diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/openBIS-premise-imaging.jar b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/openBIS-premise-imaging.jar
index 45ead497c522efa717bddc73cad091ebc4377b20..9ce77c0ca4a5774a6b963fd3a2988ff084089a31 100644
Binary files a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/openBIS-premise-imaging.jar and b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/openBIS-premise-imaging.jar differ
diff --git a/api-openbis-java/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetConfig.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetConfig.java
similarity index 100%
rename from api-openbis-java/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetConfig.java
rename to core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetConfig.java
diff --git a/api-openbis-java/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetControl.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetControl.java
similarity index 76%
rename from api-openbis-java/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetControl.java
rename to core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetControl.java
index 676549859dcc0392372795bba39b12eafbd9d042..7d5c27fe9ce8562ced6418828f8734a80d90e365 100644
--- a/api-openbis-java/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetControl.java
+++ b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetControl.java
@@ -33,6 +33,9 @@ public class ImagingDataSetControl implements Serializable
@JsonProperty
private String label;
+ @JsonProperty
+ private String section;
+
@JsonProperty
private String type;
@@ -40,7 +43,10 @@ public class ImagingDataSetControl implements Serializable
private List<String> values;
@JsonProperty
- private List<Integer> range;
+ private String unit;
+
+ @JsonProperty
+ private List<String> range;
@JsonProperty
private boolean multiselect;
@@ -50,6 +56,8 @@ public class ImagingDataSetControl implements Serializable
@JsonProperty
private List<Integer> speeds;
+ @JsonProperty
+ private List<ImagingDataSetControlVisibility> visibility;
@JsonProperty
private Map<String, String> metaData;
@@ -65,6 +73,28 @@ public class ImagingDataSetControl implements Serializable
this.label = label;
}
+ @JsonIgnore
+ public String getSection()
+ {
+ return section;
+ }
+
+ public void setSection(String section)
+ {
+ this.section = section;
+ }
+
+ @JsonIgnore
+ public String getUnit()
+ {
+ return unit;
+ }
+
+ public void setUnit(String unit)
+ {
+ this.unit = unit;
+ }
+
@JsonIgnore
public String getType()
{
@@ -121,16 +151,28 @@ public class ImagingDataSetControl implements Serializable
}
@JsonIgnore
- public List<Integer> getRange()
+ public List<String> getRange()
{
return range;
}
- public void setRange(List<Integer> range)
+ public void setRange(List<String> range)
{
this.range = range;
}
+ @JsonIgnore
+ public List<ImagingDataSetControlVisibility> getVisibility()
+ {
+ return visibility;
+ }
+
+ public void setVisibility(
+ List<ImagingDataSetControlVisibility> visibility)
+ {
+ this.visibility = visibility;
+ }
+
@JsonIgnore
public Map<String, String> getMetaData()
{
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetControlVisibility.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetControlVisibility.java
new file mode 100644
index 0000000000000000000000000000000000000000..2a364ad0745a2c5f8205090e428b27662bbaa792
--- /dev/null
+++ b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetControlVisibility.java
@@ -0,0 +1,88 @@
+/*
+ * Copyright ETH 2023 Zürich, Scientific IT Services
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+
+package ch.ethz.sis.openbis.generic.dssapi.v3.dto.imaging;
+
+import ch.systemsx.cisd.base.annotation.JsonObject;
+import com.fasterxml.jackson.annotation.JsonIgnore;
+import com.fasterxml.jackson.annotation.JsonProperty;
+
+import java.io.Serializable;
+import java.util.List;
+
+@JsonObject("dss.dto.imaging.ImagingDataSetControlVisibility")
+public class ImagingDataSetControlVisibility implements Serializable
+{
+ private static final long serialVersionUID = 1L;
+
+ @JsonProperty
+ private String label;
+ @JsonProperty
+ private List<String> values;
+ @JsonProperty
+ private List<String> range;
+ @JsonProperty
+ private String unit;
+
+ @JsonIgnore
+ public String getLabel()
+ {
+ return label;
+ }
+
+ public void setLabel(String label)
+ {
+ this.label = label;
+ }
+ @JsonIgnore
+ public List<String> getValues()
+ {
+ return values;
+ }
+
+ public void setValues(List<String> values)
+ {
+ this.values = values;
+ }
+ @JsonIgnore
+ public List<String> getRange()
+ {
+ return range;
+ }
+
+ public void setRange(List<String> range)
+ {
+ this.range = range;
+ }
+
+ @JsonIgnore
+ public String getUnit()
+ {
+ return unit;
+ }
+
+ public void setUnit(String unit)
+ {
+ this.unit = unit;
+ }
+
+ @Override
+ public String toString()
+ {
+ return "ImagingDataSetControlVisibility: " + label;
+ }
+}
diff --git a/api-openbis-java/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetExport.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetExport.java
similarity index 100%
rename from api-openbis-java/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetExport.java
rename to core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetExport.java
diff --git a/api-openbis-java/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetImage.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetImage.java
similarity index 100%
rename from api-openbis-java/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetImage.java
rename to core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetImage.java
diff --git a/api-openbis-java/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetPreview.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetPreview.java
similarity index 100%
rename from api-openbis-java/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetPreview.java
rename to core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetPreview.java
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetPropertyConfig.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetPropertyConfig.java
new file mode 100644
index 0000000000000000000000000000000000000000..7b9d9b71eb00bd109bb61218469ab131e72cc009
--- /dev/null
+++ b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/dssapi/v3/dto/imaging/ImagingDataSetPropertyConfig.java
@@ -0,0 +1,62 @@
+/*
+ * Copyright ETH 2023 Zürich, Scientific IT Services
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+
+package ch.ethz.sis.openbis.generic.dssapi.v3.dto.imaging;
+
+import ch.systemsx.cisd.base.annotation.JsonObject;
+import com.fasterxml.jackson.annotation.JsonIgnore;
+import com.fasterxml.jackson.annotation.JsonProperty;
+
+import java.io.Serializable;
+import java.util.List;
+
+@JsonObject("dss.dto.imaging.ImagingDataSetPropertyConfig")
+public class ImagingDataSetPropertyConfig implements Serializable
+{
+ private static final long serialVersionUID = 1L;
+
+ @JsonProperty
+ ImagingDataSetConfig config;
+
+ @JsonProperty
+ List<ImagingDataSetImage> images;
+
+ @JsonIgnore
+ public ImagingDataSetConfig getConfig()
+ {
+ return config;
+ }
+
+ public void setConfig(ImagingDataSetConfig config)
+ {
+ this.config = config;
+ }
+
+ @JsonIgnore
+ public List<ImagingDataSetImage> getImages()
+ {
+ return images;
+ }
+
+ public void setImages(
+ List<ImagingDataSetImage> images)
+ {
+ this.images = images;
+ }
+
+
+}
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/ImagingService.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/ImagingService.java
index b0cdb230c587d8ccb5d4899d9728cd0a9640dad1..0beb0960aee4891de964cd7913f3adde04aabff7 100644
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/ImagingService.java
+++ b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/ImagingService.java
@@ -25,6 +25,7 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.id.IDataSetId;
import ch.ethz.sis.openbis.generic.dssapi.v3.IDataStoreServerApi;
import ch.ethz.sis.openbis.generic.dssapi.v3.dto.imaging.ImagingDataSetConfig;
import ch.ethz.sis.openbis.generic.dssapi.v3.dto.imaging.ImagingDataSetImage;
+import ch.ethz.sis.openbis.generic.dssapi.v3.dto.imaging.ImagingDataSetPropertyConfig;
import ch.ethz.sis.openbis.generic.dssapi.v3.dto.service.CustomDSSServiceExecutionOptions;
import ch.ethz.sis.openbis.generic.dssapi.v3.dto.service.id.ICustomDSSServiceId;
import ch.ethz.sis.openbis.generic.server.dss.plugins.imaging.adaptor.IImagingDataSetAdaptor;
@@ -44,6 +45,7 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
import ch.systemsx.cisd.openbis.generic.shared.dto.OpenBISSessionHolder;
import com.fasterxml.jackson.annotation.JsonIgnore;
import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.databind.JsonMappingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import ch.systemsx.cisd.common.logging.LogFactory;
import org.apache.log4j.Logger;
@@ -63,21 +65,17 @@ public class ImagingService implements ICustomDSSServiceExecutor
private static final Logger
operationLog = LogFactory.getLogger(LogCategory.OPERATION, ImagingService.class);
- private static final String SCRIPT_PATH = "script-path";
-
- private String scriptPath;
public ImagingService(Properties properties)
{
this.properties = properties;
- this.scriptPath = PropertyUtils.getProperty(properties, SCRIPT_PATH);
}
@Override
public Serializable executeService(String sessionToken, ICustomDSSServiceId serviceId,
CustomDSSServiceExecutionOptions options)
{
- operationLog.info("Executing service:" + serviceId);
+ operationLog.info("Executing imaging service:" + serviceId);
ImagingDataContainer data = getDataFromParams(options.getParameters());
try
{
@@ -100,14 +98,21 @@ public class ImagingService implements ICustomDSSServiceExecutor
{
DataSet dataSet = getDataSet(sessionToken, data);
- Config config =
- readConfig(dataSet.getJsonProperty("$IMAGING_DATA_CONFIG"), Config.class);
- final String adaptorName = config.config.getAdaptor();
+ ImagingDataSetPropertyConfig config =
+ readConfig(dataSet.getJsonProperty("$IMAGING_DATA_CONFIG"), ImagingDataSetPropertyConfig.class);
+ final String adaptorName = config.getConfig().getAdaptor();
- IImagingDataSetAdaptor
- adaptor =
- ClassUtils.create(IImagingDataSetAdaptor.class, adaptorName, properties);
+ if(adaptorName == null || adaptorName.isBlank()) {
+ throw new UserFailureException("Adaptor name is missing from the config!");
+ }
+ IImagingDataSetAdaptor adaptor = null;
+ try
+ {
+ adaptor = ClassUtils.create(IImagingDataSetAdaptor.class, adaptorName, properties);
+ } catch(Exception e) {
+ throw new UserFailureException("Could not load adapter: " + adaptorName, e);
+ }
IHierarchicalContent content =
getHierarchicalContentProvider(sessionToken).asContent(
dataSet.getPermId().getPermId());
@@ -116,12 +121,13 @@ public class ImagingService implements ICustomDSSServiceExecutor
File rootFile = root.getFile();
Map<String, Serializable> previewParams = data.getPreview().getConfig();
Map<String, String> meta = data.getPreview().getMetaData();
+ String format = data.getPreview().getFormat();
ImagingServiceContext context = new ImagingServiceContext(sessionToken, getApplicationServerApi(), getDataStoreServerApi());
data.getPreview().setBytes(
adaptor.process(context,
- rootFile, previewParams, meta).toString());
+ rootFile, previewParams, meta, format).toString());
return data;
}
@@ -175,6 +181,8 @@ public class ImagingService implements ICustomDSSServiceExecutor
ObjectMapper objectMapper = getObjectMapper();
return objectMapper.readValue(new ByteArrayInputStream(val.getBytes()),
clazz);
+ } catch (JsonMappingException mappingException) {
+ throw new UserFailureException(mappingException.toString(), mappingException);
} catch (Exception e)
{
throw new UserFailureException("Could not read the parameters!", e);
@@ -210,38 +218,6 @@ public class ImagingService implements ICustomDSSServiceExecutor
return result.get(new DataSetPermId(data.getPermId()));
}
- public static final class Config
- {
- @JsonProperty
- ImagingDataSetConfig config;
-
- @JsonProperty
- List<ImagingDataSetImage> images;
-
- @JsonIgnore
- public ImagingDataSetConfig getConfig()
- {
- return config;
- }
-
- public void setConfig(ImagingDataSetConfig config)
- {
- this.config = config;
- }
-
- @JsonIgnore
- public List<ImagingDataSetImage> getImages()
- {
- return images;
- }
-
- public void setImages(
- List<ImagingDataSetImage> images)
- {
- this.images = images;
- }
- }
-
private void validateInputParams(Map<String, Object> params)
{
if (!params.containsKey("permId"))
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/adaptor/IImagingDataSetAdaptor.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/adaptor/IImagingDataSetAdaptor.java
index 2208100f55030e56f3c270fd8413113e4f836608..ea3b5ad6e14376c8023db65c17afb38b25bd6ce7 100644
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/adaptor/IImagingDataSetAdaptor.java
+++ b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/adaptor/IImagingDataSetAdaptor.java
@@ -25,6 +25,7 @@ import java.util.Map;
public interface IImagingDataSetAdaptor
{
- Serializable process(ImagingServiceContext context, File rootFile, Map<String, Serializable> previewConfig, Map<String, String> metaData);
+ Serializable process(ImagingServiceContext context, File rootFile,
+ Map<String, Serializable> previewConfig, Map<String, String> metaData, String format);
}
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/adaptor/ImagingDataSetExampleAdaptor.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/adaptor/ImagingDataSetExampleAdaptor.java
index c9385c3da83376533a5a3ddaee77c7709efa23b4..e553d1382d09354f6f82fbe4fd8b8341a7b2403d 100644
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/adaptor/ImagingDataSetExampleAdaptor.java
+++ b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/adaptor/ImagingDataSetExampleAdaptor.java
@@ -38,7 +38,8 @@ public final class ImagingDataSetExampleAdaptor implements IImagingDataSetAdapto
}
@Override
- public Serializable process(ImagingServiceContext context, File rootFile, Map<String, Serializable> previewConfig, Map<String, String> metaData)
+ public Serializable process(ImagingServiceContext context, File rootFile,
+ Map<String, Serializable> previewConfig, Map<String, String> metaData, String format)
{
BufferedImage img = new BufferedImage(WIDTH, HEIGHT, BufferedImage.TYPE_INT_ARGB);
for(int y=0;y<HEIGHT; y++)
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/adaptor/ImagingDataSetJythonAdaptor.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/adaptor/ImagingDataSetJythonAdaptor.java
index 60476537ca1c3e14a3d387381f81e5468351a0aa..51e5043ba32212f9b7e15a49cf35758776af7552 100644
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/adaptor/ImagingDataSetJythonAdaptor.java
+++ b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/adaptor/ImagingDataSetJythonAdaptor.java
@@ -40,7 +40,8 @@ public class ImagingDataSetJythonAdaptor implements IImagingDataSetAdaptor
}
}
@Override
- public Serializable process(ImagingServiceContext context, File rootFile, Map<String, Serializable> previewConfig, Map<String, String> metaData)
+ public Serializable process(ImagingServiceContext context, File rootFile,
+ Map<String, Serializable> previewConfig, Map<String, String> metaData, String format)
{
CustomDSSServiceExecutionOptions options = new CustomDSSServiceExecutionOptions();
options.withParameter("sessionToken", context.getSessionToken());
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/adaptor/ImagingDataSetPythonAdaptor.java b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/adaptor/ImagingDataSetPythonAdaptor.java
index 2720f7fc6a2736455a40f03d4bab4e12fe9e4f01..8c720261064f4fb676f5b798e79e0b274e026fa8 100644
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/adaptor/ImagingDataSetPythonAdaptor.java
+++ b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/lib/premise-sources/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/imaging/adaptor/ImagingDataSetPythonAdaptor.java
@@ -38,11 +38,11 @@ public abstract class ImagingDataSetPythonAdaptor implements IImagingDataSetAdap
@Override
public Serializable process(ImagingServiceContext context, File rootFile,
- Map<String, Serializable> previewConfig, Map<String, String> metaData)
+ Map<String, Serializable> previewConfig, Map<String, String> metaData, String format)
{
ProcessBuilder processBuilder = new ProcessBuilder(pythonPath,
- scriptPath, rootFile.getAbsolutePath(), convertMapToJson(previewConfig), convertMapToJson(metaData));
+ scriptPath, rootFile.getAbsolutePath(), convertMapToJson(previewConfig), convertMapToJson(metaData), format);
processBuilder.redirectErrorStream(false);
String fullOutput;
@@ -63,9 +63,6 @@ public abstract class ImagingDataSetPythonAdaptor implements IImagingDataSetAdap
}
String[] resultSplit = fullOutput.split("\n");
-// for(int i=0;i< resultSplit.length;i++) {
-// System.out.println("||> " + resultSplit[i].substring(0, Math.min(resultSplit[i].length(), 1000)));
-// }
return resultSplit[resultSplit.length-1];
}
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/nanonis_dat.py b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/nanonis_dat.py
index d30b24bca91bb1797072382b776bb9b625e0396a..ef2acb909668703176d5f4856f21aba2b86700e5 100644
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/nanonis_dat.py
+++ b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/nanonis_dat.py
@@ -8,6 +8,7 @@ import os
import sys
from spmpy_terry import spm # <--- class spm defines objects of type spm with their attributes and class functions
import spmpy_terry as spmpy # <--- spmpy has other methods
+from datetime import datetime
import matplotlib.pyplot as plt
# %matplotlib inline
@@ -32,6 +33,7 @@ def get_channel(img, channel_name = 'z'):
file = sys.argv[1]
params = json.loads(sys.argv[2])
meta_data = json.loads(sys.argv[3])
+format = sys.argv[4]
folder_dir = os.path.join(file, 'original')
@@ -43,43 +45,56 @@ def generate_random_image(height, width):
imarray = numpy.random.rand(height,width,3) * 255
im = Image.fromarray(imarray.astype('uint8')).convert('RGBA')
img_byte_arr = io.BytesIO()
- im.save(img_byte_arr, format='PNG')
+ im.save(img_byte_arr, format=format)
img_byte_arr = img_byte_arr.getvalue()
encoded = base64.b64encode(img_byte_arr)
return encoded
-def get_sxm_image():
- img = load_image(file_path)
- channel = get_channel(img, 'z')
- img_byte_arr = io.BytesIO()
- plt.imshow(channel[0])
- plt.savefig(img_byte_arr, format="png")
- # print(img.header)
- img_byte_arr = img_byte_arr.getvalue()
- encoded = base64.b64encode(img_byte_arr)
- return encoded
+def get_dat_image(channel_x, channel_y, x_axis, y_axis, colormap, scaling, grouping, print_legend):
+ specs = spmpy.importall(folder_dir, '', 'spec')
+ for spec in specs:
+ date_time = spec.get_param('Saved Date')
+ spec.date_time = datetime.strptime(date_time, "%d.%m.%Y %H:%M:%S")
-def get_sxm_image2():
- img = load_image(file_path)
- channel = get_channel(img, 'z')[0]
+ # sort measurements according to date
+ specs.sort(key=lambda d: d.date_time)
+ specs_sub = list(filter(lambda spec:spec.name in grouping, specs))
- min_val = numpy.min(channel)
- max_val = numpy.max(channel)
- scaled_data = (channel - min_val) / (max_val - min_val)
- img = Image.fromarray(numpy.uint8(scaled_data * 255), 'L')
+ print_legend = print_legend
+ show = False
+ fig = spmpy.specs_plot(specs_sub, channelx=channel_x, channely=channel_y, direction='forward',
+ print_legend=print_legend, show=show, colormap=colormap, scaling=scaling,
+ x_axis=x_axis, y_axis=y_axis)
img_byte_arr = io.BytesIO()
- img.save(img_byte_arr, format='PNG')
+ plt.savefig(img_byte_arr, format=format)
img_byte_arr = img_byte_arr.getvalue()
encoded = base64.b64encode(img_byte_arr)
return encoded
+
+
+
+
print(params)
if params['mode'] == '1':
- print(get_sxm_image())
+ print(generate_random_image(640, 640))
elif params['mode'] == '2':
- print(get_sxm_image2())
-elif params['mode'] == '3':
- print(generate_random_image(640, 640))
\ No newline at end of file
+ parameters = dict(
+ channel_x=params['channel x'],
+ channel_y=params['channel y'],
+ x_axis=[float(x) for x in params['x-axis']],
+ y_axis=[float(x) for x in params['y-axis']],
+ colormap=params['colormap'],
+ scaling=params['scaling'],
+ grouping=params['grouping']
+ )
+ if "color" in params:
+ parameters['color'] = params['color']
+ if "print_legend" in params:
+ parameters['print_legend'] = params['print_legend'].upper() == "TRUE"
+ else:
+ parameters['print_legend'] = True
+ print(get_dat_image(**parameters))
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/nanonis_sxm.py b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/nanonis_sxm.py
index f8e912b6018491fbea9d2b912c4281e69dc1d223..0863f13fbd4e7106b2eb2c37042e881317458fd9 100644
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/nanonis_sxm.py
+++ b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/nanonis_sxm.py
@@ -34,10 +34,11 @@ def get_channel(img, channel_name = 'z'):
channel = img.get_channel(channel_name)
return channel
-
+print("SYS.ARGV:" + str(sys.argv))
file = sys.argv[1]
params = json.loads(sys.argv[2])
meta_data = json.loads(sys.argv[3])
+format = sys.argv[4]
folder_dir = os.path.join(file, 'original')
@@ -65,8 +66,8 @@ def get_sxm_image():
fig = img.plot(show=False, show_params=False)
fig.frameon=False
# plt.title(None)
- plt.axis('off')
- plt.savefig(img_byte_arr, format="png", bbox_inches='tight')
+ # plt.axis('off')
+ plt.savefig(img_byte_arr, format=format)
# print(img.header)
img_byte_arr = img_byte_arr.getvalue()
@@ -91,7 +92,7 @@ def get_sxm_image2():
img = Image.fromarray(numpy.uint8(scaled_data * 255), 'L')
img_byte_arr = io.BytesIO()
- img.save(img_byte_arr, format='PNG')
+ img.save(img_byte_arr, format=format)
img_byte_arr = img_byte_arr.getvalue()
encoded = base64.b64encode(img_byte_arr)
@@ -104,6 +105,62 @@ def get_sxm_image2():
return encoded
+
+def get_sxm_image3(channel_name, scaling, color_scale):
+ img = load_image(file_path)
+ # channel = get_channel(img, channel_name)
+ img_byte_arr = io.BytesIO()
+
+ log = False
+ if scaling == 'logarithmic':
+ log = True
+ fig = img.plot(show=False, show_params=False, hide=True, channel=channel_name, log=log)
+ fig.frameon=False
+ # plt.title('None')
+ plt.axis('off')
+ plt.savefig(img_byte_arr, format="png", bbox_inches='tight')
+
+ pilImg = Image.open(img_byte_arr)
+ print(f"SIZE={pilImg.size}")
+ im2 = pilImg.crop(pilImg.getbbox())
+ print(f"SIZE={im2.size}")
+ img_byte_arr = io.BytesIO()
+ im2.save(img_byte_arr, format='PNG')
+
+ # print(img.header)
+ img_byte_arr = img_byte_arr.getvalue()
+ encoded = base64.b64encode(img_byte_arr)
+ print_params = img.print_params(show=False).split('\n')
+ print_params = {x: y for x, y in (s.split(':') for s in print_params)}
+ print_params = json.dumps(print_params)
+ print(f'PARAMS={print_params}')
+ header = json.dumps(img.header, cls=NumpyEncoder)
+ print(f'HEADER={header}')
+
+ return encoded
+
+def get_sxm_image4(channel_name, x_axis, y_axis, scaling, color_scale, colormap, colormap_scaling):
+ img = load_image(file_path)
+ img_byte_arr = io.BytesIO()
+
+ log = False
+ if scaling == 'logarithmic':
+ log = True
+ fig = img.plot(show=False, show_params=False, channel=channel_name, log=log, cmap=colormap,
+ color_scale=color_scale, x_axis=x_axis, y_axis=y_axis, colormap_scaling=colormap_scaling)
+ plt.savefig(img_byte_arr, format=format)
+
+ img_byte_arr = img_byte_arr.getvalue()
+ encoded = base64.b64encode(img_byte_arr)
+ print_params = img.print_params(show=False).split('\n')
+ print_params = {x: y for x, y in (s.split(':') for s in print_params)}
+ print_params = json.dumps(print_params)
+ print(f'PARAMS={print_params}')
+ header = json.dumps(img.header, cls=NumpyEncoder)
+ print(f'HEADER={header}')
+
+ return encoded
+
print(params)
if params['mode'] == '1':
# print(f'IMG={get_sxm_image()}')
@@ -113,4 +170,20 @@ elif params['mode'] == '2':
print(f'{get_sxm_image2()}')
elif params['mode'] == '3':
# print(f'IMG={generate_random_image(320, 320)}')
- print(f'{generate_random_image(256, 256)}')
\ No newline at end of file
+ print(f'{generate_random_image(256, 256)}')
+elif params['mode'] == '4':
+ channel = params['channel']
+ scaling = params['scaling']
+ color_scale = [float(x) for x in params['color-scale']]
+ print(f'{get_sxm_image3(channel, scaling, color_scale)}')
+elif params['mode'] == '5':
+ channel = params['channel']
+ x_axis = [float(x) for x in params['x-axis']]
+ y_axis = [float(x) for x in params['y-axis']]
+ color_scale = [float(x) for x in params['color-scale']]
+ colormap = params['colormap']
+ scaling = params['scaling']
+ colormap_scaling = False
+ if "colormap_scaling" in params:
+ colormap_scaling = params['colormap_scaling'].upper() == "TRUE"
+ print(f'{get_sxm_image4(channel, x_axis, y_axis, scaling, color_scale, colormap, colormap_scaling)}')
\ No newline at end of file
diff --git a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/spmpy_terry.py b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/spmpy_terry.py
index 937ca5fc2779fda4d8408fe12f6aabb714a279da..57702f4aef451c718be269e712179144f2ec8499 100644
--- a/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/spmpy_terry.py
+++ b/core-plugin-openbis/dist/core-plugins/imaging/1/dss/custom-services/imaging/spmpy_terry.py
@@ -332,11 +332,38 @@ class spm:
show_params = params['show_params']
else:
show_params = False
-
+
if 'show' in params:
show = params['show']
else:
show = True
+
+ # PREMISE - specific params
+
+ if 'hide' in params:
+ hide = params['hide']
+ else:
+ hide = False
+
+ if 'color_scale' in params:
+ color_scale = params['color_scale']
+ else:
+ color_scale = False
+
+ if 'x_axis' in params:
+ x_axis = params['x_axis']
+ else:
+ x_axis = False
+
+ if 'y_axis' in params:
+ y_axis = params['y_axis']
+ else:
+ y_axis = False
+
+ if 'colormap_scaling' in params:
+ colormap_scaling = params['colormap_scaling']
+ else:
+ colormap_scaling = False
@@ -348,41 +375,83 @@ class spm:
width = self.get_param('width')
height = self.get_param('height')
pix_y,pix_x = np.shape(chData)
-
+
+ # fig = plt.figure(figsize=(6, 4))
fig = plt.figure()#figsize=(6,4))
-
+
ImgOrigin = 'lower'
if self.get_param('scan_dir') == 'down':
ImgOrigin = 'upper'
-
-
+
+ if color_scale:
+ chData = np.clip(chData, color_scale[0], color_scale[1])
+
+ if x_axis and y_axis:
+ plt.ylim(y_axis[0], y_axis[1])
+ plt.xlim(x_axis[0], x_axis[1])
+ # plt.axis([x_axis[0], x_axis[1], y_axis[0], y_axis[1]])
+
+ plot_params = dict(
+ X = np.abs(chData) if log else chData,
+ aspect = 'equal',
+ extent = [0,width[0],0,height[0]],
+ cmap = cmap,
+ origin = ImgOrigin,
+ interpolation = 'none'
+ )
if log:
- im = plt.imshow(np.abs(chData), aspect = 'equal', extent = [0,width[0],0,height[0]], cmap = cmap, norm=LogNorm(), origin = ImgOrigin)
- else:
- im = plt.imshow(chData, aspect = 'equal',extent = [0,width[0],0,height[0]], cmap = cmap, origin = ImgOrigin)
+ plot_params['norm'] = LogNorm()
+
+ if colormap_scaling:
+ min_x = x_axis[0]
+ max_x = x_axis[1]
+ min_y = y_axis[0]
+ max_y = y_axis[1]
+
+ shape = chData.shape
+ minx = int(np.floor(shape[0] * min_x / width[0]))
+ maxx = int(np.ceil(shape[0] * max_x / width[0]))
+ miny = int(np.floor(shape[1] * min_y / height[0]))
+ maxy = int(np.ceil(shape[1] * max_y / height[0]))
+
+ mini = np.min(chData[minx:maxx, miny:maxy])
+ maxi = np.max(chData[minx:maxx, miny:maxy])
+
+ mini = int(mini*100)/100
+ maxi = int(maxi*100)/100
+ plot_params['vmin'] = mini
+ plot_params['vmax'] = maxi
+
+ im = plt.imshow(**plot_params)
+
+ # if log:
+ # im = plt.imshow(np.abs(chData), aspect = 'equal', extent = [0,width[0],0,height[0]], cmap = cmap, norm=LogNorm(), origin = ImgOrigin)
+ # else:
+ # im = plt.imshow(chData, aspect = 'equal',extent = [0,width[0],0,height[0]], cmap = cmap, origin = ImgOrigin)
if clim:
plt.clim(clim)
- im.axes.set_xticks([0,width[0]])
- im.axes.set_xticklabels([0,np.round(width[0],2)])
- im.axes.set_yticks([0,height[0]])
- im.axes.set_yticklabels([0,np.round(height[0],2)])
+ # im.axes.set_xticks([0,width[0]])
+ # im.axes.set_xticklabels([0,np.round(width[0],2)])
+ # im.axes.set_yticks([0,height[0]])
+ # im.axes.set_yticklabels([0,np.round(height[0],2)])
if show_params:
title = self.print_params(show = False);
else:
title = self.path
-
- # plt.title(title + '\n', loc='left')
- # plt.xlabel('x (%s)' % width[1])
- # plt.ylabel('y (%s)' % height[1])
-
- # cbar = plt.colorbar(im,fraction=0.046, pad=0.02, format='%.2g',shrink = 0.5,aspect=10)
- # cbar.set_label('%s (%s)' % (channel,chUnit))
+
+ if not hide:
+ # plt.title(title + '\n', loc='left')
+ plt.xlabel('x (%s)' % width[1])
+ plt.ylabel('y (%s)' % height[1])
+ print(f'AXES={im.axes}')
+ cbar = plt.colorbar(im)#,fraction=0.046, pad=0.02, format='%.2g',shrink = 0.5,aspect=10)
+ cbar.set_label('channel:%s (%s)' % (channel,chUnit))
if show:
plt.show()
@@ -561,17 +630,61 @@ def specs_plot(specs,**params):
else:
offset = 0
-
+ # PREMISE specific
+ if 'show' in params:
+ show = params['show']
+ else:
+ show = True
+
+ if 'colormap' in params:
+ colormap = params['colormap']
+ cmap = plt.get_cmap(colormap)
+ color = cmap(np.linspace(0,1,len(specs)))
+ else:
+ colormap = False
+
+ if 'scaling' in params:
+ scaling = params['scaling']
+ else:
+ scaling = False
+
+ if 'x_axis' in params:
+ x_axis = params['x_axis']
+ else:
+ x_axis = False
+
+ if 'y_axis' in params:
+ y_axis = params['y_axis']
+ else:
+ y_axis = False
+ #######
+
fig = plt.figure(figsize=(6,4))
counter = 0
- for (s,c) in zip(specs,color):
-
- (x_data,x_unit) = s.get_channel(channelx,direction=direction)
- (y_data,y_unit) = s.get_channel(channely,direction=direction)
+ for (s, c) in zip(specs, color):
-
- plt.plot(x_data,y_data+counter*offset,color = c,label = s.name)
+ (x_data, x_unit) = s.get_channel(channelx, direction=direction)
+ if x_axis:
+ x_data = np.clip(x_data, x_axis[0], x_axis[1])
+
+ (y_data, y_unit) = s.get_channel(channely, direction=direction)
+ if y_axis:
+ y_data = np.clip(y_data, y_axis[0], y_axis[1])
+
+ if scaling:
+ if scaling == 'lin-lin':
+ plt.plot(x_data, y_data, color=c, label=s.name)
+ elif scaling == "lin-log":
+ plt.semilogy(x_data, np.abs(y_data), color=c, label=s.name)
+ elif scaling == 'log-lin':
+ plt.semilogx(np.abs(x_data), y_data, color=c, label=s.name)
+ elif scaling == 'log-log':
+ plt.loglog(np.abs(x_data), np.abs(y_data), color=c, label=s.name)
+ else:
+ plt.plot(x_data, y_data, color=c, label=s.name)
+ else:
+ plt.plot(x_data,y_data+counter*offset,color = c,label = s.name)
counter = counter + 1
plt.xlabel('%s (%s)' % (channelx,x_unit))
@@ -579,8 +692,9 @@ def specs_plot(specs,**params):
if print_legend:
plt.legend()
-
- plt.show()
+
+ if show:
+ plt.show()
return fig