make html

unravel/docs/_build/html/_modules/unravel/region_stats/rstats.html

@@ -637,7 +637,7 @@ <h1>Source code for unravel.region_stats.rstats</h1><div class="highlight"><pre>
 
             <span class="n">sample_path</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">sample</span><span class="p">)</span><span class="o">.</span><span class="n">resolve</span><span class="p">()</span> <span class="k">if</span> <span class="n">sample</span> <span class="o">!=</span> <span class="n">Path</span><span class="o">.</span><span class="n">cwd</span><span class="p">()</span><span class="o">.</span><span class="n">name</span> <span class="k">else</span> <span class="n">Path</span><span class="o">.</span><span class="n">cwd</span><span class="p">()</span>
 
-            <span class="c1"># Load resolutions and dimensions of full res image for scaling </span>
+            <span class="c1"># Load resolutions from metadata</span>
             <span class="n">metadata_path</span> <span class="o">=</span> <span class="n">sample_path</span> <span class="o">/</span> <span class="n">args</span><span class="o">.</span><span class="n">metadata</span>
             <span class="n">xy_res</span><span class="p">,</span> <span class="n">z_res</span><span class="p">,</span> <span class="n">_</span><span class="p">,</span> <span class="n">_</span><span class="p">,</span> <span class="n">_</span> <span class="o">=</span> <span class="n">load_image_metadata_from_txt</span><span class="p">(</span><span class="n">metadata_path</span><span class="p">)</span>
             <span class="k">if</span> <span class="n">xy_res</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>

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

@@ -356,7 +356,7 @@ <h1>Source code for unravel.register.reg_prep</h1><div class="highlight"><pre>
 
 <span class="sd">Usage:</span>
 <span class="sd">------</span>
-<span class="sd">    reg_prep -i &lt;asterisk&gt;.czi -x &lt;x/y voxel size in microns&gt; -z &lt;z voxel size&gt; [-e &lt;list of paths to exp dirs&gt;] [-v]</span>
+<span class="sd">    reg_prep -i &lt;asterisk&gt;.czi [-e &lt;list of paths to exp dirs&gt;] [-v]</span>
 
 <span class="sd">Run command from the experiment directory w/ sample?? folder(s), a sample?? folder, or provide -e or -d arguments.</span>
 
@@ -380,7 +380,7 @@ <h1>Source code for unravel.register.reg_prep</h1><div class="highlight"><pre>
 
 <span class="kn">from</span> <span class="nn">unravel.core.argparse_utils</span> <span class="kn">import</span> <span class="n">SuppressMetavar</span><span class="p">,</span> <span class="n">SM</span>
 <span class="kn">from</span> <span class="nn">unravel.core.config</span> <span class="kn">import</span> <span class="n">Configuration</span>
-<span class="kn">from</span> <span class="nn">unravel.core.img_io</span> <span class="kn">import</span> <span class="n">load_3D_img</span><span class="p">,</span> <span class="n">resolve_path</span><span class="p">,</span> <span class="n">save_as_tifs</span><span class="p">,</span> <span class="n">save_as_nii</span>
+<span class="kn">from</span> <span class="nn">unravel.core.img_io</span> <span class="kn">import</span> <span class="n">load_3D_img</span><span class="p">,</span> <span class="n">load_image_metadata_from_txt</span><span class="p">,</span> <span class="n">resolve_path</span><span class="p">,</span> <span class="n">save_as_tifs</span><span class="p">,</span> <span class="n">save_as_nii</span>
 <span class="kn">from</span> <span class="nn">unravel.core.img_tools</span> <span class="kn">import</span> <span class="n">resample</span><span class="p">,</span> <span class="n">reorient_for_raw_to_nii_conv</span>
 <span class="kn">from</span> <span class="nn">unravel.core.utils</span> <span class="kn">import</span> <span class="n">log_command</span><span class="p">,</span> <span class="n">verbose_start_msg</span><span class="p">,</span> <span class="n">verbose_end_msg</span><span class="p">,</span> <span class="n">initialize_progress_bar</span><span class="p">,</span> <span class="n">get_samples</span><span class="p">,</span> <span class="n">print_func_name_args_times</span>
 
@@ -393,8 +393,7 @@ <h1>Source code for unravel.register.reg_prep</h1><div class="highlight"><pre>
     <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;-i&#39;</span><span class="p">,</span> <span class="s1">&#39;--input&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Full res image input path relative (rel_path) to ./sample??&#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;-x&#39;</span><span class="p">,</span> <span class="s1">&#39;--xy_res&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;x/y voxel size in microns of the input image.&#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="nb">type</span><span class="o">=</span><span class="nb">float</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="c1"># Set up   Default: get via ``io_metadata``</span>
-    <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-z&#39;</span><span class="p">,</span> <span class="s1">&#39;--z_res&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;z voxel size in microns of the input image.&#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="nb">type</span><span class="o">=</span><span class="nb">float</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="c1"># Set up   Default: get via ``io_metadata``</span>
+    <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">&#39;-md&#39;</span><span class="p">,</span> <span class="s1">&#39;--metadata&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;path/metadata.txt. Default: parameters/metadata.txt&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="s2">&quot;parameters/metadata.txt&quot;</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;-c&#39;</span><span class="p">,</span> <span class="s1">&#39;--channel&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;.czi channel number. Default: 0 for autofluo&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="mi">0</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">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;-o&#39;</span><span class="p">,</span> <span class="s1">&#39;--output&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Output path. Default: reg_inputs/autofl_50um.nii.gz&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="s2">&quot;reg_inputs/autofl_50um.nii.gz&quot;</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;-r&#39;</span><span class="p">,</span> <span class="s1">&#39;--reg_res&#39;</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">&#39;Resample input to this res in um for reg. Default: 50&#39;</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="mi">50</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">action</span><span class="o">=</span><span class="n">SM</span><span class="p">)</span>
@@ -405,8 +404,6 @@ <h1>Source code for unravel.register.reg_prep</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: The script works if -x and -z are provided. Fix it so that it works if they are not provided (i.e., get res via ``io_metadata`` output: sample??/parameters/metadata.txt)</span>
-
 
 <div class="viewcode-block" id="reg_prep">
 <a class="viewcode-back" href="../../../unravel/register/reg_prep.html#unravel.register.reg_prep.reg_prep">[docs]</a>
@@ -457,14 +454,21 @@ <h1>Source code for unravel.register.reg_prep</h1><div class="highlight"><pre>
             <span class="c1"># Define output</span>
             <span class="n">output</span> <span class="o">=</span> <span class="n">resolve_path</span><span class="p">(</span><span class="n">sample_path</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">output</span><span class="p">,</span> <span class="n">make_parents</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
             <span class="k">if</span> <span class="n">output</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;</span><span class="se">\n\n</span><span class="s2">    </span><span class="si">{</span><span class="n">output</span><span class="o">.</span><span class="n">name</span><span class="si">}</span><span class="s2"> already exists. Skipping.</span><span class="se">\n</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\n</span><span class="s2">    </span><span class="si">{</span><span class="n">args</span><span class="o">.</span><span class="n">output</span><span class="si">}</span><span class="s2"> already exists. Skipping.</span><span class="se">\n</span><span class="s2">&quot;</span><span class="p">)</span>
                 <span class="k">continue</span>
 
             <span class="c1"># Define input image path</span>
             <span class="n">img_path</span> <span class="o">=</span> <span class="n">resolve_path</span><span class="p">(</span><span class="n">sample_path</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="c1"># Load full res autofluo image [and xy and z voxel size in microns]</span>
-            <span class="n">img</span><span class="p">,</span> <span class="n">xy_res</span><span class="p">,</span> <span class="n">z_res</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">channel</span><span class="p">,</span> <span class="s2">&quot;xyz&quot;</span><span class="p">,</span> <span class="n">return_res</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">xy_res</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">xy_res</span><span class="p">,</span> <span class="n">z_res</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">z_res</span><span class="p">)</span>
+            <span class="c1"># Load resolutions from metadata</span>
+            <span class="n">metadata_path</span> <span class="o">=</span> <span class="n">sample_path</span> <span class="o">/</span> <span class="n">args</span><span class="o">.</span><span class="n">metadata</span>
+            <span class="n">xy_res</span><span class="p">,</span> <span class="n">z_res</span><span class="p">,</span> <span class="n">_</span><span class="p">,</span> <span class="n">_</span><span class="p">,</span> <span class="n">_</span> <span class="o">=</span> <span class="n">load_image_metadata_from_txt</span><span class="p">(</span><span class="n">metadata_path</span><span class="p">)</span>
+            <span class="k">if</span> <span class="n">xy_res</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="s2">&quot;    [red1]./sample??/parameters/metadata.txt is missing. Generate w/ io_metadata&quot;</span><span class="p">)</span>
+                <span class="kn">import</span> <span class="nn">sys</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="c1"># Load full res autofluo image</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">channel</span><span class="p">)</span>
 
             <span class="c1"># Prepare the autofluo image for registration</span>
             <span class="n">img_resampled</span> <span class="o">=</span> <span class="n">reg_prep</span><span class="p">(</span><span class="n">img</span><span class="p">,</span> <span class="n">xy_res</span><span class="p">,</span> <span class="n">z_res</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">reg_res</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">zoom_order</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">miracl</span><span class="p">)</span>