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aelefebv · Oct 3, 2024 · 94cc6a5 · 94cc6a5
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diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle
diff --git a/docs/_build/doctrees/nellie.feature_extraction.doctree b/docs/_build/doctrees/nellie.feature_extraction.doctree
diff --git a/docs/_build/html/_modules/nellie/feature_extraction/hierarchical.html b/docs/_build/html/_modules/nellie/feature_extraction/hierarchical.html
diff --git a/docs/_build/html/modules.html b/docs/_build/html/modules.html
@@ -13,6 +13,8 @@
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
+    <link rel="next" title="main module" href="main.html" />
+    <link rel="prev" title="Nellie documentation" href="index.html" />
 
   <link rel="stylesheet" href="_static/custom.css" type="text/css" />
 
@@ -249,11 +251,23 @@ <h1 class="logo"><a href="index.html">Nellie</a></h1>
 
 
 <h3>Navigation</h3>
+<p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
+<ul class="current">
+<li class="toctree-l1 current"><a class="current reference internal" href="#">nellie</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="main.html">main module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="nellie.html">nellie package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="nellie_napari.html">nellie_napari package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="tests.html">tests package</a></li>
+</ul>
+</li>
+</ul>
 
 <div class="relations">
 <h3>Related Topics</h3>
 <ul>
   <li><a href="index.html">Documentation overview</a><ul>
+      <li>Previous: <a href="index.html" title="previous chapter">Nellie documentation</a></li>
+      <li>Next: <a href="main.html" title="next chapter">main module</a></li>
   </ul></li>
 </ul>
 </div>

diff --git a/docs/_build/html/nellie.feature_extraction.html b/docs/_build/html/nellie.feature_extraction.html
diff --git a/docs/_build/html/nellie_napari.html b/docs/_build/html/nellie_napari.html
@@ -13,6 +13,8 @@
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
+    <link rel="next" title="tests package" href="tests.html" />
+    <link rel="prev" title="nellie.utils package" href="nellie.utils.html" />
 
   <link rel="stylesheet" href="_static/custom.css" type="text/css" />
 
@@ -485,11 +487,25 @@ <h1 class="logo"><a href="index.html">Nellie</a></h1>
 
 
 <h3>Navigation</h3>
+<p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
+<ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="modules.html">nellie</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="main.html">main module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="nellie.html">nellie package</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#">nellie_napari package</a></li>
+<li class="toctree-l2"><a class="reference internal" href="tests.html">tests package</a></li>
+</ul>
+</li>
+</ul>
 
 <div class="relations">
 <h3>Related Topics</h3>
 <ul>
   <li><a href="index.html">Documentation overview</a><ul>
+  <li><a href="modules.html">nellie</a><ul>
+      <li>Previous: <a href="nellie.utils.html" title="previous chapter">nellie.utils package</a></li>
+      <li>Next: <a href="tests.html" title="next chapter">tests package</a></li>
+  </ul></li>
   </ul></li>
 </ul>
 </div>

diff --git a/docs/_build/html/searchindex.js b/docs/_build/html/searchindex.js
diff --git a/nellie/feature_extraction/hierarchical.py b/nellie/feature_extraction/hierarchical.py
@@ -1052,6 +1052,26 @@ def run(self):
 
 
 def aggregate_stats_for_class(child_class, t, list_of_idxs):
+    """
+    Aggregates statistical metrics (mean, standard deviation, min, max, sum) for features of a given class at
+    a specific time frame.
+
+    Parameters
+    ----------
+    child_class : object
+        The class from which the feature data is extracted. It should contain a list of statistics to aggregate
+        (i.e., `stats_to_aggregate`) and corresponding feature arrays.
+    t : int
+        The time frame index for which the aggregation is performed.
+    list_of_idxs : list of lists
+        A list where each sublist contains the indices of data points that should be grouped together for aggregation.
+
+    Returns
+    -------
+    dict
+        A dictionary where the keys are feature names and the values are dictionaries containing aggregated
+        statistics for each feature (mean, standard deviation, min, max, sum).
+    """
     # initialize a dictionary to hold lists of aggregated stats for each stat name
     # aggregate_stats = {
     #     stat_name: {"mean": [], "std_dev": [], "25%": [], "50%": [], "75%": [], "min": [], "max": [], "range": [],
@@ -1330,6 +1350,23 @@ def run(self):
 
 
 def distance_check(border_mask, check_coords, spacing):
+    """
+    Calculates the minimum distance between given coordinates and a border mask using a KD-tree.
+
+    Parameters
+    ----------
+    border_mask : numpy.ndarray
+        A binary mask where the border is marked as `True`.
+    check_coords : numpy.ndarray
+        Coordinates of the points for which distances to the border will be calculated.
+    spacing : tuple or list
+        The spacing of the image dimensions (used to scale the coordinates).
+
+    Returns
+    -------
+    numpy.ndarray
+        An array of distances from each point in `check_coords` to the nearest border point.
+    """
     border_coords = np.argwhere(border_mask) * spacing
     border_tree = spatial.cKDTree(border_coords)
     dist, _ = border_tree.query(check_coords * spacing, k=1)