Briefly disable PET, and modify error logging

handler/find_img_data.py

@@ -62,28 +62,27 @@ def find_img_data(dir):
 
 find_img_data('.')
 
-
-# PET
-# TODO - These two lines take several seconds to complete, maybe can be sped up?
-pet_folders = [str(folder) for folder in is_pet.pet_folder(Path(root).resolve())]
-pet_folders = [os.path.relpath(x, root) for x in pet_folders if x != '']
-
-pet_folders = [os.path.join('.', x) for x in pet_folders]
-if pet_folders:
-    for pet_folder in pet_folders:
-        # See if we're dealing ECAT-formatted file(s)
-        ecats = [x for x in os.listdir(pet_folder) if x.endswith(tuple(['.v', '.v.gz']))]
-        if len(ecats):
-            for ecat in ecats:
-                if ecat not in pet_ecat_files_list:
-                    pet_ecat_files_list.append(f'{pet_folder}/{ecat}')
-        # See if we're dealing with DICOM files
-        dcms = [
-            x for x in os.listdir(pet_folder)
-            if not x.endswith(tuple(['.nii', '.nii.gz', '.v', '.v.gz', '.json', '.tsv']))
-        ]
-        if len(dcms) and pet_folder not in pet_dcm_dirs_list:
-            pet_dcm_dirs_list.append(pet_folder)
+# # PET
+# # TODO - Line below line take several seconds to complete, maybe can be sped up?
+# pet_folders = [str(folder) for folder in is_pet.pet_folder(Path(root).resolve())]
+# pet_folders = [os.path.relpath(x, root) for x in pet_folders if x != '']
+# pet_folders = [os.path.join('.', x) for x in pet_folders]
+
+# if pet_folders:
+#     for pet in pet_folders:
+#         # See if we're dealing ECAT-formatted file(s)
+#         ecats = [x for x in os.listdir(pet) if x.endswith(tuple(['.v', '.v.gz']))]
+#         if len(ecats):
+#             for ecat in ecats:
+#                 if ecat not in pet_ecat_files_list:
+#                     pet_ecat_files_list.append(f'{pet}/{ecat}')
+#         # See if we're dealing with DICOM files
+#         dcms = [
+#             x for x in os.listdir(pet)
+#             if not x.endswith(tuple(['.nii', '.nii.gz', '.v', '.v.gz', '.json', '.tsv']))
+#         ]
+#         if len(dcms) and pet not in pet_dcm_dirs_list:
+#             pet_dcm_dirs_list.append(pet)
 
 # MEG
 MEG_extensions = ['*.ds', '*.fif', '*.sqd', '*.con', '*.raw', '*.ave', '*.mrk', '*.kdf', '*.mhd', '*.trg', '*.chn', '*.dat']

handler/preprocess.sh

@@ -216,10 +216,10 @@ else
         # # remove error message(s) about not finding any DICOMs in folder
         line_nums=$(grep -n 'Error: Unable to find any DICOM images' $root/dcm2niix_error | cut -d: -f1)
 
-        for line_num in ${line_nums[*]}
-        do
-            sed -i "$((line_num-1)), $((line_num+1))d" $root/dcm2niix_error
-        done
+        # for line_num in ${line_nums[*]}
+        # do
+        #     sed -i "$((line_num-1)), $((line_num+1))d" $root/dcm2niix_error
+        # done
     fi
 
     # Check for pet2bids errors
@@ -229,10 +229,10 @@ else
         # # remove error message(s) about not finding any DICOMs in folder
         line_nums=$(grep -n 'Error: Unable to find any DICOM images' $root/pet2bids_error | cut -d: -f1)
 
-        for line_num in ${line_nums[*]}
-        do
-            sed -i "$((line_num-1)), $((line_num+1))d" $root/pet2bids_error
-        done
+        # for line_num in ${line_nums[*]}
+        # do
+        #     sed -i "$((line_num-1)), $((line_num+1))d" $root/pet2bids_error
+        # done
     fi
 
     # Add all transformed data (e.g. NIfTI or MEG formats) to the list file
@@ -255,8 +255,8 @@ else
 
         echo ""
         echo "Error: Could not find any MRI, PET, or MEG imaging files in upload."
-        echo "Please click the Debug section below and select Download ${err_file}"
-        echo "We recommend reaching out to the dcm2niix team for assistance: https://github.com/rordenlab/dcm2niix/issues"
+        echo "Please click the Debug (Download) section below and select the ${err_file} file."
+        echo "Please reach out to the ezBIDS team for further assistance: https://github.com/brainlife/ezbids/issues"
         exit 1
     fi