Merge pull request #31 from scitran-apps/parrecfix

Parrecfix

Dockerfile

@@ -30,7 +30,7 @@ RUN apt-get update -qq \
     python
 
 # Compile DCM2NIIX from source
-ENV DCMCOMMIT=5af76a90e46aebff790ab5d0f45846f95a940a2a
+ENV DCMCOMMIT=3d74eabceeaab57213e9ffef91c96de128ac5150
 RUN curl -#L  https://github.com/rordenlab/dcm2niix/archive/$DCMCOMMIT.zip | bsdtar -xf- -C /usr/local
 WORKDIR /usr/local/dcm2niix-${DCMCOMMIT}/build
 RUN cmake -DUSE_OPENJPEG=ON -MY_DEBUG_GE=ON ../ && \

manifest.json

@@ -8,12 +8,16 @@
   "source": "https://github.com/scitran-apps/dcm2niix",
   "license": "BSD-2-Clause",
   "flywheel": "0",
-  "version": "0.7.6_1.0.20180622_5af76a9",
+  "version": "0.7.7_1.0.20181114",
   "custom": {
-    "docker-image": "scitran/dcm2niix:0.7.6_1.0.20180622_5af76a9",
+    "docker-image": "scitran/dcm2niix:0.7.7_1.0.20181114",
     "flywheel": {
       "uid": 1000,
       "gid": 1000
+    },
+    "gear-builder": {
+      "category": "converter",
+      "image": "scitran/dcm2niix:0.7.7_1.0.20181114"
     }
   },
   "config": {

run_dcm2niix

@@ -101,6 +101,12 @@ if [[ "$input_file" == *.zip ]] ; then
   # If there is no unzipped sub-directory, check for PAR/REC files at the top-level
   if [[ -z "$dicom_input" ]]; then
       dicom_input=$(find $INPUT_DIR/* -not -path '*/\.*' -type f -name "*.par" -o -name "*.PAR" | head -1)
+      if [[ -n "$dicom_input" ]]; then
+        # Rename par/rec pair using generic names
+        dicom_input=$INPUT_DIR/inputfile.par
+        find $INPUT_DIR/* -not -path '*/\.*' -type f -name "*.par" -o -name "*.PAR" -exec mv {} $dicom_input \;
+        find $INPUT_DIR/* -not -path '*/\.*' -type f -name "*.rec" -o -name "*.REC" -exec mv {} $INPUT_DIR/inputfile.rec \;
+      fi
   fi
 
   # Zip bomb: DICOMS are at the top level -- set dicom_input to INPUT_DIR
@@ -119,6 +125,8 @@ else
   dicom_input=$INPUT_DIR
 fi
 
+echo -e "$CONTAINER $dicom_input"
+
 ##############################################################################
 # Decompression of DICOM files.
 
@@ -211,7 +219,9 @@ else
 fi
 dcm2niix_exit_code=$?
 
-mv $DCM_OUTPUT_DIR/* $OUTPUT_DIR/
+if [[ $dcm2niix_exit_code == 0 ]] || [[ $ignore_errors == "true" ]]; then
+  mv $DCM_OUTPUT_DIR/* $OUTPUT_DIR/
+fi
 
 
 ##############################################################################