use of org.vcell.vmicro.op.ImportRawTimeSeriesFromVFrapOp in project vcell by virtualcell.
the class VFrapProcess method main.
public static void main(String[] args) {
try {
File baseDir = new File(".");
// File baseDir = new File("/Users/schaff/Documents/workspace/VCell_5.4");
// initialize computing environment
//
File workingDirectory = new File(baseDir, "workingDir");
LocalWorkspace localWorkspace = new LocalWorkspace(workingDirectory);
//
// import raw image time series data from VFRAP file format (can have noise, background, etc ... can be actual microscopy data)
//
ClientTaskStatusSupport progressListener = new ClientTaskStatusSupport() {
String message = "";
int progress = 0;
@Override
public void setProgress(int progress) {
this.progress = progress;
}
@Override
public void setMessage(String message) {
this.message = message;
}
@Override
public boolean isInterrupted() {
return false;
}
@Override
public int getProgress() {
return progress;
}
@Override
public void addProgressDialogListener(ProgressDialogListener progressDialogListener) {
}
};
//
// generate fake data (and save?)
//
// ImageTimeSeries<UShortImage> simulatedFluorescence = generateFakeData(localWorkspace, progressListener);
// new ExportRawTimeSeriesToVFrapOp().exportToVFRAP(vfrapFile, simulatedFluorescence, null);
//
// analyze raw data (from file?) using Keyworthy method.
//
File vfrapFile = new File(baseDir, "vfrapPaper/rawData/sim3/workflow.txt.save");
ImageTimeSeries<UShortImage> fluorTimeSeriesImages = new ImportRawTimeSeriesFromVFrapOp().importRawTimeSeriesFromVFrap(vfrapFile);
VFrapProcessResults results = compute(fluorTimeSeriesImages, 0.85, 0.4, localWorkspace, progressListener);
new DisplayTimeSeriesOp().displayImageTimeSeries(fluorTimeSeriesImages, "raw data", null);
new DisplayImageOp().displayImage(results.cellROI_2D.getRoiImages()[0], "cell ROI", null);
new DisplayImageOp().displayImage(results.bleachROI_2D.getRoiImages()[0], "bleach ROI", null);
new DisplayDependentROIsOp().displayDependentROIs(results.imageDataROIs, results.cellROI_2D, "data rois", null);
new DisplayTimeSeriesOp().displayImageTimeSeries(results.normalizedTimeSeries, "normalized data", null);
new DisplayProfileLikelihoodPlotsOp().displayProfileLikelihoodPlots(results.profileDataOne, "one fluorescent pool", null);
new DisplayProfileLikelihoodPlotsOp().displayProfileLikelihoodPlots(results.profileDataTwoWithPenalty, "too pools", null);
} catch (Exception e) {
e.printStackTrace(System.out);
}
}
use of org.vcell.vmicro.op.ImportRawTimeSeriesFromVFrapOp in project vcell by virtualcell.
the class PhotoactivationExperimentTest method main.
public static void main(String[] args) {
try {
File baseDir = new File(".");
// File baseDir = new File("/Users/schaff/Documents/workspace/VCell_5.4");
// initialize computing environment
//
File workingDirectory = new File(baseDir, "workingDir");
LocalWorkspace localWorkspace = new LocalWorkspace(workingDirectory);
//
// import raw image time series data from VFRAP file format (can have noise, background, etc ... can be actual microscopy data)
//
ClientTaskStatusSupport progressListener = new ClientTaskStatusSupport() {
String message = "";
int progress = 0;
@Override
public void setProgress(int progress) {
this.progress = progress;
}
@Override
public void setMessage(String message) {
this.message = message;
}
@Override
public boolean isInterrupted() {
return false;
}
@Override
public int getProgress() {
return progress;
}
@Override
public void addProgressDialogListener(ProgressDialogListener progressDialogListener) {
}
};
//
// generate fake data (and save?)
//
// ImageTimeSeries<UShortImage> simulatedFluorescence = generateFakeData(localWorkspace, progressListener);
// new ExportRawTimeSeriesToVFrapOp().exportToVFRAP(vfrapFile, simulatedFluorescence, null);
//
// analyze raw data (from file?) using Keyworthy method.
//
// File vfrapFile = new File(baseDir, "vfrapPaper/photoactivation/Actin.vfrap");
File vfrapFile = new File(baseDir, "vfrapPaper/photoactivation/Actin_binding_protein.vfrap");
ImageTimeSeries<UShortImage> fluorTimeSeriesImages = new ImportRawTimeSeriesFromVFrapOp().importRawTimeSeriesFromVFrap(vfrapFile);
analyzePhotoactivation(fluorTimeSeriesImages, localWorkspace);
} catch (Exception e) {
e.printStackTrace(System.out);
}
}
use of org.vcell.vmicro.op.ImportRawTimeSeriesFromVFrapOp in project vcell by virtualcell.
the class KenworthyWorkflowTest method main.
public static void main(String[] args) {
try {
File baseDir = new File(".");
// File baseDir = new File("/Users/schaff/Documents/workspace/VCell_5.4");
// initialize computing environment
//
File workingDirectory = new File(baseDir, "workingDir");
LocalWorkspace localWorkspace = new LocalWorkspace(workingDirectory);
//
// import raw image time series data from VFRAP file format (can have noise, background, etc ... can be actual microscopy data)
//
ClientTaskStatusSupport progressListener = new ClientTaskStatusSupport() {
String message = "";
int progress = 0;
@Override
public void setProgress(int progress) {
this.progress = progress;
}
@Override
public void setMessage(String message) {
this.message = message;
}
@Override
public boolean isInterrupted() {
return false;
}
@Override
public int getProgress() {
return progress;
}
@Override
public void addProgressDialogListener(ProgressDialogListener progressDialogListener) {
}
};
//
// generate fake data (and save?)
//
// ImageTimeSeries<UShortImage> simulatedFluorescence = generateFakeData(localWorkspace, progressListener);
// new ExportRawTimeSeriesToVFrapOp().exportToVFRAP(vfrapFile, simulatedFluorescence, null);
//
// analyze raw data (from file?) using Keyworthy method.
//
File vfrapFile = new File(baseDir, "vfrapPaper/rawData/sim3/workflow.txt.save");
// File vfrapFile = new File(baseDir, "tryit.vfrap");
ImageTimeSeries<UShortImage> fluorTimeSeriesImages = new ImportRawTimeSeriesFromVFrapOp().importRawTimeSeriesFromVFrap(vfrapFile);
analyzeKeyworthy(fluorTimeSeriesImages, localWorkspace);
} catch (Exception e) {
e.printStackTrace(System.out);
}
}
use of org.vcell.vmicro.op.ImportRawTimeSeriesFromVFrapOp in project vcell by virtualcell.
the class KenworthyParticleTest method main.
public static void main(String[] args) {
try {
File baseDir = new File(".");
// File baseDir = new File("/Users/schaff/Documents/workspace/VCell_5.4");
// initialize computing environment
//
File workingDirectory = new File(baseDir, "workingDir");
LocalWorkspace localWorkspace = new LocalWorkspace(workingDirectory);
//
// analyze raw data (from file?) using Keyworthy method.
//
// File vfrapFile = new File(baseDir, "vfrapPaper/rawData/sim3/workflow.txt.save");
File vfrapFile = new File(baseDir, "tryit.vfrap");
ImageTimeSeries<UShortImage> fluorTimeSeriesImages = new ImportRawTimeSeriesFromVFrapOp().importRawTimeSeriesFromVFrap(vfrapFile);
RowColumnResultSet reducedData = new CSV().importFrom(new FileReader(new File(baseDir, "tryit.csv")));
analyzeKeyworthy(fluorTimeSeriesImages, reducedData, localWorkspace);
} catch (Exception e) {
e.printStackTrace(System.out);
}
}
use of org.vcell.vmicro.op.ImportRawTimeSeriesFromVFrapOp in project vcell by virtualcell.
the class ImportRawTimeSeriesFromVFrap method compute0.
@Override
protected void compute0(TaskContext context, ClientTaskStatusSupport clientTaskStatusSupport) throws Exception {
// get input
File vfrap_file = context.getData(vfrapFile);
// do op
ImportRawTimeSeriesFromVFrapOp op = new ImportRawTimeSeriesFromVFrapOp();
ImageTimeSeries<UShortImage> imageTimeSeries = op.importRawTimeSeriesFromVFrap(vfrap_file);
// set output
context.setData(rawTimeSeriesImages, imageTimeSeries);
}
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