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': '$tuple([d for d in dims if d not in [idx_detx, idx_dety]])'}
self.yaml['xrd']['axis_labels'] = {}
self.yaml['xrd']['metadata'] = {}
self.data_file_path = 'test_data.nxs'
self.data_file = h5.File(self.data_file_path, 'w') # this will have the axes in.
def setUp(self):
self.test_folder = tempfile.mkdtemp(suffix='template_test/')
self.tif_folder = os.path.join(self.test_folder, 'tiffs/')
os.mkdir(self.tif_folder)
# copy across the process list to the working directory
self.process_list_path = os.path.join(self.test_folder,
'xrd_template_test.nxs')
shutil.copyfile(tu.get_test_process_path('xrd_template_test.nxs'),
self.process_list_path)
utils.populate_plugins()
self.process_list = Content()
self.process_list.fopen(self.process_list_path, update=False)
for idx in self.process_list.get_positions():
self.process_list.refresh(idx)
self.detX_axis_label = {
'dim': '$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_refresh(self):
cu.populate_plugins()
path = os.path.dirname(os.path.realpath(__file__)).split('scripts')[0]
nxs_in_tests, plugins_in_tests = \
tu.get_process_list(path + '/savu/test/travis')
lists = tu.get_test_process_list(path + 'test_data/process_lists') \
+ tu.get_test_process_list(path+'test_data/test_process_lists')
nxs_used = list(set(nxs_in_tests).intersection(set(lists)))
test_path = path + '/test_data/test_process_lists'
test_path2 = path + '/test_data/process_lists'
exclude = ['simple_fit_test_XRF.nxs']
for f in [n for n in nxs_used if n not in exclude]:
print f
if os.path.exists(os.path.join(test_path, f)):
self._refresh_process_file(os.path.join(test_path, f))
else:
self._refresh_process_file(os.path.join(test_path2, f))
def test_refresh(self):
cu.populate_plugins()
path = os.path.dirname(os.path.realpath(__file__)).split('scripts')[0]
nxs_in_tests, plugins_in_tests = \
tu.get_process_list(path + '/savu/test/travis')
lists = tu.get_test_process_list(path + 'test_data/process_lists') \
+ tu.get_test_process_list(path+'test_data/test_process_lists')
nxs_used = list(set(nxs_in_tests).intersection(set(lists)))
test_path = path + '/test_data/test_process_lists'
test_path2 = path + '/test_data/process_lists'
exclude = ['simple_fit_test_XRF.nxs']
for f in [n for n in nxs_used if n not in exclude]:
print "Refreshing process list", f, "..."
if os.path.exists(os.path.join(test_path, f)):
self._refresh_process_file(os.path.join(test_path, f))
else:
self._refresh_process_file(os.path.join(test_path2, f))
def test_i08_notaux(self):
cu.populate_plugins()
data_file = tu.get_test_big_data_path('pymca_live_processing_test/i08-10471.nxs')
data = h5.File(data_file,'r')['/entry/xmapMca/data']
inputs = {}
inputs['data'] = data[0,0,0,:]
inputs['dataset_name'] = ''
inputs['xaxis_title'] = None
metaOnly = False
self.persistence = {}
self.persistence['sys_path_0_lock'] = threading.Lock()
self.persistence['sys_path_0_set'] = False
self.persistence['plugin_object'] = None
self.persistence['axis_labels'] = None
self.persistence['axis_values'] = None
self.persistence['string_key'] = None
self.persistence['parameters'] = None
self.persistence['aux'] = {}
params={}
params['config']={}
params['config']['value'] = tu.get_test_big_data_path('pymca_live_processing_test/10471.cfg')
path2plugin = pu.dawn_plugins['Pymca']['path2plugin']# set by dawn-side code
self.runSavu(path2plugin, params, metaOnly, inputs)
def test_i08_REGRESSION(self):
cu.populate_plugins()
data_file = h5.File(tu.get_test_big_data_path('pymca_live_processing_test/dawn_test_result/result.nxs'),'r')
data = data_file['/raw_entry/xmapMca/data']
inputs = {}
inputs['dataset_name'] = ''
inputs['xaxis_title'] = None
metaOnly = True
self.persistence = {}
self.persistence['sys_path_0_lock'] = threading.Lock()
self.persistence['sys_path_0_set'] = False
self.persistence['plugin_object'] = None
self.persistence['axis_labels'] = None
self.persistence['axis_values'] = None
self.persistence['string_key'] = None
self.persistence['parameters'] = None
self.persistence['aux'] = {}
params={}
params['config']={}
params['config']['value'] = tu.get_test_big_data_path('pymca_live_processing_test/10471.cfg')
path2plugin = pu.dawn_plugins['Pymca']['path2plugin']# set by dawn-side code
pts = [(39,51),
(45,25),
(18,29),
(37,96),
(8,110)] # just do 5 points for now, is full regression necessary?
for y,x in pts:
inputs['data'] = data[x,y,0,:]
out = self.runSavu(path2plugin, params, metaOnly, inputs)
aux = out['auxiliary']
entry = 'entry/auxiliary/0-Python Script - Savu/'
for key in aux.keys():
print(key,x,y)
foo=data_file[entry+key+'/data'][x,y]
self.assertAlmostEqual(aux[key],foo,delta=0.5)
def test_load_plugin(self):
cu.populate_plugins()
plugin_path = pu.dawn_plugins[dawn_plugins.keys()[0]]['path2plugin']
inst = pu.get_plugin(plugin_path)
sl = inst.__dict__['slice_list']
exp = inst.__dict__['exp']
def test_dawn_plugin_params_found(self):
cu.populate_plugins()
self.assertTrue(isinstance(
pu.dawn_plugin_params[pu.dawn_plugins.keys()[0]], dict))
def test_dawn_plugins_found(self):
cu.populate_plugins()
self.assertGreater(len(pu.dawn_plugins), 0)
def test_populate_plugins(self):
cu.populate_plugins()
# refresh
positions = content.get_positions()
for pos_str in positions:
content.refresh(pos_str)
# save
content.save(content.filename)
def generate_test(path):
def test(self):
self._refresh_process_file(path)
return test
if __name__ == "__main__":
cu.populate_plugins()
path = os.path.dirname(os.path.realpath(__file__)).split('scripts')[0]
nxs_in_tests, plugins_in_tests = \
tplu.get_process_list(path + '/savu/test/travis')
lists = tplu.get_test_process_list(path + 'test_data/process_lists') \
+ tplu.get_test_process_list(path+'test_data/test_process_lists')
nxs_used = list(set(nxs_in_tests).intersection(set(lists)))
test_path = path + '/test_data/test_process_lists'
test_path2 = path + '/test_data/process_lists'
exclude = ['multimodal/simple_fit_test_XRF.nxs']
for f in [n for n in nxs_used if n not in exclude]:
print("Refreshing process list", f, "...")
if os.path.exists(os.path.join(test_path, f)):
def test_load_plugin(self):
cu.populate_plugins()
plugin_path = pu.dawn_plugins[dawn_plugins.keys()[0]]['path2plugin']
inst = pu.get_plugin(plugin_path)
sl = inst.__dict__['slice_list']
exp = inst.__dict__['exp']
def test_dawn_plugin_params_found(self):
cu.populate_plugins()
self.assertTrue(
isinstance(pu.dawn_plugin_params[pu.dawn_plugins.keys()[0]], dict))
def test_dawn_plugins_found(self):
cu.populate_plugins()
self.assertGreater(len(pu.dawn_plugins), 0)
def test_populate_plugins(self):
cu.populate_plugins()