dealt with parameters issues (pixel-micron + arguments in fct) + some refactoring

brick/component/extension.py

@@ -46,10 +46,6 @@ import skimage.morphology as mp_
 from scipy import ndimage as im_
 
 
-ext_min_area_c = 100
-ext_selem_micron_c = 0.24050024
-
-
 class extension_t(glial_cmp_t):
     #
     # soma_uid: connected to a soma somewhere upstream
@@ -86,7 +82,7 @@ class extension_t(glial_cmp_t):
     @property
     def end_points_as_array(self) -> array_t:
         #
-        pty_name = extension_t.end_points_as_array.__name__
+        pty_name = 'end_points_as_array'
         if pty_name not in self.__cache__:
             self.__cache__[pty_name] = np_.array(self.end_points)
 
@@ -176,17 +172,15 @@ class extension_t(glial_cmp_t):
         return enhanced_img, scale_map
 
     @staticmethod
-    def CoarseMap(image: array_t, low: float, high: float, voxel_micron: array_t, ext_selem_micron=ext_selem_micron_c) -> array_t:
+    def CoarseMap(image: array_t, low: float, high: float, selem: array_t) -> array_t:
         #
         result = __HysterisisImage__(image, low, high)
-
-        selem = mp_.disk(in_.ToPixel(ext_selem_micron, voxel_micron))
         result = __MorphologicalCleaning__(result, selem)
 
         return result
 
     @staticmethod
-    def FilteredCoarseMap(map_: array_t) -> array_t:
+    def FilteredCoarseMap(map_: array_t, ext_min_area_c: int) -> array_t:
         #
         result = map_.copy()
         lmp = ms_.label(map_)

brick/processing/input.py

@@ -107,7 +107,7 @@ def FindVoxelDimensionInMicron(data_path: str) -> array_t:
         return np_.array(size_voxel_in_micron)
 
     else:
-        print('The size of a voxel is not specified in the parameters.')
+        print('/!\ The size of a voxel is not specified in the parameters.')
 
         try:
             with Image.open(data_path) as img:  # Find the voxels dimensions in micron in the metadata.
@@ -124,12 +124,12 @@ def FindVoxelDimensionInMicron(data_path: str) -> array_t:
                 voxel_size.append(re.findall(pattern, metadata)[0])
 
             voxel_size = np_.array(list(map(float, voxel_size)))
-            voxel_size_micron = 1.0e6 * voxel_size
-            print('Voxel dimension in the image is [X Y Z] =', voxel_size_micron, 'in micron.')
+            voxel_size_micron = 1.0e6 * voxel_size  # Conversion meters in micron
+            print('VOXEL DIM: [X Y Z] =', voxel_size_micron, 'micron.')
             return voxel_size_micron
 
         except:
-            print('Unable to find the voxel dimensions in micron in the metadata. Please specify it in the parameters.')
+            print('/!\ Unable to find the voxel dimensions in micron in the metadata. Please specify it in the parameters.')
 
 
 def ToPixel(micron: float, voxel_size_micron: array_t) -> int:

nutrimorph.py

@@ -89,7 +89,7 @@ start_time = tm_.time()
 
 
 # --- Images
-voxel_micron = in_.FindVoxelDimensionInMicron(data_path)
+size_voxel_in_micron = in_.FindVoxelDimensionInMicron(data_path)
 
 
 image = io_.imread(data_path)
@@ -128,7 +128,8 @@ axes = {}
 # --- Somas
 print("\n--- Soma Detection")
 
-soma_selem_c = mp_.disk(in_.ToPixel(soma_selem_micron_c, voxel_micron))
+soma_min_area_c = in_.ToPixel(soma_min_area_c, size_voxel_in_micron)
+soma_selem_c = mp_.disk(in_.ToPixel(soma_selem_micron_c, size_voxel_in_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"], soma_min_area_c)
@@ -153,9 +154,13 @@ if with_plot:
 # -- Extentions
 print("\n--- Extension Detection")
 
+ext_min_area_c = in_.ToPixel(ext_min_area_c, size_voxel_in_micron)
+ext_selem_pixel_c = mp_.disk(in_.ToPixel(ext_selem_micron_c, size_voxel_in_micron))
+
+
 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, voxel_micron)
-ext_nfo["coarse_map"], ext_lmp = extension_t.FilteredCoarseMap(ext_nfo["coarse_map"])
+ext_nfo["coarse_map"] = extension_t.CoarseMap(enhanced_ext, ext_low_c, ext_high_c, ext_selem_pixel_c)
+ext_nfo["coarse_map"], ext_lmp = extension_t.FilteredCoarseMap(ext_nfo["coarse_map"], ext_min_area_c)
 ext_nfo["map"] = extension_t.FineMapFromCoarseMap(ext_nfo["coarse_map"])
 ext_nfo["map"][som_nfo["map"] > 0] = 0
 # ext_nfo["lmp"], n_extensions = ms_.label(ext_nfo["map"], return_num=True)

parameters.ini

@@ -30,6 +30,7 @@
 # knowledge of the CeCILL license and that you accept its terms.
 
 
+# TODO: Use the .ini file instead of the .py file
 [Input]
 data_path:                  "./data/DIO_6H_6_1.70bis_2.2_3.tif"
 channel:                    'G'
@@ -39,19 +40,20 @@ size_voxel_in_micron:       None
 [Somas]
 soma_low_c:                 0.15
 soma_high_c:                0.7126
-soma_selem_micron_c:        0.48100048
+soma_selem_micron_c:        0.24050024 * 2
 # soma_selem_c = mp_.disk(2)
-soma_min_area_c:            1000
+soma_min_area_c:            0.24050024 * 1000
+;soma_min_area_c:            1000
 
 [Extensions]
 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
-ext_selem_micron_c:         0.24050024
-# ext_selem_c = mp_.disk(1) /!\ Not directly used in brick/component #TODO direct use of param ?
-ext_min_area_c:             100
-# /!\ Not directly used in brick/component  #TODO direct use of param ?
+ext_selem_micron_c:         0.24050024 * 1
+# ext_selem_c = mp_.disk(1)
+ext_min_area_c:             0.24050024 * 100
+;ext_min_area_c:             100  # pixels
 
 [Connexions]
 max_straight_sq_dist_c:     30 ** 2

parameters.py

@@ -33,7 +33,7 @@
 data_path = "./data/DIO_6H_6_1.70bis_2.2_3.tif"
 channel = 'G'
 size_voxel_in_micron = None  # -> list [X,Y,Z]
-with_plot = True
+with_plot = False
 
 soma_low_c = 0.15
 soma_high_c = 0.7126
@@ -41,14 +41,16 @@ 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_micron_c = 0.48100048
+soma_selem_micron_c = 0.24050024 * 2
 # ext_selem_c = mp_.disk(1)
-ext_selem_micron_c = 0.24050024  # /!\ Not directly used in brick/component #TODO direct use of param ?
+ext_selem_micron_c = 0.24050024 * 1
 
 max_straight_sq_dist_c = 30 ** 2
 max_weighted_length_c = 20.0
 
-soma_min_area_c = 1000
-ext_min_area_c = 100  # /!\ Not directly used in brick/component  #TODO direct use of param ?
+soma_min_area_c = 1000 * 0.24050024
+ext_min_area_c = 100 * 0.24050024
+# soma_min_area_c = 1000
+# ext_min_area_c = 100
 
 in_parallel = False