From d8226c9de50c95aae509070d97adc88a2f2b8325 Mon Sep 17 00:00:00 2001
From: jakubs <jakubs>
Date: Fri, 3 May 2013 14:23:35 +0000
Subject: [PATCH] SP-606 CCS-34 improve performance of reading c01 files
SVN: 28993
---
.../bioformats/BioFormatsImageUtils.java | 56 ++++++++++++++++++-
1 file changed, 54 insertions(+), 2 deletions(-)
diff --git a/image_readers/source/java/ch/systemsx/cisd/imagereaders/bioformats/BioFormatsImageUtils.java b/image_readers/source/java/ch/systemsx/cisd/imagereaders/bioformats/BioFormatsImageUtils.java
index ce3817be9da..9b81a4f2ca2 100644
--- a/image_readers/source/java/ch/systemsx/cisd/imagereaders/bioformats/BioFormatsImageUtils.java
+++ b/image_readers/source/java/ch/systemsx/cisd/imagereaders/bioformats/BioFormatsImageUtils.java
@@ -32,11 +32,16 @@ import java.util.UUID;
import loci.common.IRandomAccess;
import loci.common.Location;
+import loci.common.RandomAccessInputStream;
import loci.formats.FormatException;
+import loci.formats.FormatHandler;
import loci.formats.IFormatHandler;
import loci.formats.IFormatReader;
import loci.formats.ImageReader;
+import loci.formats.MetadataTools;
+import loci.formats.codec.ZlibCodec;
import loci.formats.gui.BufferedImageReader;
+import loci.formats.in.CellomicsReader;
import loci.formats.in.DefaultMetadataOptions;
import loci.formats.in.MetadataLevel;
import loci.formats.in.MetadataOptions;
@@ -55,6 +60,12 @@ final class BioFormatsImageUtils
private static final IFormatReader[] READERS = new ImageReader().getReaders();
+ static
+ {
+ MetadataTools.setDefaultDateEnabled(false);
+ CellomicsReader.setNoHiddenFiles(true);
+ }
+
/**
* Tries to create a suitable reader for the file specified with <var>fileName</var>. This is a
* factory method which returns for each invocation a new instance of a suitable reader. May
@@ -201,7 +212,7 @@ final class BioFormatsImageUtils
throws IOExceptionUnchecked, IllegalArgumentException
{
String handleId = generateHandleId(reader, imageID);
-
+
// Add to static map.
Location.mapFile(handleId, handle);
try
@@ -286,7 +297,7 @@ final class BioFormatsImageUtils
{
// Add to static map.
String handleId = generateHandleId(reader, imageID);
-
+
Location.mapFile(handleId, handle);
try
{
@@ -326,6 +337,11 @@ final class BioFormatsImageUtils
Location.mapFile(handleId, handle);
try
{
+ if (reader instanceof CellomicsReader)
+ {
+ return CellomicsReaderUtil.readSize(handleId);
+ }
+
// This does the actual parsing.
reader.setId(handleId);
reader.setSeries(imageID.getSeriesIndex());
@@ -346,6 +362,42 @@ final class BioFormatsImageUtils
}
}
+ public static class CellomicsReaderUtil
+ {
+ public static Dimension readSize(String id) throws FormatException, IOException
+ {
+ RandomAccessInputStream in = getDecompressedStream(id);
+
+ in.order(true);
+ in.skipBytes(4);
+
+ int x = in.readInt();
+ int y = in.readInt();
+
+ in.close();
+
+ return new Dimension(x, y);
+
+ }
+
+ private static RandomAccessInputStream getDecompressedStream(String filename)
+ throws FormatException, IOException
+ {
+ RandomAccessInputStream s = new RandomAccessInputStream(filename);
+ if (FormatHandler.checkSuffix(filename, "c01"))
+ {
+
+ s.seek(4);
+ ZlibCodec codec = new ZlibCodec();
+ byte[] file = codec.decompress(s, null);
+ s.close();
+
+ return new RandomAccessInputStream(file);
+ }
+ return s;
+ }
+ }
+
static Integer readImageColorDepth(IFormatReader reader, IRandomAccess handle, ImageID imageID)
throws IOExceptionUnchecked, IllegalArgumentException
{
--
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