mne.Projection#
- class mne.Projection(*, data, desc='', kind=1(FIFFV_PROJ_ITEM_FIELD), active=False, explained_var=None)[source]#
Dictionary-like object holding a projection vector.
Projection vectors are stored in a list in
inst.info["projs"]
. Each projection vector has 5 keys:active
,data
,desc
,explained_var
,kind
.Warning
This class is generally not meant to be instantiated directly, use
compute_proj_*
functions instead.- Parameters:
Methods
plot_topomap
(info, *[, sensors, show_names, ...])Plot topographic maps of SSP projections.
- plot_topomap(info, *, sensors=True, show_names=False, contours=6, outlines='head', sphere=None, image_interp='cubic', extrapolate='auto', border='mean', res=64, size=1, cmap=None, vlim=(None, None), cnorm=None, colorbar=False, cbar_fmt='%3.1f', units=None, axes=None, show=True)[source]#
Plot topographic maps of SSP projections.
- Parameters:
- info
mne.Info
The
mne.Info
object with information about the sensors and methods of measurement. Used to determine the layout.- sensorsbool |
str
Whether to add markers for sensor locations. If
str
, should be a valid matplotlib format string (e.g.,'r+'
for red plusses, see the Notes section ofplot()
). IfTrue
(the default), black circles will be used.- show_namesbool |
callable()
If
True
, show channel names next to each sensor marker. If callable, channel names will be formatted using the callable; e.g., to delete the prefix ‘MEG ‘ from all channel names, pass the functionlambda x: x.replace('MEG ', '')
. Ifmask
is notNone
, only non-masked sensor names will be shown.New in v1.2.
- contours
int
| array_like The number of contour lines to draw. If
0
, no contours will be drawn. If a positive integer, that number of contour levels are chosen using the matplotlib tick locator (may sometimes be inaccurate, use array for accuracy). If array-like, the array values are used as the contour levels. The values should be in µV for EEG, fT for magnetometers and fT/m for gradiometers. Ifcolorbar=True
, the colorbar will have ticks corresponding to the contour levels. Default is6
.- outlines‘head’ |
dict
|None
The outlines to be drawn. If ‘head’, the default head scheme will be drawn. If dict, each key refers to a tuple of x and y positions, the values in ‘mask_pos’ will serve as image mask. Alternatively, a matplotlib patch object can be passed for advanced masking options, either directly or as a function that returns patches (required for multi-axis plots). If None, nothing will be drawn. Defaults to ‘head’.
- sphere
float
| array_like | instance ofConductorModel
|None
| ‘auto’ | ‘eeglab’ The sphere parameters to use for the head outline. Can be array-like of shape (4,) to give the X/Y/Z origin and radius in meters, or a single float to give just the radius (origin assumed 0, 0, 0). Can also be an instance of a spherical
ConductorModel
to use the origin and radius from that object. If'auto'
the sphere is fit to digitization points. If'eeglab'
the head circle is defined by EEG electrodes'Fpz'
,'Oz'
,'T7'
, and'T8'
(if'Fpz'
is not present, it will be approximated from the coordinates of'Oz'
).None
(the default) is equivalent to'auto'
when enough extra digitization points are available, and (0, 0, 0, 0.095) otherwise.New in v0.20.
Changed in version 1.1: Added
'eeglab'
option.- image_interp
str
The image interpolation to be used. Options are
'cubic'
(default) to usescipy.interpolate.CloughTocher2DInterpolator
,'nearest'
to usescipy.spatial.Voronoi
or'linear'
to usescipy.interpolate.LinearNDInterpolator
.- extrapolate
str
Options:
'box'
Extrapolate to four points placed to form a square encompassing all data points, where each side of the square is three times the range of the data in the respective dimension.
'local'
(default for MEG sensors)Extrapolate only to nearby points (approximately to points closer than median inter-electrode distance). This will also set the mask to be polygonal based on the convex hull of the sensors.
'head'
(default for non-MEG sensors)Extrapolate out to the edges of the clipping circle. This will be on the head circle when the sensors are contained within the head circle, but it can extend beyond the head when sensors are plotted outside the head circle.
New in v1.2.
- border
float
| ‘mean’ Value to extrapolate to on the topomap borders. If
'mean'
(default), then each extrapolated point has the average value of its neighbours.New in v0.20.
- res
int
The resolution of the topomap image (number of pixels along each side).
- size
float
Side length of each subplot in inches.
- cmapmatplotlib colormap | (colormap, bool) | ‘interactive’ |
None
Colormap to use. If
tuple
, the first value indicates the colormap to use and the second value is a boolean defining interactivity. In interactive mode the colors are adjustable by clicking and dragging the colorbar with left and right mouse button. Left mouse button moves the scale up and down and right mouse button adjusts the range. Hitting space bar resets the range. Up and down arrows can be used to change the colormap. IfNone
,'Reds'
is used for data that is either all-positive or all-negative, and'RdBu_r'
is used otherwise.'interactive'
is equivalent to(None, True)
. Defaults toNone
.Warning
Interactive mode works smoothly only for a small amount of topomaps. Interactive mode is disabled by default for more than 2 topomaps.
- vlim
tuple
of length 2 | “joint” Lower and upper bounds of the colormap, typically a numeric value in the same units as the data. Elements of the
tuple
may also be callable functions which take in aNumPy array
and return a scalar.If both entries are
None
, the bounds are set at ± the maximum absolute value of the data (yielding a colormap with midpoint at 0), or(0, max(abs(data)))
if the (possibly baselined) data are all-positive. ProvidingNone
for just one entry will set the corresponding boundary at the min/max of the data. Ifvlim="joint"
, will compute the colormap limits jointly across all projectors of the same channel type (instead of separately for each projector), using the min/max of the data for that channel type. If vlim is"joint"
,info
must not beNone
. Defaults to(None, None)
.- cnorm
matplotlib.colors.Normalize
|None
How to normalize the colormap. If
None
, standard linear normalization is performed. If notNone
,vmin
andvmax
will be ignored. See Matplotlib docs for more details on colormap normalization, and the ERDs example for an example of its use.New in v1.2.
- colorbarbool
Plot a colorbar in the rightmost column of the figure.
- cbar_fmt
str
Formatting string for colorbar tick labels. See Format Specification Mini-Language for details.
New in v1.2.
- units
str
|None
The units to use for the colorbar label. Ignored if
colorbar=False
. IfNone
the label will be “AU” indicating arbitrary units. Default isNone
.New in v1.2.
- axesinstance of
Axes
|list
ofAxes
|None
The axes to plot into. If
None
, a newFigure
will be created with the correct number of axes. IfAxes
are provided (either as a single instance or alist
of axes), the number of axes provided must match the number of projectors. Default isNone
.- showbool
Show the figure if
True
.
- info
- Returns:
- figinstance of
Figure
Figure distributing one image per channel across sensor topography.
- figinstance of
Notes
New in v0.15.0.
Examples using mne.Projection
#
Getting started with mne.Report
Background on projectors and projections