Man page for mkevds
NAME
pymvpa2-mkevds - extract (multi-sample) events from a dataset
SYNOPSIS
pymvpa2
mkevds [
--version] [
-h]
-i DATASET [
DATASET ...] [
--event-attrs ATTR [
ATTR ...]
| --onsets [
TIME [
TIME ...]]
| --csv-events FILENAME | --fsl-ev3 FILENAME [
FILENAME ...]] [
--time-attr ATTR] [
--onset-column ATTR] [
--offset VALUE] [
--duration VALUE] [
--match-strategy {prev,next,closest}] [
--event-compression {mean,median,min,max}] [
--add-sa VALUE [
VALUE ...]] [
--add-fa VALUE [
VALUE ...]] [
--add-sa-txt VALUE [
VALUE ...]] [
--add-fa-txt VALUE [
VALUE ...]] [
--add-sa-attr FILENAME] [
--add-sa-npy VALUE [
VALUE ...]] [
--add-fa-npy VALUE [
VALUE ...]]
-o OUTPUT [
--hdf5-compression TYPE]
DESCRIPTION
Extract (multi-sample) events from a dataset
An arbitrary number of input datasets is loaded from HDF5 storage. All loaded
datasets are concatenated along the samples axis. Based on information about
onset and duration of a sequence of events corresponding samples are extracted
from the input datasets and converted into event samples. It is possible for an
event sample to consist of multiple input samples (i.e. temporal windows).
Events are defined by onset sample ID and number of consecutive samples that
comprise an event. However, events can also be defined as temporal onsets and
durations, which will be translated into sample IDs using time stamp information
in the input datasets.
Analogous to the 'mkds' command the event-related dataset can be extended with
arbitrary feature and sample attributes (one value per event for the latter).
The finished event-related dataset is written to an HDF5 file.
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.
Options for defining events (choose one):
- --event-attrs ATTR [ATTR ...]
-
define events as a unique combinations of values from
a set of sample attributes. Going through all samples
in the order in which they appear in the input
dataset, onset of events are determined by changes in
the combination of attribute values. The length of an
event is determined by the number of identical
consecutive value combinations.
- --onsets [TIME [TIME ...]]
-
reads a list of event onsets (float) from the command
line (space-separated). If this option is given, but
no arguments are provided, onsets will be read from
STDIN (one per line). If --time-attr is also given,
onsets will be interpreted as time stamps, otherwise
they are treated a integer ID of samples.
- --csv-events FILENAME
-
read event information from a CSV table. A variety of
dialects are supported. A CSV file must contain a
header line with field names as a first row. The table
must include an 'onset' column, and can optionally
include an arbitrary number of additional columns
(e.g. duration, target). All values are passed on to
the event-related samples. If '-' is given as a value
the CSV table is read from STDIN.
- --fsl-ev3 FILENAME [FILENAME ...]
-
read event information from a text file in FSL's EV3
format (one event per line, three columns: onset,
duration, intensity). One of more filenames can be
given.
Options for modifying or converting events:
- --time-attr ATTR
-
dataset attribute with time stamps for input samples.
Onset and duration for all events will be converted
using this information. All values are assumed to be
of the same units.
- --onset-column ATTR
-
name of the column in the CSV event table that
indicates event onsets
- --offset VALUE
-
fixed uniform event offset for all events. If no
--time-attr option is given, this value indicates the
number of input samples all event onsets shall be
shifted. If --time-attr is given, this is treated as a
temporal offset that needs to be given in the same
unit as the time stamp attribute (see --time-attr).
- --duration VALUE
-
fixed uniform duration for all events. If no --timeattr option is given, this value indicates the number
of consecutive input samples following an onset that
belong to an event. If --time-attr is given, this is
treated as a temporal duration that needs to be given
in the same unit as the time stamp attribute (see
--time-attr).
- --match-strategy {prev,next,closest}
-
strategy used to match time-based onsets to sample
indices. 'prev' chooses the closes preceding samples,
'next' the closest following sample and 'closest' to
absolute closest sample. Default: 'prev'
- --event-compression {mean,median,min,max}
-
specify whether and how events spanning multiple input
samples shall be compressed. A number of methods can
be chosen. Selecting, for example, 'mean' will yield
the mean of all relevant input samples for an event.
By default (when this option is not given) an event
will comprise of all concatenated input samples.
Options for attributes from the command line:
- --add-sa VALUE [VALUE ...]
-
compose a sample attribute from the command line
input. The first value is the desired attribute name,
the second value is a comma-separated list
(appropriately quoted) of actual attribute values. An
optional third value can be given to specify a data
type. Additional information on defining dataset
attributes on the command line are given in the
section "Compose attributes on the command line.
- --add-fa VALUE [VALUE ...]
-
compose a feature attribute from the command line
input. The first value is the desired attribute name,
the second value is a comma-separated list
(appropriately quoted) of actual attribute values. An
optional third value can be given to specify a data
type. Additional information on defining dataset
attributes on the command line are given in the
section "Compose attributes on the command line.
Options for attributes from text files:
- --add-sa-txt VALUE [VALUE ...]
-
load sample attribute from a text file. The first
value is the desired attribute name, the second value
is the filename the attribute will be loaded from.
Additional values modifying the way the data is loaded
are described in the section "Load data from text
files".
- --add-fa-txt VALUE [VALUE ...]
-
load feature attribute from a text file. The first
value is the desired attribute name, the second value
is the filename the attribute will be loaded from.
Additional values modifying the way the data is loaded
are described in the section "Load data from text
files".
- --add-sa-attr FILENAME
-
load sample attribute values from an legacy
'attributes file'. Column data is read as "literal".
Only two column files ('targets' + 'chunks') without
headers are supported. This option allows for reading
attributes files from early PyMVPA versions.
Options for attributes from stored Numpy arrays:
- --add-sa-npy VALUE [VALUE ...]
-
load sample attribute from a Numpy .npy file.
Compressed files (i.e. .npy.gz) are supported as well.
The first value is the desired attribute name, the
second value is the filename the data will be loaded
from. Additional values modifying the way the data is
loaded are described in the section "Load data from
Numpy NPY files".
- --add-fa-npy VALUE [VALUE ...]
-
load feature attribute from a Numpy .npy file.
Compressed files (i.e. .npy.gz) are supported as well.
The first value is the desired attribute name, the
second value is the filename the data will be loaded
from. Additional values modifying the way the data is
loaded are described in the section "Load data from
Numpy NPY files".
Output options:
- -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
Extract two events comprising of four consecutive samples from a dataset.
-
$ pymvpa2 mkevds --onsets 3 9 --duration 4 -o evds.hdf5 -i 'mydata*.hdf5'
AUTHOR
Written by Michael Hanke & Yaroslav Halchenko, and numerous other contributors.
COPYRIGHT
Copyright © 2006-2016 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
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THE SOFTWARE.