Added additional preprocessing to _img_props

slider/chart_reg.py

@@ -25,12 +25,15 @@ from slider import util
 import glymur
 
 from skimage.measure import regionprops, label
-from skimage.color import rgb2gray
-from skimage import filters, transform
+from skimage.color import rgb2gray, rgb2hsv
+from skimage import filters, transform, exposure
 from matplotlib import patches
 import numpy as np
 import matplotlib.pyplot as plt
 
+DO_PLOTS = False
+OUTDIR = None
+
 
 def register_chart_to_slide(chart, slide, slide_res, out, boundary_key=None, config=None):
 
@@ -50,10 +53,7 @@ def register_chart_to_slide(chart, slide, slide_res, out, boundary_key=None, con
     # set global variables required for summary plots
     plots = config["general"]["plots"]
 
-    global DO_PLOTS
     DO_PLOTS = plots
-
-    global OUTDIR
     OUTDIR = out
 
     #  create output dir
@@ -241,11 +241,15 @@ def _refine_edge_coord(img, img_res, edge_coords, normals):
 
 def _img_props(img, img_resolution, verbose=False):
 
-    # convert to grayscale
-    image = rgb2gray(img)
+    # # convert to grayscale
+    # image = rgb2gray(img)
 
-    # find threshold for background
-    threshold_value = filters.threshold_otsu(image)
+    # # find threshold for background
+    # threshold_value = filters.threshold_otsu(image)
+
+    image = rgb2hsv(img)[..., -1]
+    image = exposure.equalize_hist(image)
+    threshold_value = filters.threshold_li(image)
 
     if verbose:
         print(f"threshold={threshold_value}")