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teraconverter documentation incomplete #3

Open fcollman opened 7 years ago

fcollman commented 7 years ago

in particular the executable gives this documentation, which doesn't map to the web.

Also In particular, the --halve option isn't explained what integers map to which options?

USAGE:

./teraconverter -s= [-d=] [--mdata_fname=] [--ch_dir=] [--depth=] [--height=] [--width=] --sfmt= --dfmt= [--resolutions=] [--halve=] [-f=] [--info=] [--noprogressbar] [--verbose] [--V0=] [--V1=] [--H0=] [--H1=] [--D0=] [--D1=] [--isotropic] [--parallel] [--makedirs] [--metadata] [--algorithm=] ... [-p] [--imin_plugin=] [--imin_plugin_params=] [--imout_plugin=] [--imout_plugin_params=] [--dsfactor=] [--timeseries] [--libtiff_uncompress] [--libtiff_rowsperstrip=] [--] [--version] [-h]

Where:

-s=, --src= (required) Source file / root directory path.

-d=, --dst= Destination root directory path.

--mdata_fname= File containing general metadata of the image.

--ch_dir= subdirectory to store the channel (single channel in tiled 4D format only).

--depth= Slice depth.

--height= Slice height.

--width= Slice width.

--sfmt= (required) Source format ("Vaa3D raw"/"Vaa3D raw (series, 2D)"/"Vaa3D raw (tiled, 3D)"/"Vaa3D raw (tiled, 4D)"/"TIFF (3D)"/"TIFF (series, 2D)"/"TIFF (tiled, 2D)"/"TIFF (tiled, 3D)"/"TIFF (tiled, 4D)"/"TIFF (unstitched, 3D)"/"HDF5 (BigDataViewer)"/"HDF5 (Imaris IMS)"/"Mapped Volume")

--dfmt= (required) Destination format ("Vaa3D raw (series, 2D)"/"Vaa3D raw (tiled, 3D)"/"Vaa3D raw (tiled, 4D)"/"TIFF (series, 2D)"/"TIFF (tiled, 2D)"/"TIFF (tiled, 3D)"/"TIFF (tiled, 4D)"/"HDF5 (BigDataViewer)"/"HDF5 (Imaris IMS)")

--resolutions= Resolutions to be produced. Possible values are [[i]...] where i = 0 ,..,5 and 2^i is the subsampling factor.

--halve= Halving method (mean/max, default: mean).

-f=, --outFmt= Voxel format (graylevel or RGB (default)/intensity.

--info= File path of the info file to be saved.

--noprogressbar Disables progress bar and estimated time remaining

--verbose set verbosity to maximum level (to be activated ONLY for debugging)

--V0= First V vertex (included).

--V1= Last V vertex (excluded).

--H0= First H vertex (included).

--H1= Last H vertex (excluded).

--D0= First D vertex (included).

--D1= Last D vertex (excluded).

--isotropic Generate lowest resolution with voxels as much isotropic as possible. Use this flag when the high resolution image has highy anistropic voxels

--parallel Does not perform side-effect operations during the merge step. Use this flag when more merge steps are launched in parallel

--makedirs Creates the mdata.bin file of the output volume.

--metadata Creates the directory hierarchy.

--algorithm= (accepted multiple times) Forces the use of the given algorithm.

-p, --pluginsinfo Display plugins informations

--imin_plugin= Plugin that manages the input image format. Available plugins are: {"tiff2D", "IMS_HDF5", "tiff3D"}. Default is "auto".

--imin_plugin_params= A series of parameters "param1=val,param2=val,..." to configure the input image plugin (see --pluginsinfo for the list of accepted parameters)

--imout_plugin= Plugin that manages the output image format. Available plugins are: {"tiff2D", "IMS_HDF5", "tiff3D"}. Default is "auto".

--imout_plugin_params= A series of parameters "param1=val,param2=val,..." to configure the output image plugin (see --pluginsinfo for the list of accepted parameters)

--dsfactor= Dowsampling factor to be used to read the source volume (only for serie of 2D slices).

--timeseries The input is a time series.

--libtiff_uncompress Configure libtiff library to not compress output files (default: compression enabled).

--libtiff_rowsperstrip= Configure libtiff library to pack n rows per strip when compression is enabled (default: 1 row per strip).

--, --ignore_rest Ignores the rest of the labeled arguments following this flag.

--version Displays version information and exits.

-h, --help Displays usage information and exits.

abria commented 7 years ago

Hi,

you can find a more detailed usage guide for TeraConverter on the TeraStitcher wiki, see the TeraTools guide on the right menu.

The reason why not all options are on the web, is because those options are for internal / advanced / experimental use. We did not want to make the tool more complex than it is. That's also why the GUI version in Vaa3D has even fewer options than the command line.