def __init__(self, psf_filename = None, **kwds):
kwds["psf_filename"] = psf_filename
super(CRPSFFn, self).__init__(**kwds)
# Load the psf data.
with open(psf_filename, 'rb') as fp:
psf_data = pickle.load(fp)
# Use C library to calculate the PSF and it's derivatives.
psf = psf_data['psf']
self.psf_fft_c = psfFFTC.PSFFFT(psf_data['psf'])
# Additional initializations.
self.zmax = psf_data["zmax"]
self.zmin = psf_data["zmin"]
# I believe that this is the right way to scale the Z value based
# on comparisons with the pupilfn equivalent of this class. This
# is also the scaling that we use in psf_fn.py.
self.scale_gSZ = (float(psf.shape[0]) - 1.0)/(self.zmax - self.zmin)
# CR weights approximately every 25nm.
self.n_zvals = int(round((self.zmax - self.zmin)/25.0))
self.delta_xy = self.pixel_size
#self.delta_z = (self.getZMax() - self.getZMin())/float(self.n_zvals)
self.delta_z = (self.zmax - self.zmin)/float(psf.shape[0])
def __init__(self, psf_filename=None, **kwds):
super(PSFFn, self).__init__(**kwds)
# Load the PSF data.
with open(psf_filename, 'rb') as fp:
psf_data = pickle.load(fp)
# Initialize C library.
psf = psf_data['psf']
self.psf_fft_c = psfFFTC.PSFFFT(psf)
# Store some additional properties.
self.pixel_size = psf_data["pixel_size"]
self.psf_shape = psf.shape
# These are in units of nanometers.
self.zmax = psf_data["zmax"]
self.zmin = psf_data["zmin"]
self.scale_gSZ = (float(self.getZSize()) - 1.0) / (self.zmax -
self.zmin)
self.scale_rZ = 1.0e-3 * (self.zmax -
self.zmin) / (float(self.getZSize()) - 1.0)
# Sanity checks.
assert ((psf.shape[0] % 2) == 1), "Z size must be an odd number."
assert (psf.shape[1] == psf.shape[2]), "X/Y size must be the same."
assert (self.zmax == -self.zmin), "z range must be symmetric."
def test_psf_fft3():
"""
Test PSF dx calculation.
"""
dx = 0.2
[pf_psf, geo, pf] = makePSFAndPF(-0.4, 0.4, 0.05)
pfft = psfFFTC.PSFFFT(pf_psf)
pfft.translate(dx, 0.0, 0.0)
dx_exact = pfft.getPSFdx()
psf = pfft.getPSF()
pfft.translate(dx + 1.0e-6, 0.0, 0.0)
dx_calc = (pfft.getPSF() - psf) / 1.0e-6
if False:
print(numpy.max(numpy.abs(dx_exact - dx_calc)))
with tifffile.TiffWriter(
storm_analysis.getPathOutputTest("test_psf_fft3.tif")) as tf:
tf.save(dx_exact.astype(numpy.float32))
tf.save(dx_calc.astype(numpy.float32))
assert (numpy.max(numpy.abs(dx_exact - dx_calc))) < 1.0e-6
pfft.cleanup()
def test_psf_fft2():
"""
Test translated PSF calculation.
"""
dx = 0.5
dy = 0.25
dz = 0.2
[pf_psf, geo, pf] = makePSFAndPF(-0.4, 0.4, 0.05)
pfft = psfFFTC.PSFFFT(pf_psf)
pfft.translate(dy, dx, dz * (pf_psf.shape[0] - 1) / 0.8)
psf_fft = pfft.getPSF()
defocused = geo.changeFocus(pf, dz)
translated = geo.translatePf(defocused, dx, dy)
psf_pf = pupilMath.intensity(pupilMath.toRealSpace(translated))
if False:
print(numpy.max(numpy.abs(psf_fft - psf_pf)))
with tifffile.TiffWriter(
storm_analysis.getPathOutputTest("test_psf_fft2.tif")) as tf:
tf.save(psf_fft.astype(numpy.float32))
tf.save(psf_pf.astype(numpy.float32))
assert (numpy.max(numpy.abs(psf_fft - psf_pf))) < 1.0e-10
pfft.cleanup()
def test_psf_fft7():
"""
Test against the Python version, translation.
"""
dx = 0.5
dy = 0.25
dz = 0.2
[pf_psf, geo, pf] = makePSFAndPF(-0.4, 0.4, 0.05)
pfft_c = psfFFTC.PSFFFT(pf_psf)
pfft_py = psfFFTPy.PSFFFT(pf_psf)
pfft_c.translate(dx, dy, dz)
pfft_py.translate(dx, dy, dz)
psf_c = pfft_c.getPSF()
psf_py = pfft_py.getPSF()
if False:
print(numpy.max(numpy.abs(psf_c - psf_py)))
with tifffile.TiffWriter(
storm_analysis.getPathOutputTest("test_psf_fft7.tif")) as tf:
tf.save(psf_c.astype(numpy.float32))
tf.save(psf_py.astype(numpy.float32))
assert (numpy.max(numpy.abs(psf_c - psf_py))) < 1.0e-6
pfft_c.cleanup()
def test_psf_fft1():
"""
Test untranslated PSF calculation.
"""
[pf_psf, geo, pf] = makePSFAndPF(-0.4, 0.4, 0.05)
pfft = psfFFTC.PSFFFT(pf_psf)
psf_fft = pfft.getPSF()
psf_pf = pupilMath.intensity(pupilMath.toRealSpace(pf))
if False:
print(numpy.max(numpy.abs(psf_fft - psf_pf)))
with tifffile.TiffWriter(
storm_analysis.getPathOutputTest("test_psf_fft1.tif")) as tf:
tf.save(psf_fft.astype(numpy.float32))
tf.save(psf_pf.astype(numpy.float32))
assert (numpy.max(numpy.abs(psf_fft - psf_pf))) < 1.0e-10
pfft.cleanup()
def test_psf_fft10():
"""
Test against the Python version, dz.
"""
[pf_psf, geo, pf] = makePSFAndPF(-0.4, 0.4, 0.05)
pfft_c = psfFFTC.PSFFFT(pf_psf)
pfft_py = psfFFTPy.PSFFFT(pf_psf)
psf_dz_c = pfft_c.getPSFdz()
psf_dz_py = pfft_py.getPSFdz()
if False:
print(numpy.max(numpy.abs(psf_dz_c - psf_dz_py)))
with tifffile.TiffWriter(
storm_analysis.getPathOutputTest("test_psf_fft10.tif")) as tf:
tf.save(psf_dz_c.astype(numpy.float32))
tf.save(psf_dz_py.astype(numpy.float32))
assert (numpy.max(numpy.abs(psf_dz_c - psf_dz_py))) < 1.0e-6
pfft_c.cleanup()