def _extract_image_pixels(self, flex_image, frame, trusted_range):
"""Extract pixels from a single image
Params:
image The image from which to extract the pixels
frame The frame number of the current image
trusted_range The trusted range of pixel values
Returns:
The list of selected pixels
"""
from scitbx.array_family import flex
from dials.algorithms.peak_finding import flex_vec3_int
from dials.algorithms.peak_finding import mean_sdev_filter
import numpy
from time import time
# Calculate the threshold
threshold = self._calculate_threshold(flex_image, trusted_range)
# Extract the pixel indices
image = flex_image.as_numpy_array()
height, width = image.shape
image.shape = -1
index = numpy.where(image >= threshold)[0]
# Create the array of pixel coordinates
z = [frame] * len(index)
y = map(int, index // width)
x = map(int, index % width)
coords = flex_vec3_int(zip(x, y, z))
# Get the array of pixel intensities
intensity = flex.int(image[index])
# Return the pixel values
return coords, intensity
def _extract_image_pixels(self, flex_image, frame, trusted_range):
'''Extract pixels from a single image
Params:
image The image from which to extract the pixels
frame The frame number of the current image
trusted_range The trusted range of pixel values
Returns:
The list of selected pixels
'''
from scitbx.array_family import flex
from dials.algorithms.peak_finding import flex_vec3_int
from dials.algorithms.peak_finding import mean_sdev_filter
import numpy
from time import time
# Calculate the threshold
threshold = self._calculate_threshold(flex_image, trusted_range)
# Extract the pixel indices
image = flex_image.as_numpy_array()
height, width = image.shape
image.shape = -1
index = numpy.where(image >= threshold)[0]
# Create the array of pixel coordinates
z = [frame] * len(index)
y = map(int, index // width)
x = map(int, index % width)
coords = flex_vec3_int(zip(x, y, z))
# Get the array of pixel intensities
intensity = flex.int(image[index])
# Return the pixel values
return coords, intensity
def _extract_pixels(self, sweep):
"""Extract the pixels from the sweep
Params:
sweep The sweep object
Returns:
The list of selected pixels
"""
from dials.util.command_line import ProgressBar
from scitbx.array_family import flex
from dials.algorithms.peak_finding import flex_vec3_int
# Initialise the pixel arrays
coords = flex_vec3_int()
intensity = flex.int()
# Get the start index and trusted range from the sweep
start = sweep.get_array_range()[0]
trusted_range = sweep.get_detector().get_trusted_range()
# Loop through all the images in the sweep and extract the pixels
# from each of the images
progress = ProgressBar()
for frame, image in enumerate(sweep):
c, i = self._extract_image_pixels(image, frame + start,
trusted_range)
coords.extend(c)
intensity.extend(i)
progress.update(100.0 * float(frame + 1) / len(sweep))
progress.finished()
# Reuturn the pixel values
return coords, intensity
def _extract_pixels(self, sweep):
'''Extract the pixels from the sweep
Params:
sweep The sweep object
Returns:
The list of selected pixels
'''
from dials.util.command_line import ProgressBar
from scitbx.array_family import flex
from dials.algorithms.peak_finding import flex_vec3_int
# Initialise the pixel arrays
coords = flex_vec3_int()
intensity = flex.int()
# Get the start index and trusted range from the sweep
start = sweep.get_array_range()[0]
trusted_range = sweep.get_detector().get_trusted_range()
# Loop through all the images in the sweep and extract the pixels
# from each of the images
progress = ProgressBar()
for frame, image in enumerate(sweep):
c, i = self._extract_image_pixels(image, frame + start,
trusted_range)
coords.extend(c)
intensity.extend(i)
progress.update(100.0 * float(frame + 1) / len(sweep))
progress.finished()
# Reuturn the pixel values
return coords, intensity
