Object for rendering HTML.
None
| str
Name of the file containing the info dictionary.
None
The path to the directory containing the FreeSurfer subjects
reconstructions. If None
, defaults to the SUBJECTS_DIR
environment
variable.
str
| None
Subject name.
str
Title of the report.
None
| str
Name of the file containing the noise covariance.
None
| tuple
of length 2The time interval to consider as “baseline” when applying baseline
correction. If None
, do not apply baseline correction.
If a tuple (a, b)
, the interval is between a
and b
(in seconds), including the endpoints.
If a
is None
, the beginning of the data is used; and if b
is None
, it is set to the end of the interval.
If (None, None)
, the entire time interval is used.
Note
The baseline (a, b)
includes both endpoints, i.e. all
timepoints t
such that a <= t <= b
.
Correction is applied in the following way to each channel:
Calculate the mean signal of the baseline period.
Subtract this mean from the entire time period.
For Epochs
, this algorithm is run on each epoch individually.
Defaults to None
, i.e. no baseline correction.
Default image format to use (default is 'png'
).
'svg'
uses vector graphics, so fidelity is higher but can increase
file size and browser image rendering time as well.
New in version 0.15.
dict
If True, include PSD plots for raw files. Can be False (default) to
omit, True to plot, or a dict to pass as kwargs
to
mne.io.Raw.plot_psd()
.
New in version 0.17.
Whether to include topographic plots of SSP projectors, if present in
the data. Defaults to False
.
New in version 0.21.
str
| int
| None
Control verbosity of the logging output. If None
, use the default
verbosity level. See the logging documentation and
mne.verbose()
for details. Should only be passed as a keyword
argument.
Notes
See Getting started with mne.Report for an introduction to using mne.Report
.
New in version 0.8.0.
None
| str
Name of the file containing the info dictionary.
None
The path to the directory containing the FreeSurfer subjects
reconstructions. If None
, defaults to the SUBJECTS_DIR
environment
variable.
str
| None
Subject name.
str
Title of the report.
None
| str
Name of the file containing the noise covariance.
None
| tuple
of length 2The time interval to consider as “baseline” when applying baseline
correction. If None
, do not apply baseline correction.
If a tuple (a, b)
, the interval is between a
and b
(in seconds), including the endpoints.
If a
is None
, the beginning of the data is used; and if b
is None
, it is set to the end of the interval.
If (None, None)
, the entire time interval is used.
Note
The baseline (a, b)
includes both endpoints, i.e. all
timepoints t
such that a <= t <= b
.
Correction is applied in the following way to each channel:
Calculate the mean signal of the baseline period.
Subtract this mean from the entire time period.
For Epochs
, this algorithm is run on each epoch individually.
Defaults to None
, i.e. no baseline correction.
str
Default image format to use.
New in version 0.15.
dict
If True, include PSD plots for raw files. Can be False (default) to
omit, True to plot, or a dict to pass as kwargs
to
mne.io.Raw.plot_psd()
.
New in version 0.17.
Whether to include topographic plots of SSP projectors, if present in
the data. Defaults to False
.
New in version 0.21.
str
| int
| None
Control verbosity of the logging output. If None
, use the default
verbosity level. See the logging documentation and
mne.verbose()
for details. Should only be passed as a keyword
argument.
html
list
of str
A list of HTML representations for all content elements.
list
of str
Dictionary containing elements included in head.
list
of str
List of file names rendered.
list
of str
List of sections.
str
language setting for the HTML file.
Methods
|
Return the number of files processed by the report. |
|
Render a visualization of the boundary element model (BEM) surfaces. |
|
Add a code snippet (e.g., an analysis script) to the report. |
|
Add covariance to the report. |
|
Add custom CSS to the report. |
|
Add custom JavaScript to the report. |
|
Add |
|
Add events to the report. |
|
Add |
|
Add figures to the report. |
|
Add a forward solution. |
|
Add HTML content to the report. |
|
Add (a fitted) |
|
Add an image (e.g., PNG or JPEG pictures) to the report. |
|
Add an inverse operator. |
|
Render (SSP) projection vectors. |
|
Add |
|
Add a |
|
Add a MNE-Python system information to the report. |
|
Add a coregistration visualization to the report. |
|
Render all the files in the folder. |
|
Remove elements from the report. |
|
Save the report and optionally open it in browser. |
Return the number of files processed by the report.
int
The number of files processed.
Render a visualization of the boundary element model (BEM) surfaces.
str
The FreeSurfer subject name.
str
The title corresponding to the BEM image.
None
The path to the directory containing the FreeSurfer subjects
reconstructions. If None
, defaults to the SUBJECTS_DIR
environment
variable.
int
Use this decimation factor for generating MRI/BEM images (since it can be time consuming).
int
The width of the MRI images (in pixels). Larger values will have clearer surface lines, but will create larger HTML files. Typically a factor of 2 more than the number of MRI voxels along each dimension (typically 512, default) is reasonable.
int
| None
The number of jobs to run in parallel. If -1
, it is set
to the number of CPU cores. Requires the joblib
package.
None
(default) is a marker for ‘unset’ that will be interpreted
as n_jobs=1
(sequential execution) unless the call is performed under
a joblib.parallel_backend()
context manager that sets another
value for n_jobs
.
str
| str
Tags to add for later interactive filtering. Must not contain spaces.
If True
, content already present that has the same title
will be
replaced. Defaults to False
, which will cause duplicate entries in the
table of contents if an entry for title
already exists.
Notes
New in version 0.24.0.
Examples using add_bem
:
Getting started with mne.Report
Add a code snippet (e.g., an analysis script) to the report.
str
| pathlib.Path
The code to add to the report as a string, or the path to a file
as a pathlib.Path
object.
Note
Paths must be passed as pathlib.Path
object, since
strings will be treated as literal code.
str
The title corresponding to the code.
str
The programming language of code
. This will be used for syntax
highlighting. Can be 'auto'
to try to auto-detect the language.
str
| str
Tags to add for later interactive filtering. Must not contain spaces.
If True
, content already present that has the same title
will be
replaced. Defaults to False
, which will cause duplicate entries in the
table of contents if an entry for title
already exists.
Notes
New in version 0.24.0.
Examples using add_code
:
Getting started with mne.Report
Add covariance to the report.
Covariance
The Covariance
to add to the report.
Info
The Info
corresponding to cov
.
str
The title corresponding to the Covariance
object.
str
| str
Tags to add for later interactive filtering. Must not contain spaces.
If True
, content already present that has the same title
will be
replaced. Defaults to False
, which will cause duplicate entries in the
table of contents if an entry for title
already exists.
Notes
New in version 0.24.0.
Examples using add_covariance
:
Getting started with mne.Report
Add custom CSS to the report.
str
Style definitions to add to the report. The content of this string
will be embedded between HTML <style>
and </style>
tags.
Notes
New in version 0.23.
Add custom JavaScript to the report.
str
JavaScript code to add to the report. The content of this string
will be embedded between HTML <script>
and </script>
tags.
Notes
New in version 0.23.
Add Epochs
to the report.
Epochs
The epochs to add to the report.
str
The title to add.
float
If a float, the duration of data to use for creation of PSD plots, in seconds. PSD will be calculated on as many epochs as required to cover at least this duration. Epochs will be picked across the entire time range in equally-spaced distance.
Note
In rare edge cases, we may not be able to create a grid of equally-spaced epochs that cover the entire requested time range. In these situations, a warning will be emitted, informing you about the duration that’s actually being used.
If True
, add PSD plots based on all epochs
. If False
,
do not add PSD plots.
None
Whether to add SSP projector plots if projectors are present in
the data. If None
, use projs
from Report
creation.
dict
| None
Keyword arguments to pass to the topomap-generating functions.
str
The drop reasons to ignore when creating the drop log bar plot.
All epochs for which a drop reason listed here appears in
epochs.drop_log
will be excluded from the drop log plot.
str
| str
Tags to add for later interactive filtering. Must not contain spaces.
If True
, content already present that has the same title
will be
replaced. Defaults to False
, which will cause duplicate entries in the
table of contents if an entry for title
already exists.
Notes
New in version 0.24.0.
Examples using add_epochs
:
Getting started with mne.Report
Add events to the report.
array
, shape (n_events, 3)An MNE-Python events array.
str
The title corresponding to the events.
dict
A dictionary mapping event names (keys) to event codes (values).
float
The sampling frequency used while recording.
int
The first sample point in the recording. This corresponds to
raw.first_samp
on files created with Elekta/Neuromag systems.
str
| str
Tags to add for later interactive filtering. Must not contain spaces.
If True
, content already present that has the same title
will be
replaced. Defaults to False
, which will cause duplicate entries in the
table of contents if an entry for title
already exists.
Notes
New in version 0.24.0.
Examples using add_events
:
Getting started with mne.Report
Add Evoked
objects to the report.
Evoked
| list
of Evoked
The evoked data to add to the report. Multiple Evoked
objects – as returned from mne.read_evokeds
– can be passed as
a list.
str
| list
of str
| None
The titles corresponding to the evoked data. If None
, the
content of evoked.comment
from each evoked will be used as
title.
Covariance
| None
A noise covariance matrix. If provided, will be used to whiten
the evokeds
. If None
, will fall back to the cov_fname
provided upon report creation.
None
Whether to add SSP projector plots if projectors are present in
the data. If None
, use projs
from Report
creation.
int
| None
The number of equidistant time points to render. If None
,
will render each Evoked
at 21 time points, unless the data
contains fewer time points, in which case all will be rendered.
str
| str
Tags to add for later interactive filtering. Must not contain spaces.
If True
, content already present that has the same title
will be
replaced. Defaults to False
, which will cause duplicate entries in the
table of contents if an entry for title
already exists.
dict
| None
Keyword arguments to pass to the topomap-generating functions.
int
| None
The number of jobs to run in parallel. If -1
, it is set
to the number of CPU cores. Requires the joblib
package.
None
(default) is a marker for ‘unset’ that will be interpreted
as n_jobs=1
(sequential execution) unless the call is performed under
a joblib.parallel_backend()
context manager that sets another
value for n_jobs
.
Notes
New in version 0.24.0.
Examples using add_evokeds
:
Getting started with mne.Report
Add figures to the report.
matplotlib.figure.Figure
| Figure3D
| array
| array-like of matplotlib.figure.Figure
| array-like of Figure3D
| array-like of array
One or more figures to add to the report. All figures must be an
instance of matplotlib.figure.Figure
,
mne.viz.Figure3D
, or numpy.ndarray
. If
multiple figures are passed, they will be added as “slides”
that can be navigated using buttons and a slider element.
str
The title corresponding to the figure(s).
str
| array-like of str
| None
The caption(s) to add to the figure(s).
None
The image format to be used for the report, can be 'png'
,
'svg'
, or 'gif'
.
None (default) will use the default specified during Report
instantiation.
str
| str
Tags to add for later interactive filtering. Must not contain spaces.
str
| None
The name of the section (or content block) to add the content to. This feature is useful for grouping multiple related content elements together under a single, collapsible section. Each content element will retain its own title and functionality, but not appear separately in the table of contents. Hence, using sections is a way to declutter the table of contents, and to easy navigation of the report.
New in version 1.1.
If True
, content already present that has the same title
will be
replaced. Defaults to False
, which will cause duplicate entries in the
table of contents if an entry for title
already exists.
Notes
New in version 0.24.0.
Examples using add_figure
:
Getting started with mne.Report
Add a forward solution.
Forward
| path-likeThe forward solution to add to the report.
str
The title corresponding to forward solution.
str
| None
The name of the FreeSurfer subject forward
belongs to. If
provided, the sensitivity maps of the forward solution will
be visualized. If None
, will use the value of subject
passed on report creation. If supplied, also pass subjects_dir
.
None
The FreeSurfer SUBJECTS_DIR
.
str
| str
Tags to add for later interactive filtering. Must not contain spaces.
If True
, content already present that has the same title
will be
replaced. Defaults to False
, which will cause duplicate entries in the
table of contents if an entry for title
already exists.
Notes
New in version 0.24.0.
Examples using add_forward
:
Getting started with mne.Report
Add HTML content to the report.
str
The HTML content to add.
str
The title corresponding to html
.
str
| str
Tags to add for later interactive filtering. Must not contain spaces.
If True
, content already present that has the same title
will be
replaced. Defaults to False
, which will cause duplicate entries in the
table of contents if an entry for title
already exists.
Notes
New in version 0.24.0.
Examples using add_html
:
Getting started with mne.Report
Add (a fitted) ICA
to the report.
mne.preprocessing.ICA
The fitted ICA to add.
str
The title to add.
mne.io.Raw
| mne.Epochs
| None
The data to use for visualization of the effects of ICA cleaning.
To only plot the ICA component topographies, explicitly pass
None
.
int
| list
of int
| slice
| None
Indices of the independent components (ICs) to visualize.
If an integer, represents the index of the IC to pick.
Multiple ICs can be selected using a list of int or a slice.
The indices are 0-indexed, so picks=1
will
pick the second IC: ICA001
. If None
, plot all components. This only affects
the behavior of the component topography and properties plots.
mne.Evoked
| None
Evoked signal based on ECG and EOG epochs, respectively. If passed, will be used to visualize the effects of artifact rejection.
array
of float
| list
of array
of float
| None
The scores produced by mne.preprocessing.ICA.find_bads_ecg()
and mne.preprocessing.ICA.find_bads_eog()
, respectively.
If passed, will be used to visualize the scoring for each ICA
component.
int
| None
The number of jobs to run in parallel. If -1
, it is set
to the number of CPU cores. Requires the joblib
package.
None
(default) is a marker for ‘unset’ that will be interpreted
as n_jobs=1
(sequential execution) unless the call is performed under
a joblib.parallel_backend()
context manager that sets another
value for n_jobs
.
str
| str
Tags to add for later interactive filtering. Must not contain spaces.
If True
, content already present that has the same title
will be
replaced. Defaults to False
, which will cause duplicate entries in the
table of contents if an entry for title
already exists.
Notes
New in version 0.24.0.
Examples using add_ica
:
Getting started with mne.Report
Add an image (e.g., PNG or JPEG pictures) to the report.
The image to add.
str
Title corresponding to the images.
str
| None
If not None
, the caption to add to the image.
str
| str
Tags to add for later interactive filtering. Must not contain spaces.
str
| None
The name of the section (or content block) to add the content to. This feature is useful for grouping multiple related content elements together under a single, collapsible section. Each content element will retain its own title and functionality, but not appear separately in the table of contents. Hence, using sections is a way to declutter the table of contents, and to easy navigation of the report.
New in version 1.1.
If True
, content already present that has the same title
will be
replaced. Defaults to False
, which will cause duplicate entries in the
table of contents if an entry for title
already exists.
Notes
New in version 0.24.0.
Examples using add_image
:
Getting started with mne.Report
Add an inverse operator.
InverseOperator
| path-likeThe inverse operator to add to the report.
str
The title corresponding to the inverse operator object.
str
| None
The name of the FreeSurfer subject inverse_op
belongs to. If
provided, the source space the inverse solution is based on will
be visualized. If None
, will use the value of subject
passed on report creation. If supplied, also pass subjects_dir
and trans
.
None
The FreeSurfer SUBJECTS_DIR
.
Transform
| None
The head -> MRI
transformation for subject
.
str
| str
Tags to add for later interactive filtering. Must not contain spaces.
If True
, content already present that has the same title
will be
replaced. Defaults to False
, which will cause duplicate entries in the
table of contents if an entry for title
already exists.
Notes
New in version 0.24.0.
Examples using add_inverse_operator
:
Getting started with mne.Report
Render (SSP) projection vectors.
Info
| path-likeAn Info
structure or the path of a file containing one. This
is required to create the topographic plots.
mne.Projection
| path-like | None
The projection vectors to add to the report. Can be the path to a
file that will be loaded via mne.read_proj
. If None
, the
projectors are taken from info['projs']
.
str
The title corresponding to the Projection
object.
dict
| None
Keyword arguments to pass to the topomap-generating functions.
str
| str
Tags to add for later interactive filtering. Must not contain spaces.
If True
, content already present that has the same title
will be
replaced. Defaults to False
, which will cause duplicate entries in the
table of contents if an entry for title
already exists.
Notes
New in version 0.24.0.
Examples using add_projs
:
Getting started with mne.Report
Add Raw
objects to the report.
Raw
The data to add to the report.
str
The title corresponding to the raw
object.
None
Whether to add PSD plots. Overrides the raw_psd
parameter
passed when initializing the Report
. If None
, use
raw_psd
from Report
creation.
None
Whether to add SSP projector plots if projectors are present in
the data. If None
, use projs
from Report
creation.
int
Whether to add butterfly plots of the data. Can be useful to
spot problematic channels. If True
, 10 equally-spaced 1-second
segments will be plotted. If an integer, specifies the number of
1-second segments to plot. Larger numbers may take a considerable
amount of time if the data contains many sensors. You can disable
butterfly plots altogether by passing False
.
dict
| None
Scaling factors for the traces. If a dictionary where any
value is 'auto'
, the scaling factor is set to match the 99.5th
percentile of the respective data. If 'auto'
, all scalings (for all
channel types) are set to 'auto'
. If any values are 'auto'
and the
data is not preloaded, a subset up to 100 MB will be loaded. If None
,
defaults to:
dict(mag=1e-12, grad=4e-11, eeg=20e-6, eog=150e-6, ecg=5e-4,
emg=1e-3, ref_meg=1e-12, misc=1e-3, stim=1,
resp=1, chpi=1e-4, whitened=1e2)
Note
A particular scaling value s
corresponds to half of the visualized
signal range around zero (i.e. from 0
to +s
or from 0
to
-s
). For example, the default scaling of 20e-6
(20µV) for EEG
signals means that the visualized range will be 40 µV (20 µV in the
positive direction and 20 µV in the negative direction).
str
| str
Tags to add for later interactive filtering. Must not contain spaces.
If True
, content already present that has the same title
will be
replaced. Defaults to False
, which will cause duplicate entries in the
table of contents if an entry for title
already exists.
dict
| None
Keyword arguments to pass to the topomap-generating functions.
Notes
New in version 0.24.0.
Examples using add_raw
:
Getting started with mne.Report
Add a SourceEstimate
(STC) to the report.
SourceEstimate
The SourceEstimate
to add to the report.
str
The title to add.
str
| None
The name of the FreeSurfer subject the STC belongs to. The name is
not stored with the STC data and therefore needs to be specified.
If None
, will use the value of subject
passed on report
creation.
None
The FreeSurfer SUBJECTS_DIR
.
int
| None
The number of equidistant time points to render. If None
,
will render stc
at 51 time points, unless the data
contains fewer time points, in which case all will be rendered.
str
| str
Tags to add for later interactive filtering. Must not contain spaces.
If True
, content already present that has the same title
will be
replaced. Defaults to False
, which will cause duplicate entries in the
table of contents if an entry for title
already exists.
dict
Dictionary of keyword arguments to pass to
mne.SourceEstimate.plot
. Only used when plotting in 3D
mode.
Notes
New in version 0.24.0.
Examples using add_stc
:
Getting started with mne.Report
Add a MNE-Python system information to the report.
This is a convenience method that captures the output of
mne.sys_info
and adds it to the report.
str
The title to assign.
str
| str
Tags to add for later interactive filtering. Must not contain spaces.
If True
, content already present that has the same title
will be
replaced. Defaults to False
, which will cause duplicate entries in the
table of contents if an entry for title
already exists.
Notes
New in version 0.24.0.
Add a coregistration visualization to the report.
Transform
The head -> MRI
transformation to render.
Info
The Info
corresponding to trans
.
str
The title to add.
str
| None
The name of the FreeSurfer subject the trans``
belong to. The
name is not stored with the trans
and therefore needs to be
specified. If None
, will use the value of subject
passed on
report creation.
None
The FreeSurfer SUBJECTS_DIR
.
float
| None
The level of opacity to apply to the head surface. If a float, must
be between 0 and 1 (inclusive), where 1 means fully opaque. If
None
, will use the MNE-Python default value.
str
| str
Tags to add for later interactive filtering. Must not contain spaces.
If True
, content already present that has the same title
will be
replaced. Defaults to False
, which will cause duplicate entries in the
table of contents if an entry for title
already exists.
Notes
New in version 0.24.0.
Examples using add_trans
:
Getting started with mne.Report
A list of HTML representations for all content elements.
Render all the files in the folder.
str
Path to the folder containing data whose HTML report will be created.
None
| str
| list
of str
Filename pattern(s) to include in the report.
For example, [\*raw.fif, \*ave.fif]
will include Raw
as well as Evoked
files. If None
, include all supported
file formats.
Changed in version 0.23: Include supported non-FIFF files by default.
int
| None
The number of jobs to run in parallel. If -1
, it is set
to the number of CPU cores. Requires the joblib
package.
None
(default) is a marker for ‘unset’ that will be interpreted
as n_jobs=1
(sequential execution) unless the call is performed under
a joblib.parallel_backend()
context manager that sets another
value for n_jobs
.
int
Use this decimation factor for generating MRI/BEM images (since it can be time consuming).
If True
, sort the content based on tags in the order:
raw -> events -> epochs -> evoked -> covariance -> coregistration
-> bem -> forward-solution -> inverse-operator -> source-estimate.
New in version 0.24.0.
str
What to do if a file cannot be rendered. Can be ‘ignore’, ‘warn’ (default), or ‘raise’.
None
The image format to be used for the report, can be 'png'
,
'svg'
, or 'gif'
.
None (default) will use the default specified during Report
instantiation.
New in version 0.15.
If True (default), try to render the BEM.
New in version 0.16.
int
| None
The number of equidistant time points to render for Evoked
and SourceEstimate
data, respectively. If None
,
will render each Evoked
at 21 and each SourceEstimate
at 51 time points, unless the respective data contains fewer time
points, in which call all will be rendered.
New in version 0.24.0.
Whether to render butterfly plots for (decimated) Raw
data.
New in version 0.24.0.
dict
Dictionary of keyword arguments to pass to
mne.SourceEstimate.plot
. Only used when plotting in 3D
mode.
New in version 0.24.0.
dict
| None
Keyword arguments to pass to the topomap-generating functions.
New in version 0.24.0.
str
| int
| None
Control verbosity of the logging output. If None
, use the default
verbosity level. See the logging documentation and
mne.verbose()
for details. Should only be passed as a keyword
argument.
Examples using parse_folder
:
Getting started with mne.Report
Remove elements from the report.
The element to remove is searched for by its title. Optionally, tags may be specified as well to narrow down the search to elements that have the supplied tags.
str
The title of the element(s) to remove.
New in version 0.24.0.
str
| str
| None
If supplied, restrict the operation to elements with the supplied tags.
New in version 0.24.0.
Controls the behavior if multiple elements match the search
criteria. If False
(default) only the element last added to the
report will be removed. If True
, all matches will be removed.
New in version 0.24.0.
Save the report and optionally open it in browser.
None
Output filename. If the name ends with .h5
or .hdf5
, the
report is saved in HDF5 format, so it can later be loaded again
with open_report()
. For any other suffix, the report will be
saved in HTML format. If None
and Report.parse_folder()
was not called, the report is saved as report.html
in the
current working directory. If None
and
Report.parse_folder()
was used, the report is saved as
report.html
inside the data_path
supplied to
Report.parse_folder()
.
Whether to open the rendered HTML report in the default web browser after saving. This is ignored when writing an HDF5 file.
If True (default False), overwrite the destination file if it exists.
If True
, sort the content based on tags before saving in the
order:
raw -> events -> epochs -> evoked -> covariance -> coregistration
-> bem -> forward-solution -> inverse-operator -> source-estimate.
New in version 0.24.0.
str
| int
| None
Control verbosity of the logging output. If None
, use the default
verbosity level. See the logging documentation and
mne.verbose()
for details. Should only be passed as a keyword
argument.
str
The file name to which the report was saved.
Examples using save
:
Getting started with mne.Report
All tags currently used in the report.
mne.Report
#Getting started with mne.Report