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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
.. code-block:: python
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
.. code-block:: bash
# 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
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