Commit 114bf373 authored by Paul McCarthy's avatar Paul McCarthy 🚵
Browse files

DOC: fixes

parent 4b2fae25
...@@ -314,6 +314,7 @@ def relatedFiles(fname, ftypes=None): ...@@ -314,6 +314,7 @@ def relatedFiles(fname, ftypes=None):
This function assumes that the GIFTI files are named according to a This function assumes that the GIFTI files are named according to a
standard convention - the following conventions are supported: standard convention - the following conventions are supported:
- HCP-style, i.e.: ``<subject>.<hemi>.<type>.<space>.<ftype>.gii`` - HCP-style, i.e.: ``<subject>.<hemi>.<type>.<space>.<ftype>.gii``
- BIDS-style, i.e.: - BIDS-style, i.e.:
``<source_prefix>_hemi-<hemi>[_space-<space>]*_<suffix>.<ftype>.gii`` ``<source_prefix>_hemi-<hemi>[_space-<space>]*_<suffix>.<ftype>.gii``
......
...@@ -1005,7 +1005,7 @@ class Image(Nifti): ...@@ -1005,7 +1005,7 @@ class Image(Nifti):
:arg image: A string containing the name of an image file to load, :arg image: A string containing the name of an image file to load,
or a :mod:`numpy` array, or a :mod:`nibabel` image or a :mod:`numpy` array, or a :mod:`nibabel` image
object, or an ``Image``object. object, or an ``Image`` object.
:arg name: A name for the image. :arg name: A name for the image.
......
...@@ -63,7 +63,7 @@ class SubmitParams(object): ...@@ -63,7 +63,7 @@ class SubmitParams(object):
Any command line script can be submitted by the parameters by calling the `SubmitParams` object: Any command line script can be submitted by the parameters by calling the `SubmitParams` object:
.. codeblock:: python .. code-block:: python
submit = SubmitParams(minutes=1, logdir='log', wait_for=['108023', '108019']) submit = SubmitParams(minutes=1, logdir='log', wait_for=['108023', '108019'])
submit('echo finished') submit('echo finished')
...@@ -71,14 +71,14 @@ class SubmitParams(object): ...@@ -71,14 +71,14 @@ class SubmitParams(object):
This will run "echo finished" with a maximum runtime of 1 minute after the jobs with IDs 108023 and 108019 are finished. This will run "echo finished" with a maximum runtime of 1 minute after the jobs with IDs 108023 and 108019 are finished.
It is the equivalent of It is the equivalent of
.. codeblock:: bash .. code-block:: bash
fsl_sub -T 1 -l log -j 108023,108019 "echo finished" fsl_sub -T 1 -l log -j 108023,108019 "echo finished"
For python scripts that submit themselves to the cluster, it might be useful to give the user some control For python scripts that submit themselves to the cluster, it might be useful to give the user some control
over at least some of the submission parameters. This can be done using: over at least some of the submission parameters. This can be done using:
.. codeblock:: python .. code-block:: python
import argparse import argparse
parser = argparse.ArgumentParser("my script doing awesome stuff") parser = argparse.ArgumentParser("my script doing awesome stuff")
......
...@@ -606,6 +606,7 @@ class FileOrThing(object): ...@@ -606,6 +606,7 @@ class FileOrThing(object):
:arg load: Function which is called to load items for arguments :arg load: Function which is called to load items for arguments
that were set to :data:`LOAD`. Must accept the that were set to :data:`LOAD`. Must accept the
following arguments: following arguments:
- the name of the argument - the name of the argument
- path to the file to be loaded - path to the file to be loaded
......
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