def import_roi_file(self, roi_file_name):
"""
:param roi_file_name:
:return:
"""
roi_id = self._generate_id(roi_file_name, is_roi=True)
# import file
if roi_file_name.lower().endswith('.xml'):
# XML file name
roi_vec = mask_util.load_mantid_mask(self._num_pixels,
roi_file_name,
is_mask=False)
elif roi_file_name.lower().endswith(
'.h5') or roi_file_name.lower().endswith('.hdf5'):
roi_vec, two_theta, user_note = mask_util.load_pyrs_mask(
roi_file_name)
else:
raise RuntimeError(
'ROI file of type {} is not recognized and supported'
''.format(roi_file_name.split('.')[-1]))
# set
self._mask_array_dict[roi_id] = roi_vec
self._mask_info_dict[roi_id] = [None] * 2
self._mask_info_dict[roi_id] = roi_file_name
return roi_id
def _mask_detectors(counts_vec, mask_file=None):
# ignoring returns two_theta and note
mask_vec, _, _ = mask_util.load_pyrs_mask(mask_file)
if counts_vec.shape != mask_vec.shape:
raise RuntimeError('Counts vector and mask vector has different shpae')
masked_counts_vec = counts_vec * mask_vec
return masked_counts_vec
def load_mask_file(self, mask_file_name):
""" Load mask file to 1D array and auxiliary information
:param mask_file_name:
:return:
"""
mask_vec, two_theta, note = mask_util.load_pyrs_mask(mask_file_name)
# register the masks
self._loaded_mask_files.append(mask_file_name)
mask_id = os.path.basename(mask_file_name).split(
'.')[0] + '_{}'.format(hash(mask_file_name) % 100)
self._loaded_mask_dict[mask_id] = mask_vec, two_theta, mask_file_name
return two_theta, note, mask_id
def main():
# # ----------------s-----------------------------------------------------------
# wavelength = 1.296 # A
# two_theta = 30.
# Set up
# data, mask and etc
test_file_name = 'tests/testdata/LaB6_10kev_35deg-00004_Rotated_TIF.h5'
pos_mask_h5 = 'tests/testdata/masks/Chi_30.hdf5'
neg_mask_h5 = 'tests/testdata/masks/Chi_Neg30.hdf5'
mask_p10_h5 = 'tests/testdata/masks/Chi_10.hdf5'
mask_n10_h5 = 'tests/testdata/masks/Chi_Neg10.hdf5'
mask_p20_h5 = 'tests/testdata/masks/Chi_20.hdf5'
mask_n20_h5 = 'tests/testdata/masks/Chi_Neg20.hdf5'
# instrument geometry
idf_name = 'tests/testdata/xray_data/XRay_Definition_2K.txt'
# 2theta
two_theta = -35. # TODO - TONIGHT 1 - Make this user specified value
roi_vec_pos, mask_2theta, note = mask_util.load_pyrs_mask(pos_mask_h5)
roi_vec_neg, mask_2thetA, notE = mask_util.load_pyrs_mask(neg_mask_h5)
roi_p10_vec, mask_2theta, note = mask_util.load_pyrs_mask(mask_p10_h5)
roi_n10_vec, mask_2thetA, notE = mask_util.load_pyrs_mask(mask_n10_h5)
roi_p20_vec, mask_2theta, note = mask_util.load_pyrs_mask(mask_p20_h5)
roi_n20_vec, mask_2thetA, notE = mask_util.load_pyrs_mask(mask_n20_h5)
# Load, mask and reduce data
if True:
# check
instrument = calibration_file_io.import_instrument_setup(idf_name)
# calibration = [-2.28691912e-04, 3.42766839e-06, -1.99762398e-03, -5.59805308e-02, -8.32593462e-01,
# 7.66556036e-04]
# calibration = [0.] * 6
# Result from [0, 0, -0.002, -0.007, -0.922, 0] and +/- 30 degrees
# calibration = [2.33235126e-05, -1.85337378e-04, -1.87855142e-03, -2.20924269e-02,
# -1.64058209e+00, 1.41293750e+00]
# From [0...]
# calibration = [-3.90985615e-05, -2.72036598e-04, 3.91642084e-04, 5.99667751e-03,
# -8.15624721e-01, 1.42673120e+00]
# From [previous]
# calibration = [-3.81356557e-05, -2.70589009e-04, 3.91001832e-04, 5.84042046e-03,
# -8.09033785e-01, 1.42465336e+00]
# From [0] with +/- 30 and +/- 10
calibration = [-7.86738387e-05, 9.18988206e-05, -5.55805387e-05, -1.44470481e-01,
-6.45203851e-01, 1.33199903e+00]
# reduction engine
engine = reduction_manager.HB2BReductionManager()
test_data_id = engine.load_data(data_file_name=test_file_name, target_dimension=2048,
load_to_workspace=False)
roi_vec_list = [roi_vec_pos, roi_vec_neg, roi_p10_vec, roi_n10_vec]
peaks_alignment_score(calibration, engine, instrument, two_theta, roi_vec_list, plot=True)
print('RESULT EXAMINATION IS OVER')
else:
t_start = time.time()
# reduction engine
engine = reduction_manager.HB2BReductionManager()
test_data_id = engine.load_data(data_file_name=test_file_name, target_dimension=2048,
load_to_workspace=False)
# instrument
instrument = calibration_file_io.import_instrument_setup(idf_name)
# set starting values
if False:
start_calibration = [0.] * 6 # [0, 0, -0.002, -0.007, -0.922, 0]
roi_vec_list = [roi_vec_pos, roi_vec_neg]
if False:
# start value from +/- 30
start_calibration = [-3.90985615e-05, -2.72036598e-04, 3.91642084e-04, 5.99667751e-03,
-8.15624721e-01, 1.42673120e+00]
roi_vec_list = [roi_vec_pos, roi_vec_neg, roi_p10_vec, roi_n10_vec]
if False:
start_calibration = [0.] * 6
roi_vec_list = [roi_vec_pos, roi_vec_neg, roi_p10_vec, roi_n10_vec]
# result:
# Residual = 0.104224211772
# Total Time: 488.894177198
start_calibration = [0.] * 6
roi_vec_list = [roi_vec_pos, roi_vec_neg, roi_p10_vec, roi_n10_vec, roi_p20_vec, roi_n20_vec]
# optimize
GlobalParameter.global_curr_sequence = 0 # reset output
DE_Res = leastsq(peaks_alignment_score, np.array(start_calibration),
args=(engine, instrument, two_theta, roi_vec_list, False),
xtol=1e-15, maxfev=3000, epsfcn=1e-2)
t_stop = time.time()
print('Total Time: {}'.format(t_stop - t_start))
print(DE_Res[0])
print(DE_Res[1])
DD = 0.0
D_Shift = 0
Center_X = -0.002
Center_Y = -0.007
Flip = -1
Spin = 0.0
# DE_Res = leastsq(MinDifference, [-1], xtol=1e-15, maxfev=3000)
# END-IF-ELSE
return
def compare_reduced_masked(angle, calibrated, pixel_number):
"""
Compare reduced data without mask
:param angle: solid angle (integer)
:param calibrated:
:param pixel_number:
:return:
"""
# create geometry/instrument
engine, pyrs_reducer, mantid_reducer = compare_geometry_test(calibrated, pixel_number, False)
# load mask
test_mask = XRay_Masks[angle]
# load mask: mask file
print('Load masking file: {}'.format(test_mask))
mask_vec, mask_2theta, note = mask_util.load_pyrs_mask(test_mask)
print('Mask file {}: 2theta = {}'.format(test_mask, mask_2theta))
NUM_BINS = 1800
# reduce data
min_2theta = 15.
max_2theta = 55.
# reduce PyRS (pure python)
curr_id = engine.current_data_id
pyrs_returns = pyrs_reducer.reduce_to_2theta_histogram(counts_array=engine.get_counts(curr_id),
mask=mask_vec, x_range=(min_2theta, max_2theta),
num_bins=NUM_BINS)
pyrs_vec_x, pyrs_vec_y = pyrs_returns
# reduce by Mantid
data_ws = mantid_reducer.get_workspace()
reduced_data = mantid_reducer.reduce_to_2theta_histogram(data_ws.name(),
two_theta_min=min_2theta,
two_theta_max=max_2theta,
num_2theta_bins=NUM_BINS,
mask=mask_vec)
mantid_vec_x = reduced_data[0]
mantid_vec_y = reduced_data[1]
# possible convert
if mantid_vec_x.shape[0] == pyrs_vec_x.shape[0] - 1:
# partial compare result
print('Mantid ResampleX return: shape = {}, {}'.format(mantid_vec_x.shape,
mantid_vec_y.shape))
diff_y = numpy.sqrt(numpy.sum((pyrs_vec_y - mantid_vec_y)**2))/mantid_vec_y.shape[0]
print('Diff[X] = Not Calculated, Diff[Y] = {}'.format(diff_y))
plt.plot(pyrs_vec_x[:-1], pyrs_vec_y, color='blue', label='PyRS')
plt.plot(mantid_vec_x, mantid_vec_y, color='red', label='Mantid')
else:
# compare result
diff_x = numpy.sqrt(numpy.sum((pyrs_vec_x - mantid_vec_x) ** 2)) / mantid_vec_x.shape[0]
diff_y = numpy.sqrt(numpy.sum((pyrs_vec_y - mantid_vec_y)**2))/mantid_vec_y.shape[0]
print('Diff[X] = {}, Diff[Y] = {}'.format(diff_x, diff_y))
plt.plot(pyrs_vec_x[:-1], pyrs_vec_y, color='blue', label='PyRS')
plt.plot(mantid_vec_x[:-1], mantid_vec_y, color='red', label='Mantid')
plt.legend()
plt.show()
return
def main():
import os
# Set up
# data file
if False:
# pyrs_root = '/SNS/users/hcf/HFIR_TESTING/'
# test_file_name = 'LaB6_10kev_35deg-00004.xml'
# Vanadium = 'Vanadium.xml'
test_file_name = 'tests/testdata/BNT_7BT_2KNN_6kV_mm-03425-001.xml'
pos_mask_h5 = None
neg_mask_h5 = None
else:
test_file_name = 'tests/testdata/LaB6_10kev_35deg-00004_Rotated_TIF.h5'
pos_mask_h5 = 'tests/testdata/masks/Chi_30.hdf5'
neg_mask_h5 = 'tests/testdata/masks/Chi_Neg30.hdf5'
# instrument geometry
if False:
idf_name = os.path.join(pyrs_root, 'XRay_Definition_1K.xml')
else:
idf_name = 'tests/testdata/xray_data/XRay_Definition_2K.txt'
# Load, mask and reduce data
if False:
# old way
os.system('cp ' + idf_name +
' ~/.mantid/instrument/HB2B_Definition.xml')
# Load data
LoadSpice2D(Filename=hb2b_file_name, OutputWorkspace='hb2b')
LoadSpice2D(Filename=hb2b_Vfile_name, OutputWorkspace='hb2b_V')
ws_name = test_rotate_2theta(idf_name, 'hb2b', 'hb2b_rotate')
vanadium = test_rotate_2theta(idf_name, 'hb2b_V', 'hb2b_V_rotate')
vanadium_line = convert_to_2thetaVanadium(vanadium,
num_bins=1900,
Mask=None)
convert_to_2theta(ws_name, vanadium_line)
NegMask = 'NegMask'
PosMask = 'PosMask'
ZeMask = 'ZeroMask'
p10Mask = 'p10Mask'
p20Mask = 'p20Mask'
p30Mask = 'p30Mask'
n30Mask = 'n30Mask'
LoadMask(Instrument='HB2B',
InputFile='/SNS/users/hcf/HFIR_TESTING/NegZ_Mask.xml',
OutputWorkspace=NegMask)
LoadMask(Instrument='HB2B',
InputFile='/SNS/users/hcf/HFIR_TESTING/Chi_30_Mask.xml',
OutputWorkspace=p30Mask)
InvertMask(InputWorkspace=NegMask, OutputWorkspace=PosMask)
InvertMask(InputWorkspace=p30Mask, OutputWorkspace=p30Mask)
CloneWorkspace(InputWorkspace=p30Mask, OutputWorkspace=n30Mask)
MaskDetectors(Workspace=p30Mask, MaskedWorkspace=PosMask)
MaskDetectors(Workspace=n30Mask, MaskedWorkspace=NegMask)
WS_p30deg = test_rotate_2theta(idf_name, 'hb2b', 'hb2b_rotate_p30deg')
WS_n30deg = test_rotate_2theta(idf_name, 'hb2b', 'hb2b_rotate_n30deg')
MaskDetectors(WS_p30deg, MaskedWorkspace=p30Mask)
MaskDetectors(WS_n30deg, MaskedWorkspace=n30Mask)
vanadium_P30 = convert_to_2thetaVanadium(vanadium,
num_bins=1900,
Mask=p30Mask)
vanadium_N30 = convert_to_2thetaVanadium(vanadium,
num_bins=1900,
Mask=n30Mask)
elif False:
# build instrument: for FUN
instrument = calibration_file_io.import_instrument_setup(idf_name)
# 2theta
two_theta = -35. # TODO - TONIGHT 1 - Make this user specified value
calibration = [
-2.28691912e-04, 3.42766839e-06, -1.99762398e-03, -5.59805308e-02,
-8.32593462e-01, 7.66556036e-04
]
arm_length_shift = calibration[2]
center_shift_x = calibration[0]
center_shift_y = calibration[1]
rot_x_flip = calibration[3]
rot_y_flip = calibration[4]
rot_z_spin = calibration[5]
# reduction engine
engine = reduction_manager.HB2BReductionManager()
test_data_id = engine.load_data(data_file_name=test_file_name,
target_dimension=2048,
load_to_workspace=False)
# load instrument
pyrs_reducer = reduce_hb2b_pyrs.PyHB2BReduction(instrument, 1.239)
pyrs_reducer.build_instrument(two_theta, arm_length_shift,
center_shift_x, center_shift_y,
rot_x_flip, rot_y_flip, rot_z_spin)
# reduce data
min_2theta = 8.
max_2theta = 64.
num_bins = 1800
# reduce PyRS (pure python)
curr_id = engine.current_data_id
# mask
roi_vec_pos, mask_2theta, note = mask_util.load_pyrs_mask(pos_mask_h5)
roi_vec_neg, mask_2thetA, notE = mask_util.load_pyrs_mask(neg_mask_h5)
pos_2theta, pos_hist = pyrs_reducer.reduce_to_2theta_histogram(
counts_array=engine.get_counts(curr_id),
mask=roi_vec_pos,
x_range=(min_2theta, max_2theta),
num_bins=num_bins,
is_point_data=True,
use_mantid_histogram=False)
neg_2theta, neg_hist = pyrs_reducer.reduce_to_2theta_histogram(
counts_array=engine.get_counts(curr_id),
mask=roi_vec_neg,
x_range=(min_2theta, max_2theta),
num_bins=num_bins,
is_point_data=True,
use_mantid_histogram=False)
plt.plot(pos_2theta, pos_hist, color='red')
plt.plot(neg_2theta, neg_hist, color='blue')
plt.show()
print('RESULT EXAMINATION IS OVER')
else:
import time
t_start = time.time()
# reduction engine
engine = reduction_manager.HB2BReductionManager()
test_data_id = engine.load_data(data_file_name=test_file_name,
target_dimension=2048,
load_to_workspace=False)
# instrument
instrument = calibration_file_io.import_instrument_setup(idf_name)
# mask
roi_vec_pos, mask_2theta, note = mask_util.load_pyrs_mask(pos_mask_h5)
roi_vec_neg, mask_2thetA, notE = mask_util.load_pyrs_mask(neg_mask_h5)
x0 = [0, 0, -0.002, -0.007, -0.922, 0]
# x0 = [-1.]
# engine, hb2b_setup, positive_roi_vec, negative_roi_vec
DE_Res = leastsq(MinDifference,
np.array(x0),
args=(engine, instrument, roi_vec_pos, roi_vec_neg),
xtol=1e-15,
maxfev=3000,
epsfcn=1e-2)
t_stop = time.time()
print('Total Time: {}'.format(t_stop - t_start))
print(DE_Res[0])
print(DE_Res[1])
DD = 0.0
D_Shift = 0
Center_X = -0.002
Center_Y = -0.007
Flip = -1
Spin = 0.0
# DE_Res = leastsq(MinDifference, [-1], xtol=1e-15, maxfev=3000)
# END-IF-ELSE
return
def main():
# # ----------------s-----------------------------------------------------------
# wavelength = 1.296 # A
# two_theta = 30.
# Set up
# data, mask and etc
test_file_name = 'tests/testdata/LaB6_10kev_35deg-00004_Rotated_TIF.h5'
pos_mask_h5 = 'tests/testdata/masks/Chi_30.hdf5'
neg_mask_h5 = 'tests/testdata/masks/Chi_Neg30.hdf5'
# instrument geometry
idf_name = 'tests/testdata/xray_data/XRay_Definition_2K.txt'
# 2theta
two_theta = -35. # TODO - TONIGHT 1 - Make this user specified value
# Load, mask and reduce data
if True:
# check
instrument = calibration_file_io.import_instrument_setup(idf_name)
# calibration = [-2.28691912e-04, 3.42766839e-06, -1.99762398e-03, -5.59805308e-02, -8.32593462e-01,
# 7.66556036e-04]
calibration = [0.] * 6
calibration = [
2.33235126e-05, -1.85337378e-04, -1.87855142e-03, -2.20924269e-02,
-1.64058209e+00, 1.41293750e+00
]
roi_vec_pos, mask_2theta, note = mask_util.load_pyrs_mask(pos_mask_h5)
roi_vec_neg, mask_2thetA, notE = mask_util.load_pyrs_mask(neg_mask_h5)
# reduction engine
engine = reduction_manager.HB2BReductionManager()
test_data_id = engine.load_data(data_file_name=test_file_name,
target_dimension=2048,
load_to_workspace=False)
CostFunction(calibration,
engine,
instrument,
two_theta,
roi_vec_pos,
roi_vec_neg,
plot=True)
print('RESULT EXAMINATION IS OVER')
else:
t_start = time.time()
# reduction engine
engine = reduction_manager.HB2BReductionManager()
test_data_id = engine.load_data(data_file_name=test_file_name,
target_dimension=2048,
load_to_workspace=False)
# instrument
instrument = calibration_file_io.import_instrument_setup(idf_name)
# mask
roi_vec_pos, mask_2theta, note = mask_util.load_pyrs_mask(pos_mask_h5)
roi_vec_neg, mask_2thetA, notE = mask_util.load_pyrs_mask(neg_mask_h5)
start_calibration = [0, 0, -0.002, -0.007, -0.922, 0]
GlobalParameter.global_curr_sequence = 0 # reset output
DE_Res = leastsq(CostFunction,
np.array(start_calibration),
args=(engine, instrument, two_theta, roi_vec_pos,
roi_vec_neg, False),
xtol=1e-15,
maxfev=3000,
epsfcn=1e-2)
t_stop = time.time()
print('Total Time: {}'.format(t_stop - t_start))
print(DE_Res[0])
print(DE_Res[1])
DD = 0.0
D_Shift = 0
Center_X = -0.002
Center_Y = -0.007
Flip = -1
Spin = 0.0
# DE_Res = leastsq(MinDifference, [-1], xtol=1e-15, maxfev=3000)
# END-IF-ELSE
return
num_bins=1900,
Mask=None)
convert_to_2theta(ws_name, vanadium_line)
NegMask = 'NegMask'
PosMask = 'PosMask'
ZeMask = 'ZeroMask'
p10Mask = 'p10Mask'
p20Mask = 'p20Mask'
p30Mask = 'p30Mask'
n30Mask = 'n30Mask'
if True:
for solid_angle in [30,
-30]: # shall be extended to 0, +/- 10, +/- 20, +/-30
mask_vec, mask_2theta, note = mask_util.load_pyrs_mask(
'tests/testdata/masks/Chi_30.hdf5')
else:
LoadMask(Instrument='HB2B',
InputFile='/SNS/users/hcf/HFIR_TESTING/NegZ_Mask.xml',
OutputWorkspace=NegMask)
LoadMask(Instrument='HB2B',
InputFile='/SNS/users/hcf/HFIR_TESTING/Chi_30_Mask.xml',
OutputWorkspace=p30Mask)
InvertMask(InputWorkspace=NegMask, OutputWorkspace=PosMask)
InvertMask(InputWorkspace=p30Mask, OutputWorkspace=p30Mask)
CloneWorkspace(InputWorkspace=p30Mask, OutputWorkspace=n30Mask)
MaskDetectors(Workspace=p30Mask, MaskedWorkspace=PosMask)