diff --git a/brick/component/extension.py b/brick/component/extension.py index ef55dd1b3e533a2cdcd8b11e63276ba64e93b1db..9e67648ef302773ad92673c46b05f8469e21ca61 100644 --- a/brick/component/extension.py +++ b/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 diff --git a/brick/processing/input.py b/brick/processing/input.py index baaec8531ab433b53c4748aef76d21e3a3def6b2..b532ce8c14db8d4e8b4027a9e1fafa53aaa39770 100644 --- a/brick/processing/input.py +++ b/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: diff --git a/nutrimorph.py b/nutrimorph.py index d6606460be952cfe6acf2cf531424bbd7d754286..88e8471d29fc60bcdddceb3c3ae85eaa0b1a519a 100644 --- a/nutrimorph.py +++ b/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) diff --git a/parameters.py b/parameters.py index 5b514be8441d0029b40d05dad29e7669ee63ba3b..f6d7ea2c81da1ece7f116fc908fe598856fa11b5 100644 --- a/parameters.py +++ b/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