Merge pull request #23 from GReD-Clermont/dev

Add key-value pair management
Add ability to crop image when retrieving them

.omeroci/test-data

@@ -126,3 +126,11 @@ MAP2=$(omero obj new MapAnnotation)
 omero obj map-set "$MAP2" mapValue testKey1 testValue2
 omero obj map-set "$MAP2" mapValue testKey2 30
 omero obj new ImageAnnotationLink parent="$IMAGE2" child="$MAP2"
+
+MAP3=$(omero obj new MapAnnotation)
+omero obj map-set "$MAP3" mapValue key value
+omero obj new ProjectAnnotationLink parent="$PROJECT2" child="$MAP3"
+omero obj new DatasetAnnotationLink parent="$DATASET3" child="$MAP3"
+omero obj new ScreenAnnotationLink parent="$SCREEN1" child="$MAP3"
+omero obj new PlateAnnotationLink parent="$PLATE1" child="$MAP3"
+omero obj new WellAnnotationLink parent="Well:1" child="$MAP3"

README.md

@@ -9,8 +9,8 @@ A plugin for ImageJ to provide macro extensions to access OMERO.
 
 1. Install the [OMERO.insight plugin](https://omero-guides.readthedocs.io/en/latest/fiji/docs/installation.html) (if you
    haven't already).
-2. Download the JAR file for this [library](https://github.com/GReD-Clermont/simple-omero-client/releases/tag/5.16.0/).
-3. Download the JAR file ([for this plugin](https://github.com/GReD-Clermont/omero_macro-extensions/releases/tag/1.3.3/)).
+2. Download the JAR file for this [library](https://github.com/GReD-Clermont/simple-omero-client/releases/tag/5.19.0/).
+3. Download the JAR file ([for this plugin](https://github.com/GReD-Clermont/omero_macro-extensions/releases/tag/1.4.0/)).
 4. Place these JAR files in your plugins folder.
 
 ## How to use
@@ -121,6 +121,16 @@ tagName = Ext.getName("tag", tagIds[0]);
 print(tagName);
 ```
 
+* Key-Value pairs:
+
+```
+kvpairs = Ext.list("kv-pairs");
+print(kvpairs);
+kvIds = split(kvpairs,",");
+kvName = Ext.getName("kvName", kvIds[0]);
+print(kvName);
+```
+
 ### Listing objects with a given name
 
 It is also possible to list objects with a specific name:
@@ -185,6 +195,26 @@ tagName = Ext.getName("tag", tagIds[0]);
 print(tagName);
 ```
 
+Key-Value pairs can also be listed for a given object:
+
+```
+pairs = Ext.list("kv-pairs", "image", imageIds[0]);
+print(pairs);
+pairIds = split(pairs,",");
+kvs = Ext.getName("kv-pair", pairIds[0]);
+print(kvs);
+```
+or:
+```
+kvpairs = Ext.getKeyValuePairs("image", imageIds[0]);
+print(kvpairs);
+```
+or for a given key:
+```
+values = Ext.getValues("image", imageIds[0], "key", defaultValue);
+print(values);
+```
+
 Similarly, a dataset ID can be used to retrieve its images:
 
 ```
@@ -222,7 +252,7 @@ imageName = Ext.getName("image", imageIds[0]);
 print(imageName);
 ```
 
-### Creating projects, datasets and tags
+### Creating projects, datasets, tags and key-value pairs
 
 Projects can be created with *Ext.createProject*:
 
@@ -242,6 +272,12 @@ Tags can be created with *Ext.createTag*:
 tagId = Ext.createTag(name, description);
 ```
 
+Key-value pairs can be created with *Ext.createKeyValuePair*:
+
+```
+pairId = Ext.createKeyValuePair(key, value);
+```
+
 ### Linking/unlinking objects
 
 Objects can be linked with *Ext.link*, e.g.:
@@ -253,7 +289,7 @@ Ext.link("dataset", datasetId, "tag", tagId);
 They can also be unlinked with *Ext.unlink*, e.g.:
 
 ```
-Ext.unlink("dataset", datasetId, "tag", tagId);
+Ext.unlink("dataset", datasetId, "kv-pair", pairId);
 ```
 
 ### Deleting objects
@@ -272,8 +308,16 @@ Pixel intensities can be retrieved from images:
 imageplusID = Ext.getImage(imageIds[0]);
 ```
 
-Images can also be cropped on import by specifying the ROI as a String of the form:
-"x:xstart:xend,y:ystart:yend,c:cstart:cend,z:zstart:zend,t:tstart:tend".
+Images can also be cropped on import. In this case, image properties containing the position of the crop in the original 
+image can be retrieved (IMAGE_POS_X, IMAGE_POS_Y, etc.).
+
+This crop can be done by specifying the ROI in one of two ways:
+1. using the ROI ID (as a String) from OMERO, for example:
+```
+imageplusID = Ext.getImage(imageIds[0], Roi.getProperty("ROI_ID"));
+```
+
+2. as a String of the form: "x:xstart:xend,y:ystart:yend,c:cstart:cend,z:zstart:zend,t:tstart:tend". 
 For example, cropping a 512x512x3x100x5 image starting at (0,0,0,50,3) and ending at (100,100,2,99,3) can be done with:
 
 ```

pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <artifactId>pom-scijava</artifactId>
         <groupId>org.scijava</groupId>
-        <version>37.0.0</version>
+        <version>38.0.1</version>
     </parent>
 
     <groupId>fr.igred</groupId>
@@ -113,7 +113,7 @@
         <dependency>
             <groupId>fr.igred</groupId>
             <artifactId>simple-omero-client</artifactId>
-            <version>5.18.0</version>
+            <version>5.19.0</version>
         </dependency>
     </dependencies>