Command-Line Examples

Location of the binary

If you use the gradle build inside /path/to/sqy/repo, the sqy binary will be located at /path/to/sqy/repo/build/cpp/src/sqy after a successfull build. All of the following recommendations and documentation assumes that the path of sqy is setup in your current shell sesion, so that

$ sqy

will produce the sqy help successfully.

Encoding a tiff stack

To encode a tiff stack (currently only 16-bit and 8-bit encoded stacks are supported), simply do:

$ sqy enc data.tif

This assumes that data.tif contains one 3D stack where each frame is saved as it’s own TIFFDirectory. This command uses the default sqeazy pipeline “bitswap1->lz4”. Upon success, this will produce a file called data.sqy in the same directory where data.tif resides. Note, that this is a custom data format of sqeazy. If you’d like to produce the same into an hdf5 file, just use:

$ sqy enc -e ".h5" data.tif

which will produce data.h5. This produces data.h5 which will contain a dataset called sqy_stack. To change the dataset name to something meaningful like helloworld, do

$ sqy enc -e ".h5" -d "helloworld" data.tif

Inspect the produced hdf5 file with (assuming that hdf5 tools is in your PATH):

$ h5ls data.h5 
helloworld               Dataset {65, 42, 47}

Decoding a compressed sqeazy file

Decoding of both the native format as well as the hdf5 format is supported. To decode a stack, just do

$ sqy dec data.sqy

or

$ sqy dec data.h5

this will produce/overwrite data.tif. If you’d like to unpack to anything else than data.tif, use the -o flag:

$ sqy dec -o helloworld.tif data.h5

In case a hdf5 file contains multiple datasets, you can select the data set to decode manually:

$ sqy dec -d "helloworld" -o helloworld.tif data.h5