From 2fe6ea0cb010b7d688eef69277878300ce1b35fb Mon Sep 17 00:00:00 2001
From: Kimberly Meechan <kimberly.meechan@embl.de>
Date: Fri, 19 Feb 2021 16:45:23 +0000
Subject: [PATCH] more rough scripts

---
 src/test/java/develop/TestDisplayAll.java | 85 +++++++++++++++++++++++
 1 file changed, 85 insertions(+)
 create mode 100644 src/test/java/develop/TestDisplayAll.java

diff --git a/src/test/java/develop/TestDisplayAll.java b/src/test/java/develop/TestDisplayAll.java
new file mode 100644
index 0000000..4c7efb5
--- /dev/null
+++ b/src/test/java/develop/TestDisplayAll.java
@@ -0,0 +1,85 @@
+package develop;
+
+import bdv.util.BdvFunctions;
+import bdv.util.BdvOptions;
+import bdv.util.BdvStackSource;
+import com.google.gson.Gson;
+import de.embl.cba.bdv.utils.sources.LazySpimSource;
+import de.embl.schwab.crosshair.PlaneManager;
+import de.embl.schwab.crosshair.io.SettingsToSave;
+import de.embl.schwab.crosshair.utils.GeometryUtils;
+import ij3d.Content;
+import ij3d.Image3DUniverse;
+import itc.converters.AffineTransform3DToFlatString;
+import itc.converters.ElastixAffine3DToAffineTransform3D;
+import itc.converters.ElastixEuler3DToAffineTransform3D;
+import itc.transforms.elastix.ElastixAffineTransform3D;
+import itc.transforms.elastix.ElastixEulerTransform3D;
+import itc.transforms.elastix.ElastixTransform;
+import itc.utilities.TransformUtils;
+import net.imglib2.realtransform.AffineTransform3D;
+import net.imglib2.type.numeric.ARGBType;
+import org.scijava.vecmath.Vector3d;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
+
+import static de.embl.cba.tables.ij3d.UniverseUtils.addSourceToUniverse;
+
+public class TestDisplayAll {
+
+    public static void main( String[] args ) {
+
+//        final LazySpimSource afterCrop = new LazySpimSource("after_crop", "Z:\\schwab\\microCT\\PLATY_K1_2K_1um_registration\\cropped_data\\crop_after_record\\after_crop.xml");
+        final LazySpimSource beforeCrop = new LazySpimSource("before_crop", "Z:\\schwab\\microCT\\PLATY_K1_2K_1um_registration\\cropped_data\\crop_before_record\\before_crop.xml");
+        final LazySpimSource elastix = new LazySpimSource("after_elastix", "Z:\\schwab\\microCT\\PLATY_K1_2K_1um_registration\\elastix_recorded_after_to_before_cropped\\euler\\transformed.xml");
+        String beforePlanes = "Z:\\schwab\\microCT\\PLATY_K1_2K_1um_registration\\cropped_data\\transformed_before_planes.json";
+        String afterPlanes = "Z:\\schwab\\microCT\\PLATY_K1_2K_1um_registration\\elastix_recorded_after_to_before_cropped\\euler\\fitted_planes.json";
+
+
+        BdvStackSource bdvStackSource = BdvFunctions.show(beforeCrop, 1);
+        BdvFunctions.show(elastix, 1, BdvOptions.options().addTo(bdvStackSource));
+        bdvStackSource.setDisplayRange(0, 255);
+
+        Image3DUniverse universe = new Image3DUniverse();
+        universe.show();
+
+
+        // Set to arbitrary colour
+        ARGBType colour =  new ARGBType( ARGBType.rgba( 0, 0, 0, 0 ) );
+        Content beforeContent = addSourceToUniverse(universe, beforeCrop, 300 * 300 * 300, Content.VOLUME, colour, 0.7f, 0, 255 );
+        Content afterContent = addSourceToUniverse(universe, elastix, 300 * 300 * 300, Content.VOLUME, colour, 0.7f, 0, 255 );
+        // Reset colour to default for 3D viewer
+        beforeContent.setColor(null);
+        afterContent.setColor(null);
+
+        PlaneManager planeManager = new PlaneManager(bdvStackSource, universe, beforeContent);
+
+        Gson gson = new Gson();
+        FileReader fileReader = null;
+        try {
+            fileReader = new FileReader(beforePlanes);
+            SettingsToSave beforeSettings = gson.fromJson(fileReader, SettingsToSave.class);
+            fileReader = new FileReader(afterPlanes);
+            SettingsToSave afterSettings = gson.fromJson(fileReader, SettingsToSave.class);
+            Vector3d beforeNormal = beforeSettings.getPlaneNormals().get("target");
+            Vector3d afterNormal = afterSettings.getPlaneNormals().get("block");
+            planeManager.updatePlane(beforeNormal,  beforeSettings.getPlanePoints().get("target"), "before_target");
+            planeManager.updatePlane(afterNormal,  afterSettings.getPlanePoints().get("block"), "after_block");
+
+            double angle = GeometryUtils.convertToDegrees(beforeNormal.angle(afterNormal));
+            if (angle > 90) {
+                angle = 180 - angle;
+            }
+            System.out.println(angle);
+
+        } catch (FileNotFoundException e) {
+            e.printStackTrace();
+        }
+
+
+
+    }
+}