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Using land cover products to quantify urbanisation trends #51

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inesgirao opened this issue Apr 23, 2024 · 26 comments · May be fixed by #242
Open

Using land cover products to quantify urbanisation trends #51

inesgirao opened this issue Apr 23, 2024 · 26 comments · May be fixed by #242
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@inesgirao
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inesgirao commented Apr 23, 2024 •
edited by malmans2
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Data Type

Satellite ECVs - Land Biosphere

Assessment Category

Trend Assessment

Dataset Name

satellite-land-cover

Question Number

2

Workflow ID

eqctier3-e30af9a0-46df-4eb8-ae78-35519b70b8d4

Zipped Notebook

C3S2_D520.5.3.14b_Quality_Assessment_User_Questions_LULC_UQ2_v1.3.zip

Environment

name: bopen
channels:
  - conda-forge
  - defaults
dependencies:
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  - _openmp_mutex=4.5=2_gnu
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  - gstreamer=1.22.0=h25f0c4b_2
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  - h5py=3.9.0=nompi_py310h367e799_100
  - harfbuzz=6.0.0=h3ff4399_1
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  - python_abi=3.10=3_cp310
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  - requests=2.31.0=pyhd8ed1ab_0
  - rfc3339-validator=0.1.4=pyhd8ed1ab_0
  - rfc3986-validator=0.1.1=pyh9f0ad1d_0
  - rich=13.5.1=pyhd8ed1ab_0
  - rtree=1.0.1=py310h06a4308_0
  - s2n=1.3.42=h3358134_0
  - scikit-learn=1.3.0=py310h1128e8f_0
  - scipy=1.11.1=py310heeff2f4_0
  - seaborn=0.12.2=hd8ed1ab_0
  - seaborn-base=0.12.2=pyhd8ed1ab_0
  - send2trash=1.8.2=pyh41d4057_0
  - setuptools=68.0.0=py310h06a4308_0
  - shellingham=1.5.0=py310h06a4308_0
  - simplejson=3.19.2=py310h2372a71_0
  - sip=6.7.9=py310hc6cd4ac_0
  - six=1.16.0=pyhd3eb1b0_1
  - snappy=1.1.10=h9fff704_0
  - sniffio=1.3.0=pyhd8ed1ab_0
  - snowballstemmer=2.2.0=pyhd8ed1ab_0
  - snuggs=1.4.7=py_0
  - sortedcontainers=2.4.0=pyhd3eb1b0_0
  - sparse=0.14.0=pyhd8ed1ab_0
  - sphinx=6.2.1=pyhd8ed1ab_0
  - sphinx-autoapi=2.1.0=pyhd8ed1ab_0
  - sphinxcontrib-applehelp=1.0.7=pyhd8ed1ab_0
  - sphinxcontrib-devhelp=1.0.5=pyhd8ed1ab_0
  - sphinxcontrib-dotnetdomain=0.4=py_0
  - sphinxcontrib-golangdomain=0.2.0.dev0=py_0
  - sphinxcontrib-htmlhelp=2.0.4=pyhd8ed1ab_0
  - sphinxcontrib-jsmath=1.0.1=pyhd8ed1ab_0
  - sphinxcontrib-qthelp=1.0.6=pyhd8ed1ab_0
  - sphinxcontrib-serializinghtml=1.1.9=pyhd8ed1ab_0
  - sqlalchemy=2.0.20=py310h2372a71_0
  - sqlite=3.41.2=h5eee18b_0
  - stack_data=0.2.0=pyhd3eb1b0_0
  - statsmodels=0.14.0=py310h278f3c1_1
  - structlog=23.1.0=pyhd8ed1ab_0
  - tblib=1.7.0=pyhd3eb1b0_0
  - tenacity=8.2.2=py310h06a4308_0
  - terminado=0.17.1=pyh41d4057_0
  - textwrap3=0.9.2=py_0
  - threadpoolctl=2.2.0=pyh0d69192_0
  - tiledb=2.13.2=hd532e3d_0
  - tinycss2=1.2.1=pyhd8ed1ab_0
  - tk=8.6.12=h1ccaba5_0
  - toml=0.10.2=pyhd8ed1ab_0
  - tomli=2.0.1=py310h06a4308_0
  - toolz=0.12.0=py310h06a4308_0
  - tornado=6.3.2=py310h5eee18b_0
  - tqdm=4.66.1=pyhd8ed1ab_0
  - traitlets=5.7.1=py310h06a4308_0
  - typer=0.9.0=pyhd8ed1ab_0
  - typing-extensions=4.7.1=py310h06a4308_0
  - typing_extensions=4.7.1=py310h06a4308_0
  - typing_utils=0.1.0=pyhd8ed1ab_0
  - tzcode=2023c=h0b41bf4_0
  - tzdata=2023c=h04d1e81_0
  - ucx=1.14.0=h3484d09_2
  - udunits2=2.2.28=hc3e0081_0
  - ukkonen=1.0.1=py310hbf28c38_3
  - unidecode=1.3.6=pyhd8ed1ab_0
  - urllib3=1.26.16=py310h06a4308_0
  - virtualenv=20.24.3=pyhd8ed1ab_0
  - wcwidth=0.2.5=pyhd3eb1b0_0
  - websocket-client=1.6.1=pyhd8ed1ab_0
  - wheel=0.38.4=py310h06a4308_0
  - wrapt=1.15.0=py310h1fa729e_0
  - xarray=2023.8.0=pyhd8ed1ab_0
  - xarraymannkendall=1.4.5=pyhd8ed1ab_0
  - xcb-util=0.4.0=h166bdaf_0
  - xcb-util-image=0.4.0=h166bdaf_0
  - xcb-util-keysyms=0.4.0=h166bdaf_0
  - xcb-util-renderutil=0.3.9=h166bdaf_0
  - xcb-util-wm=0.4.1=h166bdaf_0
  - xerces-c=3.2.4=h8d71039_2
  - xesmf=0.7.1=pyhd8ed1ab_0
  - xhistogram=0.3.2=pyhd8ed1ab_0
  - xkeyboard-config=2.38=h0b41bf4_0
  - xorg-fixesproto=5.0=h7f98852_1002
  - xorg-inputproto=2.3.2=h7f98852_1002
  - xorg-kbproto=1.0.7=h7f98852_1002
  - xorg-libice=1.0.10=h7f98852_0
  - xorg-libsm=1.2.3=hd9c2040_1000
  - xorg-libx11=1.8.4=h0b41bf4_0
  - xorg-libxau=1.0.9=h7f98852_0
  - xorg-libxdmcp=1.1.3=h7f98852_0
  - xorg-libxext=1.3.4=h0b41bf4_2
  - xorg-libxfixes=5.0.3=h7f98852_1004
  - xorg-libxi=1.7.10=h7f98852_0
  - xorg-libxrender=0.9.10=h7f98852_1003
  - xorg-renderproto=0.11.1=h7f98852_1002
  - xorg-xextproto=7.3.0=h0b41bf4_1003
  - xorg-xf86vidmodeproto=2.3.1=h7f98852_1002
  - xorg-xproto=7.0.31=h27cfd23_1007
  - xskillscore=0.0.24=pyhd8ed1ab_0
  - xyzservices=2022.9.0=py310h06a4308_1
  - xz=5.4.2=h5eee18b_0
  - yaml=0.2.5=h7b6447c_0
  - yarl=1.9.2=py310h2372a71_0
  - zarr=2.16.1=pyhd8ed1ab_0
  - zeromq=4.3.4=h2531618_0
  - zict=2.2.0=py310h06a4308_0
  - zipp=3.11.0=py310h06a4308_0
  - zlib=1.2.13=h166bdaf_4
  - zstd=1.5.5=hc292b87_0
  - pip:
      - argon2-cffi==23.1.0
      - arrow==1.2.3
      - c3s-eqc-automatic-quality-control==0.1.2.dev84+ga57fc76
      - c3s-eqc-toolbox-template==0.2.2.dev320+g3e5c724
      - cacholote==0.4.1
      - cads-toolbox==0.0.2b0
      - cdo==1.6.0
      - cgul==0.0.4
      - coucal==0.0.1b3
      - descartes==1.1.0
      - emohawk==0.0.4b0
      - fqdn==1.5.1
      - geopandas==0.14.1
      - ipython-genutils==0.2.0
      - ipywidgets==8.1.0
      - isoduration==20.11.0
      - jsonpointer==2.4
      - jsonschema==4.18.6
      - jsonschema-specifications==2023.7.1
      - jupyter==1.0.0
      - jupyter-console==6.6.3
      - jupyter-events==0.7.0
      - jupyter-server==2.7.2
      - jupyterlab-widgets==3.0.8
      - kaleido==0.2.1
      - nbconvert==7.7.3
      - nco==1.1.0
      - notebook==7.0.2
      - pymannkendall==1.4.3
      - qtconsole==5.4.3
      - qtpy==2.3.1
      - rasterio==1.3.6
      - referencing==0.30.1
      - rioxarray==0.14.1
      - rpds-py==0.9.2
      - shapely==2.0.2
      - soupsieve==2.4.1
      - uri-template==1.3.0
      - webcolors==1.13
      - webencodings==0.5.1
      - widgetsnbextension==4.0.8

Anything else we need to know?

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@malmans2
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malmans2 commented Apr 23, 2024 •
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Hi @inesgirao,

Could you please check that you are sharing the workflow ID? (note that workflow ID is different than task ID)
I think that your q1 and q2 notebooks should share the same workflow ID.
(It's OK if you used the wrong one for the first notebook, but let's make sure that we are using the right one for this one)

@malmans2 malmans2 mentioned this issue Apr 23, 2024
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@inesgirao
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Hi @malmans2

I am sorry for missing it.
Please consider this last one as the correct one for all permalinks.
I had some problems regarding the submission of the Tier3.

Thank you

@malmans2
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OK, no need to change the one used for the first notebook.
I just wanted to make sure that you are aware of it and you're now using the correct ID.

Here is the permalink: https://github.com/ecmwf-projects/c3s2-eqc-quality-assessment/blob/08cdcb810fdf9e9844064d3a079f54c73b6244d3/Satellite_ECVs/Land_Biosphere_ECVs/satellite_satellite-land-cover_trend-assessment_q02.ipynb

Please make sure that the notebook name is correct.

If you need to make modifications (e.g., to address the reviewer's comment), please share here the new version of the notebook and I will provide a new permalink.

Let me know when the notebook is accepted, I will merge the PR into main.

@inesgirao
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Hi @malmans2

I now send the new version of this notebook.

Thank you

C3S2_D520.5.3.14b_Quality_Assessment_User_Questions_LULC_UQ2_v1.3.zip

@malmans2
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Here is the new permalink: https://github.com/ecmwf-projects/c3s2-eqc-quality-assessment/blob/523a163ae2d47c279795ebbb76130bf11d91933a/Satellite_ECVs/Land_Biosphere_ECVs/satellite_satellite-land-cover_trend-assessment_q02.ipynb

@malmans2 malmans2 added the wp5 label May 27, 2024
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Hi @inesgirao ,

Small suggestion. I noticed that in a cell you read the NUTS regions from a local file. Because of that, the notebook does not work for external people that would like to try it. You already define the NUTS url, so the fix would be very easy. Next time you request a permalink I suggest to implement this change:

- nuts = gpd.read_file('./NUTS_RG_20M_2021_4326.shp')
+ nuts = gpd.read_file(shapefile_url)

@inesgirao
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Hello @malmans2

I resend the zip file, with new template.

Thank you
C3S2_D520.5.3.14b_Quality_Assessment_User_Questions_LULC_UQ2_v1.4.zip

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malmans2 commented Jul 4, 2024

Here is the permalink: https://github.com/ecmwf-projects/c3s2-eqc-quality-assessment/blob/58e296fdcfd242ad1375e209c847e49403737948/Satellite_ECVs/Land_Biosphere_ECVs/satellite_satellite-land-cover_trend-assessment_q02.ipynb

@inesgirao
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inesgirao commented Oct 22, 2024 •
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Hello @malmans2

I resend the zip file, with new changes asked by the data provider.

Ps. I had some changes in my environment, where should i re-upload it?

Thank you

C3S2_D520.5.3.14b_Quality_Assessment_User_Questions_LULC_UQ2_v1.5.zip

@malmans2
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Hi @inesgirao,

This issue was opened a long time ago and it looks like you did not share the correct workflow ID.
Could you please send me the right Workflow ID, which looks like this: eqctier3-1123e4567-e89b-12d3-a456-42665544000

It should be clearly shown in the CIM.

@inesgirao
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Hey,

I am sorry.
Here it is:
Task: de7380fa-7054-11ef-8171-667b69cf5fd7

Workflow: eqctier3-e30af9a0-46df-4eb8-ae78-35519b70b8d4

Thank you

@malmans2
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Hi @inesgirao,

There are a few issues you need to address:

  1. You have a reference to an external figure: UrbanAreaSeriesMaps.png. This is not allowed. The figure must be attached to the notebook as explained in the template and its instructions.
  2. The title should be a level 1 heading, meaning you should use a single #. For example: # Title
  3. All sections in the template must use level 2 headings, as shown below and in the template: 
    ## 🌍 Use case: [your content]
## ❓ Quality assessment question
## 📢 Quality assessment statement
## 📋 Methodology
## 📈 Analysis and results
## ℹ️ If you want to know more
  4. Do not skip heading levels. For example, you cannot jump from ## H2 title to #### H4 title.

The first point is the most important, so please focus on that and send me the revised version of your notebook. If anything is unclear with points 2, 3, or 4, I can help fix them.

@inesgirao
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C3S2_D520.5.3.14b_Quality_Assessment_User_Questions_LULC_UQ2_v1.5.zip

Hey @malmans2

Here it goes, hopefully, everything is now proper.

Thank you

@malmans2 malmans2 linked a pull request Oct 22, 2024 that will close this issue
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Looks good now!

Permalink: https://github.com/ecmwf-projects/c3s2-eqc-quality-assessment/blob/82f75dddde88b37157557dc54988b0202bebe165/Satellite_ECVs/Land_Biosphere/satellite_satellite-land-cover_trend-assessment_q02.ipynb

Please ensure that the notebook name is correct. If you need to make any modifications (e.g., addressing the reviewer's comments), please share the new version of the notebook here, and I will provide a new permalink. Let me know once the notebook is accepted, and I will merge the PR into the main branch.

PREVIEW

@inesgirao
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Hello @malmans2

I resend the zip file, with new changes asked by the data provider.

Thank you

C3S2_D520.5.3.14b_Quality_Assessment_User_Questions_LULC_UQ2_v1.7.zip

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malmans2 commented Dec 23, 2024 •
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Hi @inesgirao,

I had to make various changes to the notebook. Here is the list:

  • You can not use external figures. You must attach the figure to the notebook as explained in the template. See here and here. The notebook must be self contained, and therefore you should not include any other file in the zip.
  • There is no need to add the notebook name to the reference section nor the title. E.g., [Bla Bla Bla](C3S2_D520.5.3.14b_Quality_Assessment_User_Questions_LULC_UQ2_v1.5.ipynb:code-section-1) is not needed, you can just use [](code-section-1). It's not a problem if you like to add the notebook name and the section title, but then you have to remember to update it. It's easy to forget about it, and indeed you had a few references out of date.
  • The quality assessment statement section is missing the admonition syntax
  • You jumped from section 3 to 5. I assume it was not intentional.

Please have a look to the notebook template and instructions as these problems are quite common in your group.

I will release the permalink in a minute.

@malmans2
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malmans2 commented Dec 23, 2024 •
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Here is the new permalink: https://github.com/ecmwf-projects/c3s2-eqc-quality-assessment/blob/dc90a43eb13953d9ad1e36d8543f9d2730c7e1d8/Satellite_ECVs/Land_Biosphere/satellite_satellite-land-cover_trend-assessment_q02.ipynb

PREVIEW

@inesgirao inesgirao changed the title Trends and Variability: Urbanization Trends Using land cover products to quantify urbanisation trends Dec 26, 2024
@inesgirao
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Hey @malmans2,

I apologise for the back and foward but i notice some small but necessary changes were needed so I resend the file. I followed your guidelines and I believe is fully ready for a permalink,

C3S2_D520.5.3.14b_Quality_Assessment_User_Questions_LULC_UQ2_v1.7.zip

Thank you for you support!

@malmans2
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Here is the new permalink: https://github.com/ecmwf-projects/c3s2-eqc-quality-assessment/blob/c209a588368b84c4e180b3552d8049f3d6260348/Satellite_ECVs/Land_Biosphere/satellite_satellite-land-cover_trend-assessment_q02.ipynb

@inesgirao
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Dear @malmans2,

I wanted to confirm if it’s acceptable that the BOPEN functions have not been implemented in this JN. I ask because they were in the JN for the FIRE dataset. Since you’ve already reviewed this, I want to ensure that proceeding without these functions won’t cause any issues down the line.

Thank you very much for your time and guidance.

@malmans2
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malmans2 commented Jan 10, 2025 •
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When evaluators contact us through the template repository, we provide support and review or optimise code when needed. However, to my knowledge, there are no constraints on the code you submit here. In fact, I only provide permalinks in this repository and do not review the code.

@inesgirao
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If I am not mistaken this JN went througth the template repository before but its true that I did not ask specifically to implement BOPEN functions. My question is more if this is ok, or the notebook needs to be revised to include the BOPEN functions.

Thank you for the feeback.

@malmans2
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I'm not sure I am following. B-Open software is imported. Which B-Open functions you are not using?

@inesgirao
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Per example, I use my own code for cell area calculation.

@malmans2
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That's not an issue as long as you are confident that the code produces correct results. We only provide technical support and do not have knowledge or understanding of the science behind all notebooks (e.g., I do not know how you obtained the scaling factors for computing the cell area, but it's not my job to check that).

B-Open reviewed the technical side of the code, and I can confirm that it's well written and runs smoothly, so no need to change anything if the results are correct.

@inesgirao
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Ok, thank you for your clarifications

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eqctier3-e30af9a0-46df-4eb8-ae78-35519b70b8d4 ecmwf-projects/c3s2-eqc-quality-assessment
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