Refactor imports (#21)

* 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 Co-authored-by: Federico Claudi <[email protected]> Co-authored-by: stephen <[email protected]>
SainsburyWellcomeCentre · Apr 16, 2020 · ae09539 · ae09539
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diff --git a/.gitignore b/.gitignore
@@ -117,3 +117,7 @@ venv.bak/
 .idea/
 .vs/
 *.~lock.*
+
+
+# macOS
+*.DS_Store
diff --git a/doc_build/main/dev/CONTRIBUTING.md b/doc_build/main/dev/CONTRIBUTING.md
@@ -28,7 +28,7 @@ clean commit history.
 
 
 #### Formatting
-`neuro` uses [Black](https://github.com/python/black) o ensure a consistent 
+`neuro` uses [Black](https://github.com/python/black) to ensure a consistent 
 code style. Please run `black ./ -l 79 --target-version py37` before making 
 any commits. To prevent any errors, it is easier to add a formatting check 
 as a [pre-commit hook](https://www.atlassian.com/git/tutorials/git-hooks). 

diff --git a/doc_build/main/user_guide/tools/cells_to_brainrender.md b/doc_build/main/user_guide/tools/cells_to_brainrender.md
@@ -5,7 +5,7 @@ To convert cell positions (e.g. in `cells_in_standard_space.xml`) to
 a format that can be used in 
 [BrainRender](https://github.com/BrancoLab/BrainRender).
 
-
+### Usage
 ```bash
     points_to_brainrender cells_in_standard_space.xml exported_cells.h5
 ```
@@ -16,7 +16,8 @@ Run `points_to_brainrender -h` to see all options.
 #### Positional
 * [Cellfinder](https://github.com/SainsburyWellcomeCentre/cellfinder) 
 cells file to be converted
-* Output filename. Should end with '.h5'
+* Output filename. Should end with '.h5'. If the containing directory doesn't 
+exist, it will be created.
 
 
 #### The following options may also need to be used:

diff --git a/doc_build/main/user_guide/tools/heatmap.md b/doc_build/main/user_guide/tools/heatmap.md
@@ -0,0 +1,47 @@
+# Heatmap generation
+
+To generate a heatmap of detected cells, which shows cell distributions in a 
+more intuitive way that showing individual cell positions:
+
+
+<img src="https://raw.githubusercontent.com/SainsburyWellcomeCentre/cellfinder/master/resources/heatmap.png" alt="heatmap" width="500"/>
+
+*Overlay on raw data and segentation from 
+[amap](https://github.com/SainsburyWellcomeCentre) added separately*
+
+
+### Usage
+```bash
+    heatmap cell_classification.xml heatmap.nii raw_data registered_atlas.nii -x 2 -y 2 -z 5
+```
+
+### Arguments
+Run `heatmap -h` to see all options.
+
+#### Positional arguments
+* [Cellfinder](https://github.com/SainsburyWellcomeCentre/cellfinder) 
+classified cells file (usually `cell_classification.xml`)
+* Output filename. Should end with '.nii'. If the containing directory doesn't 
+exist, it will be created.
+* Path to raw data (just a single channel). Used to find the shape of the 
+raw image that the detected cell positions are defined in.
+* Registered atlas file from [amap](https://github.com/SainsburyWellcomeCentre)
+ (typically run automatically in 
+ [Cellfinder](https://github.com/SainsburyWellcomeCentre/cellfinder)). File 
+ is usually `registered_atlas.nii`.
+
+
+#### Keyword arguments
+* `-x` or `--x-pixel-size` Pixel spacing of the data that the cells are 
+defined in, in the first dimension, specified in um.
+* `-y` or `--y-pixel-size` Pixel spacing of the data that the cells are 
+defined in, in the second dimension, specified in um.
+* `-z` or `--z-pixel-size` Pixel spacing of the data that the cells are 
+defined in, in the third dimension, specified in um. 
+
+
+#### The following options may also need to be used:
+* `--heatmap-bin` Heatmap bin size (um of each edge of histogram cube)
+* `--heatmap-smoothing` Gaussian smoothing sigma, in um.
+* `--no-mask-figs` Don't mask the figures (removing any areas outside the 
+brain, from e.g. smoothing)
diff --git a/docs/_sources/main/dev/CONTRIBUTING.md.txt b/docs/_sources/main/dev/CONTRIBUTING.md.txt
@@ -28,7 +28,7 @@ clean commit history.
 
 
 #### Formatting
-`neuro` uses [Black](https://github.com/python/black) o ensure a consistent 
+`neuro` uses [Black](https://github.com/python/black) to ensure a consistent 
 code style. Please run `black ./ -l 79 --target-version py37` before making 
 any commits. To prevent any errors, it is easier to add a formatting check 
 as a [pre-commit hook](https://www.atlassian.com/git/tutorials/git-hooks). 

diff --git a/docs/_sources/main/user_guide/tools/cells_to_brainrender.md.txt b/docs/_sources/main/user_guide/tools/cells_to_brainrender.md.txt
@@ -5,7 +5,7 @@ To convert cell positions (e.g. in `cells_in_standard_space.xml`) to
 a format that can be used in 
 [BrainRender](https://github.com/BrancoLab/BrainRender).
 
-
+### Usage
 ```bash
     points_to_brainrender cells_in_standard_space.xml exported_cells.h5
 ```
@@ -16,7 +16,8 @@ Run `points_to_brainrender -h` to see all options.
 #### Positional
 * [Cellfinder](https://github.com/SainsburyWellcomeCentre/cellfinder) 
 cells file to be converted
-* Output filename. Should end with '.h5'
+* Output filename. Should end with '.h5'. If the containing directory doesn't 
+exist, it will be created.
 
 
 #### The following options may also need to be used:

diff --git a/docs/_sources/main/user_guide/tools/heatmap.md.txt b/docs/_sources/main/user_guide/tools/heatmap.md.txt
@@ -0,0 +1,47 @@
+# Heatmap generation
+
+To generate a heatmap of detected cells, which shows cell distributions in a 
+more intuitive way that showing individual cell positions:
+
+
+<img src="https://raw.githubusercontent.com/SainsburyWellcomeCentre/cellfinder/master/resources/heatmap.png" alt="heatmap" width="500"/>
+
+*Overlay on raw data and segentation from 
+[amap](https://github.com/SainsburyWellcomeCentre) added separately*
+
+
+### Usage
+```bash
+    heatmap cell_classification.xml heatmap.nii raw_data registered_atlas.nii -x 2 -y 2 -z 5
+```
+
+### Arguments
+Run `heatmap -h` to see all options.
+
+#### Positional arguments
+* [Cellfinder](https://github.com/SainsburyWellcomeCentre/cellfinder) 
+classified cells file (usually `cell_classification.xml`)
+* Output filename. Should end with '.nii'. If the containing directory doesn't 
+exist, it will be created.
+* Path to raw data (just a single channel). Used to find the shape of the 
+raw image that the detected cell positions are defined in.
+* Registered atlas file from [amap](https://github.com/SainsburyWellcomeCentre)
+ (typically run automatically in 
+ [Cellfinder](https://github.com/SainsburyWellcomeCentre/cellfinder)). File 
+ is usually `registered_atlas.nii`.
+
+
+#### Keyword arguments
+* `-x` or `--x-pixel-size` Pixel spacing of the data that the cells are 
+defined in, in the first dimension, specified in um.
+* `-y` or `--y-pixel-size` Pixel spacing of the data that the cells are 
+defined in, in the second dimension, specified in um.
+* `-z` or `--z-pixel-size` Pixel spacing of the data that the cells are 
+defined in, in the third dimension, specified in um. 
+
+
+#### The following options may also need to be used:
+* `--heatmap-bin` Heatmap bin size (um of each edge of histogram cube)
+* `--heatmap-smoothing` Gaussian smoothing sigma, in um.
+* `--no-mask-figs` Don't mask the figures (removing any areas outside the 
+brain, from e.g. smoothing)
diff --git a/docs/genindex.html b/docs/genindex.html
@@ -81,6 +81,7 @@
 
               <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>
 </ul>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="main/dev/CONTRIBUTING.html">Contributing</a></li>

diff --git a/docs/index.html b/docs/index.html
@@ -81,6 +81,7 @@
 
               <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>
 </ul>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="main/dev/CONTRIBUTING.html">Contributing</a></li>
@@ -165,6 +166,7 @@ <h2>Tools<a class="headerlink" href="#tools" title="Permalink to this headline">
 <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>
 </ul>
 </div>
 </div>

diff --git a/docs/main/dev/CONTRIBUTING.html b/docs/main/dev/CONTRIBUTING.html
@@ -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="prev" title="Converting cells from cellfinder to brainrender format" href="../user_guide/tools/cells_to_brainrender.html" /> 
+    <link rel="prev" title="Heatmap generation" href="../user_guide/tools/heatmap.html" /> 
 </head>
 
 <body class="wy-body-for-nav">
@@ -81,6 +81,7 @@
 
               <ul>
 <li class="toctree-l1"><a class="reference internal" href="../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="../user_guide/tools/heatmap.html">Heatmap generation</a></li>
 </ul>
 <ul class="current">
 <li class="toctree-l1 current"><a class="current reference internal" href="#">Contributing</a><ul>
@@ -186,7 +187,7 @@ <h2>Pull requests<a class="headerlink" href="#pull-requests" title="Permalink to
 </div>
 <div class="section" id="formatting">
 <h2>Formatting<a class="headerlink" href="#formatting" title="Permalink to this headline">¶</a></h2>
-<p><code class="docutils literal notranslate"><span class="pre">neuro</span></code> uses <a class="reference external" href="https://github.com/python/black">Black</a> o ensure a consistent
+<p><code class="docutils literal notranslate"><span class="pre">neuro</span></code> uses <a class="reference external" href="https://github.com/python/black">Black</a> to ensure a consistent
 code style. Please run <code class="docutils literal notranslate"><span class="pre">black</span> <span class="pre">./</span> <span class="pre">-l</span> <span class="pre">79</span> <span class="pre">--target-version</span> <span class="pre">py37</span></code> before making
 any commits. To prevent any errors, it is easier to add a formatting check
 as a <a class="reference external" href="https://www.atlassian.com/git/tutorials/git-hooks">pre-commit hook</a>.
@@ -235,7 +236,7 @@ <h2>Dependencies<a class="headerlink" href="#dependencies" title="Permalink to t
     <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
 
 
-        <a href="../user_guide/tools/cells_to_brainrender.html" class="btn btn-neutral float-left" title="Converting cells from cellfinder to brainrender format" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+        <a href="../user_guide/tools/heatmap.html" class="btn btn-neutral float-left" title="Heatmap generation" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
 
     </div>
 

diff --git a/docs/main/user_guide/tools/cells_to_brainrender.html b/docs/main/user_guide/tools/cells_to_brainrender.html
@@ -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="Contributing" href="../../dev/CONTRIBUTING.html" />
+    <link rel="next" title="Heatmap generation" href="heatmap.html" />
     <link rel="prev" title="neuro" href="../../../index.html" /> 
 </head>
 
@@ -82,6 +82,7 @@
 
               <ul class="current">
 <li class="toctree-l1 current"><a class="current reference internal" href="#">Converting cells from cellfinder to brainrender format</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="#usage">Usage</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#arguments">Arguments</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="#positional">Positional</a></li>
 <li class="toctree-l3"><a class="reference internal" href="#the-following-options-may-also-need-to-be-used">The following options may also need to be used:</a></li>
@@ -90,6 +91,7 @@
 <li class="toctree-l2"><a class="reference internal" href="#to-visualise-this-file-in-brainrender">To visualise this file in BrainRender</a></li>
 </ul>
 </li>
+<li class="toctree-l1"><a class="reference internal" href="heatmap.html">Heatmap generation</a></li>
 </ul>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="../../dev/CONTRIBUTING.html">Contributing</a></li>
@@ -160,9 +162,12 @@ <h1>Converting cells from cellfinder to brainrender format<a class="headerlink"
 <p>To convert cell positions (e.g. in <code class="docutils literal notranslate"><span class="pre">cells_in_standard_space.xml</span></code>) to
 a format that can be used in
 <a class="reference external" href="https://github.com/BrancoLab/BrainRender">BrainRender</a>.</p>
+<div class="section" id="usage">
+<h2>Usage<a class="headerlink" href="#usage" title="Permalink to this headline">¶</a></h2>
 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>    points_to_brainrender cells_in_standard_space.xml exported_cells.h5
 </pre></div>
 </div>
+</div>
 <div class="section" id="arguments">
 <h2>Arguments<a class="headerlink" href="#arguments" title="Permalink to this headline">¶</a></h2>
 <p>Run <code class="docutils literal notranslate"><span class="pre">points_to_brainrender</span> <span class="pre">-h</span></code> to see all options.</p>
@@ -171,7 +176,8 @@ <h3>Positional<a class="headerlink" href="#positional" title="Permalink to this
 <ul class="simple">
 <li><p><a class="reference external" href="https://github.com/SainsburyWellcomeCentre/cellfinder">Cellfinder</a>
 cells file to be converted</p></li>
-<li><p>Output filename. Should end with ‘.h5’</p></li>
+<li><p>Output filename. Should end with ‘.h5’. If the containing directory doesn’t
+exist, it will be created.</p></li>
 </ul>
 </div>
 <div class="section" id="the-following-options-may-also-need-to-be-used">
@@ -208,7 +214,7 @@ <h2>To visualise this file in BrainRender<a class="headerlink" href="#to-visuali
 
     <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
 
-        <a href="../../dev/CONTRIBUTING.html" class="btn btn-neutral float-right" title="Contributing" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
+        <a href="heatmap.html" class="btn btn-neutral float-right" title="Heatmap generation" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
 
 
         <a href="../../../index.html" class="btn btn-neutral float-left" title="neuro" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>