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_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_tomo1(self):
options = tu.set_experiment('tomo')
plugin = 'savu.plugins.test_plugin'
loader_dict = {}
data_dict = {'in_datasets': ['tomo', 'tomo'], 'out_datasets': ['test']}
saver_dict = {}
all_dicts = [loader_dict, data_dict, saver_dict]
run_protected_plugin_runner_no_process_list(options, plugin,
data=all_dicts)
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_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_create_smaller_data_block(self):
options = tu.set_experiment('tomo')
plugin = 'savu.plugins.reshape.downsample_filter'
tu.set_plugin_list(options, plugin)
out_data_name = options['plugin_list'][1]['data']['out_datasets'][0]
plugin_runner = PluginRunner(options)
exp = plugin_runner._run_plugin_list()
self.assertEqual(exp.index['in_data'][out_data_name].get_shape(),
(91, 68, 80))
def framework_options_setup(self):
key1 = 'reconstruction_type'
key2 = 'number_of_iterations'
key3 = 'in_datasets'
key4 = 'out_datasets'
params = {key1: 'FBP;CGLS', key2: '1;2;3', key3: 'tomo', key4: 'tomo'}
options = tu.set_experiment('tomo')
plugin = 'savu.plugins.reconstructions.astra_recons.astra_recon_cpu'
tu.set_plugin_list(options, plugin, [{}, params, {}])
return options
def framework_options_setup(self):
key1 = 'reconstruction_type'
key2 = 'number_of_iterations'
key3 = 'in_datasets'
key4 = 'out_datasets'
params = {key1: 'FBP;CGLS', key2: '1;2;3', key3: 'tomo', key4: 'tomo'}
options = tu.set_experiment('tomo')
plugin = 'savu.plugins.reconstructions.astra_recons.astra_recon_cpu'
tu.set_plugin_list(options, plugin, [{}, params, {}])
return options
def test_create_smaller_data_block(self):
options = tu.set_experiment('tomo')
plugin = 'savu.plugins.reshape.downsample_filter'
tu.set_plugin_list(options, plugin)
out_data_name = options['plugin_list'][1]['data']['out_datasets'][0]
plugin_runner = PluginRunner(options)
exp = plugin_runner._run_plugin_list()
self.assertEqual(exp.index['in_data'][out_data_name].get_shape(),
(91, 68, 80))
def test_tomo4(self):
options = tu.set_experiment('tomo')
plugin = 'savu.plugins.test_plugin'
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']}
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 create_chunking_instance(self, current_list, nnext_list, nProcs):
current = self.create_pattern('a', current_list)
nnext = self.create_pattern('b', nnext_list)
options = tu.set_experiment('tomoRaw')
options['processes'] = range(nProcs)
# set a dummy process list
options['process_file'] = \
tu.get_test_process_path('basic_tomo_process.nxs')
exp = Experiment(options)
test_dict = {'current': current, 'next': nnext}
chunking = Chunking(exp, test_dict)
return chunking
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_tomo3(self):
options = tu.set_experiment('tomo')
plugin = 'savu.plugins.basic_operations.basic_operations'
preview = ['10:-1:10:1', '10:-1:10:1', '10:-1:10:1']
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(),
(9, 13, 15))
def framework_options_setup(self):
key1 = "preview"
key2 = "FBP_filter"
key3 = "center_of_rotation"
key4 = "in_datasets"
key5 = "out_datasets"
params = {key1: [":", "0", ":"], key2: "ram-lak;hamming", key3: "85.0;85.5;86.0", key4: "tomo", key5: "tomo"}
options = tu.set_experiment("tomo")
plugin = "savu.plugins.reconstructions.astra_recons.astra_recon_cpu"
tu.set_plugin_list(options, plugin, [{}, params, {}])
return options
def create_chunking_instance(self, current_list, nnext_list, nProcs):
current = self.create_pattern('a', current_list)
nnext = self.create_pattern('b', nnext_list)
options = tu.set_experiment('tomoRaw')
options['processes'] = range(nProcs)
# set a dummy process list
options['process_file'] = \
tu.get_test_process_path('basic_tomo_process.nxs')
exp = Experiment(options)
test_dict = {'current': current, 'next': nnext}
chunking = Chunking(exp, test_dict)
return chunking
def framework_options_setup(self):
key1 = 'interpolation'
key2 = 'iterations'
key3 = 'in_datasets'
key4 = 'out_datasets'
key5 = 'sino_pad_width'
params = {key1: 'nearest;linear', key2: '1;2;3', key3: 'tomo',
key4: 'tomo', key5: 0}
options = tu.set_experiment('tomo')
plugin = 'savu.plugins.reconstructions.scikitimage_sart'
tu.set_plugin_list(options, plugin, [{}, params, {}])
return options
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 framework_options_setup(self):
key1 = 'preview'
key2 = 'projector'
key3 = 'centre_of_rotation'
key4 = 'in_datasets'
key5 = 'out_datasets'
key6 = 'force_zero'
params = {key1: [':', '0', ':'], key2: 'line;strip',
key3: '85.0;85.5;86.0', key4: 'tomo', key5: 'tomo',
key6: '[None, None]'}
options = tu.set_experiment('tomo')
plugin = 'savu.plugins.reconstructions.astra_recons.astra_recon_cpu'
tu.set_plugin_list(options, plugin, [{}, params, {}])
return options
def framework_options_setup(self):
key1 = 'n_iterations'
key2 = 'algorithm'
key3 = 'in_datasets'
key4 = 'out_datasets'
params = OrderedDict({
key1: '1;2;3',
key2: 'FBP;CGLS',
key3: 'tomo',
key4: 'tomo'
})
options = tu.set_experiment('tomo')
plugin = 'savu.plugins.reconstructions.astra_recons.astra_recon_cpu'
tu.set_plugin_list(options, plugin, [{}, params, {}])
return options
def test_reload(self):
process_list = 'loaders/savu_nexus_loader_test1.nxs'
options1 = tu.initialise_options(data_file, experiment, process_list)
run_protected_plugin_runner(options1)
#read the output file using SavuNexusLoader
path_to_rec = options1['out_path'] + 'test_processed.nxs'
self.test_folder2 = tempfile.mkdtemp(suffix='my_test2/')
options2 = tu.set_experiment('tomo')
options2['data_file'] = path_to_rec
options2['out_path'] = os.path.join(self.test_folder2)
options2['process_file'] = tu.get_test_process_path(
'loaders/savu_nexus_loader_test2.nxs')
run_protected_plugin_runner(options2)
tu.cleanup(options1)
tu.cleanup(options2)
def framework_options_setup(self):
key1 = 'interpolation'
key2 = 'iterations'
key3 = 'in_datasets'
key4 = 'out_datasets'
key5 = 'sino_pad_width'
params = {
key1: 'nearest;linear',
key2: '1;2;3',
key3: 'tomo',
key4: 'tomo',
key5: 0
}
options = tu.set_experiment('tomo')
plugin = 'savu.plugins.reconstructions.scikitimage_sart'
tu.set_plugin_list(options, plugin, [{}, params, {}])
return options
def framework_options_setup(self):
key1 = 'preview'
key2 = 'FBP_filter'
key3 = 'center_of_rotation'
key4 = 'in_datasets'
key5 = 'out_datasets'
params = {
key1: [':', '0', ':'],
key2: 'ram-lak;hamming',
key3: '85.0;85.5;86.0',
key4: 'tomo',
key5: 'tomo'
}
options = tu.set_experiment('tomo')
plugin = 'savu.plugins.reconstructions.astra_recons.astra_recon_cpu'
tu.set_plugin_list(options, plugin, [{}, params, {}])
return options
def framework_options_setup(self):
key1 = 'preview'
key2 = 'projector'
key3 = 'centre_of_rotation'
key4 = 'in_datasets'
key5 = 'out_datasets'
key6 = 'force_zero'
params = {
key1: [':', '0', ':'],
key2: 'line;strip',
key3: '85.0;85.5;86.0',
key4: 'tomo',
key5: 'tomo',
key6: '[None, None]'
}
options = tu.set_experiment('tomo')
plugin = 'savu.plugins.reconstructions.astra_recons.astra_recon_cpu'
tu.set_plugin_list(options, plugin, [{}, params, {}])
return options
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_cgls_recon(self):
options = tu.set_experiment("tomo")
plugin = "savu.plugins.reconstructions.cgls_recon"
run_protected_plugin_runner_no_process_list(options, plugin)
def test_median_filter(self):
options = tu.set_experiment('tomo')
plugin = 'savu.plugins.filters.median_filter'
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 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_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_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 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_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_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_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_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_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_basic_operations(self):
process_file = tu.get_test_process_path('basic_operations_test.nxs')
options = tu.set_experiment('tomo')
options['process_file'] = process_file
run_protected_plugin_runner(options)
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_basic_operations(self):
process_file = tu.get_test_process_path('basic_operations_test.nxs')
options = tu.set_experiment('tomo')
options['process_file'] = process_file
run_protected_plugin_runner(options)
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 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_paganin1(self):
options = tu.set_experiment('tomoRaw')
plugin = 'savu.plugins.paganin_filter'
run_protected_plugin_runner_no_process_list(options, plugin)
def test_median_filter(self):
options = tu.set_experiment('tomo')
plugin = 'savu.plugins.filters.median_filter'
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 "r6"(self):
options = tu.set_experiment("r7")
plugin = "r8"
run_protected_plugin_runner_no_process_list(options, plugin)
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_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 = astra_recons.__name__ + ".astra_recon_cpu"
run_protected_plugin_runner_no_process_list(options, plugin)
