solved hysteresis bug - still in dvpt

brick/component/extension.py

@@ -241,6 +241,7 @@ def __HysterisisImage__(image: array_t, low: float, high: float) -> array_t:
 
     low = low * nonzero_values.min()
     high = high * image.max()
+    print("low=", low, "   high=", high)
     # lowt = low*(x_image_f-min_image_f)+max_image_f
     # hight = high*(max_image_f- min_image_f)+min_image_f
     # lowt = (image_f >lowt).astype(int)

nutrimorph.py

@@ -60,6 +60,7 @@ import skimage.io as io_
 # from skimage.segmentation import relabel_sequential
 import skimage.morphology as mp_
 import skimage.measure as ms_
+import skimage.exposure as ex_
 # import skimage.graph as gr_
 # import networkx as nx_
 # import math as mt_
@@ -132,12 +133,8 @@ image = in_.ImageVerification(image, channel)
 # iv_.image_verification(image, channel)  # -> PySide2 user interface  # TODO: must return the modified image!
 # /!\ conflicts between some versions of PySide2 and Python3
 
-image = image[:, 512:, 512:]  # 512 # 562 # Just for development
+# image = image[:, 512:, 512:]  # 512 # 562 # Just for development
 img_shape = image.shape
-# for i in range(min(img_shape)):
-#     pl_.imshow(image[i,:,:])
-#     pl_.savefig(f"D:\\MorganeNadal\\M2 report\\for the slides\\img_ini_slide{i}.png")
-#     pl_.close()
 
 #
 print(f"IMAGE: s.{img_shape} t.{image.dtype} m.{image.min()} M.{image.max()}")
@@ -194,9 +191,10 @@ if with_plot:
 #
 # -- Extentions
 print("\n--- Extension Detection")
+
+# Set to zeros the pixels belonging to the somas
 del_soma = (som_nfo["lmp"] > 0).nonzero()
 image_for_ext[del_soma] = 0
-po_.MaximumIntensityProjectionZ(image_for_ext)
 
 # Change the extensions parameters from micron to pixel dimensions
 ext_min_area_c = in_.ToPixel(ext_min_area_c, size_voxel_in_micron, dimension=(0, 1))
@@ -214,12 +212,8 @@ for value in scale_range:
 scale_range = tuple(scale_range_pixel)
 #
 scale_step = in_.ToPixel(scale_step, size_voxel_in_micron, decimals=1)
-# alpha = in_.ToPixel(alpha, size_voxel_in_micron, decimals=1)
-# beta = in_.ToPixel(beta, size_voxel_in_micron, decimals=1)
-# frangi_c = in_.ToPixel(frangi_c, size_voxel_in_micron)
 
 # Perform frangi feature enhancement (via python or c - faster - implementation)
-
 enhanced_ext, ext_scales = extension_t.EnhancedForDetection(
     image_for_ext,
     scale_range,
@@ -234,12 +228,20 @@ enhanced_ext, ext_scales = extension_t.EnhancedForDetection(
 elapsed_time = tm_.gmtime(tm_.time() - start_time)
 print(f"Elapsed Time={tm_.strftime('%Hh %Mm %Ss', elapsed_time)}\n")
 
-# enhanced_ext = in_.IntensityNormalizedImage(enhanced_ext)
+# po_.MaximumIntensityProjectionZ(enhanced_ext, cmap="OrRd")
 
 # Creation of the enhanced maps
+enhanced_ext = ex_.adjust_log(enhanced_ext, 1)  # Not necessary but better, log contrast adjustment
+enhanced_ext = ex_.equalize_hist(enhanced_ext)  # necessary, histogram equalisation (global)
+# po_.MaximumIntensityProjectionZ(enhanced_ext, cmap="OrRd")
+enhanced_ext = ex_.rescale_intensity(enhanced_ext, out_range=(0, 255))  # necessary, rescaling by stretching the values btw 0 and 255
+# po_.MaximumIntensityProjectionZ(enhanced_ext, cmap="OrRd")
 ext_nfo["coarse_map"] = extension_t.CoarseMap(enhanced_ext, ext_low_c, ext_high_c, ext_selem_pixel_c) # seuillage
+# po_.MaximumIntensityProjectionZ(ext_nfo["coarse_map"])
 ext_nfo["coarse_map"], ext_lmp = extension_t.FilteredCoarseMap(ext_nfo["coarse_map"], ext_min_area_c)  # min
+# po_.MaximumIntensityProjectionZ(ext_nfo["coarse_map"])
 ext_nfo["map"] = extension_t.FineMapFromCoarseMap(ext_nfo["coarse_map"]) # skeleton
+# po_.MaximumIntensityProjectionZ(ext_nfo["map"])
 ext_nfo["map"][som_nfo["map"] > 0] = 0
 ext_nfo["lmp"], n_extensions = ms_.label(ext_nfo["map"], return_num=True)
 # Use relabel instead of label to optimize the algorithm. BUT PROBLEM WITH THE NUMBER OF EXTENSIONS DETECTED !
@@ -388,7 +390,7 @@ if with_plot:
     pl_.show()
 
 # np_.save("D:\\MorganeNadal\\M2 report\\kmeansCHOvsDIO\\CHO_1H_2.npy", som_nfo['soma_w_ext_lmp'])
-po_.MaximumIntensityProjectionZ(som_nfo['soma_w_ext_lmp'])
+po_.MaximumIntensityProjectionZ(som_nfo['soma_w_ext_lmp'],output_image_file_name=f"D:\\MorganeNadal\\M2 report\\hysteresisCHOvsDIO\\MIP CHODIO\\DIO_3H\\{name_file}(2).png")
 
 # --- Extract all the extensions of all somas as a graph
 print('\n--- Graph extraction')

parameters.ini

@@ -49,8 +49,8 @@ parameter3                  :   None
 ; then your parameter has the value string: 'None', and not None
 
 [Input]
-data_path                  :    ./data/DIO_6H_6_1.70bis_2.2_3.tif
-#D:\\MorganeNadal\\IBA1-Microglies\\DIO_1H_16_1.58_2.1\\DIO_1H_16_1.58_2.1_9.tif
+data_path                  :    D:\\MorganeNadal\\IBA1-Microglies\\DIO_3H_F_1.82_3.1\\DIO_3H_F_1.82_3.1_1.tif
+#D:\\MorganeNadal\\IBA1-Microglies\\DIO_1H_16_1.58_2.1\\DIO_1H_16_1.58_2.1_4.tif
 #./data/DIO_6H_6_1.70bis_2.2_3.tif
 channel                    :    G
 ; Can take the values R, G or B.
@@ -71,7 +71,7 @@ soma_min_area_c            :    (0.24050024 ** 2) * 1000
 
 [Extensions]
 ; for hysteresis
-ext_low_c                  :    0.2
+ext_low_c                  :    10
 #7.5e-8
 #1e-20
 ext_high_c                 :    0.6
@@ -92,13 +92,10 @@ scale_range                :    (0.024,0.745)
 scale_step                 :    0.24
 #  1.0
 alpha                      :    0.8
-##0.19 if converted into pixels
 # 0.8
 beta                       :    0.5
-##0.12 if converted into pixels
 # 0.5
-frangi_c                   :    500
-## 3 if normalized btw 0 and 1 and converted to pixel
+frangi_c                   :    30
 ## 12.5 if normalized btw 0 and 1
 # 60.12506 # 500.0
 bright_on_dark             :    True