def zFitting(h5_name, parameters, fit_tracks):
"""
Does z fitting for the '3d' model.
"""
[wx_params, wy_params] = parameters.getWidthParams()
[min_z, max_z] = parameters.getZRange()
z_step = parameters.getAttr("z_step", 1.0e-3)
if fit_tracks:
fitzC.fitzTracks(h5_name, parameters.getAttr("cutoff"), wx_params,
wy_params, min_z, max_z, z_step)
else:
fitzC.fitzRaw(h5_name, parameters.getAttr("cutoff"), wx_params,
wy_params, min_z, max_z, z_step)
def test_fitz_c_2():
"""
Test that localizations with wx, wy values that are not near
the calibration curve are assigned z values less than z minimum.
"""
# Load 3D parameters.
settings = storm_analysis.getData("test/data/test_3d_3d.xml")
parameters = params.ParametersDAO().initFromFile(settings)
[wx_params, wy_params] = parameters.getWidthParams()
[min_z, max_z] = parameters.getZRange()
pixel_size = parameters.getAttr("pixel_size")
# Calculate widths.
z_vals = numpy.arange(-250.0, 251.0, 100)
[sx, sy] = fitzC.calcSxSy(wx_params, wy_params, z_vals)
# Create HDF5 file with these widths.
peaks = {
"x": numpy.zeros(sx.size),
"xsigma": sx / pixel_size + numpy.ones(sx.size),
"ysigma": sy / pixel_size + numpy.ones(sx.size)
}
h5_name = storm_analysis.getPathOutputTest("test_sa_hdf5.hdf5")
storm_analysis.removeFile(h5_name)
with saH5Py.SAH5Py(h5_name, is_existing=False) as h5:
h5.setMovieInformation(256, 256, 10, "XYZZY")
h5.setPixelSize(pixel_size)
h5.addLocalizations(peaks, 1)
# Calculate Z values.
fitzC.fitzRaw(h5_name, 1.5, wx_params, wy_params, min_z, max_z, 1.0e-3)
# Check Z values.
with saH5Py.SAH5Py(h5_name) as h5:
locs = h5.getLocalizationsInFrame(1)
assert (numpy.allclose(locs["z"],
min_z * numpy.ones(sx.size) - 1.0e-3))
def test_fitz_c_2():
"""
Test that localizations with wx, wy values that are not near
the calibration curve are assigned z values less than z minimum.
"""
# Load 3D parameters.
settings = storm_analysis.getData("test/data/test_3d_3d.xml")
parameters = params.ParametersDAO().initFromFile(settings)
[wx_params, wy_params] = parameters.getWidthParams()
[min_z, max_z] = parameters.getZRange()
pixel_size = parameters.getAttr("pixel_size")
# Calculate widths.
z_vals = numpy.arange(-250.0, 251.0, 100)
[sx, sy] = fitzC.calcSxSy(wx_params, wy_params, z_vals)
# Create HDF5 file with these widths.
peaks = {"x" : numpy.zeros(sx.size),
"xsigma" : sx/pixel_size + numpy.ones(sx.size),
"ysigma" : sy/pixel_size + numpy.ones(sx.size)}
h5_name = storm_analysis.getPathOutputTest("test_sa_hdf5.hdf5")
storm_analysis.removeFile(h5_name)
with saH5Py.SAH5Py(h5_name, is_existing = False) as h5:
h5.setMovieInformation(256, 256, 10, "XYZZY")
h5.setPixelSize(pixel_size)
h5.addLocalizations(peaks, 1)
# Calculate Z values.
fitzC.fitzRaw(h5_name, 1.5, wx_params, wy_params, min_z, max_z, 1.0e-3)
# Check Z values.
with saH5Py.SAH5Py(h5_name) as h5:
locs = h5.getLocalizationsInFrame(1)
assert(numpy.allclose(locs["z"], min_z*numpy.ones(sx.size)-1.0e-3))
def zFitting(h5_name, parameters, fit_tracks):
"""
Does z fitting for the '3d' model.
"""
[wx_params, wy_params] = parameters.getWidthParams()
[min_z, max_z] = parameters.getZRange()
z_step = parameters.getAttr("z_step", 1.0e-3)
if fit_tracks:
fitzC.fitzTracks(h5_name,
parameters.getAttr("cutoff"),
wx_params,
wy_params,
min_z,
max_z,
z_step)
else:
fitzC.fitzRaw(h5_name,
parameters.getAttr("cutoff"),
wx_params,
wy_params,
min_z,
max_z,
z_step)