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(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 check_user_path(self):
"""Verify user data folders were created"""
data_folders = [pathfinder.user_path(), pathfinder.data_path(),
pathfinder.thumbnails_path(), pathfinder.gates_path(),
pathfinder.plugins_path(), pathfinder.podmodels_path(),
pathfinder.colormaps_path(), pathfinder.batchoutput_path()]
self.model.check_user_path()
for folder in data_folders:
self.assertTrue(os.path.exists(folder))
def check_user_path(self):
"""Verify user data folders were created"""
data_folders = [pathfinder.user_path(), pathfinder.data_path(),
pathfinder.thumbnails_path(), pathfinder.gates_path(),
pathfinder.plugins_path(), pathfinder.podmodels_path(),
pathfinder.adamodels_path(), pathfinder.colormaps_path(),
pathfinder.batchoutput_path()]
self.model.check_user_path()
for folder in data_folders:
self.assertTrue(os.path.exists(folder))
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 check_user_path(cls):
"""Verify that user data folders exist. Creates
any missing folders."""
user_folder = pathfinder.user_path()
data_folder = pathfinder.data_path()
thumbnail_folder = pathfinder.thumbnails_path()
plugins_folder = pathfinder.plugins_path()
podmodels_folder = pathfinder.podmodels_path()
adamodels_folder = pathfinder.adamodels_path()
gates_folder = pathfinder.gates_path()
colormaps_folder = pathfinder.colormaps_path()
batch_folder = pathfinder.batchoutput_path()
for fldr in (user_folder, data_folder, thumbnail_folder, plugins_folder, podmodels_folder, gates_folder,
adamodels_folder, colormaps_folder, batch_folder):
if not os.path.exists(fldr):
os.makedirs(fldr)
def check_user_path(cls):
"""Verify that user data folders exist. Creates
any missing folders."""
user_folder = pathfinder.user_path()
data_folder = pathfinder.data_path()
thumbnail_folder = pathfinder.thumbnails_path()
plugins_folder = pathfinder.plugins_path()
podmodels_folder = pathfinder.podmodels_path()
gates_folder = pathfinder.gates_path()
colormaps_folder = pathfinder.colormaps_path()
batch_folder = pathfinder.batchoutput_path()
for fldr in (user_folder, data_folder, thumbnail_folder,
plugins_folder, podmodels_folder, gates_folder,
colormaps_folder, batch_folder):
if not os.path.exists(fldr):
os.makedirs(fldr)
def test_batchoutput_path(self):
"""Verify returning correct path to batch processing output"""
batchoutput_path = os.path.join(self.user_path, "data", "batch_output")
self.assertEqual(batchoutput_path, pathfinder.batchoutput_path())
def test_batchoutput_path(self):
"""Verify returning correct path to batch processing output"""
batchoutput_path = os.path.join(self.user_path, "data", "batch_output")
self.assertEqual(batchoutput_path, pathfinder.batchoutput_path())
