Merge branch 'dev'

README.md

@@ -1,4 +1,4 @@
-[![UNRAVEL Logo](https://github.com/b-heifets/UNRAVEL/blob/dev/unravel/docs/_static/UNRAVEL_logo.png)](https://b-heifets.github.io/UNRAVEL/)
+[![UNRAVEL Logo](https://github.com/b-heifets/UNRAVEL/blob/main/unravel/docs/_static/UNRAVEL_logo.png)](https://b-heifets.github.io/UNRAVEL/)
 
 ### UN-biased high-Resolution Analysis and Validation of Ensembles using Light sheet images
 * UNRAVEL is a [Python](https://www.python.org/) package & command line tool for the analysis of brain-wide imaging data, automating: 
@@ -19,7 +19,7 @@
 
 ---
 
-<img src="https://github.com/b-heifets/UNRAVEL/blob/dev/unravel/docs/_static/Heifets_lab_logo.png" alt="Heifets Lab" width="500">
+<img src="https://github.com/b-heifets/UNRAVEL/blob/main/unravel/docs/_static/Heifets_lab_logo.png" alt="Heifets Lab" width="500">
 
 
 
@@ -28,7 +28,7 @@
 * [UNRAVEL visualizer GitHub repo](https://github.com/MetaCell/cfos-visualizer/)
 * Developed by [MetaCell](https://metacell.us/) with support from the [Heifets lab](https://heifetslab.stanford.edu/)
 
-![UNRAVEL visualizer](https://github.com/b-heifets/UNRAVEL/blob/dev/unravel/docs/_static/UNRAVEL_visualizer.png)
+![UNRAVEL visualizer](https://github.com/b-heifets/UNRAVEL/blob/main/unravel/docs/_static/UNRAVEL_visualizer.png)
 
 ### Contact us
 If you have any questions, suggestions, or are interested in collaborations and contributions, please reach out to us. 

unravel/docs/_build/html/_modules/unravel/register/reg.html

@@ -523,7 +523,6 @@ <h1>Source code for unravel.register.reg</h1><div class="highlight"><pre>
 
                 <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;</span><span class="se">\n\n</span><span class="s1">    Generating the initial transform matrix for aligning the moving image (e.g., template) to the fixed image (e.g., tissue) </span><span class="se">\n</span><span class="s1">&#39;</span><span class="p">)</span>
                 <span class="n">command</span> <span class="o">=</span> <span class="p">[</span>
-                    <span class="s1">&#39;python&#39;</span><span class="p">,</span> 
                     <span class="s1">&#39;reg_affine_initializer&#39;</span><span class="p">,</span> 
                     <span class="s1">&#39;-f&#39;</span><span class="p">,</span> <span class="n">fixed_img_for_reg_path</span><span class="p">,</span> 
                     <span class="s1">&#39;-m&#39;</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">moving_img</span><span class="p">,</span> 

unravel/docs/_build/html/_modules/unravel/voxel_stats/vstats_prep.html

@@ -419,6 +419,7 @@ <h1>Source code for unravel.voxel_stats.vstats_prep</h1><div class="highlight"><
     <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: Fix this so -x and -z don&#39;t have to be provided if io_metadata has been run</span>
 
 <div class="viewcode-block" id="main">
 <a class="viewcode-back" href="../../../unravel/voxel_stats/vstats_prep.html#unravel.voxel_stats.vstats_prep.main">[docs]</a>
@@ -448,7 +449,7 @@ <h1>Source code for unravel.voxel_stats.vstats_prep</h1><div class="highlight"><
             <span class="c1"># Load full res image [and xy and z voxel size in microns], to be resampled [and reoriented], padded, and warped</span>
             <span class="n">img_path</span> <span class="o">=</span> <span class="nb">next</span><span class="p">(</span><span class="n">sample_path</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">args</span><span class="o">.</span><span class="n">input</span><span class="p">)),</span> <span class="kc">None</span><span class="p">)</span>
             <span class="k">if</span> <span class="n">img_path</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
-                <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;No files match the pattern </span><span class="si">{</span><span class="n">args</span><span class="o">.</span><span class="n">input</span><span class="si">}</span><span class="s2"> in </span><span class="si">{</span><span class="n">sample_path</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
+                <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="se">\n</span><span class="s2">    [red1]No files match the pattern </span><span class="si">{</span><span class="n">args</span><span class="o">.</span><span class="n">input</span><span class="si">}</span><span class="s2"> in </span><span class="si">{</span><span class="n">sample_path</span><span class="si">}</span><span class="se">\n</span><span class="s2">&quot;</span><span class="p">)</span>
                 <span class="k">continue</span>
             <span class="n">img</span> <span class="o">=</span> <span class="n">load_3D_img</span><span class="p">(</span><span class="n">img_path</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">chann_idx</span><span class="p">,</span> <span class="s2">&quot;xyz&quot;</span><span class="p">)</span>
 

unravel/docs/guide.md

@@ -244,7 +244,7 @@ unravel_commands runs ./\<repo_root_dir\>/unravel/unravel_commands.py
 
 Its help guide is here: {py:mod}`unravel.unravel_commands` 
 
-Commands are defined in the `[project.scripts]` section of the [pyproject.toml](https://github.com/b-heifets/UNRAVEL/blob/dev/pyproject.toml) in the root directory of the UNRAVEL repository (repo).
+Commands are defined in the `[project.scripts]` section of the [pyproject.toml](https://github.com/b-heifets/UNRAVEL/blob/main/pyproject.toml) in the root directory of the UNRAVEL repository (repo).
 
 If new commands are added to run new scripts (a.k.a. modules), reinstall the unravel package with pip. 
 

unravel/voxel_stats/vstats_prep.py

@@ -65,6 +65,7 @@ def parse_args():
     parser.epilog = __doc__
     return parser.parse_args()
 
+# TODO: Fix this so -x and -z don't have to be provided if io_metadata has been run
 
 def main():
     args = parse_args()
@@ -92,7 +93,7 @@ def main():
             # Load full res image [and xy and z voxel size in microns], to be resampled [and reoriented], padded, and warped
             img_path = next(sample_path.glob(str(args.input)), None)
             if img_path is None:
-                print(f"No files match the pattern {args.input} in {sample_path}")
+                print(f"\n    [red1]No files match the pattern {args.input} in {sample_path}\n")
                 continue
             img = load_3D_img(img_path, args.chann_idx, "xyz")