From 534ab1861ba47c69ec600dcf5e886deb7135a0ba Mon Sep 17 00:00:00 2001 From: Alex Gregor <111502950+alexryangregor@users.noreply.github.com> Date: Thu, 9 Nov 2023 14:03:58 +0100 Subject: [PATCH 01/18] Update index.rst Proofreading complete. --- docs/source/setup/index.rst | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/docs/source/setup/index.rst b/docs/source/setup/index.rst index 4bd0740af6..967ff603a6 100644 --- a/docs/source/setup/index.rst +++ b/docs/source/setup/index.rst @@ -1,27 +1,27 @@ Getting started with SEPAL ========================== +*Discover how to access the platform and manage your account* -Discover key requirements needed to use the platform ----------------------------------------------------- +In this section of the documentation, learn how to: -In this section of SEPAL documentation, you can learn how to: +- `register to SEPAL `__ +- `use GEE with SEPAL `__ +- `use NICFI - Planet Lab data `__ +- `exchange files with SEPAL `__ +- `manage your resources `__ +- `reset your password `__ -- `Register to SEPAL `__ -- `Use Google Earth Engine (GEE) with SEPAL `__ -- `Use Norway’s International Climate and Forests Initiative (NICFI) - Planet Lab data `__ -- `Exchange files with SEPAL `__ -- `Manage your resources `__ -- `Reset your password `__ +Navigate to other articles in each section by selecting links in the **Section navigation** pane on the left. -Navigate to other pages in this section by selecting links located in **Section navigation** in the left pane. +Navigate to other subsections of each article by selecting links in the **On this page** pane on the right. -Navigate to other sections in this article by selecting links located in **On this page** in the right pane. +Make contributions to the documentation by selecting :icon:`fa-solid fa-pencil` **Edit on GitHub** in the **On this page** pane on the right. -Make contributions to the documentation by selecting :icon:`fa-solid fa-pencil` **Edit this page** in the right pane. +If the left pane or right pane is not visible, use your browser's **Zoom out** feature. If you can't find what you're looking for, use the `GitHub issue tracker `_. -For support, `ask the community `__ or contact the SEPAL team at :email:`sepal@fao.org`. +For support, `ask the community `__. .. thumbnail:: ../_images/setup/index/planet_classification.png :title: Example of a classification for Uganda based on a combination of Sentinel-1 Timescan and Sentinel-2 CCDC slice data using the **Classification** tool in SEPAL. From 6bec889188f3ec88b47f105383ad92e7deb97772 Mon Sep 17 00:00:00 2001 From: Alex Gregor <111502950+alexryangregor@users.noreply.github.com> Date: Thu, 9 Nov 2023 14:58:29 +0100 Subject: [PATCH 02/18] Update register.rst Proofreading complete. --- docs/source/setup/register.rst | 77 +++++++++++++++++----------------- 1 file changed, 38 insertions(+), 39 deletions(-) diff --git a/docs/source/setup/register.rst b/docs/source/setup/register.rst index 3d28928d08..32923a6d3b 100644 --- a/docs/source/setup/register.rst +++ b/docs/source/setup/register.rst @@ -1,15 +1,13 @@ Register to SEPAL and other key platforms ========================================= +*Create accounts with SEPAL, GEE and CEO, and request additional SEPAL resources* -Set up your accounts and request additional resources ------------------------------------------------------ +In this article, learn how to: -In this article, you can learn how to: - -- :ref:`Create a SEPAL account ` (Mandatory) -- :ref:`Request additional SEPAL resources ` (Recommended) -- :ref:`Register and connect with Google Earth Engine ` (Recommended) -- :ref:`Register to Collect Earth Online (CEO) ` (Optional) +- :ref:`create a SEPAL account ` (mandatory) +- :ref:`request additional SEPAL resources ` (recommended) +- :ref:`register and connect with GEE ` (recommended) +- :ref:`register to CEO ` (optional) .. _create: @@ -18,25 +16,26 @@ Create a SEPAL account (Mandatory) 1. Go to `sepal.io `__. + 2. Select :guilabel:`Launch` > :guilabel:`Sign up`. .. thumbnail:: ../_images/setup/register/sepal_landing.png :width: 49% :group: landing - :title: sepal.io landing page. + :title: Landing page of the SEPAL platform .. thumbnail:: ../_images/setup/register/sepal_splash_page.png :width: 49% :group: landing - :title: sepal.io splash page. + :title: Log-in form for the SEPAL platform -3. Enter your information into the form. +3. Create a username and enter your information into the form. .. thumbnail:: ../_images/setup/register/sepal_sign_up.png :width: 60% :align: center :group: register - :title: Sign-up form. + :title: Sign-up form 4. Select :btn:` Sign up`. @@ -44,32 +43,31 @@ Create a SEPAL account :width: 40% :align: center :group: register - :title: Sign-up form. + :title: Sign-up confirmation notification. 5. Complete email verification. + 6. Create a password. .. thumbnail:: ../_images/setup/register/sepal_confirmation_email.png :width: 80% :align: center :group: register - :title: Confirmation email. + :title: Confirmation email .. tip:: - After completing registration, you can request access to the **SEPAL Users Google Group**. - - Go to https://groups.google.com/g/sepal-users and select **Ask to join group**. + After completing registration, request access to the **SEPAL Users Google Group** by going to `__ and selecting **Ask to join group**. - For support, go to the `Geographic Information Systems StackExchange `__ and ask a question to the community using the **SEPAL** tag. + For support, go to the `GIS StackExchange `__ and ask a question to the community using the **SEPAL** tag. -.. note:: With your new account, you can perform basic operations, such as visualizing and processing satellite imagery, saving recipes, and navigating through the platform; however, some SEPAL features are not fully available (e.g. in the **Tabs** bar on the left, **Terminal** and **Tools** are deactivated because these functions require an instance and a quota). To get full access, go to the :ref:`request access section `. +.. note:: With your new account, you can perform basic operations, such as visualizing and processing satellite imagery, saving recipes, and navigating through the platform. However, some SEPAL features are not fully available (e.g. The **Terminal** and **Tools** buttons – located in the vertical **Tabs** bar on the left – are deactivated because these functions require an **instance** and a **quota**). To receive full access, go to the :ref:`Request access ` section. .. thumbnail:: ../_images/setup/register/sepal_recent_disabled_buttons.png :width: 30% :align: center :group: register - :title: Newly registered account with disabled options. + :title: Newly registered account with disabled options .. _request: @@ -79,68 +77,69 @@ Request additional SEPAL resources To use SEPAL modules and acesss the command line terminal and development tools like Jupyter or RStudio, you will need to request processing resources. -1. Select **Quota** > :btn:` Request additional resources`. +1. Select the **User report** button in the lower-right corner (i.e. **$ 0/h**). +2. Select :btn:` Request additional resources`. 2. Complete the form and select :btn:` Apply`. -If you do not know how many resources you will use, go to the `resource management ` section for more information. +If you do not know how many resources you will use, go to the `Resource management ` section for more information. .. thumbnail:: ../_images/setup/register/sepal_request_button.png :width: 61% :group: request - :title: Request additional resources. + :title: Request additional resources .. thumbnail:: ../_images/setup/register/sepal_request_form.png :width: 38% :group: request - :title: Request form. + :title: Request form .. note:: Applications are evaluated by the SEPAL team to prevent bots and malicious users from accessing the platform. .. _gee: -Sign up for Google Earth Engine (GEE) -------------------------------------- +Sign up for GEE +--------------- (Recommended) .. note:: - While SEPAL can run computation on its own GEE account on your behalf, the SEPAL team highly recommends signing up for GEE to improve your experience. + While SEPAL can run computation on its own Google Earth Engine (GEE) account on your behalf, the SEPAL team highly recommends signing up for GEE to improve your experience. -If you already have a Google email address, go to https://earthengine.google.com/new_signup/ to sign up for a GEE account. +If you already have a Google email address, sign up for a GEE account by going to https://earthengine.google.com/new_signup. .. image:: ../_images/setup/register/gee_landing.png - :alt: Request access to Google Earth Engine (GEE). + :alt: Request access to GEE :align: center -If you don't have a Google email address, go to http://mail.google.com/mail/sign-up to sign up. +If you don't have a Google email address, sign up by going to http://mail.google.com/mail/sign-up. -Once you have a GEE account, go to https://code.earthengine.google.com/ to access the interface. +Once you have a GEE account, access the interface by going to https://code.earthengine.google.com. .. image:: ../_images/setup/register/gee_code.png - :alt: Google Earth Enging (GEE) code editor. + :alt: GEE code editor :align: center .. tip:: - If you experience problems registering with GEE, contact the SEPAL team at :email:`sepal@fao.org`. + If you experience problems registering with GEE, `ask the community `__. .. _ceo: -Sign up for Collect Earth Online (CEO) --------------------------------------- +Sign up for CEO +--------------- (Optional) .. note:: - To get the most out of the SEPAL platform's **Classification** and **Validation** tools, the SEPAL team highly suggests using CEO for collecting point-based training and validation data. + To get the most out of the SEPAL platform's **Classification** and **Validation** tools, the SEPAL team highly suggests using Collect Earth Online (CEO) for collecting point-based training and validation data. To create a new account: -1. Open your browser (Google Chrome, Microsoft Edge, or Mozilla Firefox). +1. Open your browser (Google Chrome, Microsoft Edge or Mozilla Firefox). 2. Go to https://collect.earth. 3. Select **Register**. -4. Complete the form and Select **Register**. -5. Log in with your **Email** and **Password**. +4. Complete the form and select **Register**. +5. Log in with your email address and password. .. image:: ../_images/setup/register/ceo_landing.png :alt: CEO landing page From 73972de7e6ab14fd99c1c048a96aad90ca1920a8 Mon Sep 17 00:00:00 2001 From: Alex Gregor <111502950+alexryangregor@users.noreply.github.com> Date: Fri, 10 Nov 2023 14:22:23 +0100 Subject: [PATCH 03/18] Update presentation.rst Copyediting complete. --- docs/source/setup/presentation.rst | 198 +++++++++++++++-------------- 1 file changed, 106 insertions(+), 92 deletions(-) diff --git a/docs/source/setup/presentation.rst b/docs/source/setup/presentation.rst index eca8e4e2e2..fa30f78dbd 100644 --- a/docs/source/setup/presentation.rst +++ b/docs/source/setup/presentation.rst @@ -1,55 +1,51 @@ Introduction to SEPAL ===================== +*Become familiar with the platform and learn how to access features to facilitate remote sensing exercises* -On this page, you will be introduced to the SEPAL interface and learn how to access SEPAL's features to facilitate the remote sensing exercises found in the rest of the documentation. +In this article, learn to: -.. note:: - - **Objectives** - - - Navigate the SEPAL interface - - Learn about the functionalities of SEPAL - -.. note:: +- navigate the interface +- use the functionalities of the platform - **Prerequisites** - - - Internet access - - SEPAL account (see "Getting Started") +Prequisities include: +- internet access +- SEPAL account (see **Register to SEPAL and other key platforms** section) Access SEPAL ------------ -Navigate to `sepal.io `_ to open SEPAL, use the log-in form and fill your username and password and, click the :btn:`Login` button. +1. Go to `sepal.io `_. +2. Select **Launch**. +3. Enter your username and password. +4. Select :btn:`Login`. .. thumbnail:: ../_images/setup/presentation/sepal_login.png - :title: SEPAL login page + :title: SEPAL log-in page :width: 70% :align: center .. tip:: - When working in SEPAL, do not click your browser's back button. This will go back to the previous webpage. Use the buttons within SEPAL to navigate to previous pages. In some instances, you may find an arrow in the upper-left or upper-right corner of the SEPAL interface to navigate to a previous window. + When working in SEPAL, do not use your browser's **Back** function. Instead, use the buttons within the SEPAL interface to navigate to previous pages. In some instances, you may find an arrow in the upper-left or upper-right corner of the interface to navigate to a previous window. -Set up language ---------------- +Select language preference +-------------------------- -The first step to create a SEPAL environment is to set up the language you want to use, follow the instructions in the video below. +Choose a language for your SEPAL environment by following the instructions in the video below. .. youtube:: Lv0HwPDQx50 - .. note:: - You can always change your language preference from SEPAL's launch page. + Language preferences can always be changed from the platform's launch page (http://sepal.io). -SEPAL is by default in English, but is also available in other languages, such as French and Spanish. To use these languages in SEPAL, return to the launch page (you may be required to logout). On this page, click on :code:`Launch`, which will provide you with access to the login page. In the upper-right side of this panel, click on the button corresponding to your language: +The default language in SEPAL is English; however, other languages are available (currently French and Spanish). -- fr: Français -- en: English -- es: Español +To change the language to either French or Spanish: -The SEPAL launch page should reload itself and the language you selected will be used by the platform for all of its tools. +1. Go to http://sepal.io. +2. Select :code:`Launch`. +3. In the upper-right corner, select **en**, **es** or **fr** (English, Spanish and French, respectively). SEPAL interface --------------- @@ -57,142 +53,160 @@ SEPAL interface Home ^^^^ -Once you are logged in, you will see the following screen. Notice that your username is displayed in the lower-right. +After logging in, you will see the following screen. .. thumbnail:: ../_images/setup/presentation/sepal_home.png :title: SEPAL home screen :align: center :width: 70% -There are four main navigation tabs in the dock on the left side of the screen: +On the left, there are four main navigation buttons in the vertical **Tabs** bar (from top to bottom): -- **Process:** Select imagery and create mosaics. -- **Files:** Navigate through your personal SEPAL folders. This is where you can download, delete, and visualize data (using the Data Visualization link). -- **Terminal:** Access the command line for the LINUX server. -- **Apps:** Follow links to a variety of pre-loaded tools. +- **Process**: Select imagery and create mosaics. +- **Files**: Navigate through your personal SEPAL folders, where you can download, delete and visualize data using the **Data visualization** link. +- **Terminal**: Access the command line for the LINUX server. +- **Apps**: Follow links to a variety of preloaded tools. -On the lower-left is the red :code:`Tasks` tab. Clicking on this brings up a list of currently-running tasks. +Below the vertical **Tabs** bar – on the left – is another button: -**Account Information** can be found on the lower-right side of the webpage by clicking the Username button. This opens an overlay that displays important user account information. +- **Tasks*: View a list of currently running tasks. -You can edit your user account info, including Name, Password, Email and Organization here. Click :code:`Save` to make those changes permanent. +In the lower-right corner there are four buttons (from right to left): -.. note:: +- **Log-out from SEPAL** (displayed as a door with an arrow) +- **User details** (displayed as your username) +- **User report** (displayed as "$ 0/h") +- **User messages** (displayed as a bell) - You cannot edit your Username in this interface. +In the **User details** pop-up window, you can: -Link your Google Earth Engine (GEE) account with your SEPAL account by clicking **Use my own Google Account** and following the instructions. If your GEE and SEPAL accounts are connected, SEPAL uses your Google Drive as a temporary storage space for data downloaded to your SEPAL workspace (e.g. any imagery tiles or mosaics that you “retrieve to SEPAL workspace” will first be saved to your Google Drive account before being saved in your SEPAL workspace). If your GEE and SEPAL accounts are not linked, data downloads to your SEPAL workspace will still be possible and the data will pass through SEPAL's Google Drive account. +- view and edit user account information (e.g. name, password, email, organization; username can not be edited); and +– link your GEE and SEPAL accounts by selecting **Use my own Google account** and following the instructions. + +If your GEE and SEPAL accounts are connected, SEPAL uses your Google Drive as a temporary storage space for data downloaded to your SEPAL workspace (e.g. any imagery tiles or mosaics that you “retrieve to SEPAL workspace” will first be saved to your Google Drive account before being saved in your SEPAL workspace). + +If your GEE and SEPAL accounts are not linked, data downloads to your SEPAL workspace will still be possible and the data will pass through SEPAL's Google Drive account. .. tip:: Unlinking your GEE and SEPAL accounts for downloading to SEPAL workspace may help if you do not have sufficient space available in your personal Google Drive. -Linking your GEE and SEPAL accounts will allow you to read and write from your GEE Assets. To save data created in SEPAL as a GEE Asset or to use your existing GEE Assets in classifications or further processing in SEPAL, you will need to have your GEE and SEPAL accounts linked. +Linking your GEE and SEPAL accounts will allow you to read and write from your GEE assets. To save data created in SEPAL as a GEE asset or to use your existing GEE assets in classifications or further processing in SEPAL, you will need to have your GEE and SEPAL accounts linked. .. tip:: - Link your SEPAL and GEE accounts in order to read and write to GEE Assets from SEPAL. + Link your SEPAL and GEE accounts in order to read and write to GEE assets from SEPAL. -Next to **Account Information** is a section called **User Report**, represented by the :code:`$ X/h`, which displays the status (used / available) of your processing and storage resources. Instance spending refers to the resources used / available to start and run cloud computers. Storage space and spending refers to the resources used / available for storage in your SEPAL workspace. If you are running any processes in your current session, they will show up here under Sessions. +In the **User report** pop-up window, you can view the status (used/available) of your processing and storage resources: +- **Instance spending** refers to the resources used/available to start and run cloud computers. +- **Storage spending** and **Storage space** refer to the resources used/available for storage in your SEPAL workspace. +- **Sessions** refers to any processes in your current session, if you are running any. .. thumbnail:: ../_images/setup/presentation/user_report_panel.png - :title: User Report panel. + :title: **User report** panel :width: 350px :align: center .. note:: - SEPAL is not to be used for long-term data storage. This is costly. The platform is best used by storing only the data necessary for processing. After processing and producing a product, data should be downloaded to your personal computer and deleted from SEPAL storage. + SEPAL should not be used for long-term data storage, as this is costly. The platform is best used by storing only the data necessary for processing. After processing and producing a product, data should be downloaded to your personal computer and deleted from SEPAL storage. -Process Tab -^^^^^^^^^^^ +Process +^^^^^^^ -Click the :code:`Process` tab on the left side of the window. +In the vertical **Tabs** bar on the left, select the :code:`Process` button. .. thumbnail:: ../_images/setup/presentation/process_tab_location.png - :title: Arrow pointing out the process tab location. + :title: Arrow pointing to the process tab location :align: center :width: 70% You should now see many options in the center of the screen: -- **Optical Mosaic** Create a mosaic using Landsat and/or Sentinel 2 data. This is what we will do in Exercise 1.2. -- **Radar Mosaic** Create a mosaic using Sentinel 1 data. -- **Planet Mosaic** Create a mosaic using NICFI / Planet basemaps (if you have permission from NICFI / Planet). -- **Classification** Use a random forest model to classify images from SEPAL or GEE. This will be the focus of Module 2. -- **Time Series** Download time series information to your SEPAL storage. -- **CCDC** Create a CCDC asset from a time series. -- **CCDC Slice** Create a slice of a CCDC asset for a specific date or date range. -- **Class Change** Create a class change map from two categorical images (either SEPAL recipes or GEE assets). -- **Index Change** Create an index change map from two single-band images (either SEPAL recipes or GEE assets). -- **Remapping** Remap categorical or continuous image bands into new categories. +- **Optical mosaic**: Create a mosaic using Landsat and/or Sentinel-2 data (for guidance, see **Exercise 1.2**). +- **Radar mosaic**: Create a mosaic using Sentinel-1 data. +- **Planet mosaic**: Create a mosaic using NICFI–Planet basemaps (if you have permission from NICFI-Planet). +- **Classification**: Use a random forest model to classify images from SEPAL or GEE (for guidance, see **Module 2**). +- **Time series**: Download time-series information to your SEPAL storage. +- **CCDC**: Create a Continuous Change Detection and Classicfication (CCDC) asset from a time series. +- **CCDC slice**: Create a slice of a CCDC asset for a specific date or date range. +- **Class change**: Create a class change map from two categorical images (either SEPAL recipes or GEE assets). +- **Index change**: Create an index change map from two single-band images (either SEPAL recipes or GEE assets). +- **Remapping**: Remap categorical or continuous image bands into new categories. -When you click on one of these options, it will open a new tab with the GUI interface that allows you to specify your desired options. +When you select one of these options, a new tab will open with the graphical user interface (GUI) interface that allows you to specify your desired options. -Files Tab -^^^^^^^^^ +Files +^^^^^ -Click the green :code:`Files` tab on the left side of the window. This will display all of your files stored in your SEPAL workspace. +In the vertical **Tabs** bar on the left, select the :code:`Files` button to display all files stored in your SEPAL workspace. -For example, click the :code:`Downloads` folder to expand it. This will display the folders containing any of the data you have downloaded in SEPAL. If you have not downloaded mosaics in SEPAL yet, this folder will be empty. +For example, select the :code:`Downloads` folder to display the folders containing any of the data you have downloaded in SEPAL. If you have not downloaded mosaics in SEPAL yet, this folder will be empty. .. thumbnail:: ../_images/setup/presentation/files_menu.png - :title: The files menu. + :title: The **Files** menu :align: center :width: 50% -Notice that there are four buttons on the upper-right side of the window. The three rightmost buttons will be inactive until you select a file. +In the upper right, there are four buttons (the three right-most buttons will be inactive until you select a file). From left to right: -- The left button will show hidden files (files and folder names starting with ‘.'). +- The first button will show hidden files (files and folder names starting with "."). - The second button will download selected data to your local computer. - The third button will delete the selected folder or file. - The last button will clear your selection. -Terminal Tab -^^^^^^^^^^^^ +Terminal +^^^^^^^^ -Click the :code:`Terminal` tab on the left side of the screen. +In the vertical **Tabs** bar on the left, select the :code:`Terminal` button. -This links you to the Linux command line that you can use in a variety of ways to manage data, load data from an outside location, or process data using a series of commands. +This links you to the Linux command line that you can use in a variety of ways to manage data, load data from an outside location or process data using a series of commands. -When you initially load the Terminal, you will see information about your usage and the available types of instances you can initialize. +When you initially load the **Terminal**, you will see information about your usage and the available types of instances you can initialize. -One of the most important features of the Terminal is the ability to start and stop instances. +One of the most important features of the **Terminal** is the ability to start and stop instances. -To start an instance, use the following steps as a guide: +To start an instance: -- First examine the “Available instance types” table. This is updated periodically but an example from September of 2020 is shown below. -- Choose an instance Type that fits your needs. Frequently a t2 or m2 is sufficient and cost-effective. -- Next to the “Select (t1):” text, type in "t2" or your chosen instance type. -- Press Enter on your keyboard. -- Wait for the new instance to start. This will take several minutes. +1. Examine the **Available instance types** table (updated periodically; see example from September 2020 below). +2. Choose an **Instance type** that fits your needs (normally, a **t2** instance or **m2** instance is sufficient and cost-effective). +3. Next to **Select (t1):**, enter **t2** (or your chosen instance type). +4. Press **Enter** on your keyboard and wait for the instance to start, which will take several minutes. -To stop an instance, type "exit" in the command line. You can then refresh the terminal page to start a new instance. You can also stop an instance by clicking on your username on the right side of the screen and accessing your account information. Under "Sessions" click on the trashcan icon to shut down your instances. +To stop an instance: -Once an instance has stopped, you can follow the instance startup steps again to select a larger instance, if necessary. +- enter **exit** into the command line (you can then refresh the terminal page to start a new instance; or +- open your **User report** by selecting the "$ 0/h" icon in the lower-right corner, then selecting the trashcan icon under **Sessions**. + +Once an instance has stopped, you can follow the instance start-up steps again to select a larger instance, if necessary. .. thumbnail:: ../_images/setup/presentation/terminal.png - :title: The terminal page, including an example of changing the instance. + :title: The **Terminal** page, including an example of changing the instance :align: center :width: 450 -Apps Tab -^^^^^^^^ +Apps +^^^^ + +In the vertical **Tabs** bar on the left, select the **Apps** button to display applications accessible through SEPAL (for more information about each app, select the rightmost **i** button). -Click the **Apps** tab on the left side of the screen. This will open up a screen that shows applications that you can access through SEPAL. Applications are pre-programmed (typically using R or Python) to perform specific, useful tasks. Applications make use of instances and running an application will use your SEPAL computing resources. +Applications are preprogrammed (typically using R or Python) to perform specific useful tasks. + +Applications make use of instances; running them will use your SEPAL computing resources. .. thumbnail:: ../_images/setup/presentation/apps_interface.png - :title: The Apps interface. + :title: The **Apps** interface :align: center :width: 70% -This will bring up a list of apps you can run in SEPAL. More information about each app is found by clicking on the “i” on the right hand side. Some of the apps include: +Some of the apps include: + +- **R Studio**: Provides access to the R environment, where you can run processing scripts and upload data to your SEPAL folder. +- **JupyterLab**: Provides access to the Python environment where you can run complex data workflows. +- **BFAST GPU**: Graphics processing unit (GPU) implementation of the Breaks for Additive Season and Trend (BFAST) algorithm to analyse time series. +- **Deforestation alert analysis**: Retrieve any type of alert on a selected area of interest (AOI). +- **Mountain Green Cover Index**: Calculates Sustainable Development Goal (SDG) 15.4.2: Mountain Green Cover Index at national/subregional scale. +- **SMFM Biota**: Calculate biomass change over time using ALOS PALSAR data (SMFM refers to Satellite Monitoring for Forest Management). -- **R Studio:** Provides access to the R environment where you can run processing scripts and upload data to your SEPAL folder. -- **JupyterLab:** Provides access to the Python environement where you can run complex data workflows. -- **BFAST GPU:** GPU implementation of the BFAST algorithm to analyse time series. -- **Deforestation alert analysis:** Retrieve any type of alert on a selected AOI. -- **Mountain Green Cover Index:** Calculates the SDG 15.4.2: Mountain Green Cover Index at national/sub-regional scale. -- **SMFM Biota:** Calculate biomass change over time using ALOS Palsar data. -- Many more that can be found in the section :doc:`../modules/index` of the documentation. +For more information on available apps, see the :doc:`../modules/index` section of the documentation. From d8c046f6683e1212b84ba2547d4a97b560121c07 Mon Sep 17 00:00:00 2001 From: Alex Gregor <111502950+alexryangregor@users.noreply.github.com> Date: Fri, 10 Nov 2023 16:37:50 +0100 Subject: [PATCH 04/18] Update gee.rst Proofreading complete. --- docs/source/setup/gee.rst | 137 +++++++++++++++++++++----------------- 1 file changed, 76 insertions(+), 61 deletions(-) diff --git a/docs/source/setup/gee.rst b/docs/source/setup/gee.rst index 8814dec8a0..089644333b 100644 --- a/docs/source/setup/gee.rst +++ b/docs/source/setup/gee.rst @@ -1,22 +1,30 @@ -Use Google Earth Engine (GEE) with SEPAL -======================================== +Use GEE with SEPAL +================== +*Sign up for a GEE account and connect with SEPAL* -Sign up for a GEE account and connect with SEPAL ------------------------------------------------- +In this article, learn how to: -In this article, you can learn how to: - -- Set up your GEE account -- Connect your GEE account and SEPAL account -- Upload files to GEE -- Use GEE assets in SEPAL +- set up your GEE account +- connect your GEE account and SEPAL account +- upload files to GEE +- use GEE assets in SEPAL GEE and SEPAL ------------- -SEPAL is closely linked to GEE, a Google-powered Earth-observation cloud-computing platform. SEPAL can access data stored in the GEE data catalog, use GEE for processing large datasets, and read and write data to GEE assets. A large part of SEPAL's existing code is based on the JavaScript GEE application programming interface (API). +SEPAL is closely linked to Google Earth Engine (GEE), a Google-powered Earth-observation cloud-computing platform. + +SEPAL can: + +- access data stored in the GEE data catalog; +- use GEE for processing large datasets; and +- read and write data to GEE assets. + +A large part of SEPAL's existing code is based on the JavaScript GEE application programming interface (API). + +All SEPAL recipes are based on GEE and run scripts written by SEPAL team members to enable access to state-of-the-art processing algorithms without having to write code. -All SEPAL recipes are based on GEE and run scripts written by SEPAL team members to enable access to state-of-the-art processing algorithms without having to write code. In the SEPAL **Applications** list, the applications tagged with the Google logo (:icon:`fa-brands fa-google`) are also running with the Python GEE API and don't require you to use big instances to run complex operations. +In the SEPAL **Apps** list, the applications tagged with the Google logo (:icon:`fa-brands fa-google`) are also running with the Python GEE API and don't require you to use big instances to run complex operations. SEPAL recipes can be run from the main SEPAL interface using default SEPAL credentials or your personal GEE access credentials; however, to run the SEPAL applications that employ GEE, you will need to link your SEPAL and GEE accounts. SEPAL applications that make use of GEE will not run (i.e. authentication will not work) if your GEE and SEPAL accounts are unlinked. @@ -30,96 +38,97 @@ A GEE account is required to properly export images and data products as GEE ass To sign up for a Google account, go to https://accounts.google.com/servicelogin. -To request a GEE account, go to https://earthengine.google.com/new_signup/. +To request a GEE account, go to https://earthengine.google.com/new_signup. .. thumbnail:: ../_images/setup/register/gee_landing.png - :title: Request access to google earth engine. + :title: Request access to GEE. :align: center -For first-time users of SEPAL, you will want to select 'Use Without a Cloud Project' as this is how non-commercial users of GEE should begin. The link between GEE and Google Cloud Projects (GCP) is evolving and SEPAL will continue to develop in order to make use of GCP correctly. For now, though...use SEPAL without a GCP. +For first-time users of SEPAL, select **Use without a cloud project** (for non-commercial users of GEE; the link between GEE and Google Cloud Projects [GCPs] is evolving and SEPAL will continue to develop in order to make use of GCPs correctly – but for now, use SEPAL without a GCP). .. thumbnail:: ../_images/setup/register/gee_gcp_declaration.png - :title: Use google earth engine without cloud project. + :title: Use GEE without a cloud project. :align: center - -Once you have a GEE account, go to https://code.earthengine.google.com/ to access the **Earth Engine Code Editor**. +Once you have a GEE account, access the **Earth Engine Code Editor** by going to https://code.earthengine.google.com. .. thumbnail:: ../_images/setup/register/gee_code.png - :title: GEE code editor + :title: GEE Code Editor :align: center .. tip:: - When you first connect to the **Earth Engine Code Editor**, it is strongly advised to take the short tour provided in the interface. + When you first connect to **Earth Engine Code Editor**, the SEPAL team recommends taking the tour of its features provided in the interface. .. thumbnail:: ../_images/setup/gee/editor_tour.png - :title: GEE code editor tour + :title: GEE Code Editor tour :align: center :width: 40% .. tip:: - If you experience trouble while linking your Google account to GEE, contact the SEPAL team at :email:`sepal@fao.org`. + If you experience trouble while linking your Google account to GEE, `ask the community `__. Initialize the **Home** folder ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -To use your GEE account in the SEPAL interface, you need to set up the **Home** folder, where all of your **Assets** (i.e. **Vectors**, **Rasters**, **Collections**, **Mosaics** and **Classifications**) will be exported. Failing to set up this folder will prevent you from successfully executing export requests. +To use your GEE account in the SEPAL interface, set up the **Home** folder, where all your **Assets** (i.e. **Vectors**, **Rasters**, **Collections**, **Mosaics** and **Classifications**) will be exported. Failing to set up this folder will prevent you from successfully executing export requests. 1. To set up the **Home** folder, go to the **Earth Engine Code Editor**. .. thumbnail:: ../_images/setup/gee/gee_code.png - :title: GEE code editor + :title: GEE Code Editor :align: center -The page is divided into three zones and a map: +The page is subdivided into three zones and a map: -**Zone 1**: Provides you with access to your GEE account information, which is divided into three panes: +**Zone 1**: Provides you with access to your GEE account information, subdivided into three panes: - - **Assets**: Displays all of the assets in your account. - - **Scripts**: Displays all of the scripts available with your account (shared and written). - - **Doc**: Displays documentation of the JS GEE API, if you need to code in this editor. + - **Assets**: Displays all of assets in your account. + - **Scripts**: Displays all scripts available with your account (shared and written). + - **Doc**: Displays documentation of the GEE JavaScript API (GEE JS API), if you need to code in this editor. **Zone 2**: Allows advanced users to code their own scripts using the GEE JS API. -**Zone 3**: Displays information about current processes, which is divided into three panes: +**Zone 3**: Displays information about current processes, divided into three panes: - **Inspector**: Transforms the arrow of the mouse into a pointer, allowing you to click anywhere on the map to view information about what you are displaying. - - **Tasks**: Displays all of the tasks of your account, as well as their statuses (i.e. *running*, *finished* or *failed*). + - **Tasks**: Displays all of the tasks of your account, as well as their statuses (i.e. **Running**, **Finished** or **Failed**). - **Console**: Displays the console panel of running scripts. -2. Go to **Zone 1** > Select **Assets** > Select **Create home folder**. +2. Go to **Zone 1** > Select **Assets** > Select **Create** Home **folder**. .. thumbnail:: ../_images/setup/gee/create_home.png - :title: gee asset creation + :title: GEE asset creation :align: center :width: 60% -3. Select the name of the folder (Note: This can only be set once and never changed; if you're not satisfied with the suggested name, you can create your own, as long as there are no spaces or special characters). +3. Select the name of the folder (this can only be set once and never changed; if you're not satisfied with the suggested name, you can create your own as long as there are no spaces or special characters). .. thumbnail:: ../_images/setup/gee/home_pop_up.png - :title: GEE popup for Home creation + :title: GEE pop-up window for **Home** folder creation :align: center :width: 50% -4. When you return to your list of **Assets** (located in the **Zone 1** panel), you should see the name you provided as the first folder at the root of the asset tree. In this example, we used *galatheetest*: +4. When you return to your list of **Assets** (located in the **Zone 1** panel), you should see the name you provided as the first folder at the root of the **Asset** tree. + +In our example, we used **galatheetest**: .. thumbnail:: ../_images/setup/gee/asset_tree.png - :title: asset tree + :title: Asset tree :align: center :width: 60% .. note:: - Now that you have initialized your GEE account, you can start the connection process between SEPAL and GEE. + After initializing your GEE account, start the connection process between GEE and SEPAL. Connection between GEE and SEPAL -------------------------------- SEPAL can work without being connected to your GEE account, but you will miss numerous opportunities to leverage the platform's potential. -In this section, the connection procedure between GEE and SEPAL will be presented. +In this subsection, we present the connection procedure between GEE and SEPAL. Connection ^^^^^^^^^^ @@ -132,17 +141,17 @@ Connection :title: SEPAL landing :align: center -3. Next to the Google logo (:icon:`fa-brands fa-google`) on the upper-right side of the **User Details** pop-up window, you will see the status of the connection between your SEPAL and GEE accounts (Note: if you have not connected your accounts, it will read *Disconnected*). +3. Next to the Google logo (:icon:`fa-brands fa-google`) in the upper-right corner of the **User details** pop-up window, the status of the connection between your GEE and SEPAL accounts is displayed (if you have not connected your accounts, it will read **Disconnected**). .. thumbnail:: ../_images/setup/gee/user_interface_disconnected.png :title: SEPAL disconnected :align: center :width: 40% -4. Select **Google account** in the lower section of the pop-up window (Note: if your GEE account is disconnected, you will see text that reminds you what functionalities are unavailable without a custom GEE account). +4. Select **Google account** in the lower section of the pop-up window (if your GEE account is disconnected, you will see text that reminds you what functionalities are unavailable without a custom GEE account). .. thumbnail:: ../_images/setup/gee/gee_disconnected.png - :title: connection pop-up + :title: Connection pop-up window :align: center :width: 40% @@ -152,9 +161,9 @@ Connection .. Note:: - You will see a message requesting your permission to authorize SEPAL's access to your Google Drive, as well as your **Assets** and **Home** folders to export recipes and module results. + You will see a message requesting your permission to authorize SEPAL's access to your Google Drive, as well as your **Assets** folder and **Home** folder to export recipes and module results. -6. After the connection process is complete, you will be redirected to the SEPAL website. If you select **User interface** again, the pop-up window will display *Connected* in green in the upper-right. +6. After the connection process is complete, you will be redirected to the SEPAL website. If you open **User details** again, the pop-up window will display *Connected* in green in the upper-right corner. .. thumbnail:: ../_images/setup/gee/user_interface_connected.png :title: SEPAL and GEE connected @@ -164,12 +173,12 @@ Connection Disconnection ^^^^^^^^^^^^^ -If you want to change accounts or remove the link between your SEPAL and GEE accounts, you can disconnect SEPAL from GEE at any time. +If you want to change accounts or disconnect your GEE and SEPAL accounts: -1. Return to the user interface and select **Google account**. You should see the following window: +1. Open **User details** and select **Google account**. You should see the following window: .. thumbnail:: ../_images/setup/gee/gee_connected.png - :title: gee connected + :title: GEE connected :align: center :width: 40% @@ -178,20 +187,25 @@ If you want to change accounts or remove the link between your SEPAL and GEE acc Upload files to GEE ------------------- -When you use SEPAL recipes and modules, you'll be asked to use GEE assets to provide rasters (:code:`ee.Image`) or vectors (:code:`ee.FeatureCollection`) to the core GEE-based algorithm. These assets can be either public assets that someone shared with you or assets that you created yourself and would like to use. +When you use SEPAL recipes and modules, you'll be asked to use GEE assets to provide rasters (:code:`ee.Image`) or vectors (:code:`ee.FeatureCollection`) to the core GEE-based algorithm. + +These assets can be either: + +- public assets that someone shared with you; or +- assets that you created yourself and would like to use. .. tip:: - For vector files, SEPAL provides an interface to upload them from your computer to the platform and eventually to GEE. This process allows you to deal with the full process directly from SEPAL without going to the **Earth Engine Code Editor** (see the :doc:`../modules/dwn/vector_manager` module documentation for more details). + For vector files, SEPAL provides an interface to upload them from your computer to the platform and eventually to GEE. This process allows you to deal with the full process directly from SEPAL without going to the **Earth Engine Code Editor** (for more information, see :doc:`../modules/dwn/vector_manager`). -1. Go to **Assets** in the **Zone 1** panel on the **Earth Engine Code Editor** page: +1. Go to **Assets** in the **Zone 1** panel in the **Earth Engine Code Editor**. .. thumbnail:: ../_images/setup/gee/gee_asset_list.png :title: GEE asset list :align: center :width: 50% -2. Select **New**. You will have several choices, including raster, shape, and table, which will be described in the following sections. +2. Select **New**. You will have several choices, including **Raster**, **Shape** and **Table**, which will be described in the following subsections. Raster ^^^^^^ @@ -199,14 +213,14 @@ Raster If you need to upload a raster image: 1. Select **Image**. -2. In the pop-up window that appears, select the file you want to upload from your computer (Note: compatible formats include :code:`.tiff`, :code:`.tif`, :code:`.json`, :code:`.tfrecord` or :code:`.tfrecord.gz`; the name of your asset can be changed in the next text field). +2. In the pop-up window, select the file you want to upload from your computer (compatible formats include :code:`.tiff`, :code:`.tif`, :code:`.json`, :code:`.tfrecord` or :code:`.tfrecord.gz`; the name of your asset can be changed in the next text field). .. tip:: - By default, the asset will be named after the base-name. + By default, the asset will be named after the basename. .. thumbnail:: ../_images/setup/gee/upload_image.png - :title: upload image + :title: Upload image :align: center :width: 50% @@ -216,10 +230,10 @@ Shape If you need to upload a shape as a :code:`ee.FeatureCollection`: 1. Select **Shape upload**. -2. In the pop-up window that appears, select the file you want to upload from your computer (note: compatible formats include :code:`.shp`, :code:`.zip`, :code:`.dbf`, :code:`.prj`, :code:`.shx`, :code:`.cpg`, :code:`.fix`, :code:`.qix`, :code:`.sbn` or :code:`.shp.xml`; if you didn't compress the file, a :code:`.shp` alone is not sufficient and must be accompanied with other files describing the shape as in the example in the image below). +2. In the pop-up window, select the file you want to upload from your computer (note: compatible formats include :code:`.shp`, :code:`.zip`, :code:`.dbf`, :code:`.prj`, :code:`.shx`, :code:`.cpg`, :code:`.fix`, :code:`.qix`, :code:`.sbn` or :code:`.shp.xml`; if you didn't compress the file, a :code:`.shp` alone is not sufficient and must be accompanied with other files describing the shape as in the example in the image below). .. thumbnail:: ../_images/setup/gee/upload_shape.png - :title: upload shp + :title: Upload .shp :align: center :width: 50% @@ -232,21 +246,22 @@ If you need to upload a table as a :code:`ee.FeatureCollection`: 2. In the pop-up window that appears, select the file you want to upload from your computer (note: compatible formats include :code:`.csv`, :code:`.json`). .. thumbnail:: ../_images/setup/gee/upload_csv.png - :title: upload csv + :title: Upload .csv :align: center :width: 50% Use your GEE assets in SEPAL ---------------------------- -Once you've uploaded your assets, you can use them in SEPAL by copying and pasting the name of each anywhere SEPAL asks for an asset name. +Once you've uploaded your assets, you can use them in SEPAL by copying and pasting the name of each whenever an asset name is requested from the interface. -To find the asset name, go back to **Assets** in the **Zone 1** pane and click on any asset in the list. The following pop-up window will appear: +To find the asset name, go back to **Assets** in the **Zone 1** pane and select any asset in the list. The following pop-up window will appear: .. thumbnail:: ../_images/setup/gee/asset_popup.png - :title: asset popup + :title: Asset pop-up window :align: center :width: 80% +If you select **Copy link**, the link will be copied to the clipboard and you can paste it into SEPAL or send it to someone for authorized use. -If you select **Copy link**, the link will be copied to the clipboard and you can paste it into SEPAL or send it to someone for authorized use. Alternatively, you can select **Share** in the pop-up window and choose between the different sharing options. +Alternatively, you can select **Share** and choose between the different sharing options. From 3682a68a5e3e4482d98f821c94ac188d1679a2e2 Mon Sep 17 00:00:00 2001 From: Alex Gregor <111502950+alexryangregor@users.noreply.github.com> Date: Mon, 13 Nov 2023 12:58:19 +0100 Subject: [PATCH 05/18] Update nicfi.rst Proofreading compete. --- docs/source/setup/nicfi.rst | 75 +++++++++++++++++++------------------ 1 file changed, 38 insertions(+), 37 deletions(-) diff --git a/docs/source/setup/nicfi.rst b/docs/source/setup/nicfi.rst index 29ec038719..f216aa93cd 100644 --- a/docs/source/setup/nicfi.rst +++ b/docs/source/setup/nicfi.rst @@ -1,13 +1,11 @@ -Use Norway’s International Climate and Forests Initiative (NICFI) - Planet Lab data +Use NICFI - Planet Lab data =================================================================================== +*Sign up for NICFI and connect with GEE* -Sign up for NICFI and connect with Google Earth Engine (GEE) ------------------------------------------------------------- +In this article, learn how to: -In this article, you can learn how to: - -- Sign up for NICFI imagery -- Access NICFI through GEE +- sign up for NICFI imagery +- access NICFI through GEE .. note:: @@ -16,9 +14,9 @@ In this article, you can learn how to: Overview -------- -Through NICFI, anyone can now access Planet’s high-resolution, analysis-ready mosaics of the world’s tropics to help reduce and reverse the loss of tropical forests, combat climate change, conserve biodiversity, and facilitate sustainable development. +Through Norway’s International Climate and Forests Initiative (NICFI), anyone can access Planet’s high-resolution, analysis-ready mosaics of the world’s tropics to help reduce and reverse the loss of tropical forests, combat climate change, conserve biodiversity and facilitate sustainable development. -In support of NICFI’s mission, you can use this data for a number of purposes, including, but not limited to: +In support of NICFI’s mission, you can use this data for a number of purposes, such as: - advancing scientific research about the world’s tropical forests and the critical services they provide; - implementing and improving policies for sustainable forest management and land use in developing tropical forest countries and jurisdictions; @@ -26,87 +24,90 @@ In support of NICFI’s mission, you can use this data for a number of purposes, - protecting and improving the rights of Indigenous Peoples and local communities in tropical forest countries; and - innovating solutions towards reducing pressure on forests from global commodities and financial markets. -The NICFI & Planet Basemaps for Tropical Forest Monitoring are now available in Google Earth Engine (GEE) and SEPAL for easy processing. In a few simple steps, you can create your own custom mosaics using the Planet basemaps. +The NICFI and Planet Basemaps for Tropical Forest Monitoring are now available in Google Earth Engine (GEE) and SEPAL for easy processing. In a few simple steps, you can create your own custom mosaics using Planet basemaps. + +The first step is to make sure you have a GEE account. -The first step is to make sure you have a GEE account. You can follow `this tutorial `__ to register for a GEE account if you don’t already have one. +If you don’t have a GEE account, register by following `this tutorial `__. Sign up for NICFI imagery ------------------------- -Sign up for NICFI Planet data access using the same email address associated with your GEE account. To sign up for access to the NICFI data program, go to ``_. +Sign up for NICFI – Planet Lab data access using the same email address associated with your GEE account. + +To sign up for access to the NICFI data program, go to ``_. .. thumbnail:: ../_images/setup/nicfi/nicfi_page.png - :title: Planet NICFI landing page. + :title: Planet NICFI landing page :group: setup_nicfi -Click on the **Sign up** button and fill in the form. +Select the **Sign up** button and fill in the form. .. thumbnail:: ../_images/setup/nicfi/signup.png - :title: Sign up form. + :title: Sign up form :group: setup_nicfi - After submitting the form, an email will be sent with a link to activate your account. -Please check your email for an invitation to complete the sign up process. +Check your email for an invitation to complete the sign-up process. -Click on the link and a new form will appear. Complete the form and you will receive a success message with a new page to sign in to your account. +Select the link and a new form will appear. Complete the form and you will receive a success message with a new page to sign in to your account. .. thumbnail:: ../_images/setup/nicfi/activate_account.png - :title: Account activation form. + :title: Account activation form :group: setup_nicfi .. tip:: - If you are already a NICFI user and would like to access the basemaps in GEE, go to ``_ to apply for access. + If you are already a NICFI user and would like to access the basemaps in GEE, apply for access by going to ``_. .. note:: - Approval for accessing NICFI-Planet Basemaps in GEE can take up to one week. - - + Approval for accessing NICFI - Planet Basemaps in GEE can take up to one week. Access NICFI through GEE ------------------------ -The NICFI Planet data can also be accessed from GEE, allowing you to use the PlanetLab imagery in SEPAL recipes, such as **Classification** or **Time series**, by authorizing your GEE account to access PlanetLab data. +NICFI – Planet Lab data can also be accessed from GEE, allowing you to use Planet Lab imagery in SEPAL recipes, such as **Classification** or **Time series**. + +To authorize your GEE account to access Planet Lab data: -1. Go to the `Planet Platform Explorer `__ and select **My Account** in the upper-right corner. +1. Go to the `Planet Platform Explorer `__. In the upper-right corner, select **My Account**. .. thumbnail:: ../_images/setup/nicfi/explorer.png - :title: The platform explorer of the PlanetLab website. The **My account** dropdown menu appears when hovering. + :title: The platform explorer of the Planet Lab website; the **My account** dropdown menu appears when hovering :group: setup_nicfi -2. Select **All Plans** (2), which should activate NICFI level 1 data access (1). If it does, select **My settings** (3) and scroll down to the bottom of the page. +2. Select **All plans** (see **2** in figure below), which should activate NICFI level 1 data access (see **1** in figure below). If it does, select **My settings** (see **3** in figure below) and scroll down to the bottom of the page. .. thumbnail:: ../_images/setup/nicfi/plans.png - :title: The plans that are linked to your NICFI account. + :title: The plans that are linked to your NICFI account :group: setup_nicfi -3. Select **Edit access** (1) in the lower-right. +3. Select **Edit access** (see **1** in figure below) in the lower right. -4. Select all of the checkboxes (2) and enter the email address (3) associated with your GEE account. +4. Select all checkboxes (see **2** in figure below) and enter the email address (see **3** in the figure below) associated with your GEE account. -5. Select **Connect to Earth Engine** (4) to finalize the registration. +5. Select **Connect to Earth Engine** (4) to finalize registration. .. note:: To connect to GEE, your GEE email address must be the same as the email address used for SEPAL. .. thumbnail:: ../_images/setup/nicfi/gee.png - :title: The registration form to authorize a GEE account to access your Planet product. + :title: The registration form to authorize a GEE account to access your Planet product :group: setup_nicfi -The next step is to make sure SEPAL is connected to the same email address that has access to NICFI-Planet Basemaps in GEE using the same process as in GEE. +The next step is to make sure SEPAL is connected to the same email address that has access to NICFI - Planet Basemaps in GEE using the same process as in GEE. -Note: If you are already connected to a Google account with access to NICFI-Planet Basemaps in GEE, you can skip the next step. +Note: If you are already connected to a Google account with access to NICFI - Planet Basemaps in GEE, you can skip this step. .. figure:: ../_images/setup/gee/user_interface_connected.png - :alt: SEPAL and GEE connected. + :alt: SEPAL and GEE connected :align: center :width: 50% -If you are either not connected to your Google account or connected via a different email address that does not have access to the NICFI-Planet Basemaps, select **Google account** and choose the email address that has access to NICFI-Planet Basemaps in GEE. +If you are either not connected to your Google account or connected via a different email address that does not have access to NICFI - Planet Basemaps, select **Google account** and choose the email address that has access to NICFI - Planet Basemaps in GEE. .. note:: @@ -114,4 +115,4 @@ If you are either not connected to your Google account or connected via a differ .. important:: - For additional information that may help when processing the NICFI/Planet high-resolution imagery in SEPAL, please refer to `the section of Planet Academy `__ dedicated to NICFI imagery. + For additional information that may help when processing high-resolution NICFI – Planet imagery in SEPAL, refer to `Planet Academy's section dedicated to NICFI imagery `__. From c3e610b11d39d7dd203f2203f36de08744bc85b4 Mon Sep 17 00:00:00 2001 From: Alex Gregor <111502950+alexryangregor@users.noreply.github.com> Date: Mon, 13 Nov 2023 14:01:08 +0100 Subject: [PATCH 06/18] Update resource.rst Proofreading complete. --- docs/source/setup/resource.rst | 44 ++++++++++++++++------------------ 1 file changed, 21 insertions(+), 23 deletions(-) diff --git a/docs/source/setup/resource.rst b/docs/source/setup/resource.rst index 11cd53d1b8..dea3e3b060 100644 --- a/docs/source/setup/resource.rst +++ b/docs/source/setup/resource.rst @@ -1,24 +1,22 @@ Manage your resources ===================== +*Monitor usage and request resources* -Monitor usage and request resources ------------------------------------ +In this article, learn how to: -In this article, you can learn how to: +- understand your **User report** +- manage instances +- request resources --Understand your **User report** --Manage instances --Request resources - -SEPAL provides free access to computation resources that are shared among registered users. To prevent exportation mistakes, new users are granted few resources that are sufficient for discovering the functionalities and running sub-regional analysis. By default, instances are closed automatically when they are not being used. +SEPAL provides free access to computation resources that are shared among registered users. To prevent exportation mistakes, new users are granted few resources that are sufficient for discovering the functionalities and running subregional analyses. By default, instances are closed automatically when they are not being used. .. note:: - The SEPAL user starter pack includes: + The **SEPAL user starter pack** includes: - 0 USD/month of instance spending - 0 USD/month of storage spending - - 0 Gb of storage + - 0 GB of storage Some actions or projects may require more storage to perform analysis at the province or country level; other actions or projects may require more instances to perform heavier computation processes. If you need more storage or instances, you can submit a quota request to the SEPAL team by following the instructions below. @@ -29,29 +27,29 @@ Some actions or projects may require more storage to perform analysis at the pro User report ----------- -In **Terminal**, **Applications** or **Recipes**, select **User report** on the lower-right side of the window to see your current instance consumption: :btn:` x.xx/h`. +In **Terminal**, **Apps** or **Process**, select **User report** in the lower-right corner to see your current instance consumption: :btn:` x.xx/h`. .. thumbnail:: ../_images/setup/resource/button_from_recipe.png - :title: The **User report** button from a **Recipe**. + :title: The **User report** button from a **Recipe** :width: 30% :group: setup_resource .. thumbnail:: ../_images/setup/resource/button_from_app.png - :title: The **User report** button from an **Application**. + :title: The **User report** button from an **App** :width: 30% :group: setup_resource .. thumbnail:: ../_images/setup/resource/button_from_terminal.png - :title: The **User report** button from a **Terminal**. + :title: The **User report** button from a **Terminal** :width: 30% :group: setup_resource -After selecting this button, the **Resource management** pop-up window will appear, displaying the current consumption of all of your resources expressed in percentages (1) (Note: a full bar indicates that you have reached one of your monthly quotas) and instances that are currently running (2). +After selecting this button, the **Resource management** pop-up window will appear, displaying the current consumption of all your **Resources** – expressed in percentages (see **1** in figure below) (a full bar indicates that you have reached one of your monthly quotas) – as well as **Instances** that are currently running (see **2** in figure below). You can request additional resources by selecting the green button. .. thumbnail:: ../_images/setup/resource/resource_management.png - :title: The **User report** pop-up window. + :title: The **User report** pop-up window :group: setup_resource Manage instances @@ -59,12 +57,12 @@ Manage instances Amazon Web Services (AWS) instances can be managed from this interface as well. -In the **User report** pop-up window, each line represents a different instance, where you can see their technical features and the hourly quota consumption. +In the **User report** pop-up window, each line represents a different instance, where you can see their technical features and hourly quota consumption. You can select the **Trashcan** icon to stop an instance. .. thumbnail:: ../_images/setup/resource/edit_instance.png - :title: Edit the instance list by removing or increasing the lifespan of any of them. + :title: Edit the instance list by removing or increasing the lifespan of any :group: setup_resource If the process you launched is a long computation (e.g. the **BFAST application** or any **Change detection algorithm**) and you want to close the SEPAL window, you can run the process in the background. @@ -76,7 +74,7 @@ Select **Edit** to open the **Instance** pop-up window, where the slider bar dis If you increase the lifespan of your instance, it will continue to consume your quota. Check regularly that your process is running effectively to avoid losing resources. .. thumbnail:: ../_images/setup/resource/change_duration.png - :title: Increase the lifespan of a specific instance. + :title: Increase the lifespan of a specific instance :group: setup_resource Request resources @@ -86,15 +84,15 @@ From the **Resource manager**, select **Request additional resources**. In order for your request to be considered, you must: -- Change the quota to values that meet your needs (e.g. more storage and fewer instances). The values entered are suggestions that the administrator will be able to change, if needed. (1) -- Provide an extensive explanation for why you need these resources, as well as the project name, the type of analysis and the area of interest (AOI). (2) +- change the quota to values that meet your needs (e.g. more storage and fewer instances); the values entered are suggestions that the administrator will be able to change, if needed (**1**); and +- provide an extensive explanation for why you need these resources, as well as the project name, the type of analysis and the area of interest (AOI) (**2**). .. thumbnail:: ../_images/setup/resource/request.png - :title: The **Resource management** request form. + :title: The **Resource management** request form :group: setup_resource Once validated, the request is sent to the SEPAL team, who will take measures in the coming days to update your profile, which may include contacting you directly if they need any extra details. .. thumbnail:: ../_images/setup/resource/notification.png - :title: The **Resource management** notification communicating that your resource request is being processed. + :title: The **Resource management** notification communicating that your resource request is being processed :group: setup_resource From ac602ebd782bb2ab839c2c2d06f10bbb9a2be0c8 Mon Sep 17 00:00:00 2001 From: Alex Gregor <111502950+alexryangregor@users.noreply.github.com> Date: Mon, 13 Nov 2023 14:15:51 +0100 Subject: [PATCH 07/18] Update password.rst Proofreading complete. --- docs/source/setup/password.rst | 49 ++++++++++++++++------------------ 1 file changed, 23 insertions(+), 26 deletions(-) diff --git a/docs/source/setup/password.rst b/docs/source/setup/password.rst index c3bc408b0a..9a514caeae 100644 --- a/docs/source/setup/password.rst +++ b/docs/source/setup/password.rst @@ -1,22 +1,20 @@ Reset password ============== +*Create a new password for your SEPAL account* -Create a new password for your SEPAL account --------------------------------------------- +In this article, learn how to: -In this article, you can learn how to: - -- Access your SEPAL account by creating new password. +- access your SEPAL account by creating a new password If you have forgotten the password for your SEPAL account, you can reset it by proving you have access to the email address associated with your account. -A password may be recovered by submitting a request by following the directions located at one of the website's sign-in forms. +A password may be recovered by submitting a request after following the directions located at one of the website's sign-in forms. .. note:: - Resetting passwords is not possible without knowing and having access to the email address used to sign in to the platform. Before requesting a new account with SEPAL, test all of your email accounts. + Resetting passwords is not possible without knowing and having access to the email address used to sign in to the platform. Before requesting a new account with SEPAL, please test all of your email accounts. -This password reset process can be performed in three steps: +The password reset process can be performed in three steps: 1. Provide your email address. 2. Complete email verification. @@ -28,40 +26,39 @@ Tell us who you are Select **Forgot password** on the SEPAL landing page. .. thumbnail:: ../_images/setup/password/landing.png - :title: SEPAL landing page where the user can find the **Forgot password?** button. + :title: SEPAL landing page where the user can find the **Forgot password?** button :group: setup_password Enter the email address you used to register for SEPAL, then select **Reset password**. .. thumbnail:: ../_images/setup/password/email-setup.png - :title: The **Reset password** page where you can insert your email address. + :title: The **Reset password** page where you can insert your email address :group: setup_password .. note:: - If the field becomes red, your email address was not found in our database. Be careful with typos and test multiple addresses, as you may have used another when you registered. + If the field becomes red, your email address was not found in the database. Be careful with typos and test multiple addresses, as you may have used another when you registered. Once your email address is validated, a confirmation email will be sent from SEPAL to your associated email account. The notification system will display a message containing this information in the upper-right corner of the screen. .. thumbnail:: ../_images/setup/password/email-confirmation.png - :title: The confirmation notification that an email to reset your password has been sent to your associated email address. + :title: Notification confirming that an email to reset your password was sent to your associated email address. :group: setup_password - Email confirmation ------------------ To reset your password, SEPAL uses an email confirmation system because: -- Attackers cannot lock the accounts of other users by guessing their usernames and utilizing the forgotten password recovery function. -- Passwords cannot be read from your email account by potential attackers. -- The reset links are only temporarily valid. -- After someone uses a password reset link, it becomes invalid and cannot be accessed again. +- attackers cannot lock the accounts of other users by guessing their usernames and utilizing the forgotten password recovery function; +- passwords cannot be read from your email account by potential attackers; +- the reset links are only temporarily valid; and +- after someone uses a password reset link, it becomes invalid and cannot be accessed again. For all of these reasons, SEPAL will send you the following email. .. thumbnail:: ../_images/setup/password/email.png - :title: Example of a **Reset password** email. + :title: Example of a **Reset password** email :group: setup_password Follow the instructions to reset your password on a new browser page. @@ -69,27 +66,27 @@ Follow the instructions to reset your password on a new browser page. Change password --------------- -In the reset password form, three fields are available: +In the **Reset password** form, three fields are available: -- **Username**: The username associated with your email address in the database. +- **Username**: the username associated with your email address in the database. - .. important:: + .. note:: Your username cannot be changed. -- **Password**: Your new password. +- **Password**: your new password. -- **Confirm password**: A security field where you need to provide your new password again. +- **Confirm password**: a security field where you need to provide your new password again. -Enter the new password in the **Password** and **Confirm Password** fields (Note: if the two fields are not exactly the same, the form cannot be validated). +Enter the new password in the **Password** and **Confirm password** fields (if the two fields are not exactly the same, the form cannot be validated). Select **Set password** to validate your new password. .. thumbnail:: ../_images/setup/password/change-password.png - :title: The **Change password** interface. + :title: The **Change password** interface :group: setup_password -Once validated, the new password will be automatically updated on your account. The user will be authenticated and a notification will be displayed in the upper-right. +Once validated, the new password will be automatically updated on your account. The user will be authenticated and a notification will be displayed in the upper right. .. thumbnail:: ../_images/setup/password/change-password-notification.png :title: The **Change password** interface. From 602a4223fa202ba67a21495301d6ec6e949824b0 Mon Sep 17 00:00:00 2001 From: Alex Gregor <111502950+alexryangregor@users.noreply.github.com> Date: Tue, 14 Nov 2023 08:48:24 +0100 Subject: [PATCH 08/18] Update index.rst Proofreading complete. --- docs/source/cookbook/index.rst | 42 ++++++++++++++++++---------------- 1 file changed, 22 insertions(+), 20 deletions(-) diff --git a/docs/source/cookbook/index.rst b/docs/source/cookbook/index.rst index 00b3ccc094..4ea186f206 100644 --- a/docs/source/cookbook/index.rst +++ b/docs/source/cookbook/index.rst @@ -1,73 +1,71 @@ SEPAL recipes ============= - -Harness high-performance cloud-based computing and modern geospatial data infrastructures with SEPAL recipes. -------------------------------------------------------------------------------------------------------------- +*Harness high-performance cloud-based computing and modern geospatial data infrastructures with SEPAL recipes* Overview -------- -SEPAL recipes are the main feature of the platform and offer users the ability to quickly and efficiently query and process satellite data, tailor their products for local needs, and produce sophisticated and relevant geospatial analyses. +SEPAL recipes are the main feature of the platform, offering users the ability to quickly and efficiently query and process satellite data, tailor their products for local needs, and produce sophisticated and relevant geospatial analyses. -A SEPAL recipe is a record of the steps and parameters used to make a dataset (e.g. optical mosaic, radar mosaic, classification, etc.). The recipe can be saved, with the same data recreated on-the-fly whenever needed or used in further analyses. A recipe is not, in itself, data. Using SEPAL recipes enables documentation of the parameters and steps used to create mosaics, composites, classifications, time series and other datasets or information products. SEPAL recipes, once saved, are available in the SEPAL interface after you sign in to the platform. Recipes can be run, deleted, or copied (e.g. to change the sensor used, while leaving all other parameters the same). +A SEPAL recipe is a record of the steps and parameters used to make a dataset (e.g. optical mosaic, radar mosaic, classification). The recipe can be saved, with the same data recreated on-the-fly whenever needed or used in further analyses. A recipe is not, in itself, data. Using SEPAL recipes enables documentation of the parameters and steps used to create mosaics, composites, classifications, time series and other datasets or information products. SEPAL recipes, once saved, are available in the SEPAL interface after you sign in to the platform. Recipes can be run, deleted or copied (e.g. to change the sensor used, while leaving all other parameters the same). With recipes, you can access the Google Earth Engine (GEE) multi-petabyte catalog of satellite imagery and utilize their planetary-scale analysis capabilities without writing a single line of code, simply by linking your Google and SEPAL accounts. .. important:: - You cannot export a recipe as an asset or a :code:`.tiff` file without a small computation quota. If you are a new user see :doc:`../setup/resource` to know more. + You cannot export a recipe as an asset or a :code:`.tiff` file without a small computation quota. If you are a new user, see :doc:`../setup/resource`. Gallery ------- .. thumbnail:: https://user-images.githubusercontent.com/149204/132474880-12333a36-dee0-4bdc-a0b4-0e9aab24b601.png :width: 30% - :title: Recipe list displayed in the web interface. + :title: Recipe list displayed in the interface :group: cookbook-index .. thumbnail:: https://user-images.githubusercontent.com/149204/132481048-6149f776-a7ed-47cb-8f75-3519aa1b8f1e.png :width: 30% - :title: Create a recipe from available workflows. + :title: Create a recipe from available workflows :group: cookbook-index .. thumbnail:: https://user-images.githubusercontent.com/149204/132482428-16ef1555-26bc-441a-8717-d65db3b62ef4.png :width: 30% - :title: Optical mosaic of the city of Rome in CIV colors. + :title: Optical mosaic of the city of Rome in CIV colors :group: cookbook-index .. thumbnail:: https://user-images.githubusercontent.com/149204/132474895-da433549-5d52-48cf-93ae-23c0ee9d47c0.png :width: 30% - :title: Norway’s International Climate & Forests Initiative (NICFI) planet composite NDVI false colors. + :title: Norway’s International Climate & Forests Initiative (NICFI) planet composite NDVI false colors :group: cookbook-index .. thumbnail:: https://user-images.githubusercontent.com/149204/132483174-154e792e-b6ce-4b22-ad08-1b8e4fdda829.png :width: 30% - :title: Sentinel1 time scan. + :title: Sentinel-1 time scan :group: cookbook-index .. thumbnail:: https://user-images.githubusercontent.com/149204/132474903-0d1db533-7427-49f6-9981-07aa5a0f6b71.png :width: 30% - :title: Sentinel1 harmonics. + :title: Sentinel-1 harmonics :group: cookbook-index .. thumbnail:: https://user-images.githubusercontent.com/149204/132474907-d4a018a1-282f-4dbd-b870-90bae470d1a0.png :width: 30% - :title: Classification. + :title: Classification :group: cookbook-index .. thumbnail:: https://user-images.githubusercontent.com/149204/132474909-3a3c9f9d-4fb9-42b8-be01-2b354c7283a3.png :width: 30% - :title: ccdc chart. + :title: CCDC chart :group: cookbook-index .. thumbnail:: https://user-images.githubusercontent.com/149204/132474911-13fdd36a-e4fd-4ad2-93e2-e0a53510b1dc.png :width: 30% - :title: visparams. + :title: visparams :group: cookbook-index .. thumbnail:: https://user-images.githubusercontent.com/149204/132478296-627a62cd-9d7b-40cf-a1aa-034c50664cf6.png :width: 30% - :title: Layers layout. + :title: Layers layout :group: cookbook-index Start a recipe @@ -80,12 +78,12 @@ Start a recipe To start a recipe, go to the **Process** tab :icon:`fa-solid fa-globe`, where you'll see the list of all saved recipes in your SEPAL account. .. thumbnail:: https://user-images.githubusercontent.com/149204/132474880-12333a36-dee0-4bdc-a0b4-0e9aab24b601.png - :title: Recipe list displayed in the web interface. + :title: Recipe list displayed in the interface Select the green :icon:`fa-solid fa-circle-plus` button in the lower-right corner to open the **Recipe type selector** pop-up window. Select any of the available recipe types and follow our tutorials to learn more about each type's usage. .. thumbnail:: https://user-images.githubusercontent.com/149204/132481048-6149f776-a7ed-47cb-8f75-3519aa1b8f1e.png - :title: Create a recipe from available workflows. + :title: Create a recipe from available workflows Save a recipe ------------- @@ -94,10 +92,14 @@ Save a recipe Using saved recipes is the recommended method for sharing parameters to developers when debugging. -Select a recipe in the main menu to display it in a tab. Then select :btn:`` in the upper-right corner and select :btn:`Export recipe`. The file will be downloaded to your computer using the following name: :code:`.json.zip`. +Select a recipe in the main menu to display it in a tab. + +Then select :btn:`` in the upper-right corner and select :btn:`Export recipe`. + +The file will be downloaded to your computer using the following name: :code:`.json.zip`. .. thumbnail:: ../_images/cookbook/index/export_recipe.png - :title: Export the recipe to your local computer. + :title: Export the recipe to your local computer Recipes ------- From 20d9090f1e0ca9bb11886b40b9343b2bf16aeb8f Mon Sep 17 00:00:00 2001 From: Alex Gregor <111502950+alexryangregor@users.noreply.github.com> Date: Tue, 14 Nov 2023 09:29:23 +0100 Subject: [PATCH 09/18] Update optical_mosaic.rst Proofreading complete. --- docs/source/cookbook/optical_mosaic.rst | 149 ++++++++++++------------ 1 file changed, 74 insertions(+), 75 deletions(-) diff --git a/docs/source/cookbook/optical_mosaic.rst b/docs/source/cookbook/optical_mosaic.rst index 90a1926274..f513b14c90 100644 --- a/docs/source/cookbook/optical_mosaic.rst +++ b/docs/source/cookbook/optical_mosaic.rst @@ -1,24 +1,22 @@ Optical mosaics =============== - -Combine images to create single raster datasets with Optical mosaics --------------------------------------------------------------------- +*Combine images to create single raster datasets with optical mosaics* Overview -------- A mosaic is a combination or fusion of two or more images. In SEPAL, you can create a single raster dataset from several raster datasets by mosaicing them together. -This can be achieved on both contiguous rasters (see first image) and overlapping images (see second image). +This can be achieved on both contiguous rasters (see first image below) and overlapping images (see second image below). .. thumbnail:: ../_images/cookbook/optical_mosaic/mosaic_contiguous.gif :width: 49% :group: optical-mosaic-recipe - :title: Contiguous rasters. + :title: Contiguous rasters .. thumbnail:: ../_images/cookbook/optical_mosaic/mosaic_overlay.png :width: 49% :group: optical-mosaic-recipe - :title: Overlapping images. + :title: Overlapping images These overlay areas can be managed in various ways. For example, you can choose to: @@ -38,20 +36,20 @@ SEPAL offers you an interactive and intuitive way to create mosaics in any area Start ----- -Once the mosaic recipe is selected, SEPAL will display the recipe process in a new tab (1) and the **AOI selection** window will appear on the lower-right side (2). +Once the mosaic recipe is selected, SEPAL will display the recipe process in a new tab (see **1** in the image below) and the **AOI selection** window will appear in the lower right (**2**). .. thumbnail:: ../_images/cookbook/optical_mosaic/landing.png :group: optical-mosaic-recipe - :title: The landing page of the optical mosaic recipe. + :title: The landing page of the optical mosaic recipe The first step is to change the name of the recipe. This name will be used to identify your files and recipes in SEPAL folders. Use the best-suited convention for your needs. Simply double-click the tab and write a new name. It will default to :code:`Optical_mosaic___`. .. thumbnail:: ../_images/cookbook/optical_mosaic/default_title.png - :title: Optical mosaics default title. + :title: Optical mosaics default title :width: 49% .. thumbnail:: ../_images/cookbook/optical_mosaic/modified_title.png - :title: Optical mosaics modified title. + :title: Optical mosaics modified title :width: 49% .. note:: @@ -61,7 +59,7 @@ The first step is to change the name of the recipe. This name will be used to id Parameters ---------- -In the lower-right corner, five tabs are available, which will allow you to customize the mosaic creation to your needs: +In the lower-right corner, five tabs are available, which allow you to customize the mosaic creation to your needs: - :guilabel:`AOI`: area of interest - :guilabel:`DAT`: target date of interest for the mosaic/composite @@ -70,10 +68,10 @@ In the lower-right corner, five tabs are available, which will allow you to cust - :guilabel:`CMP`: composition parameters .. thumbnail:: ../_images/cookbook/optical_mosaic/no_parameters.png - :title: The 5 tabs to set up SEPAL optical mosaic parameters. + :title: The five tabs to set up SEPAL optical mosaic parameters :group: optical-mosaic-recipe -AOI Selection +AOI selection ^^^^^^^^^^^^^ The data exported by the recipe will be generated from within the bounds of the AOI. There are multiple ways to select the AOI in SEPAL: @@ -94,10 +92,10 @@ Date Yearly mosaic """"""""""""" -In the :guilabel:`DAT` tab, select a year which pixels in the mosaic should come from. When the selection is done, select the :icon:`fa-solid fa-check` :guilabel:`Apply` button. +In the :guilabel:`DAT` tab, select a year which pixels in the mosaic should come from. Then select the :icon:`fa-solid fa-check` :guilabel:`Apply` button. .. thumbnail:: ../_images/cookbook/optical_mosaic/select_year.png - :title: The year selection panel. + :title: The year selection panel :group: optical-mosaic-recipe Seasonal mosaic @@ -107,14 +105,14 @@ Select :guilabel:`More` in the :guilabel:`DAT` panel to expand the date selectio Select the :icon:`fa-solid fa-calendar` (1) to open the **Date selection** pop-up window. The selected date will be the target of the mosaic (i.e. the date from which pixels in the mosaic should ideally come from). -Using the main slider (2), define a season around the target date by identifying a starting date and an ending date. SEPAL will then retrieve the mosaic images between those dates. +Using the main slider (2), define a season around the target date by identifying a start date and end date. SEPAL will then retrieve the mosaic images between those dates. -The number of images in one single season of one year may not be enough to produce a correct mosaic. SEPAL provides two secondary sliders to increase the pool of images to create the mosaic. Both count the number of seasons SEPAL can retrieve in the past (:code:`Past season` - (3)) and in the future (:code:`Future season` - (4)). +The number of images in a single season of one year may not be enough to produce a correct mosaic. SEPAL provides two secondary sliders to increase the pool of images to create the mosaic. Both count the number of seasons SEPAL can retrieve in the past (:code:`Past season` - [3]) and in the future (:code:`Future season` - [4]). When the selection is done, select the :icon:`fa-solid fa-check` :guilabel:`Apply` button. .. thumbnail:: ../_images/cookbook/optical_mosaic/select_season.png - :title: The season selection panel. + :title: The **Season selection** pane :group: optical-mosaic-recipe Sources @@ -122,34 +120,34 @@ Sources As mentioned in the introduction, a mosaic uses different raster datasets that can be obtained from multiple sources. SEPAL allows you to select data from multiple entry points. Below, you can find a description of these sources (select a link to see the corresponding dataset information): -- :guilabel:`L8`: `Landsat 8 Tier 1 `__. Landsat scenes with the highest available data quality are placed into Tier 1 and considered suitable for time-series processing analysis. Tier 1 includes Level-1 Precision Terrain (L1TP) processed data that have well-characterized radiometry and are intercalibrated across the different Landsat sensors. The geo-registration of Tier 1 scenes will be consistent and within prescribed tolerances (<=12 m root mean square error [RMSE]). All Tier 1 Landsat data can be considered consistent and intercalibrated (regardless of the sensor used) across the full collection. +- :guilabel:`L8`: `Landsat 8 Tier 1 `__. Landsat scenes with the highest available data quality are placed into **Tier 1** and considered suitable for time-series processing analysis. **Tier 1** includes Level-1 Precision Terrain (L1TP) processed data that have well-characterized radiometry and are intercalibrated across different Landsat sensors. The geo-registration of **Tier 1** scenes will be consistent and within prescribed tolerances (< = 12 m root mean square error [RMSE]). All **Tier 1** Landsat data can be considered consistent and intercalibrated (regardless of the sensor used) across the full collection. .. line-break:: -- :guilabel:`L8 T2`: `Landsat 8 Tier 2 `__. Scenes not meeting Tier 1 criteria during processing are assigned to Tier 2. This includes Systematic terrain (L1GT) and Systematic (L1GS) processed scenes, as well as any L1TP scenes that do not meet the Tier 1 specifications due to significant cloud cover, insufficient ground control, and other factors. Users interested in Tier 2 scenes can analyze the RMSE and other properties to determine the suitability for use in individual applications and studies. +- :guilabel:`L8 T2`: `Landsat 8 Tier 2 `__. Scenes not meeting **Tier 1** criteria during processing are assigned to **Tier 2**. This includes Systematic terrain (L1GT) and Systematic (L1GS) processed scenes, as well as any L1TP scenes that do not meet the **Tier 1** specifications due to significant cloud cover, insufficient ground control and other factors. Users interested in **Tier 2** scenes can analyze the RMSE and other properties to determine the suitability for use in individual applications and studies. .. line-break:: -- :guilabel:`L7`: `Landsat 7 Tier 1 `__. Landsat scenes with the highest available data quality are placed into Tier 1 and are considered suitable for time-series processing analysis. Tier 1 includes Level-1 Precision Terrain (L1TP) processed data that have well-characterized radiometry and are intercalibrated across the different Landsat sensors. The geo-registration of Tier 1 scenes will be consistent and within prescribed tolerances (<=12 m RMSE). All Tier 1 Landsat data can be considered consistent and inter-calibrated across the full collection (regardless of the sensor used). +- :guilabel:`L7`: `Landsat 7 Tier 1 `__. Landsat scenes with the highest available data quality are placed into **Tier 1** and are considered suitable for time-series processing analysis. **Tier 1** includes Level-1 Precision Terrain (L1TP) processed data that have well-characterized radiometry and are intercalibrated across different Landsat sensors. The geo-registration of **Tier 1** scenes will be consistent and within prescribed tolerances (< = 12 m RMSE). All **Tier 1** Landsat data can be considered consistent and intercalibrated across the full collection (regardless of the sensor used). .. line-break:: -- :guilabel:`L7 T2`: `Landsat 7 Tier 2 `__. Scenes not meeting Tier 1 criteria during processing are assigned to Tier 2. This includes Systematic terrain (L1GT) and Systematic (L1GS) processed scenes, as well as any L1TP scenes that do not meet the Tier 1 specifications due to significant cloud cover, insufficient ground control, and other factors. Users interested in Tier 2 scenes can analyze the RMSE and other properties to determine the suitability for use in individual applications and studies. +- :guilabel:`L7 T2`: `Landsat 7 Tier 2 `__. Scenes not meeting **Tier 1** criteria during processing are assigned to **Tier 2**. This includes Systematic terrain (L1GT) and Systematic (L1GS) processed scenes, as well as any L1TP scenes that do not meet the **Tier 1** specifications due to significant cloud cover, insufficient ground control and other factors. Users interested in **Tier 2** scenes can analyze the RMSE and other properties to determine the suitability for use in individual applications and studies. .. line-break:: -- :guilabel:`L4-5`: `Landsat 4 Tier 1 `__ combined with `Landsat 5 Tier 1 `__. Landsat scenes with the highest available data quality are placed into Tier 1 and are considered suitable for time-series processing analysis. Tier 1 includes Level-1 Precision Terrain (L1TP) processed data that have well-characterized radiometry and are inter-calibrated across the different Landsat sensors. The geo-registration of Tier 1 scenes will be consistent and within prescribed tolerances (<=12m RMSE). All Tier 1 Landsat data can be considered consistent and intercalibrated across the full collection (regardless of the sensor used). +- :guilabel:`L4-5`: `Landsat 4 Tier 1 `__ combined with `Landsat 5 Tier 1 `__. Landsat scenes with the highest available data quality are placed into **Tier 1** and are considered suitable for time-series processing analysis. **Tier 1** includes Level-1 Precision Terrain (L1TP) processed data that have well-characterized radiometry and are intercalibrated across different Landsat sensors. The geo-registration of **Tier 1** scenes will be consistent and within prescribed tolerances (< = 12 m RMSE). All **Tier 1** Landsat data can be considered consistent and intercalibrated across the full collection (regardless of the sensor used). .. line-break:: -- :guilabel:`L4-5 T2`: `Landsat 4 TM Tier 2 `__ combined with `Landsat 5 TM Tier 2 `__. Scenes not meeting Tier 1 criteria during processing are assigned to Tier 2. This includes Systematic terrain (L1GT) and Systematic (L1GS) processed scenes, as well as any L1TP scenes that do not meet the Tier 1 specifications due to significant cloud cover, insufficient ground control, and other factors. Users interested in Tier 2 scenes can analyze the RMSE and other properties to determine the suitability for use in individual applications and studies. +- :guilabel:`L4-5 T2`: `Landsat 4 TM Tier 2 `__ combined with `Landsat 5 TM Tier 2 `__. Scenes not meeting **Tier 1** criteria during processing are assigned to **Tier 2**. This includes Systematic terrain (L1GT) and Systematic (L1GS) processed scenes, as well as any L1TP scenes that do not meet the **Tier 1** specifications due to significant cloud cover, insufficient ground control and other factors. Users interested in **Tier 2** scenes can analyze the RMSE and other properties to determine the suitability for use in individual applications and studies. .. line-break:: -- :guilabel:`A+B`: `Sentinel-2 Multispectral instrument `__ is a wide-swath, high-resolution, multi-spectral imaging mission supporting Copernicus Land Monitoring studies, including the monitoring of vegetation, soil and water cover, as well as the observation of inland waterways and coastal areas. +- :guilabel:`A+B`: `Sentinel-2 Multispectral instrument `__ is a wide-swath, high-resolution, multispectral imaging mission supporting Copernicus Land Monitoring studies, including the monitoring of vegetation, soil and water cover, as well as the observation of inland waterways and coastal areas. .. thumbnail:: ../_images/cookbook/optical_mosaic/select_source.png - :title: The source selection panel. + :title: The **Source selection** pane :group: optical-mosaic-recipe To validate your selection, select the :icon:`fa-solid fa-check` :guilabel:`Apply` button. @@ -166,13 +164,13 @@ You can use multiple options to select the best scenes for your mosaic. The most Choose :guilabel:`Select scenes` and choose one of the three available :code:`Priority` options, based on the needs of your analysis (SEPAL sorts the images available for each tile): - :guilabel:`Cloud free`: Prioritizes images with zero or few clouds. -- :guilabel:`Target date`: Prioritizes images that match with the target date. +- :guilabel:`Target date`: Prioritizes images that match the target date. - :guilabel:`Balanced`: Prioritizes images that maximize both cloud and target date. To validate your selection, select the :icon:`fa-solid fa-check` :guilabel:`Apply` button. .. thumbnail:: ../_images/cookbook/optical_mosaic/scene_method.png - :title: The source selection panel. + :title: The **Source selection** pane :group: optical-mosaic-recipe Composite @@ -190,10 +188,10 @@ Composite - **Snow masking**: :guilabel:`On` - **Composing method**: :guilabel:`Medoid` -To create a mosaic, you will need to provide SEPAL with the compositing method to create the final image. See the following image for all of the possible compositing options available. +To create a mosaic, provide SEPAL with the compositing method to create the final image. See the following image for all possible compositing options available. .. thumbnail:: ../_images/cookbook/optical_mosaic/composite_options.png - :title: The panel to select the composite options of your mosaic. + :title: The pane to select the composite options of your mosaic :group: optical-mosaic-recipe Corrections @@ -201,8 +199,8 @@ Corrections This will apply corrections on the stacked pixels to improve the quality of the mosaic. -- :guilabel:`SR`: Surface reflectance improves comparison between multiple images over the same region by accounting for atmospheric effects such as aerosol scattering and thin clouds, which can help in the detection and characterization of Earth surface change. Top of atmosphere images are used if not selected. -- :guilabel:`BRDF`: Uses a bidirectional reflectance distribution function model to characterize surface reflectance anisotropy. For a given land area, the BRDF is established based on selected multiangular observations of surface reflectance. +- :guilabel:`SR`: Surface reflectance improves comparison between multiple images over the same region by accounting for atmospheric effects such as aerosol scattering and thin clouds, which can help in the detection and characterization of Earth surface change. Top-of-atmosphere images are used if not selected. +- :guilabel:`BRDF`: Uses a bidirectional reflectance distribution function (BRDF) model to characterize surface reflectance anisotropy. For a given land area, the BRDF is established based on selected multi-angular observations of surface reflectance. - :guilabel:`Calibrate`: Calibrates Sentinel and Landsat data to make them compatible. .. note:: @@ -210,7 +208,7 @@ This will apply corrections on the stacked pixels to improve the quality of the This option is only available if: - Landsat and Sentinel data are mixed; and - - BRDF and SR corrections are disabled. + - BRDF and surface reflectance (SR) corrections are disabled. Pixel filters """"""""""""" @@ -219,27 +217,27 @@ Activating any of the filters will remove some pixels from the stack. Removing p .. note:: - Each filter is applied iteratively. For example, if the normalized difference vegetation index (NDVI) is already filtering all pixels but one, there will be nothing left in the stack to be filtered by day of year. + Each filter is applied iteratively (e.g. if the normalized difference vegetation index [NDVI] is already filtering all pixels but one, there will be nothing left in the stack to be filtered by day of year). Note as well that adding filters significantly increases the creation time of the mosaic. -- **Shadow**: Filters the XX% darkest pixels of the stack. -- **Haze**: Computes a haze index and filters the XX% highest values. -- **NDVI**: Computes the NDVI and only keeps the XX% highest values. -- **Day of the year**: Computes the distance from target day in days and filters out the XX% farthest. +- **Shadow**: Filters the XX percent darkest pixels of the stack. +- **Haze**: Computes a haze index and filters the XX percent highest values. +- **NDVI**: Computes the NDVI and only keeps the XX percent highest values. +- **Day of the year**: Computes the distance from target day in days and filters out the XX percent farthest. Cloud detection """"""""""""""" Refers to the algorithm used to detect clouds. -- :guilabel:`QA bands`: Uses QA bands to identify clouds in Sentinel data. +- :guilabel:`QA bands`: Uses quality assessment (QA) bands to identify clouds in Sentinel data. - :guilabel:`Cloud score`: Uses the computed cloud score to identify clouds in Landsat data. -- :guilabel:`Pino 26`: Uses the Pino_26 algorithm to identify clouds (For more information, see `D. Simonetti, 2021 `__). +- :guilabel:`Pino 26`: Uses the Pino_26 algorithm to identify clouds (for more information, see `D. Simonetti [2021] `__). .. Note:: - This filter is only available for Sentinel exclusive source, and when both :guilabel:`BRDF` and :guilabel:`SR` correction are disabled. + This filter is only available for Sentinel exclusive source when both :guilabel:`BRDF` and :guilabel:`SR` correction are disabled. Cloud masking """"""""""""" @@ -269,7 +267,7 @@ Snow masking Defines how snowy pixels will be masked. - :guilabel:`on`: Masks snow. This tends to leave some pixels with shadowy snow. -- :guilabel:`off`: Doesn't mask snow. Note that some clouds might get misclassified as snow, and because of this, disabling snow masking might lead to cloud artifacts. +- :guilabel:`off`: Doesn't mask snow. Note that some clouds might get misclassified as snow; therefore, disabling snow masking might lead to cloud artifacts. Composing method """""""""""""""" @@ -283,14 +281,15 @@ Analysis -------- After selecting the parameters, you can start interacting with the scenes and begin the analysis. -In the upper-right corner, three tabs are available. They will allow you to customize the mosaic scene selection and export the final result. -- :btn:``: Auto-select scenes. -- :btn:``: Clear selected scenes. -- :btn:``: Retrieve mosaic. +In the upper-right corner, three tabs are available, which allow you to customize the mosaic scene selection and export the final result: + +- :btn:``: auto-select scenes +- :btn:``: clear selected scenes +- :btn:``: retrieve mosaic .. thumbnail:: ../_images/cookbook/optical_mosaic/analysis.png - :title: The three tabs to select the scenes and export mosaic. + :title: The three tabs to select the scenes and export mosaic :group: optical-mosaic-recipe .. note:: @@ -302,16 +301,16 @@ In the upper-right corner, three tabs are available. They will allow you to cust Select scenes ^^^^^^^^^^^^^ -To create a mosaic, you need to select the scenes that will be used to compute each pixel value of the mosaic. To do so, SEPAL provides a user-friendly interface that will guide you through the selection process. You don't have to select the stack for every pixel; instead, SEPAL will clip the AOI in smaller pieces called **Tiles**. These tiles correspond to the native tiling system of your dataset and are displayed on the map with circled numbers in their centroid. Each number corresponds to the number of scenes available to build the mosaic tile. Hover over these circles to see the tile boundaries appear. +To create a mosaic, select the scenes that will be used to compute each pixel value of the mosaic. SEPAL provides a user-friendly interface that will guide you through the selection process. You don't have to select the stack for every pixel; instead, SEPAL will clip the AOI in smaller pieces called **Tiles**. These tiles correspond to the native tiling system of your dataset and are displayed on the map with circled numbers in their centroid. Each number corresponds to the number of scenes available to build the mosaic tile. Hover over these circles to see the tile boundaries appear. .. note:: - Landsat and Sentinel datasets have a different grid system, which is why the selection process cannot be used if you have selected both of these datasets. If you have an idea related to the user interface (UI) that could make them work together, please let us know in our `issue tracker `__. We would be happy to implement it. + Landsat and Sentinel datasets have a different grid system, which is why the selection process cannot be used if you have selected both of these datasets. If you have an idea related to the user interface (UI) that could make them work together, let us know in our `issue tracker `__. Auto-select scene """"""""""""""""" -Selecting the :icon:`fa-solid fa-wand-magic` tab will open the **Auto-selection** panel. +Selecting the :icon:`fa-solid fa-wand-magic` tab will open the **Auto-selection** pane. Move the sliders to select the minimum and the maximum number of scenes SEPAL should select in a tile. Then, select the :guilabel:`Validate` button to apply the auto-select method. @@ -322,79 +321,79 @@ SEPAL will use the priority defined in the :guilabel:`SCN` tab to order the scen The result is never perfect but can be used as a starting point for the manual selection of scenes. .. thumbnail:: ../_images/cookbook/optical_mosaic/auto-select.png - :title: Panel to select the minimum and maximum number of scenes to auto-select in each tile. + :title: Pane to select the minimum and maximum number of scenes to auto-select in each tile. :group: optical-mosaic-recipe Clear all scenes """""""""""""""" -If at least one scene is selected, the :icon:`fa-solid fa-trash` tab will be available. Select it to open the **Clear** panel. +If at least one scene is selected, the :icon:`fa-solid fa-trash` tab will be available. Select it to open the **Clear** pane. Select :guilabel:`Clear scenes` to remove all manually and automatically selected scenes. .. thumbnail:: ../_images/cookbook/optical_mosaic/remove_all.png - :title: The panel to unselect all the scenes from the mosaic. + :title: The pane to unselect all scenes from the mosaic. :group: optical-mosaic-recipe Manual selection """""""""""""""" -To open the scene selection menu, hover over a tile circled-number and select it (1). The window will be divided into two sections: +To open the **Scene selection** menu, hover over a tile circled-number and select it (1). The window will be divided into two sections: - Available scene (2): All the available scenes according to the parameters you selected. These scenes are ordered using the :code:`priority` parameter you set in the :guilabel:`SCN` tab. - Selected scenes (3): The scenes that are currently selected. .. thumbnail:: ../_images/cookbook/optical_mosaic/select_scenes.png - :title: The pop-up window used to select individual scenes for one single tile. + :title: The pop-up window used to select individual scenes for one single tile :group: optical-mosaic-recipe -Each thumbnail represents a scene of the tile stack. You have the option to include them in the mosaic. The scenes located on the left side are the **available scenes**; the **available scene** is on the right side. In both cases, the following information can be found on the thumbnail: +Each thumbnail represents a scene of the tile stack. You have the option to include them in the mosaic. The scenes located on the left side are the **Available scenes**; the **Selected scenes** are on the right side. In both cases, the following information can be found on the thumbnail: - A small preview of the scene in the *red, blue, green* band combination. -- The exact date in yyyy-mm-dd of the scene. +- The exact date in YYYY-MM-DD of the scene. - The satellite name :icon:`fa-solid fa-satellite-dish`. -- The cloud coverage of the scene in % and its position in the stack values :icon:`fa-solid fa-cloud`. +- The cloud coverage of the scene in percent and its position in the stack values :icon:`fa-solid fa-cloud`. - The distance from target day in days within the season and its position in the stack values :icon:`fa-solid fa-calendar-check`. .. thumbnail:: ../_images/cookbook/optical_mosaic/thumbnail_available.png :width: 24% - :title: The thumbnail of a scene when it's in the available scene area. + :title: The thumbnail of a scene when it's in the available scene area :group: optical-mosaic-recipe .. thumbnail:: ../_images/cookbook/optical_mosaic/thumbnail_selected.png :width: 74% - :title: The thumbnail of a scene when it's in the selected scene area. + :title: The thumbnail of a scene when it's in the selected scene area :group: optical-mosaic-recipe -You can decide to move the scene to the **Selected** area by selecting :icon:`fa-solid fa-plus`:guilabel:`Add` or moving it back to **Available** by selecting :icon:`fa-solid fa-minus` :guilabel:`Remove`. +You can decide to move the scene to the **Selected scene** area by selecting :icon:`fa-solid fa-plus`:guilabel:`Add` or moving it back to **Available scene** pane by selecting :icon:`fa-solid fa-minus` :guilabel:`Remove`. .. thumbnail:: ../_images/cookbook/optical_mosaic/thumbnail_available_hover.png :width: 24% - :title: The thumbnail of a scene when it's in the **Available scene area** while hovering over it. + :title: The thumbnail of a scene when it's in the **Available scene** area while hovering over it :group: optical-mosaic-recipe .. thumbnail:: ../_images/cookbook/optical_mosaic/thumbnail_selected_hover.png :width: 74% - :title: The thumbnail of a scene when it's in the **Selected scene area** while hovering over it. + :title: The thumbnail of a scene when it's in the **Selected scene** area while hovering over it :group: optical-mosaic-recipe .. tip:: Scenes are moved from one side to the other so they are not duplicated and cannot be selected twice. Be careful if your connection is slow; wait for the thumbnail to move before clicking again (if you click too fast, you could select two different images instead of one). -Once you are happy with your selection, select the :guilabel:`Apply` button to close the window and use the selected scenes to compute the mosaic on this tile. When the window is closed, SEPAL resets the rendering of all the tiles. +Once you are happy with your selection, select the :guilabel:`Apply` button to close the window and use the selected scenes to compute the mosaic on this tile. When the window is closed, SEPAL resets the rendering of all tiles. Retrieve ^^^^^^^^ .. important:: - You cannot export a recipe as an asset or a :code:`.tiff` file without a small computation quota. If you are a new user see :doc:`../setup/resource` to know more. + You cannot export a recipe as an asset or a :code:`.tiff` file without a small computation quota. If you are a new user, see :doc:`../setup/resource`. -Selecting the :icon:`fa-solid fa-cloud-arrow-down` tab will open the retrieve panel where you can select the exportation parameters. +Selecting the :icon:`fa-solid fa-cloud-arrow-down` tab will open the **Retrieve** pane where you can select the exportation parameters. .. thumbnail:: ../_images/cookbook/optical_mosaic/retrieve.png - :title: The last panel of the optical mosaic: the exportation. + :title: The last pane of the optical mosaic: exportation :group: optical-mosaic-recipe Bands @@ -409,13 +408,13 @@ You need to select the band(s) to export with the mosaic. There is no maximum nu Dates ##### -- :guilabel:`dayofyear`: The Julian calendar date (day of the year). -- :guilabel:`dayfromtarget`: The distance to the target date within the season in days. +- :guilabel:`dayofyear`: the Julian calendar date (day of the year) +- :guilabel:`dayfromtarget`: the distance to the target date within the season in days Scale """"" -You can set a custom scale for exportation by changing the value of the slider in meters (m). (Note: Requesting a smaller resolution than images' native resolution will not improve the quality of the output – just its size; keep in mind that the native resolution of Sentinel data is 10 m, while Landsat is 30 m.) +You can set a custom scale for exportation by changing the value of the slider in metres (m) (note that requesting a smaller resolution than images' native resolution will not improve the quality of the output – just its size – keep in mind that the native resolution of Sentinel data is 10 m, while Landsat is 30 m.) Destination """"""""""" @@ -431,7 +430,7 @@ Select :guilabel:`Apply` to start the download process. Exportation status """""""""""""""""" -Going to the task tab (lower-left corner using the :icon:`fa-solid fa-list-check` or :icon:`fa-solid fa-spinner` buttons, depending on the loading status), you will see the list of the different loading tasks. The interface will provide you with information about the task progress and it will display an error if the exportation has failed. +In the **Tasks** tab (lower-left corner using the :icon:`fa-solid fa-list-check` or :icon:`fa-solid fa-spinner` buttons, depending on the loading status), you will see the list of the different loading tasks. The interface will provide you with information about task progress and display an error if the exportation has failed. If you are unsatisfied with the way we present information, the task can also be monitored using the `GEE task manager `__. @@ -443,12 +442,12 @@ When the task is finished, the frame will be displayed in green, as shown on the .. thumbnail:: ../_images/cookbook/time_series/download.png :width: 49% - :title: Evolution of the downloading process of the recipe displayed in the **Task manager** of SEPAL. + :title: Evolution of the download process of the recipe displayed in SEPAL's **Task manager** :group: time-series-recipe .. thumbnail:: ../_images/cookbook/time_series/download_complete.png :width: 49% - :title: Completed downloading process of the recipe displayed in the **Task manager** of SEPAL. + :title: Completed download process of the recipe displayed in SEPAL's **Task manager** :group: time-series-recipe Access @@ -469,7 +468,7 @@ Once the download process is complete, you can access the data in your SEPAL fol .. Note:: - Understanding how images are stored in an optical mosaic is only required if you want to manually use them. The SEPAL applications are bound to this tiling system and can digest this information for you. + Understanding how images are stored in an optical mosaic is only required if you want to manually use them. The SEPAL applications are bound to this tiling system and can digest the information for you. The data are stored in a folder using the name of the optical mosaic as it was created in the first section of this article. As the number of data is spatially too big to be exported at once, the data are divided into smaller pieces and brought back together in a :code:`_.vrt` file. @@ -479,4 +478,4 @@ The data are stored in a folder using the name of the optical mosaic as it was c .. important:: - Now that you have downloaded the MO to your SEPAL and/or GEE account, it can be downloaded to your computer using `FileZilla <../setup.filezilla.html>`__ or used in other SEPAL workflows. + Now that you have downloaded the optical mosaic to your SEPAL and/or GEE account, it can be downloaded to your computer using `FileZilla <../setup.filezilla.html>`__ or used in other SEPAL workflows. From a5168deb0f6b9c5d2bc3e0c9509bdc0040b1bc35 Mon Sep 17 00:00:00 2001 From: Alex Gregor <111502950+alexryangregor@users.noreply.github.com> Date: Tue, 14 Nov 2023 09:45:30 +0100 Subject: [PATCH 10/18] Update radar_mosaic.rst Proofreading complete. --- docs/source/cookbook/radar_mosaic.rst | 20 +++++++++----------- 1 file changed, 9 insertions(+), 11 deletions(-) diff --git a/docs/source/cookbook/radar_mosaic.rst b/docs/source/cookbook/radar_mosaic.rst index fb209923e3..e3edd61b22 100644 --- a/docs/source/cookbook/radar_mosaic.rst +++ b/docs/source/cookbook/radar_mosaic.rst @@ -1,8 +1,6 @@ Radar mosaics ============= - -Generate analysis-ready data (ARD) from the SAR mission with Radar mosaics --------------------------------------------------------------------------- +*Generate analysis-ready data from the SAR mission with radar mosaics* The SEPAL recipe for radar mosaics allows users to generate analysis-ready data (ARD) from the Sentinel-1 C-Band synthetic aperture radar (SAR) mission, which can be used in subsequent analysis, such as land cover classification. @@ -11,21 +9,21 @@ Quick guide: timescans The following steps demonstrate the default procedure for creating a yearly timescan, which is useful for tasks such as land cover mapping. -1. Select the **Radar mosaic** within SEPAL recipes. +1. Select **Radar mosaic** within SEPAL **Recipes**. 2. Select your area of interest (AOI) and the year. 3. Check for orbit coverage. - 3.1 De-select all processing parameters. + 3.1 Deselect all processing parameters. 3.2 Select **Ascending orbit** and let the mosaic render. - 3.3 De-select **Ascending orbit** and select **Descending orbit**. Let the mosaic render. + 3.3 Deselect **Ascending orbit** and select **Descending orbit**. Let the mosaic render. - 3.4 See if both orbits cover the entire AOI. If they do not, select the orbit that covers the entire AOI. If they do, select both and let the mosaic render; then, check for artifacts that may originate from using both orbits. + 3.4 See if both orbits cover the entire AOI. If they do not, select the orbit that covers the entire AOI. If they do, select both and let the mosaic render; then, check for artefacts that may originate from using both orbits. -4. Select **Terrain** under Geometric operations. -5. Select **Moderate** under Outlier removal. -6. Export Median, Min, Max, and STD layers for both polarization bands VV and VH. +4. Select **Terrain** under **Geometric operations**. +5. Select **Moderate** under **Outlier removal**. +6. Export **Median**, **Min**, **Max** and **STD** layers for both polarization bands **VV** and **VH**. The following video tutorial demonstrates these steps in a reproducible way: @@ -33,4 +31,4 @@ The following video tutorial demonstrates these steps in a reproducible way: :height: 315 :width: 560 -More detailed explanations of what a timescan is, how it relates to the concept of ARD, and what influences the processing parameters have will be added to this documentation at a later date. +More detailed explanations of what a timescan is, how it relates to the concept of ARD, and what influences the processing parameters have will be added to this article at a later date. From aa1d740df930feff7e2eeca56d99d78d4b88bc44 Mon Sep 17 00:00:00 2001 From: Alex Gregor <111502950+alexryangregor@users.noreply.github.com> Date: Tue, 14 Nov 2023 10:37:48 +0100 Subject: [PATCH 11/18] Update planet_mosaic.rst Proofreading complete. --- docs/source/cookbook/planet_mosaic.rst | 31 +++++++++++++------------- 1 file changed, 16 insertions(+), 15 deletions(-) diff --git a/docs/source/cookbook/planet_mosaic.rst b/docs/source/cookbook/planet_mosaic.rst index ab918b809d..bd87ad1d25 100644 --- a/docs/source/cookbook/planet_mosaic.rst +++ b/docs/source/cookbook/planet_mosaic.rst @@ -1,10 +1,13 @@ Planet mosaic ============= +*Create a composite dataset from Planet images taken at different times* Overview -------- -A mosaic is a process of combining spatially overlapping images into an individual image. In the SEPAL platform, you can create a composite dataset from Planet images taken at different times by using different techniques. For example, you can choose to keep only the pixel value from the first or last image, or combine the values of the overlapping pixels using a weighting algorithm, the average, or the maximum or minimum value. In addition, certain preprocessing tasks can be applied to mask clouds, shadows, snow, etc. These operations are complex and repetitive. SEPAL offers an interactive and intuitive way to create Planet mosaics within any area of interest (AOI). +A mosaic is a process of combining spatially overlapping images into an individual image. + +In the SEPAL platform, you can create a composite dataset from Planet images taken at different times by using different techniques. For example, you can choose to keep only the pixel value from the first or last image, or combine the values of the overlapping pixels using a weighting algorithm, the average, or the maximum or minimum value. In addition, certain preprocessing tasks can be applied to mask clouds, shadows, snow, etc. These operations are complex and repetitive. SEPAL offers an interactive and intuitive way to create Planet mosaics within any area of interest (AOI). .. thumbnail:: ../_images/cookbook/planet_mosaic/time-series.png :group: planet-mosaic-recipe @@ -19,13 +22,13 @@ A mosaic is a process of combining spatially overlapping images into an individu Start ----- -Once the :code:`Planet mosaic` recipe is selected, SEPAL will show the recipe process in a new tab (1) and the AOI selection window will appear in the lower right (2). +Once the :code:`Planet mosaic` recipe is selected, SEPAL will show the recipe process in a new tab (see **1** in the image below) and the AOI selection window will appear in the lower right (**2**). .. thumbnail:: ../_images/cookbook/planet_mosaic/landing.png :group: planet-mosaic-recipe :title: The landing page of the Planet mosaic recipe -The first step is to change the name of the recipe, which will be used to name your files and recipes in the SEPAL folders. +The first step is to change the name of the recipe, which will be used to name your files and recipes in SEPAL folders. Double-click the tab and enter a new name (it will default to :code:`Planet_mosaic__`). @@ -105,7 +108,7 @@ Select :btn:` Done` to finish the process. NICFI basemaps """""""""""""" -The NICFI basemap uses Level 1 NICFI data provided by SEPAL. +The NICFI basemap uses Level 1 NICFI data provided by SEPAL (NICFI refers to Norway’s International Climate and Forests Initiative). .. note:: @@ -180,7 +183,7 @@ Once all of the parameters have been set, the mosaic will be rendered on the fly :width: 49% .. thumbnail:: ../_images/cookbook/planet_mosaic/mosaic_nrg.png - :title: Displayed on-the-fly rendered mosaic using nir, red, and green bands + :title: Displayed on-the-fly rendered mosaic using near-infrared (NIR), red, and green bands :group: planet-mosaic-recipe :width: 49% @@ -190,7 +193,7 @@ Once all of the parameters have been set, the mosaic will be rendered on the fly :width: 49% .. thumbnail:: ../_images/cookbook/planet_mosaic/mosaic_savi.png - :title: Displayed on-the-fly rendered mosaic using SAVI in false colors + :title: Displayed on-the-fly rendered mosaic using soil-adjusted vegetation index (SAVI) in false colors :group: planet-mosaic-recipe :width: 49% @@ -201,10 +204,10 @@ Retrieve You cannot export a recipe as an asset or a :code:`.tiff` file without a small computation quota (if you are a new user, see :doc:`../setup/resource`). -Select the :btn:`` tab, which will display the **Retrieve** panel, where you can select which bands or indexes to download, as well as specify the output scale and destination. +Select the :btn:`` tab, which will display the **Retrieve** pane, where you can select which bands or indexes to download, as well as specify the output scale and destination. .. thumbnail:: ../_images/cookbook/planet_mosaic/retrieve.png - :title: The last panel of the Planet mosaic: exportation + :title: The last pane of the Planet mosaic: exportation :group: planet-mosaic-recipe Bands @@ -214,7 +217,7 @@ Select the band(s) to export in the mosaic. There is no maximum number; however, .. tip:: - There is no fixed rule to band selection. Every index will be more useful to the type of analysis you are performing. The knowledge of the study area, evolution expected, and careful selection of an adapted band combination will improve the quality of downstream analysis. + There is no fixed rule to band selection. Every index will be more useful to the type of analysis you are performing. The knowledge of the study area, evolution expected and careful selection of an adapted band combination will improve the quality of downstream analysis. Raw bands """"""""" @@ -222,7 +225,7 @@ Raw bands - :guilabel:`blue`: blue - :guilabel:`green`: green - :guilabel:`red`: red -- :guilabel:`nir`: near infrared +- :guilabel:`nir`: near-infrared Indexes @@ -238,7 +241,7 @@ Indexes Scale ^^^^^ -You can set a custom scale for exportation by changing the value in the :code:`Scale` field. Requesting a smaller resolution than the image's native resolution will not improve the quality of the output, only its size (note: PlanetLab data's native resolution is 3.0 m – 4.1 m [altitude-dependent ground sample distance; `see more info `__]). +You can set a custom scale for exportation by changing the value in the :code:`Scale` field. Requesting a smaller resolution than the image's native resolution will not improve the quality of the output, only its size (note that PlanetLab data's native resolution is 3.0–4.1 m [altitude-dependent ground sample distance; `see more info `__]). Destination ^^^^^^^^^^^ @@ -256,9 +259,7 @@ Select :btn:` Apply` to start the download process. Access ^^^^^^ -Once the download process is complete, access the data in your SEPAL folders. - -The data will be stored in the :code:`Downloads` folder using the following format: +Once the download process is complete, access the data in your SEPAL folders, stored in :code:`Downloads` in the following format: .. code-block:: @@ -275,7 +276,7 @@ The data will be stored in the :code:`Downloads` folder using the following form Understanding how images are stored in a Planet mosaic is only required if you want to use them manually. SEPAL applications are bound to this tiling system and can digest this information for you. -The data are stored in a folder using the previously chosen name of the Planet mosaic (as described in the "Start" section of this page of the documentation). Since the data is spatially too big to be exported at once, the data is divided into smaller pieces and reassembled in a :code:`_.vrt` file. +The data are stored in a folder using the previously chosen name of the Planet mosaic (as described in the **Start** section of this article). Since the data is spatially too big to be exported at once, it is divided into smaller pieces and reassembled in a :code:`_.vrt` file. .. tip:: From fdd36ab355de6c42e91fcd4a244c2b90f35a8226 Mon Sep 17 00:00:00 2001 From: Alex Gregor <111502950+alexryangregor@users.noreply.github.com> Date: Tue, 14 Nov 2023 12:44:55 +0100 Subject: [PATCH 12/18] Update classification.rst Proofreading complete. --- docs/source/cookbook/classification.rst | 214 ++++++++++++------------ 1 file changed, 108 insertions(+), 106 deletions(-) diff --git a/docs/source/cookbook/classification.rst b/docs/source/cookbook/classification.rst index 80a6344a2f..3818bacbfa 100644 --- a/docs/source/cookbook/classification.rst +++ b/docs/source/cookbook/classification.rst @@ -1,37 +1,35 @@ Classification ============== - -Build supervised classifications of mosaic images to create easy-to-use user interfaces with the Classification recipe ----------------------------------------------------------------------------------------------------------------------- +*Build supervised classifications of mosaic images to create easy-to-use user interfaces with the Classification recipe* Overview -------- -With this recipe, SEPAL will help users build a supervised classification of any mosaic image. It is built on top of the most advanced tools available on Google Earth Engine (GEE) (including the classifiers CART, RandomForest, NaiveBayes and SVM), allowing users to create an easy-to-use user interface to: +With this recipe, SEPAL helps users build supervised classifications of any mosaic image. It is built on top of the most advanced tools available on Google Earth Engine (GEE) – including the classifiers CART, RandomForest, NaiveBayes and SVM – allowing users to create an easy-to-use user interface to: -- select the image to classify; +- select an image to classify; - define the class table; and - add training data from external sources and on-the-fly selection. -In combination with the other tools of SEPAL, the classification recipe can help you provide accurate land-use maps, without writing a single line of code. +In combination with other tools of SEPAL, the **Classification** recipe can help you provide accurate land-use maps, without writing a single line of code. Start ----- -Once the classification recipe is selected, SEPAL will show the recipe process in a new tab (1) and the **Image selection** window will appear in the lower-right (2). +Once the **Classification** recipe is selected, SEPAL will show the recipe process in a new tab (see **1** in figure below); the **Image selection** window will appear in the lower right (**2**). .. thumbnail:: ../_images/cookbook/classification/landing.png :group: classification-recipe - :title: The landing page of the classification recipe. + :title: The landing page of the **Classification** recipe The first step is to change the name of the recipe. This name will be used to identify your files and recipes in SEPAL folders. Use the best-suited convention for your needs. Simply double-click the tab and enter a new name. It will default to :code:`Classification_`. .. thumbnail:: ../_images/cookbook/classification/default_title.png - :title: Classification default title. + :title: Classification default title :width: 49% .. thumbnail:: ../_images/cookbook/classification/modified_title.png - :title: Classification modified title. + :title: Classification modified title :width: 49% .. note:: @@ -43,15 +41,15 @@ Parameters In the lower-right corner, the following five tabs are available, allowing you to customize the time series to your needs: -- :guilabel:`IMG`: The image to classify. -- :guilabel:`LEG`: The legend of the classification system. -- :guilabel:`TRN`: The training data of the model. -- :guilabel:`AUX`: The auxiliary global dataset to use in the model. -- :guilabel:`CLS`: The classifier configuration. +- :guilabel:`IMG`: image to classify +- :guilabel:`LEG`: legend of the classification system +- :guilabel:`TRN`: training data of the model +- :guilabel:`AUX`: auxiliary global dataset to use in the model +- :guilabel:`CLS`: classifier configuration .. thumbnail:: ../_images/cookbook/classification/parameters.png :group: classification-recipe - :title: The parameters of the classification recipe. + :title: The parameters of the **Classification** recipe Image selection ^^^^^^^^^^^^^^^ @@ -64,13 +62,13 @@ The first step consists of selecting the image bands on which to apply the class .. note:: - If multiple images are selected, each selected image should overlap each other. If masked pixels are found in one of the bands, the classifier will mask them. + If multiple images are selected, all selected images should overlap. If masked pixels are found in one of the bands, the classifier will mask them. Select :btn:` Add`. The following screen should be displayed: .. thumbnail:: ../_images/cookbook/classification/image_source.png :group: classification-recipe - :title: The two available image sources for classification. + :title: The two available image sources for classification Image type """""""""" @@ -81,24 +79,24 @@ Users can select images coming from an **Existing recipe** or an exported **GEE - Advantages: - - All of the computed bands from SEPAL can be used. - - Any modification to the existing recipe will be propagated in the final classification. + - all of the computed bands from SEPAL can be used; and + - any modification to the existing recipe will be propagated in the final classification. - Disadvantages: - - The initial recipe will be computed at each rendering step, slowing down the classification process and potentially breaking on-the-fly rendering due to GEE timeout errors. + - the initial recipe will be computed at each rendering step, slowing down the classification process and potentially breaking on-the-fly rendering due to GEE timeout errors. - **GEE asset**: - Advantages: - - Can be shared with other users. - - The computation will be faster, as the image has already been exported. + - can be shared with other users; and + - the computation will be faster, as the image has already been exported. - Disadvantages: - - Only the exported bands will be available. - - The :code:`Image` needs to be re-exported to propagate changes. + - only the exported bands will be available; and + - the :code:`Image` needs to be re-exported to propagate changes. Both methods behave the same way in the interface. @@ -107,14 +105,14 @@ Select bands .. tip:: - For this example, we will use a public asset created with the optical mosaic tool from SEPAL. It's a Sentinel-2 mosaic of Eastern Province in Zambia during the dry season from 2012 to 2020. Multiple bands are available. + For this example, we will use a public asset created with the **Optical mosaic** tool from SEPAL. It's a Sentinel-2 mosaic of Eastern Province in Zambia during the dry season from 2012 to 2020. Multiple bands are available. Use the following asset name if you want to reproduce our workflow: :code:`projects/sepal-cookbook/assets/classification/zmb-eastern_2012_2021` Image bands ########### -Once an asset has been selected, SEPAL will load its bands in the interface. You can use any band that is native to the image as input for the classification process. Simply click on the band name to select them. The selected bands are summarized in the expansion panel title (1) and displayed in gold in the panel content (2). +Once an asset has been selected, SEPAL will load its bands in the interface. You can use any band that is native to the image as input for the classification process. Simply click on the band name to select them. The selected bands are summarized in the expansion panel title (**1**) and displayed in gold in the pane content (**2**). In this example, we selected the following: @@ -132,7 +130,7 @@ Derived bands The analysis is not limited to natively available bands. SEPAL can also build additional derived bands on-the-fly. -Select :btn:` Derived bands` at the bottom of the pop-up window and select the deriving method to. This will add a a new panel to the expansion panel with the selected method name (1). The selected method will be applied to the selected bands. +Select :btn:` Derived bands` at the bottom of the pop-up window and select the deriving method. This will add a a new panel to the expansion panel with the selected method name (**1**). The selected method will be applied to the selected bands. .. note:: @@ -148,9 +146,9 @@ Select :btn:` Derived bands` at the bottom of the pop-up windo .. note:: - You should notice that in the figure, we compute the normalized difference between :code:`nir` and :code:`red` (i.e. the NDVI). It is also precomputed in the :code:`Indexes` derived bands. + You should notice that in the figure, we compute the normalized difference between :code:`nir` and :code:`red` (i.e. the NDVI). It is also pre-computed in the :code:`Indexes` derived bands. -Once the image selection is done, select :btn:` Apply` and the pop-up window will close. The images and bands will be displayed in the :guilabel:`IMG` panel on the lower-right corner of the screen. By selecting the :btn:`` button, you will remove the image and its band from the analysis altogether. +Once image selection is complete, select :btn:` Apply` and the pop-up window will close. The images and bands will be displayed in the :guilabel:`IMG` panel in the lower-right corner of the screen. By selecting the :btn:`` button, you will remove the image and its band from the analysis altogether. .. thumbnail:: ../_images/cookbook/classification/selected_bands.png :group: classification-recipe @@ -165,7 +163,7 @@ In this step, the user will specify the legend that should be used in the output .. thumbnail:: ../_images/cookbook/classification/landing_legend.png :group: classification-recipe - :title: The landing menu of the legend parameter. + :title: The landing menu of the legend parameter .. important:: @@ -190,18 +188,18 @@ Select the :btn:` Add` button again to add an extra class line Select :btn:`HEX` (4) to display the hexadecimal value of the selected color. It can also be used to insert a known color palette by utilizing its values. -If multiple classes are created and you are not sure which one to use, you can apply colors to them by selecting a preselected color-map (5). They are provided by the `gee community `__ and will be applied to every existing class in your panel. +If multiple classes are created and you are not sure which one to use, you can apply colors to them by selecting a preselected color-map (5). They are provided by the `GEE community `__ and will be applied to every existing class in your panel. .. thumbnail:: ../_images/cookbook/classification/create_legend.png :group: classification-recipe - :title: Manual creation of a legend. + :title: Manual creation of a legend Import legend """"""""""""" If you already have a file describing your legend, you can use it, rather than identifying every legend item individually. Your legend needs to be saved in .csv format and contain the following information: -- color (stored as a hexadecimal value [e.g. "#FFFF00"] or in three columns [red, blue, green]); +- color (stored as a hexadecimal value [e.g. #FFFF00] or in three columns [red, blue, green]); - value (stored as an integer); and - class (stored as a string). @@ -226,7 +224,7 @@ For example, a .csv file containing the following information is fully qualified 95,Mangroves,#00cf75 100,Moss,#fae6a0 -This one is the same using RGB-defined colors: +Alternatively, a file containing the following information – including RGB-defined colors – is also acceptable: .. code-block:: @@ -245,21 +243,21 @@ This one is the same using RGB-defined colors: Once the fully qualified legend file has been prepared on your computer, select :btn:`` and then :code:`Import from CSV`, which will open a pop-up window where you can drag and drop the file or select it manually from your computer files. -As shown on the next image, you can then select the columns that are defining your .csv file (select :btn:`Single column` for hexadecimal-defined colors and :btn:`multiple columns` for RGB-defined colors). +As shown in the following image, you can then select the columns that are defining your .csv file (select :btn:`Single column` for hexadecimal-defined colors and :btn:`Multiple columns` for RGB-defined colors). .. thumbnail:: ../_images/cookbook/classification/import_csv.png :group: classification-recipe - :title: Import legend from csv. + :title: Import legend from a .csv file -Select :btn:` Apply` to validate your selection. The classes will be added to the legend panel and you'll be able to modify the legend using the parameters presented in the previous section. +Select :btn:` Apply` to validate your selection. The classes will be added to the legend panel and you'll be able to modify the legend using the parameters presented in the previous subsection. .. thumbnail:: ../_images/cookbook/classification/imported_csv.png :group: classification-recipe - :title: Imported legend from a .csv file. + :title: Imported legend from a .csv file Select :btn:` Done` to validate this step. -Every panel should be closed and the colors of the legend are now displayed at the bottom of the map. No classification is performed, as we didn't provide any training data. Nevertheless, this step is the last mandatory step for setting parameters. Training data can be added using the on-the-fly training functionality. +Every pane should be closed; the colors of the legend should now be displayed at the bottom of the map. No classification is performed, as we didn't provide any training data. Nevertheless, this step is the last mandatory step for setting parameters. Training data can be added using the on-the-fly training functionality. Export legend """"""""""""" @@ -291,16 +289,16 @@ This menu will help the user manage the training data of the model used. To open .. thumbnail:: ../_images/cookbook/classification/training_landing.png :group: classification-recipe - :title: Training menu opening window. + :title: Training menu opening window Collected reference data """""""""""""""""""""""" -Collected reference data are data selected on-the-fly by the user. The workflow will be explained later in the documentation. In this panel, this type of data can be managed by the user. +Collected reference data are data selected on the fly by the user. The workflow will be explained later in the documentation. -The data appear as a pair, associating coordinates to a class value, which will be used to create training data in the classification model. +In this pane, this type of data can be managed by the user. The data appear as a pair, associating coordinates to a class value, which will be used to create training data in the classification model. -If you're satisfied with the current selection and you want to share the data with others, select :btn:`` and then :code:`Export reference data to csv`. A file will be created named: :code:`_reference_data.csv` and sent to your computer. It will embed all of the gathered point data using the following convention: +If you're satisfied with the current selection and you want to share the data with others, select :btn:`` and then :code:`Export reference data to csv`. A file will be created and sent to your computer, named :code:`_reference_data.csv`. It will embed all of the gathered point data using the following convention: .. code-block:: @@ -317,7 +315,7 @@ If you are not satisfied with the selected data, select :btn:` Add` and choose the type of dat .. thumbnail:: ../_images/cookbook/classification/import-training-data.png :group: classification-recipe - :title: The different types of training data available in SEPAL. + :title: The different types of training data available in SEPAL CSV ### @@ -374,7 +372,7 @@ Selecting the :btn:` Done` button will complete the uploading .. thumbnail:: ../_images/cookbook/classification/import-training-csv-summary.png :group: classification-recipe - :title: Import a .csv file in SEPAL as training data. + :title: Import a .csv file in SEPAL as training data GEE table ######### @@ -387,24 +385,24 @@ For the other steps, please reproduce what was presented in the .csv section abo .. thumbnail:: ../_images/cookbook/classification/import-training-gee-coords.png :group: classification-recipe - :title: Import a GEE table in SEPAL as training data. + :title: Import a GEE table in SEPAL as training data .. note:: - To build the documentation example, you can use this public asset: :code:`projects/sepal-cookbook/assets/classification/zmb_eastern_esa_2012_2021_reference_data`. + To build the documentation example, use this public asset: :code:`projects/sepal-cookbook/assets/classification/zmb_eastern_esa_2012_2021_reference_data`. Sample classification ##################### -Instead of providing dataset points, SEPAL can also extract reference data from an already existing classification. It's a good way to improve an already existing classification system using an image with a better resolution. +Instead of providing dataset points, SEPAL can also extract reference data from an already existing classification – which is a good way to improve an already existing classification system using an image with a better resolution. To sample data, SEPAL will randomly select a number of points in each class and extract the class value using the provided resolution. Start by selecting btn:`Sample classification` in the opened pop-up window, where all of the the parameters can be set: -- **Sample per class**: The number of samples per class of the provided image. The more samples you request, the more accurate the model will be (if too many samples are selected though, on-the-fly visualization will never render; default to: :code:`1000`). -- **Scale to sample in**: The scale used to create the sample in the provided image (it should match the image to classify resolution; default to: :code:`30 m`). -- **EE asset ID**: The ID of the classification to sample (it should be an :code:`ee.Image` accessible to the user). +- **Sample per class**: the number of samples per class of the provided image. The more samples you request, the more accurate the model will be (if too many samples are selected, on-the-fly visualization will never render; default to: :code:`1000`). +- **Scale to sample in**: the scale used to create the sample in the provided image (it should match the image to classify resolution; default to: :code:`30 m`). +- **EE asset ID**: the ID of the classification to sample (it should be an :code:`ee.Image` accessible to the user). - **Class band**: The class to use for classification value (the dropdown menu will be filled with the bands found in the provided asset). .. note:: @@ -413,36 +411,36 @@ Start by selecting btn:`Sample classification` in the opened pop-up window, wher .. thumbnail:: ../_images/cookbook/classification/import-training-sample.png :group: classification-recipe - :title: Parameters to sample training data from an existing classification. + :title: Parameters to sample training data from an existing classification .. note:: - When all of the parameters are selected, it can take time, as SEPAL builds the sampling values on-the-fly. They will only be displayed once the sampling is validated. + When all of the parameters are selected, it can take time, as SEPAL builds the sampling values on the fly. They will only be displayed once the sampling is validated. -Select :btn:` Next` to display the sampling summary. In this panel, SEPAL displays each class of the legend (as defined in the previous section) and the number of samples created for it. +Select :btn:` Next` to display the sampling summary. In this pane, SEPAL displays each class of the legend (as defined in the previous subsection) and the number of samples created for it. -Select the :btn:`` (1) buttons to change the number of samples in a specific class. By default, SEPAL ignores the samples with a :code:`Null` value. One can select :btn:`Default` (2) for any of the classes, so that these points end up in this default class instead of being ignored. +Select the :btn:`` buttons (**1**) to change the number of samples in a specific class. By default, SEPAL ignores the samples with a :code:`Null` value. One can select :btn:`Default` (**2**) for any of the classes so that these points end up in the default class instead of being ignored. .. thumbnail:: ../_images/cookbook/classification/import-training-sample-summary.png :group: classification-recipe - :title: Parameters to sample training data from an existing classification. + :title: Parameters to sample training data from an existing classification SEPAL recipe ############ -SEPAL is also able to dirrectly apply a model built in another recipe as training data. In this case, we are not importing the points, but all of the model from the external recipe. It will not add points to the map. It's useful when the same classification needs to be applied on the same area for multiple years. The classification work can be carried out only in the first year and then applied recursively on all the others. +SEPAL is also able to directly apply a model built in another recipe as training data. In this case, we are not importing the points, but all of the model from the external recipe. It will not add points to the map. It's useful when the same classification needs to be applied on the same area for multiple years. The classification work can be carried out only in the first year and then applied recursively on all the others. Select :btn:`Saved SEPAL recipe` to open the pop-up window. In the dropdown menu, select one of the recipes saved in your SEPAL account. .. note:: - The imported recipe needs to be a classification recipe. If none are found, the dropdown menu will be empty. + The imported recipe needs to be a **Classification** recipe. If none are found, the dropdown menu will be empty. This recipe cannot come from another SEPAL account. .. thumbnail:: ../_images/cookbook/classification/import-training-recipe.png :group: classification-recipe - :title: Select an already existing SEPAL classification recipe to use its training data for your own classification. + :title: Select an already existing SEPAL **Classification** recipe to use its training data for your own classification Use auxiliary datasets ^^^^^^^^^^^^^^^^^^^^^^ @@ -457,7 +455,7 @@ Select :btn:`AUX` to open the **Auxiliaries** tab. Three sources are currently i .. thumbnail:: ../_images/cookbook/classification/auxiliary_tab.png :group: classification-recipe - :title: Select preset auxiliary datasource to improve the quality of the classification. + :title: Select preset auxiliary datasource to improve the quality of the classification Classifier configuration ^^^^^^^^^^^^^^^^^^^^^^^^ @@ -470,39 +468,39 @@ Classifier configuration The default value is a **Random Forest** classifier using 25 trees. -The classification tool used in SEPAL is based on the `Smile - Statistical Machine Intelligence and Learning Engine Javascript `__ library. Please refer to their documentation for specific descriptions of each model. +The **Classification** tool used in SEPAL is based on the `Smile - Statistical Machine Intelligence and Learning Engine Javascript `__ library (refer to their documentation for specific descriptions of each model). -Select :btn:`CLS` to open the classification parameter menu. SEPAL supports 7 classifiers: +Select :btn:`CLS` to open the **Classification parameter** menu. SEPAL supports seven classifiers: -- Random Forest -- Gradient tree boost +- random forest +- gradient tree boost - cart -- Naive Bayes +- naive bayes - SVM -- Min distance -- Decision Tree +- min distance +- decision tree For each of them, the workflow is the same: 1. Select the classifier by clicking on the corresponding name. SEPAL will display some of the parameters available. -2. Select :btn:`More` on the lower left side of the panel to fully customize your classifier. The classification results will be updated on-the-fly. +2. Select :btn:`More` on the lower-left side of the panel to fully customize your classifier. The classification results will be updated on the fly. .. thumbnail:: ../_images/cookbook/classification/cls_less.png :width: 49% :group: classification-recipe - :title: The only simple parameter of a random forest classifier (number of trees). + :title: The only simple parameter of a **random forest** classifier (number of trees) .. thumbnail:: ../_images/cookbook/classification/cls_more.png :width: 49% :group: classification-recipe - :title: All of the customization parameters of a random forest classifier. + :title: All of the customization parameters of a **random forest** classifier -On the fly training +On-the-fly training ------------------- .. note:: - This process requires a good understanding of the visualization feature of SEPAL. Please refer to the `feature <#>`__ section for more information. + This process requires a good understanding of the **Visualization** feature of SEPAL (refer to the `feature <#>`__ section for more information). Once all of the parameters are set, the user is free to add extra training data in the web interface and the new points will be added to the final model, improving the quality of the classification. @@ -513,117 +511,121 @@ In order to improve the classification, one must set up the view to display all In the following image, we displayed: -- The current recipe (1) using the class colors in categorical mode. -- The current image (what you are classifying) (2) using the NIR,RED,SWIR band combination. -- The extra visual dataset NICFI PlaneLab data (3) from 2021. +- The current recipe (**1**) using the class colors in categorical mode. +- The current image (what you are classifying) (**2**) using the NIR,RED,SWIR band combination. +- The extra visual dataset NICFI Planet Lab data (**3**) from 2021. -The number (4) indicates a cluster of existing training points. Zoom-in and they will be displayed as markers using the color of the class they mark (5). +The number (4) indicates a cluster of existing training points. Zoom in and they will be displayed as markers using the color of the class they mark (**5**). .. important:: - This initial classification has been set using sampled data. Since they are sampled from a larger image, some are out of the image. They will have no impact on the classification as they are applied to masked pixels (6). + This initial classification has been set using sampled data. Since they are sampled from a larger image, some are out of the image. They will have no impact on the classification as they are applied to masked pixels (**6**). .. thumbnail:: ../_images/cookbook/classification/classification_view.png :group: classification-recipe - :title: A classification set-up ready to add new training data. + :title: A classification setup ready to add new training data Select points ^^^^^^^^^^^^^ -To start adding points, open the training interface by selecting :btn:`` in the upper-right of the screen (1). Once selected, the background color becomes darker and the pointer of the mouse becomes a :icon:`fa-solid fa-plus`. +To start adding points, open the training interface by selecting :btn:`` in the upper right of the screen (**1**). Once selected, the background color becomes darker and the pointer of the mouse becomes a :icon:`fa-solid fa-plus`. The process to add new training data is as follows: -1. **Click on the map to select a point**: You can click in any of the panels (this is not restricted to the recipe panel), but to be useful, the point needs to be within the border of the AOI. If it's not already the case, the class selection panel will appear in the upper-right of the window (2). +1. **Click on the map to select a point**: You can click in any of the panes (not restricted to the **Recipe** pane), but to be useful, the point needs to be within the border of the AOI. If it's not already the case, the **Class selection** panel will appear in the upper right of the window (**2**). 2. **Select the class value**: The previous class value is preselected, but you can change it to any other class value from the defined legend. The legend is displayed as :code:` ()`. -You can now click elsewhere on the map to add another point. If you are satisfied with the classification, select :btn:` Close` (3) and select :btn:`` again to stop editing the points. Every time a new point is added, the classification map is recomputed and rendered in the left window. +You can now click elsewhere on the map to add another point. If you are satisfied with the classification, select :btn:` Close` (3) and select :btn:`` again to stop editing the points. Every time a new point is added, the **Classification** map is recomputed and rendered on the left side. .. thumbnail:: ../_images/cookbook/classification/add_point.png :group: classification-recipe - :title: Manually adding new training data in the model. + :title: Manually adding new training data in the model Modify existing points ^^^^^^^^^^^^^^^^^^^^^^ -To modify existing points, select the :btn:`` to open the point editing interface and follow the following steps: +To modify existing points, select the :btn:`` to open the **Point editing** interface. Then: -1. **Select a point**: To select a point, click on an existing marker. It will appear bolder than the others. If it's not already the case, the class selection panel will appear in the upper-right of the window. -2. **Change the class value**: The point class will be selected in the editing menu with a :icon:`fa-solid fa-check`. Select any other class value to change it. +1. **Select a point**: To select a point, click on an existing marker. It will appear bolder than the others. If it's not already the case, the **Class selection** pane will appear in the upper right. +2. **Change the class value**: The point class will be selected in the **Editing** menu with a :icon:`fa-solid fa-check`. Select any other class value to change it. Check the validity ^^^^^^^^^^^^^^^^^^ -SEPAL embeds information to help the user understand if the amount of training data is sufficient to produce an accurate classification model. In the recipe window, change the band combination to :code:`Class probability`. The user now sees the probability of the model (i.e. the confidence level of the level with output class for each pixel). If the value is high (>80%), then the pixel can be considered valid; if the value is low (<80%), the model needs more training data or extra bands to improve the analysis. +SEPAL embeds information to help the user understand if the amount of training data is sufficient to produce an accurate classification model. In the **Recipe** window, change the **Band combination** to :code:`Class probability`. + +The user now sees the probability of the model (i.e. the confidence level of the level with output class for each pixel). + +If the value is high (> 80 percent), then the pixel can be considered valid; if the value is low (< 80 percent), the model needs more training data or extra bands to improve the analysis. -In the example image, the lake is classified as a "permanent water body" with a confidence of 65%, which is higher than the rest of the vegetation around it. +In the example image, the lake is classified as a **permanent water body** with a confidence of 65 percent, which is higher than the rest of the vegetation around it. .. thumbnail:: ../_images/cookbook/classification/classification_confidence.png :group: classification-recipe - :title: The classification confidence around a lake in eastern Zambia. + :title: The classification confidence around a lake in eastern Zambia -This analysis can also be conducted class by class using the built-in :code:` %` bands. Select the one corresponding to the class you want to assess (as you can see in the following image) and you'll get the % of confidence for each pixel to be in the sub-mentioned class. +This analysis can also be conducted class-by-class using the built-in :code:` %` bands. Select the one corresponding to the class you want to assess (see the following image) and you'll get the percentage of confidence for each pixel to be in the sub-mentioned class. .. thumbnail:: ../_images/cookbook/classification/water_confidence.png :group: classification-recipe - :title: The classification confidence of "permanent water body" around a lake in eastern Zambia. + :title: The classification confidence of **permanent water body** around a lake in eastern Zambia Export ------ .. important:: - You cannot export a recipe as an asset or a :code:`.tiff` file without a small computation quota. If you are a new user see :doc:`../setup/resource` to know more. + You cannot export a recipe as an asset or a :code:`.tiff` file without a small computation quota. If you are a new user, see :doc:`../setup/resource`. Start download ^^^^^^^^^^^^^^ -Selecting the :icon:`fa-solid fa-cloud-arrow-down` tab will open the **Retrieve** panel where you can select the exportation parameters (1). +Selecting the :icon:`fa-solid fa-cloud-arrow-down` tab will open the **Retrieve** pane, where you can select the exportation parameters (**1**). -You need to select the band to export (2). There is no maximum number of bands; however, exporting useless bands will only increase the size and time of the output. +You need to select the band to export (**2**). There is no maximum number of bands; however, exporting useless bands will only increase the size and time of the output. -You can set a custom scale for exportation (3) by changing the value of the slider in meters (m). (Note: Requesting a smaller resolution than images' native resolution will not improve the quality of the output – just its size; keep in mind that the native resolution of Sentinel data is 10 m, while Landsat is 30 m.) +You can set a custom scale for exportation (**3**) by changing the value of the slider in metres (m). (Note: Requesting a smaller resolution than images' native resolution will not improve the quality of the output – just its size; keep in mind that the native resolution of Sentinel data is 10 m, while Landsat is 30 m.) -You can export the image to the :btn:`SEPAL workspace` or to the :btn:`Google Earth Engine Asset` list. The same image will be exported, but in the first case you will find it in :code:`.tif` format in the :code:`Downloads` folder; in the second case, the image will be exported to your GEE account asset list. +You can export the image to the :btn:`SEPAL workspace` or to the :btn:`Google Earth Engine Asset` list. The same image will be exported, but for the former, you will find it in :code:`.tif` format in the :code:`Downloads` folder; for the latter, the image will be exported to your **GEE account asset list**. .. note:: - If :btn:`Google Earth Engine Asset` is not displayed, it means that your GEE account is not connected to SEPAL. Please refer to `Connect SEPAL to GEE <../setup/gee.html>`__. + If :btn:`Google Earth Engine Asset` is not displayed, your GEE account is not connected to SEPAL. Refer to `Connect SEPAL to GEE <../setup/gee.html>`__. Select :btn:` Apply` to start the download process. .. thumbnail:: ../_images/cookbook/classification/export.png :group: classification-recipe - :title: The classification confidence of "permanent water body" around a lake in eastern Zambia. + :title: The classification confidence of **permanent water body** around a lake in eastern Zambia. Exportation status ^^^^^^^^^^^^^^^^^^ -By going to the **Task** tab (in the lower-left corner using the :btn:`` or :btn:`` buttons, depending on the loading status), you will see the list of different loading tasks. +By going to the **Tasks** tab (in the lower-left corner using the :btn:`` or :btn:`` buttons, depending on the loading status), you will see the list of different loading tasks. -The interface will provide you with information about the task progress and it will display an error if the exportation has failed. If you are unsatisfied with the way we present information, the task can also be monitored using the `GEE task manager `__. +The interface will provide you with information about the task progress and display an error if the exportation has failed. If you are unsatisfied with the way we present information, the task can also be monitored using the `GEE task manager `__. .. tip:: This operation is running between GEE and SEPAL servers in the background. You can close the SEPAL page without ending the process. -When the task is finished, the frame will be displayed in green, as shown in the second image. +When the task is finished, the frame will be displayed in green, as shown in the second image below. .. thumbnail:: ../_images/cookbook/time_series/download.png :width: 49% - :title: Evolution of the downloading process of the recipe displayed in the task manager of SEPAL. + :title: Evolution of the downloading process of the recipe displayed in the **Task manager** of SEPAL :group: classification-recipe .. thumbnail:: ../_images/cookbook/time_series/download_complete.png :width: 49% - :title: Completed downloading process of the recipe displayed in the task manager of SEPAL. + :title: Completed downloading process of the recipe displayed in the **Task manager** of SEPAL :group: classification-recipe Access ^^^^^^ -Once the download process is done, you can access the data in your SEPAL folders. The data will be stored in the :code:`Downloads` folder using the following format: +Once the download process is done, you can access the data in your **SEPAL folders**. The data will be stored in the :code:`Downloads` folder using the following format: .. code-block:: @@ -640,7 +642,7 @@ Once the download process is done, you can access the data in your SEPAL folders Understanding how images are stored in an optical mosaic is only required if you want to manually use them. The SEPAL applications are bound to this tiling system and can digest this information for you. -The data are stored in a folder using the name of the optical mosaic as it was created in the first section of this article. As the number of data is spatially too big to be exported at once, the data are divided into smaller pieces and brought back together in a :code:`_.vrt` file. +The data are stored in a folder using the name of the optical mosaic as it was created in the first section of this article. As the data are spatially too big to be exported at once, they are divided into smaller pieces and brought back together in a :code:`_.vrt` file. .. tip:: From 73581282ec22220d83c990bc2fd1ad832729a5e2 Mon Sep 17 00:00:00 2001 From: Alex Gregor <111502950+alexryangregor@users.noreply.github.com> Date: Tue, 14 Nov 2023 14:49:57 +0100 Subject: [PATCH 13/18] Update time_series.rst Proofreading complete. --- docs/source/cookbook/time_series.rst | 90 ++++++++++++++-------------- 1 file changed, 44 insertions(+), 46 deletions(-) diff --git a/docs/source/cookbook/time_series.rst b/docs/source/cookbook/time_series.rst index b61436fd47..eb8c1e25fe 100644 --- a/docs/source/cookbook/time_series.rst +++ b/docs/source/cookbook/time_series.rst @@ -1,19 +1,18 @@ Time series =========== -Create and retrieve Satellite Image Time Series (SITS) to study patterns and key changes in landscape evolution over time -------------------------------------------------------------------------------------------------------------------------- +*Create and retrieve Satellite Image Time Series to study patterns and key changes in landscape evolution over time* Overview -------- A Satellite Image Time Series (SITS) is a set of satellite images taken of the same scene at different times. A SITS makes use of different satellite sources to obtain a larger data series with a short time interval between two images. In this case, it is fundamental to observe the spatial resolution and registration constraints. -Satellite observations offer opportunities for understanding how the Earth is changing, determining the causes of these changes, and predicting future changes. Remotely-sensed data, combined with information from ecosystem models, offers an opportunity for predicting and understanding the behavior of Earth's ecosystem. Sensors with high spatial and temporal resolutions make the observation of precise spatio-temporal structures in dynamic scenes more accessible. Temporal components integrated with spectral and spatial dimensions allow the identification of complex patterns concerning applications connected with environmental monitoring and analysis of land cover dynamics. +Satellite observations offer opportunities for understanding how the Earth is changing, determining the causes of these changes and predicting future changes. Remotely sensed data, combined with information from ecosystem models, offer an opportunity for predicting and understanding the behaviour of Earth's ecosystems. Sensors with high spatial and temporal resolutions make the observation of precise spatio-temporal structures in dynamic scenes more accessible. Temporal components integrated with spectral and spatial dimensions allow the identification of complex patterns concerning applications connected with environmental monitoring and analysis of land cover dynamics. Change detection can only provide a "before and after" scenario; a time-series analysis provides an opportunity to study patterns and key changes in the landscape evolution over time. -This SEPAL recipe allows users to create and retrieve SITS based on `Landsat `__ and `Copernicus `__ programs' imagery using the Google Earth Engine (GEE) datacube. +This SEPAL recipe allows users to create and retrieve SITS based on `Landsat `__ and `Copernicus `__ programmes' imagery using the Google Earth Engine (GEE) datacube. .. attention:: @@ -22,20 +21,20 @@ This SEPAL recipe allows users to create and retrieve SITS based on `Landsat __`. .. thumbnail:: ../_images/cookbook/time_series/default_title.png - :title: Time-series default title. + :title: Time series default title :width: 49% .. thumbnail:: ../_images/cookbook/time_series/title.png - :title: Time-series modified title. + :title: Time series modified title :width: 49% .. note:: @@ -45,15 +44,15 @@ The first step is to change the name of the recipe. This name will be used to id Parameters ---------- -In the lower-right corner, four tabs are available. They will allow you to customize the time series to your needs. +In the lower-right corner, four tabs are available, allowing you to customize the time series to your needs: -- :guilabel:`AOI`: Area of interest (AOI). -- :guilabel:`DAT`: Dates of the time series. -- :guilabel:`SRC`: Source datasets of the time series. -- :guilabel:`PRC`: Pre-processing parameters. +- :guilabel:`AOI`: area of interest (AOI) +- :guilabel:`DAT`: dates of the time series +- :guilabel:`SRC`: source datasets of the time series +- :guilabel:`PRC`: pre-processing parameters .. thumbnail:: ../_images/cookbook/time_series/no_parameters.png - :title: The four tabs to set up SEPAL time-series parameters. + :title: The four tabs to set up SEPAL time series parameters :group: time-series-recipe AOI selection @@ -68,7 +67,7 @@ The data exported by the recipe will be confined to the bounds of the AOI. There For more information, go to :doc:`../feature/aoi_selector`. .. thumbnail:: ../_images/cookbook/time_series/aoi_administrative.png - :title: Select AOI based on administrative layers. + :title: Select AOI based on administrative layers :group: time-series-recipe Dates @@ -77,12 +76,12 @@ Dates In the :guilabel:`DAT` tab, you will be asked to select the start date and end date of the time series. Select the **Date** text field to open a pop-up window. Choose the :btn:` Select` button to choose a date. When both dates have been chosen, select the :btn:` Apply` button. .. thumbnail:: ../_images/cookbook/time_series/dates.png - :title: Select AOI based on EE table. + :title: Select AOI based on EE table :width: 49% :group: time-series-recipe .. thumbnail:: ../_images/cookbook/time_series/datepicker.png - :title: Select AOI based on EE table. + :title: Select AOI based on EE table :width: 49% :group: time-series-recipe @@ -94,7 +93,7 @@ As mentioned in the introduction, a SITS makes use of different satellite source When all of the data has been selected, select :btn:` Apply`. .. thumbnail:: ../_images/cookbook/time_series/sources.png - :title: The Sources panel to select the different datasets that will be used in the time-series. + :title: The **Sources** pane to select the different datasets that will be used in the time series :group: time-series-recipe Pre-processing @@ -109,7 +108,7 @@ Pre-processing - Cloud masking: :guilabel:`moderate` - Snow masking: :guilabel:`on` -Multiple pre-processing parameters can be set to improve the quality of the provided images. SEPAL has gathered four of them in the form of these interactive buttons. If you think others should be added, don't hesitate to mention it in our `issue tracker `__. +Multiple pre-processing parameters can be set to improve the quality of the provided images. SEPAL has gathered four of them in the form of these interactive buttons. If you think others should be added, tell us in the `issue tracker `__. **Correction** @@ -118,25 +117,24 @@ Multiple pre-processing parameters can be set to improve the quality of the prov **Cloud detection** -- :guilabel:`QA bands`: Use previously created QA bands from datasets. +- :guilabel:`QA bands`: Use previously created quality assessment (QA) bands from datasets. - :guilabel:`Cloud score`: Use a cloud-scoring algorithm. **Cloud masking** - :guilabel:`Moderate`: Rely only on image source QA bands for cloud masking. -- :guilabel:`Aggressive`: Rely on image source QA bands and a cloud-scoring algorithm for cloud masking. This will probably "mask" some built-up areas and other bright features. +- :guilabel:`Aggressive`: Rely on image source QA bands and a cloud-scoring algorithm for cloud masking (this will probably "mask" some built-up areas and other bright features). **Snow masking** -- :guilabel:`On`: Mask snow. This tends to leave some pixels with shadowy snow. -- :guilabel:`Off`: Don't mask snow. Note that some clouds might get misclassified as snow, and because of this, disabling snow masking might lead to cloud artifacts. - +- :guilabel:`On`: Mask snow (this tends to leave some pixels with shadowy snow). +- :guilabel:`Off`: Don't mask snow (some clouds might get misclassified as snow, and because of this, disabling snow masking might lead to cloud artefacts). .. thumbnail:: ../_images/cookbook/time_series/pre_processing.png - :title: The Pre-processing panel to select the extra filtering processes that will improve the quality of the provided images. + :title: The **Pre-processing** pane to select the extra filtering processes that will improve the quality of the provided images. :group: time-series-recipe -Available Bands +Available bands ^^^^^^^^^^^^^^^ .. note:: @@ -148,7 +146,7 @@ The time series will use a single observation for each pixel. This observation c Analysis -------- -Once all of the parameters are set, you can generate data from the recipe. Some can be directly generated on-the-fly from the interface; the rest require retrieving the data from SEPAL folders. +Once all parameters are set, you can generate data from the recipe. Some can be directly generated on the fly from the interface; the rest require retrieving the data from SEPAL folders. The analysis icons can be found in the upper-right corner of the SEPAL interface: @@ -156,7 +154,7 @@ The analysis icons can be found in the upper-right corner of the SEPAL interface - :btn:``: Retrieve data. .. thumbnail:: ../_images/cookbook/time_series/data_analysis.png - :title: The two tabs used to plot or retrieve time-series data. + :title: The two tabs used to plot or retrieve time series data. :group: time-series-recipe .. tip:: @@ -181,15 +179,15 @@ On the main graph, each point represents one valid observation (based on the pre The coordinates of the point are displayed at the top of the chart window. .. thumbnail:: ../_images/cookbook/time_series/plot.png - :title: Plot chart pop-up window providing all of the available information on one single pixel alongside the time series. + :title: **Plot chart** pop-up window providing all of the available information on one single pixel alongside the time series. :group: time-series-recipe .. attention:: - Since the plot feature is retrieving information from GEE on-the-fly and presenting it in an interactive window, this operation can take time, depending on the number of available observations and the complexity of the selected preprocessing parameters. If a spinning wheel appears in the pop-up window, you may have to wait up to two minutes to see the data displayed. + Since the plot feature is retrieving information from GEE on the fly and presenting it in an interactive window, this operation can take time, depending on the number of available observations and the complexity of the selected pre-processing parameters. If a spinning wheel appears in the pop-up window, you may have to wait up to two minutes to see the data displayed. .. thumbnail:: ../_images/cookbook/time_series/plot_loading.png - :title: Plot chart pop-up window providing all of the available information on one single pixel alongside the time series. If there are numerous observations and complex preprocessing, retrieving the data can take up to two minutes. + :title: **Plot chart** pop-up window providing all of the available information on one single pixel alongside the time series. If there are numerous observations and complex preprocessing, retrieving the data can take up to two minutes. :group: time-series-recipe Export @@ -199,17 +197,17 @@ In order for the data generated by the recipe to be used in other workflows, it .. important:: - You cannot export a recipe as an asset or a :code:`.tiff` file without a small computation quota. If you are a new user see :doc:`../setup/resource` to know more. + You cannot export a recipe as an asset or a :code:`.tiff` file without a small computation quota. If you are a new user, see :doc:`../setup/resource`. Parameters """""""""" -Select :btn:`` to open the **Download parameters** window. You will be able to select the measure to use on each observation of the time-series. This measure can be selected in the list of available bands presented above in a previous section. +Select :btn:`` to open the **Download parameters** window. You will be able to select the measure to use on each observation of the time series. This measure can be selected in the list of available bands presented above in a previous section. .. note:: - There is no fixed rule to the measure selection. Each index is more adapted to a set of analyses in a defined biome. The knowledge of the study area, the evolution expected and the careful selection of an adapted measure will improve the quality of the downstream analysis. + There is no fixed rule to the measure selection. Each index is more adapted to a set of analyses in a defined biome. The knowledge of the study area, the evolution expected and the careful selection of an adapted measure will improve the quality of downstream analysis. -You can set a custom scale for exportation by changing the value of the slider in meters (m). Keep in mind that Sentinel data native resolution is 10 m and Landsat is 30 m. +You can set a custom scale for exportation by changing the value of the slider in metres (m). Keep in mind that Sentinel data native resolution is 10 m and Landsat is 30 m. When all the data is selected, select the :btn:` apply` button. Notice that the task tab in the lower-left corner of the screen (1) will change from :btn:`` to :btn:``, meaning that the tasks are loading. @@ -221,28 +219,28 @@ When all the data is selected, select the :btn:` apply` butto Exportation status """""""""""""""""" -By selecting the task tab (bottom left corner using the :btn:`` or :btn:`` buttons, depending on the loading status), you will see the list of different tasks loading. The interface will provide you with information about the task progress and it will display an error if the exportation has failed. If you are unsatisfied with the way we present information, the task can also be monitored using the `GEE task manager `__. +By selecting the **Tasks** tab (lower-left corner using the :btn:`` or :btn:`` buttons, depending on the loading status), you will see the list of different tasks loading. The interface will provide you with information about the task progress and display an error if the exportation has failed. If you are unsatisfied with the way we present information, the task can also be monitored using the `GEE task manager `__. .. tip:: This operation is running between GEE and SEPAL servers in the background, so you can close the SEPAL page without ending the process. -When the task is finished, the frame will be displayed in green, as shown in the second image. +When the task is finished, the frame will be displayed in green, as shown in the second image below. .. thumbnail:: ../_images/cookbook/time_series/download.png :width: 49% - :title: Evolution of the downloading process of the recipe displayed in the task manager of SEPAL. + :title: Evolution of the downloading process of the recipe displayed in the **Task manager** of SEPAL. :group: time-series-recipe .. thumbnail:: ../_images/cookbook/time_series/download_complete.png :width: 49% - :title: Completed downloading process of the recipe displayed in the task manager of SEPAL. + :title: Completed downloading process of the recipe displayed in the **Task manager** of SEPAL. :group: time-series-recipe Access """""" -Once the downloading process is done, you can access the data in your SEPAL folders. The data will be stored in the :code:`Downloads` folder using the following format: +Once the download process is done, you can access the data in your **SEPAL folders** in :code:`Downloads`, using the following format: .. code-block:: @@ -267,23 +265,23 @@ Once the downloading process is done, you can access the data in your SEPAL fold .. important:: - Understanding how images are stored in a Time series is only required if you want to manually use them. The SEPAL applications are bound to this tiling system and can digest this information for you. + Understanding how images are stored in a time series is only required if you want to manually use them. The SEPAL applications are bound to this tiling system and can digest this information for you. -The data are stored in a folder using the name of the time series as it was labeled in the first section of this document. The SEPAL team was forced to use this folder structure as GEE is unable to export an :code:`ee.ImageCollection`. As the number of data is spatially too big to be exported at once, the data are divided into smaller pieces and reassembled in a :code:`stack.vrt` file. +The data are stored in a folder using the name of the time series as it was labeled in the first section of this document. The SEPAL team was forced to use this folder structure as GEE is unable to export an :code:`ee.ImageCollection`. As the data is spatially too big to be exported at once, they are divided into smaller pieces and reassembled in a :code:`stack.vrt` file. The AOI provided by the user will be divided into multiple SEPAL tiles. The AOI is a :code:`ee.FeatureCollection`; each feature is downloaded in a different tile. If the tile is bigger than 2° x 2° (EPSG:4326), then the feature is divided again until all of the tiles are smaller than the maximum 2° size. The tiles are identified by their :code:``. -To limit the size of the downloaded images, in each SEPAL tile, the time period is divided into **Chunks** of 3 months. They are identified by their :code:`_`. **Chunks** are image folders. As a SEPAL tile is still bigger than what GEE can download at once, the images are divided into GEE tiles. This tiling system uses its own identification system (000000xxxx-000000xxxx). Consequently, **Chunks** contain tile raster images. Each one of these images is composed of one band per observation date, with the value of the measure for each pixel. The bands are named with the date. +To limit the size of the downloaded images, in each SEPAL tile, the time period is divided into **Chunks** of 3 months. They are identified by their :code:`_`. **Chunks** are image folders. As a SEPAL tile is still bigger than what GEE can download at once, the images are divided into GEE tiles. This tiling process uses its own identification system (000000xxxx-000000xxxx). Consequently, **Chunks** contain tile raster images. Each one of these images is composed of one band per observation date, with the value of the measure for each pixel. The bands are named with the date. To gather all these rasters together, a first agregation on time is performed. One :code:`stack.vrt` is created per GEE tile, meaning that each :code:`stack.vrt` file contains all the :code:`*.tif` contained in each **Chunk**, reconstituting the full time period on the smallest spatial unit: the GEE tile. Each file is stored in a folder called :code:`tile-`. Finally, information is gathered spatially at the SEPAL tile level in the main :code:`stack.vrt` file. -The last file: :code:`date.csv` gathers all the observation dates in chronological order. +The last file, :code:`date.csv`, gathers all the observation dates in chronological order. .. note:: - The dates contained in :code:`date.csv` can differ from one SEPAL tile to another, due to data availability and preprocessing filters. + The dates contained in :code:`date.csv` can differ from one SEPAL tile to another, due to data availability and pre-processing filters. .. tip:: @@ -314,4 +312,4 @@ Here is an example of a real TS folder: .. important:: - Now that you have downloaded the TS to your SEPAL account, it can be downloaded to your computer using `FileZilla <../setup.filezilla.html>`__ or used in one of our `time-series analysis modules <../modules/time-series.html>`__. + Now that you have downloaded the TS to your SEPAL account, it can be downloaded to your computer using `FileZilla <../setup.filezilla.html>`__ or used in one of our `Time-series analysis modules <../modules/time-series.html>`__. From 421d337f67ad2cb5146146e03711b2e0d56724fb Mon Sep 17 00:00:00 2001 From: Alex Gregor <111502950+alexryangregor@users.noreply.github.com> Date: Tue, 14 Nov 2023 15:09:20 +0100 Subject: [PATCH 14/18] Update class_change.rst Proofreading completed. --- docs/source/cookbook/class_change.rst | 47 ++++++++++++++------------- 1 file changed, 25 insertions(+), 22 deletions(-) diff --git a/docs/source/cookbook/class_change.rst b/docs/source/cookbook/class_change.rst index 8cfbc816b9..aeb962e50e 100644 --- a/docs/source/cookbook/class_change.rst +++ b/docs/source/cookbook/class_change.rst @@ -1,10 +1,11 @@ Class change ============ +*Build a class change map between two categorical maps that share the same legend with the Class change recipe* Overview -------- -Often, we want to build the class change map between two categorical maps that share the same legend. If the two images are taken at different times, it will help us understand how the vegetation classification has evolved between these two dates. It can be tedious to build the new legend (forest -> forest, forest -> urban, etc.) and manually write the rules to identify each class. SEPAL will automatically build the legend of the resulting categorical map from the initial legend and compute all pixels automatically. +Often, we want to build the class change map between two categorical maps that share the same legend. If the two images are taken at different times, this can help us understand how the vegetation classification has evolved between two dates. It can be tedious to build the new legend (forest -> forest, forest -> urban, etc.) and manually write the rules to identify each class. SEPAL will automatically build the legend of the resulting categorical map from the initial legend and compute all pixels automatically. .. note:: @@ -13,15 +14,15 @@ Often, we want to build the class change map between two categorical maps that s Start ----- -Once the class change recipe is selected, SEPAL will present the **Process** in a new tab (1). +Once the **Class change** recipe is selected, SEPAL will present the **Process** in a new tab (see **1** in figure below). -The **Parameters** will open in the lower-right side of your screen (2). +**Parameters** will open in the lower-right side of your screen (2). .. thumbnail:: ../_images/cookbook/class_change/landing.png :group: recipe_class_change - :title: The landing page of the class change recipe. + :title: The landing page of the **Class change** recipe. -The first step is to change the name of the recipe. This name will be used to name your files and recipes in SEPAL folders. Use the best-suited convention for your need. Simply double-click the tab and enter a new name (it will default to :code:`Class_change_`). +The first step is to change the name of the recipe. This name will be used to name your files and recipes in **SEPAL folders**. Use the best-suited convention for your need. Simply double-click the tab and enter a new name (it will default to :code:`Class_change_`). .. thumbnail:: ../_images/cookbook/class_change/default_title.png :title: Class change default title @@ -36,14 +37,14 @@ Parameters In the lower-right corner, the following four tabs are available, allowing users to customize the class change to their needs: -- :guilabel:`FRM`: The source categorical image. -- :guilabel:`TO`: The destination categorical image. -- :guilabel:`LEG`: The legend of the transition classes. -- :guilabel:`OPT`: The optional parameters of the recipe. +- :guilabel:`FRM`: the source categorical image +- :guilabel:`TO`: the destination categorical image +- :guilabel:`LEG`: the legend of the transition classes +- :guilabel:`OPT`: the optional parameters of the recipe .. thumbnail:: ../_images/cookbook/class_change/parameters.png :group: recipe_class_change - :title: The four tabs to set up SEPAL class change recipe + :title: The four tabs to set up SEPAL **Class change** recipe Select images ^^^^^^^^^^^^^ @@ -52,17 +53,19 @@ The first step is to select the two images to compare. Since :guilabel:`FRM` and Select a categorical image, which can be a classification recipe or any categorical asset from your Google Earth Engine (GEE) account. In both cases, you'll need to select the band to use for the transition and the legend. -If the selected asset/recipe is a classification recipe (or its export), the legend will be automatically generated with the metadata of the file. If it's not, you'll need to upload it manually. Select :btn:`fa-solid fa-pen-to-square` to open the **Legend editing** tool. It's the same as the one described in the classification recipe (see :doc:`classification`). +If the selected asset/recipe is a **Classification** recipe (or its export), the legend will be automatically generated with the metadata of the file. If it's not, you'll need to upload it manually. + +Select :btn:`fa-solid fa-pen-to-square` to open the **Legend editing** tool. It's the same as the one described in the **Classification** recipe (see :doc:`classification`). .. thumbnail:: ../_images/cookbook/class_change/from.png :group: recipe_class_change :width: 49% - :title: The **from** image selection (in this example, a classification recipe forest/non-forest for the year 2020) + :title: The **from** image selection (in this example, a **Classification** recipe forest/non-forest [FNF] for the year 2020) .. thumbnail:: ../_images/cookbook/class_change/to.png :group: recipe_class_change :width: 49% - :title: The **to** image selection (in this example, a classification recipe forest/non-forest for the year 2021) + :title: The **to** image selection (in this example, a **Classification** recipe forest/non-forest [FNF] for the year 2021) Customize legend ^^^^^^^^^^^^^^^^ @@ -82,7 +85,7 @@ Options If the selected asset is from a SEPAL classification, it will embed a probability value for each classified pixel. SEPAL will propose clever map transitioning based on these values. -For example, a high-confidence forest pixel changes into a low-confidence non-forest piexl. The change will be taken into account only if the minimum confidence is reached by the **to** pixel. By default, no filtering is performed and the slider is set to 0. +For example, a high-confidence forest pixel changes into a low-confidence non-forest pixel. The change will be taken into account only if the minimum confidence is reached by the **to** pixel. By default, no filtering is performed and the slider is set to 0. .. note:: @@ -102,17 +105,17 @@ Export You cannot export a recipe as an asset or a :code:`.tiff` file without a small computation quota (if you are a new user, see :doc:`../setup/resource`). -Select the :icon:`fa-solid fa-cloud-arrow-down` tab to open the **Retrieve** panel, where you can select the **Exportation parameters**. +Select the :icon:`fa-solid fa-cloud-arrow-down` tab to open the **Retrieve** pane, where you can select the **Exportation parameters**. .. thumbnail:: ../_images/cookbook/class_change/export.png - :title: the last panel of the class change recipe: the exportation + :title: The last pane of the **Class change** recipe: the exportation :group: recipe_class_change Bands """"" -You need to select the band to export in the recipe. You will have access to :guilabel:`transition` (the new class change values) and :guilabel:`confidence`, if you selected **Classification recipe assets**. +Select the band to export in the recipe. You will have access to :guilabel:`transition` (the new class change values) and :guilabel:`confidence`, if you selected **Classification recipe assets**. Scale """"" @@ -122,18 +125,18 @@ You can set a custom scale for exportation by changing the value of the slider ( Destination """"""""""" -You can export the image to :guilabel:`SEPAL workspace` or to :guilabel:`GEE asset`. The same image will be exported, but in the first case you will find it in :code:`.tif` format in the :code:`Downloads` folder; in the second case, the image will be exported to your GEE account **Asset** list. +You can export the image to :guilabel:`SEPAL workspace` or to :guilabel:`GEE asset`. The same image will be exported, but in the first case, you will find it in :code:`.tif` format in the :code:`Downloads` folder; in the second case, the image will be exported to your GEE account **Asset** list. .. attention:: - If :guilabel:`GEE asset` is not displayed, it means that your GEE account is not connected to your SEPAL account (see :doc:`../setup/gee`). + If :guilabel:`GEE asset` is not displayed, your GEE account is not connected to your SEPAL account (see :doc:`../setup/gee`). Select :guilabel:`apply` to start the download process. Exportation status """""""""""""""""" -In the **Task** tab (lower-left corner using the :icon:`fa-solid fa-list-check` or :icon:`fa-solid fa-spinner` buttons, depending on the loading status), you will see the list of different loading tasks. The interface will provide you with information about the task progress and display an error if the exportation has failed. +In the **Tasks** tab (lower-left corner using the :icon:`fa-solid fa-list-check` or :icon:`fa-solid fa-spinner` buttons, depending on the loading status), you will see the list of different loading tasks. The interface will provide you with information about the task progress and display an error if the exportation has failed. If you are unsatisfied with the way we present information, the task can also be monitored using the `GEE task manager `__. @@ -145,10 +148,10 @@ When the task is finished, the frame will be displayed in green (see the second .. thumbnail:: ../_images/cookbook/class_change/download.png :width: 49% - :title: Evolution of the downloading process of the recipe displayed in the task manager of SEPAL + :title: Evolution of the downloading process of the recipe displayed in the **Task manager** of SEPAL :group: recipe_class_change .. thumbnail:: ../_images/cookbook/class_change/download_complete.png :width: 49% - :title: Completed downloading process of the recipe displayed in the task manager of SEPAL + :title: Completed downloading process of the recipe displayed in the **Task manager** of SEPAL :group: recipe_class_change From e0b7c521291a3e66a6bde6f269a1789c9a5cb60a Mon Sep 17 00:00:00 2001 From: Alex Gregor <111502950+alexryangregor@users.noreply.github.com> Date: Tue, 14 Nov 2023 15:54:08 +0100 Subject: [PATCH 15/18] Update ccdc.rst Proofreading complete. --- docs/source/cookbook/ccdc.rst | 91 ++++++++++++++++++----------------- 1 file changed, 46 insertions(+), 45 deletions(-) diff --git a/docs/source/cookbook/ccdc.rst b/docs/source/cookbook/ccdc.rst index f4e5a84aca..0abcfa4e70 100644 --- a/docs/source/cookbook/ccdc.rst +++ b/docs/source/cookbook/ccdc.rst @@ -1,5 +1,7 @@ CCDC asset creation -===================== +=================== +*Facilitate the workflow for applying the Continuous Change Detection and Classification approach with SEPAL* + Background ---------- @@ -57,10 +59,10 @@ The following steps describe the parameter selection that can be found in the lo The buttons open the following dialogues: -- :guilabel:`AOI` Area of interest (AOI) -- :guilabel:`DAT` Time of Interest (TOI), i.e. the time-span for the underlying time series -- :guilabel:`SRC` Selection of sensor(s) -- :guilabel:`PRC` Preprocessing parameters +- :guilabel:`AOI` area of interest (AOI) +- :guilabel:`DAT` time of interest (TOI) (i.e. the timespan for the underlying time series) +- :guilabel:`SRC` selection of sensor(s) +- :guilabel:`PRC` pre-processing parameters - :guilabel:`OPT` CCDC parameters AOI @@ -81,7 +83,7 @@ These are described in our documentation (see :doc:`../feature/aoi_selector`). Date range ^^^^^^^^^^ -In the :guilabel:`DAT` tab, you will be asked to select the start date and end date of the time series. +In the :guilabel:`DAT` tab, select the start date and end date of the time series. Select the **Date** text field to open the **Date selection** pop-up menu. @@ -102,11 +104,11 @@ When both dates have been chosen, select the :btn:` Apply` bu Sensor selection ^^^^^^^^^^^^^^^^ -After selecting the :guilabel:`Next` button in the **Date selection** pop-up menu, the **Sensor selection** pop-up menu will automatically open (1), where you need to specify the sensor(s) and the bands used for breakpoint detection: +After selecting the :guilabel:`Next` button in the **Date selection** pop-up menu, the **Sensor selection** pop-up menu will automatically open (see **1** in figure below), where you need to specify the sensor(s) and bands used for breakpoint detection: - :guilabel:`OPTICAL` (including the Landsat and Sentinel-2 missions); - :guilabel:`RADAR` (including the Sentinel-1 mission); and -- :guilabel:`PLANET`, where both daily imagery or monthly basemaps can be used as data inputs (if you have a valid Planet API key). +- :guilabel:`PLANET` (where both daily imagery or monthly basemaps can be used as data inputs – if you have a valid Planet API key). .. thumbnail:: ../_images/cookbook/ccdc_asset/sensor_selection_overview.png :title: Sensor selection @@ -120,22 +122,24 @@ CCDC is originally tested on optical *Landsat* satellites. In SEPAL, you have th .. attention:: - The inclusion of *Tier 2* products and *Landsat 7* may introduce artifacts due to the reduced quality of data. For recent, short-term time series, it might be better to either select the Landsat-8 or Sentinel-2 mission, which deliver imagery from 2013 and 2015, respectively; however, this will reduce the density of observations for the underlying time series. + The inclusion of *Tier 2* products and *Landsat 7* may introduce artefacts due to the reduced quality of data. For recent, short-term time series, it might be better to either select the Landsat-8 or Sentinel-2 mission, which deliver imagery from 2013 and 2015, respectively; however, this will reduce the density of observations for the underlying time series. .. attention:: - For cloud-prone regions, it is also possible to combine *Landsat* data with *Sentinel-2* data to densify the underlying time series (due to differences in the sensors – although band names are equal – and overpass time, artifacts may be introduced that will affect breakpoint detection). + For cloud-prone regions, it is also possible to combine *Landsat* data with *Sentinel-2* data to densify the underlying time series (due to differences in the sensors – although band names are equal – and overpass time, artefacts may be introduced that will affect breakpoint detection). -Breakpoint detection is at the heart of CCDC. The respective selection of bands can considerably affect the outcome of CCDC breakpoint detection. Unfortunately, there does not seem to be a one-size-fits-all preset for all kinds of applications. Scientific evidence suggests using all color bands but blue (`Zhu *et al.* [2020] `_). According to the study, the selection of additional ratio bands does not add any improvement. However, it should be noted that this assumption is based on the detection of all types of land-cover changes and that the study uses a modified version of CCDC (named *COLD*), where the change in bands are weighted differently than in the original version used in SEPAL (respectively GEE). +Breakpoint detection is at the heart of CCDC. The respective selection of bands can considerably affect the outcome of CCDC breakpoint detection. Unfortunately, there does not seem to be a one-size-fits-all preset for all kinds of applications. Scientific evidence suggests using all color bands but blue (`Zhu et al.,2020 `_). According to the study, the selection of additional ratio bands does not add any improvement. However, it should be noted that this assumption is based on the detection of all types of land-cover changes and that the study uses a modified version of CCDC (named *COLD*), where the change in bands are weighted differently than in the original version used in SEPAL. .. tip:: - Use of the color bands allows you to later select the :code:`Green` and :code:`Swir1` band as TMASK bands for CCDC's internal, multitemporal cloud removal (you can find this in the :guilabel:`OPT` button pop-up menu under :guilabel:`MORE`. + Use of the color bands allows you to later select the :code:`Green` and :code:`Swir1` band as TMASK bands for CCDC's internal, multitemporal cloud removal (see the :guilabel:`OPT` button pop-up menu under :guilabel:`MORE`). + +If the creation of the CCDC asset is aimed at the detection of both forest degradation and deforestation, the **Normalized difference fraction index** (:code:`NDFI`) might be another suitable choice as applied by `Bullock et al. (2020) `_. -If the creation of the CCDC asset is aimed at the detection of both forest degradation and deforestation, the **Normalized difference fraction index** (:code:`NDFI`) might be another suitable choice as applied by `Bullock *et al.* (2020) `_. (This article and the NDFI are specifically tested over tropical rainforest of the Brazilian Amazon. Changes in other forest types might be better captured by different ratios or color bands. For instance, one can consider the **Normalized difference moisture index** [:code:`NDMI`] when looking at mangrove forests.) +(This article and the NDFI are specifically tested over tropical rainforest of the Brazilian Amazon. Changes in other forest types might be better captured by different ratios or color bands. For instance, one can consider the **Normalized difference moisture index** [:code:`NDMI`] when looking at mangrove forests.) .. tip:: - If in doubt, use the default option (all of the color bands except blue). + If in doubt, use the default option (all color bands except blue). .. thumbnail:: ../_images/cookbook/ccdc_asset/sensor_selection_color_breakbands.png :title: Sensor selection – color breakpoint bands @@ -183,16 +187,15 @@ In case you want to use *NICFI Level-1 basemaps*, use already existing assets wi For data ordered through the Planet API (i.e. daily imagery or custom basemaps other than NICFI Level 1 data), you can specify GEE as the download location. -Using CCDC with Planet has not been explored widely, so the optimal selection of the breakpoint bands depends on testing it out. However, in accordance with Landsat-based analysis, we suggest using the green, red and NIR bands to get started. - -Preprocessing options -^^^^^^^^^^^^^^^^^^^^^ +Using CCDC with Planet has not been explored widely, so the optimal selection of the breakpoint bands depends on testing it out. However, in accordance with Landsat-based analysis, we suggest using the green, red and near-infrared (NIR) bands to get started. +Pre-processing options +^^^^^^^^^^^^^^^^^^^^^^ Optical data """""""""""" -.. attention:: +.. note:: This section is optional (as these parameters are set by default). @@ -201,11 +204,11 @@ Optical data - Cloud masking: :guilabel:`Moderate` - Snow masking: :guilabel:`On` -Multiple preprocessing parameters can be set to improve the quality of provided images. SEPAL has gathered four of them in the form of these interactive buttons. If you think others should be added, contact the SEPAL team via the `issue tracker `__. +Multiple pre-processing parameters can be set to improve the quality of provided images. SEPAL has gathered four of them in the form of these interactive buttons. If you think others should be added, contact the SEPAL team via the `issue tracker `__. **Correction** -- :guilabel:`Surface reflectance`: Use scenes' atmospherically corrected surface reflectance. +- :guilabel:`Surface reflectance`: Use scenes' atmospherically corrected surface reflectance - :guilabel:`BRDF correction`: Correct for *bidirectional reflectance distribution function* (BRDF) effects. **Cloud detection** @@ -221,13 +224,12 @@ Multiple preprocessing parameters can be set to improve the quality of provided **Snow masking** - :guilabel:`On`: Mask snow (this tends to leave some pixels with shadowy snow). -- :guilabel:`Off`: Don't mask snow (some clouds might get misclassified as snow; therefore, disabling snow masking might lead to cloud artifacts). +- :guilabel:`Off`: Don't mask snow (some clouds might get misclassified as snow; therefore, disabling snow masking might lead to cloud artefacts). .. thumbnail:: ../_images/cookbook/ccdc_asset/pre_processing.png - :title: The preprocessing panel to select extra filtering processes that will improve the quality of provided images + :title: The **Pre-processing** pane to select extra filtering processes that will improve the quality of provided images :group: time-series-recipe - Radar data """""""""" @@ -247,9 +249,9 @@ The default parameters (see following figure on the left) are optimized for perf **Orbit selection** -The orbit selection for radar satellites refers to the flight direction of the satellite (different for the sun-adverted and sun-facing sides of the planet). One distinguishes the ascending direction (from south pole towards north pole) and one distinguishes the descending direction (from north pole to south pole). Being independent from sunlight, radar satellites can acquire data during both day and night; however, they do not acquire data constantly. +The orbit selection for radar satellites refers to the flight direction of the satellite (different for the sun-adverted and sun-facing sides of the planet). One distinguishes the ascending direction (from South Pole towards North Pole) and one distinguishes the descending direction (from North Pole to South Pole). Being independent from sunlight, radar satellites can acquire data during both day and night; however, they do not acquire data constantly. -In the case of the Sentinel-1 mission, areas outside of Europe are usually only covered by either one or the other (see following figure to determine which orbit direction your AOI is covered by). +In the case of the Sentinel-1 mission, areas outside Europe are usually only covered by either one or the other (see following figure to determine which orbit direction your AOI is covered by). .. image:: https://sentinels.copernicus.eu/documents/247904/3944045/Sentinel-1-Revisit-Coverage-Frequency-Geometry-2019.jpeg :alt: Sentinel-1 observation scenario @@ -262,7 +264,7 @@ In the case of the Sentinel-1 mission, areas outside of Europe are usually only **Geometric correction** -Setting the **Geometric correction** to :guilabel:`TERRAIN` will correct for distortions of the radar backscatter signal along slopes. This is crucial for all types of land cover or biogeophysical parameter retrieval, and is therefore *highly recommended*. +Setting the **Geometric correction** to :guilabel:`TERRAIN` will correct for distortions of the radar backscatter signal along slopes. This is crucial for all types of land cover or bio-geophysical parameter retrieval, and is therefore *highly recommended*. **Speckle-filtering** @@ -270,12 +272,12 @@ Speckle filtering is a common step in radar remote sensing; it reduces the rando **Outlier removal** -Sentinel-1 data is prone to some rare artifacts, such as interferences from other radio wave sources or heavy rainfall events. SEPAL offers the option to exclude them with multitemporal outlier detection. By default, a :guilabel:`MODERATE` reduction is appropriate to remove such artifacts. More aggressive filtering might include actual change events, and is therefore not recommended. +Sentinel-1 data is prone to some rare artifacts, such as interferences from other radio wave sources or heavy rainfall events. SEPAL offers the option to exclude them with multitemporal outlier detection. By default, a :guilabel:`MODERATE` reduction is appropriate to remove such artefacts. More aggressive filtering might include actual change events, and is therefore not recommended. Planet data """"""""""" -Preprocessing parameters of Planet data are similar to the Landsat/Sentinel-2 options. The default parameters reflect a quite aggressive approach to cloud removal (see following figure). +Pre-processing parameters of Planet data are similar to the Landsat/Sentinel-2 options. The default parameters reflect a quite aggressive approach to cloud removal (see following figure). .. thumbnail:: ../_images/cookbook/ccdc_asset/prc_planet_default.png :title: PRC selection – Planet default @@ -287,7 +289,7 @@ Preprocessing parameters of Planet data are similar to the Landsat/Sentinel-2 op **Histogram matching** -Histogram matching is disabled by default. This is ok when dealing with already preprocessed monthly basemaps; however, if the collection is composed of daily imagery, it is highy recommended to :guilabel:`ENABLE` this option, as it will harmonize the radiometry between each single image. +Histogram matching is disabled by default. This is ok when dealing with already pre-processed monthly basemaps; however, if the collection is composed of daily imagery, it is highy recommended to :guilabel:`ENABLE` this option, as it will harmonize the radiometry between each single image. CCDC parameters ^^^^^^^^^^^^^^^ @@ -332,7 +334,7 @@ This option allows saving the dates in various formats (by default, SEPAL deals **TMASK BANDS** -The bands selected here are used for additional multitemporal filtering of cloud-affected pixels that have not been identified as such throughout the preprocessing of single images. For optical data from Landsat and Sentinel-2, the :guilabel:`GREEN` and :guilabel:`SWIR1` bands are recommended. +The bands selected here are used for additional multitemporal filtering of cloud-affected pixels that have not been identified as such throughout the pre-processing of single images. For optical data from Landsat and Sentinel-2, the :guilabel:`GREEN` and :guilabel:`SWIR1` bands are recommended. **Min observations** @@ -348,7 +350,7 @@ This parameter determines the minimum length of any inner-temporal segment. **LAMBDA** -The LAMBDA parameter is part of the LASSO regression used for modelling the time-series. It is used to generalize the model, thereby improving its predictive power. More specifically, it is controlling the weight of each of the parameters, and might even result in the annulation of some parameters. In practical terms, an initial third-order harmonic model might shrink to a first-order harmonic, if this provides the best generalized fit. Setting LAMBDA to 0 will lead to a regular Ordinary-Least-Square regression, not providing any generalization. Instead, a higher value will provide a more generalized model. If LAMBDA is set too high, the model will underfit, which is not desired. Since a value of 20 has been found to provide a generally good performance, the sweet spot of neither overfitting nor underfitting will be around this number. +The LAMBDA parameter is part of the LASSO regression used for modelling the time series. It is used to generalize the model, thereby improving its predictive power. More specifically, it is controlling the weight of each of the parameters, and might even result in the annulation of some parameters. In practical terms, an initial third-order harmonic model might shrink to a first-order harmonic, if this provides the best generalized fit. Setting LAMBDA to 0 will lead to a regular Ordinary-Least-Square regression, not providing any generalization. Instead, a higher value will provide a more generalized model. If LAMBDA is set too high, the model will underfit, which is not desired. Since a value of 20 has been found to provide a generally good performance, the sweet spot of neither overfitting nor underfitting will be around this number. **Max iterations** @@ -359,17 +361,17 @@ The iterations for the maximum number of runs for LASSO regression convergence. On-the-fly pixel analysis ------------------------- -Select the :btn:`` button to start the plotting tool (1). +Select the :btn:`` button to start the plotting tool (**1**). -Move the pointer to the main map; the pointer will be transformed into :icon:`fa-solid fa-plus` (2). +Move the pointer to the main map; the pointer will be transformed into :icon:`fa-solid fa-plus` (**2**). -Click anywhere in the AOI to plot data for this specific location in the pop-up window that appears. The plotting area (3) is dynamic and can be customized by the user. +Click anywhere in the AOI to plot data for this specific location in the pop-up window that appears. The plotting area (**3**) is dynamic and can be customized by the user. -Select the observation feature by selecting one of the available measures in the dropdown selector in the upper-left corner (4). The available bands are the same as those previously described. +Select the observation feature by selecting one of the available measures in the dropdown selector in the upper-left corner (**4**). The available bands are the same as those previously described. -Using the slider (5), the temporal width displayed can be changed. It cannot exceed the start and/or end date of the time series. +Using the slider (**5**), the temporal width displayed can be changed. It cannot exceed the start and/or end date of the time series. -On the main graph, the orange lines show the CCDC-modelled time series. Each of the blue points represents an actual observation. You can hover over the point or the line to let the tooltip describe the value and date of the observation, as well as the model values and the temporal extent of the specific segment. +On the main graph, the orange lines show the CCDC-modelled time series. Each of the blue points represents an actual observation. Hover over the point or line to let the tooltip describe the value and date of the observation, as well as the model values and temporal extent of the specific segment. .. thumbnail:: ../_images/cookbook/ccdc_asset/ccdc_pixel_analysis.png :title: Pixel analysis @@ -378,7 +380,7 @@ On the main graph, the orange lines show the CCDC-modelled time series. Each of .. attention:: - The plot feature is retrieving information from GEE on the fly and serving it in an interactive window. This operation can take time depending on the number of available observations and the complexity of the selected preprocessing parameters. If the pop-up window displays a spinning wheel, wait up to two minutes to see the data displayed. + The plot feature is retrieving information from GEE on the fly and serving it in an interactive window. This operation can take time depending on the number of available observations and the complexity of the selected pre-processing parameters. If the pop-up window displays a spinning wheel, wait up to two minutes to see the data displayed. Export ------ @@ -394,7 +396,7 @@ Select the :btn:`` button to open the export dialo If the area covered is relatively small and you have enough storage quota left, you can generously select most of the bands relevant for land applications (see following figure on the left). If you are more constrained by storage, you will need to decide on a subset of bands (see following figure on the right for a suggested starting point). -The scale parameter depends on the data selected and the level of detail you will need for further analysis. Landsat-based assets are usually created at 30 m. Sentinel-1 and 2 can be at 10 m, but will need nine times more space compared to 30 m resolution. +The scale parameter depends on the data selected and the level of detail you will need for further analysis. Landsat-based assets are usually created at 30 m. Sentinel-1 and Sentinel-2 can be at 10 m, but will need nine times more space compared to 30 m resolution. .. thumbnail:: ../_images/cookbook/ccdc_asset/ccdc_export_full.png :title: Export CCDC asset – full band selection @@ -406,26 +408,25 @@ The scale parameter depends on the data selected and the level of detail you wil :width: 49% :group: ccdc-asset-recipe - Exportation status ^^^^^^^^^^^^^^^^^^ -Going to the **Task** tab (lower-left corner using :btn:`` or :btn:`` buttons, depending on the loading status), you will see the list of different loading tasks. The interface will provide you with information about the task progress; it will display an error if the exportation has failed. +Going to the **Tasks** tab (lower-left corner using :btn:`` or :btn:`` buttons, depending on the loading status), you will see the list of different loading tasks. The interface will provide you with information about the task progress; it will display an error if the exportation has failed. If you are unsatisfied with the way we present information, the task can also be monitored using `GEE task manager `__. .. tip:: - This operation is running between GEE and SEPAL servers in the background; you can thus close the SEPAL page without stopping the process. + This operation is running between GEE and SEPAL servers in the background; you can close the SEPAL page without stopping the process. When the task is finished, the frame will be displayed in green (see second image below). .. thumbnail:: ../_images/cookbook/ccdc_asset/download.png :width: 49% - :title: Evolution of the downloading process of the recipe displayed in the **Task manager** of SEPAL. + :title: Evolution of the downloading process of the recipe displayed in the **Task manager** of SEPAL :group: ccdc-asset-recipe .. thumbnail:: ../_images/cookbook/ccdc_asset/download_complete.png :width: 49% - :title: Completed downloading process of the recipe displayed in the **Task manager** of SEPAL. + :title: Completed downloading process of the recipe displayed in the **Task manager** of SEPAL :group: ccdc-asset-recipe From dbe4d63d046b21bcb534cbc6824d0e7bbc09df8b Mon Sep 17 00:00:00 2001 From: Alex Gregor <111502950+alexryangregor@users.noreply.github.com> Date: Tue, 14 Nov 2023 16:14:17 +0100 Subject: [PATCH 16/18] Update ccdc_slice.rst Proofreading complete. --- docs/source/cookbook/ccdc_slice.rst | 35 +++++++++++++++-------------- 1 file changed, 18 insertions(+), 17 deletions(-) diff --git a/docs/source/cookbook/ccdc_slice.rst b/docs/source/cookbook/ccdc_slice.rst index 702fa30746..e76c7915cb 100644 --- a/docs/source/cookbook/ccdc_slice.rst +++ b/docs/source/cookbook/ccdc_slice.rst @@ -1,5 +1,6 @@ CCDC slice ========== +*Create CCDC slices out of CCDC assets* Background ---------- @@ -22,7 +23,7 @@ Once logged into the SEPAL interface, open the **Recipe** menu by selecting the .. thumbnail:: ../_images/cookbook/ccdc_slice/recipe_selection.png :group: recipe-ccdc-slice - :title: Selection menu for SEPAL recipes + :title: **Selection menu** for **SEPAL recipes** :width: 60% :align: center @@ -52,9 +53,9 @@ The following steps describe parameter selection, which can be found in the lowe The buttons open the following dialogues: -- :guilabel:`SRC` Selection of CCDC asset source -- :guilabel:`DAT` Date or date range selection -- :guilabel:`OPT` CCDC slicing parameters +- :guilabel:`SRC`: Selection of CCDC asset source +- :guilabel:`DAT`: Date or date range selection +- :guilabel:`OPT`: CCDC slicing parameters Selection of CCDC asset source @@ -64,8 +65,8 @@ CCDC slices are created out of CCDC assets. Here you have the choice to select t Two options are provided: -- Option 1 is to directly point to an existing SEPAL recipe. Note that in this case, the CCDC asset needs to be regenerated on the fly based on the parameter settings of the CCDC asset. In most cases this is computationally demanding and may lead to time-out errors. Therefore, it is rather recommended to opt for Option 2. -- Option 2 is where an existing CCDC asset is selected from GEE. In this case, the CCDC asset needs to be exported first, so you can point to its location within GEE directly. This usually allows for instant visualization, as the slicing procedure does not require lots of computing power. +- **Option 1** is to directly point to an existing SEPAL recipe. Note that in this case, the CCDC asset needs to be regenerated on the fly based on the parameter settings of the CCDC asset. In most cases, this is computationally demanding and may lead to timeout errors. Therefore, it is recommended to opt for Option 2. +- **Option 2** is where an existing CCDC asset is selected from GEE. In this case, the CCDC asset needs to be exported first, so you can point to its location within GEE directly. This usually allows for instant visualization, as the slicing procedure does not require much computing power. Date (range) selection ^^^^^^^^^^^^^^^^^^^^^^ @@ -84,20 +85,20 @@ CCDC slicing parameters Specific date """"""""""""" -In case a single date has been selected, the **Slicing parameters** will appear as shown in the following figure. +In case a single date has been selected, the **Slicing parameters** will appear, as shown in the following figure. .. thumbnail:: ../_images/cookbook/ccdc_slice/ccdc_slice_date_parameters.png :group: recipe-ccdc-slice - :title: Selection menu for CCDC slicing parameters + :title: **Selection menu** for **CCDC slicing parameters** :align: center The first parameter is the number of **Harmonics** used to extract the modelled reflectance at the given point in time. Three harmonic terms are set by default. Lowering this number will result in a smooth time series that does not depict intra-annual periodicity. Setting this value to 1 will only capture the inter-annual periodicity (i.e. annual seasonality), while a value of 0 results in the mean value over the segment's time period. The **Gap strategy** relates to the presence of gaps between two temporal segments (i.e. the presence of a break). After a detected break, CCDC reinitializes a new model (i.e. new segment) only after a couple of observations. In between, no model is available from which to extract the data. In order to avoid masked pixels, the user has the possibility to: -- :btn:`Interpolate` – Use a temporally weighted mean between the previous and subsequent model for the given data. -- :btn:`Extrapolate` – Use the extrapolated value of the closest, previous, or next model for the given data. -- :btn:`Mask` – Mask the value as *no data*. +- :btn:`Interpolate`: Use a temporally weighted mean between the previous and subsequent model for the given data. +- :btn:`Extrapolate`: Use the extrapolated value of the closest, previous or next model for the given data. +- :btn:`Mask`: Mask the value as *No data*. In case of extrapolation, the additional option, **Segment to extrapolate**, allows you to choose either the model parameters from the previous, next or closest segment with respect to the selected data. Furthermore, the **Max days to extrapolate** setting allows you to limit the number of days until this procedure is considered valid. If the difference between the selected date and the segment's valid time period is greater than this threshold value, the pixel will be automatically masked. @@ -108,7 +109,7 @@ In case a date range has been selected, the **Slicing parameters** will appear a .. thumbnail:: ../_images/cookbook/ccdc_slice/ccdc_slice_date_range_parameters.png :group: recipe-ccdc-slice - :title: Selection menu for CCDC slice parameters – date range + :title: **Selection menu** for **CCDC slice parameters – date range** :align: center The first parameter is the number of **Harmonics** used to extract the modelled reflectance at the given point in time. Three harmonic terms are set by default. Lowering this number will result in a smooth time series that does not depict intra-annual periodicity. Setting this value to 1 will only capture the inter-annual periodicity (i.e. annual seasonality), while a value of 0 results in the mean value over the segment's time period. @@ -122,7 +123,7 @@ SEPAL offers four ways of selecting the remaining break: - :guilabel:`First`: The first break within the **Slice date** range. - :guilabel:`Last`: The last break within the **Slice date** range. - :guilabel:`Magnitude`: The break with the highest magnitude of change. -- :guilabel:`Confidence`: The break with the highest confidence value (see :doc:`ccdc` for more information about confidence computation). +- :guilabel:`Confidence`: The break with the highest confidence value (for more information about confidence computation, see :doc:`ccdc`). By selecting a specific break direction, the break selection will only take into acount the break with a :guilabel:`decrease` or :guilabel:`increase` magnitude. By default, we consider :guilabel:`Any` break direction. @@ -131,15 +132,15 @@ By moving the slider, you will ignore the break with a low confidence from the a Visualization ------------- -Select the :btn:`` button to start the plotting tool (1). +Select the :btn:`` button to start the plotting tool (**1**). Move the pointer to the main map; the pointer will be transformed into :icon:`fa-solid fa-plus`. Click anywhere in the AOI to plot data for this specific location in the pop-up window that appears. -The plotting area (3) is the same as the one presented in the CCDC recipe with small adjustments to the slicing operation. Refer to :doc:`ccdc` for a complete description. +The plotting area (**3**) is the same as the one presented in the CCDC recipe with small adjustments to the slicing operation. Refer to :doc:`ccdc` for a complete description. -The plotting area covers all of the CCDC asset range (4); the user will see the slice in red (it will be a sector of the plot if a date range is selected and a red line if a single date is selected). +The plotting area covers all of the CCDC asset range (**4**); the user will see the slice in red (it will be a sector of the plot if a date range is selected and a red line if a single date is selected). .. thumbnail:: ../_images/cookbook/ccdc_slice/pixel_analysis.png :title: Pixel analysis of a date range slice of a CCDC asset @@ -147,7 +148,7 @@ The plotting area covers all of the CCDC asset range (4); the user will see the .. attention:: - The plot feature is retrieving information from GEE on the fly and serving it in an interactive window. This operation can take time, depending on the number of available observations and the complexity of the selected preprocessing parameters. If the pop-up window displays a spinning wheel, wait up to two minutes to see the data displayed. + The plot feature is retrieving information from GEE on the fly and serving it in an interactive window. This operation can take time, depending on the number of available observations and the complexity of the selected pre-processing parameters. If the pop-up window displays a spinning wheel, wait up to two minutes to see the data displayed. Export ------ From adf3d3c66598eee8255750515e77eac3b3c5dd3a Mon Sep 17 00:00:00 2001 From: dfguerrerom Date: Thu, 16 Nov 2023 11:49:31 +0100 Subject: [PATCH 17/18] style: remove trailing spaces --- docs/source/cookbook/ccdc.rst | 2 +- docs/source/cookbook/class_change.rst | 2 +- docs/source/cookbook/classification.rst | 6 +++--- docs/source/cookbook/index.rst | 4 ++-- docs/source/cookbook/planet_mosaic.rst | 2 +- docs/source/cookbook/time_series.rst | 2 +- docs/source/setup/gee.rst | 20 ++++++++++---------- docs/source/setup/index.rst | 2 +- docs/source/setup/nicfi.rst | 6 +++--- docs/source/setup/presentation.rst | 24 ++++++++++++------------ docs/source/setup/register.rst | 2 +- 11 files changed, 36 insertions(+), 36 deletions(-) diff --git a/docs/source/cookbook/ccdc.rst b/docs/source/cookbook/ccdc.rst index 0abcfa4e70..f46170e72a 100644 --- a/docs/source/cookbook/ccdc.rst +++ b/docs/source/cookbook/ccdc.rst @@ -134,7 +134,7 @@ Breakpoint detection is at the heart of CCDC. The respective selection of bands Use of the color bands allows you to later select the :code:`Green` and :code:`Swir1` band as TMASK bands for CCDC's internal, multitemporal cloud removal (see the :guilabel:`OPT` button pop-up menu under :guilabel:`MORE`). -If the creation of the CCDC asset is aimed at the detection of both forest degradation and deforestation, the **Normalized difference fraction index** (:code:`NDFI`) might be another suitable choice as applied by `Bullock et al. (2020) `_. +If the creation of the CCDC asset is aimed at the detection of both forest degradation and deforestation, the **Normalized difference fraction index** (:code:`NDFI`) might be another suitable choice as applied by `Bullock et al. (2020) `_. (This article and the NDFI are specifically tested over tropical rainforest of the Brazilian Amazon. Changes in other forest types might be better captured by different ratios or color bands. For instance, one can consider the **Normalized difference moisture index** [:code:`NDMI`] when looking at mangrove forests.) diff --git a/docs/source/cookbook/class_change.rst b/docs/source/cookbook/class_change.rst index aeb962e50e..d5e6652ff5 100644 --- a/docs/source/cookbook/class_change.rst +++ b/docs/source/cookbook/class_change.rst @@ -53,7 +53,7 @@ The first step is to select the two images to compare. Since :guilabel:`FRM` and Select a categorical image, which can be a classification recipe or any categorical asset from your Google Earth Engine (GEE) account. In both cases, you'll need to select the band to use for the transition and the legend. -If the selected asset/recipe is a **Classification** recipe (or its export), the legend will be automatically generated with the metadata of the file. If it's not, you'll need to upload it manually. +If the selected asset/recipe is a **Classification** recipe (or its export), the legend will be automatically generated with the metadata of the file. If it's not, you'll need to upload it manually. Select :btn:`fa-solid fa-pen-to-square` to open the **Legend editing** tool. It's the same as the one described in the **Classification** recipe (see :doc:`classification`). diff --git a/docs/source/cookbook/classification.rst b/docs/source/cookbook/classification.rst index 3818bacbfa..1007595c73 100644 --- a/docs/source/cookbook/classification.rst +++ b/docs/source/cookbook/classification.rst @@ -294,7 +294,7 @@ This menu will help the user manage the training data of the model used. To open Collected reference data """""""""""""""""""""""" -Collected reference data are data selected on the fly by the user. The workflow will be explained later in the documentation. +Collected reference data are data selected on the fly by the user. The workflow will be explained later in the documentation. In this pane, this type of data can be managed by the user. The data appear as a pair, associating coordinates to a class value, which will be used to create training data in the classification model. @@ -553,9 +553,9 @@ To modify existing points, select the :btn:`` to open Check the validity ^^^^^^^^^^^^^^^^^^ -SEPAL embeds information to help the user understand if the amount of training data is sufficient to produce an accurate classification model. In the **Recipe** window, change the **Band combination** to :code:`Class probability`. +SEPAL embeds information to help the user understand if the amount of training data is sufficient to produce an accurate classification model. In the **Recipe** window, change the **Band combination** to :code:`Class probability`. -The user now sees the probability of the model (i.e. the confidence level of the level with output class for each pixel). +The user now sees the probability of the model (i.e. the confidence level of the level with output class for each pixel). If the value is high (> 80 percent), then the pixel can be considered valid; if the value is low (< 80 percent), the model needs more training data or extra bands to improve the analysis. diff --git a/docs/source/cookbook/index.rst b/docs/source/cookbook/index.rst index 4ea186f206..603cc97ca6 100644 --- a/docs/source/cookbook/index.rst +++ b/docs/source/cookbook/index.rst @@ -92,9 +92,9 @@ Save a recipe Using saved recipes is the recommended method for sharing parameters to developers when debugging. -Select a recipe in the main menu to display it in a tab. +Select a recipe in the main menu to display it in a tab. -Then select :btn:`` in the upper-right corner and select :btn:`Export recipe`. +Then select :btn:`` in the upper-right corner and select :btn:`Export recipe`. The file will be downloaded to your computer using the following name: :code:`.json.zip`. diff --git a/docs/source/cookbook/planet_mosaic.rst b/docs/source/cookbook/planet_mosaic.rst index bd87ad1d25..b85eee3ea2 100644 --- a/docs/source/cookbook/planet_mosaic.rst +++ b/docs/source/cookbook/planet_mosaic.rst @@ -5,7 +5,7 @@ Planet mosaic Overview -------- -A mosaic is a process of combining spatially overlapping images into an individual image. +A mosaic is a process of combining spatially overlapping images into an individual image. In the SEPAL platform, you can create a composite dataset from Planet images taken at different times by using different techniques. For example, you can choose to keep only the pixel value from the first or last image, or combine the values of the overlapping pixels using a weighting algorithm, the average, or the maximum or minimum value. In addition, certain preprocessing tasks can be applied to mask clouds, shadows, snow, etc. These operations are complex and repetitive. SEPAL offers an interactive and intuitive way to create Planet mosaics within any area of interest (AOI). diff --git a/docs/source/cookbook/time_series.rst b/docs/source/cookbook/time_series.rst index eb8c1e25fe..a9670ef62b 100644 --- a/docs/source/cookbook/time_series.rst +++ b/docs/source/cookbook/time_series.rst @@ -34,7 +34,7 @@ The first step is to change the name of the recipe. This name will be used to id :width: 49% .. thumbnail:: ../_images/cookbook/time_series/title.png - :title: Time series modified title + :title: Time series modified title :width: 49% .. note:: diff --git a/docs/source/setup/gee.rst b/docs/source/setup/gee.rst index 089644333b..c2f24768d0 100644 --- a/docs/source/setup/gee.rst +++ b/docs/source/setup/gee.rst @@ -12,17 +12,17 @@ In this article, learn how to: GEE and SEPAL ------------- -SEPAL is closely linked to Google Earth Engine (GEE), a Google-powered Earth-observation cloud-computing platform. +SEPAL is closely linked to Google Earth Engine (GEE), a Google-powered Earth-observation cloud-computing platform. -SEPAL can: +SEPAL can: -- access data stored in the GEE data catalog; -- use GEE for processing large datasets; and -- read and write data to GEE assets. +- access data stored in the GEE data catalog; +- use GEE for processing large datasets; and +- read and write data to GEE assets. A large part of SEPAL's existing code is based on the JavaScript GEE application programming interface (API). -All SEPAL recipes are based on GEE and run scripts written by SEPAL team members to enable access to state-of-the-art processing algorithms without having to write code. +All SEPAL recipes are based on GEE and run scripts written by SEPAL team members to enable access to state-of-the-art processing algorithms without having to write code. In the SEPAL **Apps** list, the applications tagged with the Google logo (:icon:`fa-brands fa-google`) are also running with the Python GEE API and don't require you to use big instances to run complex operations. @@ -110,7 +110,7 @@ The page is subdivided into three zones and a map: :align: center :width: 50% -4. When you return to your list of **Assets** (located in the **Zone 1** panel), you should see the name you provided as the first folder at the root of the **Asset** tree. +4. When you return to your list of **Assets** (located in the **Zone 1** panel), you should see the name you provided as the first folder at the root of the **Asset** tree. In our example, we used **galatheetest**: @@ -187,11 +187,11 @@ If you want to change accounts or disconnect your GEE and SEPAL accounts: Upload files to GEE ------------------- -When you use SEPAL recipes and modules, you'll be asked to use GEE assets to provide rasters (:code:`ee.Image`) or vectors (:code:`ee.FeatureCollection`) to the core GEE-based algorithm. +When you use SEPAL recipes and modules, you'll be asked to use GEE assets to provide rasters (:code:`ee.Image`) or vectors (:code:`ee.FeatureCollection`) to the core GEE-based algorithm. These assets can be either: -- public assets that someone shared with you; or +- public assets that someone shared with you; or - assets that you created yourself and would like to use. .. tip:: @@ -262,6 +262,6 @@ To find the asset name, go back to **Assets** in the **Zone 1** pane and select :align: center :width: 80% -If you select **Copy link**, the link will be copied to the clipboard and you can paste it into SEPAL or send it to someone for authorized use. +If you select **Copy link**, the link will be copied to the clipboard and you can paste it into SEPAL or send it to someone for authorized use. Alternatively, you can select **Share** and choose between the different sharing options. diff --git a/docs/source/setup/index.rst b/docs/source/setup/index.rst index 967ff603a6..25cbb61c11 100644 --- a/docs/source/setup/index.rst +++ b/docs/source/setup/index.rst @@ -13,7 +13,7 @@ In this section of the documentation, learn how to: Navigate to other articles in each section by selecting links in the **Section navigation** pane on the left. -Navigate to other subsections of each article by selecting links in the **On this page** pane on the right. +Navigate to other subsections of each article by selecting links in the **On this page** pane on the right. Make contributions to the documentation by selecting :icon:`fa-solid fa-pencil` **Edit on GitHub** in the **On this page** pane on the right. diff --git a/docs/source/setup/nicfi.rst b/docs/source/setup/nicfi.rst index f216aa93cd..3eb6417022 100644 --- a/docs/source/setup/nicfi.rst +++ b/docs/source/setup/nicfi.rst @@ -26,14 +26,14 @@ In support of NICFI’s mission, you can use this data for a number of purposes, The NICFI and Planet Basemaps for Tropical Forest Monitoring are now available in Google Earth Engine (GEE) and SEPAL for easy processing. In a few simple steps, you can create your own custom mosaics using Planet basemaps. -The first step is to make sure you have a GEE account. +The first step is to make sure you have a GEE account. If you don’t have a GEE account, register by following `this tutorial `__. Sign up for NICFI imagery ------------------------- -Sign up for NICFI – Planet Lab data access using the same email address associated with your GEE account. +Sign up for NICFI – Planet Lab data access using the same email address associated with your GEE account. To sign up for access to the NICFI data program, go to ``_. @@ -68,7 +68,7 @@ Select the link and a new form will appear. Complete the form and you will recei Access NICFI through GEE ------------------------ -NICFI – Planet Lab data can also be accessed from GEE, allowing you to use Planet Lab imagery in SEPAL recipes, such as **Classification** or **Time series**. +NICFI – Planet Lab data can also be accessed from GEE, allowing you to use Planet Lab imagery in SEPAL recipes, such as **Classification** or **Time series**. To authorize your GEE account to access Planet Lab data: diff --git a/docs/source/setup/presentation.rst b/docs/source/setup/presentation.rst index fa30f78dbd..e7608b514a 100644 --- a/docs/source/setup/presentation.rst +++ b/docs/source/setup/presentation.rst @@ -41,9 +41,9 @@ Choose a language for your SEPAL environment by following the instructions in th The default language in SEPAL is English; however, other languages are available (currently French and Spanish). -To change the language to either French or Spanish: +To change the language to either French or Spanish: -1. Go to http://sepal.io. +1. Go to http://sepal.io. 2. Select :code:`Launch`. 3. In the upper-right corner, select **en**, **es** or **fr** (English, Spanish and French, respectively). @@ -67,7 +67,7 @@ On the left, there are four main navigation buttons in the vertical **Tabs** bar - **Terminal**: Access the command line for the LINUX server. - **Apps**: Follow links to a variety of preloaded tools. -Below the vertical **Tabs** bar – on the left – is another button: +Below the vertical **Tabs** bar – on the left – is another button: - **Tasks*: View a list of currently running tasks. @@ -78,12 +78,12 @@ In the lower-right corner there are four buttons (from right to left): - **User report** (displayed as "$ 0/h") - **User messages** (displayed as a bell) -In the **User details** pop-up window, you can: +In the **User details** pop-up window, you can: - view and edit user account information (e.g. name, password, email, organization; username can not be edited); and -– link your GEE and SEPAL accounts by selecting **Use my own Google account** and following the instructions. +– link your GEE and SEPAL accounts by selecting **Use my own Google account** and following the instructions. -If your GEE and SEPAL accounts are connected, SEPAL uses your Google Drive as a temporary storage space for data downloaded to your SEPAL workspace (e.g. any imagery tiles or mosaics that you “retrieve to SEPAL workspace” will first be saved to your Google Drive account before being saved in your SEPAL workspace). +If your GEE and SEPAL accounts are connected, SEPAL uses your Google Drive as a temporary storage space for data downloaded to your SEPAL workspace (e.g. any imagery tiles or mosaics that you “retrieve to SEPAL workspace” will first be saved to your Google Drive account before being saved in your SEPAL workspace). If your GEE and SEPAL accounts are not linked, data downloads to your SEPAL workspace will still be possible and the data will pass through SEPAL's Google Drive account. @@ -97,9 +97,9 @@ Linking your GEE and SEPAL accounts will allow you to read and write from your G Link your SEPAL and GEE accounts in order to read and write to GEE assets from SEPAL. -In the **User report** pop-up window, you can view the status (used/available) of your processing and storage resources: -- **Instance spending** refers to the resources used/available to start and run cloud computers. -- **Storage spending** and **Storage space** refer to the resources used/available for storage in your SEPAL workspace. +In the **User report** pop-up window, you can view the status (used/available) of your processing and storage resources: +- **Instance spending** refers to the resources used/available to start and run cloud computers. +- **Storage spending** and **Storage space** refer to the resources used/available for storage in your SEPAL workspace. - **Sessions** refers to any processes in your current session, if you are running any. .. thumbnail:: ../_images/setup/presentation/user_report_panel.png @@ -174,9 +174,9 @@ To start an instance: 3. Next to **Select (t1):**, enter **t2** (or your chosen instance type). 4. Press **Enter** on your keyboard and wait for the instance to start, which will take several minutes. -To stop an instance: +To stop an instance: -- enter **exit** into the command line (you can then refresh the terminal page to start a new instance; or +- enter **exit** into the command line (you can then refresh the terminal page to start a new instance; or - open your **User report** by selecting the "$ 0/h" icon in the lower-right corner, then selecting the trashcan icon under **Sessions**. Once an instance has stopped, you can follow the instance start-up steps again to select a larger instance, if necessary. @@ -191,7 +191,7 @@ Apps In the vertical **Tabs** bar on the left, select the **Apps** button to display applications accessible through SEPAL (for more information about each app, select the rightmost **i** button). -Applications are preprogrammed (typically using R or Python) to perform specific useful tasks. +Applications are preprogrammed (typically using R or Python) to perform specific useful tasks. Applications make use of instances; running them will use your SEPAL computing resources. diff --git a/docs/source/setup/register.rst b/docs/source/setup/register.rst index 32923a6d3b..0c3ed5cfd7 100644 --- a/docs/source/setup/register.rst +++ b/docs/source/setup/register.rst @@ -77,7 +77,7 @@ Request additional SEPAL resources To use SEPAL modules and acesss the command line terminal and development tools like Jupyter or RStudio, you will need to request processing resources. -1. Select the **User report** button in the lower-right corner (i.e. **$ 0/h**). +1. Select the **User report** button in the lower-right corner (i.e. **$ 0/h**). 2. Select :btn:` Request additional resources`. 2. Complete the form and select :btn:` Apply`. From 0c7448e86d33a83623b19e6639288b814fb56c28 Mon Sep 17 00:00:00 2001 From: dfguerrerom Date: Thu, 16 Nov 2023 11:58:05 +0100 Subject: [PATCH 18/18] style: lint --- docs/source/setup/presentation.rst | 4 ++-- docs/source/setup/register.rst | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/source/setup/presentation.rst b/docs/source/setup/presentation.rst index e7608b514a..7b8e24e206 100644 --- a/docs/source/setup/presentation.rst +++ b/docs/source/setup/presentation.rst @@ -69,7 +69,7 @@ On the left, there are four main navigation buttons in the vertical **Tabs** bar Below the vertical **Tabs** bar – on the left – is another button: -- **Tasks*: View a list of currently running tasks. +- **Tasks**: View a list of currently running tasks. In the lower-right corner there are four buttons (from right to left): @@ -81,7 +81,7 @@ In the lower-right corner there are four buttons (from right to left): In the **User details** pop-up window, you can: - view and edit user account information (e.g. name, password, email, organization; username can not be edited); and -– link your GEE and SEPAL accounts by selecting **Use my own Google account** and following the instructions. +- link your GEE and SEPAL accounts by selecting **Use my own Google account** and following the instructions. If your GEE and SEPAL accounts are connected, SEPAL uses your Google Drive as a temporary storage space for data downloaded to your SEPAL workspace (e.g. any imagery tiles or mosaics that you “retrieve to SEPAL workspace” will first be saved to your Google Drive account before being saved in your SEPAL workspace). diff --git a/docs/source/setup/register.rst b/docs/source/setup/register.rst index 0c3ed5cfd7..b2730fae81 100644 --- a/docs/source/setup/register.rst +++ b/docs/source/setup/register.rst @@ -79,7 +79,7 @@ To use SEPAL modules and acesss the command line terminal and development tools 1. Select the **User report** button in the lower-right corner (i.e. **$ 0/h**). 2. Select :btn:` Request additional resources`. -2. Complete the form and select :btn:` Apply`. +3. Complete the form and select :btn:` Apply`. If you do not know how many resources you will use, go to the `Resource management ` section for more information.