fixed reg_svg

Dockerfile

@@ -42,7 +42,7 @@ ENV PATH=${ANTSPATH}:${PATH}
 # Install all needed packages based on pip installation
 COPY requirements.txt ./
 RUN python3 -m pip install --no-cache-dir -r requirements.txt
-COPY . .
+#COPY . .
 
 # Download models, store in directory
 
@@ -85,14 +85,5 @@ RUN set -x \
         libxkbcommon-x11-dev \
         libxinerama-dev 
 
-
-
-# these break the build, not sure why/how to fix
-ARG USER_ID=1000
-ARG GROUP_ID=1000
-ARG USER=jacqueline
-RUN addgroup --gid 1000 jacqueline
-RUN adduser --disabled-password --gecos '' --uid 1000 --gid 1000 jacqueline
-
 # Run icvmapper when the container launches
 ENTRYPOINT /bin/bash

icvmapper/cli.py

@@ -156,7 +156,9 @@ def main(args=None):
             elif hasattr(args, 't1w'):
                 if args.t1w:
                     log_filepath = os.path.join(os.path.dirname(args.t1w), 'logs', '{}.log'.format(log_filename))
-
+						else:
+							print("Error, must provide T1")
+							exit(0)
         else:
             log_filepath = os.path.join(os.getcwd(), '{}.log'.format(log_filename))
 

icvmapper/gui.py

@@ -93,6 +93,12 @@ def capture_help_fn(fn_name):
                 'script': 'seg_qc',
                 'opts': '-t seg_qc -v img seg -f out',
                 'helpmsg': 'Creates tiled mosaic of segmentation overlaid on structural image'
+            },
+            1: {
+            		'name': 'Segmentation Reg SVG',
+                'script': 'reg_svg',
+                'opts': '',
+                'helpmsg': ''
             }
         }
     },

requirements.txt

@@ -27,7 +27,7 @@ gast==0.2.0
 grpcio==1.15.0
 h5py==2.8.0
 html5lib==0.9999999
--e git+https://github.com/AICONSlab/iCVMapp3r.git#egg=iCVMapp3r
+-e git+https://github.com/AICONSlab/iCVMapp3r.git@Jacqueline_edits#egg=iCVMapp3r
 idna==2.8
 importlib-metadata==0.8
 ipykernel==4.8.2
@@ -112,6 +112,7 @@ SimpleITK==1.2.0
 simplejson==3.16.0
 singledispatch==3.4.0.3
 six==1.11.0
+svgwrite==1.3.1
 sympy==1.3
 tables==3.5.2
 tensorboard==1.13.0