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

package sparseviewer.io;

import sparseviewer.model.ScanDataset;
import ij.IJ;

import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;

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

public class TxtTableReader {

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

        String[] referenceHeader = null;

        List<double[]> allRows = new ArrayList<double[]>();
        List<Integer> fileIndices = new ArrayList<Integer>();

        for (int fileIdx = 0; fileIdx < files.size(); fileIdx++) {
            File file = files.get(fileIdx);
            ParsedTxt parsed = readSingleFile(file);

            if (referenceHeader == null) {
                referenceHeader = parsed.channelNames;
            } else {
                if (!sameHeader(referenceHeader, parsed.channelNames)) {
                    throw new IOException(
                            "Header mismatch in file:\n" + file.getAbsolutePath()
                    );
                }
            }

            for (int i = 0; i < parsed.rows.size(); i++) {
                allRows.add(parsed.rows.get(i));
                fileIndices.add(Integer.valueOf(fileIdx));
            }
        }

        int rowCount = allRows.size();
        int colCount = referenceHeader.length;

        double[][] columns = new double[colCount][rowCount];
        int[] fileIndex = new int[rowCount];

        for (int r = 0; r < rowCount; r++) {
            double[] row = allRows.get(r);

            for (int c = 0; c < colCount; c++) {
                columns[c][r] = row[c];
            }

            fileIndex[r] = fileIndices.get(r).intValue();
        }

        IJ.log("Sparse Scan Viewer: loaded " + files.size()
                + " file(s), " + rowCount
                + " rows, " + colCount + " channels.");

        return new ScanDataset(referenceHeader, columns, rowCount, fileIndex, files);
    }

    private static ParsedTxt readSingleFile(File file) throws IOException {
        BufferedReader br = null;

        try {
            br = new BufferedReader(new FileReader(file));

            String line;
            String[] channels = null;
            int expectedRows = -1;
            List<double[]> rows = new ArrayList<double[]>();

            while ((line = br.readLine()) != null) {
                String trimmed = line.trim();

                if (trimmed.length() == 0) {
                    continue;
                }

                if (trimmed.startsWith("#table[")) {
                    HeaderInfo info = parseHeader(trimmed);
                    channels = info.channelNames;
                    expectedRows = info.expectedRows;
                    continue;
                }

                if (trimmed.startsWith("#")) {
                    continue;
                }

                if (channels == null) {
                    continue;
                }

                String[] parts = trimmed.split(";");

                if (parts.length < channels.length) {
                    continue;
                }

                double[] row = new double[channels.length];
                boolean valid = true;

                for (int i = 0; i < channels.length; i++) {
                    try {
                        row[i] = Double.parseDouble(parts[i].trim());
                    } catch (NumberFormatException e) {
                        valid = false;
                        break;
                    }
                }

                if (valid) {
                    rows.add(row);
                }
            }

            if (channels == null) {
                throw new IOException("No #table[...] header found in " + file.getName());
            }

            if (expectedRows >= 0 && expectedRows != rows.size()) {
                IJ.log("Warning: " + file.getName()
                        + " header says " + expectedRows
                        + " rows, but parsed " + rows.size() + " rows.");
            }

            ParsedTxt parsed = new ParsedTxt();
            parsed.channelNames = channels;
            parsed.rows = rows;
            return parsed;

        } finally {
            if (br != null) {
                try {
                    br.close();
                } catch (IOException ignored) {
                }
            }
        }
    }

    private static HeaderInfo parseHeader(String line) throws IOException {
        int open = line.indexOf('[');
        int close = line.indexOf(']');

        if (open < 0 || close < 0 || close <= open) {
            throw new IOException("Invalid #table header:\n" + line);
        }

        int expectedRows = -1;

        try {
            expectedRows = Integer.parseInt(line.substring(open + 1, close).trim());
        } catch (Exception ignored) {
        }

        String rest = line.substring(close + 1).trim();
        String[] rawChannels = rest.split(";");

        Vector<String> names = new Vector<String>();

        for (int i = 0; i < rawChannels.length; i++) {
            String name = rawChannels[i].trim();

            if (name.length() > 0) {
                names.add(name);
            }
        }

        if (names.isEmpty()) {
            throw new IOException("No channels found in header:\n" + line);
        }

        HeaderInfo info = new HeaderInfo();
        info.expectedRows = expectedRows;
        info.channelNames = names.toArray(new String[names.size()]);
        return info;
    }

    private static boolean sameHeader(String[] a, String[] b) {
        if (a == null || b == null) {
            return false;
        }

        if (a.length != b.length) {
            return false;
        }

        for (int i = 0; i < a.length; i++) {
            if (!a[i].equals(b[i])) {
                return false;
            }
        }

        return true;
    }

    private static class HeaderInfo {
        int expectedRows;
        String[] channelNames;
    }

    private static class ParsedTxt {
        String[] channelNames;
        List<double[]> rows;
    }
}