pymvpa2-dump - Online in the Cloud

PROGRAM:

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

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