def initPSFObjects(parameters):
"""
Create and return the PSF objects (spline, pupil function or psf FFT).
"""
psf_objects = []
# Try PSF FFT.
#
if (len(mpUtil.getPSFFFTAttrs(parameters)) > 0):
# Create PSF FFT PSF objects.
for psf_fft_attr in mpUtil.getPSFFFTAttrs(parameters):
psf_objects.append(
psfFn.PSFFn(psf_filename=parameters.getAttr(psf_fft_attr)))
# All the PSF FFT objects have to have the same Z range.
for i in range(1, len(psf_objects)):
assert (psf_objects[0].getZMin() == psf_objects[i].getZMin())
assert (psf_objects[0].getZMax() == psf_objects[i].getZMax())
# Try pupil functions.
#
elif (len(mpUtil.getPupilFnAttrs(parameters)) > 0):
# Get fitting Z range (this is in microns).
[min_z, max_z] = parameters.getZRange()
# Create pupil function PSF objects.
for pupil_fn_attr in mpUtil.getPupilFnAttrs(parameters):
psf_objects.append(
pupilFn.PupilFunction(
pf_filename=parameters.getAttr(pupil_fn_attr),
zmin=min_z * 1.0e+3,
zmax=max_z * 1.0e+3))
# Try splines.
#
elif (len(mpUtil.getSplineAttrs(parameters)) > 0):
# Create Spline PSF objects.
for spline_attr in mpUtil.getSplineAttrs(parameters):
psf_objects.append(
splineToPSF.SplineToPSF3D(
spline_file=parameters.getAttr(spline_attr)))
# All the splines have to have the same Z range.
for i in range(1, len(psf_objects)):
assert (psf_objects[0].getZMin() == psf_objects[i].getZMin())
assert (psf_objects[0].getZMax() == psf_objects[i].getZMax())
else:
raise Exception("No PSF objects found.")
return psf_objects
def initPSFObjects(parameters):
"""
Create and return the PSF objects (spline, pupil function or psf FFT).
"""
psf_objects = []
# Try PSF FFT.
#
if (len(mpUtil.getPSFFFTAttrs(parameters)) > 0):
# Create PSF FFT PSF objects.
for psf_fft_attr in mpUtil.getPSFFFTAttrs(parameters):
psf_objects.append(psfFn.PSFFn(psf_filename = parameters.getAttr(psf_fft_attr)))
# All the PSF FFT objects have to have the same Z range.
for i in range(1, len(psf_objects)):
assert (psf_objects[0].getZMin() == psf_objects[i].getZMin())
assert (psf_objects[0].getZMax() == psf_objects[i].getZMax())
# Try pupil functions.
#
elif (len(mpUtil.getPupilFnAttrs(parameters)) > 0):
# Get fitting Z range (this is in microns).
[min_z, max_z] = parameters.getZRange()
# Create pupil function PSF objects.
for pupil_fn_attr in mpUtil.getPupilFnAttrs(parameters):
psf_objects.append(pupilFn.PupilFunction(pf_filename = parameters.getAttr(pupil_fn_attr),
zmin = min_z * 1.0e+3,
zmax = max_z * 1.0e+3))
# Try splines.
#
elif (len(mpUtil.getSplineAttrs(parameters)) > 0):
# Create Spline PSF objects.
for spline_attr in mpUtil.getSplineAttrs(parameters):
psf_objects.append(splineToPSF.SplineToPSF3D(spline_file = parameters.getAttr(spline_attr)))
# All the splines have to have the same Z range.
for i in range(1, len(psf_objects)):
assert (psf_objects[0].getZMin() == psf_objects[i].getZMin())
assert (psf_objects[0].getZMax() == psf_objects[i].getZMax())
else:
raise Exception("No PSF objects found.")
return psf_objects
def planeWeighting(parameters, background, photons):
"""
This calculates and return the weights to use for each parameter at each z value.
"""
pixel_size = parameters.getAttr("pixel_size")
cr_psf_objects = []
# Try PSF FFTs.
#
if (len(mpUtil.getPSFFFTAttrs(parameters)) > 0):
# Create PSF FFT CR PSF objects.
for psf_fft_attr in mpUtil.getPSFFFTAttrs(parameters):
psf_fft_name = parameters.getAttr(psf_fft_attr)
cr_psf_objects.append(
psfFFTCramerRao.CRPSFFn(psf_filename=psf_fft_name,
pixel_size=pixel_size))
# Try pupil functions.
#
if (len(mpUtil.getPupilFnAttrs(parameters)) > 0):
# Create pupil function CR PSF objects.
[zmin, zmax] = parameters.getZRange()
for pfn_attr in mpUtil.getPupilFnAttrs(parameters):
pfn_name = parameters.getAttr(pfn_attr)
cr_psf_objects.append(
pupilFnCramerRao.CRPupilFn(psf_filename=pfn_name,
pixel_size=pixel_size,
zmax=zmax,
zmin=zmin))
# Try splines.
#
if (len(mpUtil.getSplineAttrs(parameters)) > 0):
# Create Spline CR PSF objects.
for spline_attr in mpUtil.getSplineAttrs(parameters):
spline_name = parameters.getAttr(spline_attr)
cr_psf_objects.append(
splinerCramerRao.CRSplineToPSF3D(psf_filename=spline_name,
pixel_size=pixel_size))
assert (len(cr_psf_objects) > 0), "No CR PSF objects were found."
print("Calculating Cramer-Rao bounds.")
variances = planeVariances(cr_psf_objects, background, photons)
# Clean up Cramer-Rao PSF objects (some use C libraries).
#
for cr_po in cr_psf_objects:
cr_po.cleanup()
# I believe based on simulation testing that X and Y should not be transposed here.
#
print("Correcting for mapping.")
[variances[2],
variances[3]] = xyMappingCorrect(parameters.getAttr("mapping"),
variances[2], variances[3])
weights = {
"bg": planeWeights(variances[0]),
"h": planeWeights(variances[1]),
"x": planeWeights(variances[2]),
"y": planeWeights(variances[3]),
"z": planeWeights(variances[4]),
"background": background,
"photons": photons
}
return [weights, variances]
def planeWeighting(parameters, background, photons):
"""
This calculates and return the weights to use for each parameter at each z value.
"""
pixel_size = parameters.getAttr("pixel_size")
cr_psf_objects = []
# Try PSF FFTs.
#
if (len(mpUtil.getPSFFFTAttrs(parameters)) > 0):
# Create PSF FFT CR PSF objects.
for psf_fft_attr in mpUtil.getPSFFFTAttrs(parameters):
psf_fft_name = parameters.getAttr(psf_fft_attr)
cr_psf_objects.append(psfFFTCramerRao.CRPSFFn(psf_filename = psf_fft_name,
pixel_size = pixel_size))
# Try pupil functions.
#
if (len(mpUtil.getPupilFnAttrs(parameters)) > 0):
# Create pupil function CR PSF objects.
[zmin, zmax] = parameters.getZRange()
for pfn_attr in mpUtil.getPupilFnAttrs(parameters):
pfn_name = parameters.getAttr(pfn_attr)
cr_psf_objects.append(pupilFnCramerRao.CRPupilFn(psf_filename = pfn_name,
pixel_size = pixel_size,
zmax = zmax,
zmin = zmin))
# Try splines.
#
if (len(mpUtil.getSplineAttrs(parameters)) > 0):
# Create Spline CR PSF objects.
for spline_attr in mpUtil.getSplineAttrs(parameters):
spline_name = parameters.getAttr(spline_attr)
cr_psf_objects.append(splinerCramerRao.CRSplineToPSF3D(psf_filename = spline_name,
pixel_size = pixel_size))
assert (len(cr_psf_objects) > 0), "No CR PSF objects were found."
print("Calculating Cramer-Rao bounds.")
variances = planeVariances(cr_psf_objects,
background,
photons)
# Clean up Cramer-Rao PSF objects (some use C libraries).
#
for cr_po in cr_psf_objects:
cr_po.cleanup()
# I believe based on simulation testing that X and Y should not be transposed here.
#
print("Correcting for mapping.")
[variances[2], variances[3]] = xyMappingCorrect(parameters.getAttr("mapping"),
variances[2],
variances[3])
weights = {"bg" : planeWeights(variances[0]),
"h" : planeWeights(variances[1]),
"x" : planeWeights(variances[2]),
"y" : planeWeights(variances[3]),
"z" : planeWeights(variances[4]),
"background" : background,
"photons" : photons}
return [weights, variances]