Added Dockerfile, images, masks, report_v2.html, requirements.txt, st…

…yles.css
willtack · Aug 13, 2019 · f09aad8 · f09aad8
1 parent 297d898
commit f09aad8
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diff --git a/Dockerfile b/Dockerfile
@@ -0,0 +1,39 @@
+FROM python:3
+MAINTAINER Will Tackett <william.tackett@pennmedicine.upenn.edu>
+
+# Make directory for flywheel spec (v0)
+ENV FLYWHEEL /flywheel/v0
+RUN mkdir -p ${FLYWHEEL}
+RUN mkdir -p imgs
+RUN mkdir -p masks
+RUN mkdir -p bids_dataset
+COPY manifest.json ${FLYWHEEL}/manifest.json
+
+# Set the entrypoint
+ENTRYPOINT ["/flywheel/v0/run.py"]
+
+RUN apt-get -y update
+RUN apt-get install -y zip
+
+RUN pip install flywheel-sdk \
+    && pip install nipype \
+    && pip install nilearn \
+    && pip install nibabel \
+    && pip install matplotlib \
+    && pip install bids \
+    && pip install numpy \
+    && pip install sklearn
+
+# Copy over python scripts
+COPY report.py /flywheel/v0/report.py
+COPY run.py /flywheel/v0/run.py
+COPY imgs/ /imgs/
+COPY masks/ /masks/
+COPY bids_dataset/ /bids_dataset/
+RUN chmod +x ${FLYWHEEL}/*
+
+#  ENV preservation for Flywheel Engine
+#  RUN env -u HOSTNAME -u PWD | \
+#  awk -F = '{ print "export " $1 "=\"" $2 "\"" }' > ${FLYWHEEL}/docker-#env.sh
+
+WORKDIR /flywheel/v0
diff --git a/imgs/asym_ratio_equation.png b/imgs/asym_ratio_equation.png
diff --git a/imgs/mean_signal.png b/imgs/mean_signal.png
diff --git a/imgs/std_dev.png b/imgs/std_dev.png
diff --git a/imgs/svg.png b/imgs/svg.png
diff --git a/imgs/tsnr_equation.png b/imgs/tsnr_equation.png
diff --git a/manifest.json b/manifest.json
@@ -0,0 +1,21 @@
+{
+	"name": "presurgical_report",
+	"label": "Presurgical Report Generator",
+	"description": "Generates a report from an fmri scan of an 				epilepsy patient",
+	"author": "Will Tackett",
+	"maintainer": "Will Tackett <william.tackett@pennmedicine.upenn.edu>",
+	"source": "none",
+	"url": "none",
+	"version": "3.1.1",
+	"license": "BSD-3-Clause",
+	"inputs": {
+		"fmriprepDir": {
+			"description": "Full path to directory containing 				 fmriprep results",
+			"base": "file",
+		},
+	"config": {},
+	"command": "./report.py",
+	"author": "Will Tackett",
+	"maintainer": "Will Tackett"		
+	}
+}
diff --git a/masks/ffg_left_bin.nii.gz b/masks/ffg_left_bin.nii.gz
diff --git a/masks/ffg_right_bin.nii.gz b/masks/ffg_right_bin.nii.gz
diff --git a/masks/hem_left.nii.gz b/masks/hem_left.nii.gz
diff --git a/masks/hem_right.nii.gz b/masks/hem_right.nii.gz
diff --git a/masks/hippocampus_left_bin.nii.gz b/masks/hippocampus_left_bin.nii.gz
diff --git a/masks/hippocampus_right_bin.nii.gz b/masks/hippocampus_right_bin.nii.gz
diff --git a/masks/hpf_bin.nii.gz b/masks/hpf_bin.nii.gz
diff --git a/masks/hpf_left_bin.nii.gz b/masks/hpf_left_bin.nii.gz
diff --git a/masks/hpf_right_bin.nii.gz b/masks/hpf_right_bin.nii.gz
diff --git a/masks/itg_left.nii.gz b/masks/itg_left.nii.gz
diff --git a/masks/itg_right.nii.gz b/masks/itg_right.nii.gz
diff --git a/masks/lba.nii.gz b/masks/lba.nii.gz
diff --git a/masks/mtg_left.nii.gz b/masks/mtg_left.nii.gz
diff --git a/masks/mtg_right.nii.gz b/masks/mtg_right.nii.gz
diff --git a/masks/phg_left_bin.nii.gz b/masks/phg_left_bin.nii.gz
diff --git a/masks/phg_right_bin.nii.gz b/masks/phg_right_bin.nii.gz
diff --git a/masks/rba.nii.gz b/masks/rba.nii.gz
diff --git a/masks/sfg_left.nii.gz b/masks/sfg_left.nii.gz
diff --git a/masks/sfg_right.nii.gz b/masks/sfg_right.nii.gz
diff --git a/masks/stg_left.nii.gz b/masks/stg_left.nii.gz
diff --git a/masks/stg_post_left.nii.gz b/masks/stg_post_left.nii.gz
diff --git a/masks/stg_post_right.nii.gz b/masks/stg_post_right.nii.gz
diff --git a/masks/stg_right.nii.gz b/masks/stg_right.nii.gz
diff --git a/report_v2.html b/report_v2.html
@@ -0,0 +1,140 @@
+<?xml version="1.0" encoding="utf-8" ?> <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0
+    Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> <html
+    xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> <head> <meta http-equiv="Content-Type"
+    content="text/html; charset=utf-8" /> <meta name="generator" content="Docutils 0.12:
+    http://docutils.sourceforge.net/" /> <title></title> <script
+    src="https://code.jquery.com/jquery-3.3.1.slim.min.js"
+    integrity="sha384-q8i/X+965DzO0rT7abK41JStQIAqVgRVzpbzo5smXKp4YfRvH+8abtTE1Pi6jizo"
+    crossorigin="anonymous"></script> <script
+    src="https://stackpath.bootstrapcdn.com/bootstrap/4.1.3/js/bootstrap.min.js"
+    integrity="sha384-ChfqqxuZUCnJSK3+MXmPNIyE6ZbWh2IMqE241rYiqJxyMiZ6OW/JmZQ5stwEULTy"
+    crossorigin="anonymous"></script> <link rel="stylesheet"
+    href="https://stackpath.bootstrapcdn.com/bootstrap/4.1.3/css/bootstrap.min.css"
+    integrity="sha384-MCw98/SFnGE8fJT3GXwEOngsV7Zt27NXFoaoApmYm81iuXoPkFOJwJ8ERdknLPMO" crossorigin="anonymous">
+    <style type="text/css"> .sub-report-title {} .run-title {}
+
+    h1 { padding-top: 35px; }
+    h2 { padding-top: 20px; }
+    h3 { padding-top: 15px; }
+
+    .elem-desc {}
+    .elem-filename {}
+
+    div.elem-image {
+      width: 100%;
+      page-break-before:always;
+    }
+
+    div.table {
+      display: inline-block;
+      width: 60%;
+      height: 150%;
+      margin-left: 5%;
+      vertical-align: middle;
+    }
+
+    div.barplot {
+      display: inline-block;
+      width: 55%;
+      height: 100%;
+      margin-left: -25%;
+      vertical-align: middle;
+    }
+
+    table.table-bordered > thead > tr > th{
+      border:1px solid black;
+    }
+
+    table.table-bordered > tbody > tr > td{
+      border:1px solid black;
+    }
+
+    table.table-bordered > tbody > tr > th{
+      border:1px solid black;
+    }
+
+    .elem-image object.svg-reportlet {
+        width: 100%;
+        padding-bottom: 5px;
+    }
+
+    body {
+        padding: 65px 10px 10px;
+    }
+
+    .boiler-html {
+        font-family: "Bitstream Charter", "Georgia", Times;
+        margin: 20px 25px;
+        padding: 10px;
+        background-color: #F8F9FA;
+    }
+
+    div#boilerplate pre {
+        margin: 20px 25px;
+        padding: 10px;
+        background-color: #F8F9FA;
+    }
+
+    </style>
+
+
+    </head>
+    <body>
+
+    <nav class="navbar fixed-top navbar-expand-lg navbar-light bg-light">
+    <div class="collapse navbar-collapse">
+        <ul class="navbar-nav">
+            <li class="nav-item"><a class="nav-link" href="#ses-01_task-object_run-01">Object Naming</a></li>
+            <li class="nav-item"><a class="nav-link" href="#ses-01_task-rhyme_run-01">Rhyme Matching</a></li>
+            <li class="nav-item"><a class="nav-link" href="#ses-01_task-scenemem_run-01">Scene Memory</a></li>
+            <li class="nav-item"><a class="nav-link" href="#ses-01_task-sentence_run-01">Sentence Completion</a></li>
+            <li class="nav-item"><a class="nav-link" href="#ses-01_task-wordgen_run-01">Wordgen</a></li>
+        </ul>
+    </div>
+    </nav>
+
+
+
+    <div id="Summary" style="top-padding: -20px">
+        <h1 class="sub-report-title">Summary</h1>
+    <ul class="elem-desc">
+        <li>Subject ID: sub-P69</li>
+          <li>Structural images: 1 T1-weighted </li>
+          <li>Functional series: ''' + str(len(layout.get_tasks())) + '''</li>
+               <ul class="elem-desc">
+               <li>Task: ''' + layout.get_tasks()[0] + '''</li>
+               <li>Task: ''' + layout.get_tasks()[1] + '''</li>
+               <li>Task: ''' + layout.get_tasks()[2] + '''</li>
+               <li>Task: ''' + layout.get_tasks()[3] + '''</li>
+               <li>Task: ''' + layout.get_tasks()[4] + '''</li>
+               <li>Task: ''' + layout.get_tasks()[5] + '''</li>
+               </ul>
+           <li>Resampling targets: MNI152NLin2009cAsym, T1w </li>
+        </ul>
+        <h3> Reference table </h3>
+        ''' + legend + '''
+    </div>
+
+    <div id="Functional">
+            <div id="ses-01_task-object_run-01" style="margin-top: 50px">
+                <h1 class="run-title">Object Naming</h1>
+                <h3 class="elem-title">Glass brain</h3>
+                <div class="elem-image">
+                            <object class="svg-reportlet" type="image/svg+xml" data="''' + gb['object_gb'] + '''">
+                            </object>
+                </div>
+
+                <h3 style="margin-top: 20px"><a href=''' + viewers['object_viewer'] + '''>Statistical Map Viewer</a></h3>
+
+                <h3 style="margin-top: 20px"> Statistics </h3>
+
+                <div style="border: 1px solid black;">
+                <div class="table">
+                    ''' + tables['object_table'] + '''
+                </div>
+                <div class="barplot">
+                            <object data="''' + bars['object_bar'] + '''">
+                            </object>
+                </div>
+                </div>
+    </body>
diff --git a/requirements.txt b/requirements.txt
@@ -0,0 +1,7 @@
+matplotlib
+nibabel
+nilearn
+nipype
+numpy
+pandas
+bids
diff --git a/styles.css b/styles.css
@@ -0,0 +1,63 @@
+.sub-report-title {} .run-title {} 
+
+    h1 { padding-top: 35px; }
+    h2 { padding-top: 20px; }
+    h3 { padding-top: 15px; }
+
+    .elem-desc {}
+    .elem-filename {}
+
+    div.elem-image {
+      width: 100%;
+      page-break-before:always;
+    }
+
+    div.table {
+      display: inline-block;
+      width: 60%;
+      height: 150%;
+      margin-left: 5%;
+      vertical-align: middle;
+    }
+
+    div.barplot {
+      display: inline-block;
+      width: 55%;
+      height: 100%;
+      margin-left: -25%;
+      vertical-align: middle;
+    }
+
+    table.table-bordered > thead > tr > th{
+      border:1px solid black;
+    }
+
+    table.table-bordered > tbody > tr > td{
+      border:1px solid black;
+    }
+
+    table.table-bordered > tbody > tr > th{
+      border:1px solid black;
+    }
+
+    .elem-image object.svg-reportlet {
+        width: 100%;
+        padding-bottom: 5px;
+    }
+
+    body {
+        padding: 65px 10px 10px;
+    }
+
+    .boiler-html {
+        font-family: "Bitstream Charter", "Georgia", Times;
+        margin: 20px 25px;
+        padding: 10px;
+        background-color: #F8F9FA;
+    }
+
+    div#boilerplate pre {
+        margin: 20px 25px;
+        padding: 10px;
+        background-color: #F8F9FA;
+    }