From e4fb1b914bdcd2fd453e9887a50a46e4aed90d86 Mon Sep 17 00:00:00 2001
From: Dan Levitas <dlevitas@iu.edu>
Date: Wed, 21 Feb 2024 19:55:16 +0000
Subject: [PATCH] [FIX] Address MEG issue with .ds format

---
 handler/ezBIDS_core/ezBIDS_core.py | 22 ++++++++++++++++------
 handler/find_img_data.py           |  4 +++-
 2 files changed, 19 insertions(+), 7 deletions(-)

diff --git a/handler/ezBIDS_core/ezBIDS_core.py b/handler/ezBIDS_core/ezBIDS_core.py
index 04dd40e..f1c8f4b 100755
--- a/handler/ezBIDS_core/ezBIDS_core.py
+++ b/handler/ezBIDS_core/ezBIDS_core.py
@@ -314,8 +314,9 @@ def fix_multiple_dots(uploaded_img_list):
             fix = True
             ext = '.json'
         elif img_file.endswith(tuple(MEG_extensions)) and img_file.count('.') > 1:  # for MEG
-            fix = True
-            ext = img_file.split('.')[-1]
+            if not img_file.endswith('.ds'):
+                fix = True
+                ext = '.' + img_file.split('.')[-1]
         else:
             pass
 
@@ -385,10 +386,13 @@ def generate_MEG_json_sidecars(uploaded_img_list):
         from mne_bids.config import MANUFACTURERS
 
         for meg in MEG_img_files:
-            ext = Path(meg).suffix
+            if meg.endswith('.ds'):
+                ext = '.ds'
+            else:
+                ext = Path(meg).suffix
 
             fname = f"{DATA_DIR}/{meg}"
-            json_output_name = fname.split(".")[0] + ".json"
+            json_output_name = fname.split(ext)[0] + ".json"
             raw = mne.io.read_raw(fname, verbose=0)
             acquisition_date_time = raw.info["meas_date"].strftime("%Y-%m-%dT%H:%M:%S.%f")
             acquisition_date = acquisition_date_time.split("T")[0]
@@ -481,6 +485,8 @@ def modify_uploaded_dataset_list(uploaded_img_list):
             ext = '.nii.gz'
         elif img_file.endswith('.v.gz'):
             ext = '.v.gz'
+        elif img_file.endswith('.ds'):
+            ext = '.ds'
         else:
             ext = Path(img_file).suffix
 
@@ -918,6 +924,8 @@ def generate_dataset_list(uploaded_files_list, exclude_data):
             ext = '.nii.gz'
         elif img_file.endswith('.v.gz'):
             ext = '.v.gz'
+        elif img_file.endswith('.ds'):
+            ext = '.ds'
         else:
             ext = Path(img_file).suffix
 
@@ -2931,7 +2939,10 @@ def modify_objects_info(dataset_list):
                                   "pngPaths": [],
                                   "headers": protocol["headers"]})
                 elif item.endswith(tuple(MEG_extensions)):
-                    name = Path(item).suffix
+                    if item.endswith('.ds'):
+                        name = '.ds'
+                    else:
+                        name = Path(item).suffix
                     items.append({"path": item,
                                   "name": name,
                                   "pngPaths": [],
@@ -3028,7 +3039,6 @@ def extract_series_info(dataset_list_unique_series):
 uploaded_img_list = fix_multiple_dots(uploaded_img_list)
 
 # Generate MEG json files, if MEG data was provided
-# uploaded_img_list = generate_MEG_json_sidecars(uploaded_img_list)
 generate_MEG_json_sidecars(uploaded_img_list)
 
 # Filter uploaded files list for files that ezBIDS can't use and check for ezBIDS configuration file
diff --git a/handler/find_img_data.py b/handler/find_img_data.py
index 5f54cd5..5fdd66f 100755
--- a/handler/find_img_data.py
+++ b/handler/find_img_data.py
@@ -96,8 +96,10 @@ def find_img_data(dir):
     find_cmd = os.popen(f"find . -maxdepth 9 -type {type_search} -name '{meg_ext}'").read()
     if find_cmd != '':
         meg_data_list.append(find_cmd)
+
 if len(meg_data_list):
-    meg_data_list = [x for x in meg_data_list[0].split('\n') if x != '']
+    # TODO - won't this remove different extensions?
+    meg_data_list = [x for x in meg_data_list[0].split('\n') if x != '' and 'hz.ds' not in x]
 
 # Save the MRI, PET, MEG, and NIfTI lists (if they exist) to separate files
 file = open(f'{root}/dcm2niix.list', 'w')