def analyze(movie_name, mlist_name, settings_name):
# Load parameters.
parameters = params.ParametersPSFFFT().initFromFile(settings_name, warnings = False)
# Create finding and fitting object.
finder = findPeaksStd.initFindAndFit(parameters)
# Create appropriate reader.
if parameters.hasAttr("camera_offset"):
frame_reader = analysisIO.FrameReaderStd(movie_file = movie_name,
parameters = parameters)
else:
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 = "PSF-FFT")
std_analysis.standardAnalysis(finder,
movie_reader,
data_writer,
parameters)
def analyze(movie_name, mlist_name, settings_name):
parameters = params.ParametersDAO().initFromFile(settings_name)
finder = find_peaks.initFindAndFit(parameters)
std_analysis.standardAnalysis(finder,
movie_name,
mlist_name,
parameters)
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 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 analyze(base_name, mlist_name, olist_name, settings_name):
parameters = params.ParametersMultiplane().initFromFile(settings_name)
finder = PFPeakFinder(parameters)
fitter = findPeaksStd.MPPeakFitter(parameters)
finder_fitter = PFPeakFinderFitter(parameters, finder, fitter)
reader = PFMovieReader(base_name=base_name,
bin_name=olist_name,
parameters=parameters)
stdAnalysis.standardAnalysis(finder_fitter, reader, mlist_name, parameters)
def analyze(movie_name, mlist_name, settings_name):
parameters = params.ParametersSpliner().initFromFile(settings_name,
warnings=False)
if (parameters.getAttr("use_fista", 0) != 0):
parameters = params.ParametersSplinerFISTA().initFromFile(
settings_name)
finder = find_peaks_fista.SplinerFISTAFinderFitter(parameters)
else:
parameters = params.ParametersSplinerSTD().initFromFile(settings_name)
finder = find_peaks_std.SplinerFinderFitter(parameters)
std_analysis.standardAnalysis(finder, movie_name, mlist_name, parameters)
def analyze(movie_name, mlist_name, settings_name):
parameters = params.ParametersSpliner().initFromFile(settings_name, warnings = False)
if (parameters.getAttr("use_fista", 0) != 0):
parameters = params.ParametersSplinerFISTA().initFromFile(settings_name)
finder = find_peaks_fista.SplinerFISTAFinderFitter(parameters)
else:
parameters = params.ParametersSplinerSTD().initFromFile(settings_name)
finder = find_peaks_std.SplinerFinderFitter(parameters)
std_analysis.standardAnalysis(finder,
movie_name,
mlist_name,
parameters)
def analyze(base_name, mlist_name, settings_name):
parameters = params.ParametersMultiplane().initFromFile(settings_name)
finder = findPeaksStd.MPPeakFinder(parameters)
fitter = findPeaksStd.MPPeakFitter(parameters)
finder_fitter = findPeaksStd.MPFinderFitter(parameters, finder, fitter)
reader = findPeaksStd.MPMovieReader(base_name = base_name,
parameters = parameters)
data_writer = findPeaksStd.MPDataWriter(data_file = mlist_name,
parameters = parameters)
stdAnalysis.standardAnalysis(finder_fitter,
reader,
data_writer,
parameters)
def analyze(base_name, mlist_name, settings_name):
# Load parameters.
parameters = params.ParametersMultiplaneDao().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-Dao")
stdAnalysis.standardAnalysis(finder, reader, data_writer, parameters)
def analyze(base_name, mlist_name, settings_name):
parameters = params.ParametersMultiplane().initFromFile(settings_name)
# Set to only analyze 1 frame, 1 iteration of peak finding.
parameters.setAttr("max_frame", "int", 1)
parameters.setAttr("iterations", "int", 1)
# Analyze one frame.
finder = PFPeakFinder(parameters)
fitter = PFPeakFitter(parameters)
finder_fitter = findPeaksStd.MPFinderFitter(parameters, finder, fitter)
reader = findPeaksStd.MPMovieReader(base_name=base_name,
parameters=parameters)
stdAnalysis.standardAnalysis(finder_fitter, reader, mlist_name, parameters)
# Evaluate found vs fit parameters.
hi = utilC.getHeightIndex()
xi = utilC.getXCenterIndex()
yi = utilC.getYCenterIndex()
# First identify peak pairs.
fi_x = fitted_peaks[:, xi]
fi_y = fitted_peaks[:, yi]
fo_x = found_peaks[:, xi]
fo_y = found_peaks[:, yi]
dd = utilC.peakToPeakDist(fo_x, fo_y, fi_x, fi_y)
di = utilC.peakToPeakIndex(fo_x, fo_y, fi_x, fi_y)
print(numpy.mean(dd), fi_x.size, fo_x.size)
fo_h = []
fi_h = []
for i in range(dd.size):
if (dd[i] < 2.0):
fo_h.append(found_peaks[i, hi])
fi_h.append(fitted_peaks[di[i], hi])
fi_h = numpy.array(fi_h)
fo_h = numpy.array(fo_h)
print(numpy.mean(fi_h), fi_h.size)
print(numpy.mean(fo_h), fo_h.size)
print(numpy.mean(fi_h) / numpy.mean(fo_h))
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 analyze(movie_name, mlist_name, settings_name):
# Load parameters.
parameters = params.ParametersSpliner().initFromFile(settings_name,
warnings=False)
# Check for v1.0 parameters.
if not (parameters.hasAttr("camera_gain")
or parameters.hasAttr("camera_calibration")):
raise Exception(
"Camera parameters are missing. Version 1.0 parameters?")
# Create appropriate finding and fitting object.
if (parameters.getAttr("use_fista", 0) != 0):
parameters = params.ParametersSplinerFISTA().initFromFile(
settings_name)
finder = find_peaks_fista.initFindAndFit(parameters)
else:
parameters = params.ParametersSplinerSTD().initFromFile(settings_name)
finder = find_peaks_std.initFindAndFit(parameters)
# Create appropriate reader.
if parameters.hasAttr("camera_offset"):
frame_reader = analysisIO.FrameReaderStd(movie_file=movie_name,
parameters=parameters)
else:
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="Spliner")
std_analysis.standardAnalysis(finder, movie_reader, data_writer,
parameters)
def analyze(movie_name, mlist_name, settings_name):
# Load parameters.
parameters = params.ParametersSpliner().initFromFile(settings_name, warnings = False)
# Check for v1.0 parameters.
if not (parameters.hasAttr("camera_gain") or parameters.hasAttr("camera_calibration")):
raise Exception("Camera parameters are missing. Version 1.0 parameters?")
# Create appropriate finding and fitting object.
if (parameters.getAttr("use_fista", 0) != 0):
parameters = params.ParametersSplinerFISTA().initFromFile(settings_name)
finder = find_peaks_fista.initFindAndFit(parameters)
else:
parameters = params.ParametersSplinerSTD().initFromFile(settings_name)
finder = find_peaks_std.initFindAndFit(parameters)
# Create appropriate reader.
if parameters.hasAttr("camera_offset"):
frame_reader = analysisIO.FrameReaderStd(movie_file = movie_name,
parameters = parameters)
else:
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 = "Spliner")
std_analysis.standardAnalysis(finder,
movie_reader,
data_writer,
parameters)
def analyze(movie_name, mlist_name, settings_name):
parameters = params.ParametersDAO().initFromFile(settings_name)
finder = find_peaks.initFindAndFit(parameters)
std_analysis.standardAnalysis(finder, movie_name, mlist_name, parameters)
#
# Perform spline analysis on a dax file given parameters.
#
# Hazen 01/16
#
import sys
import storm_analysis.spliner.find_peaks_fista as find_peaks_fista
import storm_analysis.spliner.find_peaks_std as find_peaks_std
import storm_analysis.sa_library.parameters as params
import storm_analysis.sa_utilities.std_analysis as std_analysis
# setup
if (len(sys.argv) == 3):
parameters = params.Parameters(sys.argv[2])
mlist_file = sys.argv[1][:-4] + "_mlist.bin"
elif (len(sys.argv) == 4):
parameters = params.Parameters(sys.argv[3])
mlist_file = sys.argv[2]
else:
print("usage: <movie> <bin> <parameters.xml>")
exit()
if hasattr(parameters, "use_fista") and (parameters.use_fista != 0):
finder = find_peaks_fista.SplinerFinderFitter(parameters)
else:
finder = find_peaks_std.SplinerFinderFitter(parameters)
std_analysis.standardAnalysis(finder, sys.argv[1], mlist_file, parameters)
