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Commit 17b427ef authored by Pietro Incardona's avatar Pietro Incardona
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Adding example files

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example/Numerics/Sussman_redistancing/image_binary_conversion/image2binary_face.ipynb 0 → 100644
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%% Cell type:code id: tags:
``` python
from tifffile import imread, imsave
import numpy as np
import os
import matplotlib.pyplot as plt
import cv2
import sys
sys.path.append("./lib")
import morphological_operations as mo
import image_process_and_save as ips
```
%% Cell type:markdown id: tags:
# Open and plot image
%% Cell type:code id: tags:
``` python
filename = '/Users/jstark/Desktop/image_examples/face.tiff'
x = imread('%s' % filename)
x = x[:, :, 0]
```
%% Cell type:code id: tags:
``` python
np.max(x), np.min(x), x.shape
```
%% Output
(255, 0, (64, 58))
%% Cell type:code id: tags:
``` python
# fig, ax = plt.subplots(figsize=(7, 7))
# ax.imshow(x, cmap='gray')
```
%% Cell type:markdown id: tags:
# Convert binary image: >1 -> -1, 0 -> +1 (indicator function)
%% Cell type:code id: tags:
``` python
x_bin = np.where(x > 1, -1, 1)
print("format of stack x_bin = ", x_bin.shape, "\n"),
print("minimum pixel value after conversion = ", np.amin(x_bin), "\n"),
print("maximum pixel value after conversion = ", np.amax(x_bin), "\n")
# fig, ax = plt.subplots(figsize=(7, 7))
# ax.imshow(x_bin[30], cmap = 'gray')
fig, ax = plt.subplots(figsize=(7, 7))
ax.imshow(x_bin, cmap='gray')
None
```
%% Output
format of stack x_bin = (64, 58)
minimum pixel value after conversion = -1
maximum pixel value after conversion = 1
%% Cell type:code id: tags:
``` python
np.min(x_bin), np.max(x_bin)
```
%% Output
(-1, 1)
%% Cell type:code id: tags:
``` python
x_bin = np.flip(x_bin)
fig, ax = plt.subplots(figsize=(7, 7))
ax.imshow(x_bin, cmap='gray')
None
```
%% Output
%% Cell type:code id: tags:
``` python
# save flat image stack as binary file
path = '/Users/jstark/Desktop/image_examples/'
filename = 'face'
ips.save_array_toBin(x_bin, path, filename)
# Save image size in #pixels / axis as csv file
dim = np.asarray(x_bin.shape)
np.savetxt('%s/size_%s.csv' % (path, filename), dim, fmt='%i', delimiter=',')
```
example/Numerics/Sussman_redistancing/image_binary_conversion/lib/image_process_and_save.py 0 → 100644
+ 26
− 0
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import os
import numpy as np
def padding(img, x_pad, y_pad, z_pad):
z, y, x = img.shape[0], img.shape[1], img.shape[2]
zp, yp, xp = z + 2*z_pad, y + 2*y_pad, x + 2*x_pad
x_padded = np.zeros((zp, yp, xp ))
x_padded[z_pad:zp-z_pad, y_pad:yp-y_pad, x_pad:xp-x_pad] = img
return x_padded
def save_zslices_toBin(numpy_array, filename):
import os
curdir = os.getcwd()
directory = '%s/%s'% (curdir, filename)
if not os.path.exists(directory):
os.makedirs(directory)
# loop through z dim and save every slice as separate binary file bc. savetxt only works for 1d or 2d arrays
z_dim = numpy_array.shape[0]
for z in range(z_dim):
numpy_array[z].astype('int8').tofile('%s/zslice_%d.bin' % (directory, z))
def save_array_toBin(numpy_array, path, filename):
if not os.path.exists(path):
os.makedirs(path)
numpy_array.astype('int8').tofile('%s/%s.bin' % (path, filename))
example/Numerics/Sussman_redistancing/image_binary_conversion/lib/morphological_operations.py 0 → 100644
+ 40
− 0
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import cv2
import numpy as np
def closure(img, kernel, iterations):
lz, ly, lx = img.shape[0], img.shape[1], img.shape[2]
erosion = np.zeros((lz, ly, lx))
dilation = np.zeros((lz, ly, lx))
# Closure
# -> connects separated regions, increase connectivity
i = 0
while i < 1:
for z_slice in range(lz):
dilation[z_slice] = cv2.dilate(img[z_slice], kernel, iterations = iterations)
img = dilation
for z_slice in range(lz):
erosion[z_slice] = cv2.erode(img[z_slice], kernel, iterations = iterations)
img = erosion
i += 1;
return img
def opening(img, kernel, iterations):
lz, ly, lx = img.shape[0], img.shape[1], img.shape[2]
erosion = np.zeros((lz, ly, lx))
dilation = np.zeros((lz, ly, lx))
# Opening
# -> removes islands / small regions
i = 0
while i < 1:
for z_slice in range(lz):
erosion[z_slice] = cv2.erode(img[z_slice], kernel, iterations = iterations)
img = erosion
for z_slice in range(lz):
dilation[z_slice] = cv2.dilate(img[z_slice], kernel, iterations = iterations)
img = dilation
i += 1;
return img
\ No newline at end of file
install
+ 4
− 4
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......@@ -414,11 +414,11 @@ fi
echo "INCLUDE_PATH=$cuda_include_dirs -Wno-deprecated-declarations $openmp_flags -I. -I$install_base/openfpm_numerics/include -I$install_base/openfpm_pdata/include/config -I$install_base/openfpm_pdata/include -I$install_base/openfpm_data/include -I$install_base/openfpm_vcluster/include -I$install_base/openfpm_io/include -I$install_base/openfpm_devices/include -I$i_dir/VCDEVEL/include -I$i_dir/METIS/include -I$i_dir/PARMETIS/include -I$i_dir/BOOST/include -I$i_dir/HDF5/include -I$i_dir/LIBHILBERT/include $lin_alg_inc" > example.mk
echo "LIBS_PATH=$openmp_flags -L$install_base/openfpm_devices/lib -L$install_base/openfpm_pdata/lib -L$install_base/openfpm_vcluster/lib -L$i_dir/VCDEVEL/lib -L$i_dir/METIS/lib -L$i_dir/PARMETIS/lib -L$i_dir/BOOST/lib -L$hdf5_lib -L$i_dir/LIBHILBERT/lib $lin_alg_dir " >> example.mk
if [ x"$gpu_support" == x"1" ]; then
echo "LIBS=-lvcluster -lofpm_pdata -lofpmmemory -lparmetis -lmetis -lboost_iostreams -lboost_program_options -lhdf5 -llibhilbert -lVc $(cat cuda_lib) $lin_alg_lib -ldl" >> example.mk
echo "LIBS_SE2=-lvcluster -lofpmmemory_se2 -lparmetis -lmetis -lboost_iostreams -lboost_program_options -lhdf5 -llibhilbert -lVc $(cat cuda_lib) $lin_alg_lib" >> example.mk
echo "LIBS=-lvcluster -lofpm_pdata -lofpmmemory -lparmetis -lmetis -lboost_iostreams -lboost_program_options -lhdf5 -llibhilbert -lVc $(cat cuda_lib) $lin_alg_lib -ldl -lboost_filesystem -lboost_system" >> example.mk
echo "LIBS_SE2=-lvcluster -lofpmmemory_se2 -lparmetis -lmetis -lboost_iostreams -lboost_program_options -lhdf5 -llibhilbert -lVc $(cat cuda_lib) $lin_alg_lib -lboost_filesystem -lboost_system" >> example.mk
else
echo "LIBS=-lvcluster -lofpm_pdata -lofpmmemory -lparmetis -lmetis -lboost_iostreams -lboost_program_options -lhdf5 -llibhilbert -lVc $lin_alg_lib -ldl" >> example.mk
echo "LIBS_SE2=-lvcluster -lofpmmemory_se2 -lparmetis -lmetis -lboost_iostreams -lboost_program_options -lhdf5 -llibhilbert -lVc $lin_alg_lib" >> example.mk
echo "LIBS=-lvcluster -lofpm_pdata -lofpmmemory -lparmetis -lmetis -lboost_iostreams -lboost_program_options -lhdf5 -llibhilbert -lVc $lin_alg_lib -ldl -lboost_filesystem -lboost_system" >> example.mk
echo "LIBS_SE2=-lvcluster -lofpmmemory_se2 -lparmetis -lmetis -lboost_iostreams -lboost_program_options -lhdf5 -llibhilbert -lVc $lin_alg_lib -lboost_filesystem -lboost_system" >> example.mk
fi
echo "INCLUDE_PATH_NVCC=-Xcompiler="-Wno-deprecated-declarations" $(cat openmp_flags) "$(cat cuda_options)" -I. -I$install_base/openfpm_numerics/include -I$install_base/openfpm_pdata/include/config -I$install_base/openfpm_pdata/include -I$install_base/openfpm_data/include -I$install_base/openfpm_vcluster/include -I$install_base/openfpm_io/include -I$install_base/openfpm_devices/include -I$i_dir/METIS/include -I$i_dir/PARMETIS/include -I$i_dir/BOOST/include -I$i_dir/HDF5/include -I$i_dir/LIBHILBERT/include $lin_alg_inc" >> example.mk
cp example.mk src/example.mk
......
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