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  • hierarchical clustering with gene expression matrix in python

    - by user248237
    how can I do a hierarchical clustering (in this case for gene expression data) in Python in a way that shows the matrix of gene expression values along with the dendrogram? What I mean is like the example here: http://www.mathworks.cn/access/helpdesk/help/toolbox/bioinfo/ug/a1060813239b1.html shown after bullet point 6 (Figure 1), where the dendrogram is plotted to the left of the gene expression matrix, where the rows have been reordered to reflect the clustering. How can I do this in Python using numpy/scipy or other tools? Also, is it computationally practical to do this with a matrix of about 11,000 genes, using euclidean distance as a metric? thanks.

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  • Passing Boost uBLAS matrices to OpenGL shader

    - by AJM
    I'm writing an OpenGL program where I compute my own matrices and pass them to shaders. I want to use Boost's uBLAS library for the matrices, but I have little idea how to get a uBLAS matrix into OpenGL's shader uniform functions. matrix<GLfloat, column_major> projection(4, 4); // Fill matrix ... GLuint projectionU = glGetUniformLocation(shaderProgram, "projection"); glUniformMatrix4fv(projectionU, 1, 0, (GLfloat *)... Um ...); Trying to cast the matrix to a GLfloat pointer causes an invalid cast error on compile.

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  • Matrix multiplication in java (RE-POST)

    - by Chapax
    Apologies for the re-post; the earlier time I'd posted I did not have all the details. My colleague, who quit the firm was a C# programmer, was forced to write Java code that involved (large, dense) matrix multiplication. He's coded his own DataTable class in Java, in order to be able to a) create indexes to sort and join with other DataTables b) do matrix multiplication. The code in its current form is NOT maintainable/extensible. I want to clean up the code, and thought using something like R within Java will help me focus on business logic rather than sorting, joining, matrix multiplication, etc. Plus, I'm very new to the concept of DataTable; I just want to replace the DataTable with 2D arrays, and let R handle the rest. (I currently do not know how to join 2 large datasets in java very efficiently Please let me know what you think. Also, are there any simple examples that I can take a look at?

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  • Performance question: Inverting an array of pointers in-place vs array of values

    - by Anders
    The background for asking this question is that I am solving a linearized equation system (Ax=b), where A is a matrix (typically of dimension less than 100x100) and x and b are vectors. I am using a direct method, meaning that I first invert A, then find the solution by x=A^(-1)b. This step is repated in an iterative process until convergence. The way I'm doing it now, using a matrix library (MTL4): For every iteration I copy all coeffiecients of A (values) in to the matrix object, then invert. This the easiest and safest option. Using an array of pointers instead: For my particular case, the coefficients of A happen to be updated between each iteration. These coefficients are stored in different variables (some are arrays, some are not). Would there be a potential for performance gain if I set up A as an array containing pointers to these coefficient variables, then inverting A in-place? The nice thing about the last option is that once I have set up the pointers in A before the first iteration, I would not need to copy any values between successive iterations. The values which are pointed to in A would automatically be updated between iterations. So the performance question boils down to this, as I see it: - The matrix inversion process takes roughly the same amount of time, assuming de-referencing of pointers is non-expensive. - The array of pointers does not need the extra memory for matrix A containing values. - The array of pointers option does not have to copy all NxN values of A between each iteration. - The values that are pointed to the array of pointers option are generally NOT ordered in memory. Hopefully, all values lie relatively close in memory, but *A[0][1] is generally not next to *A[0][0] etc. Any comments to this? Will the last remark affect performance negatively, thus weighing up for the positive performance effects?

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  • Understanding The Convolution Matrix

    - by Ryan Naddy
    I am learning about the Convolution Matrix, and I understand how they work, but I don't understand how to know before hand what the output of a Matrix will look like. For example lets say I want to add a blur to an image, I could guess 10,000+ different combinations of numbers before I get the correct one. I do know though that this formula will give me a blur effect, but I have no idea why. float[] sharpen = new float[] { 1/9f, 1/9f, 1/9f, 1/9f, 1/9f, 1/9f, 1/9f, 1/9f, 1/9f }; Can anyone either explain to me how this works or point me to some article, that explains this? I would like to know before hand what a possible output of the matrix will be without guessing. Basically I would like to know why do we put that number in the filed, and why not some other number?

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  • Multiplying two matrices from two text files with unknown dimensions

    - by wes schwertner
    This is my first post here. I've been working on this c++ question for a while now and have gotten nowhere. Maybe you guys can give me some hints to get me started. My program has to read two .txt files each containing one matrix. Then it has to multiply them and output it to another .txt file. My confusion here though is how the .txt files are setup and how to get the dimensions. Here is an example of matrix 1.txt. #ivalue #jvalue value 1 1 1.0 2 2 1 The dimension of the matrix is 2x2. 1.0 0 0 1 Before I can start multiplying these matrices I need to get the i and j value from the text file. The only way I have found out to do this is int main() { ifstream file("a.txt"); int numcol; float col; for(int x=0; x<3;x++) { file>>col; cout<<col; if(x==1) //grabs the number of columns numcol=col; } cout<<numcol; } The problem is I don't know how to get to the second line to read the number of rows. And on top of that I don't think this will give me accurate results for other matrices files. Let me know if anything is unclear. UPDATE Thanks! I got getline to work correctly. But now I am running into another problem. In matrix B it is setup like: #ivalue #jvalue Value 1 1 0.1 1 2 0.2 2 1 0.3 2 2 0.4 I need to let the program know that it needs to go down 4 lines, maybe even more (The matrices dimensions are unknown. My matrix B example is a 2x2, but it could be a 20x20). I have a while(!file.eof()) loop my program to let it loop until the end of file. I know I need a dynamic array for multiplying, but would I need one here also? #include <iostream> #include <fstream> using namespace std; int main() { ifstream file("a.txt"); //reads matrix A while(!file.eof()) { int temp; int numcol; string numrow; float row; float col; for(int x=0; x<3;x++) { file>>col; if(x==1) { numcol=col; //number of columns } } string test; getline(file, test); //next line to get rows for(int x=0; x<3; x++) { file>>test; if(x==1) { numrow=test; //sets number of rows } } cout<<numrow; cout<<numcol<<endl; } ifstream file1("b.txt"); //reads matrix 2 while(!file1.eof()) { int temp1; int numcol1; string numrow1; float row1; float col1; for(int x=0; x<2;x++) { file1>>col1; if(x==1) numcol1=col1; //sets number of columns } string test1; getline(file1, test1); //In matrix B there are four rows. getline(file1, test1); //These getlines go down a row. getline(file1, test1); //Need help here. for(int x=0; x<2; x++) { file1>>test1; if(x==1) numrow1=test1; } cout<<numrow1; cout<<numcol1<<endl; } }

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  • Matlab: Randomize and Split

    - by Null-Hypothesis
    I have following data matrix in Matlab, I am trying to actually split this into multiple segments by passing a variable to a matlab function. But before splitting I would like to shuffle the matrix. The size of my matrix is 150X4 s.data 5.1000 3.5000 1.4000 0.2000 4.9000 3.0000 1.4000 0.2000 4.7000 3.2000 1.3000 0.2000 4.6000 3.1000 1.5000 0.2000 5.0000 3.6000 1.4000 0.2000 .. s = data: [150x4 double] labels: [150x1 double] Coming from R environment I find MatLab is very strange. Initially I thought the columns in matrix has a relationshop like in a R dataframe but thats wrong in my assumption.

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  • C++ template typedef

    - by Notinlist
    I have a class template<size_t N, size_t M> class Matrix { // .... }; I want to make a typedef which creates a Vector (column vector) which is equivalent to a Matrix with sizes N and 1. Something like that: typedef Matrix<N,1> Vector<N>; Which produces compile error. The following creates something similar, but not exactly what I want: template <int N> class Vector: public Matrix<N,1> { }; Is there a solution or a not too expensive workaround / best-practice for it? Thanks in advance!

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  • How can i use the Orientation correct for images

    - by user3578109
    I´m learning android/java by myself @the moment and i have a problem with a part of my app i´m learning on. I made the code with help of the www and my problem is that if i open an image from the gallery it´s send to the edit activity but in the activity pictures what are made in portrait mode are displayed always wrong (90° to the right side).... The codes are Matrix private Bitmap rotateBitmapToOrientation(Bitmap b, int orientation){ Matrix matrix = new Matrix(); matrix.postRotate(orientation); Canvas offscreenCanvas = new Canvas(); offscreenCanvas.drawBitmap(b, matrix, null); return b; } and the other one @Override protected void onActivityResult(int requestCode, int resultCode, Intent data) { super.onActivityResult(requestCode, resultCode, data); switch (requestCode) { case PICK_IMAGE_FROM_GALLERY: { if (resultCode == RESULT_OK) { Log.d(TAG, "Got Picture!"); Log.d(TAG,"File type - " + data.getType()); Uri photoUri = data.getData(); if (photoUri != null) { try { String[] filePathColumn = {MediaStore.Images.Media.DATA}; String[] orientationColumn = {MediaStore.Images.Media.ORIENTATION}; int orientation = -1; Cursor cursor = getContentResolver().query(photoUri, filePathColumn, null, null, null); cursor.moveToFirst(); int columnIndex = cursor.getColumnIndex(filePathColumn[0]); String filePath = cursor.getString(columnIndex); cursor.close(); cursor = getContentResolver().query(photoUri, orientationColumn, null, null, null); if(cursor != null && cursor.moveToFirst()){ orientation = cursor.getInt(cursor.getColumnIndex(orientationColumn[0])); } cursor.close(); HashMap<String, Integer> pRes = this.getImageResolutionSetting(); Bitmap shrunkenBitmap = FileUtilsHelper.shrinkBitmap(filePath, pRes.get("width"), pRes.get("height")); shrunkenBitmap = rotateBitmapToOrientation(shrunkenBitmap, orientation); String res = FileUtilsHelper.saveBitmapAsJpeg(shrunkenBitmap, this); Log.d(TAG,"File Path: " + res); shrunkenBitmap.recycle(); Intent editImage = new Intent(this, EditImage.class); editImage.addFlags(Intent.FLAG_ACTIVITY_FORWARD_RESULT); editImage.putExtra("stuff.path", res); startActivity(editImage); }catch(Exception e){ Toast.makeText(this, R.string.cant_save_image,Toast.LENGTH_SHORT).show(); } } } } break; } }} I don´t know what i´m doing wrong... I could really need a teacher on that :) Thx for your help dudes!!

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  • C# - can you name a matrix with the contents of a string

    - by RHodgett
    Basically I have x amount of matrices I need to establish of y by y size. I was hoping to name the matrices: matrixnumber1 matrixnumber2..matrixnumbern I cannot use an array as its matrices I have to form. Is it possible to use a string to name a string (or a matrix in this case)? Thank you in advance for any help on this! for (int i = 1; i <= numberofmatricesrequired; i++) { string number = Convert.ToString(i); Matrix (matrixnumber+number) = new Matrix(matrixsize, matrixsize); }

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  • Stage3D Camera problem

    - by Thomas Versteeg
    I am trying to create a 2D Stage3D game where you can move the camera around the level in an RTS style. I thought about using Orthographic Matrix3D functions for this but when I try to scroll the whole "stage" also scrolls. This is the Camera code: public function Camera2D(width:int, height:int, zoom:Number = 1) { resize(width, height); _zoom = zoom; } public function resize(width:Number, height:Number):void { _width = width; _height = height; _projectionMatrix = makeMatrix(0, width, 0, height); _recalculate = true; } protected function makeMatrix(left:Number, right:Number, top:Number, bottom:Number, zNear:Number = 0, zFar:Number = 1):Matrix3D { return new Matrix3D(Vector.<Number>([ 2 / (right - left), 0, 0, 0, 0, 2 / (top - bottom), 0, 0, 0, 0, 1 / (zFar - zNear), 0, 0, 0, zNear / (zNear - zFar), 1 ])); } public function get viewMatrix():Matrix3D { if (_recalculate) { _recalculate = false; _viewMatrix.identity(); _viewMatrix.appendTranslation( -_width / 2 - _x, -_height / 2 - y, 0); _viewMatrix.appendScale(_zoom, _zoom, 1); _renderMatrix.identity(); _renderMatrix.append(_viewMatrix); _renderMatrix.append(_projectionMatrix); } return _renderMatrix; } Here are two screenshots to show what I mean: How do I only let the inside of the stage3D scroll and not the whole stage?

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  • Screen space to world space

    - by user13414
    I am writing a 2D game where my game world has x axis running left to right, y axis running top to bottom, and z axis out of the screen: Whilst my game world is top-down, the game is rendered on a slight tilt: I'm working on projecting from world space to screen space, and vice-versa. I have the former working as follows: var viewport = new Viewport(0, 0, this.ScreenWidth, this.ScreenHeight); var screenPoint = viewport.Project(worldPoint.NegateY(), this.ProjectionMatrix, this.ViewMatrix, this.WorldMatrix); The NegateY() extension method does exactly what it sounds like, since XNA's y axis runs bottom to top instead of top to bottom. The screenshot above shows this all working. Basically, I have a bunch of points in 3D space that I then render in screen space. I can modify camera properties in real time and see it animate to the new position. Obviously my actual game will use sprites rather than points and the camera position will be fixed, but I'm just trying to get all the math in place before getting to that. Now, I am trying to convert back the other way. That is, given an x and y point in screen space above, determine the corresponding point in world space. So if I point the cursor at, say, the bottom-left of the green trapezoid, I want to get a world space reading of (0, 480). The z coordinate is irrelevant. Or, rather, the z coordinate will always be zero when mapping back to world space. Essentially, I want to implement this method signature: public Vector2 ScreenPointToWorld(Vector2 point) I've tried several things to get this working but am just having no luck. My latest thinking is that I need to call Viewport.Unproject twice with differing near/far z values, calculate the resultant Ray, normalize it, then calculate the intersection of the Ray with a Plane that basically represents ground-level of my world. However, I got stuck on the last step and wasn't sure whether I was over-complicating things. Can anyone point me in the right direction on how to achieve this?

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  • What's the standard location of a 3D clipping box?

    - by Kendall Frey
    The way I understand 3D rendering, polygons are transformed using several matrices, and they are then clipped if they are not inside a certain box, before projecting the box onto the screen. Before transformation, the visible area is typically a frustum, and after transformation, I am guessing it's a cube. This cube makes the clipping math easier than a frustum would. My question is, what's the 'standard' location/size for this clipping box? I can think of 3 possibilities: (0,0,0)-(1,1,1), (-0.5,-0.5,-0.5)-(0.5,0.5,0.5), (-1,-1,-1)-(1,1,1) Or is there no standard?

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  • How to Draw texture between 2 Vector3

    - by Sparky41
    My scenario: RTS combat style, 1 unit fires beam on another unit My problem is i want to draw a flat texture between 2 Vector3 points. I have looked at various Billboarding styles but that doesn't give me a proper solution. I looked at this: http://msdn.microsoft.com/en-us/library/bb464051.aspx is BasicEffect and DrawPrimitives the correct solution just stretch the texture to the distance between point of origin to target? I used the quad class they used but i found this it seemed to inflexible So my question to you is how would i go about this sort of problem? Regards

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  • Interpolating Matrices

    - by sebf
    Hello, Apologies if I am missing something very obvious (likely!) but is there anything wrong with interpolating between two matrices by: float d = (float)(targetTime.Ticks - keyframe_start.ticks) / (float)(keyframe_end.ticks - keyframe_start.ticks); return ((keyframe_start.Transform * (1 - d)) + (keyframe_end.Transform * d)); As in my app, when I try an use this to interpolate between two keyframes, the model begins to 'shrink' - the severity based on how far between the two keyframes the target time is; its worst when the transform split is ~50/50.

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  • Billboarding restricted to an axis (cylindrical)

    - by user8709
    I have succesfully created a GLSL shader for a billboarding effect. I want to tweak this to restrict the billboarding to an arbitrary axis, i.e. a billboarded quad only rotates itself about the y-axis. I use the y-axis as an example, but essentially I would like this to be an arbitrary axis. Can anyone show me how to modify my existing shader below, or if I need to start from scratch, point me towards some resources that could be helpful? precision mediump float; uniform mat4 u_modelViewProjectionMat; uniform mat4 u_modelMat; uniform mat4 u_viewTransposeMat; uniform vec3 u_axis; // <------------ !!! the arbitrary axis to restrict rotation around attribute vec3 a_position0; attribute vec2 a_texCoord0; varying vec2 v_texCoord0; void main() { vec3 pos = (a_position0.x * u_viewTransposeMat[0] + a_position0.y * u_viewTransposeMat[1]).xyz; vec4 position = vec4(pos, 1.0); v_texCoord0 = a_texCoord0; gl_Position = u_modelViewProjectionMat * position; }

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  • Stage3D: Camera pans the whole screen

    - by Thomas Versteeg
    I am trying to create a 2D Stage3D game where you can move the camera around the level in an RTS style. I thought about using Orthographic Matrix3D functions for this but when I try to scroll the whole "stage" also scrolls. This is the Camera code: public function Camera2D(width:int, height:int, zoom:Number = 1) { resize(width, height); _zoom = zoom; } public function resize(width:Number, height:Number):void { _width = width; _height = height; _projectionMatrix = makeMatrix(0, width, 0, height); _recalculate = true; } protected function makeMatrix(left:Number, right:Number, top:Number, bottom:Number, zNear:Number = 0, zFar:Number = 1):Matrix3D { return new Matrix3D(Vector.<Number>([ 2 / (right - left), 0, 0, 0, 0, 2 / (top - bottom), 0, 0, 0, 0, 1 / (zFar - zNear), 0, 0, 0, zNear / (zNear - zFar), 1 ])); } public function get viewMatrix():Matrix3D { if (_recalculate) { _recalculate = false; _viewMatrix.identity(); _viewMatrix.appendTranslation( -_width / 2 - _x, -_height / 2 - y, 0); _viewMatrix.appendScale(_zoom, _zoom, 1); _renderMatrix.identity(); _renderMatrix.append(_viewMatrix); _renderMatrix.append(_projectionMatrix); } return _renderMatrix; } And the camera is send directly to the GPU with: c3d.setProgramConstantsFromMatrix(Context3DProgramType.VERTEX, 0, cameraMatrix, true); And these are the shaders: ------Vertex Shader------ m44 op, va0, vc0 mov v0, va1.xy mov v0.z, va0.z ------Fragment Shader------ tex ft0, v0, fs0 <2d,linear,nomip> mov oc, ft1 Here is a example and here are two screenshots to show what I mean: How do I only let the inside of the stage3D scroll and not the whole stage?

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  • 2D Skeletal Animation Transformations

    - by Brad Zeis
    I have been trying to build a 2D skeletal animation system for a while, and I believe that I'm fairly close to finishing. Currently, I have the following data structures: struct Bone { Bone *parent; int child_count; Bone **children; double x, y; }; struct Vertex { double x, y; int bone_count; Bone **bones; double *weights; }; struct Mesh { int vertex_count; Vertex **vertices; Vertex **tex_coords; } Bone->x and Bone->y are the coordinates of the end point of the Bone. The starting point is given by (bone->parent->x, bone->parent->y) or (0, 0). Each entity in the game has a Mesh, and Mesh->vertices is used as the bounding area for the entity. Mesh->tex_coords are texture coordinates. In the entity's update function, the position of the Bone is used to change the coordinates of the Vertices that are bound to it. Currently what I have is: void Mesh_update(Mesh *mesh) { int i, j; double sx, sy; for (i = 0; i < vertex_count; i++) { if (mesh->vertices[i]->bone_count == 0) { continue; } sx, sy = 0; for (j = 0; j < mesh->vertices[i]->bone_count; j++) { sx += (/* ??? */) * mesh->vertices[i]->weights[j]; sy += (/* ??? */) * mesh->vertices[i]->weights[j]; } mesh->vertices[i]->x = sx; mesh->vertices[i]->y = sy; } } I think I have everything I need, I just don't know how to apply the transformations to the final mesh coordinates. What tranformations do I need here? Or is my approach just completely wrong?

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  • How to make an object stay relative to another object

    - by Nick
    In the following example there is a guy and a boat. They have both a position, orientation and velocity. The guy is standing on the shore and would like to board. He changes his position so he is now standing on the boat. The boat changes velocity and orientation and heads off. My character however has a velocity of 0,0,0 but I would like him to stay onboard. When I move my character around, I would like to move as if the boat was the ground I was standing on. How do keep my character aligned properly with the boat? It is exactly like in World Of Warcraft, when you board a boat or zeppelin. This is my physics code for the guy and boat: this.velocity.addSelf(acceleration.multiplyScalar(dTime)); this.position.addSelf(this.velocity.clone().multiplyScalar(dTime)); The guy already has a reference to the boat he's standing on, and thus knows the boat's position, velocity, orientation (even matrices or quaternions can be used).

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  • Unity3d: calculate the result of a transform without modifying transform object itself

    - by Heisenbug
    I'm in the following situation: I need to move an object in some way, basically rotating it around its parent local position, or translating it in its parent local space (I know how to do this). The amount of rotation and translation is know at runtime (it depends on several factors, the speed of the object, enviroment factors, etc..). The problem is the following: I can perform this transformation only if the result position of the transformed object fit some criterias. An example could be this: the distance between the position before and after the transformation must be less than a given threshold. (Actually the conditions could be several and more complex) The problem is that if I use Transform.Rotate and Transform.Translate methods of my GameObject, I will loose the original Transform values. I think I can't copy the original Transform using instantiate for performance issues. How can I perform such a task? I think I have more or less 2 possibilities: First Don't modify the GameObject position through Transform. Calculate which will be the position after the transform. If the position is legal, modify transform through Translate and Rotate methods Second Store the original transform someway. Transform the object using Translate and Rotate. If the transformed position is illegal, restore the original one.

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  • Basic tutorial/introduction for 3d matrices, idealy in c++, without openGl or directX

    - by René Nyffenegger
    I am wondering if there is a simple tutorial that covers the basics of how to initialize rotation, translation and projection matrices, and how to multiply them, and how to get the screen coordinates afterwards for a 3d point. Idealy, the tutorial comes with compilable code and is not dependent on any 3rd party library. Searching the internet, I found lots of tutorials, so this is not the problem. Yet, it seemed all of these either covered openGl or directX, or they were theoretical in nature.

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  • Calculating 3D camera positions from a video

    - by Geotarget
    I need to calculate the 3D camera position and rotation for each frame in a given video. This is typically used for motion-tracking, and to insert 3D objects into a video. I'm currently using VideoTrace to calculate this for me, and I'm getting the data exported as a 3DS Maxscript file. However when I try to use the 3D camera rotations, I'm getting strange errors in my 3D calculations, as if there is an error with the 3x3 rotation matrices. Can you spot any error with the data itself? Or is it my other calculations that are erroneous? frame 1 rotation=(matrix3[-0.011938, 0.756018, -0.654442][-0.382040, -0.608284, -0.695727][-0.924068, 0.241718, 0.296091][0, 0, 0]).rotationpart position=[-0.767177, 0.308723, -0.232722] fov=57.352135 frame 2 rotation=(matrix3[-0.460922, -0.726580, -0.509541][-0.200163, 0.644491, -0.737947][ 0.864572, -0.238145, -0.442495][0, 0, 0]).rotationpart position=[-0.856630, 0.198654, -0.243853] fov=57.352135

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  • Calculating the position of an object with regards to current position using OpenGL like matrices

    - by spartan2417
    i have a 1st person camera that collides with walls, i also have a small sphere in front of my camera denoted by the camera position plus the distance ahead. I cannot get the postion of the sphere but i have the position of my camera. e.g. i need to find the position of the point or at the very least find away of calculating the position using the camera positions. code: static Float P_z = 0; P_z = -15; PushMatrix(); LoadMatrix(&Inv); Material(SCEGU_AMBIENT, 0x00000066); TranslateXYZ(0,0,P_z); ScaleXYZ(0.1f,0.1f,0.1f); pointer.Render(); PopMatrix(); where Inv is the camera positions (Inv.w.x,Inv.w.z), pointer is the sphere.

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