xenial (1) pymvpa2-dump.1.gz

NAME

       pymvpa2-dump -  export dataset components into other (file) formats

SYNOPSIS

       pymvpa2 dump [--version] [-h] -i DATASET [DATASET ...] [-s | --sa SA | --fa FA | --da DA] [-o OUTPUT] [-f
       {hdf5,nifti,npy,txt}] [--mapper-dataset DATASET [DATASET ...]] [--hdf5-compression TYPE]

DESCRIPTION

       Dump dataset components in various formats

       A single  arbitrary  dataset  component  (sample  data,  sample  attribute,  feature  attribute,  dataset
       attribute)  can  be  selected  and  exported  into  another format. A list of supported formats and their
       respective capabilities is below.

       PLAIN TEXT OUTPUT

       1D and 2D numerical data can be export as plain text. In addition lists of strings are supported as well.
       Typically  data  is  exported  with  one  element per line is, except for 2D numerical matrices, where an
       entire row is written on a single line (space-separated).

       For all unsupported data a warning is issued and a truncated textual description of the dataset component
       is given.

       HDF5 STORAGE

       Arbitrary  data  (types)  can be stored in HDF5 containers. For simple data that is natively supported by
       HDF5 a top-level HDF5 dataset is created and contains all data.  Complex,  not  natively  supported  data
       types are serialized before stored in HDF5.

       NUMPY'S NPY BINARY FILES

       This data format is for storing numerical data (with arbitrary number of dimensions in binary format).

       NIFTI FILES

       This  data format is for (multi-dimensional) spatial images. Input datasets should have a mapper that can
       reverse-map the corresponding dataset component back into the image space.

OPTIONS

       --version
              show program's version and license information and exit

       -h, --help, --help-np
              show this help message and exit. --help-np forcefully disables the use of a pager  for  displaying
              the help.

       -i DATASET [DATASET ...], --input DATASET [DATASET ...]
              path(s)  to  one  or  more PyMVPA dataset files. All datasets will be merged into a single dataset
              (vstack'ed) in order of specification. In some cases this option may need  to  be  specified  more
              than once if multiple, but separate, input datasets are required.

       -o OUTPUT, --output OUTPUT
              output  filename.  If no output file name is given output will be directed to stdout, if permitted
              by the data format

       -f {hdf5,nifti,npy,txt}, --format {hdf5,nifti,npy,txt}
              output format

       --mapper-dataset DATASET [DATASET ...]
              path to a PyMVPA dataset whose mapper should be used for reverse mapping features into  volumetric
              space for NIfTI export. By default the mapper in the input dataset is used.

   Options for selecting dataset components:
       -s, --samples
              dump the dataset samples.

       --sa SA
              name of the sample attribute to be dumped.

       --fa FA
              name of the feature attribute to be dumped.

       --da DA
              name of the dataset attribute to be dumped.

   Option for HDF5 output:
       --hdf5-compression TYPE
              compression  type  for  HDF5  storage.  Available values depend on the specific HDF5 installation.
              Typical values are: 'gzip', 'lzf', 'szip', or integers from 1 to  9  indicating  gzip  compression
              levels.

EXAMPLES

       Print a sample attribute

              $ pymvpa2 dump -i mydata.hdf5 --sa subj

       Export the sample data array into NumPy's .npy format

              $ pymvpa2 dump -i mydata.hdf5 -s -f npy -d mysamples.npy

AUTHOR

       Written by Michael Hanke & Yaroslav Halchenko, and numerous other contributors.

COPYRIGHT

       Copyright © 2006-2015 PyMVPA developers

       Permission  is  hereby  granted,  free  of  charge,  to  any person obtaining a copy of this software and
       associated documentation files (the "Software"), to deal in the Software without  restriction,  including
       without  limitation  the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
       copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to  the
       following conditions:

       The  above  copyright  notice  and  this permission notice shall be included in all copies or substantial
       portions of the Software.

       THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR  IMPLIED,  INCLUDING  BUT  NOT
       LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO
       EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
       IN  AN  ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
       THE USE OR OTHER DEALINGS IN THE SOFTWARE.