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)