Generate graphic reports for phys2bids outputs

.readthedocs.yml

@@ -8,7 +8,7 @@ version: 2
 build:
   os: "ubuntu-20.04"
   tools:
-    python: "3.7"
+    python: "3.9"
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
@@ -20,3 +20,4 @@ python:
       path: .
       extra_requirements:
         - doc
+        - reports

phys2bids/cli/run.py

@@ -189,6 +189,15 @@ def _get_parser():
         help="Only print warnings to log file. Default is False.",
         default=False,
     )
+    optional.add_argument(
+        "-report",
+        "--report",
+        dest="make_report",
+        action="store_true",
+        help="Generate a report with the data and generated folder structure. "
+        "Default is False.",
+        default=False,
+    )
     optional.add_argument("-v", "--version", action="version", version=("%(prog)s " + __version__))
 
     parser._action_groups.append(optional)

phys2bids/phys2bids.py

@@ -38,6 +38,7 @@
 from phys2bids import _version, bids, utils, viz
 from phys2bids.cli.run import _get_parser
 from phys2bids.physio_obj import BlueprintOutput
+from phys2bids.reporting.html_report import generate_report
 from phys2bids.slice4phys import slice4phys
 
 from . import __version__
@@ -145,6 +146,7 @@ def phys2bids(
     pad=9,
     ch_name=[],
     yml="",
+    make_report=False,
     debug=False,
     quiet=False,
 ):
@@ -538,6 +540,10 @@ def phys2bids(
                 ),
             )
 
+        # Only generate report if specified by the user
+        if make_report:
+            generate_report(outdir, conversion_path, logname, phys_out[key])
+
 
 def _main(argv=None):
     options = _get_parser().parse_args(argv)

phys2bids/reporting/__init__.py

@@ -0,0 +1 @@
+"""Visual reporting tools for inspecting phys2bids workflow outputs."""

phys2bids/reporting/assets/main.css

@@ -0,0 +1,102 @@
+html, body {
+    margin: 0;
+    padding: 0;
+    font-family: 'Lato', sans-serif;
+    overflow-x: hidden;
+    overflow-y: scroll;
+}
+* {
+    box-sizing: border-box;
+  }
+
+.header {
+    background: linear-gradient(90deg, rgba(0,240,141,1) 0%, rgba(0,73,133,1) 100%);
+    height: 70px;
+    width: 100%;
+    position: fixed;
+    overflow: hidden;
+    margin: 0;
+    z-index: 100;
+}
+
+.header a, span {
+    color: white;
+    text-decoration: none;
+    font-weight: 700;
+}
+
+.header_logo {
+    display: inline-block;
+    float: left;
+}
+
+.header_logo img{
+    height: 50px;
+    top: 0;
+    left: 0;
+    padding-top: 15px;
+}
+
+.header_links {
+    top: 0;
+    left: 0;
+    padding-top: 25px;
+    margin-left: 20px;
+    margin-right: 20px;
+    float: left;
+    display: inline-block;
+}
+.clear {
+    clear: both;
+}
+
+.content {
+    margin-top: 100px;
+    display: flex;
+    width: 100%;
+}
+
+.tree {
+    margin-left: 50px;
+    margin-right: 50px;
+    flex: 0.5;
+    min-width: 300px;
+    float: left;
+}
+
+.tree_text {
+    margin-top: 10px;
+    margin-bottom: 70px;
+    width: 100%;
+}
+
+.bk-root {
+    display: inline-block;
+    margin-top: 10px;
+    width: 100%;
+}
+
+.bokeh_plots {
+    margin-left: 50px;
+    margin-right: 50px;
+    flex: 1;
+    min-width: 500px;
+    float: left;
+}
+
+@media screen and (max-width: 600px) {
+    .content {
+        flex-wrap: wrap;
+    }
+    .tree {
+        flex-basis: 100%;
+    }
+    .bokeh_plots {
+        flex-basis: 100%;
+    }
+}
+
+.main{
+    margin-top: 100px;
+    margin-left: 100px;
+}