def test_tomo1(self):
options = tu.set_experiment('tomo')
plugin = 'savu.plugins.basic_operations.basic_operations'
data_dict = {'in_datasets': ['tomo', 'tomo'], 'out_datasets': ['test'],
'operations': ['tomo + tomo'], 'pattern': 'PROJECTION'}
saver_dict = {}
all_dicts = [{}, data_dict, saver_dict]
run_protected_plugin_runner_no_process_list(options, plugin,
data=all_dicts)
def test_3dto4d(self):
options = tu.set_experiment("tomo_3dto4d")
# plugin = 'savu.plugins.corrections.i12_dark_flat_field_correction'
plugin = "savu.plugins.filters.no_process_plugin"
data_dict = {"in_datasets": ["tomo"], "out_datasets": ["test"]}
all_dicts = [self.get_loader_dict(), data_dict, {}]
exp = run_protected_plugin_runner_no_process_list(options, plugin, data=all_dicts)
self.assertEqual(exp.index["in_data"]["test"].get_shape(), (181, 10, 192, 4))
def test_i12tomo(self):
options = tu.set_experiment('i12tomo')
plugin = 'savu.plugins.corrections.i12_dark_flat_field_correction'
data_dict = {'in_datasets': ['tomo'], 'out_datasets': ['test']}
all_dicts = [self.get_loader_dict(), data_dict, {}]
exp = run_protected_plugin_runner_no_process_list(options, plugin,
data=all_dicts)
self.assertEqual(exp.index['in_data']['test'].get_shape(),
(181, 10, 192, 4))
def test_i12tomo(self):
options = tu.set_experiment('i12tomo')
plugin = 'savu.plugins.corrections.i12_dark_flat_field_correction'
data_dict = {'in_datasets': ['tomo'], 'out_datasets': ['test']}
all_dicts = [self.get_loader_dict(), data_dict, {}]
exp = run_protected_plugin_runner_no_process_list(options,
plugin,
data=all_dicts)
self.assertEqual(exp.index['in_data']['test'].get_shape(),
(181, 10, 192, 4))
def test_3dto4d_previewing1(self):
options = tu.set_experiment("tomo_3dto4d")
plugin = "savu.plugins.filters.no_process_plugin"
selection = ["mid:mid+1:1:5", "0:end:1:1", "0:end:1:1", "mid:mid+1:1:1"]
loader_dict = self.get_loader_dict()
loader_dict["preview"] = selection
data_dict = {"in_datasets": ["tomo"], "out_datasets": ["test"]}
all_dicts = [loader_dict, data_dict, {}]
exp = run_protected_plugin_runner_no_process_list(options, plugin, data=all_dicts)
self.assertEqual(exp.index["in_data"]["test"].get_shape(), (5, 10, 192, 1))
def test_tomo4(self):
options = tu.set_experiment('tomo')
plugin = 'savu.plugins.basic_operations.basic_operations'
preview = ['10:-10:10:1', '10:-10:10:1', '10:-10:10:1']
loader_dict = {'preview': preview}
data_dict = {'in_datasets': ['tomo', 'tomo'], 'out_datasets': ['test'],
'operations': ['tomo + tomo'], 'pattern': 'PROJECTION'}
all_dicts = [loader_dict, data_dict, {}]
exp = run_protected_plugin_runner_no_process_list(options, plugin,
data=all_dicts)
exp = self.assertEqual(exp.index['in_data']['test'].get_shape(),
(8, 12, 15))
def test_3dto4d_previewing1(self):
options = tu.set_experiment('tomo_3dto4d')
plugin = 'savu.plugins.filters.no_process_plugin'
selection = \
['mid:mid+1:1:5', '0:end:1:1', '0:end:1:1', 'mid:mid+1:1:1']
loader_dict = self.get_loader_dict()
loader_dict['preview'] = selection
data_dict = {'in_datasets': ['tomo'], 'out_datasets': ['test']}
all_dicts = [loader_dict, data_dict, {}]
exp = run_protected_plugin_runner_no_process_list(options,
plugin,
data=all_dicts)
self.assertEqual(exp.index['in_data']['test'].get_shape(),
(5, 10, 192, 1))
def test_simple_recon(self):
options = tu.set_experiment('tomo')
plugin = 'savu.plugins.reconstructions.simple_recon'
run_protected_plugin_runner_no_process_list(options, plugin)
def test_astra_recon_gpu(self):
options = tu.set_experiment('tomo', process_names='GPU0')
plugin = astra_recons.__name__ + '.astra_recon_gpu'
run_protected_plugin_runner_no_process_list(options, plugin)
def test_astra_recon_cpu(self):
options = tu.initialise_options(None, 'tomo', None)
plugin = 'savu.plugins.reconstructions.astra_recons.astra_recon_cpu'
run_protected_plugin_runner_no_process_list(options, plugin)
tu.cleanup(options)
def test_downsample_correction(self):
options = tu.set_experiment('tomo')
plugin = 'savu.plugins.filters.downsample_filter'
run_protected_plugin_runner_no_process_list(options, plugin)
def test_simple_recon(self):
options = tu.set_experiment('tomo')
plugin = 'savu.plugins.reconstructions.simple_recon'
run_protected_plugin_runner_no_process_list(options, plugin)
def test_dezing_filter(self):
options = tu.set_experiment('tomoRaw')
plugin = 'savu.plugins.filters.dezing_filter'
run_protected_plugin_runner_no_process_list(options, plugin)
def test_band_pass(self):
options = tu.set_experiment('tomo')
plugin = 'savu.plugins.filters.band_pass'
run_protected_plugin_runner_no_process_list(options, plugin)
def test_downsample_correction(self):
options = tu.set_experiment('tomo')
plugin = 'savu.plugins.filters.downsample_filter'
run_protected_plugin_runner_no_process_list(options, plugin)
def test_paganin2(self):
options = tu.set_experiment('tomo')
plugin = 'savu.plugins.filters.paganin_filter'
run_protected_plugin_runner_no_process_list(options, plugin)
def test_sinogram_alignment(self):
options = tu.set_experiment('tomo')
plugin = 'savu.plugins.filters.sinogram_alignment'
run_protected_plugin_runner_no_process_list(options, plugin)
def test_band_pass(self):
options = tu.initialise_options(None, 'tomo', None)
plugin = 'savu.plugins.filters.band_pass'
run_protected_plugin_runner_no_process_list(options, plugin)
tu.cleanup(options)
def test_dezing_filter(self):
options = tu.set_experiment('tomoRaw')
plugin = 'savu.plugins.filters.dezinger_simple'
run_protected_plugin_runner_no_process_list(options, plugin)
def test_denoise_bregman_test(self):
options = tu.set_experiment('tomo')
plugin = 'savu.plugins.filters.denoising.denoise_bregman_filter'
run_protected_plugin_runner_no_process_list(options, plugin)
def rest_ring_artefact_removal(self):
options = tu.set_experiment('tomo')
plugin = 'savu.plugins.filters.ring_artefact_removal'
run_protected_plugin_runner_no_process_list(options, plugin)
def test_astra_recon_cpu_stxm(self):
options = tu.set_experiment('tomo')
plugin = 'savu.plugins.reconstructions.astra_recons.astra_recon_cpu'
run_protected_plugin_runner_no_process_list(options, plugin)
def test_denoise_bregman_test(self):
options = tu.set_experiment('tomo')
plugin = 'savu.plugins.filters.denoise_bregman_filter'
run_protected_plugin_runner_no_process_list(options, plugin)
def rest_ring_artefact_removal(self):
options = tu.set_experiment('tomo')
plugin = 'savu.plugins.filters.ring_artefact_removal'
run_protected_plugin_runner_no_process_list(options, plugin)
def test_astra_recon_gpu(self):
options = tu.set_experiment('tomo', process_names='GPU0')
plugin = astra_recons.__name__ + '.astra_recon_gpu'
run_protected_plugin_runner_no_process_list(options, plugin)
def test_astra_recon_cpu_stxm(self):
options = tu.set_experiment('tomo')
plugin = 'savu.plugins.reconstructions.astra_recons.astra_recon_cpu'
run_protected_plugin_runner_no_process_list(options, plugin)
def test_astra_recon_cpu_stxm(self):
options = tu.set_experiment("tomo")
plugin = astra_recons.__name__ + ".astra_recon_cpu"
run_protected_plugin_runner_no_process_list(options, plugin)
def test_sinogram_alignment(self):
options = tu.set_experiment("tomo")
plugin = "savu.plugins.filters.sinogram_alignment"
run_protected_plugin_runner_no_process_list(options, plugin)
def test_dezing_filter(self):
options = tu.initialise_options(None, 'tomoRaw', None)
plugin = 'savu.plugins.filters.dezinger_simple'
run_protected_plugin_runner_no_process_list(options, plugin)
tu.cleanup(options)
def test_cgls_recon(self):
options = tu.set_experiment("tomo")
plugin = "savu.plugins.reconstructions.cgls_recon"
run_protected_plugin_runner_no_process_list(options, plugin)
