[ENH] miscellaneous small changes and minor fixes

handler/ezBIDS_core/ezBIDS_core.py

@@ -504,9 +504,11 @@ def modify_uploaded_dataset_list(uploaded_img_list):
         elif any(x.endswith(tuple(['.v', '.v.gz'])) for x in grouped_files):
             grouped_files = [x for x in grouped_files if not x.endswith(tuple(['.v', '.v.gz']))]
 
-        # If imaging file comes with additional data (JSON, bval/bvec) add them to list for processing
-        if len(grouped_files) > 1:
-            uploaded_files_list.append(grouped_files)
+        # Don't want this section is we're allowing only NIfTI files to be uploaded (group length will only be 1).
+        # # If imaging file comes with additional data (JSON, bval/bvec) add them to list for processing
+        # if len(grouped_files) > 1:
+        #     uploaded_files_list.append(grouped_files)
+        uploaded_files_list.append(grouped_files)
 
     # Flatten uploaded_files_list
     uploaded_files_list = natsorted([file for sublist in uploaded_files_list for file in sublist])
@@ -913,7 +915,9 @@ def generate_dataset_list(uploaded_files_list, exclude_data):
     for img_file in img_list:
         # Find file extension
         if img_file.endswith('.nii.gz'):
-            ext = 'nii.gz'
+            ext = '.nii.gz'
+        elif img_file.endswith('.v.gz'):
+            ext = '.v.gz'
         else:
             ext = Path(img_file).suffix
 

handler/find_img_data.py

@@ -64,8 +64,8 @@ def find_img_data(dir):
 
 
 # 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]

handler/preprocess.sh

@@ -92,9 +92,13 @@ if [ $bids_compliant == "true" ]; then
 
     touch $root/dcm2niix_output
     touch $root/dcm2niix_error
+
+    touch $root/pet2bids_output
+    touch $root/pet2bids_error
 
     # find products (NIfTI files)
-    (cd $root && find . -maxdepth 9 -type f \( -name "*.nii.gz" \) > list)
+    (cd $root && find . -maxdepth 9 -type f \( -name "*.nii.gz" \) > $root/list)
+    (cd $root && find . -maxdepth 9 -type f \( -name "*blood.json" \) >> $root/list)
 
     echo "running ezBIDS_core (may take several minutes, depending on size of data)"
     python3 "./ezBIDS_core/ezBIDS_core.py" $root
@@ -142,13 +146,15 @@ else
 
     # determine which uploaded files/folders are PET directories or ECAT files
     echo "Finding imaging directories and files"
-    if [ ! -f $root/list]; then
-        mkdir -p $root/list
+    if [ ! -f $root/list ]; then
+        touch $root/list
     fi
     ./find_img_data.py $root
 
     # sort $root/pet2bids_dcm.list, $root/pet2bids_ecat.list, and $root/dcm2niix.list for comm.
     # Then, remove pet directories from dcm2niix list
+    touch $root/pet2bids_output
+
     if [ -f $root/pet2bids_dcm.list ]; then
         sort -o $root/pet2bids_dcm.list $root/pet2bids_dcm.list
         echo "Removing PET directories from dcm2niix list"
@@ -216,17 +222,41 @@ else
         done
     fi
 
-    # Let's add the transformed raw data (i.e. to NIfTI or MEG formats) to the list file
-
-    (cd $root && find . -maxdepth 9 -type f \( -name "*.nii.gz" \) > list)
-    (cd $root && find . -maxdepth 9 -type f \( -name "*blood.json" \) >> list)
+    # Check for pet2bids errors
+    if [[ $PET2BIDS_RUN -eq "true" ]]; then
+        # pull pet2bids error information to log file
+        { grep -B 1 --group-separator=$'\n\n' Error $root/pet2bids_output || true; } > $root/pet2bids_error
+        # # remove error message(s) about not finding any DICOMs in folder
+        line_nums=$(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
+    fi
+
+    # Add all transformed data (e.g. NIfTI or MEG formats) to the list file
+    (cd $root && find . -maxdepth 9 -type f \( -name "*.nii.gz" \) > $root/list)
+    (cd $root && find . -maxdepth 9 -type f \( -name "*blood.json" \) >> $root/list)
 
     if [ -f $root/meg.list ]; then
         cat $root/meg.list >> $root/list
     fi
 
     if [ ! -s $root/list ]; then
-        echo "Could not find any MRI, PET, or MEG imaging files in upload, aborting"
+        err_file=''
+        if [ `grep 'Error' $root/dcm2niix_error | wc -l` -ne 0 ]; then
+            err_file='dcm2niix_error'
+        fi
+
+        if [ `grep 'Error' $root/pet2bids_error | wc -l` -ne 0 ]; then
+            err_file='pet2bids_error'
+        fi
+
+        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"
         exit 1
     fi
 

ui/src/Upload.vue

@@ -149,7 +149,8 @@
 
             <div v-if="session.status == 'failed'">
                 <el-alert type="error"
-                    >ezBIDS failed.. Please check the Debug logs and contact ezBIDS team ([email protected]).</el-alert
+                    >ezBIDS failed.. Please check the Debug logs and contact the ezBIDS team
+                    ([email protected]).</el-alert
                 >
                 <br />
                 <pre class="status">{{ session.status_msg }}</pre>
@@ -190,7 +191,7 @@
                 <div v-if="!ezbids.notLoaded && !ezbids.objects.length">
                     <el-alert type="error"
                         >We couldn't find any objects. Please upload data that contains at least 1 object. Contact the
-                        ezBIDS team ([email protected]) or https://github.com/brainlife/ezbids/issues for
+                        ezBIDS team ([email protected] or https://github.com/brainlife/ezbids/issues) for
                         support</el-alert
                     >
                 </div>
@@ -213,6 +214,9 @@
                         <el-button type="warning" size="mini" @click="downloadFile('dcm2niix_error')"
                             >Download dcm2niix_error</el-button
                         >
+                        <el-button type="warning" size="mini" @click="downloadFile('pet2bids_error')"
+                            >Download pet2bids_error</el-button
+                        >
                         <el-button type="warning" size="mini" @click="downloadFile('list')">Download list</el-button>
                         <el-button type="warning" size="mini" @click="downloadFile('ezBIDS_core.json')"
                             >Download ezBIDS_core.json</el-button