modified selem (in micron) in prms + in other fcts

brick/component/extension.py

@@ -33,6 +33,7 @@ from __future__ import annotations
 
 import brick.processing.frangi3 as fg_
 import brick.processing.map_labeling as ml_
+import brick.processing.input as in_
 from brick.component.glial_cmp import glial_cmp_t
 from brick.general.type import array_t, site_h
 
@@ -45,7 +46,8 @@ import skimage.morphology as mp_
 from scipy import ndimage as im_
 
 
-min_area_c = 100
+ext_min_area_c = 100
+ext_selem_microns_c = 0.24050024
 
 
 class extension_t(glial_cmp_t):
@@ -174,10 +176,12 @@ class extension_t(glial_cmp_t):
         return enhanced_img, scale_map
 
     @staticmethod
-    def CoarseMap(image: array_t, low: float, high: float) -> array_t:
+    def CoarseMap(image: array_t, low: float, high: float, voxel_micron: array_t, ext_selem_microns=ext_selem_microns_c) -> array_t:
         #
         result = __HysterisisImage__(image, low, high)
-        result = __MorphologicalCleaning__(result)
+
+        selem = mp_.disk(in_.ToPixels(ext_selem_microns, voxel_micron))
+        result = __MorphologicalCleaning__(result, selem)
 
         return result
 
@@ -188,7 +192,7 @@ class extension_t(glial_cmp_t):
         lmp = ms_.label(map_)
 
         for region in ms_.regionprops(lmp):
-            if region.area <= min_area_c:
+            if region.area <= ext_min_area_c:
                 region_sites = (lmp == region.label).nonzero()
                 result[region_sites] = 0
                 lmp[region_sites] = 0
@@ -232,11 +236,10 @@ def __HysterisisImage__(image: array_t, low: float, high: float) -> array_t:
     return result
 
 
-def __MorphologicalCleaning__(image: array_t) -> array_t:
+def __MorphologicalCleaning__(image: array_t, selem) -> array_t:
     #
     result = image.copy()
 
-    selem = mp_.disk(1)
     for dep in range(result.shape[0]):
         result[dep, :, :] = mp_.closing(result[dep, :, :], selem)
         result[dep, :, :] = mp_.opening(result[dep, :, :], selem)

brick/general/type.py

@@ -29,12 +29,13 @@
 # The fact that you are presently reading this means that you have had
 # knowledge of the CeCILL license and that you accept its terms.
 
-from typing import Tuple, Union
+from typing import Tuple, Union, Type
 
 import numpy as np_
+# from Cython.Includes.numpy import ndarray
+from numpy.core._multiarray_umath import ndarray
 
-
-array_t = np_.ndarray
+array_t: Type[Union[ndarray, ndarray]] = np_.ndarray
 
 tintegers_h = Tuple[int, ...]
 

brick/processing/input.py

@@ -123,6 +123,19 @@ def VoxelDimensionInMicrons(data_path: str) -> array_t:
     return voxel_size_microns
 
 
+def ToPixels(micron: float, voxel_size_microns: array_t) -> int:
+    # Conversion of pixels into microns. Used in morphomath (disk structuring element mp_.disk(n_pixel)).
+    # Assumes that the axes X and Y have the same ratio pixel:microns.
+    return round(micron/voxel_size_microns[0])
+
+
+def ToMicrons(pixel: int, voxel_size_microns: array_t) -> float:
+    # May not be used. if not used, delete.
+    # Conversion of microns into pixels.
+    # Assumes that the axes X and Y have the same ratio pixel:microns.
+    return float(pixel * voxel_size_microns[0])
+
+
 def DijkstraCosts(image: array_t, som_map: array_t, ext_map: array_t) -> array_t:
     #
     # TODO: Ideally, the extension part should be dilated

nutrimorph.py

@@ -52,9 +52,8 @@ import time as tm_
 import matplotlib.pyplot as pl_
 import numpy as np_
 import skimage.io as io_
-import skimage.measure as ms_
 from skimage.segmentation import relabel_sequential
-import exifread as xf_
+import skimage.morphology as mp_
 
 print(sy_.argv, sy_.argv.__len__())
 
@@ -72,10 +71,10 @@ soma_low_c = None
 soma_high_c = None
 ext_low_c = None
 ext_high_c = None
-soma_selem_c = None
+soma_selem_microns_c = None
 max_straight_sq_dist_c = None
 max_weighted_length_c = None
-min_area_c = None
+soma_min_area_c = None
 in_parallel = None
 
 exec(open(sy_.argv[1]).read())
@@ -110,6 +109,7 @@ img_shape = image.shape
 #
 print(f"IMAGE: s.{img_shape} t.{image.dtype} m.{image.min()} M.{image.max()}")
 
+# Intensity relative normalization (between 0 and 1).
 image_for_soma = in_.IntensityNormalizedImage(image)
 image_for_ext = in_.IntensityNormalizedImage(image)
 print(f"NRM-IMG: t.{image_for_soma.dtype} m.{image_for_soma.min():.2f} M.{image_for_soma.max():.2f}")
@@ -128,8 +128,10 @@ axes = {}
 # --- Somas
 print("\n--- Soma Detection")
 
+soma_selem_c = mp_.disk(in_.ToPixels(soma_selem_microns_c, voxel_micron))
+
 som_nfo["map"] = soma_t.Map(image_for_soma, soma_low_c, soma_high_c, soma_selem_c)
-som_nfo["map"], som_lmp = soma_t.FilteredMap(som_nfo["map"], min_area_c)
+som_nfo["map"], som_lmp = soma_t.FilteredMap(som_nfo["map"], soma_min_area_c)
 # som_nfo["lmp"], n_somas= ms_.label(som_nfo["map"], return_num=True)
 som_nfo["lmp"] = relabel_sequential(som_lmp)[0]  # Use relabel instead of label to optimize the algorithm.
 n_somas = som_nfo["lmp"].max()
@@ -152,7 +154,7 @@ if with_plot:
 print("\n--- Extension Detection")
 
 enhanced_ext, ext_scales = extension_t.EnhancedForDetection(image_for_ext, in_parallel=in_parallel)
-ext_nfo["coarse_map"] = extension_t.CoarseMap(enhanced_ext, ext_low_c, ext_high_c)
+ext_nfo["coarse_map"] = extension_t.CoarseMap(enhanced_ext, ext_low_c, ext_high_c, voxel_micron)
 ext_nfo["coarse_map"], ext_lmp = extension_t.FilteredCoarseMap(ext_nfo["coarse_map"])
 ext_nfo["map"] = extension_t.FineMapFromCoarseMap(ext_nfo["coarse_map"])
 ext_nfo["map"][som_nfo["map"] > 0] = 0

parameters.py

@@ -29,8 +29,6 @@
 # The fact that you are presently reading this means that you have had
 # knowledge of the CeCILL license and that you accept its terms.
 
-import skimage.morphology as mp_
-
 
 data_path = "./data/DIO_6H_6_1.70bis_2.2_3.tif"
 channel = 'G'
@@ -41,11 +39,15 @@ soma_high_c = 0.7126
 ext_low_c = 0.2  # 0.02  # 0.2  # ext_low_c = 9.0e-4
 ext_high_c = 0.6  # 0.04  # 0.6  # high_ext = 8.0e-3
 
-soma_selem_c = mp_.disk(2)
+# soma_selem_c = mp_.disk(2)
+soma_selem_microns_c = 0.48100048
+# ext_selem_c = mp_.disk(1)
+ext_selem_microns_c = 0.24050024  # /!\ Not directly used in brick/component #TODO direct use of param ?
 
 max_straight_sq_dist_c = 30 ** 2
 max_weighted_length_c = 20.0
 
-min_area_c = 1000
+soma_min_area_c = 1000
+ext_min_area_c = 100  # /!\ Not directly used in brick/component  #TODO direct use of param ?
 
 in_parallel = False