diff --git a/screening/resource/test-data/PlatonicPlateImageDropboxTest/1_2_GFP_64x64.png b/screening/resource/test-data/PlatonicPlateImageDropboxTest/1_2_GFP_64x64.png index 8397211282bc056ce8152c3da1ecc958fbbf9c48..ad969b67d3eefb6d2fa66398ace4265c03171182 100644 Binary files a/screening/resource/test-data/PlatonicPlateImageDropboxTest/1_2_GFP_64x64.png and b/screening/resource/test-data/PlatonicPlateImageDropboxTest/1_2_GFP_64x64.png differ diff --git a/screening/resource/test-data/Simple16BitImageDropboxTest/1_2_DAPI_1392x1040.png b/screening/resource/test-data/Simple16BitImageDropboxTest/1_2_DAPI_1392x1040.png new file mode 100644 index 0000000000000000000000000000000000000000..d738c49ed5e3077fc68fae5a36e6ff8349b9e9e6 Binary files /dev/null and b/screening/resource/test-data/Simple16BitImageDropboxTest/1_2_DAPI_1392x1040.png differ diff --git a/screening/resource/test-data/SimpleImageDropboxTest/1_1_DAPI_Default.png b/screening/resource/test-data/SimpleImageDropboxTest/1_1_DAPI_Default.png index 5eaeb36b545a0f6aa138620126b2434779ad6e42..d04d59e2796be20cf6363b3ae37da7f5f89fcfba 100644 Binary files a/screening/resource/test-data/SimpleImageDropboxTest/1_1_DAPI_Default.png and b/screening/resource/test-data/SimpleImageDropboxTest/1_1_DAPI_Default.png differ diff --git a/screening/resource/test-data/SimpleImageDropboxTest/1_1_Merged_Default.png b/screening/resource/test-data/SimpleImageDropboxTest/1_1_Merged_Default.png index 26cb862e5a09974c2c70fb19adacb2b3a156e5da..4910ae51f7984c5046a1a58f6a4328687fe1051e 100644 Binary files a/screening/resource/test-data/SimpleImageDropboxTest/1_1_Merged_Default.png and b/screening/resource/test-data/SimpleImageDropboxTest/1_1_Merged_Default.png differ diff --git a/screening/resource/test-data/SimpleImageDropboxTest/1_1_Merged_Default_GFP_0_100.png b/screening/resource/test-data/SimpleImageDropboxTest/1_1_Merged_Default_GFP_0_100.png index 68655e43c38560c42ecd17c8beaec838498e1414..fd04016edf064fc2186c4a2ec6b32c39d5dad803 100644 Binary files a/screening/resource/test-data/SimpleImageDropboxTest/1_1_Merged_Default_GFP_0_100.png and b/screening/resource/test-data/SimpleImageDropboxTest/1_1_Merged_Default_GFP_0_100.png differ diff --git a/screening/resource/test-data/SimpleImageDropboxTest/1_3_DAPI_CY3_256x191.png b/screening/resource/test-data/SimpleImageDropboxTest/1_3_DAPI_CY3_256x191.png index d3ec9efc885040ce8eca066f91e8513365733f73..5b63daeb477cbfae6dd7a77e98f986507c4f17b0 100644 Binary files a/screening/resource/test-data/SimpleImageDropboxTest/1_3_DAPI_CY3_256x191.png and b/screening/resource/test-data/SimpleImageDropboxTest/1_3_DAPI_CY3_256x191.png differ diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/SimpleImageDataConfig.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/SimpleImageDataConfig.java index 17fd1b64de04e08f4d65e259fb87ce266f1d5407..cbe1118427fdf82aec58356eec8ed2952fe430ad 100644 --- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/SimpleImageDataConfig.java +++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/SimpleImageDataConfig.java @@ -217,7 +217,7 @@ abstract public class SimpleImageDataConfig private List<String> thumbnailsGenerationImageMagicParams = Collections.emptyList(); - private boolean generateThumbnailsIn8BitHighQuality = false; + private boolean generateThumbnailsIn8BitHighQuality = true; private double allowedMachineLoadDuringThumbnailsGeneration = 1.0; @@ -676,12 +676,10 @@ abstract public class SimpleImageDataConfig } /** - * If true and thumbnails generation is switched on, thumbnails will be generated with high - * quality. - * <p> - * Be careful: high quality means that the generation will take longer and the image will be - * converted to 8 bit color depth. This option is useful for segmentation images, images with 8 - * bit color depth or when no 16 bit transformation has to be applied to the images. + * By default thumbnails are created in high-quality. But this is more time consuming. + * Set to <code>false</code> suppresses thumbnail creation in high quality. But this isn't + * recommended for 12-bit or 16-bit images. + * This flag is ignored if ImageMagic should be used for thumbnail generation. */ public void setGenerateHighQuality8BitThumbnails(boolean highQualityThumbnails) { diff --git a/screening/sourceTest/core-plugins/MicroscopyImageDropboxTest/1/dss/drop-boxes/MicroscopyImageDropboxTest-drop-box/MicroscopySingleDatasetConfig.py b/screening/sourceTest/core-plugins/MicroscopyImageDropboxTest/1/dss/drop-boxes/MicroscopyImageDropboxTest-drop-box/MicroscopySingleDatasetConfig.py index 7dfb4ce3f3dff6bae92f34ecfea045d6006b10d7..5d575a97a8bece9b6d992d77d2d84ae3b65f86bf 100644 --- a/screening/sourceTest/core-plugins/MicroscopyImageDropboxTest/1/dss/drop-boxes/MicroscopyImageDropboxTest-drop-box/MicroscopySingleDatasetConfig.py +++ b/screening/sourceTest/core-plugins/MicroscopyImageDropboxTest/1/dss/drop-boxes/MicroscopyImageDropboxTest-drop-box/MicroscopySingleDatasetConfig.py @@ -57,8 +57,6 @@ class MicroscopySingleDatasetConfig(SimpleImageContainerDataConfig): # Disable thumbnail generation by ImageMagick self.setUseImageMagicToGenerateThumbnails(False) - self.setGenerateHighQuality8BitThumbnails(True) - # Enable thumbnail generation self.setGenerateThumbnails(True) diff --git a/screening/sourceTest/core-plugins/Simple16BitImageDropboxTest/1/dss/drop-boxes/Simple16BitImageDropboxTest-drop-box/hcs-dropbox.py b/screening/sourceTest/core-plugins/Simple16BitImageDropboxTest/1/dss/drop-boxes/Simple16BitImageDropboxTest-drop-box/hcs-dropbox.py index 182cfc1a9911c0af5833407d48a7112218e6ac6a..8b4e823f047c4d44a6741be4bbb00b895fc3297a 100644 --- a/screening/sourceTest/core-plugins/Simple16BitImageDropboxTest/1/dss/drop-boxes/Simple16BitImageDropboxTest-drop-box/hcs-dropbox.py +++ b/screening/sourceTest/core-plugins/Simple16BitImageDropboxTest/1/dss/drop-boxes/Simple16BitImageDropboxTest-drop-box/hcs-dropbox.py @@ -85,7 +85,6 @@ def process(transaction): imageDataset = MyImageDataSetConfig() imageDataset.setRawImageDatasetType() imageDataset.setGenerateThumbnails(True) - imageDataset.setGenerateHighQuality8BitThumbnails(True) imageDataset.setUseImageMagicToGenerateThumbnails(False) imageDataset.addGeneratedImageRepresentationWithResolution("300x300") plate = create_plate_if_needed(transaction) diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/screening/systemtests/Simple16BitImageDropboxTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/screening/systemtests/Simple16BitImageDropboxTest.java index 3f6ab2ea0ecf2dd9b5c9e0ac792bbfdc230d049f..ceae9b7ae5147fdb041bd91c49c201e808380a4e 100644 --- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/screening/systemtests/Simple16BitImageDropboxTest.java +++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/screening/systemtests/Simple16BitImageDropboxTest.java @@ -54,6 +54,8 @@ public class Simple16BitImageDropboxTest extends AbstractImageDropboxTestCase new ImageLoader(dataSet, sessionToken).tileColumn(2).channel("DAPI")); imageChecker.check(new File(getTestDataFolder(), "1_2_DAPI_256x256.png"), new ImageLoader(dataSet, sessionToken).tileColumn(2).channel("DAPI").mode("thumbnail256x256")); + imageChecker.check(new File(getTestDataFolder(), "1_2_DAPI_1392x1040.png"), + new ImageLoader(dataSet, sessionToken).tileColumn(2).channel("DAPI").mode("thumbnail1392x1040")); imageChecker.check(new File(getTestDataFolder(), "1_2_Merged_1392x1040.png"), new ImageLoader(dataSet, sessionToken).tileColumn(2).mode("thumbnail1392x1040")); imageChecker.check(new File(getTestDataFolder(), "1_2_GFP_thumbnail1392x1040.png"),