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• R + Bioconductor : combining probesets in an ExpressionSet

  - by Mike Dewar

  Hi, First off, this may be the wrong Forum for this question, as it's pretty darn R+Bioconductor specific. Here's what I have: library('GEOquery') GDS = getGEO('GDS785') cd4T = GDS2eSet(GDS) cd4T <- cd4T[!fData(cd4T)$symbol == "",] Now cd4T is an ExpressionSet object which wraps a big matrix with 19794 rows (probesets) and 15 columns (samples). The final line gets rid of all probesets that do not have corresponding gene symbols. Now the trouble is that most genes in this set are assigned to more than one probeset. You can see this by doing gene_symbols = factor(fData(cd4T)$Gene.symbol) length(gene_symbols)-length(levels(gene_symbols)) [1] 6897 So only 6897 of my 19794 probesets have unique probeset - gene mappings. I'd like to somehow combine the expression levels of each probeset associated with each gene. I don't care much about the actual probe id for each probe. I'd like very much to end up with an ExpressionSet containing the merged information as all of my downstream analysis is designed to work with this class. I think I can write some code that will do this by hand, and make a new expression set from scratch. However, I'm assuming this can't be a new problem and that code exists to do it, using a statistically sound method to combine the gene expression levels. I'm guessing there's a proper name for this also but my googles aren't showing up much of use. Can anyone help?

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• Converting python collaborative filtering code to use Map Reduce

  - by Neil Kodner

  Using Python, I'm computing cosine similarity across items. given event data that represents a purchase (user,item), I have a list of all items 'bought' by my users. Given this input data (user,item) X,1 X,2 Y,1 Y,2 Z,2 Z,3 I build a python dictionary {1: ['X','Y'], 2 : ['X','Y','Z'], 3 : ['Z']} From that dictionary, I generate a bought/not bought matrix, also another dictionary(bnb). {1 : [1,1,0], 2 : [1,1,1], 3 : [0,0,1]} From there, I'm computing similarity between (1,2) by calculating cosine between (1,1,0) and (1,1,1), yielding 0.816496 I'm doing this by: items=[1,2,3] for item in items: for sub in items: if sub >= item: #as to not calculate similarity on the inverse sim = coSim( bnb[item], bnb[sub] ) I think the brute force approach is killing me and it only runs slower as the data gets larger. Using my trusty laptop, this calculation runs for hours when dealing with 8500 users and 3500 items. I'm trying to compute similarity for all items in my dict and it's taking longer than I'd like it to. I think this is a good candidate for MapReduce but I'm having trouble 'thinking' in terms of key/value pairs. Alternatively, is the issue with my approach and not necessarily a candidate for Map Reduce?

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• Function within function in R

  - by frespider

  Can you please explain to me why th code complain saying that Samdat is not found? I am trying to switch between the models as you can see, so i declared a functions that contains these specific models and I just need to call these function as one of the argument in the get.f function where the resampling will change the structure for each design matrix in the model. the code complain the Samdat is not found when it is found. Also, is there a way I can make the condition statement as if(Model == M1()) instead I have to create another argument M to set if(M==1) Can you explain please? dat <- cbind(Y=rnorm(20),rnorm(20),runif(20),rexp(20),rnorm(20),runif(20), rexp(20),rnorm(20),runif(20),rexp(20)) nam <- paste("v",1:9,sep="") colnames(dat) <- c("Y",nam) M1 <- function(){ a1 = cbind(Samdat[,c(2:5,7,9)]) b1 = cbind(Samdat[,c(2:4,6,8,7)]) c1 = b1+a1 list(a1=a1,b1=b1,c1=c1)} M2 <- function(){ a1= cbind(Samdat[,c(2:5,7,9)])+2 b1= cbind(Samdat[,c(2:4,6,8,7)])+2 c1 = a1+b1 list(a1=a1,b1=b1,c1=c1)} M3 <- function(){ a1= cbind(Samdat[,c(2:5,7,9)])+8 b1= cbind(Samdat[,c(2:4,6,8,7)])+8 c1 = a1+b1 list(a1=a1,b1=b1,c1=c1)} ################################################################# get.f <- function(asim,Model,M){ sse <-c() for(i in 1:asim){ set.seed(i) Samdat <- dat[sample(1:nrow(dat),nrow(dat),replace=T),] Y <- Samdat[,1] if(M==1){ a2 <- Model$a1 b2 <- Model$b1 c2 <- Model$c1 s<- a2+b2+c2 fit <- lm(Y~s) cof <- sum(summary(fit)$coef[,1]) coff <-Model$cof sse <-c(sse,coff) } else if(M==2){ a2 <- Model$a1 b2 <- Model$b1 c2 <- Model$c1 s<- c2+12 fit <- lm(Y~s) cof <- sum(summary(fit)$coef[,1]) coff <-Model$cof sse <-c(sse,coff) } else { a2 <- Model$a1 b2 <- Model$b1 c2 <- Model$c1 s<- c2+a2 fit <- lm(Y~s) cof <- sum(summary(fit)$coef[,1]) coff <- Model$cof sse <-c(sse,coff) } } return(sse) } get.f(10,Model=M1(),M=1) get.f(10,Model=M2(),M=2) get.f(10,Model=M3(),M=3)

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• Create a unique ID by fuzzy matching of names (via agrep using R)

  - by tbrambor

  Using R, I am trying match on people's names in a dataset structured by year and city. Due to some spelling mistakes, exact matching is not possible, so I am trying to use agrep() to fuzzy match names. A sample chunk of the dataset is structured as follows: df <- data.frame(matrix( c("1200013","1200013","1200013","1200013","1200013","1200013","1200013","1200013", "1996","1996","1996","1996","2000","2000","2004","2004","AGUSTINHO FORTUNATO FILHO","ANTONIO PEREIRA NETO","FERNANDO JOSE DA COSTA","PAULO CEZAR FERREIRA DE ARAUJO","PAULO CESAR FERREIRA DE ARAUJO","SEBASTIAO BOCALOM RODRIGUES","JOAO DE ALMEIDA","PAULO CESAR FERREIRA DE ARAUJO"), ncol=3,dimnames=list(seq(1:8),c("citycode","year","candidate")) )) The neat version: citycode year candidate 1 1200013 1996 AGUSTINHO FORTUNATO FILHO 2 1200013 1996 ANTONIO PEREIRA NETO 3 1200013 1996 FERNANDO JOSE DA COSTA 4 1200013 1996 PAULO CEZAR FERREIRA DE ARAUJO 5 1200013 2000 PAULO CESAR FERREIRA DE ARAUJO 6 1200013 2000 SEBASTIAO BOCALOM RODRIGUES 7 1200013 2004 JOAO DE ALMEIDA 8 1200013 2004 PAULO CESAR FERREIRA DE ARAUJO I'd like to check in each city separately, whether there are candidates appearing in several years. E.g. in the example, PAULO CEZAR FERREIRA DE ARAUJO PAULO CESAR FERREIRA DE ARAUJO appears twice (with a spelling mistake). Each candidate across the entire data set should be assigned a unique numeric candidate ID. The dataset is fairly large (5500 cities, approx. 100K entries) so a somewhat efficient coding would be helpful. Any suggestions as to how to implement this?

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• vtk glyphs 3D, indenpently color and rotation

  - by user3684219

  I try to display thanks to vtk (python wrapper) several glyphs in a scene with each their own colour and rotation. Unfortunately, just the rotation (using vtkTensorGlyph) is taken in consideration by vtk. Reversely, just color is taken in consideration when I use a vtkGlyph3D. Here is a ready to use piece of code with a vtkTensorGlyph. Each cube should have a random color but there all will be in the same color. I read and read again the doc of vtk but I found no solution. Thanks in advance for any idea #!/usr/bin/env python # -*- coding: utf-8 -*- import vtk import scipy.linalg as sc import random as ra import numpy as np import itertools points = vtk.vtk.vtkPoints() # where to locate each glyph in the scene tensors = vtk.vtkDoubleArray() # rotation for each glyph tensors.SetNumberOfComponents(9) colors = vtk.vtkUnsignedCharArray() # should be the color for each glyph colors.SetNumberOfComponents(3) # let's make 10 cubes in the scene for i in range(0, 50, 5): points.InsertNextPoint(i, i, i) # position of a glyph colors.InsertNextTuple3(ra.randint(0, 255), ra.randint(0, 255), ra.randint(0, 255) ) # pick random color rot = list(itertools.chain(*np.reshape(sc.orth(np.random.rand(3, 3)).transpose(), (1, 9)).tolist())) # random rotation matrix (row major) tensors.InsertNextTuple9(*rot) polydata = vtk.vtkPolyData() # create the polydatas polydata.SetPoints(points) polydata.GetPointData().SetTensors(tensors) polydata.GetPointData().SetScalars(colors) cubeSource = vtk.vtkCubeSource() cubeSource.Update() glyphTensor = vtk.vtkTensorGlyph() glyphTensor.SetColorModeToScalars() # is it really work ? try: glyphTensor.SetInput(polydata) except AttributeError: glyphTensor.SetInputData(polydata) glyphTensor.SetSourceConnection(cubeSource.GetOutputPort()) glyphTensor.ColorGlyphsOn() # should not color all cubes independently ? glyphTensor.ThreeGlyphsOff() glyphTensor.ExtractEigenvaluesOff() glyphTensor.Update() # next is usual vtk code mapper = vtk.vtkPolyDataMapper() mapper.SetInputConnection(glyphTensor.GetOutputPort()) actor = vtk.vtkActor() actor.SetMapper(mapper) ren = vtk.vtkRenderer() ren.SetBackground(0.2, 0.5, 0.3) ren.AddActor(actor) renwin = vtk.vtkRenderWindow() renwin.AddRenderer(ren) iren = vtk.vtkRenderWindowInteractor() iren.SetInteractorStyle(vtk.vtkInteractorStyleTrackballCamera()) iren.SetRenderWindow(renwin) renwin.Render() iren.Initialize() renwin.Render() iren.Start()

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• Makefile : Build in a separate directory tree

  - by Simone Margaritelli

  My project (an interpreted language) has a standard library composed by multiple files, each of them will be built into an .so dynamic library that the interpreter will load upon user request (with an import directive). Each source file is located into a subdirectory representing its "namespace", for instance : The build process has to create a "build" directory, then when each file is compiling has to create its namespace directory inside the "build" one, for instance, when compiling std/io/network/tcp.cc he run an mkdir command with mkdir -p build/std/io/network The Makefile snippet is : STDSRC=stdlib/std/hashing/md5.cc \ stdlib/std/hashing/crc32.cc \ stdlib/std/hashing/sha1.cc \ stdlib/std/hashing/sha2.cc \ stdlib/std/io/network/http.cc \ stdlib/std/io/network/tcp.cc \ stdlib/std/io/network/smtp.cc \ stdlib/std/io/file.cc \ stdlib/std/io/console.cc \ stdlib/std/io/xml.cc \ stdlib/std/type/reflection.cc \ stdlib/std/type/string.cc \ stdlib/std/type/matrix.cc \ stdlib/std/type/array.cc \ stdlib/std/type/map.cc \ stdlib/std/type/type.cc \ stdlib/std/type/binary.cc \ stdlib/std/encoding.cc \ stdlib/std/os/dll.cc \ stdlib/std/os/time.cc \ stdlib/std/os/threads.cc \ stdlib/std/os/process.cc \ stdlib/std/pcre.cc \ stdlib/std/math.cc STDOBJ=$(STDSRC:.cc=.so) all: stdlib stdlib: $(STDOBJ) .cc.so: mkdir -p `dirname $< | sed -e 's/stdlib/stdlib\/build/'` $(CXX) $< -o `dirname $< | sed -e 's/stdlib/stdlib\/build/'`/`basename $< .cc`.so $(CFLAGS) $(LDFLAGS) I have two questions : 1 - The problem is that the make command, i really don't know why, doesn't check if a file was modified and launch the build process on ALL the files no matter what, so if i need to build only one file, i have to build them all or use the command : make path/to/single/file.so Is there any way to solve this? 2 - Any way to do this in a "cleaner" way without have to distribute all the build directories with sources? Thanks

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• Rewrite arrays using collections

  - by owca

  I have a task, which I was able to do with the use of simplest methods - arrays. Now I'd like to go further and redo it using some more complicated java features like collections, but I've never used anything more complicated than 2d matrix. What should I look at and how to start with it. Should Tower become a Collection ? And here's the task : We have two classes - Tower and Block. Towers are built from Blocks. Ande here's sample code for testing: Block k1=new Block("yellow",1,5,4); Block k2=new Block("blue",2,2,6); Block k3=new Block("green",3,4,2); Block k4=new Block("yellow",1,5,4); Tower tower=new Tower(); tower.add(k1,k2,k3); "Added 3 blocks." System.out.println(tower); "block: green, base: 4cm x 3cm, thicknes: 2 cm block: blue, base: 6cm x 2cm, thicknes: 2 cm block: yellow, base: 5cm x 4cm, thicknes: 1 cm" tower.add(k2); "Tower already contains this block." tower.add(k4); "Added 1 block." System.out.println(tower); "block: green, base: 4cm x 3cm, thicknes: 2 cm block: blue, base: 6cm x 2cm, thicknes: 2 cm block: yellow, base: 5cm x 4cm, thicknes: 1 cm block: yellow, base: 5cm x 4cm, thicknes: 1 cm" tower.delete(k1); "Deleted 1 block" tower.delete(k1); "Block not in tower" System.out.println(tower); "block: blue, base: 6cm x 2cm, thicknes: 2 cm block: yellow, base: 5cm x 4cm, thicknes: 1 cm block: yellow, base: 5cm x 4cm, thicknes: 1 cm" Let's say I will treat Tower as a collection of blocks. How to perform search for specific block among whole collection ? Or should I use other interface ?

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• Game of life in F# with accelerator

  - by jpalmer

  I'm trying to write life in F# using accelerator v2, but for some odd reason my output isn't square despite all my arrays being square - It appears that everything but a rectangular area in the top left of the matrix is being set to false. I've got no idea how this could be happening as all my operations should treat the entire array equally. Any ideas? open Microsoft.ParallelArrays open System.Windows.Forms open System.Drawing type IPA = IntParallelArray type BPA = BoolParallelArray type PAops = ParallelArrays let RNG = new System.Random() let size = 1024 let arrinit i = Array2D.init size size (fun x y -> i) let target = new DX9Target() let threearr = new IPA(arrinit 3) let twoarr = new IPA(arrinit 2) let onearr = new IPA(arrinit 1) let zeroarr = new IPA(arrinit 0) let shifts = [|-1;-1|]::[|-1;0|]::[|-1;1|]::[|0;-1|]::[|0;1|]::[|1;-1|]::[|1;0|]::[|1;1|]::[] let progress (arr:BPA) = let sums = shifts //adds up whether a neighbor is on or not |> List.fold (fun (state:IPA) t ->PAops.Add(PAops.Cond(PAops.Rotate(arr,t),onearr,zeroarr),state)) zeroarr PAops.Or(PAops.CompareEqual(sums,threearr),PAops.And(PAops.CompareEqual(sums,twoarr),arr)) //rule for life let initrandom () = Array2D.init size size (fun x y -> if RNG.NextDouble() > 0.5 then true else false) type meform () as self= inherit Form() let mutable array = new BoolParallelArray(initrandom()) let timer = new System.Timers.Timer(1.0) //redrawing timer do base.DoubleBuffered <- true do base.Size <- Size(size,size) do timer.Elapsed.Add(fun _ -> self.Invalidate()) do timer.Start() let draw (t:Graphics) = array <- array |> progress let bmap = new System.Drawing.Bitmap(size,size) target.ToArray2D array |> Array2D.iteri (fun x y t -> if not t then bmap.SetPixel(x,y,Color.Black)) t.DrawImageUnscaled(bmap,0,0) do self.Paint.Add(fun t -> draw t.Graphics) do Application.Run(new meform())

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• Setting the DataGridColumn's dataField based on XML node with the same name

  - by Rie Mino

  I am stuck. Given this XML: <matrix> <row> <column>0.51</column> <column>0.52</column> <column>0.53</column> <column>0.54</column> </row> <row> <column>0.61</column> <column>0.62</column> <column>0.63</column> <column>0.64</column> </row> I am trying to define a DataGrid such that the row nodes will represent new rows in the DataGrid and the column nodes will be used to auto-populate the DataGrid's columns. I am having a problem setting the dataField for each of the DataGridColumn ojects created. The DataGrid is created but the cell values for row 1 are all 0.51 and row 2 are 0.61. What am I doing wrong here?

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• Alternative to as3isolib?

  - by tedw4rd

  Hi everyone, I've been working on a Flash game that involves an isometric space. I've been using as3isolib for a while now, and I'm less than impressed with how easy it is to use. Whether I'm approaching it the wrong way or it's just not that great to use is a question for another post. Anyways, I've been thinking of a different way to approach the problem of isometric positions, and I think I've got an idea that might work. Essentially, each object that is to be rendered to the iso-space maintains a 3-coordinate position. Those items are then registered with a camera that projects that 3-coordinate position to a 2-coordinate point on the screen according to the math on this Wikipedia article. Then, the MovieClip is added to the stage (or to the camera's MovieClip, perhaps) at that point, and at a child index of the point's y-value. That way, I figure objects that are closer to the camera will be "above" the objects further away, and will get rendered over them. So my question, then, is two-fold: Do you think this idea will work the way I think it will? Are there any existing 3D matrix/vector packages that I should look at? I know there's a Matrix3 class in Flex 3, but we're not using Flex for this game. Thanks!

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• Azure SDK causes Node.js service bus call to run slow

  - by PazoozaTest Pazman

  I am using this piece of code to call the service bus queue from my node.js server running locally using web matrix, I have also upload to windows azure "web sites" and it still performs slowly. var sb1 = azure.createServiceBusService(config.serviceBusNamespace, config.serviceBusAccessKey); sbMessage = { "Entity": { "SerialNumbersToCreate": '0', "SerialNumberSize": config.usageRates[3], "BlobName": 'snvideos' + channel.ChannelTableName, "TableName": 'snvideos' + channel.ChannelTableName } }; sb1.getQueue('serialnumbers', function(error, queue){ if (error === null){ sb1.sendQueueMessage('serialnumbers', JSON.stringify(sbMessage), function(error) { if (!error) res.send(req.query.callback + '({data: ' + JSON.stringify({ success: true, video: newVideo }) + '});'); else res.send(req.query.callback + '({data: ' + JSON.stringify({ success: false }) + '});'); }); } else res.send(req.query.callback + '({data: ' + JSON.stringify({ success: false }) + '});'); }); It can be up to 5 seconds before the server responds back to the client with the return result. When I comment out the sb1.getQueue('serialnumbers', function(error, queue){ and just have it return without sending a queue message it performs in less than 1 second. Why is that? Is my approach to using the azure sdk service bus correct? Any help would be appreciated.

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• How to setup OpenGL camera for a racing game

  - by vian

  I need the view to show the road polygon (a rectangle 3.f * 100.f) with a vanishing point for a road being at 3/4 height of the viewport and the nearest road edge as a viewport's bottom side. See Crazy Taxi game for an example of what I wish to do. I'm using iPhone SDK 3.1.2 default OpenGL ES project template. I setup the projection matrix as follows: glMatrixMode(GL_PROJECTION); glLoadIdentity(); glFrustumf(-2.25f, 2.25f, -1.5f, 1.5f, 0.1f, 1000.0f); Then I use glRotatef to adjust for landscape mode and setup camera. glMatrixMode(GL_MODELVIEW); glLoadIdentity(); glRotatef(-90, 0.0f, 0.0f, 1.0f); const float cameraAngle = 45.0f * M_PI / 180.0f; gluLookAt(0.0f, 2.0f, 0.0f, 0.0f, 0.0f, 100.0f, 0.0f, cos(cameraAngle), sin(cameraAngle)); My road polygon triangle strip is like this: static const GLfloat roadVertices[] = { -1.5f, 0.0f, 0.0f, 1.5f, 0.0f, 0.0f, -1.5f, 0.0f, 100.0f, 1.5f, 0.0f, 100.0f, }; And I can't seem to find the right parameters for gluLookAt. My vanishing point is always at the center of the screen.

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• Matlab - Propagate points orthogonally on to the edge of shape boundaries

  - by Graham

  Hi I have a set of points which I want to propagate on to the edge of shape boundary defined by a binary image. The shape boundary is defined by a 1px wide white edge. I also have the coordinates of these points stored in a 2 row by n column matrix. The shape forms a concave boundary with no holes within itself made of around 2500 points. I want to cast a ray from each point from the set of points in an orthogonal direction and detect at which point it intersects the shape boundary at. What would be the best method to do this? Are there some sort of ray tracing algorithms that could be used? Or would it be a case of taking orthogonal unit vector and multiplying it by a scalar and testing after multiplication if the end point of the vector is outside the shape boundary. When the end point of the unit vector is outside the shape, just find the point of intersection? Thank you very much in advance for any help!

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• How to map coordinates in AxesImage to coordinates in saved image file?

  - by Vebjorn Ljosa

  I use matplotlib to display a matrix of numbers as an image, attach labels along the axes, and save the plot to a PNG file. For the purpose of creating an HTML image map, I need to know the pixel coordinates in the PNG file for a region in the image being displayed by imshow. I have found an example of how to do this with a regular plot, but when I try to do the same with imshow, the mapping is not correct. Here is my code, which saves an image and attempts to print the pixel coordinates of the center of each square on the diagonal: import numpy as np import matplotlib.pyplot as plt fig = plt.figure() ax = fig.add_axes([0.1, 0.1, 0.8, 0.8]) axim = ax.imshow(np.random.random((27,27)), interpolation='nearest') for x, y in axim.get_transform().transform(zip(range(28), range(28))): print int(x), int(fig.get_figheight() * fig.get_dpi() - y) plt.savefig('foo.png', dpi=fig.get_dpi()) Here is the resulting foo.png, shown as a screenshot in order to include the rulers: The output of the script starts and ends as follows: 73 55 92 69 111 83 130 97 149 112 … 509 382 528 396 547 410 566 424 585 439 As you see, the y-coordinates are correct, but the x-coordinates are stretched: they range from 73 to 585 instead of the expected 135 to 506, and they are spaced 19 pixels o.c. instead of the expected 14. What am I doing wrong?

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• C# images cropping,splitting,saving

  - by cheesebunz

  Hi, as stated in subject, i have an image: private Image testing; testing = new Bitmap(@"sampleimg.jpg"); I would like to split it into 3 x 3 matrix meaning 9 images in total and save it.Any tips or tricks to do this simple? I'm using visual studios 2008 and working on smart devices. Tried some ways but i can't get it. This is what i tried: int x = 0; int y = 0; int width = 3; int height = 3; int count = testing.Width / width; Bitmap bmp = new Bitmap(width, height); Graphics g = Graphics.FromImage(bmp); for (int i = 0; i < count; i++) { g.Clear(Color.Transparent); g.DrawImage(testing, new Rectangle(0, 0, width, height), new Rectangle(x, y, width, height), GraphicsUnit.Pixel); bmp.Save(Path.ChangeExtension(@"C\AndrewPictures\", String.Format(".{0}.bmp",i))); x += width; }

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• Suggestions of the easiest algorithms for some Graph operations

  - by Nazgulled

  Hi, The deadline for this project is closing in very quickly and I don't have much time to deal with what it's left. So, instead of looking for the best (and probably more complicated/time consuming) algorithms, I'm looking for the easiest algorithms to implement a few operations on a Graph structure. The operations I'll need to do is as follows: List all users in the graph network given a distance X List all users in the graph network given a distance X and the type of relation Calculate the shortest path between 2 users on the graph network given a type of relation Calculate the maximum distance between 2 users on the graph network Calculate the most distant connected users on the graph network A few notes about my Graph implementation: The edge node has 2 properties, one is of type char and another int. They represent the type of relation and weight, respectively. The Graph is implemented with linked lists, for both the vertices and edges. I mean, each vertex points to the next one and each vertex also points to the head of a different linked list, the edges for that specific vertex. What I know about what I need to do: I don't know if this is the easiest as I said above, but for the shortest path between 2 users, I believe the Dijkstra algorithm is what people seem to recommend pretty often so I think I'm going with that. I've been searching and searching and I'm finding it hard to implement this algorithm, does anyone know of any tutorial or something easy to understand so I can implement this algorithm myself? If possible, with C source code examples, it would help a lot. I see many examples with math notations but that just confuses me even more. Do you think it would help if I "converted" the graph to an adjacency matrix to represent the links weight and relation type? Would it be easier to perform the algorithm on that instead of the linked lists? I could easily implement a function to do that conversion when needed. I'm saying this because I got the feeling it would be easier after reading a couple of pages about the subject, but I could be wrong. I don't have any ideas about the other 4 operations, suggestions?

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• UML Modelling in C++Builder 2010 Professional

  - by Gordon Brandly

  I'd like to do some basic class diagram UML models in the Pro version of C++Builder 2010. Embarcadero has a C++Builder Features Matrix document, one line of which says "UML Code Visualization – at any time, get a UML model view of your source code" and has a check in the "Professional" column of that table -- I assume this means it should be available to me. Yet, when I open an existing project and do a View | Model View, there's nothing in the Model View window. The only diagram I can find is on the Graph tab of the C++ Class Explorer. I wouldn't call that a UML diagram myself -- is that what Embarcadero is referring to? Embarcadero's table shows that many UML diagrams are not available in Pro, but it looks to me like Class Diagrams should be available. Other lines in that same table indicate that both "Full two-way class diagrams with synchronization between code and diagrams" and "Diagram hyper-linking and annotations" are also supposed to be available in Pro. The Class Explorer graph is one-way only as far as I can tell, so I hope they're referring to something else I haven't been able to find so far. Thanks for any insight into this.

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• Trouble with applying a nested loop on a list

  - by user1665355

  I have a list consisting of 3 elements: datalist=list(a=datanew1,b=datanew2,c=datanew3) datalist$a : Inv_ret Firm size leverage Risk Liquidity Equity 17 0.04555968 17.34834 0.1323199 0.011292273 0.02471489 0 48 0.01405835 15.86315 0.6931730 0.002491093 0.12054914 0 109 0.04556252 16.91602 0.1714068 0.006235836 0.01194579 0 159 0.04753472 14.77039 0.3885720 0.007126830 0.06373028 0 301 0.03941040 16.94377 0.1805346 0.005450653 0.01723319 0 datalist$b : Inv_ret Firm size leverage Risk Liquidity Equity 31 0.04020832 18.13300 0.09326265 0.015235240 0.01579559 0.005025379 62 0.04439078 17.84086 0.11016402 0.005486982 0.01266566 0.006559096 123 0.04543250 18.00517 0.12215307 0.011154742 0.01531451 0.002282790 173 0.03960613 16.45457 0.10828643 0.011506857 0.02385191 0.009003780 180 0.03139643 17.57671 0.40063094 0.003447233 0.04530395 0.000000000 datalist$c : Inv_ret Firm size leverage Risk Liquidity Equity 92 0.03081029 19.25359 0.10513159 0.01635201 0.025760806 0.000119744 153 0.03280746 19.90229 0.11731517 0.01443786 0.006769735 0.011999005 210 0.04655847 20.12543 0.11622403 0.01418010 0.003125632 0.003802365 250 0.03301018 20.67197 0.13208234 0.01262499 0.009418828 0.021400052 282 0.04355975 20.03012 0.08588316 0.01918129 0.004213846 0.023657440 I am trying to create a cor.test on the datalist above : Cor.tests=sapply(datalist,function(x){ for(h in 1:length(names(x))){ for(i in 1:length(names(x$h[i]))){ for(j in 1:length(names(x$h[j]))){ cor.test(x$h[,i],x$h[,j])$p.value }}}}) But I get an error : Error in cor.test.default(x$h[, i], x$h[, j]) : 'x' must be a numeric vector Any suggestions about what I am doing wrong? P.S. If I simply have one dataframe, datanew1 : Inv_ret Firm size leverage Risk Liquidity Equity 17 0.04555968 17.34834 0.1323199 0.011292273 0.02471489 0 48 0.01405835 15.86315 0.6931730 0.002491093 0.12054914 0 109 0.04556252 16.91602 0.1714068 0.006235836 0.01194579 0 159 0.04753472 14.77039 0.3885720 0.007126830 0.06373028 0 301 0.03941040 16.94377 0.1805346 0.005450653 0.01723319 0 I use this loop : results=matrix(NA,nrow=6,ncol=6) for(i in 1:length(names(datanew1))){ for(j in 1:length(names(datanew1))){ results[i,j]<-cor.test(datanew1[,i],datanew1[,j])$p.value }} And the output is: results : [,1] [,2] [,3] [,4] [,5] [,6] [1,] 0.000000e+00 7.085663e-09 3.128975e-10 3.018239e-02 4.806400e-10 0.475139526 [2,] 7.085663e-09 0.000000e+00 2.141581e-21 0.000000e+00 2.247825e-20 0.454032499 [3,] 3.128975e-10 2.141581e-21 0.000000e+00 2.485924e-25 2.220446e-16 0.108643838 [4,] 3.018239e-02 0.000000e+00 2.485924e-25 0.000000e+00 5.870007e-15 0.006783324 [5,] 4.806400e-10 2.247825e-20 2.220446e-16 5.870007e-15 0.000000e+00 0.558827862 [6,] 4.751395e-01 4.540325e-01 1.086438e-01 6.783324e-03 5.588279e-01 0.000000000 Which is exactly what I want. But I want to get 3 matrices, one for each element of the datalist above.

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• Dimension Mismatch MatLab; cant figure out why it is mismatching

  - by Abid

  I think it may be a syntax issue, here is the code. load ([ 'C:\Users\Abid\Desktop\Inquiry Runs\dtS' ]) dtS((dtS==0))=nan; for j=2:9; maxS=max(dtS(j,:)); minS=min(dtS(j,:)); maxval(j,:)=dtS((dtS>(maxS-.1*maxS))); minval(j,:)=dtS((dtS<(minS+.1*minS))); avmax(j)=mean(maxval(j,:)); avmin(j)=mean(minval(j,:)); avs(j,:)=[avmax(j) avmin(j)] end So I know the the row matrices are different sizes every loop. For example maxval(j,:) will change depending one row it is looking through for certain values. I did this manually and I see that on the first loop the matrices are size (1,1), however, if I set the loop to run for only j=2, the row length is 13. Usually if a matrix is changing size on the loop, I only get a warning, but this time I think it is due to a reason I don't understand.

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• Need to calculate rotation-vector from Sensor.TYPE_ORIENTATION data

  - by Sponge

  I need to calculate a rotation vector out of the data i get from Sensor.TYPE_ORIENTATION. The sensor data is defined like this: the values have to be recalculated to become a correct 3d position: values[0]: Azimuth, angle between the magnetic north direction and the Y axis, around the Z axis (0 to 359). 0=North, 90=East, 180=South, 270=West values[1]: Pitch, rotation around X axis (-180 to 180), with positive values when the z-axis moves toward the y-axis. values[2]: Roll, rotation around Y axis (-90 to 90), with positive values when the x-axis moves away from the z-axis I need all three values like the Z axis value (from 0 to 360 degree). I tried a lot but cant figure out how to do this :/ i also tried to use Sensor.TYPE_ACCELEROMETER and Sensor.TYPE_MAGNETIC_FIELD to calculate this 3d vector on my own. here is the code: final float[] inR = new float[16]; // load inR matrix from current sensor data: SensorManager.getRotationMatrix(inR, null, gravityValues, geomagneticValues); float[] orientation = new float[3]; SensorManager.getOrientation(inR, orientation); mapMagAndAcclDataToVector(orientation); //here i do some *360 stuff orientetionChanged(orientation); //then the correct values are passed (in theorie) But this didn't work and i think it is much to complicated. So i bet there is a simple solution how to recalc the values of ensor.TYPE_ORIENTATION to make them a 3d rotation vector, but i just dont know how to do it. If you know the answer please tell me.

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• Warshall Algorithm Logic - Stuck

  - by stan

  I am trying to use this logic to understand what is going on with the adjacency matrix, but i am massivley confused where it says about interspacing for a b c d ..... Could anyone explain what is going on here? Thank you (tagged as java as its the language this was demonstarted to us in, so if anyone posted any code examples they could see it was in that language) http://compprog.wordpress.com/2007/11/15/all-sources-shortest-path-the-floyd-warshall-algorithm/ Here is the code: for (k = 0; k < n; ++k) { for (i = 0; i < n; ++i) for (j = 0; j < n; ++j) /* If i and j are different nodes and if the paths between i and k and between k and j exist, do */ if ((dist[i][k] * dist[k][j] != 0) && (i != j)) /* See if you can't get a shorter path between i and j by interspacing k somewhere along the current path */ if ((dist[i][k] + dist[k][j] < dist[i][j]) || (dist[i][j] == 0)) dist[i][j] = dist[i][k] + dist[k][j];

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• How to embed XBase expressions in an Xtext DSL

  - by Marcus Mathioudakis

  I am writing a simple little DSL for specifying constraints on messages, and Have been trying without success for a while to embed XBase expressions into the language. The Grammar looks like this: grammar org.xtext.businessrules.BusinessRules with org.eclipse.xtext.xbase.Xbase //import "http://www.eclipse.org/xtext/xbase/Xbase" as xbase import "http://www.eclipse.org/xtext/common/JavaVMTypes" as jvmTypes generate businessRules "http://www.xtext.org/businessrules/BusinessRules" Start: rules+=Constraint*; Constraint: {Constraint} 'FOR' 'PAYLOAD' payload=PAYLOAD 'ELEMENT' element=ID 'CONSTRAINED BY' constraint=XExpression; PAYLOAD: "SimulationSessionEvents" |"stacons" |"any" ; Range: 'above' min=INT ('below' max=INT)? |'below' max=INT ('above' min=INT)? ; When trying to parse a file such as: FOR PAYLOAD SimulationSessionEvents ELEMENT matrix CONSTRAINED BY ... I can't get it to work for ... = any kind of Arithmetic expression, although it works for ...= loop or if expression, or even just a number. As soon as I do something like '-5' or '4-5' it says Couldn't resolve reference to JvmIdentifiableElement '-', even though the Xbase.xtext Grammar looks like it allows these expressions. I don't think I'm missing any Jars, as it doesn't complain when I run the mwe workflow, but only when trying to parse the input file. Any help would be much appreciated.

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• how to create a changing variable for fsolve

  - by Shun Miyamoto

  i want fsolve to calculate the output for different uc each time (increasing uc by 0.001 each time). each output from fsolve should be sent to a simulink model seperatly. so i set a loop to do so, but i believe that at the currenty constellation (if it will work)will just calculate 1000 different values? is there a way to send out the values seperately? if not, how can i create a parameter uc. that goes from 0 to say 1000? i tried uc=0:0.001:1000, but again, the demension doen't seem to fit. how do i create a function that takes the next element of a vector/matrix each time the function is called? uc=0; for i=0:1000 x0=[1,1,1]; y=x0(1); u=x0(2); yc=x0(3); options=optimset('Display','off'); x= fsolve(@myfun,x0,options,uc,d,spacing_amplitude,spacing_width); end best regards

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• Bilinear interpolation - DirectX vs. GDI+

  - by holtavolt

  I have a C# app for which I've written GDI+ code that uses Bitmap/TextureBrush rendering to present 2D images, which can have various image processing functions applied. This code is a new path in an application that mimics existing DX9 code, and they share a common library to perform all vector and matrix (e.g. ViewToWorld/WorldToView) operations. My test bed consists of DX9 output images that I compare against the output of the new GDI+ code. A simple test case that renders to a viewport that matches the Bitmap dimensions (i.e. no zoom or pan) does match pixel-perfect (no binary diff) - but as soon as the image is zoomed up (magnified), I get very minor differences in 5-10% of the pixels. The magnitude of the difference is 1 (occasionally 2)/256. I suspect this is due to interpolation differences. Question: For a DX9 ortho projection (and identity world space), with a camera perpendicular and centered on a textured quad, is it reasonable to expect DirectX.Direct3D.TextureFilter.Linear to generate identical output to a GDI+ TextureBrush filled rectangle/polygon when using the System.Drawing.Drawing2D.InterpolationMode.Bilinear setting? For this (magnification) case, the DX9 code is using this (MinFilter,MipFilter set similarly): Device.SetSamplerState(0, SamplerStageStates.MagFilter, (int)TextureFilter.Linear); and the GDI+ path is using: g.InterpolationMode = InterpolationMode.Bilinear; I thought that "Bilinear Interpolation" was a fairly specific filter definition, but then I noticed that there is another option in GDI+ for "HighQualityBilinear" (which I've tried, with no difference - which makes sense given the description of "added prefiltering for shrinking") Followup Question: Is it reasonable to expect pixel-perfect output matching between DirectX and GDI+ (assuming all external coordinates passed in are equal)? If not, why not? Finally, there are a number of other APIs I could be using (Direct2D, WPF, GDI, etc.) - and this question generally applies to comparing the output of "equivalent" bilinear interpolated output images across any two of these. Thanks!

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• Tips on designing a .NET API for future use with F#

  - by Drew Noakes

  I'm in the process of designing a .NET API to allow developers to create RoboCup agents for the 3D simulated soccer league. I'm pretty happy with how the API work with C# code, however I would like to use this project to improve my F# skill (which is currently based on reading rather than practice). So I would like to ask what kinds of things I should consider when designing an API that is to be consumed by both C# and F# code. Some points. I make fairly heavy use of matrix and vector math. These are currently immutable classes/structs. The API currently defines a few interfaces with the consumer implements (eg: IAgent), using instances of their implementations (eg: MyAgent) to construct other API classes (eg: new Client(myAgent)). The API fires events. The API exposes a few delegate types. The API includes several enums. I'd like to release a version of the API as soon as possible and don't want to make major changes to it later if I realise it's too difficult to work with from F#. Any advice is appreciated.

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