Support Nexus in google cardboard. Small bugfix in oculus mobile

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

@@ -84,18 +84,22 @@ public static void verifyStoragePermissions(Activity activity) {
     super.onCreate(savedInstanceState);
 
 	verifyStoragePermissions(this);
+	String externalsd=android.os.Environment.getExternalStorageDirectory().getPath() + "/";
 	//intents
 	android.content.Intent intent = getIntent();
 	
 	String s=intent.getDataString();
-	String uriString="/data/local/tmp/material.ncfg";
-
+	String uriString=externalsd+"material.ncfg";
+	if (s==null)
+			android.util.Log.d("NOMADgvrT","String intent is null");
+	else
+		android.util.Log.d("NOMADgvrT","String intent is <"+ s+">");
 	if (s!=null) {
 		if (s.startsWith("content://")) {
 			try {
 				java.io.InputStream input = getContentResolver().openInputStream(intent.getData());
 				byte[] buffer = new byte[8 * 1024];
-				java.io.FileOutputStream output = new java.io.FileOutputStream("/data/local/tmp/material.ncfg");
+				java.io.FileOutputStream output = new java.io.FileOutputStream(uriString);
 				try{
 					int bytesRead;
 					while((bytesRead = input.read()) != -1){
@@ -106,24 +110,29 @@ public static void verifyStoragePermissions(Activity activity) {
 						output.close();
 					} catch (Exception e) {
 						uriString=null;
+						android.util.Log.d("NOMADgvrT","Exception closing output stream");
 					}
 					try {
 						input.close();
 					} catch (java.io.IOException e) {
 						uriString=null;
+						android.util.Log.d("NOMADgvrT","Exception closing input stream");
 					}
 				}
 			} catch (java.io.IOException e) {
 				uriString=null;
+				android.util.Log.d("NOMADgvrT","Exception saving intent to disk");
 			} 
 		if (uriString!=null)
-			nativeSetConfigFile(uriString);
+			nativeSetConfigFile(uriString, externalsd);
 		} else if (s.startsWith("file://")) {
 			uriString=s.substring(7);
-			nativeSetConfigFile(uriString);
+			nativeSetConfigFile(uriString, externalsd);
 		} else {
 			android.util.Log.d("NOMADgvrT","Unknown protocol in intent:"+ s);
 		}
+	} else { //use default
+		nativeSetConfigFile(externalsd+"Default.ncfg", externalsd);
 	}
 
     // Ensure fullscreen immersion.
@@ -277,5 +286,5 @@ public static void verifyStoragePermissions(Activity activity) {
 
   private native void nativeOnResume(long nativeTreasureHuntRenderer);
 
-  private native void nativeSetConfigFile(String s);
+  private native void nativeSetConfigFile(String s, String e);
 }

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

@@ -21,6 +21,7 @@
 #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
 
 #define JNI_METHOD(return_type, method_name) \
   JNIEXPORT return_type JNICALL              \
@@ -82,8 +83,9 @@ JNI_METHOD(void, nativeOnResume)
 }
 
 JNI_METHOD(void, nativeSetConfigFile)
-(JNIEnv *env, jobject obj, jstring s) {
+(JNIEnv *env, jobject obj, jstring s, jstring e) {
 	configPath = env->GetStringUTFChars(s , NULL ) ;
+	TMPDIR=env->GetStringUTFChars(e , NULL ) ;
 
 }
 

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

@@ -312,31 +312,32 @@ TreasureHuntRenderer::TreasureHuntRenderer(
       gvr_controller_api_(nullptr),
       gvr_viewer_type_(gvr_api_->GetViewerType()) {
 
-	eprintf ("configPath=%d", configPath);
 	if (configPath!=nullptr)
 		eprintf ("configPath=<%s>", configPath);
+	else
+		eprintf ("configPath is null");
 
-	const char *configfile="/storage/emulated/0/Oculus/NOMAD/ViveTDefault.ncfg";
-	//change cwd so that relative paths work
-	if (configPath!=nullptr)
-		configfile=configPath;
-	std::string s(configfile);
+	if (TMPDIR!=nullptr)
+		eprintf ("TMPDIR=<%s>", TMPDIR);
+	else
+		eprintf ("TMPDIR is null");
+	
+	std::string s(configPath);
 	chdir(s.substr(0, s.find_last_of("\\/")).c_str());
 	
-	int r;
 
-	if ((r=loadConfigFile(configfile))<0) {
-		if (-100<r) {
-			eprintf(loadConfigFileErrors[-r]);
+	if ((error=loadConfigFile(configPath))<0) {
+		if (-100<error) {
+			eprintf(loadConfigFileErrors[-error]);
 			eprintf("Config file reading error");
-		} else if (-200<r){
-			eprintf(readAtomsXYZErrors[-r-100]);
+		} else if (-200<error){
+			eprintf(readAtomsXYZErrors[-error-100]);
 			eprintf("XYZ file reading error");
-		} else if (-300<r) {
-			eprintf(readAtomsCubeErrors[-r-200]);
+		} else if (-300<error) {
+			eprintf(readAtomsCubeErrors[-error-200]);
 			eprintf("Cube file reading error");
 		} else {
-			eprintf(readAtomsJsonErrors[-r-300]);
+			eprintf(readAtomsJsonErrors[-error-300]);
 			eprintf("Json reading error");
 		}	
 	}
@@ -365,6 +366,12 @@ TreasureHuntRenderer::~TreasureHuntRenderer() {
 	glDeleteTextures(2, textures);
 }
 
+const char * ErrorsGL[] = {
+	"Failure compiling Unit Cell Shader", //-401
+	"Failure compiling Atom Shader NoTess", //-402;
+
+};
+
 void TreasureHuntRenderer::InitializeGl() {
   gvr_api_->InitializeGl();
 
@@ -382,35 +389,46 @@ glGenTextures(2, textures);
 	//Leave atoms until we check if android 7 has gles 3.2 or if we use the old icosahedron method with no tesselation
 	if (!PrepareUnitCellShader (&UnitCellP, &UnitCellMatrixLoc, &UnitCellColourLoc)) {
 		eprintf("OneTimeInit, failure compiling Unit Cell Shader");
+		error=-401;
 		return ;
 	}
 	
 	//rgh: for now, we don't have any tess-ready phones
 	//if (!PrepareAtomShader(&AtomsP, &AtomMatrixLoc)) {
 		hasTess=false;
-		if (!PrepareAtomShaderNoTess(&AtomsP, &AtomMatrixLoc))
+		if (!PrepareAtomShaderNoTess(&AtomsP, &AtomMatrixLoc)) {
+			error=-402;
 			eprintf ("PrepareAtomShaderNoTess failed");
+		}
 	//};
 
 	//atom texture
 	int e;
 	
 	e=atomTexture(textures[1]);
-	if (e!=GL_NO_ERROR)
+	if (e!=GL_NO_ERROR) {
 		eprintf ("atomTexture error %d", e);
+		error=-403;
+	}
 
 	e=SetupAtoms(&AtomTVAO, &AtomTBuffer);
-	if (e!=GL_NO_ERROR)
+	if (e!=GL_NO_ERROR) {
 		eprintf ("SetupAtoms error %d", e);
+		error=-404;
+	}
 
 	if (!hasTess)
 		e=SetupAtomsNoTess(&AtomVAO, &AtomBuffer, &AtomIndices);
 
-	if (e!=GL_NO_ERROR)
+	if (e!=GL_NO_ERROR) {
 		eprintf ("SetupAtomsNoTess error %d, tess=%d", e, hasTess);
+		error=-405;
+	}
 	e=SetupUnitCell(&UnitCellVAO, &UnitCellBuffer, &UnitCellIndexBuffer);
-	if (e!=GL_NO_ERROR)
+	if (e!=GL_NO_ERROR) {
 		eprintf ("SetupUnitCell error %d", e);
+		error=-406;
+	}
 
   // Because we are using 2X MSAA, we can render to half as many pixels and
   // achieve similar quality.
@@ -525,7 +543,23 @@ if (animateTimesteps) {
 
   // Draw the world.
   frame.BindBuffer(0);
-  glClearColor(0.1f, 0.1f, 0.1f, 0.5f);  // Dark background so text shows up.
+  if (error<0) {
+		if (-100<error) {
+			glClearColor(1.f, 0.f, 0.f, 1.f); 
+		} else if (-200<error){
+			glClearColor(0.f, 1.f, 0.f, 1.f); 
+		} else if (-300<error) {
+			glClearColor(0.f, 0.f, 1.f, 1.f); 
+		} else if (-400<error) {
+			glClearColor(0.f, 1.f, 1.f, 1.f); 		
+		} else {
+			glClearColor(1.f, 0.f, 1.f, 1.f); 
+		}
+  } else {
+	glClearColor(BACKGROUND[0], BACKGROUND[1], BACKGROUND[2], 0.5f);
+  }
+
+    // Dark background so text shows up.
   glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT);
   viewport_list_->GetBufferViewport(0, &scratch_viewport_);
   DrawWorld(left_eye_view, scratch_viewport_);
@@ -623,7 +657,14 @@ void TreasureHuntRenderer::DrawWorld(const gvr::Mat4f& view_matrix,
 glDisable(GL_CULL_FACE);
 modelview_=view_matrix;
 modelview_projection_cube_ = MatrixMul(perspective, modelview_);
-RenderUnitCell(modelview_projection_cube_);
+if(error)
+	return;
+if (has_abc) {
+	RenderUnitCell(modelview_projection_cube_);
+} else {
+	//atom trajectories
+	RenderAtomTrajectories(modelview_projection_cube_);
+}
 
 }
 
@@ -724,6 +765,31 @@ void TreasureHuntRenderer::RenderAtoms(const float *m) //m[16]
 	} // no tess
 }
 
+void TreasureHuntRenderer::RenderAtomTrajectories(const gvr::Mat4f eyeViewProjection)
+{
+int e;
+if (!numAtoms)
+	return;
+gvr::Mat4f trans={1,0,0,UserTranslation[0],
+		0,1,0,UserTranslation[1],
+		0,0,1,UserTranslation[2],
+		0,0,0,1};
+					
+//trans.translate(iPos).rotateX(-90).translate(UserPosition);
+gvr::Mat4f transform = MatrixMul(eyeViewProjection,trans);
+//gvr::Mat4f transform=eyeViewProjection;					
+float t[16];
+for (int i=0;i<4;i++)
+	for (int j=0;j<4;j++)
+		t[j*4+i]=transform.m[i][j];
+glUseProgram(UnitCellP);
+glUniformMatrix4fv(UnitCellMatrixLoc, 1, GL_FALSE, t);
+if ((e = glGetError()) != GL_NO_ERROR)
+	eprintf("Gl error after glUniform4fv 1 RenderAtomTrajectories: %d\n", e);
+RenderAtomTrajectoriesUnitCell();
+RenderAtoms(t);
+}
+
 void TreasureHuntRenderer::RenderAtomTrajectoriesUnitCell()
 {
 	//now trajectories
@@ -743,7 +809,7 @@ glBindVertexArray(AtomTVAO[0]);
 float color[4]={1,0,0,1};
 glUniform4fv(UnitCellColourLoc, 1, color);
 if ((e = glGetError()) != GL_NO_ERROR)
-	eprintf("Gl error after glUniform4fv 2 RenderUnitCell: %d\n", e);
+	eprintf("Gl error after glUniform4fv 2 RenderAtomTrajectoriesUnitCell: %d\n", e);
 //glEnableVertexAttribArray(0);
 //glDisableVertexAttribArray(1);
 
@@ -776,13 +842,10 @@ for (unsigned int i=0;i<atomtrajectories.size();i++) {
 
 void TreasureHuntRenderer::RenderUnitCell(const gvr::Mat4f eyeViewProjection)
 {
-	eprintf ("eyeViewProjection");
-	for (int i=0;i<4;i++)
-		for (int j=0;j<4;j++)
-			eprintf ("%d %d = %f", i, j, eyeViewProjection.m[i][j]);
-	//repetitions[0]=10;
-	//repetitions[1]=10;
-	//repetitions[2]=10;
+	//eprintf ("eyeViewProjection");
+	//for (int i=0;i<4;i++)
+	//	for (int j=0;j<4;j++)
+	//		eprintf ("%d %d = %f", i, j, eyeViewProjection.m[i][j]);
 	eprintf ("RenderUnitCell, has_abc=%d", has_abc);
 	if (!has_abc)
 		return;

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

@@ -162,9 +162,10 @@ bool animateTimesteps=false;
 void RenderAtoms(const float *m);
 void RenderUnitCell(const gvr::Mat4f eyeViewProjection);
 void RenderAtomTrajectoriesUnitCell();
+void RenderAtomTrajectories(const gvr::Mat4f eyeViewProjection);
 float UserTranslation[3]={10,0,0};
 
-
+int error=0;
 };
 
 #endif  // TREASUREHUNT_APP_SRC_MAIN_JNI_TREASUREHUNTRENDERER_H_  // NOLINT

GoogleCardboardAndroid/readme.md

+This repository contains the demos for Google cardboard using GVR Android SDK v1.20.0
+https://github.com/googlevr/gvr-android-sdk
+
+Clone that repository and add the content of this one inside the Samples directory.
+Copy the content of the ../libs directory (happyhttp, rapidjson) and NOMADVRLib into 
+NOMADgvrT/src/main/jni
+
+Enable support for ndk (tested: android-ndk-r10d) in settings.gradle:
+include ':samples:NOMADgvrT'
+
+
+List of directories
+NOMADgvrT: 
+	This program can load prepared molecular dynamics simulations, and is 
+	compatible with the TimestepData OpenVR demo.
+	Ply support is not yet implemented
+	
\ No newline at end of file

NOMADVRLib/ConfigFile.cpp

@@ -128,6 +128,7 @@ int loadConfigFile(const char * f)
 	showTrajectories = false;
 	basisvectorreps=0;
 	numClonedAtoms=0;
+	has_abc=false;
 	for (int i=0;i<3;i++)
 		repetitions[i]=1;
 	for (int i=0;i<3;i++)
@@ -249,6 +250,7 @@ int loadConfigFile(const char * f)
 			if (e<0)
 				return e-100;
 			updateTIMESTEPS (timesteps);
+			//eprintf ("After read of xyzfile, numatoms 0 =%d", numAtoms[0]);
 		}
 		else if (!strcmp(s, "cubefile")) {
 			r=readString(F, s);
@@ -345,9 +347,12 @@ int loadConfigFile(const char * f)
 				solid=new Solid(Solid::Type::Tetrahedron);
 			else
 				return -15;
-		}
-		else {
+		} else if (!strcmp (s, "\x0d")) { //discard windows newline (problem in Sebastian Kokott's phone (?!)
+			continue;
+		} else {
 			eprintf( "Unrecognized parameter %s\n", s);
+			for (int i=0;i<strlen(s);i++)
+				eprintf ("<%d>", s[i]);
 			fclose(F);
 			return -2;
 		}
@@ -381,6 +386,6 @@ int loadConfigFile(const char * f)
 		for (int i=0;i<*numAtoms;i++)
 			atomtrajectories.push_back(i);
 	}
-
+	//eprintf ("Before returning, numatoms 0 =%d", numAtoms[0]);
 	return 0;
-}
+}
\ No newline at end of file

NOMADVRLib/UnitCellShaders.cpp

@@ -5,7 +5,7 @@ const char * const UnitCellShaders [] = {"Unit Cell Renderer",
 	#ifdef WIN32
 	"#version 410\n"
 #else
-	"#version 310 es\n"
+	"#version 300 es\n"
 #endif
 	"uniform mat4 matrix;\n"
 	"layout(location = 0) in vec3 pos;\n"
@@ -18,7 +18,7 @@ const char * const UnitCellShaders [] = {"Unit Cell Renderer",
 	#ifdef WIN32
 	"#version 410\n"
 #else
-	"#version 310 es\n"
+	"#version 300 es\n"
 #endif
 	"uniform lowp vec4 color;\n"
 	"out lowp vec4 outputColor;\n"

NOMADVRLib/atoms.cpp

@@ -18,7 +18,9 @@
 #ifdef WIN32
 const char * TMPDIR="";
 #else
-const char * TMPDIR="/sdcard/Oculus/NOMAD/";
+//const char * TMPDIR="/sdcard/Oculus/NOMAD/";
+const char * TMPDIR;//filled by main
+//="/storage/540E-1AE2/";
 #endif
 
 const char * const atomNames[] =
@@ -204,6 +206,7 @@ int readAtomsXYZ(const char *const file, int **numatoms, int *timesteps, float *
 			continue; //there may be a blank line at the end of the file
 		(*timesteps)++;
 		discardline (f);
+		//eprintf ("Getting atoms, mynumatoms=%d",mynumatoms);
 		mypos.push_back(new float[mynumatoms*4]);
 		mynum.push_back(mynumatoms);
 		discardline (f); //comment
@@ -223,6 +226,7 @@ int readAtomsXYZ(const char *const file, int **numatoms, int *timesteps, float *
 	for (int i=0;i<*timesteps;i++) {
 		(*pos)[i]=mypos[i];
 		(*numatoms)[i]=mynum[i];
+		//eprintf ("Getting atoms, numatoms=%d",(*numatoms)[i]);
 	}
 
 	return 0;

NOMADVRLib/atomsGL.cpp

@@ -13,20 +13,26 @@ GLenum atomTexture(GLuint t)
 {
 	GLenum e;
 	//rgh: scale atoms here
-	for (int i = 0; i < 118; i++)
-		atomColours[i][3] *= atomScaling;
-
+	//in google cardboard, this is called again if the program is running, so leave original or atoms get progresivelly smaller!
+	float *a=new float[118*4];
+	for (int i = 0; i < 118; i++) {
+		a[i*4+0]=atomColours[i][0];
+		a[i*4+1]=atomColours[i][1];
+		a[i*4+2]=atomColours[i][2];
+		a[i*4+3]=atomColours[i][3] * atomScaling;
+	}
 	glBindTexture(GL_TEXTURE_2D, t); //atom texture
 	glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_MIN_FILTER, GL_NEAREST);
 	glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_MAG_FILTER, GL_NEAREST);