Save integer CV_32S image with OpenCV - c++

Question

I am working with TIF images containing signed integer data. After successfully inputing one and processing it I need to output the image in the same format (input and output both *.tif files).
For the input, I know that OpenCV does not know if the data is signed or unsigned, so it assumes unsigned. Using this trick solves that problem (switching the type of cv::Mat by hand).
However, when I output the image and load it again, I do not get the expected result. The file contains multiple segments (groups of pixels), and the format is as follows (I must use this format):
all pixels not belonging to any segment have the value -9999
all the pixels belonging to a single segment have the same positive integer value
(e.g. all pixels of 1st segment have value 1, second 2 etc)
And here is the example code:
void ImageProcessor::saveSegments(const std::string &filename){
cv::Mat segmentation = cv::Mat(workingImage.size().height,
workingImage.size().width,
CV_32S, cv::Scalar(-9999));
for (int i=0, szi = segmentsInput.size(); i < szi; ++i){
for (int j=0, szj = segmentsInput[i].size(); j < szj; ++j){
segmentation.at<int>(segmentsInput[i][j].Y,
ssegmentsInput[i][j].X) = i+1;
}
}
cv::imwrite(filename, segmentation);
}
You can assume that all the variables (e.g. workingImage, segmentsInput) exist as global variables.
Using this code, when I input the image and examine the values, most of the values are set to 0 while the ones that are set take a full range of integer values (in my example I had 20 segments).

Answer 1

You can't save integer matrices directly with imwrite. As the documentation states: "Only 8-bit (or 16-bit unsigned (CV_16U) in case of PNG, JPEG 2000, and TIFF) single-channel or 3-channel (with ‘BGR’ channel order) images can be saved using this function."
However, what you could do it to convert your CV_32S matrix to a CV_8UC4 and save it as a PNG with no compression. Of course, this is a bit unsafe since endianness comes into play and may change your values between different systems or compilers (especially since we're talking about signed integers here). If you use always the same system and compiler, you can use this:
cv::Mat segmentation = cv::Mat(workingImage.size().height,
workingImage.size().width,
CV_32S, cv::Scalar(-9999));
cv::Mat pngSegmentation(segmentation.rows, segmentation.cols, CV_8UC4, (cv::Vec4b*)segmentation.data);
std::vector<int> params;
params.push_back(CV_IMWRITE_PNG_COMPRESSION);
params.push_back(0);
cv::imwrite("segmentation.png", pngSegmentation, params);

Answer 2

I also save opencv mats as tifs but i don`t use the opencv tif solution. I include the libtiff lib on my own (i think libtiff is also used in opencv) and than you can use the following code to save as tiff
TIFF* tif = TIFFOpen("file.tif", "w");
if (tif != NULL) {
for (int i = 0; i < pages; i++)
{
TIFFSetField(tif, TIFFTAG_IMAGEWIDTH, TIFF_UINT64_T(x)); // set the width of the image
TIFFSetField(tif, TIFFTAG_IMAGELENGTH, TIFF_UINT64_T(y)); // set the height of the image
TIFFSetField(tif, TIFFTAG_SAMPLESPERPIXEL, 1); // set number of channels per pixel
TIFFSetField(tif, TIFFTAG_BITSPERSAMPLE, 32); // set the size of the channels 32 for CV_32F
TIFFSetField(tif, TIFFTAG_PAGENUMBER, i, pages);
TIFFSetField(tif, TIFFTAG_SAMPLEFORMAT, SAMPLEFORMAT_IEEEFP); // for CV32_F
for (uint32 row = 0; row < y; row++)
{
TIFFWriteScanline(tif, &imageDataStack[i].data[row*x*32/ 8], row, 0);
}
TIFFWriteDirectory(tif);
}
}
imageDataStack is a vector of cv::Mat objects. This code works for me to save tiff stacks.