LICENSE
MANIFEST.in
README.md
pyproject.toml
src/TraceAnalyser/__init__.py
src/TraceAnalyser/main_window.py
src/TraceAnalyser.egg-info/PKG-INFO
src/TraceAnalyser.egg-info/SOURCES.txt
src/TraceAnalyser.egg-info/dependency_links.txt
src/TraceAnalyser.egg-info/entry_points.txt
src/TraceAnalyser.egg-info/requires.txt
src/TraceAnalyser.egg-info/top_level.txt
src/TraceAnalyser/DeepFretSimulate/__init__.py
src/TraceAnalyser/DeepFretSimulate/math.py
src/TraceAnalyser/DeepFretSimulate/simulate.py
src/TraceAnalyser/DeepFretSimulate/simulation_test.py
src/TraceAnalyser/DeepFretSimulate/utils.py
src/TraceAnalyser/GUI/__init__.py
src/TraceAnalyser/GUI/bleachwindow_gui.py
src/TraceAnalyser/GUI/convert_ui_files.py
src/TraceAnalyser/GUI/correctionwindow_gui.py
src/TraceAnalyser/GUI/cropwindow_gui.py
src/TraceAnalyser/GUI/detectwindow_gui.py
src/TraceAnalyser/GUI/exportsettings_gui.py
src/TraceAnalyser/GUI/exportwindow_gui.py
src/TraceAnalyser/GUI/filterwindow_gui.py
src/TraceAnalyser/GUI/fittingwindow_gui.py
src/TraceAnalyser/GUI/groupwindow_gui.py
src/TraceAnalyser/GUI/importwindow_gui.py
src/TraceAnalyser/GUI/mainwindow_gui.py
src/TraceAnalyser/GUI/managewindow_gui.py
src/TraceAnalyser/GUI/plotsettings_gui.py
src/TraceAnalyser/GUI/simulatorwindow_gui.py
src/TraceAnalyser/GUI/smoothingwindow_gui.py
src/TraceAnalyser/InceptionTime/__init__.py
src/TraceAnalyser/InceptionTime/models/inceptiontime_model_231218_1524.h5
src/TraceAnalyser/funcs/__init__.py
src/TraceAnalyser/funcs/ebfret_utils.py
src/TraceAnalyser/funcs/gui_HMM_utils.py
src/TraceAnalyser/funcs/gui_analysis_plot_utils.py
src/TraceAnalyser/funcs/gui_bleach_utils.py
src/TraceAnalyser/funcs/gui_correction_utils.py
src/TraceAnalyser/funcs/gui_detectcrop_utils.py
src/TraceAnalyser/funcs/gui_ebfret_utils.py
src/TraceAnalyser/funcs/gui_export_utils.py
src/TraceAnalyser/funcs/gui_group_utils.py
src/TraceAnalyser/funcs/gui_import_utils.py
src/TraceAnalyser/funcs/gui_inceptiontime_utils.py
src/TraceAnalyser/funcs/gui_layout.py
src/TraceAnalyser/funcs/gui_management_utils.py
src/TraceAnalyser/funcs/gui_measure_plot_utils.py
src/TraceAnalyser/funcs/gui_simulation_utils.py
src/TraceAnalyser/funcs/gui_smoothing_utils.py
src/TraceAnalyser/funcs/gui_trace_plot_overlays.py
src/TraceAnalyser/funcs/gui_trace_plot_utils.py
src/TraceAnalyser/funcs/gui_windows.py
src/TraceAnalyser/funcs/gui_worker.py
src/ebFRET/__init__.py
src/ebFRET/ebFRET.m
src/ebFRET/+ebfret/check_matlab_version.m
src/ebFRET/+ebfret/check_parfor.m
src/ebFRET/+ebfret/ebFRET.m
src/ebFRET/+ebfret/escape_tex.m
src/ebFRET/+ebfret/join.m
src/ebFRET/+ebfret/nan_to_zero.m
src/ebFRET/+ebfret/normalize.m
src/ebFRET/+ebfret/num_to_str.m
src/ebFRET/+ebfret/struct_to_keyval.m
src/ebFRET/+ebfret/+analysis/photobleach_index.m
src/ebFRET/+ebfret/+analysis/x_lim.m
src/ebFRET/+ebfret/+analysis/+dist/+beta/log_pdf.m
src/ebFRET/+ebfret/+analysis/+dist/+dirichlet/e_step.m
src/ebFRET/+ebfret/+analysis/+dist/+dirichlet/h_step.m
src/ebFRET/+ebfret/+analysis/+dist/+dirichlet/kl_div.m
src/ebFRET/+ebfret/+analysis/+dist/+dirichlet/mean.m
src/ebFRET/+ebfret/+analysis/+dist/+dirichlet/mode.m
src/ebFRET/+ebfret/+analysis/+dist/+dirichlet/rand.m
src/ebFRET/+ebfret/+analysis/+dist/+dirichlet/tau.m
src/ebFRET/+ebfret/+analysis/+dist/+dirichlet/var.m
src/ebFRET/+ebfret/+analysis/+dist/+gamma/log_pdf.m
src/ebFRET/+ebfret/+analysis/+dist/+gamma/mean.m
src/ebFRET/+ebfret/+analysis/+dist/+gamma/mode.m
src/ebFRET/+ebfret/+analysis/+dist/+gamma/var.m
src/ebFRET/+ebfret/+analysis/+dist/+invgamma/mean.m
src/ebFRET/+ebfret/+analysis/+dist/+invgamma/mode.m
src/ebFRET/+ebfret/+analysis/+dist/+invgamma/var.m
src/ebFRET/+ebfret/+analysis/+dist/+normgamma/h_step.m
src/ebFRET/+ebfret/+analysis/+dist/+normgamma/mean.m
src/ebFRET/+ebfret/+analysis/+dist/+normgamma/mode.m
src/ebFRET/+ebfret/+analysis/+dist/+normgamma/var.m
src/ebFRET/+ebfret/+analysis/+dist/+normwish/e_step.m
src/ebFRET/+ebfret/+analysis/+dist/+normwish/h_step.m
src/ebFRET/+ebfret/+analysis/+dist/+normwish/kl_div.m
src/ebFRET/+ebfret/+analysis/+dist/+normwish/m_step.m
src/ebFRET/+ebfret/+analysis/+dist/+studt/log_pdf.m
src/ebFRET/+ebfret/+analysis/+dist/+studt/mean.m
src/ebFRET/+ebfret/+analysis/+dist/+studt/var.m
src/ebFRET/+ebfret/+analysis/+gmm/map.m
src/ebFRET/+ebfret/+analysis/+hmm/e_step.m
src/ebFRET/+ebfret/+analysis/+hmm/ebayes.m
src/ebFRET/+ebfret/+analysis/+hmm/forwback.m
src/ebFRET/+ebfret/+analysis/+hmm/forwback_native.m
src/ebFRET/+ebfret/+analysis/+hmm/guess_prior.m
src/ebFRET/+ebfret/+analysis/+hmm/h_step.m
src/ebFRET/+ebfret/+analysis/+hmm/h_step_remap.m
src/ebFRET/+ebfret/+analysis/+hmm/init_posterior.m
src/ebFRET/+ebfret/+analysis/+hmm/init_prior.m
src/ebFRET/+ebfret/+analysis/+hmm/jitter_filter.m
src/ebFRET/+ebfret/+analysis/+hmm/kl_div.m
src/ebFRET/+ebfret/+analysis/+hmm/m_step.m
src/ebFRET/+ebfret/+analysis/+hmm/report.m
src/ebFRET/+ebfret/+analysis/+hmm/valid_prior.m
src/ebFRET/+ebfret/+analysis/+hmm/vbayes.m
src/ebFRET/+ebfret/+analysis/+hmm/viterbi.m
src/ebFRET/+ebfret/+analysis/+hmm/viterbi_native.m
src/ebFRET/+ebfret/+analysis/+hmm/viterbi_vb.m
src/ebFRET/+ebfret/+batch/ebayes.m
src/ebFRET/+ebfret/+batch/vbayes.m
src/ebFRET/+ebfret/+deps/+datahash/datahash.m
src/ebFRET/+ebfret/+deps/+jsonlab/loadjson.m
src/ebFRET/+ebfret/+deps/+jsonlab/mergestruct.m
src/ebFRET/+ebfret/+deps/+jsonlab/savejson.m
src/ebFRET/+ebfret/+deps/+jsonlab/varargin2struct.m
src/ebFRET/+ebfret/+io/load_json.m
src/ebFRET/+ebfret/+io/load_raw.m
src/ebFRET/+ebfret/+io/load_sf_tracer.m
src/ebFRET/+ebfret/+io/write_json.m
src/ebFRET/+ebfret/+io/write_report.m
src/ebFRET/+ebfret/+io/write_smd.m
src/ebFRET/+ebfret/+io/+smd/create.m
src/ebFRET/+ebfret/+io/+smd/filter.m
src/ebFRET/+ebfret/+io/+smd/hash.m
src/ebFRET/+ebfret/+io/+smd/isvalid.m
src/ebFRET/+ebfret/+io/+smd/merge.m
src/ebFRET/+ebfret/+plot/cat.m
src/ebFRET/+ebfret/+plot/get_bins.m
src/ebFRET/+ebfret/+plot/get_lim.m
src/ebFRET/+ebfret/+plot/line_colors.m
src/ebFRET/+ebfret/+plot/mean.m
src/ebFRET/+ebfret/+plot/named_colors.m
src/ebFRET/+ebfret/+plot/scale.m
src/ebFRET/+ebfret/+plot/spectrum.m
src/ebFRET/+ebfret/+plot/state_dwell.m
src/ebFRET/+ebfret/+plot/state_mean.m
src/ebFRET/+ebfret/+plot/state_obs.m
src/ebFRET/+ebfret/+plot/state_stdev.m
src/ebFRET/+ebfret/+plot/time_series.m
src/ebFRET/+ebfret/+plot/whist.m
src/ebFRET/+ebfret/+python/dev.m
src/ebFRET/+ebfret/+python/python_check_running.m
src/ebFRET/+ebfret/+python/python_close_ebfret.m
src/ebFRET/+ebfret/+python/python_export_traces.m
src/ebFRET/+ebfret/+python/python_get_ebfret_instance.m
src/ebFRET/+ebfret/+python/python_launch_ebfret.m
src/ebFRET/+ebfret/+python/python_load_efficiency_data.m
src/ebFRET/+ebfret/+python/python_load_fret_data.m
src/ebFRET/+ebfret/+python/python_run_ebayes.m
src/ebFRET/+ebfret/+ui/IndexControl.m
src/ebFRET/+ebfret/+ui/PlotPanel.m
src/ebFRET/+ebfret/+ui/+dialog/assign_smd_channels.m
src/ebFRET/+ebfret/+ui/+dialog/init_priors.m
src/ebFRET/+ebfret/+ui/+dialog/remove_bleaching.m
src/ebFRET/+ebfret/+ui/+dialog/select_channels.m
src/ebFRET/+ebfret/+ui/@MainWindow/MainWindow.m
src/ebFRET/+ebfret/+ui/@MainWindow/clip_outliers.m
src/ebFRET/+ebfret/+ui/@MainWindow/close.m
src/ebFRET/+ebfret/+ui/@MainWindow/export_smd.m
src/ebFRET/+ebfret/+ui/@MainWindow/export_summary.m
src/ebFRET/+ebfret/+ui/@MainWindow/export_traces.m
src/ebFRET/+ebfret/+ui/@MainWindow/get_signal.m
src/ebFRET/+ebfret/+ui/@MainWindow/get_ui.m
src/ebFRET/+ebfret/+ui/@MainWindow/init_analysis.m
src/ebFRET/+ebfret/+ui/@MainWindow/init_priors.m
src/ebFRET/+ebfret/+ui/@MainWindow/load_data.m
src/ebFRET/+ebfret/+ui/@MainWindow/refresh.m
src/ebFRET/+ebfret/+ui/@MainWindow/remove_bleaching.m
src/ebFRET/+ebfret/+ui/@MainWindow/reset_analysis.m
src/ebFRET/+ebfret/+ui/@MainWindow/reset_posterior.m
src/ebFRET/+ebfret/+ui/@MainWindow/run_ebayes.m
src/ebFRET/+ebfret/+ui/@MainWindow/run_vbayes.m
src/ebFRET/+ebfret/+ui/@MainWindow/save_data.m
src/ebFRET/+ebfret/+ui/@MainWindow/select_analysis.m
src/ebFRET/+ebfret/+ui/@MainWindow/set_control.m
src/ebFRET/+ebfret/+ui/@MainWindow/update_priors.m