From f005360bc536274d0d24a205104dda54c0bb77ad Mon Sep 17 00:00:00 2001
From: tpylak <tpylak>
Date: Wed, 14 Sep 2011 11:19:10 +0000
Subject: [PATCH] LMS-2501 minor: better logging
SVN: 22946
---
.../jython/SimpleImageDataSetRegistrator.java | 34 +++++++++++++++----
1 file changed, 27 insertions(+), 7 deletions(-)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/SimpleImageDataSetRegistrator.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/SimpleImageDataSetRegistrator.java
index ade8c43b6de..357ee2a9112 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/SimpleImageDataSetRegistrator.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/SimpleImageDataSetRegistrator.java
@@ -346,14 +346,26 @@ public class SimpleImageDataSetRegistrator
{
String channelCode = channel.getCode();
List<File> imagePaths = chooseChannelImages(images, incomingDir, channelCode);
- operationLog.info("Computing intensity range for channel " + channelCode + ". Found "
- + imagePaths.size() + " images");
+ operationLog
+ .info(String
+ .format("Computing intensity range for channel '%s'. Found %d images in incoming directory '%s'.",
+ channelCode, imagePaths.size(), incomingDir.getName()));
Levels intensityRange =
- computeCommonIntensityRange(readerOrNull, imagePaths,
+ tryComputeCommonIntensityRange(readerOrNull, imagePaths,
simpleImageConfig.getComputeCommonIntensityRangeOfAllImagesThreshold());
- operationLog.info("Computed intensity range for channel " + channelCode + ": "
- + intensityRange);
- appendCommonIntensityRangeTransformation(channel, intensityRange);
+ if (intensityRange != null)
+ {
+ operationLog.info(String.format(
+ "Computed intensity range for channel '%s': %s (incoming directory '%s').",
+ channelCode, intensityRange.toString(), incomingDir.getName()));
+ appendCommonIntensityRangeTransformation(channel, intensityRange);
+ } else
+ {
+ operationLog
+ .warn(String
+ .format("Transformation cannot be generated for channel '%s' (incoming directory '%s').",
+ channelCode, incomingDir.getName()));
+ }
}
}
@@ -417,7 +429,7 @@ public class SimpleImageDataSetRegistrator
return normalizedCodes;
}
- private static Levels computeCommonIntensityRange(IImageReader readerOrNull,
+ private static Levels tryComputeCommonIntensityRange(IImageReader readerOrNull,
List<File> imageFiles, float threshold)
{
String libraryName = (readerOrNull == null) ? null : readerOrNull.getLibraryName();
@@ -431,6 +443,14 @@ public class SimpleImageDataSetRegistrator
{
BufferedImage image =
loadUnchangedImage(imageFile, imageIdentifier, libraryName, readerName);
+ if (IntensityRescaling.isNotGrayscale(image))
+ {
+ operationLog
+ .warn(String
+ .format("Intensity range cannot be computed because image '%s' is not in grayscale.",
+ imageFile.getPath()));
+ return null;
+ }
IntensityRescaling.addToLevelStats(histogram, image);
}
}
--
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