* properly annotate Ilastik inputs

applied-systems-biology · Sep 24, 2024 · 89d504d · 89d504d
1 parent 4a82a2d
commit 89d504d
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Showing 5 changed files with 10 additions and 17 deletions.
diff --git a/...k/src/main/java/org/hkijena/jipipe/plugins/ilastik/nodes/IlastikAutoContextAlgorithm.java b/...k/src/main/java/org/hkijena/jipipe/plugins/ilastik/nodes/IlastikAutoContextAlgorithm.java
@@ -28,6 +28,7 @@
 import org.hkijena.jipipe.api.annotation.JIPipeTextAnnotation;
 import org.hkijena.jipipe.api.annotation.JIPipeTextAnnotationMergeMode;
 import org.hkijena.jipipe.api.data.JIPipeDataSlotInfo;
+import org.hkijena.jipipe.api.data.JIPipeDataSlotRole;
 import org.hkijena.jipipe.api.data.JIPipeInputDataSlot;
 import org.hkijena.jipipe.api.data.JIPipeSlotType;
 import org.hkijena.jipipe.api.data.context.JIPipeDataContext;
@@ -76,7 +77,7 @@
 @AddJIPipeCitation("Autocontext documentation: https://www.ilastik.org/documentation/autocontext/autocontext")
 @ConfigureJIPipeNode(nodeTypeCategory = ImagesNodeTypeCategory.class, menuPath = "Ilastik")
 @AddJIPipeInputSlot(value = ImagePlusData.class, name = "Image", create = true, description = "The image(s) to classify.")
-@AddJIPipeInputSlot(value = IlastikModelData.class, name = "Project", create = true, description = "The Ilastik project. Must support pixel classification.")
+@AddJIPipeInputSlot(value = IlastikModelData.class, name = "Project", create = true, description = "The Ilastik project. Must support pixel classification.", role = JIPipeDataSlotRole.ParametersLooping)
 @AddJIPipeOutputSlot(value = ImagePlusData.class, name = "Probabilities Stage 1", description = "Multi-channel image where pixel values represent the probability that that pixel belongs to the class represented by that channel (Stage 1)")
 @AddJIPipeOutputSlot(value = ImagePlusData.class, name = "Probabilities Stage 2", description = "Multi-channel image where pixel values represent the probability that that pixel belongs to the class represented by that channel (Stage 2)")
 @AddJIPipeOutputSlot(value = ImagePlusData.class, name = "Probabilities All Stages", description = "Contains both \"Probabilities Stage 1\" and \"Probabilities Stage 2\" in a single multi-channel image")

diff --git a/...n/java/org/hkijena/jipipe/plugins/ilastik/nodes/IlastikObjectClassificationAlgorithm.java b/...n/java/org/hkijena/jipipe/plugins/ilastik/nodes/IlastikObjectClassificationAlgorithm.java
@@ -27,10 +27,7 @@
 import org.hkijena.jipipe.api.annotation.JIPipeDataAnnotationMergeMode;
 import org.hkijena.jipipe.api.annotation.JIPipeTextAnnotation;
 import org.hkijena.jipipe.api.annotation.JIPipeTextAnnotationMergeMode;
-import org.hkijena.jipipe.api.data.JIPipeDataSlot;
-import org.hkijena.jipipe.api.data.JIPipeDataSlotInfo;
-import org.hkijena.jipipe.api.data.JIPipeInputDataSlot;
-import org.hkijena.jipipe.api.data.JIPipeSlotType;
+import org.hkijena.jipipe.api.data.*;
 import org.hkijena.jipipe.api.data.context.JIPipeDataContext;
 import org.hkijena.jipipe.api.environments.JIPipeEnvironment;
 import org.hkijena.jipipe.api.nodes.AddJIPipeInputSlot;
@@ -78,7 +75,7 @@
 @AddJIPipeCitation("Object classification documentation: https://www.ilastik.org/documentation/objects/objects")
 @ConfigureJIPipeNode(nodeTypeCategory = ImagesNodeTypeCategory.class, menuPath = "Ilastik")
 @AddJIPipeInputSlot(value = ImagePlusData.class, name = "Image", create = true, description = "The image(s) to classify.")
-@AddJIPipeInputSlot(value = IlastikModelData.class, name = "Project", create = true, description = "The Ilastik project. Must support pixel classification.")
+@AddJIPipeInputSlot(value = IlastikModelData.class, name = "Project", create = true, description = "The Ilastik project. Must support pixel classification.", role = JIPipeDataSlotRole.ParametersLooping)
 @AddJIPipeOutputSlot(value = ImagePlusData.class, name = "Object Predictions", description = "A label image of the object class predictions")
 @AddJIPipeOutputSlot(value = ImagePlusData.class, name = "Object Probabilities", description = "A multi-channel image volume of object prediction probabilities instead of a label image (one channel for each prediction class)")
 @AddJIPipeOutputSlot(value = ImagePlusData.class, name = "Blockwise Object Predictions", description = "A label image of the object class predictions. " +

diff --git a/...in/java/org/hkijena/jipipe/plugins/ilastik/nodes/IlastikPixelClassificationAlgorithm.java b/...in/java/org/hkijena/jipipe/plugins/ilastik/nodes/IlastikPixelClassificationAlgorithm.java
@@ -28,6 +28,7 @@
 import org.hkijena.jipipe.api.annotation.JIPipeTextAnnotation;
 import org.hkijena.jipipe.api.annotation.JIPipeTextAnnotationMergeMode;
 import org.hkijena.jipipe.api.data.JIPipeDataSlotInfo;
+import org.hkijena.jipipe.api.data.JIPipeDataSlotRole;
 import org.hkijena.jipipe.api.data.JIPipeInputDataSlot;
 import org.hkijena.jipipe.api.data.JIPipeSlotType;
 import org.hkijena.jipipe.api.data.context.JIPipeDataContext;
@@ -75,7 +76,7 @@
 @AddJIPipeCitation("Pixel classification documentation: https://www.ilastik.org/documentation/pixelclassification/pixelclassification")
 @ConfigureJIPipeNode(nodeTypeCategory = ImagesNodeTypeCategory.class, menuPath = "Ilastik")
 @AddJIPipeInputSlot(value = ImagePlusData.class, name = "Image", create = true, description = "The image(s) to classify.")
-@AddJIPipeInputSlot(value = IlastikModelData.class, name = "Project", create = true, description = "The Ilastik project. Must support pixel classification.")
+@AddJIPipeInputSlot(value = IlastikModelData.class, name = "Project", create = true, description = "The Ilastik project. Must support pixel classification.", role = JIPipeDataSlotRole.ParametersLooping)
 @AddJIPipeOutputSlot(value = ImagePlusData.class, name = "Probabilities", description = "Multi-channel image where pixel values represent the probability that that pixel belongs to the class represented by that channel")
 @AddJIPipeOutputSlot(value = ImagePlusData.class, name = "Simple Segmentation", description = "A single-channel image where the (integer) pixel values indicate the class to which a pixel belongs. " +
         "For this image, every pixel with the same value should belong to the same class of pixels")

diff --git a/...jena/jipipe/plugins/ilastik/nodes/IlastikPredictionMapsObjectClassificationAlgorithm.java b/...jena/jipipe/plugins/ilastik/nodes/IlastikPredictionMapsObjectClassificationAlgorithm.java
@@ -27,10 +27,7 @@
 import org.hkijena.jipipe.api.annotation.JIPipeDataAnnotationMergeMode;
 import org.hkijena.jipipe.api.annotation.JIPipeTextAnnotation;
 import org.hkijena.jipipe.api.annotation.JIPipeTextAnnotationMergeMode;
-import org.hkijena.jipipe.api.data.JIPipeDataSlot;
-import org.hkijena.jipipe.api.data.JIPipeDataSlotInfo;
-import org.hkijena.jipipe.api.data.JIPipeInputDataSlot;
-import org.hkijena.jipipe.api.data.JIPipeSlotType;
+import org.hkijena.jipipe.api.data.*;
 import org.hkijena.jipipe.api.data.context.JIPipeDataContext;
 import org.hkijena.jipipe.api.environments.JIPipeEnvironment;
 import org.hkijena.jipipe.api.nodes.AddJIPipeInputSlot;
@@ -78,7 +75,7 @@
 @AddJIPipeCitation("Object classification documentation: https://www.ilastik.org/documentation/objects/objects")
 @ConfigureJIPipeNode(nodeTypeCategory = ImagesNodeTypeCategory.class, menuPath = "Ilastik")
 @AddJIPipeInputSlot(value = ImagePlusData.class, name = "Image", create = true, description = "The image(s) to classify. Requires a data annotation that contains the segmentation image.")
-@AddJIPipeInputSlot(value = IlastikModelData.class, name = "Project", create = true, description = "The Ilastik project. Must support pixel classification.")
+@AddJIPipeInputSlot(value = IlastikModelData.class, name = "Project", create = true, description = "The Ilastik project. Must support pixel classification.", role = JIPipeDataSlotRole.ParametersLooping)
 @AddJIPipeOutputSlot(value = ImagePlusData.class, name = "Object Predictions", description = "A label image of the object class predictions")
 @AddJIPipeOutputSlot(value = ImagePlusData.class, name = "Object Probabilities", description = "A multi-channel image volume of object prediction probabilities instead of a label image (one channel for each prediction class)")
 @AddJIPipeOutputSlot(value = ImagePlusData.class, name = "Blockwise Object Predictions", description = "A label image of the object class predictions. " +

diff --git a/...a/jipipe/plugins/ilastik/nodes/IlastikSegmentationImageObjectClassificationAlgorithm.java b/...a/jipipe/plugins/ilastik/nodes/IlastikSegmentationImageObjectClassificationAlgorithm.java
@@ -27,10 +27,7 @@
 import org.hkijena.jipipe.api.annotation.JIPipeDataAnnotationMergeMode;
 import org.hkijena.jipipe.api.annotation.JIPipeTextAnnotation;
 import org.hkijena.jipipe.api.annotation.JIPipeTextAnnotationMergeMode;
-import org.hkijena.jipipe.api.data.JIPipeDataSlot;
-import org.hkijena.jipipe.api.data.JIPipeDataSlotInfo;
-import org.hkijena.jipipe.api.data.JIPipeInputDataSlot;
-import org.hkijena.jipipe.api.data.JIPipeSlotType;
+import org.hkijena.jipipe.api.data.*;
 import org.hkijena.jipipe.api.data.context.JIPipeDataContext;
 import org.hkijena.jipipe.api.environments.JIPipeEnvironment;
 import org.hkijena.jipipe.api.nodes.AddJIPipeInputSlot;
@@ -79,7 +76,7 @@
 @AddJIPipeCitation("Object classification documentation: https://www.ilastik.org/documentation/objects/objects")
 @ConfigureJIPipeNode(nodeTypeCategory = ImagesNodeTypeCategory.class, menuPath = "Ilastik")
 @AddJIPipeInputSlot(value = ImagePlusData.class, name = "Image", create = true, description = "The image(s) to classify. Requires a data annotation that contains the segmentation image.")
-@AddJIPipeInputSlot(value = IlastikModelData.class, name = "Project", create = true, description = "The Ilastik project. Must support pixel classification.")
+@AddJIPipeInputSlot(value = IlastikModelData.class, name = "Project", create = true, description = "The Ilastik project. Must support pixel classification.", role = JIPipeDataSlotRole.ParametersLooping)
 @AddJIPipeOutputSlot(value = ImagePlusData.class, name = "Object Predictions", description = "A label image of the object class predictions")
 @AddJIPipeOutputSlot(value = ImagePlusData.class, name = "Object Probabilities", description = "A multi-channel image volume of object prediction probabilities instead of a label image (one channel for each prediction class)")
 @AddJIPipeOutputSlot(value = ImagePlusData.class, name = "Blockwise Object Predictions", description = "A label image of the object class predictions. " +