User corner

Batch processing

It can be convenient to convert several file in a row. Here are two small examples around h52nx that can be reused for other nxtomomill applications.

using python script

In this example we show how to retrieve a list of file to be converted and them convert them one by one

from glob import glob
from nxtomomill.converter import from_h5_to_nx
from nxtomomill.io.config import TomoHDF5Config
from tqdm import tqdm


bliss_files=glob("/home/payno/Datasets/tomography/tomwer/tomwerExtraDatasets/bamboo_hercules//*.h5")
for file_path in bliss_files:
    print(f"start conversion of {file_path}")
    config = TomoHDF5Config()
    config.input_file = file_path
    config.output_file = file_path.replace(".h5", ".nx")
    from_h5_to_nx(
        configuration=config,  # you can tune the conversion using this class
        progress=tqdm(desc="h52nx"),  # used to display advancement
    )

using bash

In this example we show how to retrieve a list of file to be converted and them convert them one by one

# source tomotools environment
source /scisoft/tomotools/activate dev

# list all bliss file to be converted
bliss_files=$(ls -d /data/visitor/{xxx}/RAW_DATA/*/*/*.h5)

for file_path in $bliss_files
do
    echo "start conversion of $file_path"
    nxtomomill h52nx $file_path   # + possible options like config file or inline options
done