IntegrationRoiManager

scanimage.components.IntegrationRoiManager, reachable as hSI.hIntegrationRoiManager, computes intensity traces from integration ROIs while an acquisition runs, and can drive analog or digital outputs from those traces.

Properties

Property	Description
`roiGroup`	`scanimage.mroi.RoiGroup` holding the integration ROIs.
`enable`	Enable the computation of intensity traces.
`enableDisplay`	Plot the traces.
`integrationHistoryLength`	Number of samples retained in the trace history. Default 1000.
`postProcessFcn`	Function handle applied to the integration values before they drive the outputs.
`outputChannelsNames`	Names of the configured output channels.
`outputChannelsPhysicalNames`	The physical terminal each output channel is bound to.
`outputChannelsEnabled`	Logical array, one per output channel.
`outputChannelsFunctions`	Cell array of function handles, one per output channel, mapping integration values to an output value.
`outputChannelsRoiNames`	The ROI each output channel evaluates.

Methods

Method	Description
`[intRois,values,timestamps,framenumbers] = hSI.hIntegrationRoiManager.getIntegrationValues()`	The most recent integration value for each ROI.
`[intRois,valueHistory,timestampHistory,framenumberHistory] = hSI.hIntegrationRoiManager.getIntegrationHistory()`	The retained history, `integrationHistoryLength` samples deep.
`hSI.hIntegrationRoiManager.refreshOutputChannelsList()`	Re-read the configured `dabs.generic.IntegrationRoiOutputChannel` devices.

hSI.hIntegrationRoiManager.enable = true;

[rois,vals,ts] = hSI.hIntegrationRoiManager.getIntegrationValues();
for idx = 1:numel(rois)
    fprintf('%s: %.3f\n',rois(idx).name,vals(idx));
end

% history, for plotting
[rois,hist,tHist] = hSI.hIntegrationRoiManager.getIntegrationHistory();
plot(tHist,hist);

Post processing and outputs

postProcessFcn runs on every update, before the output channel functions. It is the hook for closed-loop experiments: threshold a trace, and drive an output.

The signature matches the shipped default, scanimage.components.integrationRois.integrationPostProcessingFcn, which simply passes the values through:

hSI.hIntegrationRoiManager.postProcessFcn = @myPostProcess;

function integrationValues = myPostProcess(rois,integrationDone,arrayIndices, ...
        integrationValueHistory,integrationTimestampHistory,integrationFrameNumberHistory)
    integrationValues = integrationValueHistory(arrayIndices);
    % ... modify integrationValues here ...
end

Setting postProcessFcn to empty restores the default function.

Note

The post-process function and the output channel functions run inside the frame callback. Keep them short - work done here delays the display and, on a loaded system, the acquisition.

Events

updateAnalysisDisplay fires when new integration values are available; resetIntegrationRoiDisplay fires when the display should be cleared, for example when the ROI group changes.