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JPG does not support 16 bit images and with OpenCV you apparently need to convert your images explicitly to 8-bit before saving (information will be lost!)

You have commented out code that does almost that. It needs to be:

ir_img_ptr->image.convertTo(ir_img[ir_image_count],CV_8UC1,(double)(1.0/256), 0);

Notice the last parameter. Look here for convertTo for details.

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