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<!DOCTYPE html>
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<section id="usage-examples">
<h1>Usage Examples<a class="headerlink" href="#usage-examples" title="Link to this heading">¶</a></h1>
<section id="volumetric-data">
<h2>Volumetric Data<a class="headerlink" href="#volumetric-data" title="Link to this heading">¶</a></h2>
<section id="creating-a-project">
<h3>Creating a Project<a class="headerlink" href="#creating-a-project" title="Link to this heading">¶</a></h3>
<p>Programmatic creation of projects can be useful for rapid viewing of data after collection.</p>
<p>In this example, we’ll create a project file from a series of TIFFs.</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">syglass</span> <span class="kn">import</span> <span class="n">pyglass</span>
<span class="kn">import</span> <span class="nn">syglass</span> <span class="k">as</span> <span class="nn">sy</span>
<span class="kn">import</span> <span class="nn">time</span>
<span class="c1"># create a project by specifing a path and the name of the project to be created. In this case, we'll call the project autoGenProject.</span>
<span class="n">project</span> <span class="o">=</span> <span class="n">pyglass</span><span class="o">.</span><span class="n">CreateProject</span><span class="p">(</span><span class="n">pyglass</span><span class="o">.</span><span class="n">path</span><span class="p">(</span><span class="s2">"C:</span><span class="se">\\</span><span class="s2">syGlassProjects"</span><span class="p">),</span> <span class="s2">"autoGenProject"</span><span class="p">)</span>
<span class="c1"># create a DirectoryDescriptor to search a folder for TIFFs that match a pattern</span>
<span class="n">dd</span> <span class="o">=</span> <span class="n">pyglass</span><span class="o">.</span><span class="n">DirectoryDescription</span><span class="p">()</span>
<span class="c1"># show the directoryDescriptor the first image of the set, and it will create a file list of matching slices</span>
<span class="n">dd</span><span class="o">.</span><span class="n">InspectByReferenceFile</span><span class="p">(</span><span class="s2">"C:</span><span class="se">\\</span><span class="s2">raw_data</span><span class="se">\\</span><span class="s2">example0000.tif"</span><span class="p">)</span>
<span class="c1"># create a DataProvider to the dataProvider the file list</span>
<span class="n">dataProvider</span> <span class="o">=</span> <span class="n">pyglass</span><span class="o">.</span><span class="n">OpenTIFFs</span><span class="p">(</span><span class="n">dd</span><span class="o">.</span><span class="n">GetFileList</span><span class="p">(),</span> <span class="kc">False</span><span class="p">)</span>
<span class="c1"># indicate which channels to include; in this case, all channels from the file</span>
<span class="n">includedChannels</span> <span class="o">=</span> <span class="n">pyglass</span><span class="o">.</span><span class="n">IntList</span><span class="p">(</span><span class="nb">range</span><span class="p">(</span><span class="n">dataProvider</span><span class="o">.</span><span class="n">GetChannelsCount</span><span class="p">()))</span>
<span class="n">dataProvider</span><span class="o">.</span><span class="n">SetIncludedChannels</span><span class="p">(</span><span class="n">includedChannels</span><span class="p">)</span>
<span class="c1"># spawn a ConversionDriver to convert the data</span>
<span class="n">cd</span> <span class="o">=</span> <span class="n">pyglass</span><span class="o">.</span><span class="n">ConversionDriver</span><span class="p">()</span>
<span class="c1"># set the ConversionDriver input to the data provider</span>
<span class="n">cd</span><span class="o">.</span><span class="n">SetInput</span><span class="p">(</span><span class="n">dataProvider</span><span class="p">)</span>
<span class="c1"># set the ConversionDriver output to the project previously created</span>
<span class="n">cd</span><span class="o">.</span><span class="n">SetOutput</span><span class="p">(</span><span class="n">project</span><span class="p">)</span>
<span class="c1"># start the job!</span>
<span class="n">cd</span><span class="o">.</span><span class="n">StartAsynchronous</span><span class="p">()</span>
<span class="c1"># report progress</span>
<span class="k">while</span> <span class="n">cd</span><span class="o">.</span><span class="n">GetPercentage</span><span class="p">()</span> <span class="o">!=</span> <span class="mi">100</span><span class="p">:</span>
<span class="nb">print</span><span class="p">(</span><span class="n">cd</span><span class="o">.</span><span class="n">GetPercentage</span><span class="p">())</span>
<span class="n">time</span><span class="o">.</span><span class="n">sleep</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s2">"Finished!"</span><span class="p">)</span>
</pre></div>
</div>
</section>
<section id="adding-mask-data-to-projects">
<h3>Adding Mask Data to Projects<a class="headerlink" href="#adding-mask-data-to-projects" title="Link to this heading">¶</a></h3>
<p>Segmentations or masks can be added to a project, provided that they are stored in image files with the same dimensions as the project.</p>
<p>In this example, we’ll add a segmentation layer to an existing project.</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">syglass</span> <span class="kn">import</span> <span class="n">pyglass</span>
<span class="kn">import</span> <span class="nn">syglass</span> <span class="k">as</span> <span class="nn">sy</span>
<span class="kn">import</span> <span class="nn">time</span>
<span class="c1"># the mask data is stored in a syGlass project format with a special .syk extension</span>
<span class="n">project</span> <span class="o">=</span> <span class="n">pyglass</span><span class="o">.</span><span class="n">CreateProject</span><span class="p">(</span><span class="n">pyglass</span><span class="o">.</span><span class="n">path</span><span class="p">(</span><span class="s2">"C:</span><span class="se">\\</span><span class="s2">pathToExistingProject</span><span class="se">\\</span><span class="s2">"</span><span class="p">),</span> <span class="s2">"projectName.syk"</span><span class="p">,</span> <span class="kc">True</span><span class="p">)</span>
<span class="c1"># create a DirectoryDescriptor to search a folder for TIFFs that match a pattern</span>
<span class="n">dd</span> <span class="o">=</span> <span class="n">pyglass</span><span class="o">.</span><span class="n">DirectoryDescription</span><span class="p">()</span>
<span class="c1"># show the directoryDescriptor the first image of the set, and it will create a file list of matching slices</span>
<span class="n">dd</span><span class="o">.</span><span class="n">InspectByReferenceFile</span><span class="p">(</span><span class="s2">"C:</span><span class="se">\\</span><span class="s2">maskData</span><span class="se">\\</span><span class="s2">maskData_Z-00000.tiff"</span><span class="p">)</span>
<span class="c1"># create a DataProvider to the dataProvider the file list</span>
<span class="n">dataProvider</span> <span class="o">=</span> <span class="n">pyglass</span><span class="o">.</span><span class="n">OpenTIFFs</span><span class="p">(</span><span class="n">dd</span><span class="o">.</span><span class="n">GetFileList</span><span class="p">(),</span> <span class="kc">False</span><span class="p">)</span>
<span class="c1"># indicate which channels to include; in this case, all channels from the file</span>
<span class="n">includedChannels</span> <span class="o">=</span> <span class="n">pyglass</span><span class="o">.</span><span class="n">IntList</span><span class="p">(</span><span class="nb">range</span><span class="p">(</span><span class="n">dataProvider</span><span class="o">.</span><span class="n">GetChannelsCount</span><span class="p">()))</span>
<span class="n">dataProvider</span><span class="o">.</span><span class="n">SetIncludedChannels</span><span class="p">(</span><span class="n">includedChannels</span><span class="p">)</span>
<span class="c1"># spawn a ConversionDriver to convert the data</span>
<span class="n">cd</span> <span class="o">=</span> <span class="n">pyglass</span><span class="o">.</span><span class="n">ConversionDriver</span><span class="p">(</span><span class="kc">True</span><span class="p">)</span>
<span class="c1"># set the ConversionDriver input to the data provider</span>
<span class="n">cd</span><span class="o">.</span><span class="n">SetInput</span><span class="p">(</span><span class="n">dataProvider</span><span class="p">)</span>
<span class="c1"># set the ConversionDriver output to the project previously created</span>
<span class="n">cd</span><span class="o">.</span><span class="n">SetOutput</span><span class="p">(</span><span class="n">project</span><span class="p">)</span>
<span class="c1"># start the job!</span>
<span class="n">cd</span><span class="o">.</span><span class="n">StartAsynchronous</span><span class="p">()</span>
<span class="c1"># report progress</span>
<span class="k">while</span> <span class="n">cd</span><span class="o">.</span><span class="n">GetPercentage</span><span class="p">()</span> <span class="o">!=</span> <span class="mi">100</span><span class="p">:</span>
<span class="nb">print</span><span class="p">(</span><span class="n">cd</span><span class="o">.</span><span class="n">GetPercentage</span><span class="p">())</span>
<span class="n">time</span><span class="o">.</span><span class="n">sleep</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s2">"Finished!"</span><span class="p">)</span>
</pre></div>
</div>
</section>
<section id="traversing-the-volume">
<h3>Traversing the Volume<a class="headerlink" href="#traversing-the-volume" title="Link to this heading">¶</a></h3>
<p>Iterating over the entire volume is a common task. Most projects have multiple resolution levels, where higher levels are split into more and more “blocks”.</p>
<p>In this example, we’ll determine how many resolution levels are in our volume, select the highest one, and iterate over each of its blocks.</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">syglass</span> <span class="k">as</span> <span class="nn">sy</span>
<span class="n">project</span> <span class="o">=</span> <span class="n">sy</span><span class="o">.</span><span class="n">get_project</span><span class="p">(</span><span class="s2">"C:/path/to/project_file.syg"</span><span class="p">)</span>
<span class="c1"># Get a dictionary showing the number of blocks in each level</span>
<span class="n">resolution_map</span> <span class="o">=</span> <span class="n">project</span><span class="o">.</span><span class="n">get_resolution_map</span><span class="p">()</span>
<span class="c1"># Calculate the index of the highest resolution level</span>
<span class="n">max_resolution_level</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">resolution_map</span><span class="p">)</span> <span class="o">-</span> <span class="mi">1</span>
<span class="c1"># Determine the number of blocks in this level</span>
<span class="n">block_count</span> <span class="o">=</span> <span class="n">resolution_map</span><span class="p">[</span><span class="n">max_resolution_level</span><span class="p">]</span>
<span class="c1"># Retrieve a block at each index</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">block_count</span><span class="p">):</span>
<span class="c1"># Because this image volume is static, we'll always use timepoint 0</span>
<span class="n">block</span> <span class="o">=</span> <span class="n">project</span><span class="o">.</span><span class="n">get_block</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">max_resolution_level</span><span class="p">,</span> <span class="n">i</span><span class="p">)</span>
<span class="c1"># The offset between the volume's origin and the block's origin</span>
<span class="nb">print</span><span class="p">(</span><span class="n">block</span><span class="o">.</span><span class="n">offset</span><span class="p">)</span>
<span class="c1"># The volumetric data as a numpy array (z, y, x, channel)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">block</span><span class="o">.</span><span class="n">data</span><span class="p">)</span>
</pre></div>
</div>
</section>
<section id="retrieving-volumetric-data-around-points">
<h3>Retrieving Volumetric Data Around Points<a class="headerlink" href="#retrieving-volumetric-data-around-points" title="Link to this heading">¶</a></h3>
<p>You may, in some cases, be interested in analyzing the volumetric data around points. Typically these points come from annotations. For example, the image data
surrounding some counting points could be used as input for a machine learning model, with the goal of automatically counting the remaining structures.</p>
<p>The function <code class="docutils literal notranslate"><span class="pre">get_custom_block()</span></code> can be used to get a block of data of any size, at any location. It is more flexible than <code class="docutils literal notranslate"><span class="pre">get_block()</span></code> and <code class="docutils literal notranslate"><span class="pre">get_block_by_point()</span></code>,
which retrieve blocks of predetermined sizes and positions.</p>
<p>In this example, we retrieve a (100, 100, 100) voxel cube of the volume for each counting point. Each cube is centered around its corresponding annotation.</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">syglass</span> <span class="k">as</span> <span class="nn">sy</span>
<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
<span class="n">project</span> <span class="o">=</span> <span class="n">sy</span><span class="o">.</span><span class="n">get_project</span><span class="p">(</span><span class="s2">"C:/path/to/project_file.syg"</span><span class="p">)</span>
<span class="c1"># Determine the index of the highest resolution level</span>
<span class="n">resolution</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">project</span><span class="o">.</span><span class="n">get_resolution_map</span><span class="p">())</span> <span class="o">-</span> <span class="mi">1</span>
<span class="c1"># Define a side length and dimensions for our cube</span>
<span class="n">side_length</span> <span class="o">=</span> <span class="mi">100</span>
<span class="n">dimensions</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">full</span><span class="p">(</span><span class="mi">3</span><span class="p">,</span> <span class="n">side_length</span><span class="p">)</span>
<span class="c1"># Iterate over each point in each color series for the default experiment</span>
<span class="n">counts</span> <span class="o">=</span> <span class="n">project</span><span class="o">.</span><span class="n">get_counting_points</span><span class="p">()</span>
<span class="k">for</span> <span class="n">color</span> <span class="ow">in</span> <span class="n">counts</span><span class="p">:</span>
<span class="k">for</span> <span class="n">point</span> <span class="ow">in</span> <span class="n">counts</span><span class="p">[</span><span class="n">color</span><span class="p">]:</span>
<span class="c1"># Calculate the offset to each cube based on point position</span>
<span class="n">offset</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">maximum</span><span class="p">(</span><span class="n">point</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="nb">int</span><span class="p">)</span> <span class="o">-</span> <span class="n">side_length</span> <span class="o">/</span> <span class="mi">2</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="mi">3</span><span class="p">))</span>
<span class="c1"># Retrieve a full-resolution cube from the volume</span>
<span class="n">block</span> <span class="o">=</span> <span class="n">project</span><span class="o">.</span><span class="n">get_custom_block</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">resolution</span><span class="p">,</span> <span class="n">offset</span><span class="p">,</span> <span class="n">dimensions</span><span class="p">)</span>
</pre></div>
</div>
</section>
<section id="retrieving-mask-data">
<h3>Retrieving Mask Data<a class="headerlink" href="#retrieving-mask-data" title="Link to this heading">¶</a></h3>
<p>Segmentations or masks can be extracted from a project.</p>
<p>In this example, we export the segmentation from each timepoint in a time series project.</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">tifffile</span>
<span class="kn">import</span> <span class="nn">syglass</span> <span class="k">as</span> <span class="nn">sy</span>
<span class="kn">from</span> <span class="nn">syglass</span> <span class="kn">import</span> <span class="n">pyglass</span>
<span class="n">project</span> <span class="o">=</span> <span class="n">sy</span><span class="o">.</span><span class="n">get_project</span><span class="p">(</span><span class="s2">"C:/path/to/project_file.syg"</span><span class="p">)</span>
<span class="c1"># Create mask extractor</span>
<span class="n">mask_extractor</span> <span class="o">=</span> <span class="n">pyglass</span><span class="o">.</span><span class="n">MaskOctreeRasterExtractor</span><span class="p">(</span><span class="kc">None</span><span class="p">)</span>
<span class="c1"># Determine the index of the highest resolution level</span>
<span class="n">resolution_map</span> <span class="o">=</span> <span class="n">project</span><span class="o">.</span><span class="n">get_resolution_map</span><span class="p">()</span>
<span class="n">max_resolution_level</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">resolution_map</span><span class="p">)</span> <span class="o">-</span> <span class="mi">1</span>
<span class="c1"># Define the dimensions</span>
<span class="n">dimensions</span> <span class="o">=</span> <span class="n">project</span><span class="o">.</span><span class="n">get_size</span><span class="p">(</span><span class="n">max_resolution_level</span><span class="p">)</span>
<span class="c1"># Determine number of frames in project's volumetric data</span>
<span class="n">frame_count</span> <span class="o">=</span> <span class="n">project</span><span class="o">.</span><span class="n">get_timepoint_count</span><span class="p">()</span>
<span class="k">for</span> <span class="n">timepoint</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">frame_count</span><span class="p">):</span>
<span class="c1"># Determine dimensions and offset of frame</span>
<span class="n">vec3_dimensions</span> <span class="o">=</span> <span class="n">pyglass</span><span class="o">.</span><span class="n">vec3</span><span class="p">(</span><span class="nb">float</span><span class="p">(</span><span class="n">dimensions</span><span class="p">[</span><span class="mi">2</span><span class="p">]),</span> <span class="nb">float</span><span class="p">(</span><span class="n">dimensions</span><span class="p">[</span><span class="mi">1</span><span class="p">]),</span> <span class="nb">float</span><span class="p">(</span><span class="n">dimensions</span><span class="p">[</span><span class="mi">0</span><span class="p">]))</span>
<span class="n">vec3_offset</span> <span class="o">=</span> <span class="n">pyglass</span><span class="o">.</span><span class="n">vec3</span><span class="p">(</span><span class="nb">float</span><span class="p">(</span><span class="mi">0</span><span class="p">),</span> <span class="nb">float</span><span class="p">(</span><span class="mi">0</span><span class="p">),</span> <span class="nb">float</span><span class="p">(</span><span class="mi">0</span><span class="p">))</span>
<span class="c1"># Retrieve the mask as a raster image from the block</span>
<span class="n">raster</span> <span class="o">=</span> <span class="n">mask_extractor</span><span class="o">.</span><span class="n">GetCustomBlock</span><span class="p">(</span><span class="n">project</span><span class="o">.</span><span class="n">impl</span><span class="p">,</span> <span class="n">timepoint</span><span class="p">,</span> <span class="n">max_resolution_level</span><span class="p">,</span> <span class="n">vec3_offset</span><span class="p">,</span> <span class="n">vec3_dimensions</span><span class="p">)</span>
<span class="n">mask_array</span> <span class="o">=</span> <span class="n">pyglass</span><span class="o">.</span><span class="n">GetRasterAsNumpyArray</span><span class="p">(</span><span class="n">raster</span><span class="p">)</span>
<span class="c1"># Save tiff in current directory</span>
<span class="n">tifffile</span><span class="o">.</span><span class="n">imwrite</span><span class="p">(</span><span class="sa">f</span><span class="s2">"mask_image_timepoint-</span><span class="si">{</span><span class="n">timepoint</span><span class="si">}</span><span class="s2">.tif"</span><span class="p">,</span> <span class="n">mask_array</span><span class="p">)</span>
</pre></div>
</div>
</section>
</section>
<section id="counting">
<h2>Counting<a class="headerlink" href="#counting" title="Link to this heading">¶</a></h2>
<section id="changing-colors-of-counting-points">
<h3>Changing Colors of Counting Points<a class="headerlink" href="#changing-colors-of-counting-points" title="Link to this heading">¶</a></h3>
<p>Once retrieved, the color and position of counting points can be changed. Here we change the color of all of the red
counting points in an experiment to green.</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">syglass</span> <span class="k">as</span> <span class="nn">sy</span>
<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
<span class="n">project</span> <span class="o">=</span> <span class="n">sy</span><span class="o">.</span><span class="n">get_project</span><span class="p">(</span><span class="s2">"C:/path/to/project_file.syg"</span><span class="p">)</span>
<span class="c1"># Get counting points for the default experiment</span>
<span class="n">counts</span> <span class="o">=</span> <span class="n">project</span><span class="o">.</span><span class="n">get_counting_points</span><span class="p">()</span>
<span class="c1"># Copy red points to the green series, clear the red points</span>
<span class="n">counts</span><span class="p">[</span><span class="s2">"Green"</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">counts</span><span class="p">[</span><span class="s2">"Green"</span><span class="p">],</span> <span class="n">counts</span><span class="p">[</span><span class="s2">"Red"</span><span class="p">],</span> <span class="n">axis</span> <span class="o">=</span> <span class="mi">0</span><span class="p">)</span>
<span class="n">counts</span><span class="p">[</span><span class="s2">"Red"</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">empty</span><span class="p">((</span><span class="mi">0</span><span class="p">,</span> <span class="mi">3</span><span class="p">))</span>
<span class="c1"># Save result as the new counting points for the default experiment</span>
<span class="n">project</span><span class="o">.</span><span class="n">set_counting_points</span><span class="p">(</span><span class="n">counts</span><span class="p">)</span>
</pre></div>
</div>
</section>
<section id="get-and-set-the-multi-tracking-points-for-a-project">
<h3>Get and Set the Multi-tracking Points for a Project<a class="headerlink" href="#get-and-set-the-multi-tracking-points-for-a-project" title="Link to this heading">¶</a></h3>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">syglass</span> <span class="k">as</span> <span class="nn">sy</span>
<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
<span class="kn">import</span> <span class="nn">pprint</span>
<span class="c1"># get the syGlass project</span>
<span class="n">project</span> <span class="o">=</span> <span class="n">sy</span><span class="o">.</span><span class="n">get_project</span><span class="p">(</span><span class="s2">"C:/path/to/project_file.syg"</span><span class="p">)</span>
<span class="c1"># load the multi tracking points into a dict</span>
<span class="n">pts</span> <span class="o">=</span> <span class="n">project</span><span class="o">.</span><span class="n">get_multitracking_points</span><span class="p">()</span>
<span class="c1"># add two new points to the dict. One orange point and one violet point</span>
<span class="n">pts</span><span class="p">[</span><span class="s1">'Orange'</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">([</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mf">30.02</span><span class="p">,</span> <span class="mf">23.02</span><span class="p">,</span> <span class="mf">19.02</span><span class="p">]),</span> <span class="mi">235</span><span class="p">,</span> <span class="mi">3</span><span class="p">])</span> <span class="c1"># [[z,y,x], frame, series number]</span>
<span class="n">pts</span><span class="p">[</span><span class="s1">'Violet'</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">([</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mf">45.02</span><span class="p">,</span> <span class="mf">22.042</span><span class="p">,</span> <span class="mf">5.03</span><span class="p">]),</span> <span class="mi">600</span><span class="p">,</span> <span class="mi">4</span><span class="p">])</span> <span class="c1"># [[z,y,x], frame, series number]</span>
<span class="c1"># set the projects new and updated multi tracking points</span>
<span class="n">project</span><span class="o">.</span><span class="n">set_multitracking_points</span><span class="p">(</span><span class="n">pts</span><span class="p">)</span>
<span class="c1"># retrieve the updated points</span>
<span class="n">out</span> <span class="o">=</span> <span class="n">project</span><span class="o">.</span><span class="n">get_multitracking_points</span><span class="p">()</span>
<span class="c1"># display the dict with pretty print for organization</span>
<span class="n">pp</span> <span class="o">=</span> <span class="n">pprint</span><span class="o">.</span><span class="n">PrettyPrinter</span><span class="p">(</span><span class="n">indent</span><span class="o">=</span><span class="mi">4</span><span class="p">)</span>
<span class="n">pp</span><span class="o">.</span><span class="n">pprint</span><span class="p">(</span><span class="n">out</span><span class="p">)</span>
</pre></div>
</div>
</section>
</section>
<section id="tracings-swcs">
<h2>Tracings (SWCs)<a class="headerlink" href="#tracings-swcs" title="Link to this heading">¶</a></h2>
<section id="importing-swc-files">
<h3>Importing SWC Files<a class="headerlink" href="#importing-swc-files" title="Link to this heading">¶</a></h3>
<p>Import a series of SWC files for viewing inside of a syGlass project.</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">syglass</span> <span class="k">as</span> <span class="nn">sy</span>
<span class="kn">import</span> <span class="nn">glob</span>
<span class="n">project</span> <span class="o">=</span> <span class="n">sy</span><span class="o">.</span><span class="n">get_project</span><span class="p">(</span><span class="s2">"E:/empty/empty.syg"</span><span class="p">)</span>
<span class="n">l</span> <span class="o">=</span> <span class="n">glob</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="s2">"C:/swcs/*.swc"</span><span class="p">)</span>
<span class="n">outcome</span> <span class="o">=</span> <span class="n">project</span><span class="o">.</span><span class="n">import_swcs</span><span class="p">(</span><span class="n">l</span><span class="p">,</span> <span class="s2">"default"</span><span class="p">)</span>
</pre></div>
</div>
</section>
<section id="export-and-analyze">
<h3>Export and Analyze<a class="headerlink" href="#export-and-analyze" title="Link to this heading">¶</a></h3>
<p>Export tracings as SWC files, and analyze their morphology with the python module NeuroM.</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">syglass</span> <span class="k">as</span> <span class="nn">sy</span>
<span class="kn">import</span> <span class="nn">glob</span>
<span class="c1"># get the syGlass project</span>
<span class="n">project</span> <span class="o">=</span> <span class="n">sy</span><span class="o">.</span><span class="n">get_project</span><span class="p">(</span><span class="s2">"E:/empty/empty.syg"</span><span class="p">)</span>
<span class="c1"># save the tracings (will export each disconnected component as a separate SWC file)</span>
<span class="n">project</span><span class="o">.</span><span class="n">save_tracings</span><span class="p">()</span>
<span class="c1"># find all the SWC files</span>
<span class="n">matchingFiles</span> <span class="o">=</span> <span class="n">glob</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="s2">"*.swc"</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">matchingFiles</span><span class="p">)</span>
<span class="c1"># output: ['output00000.swc', 'output00001.swc', 'output00002.swc']</span>
<span class="c1"># get first SWC and load into NeuroM</span>
<span class="kn">import</span> <span class="nn">neurom</span> <span class="k">as</span> <span class="nn">nm</span>
<span class="n">nrn</span> <span class="o">=</span> <span class="n">nm</span><span class="o">.</span><span class="n">load_neuron</span><span class="p">(</span><span class="n">matchingFiles</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
<span class="n">nrnSegLen</span> <span class="o">=</span> <span class="n">nm</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">'segment_lengths'</span><span class="p">,</span> <span class="n">nrn</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="nb">sum</span><span class="p">(</span><span class="n">nrnSegLen</span><span class="p">))</span>
<span class="c1"># total length: 111945.68</span>
<span class="c1"># calculate Sholl Analysis</span>
<span class="n">nrnSholl</span> <span class="o">=</span> <span class="n">nm</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">'sholl_frequency'</span><span class="p">,</span> <span class="n">nrn</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">nrnSholl</span><span class="p">)</span>
<span class="c1"># sholl output: [ 0. 8. 24. 33. 39. 52. 69. 68. 69. 79. 84. 78. 69. 78. 61. ... ]</span>
</pre></div>
</div>
</section>
</section>
<section id="meshes-obj">
<h2>Meshes (OBJ)<a class="headerlink" href="#meshes-obj" title="Link to this heading">¶</a></h2>
<section id="import">
<h3>Import<a class="headerlink" href="#import" title="Link to this heading">¶</a></h3>
<p>Import a list of mesh files in the OBJ file format:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">syglass</span> <span class="k">as</span> <span class="nn">sy</span>
<span class="kn">import</span> <span class="nn">glob</span>
<span class="c1"># get the syGlass project</span>
<span class="n">project</span> <span class="o">=</span> <span class="n">sy</span><span class="o">.</span><span class="n">get_project</span><span class="p">(</span><span class="s2">"C:/syGlass Projects/thor/thorlabs.syg"</span><span class="p">)</span>
<span class="n">l</span> <span class="o">=</span> <span class="n">glob</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="s2">"C:/meshes/*.obj"</span><span class="p">)</span>
<span class="n">project</span><span class="o">.</span><span class="n">import_meshes</span><span class="p">(</span><span class="n">l</span><span class="p">,</span> <span class="s2">"default"</span><span class="p">)</span>
</pre></div>
</div>
</section>
</section>
<section id="rois">
<h2>ROIs<a class="headerlink" href="#rois" title="Link to this heading">¶</a></h2>
<section id="importing-and-exporting-roi-data">
<h3>Importing and Exporting ROI Data<a class="headerlink" href="#importing-and-exporting-roi-data" title="Link to this heading">¶</a></h3>
<p>Export ROI data to numpy arrays and import an ROI to syGlass:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
<span class="kn">import</span> <span class="nn">tifffile</span>
<span class="kn">import</span> <span class="nn">syglass</span> <span class="k">as</span> <span class="nn">sy</span>
<span class="c1"># get the syGlass project</span>
<span class="n">project</span> <span class="o">=</span> <span class="n">sy</span><span class="o">.</span><span class="n">get_project</span><span class="p">(</span><span class="s2">"C:/path/to/project_file.syg"</span><span class="p">)</span>
<span class="n">roi_index</span> <span class="o">=</span> <span class="mi">1</span>
<span class="c1"># get the raw ROI data block</span>
<span class="n">roi_block</span> <span class="o">=</span> <span class="n">project</span><span class="o">.</span><span class="n">get_roi_data</span><span class="p">(</span><span class="n">roi_index</span><span class="p">)</span>
<span class="c1"># save the ROI data as a tiff file</span>
<span class="n">tifffile</span><span class="o">.</span><span class="n">imsave</span><span class="p">(</span><span class="s2">"C:/path/to/roiraw_tiff_file.tiff"</span><span class="p">,</span> <span class="n">roi_block</span><span class="o">.</span><span class="n">data</span><span class="p">)</span>
<span class="c1"># get the mask block of the ROI</span>
<span class="n">mask_block</span> <span class="o">=</span> <span class="n">project</span><span class="o">.</span><span class="n">get_mask</span><span class="p">(</span><span class="n">roi_index</span><span class="p">)</span>
<span class="c1"># save the mask data as a tiff file</span>
<span class="n">tifffile</span><span class="o">.</span><span class="n">imsave</span><span class="p">(</span><span class="s2">"C:/path/to/mask_tiff_file.tiff"</span><span class="p">,</span> <span class="n">mask_block</span><span class="o">.</span><span class="n">data</span><span class="p">)</span>
<span class="c1"># import an ROI mask numpy array (z,y,x,channel count)</span>
<span class="n">incoming_mask</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">ones</span><span class="p">(</span><span class="mi">100</span><span class="p">,</span><span class="mi">100</span><span class="p">,</span><span class="mi">100</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
<span class="n">project</span><span class="o">.</span><span class="n">import_mask</span><span class="p">(</span><span class="n">incoming_mask</span><span class="p">,</span> <span class="n">roi_index</span><span class="p">)</span>
</pre></div>
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<li class="toctree-l2"><a class="reference internal" href="#volumetric-data">Volumetric Data</a><ul>
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<li class="toctree-l3"><a class="reference internal" href="#importing-swc-files">Importing SWC Files</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#importing-and-exporting-roi-data">Importing and Exporting ROI Data</a></li>
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