Merge pull request #44 from Leo-Berman/main

Updating to main

nedc_mladp/data/Example_Parameters.txt

@@ -27,3 +27,14 @@ eval_model{
     write_region_decisions=<1 if you want region decisions to be written, 0 otherwise>
     output_region_decisions_directory=<EXISTING DIRECTORY of where you want your region decisions to be written>
 }
+
+gen_graphics{
+    framesize=6000
+    imagefile="/data/isip/data/tuh_dpath_breast/deidentified/v3.0.0/svs/eval/00000739_aaaaaadc/s000_2017/breast/00000739_aaaaaadc_s000_0hne_0000_a001_lvl001_t000.svs"
+    labelfile="/data/isip/data/tuh_dpath_breast/deidentified/v3.0.0/svs/eval/00000739_aaaaaadc/s000_2017/breast/00000739_aaaaaadc_s000_0hne_0000_a001_lvl001_t000.xml"
+    output_file="test.png"
+    showframes=0
+    compression=40
+    decisions=0
+    decisions_path=""
+}

nedc_mladp/src/functs/nedc_mladp_ann_tools/nedc_mladp_ann_tools.py

@@ -65,7 +65,7 @@ def labeledFrames(labels:list,height:int,width:int,windowsize:int,framesize:int,
         # create list of tuples of coordinates compensating for column row format vs traditional
         # x,y format
         #
-        ret_coords.append((int(labeled_list[x][0][0]),int(height - labeled_list[x][0][1]+framesize)))
+        ret_coords.append((int(labeled_list[x][0][0]),int(labeled_list[x][0][1])))
 
     # return the top left coordinates of each frame and their corresponding labels
     #

nedc_mladp/src/functs/nedc_mladp_fileio_tools/nedc_mladp_fileio_tools.py

@@ -51,6 +51,7 @@ def read_feature_files(feature_file_list:list,get_header=False):
                 else:
                     row_list = list(row)
                     labels.append(row_list.pop(0)) # label
+
                     xcoords.append(row_list.pop(0)) # x coord
                     ycoords.append(row_list.pop(0)) # y coord
                     framesizes.append(row_list.pop(0)) # framesize
@@ -158,7 +159,11 @@ def parseAnnotations(file):
 
             # convert from row,column,depth into traditional (x,y) coordinates
             #
-            coords[i][j][0] = int(header['height'])-coords[i][j][0]
+            tmp1 = coords[i][j][0]
+
+            coords[i][j][0] = int(header['height']) - coords[i][j][1]
+            coords[i][j][1] = tmp1
+
             coords[i][j].pop()
             coords[i][j].reverse()
 

nedc_mladp/src/util/nedc_mladp_gen_graphics/nedc_mladp_gen_graphics.py

@@ -10,6 +10,8 @@
 #------------------------------------------------------------------------------
 from PIL import Image
 import os
+import matplotlib
+matplotlib.use('Agg')
 import matplotlib.pyplot as plt
 from matplotlib.patches import Rectangle
 
@@ -74,7 +76,7 @@ def main():
     #
     args_usage = "nedc_mladp_gen_graphics.usage"
     args_help = "nedc_mladp_gen_graphics.help"
-    parameter_file = fileio_tools.parameters_only_args(args_usage,args_help)
+    parameter_file = fileio_tools.parseArguments(args_usage,args_help)
 
     # parse parameters
     #
@@ -90,7 +92,7 @@ def main():
 
     # parse annotations
     #
-    header, ids, labels, coordinates = fileio_tools.parse_annotations(label_file)
+    header, ids, labels, coordinates = fileio_tools.parseAnnotations(label_file)
 
     # get height and width of image (in pixels) from the header
     #
@@ -99,7 +101,7 @@ def main():
 
     # get labeled regions
     #
-    labeled_regions = ann_tools.labeled_regions(coordinates)
+    labeled_regions = ann_tools.labeledRegions(coordinates)
 
 
     '''plt.figure().clear()
@@ -115,7 +117,6 @@ def main():
 
         plt.plot(x,y,color = labelsdict[labels[i]])
         plt.text(coordinates[i][0][0],coordinates[i][0][1],labels[i])
-
     # generate the background image and return the background image's filepath
     #
     image_loc = svs_to_jpg(image_file,output_file,compression)