def test_AcquisitionDataPadder(self):
reader = NexusReader(self.filename)
ad = reader.get_acquisition_data_whole()
print(ad.geometry)
cf = CenterOfRotationFinder()
cf.set_input(ad)
print("Center of rotation", cf.get_output())
self.assertAlmostEqual(86.25, cf.get_output())
adp = AcquisitionDataPadder(
acquisition_geometry=cf.get_input().geometry,
center_of_rotation=cf.get_output(),
pad_value=0)
adp.set_input(ad)
padded_data = adp.get_output()
print("Padded data shape", padded_data.shape)
print(" ", padded_data.dimension_labels)
idx = None
for k, v in padded_data.dimension_labels.items():
if v == AcquisitionGeometry.HORIZONTAL:
idx = k
padded_axis = padded_data.shape[idx]
self.assertEqual(padded_axis, math.ceil(cf.get_output() * 2))
numpy.save("pippo.npy", padded_data.as_array())
def test_CenterOfRotation(self):
reader = NexusReader(self.filename)
data = reader.get_acquisition_data_whole()
ad = data.clone()
print(ad)
cf = CenterOfRotationFinder()
cf.set_input(ad)
print("Center of rotation", cf.get_output())
self.assertAlmostEqual(86.25, cf.get_output())
#def test_CenterOfRotation_transpose(self):
#reader = NexusReader(self.filename)
#data = reader.get_acquisition_data_whole()
ad = data.clone()
ad = ad.subset(['vertical', 'angle', 'horizontal'])
print(ad)
cf = CenterOfRotationFinder()
cf.set_input(ad)
print("Center of rotation", cf.get_output())
self.assertAlmostEqual(86.25, cf.get_output())
#def test_CenterOfRotation_singleslice(self):
#reader = NexusReader(self.filename)
#data = reader.get_acquisition_data_whole()
ad = data.clone()
ad = ad.subset(vertical=67)
print(ad)
cf = CenterOfRotationFinder()
cf.set_input(ad)
print("Center of rotation", cf.get_output())
self.assertAlmostEqual(86.25, cf.get_output())
#def test_CenterOfRotation_slice(self):
#reader = NexusReader(self.filename)
#data = reader.get_acquisition_data_whole()
ad = data.clone()
print(ad)
cf = CenterOfRotationFinder()
cf.set_input(ad)
cf.set_slice(80)
print("Center of rotation", cf.get_output())
self.assertAlmostEqual(86.25, cf.get_output())
cf.set_slice()
print("Center of rotation", cf.get_output())
self.assertAlmostEqual(86.25, cf.get_output())
cf.set_slice('centre')
print("Center of rotation", cf.get_output())
self.assertAlmostEqual(86.25, cf.get_output())
labels += [data.dimension_labels[i] \
for i in range(len(data.dimension_labels)) if i != ax]
y = DataContainer( stats[:4] , False,
dimension_labels=labels)
return y
directory = r'E:\Documents\Dataset\CCPi\Nexus_test'
data_path="entry1/instrument/pco1_hw_hdf_nochunking/data"
reader = NexusReader(os.path.join( os.path.abspath(directory) , '74331.nxs'))
print ("read flat")
read_flat = NexusReader(os.path.join( os.path.abspath(directory) , '74240.nxs'))
read_flat.data_path = data_path
flatsslice = read_flat.get_acquisition_data_whole()
avg = DataStatMoments('angle')
avg.set_input(flatsslice)
flats = avg.get_output()
ave = averager()
ave.stats(flatsslice.array[:,0,0])
print ("avg" , ave.avg, flats.array[0][0][0])
print ("var" , ave.var, flats.array[1][0][0])
print ("read dark")
read_dark = NexusReader(os.path.join( os.path.abspath(directory) , '74243.nxs'))
read_dark.data_path = data_path
