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TCFile python package

A basic image processing tool of tomocube data.

Installation

pip install TCFile

Use case

from TCFile import TCFile

tcfile = TCFile('test.TCF','3D') # ready for return 3D RI images
print(f"number of snapshots : {len(tcfile)}")

## Usage 1: handling each snapshots (numpy array)
data = tcfile[0]
print(f"shape of data : {data.shape}")
# or
for data in tcfile:
    # do some operations on the data ...
    pass

## Usage 2: handling fluorescence array
tcfile_fl = TCFile('test.TCF','3DFL')
fl_data = tcfile_fl[0]

## Usage 2: handling dask array
data = tcfile.asdask() # (T, Z, Y, X) array

Limitation

It does not support TCF writer due to the difficulty of configuring metadata and interoperability with commercial Tomocube software.

TODO

  • rigorous tests
  • TCFile converter

Any suggestions and comments are welcome!

Test

# install this package in editable mode
git clone https://github.com/ehgus/TCFile.git
cd TCFile
pip install -e .
# execute pytest
pytest