update

Author: kcho

randomise_summary.py

@@ -1405,4 +1405,5 @@ def check_corrp_map_locations(corrp_map_classes):
 
     if args.html_summary:
         create_html(corrp_map_classes, df, args)
-        print(corrpMap.location.parent / 'randomise_summary.html')
+        print(f'HTML summary is saved in '
+              f"{corrpMap.location.parent / 'randomise_summary.html'}")

randomise_summary_web.py

@@ -28,6 +28,12 @@ def order_corrpMaps(corrpMaps):
 
 def create_html(corrpMaps, df, args):
     """Create html that summarizes randomise_summary.py outputs"""
+    # git version
+    command = 'git rev-parse HEAD'
+    script_dir = os.path.dirname(os.path.realpath(__file__))
+    os.chdir(script_dir)
+    git_hash = os.popen(command).read()
+
     corrpMaps = order_corrpMaps(corrpMaps)
     root = os.path.dirname(os.path.abspath(__file__))
     templates_dir = os.path.join(root, 'templates')
@@ -180,4 +186,5 @@ def create_html(corrpMaps, df, args):
             bin_sum_diff_figures=bin_sum_diff_figures,
             skel_vol_figures=skel_vol_figures,
             warped_map_figures=warped_map_figures,
+            githash=git_hash
         ))

templates/layout.html

@@ -45,8 +45,7 @@
               <a href="#" class="dropdown-toggle" data-toggle="dropdown">Dropdown <b class="caret"></b></a>
               <ul class="dropdown-menu">
                 <li><a href=https://github.com/pnlbwh/fsl_randomise target="_blank">script source</a></li>
-                <li><a href="#">Another action</a></li>
-                <li><a href="#">Something else here</a></li>
+                <li>{% block git %}{% endblock %} </li>
                 <li class="divider"></li>
                 <li><a href="#">Separated link</a></li>
               </ul>
@@ -58,6 +57,9 @@
 
     <div class="container-fluid">
       <h1>Psychiatry Neuroimaging Laboratory</h1>
+      <br>
+      <ul>Currently works the best with ENIGMA template</ul>
+
       <h2>FSL Randomise summary</h2>
       {% block subtitle %}{% endblock %}
       <br>
@@ -92,6 +94,7 @@ <h2>FSL Randomise summary</h2>
     {% block footer %}
       FSL randomise output summary by randomise_summary.py.
       If you find an error, please report it to Kevin Cho ([email protected])
+      If you have modalities detected as 'unknown', please contact Kevin about it.
     {% endblock %}
     </div>
     <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.4.1/css/bootstrap.min.css">

templates/template.html

@@ -8,26 +8,30 @@
 <li class="active"><a href="#">html created using randomise_summary.py by {{ user }}</a></li>
 {% endblock %}
 
+{% block git %}
+<a href=https://github.com/pnlbwh/fsl_randomise/commit/{{ githash }} target="_blank">
+git hash used: <code>{{ githash }}</code></a>
+{% endblock %}
+
 {% block subtitle %}
-<h4>- Data location : {{ location }}</h4>
-<h4>- Owner of the files :
+<h4><ul>Data location : <code>{{ location }}</code></ul></h4>
+<h4><ul>Owner of the files :
     {% for creater in owners %}
-        {{ creater }}
+        <code>{{ creater }}</code>
     {% endfor %}
-</h4>
-<h4>- Corrected p maps were created on :
+</ul></h4>
+<h4><ul>Corrected p maps were created on :
     {% for datec in datecs %}
         {{ datec }}
     {% endfor %}
-</h4>
+</ul></h4>
 
 {% endblock %}
 
 {% block matrixsummary %}
     <h2>Matrix summary</h2>
-    <h4>Matrix file : {{ mat_location }}
-    <h4>Total number of subjects : {{ total_number_of_subjects }}
-    <br><br>
+    <h4><ul>Matrix file : <code>{{ mat_location }}</code></ul></h4>
+    <h4><ul>Total number of subjects : <code>{{ total_number_of_subjects }}</code></ul></h4>
     <div class="table-responsive">
     {{ mat_table|safe }}
     </div>
@@ -36,8 +40,7 @@ <h4>Total number of subjects : {{ total_number_of_subjects }}
 
 {% block contrastsummary %}
     <h2>Contrast summary</h2>
-    <h4>Contrast file : {{ con_location }}
-    <br><br>
+    <h4><ul>Contrast file : <code>{{ con_location }}</code></ul></h4>
     <div class="table-responsive">
     {{ con_table|safe }}
     </div>
@@ -46,6 +49,7 @@ <h4>Contrast file : {{ con_location }}
 
 {% block outputsummary %}
     <h2>Output corrected p-map summary</h2>
+    <ul>Please bear in mind that the FSL randomise p-values are 1-p values</ul>
     <div class="table-responsive">
     {{ table|safe }}
     </div>