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Merged
merged 12 commits into from
Feb 21, 2024
Merged

Ortho before phasing #31

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6a8cb4f
implement orthogonalisation before phasing
clatlan Feb 21, 2024
f07653f
cosmetic changes
clatlan Feb 21, 2024
a55e64e
cosmetic changes + minor edits
clatlan Feb 21, 2024
81afbeb
fix bad usage of exit()
clatlan Feb 21, 2024
924f26e
cosmetic + indentation
clatlan Feb 21, 2024
f74c1e0
cosmetic: remove trailing space
clatlan Feb 21, 2024
4f78021
cosmetic: remove blank lines containing whitespace
clatlan Feb 21, 2024
d183a27
cosmetic: unnecessary parentheses
clatlan Feb 21, 2024
6d8a070
add dosctrings
clatlan Feb 21, 2024
f720b00
cosmetic changes
clatlan Feb 21, 2024
1f55481
cosmetic changes
clatlan Feb 21, 2024
1a736d8
add todo
clatlan Feb 21, 2024
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148 changes: 79 additions & 69 deletions cdiutils/converter.py
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Original file line number Diff line number Diff line change
@@ -1,11 +1,10 @@
from typing import Union, Tuple, Optional
from scipy.ndimage import center_of_mass
import matplotlib.pyplot as plt
import numpy as np
from scipy.interpolate import RegularGridInterpolator
import xrayutilities as xu

from cdiutils.utils import pretty_print, center, crop_at_center
from cdiutils.utils import center, crop_at_center
from cdiutils.geometry import Geometry


Expand All @@ -17,7 +16,7 @@ class SpaceConverter():
def __init__(
self,
geometry: Geometry,
energy: float=None
energy: float = None
):
self.geometry = geometry
# convert the geometry to xrayutilities coordinate system
Expand All @@ -36,18 +35,18 @@ def __init__(

self.q_space_shift = None

self.q_lab_interpolator: Interpolator3D=None
self.direct_lab_interpolator: Interpolator3D=None
self.xu_gridder: xu.FuzzyGridder3D=None
self.q_lab_interpolator: Interpolator3D = None
self.direct_lab_interpolator: Interpolator3D = None
self.xu_gridder: xu.FuzzyGridder3D = None

@property
def q_space_transitions(self):
return self._q_space_transitions

@q_space_transitions.setter
def q_space_transitions(self, transitions: np.array):
self._q_space_transitions = transitions

@property
def reference_voxel(self):
return self._reference_voxel
Expand All @@ -74,8 +73,8 @@ def full_shape(self, shape: tuple):

def init_q_space_area(
self,
roi: np.array or list or tuple,
det_calib_parameters: dict=None
roi: np.ndarray | list | tuple,
det_calib_parameters: dict = None
):
"""
Initialize the xrayutilites XHRD instance with the detector
Expand All @@ -91,23 +90,21 @@ def init_q_space_area(
else:
self.det_calib_parameters = det_calib_parameters

if np.all(
[
k in ["cch1", "cch2", "pwidth1", "pwidth2", "distance",
"tiltazimuth", "tilt", "detrot", "outerangle_offset"]
for k in det_calib_parameters.keys()
]
):
if np.all([
k in ["cch1", "cch2", "pwidth1", "pwidth2", "distance",
"tiltazimuth", "tilt", "detrot", "outerangle_offset"]
for k in det_calib_parameters.keys()
]):
qconversion = xu.experiment.QConversion(
sampleAxis=self.geometry.sample_circles,
detectorAxis=self.geometry.detector_circles,
r_i=self.geometry.beam_direction
)
self.hxrd = xu.HXRD(
idir=self.geometry.beam_direction, # defines the inplane
idir=self.geometry.beam_direction, # defines the inplane
# reference direction (idir points into the beam
# direction at zero angles)
ndir=[0, 0, 1], # defines the surface normal of your sample
ndir=[0, 0, 1], # defines the surface normal of your sample
# (ndir points along the innermost sample rotation axis)
en=self.energy,
qconv=qconversion
Expand Down Expand Up @@ -137,10 +134,10 @@ def init_q_space_area(

def set_q_space_area(
self,
sample_outofplane_angle: float or np.ndarray,
sample_inplane_angle: float or np.ndarray,
detector_outofplane_angle: float or np.ndarray,
detector_inplane_angle: float or np.ndarray
sample_outofplane_angle: float | np.ndarray,
sample_inplane_angle: float | np.ndarray,
detector_outofplane_angle: float | np.ndarray,
detector_inplane_angle: float | np.ndarray
):
"""
Compute the _q_space_transitions provided by xrayutilities
Expand Down Expand Up @@ -177,7 +174,7 @@ def index_det_to_q_lab(self, ijk: tuple) -> tuple:

def index_cropped_det_to_det(self, ijk: tuple) -> tuple:
"""
Transition an index of the cropped detector frame to the full
Transition an index of the cropped detector frame to the full
detector frame
"""
if self._reference_voxel is None:
Expand All @@ -190,18 +187,24 @@ def index_cropped_det_to_det(self, ijk: tuple) -> tuple:

def index_cropped_det_to_q_lab(self, ijk: tuple) -> tuple:
"""
Transition an index from the cropped detector frame to the
Transition an index from the cropped detector frame to the
reciprocal lab space frame
"""
return self.index_det_to_q_lab(self.index_cropped_det_to_det(ijk))

def index_det_to_index_of_q_lab(self, ijk: tuple) -> tuple:
def index_det_to_index_of_q_lab(
self, ijk: tuple,
interpolation_method: str = "cdiutils"
) -> tuple:
"""
Transition an index from the full detector frame to the
index-of-q lab frame
"""
cubinates = self.get_q_lab_regular_grid(arrangement="cubinates")
q_pos = self.index_det_to_q_lab(ijk) # q value
if interpolation_method in ("xu", "xrayutilities"):
cubinates = self.get_xu_q_lab_regular_grid(arrangement="cubinates")
else:
cubinates = self.get_q_lab_regular_grid(arrangement="cubinates")
q_pos = self.index_det_to_q_lab(ijk) # q value
new_ijk = np.unravel_index(
np.argmin(
np.linalg.norm(
Expand All @@ -215,11 +218,11 @@ def index_det_to_index_of_q_lab(self, ijk: tuple) -> tuple:

def index_cropped_det_to_index_of_q_lab(self, ijk: tuple) -> tuple:
"""
Transition an index from the cropped detector frame to the
Transition an index from the cropped detector frame to the
index-of-q lab frame
"""
cubinates = self.get_q_lab_regular_grid(arrangement="cubinates")
q_pos = self.index_cropped_det_to_q_lab(ijk) # q value
q_pos = self.index_cropped_det_to_q_lab(ijk) # q value
new_ijk = np.unravel_index(
np.argmin(
np.linalg.norm(
Expand All @@ -232,7 +235,7 @@ def index_cropped_det_to_index_of_q_lab(self, ijk: tuple) -> tuple:
return new_ijk

@staticmethod
def dspacing(q_lab_coordinates: np.ndarray or list or tuple)-> float:
def dspacing(q_lab_coordinates: np.ndarray | list | tuple) -> float:
"""
Compute the dspacing
"""
Expand All @@ -241,8 +244,8 @@ def dspacing(q_lab_coordinates: np.ndarray or list or tuple)-> float:
@classmethod
def lattice_parameter(
cls,
q_lab_coordinates: Union[np.ndarray, list, tuple],
hkl: Union[np.ndarray, list, tuple]
q_lab_coordinates: np.ndarray | list | tuple,
hkl: np.ndarray | list | tuple
) -> float:
"""
Compute the lattice parameter
Expand All @@ -254,7 +257,7 @@ def lattice_parameter(

@staticmethod
def do_transition(
ijk: Union[np.ndarray, list, tuple],
ijk: np.ndarray | list | tuple,
transition_matrix: np.ndarray
) -> tuple:
"""
Expand Down Expand Up @@ -317,8 +320,8 @@ def _center_shift_q_space_transitions(
def orthogonalize_to_q_lab(
self,
data: np.ndarray,
method: str="cdiutils",
shift_voxel: tuple=None
method: str = "cdiutils",
shift_voxel: tuple = None
) -> np.ndarray:
"""
Orthogonalize detector data of the reciprocal space to the lab
Expand All @@ -333,7 +336,6 @@ def orthogonalize_to_q_lab(
else:
q_space_transitions = self._q_space_transitions


if method in ("xu", "xrayutilities"):
gridder = xu.FuzzyGridder3D(*data.shape)
gridder(*q_space_transitions, data)
Expand Down Expand Up @@ -368,10 +370,10 @@ def _check_shape(self, shape: tuple) -> None:
def init_interpolator(
self,
detector_data: np.ndarray,
direct_space_data_shape: tuple=None,
direct_space_voxel_size: tuple or np.ndarray or list or float=None,
space: str="direct",
shift_voxel: tuple=None
direct_space_data_shape: tuple = None,
direct_space_voxel_size: tuple | np.ndarray | list or float = None,
space: str = "direct",
shift_voxel: tuple = None
):

if space not in (
Expand Down Expand Up @@ -416,7 +418,7 @@ def init_interpolator(
"if space is 'direct' direct_space_data_shape must be "
"provided."
)
if shape != direct_space_data_shape:
if shape != direct_space_data_shape:
raise ValueError(
"The cropped_raw_data should have the same shape as the "
"reconstructed object."
Expand Down Expand Up @@ -457,27 +459,35 @@ def init_interpolator(
target_voxel_size=direct_space_voxel_size
)


def save_interpolation_parameters(self, output_path: str):
np.savez(
output_path,
q_space_linear_transformation_matrix=(
self.q_lab_interpolator.original_to_target_matrix
),
direct_lab_linear_transformation_matrix=(
self.direct_lab_interpolator.original_to_target_matrix
),
q_space_transitions=self._q_space_transitions,
q_space_shift=self.q_space_shift,
direct_space_voxel_size=(
self.direct_lab_interpolator.target_voxel_size
"""
Save the interpolation parameters

Args:
output_path (str): where to save the parameters.
"""
if self.q_lab_interpolator is None:
print("[INFO] No interpolation parameters to save.")
else:
np.savez(
output_path,
q_space_linear_transformation_matrix=(
self.q_lab_interpolator.original_to_target_matrix
),
direct_lab_linear_transformation_matrix=(
self.direct_lab_interpolator.original_to_target_matrix
),
q_space_transitions=self._q_space_transitions,
q_space_shift=self.q_space_shift,
direct_space_voxel_size=(
self.direct_lab_interpolator.target_voxel_size
)
)
)

def load_interpolation_parameters(
self,
file_path: str,
direct_space_voxel_size: tuple or int=None
direct_space_voxel_size: tuple | int = None
):
"""
Load interpolation parameters from a file and initialize
Expand Down Expand Up @@ -523,12 +533,11 @@ def load_interpolation_parameters(
target_voxel_size=direct_space_voxel_size
)


def orthogonalize_to_direct_lab(
self,
direct_space_data: np.ndarray,
detector_data: Optional[np.ndarray]=None,
direct_space_voxel_size: Union[tuple, np.ndarray, list, float]=None,
detector_data: np.ndarray = None,
direct_space_voxel_size: tuple | np.ndarray | list | float = None,
) -> np.ndarray:
"""
Orthogonalize the direct space data (reconstructed object) to
Expand Down Expand Up @@ -672,8 +681,8 @@ def get_direct_lab_regular_grid(self, arrangement: str="list"):

@staticmethod
def lab_to_cxi_conventions(
data: Union[np.ndarray, tuple, list]
) -> Union[np.ndarray, tuple, list]:
data: np.ndarray | tuple | list
) -> np.ndarray | tuple | list:
"""
Convert the a np.ndarray, a list or a tuple from the lab frame
system to the cxi frame conventions.
Expand Down Expand Up @@ -702,10 +711,11 @@ def lab_to_cxi_conventions(
"data should be a 3D np.ndarray, a list of 3 values, a tuple "
"of 3 values or a np.ndarray of 3 values."
)

@staticmethod
def cxi_to_lab_conventions(
data: Union[np.ndarray, tuple, list]
) -> Union[np.ndarray, tuple, list]:
data: np.ndarray | tuple | list
) -> np.ndarray | tuple | list:
"""
Convert the a np.ndarray, a list or a tuple from the cxi frame
system to the lab frame conventions.
Expand Down Expand Up @@ -927,9 +937,9 @@ def _init_target_grid(self, verbose: bool=False) -> None:

@staticmethod
def zero_centered_meshgrid(
shape: np.ndarray or list or tuple,
scale: np.ndarray or list or tuple=None
) -> Tuple[np.ndarray, np.ndarray, np.ndarray]:
shape: np.ndarray | list | tuple,
scale: np.ndarray | list | tuple = None
) -> tuple[np.ndarray, np.ndarray, np.ndarray]:
"""
Return the a zero-centered meshgrid with the 'ij' indexing numpy
convention.
Expand All @@ -951,7 +961,7 @@ def _rotate_grid_axis(
grid_axis0: np.ndarray,
grid_axis1: np.ndarray,
grid_axis2: np.ndarray
) -> Tuple[np.ndarray, np.ndarray, np.ndarray]:
) -> tuple[np.ndarray, np.ndarray, np.ndarray]:
"""Rotate the grid axes to the target space."""

rotated_grid_axis0 = (
Expand Down
10 changes: 5 additions & 5 deletions cdiutils/load/bliss.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -163,10 +163,10 @@ def show_scan_attributes(
def load_motor_positions(
self,
scan: int,
sample_name: str=None,
roi: tuple[slice]=None,
binning_along_axis0: int=None,
binning_method: str="mean"
sample_name: str = None,
roi: tuple[slice] = None,
binning_along_axis0: int = None,
binning_method: str = "mean"
) -> dict:
"""
Load the motor positions and return it as a dict of:
Expand All @@ -192,7 +192,7 @@ def load_motor_positions(

for angle, name in BlissLoader.angle_names.items():
if binning_along_axis0:
angles[angle] = self.h5file[key_path + name][()]
angles[angle] = self.h5file[key_path + name][()]
else:
try:
angles[angle] = self.h5file[key_path + name][roi]
Expand Down
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