<!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD v1.0 20120330//EN" "JATS-archivearticle1.dtd">
<article xmlns:xlink="http://www.w3.org/1999/xlink">
  <front>
    <journal-meta />
    <article-meta>
      <title-group>
        <article-title>Determination of Plant Phenological Cycle from RGB Images</article-title>
      </title-group>
      <contrib-group>
        <aff id="aff0">
          <label>0</label>
          <institution>M.Yu. Kataev</institution>
        </aff>
        <aff id="aff1">
          <label>1</label>
          <institution>Tomsk University of Control Systems and Radio Electronics</institution>
          ,
          <addr-line>Tomsk</addr-line>
          ,
          <country country="RU">Russia</country>
        </aff>
      </contrib-group>
      <abstract>
        <p>Automated visual assessment of the state of the earth and plants, wilting and pests of leaves, plant growth indicators, using technical vision, can be used as a basis in smart (precision) agriculture (SA). This article discusses a brief review of the literature on the use of computer (technical) vision (CV) for analyzing the condition of agricultural fields and plants growing on them. The introduction of vision systems into real agricultural production practice is associated with the development of complex mathematical approaches that must be resistant to a variety of technical and weather changes. It is necessary to overcome image changes caused by atmospheric conditions and daily and seasonal variations in sunlight. An approach is proposed, which is based on an RGB image obtained using a typical digital camera. The results are given on the use of CV systems in solving individual tasks of agricultural production.</p>
      </abstract>
      <kwd-group>
        <kwd>technical vision</kwd>
        <kwd>mathematical methods</kwd>
        <kwd>images</kwd>
        <kwd>agriculture</kwd>
        <kwd>image classification</kwd>
        <kwd>unmanned aerial vehicle</kwd>
      </kwd-group>
    </article-meta>
  </front>
  <body>
    <sec id="sec-1">
      <title>1. Introduction</title>
      <p>An important task of smart agriculture is to monitor the
condition of plants from the moment of planting, to ripening and
harvesting [1]. This segment of research, based on CV, has still
weakly penetrated SA production. Control of large-sized and
spatially distributed plots of agricultural land is difficult and
poorly implemented in modern farms by classical methods. The
problem here is the inability to study the characteristics of soil
and plants on frequent spatial and temporal grids. Information
obtained by classical methods is rare in time and space and is
more based on the experience of agronomic workers.</p>
      <p>The problems of agricultural development are global. The
concept of sustainable development of society includes in the list
of the main issues that will need to be addressed, the following:
population growth; energy sources and new fuel; food, including
drinking water; depletion of resources; global climate change;
the problem of pollution of air, water (oceans, seas, lakes, rivers
and underground sources) and soil; the problem of limiting the
production and consumption of toxic and harmful products. The
solution to almost all of these issues, one way or another, is
associated with the successful development of agriculture,
improving the quality and quantity of products.</p>
      <p>The solution of the above problems is possible with the help
of a modern monitoring base based on the use of satellite remote
sensing (SRS) data and information obtained from unmanned
aerial vehicles (UAVs) [2]. The information obtained in this way
is unique in that it has a high temporal and spatial resolution and
is informative (the presence of multispectral information). It
should be noted that the advantages of remote sensing in SX
production are widely known, then information about the
possibility of using UAVs is just beginning to develop. The
information received from the UAV provides the ability to obtain
relevant information with high periodicity (several times a day),
the ability to cover large areas with high spatial resolution (up to
several centimeters), to receive data in a uniform form (images
in RGB or multispectral).</p>
    </sec>
    <sec id="sec-2">
      <title>2. Formulation of the problem</title>
      <p>Since the main area of agricultural land in our country is
located in areas of unsustainable and risky farming, under the
conditions of observed global climate change, increasing the
reliability of current information on current and expected
weather conditions, assessing their impact on the state and
formation of crop productivity, is of paramount importance.</p>
      <p>Factors such as weather conditions and soil quality form the
conditions for plant growth and therefore determine productivity.</p>
      <p>Changes in these factors lead to a change in productivity, which
forces us to develop methods for assessing the state of plants
throughout the entire time, from planting to ripening.</p>
      <p>The development of methods for classifying and assessing
the state of plants is one of the main areas of research in the field
of remote sensing of the earth using satellites, aircraft and
unmanned aerial vehicles. Observations of the seasonal
development of plants have been carried out in the interests of
agriculture for a long time (more than 30 years). Satellite
measurements of the spectral characteristics of radiation
reflection in the visible and infrared regions of the spectrum and
the values of vegetation indices obtained on their basis allow us
to describe the seasonal dynamics of various types of plants. One
of the necessary conditions for determining the phenological
characteristics of plants (the time of the onset of various
phenological phases, the duration of the growing season and
others) is the availability of time series of data from continuous
satellite observations. These measurements provide diverse and
accurate information on the development of plants over time.</p>
      <p>However, there are limitations associated with the frequency
(preferably at least once a week) of obtaining the necessary data
(cloud exposure). Therefore, the obtained satellite information is
important, but rather it is some benchmark information for
methods that allow you to regularly receive data on agricultural
fields and plants located on them, namely unmanned aerial
vehicles.</p>
      <p>Phenological characteristics such as start of growing season
(SOS) and end of growing season (EOS) end dates, its growing
season length (GSL), and maximum of growing date season
MGS), seasonal amplitude and some others, are widely used in
solving problems of remote sensing of plant conditions.</p>
      <p>Information on the start date of the growing season is
characterized by the widest practical relevance in solving
agricultural problems. In practice, field agricultural work, the
beginning of the growing season is established by the date of
planting, and the completion is associated with determining the
time of ripening of the plant. The duration of the phenological
cycle is determined by the type of plant. Air temperature, air and
soil humidity, illumination, the presence of chemical trace
elements necessary for plant growth in the soil are significant
factors that determine the parameters of the phenological cycle.</p>
      <p>Since the presence of moisture in the soil at the time of planting
is the main limiting factor for plant growth, the beginning of the
growing season is determined primarily by rainfall, as well as
filling the fields with snow.</p>
      <p>Modern digital cameras mounted on UAVs [3] have
technical characteristics that allow solving many practical
problems of agricultural production. This paper describes the
software necessary to solve the problem of determining the state
of crops in large areas. Obtaining this information is possible due
to the ability to obtain a set of separate images of the SA territory
in several spectral channels of a digital RGB camera or with
additional spectral channels (near IR or IR spectral region) [3].</p>
      <p>The presence of this information allows you to determine the
Copyright © 2019 for this paper by its authors. Use permitted under Creative Commons License Attribution 4.0 International (CC BY 4.0).
characteristics of plants from the calculation of various indices
(vegetation, soil, etc.), as well as texture or color analysis.</p>
      <p>Carrying out measurements at different time periods and
obtaining multi-temporal data allows us to determine the
dynamics of changes in the characteristics of crops, which is
directly related to the performed agrotechnical work. Such
studies clearly allow us to determine the area of the CX of
territories where there is a deviation from average values, for
example, due to the degradation of soil parameters close to the
surface of the water horizon, etc. The presence of field images
allows us to pose the problem of obtaining cartographic
information of the state of the SA [4] of territories , taking into
account the fact that UAVs can be equipped with high-precision
geo-referenced devices. Such geospatial information allows us to
solve the problem of combining images in space and time, as well
as embed images in geographic information systems (GIS).</p>
      <p>The presence of RGB color channels allows us to consider a
digital camera as a spectral device, which makes it possible to
make index calculations (Greeness) associated with the
normalized difference index of vegetation NDVI (Normalized
Difference Vegetation Index) [5]. The only difference is that the
calculation of NDVI requires the presence of spectral
information in the region of 0.7-1.5 μm, and the red channel of
the digital camera is located in the region of 0.6-0.7 μm.</p>
      <p>Nevertheless, selecting digital cameras with the necessary
spectral channels, it is possible to obtain reliable information
about the state of crops. Using the results of the calculation of the
Greeness index in monitoring tasks of assessing the dynamics of
characteristics, one can obtain spatio-temporal maps. The
presence of a priori information about the characteristics of the
soil and meteorological information allows us to build
mathematical models of changes in the state of agricultural crops
(amplitude and growth rate at different periods of vegetation).</p>
      <p>Such information allows you to predict in advance a possible
crop, type of harvest (given time and territory). Note that the
frequency of the survey is an important parameter that
determines the accuracy of the forecast and problem solving,
control of the performed agricultural work, monitoring of the
harvest, etc.</p>
    </sec>
    <sec id="sec-3">
      <title>3. Vegetation Indices</title>
      <p>Vegetation indices make it possible to quantify the state of a
plant at the time of measurement from a comparison of the values
of the RGB spectral channels. It is known that in the blue-green
region of the spectrum, plants have low reflectivity, which grows
significantly in the red and near infrared regions of the spectrum.
Accordingly, by comparing the values of the RGB channels in
pixels corresponding to the plant, the state of the plant can be
detected. Here are some vegetation indices that are calculated
based on RGB channels: GCC - Green Chromatic Coordinate,
RCC - Red Chromatic Coordinate, BCC - Blue Chromatic
Coordinate, ExG - Excess Green, ExR - Excess Red and NDI
Normalized Difference Index [6] .</p>
      <p>
        The calculation of the GCC, BCC and RCC indices is carried
out according to the formulas:
GCC=Green/(Blue+Green+Red), (
        <xref ref-type="bibr" rid="ref1">1</xref>
        )
BCC=Blue/(Blue+Green+Red), (
        <xref ref-type="bibr" rid="ref2">2</xref>
        )
RCC=Red/(Blue+Green+Red), (
        <xref ref-type="bibr" rid="ref3">3</xref>
        )
ExG=2∙GCC-RCC-BCC, (
        <xref ref-type="bibr" rid="ref4">4</xref>
        )
ExR=1.4∙RCC-GCC, (
        <xref ref-type="bibr" rid="ref4">4</xref>
        )
NDI=(Red-Green)/(Red+Green), (
        <xref ref-type="bibr" rid="ref5">5</xref>
        )
wherе R=Red, B=Blue, G=Green – channel values for each
image pixel.
      </p>
      <p>
        Plants in the image were distinguished using empirically
selected thresholds for each of the indices (
        <xref ref-type="bibr" rid="ref1 ref2 ref3 ref4 ref5">1-5</xref>
        ). Further, the
indices were compared and among all the results, an index with
average characteristics was selected.
      </p>
    </sec>
    <sec id="sec-4">
      <title>Results</title>
      <p>In the whole variety of tasks from image processing to
machine vision, there are no clear boundaries, however,
processes of different levels can be distinguished here. The
processes of the first level (pre-processing) include only methods
and algorithms for image processing to reduce noise, increase
contrast or improve sharpness, geometric transformations, etc.
They are characterized by the fact that there are images at the
input of the process and its output. The processes following the
first are associated with more complex image conversion tasks,
such as segmentation (dividing images into areas and selecting
objects in them), a description of the objects and their
compression to give them a convenient shape during further
computer processing, as well as the classification (recognition)
of selected objects. Note that these processes have images in the
input, and attributes and features extracted from these images,
such as borders, contours, and other distinguishing features of
objects that are also images (of a different type), are output.
Finally, processes of a different level are involved in
understanding the set of many recognized objects, correlating
them with existing templates or vice versa, forming templates.
This shows that the natural transition from image processing to
analysis of their content is the recognition area of individual
objects in the images. Thus, what is called digital image
processing is associated with processes having images at the
input and output, as well as with the processes of extracting
certain knowledge about objects located on the image.</p>
      <p>The incoming images for processing during measurements
from an unmanned aerial vehicle have specific features that are
associated with the state difference in the level of illumination
and the geometry of obtaining each image of one agricultural
field. When shooting, which is usually carried out for several
hours, the Sun changes its position and shadows from the relief,
trees or clouds may appear, the level of illumination itself, the
position of the unmanned aerial vehicle changes from the
magnitude and direction of the wind. Therefore, at the
preprocessing stage, a lot of work arises related to the preliminary
preparation of images uniform in quality (geometry and
illumination).</p>
      <p>After the images are unified in terms of quality, it is
necessary to select only plants on it, excluding from the
processing areas that are not related to plants (roads, buildings,
machinery, trees, shrubs, etc.). One way to solve this problem is
image segmentation, i.e. the selection of areas that are odd in
some ways in the image. Currently, the main classes of image
segmentation include the following classes: 1. Morphological
methods - are mainly used to work with binary (black and white)
images. These methods allow you to extract image components,
which can later be used to represent the shape of the object. 2.
Threshold methods - have intuitive properties and are easy to
implement. There are several main types of threshold
segmentation, but only two are basic: the method with an optimal
threshold and the method with an adaptive threshold. All other
methods of this class are derived from the two mentioned
algorithms. 3. Methods of growing areas - are algorithms that
recursively perform the procedure for grouping pixels in a
subregion according to predetermined criteria. One of the main
methods here is the watershed method. 4. Texture methods - are
based on the analysis on the diffuse (color, reflectivity) surface
properties of the analyzed object. The methods presented in this
category are sets of complex operators that can reduce the surface
recognition process to the simple task of distinguishing
brightness levels. Note that such approaches are dependent on
image quality and, accordingly, in our task they have the
condition of confirming the result that was obtained earlier using
greeness approaches.</p>
      <p>Remote methods for monitoring agricultural fields make it
possible to quickly identify areas of fields affected by the disease,
to determine the degree of plant ripening, etc. Identifying
problems of plant development in the early stages of
development significantly reduces the cost of labor and funds to
obtain a planned result. There are two main approaches to solving
the problem of identifying affected areas - spectrometric and
optical. The spectrometric approach allows one to determine
many problems of plant growth in the early stages of
development, however, it leads to the emergence of a large
amount of data that needs to be processed in a very short time,
which requires the development of a computing base and data
storage. Optical methods are being developed in parallel with the
spectrometric approach and have the property of simplifying
processing tasks, since the number of spectral channels is fixed
(only three - RGB). It is clear that this has its limitations on the
quality of identification of plants on the field, but it allows you
to more quickly find the necessary solutions. There are various
types of characteristics that can be used to identify plants:
geometric, morphological and color, as well as their
combinations, which can reduce the space of characters, which
simplifies identification. The main task when processing images
for plant identification is segmentation, i.e. selection of image
objects (groups of pixels), homogeneous in their color or fractal
characteristics, and assigning them to one or another predefined
class.</p>
      <p>To test the operability of the proposed algorithms, the authors
conducted a model experiment related to growing plants in
specially prepared room conditions. Observation of plant growth
(wheat) was carried out daily at noon, for two months. During
this time, the plant went through all stages of its vegetation cycle,
from ripening to wilting. The obtained daily images were
processed using the developed software, which was developed in
the C # programming language using the SimpleCV technical
vision libraries [http://simplecv.org]. The results of image
processing associated with the selection of plants are shown in
Fig. 1, from which it is clearly seen that the plant stands out well
in the image.</p>
      <p>The phenological development of plants is based on the
hereditary rhythm and periodicity of physiological processes,
called biological or phenological clocks. However, the onset of
phenophases, the duration of their passage depends on a number
of climatic factors, soil quality, as well as on human activity.
However, despite the fundamental research of domestic and
foreign scientists, phenological monitoring has not yet been
introduced in industrial monitoring system at the level of the
organizational structure of typical agricultural services. Until
now, phenological monitoring, despite the fact that the
emergence of digital forms of presenting observations of weather
and seasonal phenomena, is more attached to humans.
Phenological monitoring now refers to the system of organizing
long-term observations and recording the dates of the onset of
seasonal phenomena, the centralized collection and accumulation
of information, its statistical and analytical processing of data on
the timing of the onset of seasonal natural phenomena. The main
tasks of phenology are the observation of various changes in the
annual cycle of plant development and annual registration time
of occurrence of these changes.</p>
      <p>More specifically, phenological monitoring is associated not
only with the detection of plant conditions, but also with the
determination of the factors that determine this state, namely,
climatic factors (temperature, temperature changes,
precipitation, light exposure, cloudiness, etc.), soil factors
(humidity, types and amounts of trace elements needed for plant
nutrition), environmental factors (nearby industrial enterprises,
city, etc.). It is necessary to build mathematical models that relate
various factors to the state of vegetation. Our work is the first
step on this path when determining the state of the plant by the
phenological cycle, namely, growth rate, ripening time, etc.</p>
      <p>To use the obtained results in agricultural practice, we
calculated the number of pixels corresponding to the plant. The
calculation results for the experiment are shown in Figs. 2 and 3.
It is clearly seen that the plant at the growth stage increases the
leaf area, then saturation occurs (the leaf area does not change)
and then the plant withers, in which the leaf area decreases.</p>
      <p>Fig. 1. The selection of plants in the image (on the left - the
original image and on the right - the selected plant)
Fig. 2. The vegetation cycle of the plant in a certain number of
pixels corresponding to the plant</p>
      <p>In parallel with the calculation of the number of pixels
corresponding to the plant, we carried out the calculation of one
of the vegetative indexes ExG (see Fig. 3). Note that the shape of
the curve showing the number of pixels corresponding to the
plant is different from the shape of the vegetation index. The
figure clearly shows that the curve of the vegetation cycle has a
complex structure, which is associated with meteorological
conditions (open window, exposure to the Sun, etc.). This
indicates the sensitivity of the indices to the effects of lighting
and meteorological parameters, which can be directly used in
practice.</p>
      <p>It is possible to carry out a series of calibration measurements
(image acquisition) with simultaneous fixation of various
meteorological conditions. Based on the measurements obtained,
it is possible to obtain the functions of changing vegetation
indices depending on various conditions of plant growth. Then,
if there is a weather forecast, it is possible to predict the state of
the plants (taking into account the data in Fig. 2 and Fig. 3),
which means that it is more accurate to make decisions, for
example, about harvesting.</p>
    </sec>
    <sec id="sec-5">
      <title>3. Conclusion</title>
      <p>The article briefly describes the historical aspects of the
development of precision farming and the appearance of UAVs
in agricultural practice. The basic elements of technical vision
necessary for the analysis of the state of SA plants are shown. It
is said that in order to verify the received data from the UAV, it
is necessary to take into account the meteorological conditions
and changes in the illumination of sunlight. The results of
processing the measurement data of test growing plants under
room conditions are presented. It is shown that the proposed
approach, which is based on the RGB image, allows to obtain
information about the state of the plant over the entire time period
of the vegetation cycle. It is proposed to offer this approach for
practical use in real conditions of agricultural fields.</p>
    </sec>
    <sec id="sec-6">
      <title>4. References</title>
    </sec>
  </body>
  <back>
    <ref-list>
      <ref id="ref1">
        <mixed-citation>
          [1]
          <string-name>
            <surname>Silva</surname>
            <given-names>T.S.</given-names>
          </string-name>
          ,
          <string-name>
            <surname>Costa</surname>
            <given-names>M.P.</given-names>
          </string-name>
          ,
          <string-name>
            <surname>Melack</surname>
            <given-names>J.M.</given-names>
          </string-name>
          ,
          <string-name>
            <surname>Novo</surname>
            <given-names>E.M.</given-names>
          </string-name>
          <article-title>Remote sensing of aquatic vegetation: theory</article-title>
          and applications // Environmental Monitoring and Assessment,
          <year>2008</year>
          ,
          <volume>140</volume>
          :
          <fpage>131</fpage>
          -
          <lpage>145</lpage>
          .
        </mixed-citation>
      </ref>
      <ref id="ref2">
        <mixed-citation>
          [2]
          <string-name>
            <surname>Pantazi</surname>
            <given-names>X.E.</given-names>
          </string-name>
          ,
          <string-name>
            <surname>Moshou</surname>
            <given-names>D.</given-names>
          </string-name>
          ,
          <string-name>
            <surname>Alexandridis</surname>
            <given-names>T.</given-names>
          </string-name>
          ,
          <string-name>
            <surname>Wheton R</surname>
          </string-name>
          .L.
          <article-title>Wheat yield prediction using machine learning and advanced sensing techniques // Computers and Electronics</article-title>
          and Agriculture,
          <year>2016</year>
          , V.6,
          <string-name>
            <surname>P.</surname>
          </string-name>
          57-
          <fpage>65</fpage>
          .
        </mixed-citation>
      </ref>
      <ref id="ref3">
        <mixed-citation>
          [3]
          <string-name>
            <given-names>Xue Z.</given-names>
            ,
            <surname>Li</surname>
          </string-name>
          <string-name>
            <given-names>J</given-names>
            ., Cheng L.,
            <surname>Du</surname>
          </string-name>
          <string-name>
            <surname>P</surname>
          </string-name>
          .
          <article-title>Spectral-spatial classification of hyperspectral data via morphological component analysisbased image separation /</article-title>
          / IEEE Transaction,
          <year>2015</year>
          ,
          <string-name>
            <surname>V.</surname>
          </string-name>
          <year>53</year>
          , N.1,
          <string-name>
            <surname>P.</surname>
          </string-name>
          70-
          <fpage>84</fpage>
          .
        </mixed-citation>
      </ref>
      <ref id="ref4">
        <mixed-citation>
          [4]
          <string-name>
            <surname>Kataev</surname>
            <given-names>M.</given-names>
          </string-name>
          <string-name>
            <surname>Yu</surname>
          </string-name>
          .
          <article-title>Opportunities for space monitoring for agriculture of the Tomsk region / M. Yu</article-title>
          . Kataev,
          <string-name>
            <given-names>A. A.</given-names>
            <surname>Skugarev</surname>
          </string-name>
          , I. B. Sorokin // TUSUR reports.
          <source>- 2017</source>
          . - T.
          <volume>20</volume>
          , No. 3. - S.
          <fpage>186</fpage>
          -
          <lpage>190</lpage>
          .
        </mixed-citation>
      </ref>
      <ref id="ref5">
        <mixed-citation>
          [5]
          <string-name>
            <surname>Ide</surname>
            <given-names>R.</given-names>
          </string-name>
          ,
          <string-name>
            <surname>Oguma</surname>
            <given-names>H</given-names>
          </string-name>
          .
          <article-title>Use of digital cameras for phenological observations</article-title>
          / R. Ide, H. Oguma // Ecological Informatics.
          <article-title>-</article-title>
          <year>2010</year>
          . -N.5. - P.
          <fpage>339</fpage>
          -
          <lpage>347</lpage>
          .
        </mixed-citation>
      </ref>
      <ref id="ref6">
        <mixed-citation>
          [6]
          <string-name>
            <surname>Woebbecke</surname>
            <given-names>D.M.</given-names>
          </string-name>
          , Meyer G.E.,
          <string-name>
            <surname>Vonbargen</surname>
            <given-names>K.</given-names>
          </string-name>
          ,
          <string-name>
            <surname>Mortensen</surname>
            <given-names>D.A.</given-names>
          </string-name>
          <string-name>
            <surname>Color</surname>
          </string-name>
          <article-title>Indexes for Weed Identifiation under Various Soil</article-title>
          , Residue, and Lighting Conditions / D.M. Woebbecke, G.E. Meyer,
          <string-name>
            <given-names>K.</given-names>
            <surname>Vonbargen</surname>
          </string-name>
          ,
          <string-name>
            <surname>D.A</surname>
          </string-name>
          . Mortensen // Trans. ASABE. -
          <year>1995</year>
          . - V.
          <year>38</year>
          . - P.
          <fpage>259</fpage>
          -
          <lpage>269</lpage>
          .
        </mixed-citation>
      </ref>
    </ref-list>
  </back>
</article>