Command-line interface

Note

You may also call all of these command-line functions from within Python. For instance, to compress a dataset, you would use dclab.cli.compress():

import dclab.cli
dclab.cli.compress(
    path_out="/path/to/compressed_file.rtdc",
    path_in="/path/to/original.rtdc")

For more information please take a look at the code reference of the CLI submodule.

dclab-compress

Create a compressed version of an .rtdc file. This can be used for saving disk space (loss-less compression). The data generated during an experiment is usually not compressed.

usage: dclab-compress [-h] [--force] INPUT OUTPUT

required arguments:

  • INPUT Input path (.rtdc file)

  • OUTPUT Output path (.rtdc file)

optional arguments:

  • --force (disabled by default) Force compression, even if the input dataset is already compressed.

dclab-condense

Reduce an RT-DC measurement to its scalar-only features (i.e. without contour, image, mask, or trace). All available ancillary features are computed.

usage: dclab-condense [-h] INPUT OUTPUT

required arguments:

  • INPUT Input path (.tdms or .rtdc file)

  • OUTPUT Output path (.rtdc file)

dclab-join

Join two or more RT-DC measurements. This will produce one larger .rtdc file. The meta data of the dataset that was recorded earliest will be used in the output file. Please only join datasets that were recorded in the same measurement run.

usage: dclab-join [-h] -o OUTPUT [INPUT [INPUT ...]]

required arguments:

  • INPUT Input paths (.tdms or .rtdc files)

  • OUTPUT Output path (.rtdc file)

dclab-repack

Repack an .rtdc file. The difference to dclab-compress is that no logs are added. Other logs can optionally be stripped away. Repacking also gets rid of old clutter data (e.g. previous metadata stored in the HDF5 file).

usage: dclab-repack [-h] [--strip-logs] INPUT OUTPUT

required arguments:

  • INPUT Input path (.rtdc file)

  • OUTPUT Output path (.rtdc file)

optional arguments:

  • --strip-logs (disabled by default) Do not copy any logs to the output file.

dclab-split

Split an RT-DC measurement file (.tdms or .rtdc) into multiple smaller .rtdc files.

usage: dclab-split [-h] [--path_out PATH_OUT] [--split-events SPLIT_EVENTS]
                   [--include-empty-boundary-images]
                   PATH_IN

required arguments:

  • PATH_IN Input path (.tdms or .rtdc file)

optional arguments:

  • --path_out (default: SAME) Output directory (defaults to same directory)

  • --split-events (default: 10000) Maximum number of events in each output file

  • --include-empty-boundary-images (disabled by default) In old versions of Shape-In, the first or last images were sometimes not stored in the resulting .avi file. In dclab, such images are represented as zero-valued images. Set this option, if you wish to include these events with empty image data.

dclab-tdms2rtdc

Convert RT-DC .tdms files to the hdf5-based .rtdc file format. Note: Do not delete original .tdms files after conversion. The conversion might be incomplete.

usage: dclab-tdms2rtdc [-h] [--compute-ancillary-features]
                       [--include-empty-boundary-images]
                       TDMS_PATH RTDC_PATH

required arguments:

  • TDMS_PATH Input path (tdms file or folder containing tdms files)

  • RTDC_PATH Output path (file or folder), existing data will be overridden

optional arguments:

  • --compute-ancillary-features (disabled by default) Compute features, such as volume or emodulus, that are otherwise computed on-the-fly. Use this if you want to minimize analysis time in e.g. Shape-Out. CAUTION: ancillary feature recipes might be subject to change (e.g. if an error is found in the recipe). Disabling this option maximizes compatibility with future versions and allows to isolate the original data.

  • --include-empty-boundary-images (disabled by default) In old versions of Shape-In, the first or last images were sometimes not stored in the resulting .avi file. In dclab, such images are represented as zero-valued images. Set this option, if you wish to include these events with empty image data.

dclab-verify-dataset

Check experimental datasets for completeness. This command is used e.g. to enforce data integrity with Shape-In. The following exit codes are defined: 0: valid dataset, 1: alerts encountered, 2: violations encountered, 3: alerts and violations, 4: other error.

usage: dclab-verify-dataset [-h] PATH

required arguments:

  • PATH Path to experimental dataset