def show_image_statistics(experiments, im_type):
if im_type == "raw":
raw = True
elif im_type == "corrected":
raw = False
else:
raise ValueError(f"Unknown im_type: {im_type}")
# To show image statistics, check_format has to be true. So we have to reinstatiate
# the experiment list here
try:
experiments = ExperimentListFactory.from_json(experiments.as_json(),
check_format=True)
except OSError as e:
raise Sorry(
f"Unable to read image data. Please check {e.filename} is accessible"
)
print(f"Five number summary of the {im_type} images")
for i_expt, expt in enumerate(experiments):
for i in range(len(expt.imageset)):
identifier = os.path.basename(
expt.imageset.get_image_identifier(i))
if raw:
pnl_data = expt.imageset.get_raw_data(i)
else:
pnl_data = expt.imageset.get_corrected_data(i)
if not isinstance(pnl_data, tuple):
pnl_data = (pnl_data, )
flat_data = pnl_data[0].as_1d()
for p in pnl_data[1:]:
flat_data.extend(p.as_1d())
fns = five_number_summary(flat_data)
print(
"{}: Min: {:.1f} Q1: {:.1f} Med: {:.1f} Q3: {:.1f} Max: {:.1f}"
.format(identifier, *fns))
def test_compare_example():
experiments = ExperimentListFactory.from_json(json_is, check_format=False)
for experiment in experiments:
header = {
"DIM": "2",
"DENZO_X_BEAM": "97.185",
"RANK": "0",
"PREFIX": "step5_000009",
"BEAM_CENTER_Y": "97.13",
"BEAM_CENTER_X": "97.13",
"WAVELENGTH": "1.30432",
"OSC_START": "0",
"ADC_OFFSET": "10",
"BYTE_ORDER": "little_endian",
"DIRECT_SPACE_ABC":
"2.7790989649304656,3.721227037283121,0.616256870237976,-4.231398741367156,1.730877297917864,1.0247061633019547,2.9848502901631253,-4.645083818143041,28.595825588147285",
"OSC_RANGE": "0",
"DIALS_ORIGIN": "-97.185,97.185,-50",
"MOSFLM_CENTER_X": "97.13",
"MOSFLM_CENTER_Y": "97.13",
"CLOSE_DISTANCE": "50",
"BEAMLINE": "fake",
"TWOTHETA": "0",
"ADXV_CENTER_Y": "96.965",
"ADXV_CENTER_X": "97.185",
"HEADER_BYTES": "1024",
"DETECTOR_SN": "000",
"DISTANCE": "50",
"PHI": "0",
"SIZE1": "1765",
"SIZE2": "1765",
"XDS_ORGX": "884",
"XDS_ORGY": "884",
"DENZO_Y_BEAM": "97.185",
"TIME": "1",
"TYPE": "unsigned_short",
"PIXEL_SIZE": "0.11",
}
# the header of the simulated image, containing ground truth orientation
rsabc = (sqr([float(v)
for v in header["DIRECT_SPACE_ABC"].split(",")]) *
permute.inverse())
rsa = rsabc[0:3]
rsb = rsabc[3:6]
rsc = rsabc[6:9]
header_cryst = Crystal(rsa, rsb, rsc,
"P1").change_basis(CB_OP_C_P.inverse())
header_cryst.set_space_group(experiment.crystal.get_space_group())
print("Header crystal")
print(header_cryst)
expt_crystal = experiment.crystal
print("Integrated crystal")
print(expt_crystal)
header_ori = crystal_orientation.crystal_orientation(
header_cryst.get_A(), crystal_orientation.basis_type.reciprocal)
expt_ori = crystal_orientation.crystal_orientation(
expt_crystal.get_A(), crystal_orientation.basis_type.reciprocal)
print("Converted to cctbx")
header_ori.show()
expt_ori.show()
# assert the equivalence between dxtbx crystal object and the cctbx crystal_orientation object
assert approx_equal(header_cryst.get_U(), header_ori.get_U_as_sqr())
assert approx_equal(header_cryst.get_A(),
header_ori.reciprocal_matrix())
assert approx_equal(
header_cryst.get_B(),
sqr(header_ori.unit_cell().fractionalization_matrix()).transpose(),
)
assert approx_equal(expt_crystal.get_U(), expt_ori.get_U_as_sqr())
assert approx_equal(expt_crystal.get_A(), expt_ori.reciprocal_matrix())
assert approx_equal(
expt_crystal.get_B(),
sqr(expt_ori.unit_cell().fractionalization_matrix()).transpose(),
)
cb_op_align = sqr(
expt_ori.best_similarity_transformation(header_ori, 50, 1))
print("XYZ angles",
cb_op_align.r3_rotation_matrix_as_x_y_z_angles(deg=True))
aligned_ori = expt_ori.change_basis(cb_op_align)
U_integrated = aligned_ori.get_U_as_sqr()
U_ground_truth = header_ori.get_U_as_sqr()
missetting_rot = U_integrated * U_ground_truth.inverse()
print("determinant", missetting_rot.determinant())
assert approx_equal(missetting_rot.determinant(), 1.0)
assert missetting_rot.is_r3_rotation_matrix()
(
angle,
axis,
) = missetting_rot.r3_rotation_matrix_as_unit_quaternion(
).unit_quaternion_as_axis_and_angle(deg=True)
print("Angular offset is %13.10f deg." % (angle))
assert approx_equal(angle, 0.2609472065)
def test_compare_example():
experiments = ExperimentListFactory.from_json(json_is, check_format=False)
for experiment in experiments:
header = {
'DIM': '2',
'DENZO_X_BEAM': '97.185',
'RANK': '0',
'PREFIX': 'step5_000009',
'BEAM_CENTER_Y': '97.13',
'BEAM_CENTER_X': '97.13',
'WAVELENGTH': '1.30432',
'OSC_START': '0',
'ADC_OFFSET': '10',
'BYTE_ORDER': 'little_endian',
'DIRECT_SPACE_ABC':
'2.7790989649304656,3.721227037283121,0.616256870237976,-4.231398741367156,1.730877297917864,1.0247061633019547,2.9848502901631253,-4.645083818143041,28.595825588147285',
'OSC_RANGE': '0',
'DIALS_ORIGIN': '-97.185,97.185,-50',
'MOSFLM_CENTER_X': '97.13',
'MOSFLM_CENTER_Y': '97.13',
'CLOSE_DISTANCE': '50',
'BEAMLINE': 'fake',
'TWOTHETA': '0',
'ADXV_CENTER_Y': '96.965',
'ADXV_CENTER_X': '97.185',
'HEADER_BYTES': '1024',
'DETECTOR_SN': '000',
'DISTANCE': '50',
'PHI': '0',
'SIZE1': '1765',
'SIZE2': '1765',
'XDS_ORGX': '884',
'XDS_ORGY': '884',
'DENZO_Y_BEAM': '97.185',
'TIME': '1',
'TYPE': 'unsigned_short',
'PIXEL_SIZE': '0.11'
}
# the header of the simulated image, containing ground truth orientation
rsabc = sqr([float(v) for v in header['DIRECT_SPACE_ABC'].split(',')
]) * permute.inverse()
rsa = rsabc[0:3]
rsb = rsabc[3:6]
rsc = rsabc[6:9]
header_cryst = Crystal(rsa, rsb, rsc,
'P1').change_basis(CB_OP_C_P.inverse())
header_cryst.set_space_group(experiment.crystal.get_space_group())
print('Header crystal')
print(header_cryst)
expt_crystal = experiment.crystal
print('Integrated crystal')
print(expt_crystal)
header_ori = crystal_orientation.crystal_orientation(
header_cryst.get_A(), crystal_orientation.basis_type.reciprocal)
expt_ori = crystal_orientation.crystal_orientation(
expt_crystal.get_A(), crystal_orientation.basis_type.reciprocal)
print('Converted to cctbx')
header_ori.show()
expt_ori.show()
# assert the equivalence between dxtbx crystal object and the cctbx crystal_orientation object
assert approx_equal(header_cryst.get_U(), header_ori.get_U_as_sqr())
assert approx_equal(header_cryst.get_A(),
header_ori.reciprocal_matrix())
assert approx_equal(
header_cryst.get_B(),
sqr(header_ori.unit_cell().fractionalization_matrix()).transpose())
assert approx_equal(expt_crystal.get_U(), expt_ori.get_U_as_sqr())
assert approx_equal(expt_crystal.get_A(), expt_ori.reciprocal_matrix())
assert approx_equal(
expt_crystal.get_B(),
sqr(expt_ori.unit_cell().fractionalization_matrix()).transpose())
cb_op_align = sqr(
expt_ori.best_similarity_transformation(header_ori, 50, 1))
print('XYZ angles',
cb_op_align.r3_rotation_matrix_as_x_y_z_angles(deg=True))
aligned_ori = expt_ori.change_basis(cb_op_align)
U_integrated = aligned_ori.get_U_as_sqr()
U_ground_truth = header_ori.get_U_as_sqr()
missetting_rot = U_integrated * U_ground_truth.inverse()
print("determinant", missetting_rot.determinant())
assert approx_equal(missetting_rot.determinant(), 1.0)
assert missetting_rot.is_r3_rotation_matrix()
angle, axis = missetting_rot.r3_rotation_matrix_as_unit_quaternion(
).unit_quaternion_as_axis_and_angle(deg=True)
print("Angular offset is %13.10f deg." % (angle))
assert approx_equal(angle, 0.2609472065)
