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  • Camera closes in on the fixed point

    - by V1ncam
    I've been trying to create a camera that is controlled by the mouse and rotates around a fixed point (read: (0,0,0)), both vertical and horizontal. This is what I've come up with: camera.Eye = Vector3.Transform(camera.Eye, Matrix.CreateRotationY(camRotYFloat)); Vector3 customAxis = new Vector3(-camera.Eye.Z, 0, camera.Eye.X); camera.Eye = Vector3.Transform(camera.Eye, Matrix.CreateFromAxisAngle(customAxis, camRotXFloat * 0.0001f)); This works quit well, except from the fact that when I 'use' the second transformation (go up and down with the mouse) the camera not only goes up and down, it also closes in on the point. It zooms in. How do I prevent this? Thanks in advance.

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  • How to transform mesh components?

    - by Lea Hayes
    I am attempting to transform the components of a mesh directly using a 4x4 matrix. This is working for the vertex positions, but it is not working for the normals (and probably not the tangents either). Here is what I have: // Transform vertex positions - Works like a charm! vertices = mesh.vertices; for (int i = 0; i < vertices.Length; ++i) vertices[i] = transform.MultiplyPoint(vertices[i]); // Does not work, lighting is messed up on mesh normals = mesh.normals; for (int i = 0; i < normals.Length; ++i) normals[i] = transform.MultiplyVector(normals[i]); Note: The input matrix converts from local to world space and is needed to combine multiple meshes together.

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  • Where should i organize my matrices in a 3D Game engine?

    - by Need4Sleep
    I'm working with a group of people from around the world to create a game engine(and hopefully a game with it) within the next upcoming years. My first task was writing a camera class for the engine to use in order to add cameras to the scene, position and follow points in the scene. The problem i have is with using matrices for transformations in the class, should i keep matrices separate to each class? such as have the model matrix in the model class, camera matrix in the camera class, or have all matrices placed in one class/chuck? I could see pros and cons for each method, but i wanted to hear some input form a more professional standpoint.

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  • How should I organize my matrices in a 3D game engine?

    - by Need4Sleep
    I'm working with a group of people from around the world to create a game engine (and hopefully a game with it) within the next upcoming years. My first task is to write a camera class for the engine to use in order to add cameras to the scene, with position and follow points. The problem I have is with using matrices for transformations in the class, should I keep matrices separate to each class? Such as have the model matrix in the model class, camera matrix in the camera class, or have all matrices placed in one class/chuck? I could see pros and cons for each method, but I wanted to hear some input form a more professional standpoint.

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  • Portal View/Projection Matrix near plane

    - by melak47
    For RenderToTexture/Camera based portal rendering, the basics seems simple enough. However, with a free camera, most of the time it is going to be looking at such portals at an angle: Now a regular near clipping plane will not always work here, it will either intersect with the wall the portal is sitting on, or possibly with objects in front of the wall. The desired near clipping plane would be aligned like the portal, producing a view volume more like this: or this in 3D: So here is my question: How does one construct or "truncate" a view/projection matrix to achieve such an off-camera-normal (near) clipping plane?

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  • Visual Studio 2012 Coded UI technology matrix updated!

    - by krislankford
    The Visual Studio 2012 support matrix for Automated UI Testing (Coded UI) has been released by Microsoft and the full post can be found here. Thank you Shubhra! There are a couple of items on the list that you should definitely keep your eye on. The first item is the support for Silverlight 4  and 5. This should make the Silverlight community happy. I would also note the Planned items (blue dot) which are cross browser support and Flash/Java. Happy Coding!

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  • Matrix camera, movement concept

    - by NoFace
    I was talking to some guy. He said that my movement concept in game is bad. When left or right arrow is pressed I'm scrolling background what makes you feel that player is moving (player's X remains same). So... he told me something about matrix view. I should create all walls and platforms static and scroll only the camera and move player's rectangle. I did a little research in Google, but nothing found. Can you tell me anything about it? How to start? Maybe links, books and resources? My programming language is Java (2d). Thank you!

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  • How to write basic matrix using row and column differently

    - by kounabg
    #include<stdio.h> #include<conio.h> int main() { int a[3][3],i,j; for(i=0;i<3;i++) {printf("enter the value of row A: ",a[i]); scanf("%d",& a[i]);} for(i=0;i<3;i++) {printf("enter the value of row B: ",a[i]); scanf("%d",& a[i]);} for(i=0;i<3;i++) {printf("enter the value of row C: ",a[i]); scanf("%d",& a[i]);} } ***I did this. I want to convert it into matrix and how can I do it?

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  • wrong operator() overload called

    - by user313202
    okay, I am writing a matrix class and have overloaded the function call operator twice. The core of the matrix is a 2D double array. I am using the MinGW GCC compiler called from a windows console. the first overload is meant to return a double from the array (for viewing an element). the second overload is meant to return a reference to a location in the array (for changing the data in that location. double operator()(int row, int col) const ; //allows view of element double &operator()(int row, int col); //allows assignment of element I am writing a testing routine and have discovered that the "viewing" overload never gets called. for some reason the compiler "defaults" to calling the overload that returns a reference when the following printf() statement is used. fprintf(outp, "%6.2f\t", testMatD(i,j)); I understand that I'm insulting the gods by writing my own matrix class without using vectors and testing with C I/O functions. I will be punished thoroughly in the afterlife, no need to do it here. Ultimately I'd like to know what is going on here and how to fix it. I'd prefer to use the cleaner looking operator overloads rather than member functions. Any ideas? -Cal the matrix class: irrelevant code omitted class Matrix { public: double getElement(int row, int col)const; //returns the element at row,col //operator overloads double operator()(int row, int col) const ; //allows view of element double &operator()(int row, int col); //allows assignment of element private: //data members double **array; //pointer to data array }; double Matrix::getElement(int row, int col)const{ //transform indices into true coordinates (from sorted coordinates //only row needs to be transformed (user can only sort by row) row = sortedArray[row]; result = array[usrZeroRow+row][usrZeroCol+col]; return result; } //operator overloads double Matrix::operator()(int row, int col) const { //this overload is used when viewing an element return getElement(row,col); } double &Matrix::operator()(int row, int col){ //this overload is used when placing an element return array[row+usrZeroRow][col+usrZeroCol]; } The testing program: irrelevant code omitted int main(void){ FILE *outp; outp = fopen("test_output.txt", "w+"); Matrix testMatD(5,7); //construct 5x7 matrix //some initializations omitted fprintf(outp, "%6.2f\t", testMatD(i,j)); //calls the wrong overload }

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  • Get last row of many matrices (ASCII text files) and create a new matrix from these rows

    - by nofunsally
    I have over a thousand matrices (6 x 2000, ASCII files, comma delimited) that I generated from MATLAB. I want to get the last row of each matrix / text file and save them in a new matrix / text file. The text files have crazy names so when I load them I can name them whatever. Right now I would do this to achieve my goal: % A = load('crazyname.txt'); % B = load('crazynameagain.txt'); % C = load('crazynameyetagain.txt'); A = [5 5 5; 5 5 5; 1 1 1]; B = [5 5 5; 5 5 5; 2 2 2]; C = [5 5 5; 5 5 5; 3 3 3]; D(1,:)=A(end,:); D(2,:)=B(end,:); D(3,:)=C(end,:); I will create each command (e.g. load, building D step by step) in Excel by combining text cells to create a command. Is there a better way to do this? Could I load / assign the matrices with a name that would better suit them to be used in a for loop? Or is some other MATLAB command that would facilitate this? Thanks.

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  • Web Matrix released

    - by TATWORTH
    Microsoft have now released Web Matrix (and ASP.NET MVC3 if you so inclined!) One signifcant utility is IIS Express which will replace Cassini It is worth noting that SP1 for VS2010 should be out in Q1. Links: http://www.hanselman.com/blog/ASPNETMVC3WebMatrixNuGetIISExpressAndOrchardReleasedTheMicrosoftJanuaryWebReleaseInContext.aspx http://www.hanselman.com/blog/LinkRollupNewDocumentationAndTutorialsFromWebPlatformAndTools.aspx http://arstechnica.com/microsoft/news/2011/01/microsoft-releases-free-webmatrix-web-development-tool.ars I am impressed by the copious tutorials on MVC, which I include below: Intro to ASP.NET MVC 3 onboarding series. Scott Hanselman and Rick Anderson collaboration and Mike Pope (Editor) Both C# and VB versions: Intro to ASP.NET MVC 3 Adding a Controller Adding a View Entity Framework Code-First Development Accessing your Model's Data from a Controller Adding a Create Method and Create View Adding Validation to the Model Adding a New Field to the Movie Model and Table Implementing Edit, Details and Delete Source code for this series MVC 3 Updated and new tutorials/ API Reference on MSDN Rick Anderson (Lead Programming Writer), Keith Newman and Mike Pope (Editor) ASP.NET MVC 3 Content Map ASP.NET MVC Overview MVC Framework and Application Structure Understanding MVC Application Execution Compatibility of ASP.NET Web Forms and MVC Walkthrough: Creating a Basic ASP.NET MVC Project Walkthrough: Using Forms Authentication in ASP.NET MVC Controllers and Action Methods in ASP.NET MVC Applications Using an Asynchronous Controller in ASP.NET MVC Views and UI Rendering in ASP.NET MVC Applications Rendering a Form Using HTML Helpers Passing Data in an ASP.NET MVC Application Walkthrough: Using Templated Helpers to Display Data in ASP.NET MVC Creating an ASP.NET MVC View by Calling Multiple Actions Models and Validation in ASP.NET MVC How to: Validate Model Data Using DataAnnotations Attributes Walkthrough: Using MVC View Templates How to: Implement Remote Validation in ASP.NET MVC Walkthrough: Adding AJAX Scripting Walkthrough: Organizing an Application using Areas Filtering in ASP.NET MVC Creating Custom Action Filters How to: Create a Custom Action Filter Unit Testing in ASP.NET MVC Applications Walkthrough: Using TDD with ASP.NET MVC How to: Add a Custom ASP.NET MVC Test Framework in Visual Studio ASP.NET MVC 3 Reference System.Web.Mvc System.Web.Mvc.Ajax System.Web.Mvc.Async System.Web.Mvc.Html System.Web.Mvc.Razor

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  • transform a matrix wtih 2 columns into a multimap

    - by Derek
    Hi, I am wondering if there is a way to transform a matrix of 2 column into a multimap or list of list. The first column of the matrix is an id (with possibly duplicated entries) and the 2nd column is some value. For example, if I have to following matrix m<-matrix(c(1,2,1,3,2,4), c(3,2)) i would like to transform it into the following list [[1]] 3,4 [[2]] 2 Thanks, Derek

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  • XNA: Rotating Bones

    - by MLM
    XNA 4.0 I am trying to learn how to rotate bones on a very simple tank model I made in Cinema 4D. It is rigged by 3 bones, Root - Main - Turret - Barrel I have binded all of the objects to the bones so that all translations/rotations work as planned in C4D. I exported it as .fbx I based my test project after: http://create.msdn.com/en-US/education/catalog/sample/simple_animation I can build successfully with no errors but all the rotations I try to do to my bones have no effect. I can transform my Root successfully using below but the bone transforms have no effect: myModel.Root.Transform = world; Matrix turretRotation = Matrix.CreateRotationY(MathHelper.ToRadians(37)); Matrix barrelRotation = Matrix.CreateRotationX(barrelRotationValue); MainBone.Transform = MainTransform; TurretBone.Transform = turretRotation * TurretTransform; BarrelBone.Transform = barrelRotation * BarrelTransform; I am wondering if my model is just not right or something important I am missing in the code. Here is my Game1.cs using System; using System.Collections.Generic; using System.Linq; using Microsoft.Xna.Framework; using Microsoft.Xna.Framework.Audio; using Microsoft.Xna.Framework.Content; using Microsoft.Xna.Framework.GamerServices; using Microsoft.Xna.Framework.Graphics; using Microsoft.Xna.Framework.Input; using Microsoft.Xna.Framework.Media; namespace ModelTesting { /// <summary> /// This is the main type for your game /// </summary> public class Game1 : Microsoft.Xna.Framework.Game { GraphicsDeviceManager graphics; SpriteBatch spriteBatch; float aspectRatio; Tank myModel; public Game1() { graphics = new GraphicsDeviceManager(this); Content.RootDirectory = "Content"; } /// <summary> /// Allows the game to perform any initialization it needs to before starting to run. /// This is where it can query for any required services and load any non-graphic /// related content. Calling base.Initialize will enumerate through any components /// and initialize them as well. /// </summary> protected override void Initialize() { // TODO: Add your initialization logic here myModel = new Tank(); base.Initialize(); } /// <summary> /// LoadContent will be called once per game and is the place to load /// all of your content. /// </summary> protected override void LoadContent() { // Create a new SpriteBatch, which can be used to draw textures. spriteBatch = new SpriteBatch(GraphicsDevice); // TODO: use this.Content to load your game content here myModel.Load(Content); aspectRatio = graphics.GraphicsDevice.Viewport.AspectRatio; } /// <summary> /// UnloadContent will be called once per game and is the place to unload /// all content. /// </summary> protected override void UnloadContent() { // TODO: Unload any non ContentManager content here } /// <summary> /// Allows the game to run logic such as updating the world, /// checking for collisions, gathering input, and playing audio. /// </summary> /// <param name="gameTime">Provides a snapshot of timing values.</param> protected override void Update(GameTime gameTime) { // Allows the game to exit if (GamePad.GetState(PlayerIndex.One).Buttons.Back == ButtonState.Pressed) this.Exit(); // TODO: Add your update logic here float time = (float)gameTime.TotalGameTime.TotalSeconds; // Move the pieces /* myModel.TurretRotation = (float)Math.Sin(time * 0.333f) * 1.25f; myModel.BarrelRotation = (float)Math.Sin(time * 0.25f) * 0.333f - 0.333f; */ base.Update(gameTime); } /// <summary> /// This is called when the game should draw itself. /// </summary> /// <param name="gameTime">Provides a snapshot of timing values.</param> protected override void Draw(GameTime gameTime) { GraphicsDevice.Clear(Color.CornflowerBlue); // Calculate the camera matrices. float time = (float)gameTime.TotalGameTime.TotalSeconds; Matrix rotation = Matrix.CreateRotationY(MathHelper.ToRadians(45)); Matrix view = Matrix.CreateLookAt(new Vector3(2000, 500, 0), new Vector3(0, 150, 0), Vector3.Up); Matrix projection = Matrix.CreatePerspectiveFieldOfView(MathHelper.PiOver4, graphics.GraphicsDevice.Viewport.AspectRatio, 10, 10000); // TODO: Add your drawing code here myModel.Draw(rotation, view, projection); base.Draw(gameTime); } } } And here is my tank class: using System; using System.Collections.Generic; using System.Linq; using Microsoft.Xna.Framework; using Microsoft.Xna.Framework.Audio; using Microsoft.Xna.Framework.Content; using Microsoft.Xna.Framework.GamerServices; using Microsoft.Xna.Framework.Graphics; using Microsoft.Xna.Framework.Input; using Microsoft.Xna.Framework.Media; namespace ModelTesting { public class Tank { Model myModel; // Array holding all the bone transform matrices for the entire model. // We could just allocate this locally inside the Draw method, but it // is more efficient to reuse a single array, as this avoids creating // unnecessary garbage. public Matrix[] boneTransforms; // Shortcut references to the bones that we are going to animate. // We could just look these up inside the Draw method, but it is more // efficient to do the lookups while loading and cache the results. ModelBone MainBone; ModelBone TurretBone; ModelBone BarrelBone; // Store the original transform matrix for each animating bone. Matrix MainTransform; Matrix TurretTransform; Matrix BarrelTransform; // current animation positions float turretRotationValue; float barrelRotationValue; /// <summary> /// Gets or sets the turret rotation amount. /// </summary> public float TurretRotation { get { return turretRotationValue; } set { turretRotationValue = value; } } /// <summary> /// Gets or sets the barrel rotation amount. /// </summary> public float BarrelRotation { get { return barrelRotationValue; } set { barrelRotationValue = value; } } /// <summary> /// Load the model /// </summary> public void Load(ContentManager Content) { // TODO: use this.Content to load your game content here myModel = Content.Load<Model>("Models\\simple_tank02"); MainBone = myModel.Bones["Main"]; TurretBone = myModel.Bones["Turret"]; BarrelBone = myModel.Bones["Barrel"]; MainTransform = MainBone.Transform; TurretTransform = TurretBone.Transform; BarrelTransform = BarrelBone.Transform; // Allocate the transform matrix array. boneTransforms = new Matrix[myModel.Bones.Count]; } public void Draw(Matrix world, Matrix view, Matrix projection) { myModel.Root.Transform = world; Matrix turretRotation = Matrix.CreateRotationY(MathHelper.ToRadians(37)); Matrix barrelRotation = Matrix.CreateRotationX(barrelRotationValue); MainBone.Transform = MainTransform; TurretBone.Transform = turretRotation * TurretTransform; BarrelBone.Transform = barrelRotation * BarrelTransform; myModel.CopyAbsoluteBoneTransformsTo(boneTransforms); // Draw the model, a model can have multiple meshes, so loop foreach (ModelMesh mesh in myModel.Meshes) { // This is where the mesh orientation is set foreach (BasicEffect effect in mesh.Effects) { effect.World = boneTransforms[mesh.ParentBone.Index]; effect.View = view; effect.Projection = projection; effect.EnableDefaultLighting(); } // Draw the mesh, will use the effects set above mesh.Draw(); } } } }

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  • Creating a 2D perspective in 3D game

    - by Accatyyc
    I'm new to XNA and 3D game development in general. I'm creating a puzzle game kind of similar to tetris, built with blocks. I decided to build the game in 3D since I can do some cool animations and transitions when using 3D blocks with physics etc. However, I really do want the game to look "2D". My blocks are made up of 3D models, but I don't want that to be visible when they're not animating. I have followed some XNA tutorials and set up my scene like this: this.view = Matrix.CreateLookAt(cameraPosition, Vector3.Zero, Vector3.Up); this.aspectRatio = graphics.GraphicsDevice.Viewport.AspectRatio; this.projection = Matrix.CreatePerspectiveFieldOfView( MathHelper.ToRadians(45.0f), aspectRatio, 1.0f, 10000.0f); ... and it gives me a very 3D-ish look. For example, the blocks in the center of the screen looks exactly how I want them, but closer to the edges of the screen I can see the rotation and sides of them. My guess is that I'm not after a perspective field of view, but any help on which field of view/settings to use to get a "flat" look when the blocks aren't rotated would be great!

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  • Matrices: Arrays or separate member variables?

    - by bjz
    I'm teaching myself 3D maths and in the process building my own rudimentary engine (of sorts). I was wondering what would be the best way to structure my matrix class. There are a few options: Separate member variables: struct Mat4 { float m11, m12, m13, m14, m21, m22, m23, m24, m31, m32, m33, m34, m41, m42, m43, m44; // methods } A multi-dimensional array: struct Mat4 { float[4][4] m; // methods } An array of vectors struct Mat4 { Vec4[4] m; // methods } I'm guessing there would be positives and negatives to each. From 3D Math Primer for Graphics and Game Development, 2nd Edition p.155: Matrices use 1-based indices, so the first row and column are numbered 1. For example, a12 (read “a one two,” not “a twelve”) is the element in the first row, second column. Notice that this is different from programming languages such as C++ and Java, which use 0-based array indices. A matrix does not have a column 0 or row 0. This difference in indexing can cause some confusion if matrices are stored using an actual array data type. For this reason, it’s common for classes that store small, fixed size matrices of the type used for geometric purposes to give each element its own named member variable, such as float a11, instead of using the language’s native array support with something like float elem[3][3]. So that's one vote for method one. Is this really the accepted way to do things? It seems rather unwieldy if the only benefit would be sticking with the conventional math notation.

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  • Fastest pathfinding for static node matrix

    - by Sean Martin
    I'm programming a route finding routine in VB.NET for an online game I play, and I'm searching for the fastest route finding algorithm for my map type. The game takes place in space, with thousands of solar systems connected by jump gates. The game devs have provided a DB dump containing a list of every system and the systems it can jump to. The map isn't quite a node tree, since some branches can jump to other branches - more of a matrix. What I need is a fast pathfinding algorithm. I have already implemented an A* routine and a Dijkstra's, both find the best path but are too slow for my purposes - a search that considers about 5000 nodes takes over 20 seconds to compute. A similar program on a website can do the same search in less than a second. This website claims to use D*, which I have looked into. That algorithm seems more appropriate for dynamic maps rather than one that does not change - unless I misunderstand it's premise. So is there something faster I can use for a map that is not your typical tile/polygon base? GBFS? Perhaps a DFS? Or have I likely got some problem with my A* - maybe poorly chosen heuristics or movement cost? Currently my movement cost is the length of the jump (the DB dump has solar system coordinates as well), and the heuristic is a quick euclidean calculation from the node to the goal. In case anyone has some optimizations for my A*, here is the routine that consumes about 60% of my processing time, according to my profiler. The coordinateData table contains a list of every system's coordinates, and neighborNode.distance is the distance of the jump. Private Function findDistance(ByVal startSystem As Integer, ByVal endSystem As Integer) As Integer 'hCount += 1 'If hCount Mod 0 = 0 Then 'Return hCache 'End If 'Initialize variables to be filled Dim x1, x2, y1, y2, z1, z2 As Integer 'LINQ queries for solar system data Dim systemFromData = From result In jumpDataDB.coordinateDatas Where result.systemId = startSystem Select result.x, result.y, result.z Dim systemToData = From result In jumpDataDB.coordinateDatas Where result.systemId = endSystem Select result.x, result.y, result.z 'LINQ execute 'Fill variables with solar system data for from and to system For Each solarSystem In systemFromData x1 = (solarSystem.x) y1 = (solarSystem.y) z1 = (solarSystem.z) Next For Each solarSystem In systemToData x2 = (solarSystem.x) y2 = (solarSystem.y) z2 = (solarSystem.z) Next Dim x3 = Math.Abs(x1 - x2) Dim y3 = Math.Abs(y1 - y2) Dim z3 = Math.Abs(z1 - z2) 'Calculate distance and round 'Dim distance = Math.Round(Math.Sqrt(Math.Abs((x1 - x2) ^ 2) + Math.Abs((y1 - y2) ^ 2) + Math.Abs((z1 - z2) ^ 2))) Dim distance = firstConstant * Math.Min(secondConstant * (x3 + y3 + z3), Math.Max(x3, Math.Max(y3, z3))) 'Dim distance = Math.Abs(x1 - x2) + Math.Abs(z1 - z2) + Math.Abs(y1 - y2) 'hCache = distance Return distance End Function And the main loop, the other 30% 'Begin search While openList.Count() != 0 'Set current system and move node to closed currentNode = lowestF() move(currentNode.id) For Each neighborNode In neighborNodes If Not onList(neighborNode.toSystem, 0) Then If Not onList(neighborNode.toSystem, 1) Then Dim newNode As New nodeData() newNode.id = neighborNode.toSystem newNode.parent = currentNode.id newNode.g = currentNode.g + neighborNode.distance newNode.h = findDistance(newNode.id, endSystem) newNode.f = newNode.g + newNode.h newNode.security = neighborNode.security openList.Add(newNode) shortOpenList(OLindex) = newNode.id OLindex += 1 Else Dim proposedG As Integer = currentNode.g + neighborNode.distance If proposedG < gValue(neighborNode.toSystem) Then changeParent(neighborNode.toSystem, currentNode.id, proposedG) End If End If End If Next 'Check to see if done If currentNode.id = endSystem Then Exit While End If End While If clarification is needed on my spaghetti code, I'll try to explain.

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  • Matrix inversion in OpenCL

    - by buchtak
    Hi, I am trying to accelerate some computations using OpenCL and part of the algorithm consists of inverting a matrix. Is there any open-source library or freely available code to compute lu factorization (lapack dgetrf and dgetri) of matrix or general inversion written in OpenCL or CUDA? The matrix is real and square but doesn't have any other special properties besides that. So far, I've managed to find only basic blas matrix-vector operations implementations on gpu. The matrix is rather small, only about 60-100 rows and cols, so it could be computed faster on cpu, but it's used kinda in the middle of the algorithm, so I would have to transfer it to host, calculate the inverse, and then transfer the result back on the device where it's then used in much larger computations.

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  • How to strink matrix using array mask in Matlab?

    - by Pyrolistical
    This seems to be a very common problem of mine. data = [1 2 3; 4 5 6]; mask = [true false true]; mask = repmat(mask, 2, 1); data(mask) ==> [1; 4; 3; 6] What I wanted was [1 3; 4 6] Yes I can just reshape it to the right size, but that seems the wrong way to do it. Is there a better way? Why doesn't data(mask) return a matrix when it is actually rectangular? I understand in the general case it may not be, but in my case since my original mask is an array it always will be.

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  • plotting results of hierarchical clustering ontop of a matrix of data in python

    - by user248237
    How can I plot a dendrogram right on top of a matrix of values, reordered appropriately to reflect the clustering, in Python? An example is in the bottom of the following figure: http://www.coriell.org/images/microarray.gif I use scipy.cluster.dendrogram to make my dendrogram and perform hierarchical clustering on a matrix of data. How can I then plot the data as a matrix where the rows have been reordered to reflect a clustering induced by the cutting the dendrogram at a particular threshold, and have the dendrogram plotted alongside the matrix? I know how to plot the dendrogram in scipy, but not how to plot the intensity matrix of data with the right scale bar next to it. Any help on this would be greatly appreciated.

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  • How to get predecessor and successors from an adjacency matrix

    - by NickTFried
    Hi I am am trying to complete an assignment, where it is ok to consult the online community. I have to create a graph class that ultimately can do Breadth First Search and Depth First Search. I have been able to implement those algorithms successfully however another requirement is to be able to get the successors and predecessors and detect if two vertices are either predecessors or successors for each other. I'm having trouble thinking of a way to do this. I will post my code below, if anyone has any suggestions it would be greatly appreciated. import java.util.ArrayList; import java.util.Iterator; import java.util.LinkedList; import java.util.Queue; import java.util.Stack; public class Graph<T> { public Vertex<T> root; public ArrayList<Vertex<T>> vertices=new ArrayList<Vertex<T>>(); public int[][] adjMatrix; int size; private ArrayList<Vertex<T>> dfsArrList; private ArrayList<Vertex<T>> bfsArrList; public void setRootVertex(Vertex<T> n) { this.root=n; } public Vertex<T> getRootVertex() { return this.root; } public void addVertex(Vertex<T> n) { vertices.add(n); } public void removeVertex(int loc){ vertices.remove(loc); } public void addEdge(Vertex<T> start,Vertex<T> end) { if(adjMatrix==null) { size=vertices.size(); adjMatrix=new int[size][size]; } int startIndex=vertices.indexOf(start); int endIndex=vertices.indexOf(end); adjMatrix[startIndex][endIndex]=1; adjMatrix[endIndex][startIndex]=1; } public void removeEdge(Vertex<T> v1, Vertex<T> v2){ int startIndex=vertices.indexOf(v1); int endIndex=vertices.indexOf(v2); adjMatrix[startIndex][endIndex]=1; adjMatrix[endIndex][startIndex]=1; } public int countVertices(){ int ver = vertices.size(); return ver; } /* public boolean isPredecessor( Vertex<T> a, Vertex<T> b){ for() return true; }*/ /* public boolean isSuccessor( Vertex<T> a, Vertex<T> b){ for() return true; }*/ public void getSuccessors(Vertex<T> v1){ } public void getPredessors(Vertex<T> v1){ } private Vertex<T> getUnvisitedChildNode(Vertex<T> n) { int index=vertices.indexOf(n); int j=0; while(j<size) { if(adjMatrix[index][j]==1 && vertices.get(j).visited==false) { return vertices.get(j); } j++; } return null; } public Iterator<Vertex<T>> bfs() { Queue<Vertex<T>> q=new LinkedList<Vertex<T>>(); q.add(this.root); printVertex(this.root); root.visited=true; while(!q.isEmpty()) { Vertex<T> n=q.remove(); Vertex<T> child=null; while((child=getUnvisitedChildNode(n))!=null) { child.visited=true; bfsArrList.add(child); q.add(child); } } clearVertices(); return bfsArrList.iterator(); } public Iterator<Vertex<T>> dfs() { Stack<Vertex<T>> s=new Stack<Vertex<T>>(); s.push(this.root); root.visited=true; printVertex(root); while(!s.isEmpty()) { Vertex<T> n=s.peek(); Vertex<T> child=getUnvisitedChildNode(n); if(child!=null) { child.visited=true; dfsArrList.add(child); s.push(child); } else { s.pop(); } } clearVertices(); return dfsArrList.iterator(); } private void clearVertices() { int i=0; while(i<size) { Vertex<T> n=vertices.get(i); n.visited=false; i++; } } private void printVertex(Vertex<T> n) { System.out.print(n.label+" "); } }

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  • WPF Animate a Matrix using interpolation

    - by Mark
    I'm having a issue with my application that is using touch gestures to scale, translate and rotate my scene. I was using a TransformGroup which contained TranslateTransform, ScaleTransform and a RotateTransform but I could not get the movement correct, it always jumps and skips, so I moved to a MaxtrixTransform which I was able to use much easier to get my scene to be zoomable, rotatable and panable nicely. However, what I later found out was that you cannot animate smoothly (using interpolation) the values of a Matrix, for what reason I have no idea, but its part of the MSDN doco and the properties of the Matrix are not dependency properties anyways... Has anyone had any luck animating a matrix to make it smooth? The only idea(s) I have had is to animate a few different, custom DP which all have callbacks that I update the matrix from OR To convert the matrix to a set of Transform objects that I then animate and then afterwords convert back. Is there a smarter way to do this?

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  • Efficient calculation of matrix cumulative standard deviation in r

    - by Abiel
    I recently posted this question on the r-help mailing list but got no answers, so I thought I would post it here as well and see if there were any suggestions. I am trying to calculate the cumulative standard deviation of a matrix. I want a function that accepts a matrix and returns a matrix of the same size where output cell (i,j) is set to the standard deviation of input column j between rows 1 and i. NAs should be ignored, unless cell (i,j) of the input matrix itself is NA, in which case cell (i,j) of the output matrix should also be NA. I could not find a built-in function, so I implemented the following code. Unfortunately, this uses a loop that ends up being somewhat slow for large matrices. Is there a faster built-in function or can someone suggest a better approach? cumsd <- function(mat) { retval <- mat*NA for (i in 2:nrow(mat)) retval[i,] <- sd(mat[1:i,], na.rm=T) retval[is.na(mat)] <- NA retval } Thanks.

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  • The width of a list that contains an embedded matrix grows unexpectedly

    - by Greg Lorenz
    I have a report in reporting services 2005 that includes a list with an embedded matrix and am attempting to put a border on the list, however, when I run the report in visual studio the matrix is growing past the end of the page and therefore the boarder is growing with it causing it to grow into the second page. It appears that there was supposedly a fix for this in reporting services 2000 service pack 1 but I am still experianceing the issue in 2005. The list has a details group that limits the records on a row to 4 using the following expression: =ceiling(rownumber("list1")/4), the matrix has a column group that should recycle those based on the rownumber determined by the list using the following expression: =rowNumber("list1_Details_Group") I have also attempted to put the list in a rectangle in hopes to stop the matrix from growing to no avail. How do I effectivly stop the matrix form growing past the space allowed by the list control?

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