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use source code indentation style to 4 spaces.

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Yoshihiro OKUMURA 2022-09-29 15:13:33 +09:00
parent 565832b018
commit 8e3a599294
1 changed files with 227 additions and 225 deletions
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src/main/java/jp/riken/neurodata/tools/BioFormatsImageInfo.java
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@ -24,257 +24,259 @@ import loci.formats.tools.ImageInfo;
public class BioFormatsImageInfo { public class BioFormatsImageInfo {
protected static Map<String, Object> readImages(final IFormatReader reader) throws FormatException, IOException { protected static Map<String, Object> readImages(final IFormatReader reader) throws FormatException, IOException {
final Map<String, Object> metadata = new LinkedHashMap<String, Object>(); final Map<String, Object> metadata = new LinkedHashMap<String, Object>();
// read basic metadata // read basic metadata
final int seriesCount = reader.getSeriesCount(); final int seriesCount = reader.getSeriesCount();
final MetadataStore ms = reader.getMetadataStore(); final MetadataStore ms = reader.getMetadataStore();
final MetadataRetrieve mr = ms instanceof MetadataRetrieve ? (MetadataRetrieve) ms : null; final MetadataRetrieve mr = ms instanceof MetadataRetrieve ? (MetadataRetrieve) ms : null;
for (int j = 0; j < seriesCount; j++) { for (int j = 0; j < seriesCount; j++) {
// read basic metadata for series #j // read basic metadata for series #j
reader.setSeries(j); reader.setSeries(j);
final Map<String, Object> seriesMetadata = new LinkedHashMap<String, Object>(); final Map<String, Object> seriesMetadata = new LinkedHashMap<String, Object>();
final int imageCount = reader.getImageCount(); final int imageCount = reader.getImageCount();
final int resolutionCount = reader.getResolutionCount(); final int resolutionCount = reader.getResolutionCount();
final String seriesName = mr == null ? null : mr.getImageName(j); final String seriesName = mr == null ? null : mr.getImageName(j);
if (seriesName != null) { if (seriesName != null) {
seriesMetadata.put("name", seriesName); seriesMetadata.put("name", seriesName);
} }
// resolutions // resolutions
if (resolutionCount > 1) { if (resolutionCount > 1) {
final Map<String, Object> resolutionsMetadata = new LinkedHashMap<String, Object>(); final Map<String, Object> resolutionsMetadata = new LinkedHashMap<String, Object>();
for (int i = 0; i < resolutionCount; i++) { for (int i = 0; i < resolutionCount; i++) {
reader.setResolution(i); reader.setResolution(i);
resolutionsMetadata.put(String.format("resolution[%d]", i), resolutionsMetadata.put(String.format("resolution[%d]", i),
makeRectangle(reader.getSizeX(), reader.getSizeY())); makeRectangle(reader.getSizeX(), reader.getSizeY()));
}
seriesMetadata.put("resolutions", resolutionsMetadata);
reader.setResolution(0);
}
seriesMetadata.put("imageCount", imageCount);
seriesMetadata.put("RGB", new Object[] { reader.isRGB(), reader.getRGBChannelCount() });
seriesMetadata.put("interleaved", reader.isInterleaved());
// indexed
{
final List<Object> indexed = new ArrayList<Object>();
indexed.add(reader.isIndexed());
indexed.add(String.format("%b color", !reader.isFalseColor()));
final byte[][] table8 = reader.get8BitLookupTable();
if (table8 != null) {
indexed.add(
String.format("8-bit LUT: %d x %s", table8.length,
table8[0] == null ? "null" : "" + table8[0].length));
}
final short[][] table16 = reader.get16BitLookupTable();
if (table16 != null) {
indexed.add(String.format("16-bit LUT: %d x %s", table16.length,
table16[0] == null ? "null" : "" + table16[0].length));
}
seriesMetadata.put("indexed", indexed);
}
seriesMetadata.put("sizeX", reader.getSizeX());
seriesMetadata.put("sizeY", reader.getSizeY());
final int sizeZ = reader.getSizeZ();
seriesMetadata.put("sizeZ", makeDimension(sizeZ, sizeZ, reader.getModuloZ()));
seriesMetadata.put("sizeC",
makeDimension(reader.getSizeC(), reader.getEffectiveSizeC(), reader.getModuloC()));
final int sizeT = reader.getSizeT();
seriesMetadata.put("sizeT", makeDimension(sizeT, sizeT, reader.getModuloT()));
seriesMetadata.put("tileSize", makeRectangle(reader.getOptimalTileWidth(), reader.getOptimalTileHeight()));
seriesMetadata.put("thumbnailSize", makeRectangle(reader.getThumbSizeX(), reader.getThumbSizeY()));
seriesMetadata.put("endianness", reader.isLittleEndian() ? "little" : "big");
seriesMetadata.put("dimensionOrder",
new String[] { reader.getDimensionOrder(), reader.isOrderCertain() ? "certain" : "uncertain" });
seriesMetadata.put("pixelType", FormatTools.getPixelTypeString(reader.getPixelType()));
seriesMetadata.put("validBitsPerPixel", reader.getBitsPerPixel());
seriesMetadata.put("metadataComplete", reader.isMetadataComplete());
seriesMetadata.put("thumbnailSeries", reader.isThumbnailSeries());
// plane
{
final int[] indices;
if (imageCount > 6) {
int q = imageCount / 2;
indices = new int[] { 0, q - 2, q - 1, q, q + 1, q + 2, imageCount - 1 };
} else if (imageCount > 2) {
indices = new int[] { 0, imageCount / 2, imageCount - 1 };
} else if (imageCount > 1) {
indices = new int[] { 0, 1 };
} else {
indices = new int[] { 0 };
}
final int[][] zct = new int[indices.length][];
final int[] indices2 = new int[indices.length];
for (int i = 0; i < indices.length; i++) {
zct[i] = reader.getZCTCoords(indices[i]);
indices2[i] = reader.getIndex(zct[i][0], zct[i][1], zct[i][2]);
final Map<String, Object> planeMetadata = new LinkedHashMap<String, Object>();
planeMetadata.put("Z", zct[i][0]);
planeMetadata.put("C", zct[i][1]);
planeMetadata.put("T", zct[i][2]);
if (indices[i] != indices2[i]) {
planeMetadata.put("[mismatch]", indices2[i]);
}
seriesMetadata.put(String.format("plane[%d]", indices[i]), planeMetadata);
}
}
metadata.put(String.format("series[%d]", j), seriesMetadata);
} }
seriesMetadata.put("resolutions", resolutionsMetadata);
reader.setResolution(0);
}
seriesMetadata.put("imageCount", imageCount); return metadata;
seriesMetadata.put("RGB", new Object[] { reader.isRGB(), reader.getRGBChannelCount() }); }
seriesMetadata.put("interleaved", reader.isInterleaved());
// indexed protected static Map<String, Object> readAnnotations(final IFormatReader reader) {
{ final Map<String, Object> metadata = new LinkedHashMap<String, Object>();
final List<Object> indexed = new ArrayList<Object>(); // global metadata
indexed.add(reader.isIndexed()); final Hashtable<String, Object> globalMetadata = reader.getGlobalMetadata();
indexed.add(String.format("%b color", !reader.isFalseColor())); for (String key : MetadataTools.keys(globalMetadata)) {
final byte[][] table8 = reader.get8BitLookupTable(); metadata.put(key, globalMetadata.get(key));
if (table8 != null) {
indexed.add(
String.format("8-bit LUT: %d x %s", table8.length, table8[0] == null ? "null" : "" + table8[0].length));
} }
final short[][] table16 = reader.get16BitLookupTable(); // original metadata
if (table16 != null) { final int seriesCount = reader.getSeriesCount();
indexed.add(String.format("16-bit LUT: %d x %s", table16.length, for (int j = 0; j < seriesCount; j++) {
table16[0] == null ? "null" : "" + table16[0].length)); reader.setSeries(j);
final Hashtable<String, Object> seriesMagedata = reader.getSeriesMetadata();
if (!seriesMagedata.isEmpty()) {
final Map<String, Object> seriesMetadata = new LinkedHashMap<String, Object>();
final String[] keys = MetadataTools.keys(seriesMagedata);
for (int i = 0; i < keys.length; i++) {
seriesMetadata.put(keys[i], seriesMagedata.get(keys[i]));
}
metadata.put(String.format("series[%d]", j), seriesMetadata);
}
} }
seriesMetadata.put("indexed", indexed);
}
seriesMetadata.put("sizeX", reader.getSizeX()); return metadata;
seriesMetadata.put("sizeY", reader.getSizeY()); }
final int sizeZ = reader.getSizeZ();
seriesMetadata.put("sizeZ", makeDimension(sizeZ, sizeZ, reader.getModuloZ()));
seriesMetadata.put("sizeC", makeDimension(reader.getSizeC(), reader.getEffectiveSizeC(), reader.getModuloC()));
final int sizeT = reader.getSizeT();
seriesMetadata.put("sizeT", makeDimension(sizeT, sizeT, reader.getModuloT()));
seriesMetadata.put("tileSize", makeRectangle(reader.getOptimalTileWidth(), reader.getOptimalTileHeight()));
seriesMetadata.put("thumbnailSize", makeRectangle(reader.getThumbSizeX(), reader.getThumbSizeY()));
seriesMetadata.put("endianness", reader.isLittleEndian() ? "little" : "big");
seriesMetadata.put("dimensionOrder",
new String[] { reader.getDimensionOrder(), reader.isOrderCertain() ? "certain" : "uncertain" });
seriesMetadata.put("pixelType", FormatTools.getPixelTypeString(reader.getPixelType()));
seriesMetadata.put("validBitsPerPixel", reader.getBitsPerPixel());
seriesMetadata.put("metadataComplete", reader.isMetadataComplete());
seriesMetadata.put("thumbnailSeries", reader.isThumbnailSeries());
// plane protected static Object makeDimension(final int size, final int effSize, final Modulo modulo) {
{ final int mLength = modulo.length();
final int[] indices; if (size == effSize && mLength == 1) {
if (imageCount > 6) { return size;
int q = imageCount / 2;
indices = new int[] { 0, q - 2, q - 1, q, q + 1, q + 2, imageCount - 1 };
} else if (imageCount > 2) {
indices = new int[] { 0, imageCount / 2, imageCount - 1 };
} else if (imageCount > 1) {
indices = new int[] { 0, 1 };
} else {
indices = new int[] { 0 };
} }
final int[][] zct = new int[indices.length][]; final List<Object> ret = new ArrayList<Object>();
final int[] indices2 = new int[indices.length]; ret.add(size);
for (int i = 0; i < indices.length; i++) { if (size != effSize) {
zct[i] = reader.getZCTCoords(indices[i]); ret.add(String.format("(effectively %d)", effSize));
indices2[i] = reader.getIndex(zct[i][0], zct[i][1], zct[i][2]);
final Map<String, Object> planeMetadata = new LinkedHashMap<String, Object>();
planeMetadata.put("Z", zct[i][0]);
planeMetadata.put("C", zct[i][1]);
planeMetadata.put("T", zct[i][2]);
if (indices[i] != indices2[i]) {
planeMetadata.put("[mismatch]", indices2[i]);
}
seriesMetadata.put(String.format("plane[%d]", indices[i]), planeMetadata);
} }
} if (mLength != 1) {
metadata.put(String.format("series[%d]", j), seriesMetadata); ret.add(String.format("(%d %s x %d %s)", size / mLength, modulo.parentType, mLength, modulo.type));
}
return metadata;
}
protected static Map<String, Object> readAnnotations(final IFormatReader reader) {
final Map<String, Object> metadata = new LinkedHashMap<String, Object>();
// global metadata
final Hashtable<String, Object> globalMetadata = reader.getGlobalMetadata();
for (String key : MetadataTools.keys(globalMetadata)) {
metadata.put(key, globalMetadata.get(key));
}
// original metadata
final int seriesCount = reader.getSeriesCount();
for (int j = 0; j < seriesCount; j++) {
reader.setSeries(j);
final Hashtable<String, Object> seriesMagedata = reader.getSeriesMetadata();
if (!seriesMagedata.isEmpty()) {
final Map<String, Object> seriesMetadata = new LinkedHashMap<String, Object>();
final String[] keys = MetadataTools.keys(seriesMagedata);
for (int i = 0; i < keys.length; i++) {
seriesMetadata.put(keys[i], seriesMagedata.get(keys[i]));
} }
metadata.put(String.format("series[%d]", j), seriesMetadata);
} return ret;
} }
return metadata; protected static Map<String, Object> makeRectangle(final int width, final int height) {
} final Map<String, Object> ret = new LinkedHashMap<String, Object>();
ret.put("width", width);
ret.put("height", height);
protected static Object makeDimension(final int size, final int effSize, final Modulo modulo) { return ret;
final int mLength = modulo.length();
if (size == effSize && mLength == 1) {
return size;
}
final List<Object> ret = new ArrayList<Object>();
ret.add(size);
if (size != effSize) {
ret.add(String.format("(effectively %d)", effSize));
}
if (mLength != 1) {
ret.add(String.format("(%d %s x %d %s)", size / mLength, modulo.parentType, mLength, modulo.type));
} }
return ret; protected static String getJsonString(final Map<String, Object> map) {
} final ObjectMapper mapper = new ObjectMapper();
String json = null;
protected static Map<String, Object> makeRectangle(final int width, final int height) {
final Map<String, Object> ret = new LinkedHashMap<String, Object>();
ret.put("width", width);
ret.put("height", height);
return ret;
}
protected static String getJsonString(final Map<String, Object> map) {
final ObjectMapper mapper = new ObjectMapper();
String json = null;
try {
// json = mapper.writerWithDefaultPrettyPrinter().writeValueAsString(map);
json = mapper.writeValueAsString(map);
} catch (final Throwable e) {
// return "null" if conversion error occured
json = "null";
}
return json;
}
public static String readMetadata(final String path, final Map<String, Object> metadata)
throws BioFormatsImageException {
if (FilenameUtils.getExtension(path).toLowerCase().equals("zip")) {
// ignore if file is zip archive
throw new BioFormatsImageException("Zip is not supported");
}
String format = "";
final ImageInfo info = new ImageInfo();
final IFormatReader reader = new ImageReader();
try {
// info.parseArgs(new String[] { path, "-nopix", "-noflat", "-omexml" });
info.parseArgs(new String[] { path, "-nopix", "-noflat" });
info.setReader(reader);
info.mapLocation();
info.configureReaderPreInit();
// initialize reader
reader.setId(path);
format = reader.getFormat();
info.configureReaderPostInit();
info.checkWarnings();
// info.printOMEXML();
// info.readCoreMetadata();
metadata.put("images", readImages(reader));
info.initPreMinMaxValues();
reader.setSeries(0);
reader.setResolution(0);
// info.printGlobalMetadata();
// info.printOriginalMetadata();
final Map<String, Object> annotations = readAnnotations(reader);
if (!annotations.isEmpty()) {
metadata.put("annotations", annotations);
}
} catch (final Throwable e) {
throw new BioFormatsImageException(e);
} finally {
if (reader != null) {
try { try {
reader.close(); // json = mapper.writerWithDefaultPrettyPrinter().writeValueAsString(map);
} catch (final IOException e) { json = mapper.writeValueAsString(map);
throw new BioFormatsImageException(e); } catch (final Throwable e) {
// return "null" if conversion error occured
json = "null";
} }
}
return json;
} }
return format; public static String readMetadata(final String path, final Map<String, Object> metadata)
} throws BioFormatsImageException {
if (FilenameUtils.getExtension(path).toLowerCase().equals("zip")) {
// ignore if file is zip archive
throw new BioFormatsImageException("Zip is not supported");
}
String format = "";
final ImageInfo info = new ImageInfo();
final IFormatReader reader = new ImageReader();
try {
// info.parseArgs(new String[] { path, "-nopix", "-noflat", "-omexml" });
info.parseArgs(new String[] { path, "-nopix", "-noflat" });
info.setReader(reader);
info.mapLocation();
info.configureReaderPreInit();
// -- Main method -- // initialize reader
public static void main(final String[] args) { reader.setId(path);
boolean status = true; format = reader.getFormat();
String message = ""; info.configureReaderPostInit();
String format = ""; info.checkWarnings();
final Map<String, Object> metadata = new LinkedHashMap<String, Object>(); // info.printOMEXML();
final Map<String, Object> thumbnail = new LinkedHashMap<String, Object>(); // info.readCoreMetadata();
if (args.length != 1) { metadata.put("images", readImages(reader));
status = false; info.initPreMinMaxValues();
message = "filename argument required"; reader.setSeries(0);
} else { reader.setResolution(0);
final String path = args[0]; // info.printGlobalMetadata();
try { // info.printOriginalMetadata();
DebugTools.enableLogging("ERROR"); final Map<String, Object> annotations = readAnnotations(reader);
format = readMetadata(path, metadata); if (!annotations.isEmpty()) {
BioFormatsImageThumbnail.readThumbnail(path, thumbnail); metadata.put("annotations", annotations);
} catch (BioFormatsImageException e) { }
status = false; } catch (final Throwable e) {
message = e.getMessage(); throw new BioFormatsImageException(e);
metadata.clear(); } finally {
thumbnail.clear(); if (reader != null) {
} try {
reader.close();
} catch (final IOException e) {
throw new BioFormatsImageException(e);
}
}
}
return format;
} }
final Map<String, Object> results = new LinkedHashMap<String, Object>(); // -- Main method --
results.put("status", status); public static void main(final String[] args) {
results.put("message", message); boolean status = true;
results.put("format", format); String message = "";
results.put("thumbnail", thumbnail.isEmpty() ? null : thumbnail); String format = "";
results.put("metadata", metadata.isEmpty() ? null : metadata); final Map<String, Object> metadata = new LinkedHashMap<String, Object>();
System.out.println(getJsonString(results)); final Map<String, Object> thumbnail = new LinkedHashMap<String, Object>();
if (args.length != 1) {
status = false;
message = "filename argument required";
} else {
final String path = args[0];
try {
DebugTools.enableLogging("ERROR");
format = readMetadata(path, metadata);
BioFormatsImageThumbnail.readThumbnail(path, thumbnail);
} catch (BioFormatsImageException e) {
status = false;
message = e.getMessage();
metadata.clear();
thumbnail.clear();
}
}
if (!status) { final Map<String, Object> results = new LinkedHashMap<String, Object>();
System.exit(1); results.put("status", status);
results.put("message", message);
results.put("format", format);
results.put("thumbnail", thumbnail.isEmpty() ? null : thumbnail);
results.put("metadata", metadata.isEmpty() ? null : metadata);
System.out.println(getJsonString(results));
if (!status) {
System.exit(1);
}
} }
}
} }