Merge pull request #90 from GReD-Clermont/5_19_0

5.19.0

src/main/java/fr/igred/omero/AnnotatableWrapper.java

@@ -390,6 +390,29 @@ public Map<String, String> getKeyValuePairs(Client client)
     }
 
 
+    /**
+     * Gets the List of Key-Value pairs associated to an object.
+     *
+     * @param client The client handling the connection.
+     *
+     * @return See above.
+     *
+     * @throws ServiceException   Cannot connect to OMERO.
+     * @throws AccessException    Cannot access data.
+     * @throws ExecutionException A Facility can't be retrieved or instantiated.
+     *
+     * @deprecated This method will be renamed to {@link #getKeyValuePairs(Client)} ()} in a future version.
+     */
+    @Deprecated
+    public List<Map.Entry<String, String>> getKeyValuePairsAsList(Client client)
+    throws ServiceException, AccessException, ExecutionException {
+        return getMapAnnotations(client).stream()
+                                        .map(MapAnnotationWrapper::getContentAsEntryList)
+                                        .flatMap(List::stream)
+                                        .collect(toList());
+    }
+
+
     /**
      * Gets the value from a Key-Value pair associated to the object.
      *

src/main/java/fr/igred/omero/annotations/MapAnnotationWrapper.java

@@ -133,10 +133,7 @@ private static NamedValue toNamedValue(Entry<String, String> entry) {
      * Gets the List of NamedValue contained in the map annotation.
      *
      * @return MapAnnotationData content.
-     *
-     * @deprecated This method will be removed in a future version.
      */
-    @Deprecated
     @SuppressWarnings("unchecked")
     public List<NamedValue> getContent() {
         return (List<NamedValue>) data.getContent();

src/main/java/fr/igred/omero/annotations/TableWrapper.java

@@ -42,6 +42,7 @@
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
+import java.util.Collections;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
@@ -516,7 +517,7 @@ private void createColumn(int column, String columnName, Class<?> type) {
      */
     private Collection<Integer> getEmptyStringColumns() {
         Collection<Integer> emptyColumns = new ArrayList<>(0);
-        for (int j = 0; j < columns.length; j++) {
+        for (int j = columns.length - 1; j >= 0; j--) {
             TableDataColumn column = columns[j];
             if (column.getType().equals(String.class)) {
                 boolean empty = true;
@@ -881,7 +882,8 @@ public TableData createTable() {
             truncateRow();
         }
 
-        Collection<Integer> emptyColumns = getEmptyStringColumns();
+        List<Integer> emptyColumns = new ArrayList<>(getEmptyStringColumns());
+        emptyColumns.sort(Collections.reverseOrder());
         emptyColumns.forEach(this::removeColumn);
 
         return new TableData(columns, data);

src/main/java/fr/igred/omero/exception/ExceptionHandler.java

@@ -552,6 +552,7 @@ public interface ThrowingFunction<T, R, E extends Throwable> {
     @FunctionalInterface
     public interface OMEROFunction<T, R> extends ThrowingFunction<T, R, Exception> {
 
+        @Override
         R apply(T t) throws DSOutOfServiceException, DSAccessException, ServerError;
 
     }

src/main/java/fr/igred/omero/meta/PlaneInfoWrapper.java

@@ -35,6 +35,7 @@
 
 import static java.lang.Double.NaN;
 import static ome.formats.model.UnitsFactory.convertTime;
+import static ome.units.UNITS.MICROMETER;
 import static ome.units.UNITS.SECOND;
 
 
@@ -152,6 +153,28 @@ public static Length getMinPosition(Collection<? extends PlaneInfoWrapper> plane
     }
 
 
+    /**
+     * Retrieves the min value for the specified getter in a PlaneInfoWrapper collection.
+     *
+     * @param planesInfo A collection of PlaneInfoWrappers.
+     * @param getter     The getter function to use.
+     *
+     * @return See above.
+     */
+    public static Length getMinPosition(Collection<? extends PlaneInfoWrapper> planesInfo,
+                                        Function<? super PlaneInfoWrapper, ? extends Length> getter) {
+        Unit<ome.units.quantity.Length> unit;
+        unit = planesInfo.stream()
+                         .map(getter)
+                         .map(UnitsFactory::convertLength)
+                         .filter(Objects::nonNull)
+                         .map(ome.units.quantity.Length::unit)
+                         .findFirst()
+                         .orElse(MICROMETER);
+        return getMinPosition(planesInfo, getter, unit);
+    }
+
+
     /**
      * @return See above.
      *

src/main/java/fr/igred/omero/repository/ImageWrapper.java

@@ -121,17 +121,26 @@ private static void setCalibration(PixelsWrapper pixels, Calibration calibration
         calibration.setXUnit(positionX.getSymbol());
         calibration.setYUnit(positionY.getSymbol());
         calibration.setZUnit(positionZ.getSymbol());
-        calibration.xOrigin = positionX.getValue();
-        calibration.yOrigin = positionY.getValue();
-        calibration.zOrigin = positionZ.getValue();
+        calibration.xOrigin = -positionX.getValue();
+        calibration.yOrigin = -positionY.getValue();
+        calibration.zOrigin = -positionZ.getValue();
         if (spacingX != null) {
+            calibration.setXUnit(spacingX.getSymbol());
             calibration.pixelWidth = spacingX.getValue();
+            // positionX and spacingX should use the same unit
+            calibration.xOrigin /= calibration.pixelWidth;
         }
         if (spacingY != null) {
+            calibration.setYUnit(spacingY.getSymbol());
             calibration.pixelHeight = spacingY.getValue();
+            // positionY and spacingY should use the same unit
+            calibration.yOrigin /= calibration.pixelHeight;
         }
         if (spacingZ != null) {
+            calibration.setZUnit(spacingZ.getSymbol());
             calibration.pixelDepth = spacingZ.getValue();
+            // positionZ and spacingZ should use the same unit
+            calibration.zOrigin /= calibration.pixelDepth;
         }
         if (!Double.isNaN(stepT.getValue())) {
             calibration.setTimeUnit(stepT.getSymbol());
@@ -254,6 +263,16 @@ public String getFormat() {
     }
 
 
+    /**
+     * Returns the series.
+     *
+     * @return See above.
+     */
+    public int getSeries() {
+        return data.getSeries();
+    }
+
+
     /**
      * Returns the type of annotation link for this object.
      *
@@ -737,6 +756,9 @@ public ImagePlus toImagePlus(Client client,
 
         Calibration calibration = imp.getCalibration();
         setCalibration(pixels, calibration);
+        calibration.xOrigin -= startX;
+        calibration.yOrigin -= startY;
+        calibration.zOrigin -= startZ;
         imp.setCalibration(calibration);
 
         boolean isFloat = FormatTools.isFloatingPoint(pixelType);
@@ -794,6 +816,11 @@ public ImagePlus toImagePlus(Client client,
         imp.setPosition(1);
         if (IJ.getVersion().compareTo("1.53a") >= 0) {
             imp.setProp(IJ_ID_PROPERTY, getId());
+            imp.setProp("IMAGE_POS_X", startX);
+            imp.setProp("IMAGE_POS_Y", startY);
+            imp.setProp("IMAGE_POS_C", startC);
+            imp.setProp("IMAGE_POS_Z", startZ);
+            imp.setProp("IMAGE_POS_T", startT);
         }
         return imp;
     }
@@ -970,6 +997,46 @@ public BufferedImage getThumbnail(Client client, int size)
     }
 
 
+    /**
+     * Returns the original file paths where the image was imported from.
+     *
+     * @param client The client handling the connection.
+     *
+     * @return See above.
+     *
+     * @throws ServiceException   Cannot connect to OMERO.
+     * @throws AccessException    Cannot access data.
+     * @throws ExecutionException A Facility can't be retrieved or instantiated.
+     */
+    public List<String> getOriginalPaths(Client client)
+    throws ExecutionException, AccessException, ServiceException {
+        String error = "Cannot get original paths for " + this;
+        return call(client.getMetadata(),
+                    m -> m.getOriginalPaths(client.getCtx(), data),
+                    error);
+    }
+
+
+    /**
+     * Returns the file paths of the image in the managed repository.
+     *
+     * @param client The client handling the connection.
+     *
+     * @return See above.
+     *
+     * @throws ServiceException   Cannot connect to OMERO.
+     * @throws AccessException    Cannot access data.
+     * @throws ExecutionException A Facility can't be retrieved or instantiated.
+     */
+    public List<String> getManagedRepositoriesPaths(Client client)
+    throws ExecutionException, AccessException, ServiceException {
+        String error = "Cannot get managed repositories paths for " + this;
+        return call(client.getMetadata(),
+                    m -> m.getManagedRepositoriesPaths(client.getCtx(), data),
+                    error);
+    }
+
+
     /**
      * Downloads the original files from the server.
      *

src/main/java/fr/igred/omero/repository/PixelsWrapper.java

@@ -31,6 +31,7 @@
 import omero.gateway.model.PlaneInfoData;
 import omero.gateway.rnd.Plane2D;
 import omero.model.Length;
+import omero.model.LengthI;
 import omero.model.Time;
 
 import java.util.ArrayList;
@@ -39,8 +40,8 @@
 import java.util.concurrent.ExecutionException;
 
 import static fr.igred.omero.exception.ExceptionHandler.call;
+import static fr.igred.omero.meta.PlaneInfoWrapper.getMinPosition;
 import static ome.formats.model.UnitsFactory.convertLength;
-import static ome.units.UNITS.MICROMETER;
 
 
 /**
@@ -238,50 +239,71 @@ public Time getMeanExposureTime(int channel) {
 
 
     /**
-     * Retrieves the X stage position.
+     * Retrieves the X stage position, using the same unit as {@link #getPixelSizeX()} if possible.
      * <p>Planes information needs to be {@link #loadPlanesInfo(Client) loaded} first.</p>
      *
      * @return See above.
      */
     public Length getPositionX() {
+        Length x = getMinPosition(planesInfo, PlaneInfoWrapper::getPositionX);
+
         ome.units.quantity.Length pixSizeX = convertLength(getPixelSizeX());
+        ome.units.quantity.Length posX     = convertLength(x);
+
+        if (pixSizeX != null) {
+            Unit<ome.units.quantity.Length> unit = pixSizeX.unit();
+            if (posX.value(unit) != null) {
+                x = new LengthI(posX.value(unit).doubleValue(), unit);
+            }
+        }
 
-        Unit<ome.units.quantity.Length> unit = pixSizeX == null ? MICROMETER : pixSizeX.unit();
-        return PlaneInfoWrapper.getMinPosition(planesInfo,
-                                               PlaneInfoWrapper::getPositionX,
-                                               unit);
+        return x;
     }
 
 
     /**
-     * Retrieves the Y stage position.
+     * Retrieves the Y stage position, using the same unit as {@link #getPixelSizeY()} if possible.
      * <p>Planes information needs to be {@link #loadPlanesInfo(Client) loaded} first.</p>
      *
      * @return See above.
      */
     public Length getPositionY() {
+        Length y = getMinPosition(planesInfo, PlaneInfoWrapper::getPositionY);
+
         ome.units.quantity.Length pixSizeY = convertLength(getPixelSizeY());
+        ome.units.quantity.Length posY     = convertLength(y);
+
+        if (pixSizeY != null) {
+            Unit<ome.units.quantity.Length> unit = pixSizeY.unit();
+            if (posY.value(unit) != null) {
+                y = new LengthI(posY.value(unit).doubleValue(), unit);
+            }
+        }
 
-        Unit<ome.units.quantity.Length> unit = pixSizeY == null ? MICROMETER : pixSizeY.unit();
-        return PlaneInfoWrapper.getMinPosition(planesInfo,
-                                               PlaneInfoWrapper::getPositionY,
-                                               unit);
+        return y;
     }
 
 
     /**
-     * Retrieves the Z stage position.
+     * Retrieves the Z stage position, using the same unit as {@link #getPixelSizeZ()} if possible.
      * <p>Planes information needs to be {@link #loadPlanesInfo(Client) loaded} first.</p>
      *
      * @return See above.
      */
     public Length getPositionZ() {
+        Length z = getMinPosition(planesInfo, PlaneInfoWrapper::getPositionZ);
+
         ome.units.quantity.Length pixSizeZ = convertLength(getPixelSizeZ());
+        ome.units.quantity.Length posZ     = convertLength(z);
+
+        if (pixSizeZ != null) {
+            Unit<ome.units.quantity.Length> unit = pixSizeZ.unit();
+            if (posZ.value(unit) != null) {
+                z = new LengthI(posZ.value(unit).doubleValue(), unit);
+            }
+        }
 
-        Unit<ome.units.quantity.Length> unit = pixSizeZ == null ? MICROMETER : pixSizeZ.unit();
-        return PlaneInfoWrapper.getMinPosition(planesInfo,
-                                               PlaneInfoWrapper::getPositionZ,
-                                               unit);
+        return z;
     }
 
 

src/test/java/fr/igred/omero/ConnectionTest.java

@@ -61,6 +61,7 @@ void testRootConnection() throws ServiceException {
         try {
             testRoot.disconnect();
         } catch (RuntimeException ignored) {
+            // IGNORED
         }
         assertEquals(0L, id);
         assertEquals(GROUP1.id, groupId);
@@ -81,6 +82,7 @@ void testUserConnection() throws ServiceException {
         try {
             testUser.disconnect();
         } catch (RuntimeException ignored) {
+            // IGNORED
         }
         assertEquals(USER1.id, id);
         assertEquals(GROUP1.id, groupId);

src/test/java/fr/igred/omero/SudoTest.java

@@ -78,6 +78,7 @@ void testSudoTag() throws Exception {
             test.disconnect();
             root.disconnect();
         } catch (RuntimeException ignored) {
+            // IGNORED
         }
 
         assertNotEquals(0, images.size());