The most frequent feature request for the photo monitoring plugin is to be able to copy GPS data from the original photo to the output NDVI or DVI image. This capability now exists in the most recent version of the plugin. The entire EXIF metadata set will be copied which includes GPS data (if they exist), time image was acquired, camera setting and over a hundred other pieces of information.
One caveat is that the EXIF metadata can only be copied from JPEG images at this time but that seems to be the most frequent case.
For dual-camera processing there is an option to select if the EXIF data should come from the visible or near-infrared camera.
Another related change is that I removed the option to specify the output image format. This was causing confusion so now color index images will be output in the JPEG format and the raw floating point (decimal) NDVI and DVI images will be output in the TIFF format. At this time only the JPEG images will have the EXIF metadata copied form the original photo.
The plugin and user guide are available on the Github site: https://github.com/nedhorning/PhotoMonitoringPlugin
I also fixed a few bugs. If you have any issues running the plugin please let me know.
That pink hash is pretty cool. The hash pattern is present in the black background of both the NIR and VIS mosaics. So if you could change that to a solid field, the pattern would probably not be present in the NDVI image.
A bigger problem seems to be that the NIR and VIS mosaics, which were apparently made without ground control points, do not match perfectly. When the plugin overlays them, it does not transform them enough to produce a very good alignment. From the offset margins in the top half of the NDVI image it appears that the NDVI values are being computed from NIR and VIS values that are in some places many (10-20?) meters apart. That would greatly reduce the usefulness of the NDVI values.
This is an important issue that many people will encounter. Maybe a solution is possible. The NDVI values require only a single channel in an image file. So a standard image file has two additional channels that are not being used. When the individual photos (NIR and VIS) are aligned and used to produce an NDVI image, that output image could include one channel for NDVI and two of the channels from one of the original photos (e.g., VIS). Then those NDVI images could be stitched into a mosaic using the two VIS channels. The NDVI channel would be included in the stitched mosaic and could be displayed. This might require a stitching program that allows you to select which channels to use for stitching, although maybe stitching would work well using the entire hybrid image. The VIS channels would include the best matching information, and maybe the SIFT algorithm would rely on that and just bring the NDVI channel along for the ride. In the mosaic there would be blending of the NDVI values where images overlapped, but that might be exactly what you want.
So the first thing to try might be to modify the Fiji plugin so it output an NDVI image with a grayscale channel for NDVI and also two VIS channels (or a four-channel TIFF, but that might complicate the next step). Then see if stitching programs can stitch them together into a mosaic. Then figure out how to put the mosaic back into Fiji and display the single NDVI channel with a color lut.
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