# This file is part of cfelpyutils.
#
# cfelpyutils is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# cfelpyutils is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with cfelpyutils. If not, see <http://www.gnu.org/licenses/>.
"""
Utilities to load, manipulate and apply geometry information to
detector pixel data.
Exports:
Functions:
compute_pixel_maps: turn a CrystFEL geometry object into pixel
maps.
apply_pixel_maps: apply pixel maps to a data array. Return an
array containing data with the geometry applied.
compute_minimum_array_size: compute the minimum array size that
is required to store data to which a geometry has been
applied.
adjust_pixel_maps_for_pyqtgraph: ajust pixel maps to be used in
a PyQtGraph's ImageView widget.
"""
from __future__ import (absolute_import, division, print_function,
unicode_literals)
import collections
import numpy
PixelMaps = collections.namedtuple( # pylint: disable=C0103
typename='PixelMaps',
field_names=['x', 'y', 'r']
)
"""
Pixel maps storing data geometry.
A namedtuple that stores the pixel maps describing the geometry of a
dataset. The first two fields, named "x" and "y" respectively, store
the pixel maps for the x coordinate and the y coordinate. The third
field, named "r", is instead a pixel map storing the distance of each
pixel in the data array from the center of the reference system.
"""
def compute_pixel_maps(geometry):
"""
Compute pixel maps from a CrystFEL geometry object.
Take as input a CrystFEL-style geometry object (A dictionary
returned by the function load_crystfel_geometry function in the
crystfel_utils module) and return a PixelMap tuple . The origin the
reference system used by the pixel maps is set at the beam
interaction point.
Args:
geometry (dict): A CrystFEL geometry object (A dictionary
returned by the
:obj:`cfelpyutils.crystfel_utils.load_crystfel_geometry`
function).
Returns:
PixelMaps: A PixelMaps tuple.
"""
# Determine the max fs and ss in the geometry object.
max_slab_fs = numpy.array([
geometry['panels'][k]['max_fs']
for k in geometry['panels']
]).max()
max_slab_ss = numpy.array([
geometry['panels'][k]['max_ss']
for k in geometry['panels']
]).max()
# Create empty arrays, of the same size of the input data, that
# will store the x and y pixel maps.
x_map = numpy.zeros(
shape=(max_slab_ss + 1, max_slab_fs + 1),
dtype=numpy.float32 # pylint: disable=E1101
)
y_map = numpy.zeros(
shape=(max_slab_ss + 1, max_slab_fs + 1),
dtype=numpy.float32 # pylint: disable=E1101
)
# Iterate over the panels. For each panel, determine the pixel
# indices, then compute the x,y vectors using a comples notation.
for pan in geometry['panels']:
i, j = numpy.meshgrid(
numpy.arange(
geometry['panels'][pan]['max_ss'] -
geometry['panels'][pan]['min_ss'] +
1
),
numpy.arange(
geometry['panels'][pan]['max_fs'] -
geometry['panels'][pan]['min_fs'] +
1
),
indexing='ij'
)
d_x = (geometry['panels'][pan]['fsy'] +
1J * geometry['panels'][pan]['fsx'])
d_y = (geometry['panels'][pan]['ssy'] +
1J * geometry['panels'][pan]['ssx'])
r_0 = (geometry['panels'][pan]['cny'] +
1J * geometry['panels'][pan]['cnx'])
cmplx = i * d_y + j * d_x + r_0
x_map[
geometry['panels'][pan]['min_ss']:
geometry['panels'][pan]['max_ss'] + 1,
geometry['panels'][pan]['min_fs']:
geometry['panels'][pan]['max_fs'] + 1
] = cmplx.imag
y_map[
geometry['panels'][pan]['min_ss']:
geometry['panels'][pan]['max_ss'] + 1,
geometry['panels'][pan]['min_fs']:
geometry['panels'][pan]['max_fs'] + 1
] = cmplx.real
# Finally, compute the values for the radius pixel map.
r_map = numpy.sqrt(numpy.square(x_map) + numpy.square(y_map))
return PixelMaps(x_map, y_map, r_map)
def apply_pixel_maps(data, pixel_maps, output_array=None):
"""
Apply geometry to the input data.
Apply the geometry (in pixel maps format) to the data. In other
words, turn an array of detector pixel values into an array
containing a representation of the physical layout of the detector.
Args:
data (ndarray): array containing the data on which the geometry
will be applied.
pixel_maps (PixelMaps): a PixelMaps tuple.
output_array (Optional[ndarray]): a preallocated array (of
dtype numpy.float32) to store the function output. If
provided, this array will be filled by the function and
and returned to the user. If not provided, the function
will create a new array automatically and return it to the
user. Defaults to None (No array provided).
Returns:
ndarray: a numpy.float32 array containing the data with the
geometry applied (i.e.: a representation of the physical layout
of the detector).
"""
# If no output array was provided, create one.
if output_array is None:
output_array = numpy.zeros(
shape=data.shape,
dtype=numpy.float32 # pylint: disable=E1101
)
# Apply the pixel map geometry information the data, then return
# the resulting array.
output_array[pixel_maps.y, pixel_maps.x] = data.ravel()
return output_array
def compute_minimum_array_size(pixel_maps):
"""
Compute the minimum array size storing data with applied geometry.
Return the minimum size of an array that can store data on which
the geometry information described by the pixel maps has been
applied.
The returned array shape is big enough to display all the input
pixel values in the reference system of the physical detector. The
array is also supposed to be centered at the center of the
reference system of the detector (i.e: the beam interaction point).
Args:
pixel_maps [PixelMaps]: a PixelMaps tuple.
Returns:
Tuple[int, int]: a numpy-style shape tuple storing the minimum
array size.
"""
# Find the largest absolute values of x and y in the maps. Since
# the returned array is centered on the origin, the minimum array
# size along a certain axis must be at least twice the maximum
# value for that axis. 2 pixels are added for good measure.
x_map, y_map = pixel_maps.x, pixel_maps.y
y_minimum = 2 * int(max(abs(y_map.max()), abs(y_map.min()))) + 2
x_minimum = 2 * int(max(abs(x_map.max()), abs(x_map.min()))) + 2
# Return a numpy-style tuple with the computed shape.
return (y_minimum, x_minimum)
def adjust_pixel_maps_for_pyqtgraph(pixel_maps):
"""
Adjust pixel maps for visualization of the data in a pyqtgraph
widget.
The adjusted maps can be used for a Pyqtgraph ImageView widget.
Args:
pixel_maps (PixelMaps): a PixelMaps tuple.
Returns:
PixelMaps: A Pixelmaps tuple containing the adjusted pixel
maps. The first two fields, named "x" and "y" respectively,
store the pixel maps for the x coordinate and the y
coordinate. The third field ("r") is just set to None.
"""
# Essentially, the origin of the reference system needs to be
# moved from the beam position to the top-left of the image that
# will be displayed. First, compute the size of the array used to
# display the data, then use this information to estimate the
# magnitude of the shift that needs to be applied to the origin of
# the system.
min_shape = compute_minimum_array_size(pixel_maps)
new_x_map = numpy.array(
object=pixel_maps.x,
dtype=numpy.int
) + min_shape[1] // 2 - 1
new_y_map = numpy.array(
object=pixel_maps.y,
dtype=numpy.int
) + min_shape[0] // 2 - 1
return PixelMaps(new_x_map, new_y_map, None)