The first step is to recognize that the number of bands as well as the band order of the GeoTIFF depends on the camera that was used.
Some processing software can output orthomosaics with the band order as it was originally uploaded, rather than re-ordering by wavelength. In other words, it is important to know how your processing software outputs multispectral data sets. For reference, here are the band orders for MicaSense camera models:
RedEdge (3, M, and MX): Blue, Green, Red, Red edge, NIR
Altum (all variants): Blue, Green, Red, Red edge, NIR, LWIR
Dual Camera System: Blue-444, Blue, Green-531, Green, Red-650, Red, Red edge-705, Red edge, Red edge-740, NIR.
RedEdge-P: Same as the RedEdge-MX but the 6th band is Panchromatic.
Altum-PT: Same as Altum, but the 7th band is Panchromatic.
For more details, please see this article.
Using the QGIS Raster Calculator
This tutorial shows QGIS version 2.14.3-Essen. Your version may differ slightly.
Load your image into the Layers Panel (drag and drop or Layer > Add layer > Add raster layer...)
Open Raster Calculator from the QGIS menu bar: Raster > Raster Calculator...
The Raster calculator dialog opens.
- Specify an "Output layer" and "Output format", as a new image will be created for your index.
- Paste in one of the formulas we have provided (in the next section of this article) or use the buttons in "Operators" to enter a formula.
- Press OK when you have entered the formula.
The new image is added to the Layers Panel. Now you can create a color ramp for your index.
Color your index
To add a color map, double-click on the NDVI image in the Layers Panel (or right-click and choose "Properties" from the context menu).
The Layer Properties dialog appears.
- Make sure you are on the "Style" tab
- Change the "Render type" to "Singleband pseudocolor"
- Choose your preferred gradient and press the "Classify" button.
Press "Apply" to preview your color ramp, and press OK to make the changes.
Now that you have learned how to create an index and apply a color ramp in QGIS, here are some formulas for common indices to get you started.
Various Indices and Their Formulas
Here is a sampling of the indices used in precision agriculture. Some are calculated automatically in Atlas, while others are not. The formulas are given in QGIS raster calculator format for each camera so that you can copy and paste them. Be sure to replace the word, "image", with the actual file name of your image.
NOTE: For the Dual Camera System, your band names will vary
NDVI - Normalized Difference Vegetation Index
(NIR−RED)/(NIR + RED)
("image@5"-"image@3")/("image@5" + "image@3")
NDRE - Normalized Difference Red Edge
(NIR−RE)/(NIR + RE)
("image@5"-"image@4")/("image@5" + "image@4")
GNDVI - Green NDVI
GNDVI has wider dynamic range than NDVI and is, on average, at least five times more sensitive to chlorophyll-a concentration. GNDVI is used to sense the concentration of chlorophyll, to measure the rate of photosynthesis, and to monitor plant stress.
(NIR−GREEN)/(NIR + GREEN)
("image@5"-"image@2")/("image@5" + "image@2")
GRVI - Green RVI
GRVI is used to monitor the photosynthetically active biomass of plant canopies.