@Override
public void process(int z, int t, int p) {
// called for each z,t,p by DatasetIterator.iterateAll();
System.out.println("MagOrientProcessor.process(" + z + "," + t + "," + p + ")");
ArrayList<TaggedImage> sampleImgs = new ArrayList<TaggedImage>();
for (int i = 0; i < numSamples; i++) {
TaggedImage img = mda.getImageCache().getImage(i + 2, z, t, p);
if (img == null) {
System.out.println(
"**** " + "img==null at submit i: " + i + " z: " + z + " t: " + t + " p: " + p);
}
sampleImgs.add(img);
}
// Assuming channels : {mag,ort,0,1,2,3,4}
// TaggedImage magImage = in.getImage(0, z, t, p);
// TaggedImage ortImage = in.getImage(1, z, t, p);
// Set Parameters...
Map<String, Object> parameters = new HashMap<String, Object>();
parameters.put("Swing", 0.03);
parameters.put("BkgdCorrected", true);
parameters.put("summaryMetadata", mda.getImageCache().getSummaryMetadata());
parameters.put("sampleImages", sampleImgs);
// proc.setInputParameters(parameters);
IProcess proc = new ProcessMagOrt(this.parameters, this.data);
proc.process();
processResult(proc);
}
// Test Main =============================================================================
public static void main(String[] args) {
try {
String dir = "C:/MicroManagerData/TestDatasetGen";
String prefixIn = "pssynth_100";
String prefixOut = "processed";
//
MMgrDatasetAccessor mda = new MMgrDatasetAccessor(dir, prefixIn, false, false);
JSONObject sumMD_In = mda.getImageCache().getSummaryMetadata();
// Create new metadata based on the input dataset...
JSONObject sumMDOut =
SumMetadata.newCopyOfSummaryMetadata(sumMD_In, dir, prefixOut, true, "Extraction");
JSONObject dispMD = mda.getImageCache().getDisplayAndComments();
//
// Change /add metadata...
String[] channelNames = new String[] {"Mag", "Ort"}; // define channels
MMgrDatasetGenerator mdg = new MMgrDatasetGenerator(sumMDOut);
DimensionalExtents dsdIn = SumMetadata.getDimensionalExtents(sumMD_In);
// create processor...
ChannelSetProcessor magOrtProcessor = new MagOrientChannelSetProcessor(mda, mdg);
magOrtProcessor.addParameter("Swing", 0.03);
magOrtProcessor.addParameter("BkgdCorrected", true);
//
DatasetIterator dsIter = new DatasetIterator(SumMetadata.getDimensionalExtents(sumMD_In));
dsIter.setChannelSetProcessor(magOrtProcessor);
dsIter.iterateAll(); // run the process on all the dimensions
if (dsIter.isCancelled()) {
mdg.cancel();
}
//
System.exit(0);
} catch (Exception ex) {
}
}
private DerivedFrom createDerivedFrom(IProcess proc) {
Transform xform = new Transform(proc.getName(), proc.getInputParameters());
String antecentPath = mda.getImageCache().getDiskLocation();
String resultPath = mdg.getImageCache().getDiskLocation();
String relPath = PathUtils.getRelativePath(antecentPath, resultPath);
DerivedFrom df =
DerivedFrom.createDerivedFrom(
relPath, (List<TaggedImage>) proc.getInputParameters().get("sampleImages"), xform);
return df;
}
public void extractFrom() {
try {
MMgrDatasetAccessor datasetIn = new MMgrDatasetAccessor(inputPath, inputPrefix, false, false);
JSONObject sumMD_In = datasetIn.getImageCache().getSummaryMetadata();
// create new multi-page dataset...
JSONObject sumMDOut =
SumMetadata.newCopyOfSummaryMetadata(
sumMD_In, outputDir, outputPrefix, true, "Extraction");
// change dimensions
SumMetadata.applyDimensionalExtents(
sumMDOut, sliceIndices.length, frameIndices.length, positionIndices.length);
// change channelIndices
String[] channelNamesIn = SumMetadata.getChannelNames(sumMD_In);
String[] channelNamesNew = new String[channelIndices.length];
for (int i = 0; i < channelIndices.length; i++) {
channelNamesNew[i] = channelNamesIn[channelIndices[i]];
}
SumMetadata.setChannelsAndDisplay(sumMDOut, channelNamesNew);
//
MMgrDatasetGenerator datasetOut =
new MMgrDatasetGenerator(
sumMDOut, isMultiPage, seperateMDFile, seperateFilesForPositions);
// ***********
for (int pos = 0; pos < positionIndices.length; pos++) {
for (int frame = 0; frame < frameIndices.length; frame++) {
for (int slice = 0; slice < sliceIndices.length; slice++) {
for (int chan = 0; chan < channelIndices.length; chan++) {
TaggedImage img =
datasetIn
.getImageCache()
.getImage(
channelIndices[chan], sliceIndices[slice],
frameIndices[frame], positionIndices[pos]);
PrintWhatever.out(
channelIndices[chan],
sliceIndices[slice],
frameIndices[frame],
positionIndices[pos]);
JSONObject frameMD = img.tags;
// Change metadata to new dimensionalIndicies: (chan,slice,frame,pos)
// TODO...
PrintWhatever.out(chan, slice, frame, pos);
// System.out.println("");
// set channelName
try {
datasetOut.putImage(img);
} catch (Exception ex) {
Logger.getLogger(DatasetGenTester.class.getName()).log(Level.SEVERE, null, ex);
ex.printStackTrace();
}
}
}
}
}
datasetOut.stop();
} catch (Exception ex) {
Logger.getLogger(DatasetExtractor.class.getName()).log(Level.SEVERE, null, ex);
}
}
public MagOrientChannelSetProcessor(MMgrDatasetAccessor mda, MMgrDatasetGenerator mdg) {
this.mda = mda;
this.mdg = mdg;
in = mda.getImageCache();
}
