def OnLoadImage(self, im_file):
self.path = im_file
print('self.path=', self.path)
# read 3d image
h, self.vol = edf_read(im_file, header_size=0, verbose=True, \
autoparse_filename=True, return_header=True)
print('min in image= %d, max in image=%d' %
(np.min(self.vol), np.max(self.vol)))
self.maxim_sc.SetRange(0, np.shape(self.vol)[2] - 1)
print(np.shape(self.vol))
self.imPanel.SetImage(self.vol[:, :, 0])
def load_image(self, image_path):
print('loading image from %s' % image_path)
# read image depending on file extension
if image_path.endswith('.edf'):
image = edf_read(image_path).transpose()
elif image_path.endswith('.png'):
image = mpimg.imread(image_path)
elif image_path.endswith('.tif'):
image = TiffFile(image_path).asarray() # should we transpose here?
else:
print('Only png, tif and edf images are supported for the moment')
image = np.zeros((5, 5), dtype=np.uint8) # dummy image
return image
def OnLoadImage(self, im_file):
self.path = im_file
print 'self.path=', self.path
# read image depending on file extension (only .png .tif and .edf supported)
if self.path.endswith('.edf'):
self.im = edf_read(im_file).transpose()
elif self.path.endswith('.png'):
self.im = mpimg.imread(im_file)
elif self.path.endswith('.tif'):
self.im = TiffFile(im_file).asarray()
else:
print('Only png, tif and edf images are supported for the moment')
sys.exit(1)
print 'min in image= %d, max in image=%d' % (np.min(
self.im), np.max(self.im))
print np.shape(self.im)
self.cur_image_name.SetLabel(im_file)
self.imPanel.SetImage(self.im)
def tt_stack(scan_name,
data_dir='.',
save_edf=False,
TOPO_N=-1,
dark_factor=1.):
"""Build a topotomography stack from raw detector images.
The number of image to sum for a topograph can be determined automatically from the total number of images present
in `data_dir` or directly specified using the variable `TOPO_N`.
:param str scan_name: the name of the scan to process.
:param str data_dir: the path to the data folder.
:param bool save_edf: flag to save the tt stack as an EDF file.
:param int TOPO_N: the number of images to sum for a topograph.
:param float dark_factor: a multiplicative factor for the dark image.
"""
from pymicro.file.file_utils import edf_read, edf_write
if TOPO_N < 0:
import glob
# figure out the number of frames per topograph TOPO_N
n_frames = len(
glob.glob(os.path.join(data_dir, scan_name,
'%s*.edf' % scan_name)))
TOPO_N = int(n_frames / 90)
print('number of frames to sum for a topograph = %d' % TOPO_N)
# parse the info file
f = open(os.path.join(data_dir, scan_name, '%s.info' % scan_name))
infos = dict()
for line in f.readlines():
tokens = line.split('=')
# convert the value into int/float/str depending on the case
try:
value = int(tokens[1].strip())
except ValueError:
try:
value = float(tokens[1].strip())
except ValueError:
value = tokens[1].strip()
infos[tokens[0]] = value
print(infos)
# load dark image
dark = dark_factor * edf_read(
os.path.join(data_dir, scan_name, 'darkend0000.edf'))
# build the stack by combining individual images
tt_stack = np.empty((infos['TOMO_N'], infos['Dim_1'], infos['Dim_2']))
print(tt_stack[0].shape)
for n in range(int(infos['TOMO_N'])):
print('building topograph %d' % (n + 1))
topograph = np.zeros((infos['Dim_1'], infos['Dim_2']))
offset = TOPO_N * n
for i in range(TOPO_N):
index = offset + i + 1
frame_path = os.path.join(data_dir, scan_name,
'%s%04d.edf' % (scan_name, index))
im = edf_read(frame_path) - dark
topograph += im
tt_stack[n] = topograph
tt_stack = tt_stack.transpose((1, 2, 0))
print('done')
# save the data as edf if needed
if save_edf:
edf_write(tt_stack, os.path.join(data_dir, '%sstack.edf' % scan_name))
return tt_stack