Add gitignore

Add license to Google Cardboard
Add scaling to google cardboard.

.gitignore

+Thumbs.db
\ No newline at end of file

GoogleCardboardAndroid/NOMADgvrT/build.gradle

@@ -6,12 +6,13 @@ model {
         buildToolsVersion = "25.0.2"
 
         defaultConfig.with {
-            applicationId = "com.google.vr.ndk.samples.treasurehunt"
+            applicationId = "com.lrz.nomadvr"
             minSdkVersion.apiLevel = 19
             targetSdkVersion.apiLevel = 23
-            versionCode = 1
-            versionName = "1.0"
+            versionCode = 8
+            versionName = "1.2"
         }
+
     }
     android.buildTypes {
         release {

GoogleCardboardAndroid/NOMADgvrT/src/main/java/com/google/vr/ndk/samples/treasurehunt/Filepath.java

+/*Uses code from Stackoverflow which uses the MIT license and the CC BY-SA 3.0*/
+/*These licenses are compatible with Apache 2.0*/
+
+/*
+# Copyright 2016-2018 The NOMAD Developers Group
+ #
+ # Licensed under the Apache License, Version 2.0 (the "License");
+ # you may not use this file except in compliance with the License.
+ # You may obtain a copy of the License at
+ #
+ #     http://www.apache.org/licenses/LICENSE-2.0
+ #
+ # Unless required by applicable law or agreed to in writing, software
+ # distributed under the License is distributed on an "AS IS" BASIS,
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ # See the License for the specific language governing permissions and
+ # limitations under the License.
+*/
+
 package com.google.vr.ndk.samples.treasurehunt;
 
 //https://stackoverflow.com/questions/3401579/get-filename-and-path-from-uri-from-mediastore/7265235#7265235

GoogleCardboardAndroid/NOMADgvrT/src/main/java/com/google/vr/ndk/samples/treasurehunt/MainActivity.java

+/*Uses code from Stackoverflow which uses the MIT license and the CC BY-SA 3.0*/
+/*These licenses are compatible with Apache 2.0*/
+
+/*
+# Copyright 2016-2018 The NOMAD Developers Group
+*/
+
 /* Copyright 2017 Google Inc. All rights reserved.
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
@@ -50,6 +57,18 @@ public class MainActivity extends Activity {
     System.loadLibrary("treasurehunt_jni");
   }
 
+
+@Override
+public boolean onKeyUp(int keyCode, KeyEvent event) {
+	android.util.Log.d("NOMADgvrT","onKeyUp, keycode="+keyCode);
+	nativekeyPress(nativeTreasureHuntRenderer, keyCode);
+	return true;
+//Matthias Scheffler Bluetooth Controller, in GAME MODE @->B
+//KeyEvent.BUTTON_X, KeyEvent.BUTTON_Y, KeyEvent.BUTTON_A, KeyEvent.BUTTON_B
+
+}
+
+
 //http://stackoverflow.com/questions/8854359/exception-open-failed-eacces-permission-denied-on-android
 // Storage Permissions
 private static final int REQUEST_EXTERNAL_STORAGE = 1;
@@ -112,12 +131,6 @@ public static void verifyStoragePermissions(Activity activity) {
 	verifyStoragePermissions(this);
 
 //http://stackoverflow.com/questions/36557879/how-to-use-native-android-file-open-dialog
-/////////
-        //setContentView(R.layout.activity_main);
-
- 
-///////////
-
 
 
 	String externalsd=android.os.Environment.getExternalStorageDirectory().getPath() + "/";
@@ -337,24 +350,5 @@ public static void verifyStoragePermissions(Activity activity) {
   private native void nativeSetConfigFile(String s, String e);
   private native void nativeLoadConfigFile(long nativeTreasureHuntRenderer);
 
-  public void DisplayMessage (final String s)
-  {
-//http://stackoverflow.com/questions/3875184/cant-create-handler-inside-thread-that-has-not-called-looper-prepare
-//rgh: this hangs, need to investigate
-	new Thread()
-	{
-	    public void run()
-	    {
-		MainActivity.this.runOnUiThread(new Runnable()
-		{
-		    public void run()
-		    {
-			android.widget.Toast toast = android.widget.Toast.makeText(MainActivity.this.getApplicationContext(), s,
-				android.widget.Toast.LENGTH_LONG);		        
-		    }
-		});
-	    }
-	}.start();
-
-  }
+  private native void nativekeyPress(long nativeTreasureHuntRenderer, int k);
 }

GoogleCardboardAndroid/NOMADgvrT/src/main/jni/treasure_hunt_jni.cc

+/*Uses code from Stackoverflow which uses the MIT license and the CC BY-SA 3.0*/
+/*These licenses are compatible with Apache 2.0*/
+
+/*
+# Copyright 2016-2018 The NOMAD Developers Group
+*/
+
 /* Copyright 2017 Google Inc. All rights reserved.
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
@@ -18,12 +25,11 @@
 
 #include <memory>
 
-#include "treasure_hunt_renderer.h"  // NOLINT
 #include "vr/gvr/capi/include/gvr.h"
 #include "vr/gvr/capi/include/gvr_audio.h"
 #include "NOMADVRLib/atoms.hpp" //for TMPDIR
 
-#include "treasure_hunt_jni.h"
+#include "treasure_hunt_renderer.h" 
 
 #define JNI_METHOD(return_type, method_name) \
   JNIEXPORT return_type JNICALL              \
@@ -56,16 +62,6 @@ inline TreasureHuntRenderer *native(jlong ptr) {
     genv->CallStaticVoidMethod(jc, mid, jurl, jpath);	
 }*/
 
-void DisplayMessage (const char *s)
-{
-	JNIEnv *env;
-    	javaVM->AttachCurrentThread(&env, nullptr);
-	jstring js = env->NewStringUTF(s);
-	jclass cls = env->GetObjectClass(jo);
-	jmethodID mid = env->GetMethodID(cls, "DisplayMessage", "(Ljava/lang/String;)V");
-	env->CallVoidMethod(jo, mid, js);
-} 
-
 extern "C" {
 
 JNI_METHOD(jlong, nativeCreateRenderer)

GoogleCardboardAndroid/NOMADgvrT/src/main/jni/treasure_hunt_jni.h

-//void GetUrl (const char *url, const char *path);
-void DisplayMessage (const char *s);

GoogleCardboardAndroid/NOMADgvrT/src/main/jni/treasure_hunt_renderer.cc

+/*Uses code from Stackoverflow which uses the MIT license and the CC BY-SA 3.0*/
+/*These licenses are compatible with Apache 2.0*/
+
+/*
+# Copyright 2016-2018 The NOMAD Developers Group
+*/
 /* Copyright 2017 Google Inc. All rights reserved.
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
@@ -16,7 +22,6 @@
 #include <unistd.h>
 
 #include "treasure_hunt_renderer.h"  // NOLINT
-#include "treasure_hunt_jni.h"
 
 #include <android/log.h>
 #include <assert.h>
@@ -60,8 +65,6 @@ void eprintf( const char *fmt, ... )
 	if (*fmt=='\0')
 		LOGD("Empty format");
 	LOGD("<%s>", buffer);
-	//rgh: does not work yet
-	//DisplayMessage(buffer);
 }
 
 
@@ -99,6 +102,11 @@ gvr::Mat4f ScalingMatrix (float v[3])
 return ScalingMatrix(v[0], v[1], v[2]);
 }
 
+gvr::Mat4f ScalingMatrix (float s)
+{
+return ScalingMatrix(s,s,s);
+}
+
 //static const float kZNear = 1.0f;
 //static const float kZFar = 100.0f;
 static const float kZNear = 0.01f;
@@ -587,7 +595,7 @@ glGenTextures(2+ZLAYERS, textDepthPeeling);
 				plyfiles[p % ISOS]);
 			gvr::Mat4f trans;
 			gvr::Mat4f matFinal, matcubetrans, mvs, sc, sctrans;
-//rotateX(-90)
+
 		if (voxelSize[0]!=-1) {
 			mvs=ScalingMatrix(scaling/(float)voxelSize[0], scaling/(float)voxelSize[1],
 				scaling/(float)voxelSize[2]);
@@ -603,19 +611,12 @@ glGenTextures(2+ZLAYERS, textDepthPeeling);
 			matFinal=MatrixMul(matFinal,sc);
 			matFinal=MatrixMul(matFinal,mvs);
 		} else {
-			/*trans.m[0][0]=1;trans.m[0][1]=0;trans.m[0][2]=0; trans.m[0][3]=0;
-			trans.m[1][0]=0;trans.m[1][1]=0;trans.m[1][2]=1;trans.m[1][3]=0;
-			trans.m[2][0]=0;trans.m[2][1]=-1;trans.m[2][2]=0; trans.m[2][3]=0;
-			trans.m[3][0]=0;trans.m[3][1]=0;trans.m[3][2]=0; trans.m[3][3]=1;*/
-
 			for (int i=0;i<4;i++)
 				for(int j=0;j<4;j++)
 					matFinal.m[i][j]=(i==j);
 			for (int i=0;i<3;i++)
 				matFinal.m[i][3]=translations[p%ISOS][i];
 
-			//matFinal=MatrixMul(trans, matFinal);
-
 			trans.m[0][0]=scaling;trans.m[0][1]=0;trans.m[0][2]=0; trans.m[0][3]=0;
 			trans.m[1][0]=0;trans.m[1][1]=scaling;trans.m[1][2]=0;trans.m[1][3]=0; 
 			trans.m[2][0]=0;trans.m[2][1]=0;trans.m[2][2]=scaling; trans.m[2][3]=0;
@@ -1055,10 +1056,11 @@ void TreasureHuntRenderer::RenderAtomTrajectories(const gvr::Mat4f eyeViewProjec
 int e;
 if (!numAtoms)
 	return;
-gvr::Mat4f trans=TranslationMatrix (UserTranslation[0], UserTranslation[1], UserTranslation[2]);
+gvr::Mat4f sc=ScalingMatrix(scaling);
+gvr::Mat4f trans=TranslationMatrix (UserTranslation[0]/scaling, UserTranslation[1]/scaling, UserTranslation[2]/scaling);
 const gvr::Mat4f rot={.m={1,0,0,0, 	0,0,1,0,	0,-1,0,0,	0,0,0,1}};					
 //trans.translate(iPos).rotateX(-90).translate(UserPosition);
-gvr::Mat4f transform = MatrixMul(eyeViewProjection, MatrixMul(trans,rot));
+gvr::Mat4f transform = MatrixMul(eyeViewProjection, MatrixMul(sc, MatrixMul(trans,rot)));
 //gvr::Mat4f transform=eyeViewProjection;					
 float t[16];
 for (int i=0;i<4;i++)
@@ -1095,6 +1097,8 @@ if ((e = glGetError()) != GL_NO_ERROR)
 //glDisableVertexAttribArray(1);
 
 //LOG("atomtrajectories.size()=%d", atomtrajectories.size());
+//rgh FIXME, old code which does not work with large atom sets!
+
 glBindBuffer(GL_ARRAY_BUFFER, AtomTBuffer[0]);
 	if ((e = glGetError()) != GL_NO_ERROR)
 		eprintf("3 Gl error RenderAtomTrajectoriesUnitCell: %d\n", e);
@@ -1135,6 +1139,7 @@ void TreasureHuntRenderer::RenderUnitCell(const gvr::Mat4f eyeViewProjection)
 	int e;
 	
 	int p[3];
+	gvr::Mat4f sc=ScalingMatrix(scaling);
 	for (p[0]=0;p[0]<repetitions[0];(p[0])++)
 		for (p[1]=0;p[1]<repetitions[1];(p[1])++)
 			for (p[2]=0;p[2]<repetitions[2];(p[2])++)
@@ -1145,10 +1150,11 @@ void TreasureHuntRenderer::RenderUnitCell(const gvr::Mat4f eyeViewProjection)
 						0,1,0,delta[1]+UserTranslation[1],
 						0,0,1,delta[2]+UserTranslation[2],
 						0,0,0,1};*/
-gvr::Mat4f trans=TranslationMatrix (UserTranslation[0], UserTranslation[1], UserTranslation[2]);
+gvr::Mat4f trans=TranslationMatrix (delta[0]+UserTranslation[0]/scaling, delta[2]+UserTranslation[1]/scaling, 
+	-delta[1]+UserTranslation[2]/scaling);
 const gvr::Mat4f rot={.m={1,0,0,0, 	0,0,1,0,	0,-1,0,0,	0,0,0,1}};					
 //trans.translate(iPos).rotateX(-90).translate(UserPosition);
-gvr::Mat4f transform = MatrixMul(eyeViewProjection, MatrixMul(trans,rot));					
+gvr::Mat4f transform = MatrixMul(eyeViewProjection, MatrixMul(sc, MatrixMul(trans,rot)));					
 
 
 
@@ -1161,26 +1167,28 @@ gvr::Mat4f transform = MatrixMul(eyeViewProjection, MatrixMul(trans,rot));
 					glUseProgram(UnitCellP);
 					glUniformMatrix4fv(UnitCellMatrixLoc, 1, GL_FALSE, t);
 					if ((e = glGetError()) != GL_NO_ERROR)
-						eprintf("Gl error after glUniform4fv 1 RenderUnitCell: %d\n", e);	
-					glUniform4fv(UnitCellColourLoc, 1, unitcellcolour);
-					if ((e = glGetError()) != GL_NO_ERROR)
-						eprintf("Gl error after glUniform4fv 2 RenderUnitCell: %d\n", e);
-					glBindVertexArray(UnitCellVAO);
-	glBindBuffer(GL_ELEMENT_ARRAY_BUFFER, UnitCellIndexBuffer);
-	if ((e = glGetError()) != GL_NO_ERROR)
-		eprintf("1 Gl error RenderAtom timestep =%d: %d\n", currentSet, e);
-	glBindBuffer(GL_ARRAY_BUFFER, UnitCellBuffer);
-	glVertexAttribPointer(0, 3, GL_FLOAT, GL_FALSE, 3 * sizeof(float), (const void *)(0));
-	glEnableVertexAttribArray(0);
-	glDisableVertexAttribArray(1);
-	glDisableVertexAttribArray(2);
-	glDisableVertexAttribArray(3);
-					if ((e = glGetError()) != GL_NO_ERROR)
-						eprintf("Gl error after glBindVertexArray RenderUnitCell: %d\n", e);
-					glDrawElements(GL_LINES, 24, GL_UNSIGNED_INT, 0);
-					//glDrawElements(GL_TRIANGLES, 24, GL_UNSIGNED_INT, 0);
-					if ((e = glGetError()) != GL_NO_ERROR)
-						eprintf("Gl error after RenderUnitCell: %d\n", e);
+						eprintf("Gl error after glUniform4fv 1 RenderUnitCell: %d\n", e);
+					if (displayunitcell) {
+						glUniform4fv(UnitCellColourLoc, 1, unitcellcolour);
+						if ((e = glGetError()) != GL_NO_ERROR)
+							eprintf("Gl error after glUniform4fv 2 RenderUnitCell: %d\n", e);
+						glBindVertexArray(UnitCellVAO);
+		glBindBuffer(GL_ELEMENT_ARRAY_BUFFER, UnitCellIndexBuffer);
+		if ((e = glGetError()) != GL_NO_ERROR)
+			eprintf("1 Gl error RenderAtom timestep =%d: %d\n", currentSet, e);
+		glBindBuffer(GL_ARRAY_BUFFER, UnitCellBuffer);
+		glVertexAttribPointer(0, 3, GL_FLOAT, GL_FALSE, 3 * sizeof(float), (const void *)(0));
+		glEnableVertexAttribArray(0);
+		glDisableVertexAttribArray(1);
+		glDisableVertexAttribArray(2);
+		glDisableVertexAttribArray(3);
+						if ((e = glGetError()) != GL_NO_ERROR)
+							eprintf("Gl error after glBindVertexArray RenderUnitCell: %d\n", e);
+						glDrawElements(GL_LINES, 24, GL_UNSIGNED_INT, 0);
+						//glDrawElements(GL_TRIANGLES, 24, GL_UNSIGNED_INT, 0);
+						if ((e = glGetError()) != GL_NO_ERROR)
+							eprintf("Gl error after RenderUnitCell: %d\n", e);
+					}
 					//atom trajectories
 					RenderAtomTrajectoriesUnitCell();
 					RenderAtoms(t);

GoogleCardboardAndroid/NOMADgvrT/src/main/jni/treasure_hunt_renderer.h

+
+
 /* Copyright 2017 Google Inc. All rights reserved.
  *
  * Licensed under the Apache License, Version 2.0 (the "License");