Fix output directory tree in report

phys2bids/phys2bids.py

@@ -542,8 +542,7 @@ def phys2bids(
 
         # Only generate report if specified by the user
         if make_report:
-            generate_report(conversion_path, logname, phys_out[key])
-
+            generate_report(outdir, conversion_path, logname, phys_out[key])
 
 def _main(argv=None):
     options = _get_parser().parse_args(argv)

phys2bids/reporting/html_report.py

@@ -193,7 +193,7 @@ def _generate_bokeh_plots(phys_in, figsize=(250, 500)):
     return script, div
 
 
-def generate_report(out_dir, log_path, phys_in):
+def generate_report(out_dir, conversion_path, log_path, phys_in):
     """
     Plot all the channels for visualizations as linked line plots for dynamic report.
 
@@ -217,15 +217,15 @@ def generate_report(out_dir, log_path, phys_in):
     # Copy assets into output folder
     pkgdir = sys.modules["phys2bids"].__path__[0]
     assets_path = join(pkgdir, "reporting", "assets")
-    copy_tree(assets_path, join(out_dir, "assets"))
+    copy_tree(assets_path, join(conversion_path, "assets"))
 
     # Read log
     with open(log_path, "r") as f:
         log_content = f.read()
 
     log_content = log_content.replace("\n", "<br>")
-    log_html_path = join(out_dir, "phys2bids_report_log.html")
-    qc_html_path = join(out_dir, "phys2bids_report.html")
+    log_html_path = join(conversion_path, "phys2bids_report_log.html")
+    qc_html_path = join(conversion_path, "phys2bids_report.html")
 
     html = _save_as_html(log_html_path, log_content, qc_html_path)