def saveImage(self):
"""Dump the current frame to a file"""
outfile = datetime.datetime.now().strftime(
"%Y%m%d-%H%M%S.%f") + ".tiff"
if self.app:
module_io = self.app.get_module("io")
drc = module_io.get_experiment_directory()
drc.mkdir(exist_ok=True, parents=True)
outfile = drc / outfile
try:
flatfield, h = read_tiff(module_io.get_flatfield())
frame = apply_flatfield_correction(self.frame, flatfield)
except:
frame = self.frame
h = {}
else:
frame = self.frame
h = {}
write_tiff(outfile, frame, header=h)
print(" >> Wrote file:", outfile)
def apply_corrections(self, img, h):
if self.flatfield is not None:
img = remove_deadpixels(img, deadpixels=self.deadpixels)
h['DeadPixelCorrection'] = True
img = apply_flatfield_correction(img, flatfield=self.flatfield)
h['FlatfieldCorrection'] = True
return img, h
def __init__(
self,
buffer:
list, # image buffer, list of (index [int], image data [2D numpy array], header [dict])
camera_length: float, # virtual camera length read from the microscope
osc_angle: float, # degrees, oscillation angle of the rotation
start_angle: float, # degrees, start angle of the rotation
end_angle: float, # degrees, end angle of the rotation
rotation_axis:
float, # radians, specifies the position of the rotation axis
acquisition_time:
float, # seconds, acquisition time (exposure time + overhead)
flatfield: str = 'flatfield.tiff'):
if flatfield is not None:
flatfield, h = read_tiff(flatfield)
self.flatfield = flatfield
self.headers = {}
self.data = {}
self.smv_subdrc = "data"
while len(buffer) != 0:
i, img, h = buffer.pop(0)
self.headers[i] = h
if self.flatfield is not None:
self.data[i] = apply_flatfield_correction(img, self.flatfield)
else:
self.data[i] = img
self.untrusted_areas = []
self.observed_range = set(self.data.keys())
self.complete_range = set(
range(min(self.observed_range),
max(self.observed_range) + 1))
self.missing_range = self.observed_range ^ self.complete_range
self.data_shape = img.shape
try:
self.pixelsize = config.calibration.pixelsize_diff[
camera_length] # px / Angstrom
except KeyError:
self.pixelsize = 1
print(
f"No calibrated pixelsize for camera length={camera_length}. Setting pixelsize to 1."
)
logger.warning(
f"No calibrated pixelsize for camera length={camera_length}. Setting pixelsize to 1."
)
self.physical_pixelsize = config.camera.physical_pixelsize # mm
self.wavelength = config.microscope.wavelength # angstrom
# NOTE: Stretch correction - not sure if the azimuth and amplitude are correct anymore.
self.do_stretch_correction = True
self.stretch_azimuth = config.camera.stretch_azimuth
self.stretch_amplitude = config.camera.stretch_amplitude
self.distance = (1 / self.wavelength) * (self.physical_pixelsize /
self.pixelsize)
self.osc_angle = osc_angle
self.start_angle = start_angle
self.end_angle = end_angle
self.rotation_axis = rotation_axis
self.acquisition_time = acquisition_time
#self.rotation_speed = get_calibrated_rotation_speed(osc_angle / self.acquisition_time)
self.name = "Instamatic"
from .XDS_template import XDS_template # hook XDS_template here, because it is difficult to override as a global
self.XDS_template = XDS_template
self.check_settings(
) # check if all required parameters are present, and fill default values if needed
self.mean_beam_center, self.beam_center_std = self.get_beam_centers()
logger.debug(f"Primary beam at: {self.mean_beam_center}")