Merge pull request #84 from AICONSlab/jo-STA_workflow_fix

Release v2.2.2

.circleci/config.yml

@@ -62,7 +62,7 @@ jobs:
             # Change permissions for code directory for any Singularity user
             sed -i '/#STOPUNCOMMENT#/a # Change permissions for code dir\nchmod -R 777 /code' miracl.def && \
             # Log in to cloud.sylabs.io
-            echo $SYLABS_TOKEN_OCT_26 > tokenfile && \
+            echo $SYLABS_TOKEN_JAN_25_2023 > tokenfile && \
             singularity remote login -u aiconslab --tokenfile tokenfile && \
             # Setting trap in case image cannot be deleted
             set -e

build.sh

@@ -2,7 +2,7 @@
 
 # Build MIRACL Docker image with user information from host system
 #
-# - Checks if Docker and Docker-Compose are installed
+# - Checks if Docker and Docker Compose are installed
 # - Dynamically adds and removes user information to
 #   prevent errors in Singularity container creation
 # - Container user is the same as host user to prevent
@@ -46,7 +46,7 @@ do
   if [ "$*" = "-h" ] || [ "$*" = "--help" ];
   then
     usage
-    exit
+    exit 0
   elif [ "$*" = "-l" ] || [ "$*" = "--log" ];
   then
     write_log=true
@@ -113,16 +113,18 @@ if [ -x "$(command -v docker)" ]; then
       # Check if build process exited without errors
       build_status_code=$?
       if [ $build_status_code -eq 0 ]; then
-        printf "\nBuild was successful! Checking docker-compose installation.\n"
+        printf "\nBuild was successful! Checking Docker Compose installation.\n"
         # Remove $USER_TEXT from Dockerfile
         rm_USER_TEXT
 
         # Test if docker-compose is installed
         # Should come by default with Docker-Desktop
         if [ -x "$(command -v docker-compose)" ]; then
-          printf "Docker-Compose installation found. Run 'docker-compose up -d' to start the MIRACL container in background.\n"
+          printf "Docker Compose installation found <<$(docker-compose --version)>>). Run 'docker-compose up -d' to start the MIRACL container in background.\n"
+        elif dcex=$(docker compose --version); then
+          printf "Docker Compose installation found (<<%s>>). Run 'docker compose up -d' or use Docker Desktop (if installed) to start the MIRACL container in background.\n" "$dcex"
         else
-          printf "Docker-Compose installation not found. Please install docker-compose to run the MIRACL container.\n"
+          printf "Docker Compose installation not found. Please install Docker Compose plugin or standalone version to run the MIRACL container. Instructions on how to install Docker Compose can be found here: https://docs.docker.com/compose/install/\n"
         fi
       else
         # Return error code if build was not successful
@@ -135,4 +137,5 @@ else
     di_status_code=$?
     printf "\nDocker installation not found. Please install Docker first.\n"
     printf "Exiting with status code $di_status_code\n"
+    exit di_status_code
 fi

miracl/flow/cli_flow.py

@@ -59,10 +59,14 @@ def run_sta(parser, args):
             subprocess.Popen('%s/flow/miracl_workflow_sta.sh -h' % miracl_home,
                              shell=True)
         else:
-            bash_args = '-f %s -o %s -l %s -r %s -m %s -g %s -k %s -a %s' % (
+            bash_args = '-f %s -o %s -l %s -r %s -m %s -g %s -k %s -a %s -d %s -c %s --out_dir %s -b %s -u %s -s %s -n %s -p %s -x %s -z %s --downz %s --dilationfx %s --dilationfy %s --dilationfz %s --rk %s' % (
                 args['folder'], args['out_nii'], args['seed_label'],
                 args['clar_reg'], args['hemi'], args['dog'],
-                args['sigma'], args['angle'])
+                args['sigma'], args['angle'], args['down'], args['chan'],
+                args['out_dir'], args['brain_mask'], args['lbl_mask'],
+                args['step_length'], args['chan_num'], args['chan_pre'],
+                args['vx'], args['vz'], args['downz'], args['dilationfx'],
+                args['dilationfy'], args['dilationfz'], args['rk'])
 
             subprocess.check_call('%s/flow/miracl_workflow_sta.sh %s' % (miracl_home, bash_args), shell=True,
                                   stderr=subprocess.STDOUT)
@@ -119,6 +123,36 @@ def get_parser():
                             help="Gaussian smoothing sigma")
     parser_sta.add_argument('-a', '--angle', metavar='',
                             help="Tracking angle threshold")
+    parser_sta.add_argument('-d', '--down', metavar='',
+                            help="Downsample ratio")
+    parser_sta.add_argument('-c', '--chan', metavar='',
+                            help="Output channel name")
+    parser_sta.add_argument('--out_dir', metavar='',
+                            help="Output directory")
+    parser_sta.add_argument('-b', '--brain_mask', metavar='',
+                            help="Brain mask")
+    parser_sta.add_argument('-u', '--lbl_mask', metavar='',
+                            help="Seed mask")
+    parser_sta.add_argument('-s', '--step_length', metavar='',
+                            help="Step length")
+    parser_sta.add_argument('-n', '--chan_num', metavar='',
+                            help="Extracting single channel")
+    parser_sta.add_argument('-p', '--chan_pre', metavar='',
+                            help="Channel prefix")
+    parser_sta.add_argument('-x', '--vx', metavar='',
+                            help="Original res in x-z plane")
+    parser_sta.add_argument('-z', '--vz', metavar='',
+                            help="Original thickness")
+    parser_sta.add_argument('--downz', metavar='',
+                            help="Downsample in z")
+    parser_sta.add_argument('--dilationfx', metavar='',
+                            help="Dilation factor x")
+    parser_sta.add_argument('--dilationfy', metavar='',
+                            help="Dilation factor y")
+    parser_sta.add_argument('--dilationfz', metavar='',
+                            help="Dilation factor z")
+    parser_sta.add_argument('--rk', metavar='',
+                            help="rk2")
     parser_sta.add_argument('-h', '--help', action='store_true')
 
     parser_sta.set_defaults(func=run_sta)