Commit d9622d9a authored by Martinez-Carvajal German's avatar Martinez-Carvajal German
Browse files

adding the same parameter rw to

perform computations in cylinders smaller
than total diameter
parent db8df380
......@@ -41,7 +41,7 @@ def sector_mask(shape,centre,radius,angle_range):
return circmask*anglemask
def relabel_the_outside(image,labels):
def relabel_the_outside(image,labels, rw):
""" if pixels outside the cylinder that contains the sample have the same value for air
they will be relabeled with the value label[1]
so, if you follow the conventions for label values
......@@ -57,7 +57,7 @@ def relabel_the_outside(image,labels):
# The cylinder is supposed to be the biggest "circle" inscribed in a squared image
z,x,y = np.shape(image)[0], np.shape(image)[1], np.shape(image)[2]
center = int(x/2), int(y/2)
radius = int((x/2))
radius = int((x/2))*rw
#Selecting circular ROI (region of interest)
mask_2D = sector_mask((x,y),center,radius,(0,360 ))
mask_3D = np.zeros(image.shape, dtype = np.bool)
......@@ -67,7 +67,7 @@ def relabel_the_outside(image,labels):
print("{} pixels have been attributed to tha phase : outside the cylinder".format(np.count_nonzero(image == 1)))
return image
def compute_global_fractions_volumes_depths(r, image, sample_name, start_dl, end_dl, end_gl, path_save):
def compute_global_fractions_volumes_depths(r, image, sample_name, start_dl, end_dl, end_gl, path_save, rw):
""" r = resolution in mm/vox
start_dl = int, starting slice of the deposit layer
end_dl = int, ending slice of the deposit layer, start of the gravel layer
......@@ -131,7 +131,7 @@ def compute_global_fractions_volumes_depths(r, image, sample_name, start_dl, end
chdir(path_save)
print("Fractions for sample {}\n".format(sample_name), df)
df.to_csv('Global_Volume_Fractions_of_sample_{}.csv'.format(sample_name), sep = ';' )
df.to_csv('Global_Volume_Fractions_of_sample_{}_rw_{}.csv'.format(sample_name, rw), sep = ';' )
return (df)
......@@ -149,14 +149,15 @@ def main():
slice_start_deposit_layer = 1
slice_end_deposit_layer = 5
r = 0.035 # mm/vox
rw = 1
# Computing global fractions
chdir(path_read)
print('Reading...', path_read, file_name)
image = tifffile.imread(file_name)
print('Relabeling the outside')
labels = [1,0,128,255] # 1 = outside the cylinder, 0 = voids, 128 = fouling material, 255 = gravel
image = relabel_the_outside(image, labels)
compute_global_fractions_volumes_depths(r, image, sample_name, slice_start_deposit_layer, slice_end_deposit_layer, len(image), path_save)
image = relabel_the_outside(image, labels, rw)
compute_global_fractions_volumes_depths(r, image, sample_name, slice_start_deposit_layer, slice_end_deposit_layer, len(image), path_save, rw)
main()
print('ok global fractions')
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