How to convert vector<Mat> to vector<float>? - c++

Suppose i have a vector<Mat> called regionFeaMatand regionFeaMat.size() == 81 .In other words, regionFeaMat have 81 equal size matrix, and regionFeaMat[0].rows==256 and regionFeaMat[0].cols==1. I want to convert reginFeaMat to vector<float> reginFeaVec. I tried with following code but i got wrong result:
vector<float> regionFeaVec;
regionFeaVec.assign((float*)regionFeaMat[0].datastart, (float*)regionFeaMat[80].dataend);

You seem to have made a few wrong assumptions.
std::vector does store its elements contiguously in memory, but cv::Mat is a header containing a pointer to its internal buffer, so only pointers in vector<Mat> are stored contiguously, not the Mat data itself. Because of that, the memory that lies in between (float*)regionFeaMat[0].dataend and (float*)regionFeaMat[80].datastart is some random garbage - if it does contain other Mat's data partially, it's pure luck.
Because of the above, you can't have a one-liner assigning vector to any other vector and you have to insert each mat separately instead. Try something like this:
// prevent vector reallocation after each Mat insertion:
regionFeaVec.reserve(regionFeaMat.size()*regionFeaMat[0].cols*regionFeaMat[0].rows);
for (int i = 0; i < regionFeaMat.size(); ++i)
{
if (regionFeaMat[i].isContinuous())
regionFeaVec.insert(
regionFeaVec.end(),
(float*)regionFeaMat[i].datastart,
(float*)regionFeaMat[i].dataend
);
else
{
for (int j = 0; j < regionFeaMat[i].rows; ++j)
{
const float* row = regionFeaMat[i].ptr<float>(j);
regionFeaVec.insert(regionFeaVec.end(), row, row + regionFeaMat[i].cols);
}
}
}
Note that I'm checking if a particular Mat object is continuous, because as per OpenCV docs, each row may contain gaps at the end in some cases, and in that case we have to read the matrix row by row.
This code can be simplified, because if matrix is continuous, we may treat it as a 1D vector as per the docs referenced above:
// prevent vector reallocation after each Mat insertion:
regionFeaVec.reserve(regionFeaMat.size()*regionFeaMat[0].cols*regionFeaMat[0].rows);
for (int i = 0; i < regionFeaMat.size(); ++i)
{
cv::Size size = regionFeaMat[i].size();
if (regionFeaMat[i].isContinuous())
{
size.width *= size.height;
size.height = 1;
}
for (int j = 0; j < size.height; ++j)
{
const float* row = regionFeaMat[i].ptr<float>(j);
regionFeaVec.insert(regionFeaVec.end(), row, row + size.width);
}
}
If you want to prevent vector reallocation in more general cases, you also have to change the method of calculating the number of elements passed to reserve(). The method I use assumes all the Mat objects have only two dimensions that are equal for all the objects since this is how you described your problem.
Also, if you want to assign it to vector<float>, be sure that the element type of regionFeaMat is CV_32F.

Related

How can I reserve a fixed buffer size in OpenCV Mat?

I am rewriting some legacy code that does matrix operations on doubles using a raw C-style array. Since the code already has a dependency on OpenCV somewhere else, I want to use the cv::Mat class instead.
The specific code that bothers me works on square matrixes from size 1*1 to NN. It does so by allocating an NN buffer and uses a subset of it for smaller matrixes.
double* buf = new double[NxN];
for (int i = 1; i < N; ++i) {
// Reuse buf to create a i*i matrix and perform matrix operations
...
}
delete[] buf;
Basically, I want to replace that code to use cv::Mat objects in the loop instead. Problem is, the code requires a lot of loop iterations (there are nested loops and so on) and there are too many allocations/deallocations if I just use the naïve and clean approach. Therefore, I want to reserve the size of my matrix object beforehand and resize it for each iteration. This would ideally look like this:
cv::Mat m;
m.reserveBuffer(N * N * sizeof(double));
for (int i = 1; i < N; ++i) {
m = cv::Mat(i, i, CV_64F);
// Perform matrix operations on m
...
}
But in my understanding this would simply drop the previous instance of m and then allocate a i*i matrix. What would the right approach be?
You can create a submatix header for your buffer using cv::Mat::operator(). Pass a cv::Rect for ROI you want to process in current loop iteration ({0, 0, i, i} in your case) and it will return a view of your buffer region as another cv::Mat instance. It will not allocate new buffer but will refer to original buffer data instead.
cv::Mat m(N, N, CV_64FC1);
for (int i = 1; i < N; ++i) {
cv::Mat subM = m({0, 0, i*i});
// Perform matrix operations on "subM"
// Modifying "subM" will modify "m" buffer region that "subM" represents
}
Note that subM will not be continious, so you will need to process it row by row if you do any raw buffer processing.

C++ : Create 3D array out of stacking 2D arrays

In Python I normally use functions like vstack, stack, etc to easily create a 3D array by stacking 2D arrays one onto another.
Is there any way to do this in C++?
In particular, I have loaded a image into a Mat variable with OpenCV like:
cv::Mat im = cv::imread("image.png", 0);
I would like to make a 3D array/Mat of N layers by stacking copies of that Mat variable.
EDIT: This new 3D matrix has to be "travellable" by adding an integer to any of its components, such that if I am in the position (x1,y1,1) and I add +1 to the last component, I arrive to (x1,y1,2). Similarly for any of the coordinates/components of the 3D matrix.
SOLVED: Both answers from #Aram and #Nejc do exactly what expected. I set #Nejc 's answer as the correct one for his shorter code.
The Numpy function vstack returns a contiguous array. Any C++ solution that produces vectors or arrays of cv::Mat objects does not reflect the behaviour of vstack in this regard, becase separate "layers" belonging to individual cv::Mat objects will not be stored in contiguous buffer (unless a careful allocation of underlying buffers is done in advance of course).
I present the solution that copies all arrays into a three-dimensional cv::Mat object with a contiguous buffer. As far as the idea goes, this answer is similar to Aram's answer. But instead of assigning pixel values one by one, I take advantage of OpenCV functions. At the beginning I allocate the matrix which has a size N X ROWS X COLS, where N is the number of 2D images I want to "stack" and ROWS x COLS are dimensions of each of these images.
Then I make N steps. On every step, I obtain the pointer to the location of the first element along the "outer" dimension. I pass that pointer to the constructor of temporary Mat object that acts as a kind of wrapper around the memory chunk of size ROWS x COLS (but no copies are made) that begins at the address that is pointed-at by pointer. I then use copyTo method to copy i-th image into that memory chunk. Code for N = 2:
cv::Mat img0 = cv::imread("image0.png", CV_IMREAD_GRAYSCALE);
cv::Mat img1 = cv::imread("image1.png", CV_IMREAD_GRAYSCALE);
cv::Mat images[2] = {img0, img1}; // you can also use vector or some other container
int dims[3] = { 2, img0.rows, img0.cols }; // dimensions of new image
cv::Mat joined(3, dims, CV_8U); // same element type (CV_8U) as input images
for(int i = 0; i < 2; ++i)
{
uint8_t* ptr = &joined.at<uint8_t>(i, 0, 0); // pointer to first element of slice i
cv::Mat destination(img0.rows, img0.cols, CV_8U, (void*)ptr); // no data copy, see documentation
images[i].copyTo(destination);
}
This answer is in response to the question above of:
In Python I normally use functions like vstack, stack, etc to easily create a 3D array by stacking 2D arrays one onto another.
This is certainly possible, you can add matrices into a vector which would be your "stack"
For instance you could use a
std::vector<cv::Mat>>
This would give you a vector of mats, which would be one slice, and then you could "layer" those by adding more slices vector
If you then want to have multiple stacks you can add that vector into another vector:
std::vector<std::vector<cv::Mat>>
To add matrix to an array you do:
myVector.push_back(matrix);
Edit for question below
In such case, could I travel from one position (x1, y1, z1) to an immediately upper position doing (x1,y1,z1+1), such that my new position in the matrix would be (x1,y1,z2)?
You'll end up with something that looks a lot like this. If you have a matrix at element 1 in your vector, it doesn't really have any relationship to the element[2] except for the fact that you have added it into that point. If you want to build relationships then you will need to code that in yourself.
You can actually create a 3D or ND mat with opencv, you need to use the constructor that takes the dimensions as input. Then copy each matrix into (this case) the 3D array
#include <opencv2/opencv.hpp>
using namespace cv;
using namespace std;
int main() {
// Dimensions for the constructor... set dims[0..2] to what you want
int dims[] = {5, 5, 5}; // 5x5x5 3d mat
Mat m = Mat::zeros(5, 5, CV_8UC1);
for (size_t i = 0; i < 5; i++) {
for (size_t k = 0; k < 5; k++) {
m.at<uchar>(i, k) = i + k;
}
}
// Mat with constructor specifying 3 dimensions with dimensions sizes in dims.
Mat 3DMat = Mat(3, dims, CV_8UC1);
// We fill our 3d mat.
for (size_t i = 0; i < m2.size[0]; i++) {
for (size_t k = 0; k < m2.size[1]; k++) {
for (size_t j = 0; j < m2.size[2]; j++) {
3DMat.at<uchar>(i, k, j) = m.at<uchar>(k, j);
}
}
}
// We print it to show the 5x5x5 array.
for (size_t i = 0; i < m2.size[0]; i++) {
for (size_t k = 0; k < m2.size[1]; k++) {
for (size_t j = 0; j < m2.size[2]; j++) {
std::cout << (int) 3DMat.at<uchar>(i, k, j) << " ";
}
std::cout << endl;
}
std::cout << endl;
}
return 0;
}
Based on the question and comments, I think you are looking for something like this:
std::vector<cv::Mat> vec_im;
//In side for loop:
vec_im.push_back(im);
Then, you can access it by:
Scalar intensity_1 = vec_im[z1].at<uchar>(y, x);
Scalar intensity_2 = vec_im[z2].at<uchar>(y, x);
This assumes that the image is single channel.

Opencv Mat vector assignment to a row of a matrix, fastest way?

What is the fastest way of assigning a vector to a matrix row in a loop? I want to fill a data matrix along its rows with vectors. These vectors are computed in a loop. This loop last until all the entries of data matrix is filled those vectors.
Currently I am using cv::Mat::at<>() method for accessing the elements of the matrix and fill them with the vector, however, it seems this process is quite slow. I have tried another way by using cv::Mat::X.row(index) = data_vector, it works fast but fill my matrix X with some garbage values which I can not understand, why.
I read that there exists another way of using pointers (fastest way), however, I can not able to understand. Can somebody explain how to use them or other different methods?
Here is a part of my code:
#define OFFSET 2
cv::Mat im = cv::imread("001.png", CV_LOAD_IMAGE_GRAYSCALE);
cv::Mat X = cv::Mat((im.rows - 2*OFFSET)*(im.cols - 2*OFFSET), 25, CV_64FC1); // Holds the training data. Data contains image patches
cv::Mat patch = cv::Mat(5, 5, im.type()); // Holds a cropped image patch
typedef cv::Vec<float, 25> Vec25f;
int ind = 0;
for (int row = 0; row < (im.rows - 2*OFFSET); row++){
for (int col = 0; col < (im.cols - 2*OFFSET); col++){
cv::Mat temp_patch = im(cv::Rect(col, row, 5, 5)); // crop an image patch (5x5) at each pixel
patch = temp_patch.clone(); // Needs to do this because temp_patch is not continuous in memory
patch.convertTo(patch, CV_64FC1);
Vec25f data_vector = patch.reshape(0, 1); // make it row vector (1X25).
for (int i = 0; i < 25; i++)
{
X.at<float>(ind, i) = data_vector[i]; // Currently I am using this way (quite slow).
}
//X_train.row(ind) = patch.reshape(0, 1); // Tried this but it assigns some garbage values to the data matrix!
ind += 1;
}
}
To do it the regular opencv way you could do :-
ImageMat.row(RowIndex) = RowMat.clone();
or
RowMat.copyTo(ImageMat.row(RowIndex));
Haven't tested for correctness or speed.
Just a couple of edits in your code
double * xBuffer = X.ptr<double>(0);
for (int row = 0; row < (im.rows - 2*OFFSET); row++){
for (int col = 0; col < (im.cols - 2*OFFSET); col++){
cv::Mat temp_patch = im(cv::Rect(col, row, 5, 5)); // crop an image patch (5x5) at each pixel
patch = temp_patch.clone(); // Needs to do this because temp_patch is not continuous in memory
patch.convertTo(patch, CV_64FC1);
memcpy(xBuffer, patch.data, 25*sizeof(double));
xBuffer += 25;
}
}
Also, you dont seem to do any computation in patch just extract grey level values, so you can create X with the same type as im, and convert it to double at the end. In this way, you could memcpy each row of your patch, the address in memory beeing `unsigned char* buffer = im.ptr(row) + col
According to the docs:
if you need to process a whole row of matrix, the most efficient way is to get the pointer to the row first, and then just use plain C operator []:
// compute sum of positive matrix elements
// (assuming that M is double-precision matrix)
double sum=0;
for(int i = 0; i < M.rows; i++)
{
const double* Mi = M.ptr<double>(i);
for(int j = 0; j < M.cols; j++)
sum += std::max(Mi[j], 0.);
}

Add 1 to vector<unsigned char> value - Histogram in C++

I guess it's such an easy question (I'm coming from Java), but I can't figure out how it works.
I simply want to increment an vector element by one. The reason for this is, that I want to compute a histogram out of image values. But whatever I try I just can accomplish to assign a value to the vector. But not to increment it by one!
This is my histogram function:
void histogram(unsigned char** image, int height,
int width, vector<unsigned char>& histogramArray) {
for (int i = 0; i < width; i++) {
for (int j = 0; j < height; j++) {
// histogramArray[1] = (int)histogramArray[1] + (int)1;
// add histogram position by one if greylevel occured
histogramArray[(int)image[i][j]]++;
}
}
// display output
for (int i = 0; i < 256; i++) {
cout << "Position: " << i << endl;
cout << "Histogram Value: " << (int)histogramArray[i] << endl;
}
}
But whatever I try to add one to the histogramArray position, it leads to just 0 in the output. I'm only allowed to assign concrete values like:
histogramArray[1] = 2;
Is there any simple and easy way? I though iterators are hopefully not necesarry at this point, because I know the exakt index position where I want to increment something.
EDIT:
I'm so sorry, I should have been more precise with my question, thank you for your help so far! The code above is working, but it shows a different mean value out of the histogram (difference of around 90) than it should. Also the histogram values are way different than in a graphic program - even though the image values are exactly the same! Thats why I investigated the function and found out if I set the histogram to zeros and then just try to increase one element, nothing happens! This is the commented code above:
for (int i = 0; i < width; i++) {
for (int j = 0; j < height; j++) {
histogramArray[1]++;
// add histogram position by one if greylevel occured
// histogramArray[(int)image[i][j]]++;
}
}
So the position 1 remains 0, instead of having the value height*width. Because of this, I think the correct calculation histogramArray[image[i][j]]++; is also not working properly.
Do you have any explanation for this? This was my main question, I'm sorry.
Just for completeness, this is my mean function for the histogram:
unsigned char meanHistogram(vector<unsigned char>& histogram) {
int allOccurences = 0;
int allValues = 0;
for (int i = 0; i < 256; i++) {
allOccurences += histogram[i] * i;
allValues += histogram[i];
}
return (allOccurences / (float) allValues) + 0.5f;
}
And I initialize the image like this:
unsigned char** image= new unsigned char*[width];
for (int i = 0; i < width; i++) {
image[i] = new unsigned char[height];
}
But there shouldn't be any problem with the initialization code, since all other computations work perfectly and I am able to manipulate and safe the original image. But it's true, that I should change width and height - since I had only square images it didn't matter so far.
The Histogram is created like this and then the function is called like that:
vector<unsigned char> histogramArray(256);
histogram(array, adaptedHeight, adaptedWidth, histogramArray);
So do you have any clue why this part histogramArray[1]++; don't increases my histogram? histogramArray[1] remains 0 all the time! histogramArray[1] = 2; is working perfectly. Also histogramArray[(int)image[i][j]]++; seems to calculate something, but as I said, I think it's wrongly calculating.
I appreciate any help very much! The reason why I used a 2D Array is simply because it is asked for. I like the 1D version also much more, because it's way simpler!
You see, the current problem in your code is not incrementing a value versus assigning to it; it's the way you index your image. The way you've written your histogram function and the image access part puts very fine restrictions on how you need to allocate your images for this code to work.
For example, assuming your histogram function is as you've written it above, none of these image allocation strategies will work: (I've used char instead of unsigned char for brevity.)
char image [width * height]; // Obvious; "char[]" != "char **"
char * image = new char [width * height]; // "char*" != "char **"
char image [height][width]; // Most surprisingly, this won't work either.
The reason why the third case won't work is tough to explain simply. Suffice it to say that a 2D array like this will not implicitly decay into a pointer to pointer, and if it did, it would be meaningless. Contrary to what you might read in some books or hear from some people, in C/C++, arrays and pointers are not the same thing!
Anyway, for your histogram function to work correctly, you have to allocate your image like this:
char** image = new char* [height];
for (int i = 0; i < height; ++i)
image[i] = new char [width];
Now you can fill the image, for example:
for (int i = 0; i < height; ++i)
for (int j = 0; j < width; ++j)
image[i][j] = rand() % 256; // Or whatever...
On an image allocated like this, you can call your histogram function and it will work. After you're done with this image, you have to free it like this:
for (int i = 0; i < height; ++i)
delete[] image[i];
delete[] image;
For now, that's enough about allocation. I'll come back to it later.
In addition to the above, it is vital to note the order of iteration over your image. The way you've written it, you iterate over your columns on the outside, and your inner loop walks over the rows. Most (all?) image file formats and many (most?) image processing applications I've seen do it the other way around. The memory allocations I've shown above also assume that the first index is for the row, and the second is for the column. I suggest you do this too, unless you've very good reasons not to.
No matter which layout you choose for your images (the recommended row-major, or your current column-major,) it is in issue that you should always keep in your mind and take notice of.
Now, on to my recommended way of allocating and accessing images and calculating histograms.
I suggest that you allocate and free images like this:
// Allocate:
char * image = new char [height * width];
// Free:
delete[] image;
That's it; no nasty (de)allocation loops, and every image is one contiguous block of memory. When you want to access row i and column j (note which is which) you do it like this:
image[i * width + j] = 42;
char x = image[i * width + j];
And you'd calculate the histogram like this:
void histogram (
unsigned char * image, int height, int width,
// Note that the elements here are pixel-counts, not colors!
vector<unsigned> & histogram
) {
// Make sure histogram has enough room; you can do this outside as well.
if (histogram.size() < 256)
histogram.resize (256, 0);
int pixels = height * width;
for (int i = 0; i < pixels; ++i)
histogram[image[i]]++;
}
I've eliminated the printing code, which should not be there anyway. Note that I've used a single loop to go through the whole image; this is another advantage of allocating a 1D array. Also, for this particular function, it doesn't matter whether your images are row-major or column major, since it doesn't matter in what order we go through the pixels; it only matters that we go through all the pixels and nothing more.
UPDATE: After the question update, I think all of the above discussion is moot and notwithstanding! I believe the problem could be in the declaration of the histogram vector. It should be a vector of unsigned ints, not single bytes. Your problem seems to be that the value of the vector elements seem to stay at zero when your simplify the code and increment just one element, and are off from the values they need to be when you run the actual code. Well, this could be a symptom of numeric wrap-around. If the number of pixels in your image are a a multiple of 256 (e.g. 32x32 or 1024x1024 image) then it is natural that the sum of their number would be 0 mod 256.
I've already alluded to this point in my original answer. If you read my implementation of the histogram function, you see in the signature that I've declared my vector as vector<unsigned> and have put a comment above it that says this victor counts pixels, so its data type should be suitable.
I guess I should have made it bolder and clearer! I hope this solves your problem.

C++ Using 3D Dynamic Arrays and Vectors

I'm new to C++ and getting a bit frustrated with it. Below, in pixelsVector, I am storing each pixel RGB float-value in Pixel and want to dump
all the values to a byte array with pixelsArray so I can output to an image file. HEIGHT and WIDTH refer to the image dimensions. The code below works fine, but I need to specify
the sizes of pixelsArray at run-time, because it may not always be a 500x500 image.
// WIDTH and HEIGHT specified at run-time
vector<vector<Pixel>> pixelsVector (WIDTH, vector<Pixel> (HEIGHT));
...
unsigned char pixelsArray[500][500][3];
for (int i = 0; i < 500; i++)
{
for (int j = 0; j < 500; j++)
{
// Returns RGB components
vector<float> pixelColors = pixelArray[i][j].getColor();
for (int k = 0; k < 3; k++)
{
pixels[i][j][k] = pixelColors.at(k);
}
}
}
// write to image file
fwrite(pixelsArray, 1, 500*500*3, file);
If I put HEIGHT and WIDTH instead of 500 and 500 above, I get an error since they are not constant values. Now using a 3D vector does seem to work, but fwrite won't take a vector for its first argument. I tried using a triple-pointer array but
it doesn't seem to work at all - maybe I was using it wrong. Here it is using a 3D vector for pixelsArray:
vector<vector<Pixel>> pixelsVector (WIDTH, vector<Pixel> (HEIGHT));
...
vector< vector< vector<unsigned char> > > pixelsArray;
for (int i = 0; i < HEIGHT; i++)
{
pixels.push_back(vector< vector<unsigned char> >());
for (int j = 0; j < WIDTH; j++)
{
pixels[i].push_back(vector<unsigned char>());
vector<float> pixelColors;
pixelColors = pixelArray[i][j].getColor();
for (int k = 0; k < 3; k++)
{
pixels[i][j][k] = pixelColors.at(k);
}
}
}
// Error
fwrite(pixelsArray, 1, 500*500*3, file);
Suggestions?
You could use Boost.MultiArray insead of vectors of vectors, which lets you access he underlying memory with the .data() method.
It looks like you are trying to manipulate images, so you might want to consider using Boost.Gil.
From the last code snippet:
vector<vector<Pixel>> pixelsVector (WIDTH, vector<Pixel> (HEIGHT));
Using uppercase names for variables you risk name collisions with macros. In C++ all uppercase names are conventionally reserved for macros.
...
vector< vector< vector<unsigned char> > > pixelsArray;
Presumably this vector is the same as is called pixels below?
If so, then the standard advice is that it helps to post real code.
Anyway, in order to output those bytes in one efficient operation you need the bytes to be contiguously stored in memory. So a vector of vectors of vectors is out. Use a single vector (C++ guarantees contiguous storage for the buffer of a std::vector).
for (int i = 0; i < HEIGHT; i++)
{
pixels.push_back(vector< vector<unsigned char> >());
for (int j = 0; j < WIDTH; j++)
{
pixels[i].push_back(vector<unsigned char>());
At this point you have an inner vector but it's empty, size 0.
vector<float> pixelColors;
pixelColors = pixelArray[i][j].getColor();
Presumably pixelArray is an instance of a class you have defined?
for (int k = 0; k < 3; k++)
{
pixels[i][j][k] = pixelColors.at(k);
}
Here you're trying to assign to non-existent elements of the empty innermost vector. You can either size it properly in advance, or use the push_back method for each value.
In addition, are you sure that the float values are integers in range 0 through 255 (or more generally, 0 through UCHAR_MAX) and not, say, in the range 0 through 1?
Perhaps you need to scale those values.
}
}
// Error
fwrite(pixelsArray, 1, 500*500*3, file);
If pixelsArray had been a (non-empty) vector of bytes, then you could use &pixelsArray[0] to obtain a pointer to the first byte.
Now, I know, the above only dissects some of what's wrong, and doesn't tell you directly what's right. :-)
But some more information would be needed to give example code for doing this, like (1) what are your float values, and (2) what do you want in your file?
Anyway, hope this helps,
– Alf