def files_to_array(list_sample_files,
list_ref_files,
list_dark_files,
idx4crop=[0, -1, 0, -1]):
img = wpu.crop_matrix_at_indexes(dxchange.read_tiff(list_sample_files[0]),
idx4crop)
(nlines, ncolums) = img.shape
img_stack = np.zeros((len(list_sample_files), nlines, ncolums))
ref_stack = img_stack * 0.0
dark_im = img_stack[0, :, :] * 0.0
for i in range(len(list_dark_files)):
dark_im += wpu.crop_matrix_at_indexes(
dxchange.read_tiff(list_dark_files[i]), idx4crop)
for i in range(len(list_sample_files)):
img_stack[i, :, :] = wpu.crop_matrix_at_indexes(
dxchange.read_tiff(list_sample_files[i]), idx4crop) - dark_im
ref_stack[i, :, :] = wpu.crop_matrix_at_indexes(
dxchange.read_tiff(list_ref_files[i]), idx4crop) - dark_im
return img_stack, ref_stack
def _func(i):
wpu.print_blue("MESSAGE: loop " + str(i) + ": " + \
listOfDataFiles[i])
if idx == [0, -1, 0, -1]:
img = dxchange.read_tiff(listOfDataFiles[i]) - dark_im
else:
img = wpu.crop_matrix_at_indexes(
dxchange.read_tiff(listOfDataFiles[i]), idx) - dark_im
pv, ph = period_harm_Vert, period_harm_Horz
pv = int(period_harm_Vert / (sourceDistance + zvec[i] - zvec[0]) *
sourceDistance)
ph = int(period_harm_Horz / (sourceDistance + zvec[i] - zvec[0]) *
sourceDistance)
wgi.plot_harmonic_grid(img, [pv, ph], isFFT=False)
plt.savefig('FFT_{:04.0f}_ms_'.format(tvec[i] * 1e3) +
'{:04.0f}mm.png'.format(zvec[i] * 1e3))
plt.show(block=False)
plt.close()
# wgi.plot_harmonic_peak(img,
# [pv, ph],
# isFFT=False,
# fname='FFT_peaks_{:04.0f}_ms_'.format(tvec[i]*1e3) +
# '{:04.0f}mm.png'.format(zvec[i]*1e3))
#
#
# plt.close()
return wgi.visib_1st_harmonics(img, [pv, ph], searchRegion=10)
def read_data(idd, step):
name = '/home/beams/XYU/chip_pillar_interlace_2/projection_%06d.h5' % (idd)
fid = h5py.File(name, 'r')
# read scan positions
tmp = fid['/positions'][::step] * 70976797.5332996
scan = np.zeros([2, 1, tmp.shape[0]], dtype='float32', order='C')
nscan = tmp.shape[0]
scan[0, :, :] = tmp[:, 1] + 533
scan[1, :, :] = tmp[:, 0] + 428
ids = np.where((scan[0, 0] >= 0) * (scan[0, 0] < 1024) *
(scan[1, 0] >= 0) * (scan[1, 0] < 768))[0]
scan = np.array(scan[:, :, ids], order='C') # important!
nscan = scan.shape[2]
# import matplotlib.pyplot as plt
# plt.plot(scan[1,0], scan[0,0],'.', color='blue')
# plt.savefig('scan.png',dpi=500)
data = np.zeros([1, nscan, 256, 256], dtype='float32')
tmp = np.fft.fftshift(fid['data'][::step, :, :],
axes=(1, 2)).astype('float32')
data[0] = tmp[ids]
# read probe initial guess
prb = np.ones([1, 256, 256], dtype='complex64')
prbamp = dxchange.read_tiff(
'/home/beams/XYU/chip_pillar_interlace_2/prbamp.tiff')
prbangle = dxchange.read_tiff(
'/home/beams/XYU/chip_pillar_interlace_2/prbangle.tiff')
prb[0] = prbamp * np.exp(1j * prbangle)
# initial guess for psi (can be read)
psi = np.zeros([1, 768 + 256, 1024 + 256], dtype='complex64',
order='C') + 1
return psi, prb, scan, data
def tiff2hdf5(src_folder,
dest_folder,
dest_fname,
pattern='recon_*.tiff',
display_min=None,
display_max=None,
dtype='int8'):
dest_fname = check_fname_ext(dest_fname, 'h5')
filelist = glob.glob(os.path.join(src_folder, pattern))
filelist = sorted(filelist)
n_files = len(filelist)
temp = dxchange.read_tiff(filelist[0])
full_shape = np.array([n_files, temp.shape[0], temp.shape[1]])
if rank == 0:
if not os.path.exists(dest_folder):
os.mkdir(dest_folder)
f = h5py.File(os.path.join(dest_folder, dest_fname))
comm.Barrier()
if rank != 0:
f = h5py.File(os.path.join(dest_folder, dest_fname))
grp = f.create_group('exchange')
grp.create_dataset('data', full_shape, dtype='float32')
alloc_set = allocate_mpi_subsets(n_files, size)
dset = f['exchange/data']
for i in alloc_set[rank]:
img = dxchange.read_tiff(filelist[i])
dset[i, :, :] = img
print(' Rank: {:d}, file: {:d}'.format(rank, i))
comm.Barrier()
hdf5_cast(os.path.join(dest_folder, dest_fname),
display_min=display_min,
display_max=display_max,
dtype=dtype)
return
def files_to_array(list_sample_files, list_ref_files, list_dark_files,
idx4crop=[0, -1, 0, -1]):
img = wpu.crop_matrix_at_indexes(dxchange.read_tiff(list_sample_files[0]),
idx4crop)
(nlines, ncolums) = img.shape
img_stack = np.zeros((len(list_sample_files), nlines, ncolums))
ref_stack = img_stack*0.0
dark_im = img_stack[0, :, :]*0.0
for i in range(len(list_dark_files)):
dark_im += wpu.crop_matrix_at_indexes(dxchange.read_tiff(list_dark_files[i]),
idx4crop)
for i in range(len(list_sample_files)):
img_stack[i, :, :] = wpu.crop_matrix_at_indexes(dxchange.read_tiff(list_sample_files[i]),
idx4crop) - dark_im
ref_stack[i, :, :] = wpu.crop_matrix_at_indexes(dxchange.read_tiff(list_ref_files[i]),
idx4crop) - dark_im
return img_stack, ref_stack
def create_dataset(self, dataset_file):
"""Create a dataset for testing this module.
Only called with setUp detects that `dataset_file` has been deleted.
"""
import dxchange
delta = dxchange.read_tiff('data/delta-chip-128.tiff')[::4, ::4, ::4]
beta = dxchange.read_tiff('data/beta-chip-128.tiff')[::4, ::4, ::4]
self.original = delta + 1j * beta
self.theta = np.linspace(0, 2 * np.pi, 16, endpoint=False)
self.tilt = np.pi / 3
self.data = tike.lamino.simulate(self.original, self.theta, self.tilt)
assert self.data.shape == (16, 32, 32)
assert self.data.dtype == 'complex64', self.data.dtype
setup_data = [
self.data,
self.original,
self.theta,
self.tilt,
]
with lzma.open(dataset_file, 'wb') as file:
pickle.dump(setup_data, file)
def load_tiff_stack(path, rand_batch_size=None):
filelist = glob.glob(os.path.join(path, '*.tif*'))
if rand_batch_size is not None:
filelist = np.random.choice(filelist, rand_batch_size).tolist().sort()
temp = dxchange.read_tiff(filelist[0])
shape = np.squeeze(temp).shape
arr = np.zeros([len(filelist), shape[0], shape[1]])
for (i, f) in enumerate(filelist):
arr[i, :, :] = np.squeeze(dxchange.read_tiff(f))
return arr
def read_raw_sinogram(self,
fname,
type='tiff',
center=None,
pixel_size=1,
fin_angle=180,
max_count=None,
**kwargs):
"""
Read raw sinogram from file.
:param fname: file name
:param type: file format
:param center: rotation center
:param preprocess: whether or not to preprocess the sinogram to remove singularities
:param pixel_size: pixel size (um)
:param kwargs:
:return:
"""
if type == 'hdf5':
slice = kwargs['slice']
raw_sino = np.squeeze(
dxchange.read_aps_32id(fname, sino=(slice, slice + 1)))
else:
raw_sino = dxchange.read_tiff(fname)
raw_sino = np.copy(raw_sino)
self.raw_sino = Sinogram(raw_sino,
'raw',
coords=center,
center=center,
normalize_bg=False,
minus_log=False,
fin_angle=fin_angle,
max_count=max_count)
self.pixel_size = pixel_size
def omni_read(f_input, begin=None, end=None):
'''support tiff, tiff stack, hdf5'''
if not f_input:
return None
f_input = os.path.abspath(f_input)
matches = re.match(
r'^(?P<dirname>.*)/(?P<fname>.*)\.(?P<ext>[^:]*)($|:(?P<dataset>.*$))',
f_input)
# print(matches.groupdict())
if matches['ext'] == 'tif' or matches['ext'] == 'tiff':
if begin is not None and end is not None:
data = dxchange.read_tiff_stack(f_input, ind=range(begin, end))
else:
# print(f_input)
S, L = check_stack_len(f_input)
# print(S,L)
if L > 1:
data = dxchange.read_tiff_stack(f_input, ind=range(S, S + L))
else:
data = dxchange.read_tiff(f_input)
elif matches['ext'] == 'h5' or matches['ext'] == 'hdf5':
tokens = f_input.split(':')
dataset_name = tokens[1]
f_input = h5py.File(tokens[0], 'r')
data = np.asarray(f_input[tokens[1]])
else:
print('not implemented file type')
return data
def find_center_single(sino_name,
search_range,
search_step=1,
preprocess_single=False,
method='entropy',
output_fname='center_pos.txt'):
log = open(output_fname, 'a')
center_st, center_end = search_range
sino = dxchange.read_tiff(sino_name)
if sino.ndim == 2:
sino = sino.reshape([sino.shape[0], 1, sino.shape[1]])
if preprocess_single:
sino = preprocess(np.copy(sino))
if method == 'manual':
write_center(sino,
tomopy.angles(sino.shape[0]),
dpath='center',
cen_range=(center_st, center_end, search_step))
elif method == 'vo':
mid = sino.shape[2] / 2
smin = (center_st - mid) * 2
smax = (center_end - mid) * 2
center = find_center_vo(sino, smin=smin, smax=smax, step=search_step)
internal_print('Center is {}.'.format(center))
log.write('{}\n'.format(center))
log.close()
def _func(i):
wpu.print_blue("MESSAGE: loop " + str(i) + ": " + listOfDataFiles[i])
img = dxchange.read_tiff(listOfDataFiles[i])
darkMeanValue = np.mean(wpu.crop_matrix_at_indexes(img, idx4cropDark))
#TODO xshi, need to add option of input one value
img = img - darkMeanValue # calculate and remove dark
img = wpu.crop_matrix_at_indexes(img, idx4crop)
pv = int(period_harm_Vert / (sourceDistanceV + zvec[i]) *
(sourceDistanceV + np.min(zvec)))
ph = int(period_harm_Horz / (sourceDistanceH + zvec[i]) *
(sourceDistanceH + np.min(zvec)))
if plotFourierImages:
wgi.plot_harmonic_grid(img, [pv, ph], isFFT=False)
plt.savefig('FFT_{:.0f}mm.png'.format(zvec[i] * 1e3))
plt.show(block=False)
plt.close()
wgi.plot_harmonic_peak(img, [pv, ph], isFFT=False)
plt.savefig('FFT_peaks_{:.0f}mm.png'.format(zvec[i] * 1e3))
plt.show(block=False)
plt.close()
return wgi.visib_1st_harmonics(img, [pv, ph],
searchRegion=searchRegion,
unFilterSize=unFilterSize)
def retrieve_phase_far_field(src_fname,
save_path,
output_fname=None,
pad_length=256,
n_epoch=100,
learning_rate=0.001):
# raw data is assumed to be centered at zero frequency
prj_np = dxchange.read_tiff(src_fname)
if output_fname is None:
output_fname = os.path.basename(
os.path.splitext(src_fname)[0]) + '_recon'
# take modulus and inverse shift
prj_np = ifftshift(np.sqrt(prj_np))
obj_init = np.random.normal(50, 10, list(prj_np.shape) + [2])
obj = tf.Variable(obj_init, dtype=tf.float32, name='obj')
prj = tf.constant(prj_np, name='prj')
obj_real = tf.cast(obj[:, :, 0], dtype=tf.complex64)
obj_imag = tf.cast(obj[:, :, 1], dtype=tf.complex64)
# obj_pad = tf.pad(obj, [[pad_length, pad_length], [pad_length, pad_length], [0, 0]], mode='SYMMETRIC')
det = tf.fft2d(obj_real + 1j * obj_imag, name='detector_plane')
loss = tf.reduce_mean(tf.squared_difference(tf.abs(det), prj, name='loss'))
sess = tf.Session()
optimizer = tf.train.AdamOptimizer(learning_rate=learning_rate)
optimizer = optimizer.minimize(loss)
sess.run(tf.global_variables_initializer())
for i_epoch in range(n_epoch):
t0 = time.time()
_, current_loss = sess.run([optimizer, loss])
print('Iteration {}: loss = {}, Δt = {} s.'.format(
i_epoch, current_loss,
time.time() - t0))
det_final = sess.run(det)
obj_final = sess.run(obj)
res = np.linalg.norm(obj_final, 2, axis=2)
dxchange.write_tiff(res,
os.path.join(save_path, output_fname),
dtype='float32',
overwrite=True)
dxchange.write_tiff(fftshift(np.angle(det_final)),
os.path.join(save_path, 'detector_phase'),
dtype='float32',
overwrite=True)
dxchange.write_tiff(fftshift(np.abs(det_final)**2),
os.path.join(save_path, 'detector_mag'),
dtype='float32',
overwrite=True)
return
def search_in_folder_dnn(dest_folder,
window=((600, 600), (1300, 1300)),
dim_img=128,
seed=1337,
batch_size=50):
patch_size = (dim_img, dim_img)
nb_classes = 2
save_intermediate = False
# number of convolutional filters to use
nb_filters = 32
# size of pooling area for max pooling
nb_pool = 2
# convolution kernel size
nb_conv = 3
nb_evl = 100
fnames = glob.glob(os.path.join(dest_folder, '*.tiff'))
fnames = np.sort(fnames)
mdl = model(dim_img, nb_filters, nb_conv, nb_classes)
mdl.load_weights('weight_center.h5')
start_time = time.time()
Y_score = np.zeros((len(fnames)))
for i in range(len(fnames)):
print(fnames[i])
img = dxchange.read_tiff(fnames[i])
X_evl = np.zeros((nb_evl, dim_img, dim_img))
for j in range(nb_evl):
X_evl[j] = xlearn.img_window(img[window[0][0]:window[1][0],
window[0][1]:window[1][1]],
dim_img,
reject_bg=True,
threshold=1.2e-4,
reset_random_seed=True,
random_seed=j)
X_evl = xlearn.convolve_stack(X_evl, xlearn.get_gradient_kernel())
X_evl = xlearn.nor_data(X_evl)
if save_intermediate:
dxchange.write_tiff(X_evl,
os.path.join('debug', 'x_evl',
'x_evl_{}'.format(i)),
dtype='float32',
overwrite=True)
X_evl = X_evl.reshape(X_evl.shape[0], 1, dim_img, dim_img)
Y_evl = mdl.predict(X_evl, batch_size=batch_size)
Y_score[i] = sum(np.dot(Y_evl, [0, 1]))
# print('The evaluate score is:', Y_score[i])
# Y_score = sum(np.round(Y_score))/len(Y_score)
ind_max = np.argmax(Y_score)
best_center = float(os.path.splitext(fnames[ind_max])[0])
print('Center search done in {} s. Optimal center is {}.'.format(
time.time() - start_time, best_center))
return best_center
def _func(i):
wpu.print_blue("MESSAGE: loop " + str(i) + ": " + \
listOfDataFiles[i])
if idx == [0, -1, 0, -1]:
img = dxchange.read_tiff(listOfDataFiles[i]) - dark_im
else:
img = wpu.crop_matrix_at_indexes(dxchange.read_tiff(listOfDataFiles[i]), idx) - dark_im
pv, ph = period_harm_Vert, period_harm_Horz
pv = int(period_harm_Vert/(sourceDistance + zvec[i]-zvec[0])*sourceDistance)
ph = int(period_harm_Horz/(sourceDistance + zvec[i]-zvec[0])*sourceDistance)
return wgi.visib_1st_harmonics(img, [pv, ph], searchRegion=10)
def setUp(self):
"""Load the test dataset from the disk."""
# Model parameters
self.n = 128 # object size n x,y
self.nz = 128 # object size in z
self.ntheta = 128 * 3 // 2 # number of angles (rotations)
self.center = self.n / 2 # rotation center
self.theta = np.linspace(0, np.pi,
self.ntheta).astype('float32') # angles
self.niter = 128 # tomography iterations
self.pnz = 128 # number of slice partitions
# Load object
beta = dxchange.read_tiff(
os.path.join(testdir, 'data', 'beta-chip-128.tiff'))
delta = dxchange.read_tiff(
os.path.join(testdir, 'data', 'delta-chip-128.tiff'))
self.u0 = delta + 1j * beta
def minimum_entropy(folder, pattern='*.tiff', range=(-0.002, 0.002)):
flist = glob.glob(os.path.join(folder, pattern))
a = []
s = []
for fname in flist:
img = dxchange.read_tiff(fname)
s.append(entropy(img, range=range))
a.append(fname)
return a[np.argmin(s)]
def red_stack_tiff(path):
# path0 = 'D:/pycharm/pycharm/py/resig/data/shapp3d_160/'
files = os.listdir(path)
prj = []
# prj0 = np.zeros((len(files), size, size))
for n,file in enumerate(files):
if is_image_file(file):
p = dxchange.read_tiff(path + file)
prj.append(p)
pr = np.array(prj)
return pr
def minimum_entropy(folder, pattern='*.tiff', range=None, mask_ratio=0.9, window=None, ring_removal=True,
center_x=None, center_y=None, reliability_screening=False, verbose=False):
flist = glob.glob(os.path.join(folder, pattern))
flist.sort()
a = []
s = []
if range is None:
temp = dxchange.read_tiff(flist[int(len(flist) / 2)])
temp = temp.copy()
temp_std = np.std(temp)
temp_mean = np.mean(temp)
temp[np.where(temp > (temp_mean + temp_std * 10))] = temp_mean
temp[np.where(temp < (temp_mean - temp_std * 10))] = temp_mean
hist_min = temp.min()
hist_min = hist_min * 2 if hist_min < 0 else hist_min * 0.5
hist_max = temp.max()
hist_max = hist_max * 2 if hist_max > 0 else hist_min * 0.5
range = (hist_min, hist_max)
print('Auto-determined histogram range is ({}, {}).'.format(hist_min, hist_max))
for fname in flist:
if verbose:
print(fname)
img = dxchange.read_tiff(fname)
# if max(img.shape) > 1000:
# img = scipy.misc.imresize(img, 1000. / max(img.shape), mode='F')
# if ring_removal:
# img = np.squeeze(tomopy.remove_ring(img[np.newaxis, :, :]))
s.append(entropy(img, range=range, mask_ratio=mask_ratio, window=window, ring_removal=ring_removal,
center_x=center_x, center_y=center_y))
a.append(fname)
gc.collect()
if reliability_screening:
if a[np.argmin(s)] in [flist[0], flist[-1]]:
return None
elif abs(np.min(s) - np.mean(s)) < 0.2 * np.std(s):
return None
else:
return float(os.path.splitext(os.path.basename(a[np.argmin(s)]))[0])
else:
return float(os.path.splitext(os.path.basename(a[np.argmin(s)]))[0])
def minimum_entropy(folder, pattern='*.tiff', range=None, mask_ratio=0.9, window=None, ring_removal=True,
center_x=None, center_y=None, reliability_screening=False, verbose=False):
flist = glob.glob(os.path.join(folder, pattern))
flist.sort()
a = []
s = []
if range is None:
temp = dxchange.read_tiff(flist[int(len(flist) / 2)])
temp = temp.copy()
temp_std = np.std(temp)
temp_mean = np.mean(temp)
temp[np.where(temp > (temp_mean + temp_std * 10))] = temp_mean
temp[np.where(temp < (temp_mean - temp_std * 10))] = temp_mean
hist_min = temp.min()
hist_min = hist_min * 2 if hist_min < 0 else hist_min * 0.5
hist_max = temp.max()
hist_max = hist_max * 2 if hist_max > 0 else hist_min * 0.5
range = (hist_min, hist_max)
print('Auto-determined histogram range is ({}, {}).'.format(hist_min, hist_max))
for fname in flist:
if verbose:
print(fname)
img = dxchange.read_tiff(fname)
# if max(img.shape) > 1000:
# img = scipy.misc.imresize(img, 1000. / max(img.shape), mode='F')
# if ring_removal:
# img = np.squeeze(tomopy.remove_ring(img[np.newaxis, :, :]))
s.append(entropy(img, range=range, mask_ratio=mask_ratio, window=window, ring_removal=ring_removal,
center_x=center_x, center_y=center_y))
a.append(fname)
gc.collect()
if reliability_screening:
if a[np.argmin(s)] in [flist[0], flist[-1]]:
return None
elif abs(np.min(s) - np.mean(s)) < 0.2 * np.std(s):
return None
else:
return float(os.path.splitext(os.path.basename(a[np.argmin(s)]))[0])
else:
return float(os.path.splitext(os.path.basename(a[np.argmin(s)]))[0])
def fourier_ring_correlation(obj,
ref,
step_size=1,
save_path='frc',
save_mask=False):
if not os.path.exists(save_path):
os.makedirs(save_path)
radius_max = int(min(obj.shape) / 2)
f_obj = np_fftshift(fft2(obj))
f_ref = np_fftshift(fft2(ref))
f_prod = f_obj * np.conjugate(f_ref)
f_obj_2 = np.real(f_obj * np.conjugate(f_obj))
f_ref_2 = np.real(f_ref * np.conjugate(f_ref))
radius_ls = np.arange(1, radius_max, step_size)
fsc_ls = []
np.save(os.path.join(save_path, 'radii.npy'), radius_ls)
for rad in radius_ls:
print(rad)
if os.path.exists(
os.path.join(save_path,
'mask_rad_{:04d}.tiff'.format(int(rad)))):
mask = dxchange.read_tiff(
os.path.join(save_path,
'mask_rad_{:04d}.tiff'.format(int(rad))))
else:
mask = generate_ring(obj.shape, rad, anti_aliasing=2)
if save_mask:
dxchange.write_tiff(
mask,
os.path.join(save_path,
'mask_rad_{:04d}.tiff'.format(int(rad))),
dtype='float32',
overwrite=True)
fsc = abs(np.sum(f_prod * mask))
fsc /= np.sqrt(np.sum(f_obj_2 * mask) * np.sum(f_ref_2 * mask))
fsc_ls.append(fsc)
np.save(os.path.join(save_path, 'fsc.npy'), fsc_ls)
matplotlib.rcParams['pdf.fonttype'] = 'truetype'
fontProperties = {
'family': 'serif',
'serif': ['Times New Roman'],
'weight': 'normal',
'size': 12
}
plt.rc('font', **fontProperties)
plt.plot(radius_ls.astype(float) / radius_ls[-1], fsc_ls)
plt.xlabel('Spatial frequency (1 / Nyquist)')
plt.ylabel('FRC')
plt.savefig(os.path.join(save_path, 'frc.pdf'), format='pdf')
def global_histogram(dmin, dmax, n_bins, plot=True):
tiff_list = glob.glob('*.tiff')
mybins = np.linspace(dmin, dmax, n_bins + 1)
myhist = np.zeros(n_bins, dtype='int32')
bin_width = (dmax - dmin) / n_bins
for fname in tiff_list:
print('Now analyzing' + fname)
temp = dxchange.read_tiff(fname).flatten()
temp = np.ndarray.flatten(temp)
myhist = myhist + np.histogram(temp, bins=mybins)[0]
if plot:
plt.bar(mybins[:-1], myhist, width=bin_width)
plt.show()
return myhist, mybins
def parse_source_folder(src_dir, prefix):
flist = glob.glob(os.path.join(src_dir, prefix + '*.tif*'))
raw_img = np.squeeze(dxchange.read_tiff(flist[0]))
raw_img_shape = raw_img.shape
theta_full_ls = []
dist_ls = []
for f in flist:
i_theta = int(re.findall(r'\d+', f)[-2])
i_dist = int(re.findall(r'\d+', f)[-1])
theta_full_ls.append(i_theta)
dist_ls.append(i_dist)
theta_ls = np.unique(theta_full_ls)
n_theta = len(theta_ls)
n_dist = len(flist) // n_theta
ind_ls = np.array(theta_full_ls) * n_dist + np.array(dist_ls)
flist = np.array(flist)[np.argsort(ind_ls)]
return flist, n_theta, n_dist, raw_img_shape
def reorganize_tiffs():
tiff_list = glob.glob('*.tiff')
for fname in tiff_list:
print('Now processing ' + str(fname))
# make downsampled subdirectories
for ds in [1, 2, 4]:
# create downsample folder if not existing
folder_name = 'tiff_' + str(ds) + 'x'
if not os.path.exists(folder_name):
os.mkdir(folder_name)
# copy file if downsample level is 1
if ds == 1:
shutil.copyfile(fname, folder_name + '/' + fname)
# otherwise perform downsampling
else:
temp = dxchange.read_tiff(fname).flatten()
temp = image_downsample(temp, ds)
dxchange.write_tiff(temp, folder_name + '/' + fname)
def fourier_ring_correlation(obj, ref, step_size=1, save_path=None, save_mask=True, save_fname='fsc', threshold_curve=False):
if not os.path.exists(save_path):
os.makedirs(save_path)
if obj.ndim == 2:
fft_func = fft2
gen_mask = generate_ring
gen_kwargs = {'anti_aliasing: 2'}
elif obj.ndim == 3:
fft_func = fftn
gen_mask = generate_shell
gen_kwargs = {}
radius_max = min(obj.shape) // 2
f_obj = np_fftshift(fft_func(obj))
f_ref = np_fftshift(fft_func(ref))
f_prod = f_obj * np.conjugate(f_ref)
f_obj_2 = np.real(f_obj * np.conjugate(f_obj))
f_ref_2 = np.real(f_ref * np.conjugate(f_ref))
radius_ls = np.arange(1, radius_max, step_size)
fsc_ls = []
if save_path is not None:
np.save(os.path.join(save_path, 'radii.npy'), radius_ls)
for rad in radius_ls:
if os.path.exists(os.path.join(save_path, 'mask_rad_{:04d}.tiff'.format(int(rad)))):
mask = dxchange.read_tiff(os.path.join(save_path, 'mask_rad_{:04d}.tiff'.format(int(rad))))
else:
mask = gen_mask(obj.shape, rad, **gen_kwargs)
if save_mask:
dxchange.write_tiff(mask, os.path.join(save_path, 'mask_rad_{:04d}.tiff'.format(int(rad))),
dtype='float32', overwrite=True)
fsc = abs(np.sum(f_prod * mask))
fsc /= np.sqrt(np.sum(f_obj_2 * mask) * np.sum(f_ref_2 * mask))
fsc_ls.append(fsc)
if save_path is not None:
np.save(os.path.join(save_path, '{}.npy'.format(save_fname)), fsc_ls)
return np.array(fsc_ls)
patch_size = (dim_img, dim_img)
mdl = model(dim_img, nb_filters, nb_conv)
mdl.load_weights('transform_training_weights.h5')
print('Predicting')
folder = '../../test/test_data/'
files = [f for f in sorted(os.listdir(folder)) if re.match(r'.+.tiff', f)]
for fname in files:
time_start = time.time()
sname = fname.split('.')
time_start = time.time()
fname_save = folder + sname[0] + '_result'
img_test = dxchange.read_tiff(folder + fname)
img_rec = predict(mdl, img_test, patch_size, patch_step, batch_size, dim_img)
dxchange.write_tiff(img_rec, fname_save, dtype='float32')
print(time.time()-time_start)
for k in range(data.shape[0]):
h, e = np.histogram(data[k][:], 1000)
stend = np.where(h > np.max(h) * 0.005)
st = stend[0][0]
end = stend[0][-1]
mmin[k] = e[st]
mmax[k] = e[end + 1]
return mmin, mmax
if __name__ == "__main__":
# read data and angles
data = dxchange.read_tiff(
'/home/beams0/VNIKITIN/lamino_doga/lamalign/data/matlab_rec/matlab-recon.tif'
).astype('float32') #[:, ::4, ::4]
theta = np.load(
'/home/beams0/VNIKITIN/lamino_doga/lamalign/data/matlab_rec/angle.npy'
).astype('float32') / 180 * np.pi
idset = np.int(sys.argv[1])
data = data[idset::2]
theta = theta[idset::2]
#ids_bad = np.array([29,44,56,102,152])
phi = 61.18 / 180 * np.pi
det = data.shape[2]
ntheta = data.shape[0]
# normalize data for optical flow computations
mmin, mmax = find_min_max(data)
import os
import matplotlib.pyplot as plt
import matplotlib
# data_folder = '/raid/home/mingdu/data/VS72_Again_180_25kev_lens10x_dfocus12cm_76_y1_x0/localtomo'
data_folder = '/raid/home/mingdu/data/shirley/local_tomo'
# data_folder = '/raid/home/mingdu/data/charcoal/local_tomo'
# data_folder = '/raid/home/mingdu/data/SAMPLE_03/panos'
# full_proj_fname = 'proj_raw_mlog.tiff'
full_proj_fname = '0_norm.tiff'
# full_proj_fname = 'frame0900-2.tiff'
tile_size = (1200, 1920)
half_tile_size = np.floor((np.array(tile_size) / 2)).astype('int')
shift = 1700
central_slice = 10068
full_proj = dxchange.read_tiff(os.path.join(data_folder, full_proj_fname))
full_proj = np.squeeze(full_proj)
# pos_ls = range(0, full_proj.shape[-1] - tile_size[0] + 1, shift)
pos_ls = range(0, 12816 - tile_size[0] + 1, shift)
photon_multiplier_ls = [10, 20, 50, 100, 200, 500, 1000, 2000, 5000, 10000]
mean_diff_ls = []
for ph_mult in photon_multiplier_ls:
print('Multiplier: {}'.format(ph_mult))
abs_diff_ls = []
for i, pos in enumerate(pos_ls):
tile = full_proj[central_slice - half_tile_size[0]:central_slice +
half_tile_size[0], pos:pos + tile_size[1]]
tile = np.exp(-tile) * ph_mult
# dxchange.write_tiff(tile, os.path.join(data_folder, 'proj_tiles', '{}'.format(ph_mult), '{:02d}_poi'.format(i)),
__authors__ = "Walan Grizolli"
__copyright__ = "Copyright (c) 2016, Affiliation"
__version__ = "0.1.0"
# =============================================================================
# %% preamble. Load parameters from ini file
# =============================================================================
inifname = '.speckleAnalyses.ini'
config, ini_pars, ini_file_list = wpu.load_ini_file_terminal_dialog(inifname)
fname = ini_file_list.get('image_filename')
image = dxchange.read_tiff(fname)
image_ref = dxchange.read_tiff(ini_file_list.get('ref_filename'))
idx = list(map(int, ini_pars.get('crop').split(',')))
pixelsize = float(ini_pars.get('pixel size'))
phenergy = float(ini_pars.get('photon energy'))
distDet2sample = float(ini_pars.get('distance detector to sample'))
halfsubwidth = int(ini_pars.get('halfsubwidth'))
halfTemplateSize = int(ini_pars.get('halfTemplateSize'))
subpixelResolution = int(ini_pars.get('subpixelResolution'))
npointsmax = int(ini_pars.get('npointsmax'))
ncores = float(ini_pars.get('ncores')) / float(ini_pars.get('ncores of machine'))
saveH5 = ini_pars.get('save hdf5 files')
if subpixelResolution < 1: subpixelResolution = None
if halfTemplateSize < 1: halfTemplateSize = None
import signal
import sys
import cupy as cp
import dxchange
import numpy as np
import tomocg as pt
if __name__ == "__main__":
# Model parameters
n = 128 # object size n x,y
nz = 128 # object size in z
ntheta = 128 # number of angles (rotations)
center = n / 2 # rotation center
theta = np.linspace(0, np.pi, ntheta).astype('float32') # angles
niter = 64 # tomography iterations
pnz = 32 # number of slice partitions for simultaneous processing in tomography
# Load object
beta = dxchange.read_tiff('data/beta-chip-128.tiff')
delta = dxchange.read_tiff('data/delta-chip-128.tiff')
u0 = delta + 1j * beta
# Class gpu solver
with pt.SolverTomo(theta, ntheta, nz, n, pnz, center) as slv:
# generate data
data = slv.fwd_tomo_batch(u0)
# adjoint test
u1 = slv.adj_tomo_batch(data)
print('Adjoint test: ', np.sum(data * np.conj(data)), '=?',
np.sum(u0 * np.conj(u1)))
parser = argparse.ArgumentParser()
parser.add_argument('--epoch', default='None')
parser.add_argument('--save_path', default='cell/ptychography')
parser.add_argument('--output_folder', default='test') # Will create epoch folders under this
args = parser.parse_args()
epoch = args.epoch
if epoch == 'None':
epoch = 0
init = None
else:
epoch = int(epoch)
if epoch == 0:
init = None
else:
init_delta = dxchange.read_tiff(os.path.join(args.save_path, args.output_folder, 'epoch_{}/delta_ds_1.tiff'.format(epoch - 1)))
init_beta = dxchange.read_tiff(os.path.join(args.save_path, args.output_folder, 'epoch_{}/beta_ds_1.tiff'.format(epoch - 1)))
print(os.path.join(args.save_path, args.output_folder, 'epoch_{}/delta_ds_1.tiff'.format(epoch - 1)))
init = [np.array(init_delta[...]), np.array(init_beta[...])]
params_2d_cell = {'fname': 'data_cell_phase.h5',
'theta_st': 0,
'theta_end': 0,
'theta_downsample': 1,
'n_epochs': 200,
'obj_size': (325, 325, 1),
'alpha_d': 0,
'alpha_b': 0,
'gamma': 0,
'probe_size': (72, 72),
@author: Hannah
"""
import dxchange
import matplotlib.pyplot as plt
from xlearn.transform import train
from xlearn.transform import model
batch_size=800
nb_epoch=10
dim_img=20
nb_filters=32
nb_conv=3
patch_step=4
patch_size=(dim_img, dim_img)
img_x=dxchange.read_tiff('C:/Users/Hannah/Downloads/python programs/original_input/image235/235_normal.tif')
img_y=dxchange.read_tiff('C:/Users/Hannah/Downloads/python programs/original_input/image235/235_label.tif')
plt.imshow(img_x, cmap='Greys_r')
plt.show()
plt.imshow(img_y, cmap='Greys_r')
plt.show()
mdl=train(img_x, img_y, patch_size, patch_step, dim_img, nb_filters, nb_conv, batch_size, nb_epoch)
mdl.save_weights('training_weights.h5')
import dxchange
import numpy as np
from transform import train, predict
batch_size = 400
nb_epoch = 50
dim_img = 64
nb_filters = 40
nb_conv = 3
patch_step = 1
patch_size = (dim_img, dim_img)
smooth = 1.
test1 = dxchange.read_tiff('/home/beams/YANGX/ptychography/datatolearn/lr_0034.tiff')
ih, iw = test1.shape
img_prd = np.zeros((ih, iw))
wpath = 'th_weights/full2.h5'
img1 = test1[:ih/2, :iw/2]
img_rec1 = predict(img1, patch_size, patch_step, nb_filters, nb_conv, batch_size, dim_img, wpath)
img_prd[:ih/2, :iw/2] = img_rec1
img1 = test1[ih/2+1:, iw/2+1:]
img_rec1 = predict(img1, patch_size, patch_step, nb_filters, nb_conv, batch_size, dim_img, wpath)
img_prd[ih/2+1:, iw/2+1:] = img_rec1
img1 = test1[:ih/2, iw/2+1:]
img_rec1 = predict(img1, patch_size, patch_step, nb_filters, nb_conv, batch_size, dim_img, wpath)
img_prd[:ih/2, iw/2+1:] = img_rec1
img1 = test1[ih/2+1:, :iw/2]
from utils.image_io import *
from skimage.measure import compare_psnr
import numpy as np
import torch
import torch.nn as nn
from collections import namedtuple
import dxchange
import matplotlib
matplotlib.use('TkAgg')
import os
from crosstalk_separation import *
if __name__ == "__main__":
img = dxchange.read_tiff('data/au_ni.tiff')
img = img[114:114 + 272, 114:-114, :]
img = np.transpose(img, (2, 0, 1))
img = normalize(img)
# fig, axes = plt.subplots(1, 2, figsize=(8, 4))
# axes[0].imshow(img[0])
# axes[1].imshow(img[1])
# plt.show()
input1 = img[0].reshape([1, *img[0].shape])
input2 = img[1].reshape([1, *img[1].shape])
# Separation from two images
t = TwoImagesSeparation('input1', 'input2', input1, input2, num_iter=7000)
t.optimize()
rec_ax = plt.axes([0.15, 0.15, 0.65, 0.03], facecolor=axcolor)
rec_amp = Slider(rec_ax, 'Rec Scale', 0.1, 300.0, valinit=150)
rec_amp.on_changed(update)
proj_ax = plt.axes([0.15, 0.05, 0.65, 0.03], facecolor=axcolor)
proj_amp = Slider(proj_ax, 'Proj Scale', 0.1, 4000.0, valinit=2000)
proj_amp.on_changed(update)
while True:
cnt += 1
if cnt % 5 == 0:
proj = dxchange.read_tiff(spath + 'proj.tif')
if im1 is None:
im1 = ax1.imshow(proj, cmap='gray', vmin=0, vmax=4000)
else:
im1.set_data(proj)
im1.set_clim(0, proj_amp.val)
fig.canvas.draw_idle()
plt.pause(0.01)
recon = dxchange.read_tiff(spath + 'recon.tif')
print(recon.shape, rec_amp.val, proj_amp.val)
if im2 is None:
im2 = ax2.imshow(recon, cmap='gray', vmin=0, vmax=300)
else:
im2.set_data(recon)
fname = '../../test/test_data/1038.tiff'
ind_uncenter1 = range(1038, 1047)
ind_uncenter2 = range(1049, 1057)
uncenter1 = dxchange.read_tiff_stack(fname, ind=ind_uncenter1, digit=4)
uncenter2 = dxchange.read_tiff_stack(fname, ind=ind_uncenter2, digit=4)
uncenter = np.concatenate((uncenter1, uncenter2), axis=0)
uncenter = nor_data(uncenter)
print (uncenter.shape)
uncenter = img_window(uncenter[:, 360:1460, 440:1440], 200)
print (uncenter.shape)
uncenter_patches = extract_3d(uncenter, patch_size, 1)
np.random.shuffle(uncenter_patches)
print (uncenter_patches.shape)
# print uncenter_patches.shape
center_img = dxchange.read_tiff('../../test/test_data/1048.tiff')
center_img = nor_data(center_img)
print (center_img.shape)
center_img = img_window(center_img[360:1460, 440:1440], 400)
center_patches = extract_3d(center_img, patch_size, 1)
np.random.shuffle(center_patches)
print (center_patches.shape)
# plt.imshow(center_img, cmap='gray', interpolation= None)
# plt.show()
x_train = np.concatenate((uncenter_patches[0:50000], center_patches[0:50000]), axis=0)
x_test = np.concatenate((uncenter_patches[50000:60000], center_patches[50000:60000]), axis=0)
x_train = x_train.reshape(x_train.shape[0], 1, dim_img, dim_img)
x_test = x_test.reshape(x_test.shape[0], 1, dim_img, dim_img)
y_train = np.zeros(100000)
y_train[50000:99999] = 1
det = [64, 64] # detector size
ntheta = 256*3//2 # number of angles (rotations)
noise = True # apply discrete Poisson noise
# Reconstrucion parameters
modela = ['poisson','gaussian'] # minimization funcitonal (poisson,gaussian)
alphaa = [1e-11,3e-7] # tv regularization penalty coefficient
piter = 4 # ptychography iterations
titer = 4 # tomography iterations
NITER = 400 # ADMM iterations
ptheta = 4 # NEW: number of angular partitions for simultaneous processing in ptychography
initshift = 0.0# NEW: Initial phase shift bubles: 128:0.8, chip 128: 0.0046, 256:0.0081
# Load a 3D object
beta0 = dxchange.read_tiff('data/beta-pad2-256.tiff')[42:42+16]#[32:32+16*bbin:bbin,::bbin,::bbin]#:2,::2,::2]
delta0 = -dxchange.read_tiff('data/delta-pad2-256.tiff')[42:42+16]#[32:32+16*bbin:bbin,::bbin,::bbin]#:2,::2,::2]
beta = np.zeros([2*prbsize+beta0.shape[0],beta0.shape[1],beta0.shape[2]],dtype='float32')
delta = np.zeros([2*prbsize+beta0.shape[0],beta0.shape[1],beta0.shape[2]],dtype='float32')
beta[prbsize:-prbsize] = beta0
delta[prbsize:-prbsize] = delta0
# print(beta.shape)
maxint = maxinta[igpu]
if(maxint>0.9):
noise = False
obj = cp.array(delta+1j*beta)
prb = cp.array(objects.probe(prbsize, maxint))#,rout=1.03))
theta = cp.linspace(0, np.pi, ntheta).astype('float32')
scan = cp.array(objects.scanner3(theta, obj.shape, prbshift,
prbshift, prbsize, spiral=0, randscan=True, save=False))
src_dir = 'data_rescaled_registered'
prefix = '*'
psize_cm = 99.8e-7
dist_cm_ls = np.array([7.36, 7.42, 7.70])
energy_ev = 17500
alpha_1 = 5e-4
alpha_2 = 1e-16
energy_kev = energy_ev * 1e-3
flist, n_theta, n_dists, raw_img_shape = adorym.parse_source_folder(
src_dir, prefix)
for i_theta in range(n_theta):
prj_ls = []
for i_dist in range(n_dists):
img = np.squeeze(dxchange.read_tiff(flist[i_theta * n_dists + i_dist]))
prj_ls.append(img)
phase = multidistance_ctf(prj_ls,
dist_cm_ls,
psize_cm,
energy_kev,
kappa=50,
sigma_cut=0.01,
alpha_1=alpha_1,
alpha_2=alpha_2)
dxchange.write_tiff(np.squeeze(phase),
os.path.join(
'data_ctf_orig',
os.path.basename(flist[i_theta * n_dists])),
dtype='float32',
overwrite=True)
nu_cut = 0.6 * u_max
f = 0.5 * (1 - erf((abs_nu - nu_cut) / sigma_cut))
alpha = alpha_1 * f + alpha_2 * (1 - f)
# plt.imshow(abs(np.log(np_fftshift(fft2(prj_ls[0] - 1, axes=(-2, -1)), axes=(-2, -1)))))
# plt.imshow(alpha)
# plt.show()
# alpha = 0
phase = np.sum(
np_fftshift(fft2(prj_ls - 1, axes=(-2, -1)), axes=(-2, -1)) *
(np.sin(xi_ls) + 1. / kappa * np.cos(xi_ls)),
axis=0)
phase /= (
np.sum(2 * (np.sin(xi_ls) + 1. / kappa * np.cos(xi_ls))**2, axis=0) +
alpha)
phase = ifft2(np_ifftshift(phase, axes=(-2, -1)), axes=(-2, -1))
return np.abs(phase)
if __name__ == '__main__':
import dxchange
a = dxchange.read_tiff('data/cameraman_512_dp.tiff')
a = tf.constant(a)
sess = tf.Session()
a = sess.run(gaussian_blur(a, 5, 2) - a)
plt.imshow(a)
plt.show()
# print(sess.run(image_entropy(a)))
# print(get_gaussian_kernel(5, sigma=2))
__authors__ = "Walan Grizolli"
__copyright__ = "Copyright (c) 2016, Affiliation"
__version__ = "0.1.0"
# =============================================================================
# %% preamble. Load parameters from ini file
# =============================================================================
inifname = '.speckleAnalyses.ini'
config, ini_pars, ini_file_list = wpu.load_ini_file_terminal_dialog(inifname)
fname = ini_file_list.get('image_filename')
image = dxchange.read_tiff(fname)
image_ref = dxchange.read_tiff(ini_file_list.get('ref_filename'))
idx = list(map(int, ini_pars.get('crop').split(',')))
pixelsize = float(ini_pars.get('pixel size'))
phenergy = float(ini_pars.get('photon energy'))
distDet2sample = float(ini_pars.get('distance detector to sample'))
halfsubwidth = int(ini_pars.get('halfsubwidth'))
halfTemplateSize = int(ini_pars.get('halfTemplateSize'))
subpixelResolution = int(ini_pars.get('subpixelResolution'))
npointsmax = int(ini_pars.get('npointsmax'))
ncores = float(ini_pars.get('ncores')) / float(ini_pars.get('ncores of machine'))
saveH5 = ini_pars.get('save hdf5 files')
if subpixelResolution < 1: subpixelResolution = None
if halfTemplateSize < 1: halfTemplateSize = None
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Example script
"""
from __future__ import print_function
from convnet.transform import train
import dxchange
batch_size = 800
nb_epoch = 10
dim_img = 20
nb_filters = 32
nb_conv = 3
patch_step = 4
patch_size = (dim_img, dim_img)
# read the training data
img_x = dxchange.read_tiff('../../test/test_data/training_input.tiff')
img_y = dxchange.read_tiff('../../test/test_data/training_output.tiff')
# train and save the model
model = train(img_x, img_y, patch_size, patch_step, dim_img, nb_filters, nb_conv, batch_size, nb_epoch)
model.save_weights('transform_training_weights.h5')
# %%
if __name__ == '__main__':
# ==========================================================================
# Experimental parameters
# ==========================================================================
(list_sample_files, list_ref_files, list_dark_files,
pixelSize, stepSize) = intial_setup()
# ==========================================================================
# % % Load one image and crop
# ==========================================================================
img = dxchange.read_tiff(list_sample_files[0])
[colorlimit,
cmap] = wpu.plot_slide_colorbar(img, title='Raw Image',
xlabel=r'x [$\mu m$ ]',
ylabel=r'y [$\mu m$ ]',
extent=wpu.extent_func(img, pixelSize)*1e6)
img_croped, idx4crop = wpu.crop_graphic(zmatrix=img, verbose=True,
kargs4graph={'cmap': cmap,
'vmin': colorlimit[0],
'vmax': colorlimit[1]})
# ==========================================================================
# %% Load tiff files to numpy array
pixelsize = [0.65e-6, 0.65e-6] # vertical and horizontal pixel sizes in meters
distDet2sample = 0.18600 # in meters
sourceDistance = 100.0 # in meters, for divergence correction. to ignore it, use a big number >100
phenergy = 8e3 # in eV
wavelength = wpu.hc/phenergy # wpu has an alias for hc
kwave = 2*np.pi/wavelength
# Phase grating paremeters
gratingPeriod = 4.8e-6 # in meters
# uncomment proper pattern period:
patternPeriod = gratingPeriod/np.sqrt(2.0) # if half Pi grating
#patternPeriod = gratingPeriod/2.0 # if Pi grating
img = dxchange.read_tiff('data_example_for_single_grating/cb4p8um_halfPi_8KeV_10s_img.tif')
imgRef = dxchange.read_tiff('data_example_for_single_grating/cb4p8um_halfPi_8KeV_10s_ref.tif')
darkImg = dxchange.read_tiff('data_example_for_single_grating/10s_dark.tif')
img = img - darkImg
imgRef = imgRef - darkImg
# %% crop
img, idx4crop = wpu.crop_graphic_image(img)
imgRef = wpu.crop_matrix_at_indexes(imgRef, idx4crop)
# %% Find harmonic in the Fourier images
# calculate the theoretical position of the hamonics
period_harm_Vert_o = np.int(pixelsize[0]/patternPeriod*img.shape[0] /
mdl = model(dim_img, nb_filters, nb_conv, nb_classes)
mdl.load_weights('weight_center.h5')
print('The model loading time is %s seconds'%(time.time()-start_time))
Y_score = np.zeros((50, 501))
for i in range(50):
slice_num = (i+2)*20
datapath = '/home/oxygen/YANGX/Globus/center/test_04/slice'+str(slice_num)+'/*.tiff'
# print(datapath)
fnames = glob.glob(datapath)
fnames = np.sort(fnames)
# print(fnames)
for j in range(len(fnames)):
img = dxchange.read_tiff(fnames[j])
img = -nor_data(img)
# X_evl = np.zeros((nb_evl, dim_img, dim_img))
# for k in range(nb_evl):
# X_evl[k] = img_window(img[360:1660, 440:1640], dim_img)
X_evl = extract_patches(img[360:1660, 440:1640],
(128, 128), step=64, max_patches=None, random_state=None)
X_evl = X_evl.reshape(X_evl.shape[0], 1, dim_img, dim_img)
Y_evl = mdl.predict(X_evl, batch_size=batch_size)
Y_score[i, j] = sum(np.dot(Y_evl, [0, 1]))
# print(Y_score[i])
#print('The evaluate score is:', Y_score[i])
#Y_score = sum(np.round(Y_score))/len(Y_score)
ind_max = np.argmax(Y_score[i, :])
def _load_experimental_pars(argv):
if len(argv) == 10:
fname_img, fname_imgRef, fname_blank = argv[1:4]
pixelsize = float(argv[4])*1e-6
gratingPeriod = float(argv[5])*1e-6
pattern = argv[6]
distDet2sample = float(argv[7])*1e-3
phenergy = float(argv[8])*1e3
sourceDistance = float(argv[9])
img, imgRef, blank = (dxchange.read_tiff(fname_img),
dxchange.read_tiff(fname_imgRef),
dxchange.read_tiff(fname_blank))
elif len(argv) == 1:
(fname_img, fname_imgRef, fname_blank,
pixelsize, gratingPeriod, pattern, distDet2sample,
phenergy, sourceDistance) = _intial_gui_setup(argv[0])
img, imgRef, blank = (dxchange.read_tiff(fname_img),
dxchange.read_tiff(fname_imgRef),
dxchange.read_tiff(fname_blank))
else:
print('ERROR: wrong number of inputs: {} \n'.format(len(argv)-1) +
'Usage: \n'
'\n'
'singleGratingTalbotImaging.py : (no inputs) load dialogs \n'
'\n'
'singleGratingTalbotImaging.py [args] \n'
'\n'
'arg1: file name main image\n'
'arg2: file name reference image\n'
'arg3: file name dark image\n'
'arg4: pixel size [um]\n'
'arg5: Check Board grating period [um]\n'
"arg6: pattern, 'Edge pi' or 'Diagonal half pi' \n"
'arg7: distance detector to CB Grating [mm]\n'
'arg8: Photon Energy [KeV]\n'
'arg9: Distance to the source [m], to correct for beam\n'
' divergence (use 1e5 to ignore this, which means\n'
' source at infinity and zero divergence)\n'
'\n')
exit(-1)
img = img - blank
imgRef = imgRef - blank
pixelsize = [pixelsize, pixelsize]
# change here if you need rectangular pixel
if pattern == 'Diagonal half pi':
gratingPeriod *= 1.0/np.sqrt(2.0)
phaseShift = 'halfPi'
elif pattern == 'Edge pi':
gratingPeriod *= 1.0/2.0
phaseShift = 'Pi'
saveFileSuf = 'cb{:.2f}um_'.format(gratingPeriod*1e6)
saveFileSuf += phaseShift
saveFileSuf += '_d{:.0f}mm_'.format(distDet2sample*1e3)
saveFileSuf += '{:.1f}KeV'.format(phenergy*1e-3)
saveFileSuf = saveFileSuf.replace('.', 'p')
return (img, imgRef, saveFileSuf,
pixelsize, gratingPeriod, pattern,
distDet2sample,
phenergy, sourceDistance)
distDet2sample = 0.18600 # in meters
sourceDistance = 100.0 # in meters, for divergence correction. to ignore it, use a big number >100
phenergy = 8e3 # in eV
wavelength = wpu.hc/phenergy # wpu has an alias for hc
kwave = 2*np.pi/wavelength
# Phase grating paremeters
gratingPeriod = 4.8e-6 # in meters
# uncomment proper pattern period:
patternPeriod = gratingPeriod/np.sqrt(2.0) # if half Pi grating
#patternPeriod = gratingPeriod/2.0 # if Pi grating
img = dxchange.read_tiff('../../data4wavepy_examples/Dialens/cb_halfpi_4p8um_distace110mm_sample.tif')
imgRef = dxchange.read_tiff('../../data4wavepy_examples/Dialens/cb_halfpi_4p8um_distace110mm_ref.tif')
darkImg = dxchange.read_tiff('../../data4wavepy_examples/Dialens/dark.tif')
img = img - darkImg
imgRef = imgRef - darkImg
# %% Find harmonic in the Fourier images
# calculate the theoretical position of the hamonics
period_harm_Vert_o = np.int(pixelsize[0]/patternPeriod*img.shape[0])
period_harm_Hor_o = np.int(pixelsize[1]/patternPeriod*img.shape[1])
harmPeriod = [period_harm_Vert_o, period_harm_Hor_o]
"""
Example script
"""
from __future__ import print_function
from xlearn.transform import train
import dxchange
batch_size = 800
nb_epoch = 10
dim_img = 20
nb_filters = 32
nb_conv = 3
patch_step = 4
patch_size = (dim_img, dim_img)
# read the training data
train_folder ='/local/tomo/data/cnn/Al-10Sn-4Si-1Cu-Er-Zr/train/'
img_x = dxchange.read_tiff(train_folder + 'Slice_0563-segmentation.tiff')
img_y = dxchange.read_tiff(train_folder + 'Slice_0563.tiff')
# train and save the model
model = train(img_x, img_y, patch_size, patch_step, dim_img, nb_filters, nb_conv, batch_size, nb_epoch)
model.save_weights('transform_training_weights_al10.h5')