Esempio n. 1
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 def test_reload(self):
     data_file = tu.get_test_data_path('24737.nxs')
     process_file = tu.get_test_process_path('savu_nexus_loader_test1.nxs')
     exp = run_protected_plugin_runner(
             tu.set_options(data_file, process_file=process_file))
     data_file = exp.meta_data.get('nxs_filename')
     process_file = tu.get_test_process_path('savu_nexus_loader_test2.nxs')
     run_protected_plugin_runner(tu.set_options(data_file,
                                                process_file=process_file))
Esempio n. 2
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 def test_simple_fit_runs(self):
     data_file = tu.get_test_data_path('mm.nxs')
     process_file = tu.get_test_process_path(
         'multimodal/simple_fit_test_XRF.nxs')
     options = tu.set_options(data_file, process_file=process_file)
     self.datapath = options['out_path']
     run_protected_plugin_runner(options)
Esempio n. 3
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    def test_i08_REGRESSION(self):
        data_file = tu.get_test_big_data_path('pymca_live_processing_test/i08-10471.nxs')
        process_file = tu.get_test_process_path('i08_pymca_process.nxs')
        outdir = tempfile.mkdtemp(prefix="pymca_i08_test")

        if os.path.exists(outdir):
            shutil.rmtree(outdir)
        os.makedirs(outdir, stat.S_IRWXO | stat.S_IRWXU)

        options = tu.set_options(data_file, process_file=process_file, out_path=outdir)
        run_protected_plugin_runner(options)
        change_permissions_recursive(options['out_path'],
                                     stat.S_IRWXO | stat.S_IRWXU | stat.S_IRWXG)

        output_filename = ("%(out_path)s"+os.sep+"%(out_folder)s_processed.nxs") % options

        f_test = h5.File(output_filename, 'r')  # the result of this test
        test_path = tu.get_test_big_data_path('pymca_live_processing_test/savu_test_result/test_processed.nxs')

        f_known = h5.File(test_path, 'r')  # a known good result from the same data

        # first we just do a direct comparison of the data. This should be equal exactly.
        data = '/entry/final_result_fluo/data'
        elements = 'entry/final_result_fluo/PeakElements'

        self.assertTrue((f_test[data][...] == f_known[data][...]).any())
        self.assertListEqual(list(f_test[elements][...]),
                             list(f_known[elements][...]))
Esempio n. 4
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    def test_i08_REGRESSION(self):
        data_file = tu.get_test_big_data_path(
            'pymca_live_processing_test/i08-10471.nxs')
        process_file = tu.get_test_process_path('i08_pymca_process.nxs')
        outdir = tempfile.mkdtemp(prefix="pymca_i08_test")

        if os.path.exists(outdir):
            shutil.rmtree(outdir)
        os.makedirs(outdir, stat.S_IRWXO | stat.S_IRWXU)

        options = tu.set_options(data_file,
                                 process_file=process_file,
                                 out_path=outdir)
        run_protected_plugin_runner(options)
        change_permissions_recursive(
            options['out_path'], stat.S_IRWXO | stat.S_IRWXU | stat.S_IRWXG)

        output_filename = ("%(out_path)s" + os.sep +
                           "%(out_folder)s_processed.nxs") % options

        f_test = h5.File(output_filename, 'r')  # the result of this test
        test_path = tu.get_test_big_data_path(
            'pymca_live_processing_test/savu_test_result/test_processed.nxs')

        f_known = h5.File(test_path,
                          'r')  # a known good result from the same data

        # first we just do a direct comparison of the data. This should be equal exactly.
        data = '/entry/final_result_fluo/data'
        elements = 'entry/final_result_fluo/PeakElements'

        self.assertTrue((f_test[data][...] == f_known[data][...]).any())
        self.assertListEqual(list(f_test[elements][...]),
                             list(f_known[elements][...]))
Esempio n. 5
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    def test_i18_stxm(self):
#         data_file = '/dls/i18/data/2016/sp12601-1/processing/Savu_Test_Data/70214_Cat2_RT_1.nxs'
        data_file = tu.get_test_data_path('i18_test_data.nxs')
        process_file = tu.get_test_process_path('basic_stxm_process_i18.nxs')
#         process_file = tu.get_process_list_path('stxm_tomo_i18.nxs')
        run_protected_plugin_runner(tu.set_options(data_file,
                                                   process_file=process_file))
Esempio n. 6
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    def test_1D_data(self):
        A = 11

        X = 10
        Y = 13

        expected_output_shape = (A, X, Y)
        expected_top_corners = np.arange(A, dtype=np.float32)

        self.create_N_tiffs(A, frame_size=(X, Y))
        # create a data file with the axis information
        self.data_file['entry/A'] = np.arange(A)
        self.data_file.close()

        # edit and save the yaml
        self.yaml['xrd']['data']['shape'] = '$(len(A_vals),)'
        self.yaml['xrd']['params'].update({
            'idx_A': 0,
            'idx_detx': 1,
            'idx_dety': 2,
            'A_vals': "$dfile['entry/A'].value",
            'dims': "$range(0, 3)"
        })

        # add some axis labels
        self.yaml['xrd']['axis_labels'] = {
            0: {
                'dim': '$idx_A',
                'name': 'A',
                'value': '$A_vals',
                'units': 'pixels'
            },
            1: self.detX_axis_label,
            2: self.detY_axis_label
        }

        self.save_yaml_and_change_process_list()

        run_protected_plugin_runner(
            tu.set_options(self.data_file_path,
                           process_file=self.process_list_path,
                           out_path=self.test_folder))

        # now check the result

        result = h5.File(os.path.join(self.test_folder, 'test_processed.nxs'),
                         'r')['entry/final_result_xrd/data']
        np.testing.assert_array_equal(
            result.shape,
            expected_output_shape,
            err_msg='The output shape is not as expected.')
        result_corners = result[..., -1, -1]
        np.testing.assert_equal(
            result_corners.dtype,
            expected_top_corners.dtype,
            err_msg='The array does not output the correct type.')
        np.testing.assert_array_equal(
            result_corners,
            expected_top_corners,
            err_msg="The output values are not as expected")
Esempio n. 7
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 def test_stxm_tomo_astra(self):
     print "Hi2"
     data_file = tu.get_test_data_path('mm.nxs')
     process_file = \
         tu.get_test_process_path('simple_stxm_tomo_test_astra.nxs')
     run_protected_plugin_runner(
         tu.set_options(data_file, process_file=process_file))
Esempio n. 8
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    def test_diffraction_correction(self):
        data_file = tu.get_test_data_path('i18_test_data.nxs')

#         data_file = '/dls/i18/data/2016/sp13939-1/Experiment_1/nexus/75996_alphanitrateRT_1.nxs'
        process_file = tu.get_test_process_path('diffraction_absorption_correction_test.nxs')
        run_protected_plugin_runner(tu.set_options(data_file,
                                                   process_file=process_file))
Esempio n. 9
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    def test_simple_fit_runs(self):
#         data_file = '/dls/i13-1/data/2016/mt14190-1/raw/91318.nxs'#
        data_file = tu.get_test_data_path('i18_test_data.nxs')
        process_file = tu.get_test_process_path('pymca_test.nxs')
#         process_file = '/dls/i13-1/data/2016/mt14190-1/processing/savu/process_lists/pymca_process.nxs'
        options = tu.set_options(data_file, process_file=process_file)
        self.datapath = options['out_path']
        run_protected_plugin_runner(options)
 def test_pyfai(self):
     data_file = tu.get_test_data_path(
         'i18_test_data.nxs'
     )  #'/dls/i18/data/2016/sp12601-1/processing/Savu_Test_Data/70214_Cat2_RT_1.nxs'#
     process_file = tu.get_test_process_path(
         'PyFAI_azimuth_new_calib_i18_test.nxs')
     run_protected_plugin_runner(
         tu.set_options(data_file, process_file=process_file))
Esempio n. 11
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 def test_simple_fit_runs(self):
     #         data_file = '/dls/i13-1/data/2016/mt14190-1/raw/91318.nxs'#
     data_file = tu.get_test_data_path('i18_test_data.nxs')
     process_file = tu.get_test_process_path('pymca_test.nxs')
     #         process_file = '/dls/i13-1/data/2016/mt14190-1/processing/savu/process_lists/pymca_process.nxs'
     options = tu.set_options(data_file, process_file=process_file)
     self.datapath = options['out_path']
     run_protected_plugin_runner(options)
    def test_3D_data(self):
        A = 3
        B = 4
        C = 5

        X = 10
        Y = 13
        expected_output_shape = (A, B, C, X, Y)
        expected_top_corners = np.arange(A*B*C, dtype=np.float32).reshape((A, B, C))

        self.create_N_tiffs(A*B*C, frame_size=(X, Y))
        # create a data file with the axis information
        self.data_file['entry/A'] = np.arange(A)
        self.data_file['entry/B'] = np.arange(B)
        self.data_file['entry/C'] = np.arange(C)
        self.data_file.close()

        # edit and save the yaml
        self.yaml['xrd']['data']['shape'] = '$(len(A_vals), len(B_vals), len(C_vals))'
        self.yaml['xrd']['params'].update({'idx_A': 0,
                                           'idx_B': 1,
                                           'idx_C': 2,
                                           'idx_detx': 3,
                                           'idx_dety': 4,
                                           'A_vals': "$dfile['entry/A'].value",
                                           'B_vals': "$dfile['entry/B'].value",
                                           'C_vals': "$dfile['entry/C'].value",
                                           'dims': "$range(0, 4)"})

        self.yaml['xrd']['axis_labels'] = {0: {'dim': '$idx_A', 'name': 'A', 'value': '$A_vals', 'units': 'pixels'},
                                           1: {'dim': '$idx_B', 'name': 'B', 'value': '$B_vals', 'units': 'pixels'},
                                           2: {'dim': '$idx_C', 'name': 'C', 'value': '$C_vals', 'units': 'pixels'},
                                           3: self.detX_axis_label,
                                           4: self.detY_axis_label}

        self.save_yaml_and_change_process_list()

        run_protected_plugin_runner(tu.set_options(self.data_file_path,
                                                   process_file=self.process_list_path,
                                                   out_path=self.test_folder))

        result = h5.File(os.path.join(self.test_folder, 'test_processed.nxs'), 'r')['entry/final_result_xrd/data']
        np.testing.assert_array_equal(result.shape, expected_output_shape,
                                      err_msg='The output shape is not as expected.')
        result_corners = result[..., -1, -1]
        np.testing.assert_equal(result_corners.dtype, expected_top_corners.dtype,
                                err_msg='The array does not output the correct type.')
        np.testing.assert_array_equal(result_corners, expected_top_corners,
                                      err_msg="The output values are not as expected")
Esempio n. 13
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    def test_i08_REGRESSION(self):
        data_file = tu.get_test_big_data_path('pymca_live_processing_test/i08-10471.nxs')
        process_file = tu.get_test_process_path('i08_pymca_process.nxs')
        outdir = '/tmp/pymca_i08_test'+strftime("%Y%m%d%H%M%S", gmtime())+'/'
        if os.path.exists(outdir):
            shutil.rmtree(outdir)
        os.makedirs(outdir, stat.S_IRWXO | stat.S_IRWXU)
        options = tu.set_options(data_file,process_file=process_file,out_path=outdir)
        run_protected_plugin_runner(options)
        change_permissions_recursive(options['out_path'], stat.S_IRWXO | stat.S_IRWXU | stat.S_IRWXG)
        
        f_test = h5.File(options['out_path']+os.sep+options['out_folder']+'_processed.nxs','r') #  the result of this test
        f_known = h5.File(tu.get_test_big_data_path('pymca_live_processing_test/savu_test_result/test_processed.nxs'),'r')#  a known good result from the same data
        # first we just do a direct comparison of the data. This should be equal exactly.
        data = '/entry/final_result_fluo/data'
        elements = 'entry/final_result_fluo/PeakElements'
#         test=np.around(f_test[data][...], decimals=-1)
#         known=np.around(f_known[data][...], decimals=-1)
#         self.assertEqual(test, known)
        self.assertTrue((f_test[data][...]==f_known[data][...]).any())
#         np.testing.assert_array_almost_equal(f_test[data][...], f_known[data][...], 0) # this needs to be -1
        self.assertListEqual(list(f_test[elements][...]), list(f_known[elements][...]))
 def test_nx_stxm(self):
     data_file = tu.get_test_data_path('mm.nxs')
     process_file = tu.get_test_process_path('basic_stxm_process.nxs')
     run_protected_plugin_runner(tu.set_options(data_file,
                                                process_file=process_file))
 def test_pyfai(self):
     data_file = tu.get_test_data_path('i18_test_data.nxs')#'/dls/i18/data/2016/sp12601-1/processing/Savu_Test_Data/70214_Cat2_RT_1.nxs'#
     process_file = tu.get_test_process_path('PyFAI_azimuth_new_calib_i18_test.nxs')
     run_protected_plugin_runner(tu.set_options(data_file,
                                                process_file=process_file))
 def test_cgls_recon(self):
     data_file = tu.get_test_data_path('24737.nxs')
     process_file = tu.get_test_process_path('ccpi_cgls_recon_test.nxs')
     run_protected_plugin_runner(tu.set_options(data_file,
                                                process_file=process_file))
Esempio n. 17
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 def test_stxm_tomo_scikit(self):
     data_file = tu.get_test_data_path('mm.nxs')
     process_file = \
         tu.get_test_process_path('simple_stxm_tomo_test_scikit.nxs')
     run_protected_plugin_runner(
         tu.set_options(data_file, process_file=process_file))
 def test_chunking(self):
     data_file = tu.get_test_data_path('xrd_single_sino.nxs')
     process_file = tu.get_test_process_path(
             'pyfai_tomo_chunking_single_sino_test.nxs')
     run_protected_plugin_runner(tu.set_options(data_file,
                                                process_file=process_file))
Esempio n. 19
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 def test_process(self):
     data_file = tu.get_test_data_path('i18_test_data.nxs')
     process_file = '/dls/mx-scratch/aaron/data/I18/paper_processing/devel_process_lists/xrd_tomo_i18.nxs'
     #         process_file = tu.get_process_list_path('xrd_tomo_i18.nxs')
     run_protected_plugin_runner(
         tu.set_options(data_file, process_file=process_file))
Esempio n. 20
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 def tiff_test_stitch_dim(self):
     data_file = tu.get_test_data_path('image_test/tiffs')
     process_file = tu.get_test_process_path(
         'tiff_loader_test_change_stitching_dim.nxs')
     run_protected_plugin_runner(
         tu.set_options(data_file, process_file=process_file))
 def test_process(self):
     data_file = tu.get_test_data_path('mm.nxs')
     process_file = \
         tu.get_test_process_path('simple_stxm_tomo_test_astra.nxs')
     run_protected_plugin_runner(tu.set_options(data_file,
                                                process_file=process_file))
Esempio n. 22
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 def test_hilbert(self):
     data_file = tu.get_test_data_path('24737.nxs')
     process_file = tu.get_test_process_path('hilbert_test.nxs')
     run_protected_plugin_runner(
         tu.set_options(data_file, process_file=process_file))
Esempio n. 23
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 def test_ptycho(self):
     data_file = '/dls/mx-scratch/savu_test_data/NXptychoflipped.nxs'
     process_file = tu.get_test_process_path('ptycho_test.nxs')
     run_protected_plugin_runner(
         tu.set_options(data_file, process_file=process_file))
Esempio n. 24
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 def test_mm(self):
     data_file = tu.get_test_data_path('mm.nxs')
     process_file = tu.get_test_process_path('multiple_mm_inputs_test.nxs')
     run_protected_plugin_runner(tu.set_options(data_file,
                                                process_file=process_file))
Esempio n. 25
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 def test_ptycho(self):
     data_file = '/dls/mx-scratch/savu_test_data/NXptychoflipped.nxs'
     process_file = tu.get_test_process_path('ptycho_test.nxs')
     run_protected_plugin_runner(tu.set_options(data_file,
                                                process_file=process_file))
 def test_process(self):
     data_file = tu.get_test_big_data_path('xrd_tomo_p3_astra_recon_cpu.h5')
     process_file = tu.get_test_process_path('ica_test.nxs')
     run_protected_plugin_runner(tu.set_options(data_file,
                                                process_file=process_file))
 def test_binary_quantisation_filter(self):
     data_file = tu.get_test_data_path('24737.nxs')
     process_file = tu.get_test_process_path('threshold_filter_test.nxs')
     run_protected_plugin_runner(tu.set_options(data_file,
                                                process_file=process_file))
 def test_multi_params_tomo(self):
     data_file = tu.get_test_data_path('24737.nxs')
     process_file = tu.get_test_process_path(
         'basic_tomo_process_preview_params_test.nxs')
     run_protected_plugin_runner(tu.set_options(data_file,
                                                process_file=process_file))
Esempio n. 29
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 def test_i13_fluo(self):
     data_file = tu.get_test_data_path('i13_fluo_data.nxs')
     process_file = tu.get_test_process_path('basic_fluo_process_i13.nxs')
     run_protected_plugin_runner(
         tu.set_options(data_file, process_file=process_file))
Esempio n. 30
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 def test_stage_motion(self):
     data_file = tu.get_test_data_path('kinematics_data.nxs')
     process_file = tu.get_test_process_path('kinematic_parser_test.nxs')
     run_protected_plugin_runner(
         tu.set_options(data_file, process_file=process_file))
 def test_process(self):
     data_file = tu.get_test_data_path('fluo_single_sino.nxs')
     process_file = tu.get_test_process_path('simple_fit_test_XRF_tomo.nxs')
     run_protected_plugin_runner(tu.set_options(data_file,
                                                process_file=process_file))
Esempio n. 32
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 def test_fbp(self):
     data_file = tu.get_test_data_path('24737.nxs')
     process_file = tu.get_test_process_path('raven_filter_test.nxs')
     run_protected_plugin_runner(
         tu.set_options(data_file, process_file=process_file))
Esempio n. 33
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 def test_astra_recon_init_vol(self):
     data_file = tu.get_test_data_path('24737.nxs')
     process_file = tu.get_test_process_path('astra_init_vol_test.nxs')
     run_protected_plugin_runner(
         tu.set_options(data_file, process_file=process_file))
Esempio n. 34
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 def test_process(self):
     data_file = tu.get_test_data_path('/i12_test_data/i12_test_data.nxs')
     process_file = tu.get_test_process_path('i12_tomo_pipeline_test.nxs')
     run_protected_plugin_runner(tu.set_options(data_file,
                                                process_file=process_file))
 def test_pyfai_filtered(self):
     data_file = tu.get_test_data_path('mm.nxs')
     process_file = tu.get_test_process_path('PyFAI_azimuth_test_bragg.nxs')
     run_protected_plugin_runner(tu.set_options(data_file,
                                                process_file=process_file))
 def test_process(self):
     data_file = tu.get_test_data_path('mm.nxs')
     process_file = tu.get_test_process_path('spectrum_crop_test.nxs')
     run_protected_plugin_runner(tu.set_options(data_file,
                                                process_file=process_file))
Esempio n. 37
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 def test_process_preview(self):
     data_file = tu.get_test_data_path('24737.nxs')
     process_file = \
         tu.get_test_process_path('tomo_pipeline_preview_test.nxs')
     run_protected_plugin_runner(
         tu.set_options(data_file, process_file=process_file))
Esempio n. 38
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 def test_ccpi_regul_cpu(self):
     data_file = tu.get_test_data_path('24737.nxs')
     process_file = tu.get_test_process_path('CcpiRegulToolkitCpu_test.nxs')
     run_protected_plugin_runner(tu.set_options(data_file,
                                                process_file=process_file))
Esempio n. 39
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 def test_nx_xrd(self):
     data_file = '/dls/i18/data/2016/sp12601-1/processing/Savu_Test_Data/70214_Cat2_RT_1.nxs'
     process_file = tu.get_test_process_path('basic_xrd_process_i18.nxs')
     run_protected_plugin_runner(
         tu.set_options(data_file, process_file=process_file))
Esempio n. 40
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 def test_process(self):
     data_file = tu.get_test_data_path('mm.nxs')
     process_file = tu.get_test_process_path(
         'I18_pipeline_just_xrd_from_raw_filtered_adp_mod2.nxs')
     run_protected_plugin_runner(tu.set_options(data_file,
                                                process_file=process_file))
Esempio n. 41
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 def test_tomopy_gridrec(self):
     data_file = tu.get_test_data_path('24737.nxs')
     process_file = tu.get_test_process_path('tomopy_test.nxs')
     run_protected_plugin_runner(
         tu.set_options(data_file, process_file=process_file))
 def test_dezinger_sinogram(self):
     data_file = tu.get_test_data_path('24737.nxs')
     process_file = tu.get_test_process_path('dezinger_sinogram_test.nxs')
     run_protected_plugin_runner(tu.set_options(data_file,
                                                process_file=process_file))
Esempio n. 43
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 def test_simple_fit_XRD(self):
     data_file = tu.get_test_data_path('mm.nxs')
     process_file = tu.get_test_process_path('findpeakstest.nxs')
     run_protected_plugin_runner(tu.set_options(data_file,
                                                process_file=process_file))
 def test_multi_params_tomo(self):
     data_file = tu.get_test_data_path('24737.nxs')
     process_file = tu.get_test_process_path(
         'basic_tomo_process_preview_params_test.nxs')
     run_protected_plugin_runner(
         tu.set_options(data_file, process_file=process_file))
Esempio n. 45
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 def test_tomobar_recon(self):
     data_file = tu.get_test_data_path('24737.nxs')
     process_file = tu.get_test_process_path('tomobar2d_recon.nxs')
     run_protected_plugin_runner(tu.set_options(data_file,
                                                process_file=process_file))
Esempio n. 46
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 def test_stage_motion(self):
     data_file = tu.get_test_data_path('kinematics_data.nxs')
     process_file = tu.get_test_process_path('kinematic_parser_test.nxs')
     run_protected_plugin_runner(tu.set_options(data_file,
                                                process_file=process_file))
 def test_process_preview(self):
     data_file = tu.get_test_data_path('24737.nxs')
     process_file = \
         tu.get_test_process_path('tomo_pipeline_preview_test.nxs')
     run_protected_plugin_runner(tu.set_options(data_file,
                                                process_file=process_file))
Esempio n. 48
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 def test_image_interpolation(self):
     data_file = tu.get_test_big_data_path('speckle_tracking.h5')
     process_file = tu.get_test_process_path('to_revise/umpa_test.nxs')
     run_protected_plugin_runner(
         tu.set_options(data_file, process_file=process_file))
 def test_distortion_correction(self):
     data_file = tu.get_test_data_path('24737.nxs')
     process_file = \
         tu.get_test_process_path('distortion_correction_test.nxs')
     run_protected_plugin_runner(tu.set_options(data_file,
                                                process_file=process_file))
Esempio n. 50
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 def test_i14_software(self):
     data_file = tu.get_test_big_data_path('i14-5195.nxs')
     process_file = tu.get_test_process_path('i14_basic_process.nxs')
     run_protected_plugin_runner(tu.set_options(data_file,
                                                process_file=process_file))
Esempio n. 51
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 def test_i14_software(self):
     data_file = tu.get_test_big_data_path('i14-5195.nxs')
     process_file = tu.get_test_process_path('i14_pymca_process.nxs')
     run_protected_plugin_runner(tu.set_options(data_file,
                                                process_file=process_file))
 def test_i13_speckle_tracking(self):
     data_file = tu.get_test_big_data_path('speckle_tracking.h5')
     process_file = tu.get_test_process_path('to_revise/i13_speckle_loader_process.nxs')
     run_protected_plugin_runner(tu.set_options(data_file,
                                                process_file=process_file))
Esempio n. 53
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 def test_process(self):
     data_file = tu.get_test_big_data_path('xrd_tomo_p3_astra_recon_cpu.h5')
     process_file = tu.get_test_process_path('pca_test.nxs')
     run_protected_plugin_runner(
         tu.set_options(data_file, process_file=process_file))
 def test_subpixel_shift(self):
     data_file = tu.get_test_data_path('24737.nxs')
     process_file = \
         tu.get_test_process_path('subpixel_shift.nxs')
     run_protected_plugin_runner(tu.set_options(data_file,
                                                process_file=process_file))
Esempio n. 55
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 def test_nx_ptycho(self):
     data_file = tu.get_test_data_path('NXptycho.nxs')
     process_file = tu.get_test_process_path('basic_ptycho_process.nxs')
     run_protected_plugin_runner(
         tu.set_options(data_file, process_file=process_file))
 def test_process(self):
     data_file = tu.get_test_data_path('mm.nxs')
     process_file = tu.get_test_process_path('mm_template_processing.nxs')
     run_protected_plugin_runner(tu.set_options(data_file,
                                                process_file=process_file))