From 56c71b3691b0e18c79a2a98a18a84c738aceaec0 Mon Sep 17 00:00:00 2001
From: monadal <morgane.nadal@inria.fr>
Date: Fri, 13 Mar 2020 13:07:26 +0100
Subject: [PATCH] refactoring
---
brick/component/extension.py | 6 +++---
brick/processing/input.py | 24 ++++++++++++------------
nutrimorph.py | 6 +++---
parameters.py | 4 ++--
4 files changed, 20 insertions(+), 20 deletions(-)
diff --git a/brick/component/extension.py b/brick/component/extension.py
index ef55dd1..9e67648 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 baaec85..b532ce8 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 d660646..88e8471 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 5b514be..f6d7ea2 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
--
GitLab