The following article describes how to generate vegetation indices using the default index options and how to generate a customized index using the index calculator
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IN THIS ARTICLE
Index generator
To generate predefined indices based on the imported images.
1. Click Index above the Layers Menu. The INDEX GENERATOR tool opens.
2. Select the Source layer.
3. Select the vegetation index that you want to generate by checking the corresponding boxes.
4. Click Generate.
Available indices
| Index | Description | Formula | Image import type | Platform |
|---|---|---|---|---|
| BNDVI - Blue Normalized Difference Vegetation Index | NDVI index without red channel availability, for areas sensitive to chlorophyll content. | (nir - blue) / (nir + blue) | Multispectral (excluding Sequoia) | Drone and satellite. |
| GNDVI - Green Normalized Difference Vegetation Index | NDVI index without red channel availability, for areas sensitive to chlorophyll content. | (nir - green) / (nir + green) | Multispectral | Drone and satellite. |
| LCI - Leaf Chlorophyll Index |
Index to assess chlorophyll content in areas of complete leaf coverage. Value range clamp between -1 and 1. |
(nir - rededge) / (nir + red) | Multispectral | Drone and satellite. |
| MCARI - Modified Chlorophyll Absorption in Reflective Index | Index used to measure chlorophyll concentrations including variations in the Leaf Area Index. | 1.2 * (2.5 * (nir - red) - 1.3 * (nir - green)) / (normalized to the maximum value of red, green, and nir bands) | Multispectral | Drone and satellite. |
| NDRE - Normalized Difference Red Edge | Index sensitive to chlorophyll content in leaves against soil background effects. This index can only be formulated when the red edge band is available. | (nir - rededge) / (nir + rededge) | Multispectral | Drone and satellite. |
| NDVI - Normalized Difference Vegetation Index | Generic index used for leaf coverage and plant health. | (nir - red) / (nir + red) | Multispectral | Drone and satellite. |
| SIPI2 - Structure Intensive Pigment Index 2 |
Index used in areas with high variability in canopy structure (e.g. forestry).
|
(nir - green) / (nir - red) | Multispectral | Drone and satellite. |
| TGI - Triangular Greenness Index | RGB index for chlorophyll sensitivity. | (green - (0.39 * red) - (0.61 * blue)) /(normalized to the maximum value of red, green, and blue bands) | RGB | Drone and satellite. |
| VARI - Visible Atmospherically Resistant Index | RGB index for leaf coverage. | min(1; max(-1; (green - red) / (green + red - blue) )) | RGB | Drone and satellite. |
| NDMI - Normalized Difference Moisture Index | NDWI uses the NIR and SWIR bands to monitor changes in water content of leaves. | (nir - swir_1613) / ( nir + swir_1613) | Multispectral | Satellite |
| Note 1: min(1, max(-1, ...) is clamping the values between -1 and 1. | ||||
Index calculator
To generate a custom index using the index calculator.
1. Open the INDEX GENERATOR by clicking the icon at the top right of the window.
2. Choose the source layer.
3. Click Create custom index below the list of available indices.
4. Name the index.
5. Enter the formula either by clicking the Operations and the Available bands buttons or by using your keyboard.
When a formula is valid, the Preview button turns green.
6. Click the Preview button to preview your index.
7. When you are satisfied with the preview, click Apply
8. The generated custom index now appears in the list of layers and in the map interface.
Custom indices can be created depending on the available bands from your imported images, these are listed as buttons under Available bands.
The Operations buttons are described below:
| Operation | Description | Operation | Description |
| ( | open parenthesis | ^ | exponentiation |
| ) | close parenthesis | abs | absolute value |
| * | multiplication | exp | exponential (e^x) |
| + | addition | log | natural logarithm |
| - | subtraction | max | maximum value between two arguments, the separator is ";" (semicolon) |
| / | division | min | minimum value between two arguments, the separator is ";" (semicolon) |
| ; | (semicolon) separator for functions that take more than one parameter | sqrt | square root |
how to work with multispectral geotiff? For example I have an image with 10 bands, and I want to create my index, but when I import image is not recognized as an image with 10 bands
How do you insert formula such as MCARI into Index Calculator since it wouldnt accept ","
Hi Alex,
You will need to use ; instead of ,
I have just changed it in the article. Thanks for letting us know :-)
Hi Dusan,
Are you working with Pix4Dfields? Pix4Dfields can only process rededge and Sequoia imagery at this moment in terms of multispectral sensors. We are working on having more cameras in the database.
Hi I'm trying to use the below function from excel to convert drone measured temperatures to on ground calibration for thermal imagery. However I'm not having any luck with Pix4d recognizing the exp function as mentioned above. And I can't see it in my index calculator as an option,
Thanks
Hi Wesley, We do not have exponential in the calculator. You can use 2.71828 (value of e)^(your formula)
Is it possible to make a specific color more distinct? If I wanted to make red appear brighter and stand out over the green/yellow background.
Hi Cody,
You cannot do that in fields. You can import the map in QGIS and try playing with the symbology
Is the Index Generator available on web based application or only on the Desktop software?
Adam It is not available on cloud. However, you can upload NDVI map to cloud for sharing with clients or anyone you want.
Hello, is it possible to draw 30 regions on a reflectance map and calculate the average index map for every region, individually?
I currently have to draw a region on each of my 30 plots, one at a time, and generate the index map each time.
Hi,
I use RedEdge M sensor for image acquisition and use Pix4D to create orthoimage from each band then I do radiometric calibration in QGIS or sometimes use eCognition algorithms. As images are not radiometrically calibrated, I can't generate indices in Pix4D pipeline(step 3) but, I can use QGIS or eCognition to generate indices. When I generate indices through QGIS or in eCognition, the resolution is reduced so my question is, can I bring calibrated layers back to pix4D to generate indices using index calculator?
Thanks
Hi,
Is it necessary to do a radiometric calibration for VARI algorithm?
Nivin, Pix4Dfields does not have 100% radiometric calibration yet, it will be there shortly.
When working with common RGB cameras, keep in mind that they are probably not designed for radiometric fidelity. So indices like VARI will not have absolute values. They will give you some patterns and can be used for comparison.
@Chinthaka you are using Pix4Dfields, right? There is no way you can bring back calibrated layers to Pix4D later. Radiometric calibration will be there in fields soon. Pix4Dmapper already does radiometric calibration.
@Katherine, It seems a multiplication or division symbol is missing. Though I don't know which formula you are using, it seems there might be a multiplication sign after 0.2 and another symbol before red_edge/red. You will need to look up this formula and use the correct symbols.
@Rasmus, It is not possible to import 30 regions at a time because the values keep accumulating. You can draw 30 regions, but the index values and the statistics will be for all the 30 regions together, not for each of them. So while importing, we allow only one shp file import at a time.
Hello all, I would request you to keep Pix4Dmapper and Pix4Dfields questions separate. This page is for Pix4Dfields only, though the formulas can be used anywhere. If you have Pix4Dmapper agriculture questions, please post them on our community page: https://support.pix4d.com/hc/en-us/community/topics with the correct topic. For questions like this, the topic where you can post would be processing.
Hi Momtanu,
Is it possible to do a custom band order in Pix4dFields using the index generator or some other method (e.g. NIR-G-R or NIR-RE-G)? If so, I can't seem to figure out how.
Thanks,
Will
Will,
We do not have the feature of generating composite maps yet. However, you can generate 3 bands separately by using formula red=red, green=green and NIR=NIR by the index calculator and then use QGIS/ArcGIS to create the composite map with the 3 individual reflectance maps.
Hello Momtanu,
I have tried to insert formula red=red but it says Invalid.
If I leave red only it allows to export a 3 band file.
If I put greyscale, the same it gives a 3 bands file.
Is this 3 bands file that you recommend to export to QGIS/ARCGIS? It does not give a composite map of red in 1 single band?
Thank you
Hey Juan,
I replied to you on an internal comment. You can import the red.data.tif to ArcGIS. Please always use the red.data.tif for calculations.
To all, you can always write us into our Pix4Dfields community or you can contact us by contacting support we are more than happy to help
Cheers!
Hi,
I dont find a way to set the min and max values for the index maps? When I take process photos of both lakes and ground; I want to look only at the water surface. I would like to leave any values below min or above max at uniform value, and get the histogram only for the selected range.
Thanks
Hi Jonas,
At the moment, using Pix4Dfields you can visualize the max and min value in the distribution of values feature (see my screenshot). In this case, I am displaying just the NIR band as an example. We consider very valuable the information that you shared with us regarding selecting a range due to lakes and ground influences, and I will make sure to share this feedback with my team, in Berlin where we develop the application.
Meanwhile, we do suggest to use free software like QGIS for this. Let me know if you have more questions
I am shooting using a DuetT camera and would like to calculate TGI (manually, since we can't use and form of max functions in pix4D), but I'd like to know what the reference is to your formula:
(G-0.39R-0.61B) / max(R,G,B)
Your formula is very different from the original one in Hunt et. al.2011, and produces slightly different numbers.
Hi,
Thank you for bringing this to our attention. Our reference to the TGI index is this article.Using the wavelengths of a typical CMOS camera and normalizing by the green signal, the TGI equation is TGI = RGREEN - 0.39 * RRED - 0.61* RBLUE. We are normalizing to the maximum of the three. You can gladly contact us to trough support to determine why you are getting different numbers with our formula and the original one.
Kind regards,
please can anyone help me to correct this issue
Hi Dany,
Thank you for contacting us. In this article, we describe possible causes and solutions for that issue. Could you please contact support and attach the pdf report of your project? We will gladly help you.
Side note: I would kindly recommend all of our users to contact support or use our community when we have some questions. With our community, you can connect with other Pix4D users, and we can work together.
Thank you very much for your understanding
Hello, how are you? Hope fine!
I would like to ask a question. After the NDVI generation, for example, on both softwares Pix4D Mapper and Fields suggest me a standard interval. Can I trust on these values or do I have to change it? If I have to change which interval should I insert? Should I always enter the range from -1 to +1?
Best regards!
Hi Paulo, We are doing good. Hope you are doing well too. NDVI should always range from -1 to +1 (the interval should lie within this range, however, according to the area, the max, min values will be different). You can trust the values produced by Mapper and Fields. For Mapper, the Min/Max values in color maps and prescription are not the same values as the minimum/maximum values of the index map section. The software will cut off by default the outliers on the edge of the histogram. If you still want use the maximum/minimum value, they can be modified.
I am trying the above indices and on all of them i get invalid. What am I doing wrong?
Blue Goose Construction Can you write us a personal support ticket with the logfile, p4df file and quality report with a screenshot of your Pix4D index screen. It might happen if the images are overexposed, or have some other issues. Please make sure you are using the latest version.