agenda.md

GENERAL NOTES / KEY FEATURES

• Figure out how to integrate dialogues with point picking
• Use numpy for chromatogram data (?)
• Fix peaks table
  • https://pandas.pydata.org/docs/reference/api/pandas.plotting.table.html
  • https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.table.html
  • Probably going to need to decouple from window
• Add functionality for editing chromatogram names
• py2exe (?)
  • Ideally I want something that can install a version of python then run requirements.py
• Create custom exceptions
  • Warnings for bad inputs?
• Test referencing/normalization
• Test threshold autopicking
• Version numbering

ERROR HANDLING

• Add some bug-proofing logic to one-point picking (what if the user selects a valley or a featureless region)
• Write a better version of str.isnumeric():
  • try to convert to a float; except return false
  • possibly keep this function and validate in a separate .py file

QUALITY OF LIFE FEATURES

• "Restore defaults" option for EditChromatogram dialogue
• Keyboard shortcuts
• Chain peak picking
• Allow deleting/editing picked peaks
• Update peaks by changing values on table
• Still allow manually setting peak bounds
• Help menu
• Settings menu
• Add support for other types of data file (though I would need a sample to inspect)

UI FEATURES

• Add tooltips
• Change chromatogram order in stack
• Add a text box for printed output
• Add a crosshair cursor
  • https://stackoverflow.com/questions/63195460/how-to-have-a-fast-crosshair-mouse-cursor-for-subplots-in-matplotlib
• Dialog menus
  • Add dialogue options for all currently available analysis/peak methods
  • Add radio button subclass for methods like Chromatogram.normalize()
  • Custom class for peak picking (bounds, area mode)
  • Add title argument to dialogue class
  • http://www.java2s.com/Code/Python/GUI-Tk/Popupdialogbuildadialog.htm
• Label peak retention time and area on figure
• Highlight picked peaks (maybe plot them as separate objects with a fixed color)
• Use icons for buttons (steal them from MestReNova?)
• Color (links for reference)
  • https://stackoverflow.com/questions/42697933/colormap-with-maximum-distinguishable-colours
  • https://projects.susielu.com/viz-palette

ANALYTICAL FEATURES

• Capacity factor
• Read time scale from data file
• Chromatogram signal addition and subtraction (remove reference peaks)
• Noise and S/N ratio
• Empirically determine a better default value for NOISE_TOLERANCE
• Fix bug: plate count changes with time rescaling

SAVING/LOADING CHROMATOGRAMS

• JSON?

• Default file names

• Export plot and table to PDF

• Create a standard for saving data (similar to ascii data but with peak data, offset, scale, etc saved as well)

  • There might be a module that easily saves/loads variables
  • In that case, just export the history object and load it back in?

• reimplement plotly for exporting nice interactable chromatograms

• plt.savefig('D:\mpl_logo_with_title.png', dpi=dpi)

SETTINGS

• Default integration mode
• Error logging
• Choose derivative calculation mode (left slope, right slope, lr average)

KNOWN BUGS

• "instance.top.protocol("WM_DELETE_WINDOW", instance.cancel)" in dialogues.py does not result in instance.cancel() being called on closing out of the popup.

• When trying to undo importing the first chromatogram: Exception in Tkinter callback Traceback (most recent call last): File "C:\ProgramData\Anaconda3\lib\tkinter_init_.py", line 1892, in call return self.func(*args) File "C:\Users\epics\Documents\Code\MChroma\MChroma\main.py", line 89, in undo self.present().active().plot() File "C:\Users\epics\Documents\Code\MChroma\MChroma\main.py", line 61, in active return self.chromatograms[self.active_index] IndexError: list index out of range

• Figure scaling is really gimpy: the peak table gets cut off, and resizing the window seems to resize the plot more than the table.