def pre_process(self):
b = Ptycho.load_run(self.parameters['ptyr_file'],False) # load in the run but without the data
p = b.p
existing_scan = copy(p.scans[p.scans.keys()[0]])
p.scans.savu = existing_scan
p.scans.savu.data.source = 'savu'
p.scans.savu.data.recipe = u.Param()
p.scan.illumination = b.probe.storages['S00G00'].data
self.p = p
def setup(self):
in_datasets, out_datasets = self.get_datasets()
self.in_shape = in_datasets[0].get_shape()
in_pData, __out_pData = self.get_plugin_datasets()
in_pData[0].plugin_data_setup('PROJECTION', self.get_max_frames())
self.in_slice_dirs= np.array(in_pData[0].get_slice_directions())
self.in_core_dirs= np.sort(np.array(in_pData[0].get_core_directions()))# sort them to get in the right order
self.b = Ptycho.load_run(self.parameters['ptyr_file'],False)
self.p = self.b.p
BasePtycho.setup(self)
def pre_process(self):
b = Ptycho.load_run(self.parameters['ptyr_file'], False) # load in the run but without the data
p = b.p
existing_scan = copy(p.scans[p.scans.keys()[0]])
del p.scans[p.scans.keys()[0]]
p.scans.savu = existing_scan
p.scans.savu.data.source = 'savu'
p.scans.savu.data.recipe = u.Param()
if self.parameters['mask_file'] is not None:
p.scans.savu.data.recipe.mask = h5.File(self.parameters['mask_file'],'r')[self.parameters['mask_entry']][...]
else:
p.scans.savu.data.recipe.mask = np.ones(self.in_shape[-2:])
p.scan.illumination = b.probe.storages['S00G00'].data
self.p = p
def paramtree_from_json(json_file):
'''
generates a ptypy param tree from a json file
:param json_file: the path the json file
:return: a Param based structure.
'''
in_dict = json.load(open(json_file)) #, object_hook=byteify)
parameters_to_run = u.Param()
if in_dict['base_file'] is not None:
logging.debug("Basing this scan off of the scan in {}".format(
in_dict['base_file']))
previous_scan = Ptycho.load_run(
in_dict['base_file'],
False) # load in the run but without the data
previous_parameters = previous_scan.p
parameters_to_run.update(previous_parameters)
if in_dict['parameter_tree'] is not None:
parameters_to_run.update(in_dict['parameter_tree'], Convert=True)
return parameters_to_run