remove nickname as it is no loner supported

bioimage-io · Sep 30, 2024 · 40cc5c3 · 40cc5c3
1 parent 994ee30
commit 40cc5c3
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Showing 2 changed files with 7 additions and 22 deletions.
diff --git a/src/main/java/io/bioimage/modelrunner/runmode/ops/StardistFineTuneJdllOp.java b/src/main/java/io/bioimage/modelrunner/runmode/ops/StardistFineTuneJdllOp.java
@@ -37,6 +37,7 @@
 
 import io.bioimage.modelrunner.bioimageio.BioimageioRepo;
 import io.bioimage.modelrunner.bioimageio.description.ModelDescriptor;
+import io.bioimage.modelrunner.bioimageio.description.ModelDescriptorFactory;
 import io.bioimage.modelrunner.bioimageio.description.exceptions.ModelSpecsException;
 import io.bioimage.modelrunner.bioimageio.download.DownloadModel;
 import io.bioimage.modelrunner.engine.installation.FileDownloader;
@@ -551,8 +552,6 @@ private void setUpStardistModelFromBioimageio() throws IOException, InterruptedE
 			model = br.downloadByName(model, nModelParentPath);
 		} else if (br.selectByID(model) != null) {
 			model = br.downloadModelByID(model, nModelParentPath);
-		} else if (br.selectByNickname(model) != null) {
-			model = br.downloadByNickame(model, nModelParentPath);
 		}
 		File folder = new File(model);
 		String fineTuned = folder.getParent() + File.separator + "finetuned_" + folder.getName();
@@ -597,7 +596,7 @@ private void setUpConfigs() throws IOException, ModelSpecsException {
 	@SuppressWarnings("unchecked")
 	private void setUpConfigsBioimageio() throws IOException, ModelSpecsException {
 		String rdfDir = new File(model).getParent();
-		ModelDescriptor descriptor = ModelDescriptor.readFromLocalFile(rdfDir + File.separator + Constants.RDF_FNAME, false);
+		ModelDescriptor descriptor = ModelDescriptorFactory.readFromLocalFile(rdfDir + File.separator + Constants.RDF_FNAME);
 		Object stardistInfo = descriptor.getConfig().getSpecMap().get(StardistInferJdllOp.STARDIST_FIELD_KEY);
 
 		if (stardistInfo == null || !(stardistInfo instanceof Map)) {
@@ -629,7 +628,7 @@ private void setUpConfigsBioimageio() throws IOException, ModelSpecsException {
 
 	private void setUpKerasWeights() throws IOException, ModelSpecsException {
 		String rdfYamlFN = this.model + File.separator + Constants.RDF_FNAME;
-		ModelDescriptor descriptor = ModelDescriptor.readFromLocalFile(rdfYamlFN, false);
+		ModelDescriptor descriptor = ModelDescriptorFactory.readFromLocalFile(rdfYamlFN);
 		String stardistWeights = this.model + File.separator +  StardistInferJdllOp.STARDIST_FIELD_KEY;
 		stardistWeights += File.separator + STARDIST_WEIGHTS_FILE;
 		String stardistWeightsParent = this.model + File.separator + STARDIST_WEIGHTS_FILE;
@@ -795,9 +794,9 @@ private void findNChannels() throws Exception {
 			this.nChannelsModel = 3;
 		}
 		String rdfFileName = new File(model).getParentFile() + File.separator + Constants.RDF_FNAME;
-		ModelDescriptor descriptor = ModelDescriptor.readFromLocalFile(rdfFileName, false);
+		ModelDescriptor descriptor = ModelDescriptorFactory.readFromLocalFile(rdfFileName);
 		int cInd = descriptor.getInputTensors().get(0).getAxesOrder().indexOf("c");
-		nChannelsModel = descriptor.getInputTensors().get(0).getShape().getTileMinimumSize()[cInd];
+		nChannelsModel = descriptor.getInputTensors().get(0).getMinTileSizeArr()[cInd];
 	}
 
 	/**

diff --git a/src/main/java/io/bioimage/modelrunner/runmode/ops/StardistInferJdllOp.java b/src/main/java/io/bioimage/modelrunner/runmode/ops/StardistInferJdllOp.java
@@ -28,6 +28,7 @@
 
 import io.bioimage.modelrunner.bioimageio.BioimageioRepo;
 import io.bioimage.modelrunner.bioimageio.description.ModelDescriptor;
+import io.bioimage.modelrunner.bioimageio.description.ModelDescriptorFactory;
 import io.bioimage.modelrunner.runmode.RunMode;
 import io.bioimage.modelrunner.tensor.Tensor;
 import io.bioimage.modelrunner.utils.Constants;
@@ -243,7 +244,7 @@ public static boolean isModelFileStardist(String modelFile) {
 		if (new File(modelFile).getName().equals(Constants.RDF_FNAME) == false)
 			return false;
 		try {
-			ModelDescriptor descriptor = ModelDescriptor.readFromLocalFile(modelFile, false);
+			ModelDescriptor descriptor = ModelDescriptorFactory.readFromLocalFile(modelFile);
 			 return descriptor.getConfig().getSpecMap().keySet().contains(STARDIST_FIELD_KEY);
 		} catch (Exception e) {
 			return false;
@@ -264,8 +265,6 @@ public static boolean isModelNameStardist(String modelName) {
 			return br.selectByName(modelName).getConfig().getSpecMap().keySet().contains(STARDIST_FIELD_KEY);
 		} else if (br.selectByID(modelName) != null) {
 			return br.selectByID(modelName).getConfig().getSpecMap().keySet().contains(STARDIST_FIELD_KEY);
-		} else if (br.selectByNickname(modelName) != null) {
-			return br.selectByNickname(modelName).getConfig().getSpecMap().keySet().contains(STARDIST_FIELD_KEY);
 		}
 		return false;
 	}
@@ -283,19 +282,6 @@ public static List<String> fetchStarDistModelNamesFromBioImage() {
 		return stardistModels;
 	}
 
-	/**
-	 * Returns a list containing all the model nicknames that corresponds to 
-	 * StarDist models existing in the Bioimage.io online repository.
-	 * @return list of StarDist model nicknames from the Bioimage.io repository
-	 */
-	public static List<String> fetchStarDistModelNicknamesFromBioImage() {
-		BioimageioRepo br = BioimageioRepo.connect();
-		List<String> stardistModels = br.listAllModels(false).values().stream()
-				.filter(md -> md.getConfig().getSpecMap().keySet().contains(STARDIST_FIELD_KEY))
-				.map(md -> md.getNickname()).collect(Collectors.toList());
-		return stardistModels;
-	}
-
 	/**
 	 * Returns a list containing all the model IDs that corresponds to 
 	 * StarDist models existing in the Bioimage.io online repository.