IntroductoryPythonTutorials

Inthislabsessionyouwillrunandmodifyexamplesinthe“examples_PythonTutorial”directory(whichisasubdirectoryoftheCompuCell3Dinstallationfolder).Beforeproceedingpleasecopyentire“examples_PythonTutorial”directorytoanotherlocation,sothatifyoumessuporiginalfilesyouwillbeabletorestorethemeasily.

Formostpartofthistutorialyouwillbemodifyingcellsort_2D_steppables.pyfilewhereallthesteppablesaredefined.

Exercise1

Runcellsort_2D.xmltogetherwithcellsort_2D_info_printer.pyandobservetheoutputontheconsole.

ModifyInfoPrinterSteppableincellsort_2D_steppables.pytooutputasurfaceofthecell.Whatdoyouobserve.Why?Whatisnecessarytogetcorrectvaluesofthecellsurface?

Now,outputvaluesofthecenterofmassofeachcell(cell.xCM,cell.yCM,cell.zCM).Whatarethevaluesofthisquantity?Whatdoyouneedtodoinordertogettruecenterofmass?

Finally,tocheckwhatothercellattributesofacellareaccessiblefromPythoninsertthefollowinglineinsidetheloopthatiteratesoverallthecellsinthesimulation

print“CellAttributes”,dir(cell)

Howwouldyoumodifythesteppablesothatdir(cell)informationisprintedforonlyonecell,notallofthem?

Exercise2

Runcellsort_2D.xmltogetherwithcellsort_2D_extra_attrib.pyandobservetheoutputontheconsole.

IntheExtraAttributeCellsortsteppablemodifythelinewhereyouassignattributestothelist.Insteadof

pyAttrib[0:2]=[cell.id*mcs,cell.id*(mcs-1)]

computeandstoreinpyAttribratioandaverage“radius”ofacellcalculatedusingperimeterandsurfaceareaofthecell.Whatvaluesofthethreequantitiesshouldyougetifthecellswereperfectcircles(VissurfaceareaintheiscaseandSisaperimieter)?WhatdoyouobserveforCompuCell3Dcells?Aretheyperfectcircles?

Exercise3

Insteadofusinglistasadditionalcellattribute,usedictionaryandrepeatexercise2.Youwillneedtochangetheline

pyAttributeAdder,listAdder=CompuCellSetup.attachListToCells(sim)

inthecellsort_2D_extra_attrib.pyto:

pyAttributeAdder,dictAdder=CompuCellSetup.attachDictionaryToCells(sim)

thenmodifyExtraAttributeCellsorttoworkwithdictionaryinsteadoflist.

Whenyouattachedadictionarytocellsthefollowinglinewillreturnadictionary,i.epyAttribwillbeadictionaryinthiscase.

pyAttrib=CompuCell.getPyAttrib(cell)

Forclarityyoumaychangethislinetosomethinglikethat:

cellDictionary=CompuCell.getPyAttrib(cell)

Now,insertintothedictionaryquantitiesyoucalculatedintExersice3andprintthemout.Doyouknowhowtoprintthecontentoftheentiredictionarywithoutknowingwhatthekeysare?Searchforthesolutiononline.Whatiseasiertouselistsordictionaries?

Exercise4

Runcellsort_2D.xmltogetherwithcellsort_2D_extra_attrib.pyandobservertheoutputinthePlayer.Haveyounoticedanythinginteresting?

ModifyTypeSwitcherSteppablesteppablesothatitchangestypesinthefollowingmanner:

Every100MCSallthecelltypesarechangedto1

Every200MCSallthecelltypesarechangedto2

Every300MCSallthecelltypesarechangedtoarandommixoftypes1and2

NowchangeTypeSwitcherSteppablesteppableinsuchawaythatevery100MCSallthecelltypesarechangedtoarandommixoftypes1,2and3.Whathappens?Why?

Exercise5

Runcellsort_2D_neighbor_tracker.xmltogetherwithcellsort_2D_neighbor_tracker.pyandobservetheoutputontheconsole.

Usetheskillsthatyouhavelearnedinexercises2and3tostorecellneighborsineitherlistordictionary.

Makesureyouerasethecontentoflistordictionarybeforeyoustorenewlistofneighbors.Whydoyouneedtodothis?

ThereminderofthePythontutorialsisalittlebitmoreadvancedbecauseyouwillwriteyourownPythonscriptsinsteadofjustmodifyingexistingones.Ofcourseyouarefreetocopyexistingscriptsinsteadstartingfromscratch.

Exercise6

WritecellsortingsimulationinPythonentirely(youmaygrabitfromexamplesavailableintheCompuCell3Ddirectory).WriteaPythonsteppablethatinitializescelltypesinthefollowingway

cellsatthebottomhalfoftheblobareCondensingandcellsintheupperhalfoftheblobareNon-Condensing

Maketheabovedivisionflexible–i.e.introducenewmemberparameterofthesteppablethatdescribeswherethe"cell-typedividing"lineshouldbeplaced.

Divideblobintoquartersandinitializeoppositequarterswithsamecelltype.

Exercise7

Forthecell-sortsimulationinexercise6developasteppablethatstorescenterofmasspositionsofeverycellinthesimulationevery100MCS.Writeanewfileforevery100MCS.Makesuretoincludecellidandcelltypeinthefile.

Pickfewcellsfromthesimulation.Foreachcellyoupickedrecordcenterofmasspositionsinaseparatefile,every100MCS.

Forexample,forcellwithcell.id12openupfilecell_12.txtthatwouldlookasfollows

100 23.5 32.1 0.0

200 24.3 31.3 0.0

300 25.1 33.1 0.0

…

Plotacelltrajectoryinyourfavoritegraphingprogram(Excel,Gnuplotetc…)

Howwouldyoudopartb),i.e.plottrajectoryofselectcells,usingCompuCell3D,PlayerandPython?Hint.IntroduceextrascalarfieldinPlayerfromPythonlevel.

ThisexerciseshowshowyoucandoanalysisofsimulationdatausingPython.Playerbydefaultoutputsscreenshotsonlyandthisisnotsufficientforanyrigorousdataanalysis.UsingPythonyoucandevelopyouowntoolstorigorouslyanalyzeyoursimulation.

Exercise8

Runcell-sortsimulationandfigureoutwhencellsaremoreorlesssorted.Recordthetimeandcallit.Now,developsteppablethatatswitchescontactenergiessothatcellsproducechecker-boardpattern.Recordthetimewhencellsproducecheckerboardpattern,callit.Knowinghowlongittakesforcellstosort-outandhowlongittakesforcellstoproducecheckerboa