Opus converter

Script which helps to gather a folder of .0 files into a mat, csv or npy file. At this time it saves only AB section (raw spectra).

Requirements

Python 3

pip install numpy scipy pandas opusFC

Quick reference

usage: opus_converter.py [-h] [-f {mat,csv,npy}] [-one] [-s] [-fix] [-drop]
                         [-sep SEPARATOR] [-depth SEARCH_DEPTH] [--debug] [-q]
                         [-out OUTPUT_DIRECTORY] [-i] [-u]
                         directory

Utility for converting files from OPUS format .0 to .mat;.csv;.npy

positional arguments:
  directory             directory where to start the search

optional arguments:
  -h, --help            show this help message and exit
  -f {mat,csv,npy}, --format {mat,csv,npy}
  -one, --one-file       pack all information into one csv file (doesn't work
                        with another formats)
  -s, --split           splits sample name with --separator into columns
  -fix, --fix-table     fixes table after splitting by inserting empty cells
  -drop, --drop-last-column
                        drops last column if split was used (usually position
                        column)
  -sep SEPARATOR, --separator SEPARATOR
                        separator which used to split sample name if --split
                        is used
  -depth SEARCH_DEPTH, --search-depth SEARCH_DEPTH
  --debug
  -q, --quiet
  -out OUTPUT_DIRECTORY, --output-directory OUTPUT_DIRECTORY
  -i, --save-inplace    save result files in folder with spectra
  -u, --update          rewrites files which already exist

Examples

python opus_converter.py .
python opus_converter.py ./my_experiments

# for windows, %userprofile% is a windows variable for the current user folder
# this will find all .0 in folder C:\\Users\\current_user\\my_experiments and 
# save results into folder C:\\Users\\current_user\\my_experiments\\converted
# the maximum depth of search 3 folders.
python opus_converter.py "%USERPROFILE%/my_experiments" -out "%USERPROFILE%/my_experiments/converted"

# This will convert into one .csv file and also will split the name of file with 
# separator _
python opus_converter.py . -f csv --onefile --split

Explanation

In order to run script you should write python opus_converter.py start_folder. Where start_folder is a folder where search will start. If you want to start it in current directory you can just type . (point), that usually means current directory.

By default it doesn't go deeper than 3 folders. You can change the depth of search by passing parameter -depth n. By default it will convert into one .mat file. You can select a format by passing parameter -f format, where format can be mat, csv or npy.

Csv is the format that can be read by Excel. By default it will create 3 separate files for each folder: spectra.csv, labels.csv, wavenumbers.csv. In order to get all information in one file pass parameter -one or --onefile.

By default it creates only one column called sample_name in which it stores the name of .0 file with spectrum. It is also possible to automatically split the name of sample into another columns, e.g. Exp1_apple_3ml will be splitted into 3 columns Exp1, apple, 3ml, with names column0, column1, column2. If you want to enable split option then you need to pass -s or --split. You can also specify a separator by passing parameter -sep _ or --separator _

By default all output files will be saved in current directory, but you can specify output directory by passing -out directory. You can also save output files together with corresponded .0 files by passing -i or --save-inplace.

By default it will not rewrite result files if they exist. In order to enable this specify -u or --update

By default you will see a lot of information, in order to see only error pass -q or --quiet.