deploy: 22fa725

janelia-cellmap · Jan 30, 2025 · e8b1242 · e8b1242
1 parent 1729614
commit e8b1242
Showing 1 changed file with 16 additions and 2 deletions.
diff --git a/_modules/cellmap_segmentation_challenge/utils/utils.html b/_modules/cellmap_segmentation_challenge/utils/utils.html
@@ -270,6 +270,7 @@ <h1></h1>
 
   <h1>Source code for cellmap_segmentation_challenge.utils.utils</h1><div class="highlight"><pre>
 <span></span><span class="kn">import</span><span class="w"> </span><span class="nn">shutil</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">sys</span>
 <span class="kn">from</span><span class="w"> </span><span class="nn">tqdm</span><span class="w"> </span><span class="kn">import</span> <span class="n">tqdm</span>
 <span class="kn">from</span><span class="w"> </span><span class="nn">cellmap_segmentation_challenge.utils</span><span class="w"> </span><span class="kn">import</span> <span class="n">get_tested_classes</span>
 <span class="kn">from</span><span class="w"> </span><span class="nn">cellmap_segmentation_challenge</span><span class="w"> </span><span class="kn">import</span> <span class="n">TRUTH_PATH</span>
@@ -438,8 +439,8 @@ <h1>Source code for cellmap_segmentation_challenge.utils.utils</h1><div class="h
     <span class="k">if</span> <span class="n">UPath</span><span class="p">(</span><span class="n">destination</span><span class="p">)</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
         <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Removing existing ground truth dataset at: </span><span class="si">{</span><span class="n">destination</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
         <span class="n">shutil</span><span class="o">.</span><span class="n">rmtree</span><span class="p">(</span><span class="n">destination</span><span class="p">)</span>
-    <span class="n">ground_truth</span> <span class="o">=</span> <span class="n">zarr</span><span class="o">.</span><span class="n">open_group</span><span class="p">(</span><span class="n">destination</span><span class="p">,</span> <span class="n">mode</span><span class="o">=</span><span class="s2">&quot;w&quot;</span><span class="p">)</span>
-    <span class="c1"># ground_truth = zarr.open_group(destination, mode=&quot;a&quot;)</span>
+    <span class="c1"># ground_truth = zarr.open_group(destination, mode=&quot;w&quot;)</span>
+    <span class="n">ground_truth</span> <span class="o">=</span> <span class="n">zarr</span><span class="o">.</span><span class="n">open_group</span><span class="p">(</span><span class="n">destination</span><span class="p">,</span> <span class="n">mode</span><span class="o">=</span><span class="s2">&quot;a&quot;</span><span class="p">)</span>
 
     <span class="c1"># Make a pool for parallel processing</span>
     <span class="kn">from</span><span class="w"> </span><span class="nn">concurrent.futures</span><span class="w"> </span><span class="kn">import</span> <span class="n">ThreadPoolExecutor</span><span class="p">,</span> <span class="n">as_completed</span>
@@ -477,6 +478,7 @@ <h1>Source code for cellmap_segmentation_challenge.utils.utils</h1><div class="h
     <span class="n">zarr_file</span> <span class="o">=</span> <span class="n">zarr</span><span class="o">.</span><span class="n">open</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">mode</span><span class="o">=</span><span class="s2">&quot;r&quot;</span><span class="p">)</span>
 
     <span class="c1"># Write the dataset to the destination Zarr</span>
+    <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Writing </span><span class="si">{</span><span class="n">write_path</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">crop</span><span class="o">=</span><span class="n">crop_name</span><span class="p">,</span><span class="w"> </span><span class="n">label</span><span class="o">=</span><span class="n">class_label</span><span class="p">)</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
     <span class="n">dataset</span> <span class="o">=</span> <span class="n">ground_truth</span><span class="o">.</span><span class="n">create_dataset</span><span class="p">(</span>
         <span class="n">write_path</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">crop</span><span class="o">=</span><span class="n">crop_name</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="n">class_label</span><span class="p">),</span>
         <span class="n">data</span><span class="o">=</span><span class="n">zarr_file</span><span class="p">[</span><span class="s2">&quot;s0&quot;</span><span class="p">],</span>
@@ -489,6 +491,18 @@ <h1>Source code for cellmap_segmentation_challenge.utils.utils</h1><div class="h
     <span class="n">dataset</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="s2">&quot;translation&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">translation</span>
     <span class="n">dataset</span><span class="o">.</span><span class="n">attrs</span><span class="p">[</span><span class="s2">&quot;shape&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">shape</span></div>
 
+
+
+<span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s2">&quot;__main__&quot;</span><span class="p">:</span>
+    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">)</span> <span class="o">&lt;</span> <span class="mi">2</span><span class="p">:</span>
+        <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Usage: python utils.py &lt;path_root&gt;&quot;</span><span class="p">)</span>
+        <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span>
+    <span class="k">elif</span> <span class="nb">len</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">)</span> <span class="o">==</span> <span class="mi">2</span> <span class="ow">or</span> <span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o">==</span> <span class="s2">&quot;dataset&quot;</span><span class="p">:</span>
+        <span class="n">construct_truth_dataset</span><span class="p">(</span>
+            <span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
+        <span class="p">)</span>
+    <span class="k">elif</span> <span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o">==</span> <span class="s2">&quot;manifest&quot;</span><span class="p">:</span>
+        <span class="n">construct_test_crop_manifest</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">verbose</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
 </pre></div>
 
                 </article>