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DATE: 2018-09-07
AUTHOR: John L. Godlee
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layout: post title: "A guide about processing hemispherical photos" date: 2018-09-07
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I wrote a guide for some undergraduate students on a field course about hemispherical photography and calculating forest canopy traits. This is it. It's untested so far, so some parts may change depending on how well the field course goes. The guide may get updated, so the most up to date version can always be found here, on Github[1].
1: https://github.com/johngodlee/hemi_photo_guide
A list of tips for taking good hemispherical photos:
1. Open ImageJ
2. File -> Open, then select an image
3. Visually inspect the image to see that there isn't massive amounts of lens flare. If you have lots of lens flare, the photo should be thrown out! This is what lens flare looks like:
4. Image -> Type -> 8-bit
5. Image -> Adjust -> Threshold, manually adjust the image so all the branches are red and the sky is white, or as near as you can get it.
6. Save the newly thresholded image as a jpeg in a folder called img.
7. Rinse and repeat for all images.
The above process can be automated with a macro, but this assumes that the images are all uniformly exposed.
This is the macro, saved as a .ijm file. This is untested so use at your own risk:
// Automatically create a thresholded image for use in further analysis. Change the values of setThreshold to achieve different results.
// Partially tested
// Save as a Jpeg in the Batch macro dialog in ImageJ
run("8-bit");
run("Threshold...");
setThreshold(0, 146);
setOption("BlackBackground", false);
run("Convert to Mask");
1. Open RStudio.
2. Open a new script (File -> New File -> R Script)
3. Save the script in a folder above the images folder:
4. Enter the following preamble into the R script:
# Set working directory to location of thresholded images
setwd("LOCATION_OF_ANALYSIS")
# Source the functions used to calculate stuff
source("hemiphot.R")
# Packages
library(jpeg)
5. Add white_image.jpg to the same folder where the thresholded images are found
6. Read in all the thresholded images and create an empty data frame which will later be filled with canopy trait statistics like LAI and canopy openness.
# List all images in the directory
all_images <- list.files("img/", pattern = ".JPG")
# How many images
img_length = length(all_images)
# Create empty dataframe, 6x7 and fill it with zeroes
all_data = data.frame(matrix(data = 0, nrow = img_length, ncol = 7))
names(all_data) = c("File", "CanOpen", "LAI", "DirectAbove", "DiffAbove", "DirectBelow", "DiffBelow")
# Fill first column with image names
all_data[,1] = all_images
7. Read in the reference image (white_img.jpg) as a matrix of pixel values:
white_img <- readJPEG("img/white_image.jpg", native = F)
8. Set some parameters for the location the photos are being taken. Approximate location (0.1 degrees latitude) is good enough for our purposes. Note that the values below are for somewhere in Africa and should be changed:
location.latitude = -15 location.altitude = 200 location.day = 30 location.days = seq(15,360,30) # roughly each mid of the 12 months
9. Set some parameters for the images, cropping them to a circle and setting the threshold. These parameters are ones I have used on this camera, so don't need to be changed:
## Image parameters ### Drawing circles and identifying the image centre point hemi_dim <- dim(white_img) radius <- max(rowSums(white_img[,,1] > 0.4) / 2) ### determine using a single image and fill in here for batch processing location.cx = (hemi_dim[2] / 2) # x coordinate of center of image location.cy = (hemi_dim[1] / 2) # y coordinate of center image location.cr = radius # radius of circle location.threshold = 0.42 # Must get this to match all images, or maybe could use a lookup table / dictionary? Does R have dictionaries?
10. Set some atmospheric parameters. I've loosely estimated these for this location, but by no means is it scientific. I would not have much confidence in the statistics generated using these parameters, namely DirectAbove, DiffAbove, DirectBelow and DiffBelow.
# atmospheric parameters ## Atmospheric transmissivity - Normally set at 0.6, but can vary between 0.4-0.6 in the tropics location.tau = 0.6 ## Amount of direct light that is used as diffuse light in the Uniform Ovecast Sky (UOC) location.uoc = 0.15
11. Run a big for loop to calculate the statistics for each photo
for(i in 1:img_length){
## read file
image <- readJPEG(paste("test_img/", all_images[i], sep = ""), native = F)
## conver to Hemi image
image <- Image2Hemiphot(image)
## set cirlce parameters
image <- SetCircle(image, cx = location.cx, cy = location.cy, cr = location.cr)
## select blue channel
image <- SelectRGB(image, "B")
#threshold
image <- ThresholdImage(im = image, th = location.threshold, draw.image = F)
# canopy openness
gap.fractions <- CalcGapFractions(image)
all_data[i,2] = CalcOpenness(fractions = gap.fractions)
## calculate LAI according to Licor's LAI Analyzer
all_data[i,3] = CalcLAI(fractions = gap.fractions)
## Photosynthetic Photon Flux Density (PPDF, umol m-1 s-1) P
rad <- CalcPAR.Day(im = image,
lat = location.latitude, d = location.days,
tau = location.tau, uoc = location.uoc,
draw.tracks = F, full.day = F)
all_data[i,4] = rad[1]
all_data[i,5] = rad[2]
all_data[i,6] = rad[3]
all_data[i,7] = rad[4]
}
12. Finally, look at the output, which is stored in all_data
all_data
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The hemiphot.R source file comes from here[2].