Fast Non-Local Means Denoise with OpenCV

In this example we will use a denoise algorithm from the external OpenCV libray.

This method progressively scans through an image’s pixels, comparing a patch centered around a pixel of interest (e.g. a 5x5 patch) with patches from other pixels from the image. These patches are then averaged to eliminate gaussian noise, without the requirement of additional images for comparison.

The sample data for this example can be downloaded here.

https://media.scijava.org/scijava-ops/1.0.0/opencv_denoise_example_1.png — Results of OpenCV’s non-local means denoise algorithm with the sample data.

Denoise parameter descriptions

Parameter

Description

Value

Filter strength

Controls the decay in patch weights as a function

of distance between patches. The distance

between patches is a measure of how similar they

are. Large filter strength values allow more distant

(i.e. dissimilar) patches to have more influence on

the denoise output.

4

Patch size

The size of the patches/blocks from the input image

to be compared. Patch sizes should be odd

(default=7).

7

Search size

The size of the area in the input image to search

for similar patches to compare. Search sizes

should be odd (default=21).

21

SciJava Ops via Fiji’s scripting engine with script parameters:

#@ OpEnvironment ops
#@ ImgPlus img
#@ Integer (label="Filter strength:", value=4) strength
#@ Integer (label="Patch size:", value=7) patch
#@ Integer (label="Search size:", value=21) search
#@output ImgPlus result

import net.imglib2.type.numeric.integer.UnsignedByteType

// Get the min and max values of our input image
oldMin = ops.op("stats.min").input(img).apply()
oldMax = ops.op("stats.max").input(img).apply()

// We need to convert to 8-bit since not all data types are currently supported in OpenCV
type = new UnsignedByteType()
img8bit = ops.op("create.img").input(img, type).apply()

// Normalize our input data to the 8-bit min/max
newMin = new UnsignedByteType((int)type.getMinValue())
newMax = new UnsignedByteType((int)type.getMaxValue())

ops.op("image.normalize").input(img, oldMin, oldMax, newMin, newMax).output(img8bit).compute()

// Create a container for the denoise output
output = img8bit.copy()

// Run the denoise op
ops.op("filter.denoise").input(img8bit, strength, patch, search).output(output).compute()

// Return the denoised image
result = output

#@ OpEnvironment ops
#@ ImgPlus img
#@ Integer (label="Filter strength:", value=4) strength
#@ Integer (label="Patch size:", value=7) patch
#@ Integer (label="Search size:", value=21) search
#@output ImgPlus result

from net.imglib2.type.numeric.integer import UnsignedByteType

# Get the min and max values of our input image
old_min = ops.op("stats.min").input(img).apply()
old_max = ops.op("stats.max").input(img).apply()

# We need to convert to 8-bit since not all data types are currently supported in OpenCV
type = UnsignedByteType()
img8bit = ops.op("create.img").input(img, type).apply()

# Normalize our input data to the 8-bit min/max
new_min = UnsignedByteType(int(type.getMinValue()))
new_max = UnsignedByteType(int(type.getMaxValue()))

ops.op("image.normalize").input(img, old_min, old_max, new_min, new_max).output(img8bit).compute()

# Create a container for the denoise output
output = img8bit.copy()

# Run the denoise op
ops.op("filter.denoise").input(img8bit, strength, patch, search).output(output).compute()

# Return the denoised image
result = output