def test_run_plugin(self):
"""Verify run_plugin convenience function correctly executes"""
root, ext = os.path.splitext(os.path.basename(self.datafile))
output_fname = os.path.join(pathfinder.batchoutput_path(),
root + ".hdf5")
batchui_ctrl.run_plugin(self.toolkit_class,
self.datafile,
save_data=False)
self.assertFalse(os.path.exists(output_fname))
batchui_ctrl.run_plugin(self.toolkit_class,
self.datafile,
save_data=True)
self.assertTrue(os.path.exists(output_fname))
plugin_names, plugin_classes = self.get_available_plugins()
for idx in range(len(plugin_names)):
if plugin_names[idx] == self.toolkit_class:
plugin_instance = plugin_classes[idx]()
plugin_instance.data = dataio.get_data(self.datafile)
plugin_instance.run()
expected_data = plugin_instance.data
stored_data = dataio.get_data(output_fname)
self.assertTrue(np.array_equal(expected_data, stored_data))
break
if os.path.exists(output_fname):
try:
os.remove(output_fname)
except WindowsError: # file in use (Windows)
pass
except OSError: # other OS error
pass
def test_run_plugin(self):
"""Verify run_plugin convenience function correctly executes"""
root, ext = os.path.splitext(os.path.basename(self.datafile))
output_fname = os.path.join(pathfinder.batchoutput_path(), root + ".hdf5")
batchui_ctrl.run_plugin(self.toolkit_class, self.datafile, save_data=False)
self.assertFalse(os.path.exists(output_fname))
batchui_ctrl.run_plugin(self.toolkit_class, self.datafile, save_data=True)
self.assertTrue(os.path.exists(output_fname))
plugin_names, plugin_classes = self.get_available_plugins()
for idx in range(len(plugin_names)):
if plugin_names[idx] == self.toolkit_class:
plugin_instance = plugin_classes[idx]()
plugin_instance.data = dataio.get_data(self.datafile)
plugin_instance.run()
expected_data = plugin_instance.data
stored_data = dataio.get_data(output_fname)
self.assertTrue(np.array_equal(expected_data, stored_data))
break
if os.path.exists(output_fname):
try:
os.remove(output_fname)
except WindowsError: # file in use (Windows)
pass
except OSError: # other OS error
pass
def test_run_plugin_multi_datasets(self):
"""Verify run_plugin convenience function correctly handles datafiles with
multiple datasets"""
sample_data_folder = os.path.join(pathfinder.app_path(), 'models',
'tests', 'support_files')
sample_utwin_file = os.path.join(sample_data_folder, 'CScanData.csc')
utwin_data = dataio.get_utwin_data(sample_utwin_file)
expected_utwin_data = {}
for data_type in utwin_data.keys():
for idx in range(len(utwin_data[data_type])):
expected_utwin_data[data_type +
str(idx)] = utwin_data[data_type][idx]
output_fnames = []
root, ext = os.path.splitext(os.path.basename(sample_utwin_file))
for dataset in expected_utwin_data:
output_fnames.append(
os.path.join(pathfinder.batchoutput_path(),
root + "_" + dataset + ".hdf5"))
# Verify no output saved
batchui_ctrl.run_plugin(self.toolkit_class,
sample_utwin_file,
save_data=False)
for fname in output_fnames:
self.assertFalse(os.path.exists(fname))
# Verify output saved
batchui_ctrl.run_plugin(self.toolkit_class,
sample_utwin_file,
save_data=True)
for dataset in expected_utwin_data:
if expected_utwin_data[dataset] is not None:
fname = os.path.join(pathfinder.batchoutput_path(),
root + "_" + dataset + ".hdf5")
self.assertTrue(os.path.exists(fname))
plugin_names, plugin_classes = self.get_available_plugins()
for idx in range(len(plugin_names)):
if plugin_names[idx] == self.toolkit_class:
plugin_instance = plugin_classes[idx]()
plugin_instance.data = expected_utwin_data[dataset]
plugin_instance.run()
expected_data = plugin_instance.data
returned_data = dataio.get_data(fname)
self.assertTrue(
np.array_equal(expected_data, returned_data))
break
for fname in output_fnames:
try:
if os.path.exists(fname):
os.remove(fname)
except WindowsError: # file in use (Windows)
pass
except OSError: # other OS error
pass
def test_run_plugin_multi_datasets(self):
"""Verify run_plugin convenience function correctly handles datafiles with
multiple datasets"""
sample_data_folder = os.path.join(pathfinder.app_path(), 'models', 'tests', 'support_files')
sample_utwin_file = os.path.join(sample_data_folder, 'CScanData.csc')
utwin_data = dataio.get_utwin_data(sample_utwin_file)
expected_utwin_data = {}
for data_type in utwin_data.keys():
for idx in range(len(utwin_data[data_type])):
expected_utwin_data[data_type + str(idx)] = utwin_data[data_type][idx]
output_fnames = []
root, ext = os.path.splitext(os.path.basename(sample_utwin_file))
for dataset in expected_utwin_data:
output_fnames.append(os.path.join(pathfinder.batchoutput_path(), root + "_" + dataset + ".hdf5"))
# Verify no output saved
batchui_ctrl.run_plugin(self.toolkit_class, sample_utwin_file, save_data=False)
for fname in output_fnames:
self.assertFalse(os.path.exists(fname))
# Verify output saved
batchui_ctrl.run_plugin(self.toolkit_class, sample_utwin_file, save_data=True)
for dataset in expected_utwin_data:
if expected_utwin_data[dataset] is not None:
fname = os.path.join(pathfinder.batchoutput_path(), root + "_" + dataset + ".hdf5")
self.assertTrue(os.path.exists(fname))
plugin_names, plugin_classes = self.get_available_plugins()
for idx in range(len(plugin_names)):
if plugin_names[idx] == self.toolkit_class:
plugin_instance = plugin_classes[idx]()
plugin_instance.data = expected_utwin_data[dataset]
plugin_instance.run()
expected_data = plugin_instance.data
returned_data = dataio.get_data(fname)
self.assertTrue(np.array_equal(expected_data, returned_data))
break
for fname in output_fnames:
try:
if os.path.exists(fname):
os.remove(fname)
except WindowsError: # file in use (Windows)
pass
except OSError: # other OS error
pass
for plugin_name in available_plugins_names:
print("\t{0}".format(plugin_name))
sys.exit(1)
workers = multiprocessing.Pool()
if args.multiprocess:
print("Using multiprocessing mode, {0} simultaneous processes".format(multiprocessing.cpu_count()))
if args.input_files:
for _f in args.input_files:
paths = glob.glob(_f)
for _p in paths:
if not args.multiprocess:
print("\nProcessing {0}...".format(_p))
if args.toolkit:
batchui_ctrl.run_plugin(toolkit=args.toolkit,
input_file=_p,
toolkit_config=args.toolkit_config,
file_type=args.filetype,
save_data=args.save_output)
else:
batchui_ctrl.import_data(input_file=_p, file_type=args.filetype)
else:
print("\nAdding {0} to job list...".format(_p))
if args.toolkit:
workers.apply_async(batchui_ctrl.run_plugin,
kwds={'toolkit':args.toolkit,
'input_file':_p,
'toolkit_config':args.toolkit_config,
'file_type':args.filetype,
'save_data':args.save_output})
else:
workers.apply_async(batchui_ctrl.import_data,
print("\t{0}".format(plugin_name))
sys.exit(1)
workers = multiprocessing.Pool()
if args.multiprocess:
print("Using multiprocessing mode, {0} simultaneous processes".
format(multiprocessing.cpu_count()))
if args.input_files:
for _f in args.input_files:
paths = glob.glob(_f)
for _p in paths:
if not args.multiprocess:
print("\nProcessing {0}...".format(_p))
if args.toolkit:
batchui_ctrl.run_plugin(
toolkit=args.toolkit,
input_file=_p,
toolkit_config=args.toolkit_config,
file_type=args.filetype,
save_data=args.save_output)
else:
batchui_ctrl.import_data(input_file=_p,
file_type=args.filetype)
else:
print("\nAdding {0} to job list...".format(_p))
if args.toolkit:
workers.apply_async(batchui_ctrl.run_plugin,
kwds={
'toolkit': args.toolkit,
'input_file': _p,
'toolkit_config':
args.toolkit_config,
'file_type': args.filetype,