From 96e232c61990052a980f7af378c369e59ba0e4a1 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Wed, 8 May 2019 14:26:10 +0100
Subject: [PATCH] DOC: Fixes/updates in apidoc
---
CHANGELOG.rst | 6 +++---
doc/fsl.scripts.resample_image.rst | 7 +++++++
doc/fsl.scripts.rst | 1 +
doc/fsl.utils.image.resample.rst | 7 +++++++
doc/fsl.utils.image.rst | 12 ++++++++++++
doc/fsl.utils.parse_data.rst | 7 +++++++
doc/fsl.utils.rst | 2 ++
fsl/utils/filetree/query.py | 6 +++---
fsl/utils/image/__init__.py | 2 +-
9 files changed, 43 insertions(+), 7 deletions(-)
create mode 100644 doc/fsl.scripts.resample_image.rst
create mode 100644 doc/fsl.utils.image.resample.rst
create mode 100644 doc/fsl.utils.image.rst
create mode 100644 doc/fsl.utils.parse_data.rst
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 1088480c3..7089e91b8 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -34,7 +34,7 @@ Fixed
^^^^^
-* Minor fixes to some :mod:`.filetree` tree definitions.
+* Minor fixes to some :mod:`.filetree.filetree` tree definitions.
Deprecated
@@ -477,7 +477,7 @@ Changed
* :meth:`.MGHImage` objects now have a :meth:`.MGHImage.save` method.
* Adjustments to the ``conda`` package build and deployment process.
* The :func:`.ImageWrapper.canonicalShape` function has been moved
- to the :mod:`.image` class.
+ to the :mod:`.data.image` class.
* The :func:`.ImageWrapper.naninfrange` function has been moved
into its own :mod:`.naninfrange` module.
@@ -493,7 +493,7 @@ Deprecated
^^^^^^^^^^
-* :func:`.ImageWrapper.canonicalShape` (moved to the :mod:`.image` module)
+* :func:`.ImageWrapper.canonicalShape` (moved to the :mod:`.data.image` module)
* :func:`.ImageWrapper.naninfrange` function (moved to the :mod:`.naninfrange`
module)
diff --git a/doc/fsl.scripts.resample_image.rst b/doc/fsl.scripts.resample_image.rst
new file mode 100644
index 000000000..cf19d5d83
--- /dev/null
+++ b/doc/fsl.scripts.resample_image.rst
@@ -0,0 +1,7 @@
+``fsl.scripts.resample_image``
+==============================
+
+.. automodule:: fsl.scripts.resample_image
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/doc/fsl.scripts.rst b/doc/fsl.scripts.rst
index 2d18375d7..ece0e2b6e 100644
--- a/doc/fsl.scripts.rst
+++ b/doc/fsl.scripts.rst
@@ -9,6 +9,7 @@
fsl.scripts.imcp
fsl.scripts.imglob
fsl.scripts.immv
+ fsl.scripts.resample_image
.. automodule:: fsl.scripts
:members:
diff --git a/doc/fsl.utils.image.resample.rst b/doc/fsl.utils.image.resample.rst
new file mode 100644
index 000000000..d994581a0
--- /dev/null
+++ b/doc/fsl.utils.image.resample.rst
@@ -0,0 +1,7 @@
+``fsl.utils.image.resample``
+============================
+
+.. automodule:: fsl.utils.image.resample
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/doc/fsl.utils.image.rst b/doc/fsl.utils.image.rst
new file mode 100644
index 000000000..7b0ef37d9
--- /dev/null
+++ b/doc/fsl.utils.image.rst
@@ -0,0 +1,12 @@
+``fsl.utils.image``
+===================
+
+.. toctree::
+ :hidden:
+
+ fsl.utils.image.resample
+
+.. automodule:: fsl.utils.image
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/doc/fsl.utils.parse_data.rst b/doc/fsl.utils.parse_data.rst
new file mode 100644
index 000000000..741dfff1e
--- /dev/null
+++ b/doc/fsl.utils.parse_data.rst
@@ -0,0 +1,7 @@
+``fsl.utils.parse_data``
+========================
+
+.. automodule:: fsl.utils.parse_data
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/doc/fsl.utils.rst b/doc/fsl.utils.rst
index 76631a31b..5722c7eb4 100644
--- a/doc/fsl.utils.rst
+++ b/doc/fsl.utils.rst
@@ -12,11 +12,13 @@
fsl.utils.fslsub
fsl.utils.idle
fsl.utils.imcp
+ fsl.utils.image
fsl.utils.memoize
fsl.utils.meta
fsl.utils.naninfrange
fsl.utils.notifier
fsl.utils.path
+ fsl.utils.parse_data
fsl.utils.platform
fsl.utils.run
fsl.utils.settings
diff --git a/fsl/utils/filetree/query.py b/fsl/utils/filetree/query.py
index b1f1f46ed..e54968515 100644
--- a/fsl/utils/filetree/query.py
+++ b/fsl/utils/filetree/query.py
@@ -41,8 +41,8 @@ class FileTreeQuery(object):
a directory for files which match a specific query.
A ``FileTreeQuery`` scans the contents of a directory which is described
- by a :class:`.FileTree`, and identifies all file types (a.k.a. _templates_
- or _short names_) that are present, and the values of variables within each
+ by a :class:`.FileTree`, and identifies all file types (a.k.a. *templates*
+ or *short names*) that are present, and the values of variables within each
short name that are present. The :meth:`query` method can be used to
retrieve files which match a specific short name, and variable values.
@@ -327,7 +327,7 @@ def allVariables(
"""Identifies the ``FileTree`` variables which are actually represented
in files in the directory.
- :arg filetree: The ``FileTree``object
+ :arg filetree: The ``FileTree`` object
:arg matches: list of ``Match`` objects (e.g. as returned by :func:`scan`)
:returns: a tuple containing two dicts:
diff --git a/fsl/utils/image/__init__.py b/fsl/utils/image/__init__.py
index 8e2253364..36bde925d 100644
--- a/fsl/utils/image/__init__.py
+++ b/fsl/utils/image/__init__.py
@@ -9,7 +9,7 @@ manipulating and working with :class:`.Image` objects.
The following modules are available:
-.. autosumary::
+.. autosummary::
:nosignature
.image.resample
--
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