def process_init(path2plugin, inputs, parameters):
parameters['in_datasets'] = [inputs['dataset_name']]
parameters['out_datasets'] = [inputs['dataset_name']]
plugin = get_plugin(path2plugin.split('.py')[0] + '.py')
# print "I got this far"
plugin.exp = setup_exp_and_data(inputs, inputs['data'], plugin)
plugin._set_parameters(parameters)
plugin._set_plugin_datasets()
plugin.setup()
# print "I am her now"
axis_labels = plugin.get_out_datasets()[0].get_axis_label_keys()
foo = [type(ix) for ix in axis_labels]
# print "axis label types", foo
axis_labels.remove('idx') # get the labels
axis_values = {}
plugin._clean_up() # this copies the metadata!
for label in axis_labels:
axis_values[label] = plugin.get_out_datasets()[0].meta_data.get(label)
# print label, axis_values[label].shape
plugin.base_pre_process()
plugin.pre_process()
# print "I went here"
return plugin, axis_labels, axis_values
def test_get_plugins_path_and_load(self):
savu_path = os.path.split(savu.__path__[0])[0]
plugin_path = os.path.join(savu_path, "plugin_examples")
os.environ["SAVU_PLUGINS_PATH"] = plugin_path
pu.get_plugins_paths()
plugin = pu.get_plugin("example_median_filter")
self.assertEqual(plugin.name, "ExampleMedianFilter")
os.environ["SAVU_PLUGINS_PATH"] = ""
def test_get_plugins_path_and_load(self):
savu_path = os.path.split(savu.__path__[0])[0]
plugin_path = os.path.join(savu_path, "plugin_examples")
os.environ["SAVU_PLUGINS_PATH"] = plugin_path
pu.get_plugins_paths()
plugin = pu.get_plugin("example_median_filter")
self.assertEqual(plugin.name, "ExampleMedianFilter")
os.environ["SAVU_PLUGINS_PATH"] = ""
def _savu_setup(path2plugin, inputs, parameters):
print("running _savu_setup")
parameters['in_datasets'] = [inputs['dataset_name']]
parameters['out_datasets'] = [inputs['dataset_name']]
plugin = get_plugin(path2plugin.split('.py')[0]+'.py')
plugin.exp = setup_exp_and_data(inputs, inputs['data'], plugin)
plugin._set_parameters(parameters)
plugin._set_plugin_datasets()
plugin.setup()
return plugin
def _savu_setup(path2plugin, inputs, parameters):
print("running _savu_setup")
parameters['in_datasets'] = [inputs['dataset_name']]
parameters['out_datasets'] = [inputs['dataset_name']]
plugin = get_plugin(path2plugin.split('.py')[0]+'.py')
plugin.exp = setup_exp_and_data(inputs, inputs['data'], plugin)
plugin._set_parameters(parameters)
plugin._set_plugin_datasets()
plugin.setup()
return plugin
def plugin_runner_load_plugin(options):
plugin_runner = PluginRunner(options)
plugin_runner.exp = Experiment(options)
plugin_list = plugin_runner.exp.meta_data.plugin_list.plugin_list
exp = plugin_runner.exp
pu.plugin_loader(exp, plugin_list[0])
exp._set_nxs_file()
plugin_dict = plugin_list[1]
plugin = pu.get_plugin(plugin_dict['id'])
plugin.exp = exp
return plugin
def set_plugin_list(options, pnames, *args):
args = args[0] if args else None
plugin_names = pnames if isinstance(pnames, list) else [pnames]
options['plugin_list'] = []
ID = [options['loader']]
data = [{}, {}] if not args else [args[0], args[-1]]
for i in range(len(plugin_names)):
ID.insert(i + 1, plugin_names[i])
plugin = pu.get_plugin(plugin_names[i])
data_dict = set_data_dict(['tomo'], get_output_datasets(plugin))
data_dict = args[i + 1] if args else data_dict
data.insert(i + 1, data_dict)
for i in range(len(ID)):
name = \
''.join(x.capitalize() for x in (ID[i].split('.')[-1]).split('_'))
options['plugin_list'].append(set_plugin_entry(name, ID[i], data[i],
i))
def _add_missing_savers(self, data_names):
""" Add savers for missing datasets. """
saved_data = []
for i in self._get_savers_index():
saved_data.append(self.plugin_list[i]['data']['in_datasets'])
saved_data = set([s for sub_list in saved_data for s in sub_list])
for name in [data for data in data_names if data not in saved_data]:
process = {}
pos = int(re.search(r'\d+', self.plugin_list[-1]['pos']).group())+1
self.saver_idx.append(pos)
plugin = pu.get_plugin('savu.plugins.savers.hdf5_saver')
plugin.parameters['in_datasets'] = [name]
process['name'] = plugin.name
process['id'] = plugin.__module__
process['pos'] = str(pos)
process['data'] = plugin.parameters
process['active'] = True
process['desc'] = plugin.parameters_desc
self._add(pos, process)
def _add_missing_savers(self, data_names):
""" Add savers for missing datasets. """
saved_data = []
for i in self._get_savers_index():
saved_data.append(self.plugin_list[i]['data']['in_datasets'])
saved_data = set([s for sub_list in saved_data for s in sub_list])
for name in [data for data in data_names if data not in saved_data]:
process = {}
pos = int(re.search(r'\d+', self.plugin_list[-1]['pos']).group())+1
self.saver_idx.append(pos)
plugin = pu.get_plugin('savu.plugins.savers.hdf5_saver')
plugin.parameters['in_datasets'] = [name]
process['name'] = plugin.name
process['id'] = plugin.__module__
process['pos'] = str(pos)
process['data'] = plugin.parameters
process['active'] = True
process['desc'] = plugin.parameters_desc
self._add(pos, process)
def testfind_args(self):
plugin = pu.get_plugin(
"savu.plugins.filters.denoising.denoise_bregman_filter")
params = doc.find_args(plugin)
self.assertEqual(len(params['param']), 4)
def testGetPlugin(self):
plugin = pu.get_plugin("savu.plugins.plugin")
self.assertEqual(plugin.__class__, test_plugin.Plugin,
"Failed to load the correct class")
self.assertRaises(NotImplementedError,
plugin.process_frames, None)
def test_load_plugin(self):
cu.populate_plugins()
plugin_path = pu.dawn_plugins[dawn_plugins.keys()[0]]['path2plugin']
inst = pu.get_plugin(plugin_path)
sl = inst.__dict__['slice_list']
exp = inst.__dict__['exp']
def test_load_plugin(self):
cu.populate_plugins()
plugin_path = pu.dawn_plugins[dawn_plugins.keys()[0]]['path2plugin']
inst = pu.get_plugin(plugin_path)
sl = inst.__dict__['slice_list']
exp = inst.__dict__['exp']
def test_get_plugin_external_path(self):
savu_path = os.path.split(savu.__path__[0])[0]
plugin = pu.get_plugin(
os.path.join(savu_path, "plugin_examples",
"example_median_filter.py"))
self.assertEqual(plugin.name, "ExampleMedianFilter")
def plugin_setup(self):
ppath = 'savu.plugins.reconstructions.astra_recons.astra_recon_cpu'
plugin = pu.get_plugin(ppath)
return plugin
def testfind_args(self):
plugin = pu.get_plugin("savu.plugins.filters.denoise_bregman_filter")
params = doc.find_args(plugin)
self.assertEqual(len(params['param']), 4)
def test_get_plugin_external_path(self):
savu_path = os.path.split(savu.__path__[0])[0]
plugin = pu.get_plugin(os.path.join(savu_path, "plugin_examples",
"example_median_filter.py"))
self.assertEqual(plugin.name, "ExampleMedianFilter")
def plugin_setup(self):
ppath = 'savu.plugins.reconstructions.astra_recons.astra_recon_cpu'
plugin = pu.get_plugin(ppath)
return plugin
def testGetPlugin(self):
plugin = pu.get_plugin("savu.plugins.plugin")
self.assertEqual(plugin.__class__, test_plugin.Plugin,
"Failed to load the correct class")
self.assertRaises(NotImplementedError, plugin.process_frames, None)
