DOC: typos
Merge pull request #476 from christianmbrodbeck/doc

DOC: typos
WIP mne_kit2fiff: from KIT SQD files to fif files

Here is the beginning of a python implementation of mne_kit2fiff. It is
very much a WIP. Major points to be worked on are:
-channel coil transformation
-channel unit vectors of coord_frame.
-fix dev_head_t
-creating a synthetic trigger channel

FIX: dev_head_t, RM: excess classes, unneccesary methods

Fixed the error in dev_head_t to give proper transformation matrix.
Reduced the number of classes to three main ones:
-sqd_params, RawKIT, coreg.
Added stringdocs to all methods and classes

ENH: layout

Enhances some of the layout. Update to be done for  docstrings to match
style. PEP8 in progress. :)

ADD: test files for troubleshooting and validation

These are all the required files for creating a raw object.
-sns.txt is the sensor locations for KIT-NYU system.
-test.elp is the digitizer laser points from Polhemus.
-test.hsp is the digitizer head shape from Polhemus.
-test.sqd is the datafile acquired from the KIT-NYU system.
-test_Ykgw.mat is a mat file containing the data extracted using the
Yokogawa matlab toolkit. This is to check that the proper data is being
extracted.
-test_marker.txt is the marker coil position within the MEG.

ENH: pep8 correction

STY: update script

MV files to fiff, ADD constants

Update mne/bin/mne_kit2fiff.py

Fix error.

ADD: kit2fiff, ENH: coreg module

ADD: synthetic channel, UPDATE: constants,

ADD: unit vector

UPDATE: ch dict

Make separate package for transforms

RF: invert_transform

DOC

ENH: create translation, rotation and scaling matrices

ENH: apply transform function

ENH: add transforms/coreg module with fit_matched_pts function

ENH: add default to stim and stimthresh

ENH: standardize, new constants

ENH: remove coreg.fit, cleanup

ENH: cleanup, docstrings

FIX: kit2fiff dev-head coregistration

ENH: cosmetics, RM: print

ADD: read_sns, ENH: methods->functions

FIX: orthogonal vector computation

ENH: pep8

FIX: channel info, FIX: mne_kit2fiff command line tool

MV: files to data folder

ADD: test_kit for testing

FIX: sensitivities, and loc

ENH: file info

ADD: test data

ENH: new constants, coreg reader, FIX: new coreg

Coreg class now reads Polhemus data directly. Includes all digitization
points. Fix info.dig dict.

WIP mne_kit2fiff: from KIT SQD files to fif files

Here is the beginning of a python implementation of mne_kit2fiff. It is
very much a WIP. Major points to be worked on are:
-channel coil transformation
-channel unit vectors of coord_frame.
-fix dev_head_t
-creating a synthetic trigger channel

FIX: dev_head_t, RM: excess classes, unneccesary methods

Fixed the error in dev_head_t to give proper transformation matrix.
Reduced the number of classes to three main ones:
-sqd_params, RawKIT, coreg.
Added stringdocs to all methods and classes

ENH: layout

Enhances some of the layout. Update to be done for  docstrings to match
style. PEP8 in progress. :)

ADD: test files for troubleshooting and validation

These are all the required files for creating a raw object.
-sns.txt is the sensor locations for KIT-NYU system.
-test.elp is the digitizer laser points from Polhemus.
-test.hsp is the digitizer head shape from Polhemus.
-test.sqd is the datafile acquired from the KIT-NYU system.
-test_Ykgw.mat is a mat file containing the data extracted using the
Yokogawa matlab toolkit. This is to check that the proper data is being
extracted.
-test_marker.txt is the marker coil position within the MEG.

ENH: pep8 correction

STY: update script

Update mne/bin/mne_kit2fiff.py

Fix error.

MV files to fiff, ADD constants

ADD: kit2fiff, ENH: coreg module

ADD: synthetic channel, UPDATE: constants,

ADD: unit vector

UPDATE: ch dict

ENH: add default to stim and stimthresh

ENH: cleanup, docstrings

FIX: kit2fiff dev-head coregistration

ENH: cosmetics, RM: print

FIX: orthogonal vector computation

ENH: pep8

FIX: channel info, FIX: mne_kit2fiff command line tool

MV: files to data folder

FIX: sensitivities, and loc

ENH: file info

ENH: new constants, coreg reader, FIX: new coreg

Coreg class now reads Polhemus data directly. Includes all digitization
points. Fix info.dig dict.

FIX/ADD: reset_origin

Adds reset_origin function to reorient points centered at mid-distance
of peri-auricular points according to the mne manual, pg. 97.

ENH: downsample based on KIT.DIG_POINTS

FIX: ident, kind in dict

FIX: ch_loc, ENH: test_kit to test ch coil loc, ADD: scale option

ENH: add compability for KIT-NYUAD

ENH: addresses the comments

coreg is now a module of functions.
kit has been condensed and stripped of methods; only relevant Raw
atrributes are added to keep consistency.

Problem to be resolved:
there is a problem with deep copy. Currently there is a hack in place
to deal with it.

ENH: scipy norm instead of numpy FIX: bunch problem

ENH: filter settings read directly from rawfile

ENH: channel names, command line tool, python ref

Standardized channel names.

ENH: added comments for consistency

ENH: addresses all the comments made

RM: sqd_params class
ADD: get_sqd_params function, docstrings
cosmetic changes

RM: unneeded files

ENH: docstring

ENH: added mne_kit2fiff.py to setup.py, exclude test/data in MANIFEST.in

ENH: reduce the test data file

ENH: update fif files for test

ENH: updated fif files for comparison

So, the recently updated test_bin.py had problems loading. It may be a
function of there being too few samples. This has one sec of recording.

ENH: include the file that got away

ENH: modified mrk file

Found a way to have a smaller marker sqd file.

ENH: final changes
ENH: add kwarg to read_raw_kit, rearrange the procedure

PEP8

ENH: cosmetic changes

ENH fit_matched_pts: add tolerance parameter
ENH: remove redundancy, increase efficiency

ENH: remove unnecessary reading

DOC cosmetics
update what's new
ENH: better handle of ref channels in picks

Addresses #415 partially.
FIX: remove unintended sphinx directives
ENH: add change to other pick functions