Examples with FilePattern loci.formats.FilePattern used on opensource projects

Example 6 with FilePattern

use of loci.formats.FilePattern in project bioformats by openmicroscopy.

the class FilePatternTest method testRegex.

@Test(dataProvider = "booleanStates")
public void testRegex(Boolean createFiles) throws IOException {
    String[] names = { "z0.tif", "z1.tif" };
    Path wd = Files.createTempDirectory("");
    wd.toFile().deleteOnExit();
    String pattern = resolveToString(wd, "z.*.tif");
    FilePattern fp = new FilePattern(pattern);
    assertTrue(fp.isValid());
    assertTrue(fp.isRegex());
    assertEquals(fp.getPattern(), pattern);
    if (!createFiles) {
        // pattern matches a single (nonexistent) file with name == pattern
        assertEquals(fp.getFiles(), new String[] { pattern });
        return;
    }
    String[] fullNames = mkFiles(wd, names);
    assertEqualsNoOrder(new FilePattern(pattern).getFiles(), fullNames);
}

Example 7 with FilePattern

use of loci.formats.FilePattern in project bioformats by openmicroscopy.

the class Mass_Importer method run.

public void run(String arg) {
    // prompt user for directory to process
    DirectoryChooser dc = new DirectoryChooser("Bio-Formats Mass Importer");
    String dirPath = dc.getDirectory();
    // create a list of files we have already processed
    HashSet<String> done = new HashSet<String>();
    // list of files to actually open with Bio-Formats Importer
    ArrayList<String> filesToOpen = new ArrayList<String>();
    // process all files in the chosen directory
    File dir = new File(dirPath);
    File[] files = dir.listFiles();
    IJ.showStatus("Scanning directory");
    // image reader object, for testing whether a file is in a supported format
    try (ImageReader tester = new ImageReader()) {
        for (int i = 0; i < files.length; i++) {
            String id = files[i].getAbsolutePath();
            IJ.showProgress((double) i / files.length);
            // skip files that have already been processed
            if (done.contains(id))
                continue;
            // skip unsupported files
            if (!tester.isThisType(id, false))
                continue;
            // use FilePattern to group files with similar names
            String name = files[i].getName();
            FilePattern fp = new FilePattern(name, dirPath);
            // get a list of all files part of this group, and mark them as done
            String[] used = fp.getFiles();
            for (int j = 0; j < used.length; j++) done.add(used[j]);
            filesToOpen.add(id);
        }
    } catch (IOException e) {
        IJ.error("Sorry, an error while closing ImageReader: " + e.getMessage());
    }
    IJ.showProgress(1.0);
    IJ.showStatus("");
    // confirm that user wants to proceed in opening the file groups
    int numToOpen = filesToOpen.size();
    if (numToOpen == 0) {
        IJ.showMessage("No file groups found.");
        return;
    }
    String groups = numToOpen == 1 ? "1 file group" : (numToOpen + " file groups");
    YesNoCancelDialog confirm = new YesNoCancelDialog(IJ.getInstance(), "Bio-Formats Mass Importer", "Found " + groups + " in directory '" + dirPath + "'; proceed?");
    if (!confirm.yesPressed())
        return;
    // launch the Bio-Formats Importer plugin to open each group of files
    for (int i = 0; i < numToOpen; i++) {
        String id = (String) filesToOpen.get(i);
        String params = "location=[Local machine] " + "windowless=true " + "groupFiles=true " + "id=[" + id + "] ";
        new LociImporter().run(params);
    }
    IJ.showStatus("");
}

Example 8 with FilePattern

use of loci.formats.FilePattern in project bioformats by openmicroscopy.

the class DicomReader method scanDirectory.

// -- Utility methods --
/**
 * Scan the given directory for files that belong to this dataset.
 */
private void scanDirectory(Location dir, boolean checkSeries) throws FormatException, IOException {
    Location currentFile = new Location(currentId).getAbsoluteFile();
    FilePattern pattern = new FilePattern(currentFile.getName(), dir.getAbsolutePath());
    String[] patternFiles = pattern.getFiles();
    if (patternFiles == null)
        patternFiles = new String[0];
    Arrays.sort(patternFiles);
    // path separator normalization is inconsistent
    for (int i = 0; i < patternFiles.length; i++) {
        patternFiles[i] = new Location(patternFiles[i]).getAbsolutePath();
    }
    String[] files = dir.list(true);
    if (files == null)
        return;
    Arrays.sort(files);
    for (String f : files) {
        String file = new Location(dir, f).getAbsolutePath();
        LOGGER.debug("Checking file {}", file);
        if (!f.equals(currentId) && !file.equals(currentId) && isThisType(file) && Arrays.binarySearch(patternFiles, file) >= 0) {
            addFileToList(file, checkSeries);
        }
    }
}

Example 9 with FilePattern

use of loci.formats.FilePattern in project bioformats by openmicroscopy.

the class AxisGuesserTest method check.

private void check(// IN
String p, // IN
String order, // IN
int sZ, // IN
int sT, // IN
int sC, // IN
boolean cert, String newOrder, int[] types) {
    // OUT
    FilePattern fp = new FilePattern(p);
    AxisGuesser ag = new AxisGuesser(fp, order, sZ, sT, sC, cert);
    assertEquals(ag.getFilePattern().getPattern(), p);
    assertEquals(ag.getOriginalOrder(), order);
    assertEquals(ag.getAdjustedOrder(), newOrder);
    assertEquals(ag.getAxisTypes(), types);
    checkAxisCount(ag, types);
}

Example 10 with FilePattern

use of loci.formats.FilePattern in project bioformats by openmicroscopy.

the class DataConverter method run.

// -- Runnable methods --
@Override
public void run() {
    convert.setEnabled(false);
    includeZ.setEnabled(false);
    includeT.setEnabled(false);
    includeC.setEnabled(false);
    zChoice.setEnabled(false);
    tChoice.setEnabled(false);
    cChoice.setEnabled(false);
    input.setEditable(false);
    fps.setEnabled(false);
    if (series != null)
        series.setEnabled(false);
    forceType.setEnabled(false);
    codec.setEnabled(false);
    progress.setString("Getting ready");
    try {
        String in = input.getText();
        String out = output.getText();
        if (in.trim().equals("")) {
            msg("Please specify input files.");
            convert.setEnabled(true);
            progress.setString("");
            return;
        }
        if (out.trim().equals("")) {
            File f = new File(in);
            String name = new FilePattern(in).getPrefix();
            String stitchDir = name + "-stitched";
            new File(f.getParent() + File.separator + stitchDir).mkdir();
            out = f.getParent() + File.separator + stitchDir + File.separator + name + ".tif";
            out = out.replaceAll(File.separator + File.separator, File.separator);
            output.setText(out);
        }
        output.setEditable(false);
        swap.setId(in);
        if (series != null) {
            swap.setSeries(((Integer) series.getValue()).intValue() - 1);
        }
        writer.setFramesPerSecond(((Integer) fps.getValue()).intValue());
        try {
            writer.getWriter(out).setCompression((String) codec.getSelectedItem());
        } catch (NullPointerException npe) {
        }
        // boolean isQT = swap.getFormat().equals("QuickTime");
        // boolean useQTJ = isQT && qtJava.isSelected();
        // ((QTReader) reader.getReader(QTReader.class)).setLegacy(useQTJ);
        // swap dimensions based on user input
        String order = swap.getDimensionOrder();
        if (zLabel.getText().indexOf("Time") != -1) {
            order = order.replace('Z', 'T');
        } else if (zLabel.getText().indexOf("Channel") != -1) {
            order = order.replace('Z', 'C');
        }
        if (tLabel.getText().indexOf("Slice") != -1) {
            order = order.replace('T', 'Z');
        } else if (tLabel.getText().indexOf("Channel") != -1) {
            order = order.replace('T', 'C');
        }
        if (cLabel.getText().indexOf("Time") != -1) {
            order = order.replace('C', 'T');
        } else if (cLabel.getText().indexOf("Slice") != -1) {
            order = order.replace('C', 'Z');
        }
        swap.swapDimensions(order);
        // determine internal and external dimensions for each axis
        int internalZ = includeZ.isSelected() ? swap.getSizeZ() : 1;
        int internalT = includeT.isSelected() ? swap.getSizeT() : 1;
        int internalC = includeC.isSelected() ? swap.getEffectiveSizeC() : 1;
        int externalZ = includeZ.isSelected() ? 1 : swap.getSizeZ();
        int externalT = includeT.isSelected() ? 1 : swap.getSizeT();
        int externalC = includeC.isSelected() ? 1 : swap.getEffectiveSizeC();
        int zDigits = ("" + externalZ).length();
        int tDigits = ("" + externalT).length();
        int cDigits = ("" + externalC).length();
        progress.setMaximum(2 * swap.getImageCount());
        int star = out.lastIndexOf(".");
        if (star < 0)
            star = out.length();
        String pre = out.substring(0, star);
        String post = out.substring(star);
        // determine appropriate pixel type
        int type = swap.getPixelType();
        writer.setId(out);
        if (force && !writer.isSupportedType(type)) {
            int[] types = writer.getPixelTypes();
            for (int i = 0; i < types.length; i++) {
                if (types[i] > type) {
                    if (i == 0) {
                        type = types[i];
                        break;
                    } else {
                        type = types[i - 1];
                        break;
                    }
                }
                if (i == types.length - 1)
                    type = types[i];
            }
        } else if (!force && !writer.isSupportedType(type)) {
            throw new FormatException("Unsupported pixel type: " + FormatTools.getPixelTypeString(type) + "\nTo write to this format, the \"force\" box must be checked.\n" + "This may result in a loss of precision; for best results, " + "convert to TIFF instead.");
        }
        long start = System.currentTimeMillis();
        int plane = 0;
        for (int i = 0; i < externalZ; i++) {
            for (int j = 0; j < externalT; j++) {
                for (int k = 0; k < externalC; k++) {
                    // construct the numeric blocks
                    String zBlock = "";
                    String tBlock = "";
                    String cBlock = "";
                    if (externalZ > 1) {
                        String num = "" + i;
                        while (num.length() < zDigits) num = "0" + num;
                        zBlock = "Z" + num + "_";
                    }
                    if (externalT > 1) {
                        String num = "" + j;
                        while (num.length() < tDigits) num = "0" + num;
                        tBlock = "T" + num + "_";
                    }
                    if (externalC > 1) {
                        String num = "" + k;
                        while (num.length() < cDigits) num = "0" + num;
                        cBlock = "C" + num;
                    }
                    String outFile = pre;
                    if (zBlock.length() > 1)
                        outFile += zBlock;
                    if (tBlock.length() > 1)
                        outFile += tBlock;
                    if (cBlock.length() > 1)
                        outFile += cBlock;
                    if (outFile.endsWith("_")) {
                        outFile = outFile.substring(0, outFile.length() - 1);
                    }
                    outFile += post;
                    String outName = new File(outFile).getName();
                    int planesPerFile = internalZ * internalT * internalC;
                    int filePlane = 0;
                    for (int z = 0; z < internalZ; z++) {
                        for (int t = 0; t < internalT; t++) {
                            for (int c = 0; c < internalC; c++) {
                                int zPos = z * externalZ + i;
                                int tPos = t * externalT + j;
                                int cPos = c * externalC + k;
                                progress.setString(outName + " " + (filePlane + 1) + "/" + planesPerFile);
                                filePlane++;
                                progress.setValue(2 * (plane + 1));
                                plane++;
                                int ndx = swap.getIndex(zPos, cPos, tPos);
                                BufferedImage img = biReader.openImage(ndx);
                                writer.setId(out);
                                if (force && !writer.isSupportedType(swap.getPixelType())) {
                                    int pixelType = 0;
                                    switch(type) {
                                        case FormatTools.INT8:
                                        case FormatTools.UINT8:
                                            pixelType = DataBuffer.TYPE_BYTE;
                                            break;
                                        case FormatTools.INT16:
                                            pixelType = DataBuffer.TYPE_USHORT;
                                            break;
                                        case FormatTools.UINT16:
                                            pixelType = DataBuffer.TYPE_SHORT;
                                            break;
                                        case FormatTools.INT32:
                                        case FormatTools.UINT32:
                                            pixelType = DataBuffer.TYPE_INT;
                                            break;
                                        case FormatTools.FLOAT:
                                            pixelType = DataBuffer.TYPE_FLOAT;
                                            break;
                                        case FormatTools.DOUBLE:
                                            pixelType = DataBuffer.TYPE_DOUBLE;
                                            break;
                                    }
                                // TODO - come up with another way to do this...
                                // img = ImageTools.makeType(img, pixelType);
                                }
                                writer.setId(outFile);
                                biWriter.savePlane(filePlane, img);
                                if (shutdown)
                                    break;
                            }
                        }
                    }
                }
            }
        }
        progress.setValue(2 * swap.getImageCount());
        progress.setString("Finishing");
        if (writer != null)
            writer.close();
        long end = System.currentTimeMillis();
        double time = (end - start) / 1000.0;
        long avg = (end - start) / (swap.getImageCount());
        progress.setString(time + " s elapsed (" + avg + " ms/plane)");
        progress.setValue(0);
        if (swap != null)
            swap.close();
    } catch (FormatException exc) {
        LOGGER.info("", exc);
        String err = exc.getMessage();
        if (err == null)
            err = exc.getClass().getName();
        msg("Sorry, an error occurred: " + err);
        progress.setString("");
        progress.setValue(0);
    } catch (IOException exc) {
        LOGGER.info("", exc);
        String err = exc.getMessage();
        if (err == null)
            err = exc.getClass().getName();
        msg("Sorry, an error occurred: " + err);
        progress.setString("");
        progress.setValue(0);
    }
    convert.setEnabled(true);
    includeZ.setEnabled(true);
    includeT.setEnabled(true);
    includeC.setEnabled(true);
    zChoice.setEnabled(true);
    tChoice.setEnabled(true);
    cChoice.setEnabled(true);
    input.setEditable(true);
    output.setEditable(true);
    fps.setEnabled(true);
    if (series != null)
        series.setEnabled(true);
    forceType.setEnabled(true);
    codec.setEnabled(true);
}