dclab

0.71.8 verified Fri May 01 auth: no python

Library for real-time deformability cytometry (RT-DC) data analysis. Provides data loading, filtering, and normalization for deformability cytometry datasets. Current version 0.71.8, requires Python >=3.9, <4. Released about every 3-6 months on PyPI.

pip install dclab

Common errors

error ModuleNotFoundError: No module named 'dclab' ↓

cause dclab not installed or virtual environment not activated.

fix

Run pip install dclab or conda install -c conda-forge dclab.

error ValueError: File format not recognized. ↓

cause The file provided to `new_dataset` is not a valid .rtdc, .tdms, or .h5 file.

fix

Ensure the file has the correct extension and is valid. Use dclab.rtdc_dataset.RTDCFile for low-level checks.

Warnings

breaking In version 0.70.0, the `filter` module was restructured. `dclab.filter.xxx` is no longer available; use `dclab.features` and `dclab.features.xxx` instead. ↓

fix Replace `from dclab.filter import ...` with `from dclab.features import ...`.

breaking Python 3.9 support dropped in version 0.72.0 (upcoming). Currently requires Python >=3.9; future versions will require >=3.10. ↓

fix Update Python environment to 3.10 or later.

gotcha `new_dataset` fails silently if the file format is unsupported. It will raise a `ValueError` only if the file cannot be parsed at all. ↓

fix Always wrap `new_dataset` in a try/except block to catch `ValueError` and `OSError`.

Imports

RTDCBase
```
from dclab.rtdc_dataset import RTDCBase
```
RTDCBase is the base class for datasets; use for type checking.
new_dataset
wrong
```
import dclab.dclab
```
correct
```
from dclab import new_dataset
```
new_dataset is a top-level function; do not import from submodule.

Quickstart

Load an RT-DC dataset from a .rtdc file and print the first five area values.

import dclab
from dclab import new_dataset

ds = new_dataset('path/to/file.rtdc')
print(ds)
# Access features:
area_um = ds['area_um']
print('Area (um^2):', area_um[:5])