Refactored docstrings and added to help guides

unravel/cluster_stats/fdr.py

@@ -61,7 +61,7 @@ def parse_args():
     parser.epilog = __doc__
     return parser.parse_args()
 
-# TODO: could add optional args like in vstats.py for running the fdr command. 
+# TODO: could add optional args like in ``vstats`` for running the ``cluster_fdr`` command. 
 
 @print_func_name_args_times()
 def fdr(input_path, fdr_path, mask_path, q_value):

unravel/cluster_stats/legend.py

@@ -5,7 +5,7 @@
 
 Usage:
 ------
-    legend.py
+    cluster_legend
 
 Inputs:
     <asterisk>_valid_clusters_table.xlsx files in the working directory output from ``cluster_table``

unravel/cluster_stats/org_data.py

@@ -28,10 +28,10 @@ def parse_args():
     parser.add_argument('-p', '--pattern', help='Pattern for sample?? dirs. Use cwd if no matches.', default='sample??', action=SM)
     parser.add_argument('-d', '--dirs', help='List of sample?? dir names or paths to dirs to process', nargs='*', default=None, action=SM)
     parser.add_argument('-cvd', '--cluster_val_dirs', help='Glob pattern matching cluster validation output dirs to copy data from (relative to ./sample??/clusters/)', required=True, action=SM)
-    parser.add_argument('-vd', '--vstats_path', help='path/vstats_dir (the dir vstats.py was run from) to copy p val, info, and index files if provided', default=None, action=SM)
+    parser.add_argument('-vd', '--vstats_path', help='path/vstats_dir (the dir ``vstats`` was run from) to copy p val, info, and index files if provided', default=None, action=SM)
     parser.add_argument('-dt', '--density_type', help='Type of density data to aggregate (cell [default] or label).', default='cell', action=SM)
     parser.add_argument('-td', '--target_dir', help='path/dir to copy results. If omitted, copy data to the cwd', default=None, action=SM)
-    parser.add_argument('-pvt', '--p_val_txt', help='Name of the file w/ the corrected p value thresh (e.g., from fdr.py). Default: p_value_threshold.txt', default='p_value_threshold.txt', action=SM)
+    parser.add_argument('-pvt', '--p_val_txt', help='Name of the file w/ the corrected p value thresh (e.g., from ``cluster_fdr``). Default: p_value_threshold.txt', default='p_value_threshold.txt', action=SM)
     parser.add_argument('-v', '--verbose', help='Increase verbosity.', action='store_true', default=False)
     parser.epilog = __doc__
     return parser.parse_args()

unravel/cluster_stats/prism.py

@@ -47,7 +47,7 @@ def parse_args():
     parser = argparse.ArgumentParser(formatter_class=SuppressMetavar)
     parser.add_argument('-ids', '--valid_cluster_ids', help='Space-separated list of valid cluster IDs to include in the summary.', nargs='+', type=int, required=True, action=SM)
     parser.add_argument('-sa', '--save_all', help='Also save CSVs w/ cell_count|label_volume and cluster_volume data', action='store_true', default=False)
-    parser.add_argument('-p', '--path', help='Path to the directory containing the CSV files from validate_clusters.py. Default: current directory', action=SM)
+    parser.add_argument('-p', '--path', help='Path to the directory containing the CSV files from ``cluster_validation``. Default: current directory', action=SM)
     parser.add_argument('-v', '--verbose', help='Increase verbosity. Default: False', action='store_true', default=False)
     parser.epilog = __doc__
     return parser.parse_args()

unravel/cluster_stats/recursively_mirror_rev_cluster_indices.py

@@ -25,7 +25,7 @@
 
 def parse_args():
     parser = argparse.ArgumentParser(formatter_class=SuppressMetavar)
-    parser.add_argument('-m', '--mas_side', help='Side of the brain corresponding to the mask used for vstats.py and fdr.py (RH or LH)', choices=['RH', 'LH'], required=True, action=SM)
+    parser.add_argument('-m', '--mas_side', help='Side of the brain corresponding to the mask used for ``vstats`` and ``cluster_fdr`` (RH or LH)', choices=['RH', 'LH'], required=True, action=SM)
     parser.add_argument('-p', '--pattern', help='Glob pattern to match files. Default: **/*rev_cluster_index.nii.gz', default='**/*rev_cluster_index.nii.gz', action=SM)
     parser.add_argument('-ax', '--axis', help='Axis to flip the image along. Default: 0', default=0, type=int, action=SM)
     parser.add_argument('-s', '--shift', help='Number of voxels to shift content after flipping. Default: 2', default=2, type=int, action=SM)

unravel/cluster_stats/stats_table.py

@@ -5,7 +5,7 @@
 
 Usage:
 ------
-    stats_table -cp cluster_validation_info.csv -o cluster_validation_summary.csv
+    path/stats_table.py -cp cluster_validation_info.csv -o cluster_validation_summary.csv
 """
 
 import argparse

unravel/cluster_stats/valid_clusters_summary.ini

@@ -1,8 +1,8 @@
-# Configuration files for valid_clusters_summary.py
+# Configuration files for ``clusters_summary``
 [org_data]
 pattern = sample??
 density_type = cell # cell or label
-p_val_txt = p_value_threshold.txt # Name of the file w/ the corrected p value thresh (e.g., from fdr.py)
+p_val_txt = p_value_threshold.txt # Name of the file w/ the corrected p value thresh (e.g., from ``clusters_fdr``)
 
 [stats]
 alternate = two-sided # two-sided, greater, less (for t-test)
@@ -12,9 +12,8 @@ valid_clusters_dir = _valid_clusters
 atlas = /usr/local/unravel/atlases/gubra/gubra_ano_combined_25um.nii.gz # path/atlas.nii.gz with symmetric labels
 output_rgb_lut = True # Output sunburst_RGBs.csv if True (for Allen brain atlas coloring w/ Flourish)
 
-
 [brain]
-mirror = True # Mirror the image in the x-axis for a bilateral representation (set as false if a whole brain mask was used for vstats.py instead of a hemisphere mask)
+mirror = True # Mirror the image in the x-axis for a bilateral representation (set as false if a whole brain mask was used for ``vstats`` instead of a hemisphere mask)
 axis = 0 # Axis to flip the image along
 shift = 2 # Number of voxels to shift content after flipping (accounts for asymmetry in the gubra atlas)
 split_atlas = /usr/local/unravel/atlases/gubra/gubra_ano_split_25um.nii.gz # path/atlas.nii.gz (left label IDs increased by 20000)

unravel/docs/_build/html/_modules/unravel/cluster_stats/fdr.html

@@ -415,7 +415,7 @@ <h1>Source code for unravel.cluster_stats.fdr</h1><div class="highlight"><pre>
     <span class="k">return</span> <span class="n">parser</span><span class="o">.</span><span class="n">parse_args</span><span class="p">()</span></div>
 
 
-<span class="c1"># TODO: could add optional args like in vstats.py for running the fdr command. </span>
+<span class="c1"># TODO: could add optional args like in ``vstats`` for running the ``cluster_fdr`` command. </span>
 
 <div class="viewcode-block" id="fdr">
 <a class="viewcode-back" href="../../../unravel/cluster_stats/fdr.html#unravel.cluster_stats.fdr.fdr">[docs]</a>

unravel/docs/_build/html/_modules/unravel/cluster_stats/legend.html

@@ -356,7 +356,7 @@ <h1>Source code for unravel.cluster_stats.legend</h1><div class="highlight"><pre
 
 <span class="sd">Usage:</span>
 <span class="sd">------</span>
-<span class="sd">    legend.py</span>
+<span class="sd">    cluster_legend</span>
 
 <span class="sd">Inputs:</span>
 <span class="sd">    &lt;asterisk&gt;_valid_clusters_table.xlsx files in the working directory output from ``cluster_table``</span>

unravel/docs/_build/html/_modules/unravel/cluster_stats/org_data.html

@@ -381,10 +381,10 @@ <h1>Source code for unravel.cluster_stats.org_data</h1><div class="highlight"><p
     <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-p&#39;</span><span class="p">,</span> <span class="s1">&#39;--pattern&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Pattern for sample?? dirs. Use cwd if no matches.&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="s1">&#39;sample??&#39;</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">SM</span><span class="p">)</span>
     <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-d&#39;</span><span class="p">,</span> <span class="s1">&#39;--dirs&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;List of sample?? dir names or paths to dirs to process&#39;</span><span class="p">,</span> <span class="n">nargs</span><span class="o">=</span><span class="s1">&#39;*&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">SM</span><span class="p">)</span>
     <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-cvd&#39;</span><span class="p">,</span> <span class="s1">&#39;--cluster_val_dirs&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Glob pattern matching cluster validation output dirs to copy data from (relative to ./sample??/clusters/)&#39;</span><span class="p">,</span> <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">SM</span><span class="p">)</span>
-    <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-vd&#39;</span><span class="p">,</span> <span class="s1">&#39;--vstats_path&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;path/vstats_dir (the dir vstats.py was run from) to copy p val, info, and index files if provided&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">SM</span><span class="p">)</span>
+    <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-vd&#39;</span><span class="p">,</span> <span class="s1">&#39;--vstats_path&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;path/vstats_dir (the dir ``vstats`` was run from) to copy p val, info, and index files if provided&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">SM</span><span class="p">)</span>
     <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-dt&#39;</span><span class="p">,</span> <span class="s1">&#39;--density_type&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Type of density data to aggregate (cell [default] or label).&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="s1">&#39;cell&#39;</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">SM</span><span class="p">)</span>
     <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-td&#39;</span><span class="p">,</span> <span class="s1">&#39;--target_dir&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;path/dir to copy results. If omitted, copy data to the cwd&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">SM</span><span class="p">)</span>
-    <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-pvt&#39;</span><span class="p">,</span> <span class="s1">&#39;--p_val_txt&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Name of the file w/ the corrected p value thresh (e.g., from fdr.py). Default: p_value_threshold.txt&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="s1">&#39;p_value_threshold.txt&#39;</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">SM</span><span class="p">)</span>
+    <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-pvt&#39;</span><span class="p">,</span> <span class="s1">&#39;--p_val_txt&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Name of the file w/ the corrected p value thresh (e.g., from ``cluster_fdr``). Default: p_value_threshold.txt&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="s1">&#39;p_value_threshold.txt&#39;</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">SM</span><span class="p">)</span>
     <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-v&#39;</span><span class="p">,</span> <span class="s1">&#39;--verbose&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Increase verbosity.&#39;</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="s1">&#39;store_true&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
     <span class="n">parser</span><span class="o">.</span><span class="n">epilog</span> <span class="o">=</span> <span class="vm">__doc__</span>
     <span class="k">return</span> <span class="n">parser</span><span class="o">.</span><span class="n">parse_args</span><span class="p">()</span></div>

unravel/docs/_build/html/_modules/unravel/cluster_stats/prism.html

@@ -400,7 +400,7 @@ <h1>Source code for unravel.cluster_stats.prism</h1><div class="highlight"><pre>
     <span class="n">parser</span> <span class="o">=</span> <span class="n">argparse</span><span class="o">.</span><span class="n">ArgumentParser</span><span class="p">(</span><span class="n">formatter_class</span><span class="o">=</span><span class="n">SuppressMetavar</span><span class="p">)</span>
     <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-ids&#39;</span><span class="p">,</span> <span class="s1">&#39;--valid_cluster_ids&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Space-separated list of valid cluster IDs to include in the summary.&#39;</span><span class="p">,</span> <span class="n">nargs</span><span class="o">=</span><span class="s1">&#39;+&#39;</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="nb">int</span><span class="p">,</span> <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">SM</span><span class="p">)</span>
     <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-sa&#39;</span><span class="p">,</span> <span class="s1">&#39;--save_all&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Also save CSVs w/ cell_count|label_volume and cluster_volume data&#39;</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="s1">&#39;store_true&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
-    <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-p&#39;</span><span class="p">,</span> <span class="s1">&#39;--path&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Path to the directory containing the CSV files from validate_clusters.py. Default: current directory&#39;</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">SM</span><span class="p">)</span>
+    <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-p&#39;</span><span class="p">,</span> <span class="s1">&#39;--path&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Path to the directory containing the CSV files from ``cluster_validation``. Default: current directory&#39;</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">SM</span><span class="p">)</span>
     <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-v&#39;</span><span class="p">,</span> <span class="s1">&#39;--verbose&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Increase verbosity. Default: False&#39;</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="s1">&#39;store_true&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
     <span class="n">parser</span><span class="o">.</span><span class="n">epilog</span> <span class="o">=</span> <span class="vm">__doc__</span>
     <span class="k">return</span> <span class="n">parser</span><span class="o">.</span><span class="n">parse_args</span><span class="p">()</span></div>