corrected error in ToPixel

brick/processing/input.py

@@ -132,17 +132,15 @@ def FindVoxelDimensionInMicron(data_path: str) -> array_t:
             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:
-    # 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 ToPixel(micron: float, voxel_size_micron: array_t, dimension: int = 1, axis: int = 0) -> int:
+    # Conversion of pixels into micron.
+    return round(micron/(voxel_size_micron[axis]**dimension))
 
 
-def ToMicron(pixel: int, voxel_size_micron: array_t) -> float:
+def ToMicron(pixel: int, voxel_size_micron: array_t, dimension: int = 1, axis: int = 0) -> float:
     # May not be used. if not used, delete.
     # 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])
+    return float(pixel * (voxel_size_micron[axis])**dimension)
 
 
 def DijkstraCosts(image: array_t, som_map: array_t, ext_map: array_t) -> array_t:

nutrimorph.py

@@ -90,16 +90,17 @@ start_time = tm_.time()
 
 
 # --- Images
+# Find the dimension of the image voxels in micron
 size_voxel_in_micron = in_.FindVoxelDimensionInMicron(data_path)
 
-
 image = io_.imread(data_path)
 
 # Image size verification - simple version without user interface
 image = in_.ImageVerification(image, channel)
+# iv_.image_verification(image, channel)  # -> PySide2 interface  # TODO: must return the modified image!
 # /!\ conflicts between some versions of PySide2 and Python3
 
-image = image[:, 512:, 512:]  # 562
+image = image[:, 512:, 512:]  # 562 # Just for development
 img_shape = image.shape
 # pl_.matshow(image[image.shape[0] // 2, :, :])
 # pl_.show()
@@ -129,7 +130,7 @@ axes = {}
 # --- Somas
 print("\n--- Soma Detection")
 
-soma_min_area_c = in_.ToPixel(soma_min_area_c, size_voxel_in_micron)
+soma_min_area_c = in_.ToPixel(soma_min_area_c, size_voxel_in_micron, dimension=2)
 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)
@@ -155,7 +156,7 @@ if with_plot:
 # -- Extentions
 print("\n--- Extension Detection")
 
-ext_min_area_c = in_.ToPixel(ext_min_area_c, size_voxel_in_micron)
+ext_min_area_c = in_.ToPixel(ext_min_area_c, size_voxel_in_micron, dimension=2)
 ext_selem_pixel_c = mp_.disk(in_.ToPixel(ext_selem_micron_c, size_voxel_in_micron))
 
 
@@ -286,3 +287,5 @@ print(f"DONE: {tm_.strftime('%a, %b %d %Y @ %H:%M:%S')}")
 
 if with_plot:
     pl_.show()
+
+# graph = skl_graph_t.FromSkeleton(soma_map)  # Travailler apd squelettes (soma pas sous fore de sk)
\ No newline at end of file

parameters.ini

@@ -42,7 +42,7 @@ soma_low_c:                 0.15
 soma_high_c:                0.7126
 soma_selem_micron_c:        0.24050024 * 2
 # soma_selem_c = mp_.disk(2)
-soma_min_area_c:            0.24050024 * 1000
+soma_min_area_c:            (0.24050024 ** 2) * 1000
 ;soma_min_area_c:            1000
 
 [Extensions]
@@ -52,7 +52,7 @@ ext_high_c:                 0.6
 # 0.04  # 0.6  # high_ext = 8.0e-3
 ext_selem_micron_c:         0.24050024 * 1
 # ext_selem_c = mp_.disk(1)
-ext_min_area_c:             0.24050024 * 100
+ext_min_area_c:             (0.24050024 ** 2) * 100
 ;ext_min_area_c:             100  # pixels
 
 [Connexions]

parameters.py

@@ -37,19 +37,19 @@ with_plot = False
 
 soma_low_c = 0.15
 soma_high_c = 0.7126
-ext_low_c = 3 #1e-7 ##0.2  # 0.02  # 0.2  # ext_low_c = 9.0e-4
-ext_high_c = 1e-10 #1.2e-7 ##0.6  # 0.04  # 0.6  # high_ext = 8.0e-3
+ext_low_c = 0.2 #3 #1e-7    ##0.2  # 0.02  # 0.2  # ext_low_c = 9.0e-4
+ext_high_c = 0.6 #1e-10 #1.2e-7    ##0.6  # 0.04  # 0.6  # high_ext = 8.0e-3
 
 # soma_selem_c = mp_.disk(2)
-soma_selem_micron_c = 0.24050024 * 2
 # ext_selem_c = mp_.disk(1)
+soma_selem_micron_c = 0.24050024 * 2
 ext_selem_micron_c = 0.24050024 * 1
 
 max_straight_sq_dist_c = (30 ** 2) * 0.24050024
 max_weighted_length_c = 20.0 * 0.24050024
 
-soma_min_area_c = 1000 * 0.24050024
-ext_min_area_c = 100 * 0.24050024
+soma_min_area_c = 1000 * (0.24050024 ** 2)
+ext_min_area_c = 100 * (0.24050024 ** 2)
 # soma_min_area_c = 1000
 # ext_min_area_c = 100