From c753b56b38f9208513716f69853ab2212d3ca24d Mon Sep 17 00:00:00 2001
From: monadal <morgane.nadal@inria.fr>
Date: Wed, 11 Mar 2020 15:58:42 +0100
Subject: [PATCH] modified selem (in micron) in prms + in other fcts
---
brick/component/extension.py | 15 +++++++++------
brick/general/type.py | 7 ++++---
brick/processing/input.py | 13 +++++++++++++
nutrimorph.py | 14 ++++++++------
parameters.py | 10 ++++++----
5 files changed, 40 insertions(+), 19 deletions(-)
diff --git a/brick/component/extension.py b/brick/component/extension.py
index dc6c556..ef55dd1 100644
--- a/brick/component/extension.py
+++ b/brick/component/extension.py
@@ -33,6 +33,7 @@ from __future__ import annotations
import brick.processing.frangi3 as fg_
import brick.processing.map_labeling as ml_
+import brick.processing.input as in_
from brick.component.glial_cmp import glial_cmp_t
from brick.general.type import array_t, site_h
@@ -45,7 +46,8 @@ import skimage.morphology as mp_
from scipy import ndimage as im_
-min_area_c = 100
+ext_min_area_c = 100
+ext_selem_microns_c = 0.24050024
class extension_t(glial_cmp_t):
@@ -174,10 +176,12 @@ class extension_t(glial_cmp_t):
return enhanced_img, scale_map
@staticmethod
- def CoarseMap(image: array_t, low: float, high: float) -> array_t:
+ def CoarseMap(image: array_t, low: float, high: float, voxel_micron: array_t, ext_selem_microns=ext_selem_microns_c) -> array_t:
#
result = __HysterisisImage__(image, low, high)
- result = __MorphologicalCleaning__(result)
+
+ selem = mp_.disk(in_.ToPixels(ext_selem_microns, voxel_micron))
+ result = __MorphologicalCleaning__(result, selem)
return result
@@ -188,7 +192,7 @@ class extension_t(glial_cmp_t):
lmp = ms_.label(map_)
for region in ms_.regionprops(lmp):
- if region.area <= min_area_c:
+ if region.area <= ext_min_area_c:
region_sites = (lmp == region.label).nonzero()
result[region_sites] = 0
lmp[region_sites] = 0
@@ -232,11 +236,10 @@ def __HysterisisImage__(image: array_t, low: float, high: float) -> array_t:
return result
-def __MorphologicalCleaning__(image: array_t) -> array_t:
+def __MorphologicalCleaning__(image: array_t, selem) -> array_t:
#
result = image.copy()
- selem = mp_.disk(1)
for dep in range(result.shape[0]):
result[dep, :, :] = mp_.closing(result[dep, :, :], selem)
result[dep, :, :] = mp_.opening(result[dep, :, :], selem)
diff --git a/brick/general/type.py b/brick/general/type.py
index a1820df..c9292db 100644
--- a/brick/general/type.py
+++ b/brick/general/type.py
@@ -29,12 +29,13 @@
# The fact that you are presently reading this means that you have had
# knowledge of the CeCILL license and that you accept its terms.
-from typing import Tuple, Union
+from typing import Tuple, Union, Type
import numpy as np_
+# from Cython.Includes.numpy import ndarray
+from numpy.core._multiarray_umath import ndarray
-
-array_t = np_.ndarray
+array_t: Type[Union[ndarray, ndarray]] = np_.ndarray
tintegers_h = Tuple[int, ...]
diff --git a/brick/processing/input.py b/brick/processing/input.py
index 56a081f..cbe0996 100644
--- a/brick/processing/input.py
+++ b/brick/processing/input.py
@@ -123,6 +123,19 @@ def VoxelDimensionInMicrons(data_path: str) -> array_t:
return voxel_size_microns
+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 ToMicrons(pixel: int, voxel_size_microns: 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])
+
+
def DijkstraCosts(image: array_t, som_map: array_t, ext_map: array_t) -> array_t:
#
# TODO: Ideally, the extension part should be dilated
diff --git a/nutrimorph.py b/nutrimorph.py
index 52d993c..c51aaff 100644
--- a/nutrimorph.py
+++ b/nutrimorph.py
@@ -52,9 +52,8 @@ import time as tm_
import matplotlib.pyplot as pl_
import numpy as np_
import skimage.io as io_
-import skimage.measure as ms_
from skimage.segmentation import relabel_sequential
-import exifread as xf_
+import skimage.morphology as mp_
print(sy_.argv, sy_.argv.__len__())
@@ -72,10 +71,10 @@ soma_low_c = None
soma_high_c = None
ext_low_c = None
ext_high_c = None
-soma_selem_c = None
+soma_selem_microns_c = None
max_straight_sq_dist_c = None
max_weighted_length_c = None
-min_area_c = None
+soma_min_area_c = None
in_parallel = None
exec(open(sy_.argv[1]).read())
@@ -110,6 +109,7 @@ img_shape = image.shape
#
print(f"IMAGE: s.{img_shape} t.{image.dtype} m.{image.min()} M.{image.max()}")
+# Intensity relative normalization (between 0 and 1).
image_for_soma = in_.IntensityNormalizedImage(image)
image_for_ext = in_.IntensityNormalizedImage(image)
print(f"NRM-IMG: t.{image_for_soma.dtype} m.{image_for_soma.min():.2f} M.{image_for_soma.max():.2f}")
@@ -128,8 +128,10 @@ axes = {}
# --- Somas
print("\n--- Soma Detection")
+soma_selem_c = mp_.disk(in_.ToPixels(soma_selem_microns_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"], min_area_c)
+som_nfo["map"], som_lmp = soma_t.FilteredMap(som_nfo["map"], soma_min_area_c)
# som_nfo["lmp"], n_somas= ms_.label(som_nfo["map"], return_num=True)
som_nfo["lmp"] = relabel_sequential(som_lmp)[0] # Use relabel instead of label to optimize the algorithm.
n_somas = som_nfo["lmp"].max()
@@ -152,7 +154,7 @@ if with_plot:
print("\n--- Extension Detection")
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)
+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["map"] = extension_t.FineMapFromCoarseMap(ext_nfo["coarse_map"])
ext_nfo["map"][som_nfo["map"] > 0] = 0
diff --git a/parameters.py b/parameters.py
index d6af36f..ee09ffe 100644
--- a/parameters.py
+++ b/parameters.py
@@ -29,8 +29,6 @@
# The fact that you are presently reading this means that you have had
# knowledge of the CeCILL license and that you accept its terms.
-import skimage.morphology as mp_
-
data_path = "./data/DIO_6H_6_1.70bis_2.2_3.tif"
channel = 'G'
@@ -41,11 +39,15 @@ soma_high_c = 0.7126
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_c = mp_.disk(2)
+soma_selem_microns_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 ?
max_straight_sq_dist_c = 30 ** 2
max_weighted_length_c = 20.0
-min_area_c = 1000
+soma_min_area_c = 1000
+ext_min_area_c = 100 # /!\ Not directly used in brick/component #TODO direct use of param ?
in_parallel = False
--
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