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Support 0.5 models #8

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Merged
alanocallaghan merged 11 commits into from
Feb 12, 2025
Merged

Support 0.5 models #8

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c1c8377
Potentially implement 0.5 models
alanocallaghan Jan 7, 2025
ffd505e
Deprecations and linting
alanocallaghan Jan 10, 2025
397befc
Update to refactored spec
alanocallaghan Jan 23, 2025
ce35250
Fix typo and method names
alanocallaghan Feb 3, 2025
a313fe1
Implement simple checks for 2D image with one input/output
alanocallaghan Feb 5, 2025
cf88a7c
Simpler check for space axes
alanocallaghan Feb 5, 2025
e2430c6
Revert axis type simplification to handle 0.4 models
alanocallaghan Feb 5, 2025
ea8f3fc
Bump upload V
alanocallaghan Feb 5, 2025
2a27ac5
Title
alanocallaghan Feb 6, 2025
2235700
Make less public
alanocallaghan Feb 7, 2025
424f486
Remove useless jdocs
alanocallaghan Feb 7, 2025
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40 changes: 23 additions & 17 deletions src/main/java/qupath/ext/bioimageio/BioimageIoCommand.java
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Original file line number Diff line number Diff line change
Expand Up @@ -30,6 +30,7 @@

import javax.swing.SwingUtilities;

import javafx.stage.FileChooser;
import org.bytedeco.javacpp.PointerScope;
import org.bytedeco.opencv.global.opencv_core;
import org.bytedeco.opencv.opencv_core.Mat;
Expand Down Expand Up @@ -60,10 +61,11 @@
import javafx.util.StringConverter;
import qupath.bioimageio.spec.BioimageIoSpec;
import qupath.bioimageio.spec.BioimageIoSpec.BioimageIoModel;
import qupath.fx.dialogs.FileChoosers;
import qupath.imagej.tools.IJTools;
import qupath.lib.common.GeneralTools;
import qupath.lib.gui.QuPathGUI;
import qupath.lib.gui.dialogs.Dialogs;
import qupath.fx.dialogs.Dialogs;
import qupath.lib.gui.tools.PaneTools;
import qupath.lib.images.ImageData;
import qupath.lib.images.servers.ColorTransforms;
Expand All @@ -80,6 +82,9 @@
import qupath.opencv.tools.NumpyTools;
import qupath.opencv.tools.OpenCVTools;

import static qupath.bioimageio.spec.BioimageIoSpec.getAxesString;


/**
* Very early exploration of BioImage Model Zoo support within QuPath.
*
Expand All @@ -102,7 +107,8 @@ public class BioimageIoCommand {
public void promptForModel() {

// TODO: In the future consider handling .zip files
var file = Dialogs.promptForFile(title, null, "BioImage Model Zoo spec", "", ".yml", ".yaml");
var file = FileChoosers.promptForFile(title,
new FileChooser.ExtensionFilter("BioImage Model Zoo YAML file", "*.yml", "*.yaml"));
if (file == null)
return;

Expand Down Expand Up @@ -134,14 +140,15 @@ public void promptForModel() {
showLoadPixelClassifier = true;
}
} else {
var fileSaved = Dialogs.promptToSaveFile(title, null, null, "Pixel classifier", ".json");
var fileSaved = FileChoosers.promptToSaveFile(title,
FileChoosers.promptToSaveFile(new FileChooser.ExtensionFilter("Pixel classifier", "*.json")));
if (fileSaved != null) {
PixelClassifiers.writeClassifier(classifier, fileSaved.toPath());
Dialogs.showInfoNotification(title, "Pixel classifier saved to \n" + fileSaved.getAbsolutePath());
}
}


// Offer to show the prediction in the current image, if it's small enough
var imageData = qupath.getImageData();
if (imageData != null) {
Expand All @@ -164,7 +171,8 @@ public void promptForModel() {


} catch (Exception e) {
Dialogs.showErrorMessage(title, e);
Dialogs.showErrorMessage(title, "Error loading or running model. See the log for more details.");
logger.error("Error loading model", e);
}
}

Expand All @@ -189,18 +197,16 @@ static void showDialog(ImageData<?> imageData, String path) throws IOException {

static class DnnBuilderPane {

private QuPathGUI qupath;
private String title;
private final QuPathGUI qupath;
private final String title;

private static Font font = Font.font("Arial");
private static final Font font = Font.font("Arial");

private DnnBuilderPane(QuPathGUI qupath, String title) {
this.qupath = qupath;
this.title = title;
}

private GridPane pane;


private PatchClassifierParams promptForParameters(BioimageIoModel model, ImageData<?> imageData) {

Objects.requireNonNull(imageData, "ImageData must not be null!");
Expand All @@ -213,8 +219,8 @@ private PatchClassifierParams promptForParameters(BioimageIoModel model, ImageDa

int nChannels = params.getInputChannels().size();
int nOutputClasses = params.getOutputClasses().size();
pane = new GridPane();

GridPane pane = new GridPane();
pane.setHgap(5);
pane.setVgap(5);

Expand All @@ -234,8 +240,7 @@ private PatchClassifierParams promptForParameters(BioimageIoModel model, ImageDa
, row++);

addSeparatorRow(pane, row++);



// Handle input channels & their order
addTitleRow(pane, "Input channels", row++);
addDescriptionRow(pane, "The image channels provided as input to the model", row++);
Expand Down Expand Up @@ -307,8 +312,9 @@ private PatchClassifierParams promptForParameters(BioimageIoModel model, ImageDa
int[] shape = output.getShape().getShape();
int[] steps = output.getShape().getShapeStep();
int[] minSize = output.getShape().getShapeMin();
int indX = output.getAxes().toLowerCase().indexOf("x");
int indY = output.getAxes().toLowerCase().indexOf("y");
String outputAxes = getAxesString(output.getAxes()).toLowerCase();
int indX = outputAxes.indexOf("x");
int indY = outputAxes.indexOf("y");
if (indX >= 0 && indY >= 0) {
if (minSize.length > 0) {
width = minSize[indX];
Expand Down
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