def testingParametersSCMOS():
"""
Create a sCMOS parameters object.
"""
params = parameters.ParametersSCMOS()
params.setAttr("max_frame", "int", -1)
params.setAttr("start_frame", "int", -1)
params.setAttr("background_sigma", "float", 8.0)
params.setAttr("camera_calibration", "filename", "calib.npy")
params.setAttr("find_max_radius", "int", 5)
params.setAttr("foreground_sigma", "float", 1.5)
params.setAttr("iterations", "int", settings.iterations)
params.setAttr("model", "string", "2dfixed")
params.setAttr("pixel_size", "float", settings.pixel_size)
params.setAttr("sigma", "float", 150.0 / settings.pixel_size)
params.setAttr("threshold", "float", 6.0)
# Don't do tracking.
params.setAttr("descriptor", "string", "1")
params.setAttr("radius", "float", "0.0")
# 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 test_scmos_scmos_cal():
"""
Test that scmos calibration data is initialized correctly.
"""
settings = storm_analysis.getData("test/data/test_sc_2d_fixed.xml")
parameters = params.ParametersSCMOS().initFromFile(settings)
# Create analysis object and reach deep into it..
find_fit = findPeaks.initFindAndFit(parameters)
fitter = find_fit.peak_fitter
mfitter = fitter.mfitter
# Get sCMOS calibration value.
scmos_cal_value = mfitter.scmos_cal[0, 0]
# Initialize with an image.
image = numpy.ones(mfitter.scmos_cal.shape)
fitter.newImage(image)
# Verify that the image has the sCMOS term added.
resp = mfitter.getResidual()
assert (numpy.max(resp - (1.0 + scmos_cal_value)) < 1.0e-6)
# Cleanup.
fitter.cleanUp()
def analyze(movie_name, mlist_name, settings_name):
# Load parameters.
parameters = params.ParametersSCMOS().initFromFile(settings_name)
# Check for possibly v1.0 parameters.
if not parameters.hasAttr("background_sigma"):
raise Exception(
"Parameter 'background_sigma' is missing. Version 1.0 parameters?")
# Create finding and fitting object.
finder = find_peaks.initFindAndFit(parameters)
# Create object for reading sCMOS camera frames.
frame_reader = analysisIO.FrameReaderSCMOS(movie_file=movie_name,
parameters=parameters)
# Create movie reader (uses frame reader).
movie_reader = analysisIO.MovieReader(frame_reader=frame_reader,
parameters=parameters)
# Create localization file writer.
data_writer = analysisIO.DataWriterHDF5(data_file=mlist_name,
parameters=parameters,
sa_type='sCMOS')
# Run the analysis.
std_analysis.standardAnalysis(finder, movie_reader, data_writer,
parameters)
def testingParameters():
"""
Create a sCMOS parameters object.
"""
params = parameters.ParametersSCMOS()
params.setAttr("max_frame", "int", -1)
params.setAttr("start_frame", "int", -1)
params.setAttr("background_sigma", "float", 8.0)
params.setAttr("camera_calibration", "filename", "calib.npy")
params.setAttr("find_max_radius", "int", 5)
params.setAttr("foreground_sigma", "float", 1.5)
params.setAttr("iterations", "int", settings.iterations)
params.setAttr("model", "string", settings.model)
params.setAttr("pixel_size", "float", settings.pixel_size)
params.setAttr("sigma", "float", 150.0 / settings.pixel_size)
params.setAttr("threshold", "float", 6.0)
# Don't do tracking.
params.setAttr("descriptor", "string", "1")
params.setAttr("radius", "float", "0.0")
# 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)
# Z fitting.
#
# These are nonsense values. We test either '2D' of '3D' mode
# and check how will we do at fitting the localization widths.
#
params.setAttr("do_zfit", "int", 0)
params.setAttr("cutoff", "float", 0.0)
params.setAttr("max_z", "float", 0.5)
params.setAttr("min_z", "float", -0.5)
params.setAttr("z_value", "float", 0.0)
params.setAttr("z_step", "float", 1.0)
params.setAttr("wx_wo", "float", 1.0)
params.setAttr("wx_c", "float", 1.0)
params.setAttr("wx_d", "float", 1.0)
params.setAttr("wxA", "float", 0.0)
params.setAttr("wxB", "float", 0.0)
params.setAttr("wxC", "float", 0.0)
params.setAttr("wxD", "float", 0.0)
params.setAttr("wy_wo", "float", 1.0)
params.setAttr("wy_c", "float", 1.0)
params.setAttr("wy_d", "float", 1.0)
params.setAttr("wyA", "float", 0.0)
params.setAttr("wyB", "float", 0.0)
params.setAttr("wyC", "float", 0.0)
params.setAttr("wyD", "float", 0.0)
return params
def sCMOSXML():
"""
Create an sCMOS analysis file.
"""
params = parameters.ParametersSCMOS()
params.setAttr("max_frame", "int", 1)
params.setAttr("start_frame", "int", 0)
params.setAttr("background_sigma", "float", 8.0)
params.setAttr("camera_calibration", "filename", "calib.npy")
params.setAttr("find_max_radius", "int", 5)
params.setAttr("foreground_sigma", "float", 1.5)
params.setAttr("iterations", "int", 1)
params.setAttr("model", "string", "2dfixed")
params.setAttr("pixel_size", "float", pixel_size)
params.setAttr("roi_size", "int", 9)
params.setAttr("sigma", "float", 1.5)
params.setAttr("threshold", "float", 20.0)
# Don't do tracking.
params.setAttr("descriptor", "string", "1")
params.setAttr("radius", "float", "0.0")
# 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)
# Z fitting.
params.setAttr("do_zfit", "int", 0)
params.setAttr("cutoff", "float", 0.0)
params.setAttr("max_z", "float", 0.5)
params.setAttr("min_z", "float", -0.5)
params.setAttr("z_value", "float", 0.0)
params.setAttr("z_step", "float", 1.0)
params.setAttr("wx_wo", "float", 1.0)
params.setAttr("wx_c", "float", 1.0)
params.setAttr("wx_d", "float", 1.0)
params.setAttr("wxA", "float", 0.0)
params.setAttr("wxB", "float", 0.0)
params.setAttr("wxC", "float", 0.0)
params.setAttr("wxD", "float", 0.0)
params.setAttr("wy_wo", "float", 1.0)
params.setAttr("wy_c", "float", 1.0)
params.setAttr("wy_d", "float", 1.0)
params.setAttr("wyA", "float", 0.0)
params.setAttr("wyB", "float", 0.0)
params.setAttr("wyC", "float", 0.0)
params.setAttr("wyD", "float", 0.0)
params.toXMLFile("scmos.xml")
def test_remove_paths():
"""
Test that saving does / does not remove path information.
"""
output = storm_analysis.getPathOutputTest("test_rp.xml")
# Create parameters.
p1 = params.ParametersSCMOS()
p1.changeAttr("camera_calibration", "weird_path/foo.npy")
# Save without path information
p1.toXMLFile(output, pretty=True)
p2 = params.ParametersSCMOS().initFromFile(output)
assert (not "weird_path" in p2.getAttr("camera_calibration"))
# Save with path information
p1.toXMLFile(output, pretty=True, remove_paths=False)
p2 = params.ParametersSCMOS().initFromFile(output)
assert ("weird_path" in p2.getAttr("camera_calibration"))
def analyze(movie_name, mlist_name, settings_name):
parameters = params.ParametersSCMOS().initFromFile(settings_name)
finder = find_peaks.initFindAndFit(parameters)
std_analysis.standardAnalysis(finder, movie_name, mlist_name, parameters)
