Run:
pip install .
to install this package.
cif2lmdb can be used as follows:
Usage: cif2lmdb [OPTIONS] CIF
Options:
--output FILE Output filename. If not set, cif-filename is taken with
lmdb extension.
--channels INTEGER Images from these channels will be extracted. Default is
to extract all. 1-based index.
--names TEXT Names to assign to channels.
--debug Show debugging information. Limits output to 100 first
cells.
--overwrite Overwrite lmdb if it exists.
--targets-npy FILE Numpy binary file containing targets.
--skip-npy FILE Numpy binary file containing instances to be skipped.
--help Show this message and exit.
Here is an example command:
cif2lmdb --channels 1 --channels 6 --channels 9 --names BF --names SSC --names BF2 --output tmp.lmdb --debug --overwrite input.cif
It takes input.cif as input and outputs output.lmdb, an lmdb-file containing 100 (see debug flag) 3-channel images with names BF, SSC and BF2.
Please see the imglmdb.ipynb notebook for usage examples of the imglmdb package.
Docker images are available for cif2lmdb (tag cif2lmdb), the jupyter lab environment (tag jupyter-lab-env), and the notebooks in this repository (tag notebooks).
For using cif2lmdb, run:
docker run --rm -v /path/to/data/dir:/data maximlippeveld/ifcimglib:cif2lmdb [OPTIONS] /data/example.cif
For using the jupyter environment, run:
docker run --it -v /path/to/data/dir:/data -v /path/to/your/code/dir:/app -p [your-port]:8888 maximlippeveld/ifcimglib:jupyter-lab-env
Fur using the notebooks in this repository, run:
docker run --it -v /path/to/data/dir:/data -p [your-port]:8888 maximlippeveld/ifcimglib:notebooks