Sum of each column opencv - opencv

In Matlab, If A is a matrix, sum(A) treats the columns of A as vectors, returning a row vector of the sums of each column.
sum(Image); How could it be done with OpenCV?

Using cvReduce has worked for me. For example, if you need to store the column-wise sum of a matrix as a row matrix you could do this:
CvMat * MyMat = cvCreateMat(height, width, CV_64FC1);
// Fill in MyMat with some data...
CvMat * ColSum = cvCreateMat(1, MyMat->width, CV_64FC1);
cvReduce(MyMat, ColSum, 0, CV_REDUCE_SUM);
More information is available in the OpenCV documentation.

EDIT after 3 years:
The proper function for this is cv::reduce.
Reduces a matrix to a vector.
The function reduce reduces the matrix to a vector by treating the
matrix rows/columns as a set of 1D vectors and performing the
specified operation on the vectors until a single row/column is
obtained. For example, the function can be used to compute horizontal
and vertical projections of a raster image. In case of REDUCE_MAX and
REDUCE_MIN , the output image should have the same type as the source
one. In case of REDUCE_SUM and REDUCE_AVG , the output may have a
larger element bit-depth to preserve accuracy. And multi-channel
arrays are also supported in these two reduction modes.
OLD:
I've used ROI method: move ROI of height of the image and width 1 from left to right and calculate means.
Mat src = imread(filename, 0);
vector<int> graph( src.cols );
for (int c=0; c<src.cols-1; c++)
{
Mat roi = src( Rect( c,0,1,src.rows ) );
graph[c] = int(mean(roi)[0]);
}
Mat mgraph( 260, src.cols+10, CV_8UC3);
for (int c=0; c<src.cols-1; c++)
{
line( mgraph, Point(c+5,0), Point(c+5,graph[c]), Scalar(255,0,0), 1, CV_AA);
}
imshow("mgraph", mgraph);
imshow("source", src);
EDIT:
Just out of curiosity, I've tried resize to height 1 and the result was almost the same:
Mat test;
cv::resize(src,test,Size( src.cols,1 ));
Mat mgraph1( 260, src.cols+10, CV_8UC3);
for(int c=0; c<test.cols; c++)
{
graph[c] = test.at<uchar>(0,c);
}
for (int c=0; c<src.cols-1; c++)
{
line( mgraph1, Point(c+5,0), Point(c+5,graph[c]), Scalar(255,255,0), 1, CV_AA);
}
imshow("mgraph1", mgraph1);

cvSum respects ROI, so if you move a 1 px wide window over the whole image, you can calculate the sum of each column.
My c++ got a little rusty so I won't provide a code example, though the last time I did this I used OpenCVSharp and it worked fine. However, I'm not sure how efficient this method is.
My math skills are getting rusty too, but shouldn't it be possible to sum all elements in columns in a matrix by multiplying it by a vector of 1s?

For an 8 bit greyscale image, the following should work (I think).
It shouldn't be too hard to expand to different image types.
int imgStep = image->widthStep;
uchar* imageData = (uchar*)image->imageData;
uint result[image->width];
memset(result, 0, sizeof(uchar) * image->width);
for (int col = 0; col < image->width; col++) {
for (int row = 0; row < image->height; row++) {
result[col] += imageData[row * imgStep + col];
}
}
// your desired vector is in result

Related

Column-Wise Standard Deviation in OpenCV

Is there a direct way to compute the column-wise standard deviation for a matrix in opencv? Similar to std in Matlab. I've found one for the mean:
cv::Mat col_mean;
reduce(A, col_mean, 1, CV_REDUCE_AVG);
but I cannot find such a function for the standard deviation.
Here's a quick answer to what you're looking for. I added both the standard deviation and mean for each column. The code can easily be modified for rows.
cv::Mat A = ...; // FILL IN THE DATA FOR YOUR INPUT MATRIX
cv::Mat meanValue, stdValue;
cv::Mat colSTD(1, A.cols, CV_64FC1);
cv::Mat colMEAN(1, A.cols, CV_64FC1);
for (int i = 0; i < A.cols; i++){
cv::meanStdDev(A.col(i), meanValue, stdValue);
colSTD.at<double>(i) = stdValue.at<double>(0);
colMEAN.at<double>(i) = meanValue.at<double>(0);
}
The following is not in a single line,but it is another version without loops:
reduce(A, meanOfEachCol, 0, CV_REDUCE_AVG); // produces single row of columnar means
Mat repColMean;
cv::repeat(meanOfEachCol, rows, 1, repColMean); // repeat mean vector 'rows' times
Mat diffMean = A - repColMean; // get difference
Mat diffMean2 = diffMean.mul(diffMean); // per element square
Mat varMeanF;
cv::reduce(diffMean2, varMeanF, 0, CV_REDUCE_AVG); // sum each column's elements to get single row
Mat stdMeanF;
cv::sqrt(varMeanF, stdMeanF); // get standard deviation

Distinguish rock scences using opencv

I am struggling with finding the appropriate contour algorithm for a low quality image. The example image shows a rock scene:
What I am trying to achieve is to find contours arround features such as:
light areas
dark areas
grey1 areas
grey2 areas
etc. until grey-n areas
(The number of areas shall be a parameter of choice)
I do not want to take a simple binary-threshold but rather use some sort of contour-finding (for example watershed or other). The major feature-lines shall be kept, noise within a feature-are can be flattened.
The result of my code can be seen on the images to the right.
Unfortunately, as you can easily tell, the colors do not really represent the original large-scale image features! For example: check out the two areas that I circled with red - these features are almost completely flooded with another color. What I imagine is that at least the very light and the very dark areas are covered by its own color.
cv::Mat cv_src = cv::imread(argv[1]);
cv::Mat output;
cv::Mat cv_src_gray;
cv::cvtColor(cv_src, cv_src_gray, cv::COLOR_RGB2GRAY);
double clipLimit = 0.1;
cv::Size titleGridSize = cv::Size(8,8);
cv::Ptr<cv::CLAHE> clahe = cv::createCLAHE(clipLimit, titleGridSize);
clahe->apply(cv_src_gray, output);
cv::equalizeHist(output, output);
cv::cvtColor(output, cv_src, cv::COLOR_GRAY2RGB);
// Create binary image from source image
cv::Mat bw;
cv::cvtColor(cv_src, bw, cv::COLOR_BGR2GRAY);
cv::threshold(bw, bw, 180, 255, cv::THRESH_BINARY);
// Perform the distance transform algorithm
cv::Mat dist;
cv::distanceTransform(bw, dist, cv::DIST_L2, CV_32F);
// Normalize the distance image for range = {0.0, 1.0}
cv::normalize(dist, dist, 0, 1., cv::NORM_MINMAX);
// Threshold to obtain the peaks
cv::threshold(dist, dist, .2, 1., cv::THRESH_BINARY);
// Create the CV_8U version of the distance image
cv::Mat dist_8u;
dist.convertTo(dist_8u, CV_8U);
// Find total markers
std::vector<std::vector<cv::Point> > contours;
cv::findContours(dist_8u, contours, cv::RETR_EXTERNAL, cv::CHAIN_APPROX_SIMPLE);
int ncomp = contours.size();
// Create the marker image for the watershed algorithm
cv::Mat markers = cv::Mat::zeros(dist.size(), CV_32S);
// Draw the foreground markers
for (int i = 0; i < ncomp; i++)
cv::drawContours(markers, contours, i, cv::Scalar::all(i+1), -1);
// Draw the background marker
cv::circle(markers, cv::Point(5,5), 3, CV_RGB(255,255,255), -1);
// Perform the watershed algorithm
cv::watershed(cv_src, markers);
// Generate random colors
std::vector<cv::Vec3b> colors;
for (int i = 0; i < ncomp; i++)
{
int b = cv::theRNG().uniform(0, 255);
int g = cv::theRNG().uniform(0, 255);
int r = cv::theRNG().uniform(0, 255);
colors.push_back(cv::Vec3b((uchar)b, (uchar)g, (uchar)r));
}
// Create the result image
cv::Mat dst = cv::Mat::zeros(markers.size(), CV_8UC3);
// Fill labeled objects with random colors
for (int i = 0; i < markers.rows; i++)
{
for (int j = 0; j < markers.cols; j++)
{
int index = markers.at<int>(i,j);
if (index > 0 && index <= ncomp)
dst.at<cv::Vec3b>(i,j) = colors[index-1];
else
dst.at<cv::Vec3b>(i,j) = cv::Vec3b(0,0,0);
}
}
// Show me what you got
imshow("final_result", dst);
I think you can use a simple clustering such as k-means for this, then examine the cluster centers (or the mean and standard deviations of each cluster). I quickly tried it in matlab.
im = imread('tvBqt.jpg');
gr = rgb2gray(im);
x = double(gr(:));
idx = kmeans(x, 4);
cl = reshape(idx, 600, 472);
figure,
subplot(1, 2, 1), imshow(gr, []), title('original')
subplot(1, 2, 2), imshow(label2rgb(cl), []), title('clustered')
The result:
You could try using SLIC Superpixels. I tried it and showed some good results. You could vary the parameters to get better clustering.
SLIC Superpixels
SLIC Superpixels with OpenCV C++
SLIC Superpixels with OpenCV Python

OpenCV 2.4.7 Mat::convertTo() 32-bit to 16-bit truncate

I've noticed that using convertTo to convert a matrix from 32-bit to 16-bit "rounds" number to the upper boud. So, values bigger than 0x0000FFFF in the source matrix will be set as 0xFFFF in the destination matrix.
What I want for my application is instead to mask the values, setting in the destination just the 2 LSB of the values.
Here is an example:
Mat mat32;
Mat mat16;
mat32 = Mat(2,2,CV_32SC1);
for(int y = 0; y < 2; y++)
for(int x = 0; x < 2; x++)
mat32.at<unsigned int>(cv::Point(x,y)) = 0x0000FFFE + (y*2+x);
mat32.convertTo(mat16, CV_16UC1);
The matrixes have these values:
32 bits matrix:
0000FFFE 0000FFFF
00010000 00010001
16 bits matrix:
0000FFFE 0000FFFF
0000FFFF 0000FFFF
In the second row of 16-bit matrix I want to have
00000000 00000001
I can do this by scanning the source matrix value-by-value and masking the values, but the performances are low.
Is there an OpenCV function that does this?
Thanks to everyone!
MIX
This can be done, but this requires a somewhat dirty trick, so it is up to you to use this approach or not. So this is how it can be done:
For this example lets create 1000x1000 32-bit matrix and set all its values to 65541 (=256*256+5). So after the conversion we expect to have a matrix filled with fives.
Mat M1(1000, 1000, CV_32S, Scalar(65541));
And here is the trick:
Mat M2(1000, 1000, CV_16SC2, M1.data);
We created matrix M2 over the same memory buffer as M1, but M2 'think' that this is a buffer of 2-channel 16-bit image. Now the last thing to do is to copy the channel you need to the place you need. This can be done by split() or mixChannels() functions. For example:
Mat M3(1000, 1000, CV_16S);
int fromto[] = {0,0};
Mat inpu[] = {M2}, outpu[] = {M3};
mixChannels(inpu, 1, outpu, 1, fromto, 1);
cout << M3.at<short>(10,10) << endl;
Ye I know that the format of mixChannels looks weird and makes the code even less readable, but it works... If you prefer split() function:
vector<Mat> v;
split(M2,v);
cout << v[0].at<short>(10,10) << " " << v[1].at<short>(10,10) << endl;
There is no OpenCV function (that I know of) which does the conversion like you want, so either you code it yourself or like you said you go through a masking step first to remove the 16 high bits.
The mask can be applied using the bitwise_and in C++ or cvAndS in C. See here.
You could also have made your hand-written code more efficient. In general, you should avoid OpenCV pixel accessors in loops because they have bad performance. I don't have an OpenCV install at hand so this could be slighlty off -- the idea is to use the data field directly, and step which is the number of bytes per row:
for(int y = 0; y < mat32.height; ++) {
int* row = (int*)( (char*)mat32.data + y * mat32.step);
for(int x = 0; x < mat32.step/ 4)
row[x] &= 0xffff;
Then, once the mask is applied, all values fit in 16 bits, and convertTo will just truncate the 16 upper bits.
The other solution is to code the conversion by hand:
mat16.resize( mat32.size() );
for(int y = 0; y < mat32.height; ++) {
const int* row32 = (const int*)( (char*)mat32.data + y * mat32.step);
short* row16 = (short*) ( (char*)mat16.data + y * mat16.step);
for(int x = 0; x < mat32.step/ 4)
row16[x] = short(row32[x]);

OpenCV displaying a 2-channel image (optical flow)

I have optical flow stored in a 2-channel 32F matrix. I want to visualize the contents, what's the easiest way to do this?
How do I convert a CV_32FC2 to RGB with an empty blue channel, something imshow can handle? I am using OpenCV 2 C++ API.
Super Bonus Points
Ideally I would get the angle of flow in hue and the magnitude in brightness (with saturation at a constant 100%).
imshow can handle only 1-channel gray-scale and 3-4 channel BRG/BGRA images. So you need do a conversion yourself.
I think you can do something similar to:
//extraxt x and y channels
cv::Mat xy[2]; //X,Y
cv::split(flow, xy);
//calculate angle and magnitude
cv::Mat magnitude, angle;
cv::cartToPolar(xy[0], xy[1], magnitude, angle, true);
//translate magnitude to range [0;1]
double mag_max;
cv::minMaxLoc(magnitude, 0, &mag_max);
magnitude.convertTo(magnitude, -1, 1.0 / mag_max);
//build hsv image
cv::Mat _hsv[3], hsv;
_hsv[0] = angle;
_hsv[1] = cv::Mat::ones(angle.size(), CV_32F);
_hsv[2] = magnitude;
cv::merge(_hsv, 3, hsv);
//convert to BGR and show
cv::Mat bgr;//CV_32FC3 matrix
cv::cvtColor(hsv, bgr, cv::COLOR_HSV2BGR);
cv::imshow("optical flow", bgr);
cv::waitKey(0);
The MPI Sintel Dataset provides C and MatLab code for visualizing computed flow. Download the ground truth optical flow of the training set from here. The archive contains a folder flow_code containing the mentioned source code.
You can port the code to OpenCV, however, I wrote a simple OpenCV wrapper to easily use the provided code. Note that the method MotionToColor is taken from the color_flow.cpp file. Note the comments in the listing below.
// Important to include this before flowIO.h!
#include "imageLib.h"
#include "flowIO.h"
#include "colorcode.h"
// I moved the MotionToColor method in a separate header file.
#include "motiontocolor.h"
cv::Mat flow;
// Compute optical flow (e.g. using OpenCV); result should be
// 2-channel float matrix.
assert(flow.channels() == 2);
// assert(flow.type() == CV_32F);
int rows = flow.rows;
int cols = flow.cols;
CFloatImage cFlow(cols, rows, 2);
// Convert flow to CFLoatImage:
for (int i = 0; i < rows; i++) {
for (int j = 0; j < cols; j++) {
cFlow.Pixel(j, i, 0) = flow.at<cv::Vec2f>(i, j)[0];
cFlow.Pixel(j, i, 1) = flow.at<cv::Vec2f>(i, j)[1];
}
}
CByteImage cImage;
MotionToColor(cFlow, cImage, max);
cv::Mat image(rows, cols, CV_8UC3, cv::Scalar(0, 0, 0));
// Compute back to cv::Mat with 3 channels in BGR:
for (int i = 0; i < rows; i++) {
for (int j = 0; j < cols; j++) {
image.at<cv::Vec3b>(i, j)[0] = cImage.Pixel(j, i, 0);
image.at<cv::Vec3b>(i, j)[1] = cImage.Pixel(j, i, 1);
image.at<cv::Vec3b>(i, j)[2] = cImage.Pixel(j, i, 2);
}
}
// Display or output the image ...
Below is the result when using the Optical Flow code and example images provided by Ce Liu.

OpenCV PCA question

I'm trying to create a PCA model in OpenCV to hold pixel coordinates. As an experiment I have two sets of pixel coordinates that maps out two approximate circles. Each set of coordiantes has 48 x,y pairs. I was experimenting with the following code which reads the coordinates from a file and stores them in a Mat structure. However, I don't think it is right and PCA in openCV seems very poorly covered on the Internet.
Mat m(2, 48, CV_32FC2); // matrix with 2 rows of 48 cols of floats held in two channels
pFile = fopen("data.txt", "r");
for (int i=0; i<48; i++){
int x, y;
fscanf(pFile, "%d%c%c%d%c", &x, &c, &c, &y, &c);
m.at<Vec2f>( 0 , i )[0] = (float)x; // store x in row 0, col i in channel 0
m.at<Vec2f>( 0 , i )[1] = (float)y; // store y in row 0, col i in channel 1
}
for (int i=0; i<48; i++){
int x, y;
fscanf(pFile, "%d%c%c%d%c", &x, &c, &c, &y, &c);
m.at<Vec2f>( 1 , i )[0] = (float)x; // store x in row 1, col i in channel 0
m.at<Vec2f>( 1 , i )[1] = (float)y; // store y in row 1, col i in channel 1
}
PCA pca(m, Mat(), CV_PCA_DATA_AS_ROW, 2); // 2 principle components??? Not sure what to put here e.g. is it 2 for two data sets or 48 for number of elements?
for (int i=0; i<48; i++){
float x = pca.mean.at<Vec2f>(i,0)[0]; //get average x
float y = pca.mean.at<Vec2f>(i,0)[1]; //get average y
printf("\n x=%f, y=%f", x, y);
}
However, this crashes when creating the pca object. I know this is a very basic question but I am a bit lost and was hoping that someone could get me started with pca in open cv.
Perhaps it would be helpful if you described in further detail what you need to use PCA for and what you hope to achieve (output?).
I am fairly sure that the reason your program crashes is because the input Mat is CV_32FC2, when it should be CV_32FC1. You need to reshape your data into 1 dimensional row vectors before using PCA, not knowing what you need I can't say how to reshape your data. (The common application with images is eigenFace which requires an image to be reshaped into a row vector). Additionally you will need to normalize your input data between 0 and 1.
As a further aside, usually you would choose to keep 1 less principal component than the number of input samples because the last principal component is simply orthogonal to the others.
I have worked with opencv PCA before and would like to help further. I would also refer you to this blog: http://www.bytefish.de/blog/pca_in_opencv which helped me get started with PCA in openCV.

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