xenial (1) pymvpa2-exec.1.gz

NAME

       pymvpa2-exec -  evaluate arbitrary Python expressions for tests and assertions

SYNOPSIS

       pymvpa2  exec  [--version]  [-h]  [-i  [DATASET  [DATASET ...]]] -e EXPR [-s NAME [NAME ...]] [-o OUTPUT]
       [--hdf5-compression TYPE]

DESCRIPTION

       Execute arbitrary Python expressions (on datasets)

       This command can be used to execute arbitrary Python scripts while avoiding unnecessary boilerplate  code
       to load datasets and store results. This command is also useful for testing functionality and results via
       the commandline interface and for asserting arbitrary conditions in scripts.

       First, optional dataset(s) are  loaded  from  one  or  more  sources.  Afterwards  any  number  of  given
       expressions  (see  --exec)  are  executed. An expression can be given as an argument on the command line,
       read from a file, or from STDIN. The return value of any  given  expression  is  ignored  (not  evaluated
       anyhow),  only  exceptions  are  treated  as  errors and cause the command to exit with a non-zero return
       value.  To implement tests and assertions it is best to utilize  a  Python  unittest  framework  such  as
       'nose'.

       In the namespace in which all expressions are evaluated the NumPy module is available via the alias 'np',
       and the nose.tools under the alias 'nt' (if installed). Any loaded datasets are available as a list named
       ``dss``. The first dataset in that list (if any) is available under the name ``ds``.

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.

       -e EXPR, --exec EXPR
              Python expression, or filename of a Python script, or '-' to read expressions from STDIN.

   Output options:
       -s NAME [NAME ...], --store NAME [NAME ...]
              One or more names of variables or  objects  to  extract  from  the  local  name  space  after  all
              expressions  have  been  executed.  They  will  be stored in a dictionary in HDF5 format (requires
              --output).

       -o OUTPUT, --output OUTPUT
              output filename ('.hdf5' extension is added automatically if necessary). NOTE: The  output  format
              is  suitable  for  data  exchange  between  PyMVPA  commands, but is not recommended for long-term
              storage or exchange as its specific content may vary depending on the actual software environment.
              For long-term storage consider conversion into other data formats (see 'dump' command).

       --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

       Assert some condition

              $ pymvpa2 exec -e 'assert(4==4)'

       Check for the presence of a particular sample attribute in a dataset

              $ pymvpa2 exec -e 'dss[0].sa.subj3' -i mydata.hdf5

       Extract and store results

              $ pymvpa2 exec -e 'a=5' -e 'print a' --store a -o mylittlea.hdf5

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.