updated so that input file names can be more generic. kitchell#10

added config.json.sample
updated README slightly

README.md

@@ -1,5 +1,5 @@
 [![Abcdspec-compliant](https://img.shields.io/badge/ABCD_Spec-v1.1-green.svg)](https://github.com/brain-life/abcd-spec)
-[![Run on Brainlife.io](https://img.shields.io/badge/Brainlife-bl.app.1-blue.svg)](https://doi.org/10.25663/bl.app.1)
+[![Run on Brainlife.io](https://img.shields.io/badge/Brainlife-bl.app.108-blue.svg)](https://doi.org/10.25663/bl.app.108)
 
 # app-generatetractsurfaces
 
@@ -48,7 +48,6 @@ Otherwise:
 
 If you don't have your own input file, you can download sample datasets from Brainlife.io, or you can use [Brainlife CLI](https://github.com/brain-life/cli).
 
-
 ## Output
 
 The main output of this App is a folder called 'surfaces'. This folder contains one surface mesh file for each input binary voxel file. 

config.json.sample

@@ -0,0 +1,4 @@
+{
+    "maskdir": "../app-tractseg/tractseg_output/bundle_segmentations",
+    "filetype": "vtk"
+}

main

@@ -1,44 +1,19 @@
 #!/bin/bash
 
-
 #clean up previous job (just in case)
 rm -f finished
 
-
-#if [ $ENV == "IUHPC" ]; then
-#	module unload python
-#	if [ $HPC == "KARST" ]; then
-#		module load anaconda2
-#	fi
-#	if [ $HPC == "CARBONATE" ]; then
-#		module load anaconda/python2.7/4.3.1
-#	fi
-
-#fi
-
-	#module unload python/2.7.3
-
-module load singularity 2> /dev/null
-
-
 # remove surface directory
 rm -rf surfaces
 
 echo "counting files"
-NUMFILES=`numfiles.py`
+NUMFILES=`python numfiles.py`
 echo "there are $NUMFILES files" 
 echo "starting main"
 
-#singularity exec -e docker://lukin0110/docker-vtk-python ./main.py
 singularity exec -e docker://brainlife/pythonvtk ./main.py
 
-#nohup time python main.py > stdout.log 2> stderr.log
-
-#check for output files
-#if [ -s Right_Uncinate_surf.vtk ];
-
 count=$(ls surfaces/* | wc -l)
-
 if [ "$count" == "$NUMFILES" ] 
 then
 	echo 0 > finished

main.py

@@ -21,8 +21,11 @@
 filetype = config["filetype"]
 for file in glob.glob(config["maskdir"] + "/*.nii.gz"):
     print(file)
-    split_name = os.path.basename(file).split('_')
-    split_name[-1] = 'surf.' + filetype
-    surfname = '_'.join(split_name)
+    #split_name = os.path.basename(file).split('_')
+    #split_name[-1] = 'surf.' + filetype
+    #surfname = '_'.join(split_name)
+    #trim .nii.gz
+    split_name = os.path.basename(file).split('.nii.gz')
+    surfname = split_name[0]+"."+filetype
     print(surfname)
     niftiMask2Surface(file, 'surfaces/'+surfname, 10, filetype)

numfiles.py

@@ -4,8 +4,6 @@
 import fnmatch
 import json
 
-
-
 with open('config.json') as config_json:
     config = json.load(config_json)