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[EEG Browser] Annotations: Add new and HED tags #8236

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Merged
merged 6 commits into from
Dec 1, 2022
Merged

[EEG Browser] Annotations: Add new and HED tags #8236

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9d65c26
[EEG Browser][Feature] Ability to add new annotations from module
Nov 16, 2021
5e7d0ec
phpcs
Nov 16, 2021
7c1f995
amend props in annotation form
Nov 23, 2021
93d282d
Amend metadata to include current user as annotation author
Jan 5, 2022
9f75ebe
Timeline nav, annotations form and HED tags
laemtl Nov 22, 2022
e815709
Review request changes
laemtl Nov 28, 2022
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34 changes: 33 additions & 1 deletion modules/electrophysiology_browser/css/electrophysiology_browser.css
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Original file line number Diff line number Diff line change
Expand Up @@ -42,11 +42,43 @@ svg {
user-select: none;
}

.annotation.list-group-item {
.list-group-item {
position: relative;
display: flex;
flex-direction: row;
justify-content: space-between;
align-items: center;
}

.annotation {
background: #fffae6;
border-left: 5px solid #ff6600;
}

.epoch-details {
padding-right: 100px;
}

.epoch-action {
display: flex;
flex-direction: row;
justify-content: center;
align-items: center;
position: absolute;
right: 0;
}

.epoch-tag {
padding: 5px;
background: #e7e4e4;
border-left: 5px solid #797878;
}

.epoch-tag p {
word-wrap: break-word;
width: 95%;
}

.event-list .btn.btn-primary {
color: #555;
border: 1px solid #555;
Expand Down
2 changes: 1 addition & 1 deletion modules/electrophysiology_browser/jsx/components/DownloadPanel.js
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Original file line number Diff line number Diff line change
Expand Up @@ -91,7 +91,7 @@ class DownloadPanel extends Component {
>Not Available</a>
: <a
className='btn btn-primary download col-xs-6'
href={this.state.outputType == 'derivative' &&
href={
(download.type ==
'physiological_annotation_files' ||
download.type == 'all_files') ?
Expand Down
288 changes: 149 additions & 139 deletions modules/electrophysiology_browser/jsx/electrophysiologySessionView.js
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Original file line number Diff line number Diff line change
Expand Up @@ -145,6 +145,8 @@ class ElectrophysiologySessionView extends Component {
chunksURL: null,
epochsURL: null,
electrodesURL: null,
events: null,
annotations: null,
splitData: null,
},
],
Expand Down Expand Up @@ -192,10 +194,10 @@ class ElectrophysiologySessionView extends Component {
}
return resp.json();
})
.then((data) => {
.then((data) => {
const database = data.database.map((dbEntry) => ({
...dbEntry,
// EEG Visualization parameters
// EEG Visualization urls
chunksURLs:
dbEntry
&& dbEntry.file.chunks_urls.map(
Expand All @@ -218,7 +220,10 @@ class ElectrophysiologySessionView extends Component {
&& loris.BaseURL
+ '/electrophysiology_browser/file_reader/?file='
+ group.links[1].file
),
),
events:
dbEntry
&& dbEntry.file.events,
annotations:
dbEntry
&& dbEntry.file.annotations,
Expand Down Expand Up @@ -305,13 +310,13 @@ class ElectrophysiologySessionView extends Component {
render() {
if (!this.state.isLoaded) {
return (
<button className='btn-info has-spinner'>
<button className='btn-info has-spinner'>
Loading
<span
className='glyphicon glyphicon-refresh glyphicon-refresh-animate'>
className='glyphicon glyphicon-refresh glyphicon-refresh-animate'>
</span>
</button>
);
</button>
);
}

if (this.state.isLoaded) {
Expand All @@ -320,153 +325,158 @@ class ElectrophysiologySessionView extends Component {
const {
chunksURLs,
epochsURL,
electrodesURL,
events,
annotations,
electrodesURL,
} = this.state.database[i];
const file = this.state.database[i].file;
const splitPagination = [];
for (const j of Array(file.splitData?.splitCount).keys()) {
splitPagination.push(
<a
key={j}
className={
'btn btn-xs btn-primary split-nav'
+ (file.splitData?.splitIndex === j ? ' active' : '')
}
onClick={() => this.getSplitData(file.id, i, j)}
>{j+1}</a>
);
<a
key={j}
className={
'btn btn-xs btn-primary split-nav'
+ (file.splitData?.splitIndex === j ? ' active' : '')
}
onClick={() => this.getSplitData(file.id, i, j)}
>{j+1}</a>
);
}
database.push(
<div key={i}>
<div key={i}>
<FilePanel
id={'filename_panel_' + i}
title={this.state.database[i].file.name}
data={this.state.database[i].file.details}
id={'filename_panel_' + i}
title={this.state.database[i].file.name}
data={this.state.database[i].file.details}
>
<div className="react-series-data-viewer-scoped col-xs-12">
<EEGLabSeriesProvider
chunksURL={
chunksURLs?.[file.splitData?.splitIndex] || chunksURLs
}
epochsURL={epochsURL}
electrodesURL={electrodesURL}
<div className="react-series-data-viewer-scoped col-xs-12">
<EEGLabSeriesProvider
chunksURL={
chunksURLs?.[file.splitData?.splitIndex] || chunksURLs
}
epochsURL={epochsURL}
events={events}
annotations={annotations}
>
<Panel
id='channel-viewer'
title={
'Signal Viewer' + (file.splitData
? ' [split '+(file.splitData?.splitIndex+1)+']'
: ''
)
}
>
{file.splitData &&
<>
<span
style={{
color: '#064785',
fontWeight: 'bold',
fontSize: '14px',
paddingRight: '15px',
}}
>
Viewing signal split file:
</span>
<a
className={
'btn btn-xs btn-default split-nav'
+ (file.splitData.splitIndex === 0
? ' disabled'
: '')
}
onClick={() => this.getSplitData(
file.id,
i,
file.splitData.splitIndex-1
)}
>
{'<'}
</a>
{splitPagination}
<a
className={
'btn btn-xs btn-default split-nav'
+ (file.splitData.splitIndex
=== (file.splitData.splitCount-1)
? ' disabled'
: '')
}
onClick={
() => this.getSplitData(
file.id,
i,
file.splitData.splitIndex+1
)
}
>
{'>'}
</a>
</>
}
<SeriesRenderer />
</Panel>
<div className='row'>
<div className='col-md-6 col-lg-4'>
<SummaryPanel
id={'filename_summary_' + i}
data={this.state.database[i].file.summary}
/>
</div>
<EEGMontage />
<div className='col-md-6 col-lg-4'>
<DownloadPanel
id={'file_download_' + i}
downloads={this.state.database[i].file.downloads}
physioFileID={this.state.database[i].file.id}
outputType={this.state.database[i].file.output_type}
/>
</div>
</div>
</EEGLabSeriesProvider>
</div>
</FilePanel>
</div>
);
electrodesURL={electrodesURL}
>
<Panel
id='channel-viewer'
title={
'Signal Viewer' + (file.splitData
? ' [split '+(file.splitData?.splitIndex+1)+']'
: ''
)
}
>
{file.splitData &&
<>
<span
style={{
color: '#064785',
fontWeight: 'bold',
fontSize: '14px',
paddingRight: '15px',
}}
>
Viewing signal split file:
</span>
<a
className={
'btn btn-xs btn-default split-nav'
+ (file.splitData.splitIndex === 0
? ' disabled'
: '')
}
onClick={() => this.getSplitData(
file.id,
i,
file.splitData.splitIndex-1
)}
>
{'<'}
</a>
{splitPagination}
<a
className={
'btn btn-xs btn-default split-nav'
+ (file.splitData.splitIndex
=== (file.splitData.splitCount-1)
? ' disabled'
: '')
}
onClick={
() => this.getSplitData(
file.id,
i,
file.splitData.splitIndex+1
)
}
>
{'>'}
</a>
</>
}
<SeriesRenderer
physioFileID={this.state.database[i].file.id}
annotationMetadata={annotations}
/>
</Panel>
<div className='row'>
<div className='col-md-6 col-lg-4'>
<SummaryPanel
id={'filename_summary_' + i}
data={this.state.database[i].file.summary}
/>
</div>
<EEGMontage />
<div className='col-md-6 col-lg-4'>
<DownloadPanel
id={'file_download_' + i}
downloads={this.state.database[i].file.downloads}
physioFileID={this.state.database[i].file.id}
outputType={this.state.database[i].file.output_type}
/>
</div>
</div>
</EEGLabSeriesProvider>
</div>
</FilePanel>
</div>
);
}

return (
<div id='lorisworkspace'>
<div id='lorisworkspace'>
<StaticDataTable
Headers={[
'PSCID',
'DCCID',
'Visit Label',
'Site',
'DOB',
'Sex',
'Output Type',
'Cohort',
]}
Data={[
[
this.state.patient.info.pscid,
this.state.patient.info.dccid,
this.state.patient.info.visit_label,
this.state.patient.info.site,
this.state.patient.info.dob,
this.state.patient.info.sex,
this.state.patient.info.output_type,
this.state.patient.info.cohort,
],
]}
freezeColumn='PSCID'
Hide={{rowsPerPage: true, downloadCSV: true, defaultColumn: true}}
/>
{database}
</div>
);
Headers={[
'PSCID',
'DCCID',
'Visit Label',
'Site',
'DOB',
'Sex',
'Output Type',
'Cohort',
]}
Data={[
[
this.state.patient.info.pscid,
this.state.patient.info.dccid,
this.state.patient.info.visit_label,
this.state.patient.info.site,
this.state.patient.info.dob,
this.state.patient.info.sex,
this.state.patient.info.output_type,
this.state.patient.info.cohort,
],
]}
freezeColumn='PSCID'
Hide={{rowsPerPage: true, downloadCSV: true, defaultColumn: true}}
/>
{database}
</div>
);
}
}
}
Expand Down
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