bump (#27)

* points to brainrender * update testing * refactor * refactor * badges * notes * initial inj finder commit (#11) * formatting with black * add .DS_store to gitignore * typo * update imports * update imports * deal with no obj path given * error typo * move utils too imlib * remove amap imports * optional logging to file * tidy * registration moved to imlib * keep largest object * reduce RAM usage * remove unnecessary logging args * adds lesion and track estimation and generic tools * add missing dir support for cell export * add missing dir support for cell export * reduce mem requirements * remove old code * remove old code * refactor scaling * fix failing heatmap test * update docs * ensure output directory exists * make pixel sizes mandatory * make pixel sizes mandatory (#17) * move functionality to imlib * remove hard coded smoothing * Refactor (#19) * make pixel sizes mandatory * move functionality to imlib * remove hard coded smoothing * update docs * Injectionsite (#20) * refactors code from SL to import from neuro and imlib only * moves amap_vis to neuro and removes amap and cellfinder dependencies; * format with black * amap_vis * bump * remove cellfinder dependency * cli entry point for fibre track segmentation * refactor seg tools * start manual seg * remove hardocoding in manual region segmentation * refactor paths * bump * update docs * update docs * update docs * update docs * support multiple objects * color objects * bump * update reqs * improve rendering of flat objects * bump * prevent saving unnecessary common volume * allow ROIs to be edited * label regions * bump * bump Co-authored-by: Federico Claudi <[email protected]> Co-authored-by: stephen <[email protected]>
SainsburyWellcomeCentre · Apr 22, 2020 · 33573d5 · 33573d5
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diff --git a/doc_build/main/user_guide/tools/manual_segmentation.md b/doc_build/main/user_guide/tools/manual_segmentation.md
@@ -36,8 +36,6 @@ Run `manual_region_seg -h` to see all options.
 `/home/analysis/cellfinder_output/registration/`)
 
 ##### The following options may also need to be used:
-* `--save-image` Store the resulting segmented region image (e.g. for
-inspecting in 2D. (default: False)
 * `--preview` Preview the segmented regions in brainrender (default:False)
 * `--debug` Debug mode. Will increase verbosity of logging and save all 
 intermediate files for diagnosis of software issues. (default: False)
@@ -51,25 +49,32 @@ take a few minutes) and then display the image in a
 <img src="https://raw.githubusercontent.com/SainsburyWellcomeCentre/neuro/master/resources/manual_segmentation_window.png" alt="manual_seg_window" width="700"/>
 
 ##### To segment regions:
-* Ensure that the "Regions" tab is selected (left hand side)
+* Ensure that the "new_region" tab is selected (left hand side)
+* Rename this region (by selecting the "new_region" text)
 * Navigate to where you want to draw your region of interest.
     * Use the scroll bar at the bottom (or left/right keys) to navigate 
     through the image stack
     * Use the mouse scrollwheel to zoom in or out
     * Drag with the mouse the pan the view
 
-* Select a label ID (by pressing the `+` button in the `label` row, top-left),
-the ID is not important, but `0` refers to no label, so you may as well start 
-from 1.
-* Choose a brush size (also in top left box)
+* Choose a brush size (top left box)
 * Activate painting mode (by selecting the paintbrush, top left). You can 
 go back to the navigation mode by selecting the magnifying glass.
 * Colour in your region that you want to segment, ensuring that you make a 
 solid object. 
 * Selecting the `ndim` toggle in the top left will extend the brush size in 
 three dimensions (so it will colour in multiple layers).
 
+* To add a new region press `Control+N`
 * Repeat above for each region you wish to segment.
+
 * Press `Control+S` on your keyboard to save the regions. If you used the
  `--preview flag`, once they are saved, they will be displayed in a brainrender
  window.
+
+
+##### Editing regions:
+If you have already run `manual_region_seg`, and run it again, the segmented 
+regions will be shown. You can edit them, and press `Control+S` to resave them. 
+If you don't want to save any changes, press `Control+X` to exit. The regions
+ will still be previewed if you have selected that option.
diff --git a/docs/.buildinfo b/docs/.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: ed007dbdf8172460ccc81a16ac8bf976
+config: 21f1b720085db93f2bf3fb4298a3bb15
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/_sources/main/user_guide/tools/manual_segmentation.md.txt b/docs/_sources/main/user_guide/tools/manual_segmentation.md.txt
@@ -36,8 +36,6 @@ Run `manual_region_seg -h` to see all options.
 `/home/analysis/cellfinder_output/registration/`)
 
 ##### The following options may also need to be used:
-* `--save-image` Store the resulting segmented region image (e.g. for
-inspecting in 2D. (default: False)
 * `--preview` Preview the segmented regions in brainrender (default:False)
 * `--debug` Debug mode. Will increase verbosity of logging and save all 
 intermediate files for diagnosis of software issues. (default: False)
@@ -51,25 +49,32 @@ take a few minutes) and then display the image in a
 <img src="https://raw.githubusercontent.com/SainsburyWellcomeCentre/neuro/master/resources/manual_segmentation_window.png" alt="manual_seg_window" width="700"/>
 
 ##### To segment regions:
-* Ensure that the "Regions" tab is selected (left hand side)
+* Ensure that the "new_region" tab is selected (left hand side)
+* Rename this region (by selecting the "new_region" text)
 * Navigate to where you want to draw your region of interest.
     * Use the scroll bar at the bottom (or left/right keys) to navigate 
     through the image stack
     * Use the mouse scrollwheel to zoom in or out
     * Drag with the mouse the pan the view
 
-* Select a label ID (by pressing the `+` button in the `label` row, top-left),
-the ID is not important, but `0` refers to no label, so you may as well start 
-from 1.
-* Choose a brush size (also in top left box)
+* Choose a brush size (top left box)
 * Activate painting mode (by selecting the paintbrush, top left). You can 
 go back to the navigation mode by selecting the magnifying glass.
 * Colour in your region that you want to segment, ensuring that you make a 
 solid object. 
 * Selecting the `ndim` toggle in the top left will extend the brush size in 
 three dimensions (so it will colour in multiple layers).
 
+* To add a new region press `Control+N`
 * Repeat above for each region you wish to segment.
+
 * Press `Control+S` on your keyboard to save the regions. If you used the
  `--preview flag`, once they are saved, they will be displayed in a brainrender
  window.
+
+
+##### Editing regions:
+If you have already run `manual_region_seg`, and run it again, the segmented 
+regions will be shown. You can edit them, and press `Control+S` to resave them. 
+If you don't want to save any changes, press `Control+X` to exit. The regions
+ will still be previewed if you have selected that option.
diff --git a/docs/_static/basic.css b/docs/_static/basic.css
@@ -4,7 +4,7 @@
  *
  * Sphinx stylesheet -- basic theme.
  *
- * :copyright: Copyright 2007-2019 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2020 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */

diff --git a/docs/_static/doctools.js b/docs/_static/doctools.js
@@ -4,7 +4,7 @@
  *
  * Sphinx JavaScript utilities for all documentation.
  *
- * :copyright: Copyright 2007-2019 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2020 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -283,10 +283,11 @@ var Documentation = {
   },
 
   initOnKeyListeners: function() {
-    $(document).keyup(function(event) {
+    $(document).keydown(function(event) {
       var activeElementType = document.activeElement.tagName;
       // don't navigate when in search box or textarea
-      if (activeElementType !== 'TEXTAREA' && activeElementType !== 'INPUT' && activeElementType !== 'SELECT') {
+      if (activeElementType !== 'TEXTAREA' && activeElementType !== 'INPUT' && activeElementType !== 'SELECT'
+          && !event.altKey && !event.ctrlKey && !event.metaKey && !event.shiftKey) {
         switch (event.keyCode) {
           case 37: // left
             var prevHref = $('link[rel="prev"]').prop('href');

diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js
@@ -5,6 +5,7 @@ var DOCUMENTATION_OPTIONS = {
     COLLAPSE_INDEX: false,
     BUILDER: 'html',
     FILE_SUFFIX: '.html',
+    LINK_SUFFIX: '.html',
     HAS_SOURCE: true,
     SOURCELINK_SUFFIX: '.txt',
     NAVIGATION_WITH_KEYS: false

diff --git a/docs/_static/language_data.js b/docs/_static/language_data.js
@@ -5,7 +5,7 @@
  * This script contains the language-specific data used by searchtools.js,
  * namely the list of stopwords, stemmer, scorer and splitter.
  *
- * :copyright: Copyright 2007-2019 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2020 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */

diff --git a/docs/_static/searchtools.js b/docs/_static/searchtools.js
@@ -4,7 +4,7 @@
  *
  * Sphinx JavaScript utilities for the full-text search.
  *
- * :copyright: Copyright 2007-2019 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2020 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -63,6 +63,11 @@ var Search = {
       htmlElement.innerHTML = htmlString;
       $(htmlElement).find('.headerlink').remove();
       docContent = $(htmlElement).find('[role=main]')[0];
+      if(docContent === undefined) {
+          console.warn("Content block not found. Sphinx search tries to obtain it " +
+                       "via '[role=main]'. Could you check your theme or template.");
+          return "";
+      }
       return docContent.textContent || docContent.innerText;
   },
 
@@ -245,6 +250,8 @@ var Search = {
       if (results.length) {
         var item = results.pop();
         var listItem = $('<li style="display:none"></li>');
+        var requestUrl = "";
+        var linkUrl = "";
         if (DOCUMENTATION_OPTIONS.BUILDER === 'dirhtml') {
           // dirhtml builder
           var dirname = item[0] + '/';
@@ -253,23 +260,25 @@ var Search = {
           } else if (dirname == 'index/') {
             dirname = '';
           }
-          listItem.append($('<a/>').attr('href',
-            DOCUMENTATION_OPTIONS.URL_ROOT + dirname +
-            highlightstring + item[2]).html(item[1]));
+          requestUrl = DOCUMENTATION_OPTIONS.URL_ROOT + dirname;
+          linkUrl = requestUrl;
+
         } else {
           // normal html builders
-          listItem.append($('<a/>').attr('href',
-            item[0] + DOCUMENTATION_OPTIONS.FILE_SUFFIX +
-            highlightstring + item[2]).html(item[1]));
+          requestUrl = DOCUMENTATION_OPTIONS.URL_ROOT + item[0] + DOCUMENTATION_OPTIONS.FILE_SUFFIX;
+          linkUrl = item[0] + DOCUMENTATION_OPTIONS.LINK_SUFFIX;
         }
+        listItem.append($('<a/>').attr('href',
+            linkUrl +
+            highlightstring + item[2]).html(item[1]));
         if (item[3]) {
           listItem.append($('<span> (' + item[3] + ')</span>'));
           Search.output.append(listItem);
           listItem.slideDown(5, function() {
             displayNextItem();
           });
         } else if (DOCUMENTATION_OPTIONS.HAS_SOURCE) {
-          $.ajax({url: DOCUMENTATION_OPTIONS.URL_ROOT + item[0] + DOCUMENTATION_OPTIONS.FILE_SUFFIX,
+          $.ajax({url: requestUrl,
                   dataType: "text",
                   complete: function(jqxhr, textstatus) {
                     var data = jqxhr.responseText;

diff --git a/docs/genindex.html b/docs/genindex.html
@@ -22,10 +22,10 @@
 
 
       <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
-        <script type="text/javascript" src="_static/jquery.js"></script>
-        <script type="text/javascript" src="_static/underscore.js"></script>
-        <script type="text/javascript" src="_static/doctools.js"></script>
-        <script type="text/javascript" src="_static/language_data.js"></script>
+        <script src="_static/jquery.js"></script>
+        <script src="_static/underscore.js"></script>
+        <script src="_static/doctools.js"></script>
+        <script src="_static/language_data.js"></script>
 
     <script type="text/javascript" src="_static/js/theme.js"></script>
 
@@ -79,15 +79,8 @@
 
 
 
-              <ul>
-<li class="toctree-l1"><a class="reference internal" href="main/user_guide/tools/cells_to_brainrender.html">Converting cells from cellfinder to brainrender format</a></li>
-<li class="toctree-l1"><a class="reference internal" href="main/user_guide/tools/heatmap.html">Heatmap generation</a></li>
-<li class="toctree-l1"><a class="reference internal" href="main/user_guide/tools/manual_segmentation.html">Manual segmentation</a></li>
-</ul>
-<ul>
-<li class="toctree-l1"><a class="reference internal" href="main/dev/CONTRIBUTING.html">Contributing</a></li>
-</ul>
-
+              <!-- Local TOC -->
+              <div class="local-toc"></div>
 
 
         </div>

diff --git a/docs/index.html b/docs/index.html
@@ -21,10 +21,10 @@
 
 
       <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
-        <script type="text/javascript" src="_static/jquery.js"></script>
-        <script type="text/javascript" src="_static/underscore.js"></script>
-        <script type="text/javascript" src="_static/doctools.js"></script>
-        <script type="text/javascript" src="_static/language_data.js"></script>
+        <script src="_static/jquery.js"></script>
+        <script src="_static/underscore.js"></script>
+        <script src="_static/doctools.js"></script>
+        <script src="_static/language_data.js"></script>
 
     <script type="text/javascript" src="_static/js/theme.js"></script>
 
@@ -35,7 +35,7 @@
   <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
-    <link rel="next" title="Converting cells from cellfinder to brainrender format" href="main/user_guide/tools/cells_to_brainrender.html" /> 
+    <link rel="next" title="&lt;no title&gt;" href="main/user_guide/tools/cells_to_brainrender.html" /> 
 </head>
 
 <body class="wy-body-for-nav">
@@ -79,15 +79,17 @@
 
 
 
-              <ul>
-<li class="toctree-l1"><a class="reference internal" href="main/user_guide/tools/cells_to_brainrender.html">Converting cells from cellfinder to brainrender format</a></li>
-<li class="toctree-l1"><a class="reference internal" href="main/user_guide/tools/heatmap.html">Heatmap generation</a></li>
-<li class="toctree-l1"><a class="reference internal" href="main/user_guide/tools/manual_segmentation.html">Manual segmentation</a></li>
+              <!-- Local TOC -->
+              <div class="local-toc"><ul>
+<li><a class="reference internal" href="#">neuro</a><ul>
+<li><a class="reference internal" href="#introduction">Introduction:</a></li>
+<li><a class="reference internal" href="#installation">Installation:</a></li>
+<li><a class="reference internal" href="#tools">Tools</a></li>
+<li><a class="reference internal" href="#developers">Developers</a></li>
 </ul>
-<ul>
-<li class="toctree-l1"><a class="reference internal" href="main/dev/CONTRIBUTING.html">Contributing</a></li>
+</li>
 </ul>
-
+</div>
 
 
         </div>
@@ -165,19 +167,11 @@ <h2>Installation:<a class="headerlink" href="#installation" title="Permalink to
 <div class="section" id="tools">
 <h2>Tools<a class="headerlink" href="#tools" title="Permalink to this headline">¶</a></h2>
 <div class="toctree-wrapper compound">
-<ul>
-<li class="toctree-l1"><a class="reference internal" href="main/user_guide/tools/cells_to_brainrender.html">Converting cells from cellfinder to brainrender format</a></li>
-<li class="toctree-l1"><a class="reference internal" href="main/user_guide/tools/heatmap.html">Heatmap generation</a></li>
-<li class="toctree-l1"><a class="reference internal" href="main/user_guide/tools/manual_segmentation.html">Manual segmentation</a></li>
-</ul>
 </div>
 </div>
 <div class="section" id="developers">
 <h2>Developers<a class="headerlink" href="#developers" title="Permalink to this headline">¶</a></h2>
 <div class="toctree-wrapper compound">
-<ul>
-<li class="toctree-l1"><a class="reference internal" href="main/dev/CONTRIBUTING.html">Contributing</a></li>
-</ul>
 </div>
 </div>
 </div>
@@ -190,7 +184,7 @@ <h2>Developers<a class="headerlink" href="#developers" title="Permalink to this
 
     <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
 
-        <a href="main/user_guide/tools/cells_to_brainrender.html" class="btn btn-neutral float-right" title="Converting cells from cellfinder to brainrender format" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
+        <a href="main/user_guide/tools/cells_to_brainrender.html" class="btn btn-neutral float-right" title="&lt;no title&gt;" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
 
 
     </div>