def _read_images(self):
"""Read diffraction patterns and save them within the object."""
#should I normalize images??
list_of_all_files = os.listdir("output")
list_of_images = [
f for f in list_of_all_files if re.search("^image_[0-9]{4}.h5$", f)
]
prefix = "output"
if len(list_of_images) == 0:
# maybe this is an old run with images output in debug
list_of_all_files = os.listdir("debug")
list_of_images = [
f for f in list_of_all_files
if re.search("^image_[0-9]{4}.h5$", f)
]
prefix = "debug"
if len(list_of_images) == 0:
self.read_error.emit()
self._number_of_images = len(list_of_images)
for i in range(self._number_of_images):
try:
image, mask = sphelper.import_spimage(
"%s/image_%.4d.h5" % (prefix, i), ['image', 'mask'])
except IOError:
print "{0} is bad".format(i)
image = numpy.zeros(self._images[0].shape, dtype="float32")
mask = numpy.zeros(self._images[0].shape, dtype="int32")
self._images.append(image)
self._masks.append(mask)
def get_mask(self, iteration):
"""Return the mask of the 3D model as an array for the requested iteration."""
try:
if iteration >= 0:
mask = sphelper.import_spimage('%s_%.4d.h5' % (self._file_prefix, iteration), ['mask'])
elif iteration == -1:
mask = sphelper.import_spimage('%s_init.h5' % (self._file_prefix), ['mask'])
elif iteration == -2:
mask = sphelper.import_spimage('%s_final.h5' % (self._file_prefix), ['mask'])
except IOError:
self.read_error.emit()
return
if self._side != mask.shape[0]:
self._side = mask.shape[0]
self.properties_changed.emit()
return mask
def get_image(self, index, reload_data=False):
"""Get image of certain index."""
if index >= self._number_of_images:
raise ValueError("Image index out of range. %d is above %d" % (index, self._number_of_images))
if index in self._images.keys() and not reload_data:
return abs(self._images[index])
self._images[index] = sphelper.import_spimage("output/image_%.4d.h5" % index, ["image"])
return abs(self._images[index])
def get_map(self, iteration):
"""Return the 3D model as an array for the requested iteration."""
try:
if iteration >= 0:
modelmap = sphelper.import_spimage('%s_%.4d.h5' % (self._file_prefix, iteration), ['image'])
elif iteration == -1:
modelmap = sphelper.import_spimage('%s_init.h5' % (self._file_prefix), ['image'])
elif iteration == -2:
modelmap = sphelper.import_spimage('%s_final.h5' % (self._file_prefix), ['image'])
except (IOError, KeyError):
self.read_error.emit()
if self._side:
return numpy.zeros((self._side, )*3)
else:
return numpy.zeros((10, )*3)
if self._side != modelmap.shape[0]:
self._side = modelmap.shape[0]
self.properties_changed.emit()
return modelmap
def get_image(self, index, reload_data=False):
"""Get image of certain index."""
if index >= self._number_of_images:
raise ValueError("Image index out of range. %d is above %d" %
(index, self._number_of_images))
if index in self._images.keys() and not reload_data:
return abs(self._images[index])
self._images[index] = sphelper.import_spimage(
"output/image_%.4d.h5" % index, ["image"])
return abs(self._images[index])
def get_mask(self, iteration):
"""Return the mask of the 3D model as an array for the requested iteration."""
try:
if iteration >= 0:
mask = sphelper.import_spimage(
'%s_%.4d.h5' % (self._file_prefix, iteration), ['mask'])
elif iteration == -1:
mask = sphelper.import_spimage(
'%s_init.h5' % (self._file_prefix), ['mask'])
elif iteration == -2:
mask = sphelper.import_spimage(
'%s_final.h5' % (self._file_prefix), ['mask'])
except IOError:
self.read_error.emit()
return
if self._side != mask.shape[0]:
self._side = mask.shape[0]
self.properties_changed.emit()
return mask
def get_map(self, iteration):
"""Return the 3D model as an array for the requested iteration."""
try:
if iteration >= 0:
modelmap = sphelper.import_spimage(
'%s_%.4d.h5' % (self._file_prefix, iteration), ['image'])
elif iteration == -1:
modelmap = sphelper.import_spimage(
'%s_init.h5' % (self._file_prefix), ['image'])
elif iteration == -2:
modelmap = sphelper.import_spimage(
'%s_final.h5' % (self._file_prefix), ['image'])
except (IOError, KeyError):
self.read_error.emit()
if self._side:
return numpy.zeros((self._side, ) * 3)
else:
return numpy.zeros((10, ) * 3)
if self._side != modelmap.shape[0]:
self._side = modelmap.shape[0]
self.properties_changed.emit()
return modelmap
def read_images(directory, number_of_images):
images = []
masks = []
for i in range(number_of_images):
try:
image, mask = sphelper.import_spimage("%s/image_%.4d.h5" % (directory, i), ['image', 'mask'])
except IOError:
#print "Problem reading file %s" % ("%s/image_%.4d.h5" % (directory, i))
raise IOError("Problem reading file %s" % ("%s/image_%.4d.h5" % (directory, i)))
mask = bool8(mask)
image[-mask] = 0.
images.append(image)
masks.append(mask)
return array(images), bool8(array(masks))
def _read_image_and_mask(self, index):
"""Load the image and mask if they have not been viewed before."""
if index in self._images and index in self._masks:
return
prefix = "output"
try:
image, mask = sphelper.import_spimage(os.path.join(prefix, "image_{0:04}.h5".format(index)), ["image", "mask"])
except IOError:
print "Image {0} is bad".format(index)
self._images[index] = numpy.zeros(self._images[0].shape, dtype="float64")
self._masks[index] = numpy.zeros(self._images[0].shape, dtype="int32")
return
self._images[index] = image
self._masks[index] = mask
def _read_image_and_mask(self, index):
"""Load the image and mask if they have not been viewed before."""
if index in self._images and index in self._masks:
return
prefix = "output"
try:
image, mask = sphelper.import_spimage(
os.path.join(prefix, "image_{0:04}.h5".format(index)),
["image", "mask"])
except IOError:
print "Image {0} is bad".format(index)
self._images[index] = numpy.zeros(self._images[0].shape,
dtype="float64")
self._masks[index] = numpy.zeros(self._images[0].shape,
dtype="int32")
return
self._images[index] = image
self._masks[index] = mask
def _read_images(self):
"""Read diffraction patterns and save them within the object."""
#should I normalize images??
list_of_all_files = os.listdir("output")
list_of_images = [f for f in list_of_all_files if re.search("^image_[0-9]{4}.h5$", f)]
prefix = "output"
if len(list_of_images) == 0:
# maybe this is an old run with images output in debug
list_of_all_files = os.listdir("debug")
list_of_images = [f for f in list_of_all_files if re.search("^image_[0-9]{4}.h5$", f)]
prefix = "debug"
if len(list_of_images) == 0:
self.read_error.emit()
self._number_of_images = len(list_of_images)
for i in range(self._number_of_images):
try:
image, mask = sphelper.import_spimage("%s/image_%.4d.h5" % (prefix, i), ['image', 'mask'])
except IOError:
print "{0} is bad".format(i)
image = numpy.zeros(self._images[0].shape, dtype="float32")
mask = numpy.zeros(self._images[0].shape, dtype="int32")
self._images.append(image)
self._masks.append(mask)
