Update dependencies

Fix variable name changes
BIOP · Sep 19, 2024 · 49fec1b · 49fec1b
1 parent 8a0fa48
commit 49fec1b
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Showing 5 changed files with 9 additions and 9 deletions.
diff --git a/pom.xml b/pom.xml
@@ -108,8 +108,8 @@
 
 		<!-- bdv playground related dependencies -->
 		<bigdataviewer-playground.version>0.10.5</bigdataviewer-playground.version>
-		<bigdataviewer-image-loaders.version>0.8.2</bigdataviewer-image-loaders.version>
-		<bigdataviewer-biop-tools.version>0.10.5</bigdataviewer-biop-tools.version>
+		<bigdataviewer-image-loaders.version>0.8.6</bigdataviewer-image-loaders.version>
+		<bigdataviewer-biop-tools.version>0.10.6</bigdataviewer-biop-tools.version>
 		<bigdataviewer-selector.version>0.2.7</bigdataviewer-selector.version>
 
 		<!-- maths -->

diff --git a/src/main/java/ch/epfl/biop/atlas/aligner/command/ImportSlicesFromQuPathCommand.java b/src/main/java/ch/epfl/biop/atlas/aligner/command/ImportSlicesFromQuPathCommand.java
@@ -50,7 +50,7 @@ public void run() {
             }
             AbstractSpimData<?> spimdata = (AbstractSpimData<?>) command_service
                     .run(CreateBdvDatasetQuPathCommand.class,true,
-                            "quPathProject", qupath_project,
+                            "qupath_project", qupath_project,
                             "unit", "MILLIMETER").get().getOutput("spimData");
             SourceAndConverter<?>[] sacs =
                     sac_service.getSourceAndConverterFromSpimdata(spimdata)

diff --git a/src/main/java/ch/epfl/biop/atlas/aligner/command/RegisterSlicesElastixAffineCommand.java b/src/main/java/ch/epfl/biop/atlas/aligner/command/RegisterSlicesElastixAffineCommand.java
@@ -36,10 +36,10 @@ public void runValidated() {
         ElastixHelper.checkOrSetLocal(this.mp.getContext());
 
         Map<String, Object> parameters = new HashMap<>();
-        parameters.put("showImagePlusRegistrationResult", show_imageplus_registration_result);
+        parameters.put("show_image_registration", show_imageplus_registration_result);
         parameters.put("background_offset_value_moving", background_offset_value_moving);
         parameters.put("background_offset_value_fixed", background_offset_value_fixed);
-        parameters.put("pxSizeInCurrentUnit", pixel_size_micrometer/1000.0);
+        parameters.put("px_size_in_current_unit", pixel_size_micrometer/1000.0);
 
         mp.registerSelectedSlices(Elastix2DAffineRegistration.class,
                 getFixedFilter(),

diff --git a/src/main/java/ch/epfl/biop/atlas/aligner/command/RegisterSlicesElastixSplineCommand.java b/src/main/java/ch/epfl/biop/atlas/aligner/command/RegisterSlicesElastixSplineCommand.java
@@ -46,11 +46,11 @@ public void runValidated() {
 
         //mp.registerElastixSpline(getFixedFilter(), getMovingFilter(), nbControlPointsX, showIJ1Result);
         Map<String, Object> parameters = new HashMap<>();
-        parameters.put("showImagePlusRegistrationResult", show_imageplus_registration_result);
-        parameters.put("nbControlPointsX", nb_control_points_x);
+        parameters.put("show_image_registration", show_imageplus_registration_result);
+        parameters.put("num_ctrl_points_x", nb_control_points_x);
         parameters.put("background_offset_value_moving", background_offset_value_moving);
         parameters.put("background_offset_value_fixed", background_offset_value_fixed);
-        parameters.put("pxSizeInCurrentUnit", pixel_size_micrometer/1000.0);
+        parameters.put("px_size_in_current_unit", pixel_size_micrometer/1000.0);
 
         mp.registerSelectedSlices(Elastix2DSplineRegistration.class,
                 getFixedFilter(),

diff --git a/src/test/java/ch/epfl/biop/abba/pluginexample/py/TestExternalRegistrationPlugin.java b/src/test/java/ch/epfl/biop/abba/pluginexample/py/TestExternalRegistrationPlugin.java
@@ -57,7 +57,7 @@ public static void main (String... args) throws Error, Exception{
         ImagePlus demoSlice = IJ.openImage("src/test/resources/demoSlice.tif");
         demoSlice.show();
 
-        ij.command().run(SourceFromImagePlusCommand.class, true, "imagePlus", demoSlice).get();
+        ij.command().run(SourceFromImagePlusCommand.class, true, "image", demoSlice).get();
 
         SourceAndConverter[] sac = ij.convert().convert(demoSlice.getTitle(), SourceAndConverter[].class);