public void setChannelColor(Color color, int imageIndex, int channelIndex) { // Parents: {u'Pixels': {u'Image': {u'OME': None}}} // Color is not a reference OME o0 = root; if (o0.sizeOfImageList() == imageIndex) { o0.addImage(new Image()); } Image o1 = o0.getImage(imageIndex); if (o1.getPixels() == null) { o1.setPixels(new Pixels()); } Pixels o2 = o1.getPixels(); if (o2.sizeOfChannelList() == channelIndex) { o2.addChannel(new Channel()); } Channel o3 = o2.getChannel(channelIndex); o3.setColor(color); }
setSizeT(PositiveInteger.valueOf( element.getAttribute("SizeT"))); setDimensionOrder(DimensionOrder.fromString( element.getAttribute("DimensionOrder"))); unitSymbol = getPhysicalSizeZUnitXsdDefault(); setPhysicalSizeZ(UnitsLengthEnumHandler.getQuantity(baseValue, modelUnit)); unitSymbol = getPhysicalSizeYUnitXsdDefault(); setPhysicalSizeY(UnitsLengthEnumHandler.getQuantity(baseValue, modelUnit)); unitSymbol = getPhysicalSizeXUnitXsdDefault(); setPhysicalSizeX(UnitsLengthEnumHandler.getQuantity(baseValue, modelUnit)); setSizeX(PositiveInteger.valueOf( element.getAttribute("SizeX"))); setSizeY(PositiveInteger.valueOf( element.getAttribute("SizeY"))); setSizeZ(PositiveInteger.valueOf( element.getAttribute("SizeZ"))); setBigEndian(Boolean.valueOf( element.getAttribute("BigEndian")));
/** @see OMEXMLService#removeTiffData(OMEXMLMetadata) */ @Override public void removeTiffData(OMEXMLMetadata omexmlMeta) { omexmlMeta.resolveReferences(); OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) omexmlMeta.getRoot(); List<Image> images = root.copyImageList(); for (Image img : images) { Pixels pix = img.getPixels(); List<TiffData> tiffData = pix.copyTiffDataList(); for (TiffData tiff : tiffData) { pix.removeTiffData(tiff); } pix.setMetadataOnly(null); } omexmlMeta.setRoot(root); }
/** @see OMEXMLService#removeBinData(OMEXMLMetadata) */ @Override public void removeBinData(OMEXMLMetadata omexmlMeta) { omexmlMeta.resolveReferences(); OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) omexmlMeta.getRoot(); List<Image> images = root.copyImageList(); for (Image img : images) { Pixels pix = img.getPixels(); List<BinData> binData = pix.copyBinDataList(); for (BinData bin : binData) { pix.removeBinData(bin); } pix.setMetadataOnly(null); } omexmlMeta.setRoot(root); }
image.setID("Image:" + index); Pixels pixels = new Pixels(); pixels.setID("Pixels:" + index); pixels.setSizeX(new PositiveInteger(SIZE_X)); pixels.setSizeY(new PositiveInteger(SIZE_Y)); pixels.setSizeZ(new PositiveInteger(SIZE_Z)); pixels.setSizeC(new PositiveInteger(SIZE_C)); pixels.setSizeT(new PositiveInteger(SIZE_T)); pixels.setDimensionOrder(DIMENSION_ORDER); pixels.setType(PIXEL_TYPE); binData.setLength(new NonNegativeLong( (long) (SIZE_X * SIZE_Y * BYTES_PER_PIXEL))); pixels.addBinData(binData); Channel channel = new Channel(); channel.setID("Channel:" + i); pixels.addChannel(channel);
image.setStageLabel(createStageLabel()); Pixels pixels = new Pixels(); pixels.setID("Pixels:"+index); pixels.setSizeX(new PositiveInteger(SIZE_X)); pixels.setSizeY(new PositiveInteger(SIZE_Y)); pixels.setSizeZ(new PositiveInteger(SIZE_Z)); pixels.setSizeC(new PositiveInteger(SIZE_C)); pixels.setSizeT(new PositiveInteger(SIZE_T)); pixels.setPhysicalSizeX(new Length(1, UNITS.MICROMETER)); pixels.setPhysicalSizeY(new Length(1, UNITS.MICROMETER)); pixels.setPhysicalSizeZ(new Length(1, UNITS.MICROMETER)); pixels.setDimensionOrder(DIMENSION_ORDER); pixels.setType(PIXEL_TYPE); if (!metadata) { BinData data; for (int i = 0; i < SIZE_Z*SIZE_C*SIZE_T; i++) { data = createBinData(SIZE_X, SIZE_Y, BYTES_PER_PIXEL); pixels.addBinData(data); for (int t = 0; t < SIZE_T; t++) { for (int c = 0; c < SIZE_C; c++) { pixels.addPlane(createPlane(z, c, t)); j++; pixels.addChannel(channel);
Pixels pixels = new Pixels(); pixels.setID("Pixels:0"); Channel channel = new Channel(); channel.setID("Channel:0"); settings.setID("LightSource:0"); channel.setLightSourceSettings(settings); pixels.addChannel(channel); image.setPixels(pixels); ome.addImage(image);
public void setPixelsBinDataCompression(Compression compression, int imageIndex, int binDataIndex) { // Parents: {u'BinaryFile': {u'FileAnnotation': {u'StructuredAnnotations': {u'OME': None}}}, u'Mask': None, u'Pixels': {u'Image': {u'OME': None}}} // Compression is not a reference OME o0 = root; if (o0.sizeOfImageList() == imageIndex) { o0.addImage(new Image()); } Image o1 = o0.getImage(imageIndex); if (o1.getPixels() == null) { o1.setPixels(new Pixels()); } Pixels o2 = o1.getPixels(); if (o2.sizeOfBinDataList() == binDataIndex) { o2.addBinData(new BinData()); } BinData o3 = o2.getBinData(binDataIndex); o3.setCompression(compression); }
public void setPixelsID(String id, int imageIndex) { // Parents: {u'Image': {u'OME': None}} // ID is not a reference OME o0 = root; if (o0.sizeOfImageList() == imageIndex) { o0.addImage(new Image()); } Image o1 = o0.getImage(imageIndex); if (o1.getPixels() == null) { o1.setPixels(new Pixels()); } Pixels o2 = o1.getPixels(); model.addModelObject(id, o2); o2.setID(id); }
public void setPlaneDeltaT(Time deltaT, int imageIndex, int planeIndex) { // Parents: {u'Pixels': {u'Image': {u'OME': None}}} // DeltaT is not a reference OME o0 = root; if (o0.sizeOfImageList() == imageIndex) { o0.addImage(new Image()); } Image o1 = o0.getImage(imageIndex); if (o1.getPixels() == null) { o1.setPixels(new Pixels()); } Pixels o2 = o1.getPixels(); if (o2.sizeOfPlaneList() == planeIndex) { o2.addPlane(new Plane()); } Plane o3 = o2.getPlane(planeIndex); o3.setDeltaT(deltaT); }
Image img = images.get(i); Pixels pix = img.getPixels(); List<Plane> planes = pix.copyPlaneList(); for (int p=0; p<planes.size(); p++) { Plane plane = planes.get(p); plane.getTheT().getValue() >= core.get(i, 0).sizeT) pix.removePlane(planes.get(p)); pix.setMetadataOnly(null); List<Channel> channels = pix.copyChannelList(); for (int c=0; c<channels.size(); c++) { if (c < cBounds.get(i)[0] || c > cBounds.get(i)[1]) { pix.removeChannel(channels.get(c));
public void setPixelsSizeT(PositiveInteger sizeT, int imageIndex) { // Parents: {u'Image': {u'OME': None}} // SizeT is not a reference OME o0 = root; if (o0.sizeOfImageList() == imageIndex) { o0.addImage(new Image()); } Image o1 = o0.getImage(imageIndex); if (o1.getPixels() == null) { o1.setPixels(new Pixels()); } Pixels o2 = o1.getPixels(); o2.setSizeT(sizeT); }
public void setPixelsSizeC(PositiveInteger sizeC, int imageIndex) { // Parents: {u'Image': {u'OME': None}} // SizeC is not a reference OME o0 = root; if (o0.sizeOfImageList() == imageIndex) { o0.addImage(new Image()); } Image o1 = o0.getImage(imageIndex); if (o1.getPixels() == null) { o1.setPixels(new Pixels()); } Pixels o2 = o1.getPixels(); o2.setSizeC(sizeC); }
public void setPixelsSizeY(PositiveInteger sizeY, int imageIndex) { // Parents: {u'Image': {u'OME': None}} // SizeY is not a reference OME o0 = root; if (o0.sizeOfImageList() == imageIndex) { o0.addImage(new Image()); } Image o1 = o0.getImage(imageIndex); if (o1.getPixels() == null) { o1.setPixels(new Pixels()); } Pixels o2 = o1.getPixels(); o2.setSizeY(sizeY); }
public void setPixelsDimensionOrder(DimensionOrder dimensionOrder, int imageIndex) { // Parents: {u'Image': {u'OME': None}} // DimensionOrder is not a reference OME o0 = root; if (o0.sizeOfImageList() == imageIndex) { o0.addImage(new Image()); } Image o1 = o0.getImage(imageIndex); if (o1.getPixels() == null) { o1.setPixels(new Pixels()); } Pixels o2 = o1.getPixels(); o2.setDimensionOrder(dimensionOrder); }
public void setPixelsSizeX(PositiveInteger sizeX, int imageIndex) { // Parents: {u'Image': {u'OME': None}} // SizeX is not a reference OME o0 = root; if (o0.sizeOfImageList() == imageIndex) { o0.addImage(new Image()); } Image o1 = o0.getImage(imageIndex); if (o1.getPixels() == null) { o1.setPixels(new Pixels()); } Pixels o2 = o1.getPixels(); o2.setSizeX(sizeX); }
public void setPixelsType(PixelType type, int imageIndex) { // Parents: {u'Image': {u'OME': None}} // Type is not a reference OME o0 = root; if (o0.sizeOfImageList() == imageIndex) { o0.addImage(new Image()); } Image o1 = o0.getImage(imageIndex); if (o1.getPixels() == null) { o1.setPixels(new Pixels()); } Pixels o2 = o1.getPixels(); o2.setType(type); }
public void setPixelsSizeZ(PositiveInteger sizeZ, int imageIndex) { // Parents: {u'Image': {u'OME': None}} // SizeZ is not a reference OME o0 = root; if (o0.sizeOfImageList() == imageIndex) { o0.addImage(new Image()); } Image o1 = o0.getImage(imageIndex); if (o1.getPixels() == null) { o1.setPixels(new Pixels()); } Pixels o2 = o1.getPixels(); o2.setSizeZ(sizeZ); }
public void setPixelsPhysicalSizeX(Length physicalSizeX, int imageIndex) { // Parents: {u'Image': {u'OME': None}} // PhysicalSizeX is not a reference OME o0 = root; if (o0.sizeOfImageList() == imageIndex) { o0.addImage(new Image()); } Image o1 = o0.getImage(imageIndex); if (o1.getPixels() == null) { o1.setPixels(new Pixels()); } Pixels o2 = o1.getPixels(); o2.setPhysicalSizeX(physicalSizeX); }
public void setPixelsPhysicalSizeY(Length physicalSizeY, int imageIndex) { // Parents: {u'Image': {u'OME': None}} // PhysicalSizeY is not a reference OME o0 = root; if (o0.sizeOfImageList() == imageIndex) { o0.addImage(new Image()); } Image o1 = o0.getImage(imageIndex); if (o1.getPixels() == null) { o1.setPixels(new Pixels()); } Pixels o2 = o1.getPixels(); o2.setPhysicalSizeY(physicalSizeY); }