From aa7b9f32d593bcb368df1f415426848c66502d73 Mon Sep 17 00:00:00 2001
From: tpylak <tpylak>
Date: Wed, 11 May 2011 12:37:45 +0000
Subject: [PATCH] matlab hcs API: getImagesMetadata, formatting
SVN: 21237
---
screening/source/java/OpenBISScreeningML.java | 194 +++++++++++-------
1 file changed, 118 insertions(+), 76 deletions(-)
diff --git a/screening/source/java/OpenBISScreeningML.java b/screening/source/java/OpenBISScreeningML.java
index cbed7e8d13b..d69d9549e80 100644
--- a/screening/source/java/OpenBISScreeningML.java
+++ b/screening/source/java/OpenBISScreeningML.java
@@ -77,9 +77,8 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellPosition;
* </pre>
*
* <i>Note: using this login your password will end up in the Matlab command history. An alternative
- * that avoids this is to call the
- * {@link ch.systemsx.cisd.openbis.generic.client.cli.Login} class. Logging in on the
- * console will grant this class access to the openBIS server.</i>
+ * that avoids this is to call the {@link ch.systemsx.cisd.openbis.generic.client.cli.Login} class.
+ * Logging in on the console will grant this class access to the openBIS server.</i>
*
* @author Bernd Rinn
*/
@@ -88,13 +87,16 @@ public class OpenBISScreeningML
private static interface ITileNumberIterable extends Iterable<Integer>
{
public void setMaximumNumberOfTiles(int numberOfTiles);
+
public int getMaximumNumberOfTiles();
}
-
+
private static final class ImageReferenceAndFile
{
private final PlateImageReference imageReference;
+
private final File imageFile;
+
private BufferedOutputStream outputStream;
ImageReferenceAndFile(PlateImageReference imageReference, File imageFile)
@@ -112,7 +114,7 @@ public class OpenBISScreeningML
{
return imageFile;
}
-
+
public OutputStream open() throws IOException
{
if (outputStream == null)
@@ -121,7 +123,7 @@ public class OpenBISScreeningML
}
return outputStream;
}
-
+
public void close() throws IOException
{
if (outputStream != null)
@@ -131,13 +133,13 @@ public class OpenBISScreeningML
outputStream = null;
}
}
-
+
static final String DATASETS_FOLDER = "openbis_datasets";
-
+
private static File temporarySessionDir;
-
+
private static Map<PlateImageReference, File> loadedImages;
-
+
static IScreeningOpenbisServiceFacadeFactory facadeFactory =
ScreeningOpenbisServiceFacadeFactory.INSTANCE;
@@ -188,6 +190,7 @@ public class OpenBISScreeningML
static File tempDir = new File(System.getProperty("java.io.tmpdir"));
static final String TEMP_DIR_PREFIX = "openbis_";
+
static final String TEMP_DIR_POSTFIX = "_temp_dir";
//
@@ -225,7 +228,9 @@ public class OpenBISScreeningML
{
throw new RuntimeException("Couldn't create a data set directory.");
}
- temporarySessionDir = new File(tempDir, TEMP_DIR_PREFIX + System.currentTimeMillis() / 1000 + TEMP_DIR_POSTFIX);
+ temporarySessionDir =
+ new File(tempDir, TEMP_DIR_PREFIX + System.currentTimeMillis() / 1000
+ + TEMP_DIR_POSTFIX);
if (temporarySessionDir.mkdirs() == false)
{
throw new RuntimeException("Couldn't create a temporary directory.");
@@ -278,7 +283,7 @@ public class OpenBISScreeningML
delete(temporarySessionDir);
openbis = null;
}
-
+
private static void delete(File file)
{
if (file.isDirectory())
@@ -361,7 +366,7 @@ public class OpenBISScreeningML
checkLoggedIn();
return listPlates(plates);
}
-
+
/**
* Lists the plates of <var>experiment</var>.
* <p>
@@ -403,23 +408,18 @@ public class OpenBISScreeningML
{
final Object[] annotations =
new Object[]
- {
- list.get(i).getAugmentedCode(),
- plates.get(i).getPermId(),
- list.get(i).tryGetSpaceCode(),
- plates.get(i).getPlateCode(),
- list.get(i).getExperimentIdentifier()
- .getAugmentedCode(),
+ { list.get(i).getAugmentedCode(), plates.get(i).getPermId(),
+ list.get(i).tryGetSpaceCode(), plates.get(i).getPlateCode(),
+ list.get(i).getExperimentIdentifier().getAugmentedCode(),
list.get(i).getExperimentIdentifier().getPermId(),
list.get(i).getExperimentIdentifier().getSpaceCode(),
list.get(i).getExperimentIdentifier().getProjectCode(),
- list.get(i).getExperimentIdentifier()
- .getExperimentCode(), };
+ list.get(i).getExperimentIdentifier().getExperimentCode(), };
System.arraycopy(annotations, 0, result[i], 0, annotations.length);
}
return result;
}
-
+
/**
* Returns the properties of specified well for specified plate.
* <p>
@@ -437,11 +437,10 @@ public class OpenBISScreeningML
* @param augmentedPlateCode The augmented plate code
* @param row The row in the plate to get the well properties for
* @param column The column in the plate to get the well properties for
- * @return A two dimensional array where the first column contains the property
- * codes and the second column the corresponding property values.
+ * @return A two dimensional array where the first column contains the property codes and the
+ * second column the corresponding property values.
*/
- public static Object[][] getWellProperties(String augmentedPlateCode, int row,
- int column)
+ public static Object[][] getWellProperties(String augmentedPlateCode, int row, int column)
{
checkLoggedIn();
WellPosition wellPosition = new WellPosition(row, column);
@@ -452,11 +451,12 @@ public class OpenBISScreeningML
Object[][] result = new Object[list.size()][2];
for (int i = 0; i < list.size(); i++)
{
- result[i] = new Object[] {list.get(i).getKey(), list.get(i).getValue()};
+ result[i] = new Object[]
+ { list.get(i).getKey(), list.get(i).getValue() };
}
return result;
}
-
+
/**
* Updates properties of specified well for specified plate.
* <p>
@@ -471,18 +471,18 @@ public class OpenBISScreeningML
* @param augmentedPlateCode The augmented plate code
* @param row The row in the plate to get the well properties for
* @param column The column in the plate to get the well properties for
- * @param properties A two dimensional array where the first column contains the property
- * codes and the second column the corresponding property values.
+ * @param properties A two dimensional array where the first column contains the property codes
+ * and the second column the corresponding property values.
*/
- public static void updateWellProperties(String augmentedPlateCode, int row,
- int column, Object[][] properties)
+ public static void updateWellProperties(String augmentedPlateCode, int row, int column,
+ Object[][] properties)
{
checkLoggedIn();
WellPosition wellPosition = new WellPosition(row, column);
WellIdentifier wellIdentifier = getWell(augmentedPlateCode, wellPosition);
openbis.updateWellProperties(wellIdentifier, createMap(properties));
}
-
+
private static WellIdentifier getWell(String augmentedPlateCode, WellPosition wellPosition)
{
Plate plate = getPlate(augmentedPlateCode);
@@ -498,6 +498,43 @@ public class OpenBISScreeningML
+ wellPosition + ".");
}
+ /**
+ * Fetches metadata of the image datasets for the specified <var>plate</var>.
+ * <p>
+ * Matlab example:
+ *
+ * <pre>
+ * % Get the metadata of image datasets of plate P005 from space SPACE
+ * imagesMetadata = OpenBISScreeningML.getImagesMetadata('/SPACE/P005');
+ * % How many image datasets do we have? Usually there will be just one.
+ * length(imagesMetadata)
+ * % What is the number of tiles in the first image dataset?
+ * imagesMetadata(1, 3)
+ * </pre>
+ *
+ * @param augmentedPlateCode The augmented plate code.
+ * @return <code>{ number of plate rows, number of plate columns, number of tiles in the well,
+ * number of tiles rows, number of tiles columns }</code> .
+ */
+ public static Object[][] getImagesMetadata(String augmentedPlateCode)
+ {
+ checkLoggedIn();
+ final Plate plateId = getPlate(augmentedPlateCode);
+ final List<ImageDatasetReference> imageDatasets = listRawImageDatasets(plateId);
+ final List<ImageDatasetMetadata> metaList = openbis.listImageMetadata(imageDatasets);
+
+ Object[][] result = new Object[metaList.size()][];
+ for (int i = 0; i < metaList.size(); ++i)
+ {
+ ImageDatasetMetadata meta = metaList.get(i);
+ result[i] =
+ new Object[]
+ { meta.getWidth(), meta.getHeight(), meta.getNumberOfTiles(),
+ meta.getTilesRows(), meta.getTilesCols() };
+ }
+ return result;
+ }
+
/**
* Lists all channels measured in <var>experiment</var>.
* <p>
@@ -549,10 +586,9 @@ public class OpenBISScreeningML
return result;
}
- @SuppressWarnings("deprecation")
private static List<String> getChannelCodes(final List<ImageDatasetMetadata> meta)
{
- return meta.get(0).getChannelNames();
+ return meta.get(0).getChannelCodes();
}
/**
@@ -606,7 +642,7 @@ public class OpenBISScreeningML
{
return openbis.listAvailableFeatureNames(Arrays.asList(featureDatasets.get(0)));
}
-
+
//
// Data Sets
//
@@ -632,7 +668,8 @@ public class OpenBISScreeningML
* <p>
* <code>{ data set code, data set root path }</code>
*/
- public static Object[][] loadDataSets(String augmentedPlateCode) {
+ public static Object[][] loadDataSets(String augmentedPlateCode)
+ {
checkLoggedIn();
Plate plateIdentifier = getPlate(augmentedPlateCode);
@@ -649,7 +686,8 @@ public class OpenBISScreeningML
{
file = dataSet.getLinkOrCopyOfContents(null, dataSetsDir);
}
- result[i] = new Object[] {code, file.getPath()};
+ result[i] = new Object[]
+ { code, file.getPath() };
}
return result;
} catch (Exception ex)
@@ -714,7 +752,7 @@ public class OpenBISScreeningML
}
return map;
}
-
+
//
// Images
//
@@ -773,7 +811,7 @@ public class OpenBISScreeningML
* @param plate The augmented plate code
* @param row The row in the plate to get the images for
* @param col The column in the plate to get the images for
- * @param tile The tile number. Starts with 0.
+ * @param tile The tile number. Starts with 0.
* @return <code>{ names of TIFF files, image annotation }</code>
* <p>
* Each of <code>names of TIFF files</code> and <code>image annotation</code> is a
@@ -842,7 +880,7 @@ public class OpenBISScreeningML
return new Iterator<Integer>()
{
private int index;
-
+
public boolean hasNext()
{
return index < maximumNumberOfTiles;
@@ -881,7 +919,7 @@ public class OpenBISScreeningML
* @param plate The augmented plate code
* @param row The row in the plate to get the images for
* @param col The column in the plate to get the images for
- * @param tile The tile number. Starts with 0.
+ * @param tile The tile number. Starts with 0.
* @param channels The names of the channels to get the images for
* @return <code>{ names of TIFF files, image annotation }</code>
* <p>
@@ -938,14 +976,13 @@ public class OpenBISScreeningML
}
});
}
-
+
private static Object[][][] loadImages(String plate, int row, int col, String[] channels,
ITileNumberIterable tileNumberIterable)
{
checkLoggedIn();
final Plate plateId = getPlate(plate);
- final List<ImageDatasetReference> imageDatasets =
- openbis.listRawImageDatasets(Arrays.asList(plateId));
+ final List<ImageDatasetReference> imageDatasets = listRawImageDatasets(plateId);
final List<ImageDatasetMetadata> meta = openbis.listImageMetadata(imageDatasets);
if (meta.isEmpty())
{
@@ -961,7 +998,7 @@ public class OpenBISScreeningML
imageChannels = Arrays.asList(channels);
}
final List<ImageReferenceAndFile> imageReferencesAndFiles =
- new ArrayList<ImageReferenceAndFile>(imageDatasets.size());
+ new ArrayList<ImageReferenceAndFile>(imageDatasets.size());
final Object[][][] result = new Object[2][][];
tileNumberIterable.setMaximumNumberOfTiles(meta.get(0).getNumberOfTiles());
int numberOfTiles = tileNumberIterable.getMaximumNumberOfTiles();
@@ -980,19 +1017,20 @@ public class OpenBISScreeningML
final File imageFile = createImageFileName(plateId, ref);
imageReferencesAndFiles.add(new ImageReferenceAndFile(ref, imageFile));
result[0][resultIdx][0] = imageFile.getPath();
+ PlateIdentifier plateIdentifier = ds.getPlate();
+ ExperimentIdentifier expIdentifier = ds.getExperimentIdentifier();
final Object[] annotations =
new Object[]
{ channel, tile,
- createPlateWellDescription(ds.getPlate(), row, col),
- ds.getPlate().getAugmentedCode(),
- ds.getPlate().getPermId(), ds.getPlate().tryGetSpaceCode(),
- ds.getPlate().getPlateCode(), row, col,
- ds.getExperimentIdentifier().getAugmentedCode(),
- ds.getExperimentIdentifier().getPermId(),
- ds.getExperimentIdentifier().getSpaceCode(),
- ds.getExperimentIdentifier().getProjectCode(),
- ds.getExperimentIdentifier().getExperimentCode(),
- ds.getPermId(), };
+ createPlateWellDescription(plateIdentifier, row, col),
+ plateIdentifier.getAugmentedCode(),
+ plateIdentifier.getPermId(),
+ plateIdentifier.tryGetSpaceCode(),
+ plateIdentifier.getPlateCode(), row, col,
+ expIdentifier.getAugmentedCode(),
+ expIdentifier.getPermId(), expIdentifier.getSpaceCode(),
+ expIdentifier.getProjectCode(),
+ expIdentifier.getExperimentCode(), ds.getPermId(), };
System.arraycopy(annotations, 0, result[1][resultIdx], 0, annotations.length);
resultIdx++;
}
@@ -1008,7 +1046,12 @@ public class OpenBISScreeningML
}
return result;
}
-
+
+ private static List<ImageDatasetReference> listRawImageDatasets(final Plate plateId)
+ {
+ return openbis.listRawImageDatasets(Arrays.asList(plateId));
+ }
+
/**
* Saves images for a given list of image references (given by data set code, well position,
* channel and tile) and files.
@@ -1052,21 +1095,20 @@ public class OpenBISScreeningML
}
}
}
-
+
private static File createImageFileName(Plate plate, PlateImageReference image)
{
final WellPosition well = image.getWellPosition();
File imageDir = new File(temporarySessionDir, "images");
imageDir.mkdirs();
final File f =
- new File(imageDir, "img_" + plate.getPlateCode() + "_"
- + image.getDatasetCode() + "_row" + well.getWellRow() + "_col"
- + well.getWellColumn() + "_" + image.getChannel() + "_tile"
- + image.getTile() + ".tiff");
+ new File(imageDir, "img_" + plate.getPlateCode() + "_" + image.getDatasetCode()
+ + "_row" + well.getWellRow() + "_col" + well.getWellColumn() + "_"
+ + image.getChannel() + "_tile" + image.getTile() + ".tiff");
f.deleteOnExit();
return f;
}
-
+
//
// Feature matrix
//
@@ -1160,8 +1202,8 @@ public class OpenBISScreeningML
}
final List<FeatureVectorWithDescription> featureVectors =
openbis.loadFeaturesForPlateWells(experimentId, new MaterialIdentifier(
- MaterialTypeIdentifier.GENE, gene), (features == null) ? null : Arrays
- .asList(features));
+ MaterialTypeIdentifier.GENE, gene),
+ (features == null) ? null : Arrays.asList(features));
final List<String> featureNameList =
featureVectors.get(featureVectors.size() - 1).getFeatureNames();
final Object[][][] result = new Object[3][][];
@@ -1280,8 +1322,8 @@ public class OpenBISScreeningML
checkLoggedIn();
final List<FeatureVectorWithDescription> featureVectors =
openbis.loadFeaturesForPlateWells(new MaterialIdentifier(
- MaterialTypeIdentifier.GENE, gene), (features == null) ? null : Arrays
- .asList(features));
+ MaterialTypeIdentifier.GENE, gene),
+ (features == null) ? null : Arrays.asList(features));
final List<String> featureNameList =
featureVectors.get(featureVectors.size() - 1).getFeatureNames();
final Object[][][] result = new Object[3][][];
@@ -1400,9 +1442,9 @@ public class OpenBISScreeningML
{
checkLoggedIn();
final List<FeatureVectorDataset> featureVectors =
- openbis.loadFeaturesForPlates(Arrays.asList(PlateIdentifier
- .createFromAugmentedCode(plate)), (features == null) ? null : Arrays
- .asList(features));
+ openbis.loadFeaturesForPlates(
+ Arrays.asList(PlateIdentifier.createFromAugmentedCode(plate)),
+ (features == null) ? null : Arrays.asList(features));
FeatureVectorDataset last = featureVectors.get(featureVectors.size() - 1);
final List<String> featureCodeList = getFeatureCodes(last);
final Object[][][] result = new Object[3][][];
@@ -1485,9 +1527,7 @@ public class OpenBISScreeningML
{
checkLoggedIn();
final List<PlateWellMaterialMapping> mappingList =
- openbis
- .listPlateMaterialMapping(toPlates(platesCodes),
- MaterialTypeIdentifier.GENE);
+ openbis.listPlateMaterialMapping(toPlates(platesCodes), MaterialTypeIdentifier.GENE);
int size = 0;
for (PlateWellMaterialMapping mapping : mappingList)
{
@@ -1542,7 +1582,8 @@ public class OpenBISScreeningML
Plate plateIdentifier = plateCodeToPlateMap.get(augmentedPlateCode);
if (plateIdentifier == null)
{
- throw new RuntimeException("No plate with that code '" + augmentedPlateCode + "' found.");
+ throw new RuntimeException("No plate with that code '" + augmentedPlateCode
+ + "' found.");
}
return plateIdentifier;
}
@@ -1604,7 +1645,8 @@ public class OpenBISScreeningML
final String serverUrl = br.readLine();
br.close();
br = null;
- IScreeningOpenbisServiceFacade facade = facadeFactory.tryToCreate(token, serverUrl);
+ IScreeningOpenbisServiceFacade facade =
+ facadeFactory.tryToCreate(token, serverUrl);
if (facade == null)
{
throw new RuntimeException("Login failed.");
--
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