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Renamed project and switched to simple-omero-client 5.8.3 (#3)
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* Fixed createProject function, corrected README and updated dependency

* Removed expected ij version from pom.xml

* Added catch for new expected exceptions

* Added optional parameters to "addToTable" and "getROIs".

* Restructured addTable() and fixed testTable() test
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@ppouchin
ppouchin authored Nov 23, 2021
1 parent e683a8b commit 7b7086c
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25 changes: 14 additions & 11 deletions README.md
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Original file line number Diff line number Diff line change
@@ -1,14 +1,16 @@
[![Java CI with Maven](https://github.com/GReD-Clermont/omero_macroextensions/actions/workflows/maven.yml/badge.svg)](https://github.com/GReD-Clermont/omero_macroextensions/actions/workflows/maven.yml)
[![Java CI with Maven](https://github.com/GReD-Clermont/omero_macro-extensions/actions/workflows/maven.yml/badge.svg)](https://github.com/GReD-Clermont/omero_macro-extensions/actions/workflows/maven.yml)

# omero_macroextensions
# OMERO Macro Extensions

A plugin for ImageJ to provide macro extensions to access OMERO.

## How to install

1. Install the [OMERO.insight plugin for Fiji](https://omero-guides.readthedocs.io/en/latest/fiji/docs/installation.html) (if you haven't already).
1. Install
the [OMERO.insight plugin for Fiji](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/latest/).
3. Download the JAR file ([for this plugin](https://github.com/GReD-Clermont/omero_macroextensions/releases/latest/)).
3. Download the JAR file ([for this plugin](https://github.com/GReD-Clermont/omero_macro-extensions/releases/latest/)).
4. Place these JAR files in your plugins folder.

## How to use
Expand Down Expand Up @@ -156,7 +158,7 @@ projectId = Ext.createProject(name, description);
Datasets can be created with *Ext.createDataset*:

```
datasetId = Ext.createDataset(projectId, name, description);
datasetId = Ext.createDataset(name, description, projectId);
```

Tags can be created with *Ext.createTag*:
Expand Down Expand Up @@ -189,14 +191,17 @@ Pixel intensities can be retrieved from images:
imageplusID = Ext.getImage(imageIds[0]);
```

ROIs from OMERO can also be added to the ROI manager (and the current image):
ROIs from OMERO can also be added to the ROI manager (and the current image). ROIs composed of multiple shapes (eg
3D/4D) will share the same values in the "ROI" and "ROI_ID" properties in ImageJ. These can be optionnally changed with
the "property" parameter: local indices will be in "property" while OMERO IDs will be in "property + _ID".
This is achieved through:

```
nIJROIs = Ext.getROIs(imageIds[0]);
nIJROIs = Ext.getROIs(imageIds[0], property);
```

Conversely, ImageJ ROIs can also be saved to OMERO (the property is used to group ImageJ shapes into a single 3D/4D ROI
on OMERO):
on OMERO, if the string is empty, "ROI" is used):

```
nROIS = Ext.saveROIs(imageId, property);
Expand Down Expand Up @@ -229,7 +234,7 @@ Ext.deleteFile(fileId);
A table can be created/updated using the results with *Ext.addToTable*:

```
Ext.addToTable(tableName, resultsName, imageId);
Ext.addToTable(tableName, resultsName, imageId, roiProperty);
```

If a column named ROI containing ROI IDs is present, these will be added to the table. Alternatively, if ROIs that were
Expand All @@ -240,14 +245,12 @@ The table can then be saved to a project/dataset/image through *Ext.saveTable*:

```
Ext.saveTable(tableName, 'dataset', datasetId);
```

It can then be saved to a tab-separated text file through *Ext.saveTableAsTXT*:

```
Ext.saveTableAsTXT(tableName, pathToTXT);
```

### Work as another user (sudo)
Expand Down
19 changes: 9 additions & 10 deletions pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -10,12 +10,12 @@
</parent>

<groupId>fr.igred</groupId>
<artifactId>omero_macroextensions</artifactId>
<artifactId>omero_macro-extensions</artifactId>
<version>1.0.1</version>

<name>ImageJ OMERO macro extensions</name>
<description>Plugin providing macro extensions for OMERO.</description>
<url>https://github.com/GReD-Clermont/omero_macroextensions</url>
<url>https://github.com/GReD-Clermont/omero_macro-extensions</url>
<inceptionYear>2021</inceptionYear>

<organization>
Expand Down Expand Up @@ -63,24 +63,24 @@
</mailingLists>

<scm>
<connection>scm:git:git://github.com/GReD-Clermont/omero_macroextensions</connection>
<developerConnection>scm:git:[email protected]:GReD-Clermont/omero_macroextensions</developerConnection>
<connection>scm:git:git://github.com/GReD-Clermont/omero_macro-extensions</connection>
<developerConnection>scm:git:[email protected]:GReD-Clermont/omero_macro-extensions</developerConnection>
<tag>HEAD</tag>
<url>https://github.com/GReD-Clermont/omero_macroextensions</url>
<url>https://github.com/GReD-Clermont/omero_macro-extensions</url>
</scm>
<issueManagement>
<system>GitHub Issues</system>
<url>https://github.com/GReD-Clermont/omero_macroextensions/issues</url>
<url>https://github.com/GReD-Clermont/omero_macro-extensions/issues</url>
</issueManagement>
<ciManagement>
<system>GitHub Actions</system>
<url>https://github.com/GReD-Clermont/omero_macroextensions/actions</url>
<url>https://github.com/GReD-Clermont/omero_macro-extensions/actions</url>
</ciManagement>
<distributionManagement>
<repository>
<id>github</id>
<name>GitHub GReD-Clermont Apache Maven Packages</name>
<url>https://maven.pkg.github.com/GReD-Clermont/omero_macroextensions</url>
<url>https://maven.pkg.github.com/GReD-Clermont/omero_macro-extensions</url>
</repository>
</distributionManagement>

Expand All @@ -91,7 +91,7 @@
<license.licenseName>gpl_v2</license.licenseName>
<license.copyrightOwners>GReD</license.copyrightOwners>
<allowedDuplicateClasses>com.esotericsoftware.kryo.*,com.esotericsoftware.minlog.*,com.esotericsoftware.reflectasm.*</allowedDuplicateClasses>
<soc.version>5.8.2</soc.version>
<soc.version>5.8.3</soc.version>
</properties>

<dependencyManagement>
Expand Down Expand Up @@ -122,7 +122,6 @@
<dependency>
<groupId>net.imagej</groupId>
<artifactId>ij</artifactId>
<version>1.53c</version>
<scope>provided</scope>
</dependency>
<dependency>
Expand Down
76 changes: 45 additions & 31 deletions ...va/fr/igred/ij/plugin/OMEROExtension.java → .../igred/ij/plugin/OMEROMacroExtension.java
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Original file line number Diff line number Diff line change
Expand Up @@ -52,7 +52,7 @@
import static ij.macro.ExtensionDescriptor.newDescriptor;


public class OMEROExtension implements PlugIn, MacroExtension {
public class OMEROMacroExtension implements PlugIn, MacroExtension {

private static final String PROJECT = "project";
private static final String DATASET = "dataset";
Expand All @@ -65,11 +65,12 @@ public class OMEROExtension implements PlugIn, MacroExtension {
newDescriptor("switchGroup", this, ARG_NUMBER),
newDescriptor("list", this, ARG_STRING, ARG_STRING + ARG_OPTIONAL, ARG_NUMBER + ARG_OPTIONAL),
newDescriptor("createDataset", this, ARG_STRING, ARG_STRING, ARG_NUMBER + ARG_OPTIONAL),
newDescriptor("createProject", this, ARG_NUMBER, ARG_STRING, ARG_STRING),
newDescriptor("createProject", this, ARG_STRING, ARG_STRING),
newDescriptor("createTag", this, ARG_STRING, ARG_STRING),
newDescriptor("link", this, ARG_STRING, ARG_NUMBER, ARG_STRING, ARG_NUMBER),
newDescriptor("addFile", this, ARG_STRING, ARG_NUMBER, ARG_STRING),
newDescriptor("addToTable", this, ARG_STRING, ARG_STRING + ARG_OPTIONAL, ARG_NUMBER + ARG_OPTIONAL),
newDescriptor("addToTable", this, ARG_STRING,
ARG_STRING + ARG_OPTIONAL, ARG_NUMBER + ARG_OPTIONAL, ARG_STRING + ARG_OPTIONAL),
newDescriptor("saveTable", this, ARG_STRING, ARG_STRING, ARG_NUMBER),
newDescriptor("saveTableAsTXT", this, ARG_STRING, ARG_STRING),
newDescriptor("clearTable", this, ARG_STRING),
Expand All @@ -78,8 +79,8 @@ public class OMEROExtension implements PlugIn, MacroExtension {
newDescriptor("delete", this, ARG_STRING, ARG_NUMBER),
newDescriptor("getName", this, ARG_STRING, ARG_NUMBER),
newDescriptor("getImage", this, ARG_NUMBER),
newDescriptor("getROIs", this, ARG_NUMBER),
newDescriptor("saveROIs", this, ARG_NUMBER, ARG_STRING),
newDescriptor("getROIs", this, ARG_NUMBER, ARG_STRING + ARG_OPTIONAL),
newDescriptor("saveROIs", this, ARG_NUMBER, ARG_STRING + ARG_OPTIONAL),
newDescriptor("sudo", this, ARG_STRING),
newDescriptor("endSudo", this),
newDescriptor("disconnect", this),
Expand Down Expand Up @@ -109,6 +110,18 @@ private static String singularType(String type) {
}


private static Long doubleToLong(Double d) {
if (d != null) return d.longValue();
else return null;
}


private static ResultsTable getTable(String resultsName) {
if (resultsName == null) return ResultsTable.getResultsTable();
else return ResultsTable.getResultsTable(resultsName);
}


private GenericObjectWrapper<?> getObject(String type, long id) {
String singularType = singularType(type);

Expand Down Expand Up @@ -144,7 +157,7 @@ private GenericRepositoryObjectWrapper<?> getRepositoryObject(String type, long
default:
IJ.error(INVALID + ": " + type + ".");
}
} catch (ServiceException | AccessException e) {
} catch (ServiceException | AccessException | ExecutionException e) {
IJ.error("Could not retrieve object: " + e.getMessage());
}
return object;
Expand All @@ -156,7 +169,7 @@ public boolean connect(String host, int port, String username, String password)
try {
client.connect(host, port, username, password.toCharArray());
connected = true;
} catch (ServiceException | ExecutionException e) {
} catch (ServiceException e) {
IJ.error("Could not connect: " + e.getMessage());
}
return connected;
Expand All @@ -167,7 +180,7 @@ public String downloadImage(long imageId, String path) {
List<File> files = new ArrayList<>();
try {
files = client.getImage(imageId).download(client, path);
} catch (ServiceException | AccessException | OMEROServerError e) {
} catch (ServiceException | AccessException | OMEROServerError | ExecutionException e) {
IJ.error("Could not download image: " + e.getMessage());
}
return files.stream().map(File::toString).collect(Collectors.joining(","));
Expand Down Expand Up @@ -227,23 +240,16 @@ public void deleteFile(long fileId) {
}


public void addToTable(String tableName, String resultsName, Long imageId) {
ResultsTable rt;
if (tableName == null) rt = ResultsTable.getResultsTable();
else rt = ResultsTable.getResultsTable(resultsName);

RoiManager rm = RoiManager.getRoiManager();
List<Roi> ijRois = Arrays.asList(rm.getRoisAsArray());

public void addToTable(String tableName, ResultsTable results, Long imageId, List<Roi> ijRois, String property) {
TableWrapper table = tables.get(tableName);

try {
if (table == null) {
table = new TableWrapper(client, rt, imageId, ijRois, ROIWrapper.IJ_PROPERTY);
table = new TableWrapper(client, results, imageId, ijRois, property);
table.setName(tableName);
tables.put(tableName, table);
} else {
table.addRows(client, rt, imageId, ijRois, ROIWrapper.IJ_PROPERTY);
table.addRows(client, results, imageId, ijRois, property);
}
} catch (ExecutionException | ServiceException | AccessException e) {
IJ.error("Could not add results to table: " + e.getMessage());
Expand Down Expand Up @@ -384,7 +390,7 @@ public String list(String type) {
default:
IJ.error(INVALID + ": " + type + ". Possible values are: projects, datasets, images or tags.");
}
} catch (ServiceException | AccessException | OMEROServerError e) {
} catch (ServiceException | AccessException | OMEROServerError | ExecutionException e) {
IJ.error("Could not retrieve " + type + ": " + e.getMessage());
}
return results;
Expand Down Expand Up @@ -416,7 +422,7 @@ public String list(String type, String name) {
default:
IJ.error(INVALID + ": " + type + ". Possible values are: projects, datasets, images or tags.");
}
} catch (ServiceException | AccessException | OMEROServerError e) {
} catch (ServiceException | AccessException | OMEROServerError | ExecutionException e) {
IJ.error("Could not retrieve project name: " + e.getMessage());
}
return results;
Expand Down Expand Up @@ -585,7 +591,7 @@ public ImagePlus getImage(long id) {
}


public int getROIs(long id) {
public int getROIs(long id, String property) {
List<ROIWrapper> rois = new ArrayList<>();
try {
ImageWrapper image = client.getImage(id);
Expand All @@ -596,7 +602,7 @@ public int getROIs(long id) {

ImagePlus imp = IJ.getImage();

List<Roi> ijRois = ROIWrapper.toImageJ(rois);
List<Roi> ijRois = ROIWrapper.toImageJ(rois, property);

RoiManager rm = RoiManager.getInstance();
if (rm == null) rm = RoiManager.getRoiManager();
Expand Down Expand Up @@ -631,7 +637,7 @@ public int saveROIs(long id, String property) {
}
result = rois.size();
rm.reset();
this.getROIs(id);
this.getROIs(id, property);
} catch (ServiceException | AccessException | ExecutionException e) {
IJ.error("Could not save ROIs to image: " + e.getMessage());
}
Expand Down Expand Up @@ -707,8 +713,7 @@ public String handleExtension(String name, Object[] args) {
break;

case "createDataset":
Long projectId = null;
if (args[2] != null) projectId = ((Double) args[2]).longValue();
Long projectId = doubleToLong((Double) args[2]);
id = createDataset((String) args[0], (String) args[1], projectId);
results = String.valueOf(id);
break;
Expand All @@ -726,13 +731,20 @@ public String handleExtension(String name, Object[] args) {
case "addToTable":
tableName = (String) args[0];
String resultsName = (String) args[1];
Long imageId = null;
if (args[2] != null) imageId = ((Double) args[2]).longValue();
addToTable(tableName, resultsName, imageId);
Long imageId = doubleToLong((Double) args[2]);
String property = (String) args[3];

ResultsTable rt = getTable(resultsName);
RoiManager rm = RoiManager.getRoiManager();
List<Roi> ijRois = Arrays.asList(rm.getRoisAsArray());

addToTable(tableName, rt, imageId, ijRois, property);
break;

case "saveTableAsTXT":
saveTableAsTXT((String) args[0], (String) args[1]);
tableName = (String) args[0];
path = (String) args[1];
saveTableAsTXT(tableName, path);
break;

case "saveTable":
Expand Down Expand Up @@ -791,13 +803,15 @@ public String handleExtension(String name, Object[] args) {
break;

case "getROIs":
int nIJRois = getROIs(((Double) args[0]).longValue());
id = ((Double) args[0]).longValue();
property = (String) args[1];
int nIJRois = getROIs(id, property);
results = String.valueOf(nIJRois);
break;

case "saveROIs":
id = ((Double) args[0]).longValue();
String property = ((String) args[1]);
property = (String) args[1];
int nROIs = saveROIs(id, property);
results = String.valueOf(nROIs);
break;
Expand Down
2 changes: 1 addition & 1 deletion src/main/resources/omero.extensions.plugins.config
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Original file line number Diff line number Diff line change
@@ -1 +1 @@
Plugins>OMERO, "OMERO Extensions", fr.igred.ij.plugin.OMEROExtension("")
Plugins>OMERO, "OMERO Extensions", fr.igred.ij.plugin.OMEROMacroExtension("")
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