pvc-export 0.0.1.2023.6.28.1635

Implen spectra export(er)

Intention:

• extract XY (absorption spectrum) data from PVC wavescan files created by "Implen NanoPhotometer Pearl P300"
• export the data as a "CSV" (TAB-separated) table, original and smoothed
• find most prominent peaks in the spectrum and export them as a separate CSV table
• plot the data and save the image
• support loading of multiple PVC files, plotting them together in one figure and exporting them into a single table
• if a custom configuration file (*.yaml) provided (by the-coption), read it, merge it with the default configuration and use to style the plot(s)
• if requested (by the--ccoption), create a custom configuration file template

Implementation:

• Import the default configuration from cfg.py as dict cfg
• Read a custom config and merge it with the default one, reconstruct missing values
• XY (absorption spectrum) array in PVC file is on the line starting with '$PVC '
  Find and read the line, reshape the array, apply transformations specified in the config file
• Create a dict data holding all the read data and merged configuration
• Use scipy.signal.savgol_filter() to smooth the raw data
• Usescipy.signal.find_peaks()to find peaks in spectra
• Plot loaded data on matplotlib.Figure() , reserve a large part of the figure for the plot descriptions,
  so that most of the images created with this tool have the same dimensions of the plot area.
• Create Pillow.Image() from the figure.
• Remove excessive white borders from the image with Pillow.Image.crop()
• Add borders (padding) of the size defined by config.
• Save (export) the figure image and CSV files with the loaded data

Installation:

• Either install the package directly from pypi
  pipx install pvc-export,
• Or download a .whl file from the latest release page
  and install the package from the file
  pipx install <the-downloaded-file>.whl
• In command shell, the script can be started with
  pvc-export or python3 -m pvc_export
• In Windows, to add right click menu actions for PVC and YAML files,
  consult the included win-install.reg file.
  Note that the suggested approach does not support combining multiple files into a single figure or CSV table via the right-click menu.

Some command line examples:

pvc-export *.pvc
    => from all found *.pvc files produce:
    export.png       - figure
    export.csv       - plot data
    export.peaks.csv - peaks data

pvc-export *.pvc -e <name>
    => from all found *.pvc files produce:
    <name>.png       - figure
    <name>.csv       - plot data
    <name>.peaks.csv - peaks data

pvc-export --cc "config"
    => create "config.yaml" template,
    do not export figure or data

pvc-export *.pvc --cc "config"
    => create "config.yaml" listing inside all found *.pvc files with the default styles assigned,
    do not export figure or data

pvc-export -c "config.yaml"
    => use "config.yaml" to save
    figure, plot data, and peaks data with the styles and locations defined inside "config.yaml"

pvc-export *.pvc -c "config.yaml"
    => use "config.yaml" for styles and locations to save all found .pvc files
    <name>.png       - figure,
    <name>.csv       - plot data,
    <name>.peaks.csv - peaks data,
    where <name> is set in advance in CONFIG:export:path

Variables, like "$HOME", and globs, like "*", are expanded in *.pvc file names, "~" is not.
Globs are only expanded if a file path is not absolute.