Automatically parse image files from Opera Phenix imaging experiments

from scportrait.tools.parse import PhenixParser
from scportrait.data._datasets import dataset_parsing_example_flatfield_corrected

input_dir = (
    dataset_parsing_example_flatfield_corrected()
)  # do not need to go to the image directory, the main directory is sufficient

print("Beginning Parsing")
parser = PhenixParser(input_dir, overwrite=True)
parser.parse()
print("Parsing completed.")

Beginning Parsing
Experiment contains the following image channels:
  id         label
0  1  HOECHST33342
1  2      Alexa488

Channel Lookup table saved to file at /Users/sophia/Documents/GitHub/scPortrait/src/scportrait/scportrait_data/parsing_example_flatfield/flat_field_corrected/channel_lookuptable.csv

Parsing XML file from HarmonyV7 version.
Starting copy process...

Copy process completed.
Checking for missing images...
No missing tiles found.
Metadata used to parse images saved to file /Users/sophia/Documents/GitHub/scPortrait/src/scportrait/scportrait_data/parsing_example_flatfield/flat_field_corrected/metadata_image_parsing.csv
Parsing completed.