Merge branch 'ME-ICA:main' into main

docs/outputs.rst

@@ -527,6 +527,22 @@ should not overly focus on carpet plots and should examine these results in cont
   :height: 400px
 
 
+************************
+T2* and S0 Summary Plots
+************************
+
+Below the carpet plots are summary plots for the T2* and S0 maps.
+Each map has two figures: a spatial map of the values and a histogram of the voxelwise values.
+The T2* map should look similar to T2 maps and be brightest in the ventricles and darkest in areas of largest susceptibility.
+The S0 map should roughly follow the signal-to-noise ratio and will be brightest near the surface near RF coils.
+
+It is important to note that the histogram is limited from 0 to the 98th percentile of the data to improve readability.
+
+.. image:: /_static/t2star_plots.png
+  :align: center
+  :height: 400px
+
+
 **************************
 Citable workflow summaries
 **************************

tedana/reporting/data/html/report_body_template.html

@@ -1,4 +1,9 @@
 <style type="text/css">
+  .brainplot {
+    width: 50%;
+    height: auto;
+  }
+
   .report {
     display: flex;
     flex-direction: column;
@@ -174,21 +179,39 @@ <h1>Carpet plots</h1>
       <img id="imgCarpetPlot" src="$initialCarpet" />
     </div>
   </div>
-  <div class="info">
-    <h1>Info</h1>
-    $info
+</div>
+<div class="carpet-plots">
+  <h1>T2* and S0</h1>
+  <h2>T2*</h2>
+  <div class="carpet-plots-image">
+    <img id="t2starBrainPlot" src="$t2starBrainPlot" class="brainplot" />
+  </div>
+  <div class="carpet-plots-image">
+    <img id="t2starHistogram" src="$t2starHistogram" />
   </div>
-  <div class="about">
-    <h1>About tedana</h1>
-    $about
+  <h2>S0</h2>
+  <div class="carpet-plots-image">
+    <img id="s0BrainPlot" src="$s0BrainPlot" class="brainplot" />
   </div>
-  <div class="content references">
-    <h1>References</h1>
-    <ul>
-      $references
-    </ul>
+  <div class="carpet-plots-image">
+    <img id="s0Histogram" src="$s0Histogram" />
   </div>
 </div>
+</div>
+<div class="info">
+  <h1>Info</h1>
+  $info
+</div>
+<div class="about">
+  <h1>About tedana</h1>
+  $about
+</div>
+<div class="content references">
+  <h1>References</h1>
+  <ul>
+    $references
+  </ul>
+</div>
 
 <script type="text/javascript">
   function updateCarpetPlot(name) {

tedana/reporting/html_report.py

@@ -14,7 +14,7 @@
 from pybtex.plugin import find_plugin
 
 from tedana import __version__
-from tedana.io import load_json
+from tedana.io import OutputGenerator, load_json
 from tedana.reporting import dynamic_figures as df
 
 LGR = logging.getLogger("GENERAL")
@@ -143,6 +143,12 @@ def _update_template_bokeh(bokeh_id, info_table, about, prefix, references, boke
     # Initial carpet plot (default one)
     initial_carpet = f"./figures/{prefix}carpet_optcom.svg"
 
+    # T2* and S0 images
+    t2star_brain = f"./figures/{prefix}t2star_brain.svg"
+    t2star_histogram = f"./figures/{prefix}t2star_histogram.svg"
+    s0_brain = f"./figures/{prefix}s0_brain.svg"
+    s0_histogram = f"./figures/{prefix}s0_histogram.svg"
+
     # Convert bibtex to html
     references, bibliography = _bib2html(references)
 
@@ -159,6 +165,10 @@ def _update_template_bokeh(bokeh_id, info_table, about, prefix, references, boke
         about=about,
         prefix=prefix,
         initialCarpet=initial_carpet,
+        t2starBrainPlot=t2star_brain,
+        t2starHistogram=t2star_histogram,
+        s0BrainPlot=s0_brain,
+        s0Histogram=s0_histogram,
         references=references,
         javascript=bokeh_js,
         buttons=buttons,
@@ -212,18 +222,17 @@ def _generate_info_table(info_dict):
     return info_html
 
 
-def generate_report(io_generator):
+def generate_report(io_generator: OutputGenerator) -> None:
     """Generate an HTML report.
 
     Parameters
     ----------
-    io_generator : tedana.io.OutputGenerator
+    io_generator : :obj:`tedana.io.OutputGenerator`
         io_generator object for this workflow's output
 
-    Returns
-    -------
-    HTML : file
-        A generated HTML report
+    Notes
+    -----
+    This writes out an HTML report to a file.
     """
     # Load the component time series
     comp_ts_path = io_generator.get_name("ICA mixing tsv")