def _generate_regist_command(self, item):
""" generate the registration command(s)
:param dict item: dictionary with registration params
:return str|list(str): the execution commands
"""
path_im_ref, path_im_move, _, _ = self._get_paths(item,
prefer_pproc=True)
path_dir = self._get_path_reg_dir(item)
config = self.DEFAULT_PARAMS
config = dict_deep_update(config,
load_config_yaml(self.params['path_config']))
assert config['bUnwarpJ']['mode'] < 2, 'Mono mode does not supports inverse transform' \
' which is need for landmarks warping.'
config_sift = [config['SIFT'][k] for k in self.REQUIRED_PARAMS_SIFT] \
if config.get('SIFT', False) else []
config_bunwarpj = [
config['bUnwarpJ'][k] for k in self.REQUIRED_PARAMS_BUNWARPJ
]
path_reg_script = self.PATH_SCRIPT_REGISTRATION_SIFT if config_sift \
else self.PATH_SCRIPT_REGISTRATION_BASE
cmd = self.COMMAND_REGISTRATION % {
'exec_Fiji': self.params['exec_Fiji'],
'path_bsh': path_reg_script,
'target': path_im_ref,
'source': path_im_move,
'output': path_dir,
'params': ' '.join(map(str, config_sift + config_bunwarpj)),
}
return cmd
def _generate_regist_command(self, item):
""" generate the registration command(s)
:param dict item: dictionary with registration params
:return str|list(str): the execution commands
"""
path_im_ref, path_im_move, _, _ = self._get_paths(item, prefer_pproc=True)
path_dir = self._get_path_reg_dir(item)
# creating the internal folders
path_dir_in = os.path.join(path_dir, self.DIR_INPUTS)
path_dir_out = os.path.join(path_dir, self.DIR_OUTPUTS)
for p_dir in (path_dir_in, path_dir_out):
os.mkdir(p_dir)
# copy both images
name_ref = os.path.basename(path_im_ref)
shutil.copy(path_im_ref, os.path.join(path_dir_in, name_ref))
shutil.copy(path_im_move, os.path.join(path_dir_in, os.path.basename(path_im_move)))
config = self.DEFAULT_PARAMS
config = dict_deep_update(config, load_config_yaml(self.params['path_config']))
config_rvss = [config['RVSS'][k] for k in self.REQUIRED_PARAMS_RVSS]
config_sift = [config['SIFT'][k] for k in BmUnwarpJ.REQUIRED_PARAMS_SIFT]
cmd = self.COMMAND_REGISTRATION % {
'exec_Fiji': self.params['exec_Fiji'],
'path_bsh': self.PATH_SCRIPT_REGISTRATION,
'dir_input': path_dir_in,
'dir_output': path_dir_out,
'ref_name': name_ref,
'params': ' '.join(map(str, config_rvss + config_sift)),
}
return cmd