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Vysoké Učení Technické V Brně Brno University of Technology

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Vysoké Učení Technické V Brně Brno University of Technology 1 Faculty of Electrical Engineering and Communication VYSOKÉ UČENÍ TECHNICKÉ V BRNĚ BRNO UNIVERSITY OF TECHNOLOGY FAKULTA ELEKTROTECHNIKY A KOMUNIKAČNÍCH TECHNOLOGIÍ FACULTY OF ELECTRICAL ENGINEERING AND COMMUNICATION ÚSTAV BIOMEDICÍNSKÉHO INŽENÝRSTVÍ DEPARTMENT OF BIOMEDICAL ENGINEERING MODELOVÁNÍ A ANIMACE BIOLOGICKÝCH STRUKTUR Modelling and animation of biological structures DIPLOMOVÁ PRÁCE MASTER’S THESIS AUTOR PRÁCE Bc. Martin Matulík AUTHOR VEDOUCÍ PRÁCE doc. Ing. Jiří Maxa, Ph.D. SUPERVISOR BRNO 2017 2 Faculty of Electrical Engineering and Communication 3 Faculty of Electrical Engineering and Communication Anotace Následující práce se zabývá problematikou digitálního modelování a animace biologických struktur. Probrány jsou v praxi používané softwarové nástroje pro počítačové generování obrazů (CGI) i nástroje pro specifické činnosti dostupné uvnitř vybraného programového prostředí. Z modelovacích přístupů jsou diskutovány nástroje vhodné k vytvoření a znázornění zvolených struktur, stejně jako nástroje nepostradatelné pro jejich následnou animaci. Diskutovány jsou také možné renderovací přístupy a jejich parametry ve vztahu k vlastnostem výsledných počítačově generovaných obrazů. Výše uvedené postupy jsou použity pro modelování, fyzikální simulaci a animaci průtoku erytrocytů cévou krevního řečiště v softwarovém prostředí Autodesk MAYA®. Výstupem je videosoubor obsahující výše uvedenou animaci ve formě stravitelné koncovým uživatelem. Abstract Following work deals with subject matter of digital modelling and animation of biological structures. Software tools for computer generated images (CGI), well proven in common practice, are evaluated, as well as tools for specific activities, available inside chosen software environment. Among vast pool of modelling approaches are discussed tools suitable for creation and representation of selected structures, along with tools essential for their consequent animation. Possible rendering approaches and their parameters in relation to qualities of resulting computer-generated images are discussed as well. Above-mentioned approaches are then consequently utilized for modelling, physical simulation and animation of erythrocyte’s flow throughout a blood vessel within Autodesk MAYA® software envirnment. Resulting output is a video-file containing such animation in end-user digestible form. 4 Faculty of Electrical Engineering and Communication Klíčová slova Biovizualizace, vědecká komunikace, vizuálně atraktivní obsah, řeč obrazů, struktura dramatu, získávání dat, modelování biologických struktur, animace, animační přístupy, fyzikální simulace, simulace částic, instancér, MASH, počítačově generované obrazy, CGI, renderování, renderovací vrstvy, dávkové zpracování souborů, kamerový sekvencér, Autodesk MAYA, krevní oběh, polygonální modelování, standardní shadery, procedurální materiály, fyzikálně správné osvětlení. Keywords Bio-visualization, scientific communication, visually appealing content, visual language, dramatic structure, data acquisition, biological structures modelling, animation, animation approaches, physical simulation, particle simulation, instancer, MASH, computer generated imagery, CGI, rendering, rendering layers, batch processing, camera sequencer, Autodesk MAYA, blood flow, standard shaders, procedural materials, physically accurate lighting. 5 Faculty of Electrical Engineering and Communication Bibliografická citace MATULÍK, M. Modelování a animace biologických struktur. Brno: Vysoké učení technické v Brně, Fakulta elektrotechniky a komunikačních technologií, 2017. 40 s. Vedoucí diplomové práce doc. Ing. Jiří Maxa, Ph.D.. Prohlášení Prohlašuji, že svou diplomovou práci na téma „Modelování a animace biologických struktur“ jsem vypracoval samostatně pod vedením vedoucího semestrálního projektu s použitím odborné literatury a dalších informačních zdrojů, které jsou všechny citovány v práci a uvedeny v seznamu literatury na konci práce. Jako autor uvedené diplomové práce dále prohlašuji, že v souvislosti s vytvořením tohoto projektu jsem neporušil autorská práva třetích osob, zejména jsem nezasáhl nedovoleným způsobem do cizích autorských práv osobnostních a jsem si plně vědom následků porušení ustanovení § 11 a následujících autorského zákona č. 121/2000 Sb., včetně možných trestněprávních důsledků vyplývajících z ustanovení § 152 trestního zákona č. 140/1961 Sb. V Brně dne 17. května 2017 ............................................ podpis autora Poděkování Děkuji vedoucímu diplomové práce doc. Ing. Jiřímu Maxovi za účinnou metodickou, pedagogickou a odbornou pomoc, zejména v oblasti modelování a simulací počítačově generovaných obrazů a další cenné rady při zpracování projektu. Děkuji taktéž společnosti Autodesk za poskytnutí studentské licence softwarového prostředí „Autodesk MAYA®“, v němž byla převážná část diplomové práce realizována. V Brně dne 17. května 2017 ............................................ podpis autora 6 Faculty of Electrical Engineering and Communication Content INTRODUCTION ................................................................................................................................14 1 COMMUNICATING SCIENCE .....................................................................................................15 1.1 FUNDAMENTAL COMPETENCIES ...............................................................................................17 1.1.1 INTEGRATING ABILITIES ...................................................................................................18 1.1.2 OPTIMIZING RESULTS ........................................................................................................18 1.2 VISUAL LANGUAGE ....................................................................................................................19 1.2.1 DEPTH PERCEPTION CLUES ...............................................................................................19 1.2.2 FOCUS & SUBTEXT ...........................................................................................................20 1.3 ENHANCING REALITY ................................................................................................................21 1.4 DRAMATIC STRUCTURE .............................................................................................................22 1.5 MULTIDISCIPLINARY CAPTURING METHODS ...........................................................................24 1.5.1 CINEMATOGRAPHICAL FILM MILESTONES ........................................................................24 1.5.2 FAST EVENTS IMAGING .....................................................................................................25 1.5.3 MOTION CAPTURE & VIRTUAL REALITY ..........................................................................27 1.6 SCIENTIFIC APPROACHES ..........................................................................................................28 1.6.1 RECONSTRUCTING MEDICAL IMAGES ...............................................................................29 1.6.2 DETERMINING MOLECULAR STRUCTURES ........................................................................30 1.6.3 PROTEIN DATA-BANK (PDB) ............................................................................................31 1.6.4 BASIC VISUALIZATION TOOLS ...........................................................................................32 1.7 DIGITAL MODELLING .................................................................................................................33 1.7.1 ANIMATION SOFTWARE ....................................................................................................33 1.7.2 IMAGE CREATION WORKFLOW ..........................................................................................34 1.7.3 ANIMATION TECHNIQUES ..................................................................................................34 1.8 BEST OF ALL WORLDS ................................................................................................................35 1.9 EXAMPLE: BLOOD FLOW ANIMATION ......................................................................................36 7 Faculty of Electrical Engineering and Communication 2 AUTODESK MAYA® .......................................................................................................................39 2.1 SOFTWARE INTERFACE ..............................................................................................................40 2.1.1 OVERVIEW WINDOWS .......................................................................................................41 2.1.2 MENUS & LINES ................................................................................................................43 2.1.3 NAVIGATION .....................................................................................................................45 2.1.4 COMMUNICATING WITH MAYA .......................................................................................47 2.2 MODELLING TOOLS....................................................................................................................48 2.2.1 NURBS VS. POLYGONS ....................................................................................................48 2.2.2 POLYGONAL MODELLING ..................................................................................................49 2.2.3 ADJUSTING ATTRIBUTES ...................................................................................................50
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