From d84ad67e31ab7648fb54701104ae3dbae4662b6d Mon Sep 17 00:00:00 2001
From: monadal <morgane.nadal@inria.fr>
Date: Tue, 17 Mar 2020 09:38:13 +0100
Subject: [PATCH] dealt with parameters issues (pixel-micron + arguments in
fct) + some refactoring
---
brick/component/extension.py | 12 +++---------
brick/processing/input.py | 8 ++++----
nutrimorph.py | 13 +++++++++----
parameters.ini | 14 ++++++++------
parameters.py | 12 +++++++-----
5 files changed, 31 insertions(+), 28 deletions(-)
diff --git a/brick/component/extension.py b/brick/component/extension.py
index 9e67648..e7a61ed 100644
--- a/brick/component/extension.py
+++ b/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_)
diff --git a/brick/processing/input.py b/brick/processing/input.py
index f3bcee7..efdffb4 100644
--- a/brick/processing/input.py
+++ b/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:
diff --git a/nutrimorph.py b/nutrimorph.py
index 88e8471..9081477 100644
--- a/nutrimorph.py
+++ b/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)
diff --git a/parameters.ini b/parameters.ini
index abd635a..14da703 100644
--- a/parameters.ini
+++ b/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
diff --git a/parameters.py b/parameters.py
index f6d7ea2..a39bf75 100644
--- a/parameters.py
+++ b/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
--
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