Beispiel #1
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    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)
Beispiel #2
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    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)
Beispiel #3
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    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)
Beispiel #4
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 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)
Beispiel #5
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 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)               
Beispiel #6
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 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)
Beispiel #7
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 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)
Beispiel #8
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 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)
Beispiel #9
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 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)
Beispiel #10
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 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)
Beispiel #11
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 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)
Beispiel #12
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 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)
Beispiel #14
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 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)
Beispiel #15
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 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)
Beispiel #17
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 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)
Beispiel #18
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 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)
Beispiel #19
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 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)
Beispiel #20
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 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)
Beispiel #21
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 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)
Beispiel #22
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 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)
Beispiel #23
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 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)
Beispiel #26
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 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)
Beispiel #27
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 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)
Beispiel #28
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 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)
Beispiel #29
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 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)
Beispiel #30
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 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)