Merge pull request freesurfer#1317 from jnolan14/dev

Fixed bug calling the dissection_photo_gui tool on MacOS

Author: jnolan14

dissection_photo/dissection_photo/CMakeLists.txt

@@ -22,11 +22,10 @@ if(BUILD_GUIS)
 
   if(APPLE)
     mac_deploy_qt(TARGET dissection_photo BUNDLE bin/dissection_photo PLIST Info.plist)
-    install(PROGRAMS mac_wrapper DESTINATION bin RENAME dissection_photo)
+    install(PROGRAMS mac_wrapper DESTINATION bin RENAME dissection_photo_gui.sh)
   else()
     install(TARGETS dissection_photo DESTINATION bin)
+    install_configured(dissection_photo_gui.sh DESTINATION bin)
   endif()
 
-  install_configured(dissection_photo_gui.sh DESTINATION bin)
-
 endif()

dissection_photo/dissection_photo/mac_wrapper

@@ -1,3 +1,48 @@
 #!/usr/bin/env bash
-$FREESURFER_HOME/bin/dissection_photo.app/Contents/MacOS/dissection_photo "$@"
+
+# check for required env vars
+if [ ! -e "$FREESURFER_HOME" ]; then
+    echo "error: FREESURFER_HOME has not been properly set"
+    exit 1
+fi
+
+if [ ! -e "$NNUNET_MODEL_DIR" ]; then
+    echo "WARNING: NNUNET_MODEL_DIR is not set"
+    echo "This should be the path to the directory containing the model"
+    echo "dependency 'nnUNetTrainer__nnUNetPlans__2d'"
+    echo "Setting NNUNET_MODEL_DIR to be: $FREESURFER_HOME_FSPYTHON/models/nnUNetTrainer__nnUNetPlans__2d"
+    export NNUNET_MODEL_DIR=$FREESURFER_HOME_FSPYTHON/models/nnUNetTrainer__nnUNetPlans__2d
+fi
+
+if [ ! -e "$NNUNET_SCRIPT_DIR" ]; then
+    echo "WARNING: NNUNET_SCRIPT_DIR is not set"
+    echo "Setting NNUNET_SCRIPT_DIR to be: $FREESURFER_HOME_FSPYTHON/python/packages/nnUNet_v2"
+    export NNUNET_SCRIPT_DIR=$FREESURFER_HOME_FSPYTHON/python/packages/nnUNet_v2
+fi
+
+# sanity check that the model files exist
+ls "$NNUNET_MODEL_DIR/plans.json"
+if [ $? -ne 0 ]; then
+    echo "Unable to detect the required files in NNUNET_MODEL_DIR: $NNUNET_MODEL_DIR"
+    echo "If this is your first time using this util, follow the instructions"
+    echo "below to download, unpack, install, and configure the model files."
+    echo ""
+    echo "  1. Download the model file from the FTP server. Copying the following link"
+    echo "     into your browser will begin the download: https://ftp.nmr.mgh.harvard.edu/pub/dist/lcnpublic/dist/dissection_photo_model/nnUNetTrainer__nnUNetPlans__2d.tar.gz"
+    echo ""
+    echo "  2. Move the tarball to the FreeSurfer modles/ dir and cd into it:"
+    echo "     mv nnUNetTrainer__nnUNetPlans__2d.tar.gz \$FREESURFER_HOME/models"
+    echo "     cd \$FREESURFER_HOME/models"
+    echo ""
+    echo "  3. Unpack the tarball:"
+    echo "     tar -xzf nnUNetTrainer__nnUNetPlans__2d.tar.gz"
+    echo ""
+    echo "  4. Configure the nnUNet environment variables:"
+    echo "     export NNUNET_MODEL_DIR=\$FREESURFER_HOME/models/nnUNetTrainer__nnUNetPlans__2d"
+    echo "     export NNUNET_SCRIPTS_DIR=\$FREESURFER_HOME/python/packages/nnUNet_v2"
+    echo ""
+    exit 1
+fi
+
+$FREESURFER_HOME/bin/dissection_photo/Contents/MacOS/dissection_photo "$@"
 exit $?