def import_int_file(self, init):
""" Replaces path settings in imported image object with new settings
NEED TO RE-DO LATER """
# Generate paths to output files
self.params = init.params
self.main_log = init.logfile
self.input_base = init.input_base
self.conv_base = init.conv_base
self.int_base = init.int_base
self.obj_base = init.obj_base
self.fin_base = init.fin_base
self.viz_base = init.viz_base
self.obj_path = misc.make_image_path(self.conv_img, self.input_base, self.obj_base)
self.obj_file = os.path.abspath(os.path.join(self.obj_path,
os.path.basename(self.conv_img).split('.')[0] + ".int"))
self.fin_path = misc.make_image_path(self.conv_img, self.input_base, self.fin_base)
self.fin_file = os.path.abspath(os.path.join(self.fin_path,
os.path.basename(self.conv_img).split('.')[0] + "_int.pickle"))
self.final['final'] = self.fin_file
self.final['img'] = self.conv_img
if self.viz_base != None:
self.viz_path = misc.make_image_path(self.raw_img, self.input_base, self.viz_base)
self.viz_file = os.path.join(self.viz_path,
os.path.basename(self.conv_img).split('.')[0] + "_int.png")
# Generate output folders and files:
# Grid search subfolder or final integration subfolder
if not os.path.isdir(self.obj_path):
os.makedirs(self.obj_path)
if not os.path.isdir(self.fin_path):
os.makedirs(self.fin_path)
# Grid search / integration log file
self.int_log = os.path.join(self.fin_path,
os.path.basename(self.conv_img).split('.')[0] + '.log')
# Visualization subfolder
if self.viz_path != None and not os.path.isdir(self.viz_path):
os.makedirs(self.viz_path)
# Reset status to 'grid search' to pick up at selection (if no fail)
if self.fail == None:
self.status = 'grid search'
return self
def convert_image(self):
""" Converts images into pickle format; crops and masks out beamstop if
selected """
self.status = 'imported'
img_data, self.img_type = self.load_image()
info = []
self.log_info.append('\n{:-^100}\n'.format(self.raw_img))
self.log_info.append('Imported image : {}'.format(self.raw_img))
self.log_info.append('Parameters : BEAM_X = {:<4.2f}, BEAM_Y = {:<4.2f}, '\
'PIXEL_SIZE = {:<8.6f}, IMG_SIZE = {:<4} X {:<4}, '\
'DIST = {}'.format(img_data['BEAM_CENTER_X'],
img_data['BEAM_CENTER_Y'],
img_data['PIXEL_SIZE'],
img_data['SIZE1'],
img_data['SIZE2'],
img_data['DISTANCE']))
if self.params.image_conversion.beamstop != 0 or\
self.params.image_conversion.beam_center.x != 0 or\
self.params.image_conversion.beam_center.y != 0 or\
self.params.image_conversion.distance != 0 or\
self.params.image_conversion.rename_pickle_prefix != 'Auto' or\
self.params.image_conversion.rename_pickle_prefix != None:
self.status = 'unconverted'
if self.img_type == 'unconverted':
# Check for and/or create a converted pickles folder
try:
if not os.path.isdir(self.conv_base):
os.makedirs(self.conv_base)
except OSError:
pass
# Generate converted image pickle filename
if self.params.image_conversion.rename_pickle_prefix != None:
if str(self.params.image_conversion.rename_pickle_prefix).lower() == "auto":
prefix = os.getlogin()
suffix = int(os.path.basename(self.conv_base))
else:
prefix = self.params.image_conversion.rename_pickle_prefix
suffix = int(os.path.basename(self.conv_base))
self.conv_img = os.path.abspath(os.path.join(self.conv_base,
"{}_{}_{:05d}.pickle".format(prefix, suffix, self.img_index)))
else:
img_path = misc.make_image_path(self.raw_img, self.input_base, self.conv_base)
self.conv_img = os.path.abspath(os.path.join(img_path,
os.path.basename(self.raw_img).split('.')[0] + ".pickle"))
# Make subfolder for converted pickles
try:
if not os.path.isdir(img_path):
os.makedirs(img_path)
except OSError:
pass
# Convert raw image to image pickle
beamstop = self.params.image_conversion.beamstop
distance = self.params.image_conversion.distance
beam_center = [self.params.image_conversion.beam_center.x,
self.params.image_conversion.beam_center.y]
square = self.params.image_conversion.square_mode
if beam_center != [0,0]:
pixel_size = img_data['PIXEL_SIZE']
img_data['BEAM_CENTER_X'] = int(round(beam_center[0] * pixel_size))
img_data['BEAM_CENTER_Y'] = int(round(beam_center[1] * pixel_size))
if distance != 0:
img_data['DISTANCE'] = distance
if square != "None":
img_data = self.square_pickle(img_data)
if beamstop != 0:
img_data = self.mask_image(img_data)
self.log_info.append('Converted image : {}'.format(self.conv_img))
self.log_info.append('Parameters : BEAM_X = {:<4.2f}, BEAM_Y = {:<4.2f}, '\
'PIXEL_SIZE = {:<8.6f}, IMG_SIZE = {:<4} X {:<4}, '\
'DIST = {}'.format(img_data['BEAM_CENTER_X'],
img_data['BEAM_CENTER_Y'],
img_data['PIXEL_SIZE'],
img_data['SIZE1'],
img_data['SIZE2'],
img_data['DISTANCE']))
self.img_type = 'converted'
self.input_base = self.conv_base
# Save converted image pickle
ep.dump(self.conv_img, img_data)
self.status = 'converted'
if self.params.image_triage.flag_on and self.status == 'converted':
self.fail = self.triage_image()
self.status = 'triaged'
else:
self.fail = None
# Generate names for output folders and files:
if not self.params.image_conversion.convert_only:
self.obj_path = misc.make_image_path(self.conv_img, self.input_base, self.obj_base)
self.obj_file = os.path.abspath(os.path.join(self.obj_path,
os.path.basename(self.conv_img).split('.')[0] + ".int"))
self.fin_path = misc.make_image_path(self.conv_img, self.input_base, self.fin_base)
self.fin_file = os.path.abspath(os.path.join(self.fin_path,
"int_{}.pickle".format(os.path.basename(self.conv_img).split('.')[0])))
self.final['final'] = self.fin_file
self.final['img'] = self.conv_img
self.int_log = os.path.join(self.fin_path,
os.path.basename(self.conv_img).split('.')[0] + '.log')
if self.viz_base != None:
self.viz_path = misc.make_image_path(self.conv_img, self.input_base, self.viz_base)
self.viz_file = os.path.join(self.viz_path,
"int_{}.png".format(os.path.basename(self.conv_img).split('.')[0]))
# Create actual folders (if necessary)
try:
if not os.path.isdir(self.obj_path):
os.makedirs(self.obj_path)
if not os.path.isdir(self.fin_path):
os.makedirs(self.fin_path)
if self.viz_base != None:
if not os.path.isdir(self.viz_path):
os.makedirs(self.viz_path)
except OSError:
pass
# Save image object to file
ep.dump(self.obj_file, self)
return self
