@Override public boolean isThisType(String name) { if (!super.isThisType(name)) { return false; } if (resolutionData.size() > 0) { return true; } MetadataRetrieve r = getMetadataRetrieve(); if (!(r instanceof IPyramidStore)) { return false; } return ((IPyramidStore) r).getResolutionCount(0) > 1; }
public static void populatePixelsOnly(MetadataStore store, IFormatReader r) { int oldSeries = r.getSeries(); for (int i=0; i<r.getSeriesCount(); i++) { r.setSeries(i); String pixelType = FormatTools.getPixelTypeString(r.getPixelType()); populatePixelsOnly(store, i, r.isLittleEndian(), r.getDimensionOrder(), pixelType, r.getSizeX(), r.getSizeY(), r.getSizeZ(), r.getSizeC(), r.getSizeT(), r.getRGBChannelCount()); if (store instanceof IPyramidStore) { for (int res=1; res<r.getResolutionCount(); res++) { r.setResolution(res); ((IPyramidStore) store).setResolutionSizeX( new PositiveInteger(r.getSizeX()), i, res); ((IPyramidStore) store).setResolutionSizeY( new PositiveInteger(r.getSizeY()), i, res); } r.setResolution(0); } } r.setSeries(oldSeries); }
protected int getSizeX() throws FormatException { MetadataRetrieve r = getMetadataRetrieve(); if (r == null) { throw new FormatException("MetadataRetrieve cannot be null"); } PositiveInteger x = null; if (getResolution() == 0) { x = r.getPixelsSizeX(getSeries()); } else if (hasResolutions()) { x = resolutionData.get(getSeries()).get(getResolution() - 1).sizeX; } else { x = ((IPyramidStore) r).getResolutionSizeX(getSeries(), getResolution()); } if (x == null) { throw new FormatException("Size X must not be null"); } return x.getValue().intValue(); }
protected int getSizeY() throws FormatException { MetadataRetrieve r = getMetadataRetrieve(); if (r == null) { throw new FormatException("MetadataRetrieve cannot be null"); } PositiveInteger y = null; if (getResolution() == 0) { y = r.getPixelsSizeY(getSeries()); } else if (hasResolutions()) { y = resolutionData.get(getSeries()).get(getResolution() - 1).sizeY; } else { y = ((IPyramidStore) r).getResolutionSizeY(getSeries(), getResolution()); } if (y == null) { throw new FormatException("Size Y must not be null"); } return y.getValue().intValue(); }
public static void populatePixelsOnly(MetadataStore store, IFormatReader r) { int oldSeries = r.getSeries(); for (int i=0; i<r.getSeriesCount(); i++) { r.setSeries(i); String pixelType = FormatTools.getPixelTypeString(r.getPixelType()); populatePixelsOnly(store, i, r.isLittleEndian(), r.getDimensionOrder(), pixelType, r.getSizeX(), r.getSizeY(), r.getSizeZ(), r.getSizeC(), r.getSizeT(), r.getRGBChannelCount()); if (store instanceof IPyramidStore) { for (int res=1; res<r.getResolutionCount(); res++) { r.setResolution(res); ((IPyramidStore) store).setResolutionSizeX( new PositiveInteger(r.getSizeX()), i, res); ((IPyramidStore) store).setResolutionSizeY( new PositiveInteger(r.getSizeY()), i, res); } r.setResolution(0); } } r.setSeries(oldSeries); }
protected int getSizeX() throws FormatException { MetadataRetrieve r = getMetadataRetrieve(); if (r == null) { throw new FormatException("MetadataRetrieve cannot be null"); } PositiveInteger x = null; if (getResolution() == 0) { x = r.getPixelsSizeX(getSeries()); } else if (hasResolutions()) { x = resolutionData.get(getSeries()).get(getResolution() - 1).sizeX; } else { x = ((IPyramidStore) r).getResolutionSizeX(getSeries(), getResolution()); } if (x == null) { throw new FormatException("Size X must not be null"); } return x.getValue().intValue(); }
protected int getSizeY() throws FormatException { MetadataRetrieve r = getMetadataRetrieve(); if (r == null) { throw new FormatException("MetadataRetrieve cannot be null"); } PositiveInteger y = null; if (getResolution() == 0) { y = r.getPixelsSizeY(getSeries()); } else if (hasResolutions()) { y = resolutionData.get(getSeries()).get(getResolution() - 1).sizeY; } else { y = ((IPyramidStore) r).getResolutionSizeY(getSeries(), getResolution()); } if (y == null) { throw new FormatException("Size Y must not be null"); } return y.getValue().intValue(); }
((IPyramidStore) meta).setResolutionSizeX( new PositiveInteger(widths[p] / scale), p, r); ((IPyramidStore) meta).setResolutionSizeY( new PositiveInteger(heights[p] / scale), p, r);
@Override public boolean isThisType(String name) { if (!super.isThisType(name)) { return false; } if (resolutionData.size() > 0) { return true; } MetadataRetrieve r = getMetadataRetrieve(); if (!(r instanceof IPyramidStore)) { return false; } return ((IPyramidStore) r).getResolutionCount(0) > 1; }
for (int res=1; res<r.getResolutionCount(); res++) { r.setResolution(res); ((IPyramidStore) store).setResolutionSizeX( new PositiveInteger(r.getSizeX()), i, res); ((IPyramidStore) store).setResolutionSizeY( new PositiveInteger(r.getSizeY()), i, res);
@Override public int getResolutionCount() { if (hasResolutions()) { return resolutionData.get(getSeries()).size() + 1; } MetadataRetrieve r = getMetadataRetrieve(); if (r instanceof IPyramidStore) { return ((IPyramidStore) r).getResolutionCount(getSeries()); } return 1; }
for (int res=1; res<r.getResolutionCount(); res++) { r.setResolution(res); ((IPyramidStore) store).setResolutionSizeX( new PositiveInteger(r.getSizeX()), i, res); ((IPyramidStore) store).setResolutionSizeY( new PositiveInteger(r.getSizeY()), i, res);
@Override public int getResolutionCount() { if (hasResolutions()) { return resolutionData.get(getSeries()).size() + 1; } MetadataRetrieve r = getMetadataRetrieve(); if (r instanceof IPyramidStore) { return ((IPyramidStore) r).getResolutionCount(getSeries()); } return 1; }