x11ma/plugins/fiji/sparseviewer/io/MdaReader.java

package sparseviewer.io;

import sparseviewer.mda.MdaDetector;
import sparseviewer.mda.MdaPositioner;
import sparseviewer.mda.MdaScan;
import sparseviewer.mda.XdrInput;
import sparseviewer.model.ScanDataset;
import sparseviewer.mda.MdaFileData;

import ij.IJ;

import java.io.File;
import java.io.IOException;

import java.util.ArrayList;
import java.util.List;

public class MdaReader {

    public static ScanDataset readFiles(List<File> files) throws IOException {
        if (files == null || files.isEmpty()) {
            throw new IOException("No MDA file selected.");
        }

        if (files.size() > 1) {
            throw new IOException("MDA support currently expects a single file.");
        }

    File file = files.get(0);

    MdaFileData mda = readMdaFile(file);

        if (mda.rank == 1) {
        return toScanDatasetRank1(mda, file);
        }

                if (mda.rank == 2) {
        return toScanDatasetRank2(mda, file);
        }

                throw new IOException("Only MDA rank 1 and rank 2 are supported currently. File rank = " + mda.rank);
    }
    private static MdaFileData readMdaFile(File file) throws IOException {
    XdrInput in = new XdrInput(file);

    try {
        MdaFileData data = new MdaFileData();

        data.version = in.readFloat();

        if (Math.abs(data.version - 1.3f) > 0.02f
                && Math.abs(data.version - 1.4f) > 0.02f) {
            throw new IOException("Unsupported MDA version: " + data.version);
        }

        data.scanNumber = in.readInt();
        data.rank = in.readInt();

        if (data.rank < 1 || data.rank > 4) {
            throw new IOException("Invalid MDA rank: " + data.rank);
        }

        data.dimensions = in.readIntArray(data.rank);
        data.isRegular = in.readInt();
        data.pExtra = in.readInt();

        long mainScanOffset = in.getFilePointer();

        data.mainScan = readScan(in, mainScanOffset);

        if (data.rank == 2) {
            readRank2InnerScans(in, data);
        }

        IJ.log("MDA loaded: " + file.getName()
                + ", version=" + data.version
                + ", rank=" + data.rank
                + ", scanNumber=" + data.scanNumber);

        return data;

    } finally {
        in.close();
    }
}
    private static void readRank2InnerScans(XdrInput in, MdaFileData data) throws IOException {
    MdaScan outer = data.mainScan;

    if (outer.lowerScanOffsets == null) {
        throw new IOException("Rank 2 MDA file has no lower scan offsets.");
    }

    int nOuter = Math.min(outer.currPt, outer.lowerScanOffsets.length);

    for (int i = 0; i < nOuter; i++) {
        int offset = outer.lowerScanOffsets[i];

        if (offset <= 0) {
            data.innerScans.add(null);
            continue;
        }

        MdaScan inner = readScan(in, offset);
        data.innerScans.add(inner);
    }
}
    private static MdaScan readScan(XdrInput in, long offset) throws IOException {
        in.seek(offset);

        MdaScan scan = new MdaScan();

        scan.rank = in.readInt();

        if (scan.rank < 0 || scan.rank > 20) {
            throw new IOException("Invalid scan rank at offset " + offset + ": " + scan.rank);
        }

        scan.npts = in.readInt();
        scan.currPt = in.readInt();

        if (scan.rank > 1) {
            scan.lowerScanOffsets = in.readIntArray(scan.npts);
        }

        scan.name = in.readStringWithLeadingLength();
        scan.time = in.readStringWithLeadingLength();

        scan.np = in.readInt();
        scan.nd = in.readInt();
        scan.nt = in.readInt();

        for (int i = 0; i < scan.np; i++) {
            MdaPositioner p = new MdaPositioner();

            p.number = in.readInt();
            p.fieldName = posName(p.number);

            p.name = in.readStringWithLeadingLength();
            p.desc = in.readStringWithLeadingLength();
            p.stepMode = in.readStringWithLeadingLength();
            p.unit = in.readStringWithLeadingLength();

            p.readbackName = in.readStringWithLeadingLength();
            p.readbackDesc = in.readStringWithLeadingLength();
            p.readbackUnit = in.readStringWithLeadingLength();

            scan.positioners.add(p);
        }

    for (int i = 0; i < scan.nd; i++) {
        MdaDetector d = new MdaDetector();

        d.number = in.readInt();
        d.fieldName = detName(d.number);

        d.name = in.readStringWithLeadingLength();
        d.desc = in.readStringWithLeadingLength();
        d.unit = in.readStringWithLeadingLength();

        scan.detectors.add(d);
    }

    // Triggers are not needed for ScanDataset, but must be consumed.
    for (int i = 0; i < scan.nt; i++) {
        in.readInt(); // trigger number
        in.readStringWithLeadingLength(); // trigger name
        in.readFloat(); // command
    }

    readScanData(in, scan);

    return scan;
}
    private static void readScanData(XdrInput in, MdaScan scan) throws IOException {
    for (int p = 0; p < scan.np; p++) {
        double[] values = new double[scan.npts];

        for (int i = 0; i < scan.npts; i++) {
            values[i] = in.readDouble();
        }

        scan.positioners.get(p).data = values;
    }

    for (int d = 0; d < scan.nd; d++) {
        float[] values = new float[scan.npts];

        for (int i = 0; i < scan.npts; i++) {
            values[i] = in.readFloat();
        }

        scan.detectors.get(d).data = values;
    }
}
    private static ScanDataset toScanDatasetRank1(MdaFileData mda, File file) {
    MdaScan scan = mda.mainScan;

    int rowCount = scan.currPt;
    int channelCount = scan.np + scan.nd;

    String[] channelNames = new String[channelCount];
    double[][] columns = new double[channelCount][rowCount];
    int[] fileIndex = new int[rowCount];

    int c = 0;

    for (int p = 0; p < scan.np; p++) {
        MdaPositioner pos = scan.positioners.get(p);
        channelNames[c] = makePositionerName("rank1", pos);

        for (int i = 0; i < rowCount; i++) {
            columns[c][i] = safeDouble(pos.data, i);
        }

        c++;
    }

    for (int d = 0; d < scan.nd; d++) {
        MdaDetector det = scan.detectors.get(d);
        channelNames[c] = makeDetectorName("rank1", det);

        for (int i = 0; i < rowCount; i++) {
            columns[c][i] = safeFloat(det.data, i);
        }

        c++;
    }

    for (int i = 0; i < rowCount; i++) {
        fileIndex[i] = 0;
    }

    List<File> sourceFiles = new ArrayList<File>();
    sourceFiles.add(file);

    IJ.log("MDA rank 1 converted to ScanDataset: "
            + rowCount + " rows, " + channelCount + " channels.");

    return new ScanDataset(channelNames, columns, rowCount, fileIndex, sourceFiles);
}
    private static ScanDataset toScanDatasetRank2(MdaFileData mda, File file) throws IOException {
    MdaScan outer = mda.mainScan;

    MdaScan firstInner = findFirstInnerScan(mda);

    if (firstInner == null) {
        throw new IOException("Rank 2 MDA file contains no readable inner scan.");
    }

    int rowCount = 0;

    for (int j = 0; j < mda.innerScans.size(); j++) {
        MdaScan inner = mda.innerScans.get(j);

        if (inner != null) {
            rowCount += inner.currPt;
        }
    }

    int channelCount = outer.np + outer.nd + firstInner.np + firstInner.nd;

    String[] channelNames = new String[channelCount];
    double[][] columns = new double[channelCount][rowCount];
    int[] fileIndex = new int[rowCount];

    int c = 0;

    for (int p = 0; p < outer.np; p++) {
        channelNames[c++] = makePositionerName("outer", outer.positioners.get(p));
    }

    for (int d = 0; d < outer.nd; d++) {
        channelNames[c++] = makeDetectorName("outer", outer.detectors.get(d));
    }

    for (int p = 0; p < firstInner.np; p++) {
        channelNames[c++] = makePositionerName("inner", firstInner.positioners.get(p));
    }

    for (int d = 0; d < firstInner.nd; d++) {
        channelNames[c++] = makeDetectorName("inner", firstInner.detectors.get(d));
    }

    int row = 0;

    for (int j = 0; j < mda.innerScans.size(); j++) {
        MdaScan inner = mda.innerScans.get(j);

        if (inner == null) {
            continue;
        }

        int innerRows = inner.currPt;

        for (int k = 0; k < innerRows; k++) {
            c = 0;

            for (int p = 0; p < outer.np; p++) {
                columns[c++][row] = safeDouble(outer.positioners.get(p).data, j);
            }

            for (int d = 0; d < outer.nd; d++) {
                columns[c++][row] = safeFloat(outer.detectors.get(d).data, j);
            }

            for (int p = 0; p < firstInner.np; p++) {
                if (p < inner.positioners.size()) {
                    columns[c++][row] = safeDouble(inner.positioners.get(p).data, k);
                } else {
                    columns[c++][row] = Double.NaN;
                }
            }

            for (int d = 0; d < firstInner.nd; d++) {
                if (d < inner.detectors.size()) {
                    columns[c++][row] = safeFloat(inner.detectors.get(d).data, k);
                } else {
                    columns[c++][row] = Double.NaN;
                }
            }

            fileIndex[row] = 0;
            row++;
        }
    }

    List<File> sourceFiles = new ArrayList<File>();
    sourceFiles.add(file);

    IJ.log("MDA rank 2 converted to ScanDataset: "
            + rowCount + " rows, " + channelCount + " channels.");

    return new ScanDataset(channelNames, columns, rowCount, fileIndex, sourceFiles);
}
    private static MdaScan findFirstInnerScan(MdaFileData mda) {
    for (int i = 0; i < mda.innerScans.size(); i++) {
        MdaScan scan = mda.innerScans.get(i);

        if (scan != null) {
            return scan;
        }
    }

    return null;
}
    private static String makePositionerName(String prefix, MdaPositioner p) {
    String pv = clean(p.name);
    String desc = clean(p.desc);

    if (pv.length() > 0 && desc.length() > 0) {
        return prefix + "/" + p.fieldName + "/" + pv + " {" + desc + "}";
    }

    if (pv.length() > 0) {
        return prefix + "/" + p.fieldName + "/" + pv;
    }

    if (desc.length() > 0) {
        return prefix + "/" + p.fieldName + "/{" + desc + "}";
    }

    return prefix + "/" + p.fieldName;
}
    private static String makeDetectorName(String prefix, MdaDetector d) {
    String pv = clean(d.name);
    String desc = clean(d.desc);

    if (pv.length() > 0 && desc.length() > 0) {
        return prefix + "/" + d.fieldName + "/" + pv + " {" + desc + "}";
    }

    if (pv.length() > 0) {
        return prefix + "/" + d.fieldName + "/" + pv;
    }

    if (desc.length() > 0) {
        return prefix + "/" + d.fieldName + "/{" + desc + "}";
    }

    return prefix + "/" + d.fieldName;
}
    private static String clean(String s) {
    return s == null ? "" : s.trim();
}
    private static double safeDouble(double[] data, int index) {
    if (data == null || index < 0 || index >= data.length) {
        return Double.NaN;
    }

    return data[index];
}
    private static double safeFloat(float[] data, int index) {
    if (data == null || index < 0 || index >= data.length) {
        return Double.NaN;
    }

    return data[index];
}
    private static String posName(int i) {
    if (i < 4) {
        return "P" + (i + 1);
    }

    return "?";
}
    private static String detName(int i) {
    if (i < 100) {
        int n = i + 1;

        if (n < 10) {
            return "D0" + n;
        }

        return "D" + n;
    }

    return "?";
}
}