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)