mne.Report¶
- class mne.Report(info_fname=None, subjects_dir=None, subject=None, title=None, cov_fname=None, baseline=None, image_format='png', raw_psd=False, projs=False, verbose=None)[source]¶
Object for rendering HTML.
- Parameters
- info_fname
None
|str
Name of the file containing the info dictionary.
- subjects_dir
str
|pathlib.Path
|None
The path to the directory containing the FreeSurfer subjects reconstructions. If
None
, defaults to theSUBJECTS_DIR
environment variable.- subject
str
|None
Subject name.
- title
str
Title of the report.
- cov_fname
None
|str
Name of the file containing the noise covariance.
- baseline
None
|tuple
of length 2 The 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 betweena
andb
(in seconds), including the endpoints. Ifa
isNone
, the beginning of the data is used; and ifb
isNone
, 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 timepointst
such thata <= 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 toNone
, i.e. no baseline correction.- image_format‘png’ | ‘svg’ | ‘gif’
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.
- raw_psdbool |
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
tomne.io.Raw.plot_psd()
.New in version 0.17.
- projsbool
Whether to include topographic plots of SSP projectors, if present in the data. Defaults to
False
.New in version 0.21.
- verbosebool |
str
|int
|None
Control verbosity of the logging output. If
None
, use the default verbosity level. See the logging documentation andmne.verbose()
for details. Should only be passed as a keyword argument.
- info_fname
Notes
See Getting started with mne.Report for an introduction to using
mne.Report
.New in version 0.8.0.
- Attributes
- info_fname
None
|str
Name of the file containing the info dictionary.
- subjects_dir
str
|pathlib.Path
|None
The path to the directory containing the FreeSurfer subjects reconstructions. If
None
, defaults to theSUBJECTS_DIR
environment variable.- subject
str
|None
Subject name.
- title
str
Title of the report.
- cov_fname
None
|str
Name of the file containing the noise covariance.
- baseline
None
|tuple
of length 2 The 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 betweena
andb
(in seconds), including the endpoints. Ifa
isNone
, the beginning of the data is used; and ifb
isNone
, 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 timepointst
such thata <= 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 toNone
, i.e. no baseline correction.- image_format
str
Default image format to use.
New in version 0.15.
- raw_psdbool |
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
tomne.io.Raw.plot_psd()
.New in version 0.17.
- projsbool
Whether to include topographic plots of SSP projectors, if present in the data. Defaults to
False
.New in version 0.21.
- verbosebool |
str
|int
|None
Control verbosity of the logging output. If
None
, use the default verbosity level. See the logging documentation andmne.verbose()
for details. Should only be passed as a keyword argument.- html
list
ofstr
Contains items of html-page.
- include
list
ofstr
Dictionary containing elements included in head.
- fnames
list
ofstr
List of file names rendered.
- sections
list
ofstr
List of sections.
- lang
str
language setting for the HTML file.
- info_fname
Methods
__hash__
(/)Return hash(self).
__len__
()Return the number of files processed by the report.
add_bem
(subject, title, *[, subjects_dir, ...])Render a visualization of the boundary element model (BEM) surfaces.
add_bem_to_section
(subject[, caption, ...])Warning
DEPRECATED: Use
add_bem()
instead.add_code
(code, title, *[, language, tags, ...])Add a code snippet (e.g., an analysis script) to the report.
add_covariance
(cov, *, info, title[, tags, ...])Add covariance to the report.
add_custom_css
(css)Add custom CSS to the report.
add_custom_js
(js)Add custom JavaScript to the report.
add_epochs
(epochs, title, *[, psd, projs, ...])Add
Epochs
to the report.add_events
(events, title, *[, event_id, ...])Add events to the report.
add_evokeds
(evokeds, *[, titles, noise_cov, ...])Add
Evoked
objects to the report.add_figs_to_section
(figs, captions[, ...])Warning
DEPRECATED: Use
add_figure()
instead.add_figure
(fig, title, *[, caption, ...])Add figures to the report.
add_forward
(forward, title, *[, subject, ...])Add a forward solution.
add_html
(html, title, *[, tags, replace])Add HTML content to the report.
add_htmls_to_section
(htmls, captions[, ...])Warning
DEPRECATED: Use
add_html()
instead.add_ica
(ica, title, *, inst[, picks, ...])Add (a fitted)
ICA
to the report.add_image
(image, title, *[, caption, tags, ...])Add an image (e.g., PNG or JPEG pictures) to the report.
add_images_to_section
(fnames, captions[, ...])Warning
DEPRECATED: Use
add_image()
instead.add_inverse_operator
(inverse_operator, title, *)Add an inverse operator.
add_projs
(*, info[, projs, topomap_kwargs, ...])Render (SSP) projection vectors.
add_raw
(raw, title, *[, psd, projs, ...])Add
Raw
objects to the report.add_slider_to_section
(figs[, captions, ...])Warning
DEPRECATED: Use
add_figure()
instead.add_stc
(stc, title, *[, subject, ...])Add a
SourceEstimate
(STC) to the report.add_sys_info
(title, *[, tags])Add a MNE-Python system information to the report.
add_trans
(trans, *, info, title[, subject, ...])Add a coregistration visualization to the report.
parse_folder
(data_path[, pattern, n_jobs, ...])Render all the files in the folder.
remove
([caption, section, title, tags, ...])Remove elements from the report.
save
([fname, open_browser, overwrite, ...])Save the report and optionally open it in browser.
- __len__()[source]¶
Return the number of files processed by the report.
- Returns
- n_files
int
The number of files processed.
- n_files
- add_bem(subject, title, *, subjects_dir=None, decim=2, width=512, n_jobs=1, tags=('bem',), replace=False)[source]¶
Render a visualization of the boundary element model (BEM) surfaces.
- Parameters
- subject
str
The FreeSurfer subject name.
- title
str
The title corresponding to the BEM image.
- subjects_dir
str
|pathlib.Path
|None
The path to the directory containing the FreeSurfer subjects reconstructions. If
None
, defaults to theSUBJECTS_DIR
environment variable.- decim
int
Use this decimation factor for generating MRI/BEM images (since it can be time consuming).
- width
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.
- n_jobs
int
The number of jobs to run in parallel (default
1
). If-1
, it is set to the number of CPU cores. Requires thejoblib
package.- tagscollections of
str
Tags to add for later interactive filtering.
- replacebool
If
True
, content already present that has the sametitle
will be replaced. Defaults toFalse
, which will cause duplicate entries in the table of contents if an entry fortitle
already exists.
- subject
Notes
New in version 0.24.0.
Examples using
add_bem
:
- add_bem_to_section(subject, caption='BEM', section='bem', decim=2, n_jobs=1, subjects_dir=None, replace=False, width=512, verbose=None)[source]¶
Warning
DEPRECATED: Use
add_bem()
instead.Render a bem slider html str.
- Parameters
- subject
str
Subject name.
- caption
str
A caption for the BEM.
- section
str
Name of the section. If it already exists, the BEM will be appended to the end of the existing section.
- decim
int
Use this decimation factor for generating MRI/BEM images (since it can be time consuming).
- n_jobs
int
The number of jobs to run in parallel (default
1
). If-1
, it is set to the number of CPU cores. Requires thejoblib
package.- subjects_dir
str
|pathlib.Path
|None
The path to the directory containing the FreeSurfer subjects reconstructions. If
None
, defaults to theSUBJECTS_DIR
environment variable.- replacebool
If
True
, figures already present that have the same caption will be replaced. Defaults toFalse
.- width
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.
New in version 0.23.
- verbosebool |
str
|int
|None
Control verbosity of the logging output. If
None
, use the default verbosity level. See the logging documentation andmne.verbose()
for details. Should only be passed as a keyword argument. Defaults to self.verbose.
- subject
Notes
New in version 0.9.0.
- add_code(code, title, *, language='python', tags=('code',), replace=False)[source]¶
Add a code snippet (e.g., an analysis script) to the report.
- Parameters
- code
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.- title
str
The title corresponding to the code.
- language
str
The programming language of
code
. This will be used for syntax highlighting. Can be'auto'
to try to auto-detect the language.- tagscollections of
str
Tags to add for later interactive filtering.
- replacebool
If
True
, content already present that has the sametitle
will be replaced. Defaults toFalse
, which will cause duplicate entries in the table of contents if an entry fortitle
already exists.
- code
Notes
New in version 0.24.0.
Examples using
add_code
:
- add_covariance(cov, *, info, title, tags=('covariance',), replace=False)[source]¶
Add covariance to the report.
- Parameters
- covpath-like | instance of
Covariance
The
Covariance
to add to the report.- infopath-like | instance of
Info
The
Info
corresponding tocov
.- title
str
The title corresponding to the
Covariance
object.- tagscollections of
str
Tags to add for later interactive filtering.
- replacebool
If
True
, content already present that has the sametitle
will be replaced. Defaults toFalse
, which will cause duplicate entries in the table of contents if an entry fortitle
already exists.
- covpath-like | instance of
Notes
New in version 0.24.0.
Examples using
add_covariance
:
- add_custom_css(css)[source]¶
Add custom CSS to the report.
- Parameters
- css
str
Style definitions to add to the report. The content of this string will be embedded between HTML
<style>
and</style>
tags.
- css
Notes
New in version 0.23.
- add_custom_js(js)[source]¶
Add custom JavaScript to the report.
- Parameters
- js
str
JavaScript code to add to the report. The content of this string will be embedded between HTML
<script>
and</script>
tags.
- js
Notes
New in version 0.23.
- add_epochs(epochs, title, *, psd=True, projs=None, tags=('epochs',), replace=False, topomap_kwargs=None)[source]¶
Add
Epochs
to the report.- Parameters
- epochspath-like | instance of
Epochs
The epochs to add to the report.
- title
str
The title to add.
- psdbool |
None
Whether to add PSD plots.
- projsbool |
None
Whether to add SSP projector plots if projectors are present in the data. If
None
, useprojs
fromReport
creation.- tagscollections of
str
Tags to add for later interactive filtering.
- replacebool
If
True
, content already present that has the sametitle
will be replaced. Defaults toFalse
, which will cause duplicate entries in the table of contents if an entry fortitle
already exists.- topomap_kwargs
dict
|None
Keyword arguments to pass to topomap functions (
mne.viz.plot_evoked_topomap()
,mne.viz.plot_projs_topomap()
, etc.).
- epochspath-like | instance of
Notes
New in version 0.24.0.
Examples using
add_epochs
:
- add_events(events, title, *, event_id=None, sfreq, first_samp=0, tags=('events',), replace=False)[source]¶
Add events to the report.
- Parameters
- eventspath-like |
array
, shape (n_events, 3) An MNE-Python events array.
- title
str
The title corresponding to the events.
- event_id
dict
A dictionary mapping event names (keys) to event codes (values).
- sfreq
float
The sampling frequency used while recording.
- first_samp
int
The first sample point in the recording. This corresponds to
raw.first_samp
on files created with Elekta/Neuromag systems.- tagscollections of
str
Tags to add for later interactive filtering.
- replacebool
If
True
, content already present that has the sametitle
will be replaced. Defaults toFalse
, which will cause duplicate entries in the table of contents if an entry fortitle
already exists.
- eventspath-like |
Notes
New in version 0.24.0.
Examples using
add_events
:
- add_evokeds(evokeds, *, titles=None, noise_cov=None, projs=None, n_time_points=None, tags=('evoked',), replace=False, topomap_kwargs=None, n_jobs=1)[source]¶
Add
Evoked
objects to the report.- Parameters
- evokedspath-like | instance of
Evoked
|list
ofEvoked
The evoked data to add to the report. Multiple
Evoked
objects – as returned frommne.read_evokeds
– can be passed as a list.- titles
str
|list
ofstr
|None
The titles corresponding to the evoked data. If
None
, the content ofevoked.comment
from each evoked will be used as title.- noise_covpath-like | instance of
Covariance
|None
A noise covariance matrix. If provided, will be used to whiten the
evokeds
. IfNone
, will fall back to thecov_fname
provided upon report creation.- projsbool |
None
Whether to add SSP projector plots if projectors are present in the data. If
None
, useprojs
fromReport
creation.- n_time_points
int
|None
The number of equidistant time points to render. If
None
, will render eachEvoked
at 21 time points, unless the data contains fewer time points, in which case all will be rendered.- tagscollections of
str
Tags to add for later interactive filtering.
- replacebool
If
True
, content already present that has the sametitle
will be replaced. Defaults toFalse
, which will cause duplicate entries in the table of contents if an entry fortitle
already exists.- topomap_kwargs
dict
|None
Keyword arguments to pass to topomap functions (
mne.viz.plot_evoked_topomap()
,mne.viz.plot_projs_topomap()
, etc.).- n_jobs
int
The number of jobs to run in parallel (default
1
). If-1
, it is set to the number of CPU cores. Requires thejoblib
package.
- evokedspath-like | instance of
Notes
New in version 0.24.0.
Examples using
add_evokeds
:
- add_figs_to_section(figs, captions, section='custom', scale=None, image_format=None, comments=None, replace=False, auto_close=True)[source]¶
Warning
DEPRECATED: Use
add_figure()
instead.Append custom user-defined figures.
- Parameters
- figs
matplotlib.figure.Figure
|mlab.Figure
|array
|list
A figure or a list of figures to add to the report. Each figure in the list can be an instance of
matplotlib.figure.Figure
,mayavi.core.api.Scene
, ornumpy.ndarray
.- captions
str
|list
ofstr
A caption or a list of captions to the figures.
- section
str
Name of the section to place the figures in. If it already exists, the figures will be appended to the end of the existing section.
- scale
float
|None
|callable()
Scale the images maintaining the aspect ratio. If None, no scaling is applied. If float, scale will determine the relative scaling (might not work for scale <= 1 depending on font sizes). If function, should take a figure object as input parameter. Defaults to None.
- image_format‘png’ | ‘svg’ | ‘gif’ |
None
The image format to be used for the report, can be
'png'
,'svg'
, or'gif'
. None (default) will use the default specified duringReport
instantiation.- comments
None
|str
|list
ofstr
A string of text or a list of strings of text to be appended after the figure.
- replacebool
If
True
, figures already present that have the same caption will be replaced. Defaults toFalse
.- auto_closebool
If True, the plots are closed during the generation of the report. Defaults to True.
- figs
- add_figure(fig, title, *, caption=None, image_format=None, tags=('custom-figure',), replace=False)[source]¶
Add figures to the report.
- Parameters
- fig
matplotlib.figure.Figure
|mlab.Figure
|array
| collections ofmatplotlib.figure.Figure
| collections ofmlab.Figure
| collections ofarray
One or more figures to add to the report. All figures must be an instance of
matplotlib.figure.Figure
,mayavi.core.api.Scene
, ornumpy.ndarray
. If multiple figures are passed, they will be added as “slides” that can be navigated using buttons and a slider element.- title
str
The title corresponding to the figure(s).
- caption
str
| collections ofstr
|None
The caption(s) to add to the figure(s).
- image_format‘png’ | ‘svg’ | ‘gif’ |
None
The image format to be used for the report, can be
'png'
,'svg'
, or'gif'
. None (default) will use the default specified duringReport
instantiation.- tagscollections of
str
Tags to add for later interactive filtering.
- replacebool
If
True
, content already present that has the sametitle
will be replaced. Defaults toFalse
, which will cause duplicate entries in the table of contents if an entry fortitle
already exists.
- fig
Notes
New in version 0.24.0.
Examples using
add_figure
:
- add_forward(forward, title, *, subject=None, subjects_dir=None, tags=('forward-solution',), replace=False)[source]¶
Add a forward solution.
- Parameters
- forwardinstance of
Forward
| path-like The forward solution to add to the report.
- title
str
The title corresponding to forward solution.
- subject
str
|None
The name of the FreeSurfer subject
forward
belongs to. If provided, the sensitivity maps of the forward solution will be visualized. IfNone
, will use the value ofsubject
passed on report creation. If supplied, also passsubjects_dir
.- subjects_dirpath-like |
None
The FreeSurfer
SUBJECTS_DIR
.- tagscollections of
str
Tags to add for later interactive filtering.
- replacebool
If
True
, content already present that has the sametitle
will be replaced. Defaults toFalse
, which will cause duplicate entries in the table of contents if an entry fortitle
already exists.
- forwardinstance of
Notes
New in version 0.24.0.
Examples using
add_forward
:
- add_html(html, title, *, tags=('custom-html',), replace=False)[source]¶
Add HTML content to the report.
- Parameters
- html
str
The HTML content to add.
- title
str
The title corresponding to
html
.- tagscollections of
str
Tags to add for later interactive filtering.
- replacebool
If
True
, content already present that has the sametitle
will be replaced. Defaults toFalse
, which will cause duplicate entries in the table of contents if an entry fortitle
already exists.
- html
Notes
New in version 0.24.0.
- add_htmls_to_section(htmls, captions, section='custom', replace=False)[source]¶
Warning
DEPRECATED: Use
add_html()
instead.Append htmls to the report.
- Parameters
- htmls
str
|list
ofstr
An html str or a list of html str.
- captions
str
|list
ofstr
A caption or a list of captions to the htmls.
- section
str
Name of the section. If section already exists, the images will be appended to the end of the section.
- replacebool
If
True
, figures already present that have the same caption will be replaced. Defaults toFalse
.
- htmls
Notes
New in version 0.9.0.
- add_ica(ica, title, *, inst, picks=None, ecg_evoked=None, eog_evoked=None, ecg_scores=None, eog_scores=None, n_jobs=1, tags=('ica',), replace=False)[source]¶
Add (a fitted)
ICA
to the report.- Parameters
- icapath-like | instance of
mne.preprocessing.ICA
The fitted ICA to add.
- title
str
The title to add.
- instpath-like |
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
.- picks
int
|list
ofint
|slice
|None
Indices of the ICA components to visualize. If
None
, plot all components. This only affects the behavior of the component topography and properties plots.- ecg_evoked, eog_evokedpath-line |
mne.Evoked
|None
Evoked signal based on ECG and EOG epochs, respectively. If passed, will be used to visualize the effects of artifact rejection.
- ecg_scores, eog_scores
array
offloat
|list
ofarray
offloat
|None
The scores produced by
mne.preprocessing.ICA.find_bads_ecg()
andmne.preprocessing.ICA.find_bads_eog()
, respectively. If passed, will be used to visualize the scoring for each ICA component.- n_jobs
int
The number of jobs to run in parallel (default
1
). If-1
, it is set to the number of CPU cores. Requires thejoblib
package.- tagscollections of
str
Tags to add for later interactive filtering.
- replacebool
If
True
, content already present that has the sametitle
will be replaced. Defaults toFalse
, which will cause duplicate entries in the table of contents if an entry fortitle
already exists.
- icapath-like | instance of
Notes
New in version 0.24.0.
Examples using
add_ica
:
- add_image(image, title, *, caption=None, tags=('custom-image',), replace=False)[source]¶
Add an image (e.g., PNG or JPEG pictures) to the report.
- Parameters
- imagepath-like
The image to add.
- title
str
Title corresponding to the images.
- caption
str
|None
If not
None
, the caption to add to the image.- tagscollections of
str
Tags to add for later interactive filtering.
- replacebool
If
True
, content already present that has the sametitle
will be replaced. Defaults toFalse
, which will cause duplicate entries in the table of contents if an entry fortitle
already exists.
Notes
New in version 0.24.0.
Examples using
add_image
:
- add_images_to_section(fnames, captions, scale=None, section='custom', comments=None, replace=False)[source]¶
Warning
DEPRECATED: Use
add_image()
instead.Append custom user-defined images.
- Parameters
- fnames
str
|list
ofstr
A filename or a list of filenames from which images are read. Images can be PNG, GIF or SVG.
- captions
str
|list
ofstr
A caption or a list of captions to the images.
- scale
float
|None
Scale the images maintaining the aspect ratio. Defaults to None. If None, no scaling will be applied.
- section
str
Name of the section. If section already exists, the images will be appended to the end of the section.
- comments
None
|str
|list
ofstr
A string of text or a list of strings of text to be appended after the image.
- replacebool
If
True
, figures already present that have the same caption will be replaced. Defaults toFalse
.
- fnames
- add_inverse_operator(inverse_operator, title, *, subject=None, subjects_dir=None, trans=None, tags=('inverse-operator',), replace=False)[source]¶
Add an inverse operator.
- Parameters
- inverse_operatorinstance of
InverseOperator
| path-like The inverse operator to add to the report.
- title
str
The title corresponding to the inverse operator object.
- subject
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. IfNone
, will use the value ofsubject
passed on report creation. If supplied, also passsubjects_dir
andtrans
.- subjects_dirpath-like |
None
The FreeSurfer
SUBJECTS_DIR
.- transpath-like | instance of
Transform
|None
The
head -> MRI
transformation forsubject
.- tagscollections of
str
Tags to add for later interactive filtering.
- replacebool
If
True
, content already present that has the sametitle
will be replaced. Defaults toFalse
, which will cause duplicate entries in the table of contents if an entry fortitle
already exists.
- inverse_operatorinstance of
Notes
New in version 0.24.0.
Examples using
add_inverse_operator
:
- add_projs(*, info, projs=None, title, topomap_kwargs=None, tags=('ssp',), replace=False)[source]¶
Render (SSP) projection vectors.
- Parameters
- infoinstance of
Info
| path-like An
Info
structure or the path of a file containing one. This is required to create the topographic plots.- projsiterable of
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
. IfNone
, the projectors are taken frominfo['projs']
.- title
str
The title corresponding to the
Projection
object.- topomap_kwargs
dict
|None
Keyword arguments to pass to topomap functions (
mne.viz.plot_evoked_topomap()
,mne.viz.plot_projs_topomap()
, etc.).- tagscollections of
str
Tags to add for later interactive filtering.
- replacebool
If
True
, content already present that has the sametitle
will be replaced. Defaults toFalse
, which will cause duplicate entries in the table of contents if an entry fortitle
already exists.
- infoinstance of
Notes
New in version 0.24.0.
Examples using
add_projs
:
- add_raw(raw, title, *, psd=None, projs=None, butterfly=True, tags=('raw',), replace=False, topomap_kwargs=None)[source]¶
Add
Raw
objects to the report.- Parameters
- rawpath-like | instance of
Raw
The data to add to the report.
- title
str
The title corresponding to the
raw
object.- psdbool |
None
Whether to add PSD plots. Overrides the
raw_psd
parameter passed when initializing theReport
. IfNone
, useraw_psd
fromReport
creation.- projsbool |
None
Whether to add SSP projector plots if projectors are present in the data. If
None
, useprojs
fromReport
creation.- butterflybool
Whether to add a butterfly plot of the (decimated) data. Can be useful to spot segments marked as “bad” and problematic channels.
- tagscollections of
str
Tags to add for later interactive filtering.
- replacebool
If
True
, content already present that has the sametitle
will be replaced. Defaults toFalse
, which will cause duplicate entries in the table of contents if an entry fortitle
already exists.- topomap_kwargs
dict
|None
Keyword arguments to pass to topomap functions (
mne.viz.plot_evoked_topomap()
,mne.viz.plot_projs_topomap()
, etc.).
- rawpath-like | instance of
Notes
New in version 0.24.0.
Examples using
add_raw
:
- add_slider_to_section(figs, captions=None, section='custom', title='Slider', scale=None, image_format=None, replace=False, auto_close=True)[source]¶
Warning
DEPRECATED: Use
add_figure()
instead.Render a slider of figs to the report.
- Parameters
- figs
list
ofFigure
Each figure in the list can be an instance of
matplotlib.figure.Figure
,mayavi.core.api.Scene
, ornumpy.ndarray
.- captions
list
ofstr
|list
offloat
|None
A list of captions to the figures. If
None
, it will default toData slice [i]
.- section
str
Name of the section. If section already exists, the figures will be appended to the end of the section.
- title
str
The title of the slider.
- scale
float
|None
|callable()
Scale the images maintaining the aspect ratio. If None, no scaling is applied. If float, scale will determine the relative scaling (might not work for scale <= 1 depending on font sizes). If function, should take a figure object as input parameter. Defaults to None.
- image_format‘png’ | ‘svg’ | ‘gif’ |
None
The image format to be used for the report, can be
'png'
,'svg'
, or'gif'
. None (default) will use the default specified duringReport
instantiation.- replacebool
If
True
, figures already present that have the same caption will be replaced. Defaults toFalse
.- auto_closebool
If True, the plots are closed during the generation of the report. Defaults to True.
New in version 0.23.
- figs
Notes
New in version 0.10.0.
- add_stc(stc, title, *, subject=None, subjects_dir=None, n_time_points=None, tags=('source-estimate',), replace=False, stc_plot_kwargs=None)[source]¶
Add a
SourceEstimate
(STC) to the report.- Parameters
- stcpath-like | instance of
SourceEstimate
The
SourceEstimate
to add to the report.- title
str
The title to add.
- subject
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 ofsubject
passed on report creation.- subjects_dirpath-like |
None
The FreeSurfer
SUBJECTS_DIR
.- n_time_points
int
|None
The number of equidistant time points to render. If
None
, will renderstc
at 51 time points, unless the data contains fewer time points, in which case all will be rendered.- tagscollections of
str
Tags to add for later interactive filtering.
- replacebool
If
True
, content already present that has the sametitle
will be replaced. Defaults toFalse
, which will cause duplicate entries in the table of contents if an entry fortitle
already exists.- stc_plot_kwargs
dict
Dictionary of keyword arguments to pass to
mne.SourceEstimate.plot
. Only used when plotting in 3D mode.
- stcpath-like | instance of
Notes
New in version 0.24.0.
Examples using
add_stc
:
- add_sys_info(title, *, tags=('mne-sysinfo',))[source]¶
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.- Parameters
- title
str
The title to assign.
- tagscollections of
str
Tags to add for later interactive filtering.
- title
Notes
New in version 0.24.0.
- add_trans(trans, *, info, title, subject=None, subjects_dir=None, tags=('coregistration',), replace=False)[source]¶
Add a coregistration visualization to the report.
- Parameters
- transpath-like | instance of
Transform
The
head -> MRI
transformation to render.- infopath-like | instance of
Info
The
Info
corresponding totrans
.- title
str
The title to add.
- subject
str
|None
The name of the FreeSurfer subject the
trans``
belong to. The name is not stored with thetrans
and therefore needs to be specified. IfNone
, will use the value ofsubject
passed on report creation.- subjects_dirpath-like |
None
The FreeSurfer
SUBJECTS_DIR
.- tagscollections of
str
Tags to add for later interactive filtering.
- replacebool
If
True
, content already present that has the sametitle
will be replaced. Defaults toFalse
, which will cause duplicate entries in the table of contents if an entry fortitle
already exists.
- transpath-like | instance of
Notes
New in version 0.24.0.
Examples using
add_trans
:
- parse_folder(data_path, pattern=None, n_jobs=1, mri_decim=2, sort_content=True, sort_sections=None, on_error='warn', image_format=None, render_bem=True, *, n_time_points_evokeds=None, n_time_points_stcs=None, raw_butterfly=True, stc_plot_kwargs=None, topomap_kwargs=None, verbose=None)[source]¶
Render all the files in the folder.
- Parameters
- data_path
str
Path to the folder containing data whose HTML report will be created.
- pattern
None
|str
|list
ofstr
Filename pattern(s) to include in the report. For example,
[\*raw.fif, \*ave.fif]
will includeRaw
as well asEvoked
files. IfNone
, include all supported file formats.Changed in version 0.23: Include supported non-FIFF files by default.
- n_jobs
int
The number of jobs to run in parallel (default
1
). If-1
, it is set to the number of CPU cores. Requires thejoblib
package.- mri_decim
int
Use this decimation factor for generating MRI/BEM images (since it can be time consuming).
- sort_contentbool
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.
- sort_sectionsbool
If
True
, sort the content based on tags in the order: raw -> events -> epochs -> evoked -> covariance -> coregistration -> bem -> forward-solution -> inverse-operator -> source-estimate.Deprecated since version 0.24.0: This parameter is scheduled for removal. Use
sort_content
instead.- on_error
str
What to do if a file cannot be rendered. Can be ‘ignore’, ‘warn’ (default), or ‘raise’.
- image_format‘png’ | ‘svg’ | ‘gif’ |
None
The image format to be used for the report, can be
'png'
,'svg'
, or'gif'
. None (default) will use the default specified duringReport
instantiation.New in version 0.15.
- render_bembool
If True (default), try to render the BEM.
New in version 0.16.
- n_time_points_evokeds, n_time_points_stcs
int
|None
The number of equidistant time points to render for
Evoked
andSourceEstimate
data, respectively. IfNone
, will render eachEvoked
at 21 and eachSourceEstimate
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.
- raw_butterflybool
Whether to render butterfly plots for (decimated)
Raw
data.New in version 0.24.0.
- stc_plot_kwargs
dict
Dictionary of keyword arguments to pass to
mne.SourceEstimate.plot
. Only used when plotting in 3D mode.New in version 0.24.0.
- topomap_kwargs
dict
|None
Keyword arguments to pass to topomap functions (
mne.viz.plot_evoked_topomap()
,mne.viz.plot_projs_topomap()
, etc.).New in version 0.24.0.
- verbosebool |
str
|int
|None
Control verbosity of the logging output. If
None
, use the default verbosity level. See the logging documentation andmne.verbose()
for details. Should only be passed as a keyword argument. Defaults to self.verbose.
- data_path
Examples using
parse_folder
:
- remove(caption=None, section=None, *, title=None, tags=None, remove_all=False)[source]¶
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.
- Parameters
- caption
str
Remove content based on its caption.
Deprecated since version 0.24.0: This parameter is scheduled for removal. Use
title
instead.- section
str
|None
If supplied, restrict the operation to elements within the supplied section.
Deprecated since version 0.24.0: This parameter is scheduled for removal. Use
tags
instead.- title
str
The title of the element(s) to remove.
New in version 0.24.0.
- tagscollections of
str
|None
If supplied, restrict the operation to elements with the supplied tags.
New in version 0.24.0.
- remove_allbool
Controls the behavior if multiple elements match the search criteria. If
False
(default) only the element last added to the report will be removed. IfTrue
, all matches will be removed.New in version 0.24.0.
- caption
- Returns
- save(fname=None, open_browser=True, overwrite=False, sort_content=False, *, verbose=None)[source]¶
Save the report and optionally open it in browser.
- Parameters
- fnamepath-like |
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 withopen_report()
. For any other suffix, the report will be saved in HTML format. IfNone
andReport.parse_folder()
was not called, the report is saved asreport.html
in the current working directory. IfNone
andReport.parse_folder()
was used, the report is saved asreport.html
inside thedata_path
supplied toReport.parse_folder()
.- open_browserbool
Whether to open the rendered HTML report in the default web browser after saving. This is ignored when writing an HDF5 file.
- overwritebool
If True (default False), overwrite the destination file if it exists.
- sort_contentbool
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.
- verbosebool |
str
|int
|None
Control verbosity of the logging output. If
None
, use the default verbosity level. See the logging documentation andmne.verbose()
for details. Should only be passed as a keyword argument. Defaults to self.verbose.
- fnamepath-like |
- Returns
- fname
str
The file name to which the report was saved.
- fname
Examples using
save
:
- property tags¶
All tags currently used in the report.