Examples with AstroImageJ ij.astro.AstroImageJ used on opensource projects

Example 21 with AstroImageJ

use of ij.astro.AstroImageJ in project astroimagej by keastrid.

the class Opener method getFileType.

/**
 *	Attempts to determine the image file type by looking for
 *	'magic numbers' and the file name extension.
 */
@AstroImageJ(reason = "Add more file types; extend how fits file is checked; " + "skip read check for files within a zip; add option to ignore unopenable file; " + "add extension check for pngs", modified = true)
private int getFileType(String path, boolean checkOpenable) {
    if (openUsingPlugins && !path.endsWith(".txt") && !path.endsWith(".java"))
        return UNKNOWN;
    File file = new File(path);
    String name = file.getName();
    InputStream is;
    byte[] buf = new byte[132];
    try {
        if (checkOpenable) {
            is = new FileInputStream(file);
            is.read(buf, 0, 132);
            is.close();
        }
    } catch (IOException e) {
        return UNKNOWN;
    }
    int b0 = buf[0] & 255, b1 = buf[1] & 255, b2 = buf[2] & 255, b3 = buf[3] & 255;
    // Combined TIFF and DICOM created by GE Senographe scanners
    if (buf[128] == 68 && buf[129] == 73 && buf[130] == 67 && buf[131] == 77 && ((b0 == 73 && b1 == 73) || (b0 == 77 && b1 == 77)))
        return TIFF_AND_DICOM;
    // Big-endian TIFF ("MM")
    if (name.endsWith(".lsm"))
        // The LSM	Reader plugin opens these files
        return UNKNOWN;
    if (b0 == 73 && b1 == 73 && b2 == 42 && b3 == 0 && !(bioformats && name.endsWith(".flex")))
        return TIFF;
    // Little-endian TIFF ("II")
    if (b0 == 77 && b1 == 77 && b2 == 0 && b3 == 42)
        return TIFF;
    // JPEG
    if (b0 == 255 && b1 == 216 && b2 == 255)
        return JPEG;
    // GIF ("GIF8")
    if (b0 == 71 && b1 == 73 && b2 == 70 && b3 == 56)
        return GIF;
    name = name.toLowerCase(Locale.US);
    // DICOM ("DICM" at offset 128)
    if (buf[128] == 68 && buf[129] == 73 && buf[130] == 67 && buf[131] == 77 || name.endsWith(".dcm")) {
        return DICOM;
    }
    // ACR/NEMA with first tag = 00002,00xx or 00008,00xx
    if ((b0 == 8 || b0 == 2) && b1 == 0 && b3 == 0 && !name.endsWith(".spe") && !name.equals("fid"))
        return DICOM;
    // PGM ("P1", "P4", "P2", "P5", "P3" or "P6")
    if (b0 == 80 && (b1 == 49 || b1 == 52 || b1 == 50 || b1 == 53 || b1 == 51 || b1 == 54) && (b2 == 10 || b2 == 13 || b2 == 32 || b2 == 9))
        return PGM;
    // Lookup table
    if (name.endsWith(".lut"))
        return LUT;
    // PNG
    if ((b0 == 137 && b1 == 80 && b2 == 78 && b3 == 71) || name.endsWith(".png"))
        return PNG;
    // ZIP containing a TIFF
    if (name.endsWith(".zip"))
        return ZIP;
    // FITS ("SIMP")
    if ((b0 == 83 && b1 == 73 && b2 == 77 && b3 == 80) || name.endsWith(".fts.gz") || name.endsWith(".fits.gz") || name.endsWith(".fit.gz") || name.endsWith(".fts.fz") || name.endsWith(".fits.fz") || name.endsWith(".fit.fz") || name.endsWith(".fits"))
        return FITS;
    // Java source file, text file or macro
    if (name.endsWith(".java") || name.endsWith(".txt") || name.endsWith(".ijm") || name.endsWith(".js") || name.endsWith(".bsh") || name.endsWith(".py") || name.endsWith(".html"))
        return JAVA_OR_TEXT;
    // ImageJ, NIH Image, Scion Image for Windows ROI
    if (// "Iout"
    b0 == 73 && b1 == 111)
        return ROI;
    // ObjectJ project
    if ((b0 == 'o' && b1 == 'j' && b2 == 'j' && b3 == 0) || name.endsWith(".ojj"))
        return OJJ;
    // Results table (tab-delimited or comma-separated tabular text)
    if (name.endsWith(".xls") || name.endsWith(".csv") || name.endsWith(".dat") || name.endsWith(".tbl") || name.endsWith(".prn") || name.endsWith(".spc"))
        return TABLE;
    // AVI
    if (name.endsWith(".avi"))
        return AVI;
    // Text file
    boolean isText = true;
    for (int i = 0; i < 10; i++) {
        int c = buf[i] & 255;
        if ((c < 32 && c != 9 && c != 10 && c != 13) || c > 126) {
            isText = false;
            break;
        }
    }
    if (isText)
        return TEXT;
    // BMP ("BM")
    if ((b0 == 66 && b1 == 77) || name.endsWith(".dib"))
        return BMP;
    // RAW
    if (name.endsWith(".raw") && !Prefs.skipRawDialog)
        return RAW;
    return UNKNOWN;
}

Example 22 with AstroImageJ

use of ij.astro.AstroImageJ in project astroimagej by keastrid.

the class Opener method getImageFromPath.

/**
 * Get image from the path. If it is in a zip file, it will open the zip
 */
@AstroImageJ(reason = "Open zip of pngs as folder")
private BufferedImage getImageFromPath(String path) throws IOException {
    if (path.contains(".zip")) {
        var s = path.split("\\.zip");
        var zip = new ZipFile(s[0] + ".zip");
        var img = ImageIO.read(zip.getInputStream(zip.getEntry(s[1].substring(1))));
        zip.close();
        return img;
    }
    return ImageIO.read(new File(path));
}

Example 23 with AstroImageJ

use of ij.astro.AstroImageJ in project astroimagej by keastrid.

the class FolderOpener method getFileCount.

/**
 * @return first = file count, second = size in MB
 */
@AstroImageJ(reason = "Obtain filtered file count")
private Pair.IntFloatPair getFileCount(GenericDialog gd) {
    var filter = ((TextField) gd.getStringFields().get(1)).getText();
    if (legacyRegex != null)
        filter = "(" + legacyRegex + ")";
    var directory = this.directory;
    directory = ((TextField) gd.getStringFields().get(0)).getText();
    File file = new File(directory);
    String[] list = file.list();
    // Zip as folder
    ZipOpenerUtil.InternalZipFile[] zipEntries = null;
    if (list == null) {
        zipEntries = ZipOpenerUtil.getFilesInZip(directory);
        list = ZipOpenerUtil.InternalZipFile.getPaths(zipEntries);
        if (list.length == 0)
            list = null;
    }
    if (list == null) {
        String parent = file.getParent();
        file = new File(parent);
        list = file.list();
        if (list != null)
            directory = parent;
        else {
            return Pair.IntFloatPair.empty();
        }
    }
    // remove subdirectories from list
    ArrayList<String> fileList = new ArrayList<>();
    for (String s : list) {
        File f = (new File(directory + s));
        if (!f.isDirectory())
            fileList.add(s);
    }
    if (fileList.size() < list.length)
        list = fileList.toArray(new String[fileList.size()]);
    list = trimFileList(list);
    if (list == null)
        return Pair.IntFloatPair.empty();
    // Dynamic filter does not support legacy regex
    list = getFilteredList(list, filter, null);
    if (list == null)
        return Pair.IntFloatPair.empty();
    // Get file sizes by locating a prototypical image file manually calculating its byte size in memory
    var width = 0;
    var height = 0;
    var bitDepth = 0;
    long sizeInBytes = 0;
    var stackCountPerImage = 1;
    for (String sf : list) {
        Opener opener = new Opener();
        opener.setSilentMode(true);
        IJ.redirectErrorMessages(true);
        ImagePlus imp = opener.openImage(directory, sf);
        IJ.redirectErrorMessages(false);
        if (imp != null) {
            width = imp.getWidth();
            height = imp.getHeight();
            bitDepth = imp.getBytesPerPixel();
            stackCountPerImage = imp.getImageStackSize();
            break;
        }
    }
    var increment = safeParse(((TextField) gd.getNumericFields().get(1)).getText(), 1);
    var count = safeParse(((TextField) gd.getStringFields().get(2)).getText(), list.length);
    var start = safeParse(((TextField) gd.getNumericFields().get(0)).getText(), 1);
    sizeInBytes = (long) bitDepth * width * height * ((long) ((count - start + 1) / increment) * stackCountPerImage);
    return new Pair.IntFloatPair(list.length, sizeInBytes / 1_000_000F);
}

Example 24 with AstroImageJ

use of ij.astro.AstroImageJ in project astroimagej by keastrid.

the class TextPanel method copySelection.

/**
 *	Copies the current selection to the system clipboard.
 *	Returns the number of characters copied.
 */
@AstroImageJ(reason = "Limit selection to tabs", modified = true)
public int copySelection() {
    if (Recorder.record && title.equals("Results"))
        Recorder.record("String.copyResults");
    if (selStart == -1 || selEnd == -1)
        return copyAll();
    StringBuffer sb = new StringBuffer();
    ResultsTable rt2 = getResultsTable();
    boolean hasRowNumers = rt2 != null && rt2.showRowNumbers();
    if (Prefs.copyColumnHeaders && labels != null && !labels.equals("") && selStart == 0 && selEnd == iRowCount - 1) {
        if (hasRowNumers && Prefs.noRowNumbers) {
            String s = labels;
            int index = s.indexOf("\t", s.indexOf("\t") + 1);
            if (index != -1)
                s = s.substring(index + 1, s.length());
            sb.append(s);
        } else
            sb.append(labels);
        sb.append('\n');
    }
    for (int i = selStart; i <= selEnd; i++) {
        char[] chars = (char[]) (vData.elementAt(i));
        String s = new String(chars);
        if (s.endsWith("\t"))
            s = s.substring(0, s.length() - 1);
        if (hasRowNumers && Prefs.noRowNumbers && labels != null && !labels.equals("")) {
            int index = s.indexOf("\t");
            if (index != -1)
                s = s.substring(index + 1, s.length());
            sb.append(s);
        } else
            sb.append(s);
        if (i < selEnd || selEnd > selStart)
            sb.append('\n');
    }
    String s = new String(sb);
    Clipboard clip = getToolkit().getSystemClipboard();
    if (clip == null)
        return 0;
    StringSelection cont = new StringSelection(s);
    clip.setContents(cont, this);
    if (s.length() > 0) {
        IJ.showStatus((selEnd - selStart + 1) + " lines copied to clipboard");
        if (this.getParent() instanceof ImageJ)
            Analyzer.setUnsavedMeasurements(false);
    }
    return s.length();
}

Example 25 with AstroImageJ

use of ij.astro.AstroImageJ in project astroimagej by keastrid.

the class TextPanel method rename.

@AstroImageJ(reason = "Add check for AIJ windows", modified = true)
void rename(String title2) {
    ResultsTable rt2 = getOrCreateResultsTable();
    if (rt2 == null)
        return;
    if (title2 != null && title2.equals(""))
        title2 = null;
    TextWindow tw = getTextWindow();
    if (tw == null)
        return;
    if (title2 == null) {
        GenericDialog gd = new GenericDialog("Rename", tw);
        gd.addStringField("Title:", tw.getTitle().contains("Measure") ? tw.getTitle() + "_2" : "Results2", 40);
        gd.showDialog();
        if (gd.wasCanceled())
            return;
        title2 = gd.getNextString();
    }
    String title1 = title;
    if (title != null && title.equals("Results")) {
        IJ.setTextPanel(null);
        Analyzer.setUnsavedMeasurements(false);
        Analyzer.setResultsTable(null);
        Analyzer.resetCounter();
    }
    if (title2.equals("Results")) {
        // tw.setVisible(false);
        tw.dispose();
        WindowManager.removeWindow(tw);
        flush();
        rt2.show("Results");
    } else {
        tw.setTitle(title2);
        int mbSize = tw.mb != null ? tw.mb.getMenuCount() : 0;
        if (mbSize > 0 && tw.mb.getMenu(mbSize - 1).getLabel().equals("Results"))
            tw.mb.remove(mbSize - 1);
        title = title2;
        rt2.show(title);
    }
    Menus.updateWindowMenuItem(title1, title2);
    if (Recorder.record) {
        if (Recorder.scriptMode())
            Recorder.recordString("IJ.renameResults(\"" + title1 + "\", \"" + title2 + "\");\n");
        else
            Recorder.record("Table.rename", title1, title2);
    }
}