Commit 6bbfb8bc authored by Michael Waskom's avatar Michael Waskom

Merge pull request #138 from mwaskom/update_docs

Prepare for 0.6 release
parents a671d73f 26c051c8
.. _config_file:
The Config File
===============
There are several aspects of how PySurfer looks and behaves that you may
wish to customize but do not want to have to alter every time you
instantiate a Brain object or use the command-line interface. To
facilitate this, PySurfer allows you to set certain options with a
standard Python config file.
When a new Brain object is created (either in a script or via the
command-line), it can read configuration options from one of two places:
first, in the local folder in a file called ``surfer.cfg``, and next in
your home directory, from a file called ``.surfer.cfg``. The file is
divided into the following sections:
Visual
------
*background*
What color the display background should be. (Possible values:
any HTML color name or 256 color hex code.
*cortex*
What colormap should be used for the binarized curvature on the
cortex. (Possible values: any cortical curvature color scheme name.)
*size*
How large the sides of the display window should be (measured in
pixels.) When using this option, the window will be square, and
"size" it will be used for the height and width. (Possible values:
any positive number.)
*width* and *height*
The size of the window. This is an alternative to size, allowing
the width and height to be set independently. (Possible values:
any positive number.)
*default_view*
Which view should be shown at the beginning of a visualization
session. (Possible values: ``lateral``, ``medial``, ``rostral``,
``caudal``, ``dorsal``, ``ventral``, ``frontal``, ``parietal``.)
Overlay
-------
*min_thresh*
What the default minimum threshold should be if not provided when
calling the :meth:`Brain.add_overlay` method. (Possible values: any
float, ``robust_min``, ``actual_min``.)
*max_thresh*
What the default saturation point of the colormap should be if not
provided when calling the :meth:`Brain.add_overlay` method.
(Possible values: any float, ``robust_max``, ``actual_max``.)
Options
-------
*logging_level*
Amount of verbosity to use in outputting status messages.
(Possible values: ``DEBUG``, ``INFO``, ``WARNING``, ``ERROR``.)
......@@ -8,5 +8,3 @@ Detailed Documentation
./command_line
./custom_viz
./split_brain
./config_file
......@@ -60,7 +60,7 @@ parser.add_argument("-sign", default="abs", choices=["abs", "pos", "neg"],
help="overlay sign")
parser.add_argument("-name",
help="name to use for the overlay")
parser.add_argument("-size", default=800,
parser.add_argument("-size", default=800, nargs="?",
help="size of the display window (in pixels)")
parser.add_argument("-background", metavar="COLOR", default="black",
help="background color for display")
......
......@@ -477,7 +477,7 @@ class Brain(object):
# old option "size" sets both width and height
try:
width, height = size
except TypeError:
except (TypeError, ValueError):
width, height = size, size
self._scene_size = height, width
......
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