Commit a0ea64ae authored by Paul McCarthy's avatar Paul McCarthy 🚵
Browse files

Merge branch 'mnt/doc' into 'master'

Mnt/doc

See merge request fsl/fslpy!239
parents 56bf8834 d8b2a0fb
...@@ -2,6 +2,18 @@ This document contains the ``fslpy`` release history in reverse chronological ...@@ -2,6 +2,18 @@ This document contains the ``fslpy`` release history in reverse chronological
order. order.
3.2.1 (Tuesday 23rd June 2020)
------------------------------
Changed
^^^^^^^
* Minor updates to documentation.
3.2.0 (Thursday 11th June 2020) 3.2.0 (Thursday 11th June 2020)
------------------------------- -------------------------------
......
...@@ -361,26 +361,12 @@ epub_exclude_files = ['search.html'] ...@@ -361,26 +361,12 @@ epub_exclude_files = ['search.html']
# special-members flag) # special-members flag)
autoclass_content = 'class' autoclass_content = 'class'
# Document private members and special members (e.g. __init__)
autodoc_default_flags = ['private-members', 'special-members']
# Documentation for python modules is in the same order autodoc_default_options = {
# as the source code. 'special-members' : True,
autodoc_member_order = 'bysource' 'private-members' : True,
'undoc-members' : True,
def autodoc_skip_member(app, what, name, obj, skip, options): 'member-order' : 'bysource',
}
# Do not document the _sync_* properties
# that are added by the props package to
# all SyncableHasProperties classes.
if what == 'class':
attName = name.split('.')[-1]
return skip or attName.startswith('_sync_')
return skip or False
def setup(app):
app.connect('autodoc-skip-member', autodoc_skip_member)
graphviz_output_format = 'svg' graphviz_output_format = 'svg'
...@@ -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.
......
...@@ -82,6 +82,12 @@ the reference image, and may contain: ...@@ -82,6 +82,12 @@ the reference image, and may contain:
the source image coordinates which correspond to those reference image the source image coordinates which correspond to those reference image
coordinates. coordinates.
.. note:: FNIRT deformation field files give no indication as to whether they
contain relative displacements or absolute coordinates, so heuristics
must be used to infer what is stored in a a particular file. The
:func:`.nonlinear.detectDeformationType` function can be used to
determine whether a file contains relative displacements or absolute
coordinates.
If an initial linear registration was used as the starting point for FNIRT, If an initial linear registration was used as the starting point for FNIRT,
this is encoded into the displacements/coordinates themselves, so they can be this is encoded into the displacements/coordinates themselves, so they can be
......
...@@ -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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