06.2026
This commit is contained in:
gac-x11ma
@@ -0,0 +1,419 @@
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package sparseviewer.io;
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import sparseviewer.mda.MdaDetector;
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import sparseviewer.mda.MdaPositioner;
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import sparseviewer.mda.MdaScan;
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import sparseviewer.mda.XdrInput;
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import sparseviewer.model.ScanDataset;
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import sparseviewer.mda.MdaFileData;
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import ij.IJ;
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import java.io.File;
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import java.io.IOException;
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import java.util.ArrayList;
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import java.util.List;
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public class MdaReader {
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public static ScanDataset readFiles(List<File> files) throws IOException {
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if (files == null || files.isEmpty()) {
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throw new IOException("No MDA file selected.");
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}
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if (files.size() > 1) {
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throw new IOException("MDA support currently expects a single file.");
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}
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File file = files.get(0);
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MdaFileData mda = readMdaFile(file);
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if (mda.rank == 1) {
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return toScanDatasetRank1(mda, file);
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}
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if (mda.rank == 2) {
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return toScanDatasetRank2(mda, file);
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}
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throw new IOException("Only MDA rank 1 and rank 2 are supported currently. File rank = " + mda.rank);
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}
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private static MdaFileData readMdaFile(File file) throws IOException {
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XdrInput in = new XdrInput(file);
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try {
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MdaFileData data = new MdaFileData();
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data.version = in.readFloat();
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if (Math.abs(data.version - 1.3f) > 0.02f
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&& Math.abs(data.version - 1.4f) > 0.02f) {
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throw new IOException("Unsupported MDA version: " + data.version);
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}
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data.scanNumber = in.readInt();
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data.rank = in.readInt();
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if (data.rank < 1 || data.rank > 4) {
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throw new IOException("Invalid MDA rank: " + data.rank);
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}
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data.dimensions = in.readIntArray(data.rank);
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data.isRegular = in.readInt();
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data.pExtra = in.readInt();
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long mainScanOffset = in.getFilePointer();
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data.mainScan = readScan(in, mainScanOffset);
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if (data.rank == 2) {
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readRank2InnerScans(in, data);
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}
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IJ.log("MDA loaded: " + file.getName()
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+ ", version=" + data.version
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+ ", rank=" + data.rank
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+ ", scanNumber=" + data.scanNumber);
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return data;
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} finally {
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in.close();
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}
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}
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private static void readRank2InnerScans(XdrInput in, MdaFileData data) throws IOException {
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MdaScan outer = data.mainScan;
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if (outer.lowerScanOffsets == null) {
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throw new IOException("Rank 2 MDA file has no lower scan offsets.");
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}
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int nOuter = Math.min(outer.currPt, outer.lowerScanOffsets.length);
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for (int i = 0; i < nOuter; i++) {
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int offset = outer.lowerScanOffsets[i];
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if (offset <= 0) {
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data.innerScans.add(null);
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continue;
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}
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MdaScan inner = readScan(in, offset);
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data.innerScans.add(inner);
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}
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}
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private static MdaScan readScan(XdrInput in, long offset) throws IOException {
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in.seek(offset);
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MdaScan scan = new MdaScan();
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scan.rank = in.readInt();
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if (scan.rank < 0 || scan.rank > 20) {
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throw new IOException("Invalid scan rank at offset " + offset + ": " + scan.rank);
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}
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scan.npts = in.readInt();
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scan.currPt = in.readInt();
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if (scan.rank > 1) {
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scan.lowerScanOffsets = in.readIntArray(scan.npts);
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}
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scan.name = in.readStringWithLeadingLength();
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scan.time = in.readStringWithLeadingLength();
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scan.np = in.readInt();
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scan.nd = in.readInt();
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scan.nt = in.readInt();
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for (int i = 0; i < scan.np; i++) {
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MdaPositioner p = new MdaPositioner();
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p.number = in.readInt();
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p.fieldName = posName(p.number);
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p.name = in.readStringWithLeadingLength();
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p.desc = in.readStringWithLeadingLength();
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p.stepMode = in.readStringWithLeadingLength();
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p.unit = in.readStringWithLeadingLength();
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p.readbackName = in.readStringWithLeadingLength();
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p.readbackDesc = in.readStringWithLeadingLength();
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p.readbackUnit = in.readStringWithLeadingLength();
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scan.positioners.add(p);
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}
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for (int i = 0; i < scan.nd; i++) {
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MdaDetector d = new MdaDetector();
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d.number = in.readInt();
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d.fieldName = detName(d.number);
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d.name = in.readStringWithLeadingLength();
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d.desc = in.readStringWithLeadingLength();
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d.unit = in.readStringWithLeadingLength();
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scan.detectors.add(d);
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}
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// Triggers are not needed for ScanDataset, but must be consumed.
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for (int i = 0; i < scan.nt; i++) {
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in.readInt(); // trigger number
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in.readStringWithLeadingLength(); // trigger name
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in.readFloat(); // command
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}
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readScanData(in, scan);
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return scan;
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}
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private static void readScanData(XdrInput in, MdaScan scan) throws IOException {
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for (int p = 0; p < scan.np; p++) {
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double[] values = new double[scan.npts];
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for (int i = 0; i < scan.npts; i++) {
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values[i] = in.readDouble();
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}
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scan.positioners.get(p).data = values;
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}
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for (int d = 0; d < scan.nd; d++) {
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float[] values = new float[scan.npts];
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for (int i = 0; i < scan.npts; i++) {
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values[i] = in.readFloat();
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}
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scan.detectors.get(d).data = values;
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}
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}
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private static ScanDataset toScanDatasetRank1(MdaFileData mda, File file) {
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MdaScan scan = mda.mainScan;
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int rowCount = scan.currPt;
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int channelCount = scan.np + scan.nd;
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String[] channelNames = new String[channelCount];
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double[][] columns = new double[channelCount][rowCount];
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int[] fileIndex = new int[rowCount];
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int c = 0;
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for (int p = 0; p < scan.np; p++) {
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MdaPositioner pos = scan.positioners.get(p);
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channelNames[c] = makePositionerName("rank1", pos);
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for (int i = 0; i < rowCount; i++) {
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columns[c][i] = safeDouble(pos.data, i);
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}
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c++;
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}
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for (int d = 0; d < scan.nd; d++) {
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MdaDetector det = scan.detectors.get(d);
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channelNames[c] = makeDetectorName("rank1", det);
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for (int i = 0; i < rowCount; i++) {
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columns[c][i] = safeFloat(det.data, i);
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}
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c++;
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}
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for (int i = 0; i < rowCount; i++) {
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fileIndex[i] = 0;
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}
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List<File> sourceFiles = new ArrayList<File>();
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sourceFiles.add(file);
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IJ.log("MDA rank 1 converted to ScanDataset: "
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+ rowCount + " rows, " + channelCount + " channels.");
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return new ScanDataset(channelNames, columns, rowCount, fileIndex, sourceFiles);
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}
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private static ScanDataset toScanDatasetRank2(MdaFileData mda, File file) throws IOException {
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MdaScan outer = mda.mainScan;
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MdaScan firstInner = findFirstInnerScan(mda);
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if (firstInner == null) {
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throw new IOException("Rank 2 MDA file contains no readable inner scan.");
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}
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int rowCount = 0;
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for (int j = 0; j < mda.innerScans.size(); j++) {
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MdaScan inner = mda.innerScans.get(j);
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if (inner != null) {
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rowCount += inner.currPt;
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}
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}
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int channelCount = outer.np + outer.nd + firstInner.np + firstInner.nd;
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String[] channelNames = new String[channelCount];
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double[][] columns = new double[channelCount][rowCount];
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int[] fileIndex = new int[rowCount];
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int c = 0;
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for (int p = 0; p < outer.np; p++) {
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channelNames[c++] = makePositionerName("outer", outer.positioners.get(p));
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}
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for (int d = 0; d < outer.nd; d++) {
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channelNames[c++] = makeDetectorName("outer", outer.detectors.get(d));
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}
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for (int p = 0; p < firstInner.np; p++) {
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channelNames[c++] = makePositionerName("inner", firstInner.positioners.get(p));
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}
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for (int d = 0; d < firstInner.nd; d++) {
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channelNames[c++] = makeDetectorName("inner", firstInner.detectors.get(d));
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}
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int row = 0;
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for (int j = 0; j < mda.innerScans.size(); j++) {
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MdaScan inner = mda.innerScans.get(j);
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if (inner == null) {
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continue;
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}
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int innerRows = inner.currPt;
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for (int k = 0; k < innerRows; k++) {
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c = 0;
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for (int p = 0; p < outer.np; p++) {
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columns[c++][row] = safeDouble(outer.positioners.get(p).data, j);
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}
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for (int d = 0; d < outer.nd; d++) {
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columns[c++][row] = safeFloat(outer.detectors.get(d).data, j);
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}
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for (int p = 0; p < firstInner.np; p++) {
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if (p < inner.positioners.size()) {
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columns[c++][row] = safeDouble(inner.positioners.get(p).data, k);
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} else {
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columns[c++][row] = Double.NaN;
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}
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}
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for (int d = 0; d < firstInner.nd; d++) {
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if (d < inner.detectors.size()) {
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columns[c++][row] = safeFloat(inner.detectors.get(d).data, k);
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} else {
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columns[c++][row] = Double.NaN;
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}
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}
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fileIndex[row] = 0;
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row++;
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}
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}
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List<File> sourceFiles = new ArrayList<File>();
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sourceFiles.add(file);
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IJ.log("MDA rank 2 converted to ScanDataset: "
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+ rowCount + " rows, " + channelCount + " channels.");
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return new ScanDataset(channelNames, columns, rowCount, fileIndex, sourceFiles);
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}
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private static MdaScan findFirstInnerScan(MdaFileData mda) {
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for (int i = 0; i < mda.innerScans.size(); i++) {
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MdaScan scan = mda.innerScans.get(i);
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if (scan != null) {
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return scan;
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}
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}
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return null;
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}
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private static String makePositionerName(String prefix, MdaPositioner p) {
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String pv = clean(p.name);
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String desc = clean(p.desc);
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if (pv.length() > 0 && desc.length() > 0) {
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return prefix + "/" + p.fieldName + "/" + pv + " {" + desc + "}";
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}
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if (pv.length() > 0) {
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return prefix + "/" + p.fieldName + "/" + pv;
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}
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if (desc.length() > 0) {
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return prefix + "/" + p.fieldName + "/{" + desc + "}";
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}
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return prefix + "/" + p.fieldName;
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}
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private static String makeDetectorName(String prefix, MdaDetector d) {
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String pv = clean(d.name);
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String desc = clean(d.desc);
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if (pv.length() > 0 && desc.length() > 0) {
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return prefix + "/" + d.fieldName + "/" + pv + " {" + desc + "}";
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}
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if (pv.length() > 0) {
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return prefix + "/" + d.fieldName + "/" + pv;
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}
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if (desc.length() > 0) {
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return prefix + "/" + d.fieldName + "/{" + desc + "}";
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}
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return prefix + "/" + d.fieldName;
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}
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private static String clean(String s) {
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return s == null ? "" : s.trim();
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}
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private static double safeDouble(double[] data, int index) {
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if (data == null || index < 0 || index >= data.length) {
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return Double.NaN;
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}
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return data[index];
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}
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private static double safeFloat(float[] data, int index) {
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if (data == null || index < 0 || index >= data.length) {
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return Double.NaN;
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}
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return data[index];
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}
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private static String posName(int i) {
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if (i < 4) {
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return "P" + (i + 1);
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}
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return "?";
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}
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private static String detName(int i) {
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if (i < 100) {
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int n = i + 1;
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if (n < 10) {
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return "D0" + n;
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}
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return "D" + n;
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}
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return "?";
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}
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}
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