2

I am new to image processing in R. To start with, I am using the EBImage R package for this. I have a 260 by 134 Matrix which I converted to an image using 

> image1 <- as.Image(matrix1)

And, here is the image object summary

> image1 
  colorMode    : Grayscale 
  storage.mode : double 
  dim          : 260 134 
  frames.total : 1 
  frames.render: 1 

imageData(object)[1:5,1:6]
     [,1] [,2] [,3] [,4] [,5] [,6]
[1,]    0    0    0    0    0    0
[2,]    0    0    0    0    0    0
[3,]    0    0    0    0    0    0
[4,]    0    0    0    0    0    0
[5,]    0    0    0    0    0    0

A value greater than zero for a specific cell in the image object looks like this:

> imageData(image1)[9,2]
[1] 3686.308

I then use the display function in the EBImage package to view the image which is build from the matrix data. 

> display(image1, method = "raster")

However, I get a binary image i.e just black and white pixels. I have shown it below. My data does not just consist of 0 and 1. The background values are zero but the regions with the actual image pattern have values higher than 1. How do I display the image using grayscale and using the functions in this package? Did someone face a similar issue? I also could not find a parameter to specify a gradient level.

enter image description here

novicegeek
  • 773
  • 2
  • 9
  • 29

1 Answers1

2

The reason why the image renders only as black and white is because the display function expects values in the range [0, 1]. Values higher than 1 are clipped and effectively display as 1 (white).

To properly visualize your data you first need to scale the pixel intensity values to the [0, 1] range. This can be done with the help of the normalize function:

image1 <- normalize(image1)
display(image1, method = "raster")
aoles
  • 1,525
  • 10
  • 17