def setUp(self):
self.test_folder = tempfile.mkdtemp(suffix='template_test/')
self.tif_folder = os.path.join(self.test_folder, 'tiffs/')
os.mkdir(self.tif_folder)
# copy across the process list to the working directory
self.process_list_path = os.path.join(self.test_folder, 'xrd_template_test.nxs')
shutil.copyfile(tu.get_test_process_path('xrd_template_test.nxs'),
self.process_list_path)
utils.populate_plugins()
self.process_list = Content()
self.process_list.fopen(self.process_list_path, update=False)
for idx in self.process_list.get_positions():
self.process_list.refresh(idx)
self.detX_axis_label = {'dim': '$idx_detx', 'name': 'detector_x', 'value': None, 'units': 'pixels'}
self.detY_axis_label = {'dim': '$idx_dety', 'name': 'detector_y', 'value': None, 'units': 'pixels'}
self.yaml = OrderedDict()
# now make some standard modifications
self.yaml['inherit'] = [tu.get_test_data_path(os.path.join('i18_templates', 'xrd_calibration.yml'))]
self.yaml['xrd'] = OrderedDict()
self.yaml['xrd']['params'] = {}
self.yaml['xrd']['data'] = {}
self.yaml['xrd']['data']['folder'] = self.tif_folder
self.yaml['xrd']['params']['cfile'] = \
"$h5py.File('%s', 'r')" % tu.get_test_data_path('LaB6_calibration_new.nxs')
self.yaml['xrd']['patterns'] = {}
self.yaml['xrd']['patterns']['DIFFRACTION'] = {'core_dims': '$(idx_detx, idx_dety)',
'slice_dims': '$tuple([d for d in dims if d not in [idx_detx, idx_dety]])'}
self.yaml['xrd']['axis_labels'] = {}
self.yaml['xrd']['metadata'] = {}
self.data_file_path = 'test_data.nxs'
self.data_file = h5.File(self.data_file_path, 'w') # this will have the axes in.
def test_process(self):
options = {
"transport": "hdf5",
"process_names": "CPU0",
"data_file": tu.get_test_data_path('xrd_test.nxs'),
"process_file": tu.get_test_data_path('PyFAI_azimuth_test.nxs'),
"out_path": tempfile.mkdtemp()
}
run_protected_plugin_runner(options)
def test_process(self):
options = {
"transport": "hdf5",
"process_names": "CPU0",
"data_file": tu.get_test_data_path('stxm.nxs'),
"process_file": tu.get_test_data_path('basic_stxm_process.nxs'),
"out_path": tempfile.mkdtemp()
}
run_protected_plugin_runner(options)
def test_FastXrf(self):
options = {
"transport": "hdf5",
"process_names": "CPU0",
"data_file": tu.get_test_data_path('fluo.nxs'),
"process_file": tu.get_test_data_path('basic_fastxrf_process.nxs'),
"out_path": tempfile.mkdtemp()
}
PluginRunner(options)
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))
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))
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_monitor_correction(self):
options = {
"transport": "hdf5",
"process_names": "CPU0",
"data_file": tu.get_test_data_path('mm.nxs'),
"process_file": tu.get_test_process_path('monitor_correction_test.nxs'),
"out_path": tempfile.mkdtemp()
}
run_protected_plugin_runner(options)
def test_fbp(self):
options = {
"transport": "hdf5",
"process_names": "CPU0",
"data_file": tu.get_test_data_path('24737.nxs'),
"process_file": tu.get_test_process_path('miro_test.nxs'),
"out_path": tempfile.mkdtemp()
}
run_protected_plugin_runner(options)
def test_process(self):
options = {
"transport": "hdf5",
"process_names": "CPU0",
"data_file": tu.get_test_data_path("mm.nxs"),
"process_file": tu.get_process_list_path("I18_pipeline_just_xrd.nxs"),
"out_path": tempfile.mkdtemp(),
}
run_protected_plugin_runner(options)
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))
def test_stxm_tomo_astra(self):
options = {
"transport": "hdf5",
"process_names": "CPU0",
"data_file": tu.get_test_data_path('mm.nxs'),
"process_file": tu.get_test_process_path('simple_stxm_tomo_test_astra.nxs'),
"out_path": tempfile.mkdtemp()
}
run_protected_plugin_runner(options)
def test_cgls_astra(self):
process = 'basic_tomo_iterative_process.nxs'
options = {
"transport": "hdf5",
"process_names": "CPU0",
"data_file": tu.get_test_data_path('24737.nxs'),
"process_file": tu.get_test_process_path(process),
"out_path": tempfile.mkdtemp()
}
run_protected_plugin_runner(options)
def test_mm(self):
options = {
"transport": "hdf5",
"process_names": "CPU0",
"data_file": tu.get_test_data_path('mm.nxs'),
"process_file": tu.get_test_process_path(
'multiple_mm_inputs_test.nxs'),
"out_path": tempfile.mkdtemp()
}
run_protected_plugin_runner(options)
def test_multi_params_tomo(self):
process = 'basic_tomo_process_preview_params_test.nxs'
options = {
"transport": "hdf5",
"process_names": "CPU0",
"data_file": tu.get_test_data_path('24737.nxs'),
"process_file": tu.get_test_process_path(process),
"out_path": tempfile.mkdtemp()
}
run_protected_plugin_runner(options)
def test_process(self):
options = {
"transport": "hdf5",
"process_names": "CPU0",
"data_file": tu.get_test_data_path('mm.nxs'),
# "process_file": tu.get_test_process_path('simplefitreconstest.nxs'),
"process_file": tu.get_test_process_path(
'testing_mm_sart_recon.nxs'),
"out_path": tempfile.mkdtemp()
}
run_protected_plugin_runner(options)
def test_multi_params_i12tomo(self):
process = 'i12_tomo_pipeline_test.nxs'
options = {
"transport": "hdf5",
"process_names": "CPU0",
"data_file": tu.get_test_data_path(
'i12_test_data/i12_test_data.nxs'),
"process_file": tu.get_test_process_path(process),
"out_path": tempfile.mkdtemp()
}
run_protected_plugin_runner(options)
def test_process_preview(self):
options = {
"transport": "hdf5",
"process_names": "CPU0",
"data_file": tu.get_test_data_path(
'/i12_test_data/i12_test_data.nxs'),
"process_file": tu.get_test_process_path(
'i12_tomo_pipeline_preview_test.nxs'),
"out_path": tempfile.mkdtemp()
}
run_protected_plugin_runner(options)
def test_Pyfai(self):
options = {
"transport": "hdf5",
"process_names": "CPU0",
"data_file": '/media/My Passport/Steve_data/xrd_tester2.nxs',
"process_file": tu.get_test_data_path('PyFAI_azimuth_test.nxs'),
"out_path": tempfile.mkdtemp()
}
try:
PluginRunner(options)
except ImportError as e:
print("Failed to run test as libraries not available (%s)," % (e) +
" passing test")
pass
def test_ccpi_denoise_gpu(self):
data_file = tu.get_test_data_path('24737.nxs')
process_file = tu.get_test_process_path('ccpi_denoising_gpu_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('i18_test_data.nxs')
process_file = tu.get_process_list_path('multimodal_tomo_i18.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('mm.nxs')
process_file = tu.get_test_process_path('pyfai_tomo_chunking_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_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))
def test_ring_removal_regularization(self):
data_file = tu.get_test_data_path('24737.nxs')
process_file = tu.get_test_process_path(
'ring_removal_regularization_test.nxs')
run_protected_plugin_runner(tu.set_options(data_file,
process_file=process_file))
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 get_conf_path(self):
path = self.parameters['config']
if path.split(os.sep)[0] == 'Savu':
path = tu.get_test_data_path(path.split('/test_data/data')[1])
return path
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))
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))
def test_ring_removal(self):
data_file = tu.get_test_data_path('24737.nxs')
process_file = tu.get_test_process_path('ccpi_ring_artefact_test.nxs')
run_protected_plugin_runner(tu.set_options(data_file,
process_file=process_file))
def set_data_options(self):
options = tu.set_options(tu.get_test_data_path('24737.nxs'))
options['process_file'] = \
tu.get_test_process_path('checkpoint_process2.nxs')
return options
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))
def test_nx_fluo(self):
data_file = tu.get_test_data_path('mm.nxs')
process_file = tu.get_test_process_path('basic_fluo_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('/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_median_filter(self):
data_file = tu.get_test_data_path('24737.nxs')
process_file = tu.get_test_process_path('median_filter_test.nxs')
run_protected_plugin_runner(
tu.set_options(data_file, process_file=process_file))
def test_mcnear(self):
data_file = tu.get_test_data_path('i18_test_data.nxs')
process_file = tu.get_test_process_path(
'mcnear_absorption_correction.nxs')
run_protected_plugin_runner(
tu.set_options(data_file, process_file=process_file))
def get_dummyhdf_path(self):
return tu.get_test_data_path('i18_test_data.nxs')
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))
def get_cal_path(self):
path = self.parameters['calibration_path']
if path.split(os.sep)[0] == 'Savu':
path = tu.get_test_data_path(path.split('/test_data/data')[1])
return path
def test_histogram(self):
data_file = tu.get_test_data_path('mm.nxs')
process_file = tu.get_test_process_path('histogramtest.nxs')
run_protected_plugin_runner(tu.set_options(data_file,
process_file=process_file))
def test_nx_multimodal(self):
data_file = tu.get_test_data_path('mm.nxs')
process_file = tu.get_test_process_path('MMtest.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_simple_fit_XRF(self):
data_file = tu.get_test_data_path('mm.nxs')
process_file = tu.get_test_process_path('simple_fit_test_XRF.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(
'I18_pipeline_just_xrd_from_raw_filtered_adp_mod2.nxs')
run_protected_plugin_runner(
tu.set_options(data_file, process_file=process_file))
logging.info("Starting the test process")
logging.debug("Rank : %i - Size : %i", RANK, SIZE)
IP = socket.gethostbyname(socket.gethostname())
logging.debug("ip address is : %s", IP)
call_mpi_barrier()
import os
logging.debug(os.getenv('LD_LIBRARY_PATH'))
call_mpi_barrier()
process_filename = tu.get_test_data_path(options.process_filename)
process_list = ProcessList()
process_list.populate_process_list(process_filename)
first_plugin = pu.load_plugin(process_list.process_list[0]['id'])
input_data = tu.get_appropriate_input_data(first_plugin)[0]
process.run_process_list(input_data,
process_list,
options.directory,
mpi=True,
processes=ALL_PROCESSES,
process=RANK)
call_mpi_barrier()
def test_basic_operations(self):
data_file = tu.get_test_data_path('image_test/tiffs')
process_file = tu.get_test_process_path('tiff_loader_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('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))
def test_process(self):
data_file = tu.get_test_data_path('24737.nxs')
process_file = \
tu.get_test_process_path('simple_recon_test_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('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))
def test_monitor_correction(self):
data_file = tu.get_test_data_path('mm.nxs')
process_file = tu.get_test_process_path('monitor_correction_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))
def test_sinogram_alignment(self):
data_file = tu.get_test_data_path('24737.nxs')
process_file = tu.get_test_process_path('sino_alignment_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))
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))
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))
def get_path(self,field):
path = self.parameters[field]
if path.split(os.sep)[0] == 'Savu':
path = tu.get_test_data_path(path.split('/test_data/data')[1])
return path
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_correction2(self):
data_file = tu.get_test_data_path('24737.nxs')
process_file = \
tu.get_test_process_path('time_based_correction_test2.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_nx_xrd(self):
data_file = tu.get_test_data_path('i18_test_data.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))
