deploy: ea35460

guiwitz · Dec 16, 2024 · 98301ec · 98301ec
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diff --git a/.buildinfo b/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: b0ea98e53a476ddd1b69093bd3b02909
+config: 4224b0491710a281498ab6e51e5d7746
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/README.html b/README.html
diff --git a/_downloads/67c82d7386509b69c0fdc3a99f60af43/environment.yml b/_downloads/67c82d7386509b69c0fdc3a99f60af43/environment.yml
@@ -0,0 +1,14 @@
+name: microfilm
+channels:
+  - conda-forge
+dependencies:
+  - python>=3.8
+  - pandas
+  - jupyter
+  - jupyterlab
+  - ipywidgets
+  - pip
+  - ipympl
+  - pip:
+    - tqdm
+    - microfilm
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diff --git a/_panels_static/panels-main.c949a650a448cc0ae9fd3441c0e17fb0.css b/_panels_static/panels-main.c949a650a448cc0ae9fd3441c0e17fb0.css
diff --git a/_panels_static/panels-variables.06eb56fa6e07937060861dad626602ad.css b/_panels_static/panels-variables.06eb56fa6e07937060861dad626602ad.css
diff --git a/_sources/README.md b/_sources/README.md
@@ -30,6 +30,32 @@ To test the package via the Jupyter interface and the notebooks available [here]
 conda env create -f environment.yml
 ```
 
+### Optional installs
+
+If you want to use the ```dataset``` submodule (see below in Additional functionalities) and need to handle multipage tiff files or nd2 files, use:
+
+```
+pip install "microfilm[multipage]"
+```
+
+or 
+
+```
+pip install "microfilm[nd2]"
+```
+
+If you plan to not just use simple plotting but want to create animations, you need to install:
+
+```
+pip install "microfilm[animation]"
+```
+
+To install all options use:
+
+```
+pip install "microfilm[all]"
+```
+
 ## Simple plot
 
 It is straightforward to create a ready-to-use plot of a multi-channel image dataset. In the following code snippet, we load a Numpy array of a multi-channel time-lapse dataset with shape ```CTXY``` (three channels). The figure below showing the time-point ```t=10``` is generated in a single command with a few options and saved as a png:

diff --git a/_sources/docs/first_plot.ipynb b/_sources/docs/first_plot.ipynb
diff --git a/_sources/docs/source/microfilm.rst b/_sources/docs/source/microfilm.rst
@@ -36,14 +36,6 @@ microfilm.microplot module
    :undoc-members:
    :show-inheritance:
 
-microfilm.version module
-------------------------
-
-.. automodule:: microfilm.version
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
 Module contents
 ---------------
 

diff --git a/_sources/notebooks/create_animations.ipynb b/_sources/notebooks/create_animations.ipynb
diff --git a/_sources/notebooks/create_illustrations.ipynb b/_sources/notebooks/create_illustrations.ipynb
diff --git a/_sources/notebooks/create_panels.ipynb b/_sources/notebooks/create_panels.ipynb
diff --git a/_sources/notebooks/create_plots.ipynb b/_sources/notebooks/create_plots.ipynb
diff --git a/_sphinx_design_static/design-tabs.js b/_sphinx_design_static/design-tabs.js
@@ -0,0 +1,101 @@
+// @ts-check
+
+// Extra JS capability for selected tabs to be synced
+// The selection is stored in local storage so that it persists across page loads.
+
+/**
+ * @type {Record<string, HTMLElement[]>}
+ */
+let sd_id_to_elements = {};
+const storageKeyPrefix = "sphinx-design-tab-id-";
+
+/**
+ * Create a key for a tab element.
+ * @param {HTMLElement} el - The tab element.
+ * @returns {[string, string, string] | null} - The key.
+ *
+ */
+function create_key(el) {
+  let syncId = el.getAttribute("data-sync-id");
+  let syncGroup = el.getAttribute("data-sync-group");
+  if (!syncId || !syncGroup) return null;
+  return [syncGroup, syncId, syncGroup + "--" + syncId];
+}
+
+/**
+ * Initialize the tab selection.
+ *
+ */
+function ready() {
+  // Find all tabs with sync data
+
+  /** @type {string[]} */
+  let groups = [];
+
+  document.querySelectorAll(".sd-tab-label").forEach((label) => {
+    if (label instanceof HTMLElement) {
+      let data = create_key(label);
+      if (data) {
+        let [group, id, key] = data;
+
+        // add click event listener
+        // @ts-ignore
+        label.onclick = onSDLabelClick;
+
+        // store map of key to elements
+        if (!sd_id_to_elements[key]) {
+          sd_id_to_elements[key] = [];
+        }
+        sd_id_to_elements[key].push(label);
+
+        if (groups.indexOf(group) === -1) {
+          groups.push(group);
+          // Check if a specific tab has been selected via URL parameter
+          const tabParam = new URLSearchParams(window.location.search).get(
+            group
+          );
+          if (tabParam) {
+            console.log(
+              "sphinx-design: Selecting tab id for group '" +
+                group +
+                "' from URL parameter: " +
+                tabParam
+            );
+            window.sessionStorage.setItem(storageKeyPrefix + group, tabParam);
+          }
+        }
+
+        // Check is a specific tab has been selected previously
+        let previousId = window.sessionStorage.getItem(
+          storageKeyPrefix + group
+        );
+        if (previousId === id) {
+          // console.log(
+          //   "sphinx-design: Selecting tab from session storage: " + id
+          // );
+          // @ts-ignore
+          label.previousElementSibling.checked = true;
+        }
+      }
+    }
+  });
+}
+
+/**
+ *  Activate other tabs with the same sync id.
+ *
+ * @this {HTMLElement} - The element that was clicked.
+ */
+function onSDLabelClick() {
+  let data = create_key(this);
+  if (!data) return;
+  let [group, id, key] = data;
+  for (const label of sd_id_to_elements[key]) {
+    if (label === this) continue;
+    // @ts-ignore
+    label.previousElementSibling.checked = true;
+  }
+  window.sessionStorage.setItem(storageKeyPrefix + group, id);
+}
+
+document.addEventListener("DOMContentLoaded", ready, false);
diff --git a/_sphinx_design_static/sphinx-design.min.css b/_sphinx_design_static/sphinx-design.min.css
diff --git a/_static/__init__.py b/_static/__init__.py
diff --git a/_static/__pycache__/__init__.cpython-39.pyc b/_static/__pycache__/__init__.cpython-39.pyc
diff --git a/_static/basic.css b/_static/basic.css
@@ -4,7 +4,7 @@
  *
  * Sphinx stylesheet -- basic theme.
  *
- * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -222,7 +222,7 @@ table.modindextable td {
 /* -- general body styles --------------------------------------------------- */
 
 div.body {
-    min-width: 450px;
+    min-width: 360px;
     max-width: 800px;
 }
 
@@ -237,14 +237,8 @@ a.headerlink {
     visibility: hidden;
 }
 
-a.brackets:before,
-span.brackets > a:before{
-    content: "[";
-}
-
-a.brackets:after,
-span.brackets > a:after {
-    content: "]";
+a:visited {
+    color: #551A8B;
 }
 
 h1:hover > a.headerlink,
@@ -335,12 +329,16 @@ p.sidebar-title {
     font-weight: bold;
 }
 
+nav.contents,
+aside.topic,
 div.admonition, div.topic, blockquote {
     clear: left;
 }
 
 /* -- topics ---------------------------------------------------------------- */
 
+nav.contents,
+aside.topic,
 div.topic {
     border: 1px solid #ccc;
     padding: 7px;
@@ -379,13 +377,17 @@ div.body p.centered {
 
 div.sidebar > :last-child,
 aside.sidebar > :last-child,
+nav.contents > :last-child,
+aside.topic > :last-child,
 div.topic > :last-child,
 div.admonition > :last-child {
     margin-bottom: 0;
 }
 
 div.sidebar::after,
 aside.sidebar::after,
+nav.contents::after,
+aside.topic::after,
 div.topic::after,
 div.admonition::after,
 blockquote::after {
@@ -428,10 +430,6 @@ table.docutils td, table.docutils th {
     border-bottom: 1px solid #aaa;
 }
 
-table.footnote td, table.footnote th {
-    border: 0 !important;
-}
-
 th {
     text-align: left;
     padding-right: 5px;
@@ -615,19 +613,26 @@ ul.simple p {
     margin-bottom: 0;
 }
 
-dl.footnote > dt,
-dl.citation > dt {
+aside.footnote > span,
+div.citation > span {
     float: left;
-    margin-right: 0.5em;
 }
-
-dl.footnote > dd,
-dl.citation > dd {
+aside.footnote > span:last-of-type,
+div.citation > span:last-of-type {
+  padding-right: 0.5em;
+}
+aside.footnote > p {
+  margin-left: 2em;
+}
+div.citation > p {
+  margin-left: 4em;
+}
+aside.footnote > p:last-of-type,
+div.citation > p:last-of-type {
     margin-bottom: 0em;
 }
-
-dl.footnote > dd:after,
-dl.citation > dd:after {
+aside.footnote > p:last-of-type:after,
+div.citation > p:last-of-type:after {
     content: "";
     clear: both;
 }
@@ -644,10 +649,6 @@ dl.field-list > dt {
     padding-right: 5px;
 }
 
-dl.field-list > dt:after {
-    content: ":";
-}
-
 dl.field-list > dd {
     padding-left: 0.5em;
     margin-top: 0em;
@@ -673,6 +674,16 @@ dd {
     margin-left: 30px;
 }
 
+.sig dd {
+    margin-top: 0px;
+    margin-bottom: 0px;
+}
+
+.sig dl {
+    margin-top: 0px;
+    margin-bottom: 0px;
+}
+
 dl > dd:last-child,
 dl > dd:last-child > :last-child {
     margin-bottom: 0;
@@ -741,6 +752,14 @@ abbr, acronym {
     cursor: help;
 }
 
+.translated {
+    background-color: rgba(207, 255, 207, 0.2)
+}
+
+.untranslated {
+    background-color: rgba(255, 207, 207, 0.2)
+}
+
 /* -- code displays --------------------------------------------------------- */
 
 pre {

diff --git a/_static/copybutton.css b/_static/copybutton.css
@@ -35,7 +35,8 @@ div.highlight  {
     position: relative;
 }
 
-.highlight:hover button.copybtn {
+/* Show the copybutton */
+.highlight:hover button.copybtn, button.copybtn.success {
 	opacity: 1;
 }