mirror of
https://github.com/paulscherrerinstitute/ch.psi.imagej.hdf5.git
synced 2025-06-04 09:40:39 +02:00
Further cleanup reader ...
This commit is contained in:
parent
1ad581d126
commit
10b0052c6f
@ -127,13 +127,13 @@ public class HDF5Reader implements PlugIn {
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wholeDataset = checkUnsigned(datatype, wholeDataset);
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ImageStack stack = new ImageStack((int) dimensions[3], (int) dimensions[2]);
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long stackSize = dimensions[2] * dimensions[3];
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long singleVolumeSize = dimensions[1] * stackSize;
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int stackSize = (int) (dimensions[2] * dimensions[3]);
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int singleVolumeSize = (int) (dimensions[1] * stackSize);
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for (int volIDX = 0; volIDX < dimensions[0]; ++volIDX) {
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for (int lev = 0; lev < dimensions[1]; ++lev) {
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int startIdx = (int) ((volIDX * singleVolumeSize * 3) + (lev * stackSize * 3));
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int endIdx = (int) (startIdx + stackSize * 3 - 1);
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copyPixels3(datatypeIfUnsupported, (int) dimensions[2], (int) dimensions[3], stack, wholeDataset, (int) stackSize, startIdx, endIdx);
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int startIdx = (volIDX * singleVolumeSize * 3) + (lev * stackSize * 3);
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int endIdx = startIdx + stackSize * 3 - 1;
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copyPixels4D_RGB(datatypeIfUnsupported, (int) dimensions[2], (int) dimensions[3], stack, wholeDataset, (int) stackSize, startIdx, endIdx);
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}
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}
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@ -164,7 +164,7 @@ public class HDF5Reader implements PlugIn {
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int startIdx = (int) (lev * stackSize);
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int endIdx = (int) (startIdx + stackSize - 1);
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int size = (int) (dimensions[2] * dimensions[1]);
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copyPixels1((int) dimensions[1], (int) dimensions[2], stack, wholeDataset, size, startIdx, endIdx);
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copyPixels3D_RGB((int) dimensions[1], (int) dimensions[2], stack, wholeDataset, size, startIdx, endIdx);
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}
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ImagePlus imp = new ImagePlus(directory + name + " " + datasetName, stack);
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@ -219,7 +219,7 @@ public class HDF5Reader implements PlugIn {
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wholeDataset = checkUnsigned(datatype, wholeDataset);
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ImageStack stack = new ImageStack((int) dimensions[1], (int) dimensions[0]);
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copyPixels2((int) dimensions[0], (int) dimensions[1], stack, wholeDataset, (int) (dimensions[1] * dimensions[0]));
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copyPixels2D_RGB((int) dimensions[0], (int) dimensions[1], stack, wholeDataset, (int) (dimensions[1] * dimensions[0]));
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ImagePlus imp = new ImagePlus(directory + name + " " + datasetName, stack);
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imp.setDimensions(3, 1, 1);
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@ -241,10 +241,10 @@ public class HDF5Reader implements PlugIn {
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wholeDataset = checkUnsigned(datatype, wholeDataset);
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ImageStack stack = new ImageStack((int) dimensions[2], (int) dimensions[1]);
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long stackSize = dimensions[1] * dimensions[2];
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int stackSize = (int) (dimensions[1] * dimensions[2]);
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for (int lev = 0; lev < dimensions[0]; ++lev) {
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int startIdx = (int) (lev * stackSize);
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int endIdx = (int) (startIdx + stackSize);
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int startIdx = lev * stackSize;
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int endIdx = startIdx + stackSize;
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convertDatatypesAndSlice(datatypeIfUnsupported, stack, wholeDataset, startIdx, endIdx);
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}
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@ -268,24 +268,24 @@ public class HDF5Reader implements PlugIn {
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} else if (wholeDataset instanceof int[]) {
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int[] tmp = (int[]) wholeDataset;
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if (datatypeIfUnsupported.getDatatypeClass() == Datatype.CLASS_FLOAT) {
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stack.addSlice(null, convertInt32ToFloat(tmp));
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stack.addSlice(null, HDF5Utilities.convertToFloat(tmp));
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}
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if (datatypeIfUnsupported.getDatatypeClass() == Datatype.CLASS_INTEGER) {
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stack.addSlice(null, convertInt32ToShort(tmp));
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stack.addSlice(null, HDF5Utilities.convertToShort(tmp));
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}
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} else if (wholeDataset instanceof long[]) {
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long[] tmp = (long[]) wholeDataset;
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if (datatypeIfUnsupported.getDatatypeClass() == Datatype.CLASS_FLOAT) {
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stack.addSlice(null, convertInt64ToFloat(tmp));
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stack.addSlice(null, HDF5Utilities.convertToFloat(tmp));
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}
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if (datatypeIfUnsupported.getDatatypeClass() == Datatype.CLASS_INTEGER) {
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stack.addSlice(null, convertInt64ToShort(tmp));
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stack.addSlice(null, HDF5Utilities.convertToShort(tmp));
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}
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} else if (wholeDataset instanceof float[]) {
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float[] tmp = (float[]) wholeDataset;
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stack.addSlice(null, tmp);
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} else if (wholeDataset instanceof double[]) {
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float[] tmp = convertDoubleToFloat((double[]) wholeDataset);
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float[] tmp = HDF5Utilities.convertToFloat((double[]) wholeDataset);
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stack.addSlice(null, tmp);
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} else {
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// try to put pixels on stack
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@ -329,20 +329,22 @@ public class HDF5Reader implements PlugIn {
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*/
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private Object checkUnsigned(Datatype datatype, Object wholeDataset) {
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// check for unsigned datatype
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int unsignedConvSelec = 0;
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boolean isSigned16Bit = !datatype.isUnsigned() && (datatype.getDatatypeClass() == Datatype.CLASS_INTEGER) && (datatype.getDatatypeSize() == 2);
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if (isSigned16Bit) {
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GenericDialog convDiag = new GenericDialog("Unsigend to signed conversion");
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convDiag.addMessage("Detected unsigned datatype, which " + "is not supported.");
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String[] convOptions = new String[2];
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convOptions[0] = "cut off values";
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convOptions[1] = "convert to float";
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convDiag.addChoice("Please select an conversion option:", convOptions, convOptions[0]);
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convDiag.showDialog();
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if (convDiag.wasCanceled())
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return wholeDataset;
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unsignedConvSelec = convDiag.getNextChoiceIndex();
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wholeDataset = convertToUnsigned(wholeDataset, unsignedConvSelec);
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if (!datatype.isUnsigned() && (datatype.getDatatypeClass() == Datatype.CLASS_INTEGER) && (datatype.getDatatypeSize() == 2)) {
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GenericDialog dialog = new GenericDialog("Unsigned to signed conversion");
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dialog.addMessage("Detected unsigned datatype, which is not supported.");
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String[] convOptions = {"cut off values", "convert to float"};
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dialog.addChoice("Please select an conversion option:", convOptions, convOptions[0]);
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dialog.showDialog();
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if (!dialog.wasCanceled()){
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int unsignedConvSelec = dialog.getNextChoiceIndex();
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if (wholeDataset instanceof short[]) {
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if (unsignedConvSelec == 0) {
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wholeDataset = HDF5Utilities.cutoffNegative((short[]) wholeDataset);
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} else if (unsignedConvSelec == 1) {
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wholeDataset = HDF5Utilities.convertToFloat((short[]) wholeDataset);
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}
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}
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}
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}
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return wholeDataset;
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}
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@ -355,30 +357,25 @@ public class HDF5Reader implements PlugIn {
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*/
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private Datatype checkIfDatatypeSupported(Datatype datatype) {
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Datatype datatypeIfUnsupported = null;
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// check if we have an unsupported datatype
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if (datatype.getDatatypeClass() == Datatype.CLASS_INTEGER && (datatype.getDatatypeSize() == 4 || datatype.getDatatypeSize() == 8)) {
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logger.info("Datatype not supported by ImageJ");
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GenericDialog typeSelDiag = new GenericDialog("Datatype Selection");
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typeSelDiag.addMessage("The datatype `" + datatype.getDatatypeDescription() + "` is not supported by ImageJ.\n\n");
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typeSelDiag.addMessage("Please select your wanted datatype.\n");
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typeSelDiag.addMessage("Please select datatype to convert to.\n");
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String[] choices = new String[2];
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choices[0] = "float";
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choices[1] = "short";
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typeSelDiag.addChoice(" Possible types are", choices, "float");
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typeSelDiag.showDialog();
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if (typeSelDiag.wasCanceled()) {
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return null;
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}
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int selection = typeSelDiag.getNextChoiceIndex();
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if (selection == 0) {
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logger.info("float selected");
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datatypeIfUnsupported = new H5Datatype(Datatype.CLASS_FLOAT, Datatype.NATIVE, Datatype.NATIVE, -1);
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}
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if (selection == 1) {
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logger.info("short selected");
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int typeSizeInByte = 2;
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datatypeIfUnsupported = new H5Datatype(Datatype.CLASS_INTEGER, typeSizeInByte, Datatype.NATIVE, -1);
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if (!typeSelDiag.wasCanceled()) {
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int selection = typeSelDiag.getNextChoiceIndex();
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if (selection == 0) {
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datatypeIfUnsupported = new H5Datatype(Datatype.CLASS_FLOAT, Datatype.NATIVE, Datatype.NATIVE, -1);
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}
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if (selection == 1) {
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datatypeIfUnsupported = new H5Datatype(Datatype.CLASS_INTEGER, 2, Datatype.NATIVE, -1);
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}
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}
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}
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return datatypeIfUnsupported;
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@ -479,24 +476,24 @@ public class HDF5Reader implements PlugIn {
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} else if (wholeDataset instanceof int[]) {
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int[] tmp = Arrays.copyOfRange((int[]) wholeDataset, startIdx, endIdx);
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if (datatypeIfUnsupported.getDatatypeClass() == Datatype.CLASS_FLOAT) {
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stack.addSlice(null, convertInt32ToFloat(tmp));
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stack.addSlice(null, HDF5Utilities.convertToFloat(tmp));
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}
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if (datatypeIfUnsupported.getDatatypeClass() == Datatype.CLASS_INTEGER) {
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stack.addSlice(null, convertInt32ToShort(tmp));
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stack.addSlice(null, HDF5Utilities.convertToShort(tmp));
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}
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} else if (wholeDataset instanceof long[]) {
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long[] tmp = Arrays.copyOfRange((long[]) wholeDataset, startIdx, endIdx);
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if (datatypeIfUnsupported.getDatatypeClass() == Datatype.CLASS_FLOAT) {
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stack.addSlice(null, convertInt64ToFloat(tmp));
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stack.addSlice(null, HDF5Utilities.convertToFloat(tmp));
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}
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if (datatypeIfUnsupported.getDatatypeClass() == Datatype.CLASS_INTEGER) {
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stack.addSlice(null, convertInt64ToShort(tmp));
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stack.addSlice(null, HDF5Utilities.convertToShort(tmp));
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}
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} else if (wholeDataset instanceof float[]) {
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float[] tmp = Arrays.copyOfRange((float[]) wholeDataset, startIdx, endIdx);
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stack.addSlice(null, tmp);
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} else if (wholeDataset instanceof double[]) {
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float[] tmp = convertDoubleToFloat(Arrays.copyOfRange((double[]) wholeDataset, startIdx, endIdx));
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float[] tmp = HDF5Utilities.convertToFloat(Arrays.copyOfRange((double[]) wholeDataset, startIdx, endIdx));
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stack.addSlice(null, tmp);
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} else {
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logger.warning("Not supported array type");
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@ -514,7 +511,7 @@ public class HDF5Reader implements PlugIn {
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* @param startIdx
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* @param endIdx
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*/
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private void copyPixels3(Datatype datatypeIfUnsupported, int nRows, int nColumns, ImageStack stack, Object wholeDataset, int size, int startIdx, int endIdx) {
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private void copyPixels4D_RGB(Datatype datatypeIfUnsupported, int nRows, int nColumns, ImageStack stack, Object wholeDataset, int size, int startIdx, int endIdx) {
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if (wholeDataset instanceof byte[]) {
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byte[] tmp = Arrays.copyOfRange((byte[]) wholeDataset, startIdx, endIdx);
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byte[] rChannel = new byte[size];
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@ -551,7 +548,7 @@ public class HDF5Reader implements PlugIn {
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stack.addSlice(null, bChannel);
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} else if (wholeDataset instanceof int[]) {
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if (datatypeIfUnsupported.getDatatypeClass() == Datatype.CLASS_FLOAT) {
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float[] tmp = convertInt32ToFloat(Arrays.copyOfRange((int[]) wholeDataset, startIdx, endIdx));
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float[] tmp = HDF5Utilities.convertToFloat(Arrays.copyOfRange((int[]) wholeDataset, startIdx, endIdx));
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float[] rChannel = new float[size];
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float[] gChannel = new float[size];
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float[] bChannel = new float[size];
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@ -569,7 +566,7 @@ public class HDF5Reader implements PlugIn {
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stack.addSlice(null, bChannel);
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}
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if (datatypeIfUnsupported.getDatatypeClass() == Datatype.CLASS_INTEGER) {
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short[] tmp = convertInt32ToShort(Arrays.copyOfRange((int[]) wholeDataset, startIdx, endIdx));
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short[] tmp = HDF5Utilities.convertToShort(Arrays.copyOfRange((int[]) wholeDataset, startIdx, endIdx));
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short[] rChannel = new short[size];
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short[] gChannel = new short[size];
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short[] bChannel = new short[size];
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@ -588,7 +585,7 @@ public class HDF5Reader implements PlugIn {
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}
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} else if (wholeDataset instanceof long[]) {
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if (datatypeIfUnsupported.getDatatypeClass() == Datatype.CLASS_FLOAT) {
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float[] tmp = convertInt64ToFloat(Arrays.copyOfRange((long[]) wholeDataset, startIdx, endIdx));
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float[] tmp = HDF5Utilities.convertToFloat(Arrays.copyOfRange((long[]) wholeDataset, startIdx, endIdx));
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float[] rChannel = new float[size];
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float[] gChannel = new float[size];
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float[] bChannel = new float[size];
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@ -606,7 +603,7 @@ public class HDF5Reader implements PlugIn {
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stack.addSlice(null, bChannel);
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}
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if (datatypeIfUnsupported.getDatatypeClass() == Datatype.CLASS_INTEGER) {
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short[] tmp = convertInt64ToShort(Arrays.copyOfRange((long[]) wholeDataset, startIdx, endIdx));
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short[] tmp = HDF5Utilities.convertToShort(Arrays.copyOfRange((long[]) wholeDataset, startIdx, endIdx));
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short[] rChannel = new short[size];
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short[] gChannel = new short[size];
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short[] bChannel = new short[size];
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@ -641,7 +638,7 @@ public class HDF5Reader implements PlugIn {
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stack.addSlice(null, gChannel);
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stack.addSlice(null, bChannel);
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} else if (wholeDataset instanceof double[]) {
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float[] tmp = convertDoubleToFloat(Arrays.copyOfRange((double[]) wholeDataset, startIdx, endIdx));
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float[] tmp = HDF5Utilities.convertToFloat(Arrays.copyOfRange((double[]) wholeDataset, startIdx, endIdx));
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float[] rChannel = new float[size];
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float[] gChannel = new float[size];
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float[] bChannel = new float[size];
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@ -670,7 +667,7 @@ public class HDF5Reader implements PlugIn {
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* @param wholeDataset
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* @param size
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*/
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private void copyPixels2(int nRows, int nColumns, ImageStack stack, Object wholeDataset, int size) {
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private void copyPixels2D_RGB(int nRows, int nColumns, ImageStack stack, Object wholeDataset, int size) {
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if (wholeDataset instanceof byte[]) {
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byte[] tmp = (byte[]) wholeDataset;
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byte[] rChannel = new byte[size];
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@ -776,7 +773,6 @@ public class HDF5Reader implements PlugIn {
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}
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}
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/**
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* @param nRows
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* @param nColumns
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@ -786,7 +782,7 @@ public class HDF5Reader implements PlugIn {
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* @param endIdx
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* @param size
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*/
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private void copyPixels1(int nRows, int nColumns, ImageStack stack, Object wholeDataset, int size, int startIdx, int endIdx) {
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private void copyPixels3D_RGB(int nRows, int nColumns, ImageStack stack, Object wholeDataset, int size, int startIdx, int endIdx) {
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if (wholeDataset instanceof byte[]) {
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byte[] tmp = Arrays.copyOfRange((byte[]) wholeDataset, startIdx, endIdx);
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byte[] rChannel = new byte[size];
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@ -892,71 +888,8 @@ public class HDF5Reader implements PlugIn {
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}
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}
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private float[] convertDoubleToFloat(double[] dataIn) {
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float[] dataOut = new float[dataIn.length];
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for (int index = 0; index < dataIn.length; index++) {
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dataOut[index] = (float) dataIn[index];
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}
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return dataOut;
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}
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private float[] convertInt32ToFloat(int[] array) {
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float[] narray = new float[array.length];
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for (int index = 0; index < array.length; index++) {
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narray[index] = array[index];
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}
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return narray;
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}
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private short[] convertInt32ToShort(int[] array) {
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short[] narray = new short[array.length];
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for (int index = 0; index < array.length; index++) {
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narray[index] = (short) array[index];
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}
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return narray;
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}
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private float[] convertInt64ToFloat(long[] array) {
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float[] narray = new float[array.length];
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for (int index = 0; index < array.length; index++) {
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narray[index] = array[index];
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}
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return narray;
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}
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private short[] convertInt64ToShort(long[] array) {
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short[] narray = new short[array.length];
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for (int index = 0; index < array.length; index++) {
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narray[index] = (short) array[index];
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}
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return narray;
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}
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private Object convertToUnsigned(Object dataIn, int unsignedConvSelec) {
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Object dataOut = null;
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if (unsignedConvSelec == 0) {
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// cut off values
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if (dataIn instanceof short[]) {
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short[] tmp = (short[]) dataIn;
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for (int i = 0; i < tmp.length; i++)
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if (tmp[i] < 0)
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tmp[i] = 0;
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dataOut = tmp;
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}
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} else if (unsignedConvSelec == 1) {
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// convert to float
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if (dataIn instanceof short[]) {
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logger.info("Converting to float");
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short[] tmpIn = (short[]) dataIn;
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float[] tmp = new float[tmpIn.length];
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for (int i = 0; i < tmp.length; i++)
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tmp[i] = (float) tmpIn[i];
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dataOut = tmp;
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}
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}
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return dataOut;
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}
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/** Adds AWT scroll bars to the given container. */
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public static void addScrollBars(Container pane) {
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@ -222,4 +222,98 @@ public class HDF5Utilities {
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}
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return datasets;
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}
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/**
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* Cut of negative values from array. This function will modify the passed array!
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* @param array Array with values to cut off
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* @return array holding cut off values
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*/
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public static short[] cutoffNegative(short[] array) {
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for (int i = 0; i < array.length; i++) {
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if (array[i] < 0) {
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array[i] = 0;
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}
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}
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return array;
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}
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/**
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* Convert short to float array
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* @param array short array to convert
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* @return Converted float array
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*/
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public static float[] convertToFloat(short[] array) {
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float[] narray = new float[array.length];
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for (int i = 0; i < array.length; i++) {
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narray[i] = (float) array[i];
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}
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return narray;
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}
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/**
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* Convert double to float array
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* @param array double array to convert
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* @return Converted float array
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*/
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public static float[] convertToFloat(double[] array) {
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float[] narray = new float[array.length];
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for (int index = 0; index < array.length; index++) {
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narray[index] = (float) array[index];
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}
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return narray;
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* Convert int to float array
|
||||
* @param array int array to convert
|
||||
* @return Converted short array
|
||||
*/
|
||||
public static float[] convertToFloat(int[] array) {
|
||||
float[] narray = new float[array.length];
|
||||
for (int index = 0; index < array.length; index++) {
|
||||
narray[index] = array[index];
|
||||
}
|
||||
return narray;
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* Convert int to short array
|
||||
* @param array int array to convert
|
||||
* @return Converted short array
|
||||
*/
|
||||
public static short[] convertToShort(int[] array) {
|
||||
short[] narray = new short[array.length];
|
||||
for (int index = 0; index < array.length; index++) {
|
||||
narray[index] = (short) array[index];
|
||||
}
|
||||
return narray;
|
||||
}
|
||||
|
||||
/**
|
||||
* Convert long (or int64) to float
|
||||
* @param array long array to convert
|
||||
* @return Converted short array
|
||||
*/
|
||||
public static float[] convertToFloat(long[] array) {
|
||||
float[] narray = new float[array.length];
|
||||
for (int index = 0; index < array.length; index++) {
|
||||
narray[index] = array[index];
|
||||
}
|
||||
return narray;
|
||||
}
|
||||
|
||||
/**
|
||||
* Convert long (or int64) to short
|
||||
* @param array long array to convert
|
||||
* @return Converted short array
|
||||
*/
|
||||
public static short[] convertToShort(long[] array) {
|
||||
short[] narray = new short[array.length];
|
||||
for (int index = 0; index < array.length; index++) {
|
||||
narray[index] = (short) array[index];
|
||||
}
|
||||
return narray;
|
||||
}
|
||||
}
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user