refactoring

brick/component/extension.py

@@ -47,7 +47,7 @@ from scipy import ndimage as im_
 
 
 ext_min_area_c = 100
-ext_selem_microns_c = 0.24050024
+ext_selem_micron_c = 0.24050024
 
 
 class extension_t(glial_cmp_t):
@@ -176,11 +176,11 @@ 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_microns=ext_selem_microns_c) -> array_t:
+    def CoarseMap(image: array_t, low: float, high: float, voxel_micron: array_t, ext_selem_micron=ext_selem_micron_c) -> array_t:
         #
         result = __HysterisisImage__(image, low, high)
 
-        selem = mp_.disk(in_.ToPixels(ext_selem_microns, voxel_micron))
+        selem = mp_.disk(in_.ToPixel(ext_selem_micron, voxel_micron))
         result = __MorphologicalCleaning__(result, selem)
 
         return result

brick/processing/input.py

@@ -101,7 +101,7 @@ def IntensityNormalizedImage(image: array_t) -> array_t:
     # return result
 
 
-def FindVoxelDimensionInMicrons(data_path: str) -> array_t:
+def FindVoxelDimensionInMicron(data_path: str) -> array_t:
     #
     if size_voxel_in_micron is not None:
         return np_.array(size_voxel_in_micron)
@@ -124,25 +124,25 @@ def FindVoxelDimensionInMicrons(data_path: str) -> array_t:
                 voxel_size.append(re.findall(pattern, metadata)[0])
 
             voxel_size = np_.array(list(map(float, voxel_size)))
-            voxel_size_microns = 1.0e6 * voxel_size
-            print('Voxel dimension in the image is [X Y Z] =', voxel_size_microns, 'in microns.')
-            return voxel_size_microns
+            voxel_size_micron = 1.0e6 * voxel_size
+            print('Voxel dimension in the image is [X Y Z] =', voxel_size_micron, 'in micron.')
+            return voxel_size_micron
 
         except:
             print('Unable to find the voxel dimensions in micron in the metadata. Please specify it in the parameters.')
 
 
-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 ToPixel(micron: float, voxel_size_micron: array_t) -> int:
+    # Conversion of pixels into micron. Used in morphomath (disk structuring element mp_.disk(n_pixel)).
+    # Assumes that the axes X and Y have the same ratio pixel:micron.
+    return round(micron/voxel_size_micron[0])
 
 
-def ToMicrons(pixel: int, voxel_size_microns: array_t) -> float:
+def ToMicron(pixel: int, voxel_size_micron: 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])
+    # Conversion of micron into pixels.
+    # Assumes that the axes X and Y have the same ratio pixel:micron.
+    return float(pixel * voxel_size_micron[0])
 
 
 def DijkstraCosts(image: array_t, som_map: array_t, ext_map: array_t) -> array_t:

nutrimorph.py

@@ -71,7 +71,7 @@ soma_low_c = None
 soma_high_c = None
 ext_low_c = None
 ext_high_c = None
-soma_selem_microns_c = None
+soma_selem_micron_c = None
 max_straight_sq_dist_c = None
 max_weighted_length_c = None
 soma_min_area_c = None
@@ -89,7 +89,7 @@ start_time = tm_.time()
 
 
 # --- Images
-voxel_micron = in_.FindVoxelDimensionInMicrons(data_path)
+voxel_micron = in_.FindVoxelDimensionInMicron(data_path)
 
 
 image = io_.imread(data_path)
@@ -128,7 +128,7 @@ axes = {}
 # --- Somas
 print("\n--- Soma Detection")
 
-soma_selem_c = mp_.disk(in_.ToPixels(soma_selem_microns_c, voxel_micron))
+soma_selem_c = mp_.disk(in_.ToPixel(soma_selem_micron_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"], soma_min_area_c)

parameters.py

@@ -41,9 +41,9 @@ 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_microns_c = 0.48100048
+soma_selem_micron_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 ?
+ext_selem_micron_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