resolve sharpness/saturation terminology issue, updated package names and code cleanup

turbidity/plot.go

@@ -6,7 +6,7 @@ AUTHORS
   Russell Stanley <russell@ausocean.org>
 
 LICENSE
-  Copyright (C) 2020 the Australian Ocean Lab (AusOcean)
+  Copyright (C) 2021-2022 the Australian Ocean Lab (AusOcean)
 
   It is free software: you can redistribute it and/or modify them
   under the terms of the GNU General Public License as published by the
@@ -22,7 +22,7 @@ LICENSE
   in gpl.txt.  If not, see http://www.gnu.org/licenses.
 */
 
-package main
+package turbidity
 
 import (
 	"fmt"
@@ -63,15 +63,13 @@ func normalize(slice []float64) []float64 {
 // Return the average of a slice.
 func average(slice []float64) float64 {
 	var out float64
-
-	// Sum all elements in the slice.
 	for i := range slice {
 		out += slice[i]
 	}
 	return out / float64(len(slice))
 }
 
-func plotResults(x, saturation, contrast []float64) error {
+func plotResults(x, sharpness, contrast []float64) error {
 	err := plotToFile(
 		"Results",
 		"Almond Milk (ml)",
@@ -79,7 +77,7 @@ func plotResults(x, saturation, contrast []float64) error {
 		func(p *plot.Plot) error {
 			return plotutil.AddLinePoints(p,
 				"Contrast", plotterXY(x, contrast),
-				"Saturation", plotterXY(x, saturation),
+				"Sharpness", plotterXY(x, sharpness),
 			)
 		},
 	)

turbidity/results.go

@@ -9,7 +9,7 @@ AUTHORS
   Russell Stanley <russell@ausocean.org>
 
 LICENSE
-  Copyright (C) 2020 the Australian Ocean Lab (AusOcean)
+  Copyright (C) 2021-2022 the Australian Ocean Lab (AusOcean)
 
   It is free software: you can redistribute it and/or modify them
   under the terms of the GNU General Public License as published by the
@@ -25,27 +25,26 @@ LICENSE
   in gpl.txt.  If not, see http://www.gnu.org/licenses.
 */
 
-package main
+package turbidity
 
 import "fmt"
 
 // Results holds the results of the turbidity sensor.
 type Results struct {
 	Turbidity []float64
-	Saturation []float64
+	Sharpness []float64
 	Contrast  []float64
 }
 
-// NewResults constructs the results object.
+// NewResults returns a new Results
 func NewResults(n int) (*Results, error) {
-
 	if n <= 0 {
-		return nil, fmt.Errorf("invalid result size: %v.", n)
+		return nil, fmt.Errorf("invalid result size: %v", n)
 	}
 
 	r := new(Results)
 	r.Turbidity = make([]float64, n)
-	r.Saturation = make([]float64, n)
+	r.Sharpness = make([]float64, n)
 	r.Contrast = make([]float64, n)
 
 	return r, nil
@@ -53,7 +52,7 @@ func NewResults(n int) (*Results, error) {
 
 // Update adds new values to slice at specified index.
 func (r *Results) Update(newSat, newCont, newTurb float64, index int) {
-	r.Saturation[index] = newSat
+	r.Sharpness[index] = newSat
 	r.Contrast[index] = newCont
 	r.Turbidity[index] = newTurb
 }

turbidity/turbidity.go

@@ -3,14 +3,16 @@
 
 /*
 DESCRIPTION
-  Holds the turbidity sensor struct. Can evaluate 4x4 chessboard markers
+  Holds the turbidity sensor struct. Can evaluate 4x4 chessboard markers in an
-  in an image to measure the sharpness and contrast.
+  image to measure the sharpness and contrast. This implementation is based off
+  a master thesis from Aalborg University, Turbidity measurement based on computer vision.
+  The full paper is avaible at https://projekter.aau.dk/projekter/files/306657262/master.pdf
 
 AUTHORS
   Russell Stanley <russell@ausocean.org>
 
 LICENSE
-  Copyright (C) 2020 the Australian Ocean Lab (AusOcean)
+  Copyright (C) 2021-2022 the Australian Ocean Lab (AusOcean)
 
   It is free software: you can redistribute it and/or modify them
   under the terms of the GNU General Public License as published by the
@@ -26,7 +28,7 @@ LICENSE
   in gpl.txt.  If not, see http://www.gnu.org/licenses.
 */
 
-package main
+package turbidity
 
 import (
 	"errors"
@@ -37,7 +39,7 @@ import (
 	"gocv.io/x/gocv"
 )
 
-// TurbiditySensor is a software based turbidity sensor that uses CV to determine saturation and constrast level
+// TurbiditySensor is a software based turbidity sensor that uses CV to determine sharpness and constrast level
 // of a chessboard-like target submerged in water that can be correlated to turbidity/visibility values.
 type TurbiditySensor struct {
 	template, templateCorners gocv.Mat
@@ -46,7 +48,7 @@ type TurbiditySensor struct {
 	scale, alpha              float64
 }
 
-// NewTurbiditySensor constructor for a turbidity sensor.
+// NewTurbiditySensor returns a new TurbiditySensor.
 func NewTurbiditySensor(template, standard gocv.Mat, k1, k2, sobelFilterSize int, scale, alpha float64) (*TurbiditySensor, error) {
 	ts := new(TurbiditySensor)
 	templateCorners := gocv.NewMat()
@@ -54,7 +56,7 @@ func NewTurbiditySensor(template, standard gocv.Mat, k1, k2, sobelFilterSize int
 
 	// Validate template image is not empty and has valid corners.
 	if template.Empty() {
-		return nil, errors.New("template image is empty.")
+		return nil, errors.New("template image is empty")
 	}
 	if !gocv.FindChessboardCorners(template, image.Pt(3, 3), &templateCorners, gocv.CalibCBNormalizeImage) {
 		return nil, errors.New("could not find corners in template image")
@@ -64,7 +66,7 @@ func NewTurbiditySensor(template, standard gocv.Mat, k1, k2, sobelFilterSize int
 
 	// Validate standard image is not empty and has valid corners.
 	if standard.Empty() {
-		return nil, errors.New("standard image is empty.")
+		return nil, errors.New("standard image is empty")
 	}
 	if !gocv.FindChessboardCorners(standard, image.Pt(3, 3), &standardCorners, gocv.CalibCBNormalizeImage) {
 		return nil, errors.New("could not find corners in standard image")
@@ -74,7 +76,6 @@ func NewTurbiditySensor(template, standard gocv.Mat, k1, k2, sobelFilterSize int
 
 	ts.k1, ts.k2, ts.sobelFilterSize = k1, k2, sobelFilterSize
 	ts.alpha, ts.scale = alpha, scale
-
 	return ts, nil
 }
 
@@ -82,28 +83,22 @@ func NewTurbiditySensor(template, standard gocv.Mat, k1, k2, sobelFilterSize int
 func (ts TurbiditySensor) Evaluate(imgs []gocv.Mat) (*Results, error) {
 	result, err := NewResults(len(imgs))
 	if err != nil {
-		return result, err
+		return nil, fmt.Errorf("could not create results: %w", err)
 	}
 
 	for i := range imgs {
-		// Transform image.
 		marker, err := ts.transform(imgs[i])
 		if err != nil {
-			return result, fmt.Errorf("image %v: %w", i, err)
+			return nil, fmt.Errorf("could not transform image: %d: %w", i, err)
 		}
-
-		// Apply sobel filter.
 		edge := ts.sobel(marker)
 
-		// Evaluate image.
 		sharpScore, contScore, err := ts.EvaluateImage(marker, edge)
 		if err != nil {
 			return result, err
 		}
-
 		result.Update(sharpScore, contScore, float64(i), i)
 	}
-
 	return result, nil
 }
 
@@ -115,19 +110,16 @@ func (ts TurbiditySensor) EvaluateImage(img, edge gocv.Mat) (float64, float64, e
 	if img.Rows()%ts.k1 != 0 || img.Cols()%ts.k2 != 0 {
 		return math.NaN(), math.NaN(), fmt.Errorf("dimensions not compatible (%v, %v)", ts.k1, ts.k2)
 	}
-
 	lStep := img.Rows() / ts.k1
 	kStep := img.Cols() / ts.k2
 
 	for l := 0; l < img.Rows(); l += lStep {
 		for k := 0; k < img.Cols(); k += kStep {
 			// Enhancement Measure Estimation (EME), provides a measure of the sharpness.
-			sharpValue := ts.evaluateBlockEME(edge, l, k, l+lStep, k+kStep)
+			sharpness += ts.evaluateBlockEME(edge, l, k, l+lStep, k+kStep)
-			sharpness += sharpValue
 
 			// AMEE, provides a measure of the contrast.
-			contValue := ts.evaluateBlockAMEE(img, l, k, l+lStep, k+kStep)
+			contrast += ts.evaluateBlockAMEE(img, l, k, l+lStep, k+kStep)
-			contrast += contValue
 		}
 	}
 
@@ -165,7 +157,7 @@ func (ts TurbiditySensor) minMax(img gocv.Mat, xStart, yStart, xEnd, yEnd int) (
 func (ts TurbiditySensor) evaluateBlockEME(img gocv.Mat, xStart, yStart, xEnd, yEnd int) float64 {
 	max, min := ts.minMax(img, xStart, yStart, xEnd, yEnd)
 
-	// Blocks which have no information are ignored.
+	// Blocks where all pixel values are equal are ignored to avoid division by 0.
 	if max != -math.MaxFloat64 && min != math.MaxFloat64 && max != min {
 		return math.Log(max / min)
 	}
@@ -176,7 +168,7 @@ func (ts TurbiditySensor) evaluateBlockEME(img gocv.Mat, xStart, yStart, xEnd, y
 func (ts TurbiditySensor) evaluateBlockAMEE(img gocv.Mat, xStart, yStart, xEnd, yEnd int) float64 {
 	max, min := ts.minMax(img, xStart, yStart, xEnd, yEnd)
 
-	// Blocks which have no information are ignored.
+	// Blocks where all pixel values are equal are ignored to avoid division by 0.
 	if max != -math.MaxFloat64 && min != math.MaxFloat64 && max != min {
 		contrast := (max + min) / (max - min)
 		return math.Pow(ts.alpha*(contrast), ts.alpha) * math.Log(contrast)
@@ -189,8 +181,12 @@ func (ts TurbiditySensor) transform(img gocv.Mat) (gocv.Mat, error) {
 	out := gocv.NewMat()
 	mask := gocv.NewMat()
 	imgCorners := gocv.NewMat()
+	const (
+		ransacThreshold = 3.0   // Maximum allowed reprojection error to treat a point pair as an inlier.
+		maxIter         = 2000  // The maximum number of RANSAC iterations.
+		confidence      = 0.995 // Confidence level, between 0 and 1.
+	)
 
-	// Check image is valid.
 	if img.Empty() {
 		return out, errors.New("image is empty, cannot transform")
 	}
@@ -200,7 +196,7 @@ func (ts TurbiditySensor) transform(img gocv.Mat) (gocv.Mat, error) {
 	}
 
 	// Find and apply transformation.
-	H := gocv.FindHomography(imgCorners, &ts.templateCorners, gocv.HomograpyMethodRANSAC, 3.0, &mask, 2000, 0.995)
+	H := gocv.FindHomography(imgCorners, &ts.templateCorners, gocv.HomograpyMethodRANSAC, ransacThreshold, &mask, maxIter, confidence)
 	gocv.WarpPerspective(img, &out, H, image.Pt(ts.template.Rows(), ts.template.Cols()))
 
 	return out, nil

turbidity/turbidity_test.go

@@ -7,7 +7,7 @@ AUTHORS
   Russell Stanley <russell@ausocean.org>
 
 LICENSE
-  Copyright (C) 2020 the Australian Ocean Lab (AusOcean)
+  Copyright (C) 2021-2022 the Australian Ocean Lab (AusOcean)
 
   It is free software: you can redistribute it and/or modify them
   under the terms of the GNU General Public License as published by the
@@ -23,7 +23,7 @@ LICENSE
   in gpl.txt.  If not, see http://www.gnu.org/licenses.
 */
 
-package main
+package turbidity
 
 import (
 	"fmt"
@@ -35,10 +35,16 @@ import (
 const (
 	nImages   = 13  // Number of images to test. (Max 13)
 	nSamples  = 10  // Number of samples for each image. (Max 10)
-	increment = 2.5
+	increment = 2.5 // Increment of the turbidity level
 )
 
 func TestImages(t *testing.T) {
+	const (
+		k1, k2       = 8, 8
+		filterSize   = 3
+		scale, alpha = 1.0, 1.0
+	)
+
 	// Load template and standard image.
 	template := gocv.IMRead("images/template.jpg", gocv.IMReadGrayScale)
 	standard := gocv.IMRead("images/default.jpg", gocv.IMReadGrayScale)
@@ -54,15 +60,15 @@ func TestImages(t *testing.T) {
 	}
 
 	// Create turbidity sensor.
-	ts, err := NewTurbiditySensor(template, standard, 8, 8, 3, 1.0, 1.0)
+	ts, err := NewTurbiditySensor(template, standard, k1, k2, filterSize, scale, alpha)
 	if err != nil {
-		t.Fatal(err)
+		t.Fatal("could not create turbidity sensor: %w", err)
 	}
 
 	// Create results.
 	results, err := NewResults(nImages)
 	if err != nil {
-		t.Fatal(err)
+		t.Fatal("could not create results: %w", err)
 	}
 
 	// Score each image by calculating the average score from camera burst.
@@ -70,19 +76,19 @@ func TestImages(t *testing.T) {
 		// Evaluate camera burst.
 		sample_result, err := ts.Evaluate(imgs[i])
 		if err != nil {
-			t.Fatalf("Evaluation Failed: %v", err)
+			t.Fatalf("evaluation Failed: %w", err)
 		}
 
 		// Add the average result from camera burst.
-		results.Update(average(sample_result.Saturation), average(sample_result.Contrast), float64(i)*increment, i)
+		results.Update(average(sample_result.Sharpness), average(sample_result.Contrast), float64(i)*increment, i)
 	}
 
 	// Plot the final results.
-	err = plotResults(results.Turbidity, normalize(results.Saturation), normalize(results.Contrast))
+	err = plotResults(results.Turbidity, normalize(results.Sharpness), normalize(results.Contrast))
 	if err != nil {
-		t.Fatalf("Plotting Failed: %v", err)
+		t.Fatalf("plotting Failed: %w", err)
 	}
 
-	t.Logf("Saturation: %v", results.Saturation)
+	t.Logf("Sharpness: %v", results.Sharpness)
 	t.Logf("Contrast: %v", results.Contrast)
 }