def test_tomobar3d_fast(self):
process_list = 'reconstruction/tomobar/tomobar3d_gpu_recon.nxs'
options1 = tu.initialise_options(data_file, experiment, process_list)
run_protected_plugin_runner(options1)
#read the output file using SavuNexusLoader
data_file2 = options1['out_path'] + 'test_processed.nxs'
options2 = tu.initialise_options(data_file2, 'load_data', 'loaders/savu_nexus_loader_test4.nxs')
run_protected_plugin_runner(options2)
tu.cleanup(options1)
tu.cleanup(options2)
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
data_file2 = options1['out_path'] + 'test_processed.nxs'
options2 = tu.initialise_options(
data_file2, 'load_data', 'loaders/savu_nexus_loader_test2.nxs')
run_protected_plugin_runner(options2)
tu.cleanup(options1)
tu.cleanup(options2)
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 test_astra_recon_init_vol(self):
process_list = 'reconstruction/astra_init_vol_test.nxs'
options = tu.initialise_options(data_file, experiment, process_list)
run_protected_plugin_runner(options)
tu.cleanup(options)
def test_process_preview(self):
process_list = 'map3dto4d_pipeline_preview_test.nxs'
options = tu.initialise_options(data_file, experiment, process_list)
run_protected_plugin_runner(options)
tu.cleanup(options)
def test_i18_mm(self):
process_list = 'loaders/MM_i18_test.nxs'
options = tu.initialise_options(data_file, experiment, process_list)
run_protected_plugin_runner(options)
tu.cleanup(options)
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_gmm(self):
process_list = 'segmentation/gmm/gmm_test.nxs'
options = tu.initialise_options(data_file, experiment, process_list)
run_protected_plugin_runner(options)
tu.cleanup(options)
def test_correction(self):
process_list = 'corrections/camera_rot_corr_test.nxs'
options = tu.initialise_options(data_file, experiment, process_list)
run_protected_plugin_runner(options)
tu.cleanup(options)
def test_GeoDistance3d(self):
process_list = 'segmentation/geodistance/geodistance3d_test.nxs'
options = tu.initialise_options(data_file, experiment, process_list)
run_protected_plugin_runner(options)
tu.cleanup(options)
def test_process(self):
process_list = 'pymca/interpolation_test.nxs'
options = tu.initialise_options(data_file, experiment, process_list)
run_protected_plugin_runner(options)
tu.cleanup(options)
def test_simple_fit_XRD(self):
process_list = 'multimodal/findpeakstest.nxs'
options = tu.initialise_options(data_file, experiment, process_list)
run_protected_plugin_runner(options)
tu.cleanup(options)
def test_diffraction_correction(self):
process_list = 'diffraction/diffraction_absorption_correction_test.nxs'
options = tu.initialise_options(data_file, None, process_list)
run_protected_plugin_runner(options)
tu.cleanup(options)
def test_binary_quantisation_filter(self):
process_list = 'threshold_filter_test.nxs'
options = tu.initialise_options(data_file, experiment, process_list)
run_protected_plugin_runner(options)
tu.cleanup(options)
def test_MaskInitialiser(self):
process_list = 'segmentation/morphsnakes/mask_init_test.nxs'
options = tu.initialise_options(data_file, experiment, process_list)
run_protected_plugin_runner(options)
tu.cleanup(options)
def test_ccpi_denoise_gpu(self):
process_list = 'filters/ccpi/ccpi_denoising_gpu_test.nxs'
options = tu.initialise_options(data_file, experiment, process_list)
run_protected_plugin_runner(options)
tu.cleanup(options)
def test_histogram(self):
process_list = 'multimodal/histogramtest.nxs'
options = tu.initialise_options(data_file, experiment, process_list)
run_protected_plugin_runner(options)
tu.cleanup(options)
def test_image_saver(self):
process_list = 'imagesavers/image_saver_test.nxs'
options = tu.initialise_options(data_file, experiment, process_list)
run_protected_plugin_runner(options)
tu.cleanup(options)
def test_fresnel_fbp(self):
process_list = 'fresnel_filter_test.nxs'
options = tu.initialise_options(data_file, experiment, process_list)
run_protected_plugin_runner(options)
tu.cleanup(options)
def test_tomobar3d_full(self):
process_list = 'reconstruction/tomobar/tomobar_fully3d_gpu_recon.nxs'
options = tu.initialise_options(data_file, experiment, process_list)
run_protected_plugin_runner(options)
tu.cleanup(options)
def test_downsample_correction(self):
process_list = 'downsample_filter_test.nxs'
options = tu.initialise_options(data_file, experiment, process_list)
run_protected_plugin_runner(options)
tu.cleanup(options)
def test_fbp(self):
process_list = 'reconstruction/simple_recon_test_process.nxs'
options = tu.initialise_options(data_file, experiment, process_list)
run_protected_plugin_runner(options)
tu.cleanup(options)
def test_sinogram_alignment(self):
process_list = 'sino_alignment_test.nxs'
options = tu.initialise_options(data_file, experiment, process_list)
run_protected_plugin_runner(options)
tu.cleanup(options)
def test_background_estimator(self):
process_list = 'multimodal/poly_background_test.nxs'
options = tu.initialise_options(data_file, experiment, process_list)
run_protected_plugin_runner(options)
tu.cleanup(options)
def test_median_gpu_filter(self):
process_list = 'filters/denoise/median_filter_gpu_test.nxs'
options = tu.initialise_options(data_file, experiment, process_list)
run_protected_plugin_runner(options)
tu.cleanup(options)
def test_quantification_tomophantom(self):
process_list = 'simulation/tomophantom/tomophant_quantif_test.nxs'
options = tu.initialise_options(data_file, experiment, process_list)
run_protected_plugin_runner(options)
tu.cleanup(options)
def test_nx_tomo(self):
process_list = 'loaders/basic_tomo_process.nxs'
options = tu.initialise_options(data_file, experiment, process_list)
run_protected_plugin_runner(options)
tu.cleanup(options)
def test_morphremoval(self):
process_list = 'segmentation/morphproc/morphremove_objects_test.nxs'
options = tu.initialise_options(data_file, experiment, process_list)
run_protected_plugin_runner(options)
tu.cleanup(options)
def test_dezinger_sinogram(self):
process_list = 'filters/dezinger/dezinger_sinogram_test.nxs'
options = tu.initialise_options(data_file, experiment, process_list)
run_protected_plugin_runner(options)
tu.cleanup(options)
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)