def initSaveParameters(self,
save_path,
save_fident,
orig_img_path=[None, None],
orig_psf_path=[None, None],
overwrite=False):
""""""
self.save_fident = save_fident
self.overwrite = overwrite
util.createAllPaths(save_path)
if not util.isEmptyDir(save_path) and not overwrite:
raise ValueError(
'Save destination is not empty and overwriting is disabled.')
else:
self.save_path = save_path
if util.checkAllPaths(orig_img_path[0]):
self.orig_img_path = orig_img_path[0]
self.orig_img_fident = orig_img_path[1]
else:
raise ValueError('Given path for original image is not valid.')
if util.checkAllPaths(orig_psf_path):
self.orig_psf_path = orig_psf_path[0]
self.orig_psf_fident = orig_psf_path[1]
else:
raise ValueError('Given path for original psf is not valid.')
def initSaveParameters(self, save_path, save_fident, overwrite=False):
""""""
self.save_fident = save_fident
self.overwrite = overwrite
util.createAllPaths(save_path)
if not util.isEmptyDir(save_path) and not overwrite:
raise ValueError(
'Save destination is not empty and overwriting is disabled.')
else:
self.save_path = save_path
def write_image_stack(img_stack, path, f_ident, n_start, meta_data = None, meta_only = False):
""""""
util.createAllPaths(path)
if not img_stack.dtype == 'uint8':
raise TypeError
if meta_data:
if isinstance(meta_data, MetaData):
meta_data = meta_data.toList()
if not isinstance(meta_data, list):
raise TypeError
if not meta_only:
for ind in range(img_stack.shape[2]):
temp_img = img_stack[:,:,ind].copy()
_writeImage(temp_img, path, f_ident, ind)
if meta_data:
print('Writing Meta...')
_writeMeta(meta_data, path, f_ident)
def create_sub_crops_overlap():
""""""
f_ident = 'cyto_sim_{:0>3}.tif'
in_main_path = util.ptjoin(util.SIM_DATA, 'cyto_sim_full')
path_full = util.ptjoin(in_main_path, 'full_res_[0.2,0.2,0.2]')
path_down = util.ptjoin(in_main_path, 'downsample_res_[0.2,0.2,0.2]')
crop_diviser = 3
crop_paths_full = [
'full_overlap_crop_{}_{}_res_[0.2,0.2,0.2]'.format(
i / crop_diviser, i % crop_diviser) for i in range(crop_diviser**2)
]
crop_paths_down = [
'downsampled_overlap_crop_{}_{}_res_[0.2,0.2,0.2]'.format(
i / crop_diviser, i % crop_diviser) for i in range(crop_diviser**2)
]
crop_paths_full = [util.ptjoin(in_main_path, pt) for pt in crop_paths_full]
crop_paths_down = [util.ptjoin(in_main_path, pt) for pt in crop_paths_down]
util.createAllPaths(crop_paths_full)
util.createAllPaths(crop_paths_down)
full_stack = util.stack_loader.read_image_stack(path_full,
f_ident,
meta=False)
full_meta = util.stack_loader.read_meta_data_only(path_full, f_ident)
t_reduced_shape = [
sh / crop_diviser if sh % 2 == 0 else 1 + sh / crop_diviser
for sh in full_stack.shape
]
meta_comment = full_meta.comment
for i, crop_path in enumerate(crop_paths_full):
x_ind = i / crop_diviser
y_ind = i % crop_diviser
sh_bool2 = [sh % 2 == 0 for sh in t_reduced_shape]
ind_slice = [
slice(
x_ind * (t_reduced_shape[0] / 2) if sh_bool2[0] else x_ind *
((t_reduced_shape[0] - 1) / 2),
(x_ind + 2) * (t_reduced_shape[0] / 2) if sh_bool2[0] else 1 +
(x_ind + 2) * (t_reduced_shape[0] - 1) / 2, 1),
slice(
y_ind * (t_reduced_shape[1] / 2) if sh_bool2[1] else y_ind *
((t_reduced_shape[1] - 1) / 2),
(y_ind + 2) * (t_reduced_shape[1] / 2) if sh_bool2[1] else 1 +
(y_ind + 2) * (t_reduced_shape[1] - 1) / 2, 1),
slice(None, None, 1)
]
cropped_stack = full_stack[ind_slice].copy()
full_meta.comment = meta_comment + '; Cropped; Crop_index=[{},{}]'.format(
x_ind, y_ind)
util.stack_loader.write_image_stack(cropped_stack,
crop_path,
f_ident,
0,
meta_data=full_meta.toList())
down_stack = util.stack_loader.read_image_stack(path_down,
f_ident,
meta=False)
down_meta = util.stack_loader.read_meta_data_only(path_down, f_ident)
t_reduced_shape = [
sh / crop_diviser if sh % 2 == 0 else 1 + sh / crop_diviser
for sh in down_stack.shape
]
meta_comment = down_meta.comment
for i, crop_path in enumerate(crop_paths_down):
x_ind = i / crop_diviser
y_ind = i % crop_diviser
sh_bool2 = [sh % 2 == 0 for sh in t_reduced_shape]
ind_slice = [
slice(
x_ind * (t_reduced_shape[0] / 2) if sh_bool2[0] else x_ind *
((t_reduced_shape[0] - 1) / 2),
(x_ind + 2) * (t_reduced_shape[0] / 2) if sh_bool2[0] else 1 +
(x_ind + 2) * (t_reduced_shape[0] - 1) / 2, 1),
slice(
y_ind * (t_reduced_shape[1] / 2) if sh_bool2[1] else y_ind *
((t_reduced_shape[1] - 1) / 2),
(y_ind + 2) * (t_reduced_shape[1] / 2) if sh_bool2[1] else 1 +
(y_ind + 2) * (t_reduced_shape[1] - 1) / 2, 1),
slice(None, None, 1)
]
cropped_stack = down_stack[ind_slice].copy()
down_meta.comment = meta_comment + '; Cropped; Crop_index=[{},{}]'.format(
x_ind, y_ind)
util.stack_loader.write_image_stack(cropped_stack,
crop_path,
f_ident,
0,
meta_data=down_meta.toList())
def createSupCrops_forDownsample():
""""""
main_path = util.ptjoin(util.SIM_DATA, 'cyto_sim_full')
res_path_add = 'downsample_res_[0.2,0.2,0.2]'
f_ident = 'cyto_sim_{:0>3}.tif'
out_path_add = 'cyto_sim_crop_{}_{}'
crop_diviser = 2
path_in = util.ptjoin(main_path, res_path_add)
in_stack = util.stack_loader.read_image_stack(path_in, f_ident, meta=False)
in_meta = util.stack_loader.read_meta_data_only(path_in, f_ident)
red_shape = [sh / crop_diviser for sh in in_stack.shape]
meta_comment = in_meta.comment
for x_ind in range(crop_diviser):
for y_ind in range(crop_diviser):
cur_path_out = util.ptjoin(util.SIM_DATA,
out_path_add.format(x_ind, y_ind),
res_path_add)
print('Processing path: {}').format(cur_path_out)
util.createAllPaths(cur_path_out)
ind_slice = [
slice(x_ind * red_shape[0], (x_ind + 1) * red_shape[0], 1),
slice(y_ind * red_shape[1], (y_ind + 1) * red_shape[1], 1),
slice(None, None, 1)
]
cropped_stack = in_stack[ind_slice].copy()
in_meta.comment = meta_comment + '; Cropped; Crop_index=[{},{}]'.format(
x_ind, y_ind)
util.stack_loader.write_image_stack(cropped_stack,
cur_path_out,
f_ident,
0,
meta_data=in_meta.toList())
out_path_add = 'cyto_sim_crop_overlap_{}_{}'
for x_ind in range(crop_diviser + 1):
for y_ind in range(crop_diviser + 1):
cur_path_out = util.ptjoin(util.SIM_DATA,
out_path_add.format(x_ind, y_ind),
res_path_add)
print('Processing path:{}'.format(cur_path_out))
util.createAllPaths(cur_path_out)
ind_slice = [
slice(x_ind * (red_shape[0] / 2),
(x_ind + 2) * (red_shape[0] / 2), 1),
slice(y_ind * (red_shape[1] / 2),
(y_ind + 2) * (red_shape[1] / 2), 1),
slice(None, None, 1)
]
print(ind_slice)
cropped_stack = in_stack[ind_slice].copy()
in_meta.comment = meta_comment + '; Cropped; Crop_index=[{},{}]'.format(
x_ind, y_ind)
util.stack_loader.write_image_stack(cropped_stack,
cur_path_out,
f_ident,
0,
meta_data=in_meta.toList())
def testFISTA():
""""""
#gauss_single = [0.05, 0.15, 0.25, 0.5]
gauss_single = [0.05, 0.5]
gauss_multi = [ #[0.05, 0., 0.15],
#[0.05, 0., 0.2],
[0.05, 0., 0.25],
#[0.05, 0., 0.4],
[0.1, 0., 0.15],
#[0.1, 0., 0.2],
#[0.1, 0., 0.25],
#[0.1, 0., 0.4],
[0.2, 0., 0.15],
#[0.2, 0., 0.2],
[0.2, 0., 0.25]
]
#[0.2, 0., 0.4]]
defocus = []
"""
defocus = [[0.3, 2000, 400],
#[0.3, 2000, 200],
[0.3, 2000, 100],
#[0.3, 800, 400],
[0.3, 800, 200],
#[0.3, 800, 100],
[0.1, 2000, 400],
#[0.1, 2000, 200],
#[0.1, 2000, 100],
#[0.1, 800, 400],
[0.1, 800, 200],
#[0.1, 800, 100],
[0.05, 2000, 400],
#[0.05, 2000, 200],
[0.05, 2000, 100],
#[0.05, 800, 400],
#[0.05, 800, 200],
[0.05, 800, 100]]
"""
dict_paths = []
orig_path = util.ptjoin(util.SIM_DATA, 'cyto_sim_full',
'full_res_[0.4,0.4,0.4]')
orig_fident = 'cyto_sim_{:0>3}.tif'
for fl in gauss_single:
conv_path = 'cyto_gauss_simple_sig-{:.2f}'.format(fl)
conv_f_ident = 'cyto_conv_gauss_simple_{:0>3}.tif'
#conv_path = util.ptjoin(util.SIM_CONVOLUTED, path, 'full_res_[0.2,0.2,0.2]')
psf_path = 'gauss_simple_sig-{:.2f}'.format(fl)
psf_f_ident = 'psf_gauss_simple_{:0>3}.tif'
#psf_path = util.ptjoin(util.SIM_PSF, 'odd', psf_path, 'res_[0.2,0.2,0.2]')
dict_paths.append({
'conv_path': conv_path,
'conv_fident': conv_f_ident,
'psf_path': psf_path,
'psf_fident': psf_f_ident
})
for lis in gauss_multi:
conv_path = 'cyto_gauss_sig0-{0[0]:.2f}_sig1-{0[1]:.2f}_sig2-{0[2]:.2f}'.format(
lis)
conv_f_ident = 'cyto_conv_gauss_{:0>3}.tif'
#conv_path = util.ptjoin(util.SIM_CONVOLUTED, path, 'full_res[0.2,0.2,0.2]')
psf_path = 'gauss_sig0-{0[0]:.2f}_sig1-{0[1]:.2f}_sig2-{0[2]:.2f}'.format(
lis)
psf_f_ident = 'psf_gauss_{:0>3}.tif'
#psf_path = util.ptjoin(util.SIM_PSF, 'odd', psf_path, 'res_[0.2,0.2,0.2]')
dict_paths.append({
'conv_path': conv_path,
'conv_fident': conv_f_ident,
'psf_path': psf_path,
'psf_fident': psf_f_ident
})
for lis in defocus:
conv_path = 'cyto_defocus_sig-{0[0]:.2f}_zi-{0[1]}_K-{0[2]}'.format(
lis)
conv_f_ident = 'cyto_conv_defocus_{:0>3}.tif'
#conv_path = util.ptjoin(util.SIM_CONVOLUTED, path, 'full_res[0.2,0.2,0.2]')
psf_path = 'defocussing_sig-{0[0]:.2f}_zi-{0[1]}_K-{0[2]}'.format(lis)
psf_f_ident = 'psf_defocus_{:0>3}.tif'
#psf_path = util.ptjoin(util.SIM_PSF, 'odd', psf_path, 'res_[0.2,0.2,0.2]')
dict_paths.append({
'conv_path': conv_path,
'conv_fident': conv_f_ident,
'psf_path': psf_path,
'psf_fident': psf_f_ident
})
orig_stack, orig_meta = util.stack_loader.read_image_stack(orig_path,
orig_fident,
meta=True)
#lambdas = [0.8, 0.85, 0.87, 0.9, 0.92, 0.94, 0.96, 0.98, 1., 1.02, 1.04, 1.06, 1.08, 1.1, 1.13, 1.15, 1.2]
lambdas = [0.87, 0.94, 0.98, 1., 1.02, 1.06, 1.13]
for paths in dict_paths:
for lam in lambdas:
conv_path = util.ptjoin(util.SIM_CONVOLUTED, paths['conv_path'],
'full_res_[0.4,0.4,0.4]')
psf_path = util.ptjoin(util.SIM_PSF, 'odd', paths['psf_path'],
'res_[0.4,0.4,0.4]')
psf_stack, psf_meta = util.stack_loader.read_image_stack(
psf_path, paths['psf_fident'], meta=True)
conv_stack, conv_meta = util.stack_loader.read_image_stack(
conv_path, paths['conv_fident'], meta=True)
recon_path = util.ptjoin(util.SIM_RECON, 'test_FISTA',
paths['conv_path'], 'res_[0.4,0.4,0.4]')
util.createAllPaths(recon_path)
recon_fident = 'recon_{:0>3}.tif'
fista = wave.FISTA(conv_stack,
psf=psf_stack,
groundTruth=orig_stack,
iterSteps=200,
saveIntermediateSteps=50,
compareWithTruth=True,
debugInt=3)
fista.initSaveParameters(recon_path, recon_fident)
fista.prepare()
fista.solve()
fista.saveSolution()
def sample_noise_additions():
""""""
convs = {
'defocus1': [
'cyto_defocus_sig-0.10_zi-1000_K-200', ['res_[0.2,0.2,0.2]'],
'cyto_conv_{:0>3}.tif', [['cnr', 30.], ['cnr', 10.], ['cnr', 5.]]
],
'defocus2': [
'cyto_defocus_sig-0.05_zi-2000_K-200', ['res_[0.2,0.2,0.2]'],
'cyto_conv_{:0>3}.tif', [['cnr', 30.], ['cnr', 10.], ['cnr', 5.]]
],
'defocus3': [
'cyto_defocus_sig-0.05_zi-1000_K-200', ['res_[0.2,0.2,0.2]'],
'cyto_conv_{:0>3}.tif', [['cnr', 30.], ['cnr', 10.], ['cnr', 5.]]
],
'defocus4': [
'cyto_defocus_sig-0.05_zi-800_K-100',
['res_[0.1,0.1,0.1]', 'res_[0.2,0.2,0.2]'], 'cyto_conv_{:0>3}.tif',
[['cnr', 30.], ['cnr', 10.], ['cnr', 5.]]
],
'gauss1': [
'cyto_gauss_sig0-0.15_sig1-0.00_sig2-0.22',
['res_[0.1,0.1,0.1]', 'res_[0.2,0.2,0.2]'], 'cyto_conv_{:0>3}.tif',
[['cnr', 30.], ['cnr', 10.], ['cnr', 5.]]
],
'gauss_simple1': [
'cyto_gauss_simple_sig-0.15',
['res_[0.1,0.1,0.1]', 'res_[0.2,0.2,0.2]'], 'cyto_conv_{:0>3}.tif',
[['cnr', 30.], ['cnr', 10.], ['cnr', 5.]]
],
'gauss_simple2': [
'cyto_gauss_simple_sig-0.30', ['res_[0.1,0.1,0.1]'],
'cyto_conv_{:0>3}.tif', [['cnr', 30.], ['cnr', 10.], ['cnr', 5.]]
],
}
main_path = util.SIM_CONVOLUTED
for name, parameters in psfs.items():
print('Processing Convoluted Image Stack: {}'.format(name))
add_path = parameters[0]
res_folders = parameters[1]
f_ident = parameters[2]
noise_params = parameters[3]
for res in res_folders:
for noise in noise_params:
noise_free_path = util.ptjoin(main_path, add_path, res)
new_path = util.ptjoin(
main_path, add_path,
'{}_{}-{}'.format(res, noise[0], noise[1]))
util.createAllPaths(new_path)
temp_stack = util.stack_loader.read_image_stack(
noise_free_path, f_ident, meta=True)
t_noise_dict = {
'noise_def': convoluter.Noise_Adder.NOISE_DEF[noise[0]],
noise[0]: noise[1]
}
temp_noise = convoluter.Noise_Adder(temp_stack[0],
old_meta=temp_stack[1],
img_type='sample',
noise_type='gaussian',
noise_params=t_noise_dict,
debug_int=3)
temp_noise.addNoise()
temp_noise.initSaveParameters(
new_path,
f_ident,
orig_img_path=[noise_free_path, f_ident],
overwrite=True)
temp_noise.saveSolution()
def PSF_noise_additions_batch():
""""""
main_path = util.SIM_PSF
#path_adds = ['odd', 'even']
path_adds = ['odd']
#res_list = [[0.1,0.1,0.1], [0.2,0.2,0.2]]
#res_list = [[0.4,0.4,0.4]]
res_list = [[0.8, 0.8, 0.8]]
res_path_def = 'res_[{0[0]:.1f},{0[1]:.1f},{0[2]:.1f}]'
#Defocus parameter lists
sig_defocus_list = [.05, 0.1, 0.2, 0.3]
zi_list = [800, 1000, 2000]
K_list = [100, 200, 300, 400]
defocus_noise_list = [['snr', 60.], ['snr', 30.], ['snr', 15.],
['snr', 10.], ['snr', 5.], ['snr', 2.]]
f_ident_defocus = 'psf_defocus_{:0>3}.tif'
path_def_defocus = 'defocussing_sig-{:.2f}_zi-{:.0f}_K-{:.0f}'
for oddity in path_adds:
for res in res_list:
for sig in sig_defocus_list:
for zi in zi_list:
for K in K_list:
for noise_par in defocus_noise_list:
t_noise_free_path = util.ptjoin(
main_path, oddity,
path_def_defocus.format(sig, zi, K),
res_path_def.format(res))
t_new_path = util.ptjoin(
main_path, oddity,
path_def_defocus.format(sig, zi, K),
'res_[{0[0]:.1f},{0[1]:.1f},{0[2]:.1f}]_{1}-{2}'
.format(res, noise_par[0], noise_par[1]))
util.createAllPaths(t_new_path)
temp_stack = util.stack_loader.read_image_stack(
t_noise_free_path, f_ident_defocus, meta=True)
t_noise_dict = {
'noise_def':
convoluter.Noise_Adder.NOISE_DEF[noise_par[0]],
noise_par[0]:
noise_par[1]
}
temp_noise = convoluter.Noise_Adder(
temp_stack[0],
old_meta=temp_stack[1],
img_type='psf',
noise_type='gaussian',
noise_params=t_noise_dict,
debug_int=3)
temp_noise.addNoise()
temp_noise.initSaveParameters(
t_new_path,
f_ident_defocus,
orig_img_path=[
t_noise_free_path, f_ident_defocus
],
overwrite=True)
temp_noise.saveSolution()
#Gaussian parameter lists
sig0_list = [0.05, 0.10, 0.15, 0.2, 0.3, 0.4]
sig1_list = [0]
sig2_list = [0.15, 0.2, 0.25, 0.3, 0.4]
gauss_noise_list = [['snr', 60.], ['snr', 30.], ['snr', 15.], ['snr', 10.],
['snr', 5.], ['snr', 2.]]
f_ident_gauss = 'psf_gauss_{:0>3}.tif'
path_def_gauss = 'gauss_sig0-{:.2f}_sig1-{:.2f}_sig2-{:.2f}'
for oddity in path_adds:
for res in res_list:
for sig0 in sig0_list:
for sig1 in sig1_list:
for sig2 in sig2_list:
for noise_par in gauss_noise_list:
t_noise_free_path = util.ptjoin(
main_path, oddity,
path_def_gauss.format(sig0, sig1, sig2),
res_path_def.format(res))
t_new_path = util.ptjoin(
main_path, oddity,
path_def_gauss.format(sig0, sig1, sig2),
'res_[{0[0]:.1f},{0[1]:.1f},{0[2]:.1f}]_{1}-{2}'
.format(res, noise_par[0], noise_par[1]))
util.createAllPaths(t_new_path)
temp_stack = util.stack_loader.read_image_stack(
t_noise_free_path, f_ident_gauss, meta=True)
t_noise_dict = {
'noise_def':
convoluter.Noise_Adder.NOISE_DEF[noise_par[0]],
noise_par[0]:
noise_par[1]
}
temp_noise = convoluter.Noise_Adder(
temp_stack[0],
old_meta=temp_stack[1],
img_type='psf',
noise_type='gaussian',
noise_params=t_noise_dict,
debug_int=3)
temp_noise.addNoise()
temp_noise.initSaveParameters(
t_new_path,
f_ident_gauss,
orig_img_path=[
t_noise_free_path, f_ident_gauss
],
overwrite=True)
temp_noise.saveSolution()
#Gaussian simple lists
sig_gauss_simple_list = [0.05, 0.1, 0.15, 0.2, 0.25, 0.3, 0.4, 0.5]
gauss_simple_noise_list = [['snr', 60.], ['snr', 30.], ['snr', 15.],
['snr', 10.], ['snr', 5.], ['snr', 2.]]
f_ident_gauss_simple = 'psf_gauss_simple_{:0>3}.tif'
path_def_gauss_simple = 'gauss_simple_sig-{:.2f}'
for oddity in path_adds:
for res in res_list:
for sig in sig_gauss_simple_list:
for noise_par in gauss_simple_noise_list:
t_noise_free_path = util.ptjoin(
main_path, oddity, path_def_gauss_simple.format(sig),
res_path_def.format(res))
t_new_path = util.ptjoin(
main_path, oddity, path_def_gauss_simple.format(sig),
'res_[{0[0]:.1f},{0[1]:.1f},{0[2]:.1f}]_{1}-{2}'.
format(res, noise_par[0], noise_par[1]))
util.createAllPaths(t_new_path)
temp_stack = util.stack_loader.read_image_stack(
t_noise_free_path, f_ident_gauss_simple, meta=True)
t_noise_dict = {
'noise_def':
convoluter.Noise_Adder.NOISE_DEF[noise_par[0]],
noise_par[0]: noise_par[1]
}
temp_noise = convoluter.Noise_Adder(
temp_stack[0],
old_meta=temp_stack[1],
img_type='psf',
noise_type='gaussian',
noise_params=t_noise_dict,
debug_int=3)
temp_noise.addNoise()
temp_noise.initSaveParameters(t_new_path,
f_ident_gauss_simple,
orig_img_path=[
t_noise_free_path,
f_ident_gauss_simple
],
overwrite=True)
temp_noise.saveSolution()
