BSComputer ScienceMedical Report Analyzer (MRA) 15621006540500BYTania Sahito CMS-ID: 023-14-0026Nimra Mughal CMS-ID 053-14-0007THESIS SUPERVISORDr Sajid KhanDEPARTMENT OF COMPUTER SCIENCESUKKUR IBA UNIVERSITY2018Medical Report AnalyzerbyNimra Mughal 053-Tania Sahito 023-14-0026SUBMITTED TO THE DEPARTMENT OF COMPUTER SCIENCE IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OFBACHELOR OF SCIENCE IN COMPUTERR SCIENCEat theSUKKUR IBA UNIVERSITYJuly,2018 © 2013 MRA Team. All rights reserved.The author hereby grants permission to Sukkur IBA to reproduce and distribute publicly paper and electronic copies of this thesis and grant others the right to do so.Signature of Author 1 NimraDepartment of Computer ScienceSignature of Author 2TaniaDepartment of Computer ScienceCertified by:Internal Examiner SignatureSajid KhanAssociate ProfessorThesis SupervisorExternal Examiner Signature.
Accepted by:Dr. Abdul Rehman SoomraniHead, Department of Computer ScienceContents TOC o “1-3” h z u List of Figures PAGEREF _Toc520588117 h 5Acronyms and Abbreviations PAGEREF _Toc520588118 h 8Abstract PAGEREF _Toc520588119 h 9Introduction PAGEREF _Toc520588120 h 111.1 Problem Statement PAGEREF _Toc520588121 h 111.
2 Project Background PAGEREF _Toc520588122 h 121.3 Project Scope PAGEREF _Toc520588123 h 121.4 Out of Scope PAGEREF _Toc520588124 h 121.5 Objectives PAGEREF _Toc520588125 h 121.6 Functional Requirements PAGEREF _Toc520588126 h 131.
7 Nonfunctional Requirements PAGEREF _Toc520588127 h 13?Performance Requirements PAGEREF _Toc520588128 h 13?Safety Requirements PAGEREF _Toc520588129 h 13?Security Requirements PAGEREF _Toc520588130 h 13Literature Review PAGEREF _Toc520588131 h 152.1 Motivation PAGEREF _Toc520588132 h 162.2 Research on Related Projects PAGEREF _Toc520588133 h 162.2.1 Medical Tests Analyzer PAGEREF _Toc520588134 h 162.2.
2 Lab Test Analyzer (LTA) PAGEREF _Toc520588135 h 192.3 Study Results PAGEREF _Toc520588136 h 20Methodology PAGEREF _Toc520588137 h 213.1 Purpose and Scope PAGEREF _Toc520588138 h 223.2 Software Development Methodology PAGEREF _Toc520588139 h 233.2.
1 The Agile Methodology PAGEREF _Toc520588140 h 233.3 UML Diagraming PAGEREF _Toc520588141 h 243.3.1 Proposed System Modules PAGEREF _Toc520588142 h 243.4 Activity Diagram PAGEREF _Toc520588143 h 303.5 Sequence Diagrams PAGEREF _Toc520588144 h 343.6 Application Architecture Description PAGEREF _Toc520588145 h 363.6.
1 Overview of Components PAGEREF _Toc520588146 h 363.7 Detailed Description of Components PAGEREF _Toc520588147 h 373.7.1 Component Diagram PAGEREF _Toc520588148 h 373.7.
2 Deployment Diagram PAGEREF _Toc520588149 h 38Implementation PAGEREF _Toc520588150 h 394.1 Android Studio PAGEREF _Toc520588151 h 404.2 Java PAGEREF _Toc520588152 h 414.3 OCR Google Vision API PAGEREF _Toc520588153 h 424.4 Firebase PAGEREF _Toc520588154 h 434.5 Medical Report Analyzer (MRA) PAGEREF _Toc520588155 h 44Conclusion PAGEREF _Toc520588156 h 46Future Works PAGEREF _Toc520588157 h 46Code PAGEREF _Toc520588158 h 47MRA Screenshots PAGEREF _Toc520588159 h 48References PAGEREF _Toc520588160 h 49List of FiguresFigure 01: MTA Home PageFigure 02: MTA Input Data PageFigure 03: MTA Results PageFigure 4: Main Interface of LTAFigure 05: Sign-in Use-CaseFigure 06: Report Upload Image Use-CaseFigure 07: Report Image Capture Use-CaseFigure 08: History Use-CaseFigure 09: Activity Diagram for Sign-inFigure 10: Log-out Activity DiagramFigure 11: Activity Diagram for Text ExtractionFigure 12: Activity Diagram HistoryFigure 13: Upload Image Sequence DiagramFigure 14: Capture Image Using Camera Sequence DiagramFigure 15: Show History Sequence DiagramFigure 16: MRA Domain ModelFigure 17: MRA Component DiagramFigure 18: MRA Deployment DiagramEXORDIUMIn the name of Allah, the Compassionate, the Merciful.
Praise be to Allah, Lord of Creation, The Compassionate, theMerciful, King of Judgment-day!DedicationAcronyms and AbbreviationsMRA- Smart Medical Report AnalyzerOS – Operating SystemCBC-Complete Blood CountAbstractThis is the era of technology and it is developing very quickly. Advancement in the technology has paved ways to the solution of many social life problems and has facilitated humans 1-3. Specifically, Artificial Intelligence (A.I) has a very strong and positive impact on human life.
The field of medical science has a strong dependency on A.I 4.Though technology has changed the way medical treatments were done earlier.
Common man is unaware of the medical tests reports which he gets done by any medical laboratory. Sometimes doctors encounter difficulties to find the sensitive information which is not related to their specialization area. Because of this patient may get wrongly prescribed and suffer side-effects.In this project, an attempt will be made to develop a system which could extract information from the medical test reports and could have a summarized version of the information which would be easily understood by a layman. It will also assist doctors to get the information of the fields other than their specialization.
In this way, doctors can prescribe the patients properly and patients could suffer no or minimum side-effects.Chapter No. 1Introduction1.1 Problem StatementHuman has benefited greatly from the advancement of medical science.
It is mostly because of rapid growth in the technology. Today, humans can also avail services of doctors who are thousands of kilometers away from the hospitals. Successful transplantations have been performed too.Though all the advancements have eased human life, they are mostly concerned with doctors whereas patients can only utilize these services. A layman or a doctor that is specialized in field other than that of report is still unable to even interpret his/her lab test report. These facts led towards the idea of Medical Report Analyzer (MRA), an app that will analyze medical test report and provide conclusion in a very simple words.
Not only this, it aims to make personalized recommendations to its users so that effect of disease could be lessen somehow. Such as system will recommend user few edibles which can help him/her improve his health.1.
2 Project BackgroundMRA is an android app dedicated for the layman patients who cannot know their test report unless they visit a doctor. Doctors can also use this app to know the patient’s current condition through his/her previous reports. Also, this app maintains history of the reports which users have already analyzed using MRA. Any user can check his/her previous reports data and MRA analysis and recommendations. 1.3 Project ScopeThe purpose of the Medical Report Analyzer is to ease medical report analysis and to generate a comprehensive and easy-to-understand results for those doctors and patients who are trying to understand what feature values in a medical report explains. The system is based on a firebase storage which will store various conditions for some selected diseases.
The knowledge base will be online as well as offline so that it could be update/maintained easily. We will be having mechanism to extract text from medical test reports as well. Above all, we hope to provide a comfortable user experience along with the reasonable pricing available. 1.4 Out of ScopeOur system will only scan medical test report and generate results with expected disease and some recommendation to lower it. Right now, it is not in the scope of the system to recommend a doctor for detected disease. 1.
5 ObjectivesThe main objective of the project is to develop a system named Medical Report Analyzer (MRA), an android application, that takes scanned medical test reports as an input and to interpret the report statistics in meaningful form. User just needs scan his/her medical test report and will be able to get the simple and meaningful summary. The other main objective of the system is that it also facilitates the user to record all its summaries which may be helpful for the future. Next time, he/she can access the history of reports anytime.1.6 Functional RequirementsMRA has following functional requirementsTo upload/ capture test imageTo extract text from test reportTo compare extracted features values with normal values from serverTo generate a simple summary To maintain history1.7 Nonfunctional RequirementsNon-functional requirements are those which are in directly connected with system.
Following are Non-functional requirements are;Performance Requirements The system must be interactive, user friendly and the delays involved must be less. So, in every action-response of the system, there will be less delay. In case of data extraction, system should not take much time to extract data from medical test report and extracting data from the knowledge base must be a quick process so that user can enjoy interacting with the system and achieve its goal at priority. System also provides offline services so in case if there is no internet/ slow internet connection, user gets full access to its functionality.Safety Requirements As we know that medical information is the most sensitive of all the information, so the system should be capable enough to handle it very carefully. As our app is supposed to use an online knowledge base it means it needs to send request to the knowledge base server so that appropriate results be generated.
Security Requirements Every user of the app will create his/her account on our server and whenever they need to analyze their report/record, they will first need to get logged in and then access the knowledge base. Chapter No. 2Literature Review2.1 MotivationIn existing test analyzers, user needs to manually enter each feature value from the report into the system which is very hectic job for everyone, even for those who are good at typing. The other problem with existing system is, it generates the report which contains medical terms in a bulk quantity which is again not understandable for a person who has less knowledge of medical science and its various terms. Our android based medical report analyzer covers all above-mentioned problems.
User just needs to scan his/her medical test report and then system generates an easily understandable summary of his report analysis. Also, if user wants, system will maintain history of his/her reports. The summary would contain expected disease information and some recommendations to lower it at some level.
2.2 Research on Related Projects2.2.1 Medical Tests AnalyzerIt is basically a solution for efficient, reliable and modern managing of patient’s medical lab results history. This tool provides a short overview and some tips on how to translate the results, and what they mean. Medical Test Analyzer takes data values from the user and then gives the results. It is not much layman friendly because it also uses some medical terms. Once data values are entered in the system, it generates results which also contain some numeric values.
0374015MTA Home PageFigure 01: MTA Home Pageright29718000Figure 02: MTA Input Data PageResults PageFigure 03: MTA Results PageNote: This image was taken after the MRA trial expiry; that is why, it is not showing the results as we have mentioned in the report.2.2.2 Lab Test Analyzer (LTA)Lab Test Analyzer is a digital health advisor, making recommendations based on analysis of the lab results. LTA is a user-friendly and is as accessible as possible, so user don’t need to be a tech geek to use it. It is a web application.
It has certain steps to follow for its proper working and those are:User must input all data values for his/her test of interest. Data Values are stored for future use. Once data is uploaded, the results will provide you with recommendations and tips to help improve user’s health.It costs much and that is why many avoid using this system.266700344170Figure 4: Main Interface of LTA2.3 Study ResultsAfter reviewing all the above application, we conclude that one or other way they are not much user friendly as they claim that they are user-friendly because;In these systems, user needs to input feature values of his/her report that is a time-consuming task for a person and is unfavorable Today, most of the people feel comfortable in mobility that smartphones provide instead using desktops. They prefer these huge systems for office works only.
Medical Test Analyzer is a desktop application while Lab test Analyzer is a web applicationBoth are not free of cost MTA uses medical terms in test report results. It is not layman-friendly. All above mentioned points led us to think of an idea which could use mobile camera to collect lab reports data and generate a summary-based result.
Consequently, we thought to develop an app which does not require desktops, does not demand user to enter medical report data values, instead which will take an image captured using camera. After taking images of report, our app will apply text extraction techniques for getting useful textual information from images of lab reports. After the text is usefully extracted, system will generate results based on comparison of extracted features with the normal ranges of values. In last step, app will produce a summary which will be easily understandable and interpretable for a layman as well. App will indicate the things patients need to take care about to improve his/her health by making some recommendations.Chapter No.
3MethodologyThis project is based on a real-life scenario happened to one of the team member who was suffer from some abdominal disease. When doctors suggested her for some medical test reports. She observed herself incapable to interpret the meaning of those values in the test report. There was no application which could provide the simplified meaning of those values and could recommend tips to improve her health. The motivation to start and develop such an app came fromA layman/ a doctor who does not refereed any report could not understand/ interpret report data valuesIn these systems, user needed to put all the data values of the report manuallyThese systems also used some medical science terms in their analysis results3.1 Purpose and ScopeThe purpose of this document id to specify through design what type of basic components our system has and how they work to achieve the goal. How the user interacts with application to get desired output, by drawing UML diagrams and appropriate documentationsExisting systems only accepted manual input of the feature values of the medical test report. Also produce analysis results in a way which contain some numeric medical terms.
They are less-user friendly in a sense a layman cannot facilitate himself. MRA is very simple to use and its analysis results are also easily understandable because it returns a summarized value of the report analysis. Anyone can use it.
3.2 Software Development MethodologyIn this section of the chapter, we are going to discuss software development methodology in a very precise way. For a software engineer, it becomes a necessity to select that software development methodology which suits best to the context of the application. Hence, considering this fact, we applied Agile Development Methodology to give life to idea of an app we call today MRA. This idea feels so simple but while working on this we observed that to work on a field which was mostly alien to us, we could not achieve the goal unless we followed Agile Development MethodologyLet’s discuss very shortly on development methodology3.
2.1 The Agile MethodologyAgile software development methods are an iterative approach to software specification, development and delivery 12.Agile is an iterative, team-based approach to development. We don’t create c tasks and schedules, rather it completely focused on phases called “sprints.”Some advantages, as per our app requirement, dragged us to use Agile methodology.Early opportunity to see the work and decide for changes Development is much user focused Incremental DeliveryMaintain Simplicity3.3 UML Diagraming The project designing is done in UML (Uniform Modeling Language) notation and we have described and designed below the main activities of the project. 3.
3.1 Proposed System ModulesComponent DescriptionImage Upload User can upload image from gallery of his/her mobile phone and, system will extract feature values from reportImage Capture System also provides the feature to user that he/she can also capture image of the report using the camera of mobile phoneHistory To keep aware user about his/her previous reports, we have added the feature of storing reports data and its analysis.Sign-in /Sign-up Form To ensure that only authenticated owner of the reports can access his/her reports and the respective analysis, we offer user to register himself/herself. Once he/she is registered they can perform above mentioned activities easilyText Extraction To perform analysis on feature values of the report, text extraction is done. This would give all the variables and their respective values of the report.Table 01: Proposed System ComponentsUse case illustrates a unit of functionality provided by system.
The main purpose of the use-case diagrams is to help development teams visualize the functional requirements of the system, including the relationship of the actors (human beings or any other systems who offer their services to our system) to essential processes, as well as the relationship among different use cases. We used UML 2.0 for drawing UML diagram to describe the functionality of the system and which actors are connected to each functionality.3.3.2 Sign-in Use-CaseUse Case #01Name Sign-inActor UserPre-Condition User should have username and passwordPost-Condition User Logged-InDescription User enters username and password for authenticated use of his/her data.
left309245Figure 05: Sign-in Use-Case3.3.3 Report Upload Image Use-CaseUse Case #02Name Report Upload ImageActor UserPre-Condition User must be logged in. Test Report Image should be stored in the phone gallery.Post-Condition Report image should be successfully uploaded. Feature values extraction should be performed then. Description User goes to gallery to upload report image.
Figure 06: Report Upload Image Use-Case3.3.4 Report Image Capture Use-CaseUse Case #03Name Report Image CaptureActor App UserPre-Condition User must be logged in. Post-Condition When user captures image of the report.
It should be available to MRA for text extraction. Description This use case shows that how user can capture image of the report and then text features can be extracted.-180975313690Figure 07: Report Image Capture Use-Case3.3.5 History Use-CaseUse Case #04Name HistoryActor App UserPre-Condition User must be logged in. Post-Condition History should be successfully shown to user.Description This use case simply describes how the user who has some history for his/her previous records can access that.
Figure 08: History Use-Case3.3.6 Domain Model of MRA114300281305Figure 16: MRA Domain Model3.4 Activity DiagramTo understand flow of the activities of MRA, we can draw activity diagrams. Before drawing the diagram, let’s revise what activity diagram is.Activity diagrams show the procedural flow of control between two or more class objects while processing and activity. Activity diagrams can be used to model higher-level business process at the business unit level, or to model low-level internal class action.
Basically, we can easily elaborate the processing of the flow of the company activities such as to know how the company develops/produces a product, how the delivery is made etc. With activity diagrams it becomes very easy for anyone to interpret the processing because they are less-technical as sequence diagrams are.3.4.1 Activity Diagram for Sign-in1562100171450Figure 09: Activity Diagram for Sign-in3.
4.2 Activity Diagram for Log-out173355013335Figure 10: Log-out Activity Diagram3.4.3 Activity Diagram for Text Extraction11239502349500Figure 11: Activity Diagram for Text Extraction3.4.4 Activity Diagram for HistoryFigure 12: Activity Diagram History3.
5 Sequence DiagramsWe learnt that before developing any project, it is very necessary that we know that how different objects interact with each other. They capture the interaction between objects in the context of a collaboration. Sequence Diagrams are time focus and they show the order of the interaction visually by using the vertical axis of the diagram to represent time what messages are sent and when.3.
5.1 Upload Image Sequence Diagram-66675253365Figure 13: Upload Image Sequence Diagram3.5.2 Capture Image Using Camera Sequence DiagramFigure 14: Capture Image Using Camera Sequence Diagram3.5.3 Show History Sequence Diagram-270510251460Figure 15: Show History Sequence Diagram3.6 Application Architecture Description3.6.
1 Overview of ComponentsMedical Report Analysis is composed of the following componentsLoginUpload ImageCapture ImageMaintain HistoryText Extraction3.7 Detailed Description of Components3.7.
1 Component DiagramA component diagram in UML gives a bird’s-eye view of your software system. Component Diagram contains components and dependencies. Component Diagram does not describe the functionality of the system, but it describes the components used to make those functionalities. Simply we can say that component diagrams help visualize physical components in a system.
These components may include libraries, packages, files, etc. Below given is the simplest component diagram of Medical Report Analyzer. Basically, MRA uses OCR Google Vision Library to extract text from images of the report. We also have Firebase component to manage data.
center27305000Figure 17: MRA Component Diagram3.7.2 Deployment DiagramWe saw the very basic component diagram of MRA.
Let’s draw the deployment diagram of the system. Before we saw its deployment diagram, let’s review what a deployment diagram is.Deployment diagram is a structural diagramming because it describes the system itself. It maps system’s software artifacts to the hardware that will execute them. It models a system’s logical elements, physical location, and how they communicate.
Remember, in the world of deployment diagrams, systems refer to the software you develop and the software and hardware that enabled your developed software to run. Figure 18: MRA Deployment DiagramChapter 4ImplementationThis may be the most awaited chapter of the report. In this chapter we have discussed the tools and technologies we used to develop Medical Report Analyzer (MRA). We have used following tools to develop the system we owe today.Android StudioJavaOCR Google Vision LibraryRegexFirebaseLet’s have a short overview of the above mentions.
4.1 Android Studio65341501270000We know that Android Studio is the official Integrated Development Environment (IDE) for Android application development. It is built on JetBrains’ IntelliJ IDE1.
We have used Android Studio 3.0 to develop MRA. Though we could also use Eclipse with Android Plugin, we preferred Android Studio because offers even more features that enhance the productivity when building Android apps, such as 2:A flexible Gradle-based build systemA fast and feature-rich emulatorA unified environment where you can develop for all Android devicesInstant Run to push changes to your running app without building a new APKCode templates and GitHub integration to help you build common app features and import sample codeExtensive testing tools and frameworksLint tools to catch performance, usability, version compatibility, and other problemsC++ and NDK supportBuilt-in support for Google Cloud Platform, making it easy to integrate Google Cloud Messaging and App Engine4.
2 Java4762500571500When it comes time to develop Android apps, the first and most popular option is Java. Java is the official language of Android development, meaning it is the one that has the most support from Google and the one that most apps on the Play Store are built with.We could also use other languages such as C++/ C# to develop, but we selected Java. The very basic reason may be that we are comfortable with this language to code in android studio and as it is official language of Android Studio, this can also be considered as a reason we used Java.Why we used Java?Formerly Speaking, after we observed following striking features of Java which drag most of the programmers to code apps in Android Studio, it also gave us such a great motivation to use it for MRA development.SimpleJava is very easy and simple to learn because of its simple syntax According to Sun, Java language is a simple programming language 11Object-Oriented Programming Language It is based on the concept of class and objects.
Everything in Java is an object4800600137160Platform Independent Java is different from other languages like C, C++ etc. which are compiled into platform specific machines while it is a write once, run anywhere language. Java provides software-based platform 3.Given picture elaborates how Java provides platform independency.
It is basically a .class file that contains byte code that can run on Java Virtual Machine. Interpreted Java language is known to be compiled to byte-codes, which are then interpreted to Java Run-Time Environment.
Secure Java provides one with the most secure environment. Even though it is running on a network, one can be sure about the online security with java run-time environment.Portability It is portable only because of the byte code.RobustJava is robust because it uses strong memory management, lack of pointers, automatic garbage collections, and exception handling and type checking mechanism.
4.3 OCR Google Vision APIThe Google Vision API was released on December 2nd 2015. It provides an interface that quickly analyses image content. This interface hides the complexity of continuously evolving machine learning models and image processing algorithms.
Moreover, Google Vision API enables developers to understand the content of an image by encapsulating powerful machine learning models in an easy to use REST API.This API provides following features to annotate images LABEL_DETECTIONTEXT_DETECTIONFACE_DETECTIONLANDMARK_DETECTIONLOGO_DETECTIONLOGO_DETECTIONAs we have used its second feature; that is TEXT_EXTRACTION so we are discussing it only that at this point.Optical Character Recognition (OCR) refers to the process of automatically identifying from an image characters or symbols belonging to a specified alphabet. OCR is a prevailing problem in the field of image analysis because it often requires high-resolution images, an incredibly precise text extraction algorithm, and very little perspective distortion.4.
4 Firebase467677513970Firebase started out as a Backend-as-a-Service?(BaaS). It is used to develop applications in Google Cloud Platform. In Firebase you can customize things according to your need.
But we must keep in mind that firebase is the everything for everybody. We must consider context of the application. Let’s discuss few advantages of the firebase.The AuthenticationIts auth includes a built-in email/password authentication system. The HostingFirebase provides easy-to-use service for hosting for all your static files.The Real-Time Syncing of Data It offers real-time synchronization of data across all clients be it Android, iOS or web will come in very handy.Free hostingWe have used its features like firebase authentication for users and firebase real-time storage for data.Why We Used Firebase for MRA?The basics reasons are as given below.
The AuthenticationAs we have already mentioned, firebase provides very easy-to-use platform to modify it as per requirement or context of the application. Firebase Authentication provides backend services, easy-to-use SDKs, and ready-made UI libraries to authenticate users to your app 6. This created much easy for ease to go for firebase it offers everything one want for security of the app.The Real-Time DatastoreFirebase is cloud based document store that is suitable for real time applications. We used firebase for it gives us advantage of real-time access.
Firebase if different than MySQL or SQLite because Firebase is indeed a hierarchical data structure: it’s just a JSON tree in the cloud, thought MYSQL is a relational database.4.5 Medical Report Analyzer (MRA)Medical Report Analyzer is developed to analyze reports and generate result in a summarized form which would be easier for a layman to interpret.
Also, it maintains history of the user’s analysis for his/her reports. It uses login authentication for we believed that test report analysis or the history should be limited to the authenticated users only.4.5.1 How the System Operates?There are some basic activities to achieve the goal.Login Capture Image Upload Image form GalleryText ExtractionMaintain HistoryChapter 5ConclusionConclusionMRA is a very little effort to give life to an idea that a layman cannot interpret the reports data features in a way he/she/ may want like our team member wanted to. There is some application as we also mention their names like Medical Tests Analyzer and Lab Report Analyzer. They offer report analysis services as well.
But MRA is aimed to be bit different. It is mainly designed to analyze reports and generate the summaries from them in a way layman could get it. We think that this is a very small effort that our team has made to facilitate those people who want to know want their reports tell them about their health. We focused on this thing as well that it should give some tips to improve health.Future WorksTo enrich the app by adding the feature of sending reports to the respective doctors, if user is a patient.
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