def crop_image(in_file, out_file, side, center=None):
"""Function to crop an h5 image and pad with zeros around it"""
img = spimage.sp_image_read(in_file, 0)
if not center:
center = img.detector.image_center[:2]
shifted = 0
if img.shifted:
shifted = 1
img = spimage.sp_image_shift(img)
cropped = spimage.sp_image_alloc(side, side, 1)
cropped.image[:, :] = image_manipulation.crop_and_pad(
img.image, center, side)
cropped.mask[:, :] = image_manipulation.crop_and_pad(
img.mask, center, side)
if shifted:
cropped = spimage.sp_image_shift(cropped)
spimage.sp_image_write(cropped, out_file, 16)
spimage.sp_image_free(img)
spimage.sp_image_free(cropped)
print("end")
def intensities_array_to_h5(img0,msk0,cx=None,cy=None,cropLength=None,save_to_file=None):
import spimage,imgtools
Nx = img0.shape[1]
Ny = img0.shape[0]
img = img0
msk = msk0
if cropLength != None:
img = imgtools.crop(img0,cropLength,center=[cy,cx])
msk = imgtools.crop(msk0,cropLength,center=[cy,cx])
Nx = cropLength
Ny = cropLength
elif cx != None and cy != None:
img = imgtools.recenter(img0,cx,cy)
msk = imgtools.recenter(msk0,cx,cy)
I = spimage.sp_image_alloc(Nx,Ny,1)
I.image[:,:] = img[:,:]
I.mask[:,:] = msk[:,:]
I2 = spimage.sp_image_shift(I)
I2.shifted = 0
I2.phased = 0
spimage.sp_image_free(I)
if save_to_file != None:
spimage.sp_image_write(I2,save_to_file,0)
else:
return I2
def crop_image(in_file, out_file, sideX, sideY = 0):
if sideY == 0:
sideY = sideX
try:
img = spimage.sp_image_read(in_file,0)
except:
print "Error: %s is not a readable .h5 file\n" % in_file
exit(1)
shifted = 0
if img.shifted:
shifted = 1
img = spimage.sp_image_shift(img)
print "shifted = ", shifted
lowX = img.detector.image_center[0]-(sideX/2.0-0.5)
highX = img.detector.image_center[0]+(sideX/2.0-0.5)
lowY = img.detector.image_center[1]-(sideY/2.0-0.5)
highY = img.detector.image_center[1]+(sideY/2.0-0.5)
print lowX, " ", highX
print lowY, " ", highY
if lowX != pylab.floor(lowX):
lowX = int(pylab.floor(lowX))
highX = int(pylab.floor(highX))
img.detector.image_center[0] -= 0.5
else:
lowX = int(lowX)
highX = int(highX)
if lowY != pylab.floor(lowY):
lowY = int(pylab.floor(lowY))
highY = int(pylab.floor(highY))
img.detector.image_center[1] -= 0.5
else:
lowY = int(lowY)
highY = int(highY)
cropped = spimage.rectangle_crop(img,lowX,lowY,highX,highY)
print "did crop"
if shifted:
cropped = spimage.sp_image_shift(cropped)
print "shifted (or not)"
print "write ", out_file
#print "orientation = ", cropped.detector.orientation
#print spimage.sp_3matrix_get(cropped.detector.orientation,0,0,0)
try:
spimage.sp_image_write(cropped,out_file,16)
except:
print "Error: can not write to %s\n" % out_file
print "end"
def prep_emc_output_for_phasing(input_file, output_file, corner_to_zero=False):
"Sets all negative values in image to 0 and create a rectangular mask"
img = spimage.sp_image_read(input_file, 0)
#set all negative values to 0:
img.image[:, :, :] = img.image.clip(0)
#set corners of mask to 1:
r_array = stuff.r_array_3D(img.image.shape[0])
img.mask[r_array > img.image.shape[0] / 2. + 0.5] = 1
if corner_to_zero:
img.image[r_array > img.image.shape[0]] = 0.
spimage.sp_image_write(img, output_file, 0)
def to_png(input_dir, output_dir, plot_setup):
files = read_files(input_dir)
support_function = get_support_function(plot_setup.get_mask())
for f in files:
img = spimage.sp_image_read(f, 0)
support_function(img)
img = spimage.sp_image_shift(img)
output_file = output_dir + "/" + f[:-2] + "png"
spimage.sp_image_write(img, output_file, plot_setup.get_color())
spimage.sp_image_free(img)
def mask_center_and_negatives(img_file_name,
radius,
output_file_name,
save_file=True):
"""Creates a new mask around the center with given radius as well as masking out regions with negative values in the image."""
msk = mask_center(img_file_name, radius, output_file_name, save_file=False)
img = spimage.sp_image_read(img_file_name, 0)
msk.mask[real(img.image) < 0.] = 0
if save_file:
spimage.sp_image_write(msk, output_file_name, 0)
else:
return (msk)
def to_png(*arguments):
color,shift_flag,support_flag = evaluate_arguments(arguments)
files = read_files()
shift_function = get_shift_function(shift_flag)
support_function = get_support_function(support_flag)
for f in files:
img = spimage.sp_image_read(f,0)
support_function(img)
img = sp_image_shift(img)
spimage.sp_image_write(img,f[:-2]+"png",color)
spimage.sp_image_free(img)
def image_to_png(in_filename, out_filename, colorscale, shift):
try:
img = spimage.sp_image_read(in_filename,0)
except:
raise TypeError("%s is not a readable file" % in_filename)
if shift == 1:
img = spimage.sp_image_shift(img)
try:
spimage.sp_image_write(img,out_filename,colorscale)
except:
raise TypeError("Can not write %s" % out_filename)
def to_png(input_dir, output_dir, plot_setup):
#color,shift_flag,support_flag = evaluate_arguments(arguments)
files = read_files(input_dir)
shift_function = get_shift_function(plot_setup.get_shift())
support_function = get_support_function(plot_setup.get_mask())
for f in files:
img = spimage.sp_image_read(f,0)
support_function(img)
img = sp_image_shift(img)
spimage.sp_image_write(img,output_dir+"/"+f[:-2]+"png",plot_setup.get_color())
spimage.sp_image_free(img)
def image_to_png(in_filename, out_filename, colorscale, shift):
try:
img = spimage.sp_image_read(in_filename, 0)
except IOError:
raise TypeError(f"{in_filename} is not a readable file")
if shift == 1:
img = spimage.sp_image_shift(img)
try:
spimage.sp_image_write(img, out_filename, colorscale)
except IOError:
raise TypeError(f"Can not write {out_filename}")
def shift_image(in_file,out_file = 0):
try:
img = spimage.sp_image_read(in_file,0)
except:
raise IOError("Can't read %s" % in_file)
img_s = spimage.sp_image_shift(img)
if out_file == 0:
out_file = in_file
try:
spimage.sp_image_write(img_s,out_file,0)
except:
print "Error: Can not write to %s" % out_file
def pnccd_to_image(infile, outfile):
try:
f = h5py.File(infile)
except:
raise IOError("Can't read %s. It may not be a pnCCD file." % filename)
i1 = f.keys().index("data")
i2 = f.values()[i1].keys().index("data1")
data = f.values()[i1].values()[i2].value
img = spimage.sp_image_alloc(pylab.shape(data)[0], pylab.shape(data)[1], 1)
img.image[:, :] = data[:, :]
spimage.sp_image_write(img, outfile, 0)
spimage.sp_image_free(img)
def shift_image(in_file, out_file=0):
try:
img = spimage.sp_image_read(in_file, 0)
except IOError:
raise IOError(f"Can't read {in_file}")
img_s = spimage.sp_image_shift(img)
if out_file == 0:
out_file = in_file
try:
spimage.sp_image_write(img_s, out_file, 0)
except IOError:
print(f"Error: Can not write to {out_file}")
def split_pnccd(filename):
f = h5py.File(filename)
i1 = f.keys().index('data')
i2 = f.values()[i1].keys().index('data1')
i2 = f.values()[i1].keys().index('data1')
data2 = f.values()[i1].values()[i2].value
data2_1 = spimage.sp_image_alloc(data2.shape[1]/2,data2.shape[0],1)
data2_2 = spimage.sp_image_alloc(data2.shape[1]/2,data2.shape[0],1)
data2_1.image[:,:] = data2[:,:(data2.shape[1]/2)]
data2_2.image[:,:] = data2[:,(data2.shape[1]/2):]
spimage.sp_image_write(data2_1,filename[:-3]+"_part1.h5",0)
spimage.sp_image_write(data2_2,filename[:-3]+"_part2.h5",0)
def mask_center(img_file_name, radius, output_file_name=None, save_file=True):
"""Create a new mask around the center with given radius"""
img = spimage.sp_image_read(img_file_name, 0)
r_array = stuff.r_array_3D(img.image.shape[0])
img.mask[r_array < radius] = 0
img.mask[r_array > radius] = 1
new_mask = spimage.sp_image_alloc(*np.shape(img.mask))
new_mask.mask[:, :, :] = img.mask
new_mask.image[:, :, :] = img.image
new_mask.shifted = img.shifted
new_mask.scaled = img.scaled
new_mask.detector = img.detector
if save_file:
spimage.sp_image_write(new_mask, output_file_name, 0)
else:
return (new_mask)
def add_new_mask(img_file_name,
new_mask_file_name,
output_file_name,
imgtimesmask=False):
img = spimage.sp_image_read(img_file_name, 0)
new_mask = spimage.sp_image_read(new_mask_file_name, 0)
new_img = spimage.sp_image_alloc(*shape(img.image))
new_img.image[:, :, :] = img.image
new_img.shifted = img.shifted
new_img.scaled = img.scaled
new_img.detector = img.detector
new_img.mask[:, :, :] = new_mask.mask
spimage.sp_image_write(new_img, output_file_name, 0)
if imgtimesmask:
new_img.image[:, :, :] = img.image * new_mask.mask
spimage.sp_image_write(new_img, 'imgtimesmask.h5', 0)
def shift_image(in_file,out_file = 0):
try:
img = spimage.sp_image_read(in_file,0)
except:
print "Error: Can not read image %s" % in_file
return
img_s = spimage.sp_image_shift(img)
if out_file == 0:
out_file = in_file
try:
spimage.sp_image_write(img_s,out_file,0)
except:
print "Error: Can not write to %s" % out_file
def center_image(filename, outfile, sigma=3):
"""Finds a localized strong object and puts it in the center. The
sigma variable describes the size of the object"""
print("foo")
if not os.path.isfile(filename):
raise IOError("Can not find file {0}".format(filename))
img = spimage.sp_image_read(filename, 0)
x = (numpy.arange(img.image.shape[0], dtype='float64') -
img.image.shape[0] / 2. + 0.5)
y = (numpy.arange(img.image.shape[1], dtype='float64') -
img.image.shape[1] / 2. + 0.5)
z = (numpy.arange(img.image.shape[2], dtype='float64') -
img.image.shape[2] / 2. + 0.5)
kernel = numpy.exp(-(x[:, numpy.newaxis, numpy.newaxis]**2 +
y[numpy.newaxis, :, numpy.newaxis]**2 +
y[numpy.newaxis, numpy.newaxis, :]**2) / 2.0 /
sigma**2)
img_ft = numpy.fft.fft2(numpy.fft.fftshift(img.image))
kernel_ft = numpy.fft.fft2(numpy.fft.fftshift(kernel))
kernel_ft *= numpy.conj(img_ft)
bt = numpy.fft.ifft2(kernel_ft)
min_v = 0.
min_x = 0
min_y = 0
min_z = 0
for x in range(bt.shape[0]):
for y in range(bt.shape[1]):
for z in range(bt.shape[2]):
if abs(bt[z, y, x]) > min_v:
min_v = abs(bt[z, y, x])
min_x = x
min_y = y
min_z = z
print(min_x, min_y, min_z)
spimage.sp_image_translate(img, -(-min_z + bt.shape[0] // 2),
-(-min_y + bt.shape[1] // 2),
-(-min_x + bt.shape[2] // 2),
spimage.SP_TRANSLATE_WRAP_AROUND)
shift = img
spimage.sp_image_write(shift, outfile, 0)
spimage.sp_image_free(img)
def add_mask(path, number_of_files, output_file):
"""Reads in files in paths, outputs h5 file output_file with accumulative mask from input images saved in both image and mask"""
imgs = [
os.path.join(path, i) for i in os.listdir(path) if i.endswith('.h5')
]
for img_file in imgs[:number_of_files]:
img = spimage.sp_image_read(img_file, 0)
try:
msk_array = msk_array + img.mask
except NameError:
msk_array = img.mask
msk_array[msk_array < msk_array.max()] = 0
msk_array[msk_array != 0] = 1
new = spimage.sp_image_alloc(
numpy.shape(img.image)[0],
numpy.shape(img.image)[1], 1)
new.mask[:, :] = msk_array
new.image[:, :] = msk_array
spimage.sp_image_write(new, output_file, 0)
def calc_average_img(r2, r1=0, r_skip=None, iteration=None):
rundir_range = range(r1, r2)
if r_skip != None:
for i in r_skip:
rundir_range.remove(i)
fail = 0
for r in rundir_range:
run_dir = 'run_%04d' % r
print run_dir
if iteration == None:
iteration = return_last_iteration_integer(
'{r}/output_mnt/'.format(r=run_dir))
with h5py.File('{r}/output_mnt/fmodel_{i}.h5'.format(
r=run_dir, i=iteration)) as f:
try:
added_real += f['real'][...]
added_imag += f['imag'][...]
except NameError:
added_real = f['real'][...]
added_imag = f['imag'][...]
except KeyError:
print 'fail'
fail += 1
if r == r2 - 1:
mask = f['mask'][:]
added_real /= float(len(rundir_range) - fail)
added_imag /= float(len(rundir_range) - fail)
complex_fmodel = added_real + 1j * added_imag
new = spimage.sp_image_alloc(*np.shape(added_real))
new.phased = 1
new.mask[:] = mask
new.image[:] = complex_fmodel
spimage.sp_image_write(
new, 'avg_fmodel_runs_{i}_{j}_iteration{k}.h5'.format(i=r1,
j=r2,
k=iteration), 0)
new.image[:, :, :] = fft.fftn(complex_fmodel)
spimage.sp_image_write(
new, 'avg_model_runs_{i}_{j}_iteration{k}.h5'.format(i=r1,
j=r2,
k=iteration), 0)
def calc_average_img_translated(r2,
r1=0,
r_skip=None,
iteration=None,
reference_model=None):
rundir_range = range(r1, r2)
if r_skip != None:
for i in r_skip:
rundir_range.remove(i)
for r in rundir_range:
run_dir = 'run_%04d' % r
print run_dir
if iteration == None:
iteration = return_last_iteration_integer(
'{r}/output_mnt/'.format(r=run_dir))
f = spimage.sp_image_read(
'{r}/output_mnt/fmodel_{i}.h5'.format(r=run_dir, i=iteration), 0)
if r == r1:
if reference_model == None:
ref = f
else:
ref = reference_model
added_img = f.image[:]
mask = f.mask[:]
if r != r1:
spimage.sp_image_superimpose(ref, f, 0)
added_img += f.image[:]
added_img /= float(len(rundir_range))
new = spimage.sp_image_alloc(*np.shape(added_img))
new.phased = 1
new.mask[:] = mask
new.image[:] = added_img
spimage.sp_image_write(
new, 'avg_fmodel_runs_{i}_{j}_iteration{k}.h5'.format(i=r1,
j=r2,
k=iteration), 0)
new.image[:, :, :] = fft.fftn(added_img)
spimage.sp_image_write(
new, 'avg_model_runs_{i}_{j}_iteration{k}.h5'.format(i=r1,
j=r2,
k=iteration), 0)
def slice_3D(fn, output_dir=''):
#Takes 3 slices through the center along x,y and z from a 3D image and saves it as three new 2D images.
img_3D = spimage.sp_image_read(fn, 0)
dim = shape(img_3D.image)[0]
img_2D = spimage.sp_image_alloc(dim, dim, 1)
img_2D.shifted = img_3D.shifted
img_2D.scaled = img_3D.scaled
if img_3D.shifted == 0:
s = dim / 2
else:
s = 0
img_2D.image[:, :] = img_3D.image[s, :, :]
img_2D.mask[:, :] = img_3D.mask[s, :, :]
spimage.sp_image_write(img_2D,
output_dir + fn.split('.')[0] + '_x_slice.h5', 0)
img_2D.image[:, :] = img_3D.image[:, s, :]
img_2D.mask[:, :] = img_3D.mask[:, s, :]
spimage.sp_image_write(img_2D,
output_dir + fn.split('.')[0] + '_y_slice.h5', 0)
img_2D.image[:, :] = img_3D.image[:, :, s]
img_2D.mask[:, :] = img_3D.mask[:, :, s]
spimage.sp_image_write(img_2D,
output_dir + fn.split('.')[0] + '_z_slice.h5', 0)
def calc_average_img(path, cutoff=None):
if cutoff == None:
run_folders = []
run_folders = select_by_error_cutoff(path, cutoff)['run']
for r in run_folders:
img = spimage.sp_image_read(
r +
'/output_mnt/model_{n}.h5'.format(n=return_last_iteration_integer(
os.path.join(r, 'output_mnt'))), 0)
try:
added_imgs = added_imgs + img.image
except NameError:
added_imgs = img.image
avg_img = added_imgs / float(len(run_folders))
new = spimage.sp_image_alloc(*np.shape(img.image))
new.image[:, :, :] = avg_img
spimage.sp_image_write(
new,
'{p}/average_final_model_{c}_{t}.h5'.format(p=path,
c=cutoff,
t=time.strftime('%Y%m%d')),
0)
def crop_image(in_file, out_file, side, center=None):
"""Function to crop an h5 image and pad with zeros around it"""
img = spimage.sp_image_read(in_file, 0)
if not center:
center = img.detector.image_center[:2]
shifted = 0
if img.shifted:
shifted = 1
img = spimage.sp_image_shift(img)
print "shifted = ", shifted
# cropped = spimage.rectangle_crop(img,lowX,lowY,highX,highY)
cropped = spimage.sp_image_alloc(side, side, 1)
cropped.image[:, :] = image_manipulation.crop_and_pad(img.image, center, side)
cropped.mask[:, :] = image_manipulation.crop_and_pad(img.mask, center, side)
print "did crop"
if shifted:
cropped = spimage.sp_image_shift(cropped)
print "shifted (or not)"
print "write ", out_file
# print "orientation = ", cropped.detector.orientation
# print spimage.sp_3matrix_get(cropped.detector.orientation,0,0,0)
spimage.sp_image_write(cropped, out_file, 16)
spimage.sp_image_free(img)
spimage.sp_image_free(cropped)
print "end"
spimage.sp_phaser_init_model(phaser, None, spimage.SpModelRandomPhases)
spimage.sp_phaser_init_support(phaser, support, 0, 0)
def run_it(number_of_iterations):
spimage.sp_phaser_iterate(phaser, number_of_iterations)
run_it(NUMBER_OF_ITERATIONS)
phaser.algorithm = phase_alg_refine
run_it(NUMBER_OF_REFINE_ITERATIONS)
# Output data
model = spimage.sp_phaser_model(phaser)
support = spimage.sp_phaser_support(phaser)
fmodel = spimage.sp_phaser_fmodel(phaser)
spimage.sp_image_write(model, OUTPUT_DIR + "run_{}_model.h5".format(run_id), 0)
spimage.sp_image_write(support,
OUTPUT_DIR + "run_{}_support.h5".format(run_id), 0)
spimage.sp_image_write(fmodel, OUTPUT_DIR + "run_{}_fmodel.h5".format(run_id),
0)
ereal = spimage.sp_phaser_ereal(phaser)
efourier = spimage.sp_phaser_efourier(phaser)
filename = OUTPUT_DIR + '/run_{}_error.h5'.format(run_id)
with h5py.File(filename, "w") as file_handle:
file_handle.create_dataset('ereal', data=ereal)
file_handle.create_dataset('efourier', data=efourier)
# create phaser
phaser = _spimage.sp_phaser_alloc()
_spimage.sp_phaser_init(phaser, phase_alg, sup_alg, _spimage.SpEngineCUDA)
_spimage.sp_phaser_set_amplitudes(phaser, amplitudes)
_spimage.sp_phaser_init_model(phaser, real_space, 0)
_spimage.sp_phaser_init_support(phaser, support, 0, 0)
#real_space_s = _spimage.sp_image_shift(real_space)
fourier_space = _spimage.sp_image_ifftw3(real_space)
ereal_start = _numpy.sqrt((abs(real_space.image[~_numpy.bool8(support.image)])**2).sum() / (abs(real_space.image)**2).sum())
efourier_start = _numpy.sqrt(((abs(fourier_space.image[_numpy.bool8(amplitudes.mask)]) - abs(amplitudes.image[_numpy.bool8(amplitudes.mask)]))**2).sum() / ((abs(amplitudes.image[_numpy.bool8(amplitudes.mask)])**2).sum() + (abs(fourier_space.image[~_numpy.bool8(amplitudes.mask)])**2).sum()))
_spimage.sp_phaser_iterate(phaser, options.number_of_iterations)
model_out = _spimage.sp_phaser_model(phaser)
support_out = _spimage.sp_phaser_support(phaser)
fmodel_out = _spimage.sp_phaser_fmodel(phaser)
real_space_end = _spimage.sp_phaser_model_before_projection(phaser)
fourier_space_end = _spimage.sp_phaser_fmodel(phaser)
ereal_end = _numpy.sqrt((abs(real_space_end.image[~_numpy.bool8(support.image)])**2).sum() / (abs(real_space_end.image)**2).sum())
efourier_end = _numpy.sqrt(((abs(fourier_space_end.image[_numpy.bool8(amplitudes.mask)]) - abs(amplitudes.image[_numpy.bool8(amplitudes.mask)]))**2).sum() / ((abs(amplitudes.image[_numpy.bool8(amplitudes.mask)])**2).sum() + (abs(fourier_space_end.image[~_numpy.bool8(amplitudes.mask)])**2).sum()))
_spimage.sp_image_write(model_out, "%s/real_space-%s.h5" % (options.output_dir, options.output_affix), 0)
_spimage.sp_image_write(support_out, "%s/support-%s.h5" % (options.output_dir, options.output_affix), 0)
_spimage.sp_image_write(fmodel_out, "%s/fourier_space-%s.h5" % (options.output_dir, options.output_affix), 0)
print "Ereal: %g -> %g" % (ereal_start, ereal_end)
print "Efourier: %g -> %g" % (efourier_start, efourier_end)
np3 = np1[np.newaxis, np.newaxis, :] + a
number_of_scattered_photons = 10**int(
np3.flatten()[index]) * (particle_size / 20)**2 #10 is smallest radius
array_size = particle_size + 5
#Generate diffraction pattern
particle = ElserParticle(array_size, particle_size, feature_size)
detected_intensity, diffracted_wave, support = particle.generate_pattern(
pattern_size_pixels, detector_distance, detector_pixel_size, wavelength,
number_of_scattered_photons)
#Write to file
img_detected_intensity = spimage_tools.image_from_array(detected_intensity)
img_diffracted_wave = spimage_tools.image_from_array(diffracted_wave)
img_support = spimage_tools.image_from_array(support)
version = 'testrun'
output_dir = '/scratch/fhgfs/elsin/' + version + '/particles/'
shell_functions.mkdir_p(output_dir)
filename1 = output_dir + '/p{0:06d}'.format(index) + '_detected_intensity.h5'
filename2 = output_dir + '/p{0:06d}'.format(index) + '_diffracted_wave.h5'
filename3 = output_dir + '/p{0:06d}'.format(index) + '_support.h5'
spimage.sp_image_write(img_detected_intensity, filename1, 0)
spimage.sp_image_write(img_diffracted_wave, filename2, 0)
spimage.sp_image_write(img_support, filename3, 0)
image = np.fft.fftshift(np.fft.fft2(np.fft.fftshift(diffracted_wave)))
plt.imsave(output_dir + '/p{0:06d}'.format(index) + 'img.png', abs(image))
def process(self, f):
img = spimage.sp_image_read(f,0)
img = self.process_function(img)
spimage.sp_image_write(img,self.out_dir+"/"+f[:-2]+"png",self.color)
spimage.sp_image_free(img)
def process(self, f):
img = spimage.sp_image_read(f, 0)
img = self.process_function(img)
output_file = self.out_dir + "/" + f[:-2] + "png"
spimage.sp_image_write(img, output_file, self.color)
spimage.sp_image_free(img)
def run_it(number_of_iterations):
spimage.sp_phaser_iterate(phaser, number_of_iterations)
run_it(NUMBER_OF_ITERATIONS)
phaser.algorithm = phase_alg_refine
run_it(NUMBER_OF_REFINE_ITERATIONS)
#Output data
model = spimage.sp_phaser_model(phaser)
support = spimage.sp_phaser_support(phaser)
fmodel = spimage.sp_phaser_fmodel(phaser)
spimage.sp_image_write(
model, OUTPUT_DIR + "index{0:06d}".format(index) +
"run{0:06d}model.h5".format(run), 0)
spimage.sp_image_write(
support, OUTPUT_DIR + "index{0:06d}".format(index) +
"run{0:06d}support.h5".format(run), 0)
spimage.sp_image_write(
fmodel, OUTPUT_DIR + "index{0:06d}".format(index) +
"run{0:06d}fmodel.h5".format(run), 0)
ereal = spimage.sp_phaser_ereal(phaser)
efourier = spimage.sp_phaser_efourier(phaser)
filename = OUTPUT_DIR + 'index{0:06d}'.format(
index) + 'run{0:06d}error.h5'.format(run)
with h5py.File(filename, 'w') as file_handle:
img_real_space = spimage_tools.image_from_array(real_space)
img_real_space.phased = 0
img_real_space.shifted = 0
img_real_space.detector.detector_distance = settings['detector_distance']
img_real_space.detector.pixel_size[:] = settings['detector_pixel_size']
img_real_space.detector.wavelength = settings['wavelength']
output_dir = output_dir + 'particle_' + particle_id
shell_functions.mkdir_p(output_dir)
file1 = output_dir + '/particle_detected_intensity.h5'
file2 = output_dir + '/particle_diffracted_wave.h5'
file3 = output_dir + '/particle_support.h5'
file4 = output_dir + '/particle_shape.hdf5'
file5 = output_dir + '/particle_real_space.h5'
spimage.sp_image_write(img_detected_intensity, file1, 0)
spimage.sp_image_write(img_diffracted_wave, file2, 0)
spimage.sp_image_write(img_support, file3, 0)
spimage.sp_image_write(img_real_space, file5, 0)
with h5py.File(file4, "w") as f:
dset = f.create_dataset("particle_matrix", data=particle.particle)
dset.attrs['particle_size'] = particle_size
dset.attrs['feature_size'] = feature_size
dset.attrs['n_photons'] = settings['number_of_photons']
image = np.fft.fftshift(np.fft.fft2(np.fft.fftshift(diffracted_wave)))
plt.imsave(output_dir + '/particle_projection_img.png', abs(image))
def to_png(*arguments):
if len(arguments) <= 0:
print("""
This program converts all h5 files in the curren directory to png.
Usage: python_script_new_to_png [colorscale]
Colorscales:
Jet
Gray
PosNeg
InvertedPosNeg
Phase
InvertedPhase
Log (can be combined with the others)
Shift (can be combined with the others)
Support
""")
return
elif not (isinstance(arguments, list) or isinstance(arguments, tuple)):
print("function to_png takes must have a list or string input")
return
files = os.listdir('.')
expr = re.compile('.h5$')
h5_files = list(filter(expr.search, files))
expr = re.compile('.png$')
png_files = list(filter(expr.search, files))
files = [f for f in h5_files if f[:-2]+"png" not in png_files]
files.sort()
print("Converting %d files" % len(files))
log_flag = 0
shift_flag = 0
support_flag = 0
color = 16
for flag in arguments:
if flag == 'PosNeg':
color = 8192
elif flag == 'InvertedPosNeg':
color = 16384
elif flag == 'Phase':
color = 256
elif flag == 'InvertedPhase':
color = 4096
elif flag == 'Jet':
color = 16
elif flag == 'Gray':
color = 1
elif flag == 'Log':
log_flag = 1
elif flag == 'Shift':
shift_flag = 1
elif flag == 'Support':
support_flag = 1
else:
print("unknown flag %s" % flag)
if log_flag == 1:
color += 128
# for f in files:
# img = spimage.sp_image_read(f[:-1],0)
if shift_flag:
def shift_function(img):
ret = spimage.sp_image_shift(img)
spimage.sp_image_free(img)
return ret
else:
def shift_function(img):
return img
if support_flag:
for f in files:
img = spimage.sp_image_read(f, 0)
spimage.sp_image_mask_to_image(img, img)
img = shift_function(img)
spimage.sp_image_write(img, f[:-2]+"png", color)
spimage.sp_image_free(img)
else:
for f in files:
img = spimage.sp_image_read(f, 0)
img = shift_function(img)
spimage.sp_image_write(img, f[:-2]+"png", color)
spimage.sp_image_free(img)
def image_to_png(arguments):
if isinstance(arguments,str):
arguments = [arguments]
elif not isinstance(arguments,list):
print "function to_png takes must have a list or string input"
return
if len(sys.argv) <= 1:
print """
Usage: python_script_image_to_png <image_in.h5> <image_out.h5> [colorscale]
Colorscales:
Jet
Gray
PosNeg
InvertedPosNeg
Phase
InvertedPhase
Log (can be combined with the others)
Shift (can be combined with the others)
"""
exit(1)
try:
img = spimage.sp_image_read(arguments[0],0)
except:
print "Error: %s is not a readable .h5 file\n" % arguments[0]
exit(1)
log_flag = 0
shift_flag = 0
for flag in arguments[2:]:
if flag == 'PosNeg':
color = 8192
elif flag == 'InvertedPosNeg':
color = 16384
elif flag == 'Phase':
color = 256
elif flag == 'InvertedPhase':
color = 4096
elif flag == 'Jet':
color = 16
elif flag == 'Gray':
color = 1
elif flag == 'Log':
log_flag = 1
elif flag == 'Shift':
shift_flag = 1
else:
print "unknown flag %s" % flag
if log_flag == 1:
color += 128
if shift_flag == 1:
img = spimage.sp_image_shift(img)
try:
spimage.sp_image_write(img,arguments[1],color)
except:
print "Error: Can not write %s\n" % arguments[1]
exit(1)
def to_png(*arguments):
if len(arguments) <= 0:
print """
This program converts all h5 files in the curren directory to png.
Usage: python_script_new_to_png [colorscale]
Colorscales:
Jet
Gray
PosNeg
InvertedPosNeg
Phase
InvertedPhase
Log (can be combined with the others)
Shift (can be combined with the others)
Support
"""
return
elif not (isinstance(arguments,list) or isinstance(arguments,tuple)):
print "function to_png takes must have a list or string input"
return
#l = os.popen('ls').readlines()
l = os.listdir('.')
expr = re.compile('.h5$')
h5_files = filter(expr.search,l)
expr = re.compile('.png$')
png_files = filter(expr.search,l)
files = [f for f in h5_files if f[:-2]+"png" not in png_files]
files.sort()
print "Converting %d files" % len(files)
log_flag = 0
shift_flag = 0
support_flag = 0
color = 16
for flag in arguments:
if flag == 'PosNeg':
color = 8192
elif flag == 'InvertedPosNeg':
color = 16384
elif flag == 'Phase':
color = 256
elif flag == 'InvertedPhase':
color = 4096
elif flag == 'Jet':
color = 16
elif flag == 'Gray':
color = 1
elif flag == 'Log':
log_flag = 1
elif flag == 'Shift':
shift_flag = 1
elif flag == 'Support':
support_flag = 1
else:
print "unknown flag %s" % flag
if log_flag == 1:
color += 128
# for f in files:
# img = spimage.sp_image_read(f[:-1],0)
def shift_function(img):
return img
if shift_flag:
def shift_function(img):
ret = spimage.sp_image_shift(img)
spimage.sp_image_free(img)
return ret
if support_flag:
for f in files:
img = spimage.sp_image_read(f,0)
spimage.sp_image_mask_to_image(img,img)
img = shift_function(img)
spimage.sp_image_write(img,f[:-2]+"png",color)
spimage.sp_image_free(img)
else:
for f in files:
img = spimage.sp_image_read(f,0)
img = shift_function(img)
spimage.sp_image_write(img,f[:-2]+"png",color)
spimage.sp_image_free(img)
def process(self, f):
#for f in files:
img = spimage.sp_image_read(f,0)
img = self.process_function(img)
spimage.sp_image_write(img,f[:-2]+"png",self.color)
spimage.sp_image_free(img)
def put_neg_to_zero(image_file_name, output_file_name):
img = spimage.sp_image_read(image_file_name, 0)
new_img = img.image
new_img[real(img.image) < 0.] = 0.
img.image[:, :] = new_img
spimage.sp_image_write(img, output_file_name, 0)
mask = _numpy.bool8(amplitudes.mask)
efourier_start = _numpy.sqrt(
((abs(fourier_space.image[mask]) - abs(amplitudes.image[mask]))**
2).sum() / ((abs(amplitudes.image[mask])**2).sum() +
(abs(fourier_space.image[~mask])**2).sum()))
_spimage.sp_phaser_iterate(phaser, args.number_of_iterations)
model_out = _spimage.sp_phaser_model(phaser)
support_out = _spimage.sp_phaser_support(phaser)
fmodel_out = _spimage.sp_phaser_fmodel(phaser)
real_space_end = _spimage.sp_phaser_model_before_projection(phaser)
fourier_space_end = _spimage.sp_phaser_fmodel(phaser)
ereal_end = _numpy.sqrt((abs(real_space_end.image[~support])**2).sum() /
(abs(real_space_end.image)**2).sum())
efourier_end = _numpy.sqrt(
((abs(fourier_space_end.image[mask]) - abs(amplitudes.image[mask]))**
2).sum() / ((abs(amplitudes.image[mask])**2).sum() +
(abs(fourier_space_end.image[~mask])**2).sum()))
_spimage.sp_image_write(model_out,
f"{args.outdir}/real_space-{args.affix}.h5", 0)
_spimage.sp_image_write(support_out,
f"{args.outdir}/support-{args.affix}.h5", 0)
_spimage.sp_image_write(fmodel_out,
f"{args.outdir}/fourier_space-{args.affix}.h5", 0)
print("Ereal: %g -> %g" % (ereal_start, ereal_end))
print("Efourier: %g -> %g" % (efourier_start, efourier_end))