Merge pull request #17 from tinalasisi/updates

Reverted to morphological_chan_vese instead of chan_vese & added bina…

Author: tinalasisi

fibermorph/fibermorph.py

@@ -460,13 +460,13 @@ def crop_section(img, im_name, resolution, minpixel, maxpixel, im_center):
 
 def segment_section(crop_im, im_name, resolution, minpixel, maxpixel, im_center):
     try:
+        thresh = skimage.filters.threshold_minimum(crop_im)
+        bin_img = skimage.segmentation.clear_border(crop_im < thresh)
 
-        seg_im_inv = skimage.segmentation.chan_vese(crop_im)
-        # seg_im = skimage.segmentation.morphological_chan_vese(np.asarray(crop_im), 35, init_level_set='checkerboard', smoothing=2)
-        
-        # seg_im_inv = np.asarray(seg_im != 0)
+        # seg_im_inv = skimage.segmentation.chan_vese(crop_im, max_iter=200, init_level_set=bin_img)
+        seg_im = skimage.segmentation.morphological_chan_vese(np.asarray(crop_im), 40, init_level_set=bin_img, smoothing=4)
 
-        # seg_im_inv = invert(seg_im.astype(np.uint8).astype(np.bool))
+        seg_im_inv = np.asarray(seg_im != 0)
 
         crop_label_im, num_elem = skimage.measure.label(seg_im_inv, connectivity=2, return_num=True)
 

fibermorph/test/test_fibermorph.py

@@ -208,8 +208,8 @@ def test_segment_section():
 
 
     #input
-    input_directory = pathlib.Path("/Users/tinalasisi/Desktop/Nov01_2338_ValidationTest_Section/ValidationData")
-    # input_directory = pathlib.Path("/Users/tinalasisi/Desktop/Nov3_TestSectionsImages")
+    # input_directory = pathlib.Path("/Users/tinalasisi/Desktop/Nov01_2338_ValidationTest_Section/ValidationData")
+    input_directory = pathlib.Path("/Users/tinalasisi/Desktop/Nov3_RealSections/Images")
     file_list = fibermorph.list_images(input_directory)
     main_output_path = "/Users/tinalasisi/Desktop"
     output_path = main_output_path