Detection Of Leaf Rust Disease In Wheat Crops

Using Image Processing Techniques And AI

No Author Given

No Institute Given

Abstract. Wheat crop suffers from different varieties of rust-diseases,

which mainly affect the leaves and stem of the plant. In this paper,
an image processing and analysis system has been discussed which has
been developed to detect the presence of rust diseases in wheat leaves,
using an Artificial Neural Network (ANN), based on various features
extracted from leaf-images. 264 wheat-leaf images were available during
the experiment and the designed system was able to detect the presence
of rust diseases and could successfully grade diseased leaves in 99.2424
% cases.

1 Introduction

Wheat(T riticum aestivum) crop being rich in many essential vitamins, miner-
als, enzymes and antioxidants, is considered to be a staple food crop worldwide.
India is presently considered to be the third highest producer of wheat, with an
area of 285, 00, 000 hectors of land being used to cultivate this particular crop,
each hector yielding an average of 28 tonnes of wheat annually. However, the
efforts towards high quality and quantity production are greatly hampered by a
number diseases that infect the crops. Wheat crops are greatly affected by vari-
ous fungal diseases, Rust disease being the most common one. In the agriculture
industry, rust is considered to be the most devastating fungal disease of all kinds
of cereal crops till known.
It is a general practice among agricultural experts to detect and grade dis-
eases based on naked-eye observations. This process requires a constant monitor-
ing of crops by experts, which is prohibitively expensive in vast farming systems
in a third world country like ours. Also, due to their lack of knowledge, cul-
tivators frequently fail to notice the various symptoms of plant diseases until
contamination occurs at an alarming rate. Thus even before the experts could
be informed, huge production loss has already occurred. In such a scenario, au-
tomated disease-detection systems have become an essential research domain, as
such systems have been proved to be beneficial in monitoring plant health, due
to the fact that they can easily detect the presence of diseases in plant parts as
soon as they occur, with high accuracy.
The use of various image processing techniques and machine learning al-
gorithms in detection of plant health conditions is a recent trend in such ap-
proaches. Stereo- microscopic method and image analysis method have been
compared for usefulness of image analysis as an efficient and precise method to
measure fruit traits by Mix and Pico [2].
Ying and others studied methods of image pre-processing for recognition
of cucumber-crop diseases in [3]. Method for fast and accurate detection and
classification of plant diseases has been proposed in [4] and [5].
Paper [7] proposes automatic detection and calculating area of infection on
leaves of a whitefly (Trialeurodes vaporariorum Westwood ) at a mature stage.
The authors have proposed an algorithm which provides object extraction and
feature extraction on a given image. When the algorithm is used on the image of
a pest-affected leaf, the object extraction method detects the pests by applying
background subtraction and filtering methods, whereas the size and shape of the
pests can be measured by applying an edge detection method.
Paper[10] reports that the various features of a cotton crop leaf could be
extracted using self organizing feature map together with a back-propagation
neural network to recognize colour of image and this information can be utilized
to segment the image depending on pixel values, thus proving a way to find
minute details and better diagnosis of diseases.
Correct diagnosis is the first step in fighting against any disease. In case
of wheat crops, proper diagnosis and detection becomes a tedious job due to
the similarities in appearance between diseased and disease free leaves. In this
paper, an automated method of detection of rust diseases in wheat-leaves has
been discussed. The system includes the knowledge and experience gathered by
the domain experts and aims at providing a safe, fast and reliable response.
Before presenting the architecture of the developed system, an account of the
various types of diseases that can infect wheat crops has been provided.

2 Diseases of wheat crop and their gradations

The rust disease in wheat has 3 variations, caused by 3 related fungi.

1. Stem Rust: Caused by Puccinia Striiformis.

2. Strip Rust: Caused by Puccinia Graminis.
3. Leaf Rust: Caused by Puccinia Triticina.

Amongst the above mentioned diseases, leaf rust, in-spite of being more com-
mon than the other two varieties, has not caused any spectacular damage till
now. However, the scenario is changing very fast as this particular disease has
started invading new areas at an alarming rate and perhaps has more damaging
capabilities now that large areas are being cultivated with genetically closely
related varieties of the crop. In India, an annual average loss of 3% has been
estimated, although a much greater loss may actually occur at areas where the
cultivated crop varieties are susceptible to this fungal infection. A wheat leaf
may be infected by the following diseases.

1. Powdery Mildew: It is a fungal disease in which fungal colonies grow in

elliptical blotches along the leaf surfaces.
 Fig. 1: Sample Images

2. Septoria Leaf Spot: In this disease, elliptical yellow coloured blotches first
appear, and with the advancement of the disease dark brown or black spots
appear in the infected region
3. Tan spot or Yellow Leaf : Dark tan coloured spots appear in the leaves,
hence the name
4. Snow Molds: In this case, the infected leaves appear to be bleached or
brown in colour, and eventually they get dried. If the crowns of the crop
are not infected, new leaves may still grow along the diseased leaves and
the plant may still live. However when the crowns are infected, chances of
survival are nil.

All of the above mentioned diseases are considered to be various manifesta-

tions of the wheat leaf rust infection of various gradations.
In the method being discussed in this paper, the system has been configured
such that it can detect and grade wheat leaves into the two categories : Diseased
and Non-diseased.

3 Architecture of the proposed system

The system has been designed to operate in two phases: the off-line phase
or the training phase and the on-line phase or the testing phase. In the on-
line phase, some pre-categorized training images are first provided to the image
analyzer, which performs the following operations on them -
1. Image Enhancement.
2. Image Segmentation.
3. Feature Extraction

The extracted features are then provided to the classifier, along with the
predetermined gradations of the images. The relations between the values of the
features extracted and the gradations given to the respective images are then
calculated by the classifier and are stored in the feature repository.
In the on-line phase, when a test image is produced to the system, the image
analyzer operates on it and extracts the predefined features. The values of these
features are then compared with those stored in the repository and the diagnosis
made by the classifier depends entirely on the result of this comparison.
 Fig. 2: Architecture of proposed system

The various phases of the system have been discussed in details in the fol-
lowing sections. The image analyzer component has been discussed in section 4
and section 5 deals with the details of the classifier.

4 The Image Analyzer

Both the training and test images are at first produced to the image analyser
which pre-processes the images in order to extract useful features.

4.1 Image Enhancement

The following Image Enhancement techniques were applied on both the training
and test images:

1. Re-sizing an image: The images obtained varied greatly in size, so they

were uniformly re-sized first, the specifications being 512 X 512.
2. RGB to HSI Transformation: The primary visual symptoms of the wheat
leaf rust disease are the reddish-brown spots that appear on the upper sur-
faces of the leaves. By inspection of the diseased leaves, it was found that
the disease infected parts have higher intensity values of the pixels as com-
pared to the non-infected parts. In order to extract these damaged tissues,
the acquired RGB colour image was transformed into gray-level image us-
ing Hue-Saturation-Intensity(HSI) transformation. In the next stage of the
work, these grey-level images were used to produce binary images.
4.2 Image Segmentation

The mostly green areas of the wheat images represent the healthy plant tissues.
These regions could be easily recognized from the infected or diseased parts,
using the method of image segmentation.
Segmentation of the diseased wheat leaves involves distributing the pixel
intensity values into two classes or clusters: one class containing the higher in-
tensity values of the rust-spots and the other class consisting of the lower in-
tensity values of pixels belonging to the non-infected or healthy tissue-regions.
The Otsu’s threshold method was implemented to perform the segmentation
operation.In the resulting binary image,the white regions represent the disease
affected regions whereas the darker regions represent the healthy tissues.
This step was performed to ensure that long processing times were not spent
in extracting features from these healthy areas, as such feature values are irrel-
evant to our problem.

RGB Image

Gray Image

Binary Image

Fig. 4: Acquired RGB images of wheat leaves with corresponding HSI transformed and
segmented images.
4.3 Feature Extraction Phase
The next phase is the feature extraction phase. This phase becomes necessary
in order to reduce the total amount of data that is being considered: instead of
processing the whole image, we have processed some of its feature-values, thus
reducing the computation required.
1. Green Density: The number of green pixels in the image which are above
a predefined threshold are calculated, in order to determine the health of the
leaf.
2. Estimation of infected area: The color image was first converted into a
gray-level image by HSI transformation. This gray-level image is then con-
verted into binary image after application of segmentation operation , as
discussed in the previous section.
The black areas of the binary image represent the healthy tissues of the
leaf and the white regions represent the infected tissues. let AHT denote the
healthy-tissue count. Also, let ADT denote the count of the infected tissues.
Therefore,
ADT
Inf ectedArea = (1)
A
where A= AHT + ADT .
3. Texture based features : In case of feature extraction based on texture of
the image, the gray level co-occurrence matrix was used. The co-occurrence
matrix C(i, j) counts the number of co-occurrence of pixels with gray-levels
i and j respectively, at a given distance d, where d is the distance defined in
polar coordinates (d, θ) with discrete length and orientation. θ takes values
0, 45, 90, 135, 180, 225, 270 and 315.
The texture features that have been obtained from the co-occurrence matrix
of the gray-level image, are:
(a) Energy: It measures the sum of squared elements in the matrix.

Energy = ΣΣ(c(i, j))2 . (2)

(b) Entropy: Entropy is the minimum amount of data that is sufficient to
describe the GLCM without losing information.

Entropy = −ΣPr (rk )logPr (rk ). (3)

(c) Contrast: Also known as variance and inertia, contrast is the measure-
ment of the local variations in the matrix.

Inertia = ΣΣ(i − j)2 ∗ (c(i, j)). (4)

(d) Correlation: It measures the sum of joint probabilities of occurrences
of every possible gray-level pair i and j of the GLCM.
4. Mode: The mode of an image denotes the pixel intensity value of the image
which occurs the maximum number of times in that image. It can also be
defined as the pixel intensity value for which the histogram of the image
attains the maximum height.
 5. Variance: The variance (or standard deviation) is a measure of contrast in
the neighborhood S(x, y).
6. Number of peaks in the histogram: A peak in a histogram is defined as
that value which is greater than its nearest two neighbours. Such peaks were
counted from the histograms of the gray-level images of the wheat leaves.
After the feature extraction phase was complete, the values of the above
mentioned features were produced to the classifier for the purpose of correct
diagnosis and detection. A Multi- Layer Perceptron (MLP) network was used
for this purpose, details of which have been discussed in the next section.

5 The Classifier
Before the system goes on-line, it needs to be manually trained using a set of
training samples. An Artificial neural network (ANN), specifically a Multi-layer
Perceptron (MLP) was used to in the classification phase. This type of Artificial
Neural Network is excellent for performing pattern recognition and classification
tasks.
The topology of the neural network, which consists of the number of nodes
and layers present and the number of training samples, decides the success of
the experiment. It is a known fact that too many layers and too many nodes
in each layer results in long training time and local minima, thus degrading the
performance of the neural network. Large number of connections may also lead to
loss of generalization capacity, thus causing over-fitting. On the other hand, if the
number of nodes and layers are fewer than that required, the designed network
may not be able to adjust to the dynamic nature of the problem. Unfortunately,
there are no specific rules so as to consider the exact number of nodes and layers
of the network for a specific problem. The most widely method used for this
purpose is trial and error.
The MLP used in this experiment consists of two hidden layers, the first
one with 10 nodes and the second one with 5 nodes.

6 Experimental Results
The experiment was conducted on a 32-bit Windows 7 operating-system sup-
ported machine. The image-processing tool ImageJ was used for the feature
extraction purpose and the data-mining tool Weka was used for the training and
testing of the ANN.
The MLP was trained using the 10 input images.
– 5 images of disease-free category leaves.
– 5 images of diseased category leaves.
In the testing phase of the experiment, 58 image of diseased wheat-leaves,
and 204 images of non-diseased variety, as classified by the experts were used.
The total number of correctly classified instances was 262 and incorrectly clas-
sified instances was 2, yielding a success-rate of 99.2424%.
The following figure depicts the results obtained in this experiment:
 Fig. 5: Experimental Results

7 Conclusion and Future Scope

In this paper, an integrated image processing and analysis system has been
discussed, which can be used in detecting the presence of rust diseases in wheat
leaves.
This approach can also be used to detect various other diseases or pests in
crops other than wheat. However, the features to be extracted from the images
need to be carefully decided in those cases.
The system can actually be transformed into a working model, such that
both cultivators and agricultural scientists can utilize the system in order to get
fast and accurate test results. The Government of India already supports various
help-lines and other aids to cultivators so as to guide them in maintaining the
quality of the crops. The proposed system has the potential to become a source
of great help to the farmers, if the concerned government departments utilize
it. However, the methods, platforms and architecture to physically model this
system would require further research and implementation.

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