Update BoneJ_Module_Example_Batch.py

Added arguments for fiji path and roi file path

Examples/BoneJ_Module_Example_Batch.py

@@ -10,24 +10,44 @@
 import sys, os
 from glob import glob
 import csv 
-# sys.path.append('/gpfs_projects/sriharsha.marupudi/BoneJ_Headless-main/BoneJ_Scripts/')
+from argparse import ArgumentParser
+
 from BoneJ_Module import Thickness
 from BoneJ_Module import Spacing
 from BoneJ_Module import Area_VolumeFraction
 from BoneJ_Module import Connectivity
 from BoneJ_Module import Anisotropy
 from BoneJ_Module import Ellipsoid_Factor
 
-filepath = "/BoneJ_Headless-main/ROIs/"
 voxel_size = [25,25,25] #microns 
-fiji_path = "~/Fiji.app/ImageJ-linux64"
 outdir = "/BoneJ_Headless-main/ROIs/"
 csv_path = outdir + "output_metrics.csv"
 
 with open(csv_path, 'w', newline='') as csv_file:
     csvwriter = csv.writer(csv_file)
     csvwriter.writerow(["ROI Name", "Tb.Th Mean (µm)", "Tb.Sp Mean (µm)", "DA", "BV/TV", "Conn.D (µm⁻³)", "Median EF"])
 if __name__ == "__main__":
+
+    parser = ArgumentParser()
+    parser.add_argument("-i", "--input", "--ROI", dest="ROI", default=os.path.join(os.path.dirname(os.path.dirname(__file__)), "ROIs/emu.nrrd"))
+    parser.add_argument("-f", "--fiji", "--fiji-path", dest="fiji_path", default="~/Fiji.app/ImageJ-linux64")
+    args = parser.parse_args()
+
+    fiji_path = args.fiji_path
+    filepath = args.ROI
+
+
+    # Check that those filepaths actually exist
+    if os.path.exists(fiji_path):
+      print(f"Fiji installation specified: {fiji_path}")
+    else:
+      print(f"Unrecognized file path: {fiji_path}")
+
+    if os.path.exists(filepath):
+      print(f"Loading ROI from {filepath}")
+    else:
+      raise Exception(f"Unrecognized file path: {filepath}")
+
     Dir = glob(filepath+"*.nrrd")
     for file in Dir: