def runPlaneWeighting(xml, output, background, photons, no_plots=False):
"""
xml - The analysis XML file.
output - File name to save the weights in.
background - Per pixel background in e- for each plane (as a list).
photons - Integrated peak intensity in e-.
no_plots - Don't show any plots.
"""
parameters = params.ParametersMultiplaneArb().initFromFile(xml)
[weights, variances] = planeWeighting(parameters, background, photons)
with open(output, 'wb') as fp:
pickle.dump(weights, fp)
#
# Plot results.
#
if not no_plots:
for i, name in enumerate(["bg", "h", "x", "y", "z"]):
# Plot per channel standard deviation.
sd = numpy.sqrt(variances[i])
x = numpy.arange(sd.shape[0])
fig = pyplot.figure()
for j in range(sd.shape[1]):
pyplot.plot(x, sd[:, j])
sd = 1.0 / numpy.sqrt(numpy.sum(1.0 / variances[i], axis=1))
pyplot.plot(x, sd, color="black")
pyplot.title(name)
pyplot.xlabel("scaled z")
pyplot.ylabel("standard deviation (nm)")
pyplot.ylim(ymin=0)
pyplot.show()
def testingParametersMC():
"""
Create a Multiplane parameters object.
"""
params = parameters.ParametersMultiplaneArb()
params.setAttr("max_frame", "int", -1)
params.setAttr("start_frame", "int", -1)
params.setAttr("background_sigma", "float", 8.0)
params.setAttr("find_max_radius", "int", 2)
params.setAttr("independent_heights", "int", settings.independent_heights)
params.setAttr("iterations", "int", settings.iterations)
params.setAttr("mapping", "filename", "map.map")
params.setAttr("no_fitting", "int", 0)
params.setAttr("pixel_size", "float", settings.pixel_size)
params.setAttr("sigma", "float", 1.5)
params.setAttr("threshold", "float", 6.0)
params.setAttr("weights", "filename", "weights.npy")
params.setAttr("z_value", "float-array", settings.z_value)
params.setAttr("channel0_cal", "filename", "calib.npy")
params.setAttr("channel1_cal", "filename", "calib.npy")
params.setAttr("channel2_cal", "filename", "calib.npy")
params.setAttr("channel3_cal", "filename", "calib.npy")
params.setAttr("channel0_ext", "string", "_c1.dax")
params.setAttr("channel1_ext", "string", "_c2.dax")
params.setAttr("channel2_ext", "string", "_c3.dax")
params.setAttr("channel3_ext", "string", "_c4.dax")
params.setAttr("channel0_offset", "int", 0)
params.setAttr("channel1_offset", "int", 0)
params.setAttr("channel2_offset", "int", 0)
params.setAttr("channel3_offset", "int", 0)
params.setAttr("spline0", "filename", "c1_psf.spline")
params.setAttr("spline1", "filename", "c2_psf.spline")
params.setAttr("spline2", "filename", "c3_psf.spline")
params.setAttr("spline3", "filename", "c4_psf.spline")
# Do tracking (localization color analysis depends on the tracks).
params.setAttr("descriptor", "string", "1")
params.setAttr("radius", "float", "1.0")
params.setAttr("max_z", "float", str(0.001 * settings.psf_z_range))
params.setAttr("min_z", "float", str(-0.001 * settings.psf_z_range))
# Don't do drift-correction.
params.setAttr("d_scale", "int", 2)
params.setAttr("drift_correction", "int", 0)
params.setAttr("frame_step", "int", 500)
params.setAttr("z_correction", "int", 0)
return params
def multiplaneXML():
"""
Create a Multiplane parameters object.
"""
params = parameters.ParametersMultiplaneArb()
params.setAttr("max_frame", "int", -1)
params.setAttr("start_frame", "int", -1)
params.setAttr("background_sigma", "float", 8.0)
params.setAttr("find_max_radius", "int", 2)
params.setAttr("independent_heights", "int", 0)
params.setAttr("iterations", "int", 20)
params.setAttr("mapping", "filename", "map.map")
params.setAttr("no_fitting", "int", 0)
params.setAttr("pixel_size", "float", pixel_size)
params.setAttr("sigma", "float", 1.5)
params.setAttr("threshold", "float", 6.0)
params.setAttr("weights", "filename", "weights.npy")
params.setAttr("z_value", "float-array", z_value)
params.setAttr("channel0_cal", "filename", "calib.npy")
params.setAttr("channel1_cal", "filename", "calib.npy")
params.setAttr("channel0_ext", "string", "_c1.dax")
params.setAttr("channel1_ext", "string", "_c2.dax")
params.setAttr("channel0_offset", "int", 0)
params.setAttr("channel1_offset", "int", 0)
params.setAttr("spline0", "filename", "c1_psf.spline")
params.setAttr("spline1", "filename", "c2_psf.spline")
# Don't do tracking.
params.setAttr("descriptor", "string", "1")
params.setAttr("radius", "float", "0.0")
params.setAttr("max_z", "float", str(spline_z_range + 0.001))
params.setAttr("min_z", "float", str(-(spline_z_range - 0.001)))
# Don't do drift-correction.
params.setAttr("d_scale", "int", 2)
params.setAttr("drift_correction", "int", 0)
params.setAttr("frame_step", "int", 500)
params.setAttr("z_correction", "int", 0)
params.toXMLFile("multiplane.xml")
def testingParameters():
"""
Create a Multiplane parameters object.
"""
params = parameters.ParametersMultiplaneArb()
params.setAttr("max_frame", "int", -1)
params.setAttr("start_frame", "int", -1)
params.setAttr("background_sigma", "float", 8.0)
params.setAttr("find_max_radius", "int", 2)
params.setAttr("independent_heights", "int", settings.independent_heights)
params.setAttr("iterations", "int", settings.iterations)
params.setAttr("mapping", "filename", "map.map")
params.setAttr("no_fitting", "int", 0)
params.setAttr("pixel_size", "float", settings.pixel_size)
params.setAttr("sigma", "float", 1.5)
params.setAttr("threshold", "float", 6.0)
params.setAttr("weights", "filename", "weights.npy")
params.setAttr("z_value", "float-array", settings.z_value)
params.setAttr("channel0_cal", "filename", "calib.npy")
params.setAttr("channel1_cal", "filename", "calib.npy")
params.setAttr("channel0_ext", "string", "_c1.dax")
params.setAttr("channel1_ext", "string", "_c2.dax")
params.setAttr("channel0_offset", "int", 0)
params.setAttr("channel1_offset", "int", 0)
params.setAttr("pupilfn0", "filename", "c1_pupilfn.pfn")
params.setAttr("pupilfn1", "filename", "c2_pupilfn.pfn")
# Don't do tracking.
params.setAttr("descriptor", "string", "1")
params.setAttr("radius", "float", "0.0")
params.setAttr("max_z", "float", str(settings.pupilfn_z_range))
params.setAttr("min_z", "float", str(-settings.pupilfn_z_range))
# Don't do drift-correction.
params.setAttr("d_scale", "int", 2)
params.setAttr("drift_correction", "int", 0)
params.setAttr("frame_step", "int", 500)
params.setAttr("z_correction", "int", 0)
return params
def analyze(base_name, mlist_name, settings_name):
# Load parameters.
parameters = params.ParametersMultiplaneArb().initFromFile(settings_name)
# Create finding and fitting object.
finder = findPeaksStd.initFindAndFit(parameters)
# Create multiplane (sCMOS) reader.
reader = analysisIO.MPMovieReader(base_name = base_name,
parameters = parameters)
# Create multiplane localization file(s) writer.
data_writer = analysisIO.MPDataWriter(data_file = mlist_name,
parameters = parameters,
sa_type = "Multiplane-Arb")
stdAnalysis.standardAnalysis(finder,
reader,
data_writer,
parameters)
def testingParameters(psf_model):
"""
Create a Multiplane parameters object.
"""
params = parameters.ParametersMultiplaneArb()
params.setAttr("max_frame", "int", -1)
params.setAttr("start_frame", "int", -1)
params.setAttr("background_sigma", "float", 8.0)
params.setAttr("find_max_radius", "int", 2)
params.setAttr("independent_heights", "int", settings.independent_heights)
params.setAttr("iterations", "int", settings.iterations)
params.setAttr("mapping", "filename", "map.map")
params.setAttr("no_fitting", "int", 0)
params.setAttr("pixel_size", "float", settings.pixel_size)
params.setAttr("sigma", "float", 1.5)
params.setAttr("threshold", "float", 6.0)
params.setAttr("weights", "filename", "weights.npy")
params.setAttr("z_value", "float-array", settings.z_value)
params.setAttr("channel0_cal", "filename", "calib.npy")
params.setAttr("channel1_cal", "filename", "calib.npy")
params.setAttr("channel0_ext", "string", "_c1.dax")
params.setAttr("channel1_ext", "string", "_c2.dax")
params.setAttr("channel0_offset", "int", 0)
params.setAttr("channel1_offset", "int", 0)
if (psf_model == "psf_fft"):
params.setAttr("psf0", "filename", "c1_psf_fft.psf")
params.setAttr("psf1", "filename", "c2_psf_fft.psf")
elif (psf_model == "pupilfn"):
params.setAttr("pupilfn0", "filename", "c1_pupilfn.pfn")
params.setAttr("pupilfn1", "filename", "c2_pupilfn.pfn")
elif (psf_model == "spline"):
params.setAttr("spline0", "filename", "c1_psf.spline")
params.setAttr("spline1", "filename", "c2_psf.spline")
else:
raise Exception("Unknown PSF model " + args.psf_model)
# Don't do tracking.
params.setAttr("descriptor", "string", "1")
params.setAttr("radius", "float", "0.0")
if (psf_model == "psf_fft"):
params.setAttr("max_z", "float", str(settings.psf_z_range + 0.001))
params.setAttr("min_z", "float", str(-(settings.psf_z_range - 0.001)))
elif (psf_model == "pupilfn"):
params.setAttr("max_z", "float", str(settings.pupilfn_z_range))
params.setAttr("min_z", "float", str(-settings.pupilfn_z_range))
elif (psf_model == "spline"):
params.setAttr("max_z", "float", str(settings.spline_z_range + 0.001))
params.setAttr("min_z", "float",
str(-(settings.spline_z_range - 0.001)))
# Don't do drift-correction.
params.setAttr("d_scale", "int", 2)
params.setAttr("drift_correction", "int", 0)
params.setAttr("frame_step", "int", 500)
params.setAttr("z_correction", "int", 0)
# 'peak_locations' testing.
if hasattr(settings, "peak_locations") and (settings.peak_locations
is not None):
params.setAttr("peak_locations", "filename", settings.peak_locations)
return params