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This is a repo for a Python based application to open SMS .h5 files, and perform the initial analysis and exporting.

Home Page: https://up-biophysics-sms.readthedocs.io/en/latest/index.html

License: Other

Python 99.24% MATLAB 0.43% Jupyter Notebook 0.21% Inno Setup 0.12%
analysis change-point-detection fluorescence fluorescence-intensity fluorescence-lifetime fluorescence-spectra hdf5 intensity-level-grouping lifetime-fitting photon-burst-detection pyqt5-gui python python3 single-molecule spectroscopy tcspc time-correlated-single-photon time-taged-time-resolved tttr

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full_sms's Issues

Fitting results not showing

Fitting results for the lifetime of a particle isn't displayed in the box on the right-hand side if more than one exponential
function is used for the fit. A measured IRF was loaded which was successful.
Error message in dialog window:
"unsupported format string passed to numpy.ndarray.__format__"

Raised by Francios by email

Cannot run main.py

Issue trying to run software from source. Windows 10, python 3.9.

Created new environment and installed packages listed in installation instructions
https://up-biophysics-sms.readthedocs.io/en/latest/usage/installation.html

cloned source code from git hub

python main.py in \src directory gives the following error:

Currently used style: QWindowsVistaStyle
Available styles: ['windowsvista', 'Windows', 'Fusion']
2024-05-16 13:11:02,192 -> MainThread -> main -> main: App created
2024-05-16 13:11:02,192 -> MainThread -> main -> __init__: Multi-threading with maximum 8 threads
2024-05-16 13:11:02,192 -> MainThread -> main -> __init__: System -> Windows
Process Process-1:
Traceback (most recent call last):
  File "\miniconda3\envs\fullsms\lib\multiprocessing\process.py", line 315, in _bootstrap
    self.run()
  File "\miniconda3\envs\fullsms\lib\multiprocessing\process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "\Full_SMS\src\main.py", line 1526, in main
    main_window = MainWindow()
  File "\Full_SMS\src\main.py", line 146, in __init__
    self.spectra_controller = SpectraController(main_window=self)
  File "\Full_SMS\src\controllers.py", line 3188, in __init__
    self.main_window.pgSpectra_Image_View = pg.ImageView(view=pg.PlotItem(), roi=myPlotROI(size=(10, 200)))
TypeError: __init__() got an unexpected keyword argument 'roi'

Exporting once breaks further exporting

After exporting one file of fitting results to a folder it becomes impossible to do so again if the program isn't restarted.
Error message in dialog window:
"QObject::setParent: Cannot set parent, new parent is in a different thread"

Raised by Francios by email

Fits not included in exported file

When exporting the fitting results using the Export tab the Durbin-Watson parameters of the fits aren't included in the exported file.

Raised by Francios by email

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