Examples with MetadataRetrieve loci.formats.meta.MetadataRetrieve used on opensource projects

Example 21 with MetadataRetrieve

use of loci.formats.meta.MetadataRetrieve in project bioformats by openmicroscopy.

the class OMEXMLWriter method saveBytes.

// -- IFormatWriter API methods --
/**
 * @see loci.formats.IFormatWriter#saveBytes(int, byte[], int, int, int, int)
 */
@Override
public void saveBytes(int no, byte[] buf, int x, int y, int w, int h) throws FormatException, IOException {
    checkParams(no, buf, x, y, w, h);
    if (!isFullPlane(x, y, w, h)) {
        throw new FormatException("OMEXMLWriter does not yet support saving image tiles.");
    }
    MetadataRetrieve retrieve = getMetadataRetrieve();
    if (no == 0) {
        out.writeBytes(xmlFragments.get(series));
    }
    String type = retrieve.getPixelsType(series).toString();
    int pixelType = FormatTools.pixelTypeFromString(type);
    int bytes = FormatTools.getBytesPerPixel(pixelType);
    int nChannels = getSamplesPerPixel();
    int sizeX = retrieve.getPixelsSizeX(series).getValue().intValue();
    int sizeY = retrieve.getPixelsSizeY(series).getValue().intValue();
    int planeSize = sizeX * sizeY * bytes;
    boolean bigEndian = false;
    if (retrieve.getPixelsBigEndian(series) != null) {
        bigEndian = retrieve.getPixelsBigEndian(series).booleanValue();
    } else if (retrieve.getPixelsBinDataCount(series) == 0) {
        bigEndian = retrieve.getPixelsBinDataBigEndian(series, 0).booleanValue();
    }
    String namespace = "xmlns=\"http://www.openmicroscopy.org/Schemas/OME/" + service.getLatestVersion() + "\"";
    for (int i = 0; i < nChannels; i++) {
        byte[] b = ImageTools.splitChannels(buf, i, nChannels, bytes, false, interleaved);
        byte[] encodedPix = compress(b);
        final StringBuilder plane = new StringBuilder("\n<BinData ");
        plane.append(namespace);
        plane.append(" Length=\"");
        plane.append(planeSize);
        plane.append("\"");
        plane.append(" BigEndian=\"");
        plane.append(bigEndian);
        plane.append("\"");
        if (compression != null && !compression.equals("Uncompressed")) {
            plane.append(" Compression=\"");
            plane.append(compression);
            plane.append("\"");
        }
        plane.append(">");
        plane.append(new String(encodedPix, Constants.ENCODING));
        plane.append("</BinData>");
        out.writeBytes(plane.toString());
    }
}

Example 22 with MetadataRetrieve

use of loci.formats.meta.MetadataRetrieve in project bioformats by openmicroscopy.

the class AVIWriter method setId.

/* @see loci.formats.FormatWriter#setId(String) */
@Override
public void setId(String id) throws FormatException, IOException {
    super.setId(id);
    savedbLength = new ArrayList<Long>();
    if (out.length() > 0) {
        RandomAccessInputStream in = new RandomAccessInputStream(currentId);
        in.order(true);
        in.seek(FRAME_OFFSET);
        planesWritten = in.readInt();
        in.seek(SAVE_FILE_SIZE);
        endPos = in.readInt() + SAVE_FILE_SIZE + 4;
        in.seek(SAVE_LIST2_SIZE);
        idx1Pos = in.readInt() + SAVE_LIST2_SIZE + 4;
        saveidx1Length = idx1Pos + 4;
        if (planesWritten > 0)
            in.seek(saveidx1Length + 4);
        for (int z = 0; z < planesWritten; z++) {
            in.skipBytes(8);
            savedbLength.add(in.readInt() + 4 + SAVE_MOVI);
            in.skipBytes(4);
        }
        in.close();
        out.seek(idx1Pos);
    } else {
        planesWritten = 0;
    }
    out.order(true);
    MetadataRetrieve meta = getMetadataRetrieve();
    tDim = meta.getPixelsSizeZ(series).getValue().intValue();
    zDim = meta.getPixelsSizeT(series).getValue().intValue();
    yDim = meta.getPixelsSizeY(series).getValue().intValue();
    xDim = meta.getPixelsSizeX(series).getValue().intValue();
    String type = meta.getPixelsType(series).toString();
    int pixelType = FormatTools.pixelTypeFromString(type);
    bytesPerPixel = FormatTools.getBytesPerPixel(pixelType);
    bytesPerPixel *= getSamplesPerPixel();
    xPad = 0;
    int xMod = xDim % 4;
    if (xMod != 0) {
        xPad = 4 - xMod;
        xDim += xPad;
    }
    byte[][] lut = null;
    if (getColorModel() instanceof IndexColorModel) {
        lut = new byte[4][256];
        IndexColorModel model = (IndexColorModel) getColorModel();
        model.getReds(lut[0]);
        model.getGreens(lut[1]);
        model.getBlues(lut[2]);
        model.getAlphas(lut[3]);
    }
    if (out.length() == 0) {
        // signature
        out.writeBytes("RIFF");
        // Bytes 4 thru 7 contain the length of the file. This length does
        // not include bytes 0 thru 7.
        // for now write 0 for size
        out.writeInt(0);
        // RIFF type
        out.writeBytes("AVI ");
        // Write the first LIST chunk, which contains
        // information on data decoding
        // CHUNK signature
        out.writeBytes("LIST");
        // Write the length of the LIST CHUNK not including the first 8 bytes
        // with LIST and size. Note that the end of the LIST CHUNK is followed
        // by JUNK.
        out.writeInt((bytesPerPixel == 1) ? 1240 : 216);
        // CHUNK type
        out.writeBytes("hdrl");
        // Write the avih sub-CHUNK
        out.writeBytes("avih");
        // Write the length of the avih sub-CHUNK (38H) not including the
        // the first 8 bytes for avihSignature and the length
        out.writeInt(0x38);
        // dwMicroSecPerFrame - Write the microseconds per frame
        microSecPerFrame = (int) (1.0 / fps * 1.0e6);
        out.writeInt(microSecPerFrame);
        // Write the maximum data rate of the file in bytes per second
        // dwMaxBytesPerSec
        out.writeInt(0);
        // dwReserved1 - set to 0
        out.writeInt(0);
        // dwFlags - just set the bit for AVIF_HASINDEX
        out.writeInt(0x10);
        // 10H AVIF_HASINDEX: The AVI file has an idx1 chunk containing
        // an index at the end of the file. For good performance, all
        // AVI files should contain an index.
        // 20H AVIF_MUSTUSEINDEX: Index CHUNK, rather than the physical
        // ordering of the chunks in the file, must be used to determine the
        // order of the frames.
        // 100H AVIF_ISINTERLEAVED: Indicates that the AVI file is interleaved.
        // This is used to read data from a CD-ROM more efficiently.
        // 800H AVIF_TRUSTCKTYPE: USE CKType to find key frames
        // 10000H AVIF_WASCAPTUREFILE: The AVI file is used for capturing
        // real-time video. Applications should warn the user before
        // writing over a file with this fla set because the user
        // probably defragmented this file.
        // 20000H AVIF_COPYRIGHTED: The AVI file contains copyrighted data
        // and software. When, this flag is used, software should not
        // permit the data to be duplicated.
        // dwTotalFrames - total frame number
        out.writeInt(0);
        // dwInitialFrames -Initial frame for interleaved files.
        // Noninterleaved files should specify 0.
        out.writeInt(0);
        // dwStreams - number of streams in the file - here 1 video and
        // zero audio.
        out.writeInt(1);
        // dwSuggestedBufferSize - Suggested buffer size for reading the file.
        // Generally, this size should be large enough to contain the largest
        // chunk in the file.
        out.writeInt(0);
        // dwWidth - image width in pixels
        out.writeInt(xDim - xPad);
        // dwHeight - height in pixels
        out.writeInt(yDim);
        // dwReserved[4] - Microsoft says to set the following 4 values to 0.
        out.writeInt(0);
        out.writeInt(0);
        out.writeInt(0);
        out.writeInt(0);
        // Write the Stream line header CHUNK
        out.writeBytes("LIST");
        // Write the size of the first LIST subCHUNK not including the first 8
        // bytes with LIST and size. Note that saveLIST1subSize = saveLIST1Size
        // + 76, and that the length written to saveLIST1subSize is 76 less than
        // the length written to saveLIST1Size. The end of the first LIST
        // subCHUNK is followed by JUNK.
        out.writeInt((bytesPerPixel == 1) ? 1164 : 140);
        // Write the chunk type
        out.writeBytes("strl");
        // Write the strh sub-CHUNK
        out.writeBytes("strh");
        // Write length of strh sub-CHUNK
        out.writeInt(56);
        // fccType - Write the type of data stream - here vids for video stream
        out.writeBytes("vids");
        // Write DIB for Microsoft Device Independent Bitmap.
        // Note: Unfortunately, at least 3 other four character codes are
        // sometimes used for uncompressed AVI videos: 'RGB ', 'RAW ',
        // 0x00000000
        out.writeBytes("DIB ");
        // dwFlags
        out.writeInt(0);
        // 0x00000001 AVISF_DISABLED The stram data should be rendered only when
        // explicitly enabled.
        // 0x00010000 AVISF_VIDEO_PALCHANGES Indicates that a palette change is
        // included in the AVI file. This flag warns the playback software that
        // it will need to animate the palette.
        // dwPriority - priority of a stream type. For example, in a file with
        // multiple audio streams, the one with the highest priority might be
        // the default one.
        out.writeInt(0);
        // dwInitialFrames - Specifies how far audio data is skewed ahead of
        // video frames in interleaved files. Typically, this is about 0.75
        // seconds. In interleaved files specify the number of frames in the
        // file prior to the initial frame of the AVI sequence.
        // Noninterleaved files should use zero.
        out.writeInt(0);
        // rate/scale = samples/second
        // dwScale
        out.writeInt(1);
        // dwRate - frame rate for video streams
        out.writeInt(fps);
        // dwStart - this field is usually set to zero
        out.writeInt(0);
        // dwLength - playing time of AVI file as defined by scale and rate
        // Set equal to the number of frames
        out.writeInt(tDim * zDim);
        // dwSuggestedBufferSize - Suggested buffer size for reading the stream.
        // Typically, this contains a value corresponding to the largest chunk
        // in a stream.
        out.writeInt(0);
        // dwQuality - encoding quality given by an integer between 0 and
        // 10,000. If set to -1, drivers use the default quality value.
        out.writeInt(-1);
        // dwSampleSize #
        // 0 if the video frames may or may not vary in size
        // If 0, each sample of data(such as a video frame) must be in a
        // separate chunk. If nonzero, then multiple samples of data can be
        // grouped into a single chunk within the file.
        out.writeInt(0);
        // rcFrame - Specifies the destination rectangle for a text or video
        // stream within the movie rectangle specified by the dwWidth and
        // dwHeight members of the AVI main header structure. The rcFrame member
        // is typically used in support of multiple video streams. Set this
        // rectangle to the coordinates corresponding to the movie rectangle to
        // update the whole movie rectangle. Units for this member are pixels.
        // The upper-left corner of the destination rectangle is relative to the
        // upper-left corner of the movie rectangle.
        // left
        out.writeShort((short) 0);
        // top
        out.writeShort((short) 0);
        // right
        out.writeShort((short) 0);
        // bottom
        out.writeShort((short) 0);
        // Write the size of the stream format CHUNK not including the first 8
        // bytes for strf and the size. Note that the end of the stream format
        // CHUNK is followed by strn.
        // Write the stream format chunk
        out.writeBytes("strf");
        // write the strf CHUNK size
        out.writeInt((bytesPerPixel == 1) ? 1068 : 44);
        // Applications should use this size to determine which BITMAPINFO
        // header structure is being used. This size includes this biSize field.
        // biSize- Write header size of BITMAPINFO header structure
        out.writeInt(40);
        // biWidth - image width in pixels
        out.writeInt(xDim);
        // biHeight - image height in pixels. If height is positive, the bitmap
        // is a bottom up DIB and its origin is in the lower left corner. If
        // height is negative, the bitmap is a top-down DIB and its origin is
        // the upper left corner. This negative sign feature is supported by the
        // Windows Media Player, but it is not supported by PowerPoint.
        out.writeInt(yDim);
        // biPlanes - number of color planes in which the data is stored
        // This must be set to 1.
        out.writeShort(1);
        int bitsPerPixel = (bytesPerPixel == 3) ? 24 : 8;
        // biBitCount - number of bits per pixel #
        // 0L for BI_RGB, uncompressed data as bitmap
        out.writeShort((short) bitsPerPixel);
        // biSizeImage #
        out.writeInt(0);
        // biCompression - compression type
        out.writeInt(0);
        // biXPelsPerMeter - horizontal resolution in pixels
        out.writeInt(0);
        // biYPelsPerMeter - vertical resolution in pixels per meter
        out.writeInt(0);
        int nColors = 256;
        out.writeInt(nColors);
        // biClrImportant - specifies that the first x colors of the color table
        // are important to the DIB. If the rest of the colors are not
        // available, the image still retains its meaning in an acceptable
        // manner. When this field is set to zero, all the colors are important,
        // or, rather, their relative importance has not been computed.
        out.writeInt(0);
        // written: blue byte, green byte, red byte, 0 byte
        if (bytesPerPixel == 1) {
            if (lut != null) {
                for (int i = 0; i < 256; i++) {
                    out.write(lut[2][i]);
                    out.write(lut[1][i]);
                    out.write(lut[0][i]);
                    out.write(lut[3][i]);
                }
            } else {
                byte[] lutWrite = new byte[4 * 256];
                for (int i = 0; i < 256; i++) {
                    // blue
                    lutWrite[4 * i] = (byte) i;
                    // green
                    lutWrite[4 * i + 1] = (byte) i;
                    // red
                    lutWrite[4 * i + 2] = (byte) i;
                    lutWrite[4 * i + 3] = 0;
                }
                out.write(lutWrite);
            }
        }
        out.seek(SAVE_STRF_SIZE);
        out.writeInt((int) (SAVE_STRN_POS - (SAVE_STRF_SIZE + 4)));
        out.seek(SAVE_STRN_POS);
        // Use strn to provide zero terminated text string describing the stream
        out.writeBytes("strn");
        // Write length of strn sub-CHUNK
        out.writeInt(16);
        out.writeBytes("FileAVI write  ");
        out.seek(SAVE_LIST1_SIZE);
        out.writeInt((int) (SAVE_JUNK_SIG - (SAVE_LIST1_SIZE + 4)));
        out.seek(SAVE_LIST1_SUBSIZE);
        out.writeInt((int) (SAVE_JUNK_SIG - (SAVE_LIST1_SUBSIZE + 4)));
        out.seek(SAVE_JUNK_SIG);
        // write a JUNK CHUNK for padding
        out.writeBytes("JUNK");
        out.writeInt((int) PADDING_BYTES);
        for (int i = 0; i < PADDING_BYTES / 2; i++) {
            out.writeShort((short) 0);
        }
        // Write the second LIST chunk, which contains the actual data
        out.writeBytes("LIST");
        // For now write 0
        out.writeInt(4);
        // Write CHUNK type 'movi'
        out.writeBytes("movi");
        idx1Pos = out.getFilePointer();
    }
}

Example 23 with MetadataRetrieve

use of loci.formats.meta.MetadataRetrieve in project bioformats by openmicroscopy.

the class ICSWriter method setId.

// -- IFormatHandler API methods --
/* @see loci.formats.FormatWriter#setId(String) */
@Override
public void setId(String id) throws FormatException, IOException {
    super.setId(id);
    if (!uniqueFiles.contains(id)) {
        uniqueFiles.add(id);
    }
    if (checkSuffix(currentId, "ids")) {
        String metadataFile = currentId.substring(0, currentId.lastIndexOf("."));
        metadataFile += ".ics";
        out.close();
        out = new RandomAccessOutputStream(metadataFile);
    }
    if (out.length() == 0) {
        out.writeBytes("\t\n");
        if (checkSuffix(id, "ids")) {
            out.writeBytes("ics_version\t1.0\n");
        } else {
            out.writeBytes("ics_version\t2.0\n");
        }
        out.writeBytes("filename\t" + currentId + "\n");
        out.writeBytes("layout\tparameters\t6\n");
        MetadataRetrieve meta = getMetadataRetrieve();
        MetadataTools.verifyMinimumPopulated(meta, series);
        int pixelType = FormatTools.pixelTypeFromString(meta.getPixelsType(series).toString());
        dimensionOffset = out.getFilePointer();
        int[] sizes = overwriteDimensions(meta);
        dimensionLength = (int) (out.getFilePointer() - dimensionOffset);
        if (validBits != 0) {
            out.writeBytes("layout\tsignificant_bits\t" + validBits + "\n");
        }
        boolean signed = FormatTools.isSigned(pixelType);
        boolean littleEndian = false;
        if (meta.getPixelsBigEndian(series) != null) {
            littleEndian = !meta.getPixelsBigEndian(series).booleanValue();
        } else if (meta.getPixelsBinDataCount(series) == 0) {
            littleEndian = !meta.getPixelsBinDataBigEndian(series, 0).booleanValue();
        }
        out.writeBytes("representation\tformat\t" + (pixelType == FormatTools.FLOAT ? "real\n" : "integer\n"));
        out.writeBytes("representation\tsign\t" + (signed ? "signed\n" : "unsigned\n"));
        out.writeBytes("representation\tcompression\tuncompressed\n");
        out.writeBytes("representation\tbyte_order\t");
        for (int i = 0; i < sizes[0] / 8; i++) {
            if ((littleEndian && (sizes[0] < 32 || pixelType == FormatTools.FLOAT)) || (!littleEndian && sizes[0] >= 32 && pixelType != FormatTools.FLOAT)) {
                out.writeBytes((i + 1) + "\t");
            } else {
                out.writeBytes(((sizes[0] / 8) - i) + "\t");
            }
        }
        out.writeBytes("\nparameter\tscale\t1.000000\t");
        final StringBuilder units = new StringBuilder();
        for (int i = 0; i < outputOrder.length(); i++) {
            char dim = outputOrder.charAt(i);
            Number value = 1.0;
            if (dim == 'X') {
                if (meta.getPixelsPhysicalSizeX(0) != null) {
                    value = meta.getPixelsPhysicalSizeX(0).value(UNITS.MICROMETER).doubleValue();
                }
                units.append("micrometers\t");
            } else if (dim == 'Y') {
                if (meta.getPixelsPhysicalSizeY(0) != null) {
                    value = meta.getPixelsPhysicalSizeY(0).value(UNITS.MICROMETER).doubleValue();
                }
                units.append("micrometers\t");
            } else if (dim == 'Z') {
                if (meta.getPixelsPhysicalSizeZ(0) != null) {
                    value = meta.getPixelsPhysicalSizeZ(0).value(UNITS.MICROMETER).doubleValue();
                }
                units.append("micrometers\t");
            } else if (dim == 'T') {
                Time valueTime = meta.getPixelsTimeIncrement(0);
                if (valueTime != null) {
                    value = valueTime.value(UNITS.SECOND);
                    units.append("seconds\t");
                }
            }
            out.writeBytes(value + "\t");
        }
        out.writeBytes("\nparameter\tunits\tbits\t" + units.toString() + "\n");
        out.writeBytes("\nend\n");
        pixelOffset = out.getFilePointer();
    } else if (checkSuffix(currentId, "ics")) {
        RandomAccessInputStream in = new RandomAccessInputStream(currentId);
        in.findString("\nend\n");
        pixelOffset = in.getFilePointer();
        in.close();
    }
    if (checkSuffix(currentId, "ids")) {
        pixelOffset = 0;
    }
}

Example 24 with MetadataRetrieve

use of loci.formats.meta.MetadataRetrieve in project bioformats by openmicroscopy.

the class OMETiffWriter method setId.

// -- FormatWriter API methods --
/* @see FormatWriter#setId(String) */
@Override
public void setId(String id) throws FormatException, IOException {
    if (id.equals(currentId))
        return;
    super.setId(id);
    if (imageLocations == null) {
        MetadataRetrieve r = getMetadataRetrieve();
        imageLocations = new String[r.getImageCount()][];
        for (int i = 0; i < imageLocations.length; i++) {
            setSeries(i);
            imageLocations[i] = new String[planeCount()];
        }
        setSeries(0);
    }
}

Example 25 with MetadataRetrieve

use of loci.formats.meta.MetadataRetrieve in project bioformats by openmicroscopy.

the class OMETiffWriter method planeCount.

private int planeCount() {
    MetadataRetrieve r = getMetadataRetrieve();
    int z = r.getPixelsSizeZ(series).getValue().intValue();
    int t = r.getPixelsSizeT(series).getValue().intValue();
    int c = r.getChannelCount(series);
    String pixelType = r.getPixelsType(series).getValue();
    int bytes = FormatTools.getBytesPerPixel(pixelType);
    if (bytes > 1 && c == 1) {
        c = r.getChannelSamplesPerPixel(series, 0).getValue();
    }
    return z * c * t;
}