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refactor method
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@carlosuc3m
carlosuc3m committed Sep 24, 2024
1 parent f0c566a commit 568aa53
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Showing 10 changed files with 42 additions and 39 deletions.
8 changes: 4 additions & 4 deletions src/main/java/io/bioimage/modelrunner/bioimageio/TileCalculator.java
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Expand Up @@ -71,13 +71,13 @@ public List<TileInfo> getOptimalTileSize(List<ImageInfo> inputInfo) {
List<TileInfo> firstIterationInputs = new ArrayList<TileInfo>();
for (TensorSpec tt : this.descriptor.getInputTensors()) {
ImageInfo im = inputInfo.stream()
.filter(ii -> ii.getTensorName().equals(tt.getTensorID())).findFirst().orElse(null);
.filter(ii -> ii.getTensorName().equals(tt.getName())).findFirst().orElse(null);
if (im == null)
throw new IllegalArgumentException("No data was provided for input tensor: " + tt.getTensorID());
throw new IllegalArgumentException("No data was provided for input tensor: " + tt.getName());

long[] tileSize = getOptimalTileSize(tt, im.getAxesOrder(), im.getDimensions());

firstIterationInputs.add(TileInfo.build(tt.getTensorID(), im.getDimensions(), im.getAxesOrder(), tileSize, im.getAxesOrder()));
firstIterationInputs.add(TileInfo.build(tt.getName(), im.getDimensions(), im.getAxesOrder(), tileSize, im.getAxesOrder()));
}

if (!tiling)
Expand Down Expand Up @@ -174,7 +174,7 @@ private List<TileInfo> checkOutputSize(List<TileInfo> inputs, List<TensorSpec> a
if (ax.getReferenceTensor() == null)
continue;
TensorSpec inputT = this.descriptor.findInputTensor(ax.getReferenceTensor());
TileInfo im = inputs.stream().filter(in -> in.getName().equals(inputT.getTensorID())).findFirst().orElse(null);
TileInfo im = inputs.stream().filter(in -> in.getName().equals(inputT.getName())).findFirst().orElse(null);
String refAxis = ax.getReferenceAxis();
int index = im.getTileAxesOrder().indexOf(refAxis);
Axis inAx = inputT.getAxesInfo().getAxis(refAxis);
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2 changes: 1 addition & 1 deletion src/main/java/io/bioimage/modelrunner/bioimageio/description/ModelDescriptor.java
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Original file line number Diff line number Diff line change
Expand Up @@ -161,7 +161,7 @@ public static TensorSpec findTensorInList(String name, List<TensorSpec> tts)
}

return tts.stream()
.filter(t -> t.getTensorID().equals(name))
.filter(t -> t.getName().equals(name))
.findAny().orElse(null);
}

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4 changes: 2 additions & 2 deletions src/main/java/io/bioimage/modelrunner/bioimageio/description/ModelDescriptorV04.java
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Expand Up @@ -611,7 +611,7 @@ public TensorSpec findInputTensor(String name)
}

return input_tensors.stream()
.filter(t -> t.getTensorID().equals(name))
.filter(t -> t.getName().equals(name))
.findAny().orElse(null);
}

Expand All @@ -630,7 +630,7 @@ public TensorSpec findOutputTensor(String name)
}

return output_tensors.stream()
.filter(t -> t.getTensorID().equals(name))
.filter(t -> t.getName().equals(name))
.findAny().orElse(null);
}

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4 changes: 2 additions & 2 deletions src/main/java/io/bioimage/modelrunner/bioimageio/description/ModelDescriptorV05.java
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Original file line number Diff line number Diff line change
Expand Up @@ -476,7 +476,7 @@ public TensorSpec findInputTensor(String name)
}

return input_tensors.stream()
.filter(t -> t.getTensorID().equals(name))
.filter(t -> t.getName().equals(name))
.findAny().orElse(null);
}

Expand All @@ -495,7 +495,7 @@ public TensorSpec findOutputTensor(String name)
}

return output_tensors.stream()
.filter(t -> t.getTensorID().equals(name))
.filter(t -> t.getName().equals(name))
.findAny().orElse(null);
}

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2 changes: 1 addition & 1 deletion src/main/java/io/bioimage/modelrunner/bioimageio/description/TensorSpec.java
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Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,7 @@ public interface TensorSpec {



public String getTensorID();
public String getName();

public String getDescription();

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2 changes: 1 addition & 1 deletion src/main/java/io/bioimage/modelrunner/bioimageio/description/TensorSpecV04.java
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Expand Up @@ -120,7 +120,7 @@ protected void setTestTensor(String testTensorName) {
this.testTensorName = testTensorName;
}

public String getTensorID() {
public String getName() {
return this.id;
}

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2 changes: 1 addition & 1 deletion src/main/java/io/bioimage/modelrunner/bioimageio/description/TensorSpecV05.java
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Original file line number Diff line number Diff line change
Expand Up @@ -123,7 +123,7 @@ protected TensorSpecV05(Map<String, Object> tensorSpecMap, boolean input)
}
}

public String getTensorID() {
public String getName() {
return this.id;
}

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25 changes: 14 additions & 11 deletions src/main/java/io/bioimage/modelrunner/example/ExampleLoadAndRunAllBmzModels.java
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Original file line number Diff line number Diff line change
Expand Up @@ -39,6 +39,8 @@

import net.imglib2.img.ImgFactory;
import net.imglib2.img.array.ArrayImgFactory;
import net.imglib2.type.NativeType;
import net.imglib2.type.numeric.RealType;
import net.imglib2.type.numeric.real.FloatType;

/**
Expand Down Expand Up @@ -121,11 +123,12 @@ public static void main(String[] args) {
* descriptor containing the rdf.yaml information
* @throws Exception if any error occurs
*/
public static void loadAndRunModel(String modelFolder, ModelDescriptor descriptor) throws Exception {
public static <T extends RealType<T> & NativeType<T>, R extends RealType<R> & NativeType<R>>
void loadAndRunModel(String modelFolder, ModelDescriptor descriptor) throws Exception {
Model model = Model.createBioimageioModel(modelFolder, ENGINES_DIR);
model.loadModel();
List<Tensor<?>> inputs = createInputs(descriptor);
List<Tensor<?>> outputs = createOutputs(descriptor);
List<Tensor<T>> inputs = createInputs(descriptor);
List<Tensor<R>> outputs = createOutputs(descriptor);
model.runModel(inputs, outputs);
for (Tensor<?> tt : outputs) {
if (tt.isEmpty())
Expand All @@ -144,19 +147,19 @@ public static void loadAndRunModel(String modelFolder, ModelDescriptor descripto
* file containing the information
* @return the input Tensor list
*/
private static List<Tensor<?>> createInputs(ModelDescriptor descriptor) {
List<Tensor<?>> inputs = new ArrayList<Tensor<?>>();
private static <T extends RealType<T> & NativeType<T>> List<Tensor<T>> createInputs(ModelDescriptor descriptor) {
List<Tensor<T>> inputs = new ArrayList<Tensor<T>>();
final ImgFactory< FloatType > imgFactory = new ArrayImgFactory<>( new FloatType() );

for ( TensorSpec it : descriptor.getInputTensors()) {
String axesStr = it.getAxesOrder();
String name = it.getName();
int[] min = it.getShape().getTileMinimumSize();
int[] step = it.getShape().getTileStep();
int[] min = it.getMinTileSizeArr();
int[] step = it.getTileStepArr();
long[] imSize = LongStream.range(0, step.length)
.map(i -> min[(int) i] + step[(int) i]).toArray();
Tensor<FloatType> tt = Tensor.build(name, axesStr, imgFactory.create(imSize));
inputs.add(tt);
inputs.add((Tensor<T>) tt);
}
return inputs;
}
Expand All @@ -168,13 +171,13 @@ private static List<Tensor<?>> createInputs(ModelDescriptor descriptor) {
* file containing the information
* @return the output Tensor list
*/
private static List<Tensor<?>> createOutputs(ModelDescriptor descriptor) {
List<Tensor<?>> outputs = new ArrayList<Tensor<?>>();
private static <T extends RealType<T> & NativeType<T>> List<Tensor<T>> createOutputs(ModelDescriptor descriptor) {
List<Tensor<T>> outputs = new ArrayList<Tensor<T>>();

for ( TensorSpec ot : descriptor.getOutputTensors()) {
String axesStr = ot.getAxesOrder();
String name = ot.getName();
Tensor<?> tt = Tensor.buildEmptyTensor(name, axesStr);
Tensor<T> tt = Tensor.buildEmptyTensor(name, axesStr);
outputs.add(tt);
}
return outputs;
Expand Down
4 changes: 2 additions & 2 deletions src/main/java/io/bioimage/modelrunner/model/Model.java
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Original file line number Diff line number Diff line change
Expand Up @@ -678,8 +678,8 @@ else if (descriptor == null)
List<Tensor<T>> runTiling(List<Tensor<R>> inputTensors, TileMaker tiles, TilingConsumer tileCounter) throws RunModelException {
List<Tensor<T>> outputTensors = new ArrayList<Tensor<T>>();
for (TensorSpec tt : descriptor.getOutputTensors()) {
long[] dims = tiles.getOutputImageSize(tt.getTensorID());
outputTensors.add((Tensor<T>) Tensor.buildBlankTensor(tt.getTensorID(),
long[] dims = tiles.getOutputImageSize(tt.getName());
outputTensors.add((Tensor<T>) Tensor.buildBlankTensor(tt.getName(),
tt.getAxesOrder(),
dims,
(T) new FloatType()));
Expand Down
28 changes: 14 additions & 14 deletions src/main/java/io/bioimage/modelrunner/tiling/TileMaker.java
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Original file line number Diff line number Diff line change
Expand Up @@ -77,7 +77,7 @@ private void getOutputTiles() {
TensorSpec intt = descriptor.getInputTensors().stream()
.filter(t -> t.isImage()).findFirst().orElse(null);
TileInfo inTile = inputTileInfo.stream()
.filter(t -> t.getName().equals(intt.getTensorID())).findFirst().orElse(null);
.filter(t -> t.getName().equals(intt.getName())).findFirst().orElse(null);
int indTile = inTile.getTileAxesOrder().indexOf(ax.getAxis());
int indIm = inTile.getImageAxesOrder().indexOf(ax.getAxis());
if (indTile == -1 || indIm == -1)
Expand Down Expand Up @@ -112,7 +112,7 @@ private void getOutputTiles() {
+ " so we can troubleshoot at: " + Constants.ISSUES_LINK);
}
}
outputTileInfo.add(TileInfo.build(tt.getTensorID(), imagSize, outAxesOrder, tileSize, outAxesOrder));
outputTileInfo.add(TileInfo.build(tt.getName(), imagSize, outAxesOrder, tileSize, outAxesOrder));
}
}

Expand Down Expand Up @@ -247,9 +247,9 @@ private void checkTilesCombine() {
private void checkAllTensorsDefined() {
for (TensorSpec tensor : this.descriptor.getInputTensors()) {
TileInfo info = inputTileInfo.stream()
.filter(tt -> tt.getName().equals(tensor.getTensorID())).findFirst().orElse(null);
.filter(tt -> tt.getName().equals(tensor.getName())).findFirst().orElse(null);
if (info == null) {
throw new IllegalArgumentException("Tiling info for input tensor '" + tensor.getTensorID()
throw new IllegalArgumentException("Tiling info for input tensor '" + tensor.getName()
+ "' not defined.");
}
}
Expand All @@ -258,17 +258,17 @@ private void checkAllTensorsDefined() {
private void calculate() {
for (TensorSpec tt : this.descriptor.getInputTensors()) {
TileInfo tile = inputTileInfo.stream()
.filter(til -> til.getName().equals(tt.getTensorID())).findFirst().orElse(null);
.filter(til -> til.getName().equals(tt.getName())).findFirst().orElse(null);
PatchSpec patch = computePatchSpecs(tt, tile);
input.put(tt.getTensorID(), patch);
inputGrid.put(tt.getTensorID(), TileGrid.create(patch));
input.put(tt.getName(), patch);
inputGrid.put(tt.getName(), TileGrid.create(patch));
}
for (TensorSpec tt : this.descriptor.getOutputTensors()) {
TileInfo tile = outputTileInfo.stream()
.filter(til -> til.getName().equals(tt.getTensorID())).findFirst().orElse(null);
.filter(til -> til.getName().equals(tt.getName())).findFirst().orElse(null);
PatchSpec patch = computePatchSpecs(tt, tile);
output.put(tt.getTensorID(), patch);
outputGrid.put(tt.getTensorID(), TileGrid.create(patch));
output.put(tt.getName(), patch);
outputGrid.put(tt.getName(), TileGrid.create(patch));
}
}

Expand Down Expand Up @@ -321,11 +321,11 @@ private PatchSpec computePatchSpecs(TensorSpec spec, TileInfo tile)
.map(i -> (int) Math.max( paddingSize[1][i],
tileSize[i] - imSize[i] - paddingSize[0][i])).toArray();

return PatchSpec.create(spec.getTensorID(), tileSize, patchGridSize, paddingSize, imSize);
return PatchSpec.create(spec.getName(), tileSize, patchGridSize, paddingSize, imSize);
}

public int getNumberOfTiles() {
return inputGrid.get(this.descriptor.getInputTensors().get(0).getTensorID()).getRoiPostionsInImage().size();
return inputGrid.get(this.descriptor.getInputTensors().get(0).getName()).getRoiPostionsInImage().size();
}

public Map<String, Integer> getTilesPerAxis() {
Expand All @@ -352,7 +352,7 @@ public void getOutputInsertionPoints(String tensorID, int nTile, String axes) {
*/
public List<String> getInputTensorNames() {
return descriptor.getInputTensors().stream()
.map(tt -> tt.getTensorID()).collect(Collectors.toList());
.map(tt -> tt.getName()).collect(Collectors.toList());
}

/**
Expand All @@ -361,7 +361,7 @@ public List<String> getInputTensorNames() {
*/
public List<String> getOutputTensorNames() {
return descriptor.getOutputTensors().stream()
.map(tt -> tt.getTensorID()).collect(Collectors.toList());
.map(tt -> tt.getName()).collect(Collectors.toList());
}

/**
Expand Down

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