A Crop Field Image Dataset for the Evaluation of Computer Vision

Based growth comparison Agriculture Tasks

Abstract

Rainfall and crops production is playing a most important role for countries

economic growth and development. In this project we propose a benchmark dataset

for crop / weed discrimination, single plant phenotyping and other open computer

vision tasks in growth comparison agriculture. The dataset comprises 60 images

with annotations and is available online . All images were acquired with the

autonomous field robot Bonirob in an organic carrot farm while the carrot plants

were in early true leaf growth stage. Using K-Means segmentation algorithm

separate clusters in dataset image. After segmentation calculate growth area in

present data and existing data. Depends upon pixels area we calculate the growth.
 CHAPTER 1

INTRODUCTION

1.1 INTRODUCTION ABOUT CROP GROWTH

India is an agriculture based country. Two -third of population relies upon

agriculture directly or indirectly. It is not merely a source of livelihood but a way
of life. It is the main source of food, fodder and fuel. It is the basic foundation of
economic development. It provides highest contribution to national income. In
addition to this, agriculture also provides employment opportunities to very large
percentage of population. The climate conditions of our country is isotropic, still
we are not been able to utilize agriculture resources. The reason behind this is the
lack of rains and scarcity of water. Another cause may be unplanned use of water
due to which a remarkable amount of water goes in vain.

At the present era, the farmers have been using various pesticides for crop at
regular intervals. Presence of pests and disease affect the rate of crop cultivation. It
reduces crop yield in a significant amount and as a result there will be an increase
in poverty, food insecurity and mortality rate. The current system relies on visual
observation which is a time consuming process. This problem can be completely
resolved if we use automatic control of using pesticides in which the pesticides will
be used based on the growth of the crop. With the advancement in image
processing technology, it is feasible to create an automated mechanism for the
detection of pests.
In biological studies, plant growth and health assessments are still evaluated
manually by human observations, which are time consuming and destructive.
Because of this there is an increasing demand for objectivity and efficiency. Thus,
automatic image analysis technique has become a useful tool in biological
researches. Image analysis method is a non-invasive and non-destructive sensing
system. It can be used to extract and quantify different kinds of information like
size, shape, colour, and moisture and growth rate of a targeted object.
1.2 LITRATURE SURVEY

This paper presents recent developments of image analysis applications in plant

growth and health assessment. Almost all monitoring systems using image analysis
techniques involves seven basic steps like image recording, pre-processing, image
segmentation, detection, extraction, classification and finally validation. Examples
of image monitoring application includes satellite image analysis, aerial
photographs and video graphs, 3D images, acoustic images, MR images and
images in electron microscopy (Nilsson, 2009).
Image analysis systems have a great potential in the assessment of plant growth
and health with high accuracy (Du and Sun, 2004). The automatic image analysis
systems offer flexibility in application. To develop an automatic monitoring tool
for the plant growth and health assessment, image analysis is usually integrated
into the mechanical devices to replace manual assessments by humans (Du and
Sun, 2004). The image analysis system is used to control the operation of the
machinery. There are five main steps in image analysis, including: image
recordings, pre-analysing, segmentation, detection and classification (Du and Sun,
2004).
Image processing can reduce the total information of plant image to a
manageable amount, by increasing edges and making geometrical corrections,
before the analysis of measurements and identification of some specific details
such as size, area and shape (Nilsson, 2009). The biggest benefit of image analysis
is that it can view specific areas and contrast colours. This allows visual
explication and interactive analysis by the computer. The analysed images can also
be stored in a mass memory. When a PC is bonded to a net, it is very easy to
transfer data among scientists from different cities or countries (Nilsson, 2009).

In today’s technology, image analysis finds itself a great use to monitor and
assess plant growth and health. Data collected for this purpose allows creating or
increasing the performance of the health and growth models. Studies related to the
growth and health of plants is mainly focused on leaf area as a feature parameter
(Tarbell and Raid, 1991). Thus, plant leaf area can be used to predict the growth of
plants as functions of environmental conditions. Disruptive harvesting of plants by
sampling of leaves is the most accurate way to measure the leaf area, but it is not
good to make repeated measurements on the same plants or remote measurement
of plants.
Moreover, the areas of the leaves can be predicted based on the correlations
between the area and dimensions of leaf size and shape (Baker, 1996).
Nevertheless, these recordings can be boring and time consuming, particularly
during periods when leaf area is growing quickly. Non-destructive recordings using
vision technology have the potential to provide a reliable prediction of area without
harvesting the plants. Leaf areas can be obtained by a video camera and processed
with a computer (Baker, 1996). Eguchi et al., (1983) tried to adapt an image
analysis system for researches of plant growth. In later years, image processing
was used by Meyer and Davidson, (1987) to investigate plant growth, by
measuring the leaf area; stem chamber and leaf. They also concluded in their study
that system accuracy and applicability can be limited by the camera resolution.
The problem of predicting plants biomass with respect to their growth using
vision monitoring techniques was discussed by Evers et al., (1987). Hack, (1989)
investigated the relationship between fresh weight of the lettuce plant and the
recorded leaf area of it in the greenhouse, by image processing system. To
determine the plant fresh weight and transpiration, a weighing scale was used in a
hydroponic system. This time, the correlation between fresh weight and leaf area
gave the best results with an exponential regression equation and with a
determination coefficient (R2) of 0.90. Special software was developed by Tarbell
and Reid, (1991) to scan corn plants images. Plant growth and development could
be monitored by this image-based monitoring system. Another simulation model
was also developed to detect the leaf area in potato plants (Trooien and Heermann,
1992). They have tested several experimental procedures on the simulated potato
canopy where they compared the image processed and measured leaf area.
In another research, for hazelnut plants a high correlation between leaf areas
obtained with an area meter and canopy silhouette areas measured with image
processing was found by Bignami and Rossini, (1996). Nyakwende et al., (2015)
found a correlation between true leaf area of intact tomato plants and areas
measured using image analysis. The images were obtained from the plants as top-
view, side-view and with an oblique angle. Additionally, they investigated the taut-
string boundary which provided information about the compactness of the plants as
they grow.
Another system using digital video and image analysis was demonstrated by
Leister et al., (1999) to non-destructively define the plant size by measuring plant
leaf area. The system provided a non-destructive method to assess the plant growth
and growth rates by monitoring and quantifying feature parameters of the plant. In
another study, plant growth and health in a controlled environment was
continuously monitored by Kacira and Ling, (2001) using a vision monitoring
approach. Canopy area is also an important variable concerning plant growth. The
canopy area of a plant is certainly commensurate to its dry weight. In addition, the
plant growth is also expressly correlated to its dry weight. Measuring plant canopy
area, or in other terms plant canopy cover, by the means of image processing can
give valuable information for plant growth monitoring.
A pattern recognition algorithm was tested by Han and Hayes, (1990) to
distinguish crop canopies from the background soil. In another study, the image
classification method was used by Han and Hayes, (1990) with soil colour
information. Further models were also studied by Vanhenten and Bontsema, (1995)
to find the relationship between the soil coverage of lettuce canopy which is
measured by image analysis and its dry weight. It was concluded that the dry
weight could predicted with 95% accuracy from the soil coverage.
Ewing and Horton, (1999) developed special algorithm to extract some
information from colour images. The software allowed obtaining some data from
colour images like photographs of plant canopies. Percent canopy cover could also
be measured using this software. Growth rates of plants can also be measured
directly using image analysis techniques. The stem length and growth rates were
measured by image analysis of Verbena bonariensis L. plant by Shimizu and Heins,
(1995). Motion in dynamic image sequences of dicot leaves were analysed by
Schmundt et al., (1998). By the developed algorithms growth rate could be
measured at less than 1% per hour.
 CHAPTER 2

METHODOLOGY

2.1 OBJECTIVES
The objective of this study was to review current image processing techniques
to assess the plant growth. Furthermore, the role of the image analysis systems in
the plant growth was explained.

2.2 Proposed system

Contrast K-means Area

First image
enhancement segmentation calculation

Crop growth
detection

Contrast K-means Area

Second image
enhancement segmentation calculation

Fig.3.1 Block Diagram of Proposed system

In this project, we propose crop growth detection method using k means

segmentation algorithm. The algorithm starts by acquiring the digital image from
the environment and loading them as the filter construction images, following
acquisition the color transformation structure for the RGB plant images was
created. Contrast enhancement applies the first image and second image. After
applying k-means algorithm, image segmented into clusters. After segmentation
cluster converted into binary image .Calculate image region of two images and also
calculate crop growth.

2.3 K-means Clustering

K-means is an unsupervised clustering technique. It partitions the given

image by defining k clusters with a centroid value for each one. A distance function
is calculated for each pixel to define the cluster. Below steps shows the steps of K-
means that takes a two dimensional image as input.

1: Copy image values into an array and iterate.

2: Initialize a seed point (centroid) as mean of the array.

3: Find the distance of pixels and seed point

4: Calculate the bandwidth for cluster center

5: Find a new seed as mean of qualified values that their distance are less than
the bandwidth.

6: If the new seed is equal to the old seed, remove qualified values and update
the center. Then, return to step 2.

7: Store the new seed among centroids.

8: Sort the seeds at the end of the number of iterations.

9: Find the difference between every two consecutive centers and the minimum
distance between centroids.
 10: Discard cluster centroids less than distance.

11: Make a clustered image using these centers.

2.4 Area calculation

In MATLAB, the function ‘regionprops’ is used to measure the image properties.

Here are some basic properties computed without using the function.
Read an image and find the connected components using ‘bwlabel’ function.
Using the Labeled matrix as an input, the properties can be measured.

Example:
A= [1 0 0 1
1111
0 0 1 1]

To find Area:
 The total number of ‘ON’ pixels in the image.
 CHAPTER 3

RESULTS & DISCUSSON

3.1 Matlab Software Details

MATLAB is a high-performance language for technical computing. It integrates

computation, visualization, and programming in an easy-to-use environment where
problems and solutions are expressed in familiar mathematical notation. Typical
uses include:

 Math and computation

 Algorithm development

 Modeling, simulation, and prototyping

 Data analysis, exploration, and visualization

 Scientific and engineering graphics

 Application development, including Graphical User Interface building

 An interactive numerical computing environment

 Matrix computations

 Graphics

 Programming (M-files)

 Toolboxes (signal processing, statistics, optimization, symbolic math)

 MATLAB is an interactive system whose basic data element is an array that
does not require dimensioning. This allows you to solve many technical computing
problems, especially those with matrix and vector formulations, in a fraction of the
time it would take to write a program in a scalar non-interactive language such as
C or Fortran.

The name MATLAB stands for matrix laboratory. MATLAB was originally
written to provide easy access to matrix software developed by the LINPACK and
EISPACK projects, which together represent the state-of-the-art in software for
matrix computation.

MATLAB has evolved over a period of years with input from many users. In
university environments, it is the standard instructional tool for introductory and
advanced courses in mathematics, engineering, and science. In industry, MATLAB
is the tool of choice for high-productivity research, development, and analysis.

MATLAB features a family of application-specific solutions called

toolboxes. Very important to most users of MATLAB, toolboxes allow you to
learn and apply specialized technology. Toolboxes are comprehensive collections
of MATLAB functions (M-files) that extend the MATLAB environment to solve
particular classes of problems. Areas in which toolboxes are available include
signal processing, control systems, neural networks, fuzzy logic, wavelets,
simulation, and many others.

Matlab (matrix laboratory) is a numerical computing environment and

fourth-generation programming language. developed by math-works, Matlab
allows matrix manipulations, plotting of functions and data, implementation of
algorithms, creation of user interfaces, and interfacing with programs written in
other languages, including c, c++, java, and Fortran.
 Although Matlab is intended primarily for numerical computing, an optional
toolbox uses the mupad symbolic engine, allowing access to symbolic computing
capabilities. An additional package, Simulink, adds graphical multi-domain
simulation and model-based design for dynamic and embedded systems.

In 2003, Matlab had around one million users across industry and academia.
Matlab users come from various backgrounds of engineering, science, and
economics. Matlab is widely used in academic and research institutions as well as
industrial enterprises.

3.2 The MATLAB System

The MATLAB system consists of five main parts:

3.2.1 The MATLAB language

This is a high-level matrix/array language with control flow statements,

functions, data structures, input/output, and object-oriented programming features.
It allows both "programming in the small" to rapidly create quick and dirty throw-
away programs, and "programming in the large" to create complete large and
complex application programs.

3.2.2 The MATLAB working environment

This is the set of tools and facilities that you work with as the MATLAB
user or programmer. It includes facilities for managing the variables in your
workspace and importing and exporting data. It also includes tools for developing,
managing, debugging, and profiling M-files, MATLAB's applications.
3.2.3 Handle Graphics
This is the MATLAB graphics system. It includes high-level commands for
two-dimensional and three-dimensional data visualization, image processing,
animation, and presentation graphics. It also includes low-level commands that
allow you to fully customize the appearance of graphics as well as to build
complete Graphical User Interfaces on your MATLAB applications.

The MATLAB mathematical function library

This is a vast collection of computational algorithms ranging from
elementary functions like sum, sine, cosine, and complex arithmetic, to more
sophisticated functions like matrix inverse, matrix eigenvalues, Bessel functions,
and fast Fourier transforms.

The MATLAB Application Program Interface (API)

This is a library that allows you to write C and Fortran programs that interact
with MATLAB. It include facilities for calling routines from MATLAB (dynamic
linking), calling MATLAB as a computational engine, and for reading and writing
MAT-files.

Starting MATLAB

After logging into your account, you can enter MATLAB by double-clicking
on the MATLAB shortcut icon (MATLAB 2013a) on your Windows desktop.
When you start MATLAB, a special window called the MATLAB desktop appears.
The desktop is a window that contains other windows. The major tools within or
accessible from the desktop are:

• The Command Window

• The Command History

 • The Workspace

• The Current Directory

• The Help Browser

• The Start button

Syntax

The MATLAB application is built around the MATLAB scripting language.

Common usage of the MATLAB application involves using the Command
Window as an interactive mathematical shell or executing text files containing
MATLAB code.

Structures

MATLAB has structure data types. Since all variables in MATLAB are
arrays, a more adequate name is "structure array", where each element of the array
has the same field names. In addition, MATLAB supports dynamic field names
(field look-ups by name, field manipulations, etc.). Unfortunately, MATLAB JIT
does not support MATLAB structures; therefore just a simple bundling of various
variables into a structure will come at a cost.

Functions

When creating a MATLAB function, the name of the file should match the
name of the first function in the file. Valid function names begin with an alphabetic
character, and can contain letters, numbers, or underscores.

Function handles
 MATLAB supports elements of lambda calculus by introducing function
handles, or function references, which are implemented either in .m files or
anonymous/nested functions.

Classes and object-oriented programming

MATLAB's support for object-oriented programming includes classes,

inheritance, virtual dispatch, packages, pass-by-value semantics, and pass-by-
reference semantics. However, the syntax and calling conventions are significantly
different from other languages. MATLAB has value classes and reference classes,
depending on whether the class has handle as a super-class (for reference classes)
or not (for value classes).

3.3 APPLICATIONS OF MATLAB:

 Mathematical Calculations

 Data Analysis & Visualization

 Software Development

 Simulation

3.4 ADVANTAGES:

 It's very easy for a beginner in computer programming.

 It comes with well-written manuals.

 Large user community, sharing free codes. It lets you work in Matrices easily. It
lets you do some complicated calculations quickly, without having to write a whole
program or spreadsheet. Tons of add-ons and workbenches available to do a variety
of tasks.

 Easy, interactive environment

 Fast numerical algorithms

 Inexpensive software

 Fun and easy environment for learning Linear Algebra!!

Fig 3.1 GUI for crop growth detection

Fig 3.2 Output of first image contrast enhancement
Fig 3.3 Output of K-Means segmentation with clusters
Fig 3.4 Output of cluster gray scale image
Fig 3.5 Output of cluster binary image
Fig 3.6 GUI for second image selection
Fig 3.7 Output of second image contrast enhancement
Fig 3.8 Output of K-Means segmentation with clusters
Fig 3.9 Output of cluster gray scale image
 Fig 3.10 Output of cluster binary image

Fig 3.11 GUI for crop growth area detection

 CHAPTER 4

CONCLUSION

The role of image monitoring systems to evaluate plant growth was

reviewed in this manuscript. Various image analysis systems were used to assess
the plant growth and health in literature with various degrees of success. Area
feature were used to detect the object in the plant image and to assess the growth
by image processing. Developing the image analysis algorithms can increase the
accuracy and speed to fulfill the needs of systems. However, integrating image
analysis algorithms into special hardware can fairly reduce the time consuming.
With developed fast algorithms and cheap hardware solutions, image
processing methods will have an increasingly important role in growth and health
of plants assessment in the future. This method can also help to protect the natural
balance of the ecosystem.
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