Mercurial > hg > digilib-old

annotate common-bioformats/src/main/java/digilib/image/BioFormatsDocuImage.java @ 1132:d47513632da5

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additional annotationSafeTokenUrl for https url, used with passwords. we don't always use https for issues with self-signed certs.
author robcast
date Tue, 13 Nov 2012 19:29:23 +0100
parents f34891279a6e
children
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1 /**
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2 *
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3 */
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4 package digilib.image;
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5
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6 import java.awt.RenderingHints;
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7 import java.awt.geom.AffineTransform;
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8 import java.awt.image.AffineTransformOp;
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9 import java.awt.image.BufferedImage;
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10 import java.io.File;
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11 import java.io.FileInputStream;
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12 import java.io.IOException;
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13 import java.io.OutputStream;
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14
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15 import ome.xml.model.primitives.PositiveInteger;
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16
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17 import loci.common.services.DependencyException;
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18 import loci.common.services.ServiceException;
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19 import loci.common.services.ServiceFactory;
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20 import loci.formats.FormatException;
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21 import loci.formats.IFormatWriter;
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22 import loci.formats.ImageReader;
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23 import loci.formats.ImageWriter;
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24 import loci.formats.gui.BufferedImageReader;
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25 import loci.formats.gui.BufferedImageWriter;
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26 import loci.formats.meta.DummyMetadata;
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27 import loci.formats.meta.IMetadata;
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28 import loci.formats.meta.MetadataRetrieve;
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29 import loci.formats.meta.MetadataStore;
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30 import loci.formats.ome.OMEXMLMetadata;
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31 import loci.formats.services.OMEXMLService;
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32
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33 import digilib.io.FileOpException;
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34 import digilib.io.ImageInput;
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35 import digilib.util.ImageSize;
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36
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37 /**
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38 * @author casties
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39 *
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40 */
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41 public class BioFormatsDocuImage extends DocuImageImpl {
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42
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43 private BufferedImage img;
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44 private Object imageSize;
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45 private RenderingHints renderHint;
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46 private ImageReader reader;
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47 private OMEXMLMetadata meta;
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48
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49 /*
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50 * (non-Javadoc)
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51 *
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52 * @see digilib.image.DocuImageImpl#identify(digilib.io.ImageInput)
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53 */
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54 @Override
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55 public ImageInput identify(ImageInput ii) throws IOException {
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56 ImageReader reader = new ImageReader();
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57 try {
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58 reader.setId(ii.getFile().getAbsolutePath());
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59 } catch (FormatException e) {
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60 // TODO Auto-generated catch block
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61 e.printStackTrace();
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62 }
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63 int width = reader.getSizeX();
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64 int height = reader.getSizeY();
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65 String fmt = reader.getFormat();
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66
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67 String mt = "";
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68 if (fmt.equalsIgnoreCase("Tagged Image File Format")) {
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69 mt = "image/tiff";
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70 } else if (fmt.equalsIgnoreCase("JPEG")) {
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71 mt = "image/jpeg";
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72 }
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73
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74 logger.debug("BioFormats identify: width=" + width + " height=" + height + " format=" + fmt + " mimetype=" + mt);
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75 ii.setSize(new ImageSize(width, height));
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76 ii.setMimetype(mt);
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77 return ii;
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78 }
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79
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80 @Override
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81 public void loadImage(ImageInput ii) throws FileOpException {
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82 logger.debug("loadImage: " + ii);
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83 this.input = ii;
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84 reader = new ImageReader();
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85 try {
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86 // construct the object that stores OME-XML metadata
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87 ServiceFactory factory = new ServiceFactory();
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88 OMEXMLService service = factory.getInstance(OMEXMLService.class);
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89 meta = service.createOMEXMLMetadata();
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90
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91 // set up the reader and associate it with the input file
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92 reader = new ImageReader();
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93 reader.setMetadataStore(meta);
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94 reader.setId(ii.getFile().getAbsolutePath());
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95 BufferedImageReader biReader = BufferedImageReader.makeBufferedImageReader(reader);
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96 img = biReader.openImage(0);
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97 logger.debug("image loaded: " + img);
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98 } catch (FormatException e) {
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99 throw new FileOpException("Unable to load image format: " + e);
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100 } catch (IOException e) {
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101 throw new FileOpException("Unable to load image file: " + e);
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102 } catch (ServiceException e) {
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103 // TODO Auto-generated catch block
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104 e.printStackTrace();
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105 } catch (DependencyException e) {
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106 // TODO Auto-generated catch block
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107 e.printStackTrace();
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108 }
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109 }
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110
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111 @Override
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112 public void scale(double scaleX, double scaleY) throws ImageOpException {
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113 logger.debug("scale: " + scaleX);
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114 /* for downscaling in high quality the image is blurred first */
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115 if ((scaleX <= 0.5) && (quality > 1)) {
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116 int bl = (int) Math.floor(1 / scaleX);
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117 // blur(bl);
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118 }
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119 /* then scaled */
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120 AffineTransformOp scaleOp = new AffineTransformOp(AffineTransform.getScaleInstance(scaleX, scaleY), renderHint);
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121 img = scaleOp.filter(img, null);
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122 logger.debug("scaled to " + img.getWidth() + "x" + img.getHeight() + " img=" + img);
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123 // invalidate image size
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124 imageSize = null;
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125 }
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126
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127 public void setQuality(int qual) {
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128 quality = qual;
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129 renderHint = new RenderingHints(null);
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130 // hint.put(RenderingHints.KEY_ANTIALIASING,
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131 // RenderingHints.VALUE_ANTIALIAS_OFF);
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132 // setup interpolation quality
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133 if (qual > 0) {
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134 logger.debug("quality q1");
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135 renderHint.put(RenderingHints.KEY_INTERPOLATION, RenderingHints.VALUE_INTERPOLATION_BICUBIC);
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136 } else {
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137 logger.debug("quality q0");
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138 renderHint.put(RenderingHints.KEY_INTERPOLATION, RenderingHints.VALUE_INTERPOLATION_NEAREST_NEIGHBOR);
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139 }
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140 }
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141
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142 public void crop(int x_off, int y_off, int width, int height) throws ImageOpException {
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143 // setup Crop
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144 img = img.getSubimage(x_off, y_off, width, height);
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145 logger.debug("CROP:" + img.getWidth() + "x" + img.getHeight());
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146 // invalidate image size
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147 imageSize = null;
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148 }
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149
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150 @Override
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151 public void writeImage(String mt, OutputStream ostream) throws ImageOpException, FileOpException {
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152 logger.debug("writeImage");
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153 File outFile;
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154 String filext = ".jpg";
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155 if (mt.equals("image/png")) {
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156 filext = ".png";
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157 }
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158 try {
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159 outFile = File.createTempFile("biof_temp", filext);
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160 } catch (IOException e) {
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161 throw new FileOpException(e.toString());
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162 }
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163 // save image to file
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164 ImageWriter iw = new ImageWriter();
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165 /*
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166 * try { //iw.setMetadataRetrieve(new DummyMetadata());
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167 * //iw.setSeries(0); //iw.setId(outFile.getAbsolutePath());
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168 * //logger.debug("writer="+iw); } catch (FormatException e) { throw new
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169 * FileOpException(e.toString()); } catch (IOException e) { // TODO
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170 * Auto-generated catch block e.printStackTrace(); } /* if
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171 * (mt.endsWith("png")) { iw = }
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172 */
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173 BufferedImageWriter writer = BufferedImageWriter.makeBufferedImageWriter(iw);
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174 try {
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175 logger.debug("setting metadata "+meta);
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176 iw.setMetadataRetrieve(meta);
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177 logger.debug("writing to file " + outFile);
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178 writer.setId(outFile.getAbsolutePath());
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179 logger.debug("fixing metadata "+meta);
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180 iw.setInterleaved(reader.isInterleaved());
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181 iw.setWriteSequentially(true);
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182 meta.setPixelsSizeX(new PositiveInteger(img.getWidth()), 0);
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183 meta.setPixelsSizeY(new PositiveInteger(img.getHeight()), 0);
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184 meta.setPixelsSizeC(new PositiveInteger(img.getColorModel().getNumComponents()), 0);
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185 logger.debug("saving image " + img);
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186 writer.saveImage(0, img);
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187 logger.debug("closing file");
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188 writer.close();
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189 } catch (FormatException e1) {
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190 // TODO Auto-generated catch block
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191 e1.printStackTrace();
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192 } catch (IOException e1) {
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193 // TODO Auto-generated catch block
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194 e1.printStackTrace();
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195 }
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196 // now send file
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197 FileInputStream inFile = null;
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198 try {
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199 inFile = new FileInputStream(outFile);
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200 byte dataBuffer[] = new byte[4096];
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201 int len;
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202 while ((len = inFile.read(dataBuffer)) != -1) {
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203 // copy out file
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204 ostream.write(dataBuffer, 0, len);
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205 }
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206 } catch (IOException e) {
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207 throw new FileOpException(e.toString());
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208 } finally {
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209 try {
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210 if (inFile != null) {
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211 inFile.close();
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212 }
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213 } catch (IOException e) {
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214 // nothing to do
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215 }
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216 }
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217
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218 }
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219
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220 }