-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathsearchindex.js
1 lines (1 loc) · 27.8 KB
/
searchindex.js
1
Search.setIndex({docnames:["api","api/app","api/app/application","api/app/plugin_manager","api/app/script_editor","api/app/script_namespace","api/app/settings_editor","api/app/syntax","api/app/terminal","api/flika","api/flikaflika","api/global_vars","api/process","api/process/BaseProcess","api/process/binary","api/process/color","api/process/file_","api/process/filters","api/process/math_","api/process/measure","api/process/overlay","api/process/progress_bar","api/process/roi","api/process/stacks","api/roi","api/tracefig","api/utils","api/window","changelog","contact","contents","contributing","example/index","getting-started","index","license","plugins","similar_projects","starting_flika","writing_plugins"],envversion:53,filenames:["api.rst","api/app.rst","api/app/application.rst","api/app/plugin_manager.rst","api/app/script_editor.rst","api/app/script_namespace.rst","api/app/settings_editor.rst","api/app/syntax.rst","api/app/terminal.rst","api/flika.rst","api/flikaflika.rst","api/global_vars.rst","api/process.rst","api/process/BaseProcess.rst","api/process/binary.rst","api/process/color.rst","api/process/file_.rst","api/process/filters.rst","api/process/math_.rst","api/process/measure.rst","api/process/overlay.rst","api/process/progress_bar.rst","api/process/roi.rst","api/process/stacks.rst","api/roi.rst","api/tracefig.rst","api/utils.rst","api/window.rst","changelog.rst","contact.rst","contents.rst","contributing.rst","example/index.rst","getting-started.rst","index.rst","license.rst","plugins.rst","similar_projects.rst","starting_flika.rst","writing_plugins.rst"],objects:{"":{flika:[9,0,0,"-"]},"flika.app":{application:[2,0,0,"-"],plugin_manager:[3,0,0,"-"],script_editor:[4,0,0,"-"],script_namespace:[5,0,0,"-"],settings_editor:[6,0,0,"-"],syntax:[7,0,0,"-"],terminal:[8,0,0,"-"]},"flika.app.application":{ClickableLabel:[2,1,1,""],FlikaApplication:[2,1,1,""],Logger:[2,1,1,""]},"flika.app.application.FlikaApplication":{clear:[2,2,1,""],closeEvent:[2,2,1,""],dragEnterEvent:[2,2,1,""],dropEvent:[2,2,1,""]},"flika.app.application.Logger":{flush:[2,2,1,""],keyPressEvent:[2,2,1,""],status_light:[2,3,1,""],write:[2,2,1,""]},"flika.app.plugin_manager":{Load_Local_Plugins_Thread:[3,1,1,""],PluginManager:[3,1,1,""],str2func:[3,5,1,""]},"flika.app.plugin_manager.Load_Local_Plugins_Thread":{run:[3,2,1,""]},"flika.app.plugin_manager.PluginManager":{close:[3,4,1,""],closeEvent:[3,2,1,""],show:[3,4,1,""],sigPluginLoaded:[3,3,1,""]},"flika.app.script_editor":{Editor:[4,1,1,""],ScriptEditor:[4,1,1,""]},"flika.app.script_editor.ScriptEditor":{close:[4,4,1,""],closeEvent:[4,2,1,""],dragEnterEvent:[4,2,1,""],dropEvent:[4,2,1,""],keyPressEvent:[4,2,1,""],show:[4,4,1,""]},"flika.app.script_namespace":{getnamespace:[5,5,1,""]},"flika.app.settings_editor":{SettingsEditor:[6,1,1,""],pencilSettings:[6,5,1,""],pointSettings:[6,5,1,""],rectSettings:[6,5,1,""]},"flika.app.settings_editor.SettingsEditor":{show:[6,4,1,""]},"flika.app.syntax":{PythonHighlighter:[7,1,1,""],format:[7,5,1,""]},"flika.app.syntax.PythonHighlighter":{highlightBlock:[7,2,1,""],match_multiline:[7,2,1,""]},"flika.app.terminal":{EmbeddedIPythonWidget:[8,1,1,""],EmbeddedQtKernel:[8,1,1,""],EmbeddedQtKernelApp:[8,1,1,""],Terminal:[8,1,1,""],connected_console:[8,5,1,""],default_kernel_app:[8,5,1,""],default_manager:[8,5,1,""],in_process_console:[8,5,1,""],ipython_terminal:[8,5,1,""],redirect_output:[8,5,1,""]},"flika.app.terminal.EmbeddedQtKernel":{do_one_iteration:[8,2,1,""],execute_request:[8,2,1,""]},"flika.app.terminal.EmbeddedQtKernelApp":{init_kernel:[8,2,1,""],start:[8,2,1,""]},"flika.flika":{start_flika:[10,5,1,""]},"flika.global_vars":{Settings:[11,1,1,""],alert:[11,5,1,""],currentTrace:[11,6,1,""],currentWindow:[11,6,1,""],m:[11,6,1,""],traceWindows:[11,6,1,""],win:[11,6,1,""],windows:[11,6,1,""]},"flika.global_vars.Settings":{load:[11,2,1,""],save:[11,2,1,""]},"flika.process":{binary:[14,0,0,"-"],color:[15,0,0,"-"],file_:[16,0,0,"-"],filters:[17,0,0,"-"],math_:[18,0,0,"-"],measure:[19,0,0,"-"],overlay:[20,0,0,"-"],progress_bar:[21,0,0,"-"],roi:[22,0,0,"-"],stacks:[23,0,0,"-"]},"flika.process.binary":{Adaptive_threshold:[14,1,1,""],Binary_Dilation:[14,1,1,""],BlocksizeSlider:[14,1,1,""],Canny_edge_detector:[14,1,1,""],Logically_combine:[14,1,1,""],Remove_small_blobs:[14,1,1,""],Threshold:[14,1,1,""]},"flika.process.color":{Split_channels:[15,1,1,""]},"flika.process.file_":{close:[16,5,1,""],get_permutation_tuple:[16,5,1,""],open_file:[16,5,1,""],open_image_sequence:[16,5,1,""],open_points:[16,5,1,""],save_file:[16,5,1,""],save_movie:[16,5,1,""],save_points:[16,5,1,""]},"flika.process.filters":{Bilateral_filter:[17,1,1,""],Boxcar_differential_filter:[17,1,1,""],Butterworth_filter:[17,1,1,""],Difference_filter:[17,1,1,""],Difference_of_Gaussians:[17,1,1,""],Fourier_filter:[17,1,1,""],Gaussian_blur:[17,1,1,""],Mean_filter:[17,1,1,""],Median_filter:[17,1,1,""],Variance_filter:[17,1,1,""],Wavelet_filter:[17,1,1,""]},"flika.process.math_":{Divide:[18,1,1,""],Divide_trace:[18,1,1,""],Multiply:[18,1,1,""],Power:[18,1,1,""],Ratio:[18,1,1,""],Subtract:[18,1,1,""],Subtract_trace:[18,1,1,""]},"flika.process.measure":{Measure:[19,1,1,""]},"flika.process.measure.Measure":{"export":[19,2,1,""]},"flika.process.overlay":{Scale_Bar:[20,1,1,""],ShowCheckbox:[20,1,1,""],Time_Stamp:[20,1,1,""]},"flika.process.progress_bar":{ProcessLauncher:[21,1,1,""],ProgressBar:[21,1,1,""]},"flika.process.roi":{Set_value:[22,1,1,""]},"flika.process.stacks":{Change_datatype:[23,1,1,""],Concatenate_stacks:[23,1,1,""],Deinterleave:[23,1,1,""],Frame_binning:[23,1,1,""],Image_calculator:[23,1,1,""],Pixel_binning:[23,1,1,""],Resize:[23,1,1,""],Trim:[23,1,1,""],ZProject:[23,1,1,""]},"flika.roi":{ROI_Base:[24,1,1,""],ROI_line:[24,1,1,""],ROI_rect_line:[24,1,1,""],ROI_rectangle:[24,1,1,""],makeROI:[24,5,1,""],open_rois:[24,5,1,""]},"flika.roi.ROI_Base":{"delete":[24,2,1,""],_str:[24,2,1,""],colorDialog:[24,3,1,""],colorSelected:[24,2,1,""],getTrace:[24,2,1,""],linkedROIs:[24,3,1,""],plot:[24,2,1,""],pts:[24,3,1,""],traceWindow:[24,3,1,""],unplot:[24,2,1,""]},"flika.roi.ROI_line":{kymograph:[24,3,1,""]},"flika.roi.ROI_rect_line":{kymograph:[24,3,1,""],setWidth:[24,2,1,""]},"flika.roi.ROI_rectangle":{crop:[24,2,1,""]},"flika.tracefig":{TraceFig:[25,1,1,""]},"flika.tracefig.TraceFig":{p1:[25,3,1,""],p2:[25,3,1,""],rois:[25,3,1,""]},"flika.utils.app":{get_qapp:[26,5,1,""]},"flika.utils.misc":{load_ui:[26,5,1,""],nonpartial:[26,5,1,""],open_file_gui:[26,5,1,""],random_color:[26,5,1,""],save_file_gui:[26,5,1,""]},"flika.window":{Window:[27,1,1,""]},"flika.window.Window":{closeEvent:[27,2,1,""],closed:[27,3,1,""],commands:[27,3,1,""],currentROI:[27,3,1,""],dtype:[27,3,1,""],filename:[27,3,1,""],framerate:[27,3,1,""],getScatterPts:[27,2,1,""],imageArray:[27,2,1,""],keyPressEvent:[27,2,1,""],link:[27,2,1,""],metadata:[27,3,1,""],mouseClickEvent:[27,2,1,""],mouseMoved:[27,2,1,""],mousePressEvent:[27,2,1,""],mt:[27,3,1,""],mx:[27,3,1,""],my:[27,3,1,""],name:[27,3,1,""],paste:[27,2,1,""],resizeEvent:[27,2,1,""],rois:[27,3,1,""],save:[27,2,1,""],save_rois:[27,2,1,""],setAsCurrentWindow:[27,2,1,""],setIndex:[27,2,1,""],setName:[27,2,1,""],unlink:[27,2,1,""]},flika:{flika:[10,0,0,"-"],global_vars:[11,0,0,"-"],roi:[24,0,0,"-"],tracefig:[25,0,0,"-"],utils:[26,0,0,"-"],window:[27,0,0,"-"]}},objnames:{"0":["py","module","Python module"],"1":["py","class","Python class"],"2":["py","method","Python method"],"3":["py","attribute","Python attribute"],"4":["py","staticmethod","Python static method"],"5":["py","function","Python function"],"6":["py","data","Python data"]},objtypes:{"0":"py:module","1":"py:class","2":"py:method","3":"py:attribute","4":"py:staticmethod","5":"py:function","6":"py:data"},terms:{"03d":16,"128x128":23,"256x256":23,"abstract":24,"boolean":[14,17],"case":32,"class":[2,3,4,6,7,8,11,14,15,17,18,19,20,21,22,23,25,27],"default":[6,17,26],"export":[16,19,24,37],"final":31,"float":[14,17,18,20,27],"function":[3,5,7,14,17,19,26,27,37,39],"import":[3,9,11,24,26,33,36,37,38,39],"int":[14,16,17,18,20,22,23,24,25,27],"jyv\u00e4skyl\u00e4":37,"new":[14,15,23,24,26,28,29],"return":[2,7,8,10,14,15,16,17,18,20,22,23,24,26,27],"static":[3,4,6],"true":[7,14,17,20,23,24,27],AND:35,BUT:35,FOR:35,For:[11,32,33,36,37],NOT:35,OME:37,THE:35,That:36,The:[2,8,11,14,16,17,18,19,20,22,23,24,26,27,31,32,35,37,39],Then:33,There:[27,31,36],USE:35,Using:[30,37],WITH:35,Will:16,__all__:5,__init__:[24,39],_build:31,_str:24,abl:36,about:[31,36,39],abov:[8,17,35],absolute_valu:18,access:[9,11,27,33,38],accord:[14,18],act:[11,24],action:[3,35,39],adapative_threshold:12,adapt:14,adaptive_threshold:14,add:[20,31,34,36,38],added:[8,19,28],addit:24,address:[16,37],adjust:24,advantag:37,aid:37,aim:32,alert:11,algorithm:34,alia:9,align:37,alik:37,all:[2,5,11,14,16,19,24,27,31,35,36],allow:37,almost:27,along:33,also:[31,32,37],alter:[22,27],alwai:31,anaconda:33,analysi:[34,37],analyz:[34,37],ani:[8,11,16,31,32,35],annot:37,anoth:[8,16,17,27],answer:[29,32],anyon:31,anywher:[26,37],api:[28,30],app:[0,2,3,4,5,6,7,8,28],append:38,appli:[7,14,17,33],applic:[1,10,26,37],appreci:31,approach:37,architectur:34,archiv:[37,39],arg:[8,21,26],argument:[3,19,24,26],aris:[35,37],around:37,arrai:[18,24,27],articl:31,artifact:37,ascii:19,associ:35,attribut:7,author:[31,35,39],autoclass:18,autom:[34,37],automat:[27,34,37],avail:31,averag:[17,18,24,25],axes:[16,17],background:[20,26],bandpass:17,banner:8,base:[31,34,37],basedialog:12,baseprocess:[12,19],baseprocess_nopriorwindow:12,basic:32,batch:37,becaus:31,becom:[14,27],been:[11,27,34,36,37],befor:38,begin:10,below:[14,17],beta:17,between:[17,23,24],bilateral_filt:12,bin:23,binari:12,binary_dil:12,bind:37,bio:37,biolog:[34,37],biologist:37,bit:37,black:[20,26],black_level:18,block:7,block_siz:14,blocksizeslid:12,blog:31,blur:[17,33],bool:[3,4,14,17,20,22,23,27],bottom:25,bound:24,box:17,boxcar:17,boxcar_differential_filt:12,branch:31,brett:34,bright:26,bug:29,bugfix:31,build:[31,38],built:[31,37],butterworth:17,butterworth_filt:12,calcium:[34,37],calcul:14,call:[3,26],camera:34,can:[2,11,14,17,27,31,36,37,38,39],cancel:26,canny_edge_detector:12,cbg:37,cell:[34,37],cellular:37,center:[24,31],central:[27,31],chang:[7,11,27,31,38],change_datatyp:12,changelog:[30,31],channel:[15,23,30,37],charg:35,check:31,check_upd:28,checkbox:12,checkout:31,cite:34,claim:35,classif:37,clear:[2,6],click:[2,3,19,27],clickablelabel:1,client:37,clone:31,close:[2,3,4,11,12,27],closeev:[2,3,4,24,27],code:[33,34,38],col0:27,col1:27,col2:27,collabor:[36,37],colleagu:37,collect:[24,37],color:[6,7,12,20,24,26,27,37],colordialog:24,colorselect:24,colorselector:12,column:19,com:[29,31,32,39],combin:[14,18,23],combobox:12,come:[32,39],command:[16,27,31,33,34,38],commerci:37,commit:31,common:24,commun:[29,34],compar:[17,31],complementari:31,complet:37,comprehens:32,compris:4,comput:[24,37],concaten:23,concatenate_stack:12,condit:35,configur:8,conform:31,connect:[8,14,24,35],connected_consol:8,conquer:37,consist:37,consol:[4,8,33,38],console_class:8,constructor:3,consult:34,contact:[30,32,37,39],contain:[27,32,37,39],content:34,contigu:14,contract:35,contribut:[29,30,32,34,39],control:20,conveni:31,converg:17,convert:[11,14],coord:24,coordin:24,copi:[24,31,35],copyright:35,core:31,correct:[24,27,37],correspond:[7,18],could:31,count:[31,37],creat:[8,11,14,23,24,26,27,31,34,37],crop:24,cross:37,current:[6,8,11,16,18,22,24,26,27,31,33,37],currentroi:[24,27],currenttrac:11,currentwindow:[6,11,14,16,24],cutoff:17,damag:35,darkbackground:14,data:[10,19,21,31,34,37],databas:3,dataset:37,datatyp:[23,27],deal:35,declar:24,deconvolut:37,default_kernel_app:8,default_manag:8,defin:5,deinterleav:12,delet:[23,24],delimit:7,demic:14,demo:37,demonstr:31,depend:[28,33,39],dependency_name_1:39,dependency_name_2:39,deploy:38,describ:31,design:[11,37],desir:[16,22],detail:31,detect:[34,37],determin:14,develop:[29,31,37],deviat:[17,18],diagon:14,dialog:[2,24,26],dict:[25,27],dictionari:[11,27],differ:[24,37],difference_filt:12,difference_of_gaussian:12,differenti:17,dilat:14,dimens:[14,27],dimension:37,directli:31,directori:[26,27,31,36,38,39],discard:14,discuss:31,displai:[2,3,11,16,20,25,26,27,31,39],distanc:14,distribut:[34,35,37],divid:[12,37],divide_trac:12,divison:37,django:37,do_one_iter:8,doc:[28,31],docstr:31,document:[7,28,32,35,38],doesn:31,domain:17,don:[26,31],doubl:[7,23],down:27,download:[31,33,36,38,39],dragenterev:[2,4],draw:24,draw_from_point:24,dresden:37,dropev:[2,4],dst:16,dtype:27,dynam:37,each:[14,16,17,18,19,24,34,37],easi:[9,24,34,36,39],easier:31,easili:37,edg:17,edit:[4,31],editor:[4,33],effect:22,either:[14,18,31,33],element:14,ellefsen:[34,35],emb:8,embeddedipythonwidget:8,embeddedqtkernel:8,embeddedqtkernelapp:8,emit:25,empti:[26,39],enabl:37,encount:32,end:17,engin:37,english:31,enhanc:[31,34],enough:26,entir:[18,25],entiti:37,equal:23,error:2,escap:2,etc:16,even:31,event:[2,10,27,35,38],eventloop:8,eventu:17,everi:[17,23,31],exactli:31,exampl:[23,24,30,33,37],excel:31,excepthook:2,execut:38,execute_request:8,exist:[3,16,26],exit:[2,10],expandus:38,experi:37,experiment:37,explain:31,expon:18,express:35,extend:[24,34,39],extens:[24,26],extern:34,extra:[8,26],extract:37,extrem:17,factor:23,fals:[14,15,16,17,18,22,23,27],far:34,favourit:31,featur:[29,33],feel:31,few:[33,37],fewer:14,ffmpeg:16,field:37,file:[10,11,16,19,23,24,26,27,31,35,38,39],file_:12,file_loc:3,file_or_submodule_containing_function1:39,file_or_submodule_containing_function2:39,filenam:[16,19,24,27],fileselector:12,filetyp:[26,34],filter:[12,26,31,33],filter_ord:17,find:[14,31],fine:31,finish:[7,24,25],finisheddrawingsign:25,finland:37,first:[16,17,18,22,23],first_fram:18,firstfram:[22,23],fit:35,fix:[28,34],flatiron:37,flika:[0,2,3,4,5,6,7,8,11,14,15,16,17,18,19,20,21,22,23,24,25,26,27,29,32,36,37,39],flika_dir:38,flika_plugin_templ:[31,39],flikaappl:1,fluoresc:37,flush:2,follow:[16,24,31,32,35,37,38,39],font:20,font_siz:20,forget:31,fork:31,format:[7,37],found:31,foundat:37,fourier:17,fourier_filt:12,frame:[14,16,17,18,20,22,23,25,27],frame_bin:12,frame_r:17,frameat:17,framer:[16,17,20,27],framework:37,free:[31,34,35,37],freehand:24,frequenc:17,friendli:37,from:[3,8,9,11,14,16,17,18,22,23,24,26,27,33,34,35,36,37],from_gui:16,fucntion:27,full:[24,27,34],func:26,function1_nam:39,function2_nam:39,functool:26,furnish:35,gaussian:[17,33],gaussian_blur:[12,33],gener:[2,26,33,34],generate_random_imag:33,germani:37,get:[3,5,26,30,32,34],get_permtation_tupl:16,get_permutation_tupl:12,get_qapp:26,getmask:24,getnamespac:5,getpoint:24,getscatterpt:27,gettrac:24,git:31,github:[29,34,38,39],given:[7,24,31],global:26,global_var:[0,9],gmail:29,goe:5,going:[17,33],good:37,grant:[34,35],graph:19,grayscal:37,greater:14,group:[24,37],grow:[32,34,37],grown:34,guassian:17,gui:[3,33,38],guid:[29,31,34],handl:[3,8,24,26,37],handler:27,happi:31,hard:17,hardwar:37,has:[27,34,36,37],hasn:36,have:[9,11,14,16,17,31,32,39],haven:32,head:31,health:34,hear:31,heigh:27,height:[6,24],help:[29,31],hemodynam:37,here:[31,32,33],herebi:35,hesit:31,hide:2,high:17,higher:17,highli:[31,37],highlight:7,highlightblock:7,hijack:8,histolog:37,histori:30,holder:35,home:39,hover:25,how:[14,31,36],html:[31,39],http:[31,39],ian:34,icon:[2,26,28],icon_path:26,ident:8,identifi:[34,37],imag:[11,14,16,17,18,23,24,26,27,33,37],image_calcul:12,imagearrai:27,immedi:36,implement:24,impli:35,in_process_consol:8,in_stat:7,includ:[24,27,31,34,35,37],incompat:31,increasingli:37,increment:23,indeped:37,independ:14,index:[17,23,25,27,31],indexchang:25,individu:16,info:39,inform:[25,31,33],init_kernel:8,initi:[3,26],input:[16,26],insid:[7,11,17,27,31,33,38],instal:[3,30,31,32,37,38],instanc:[8,11,26],instead:31,institut:[34,37],instruct:[34,36,39],integ:7,integr:[37,38],intend:37,interact:37,interest:[24,33,37],interfac:[2,24,31],interpol:23,interpret:[5,8,31],introductori:32,ipkernelapp:8,ipykernel:33,ipython:8,ipython_termin:8,isol:26,issu:[29,31,34,37],iter:[14,17],ith:23,its:[18,24,31],itself:8,join:[16,38],jpg:16,json:11,juli:37,just:8,karg:24,keep:31,keepsourcewindow:[14,15,17,18,22,23],kei:[2,25],kept:23,kernel:[8,17,31],kevin:34,keypressev:[2,4,27],keypresssign:25,keyword:8,kind:[24,35],kwarg:[8,26],kyle:[34,35],kyleellefsen:29,kymograph:24,lab:36,label:[31,37],languag:[7,37],larg:37,laser:37,last:[16,22,23],lastfram:[22,23],later:31,latest:33,lazili:37,learn:33,left:[20,27],let:[33,37],level:[9,37],liabil:35,liabl:35,librari:31,licens:30,like:[11,26,31,32,34,39],limit:35,line:[7,16,24,33,38],linesegmentroi:24,link:[24,27],linkedroi:24,linux:34,list:[10,11,15,16,24,25,27,31,32,34,36,37],littl:31,live:31,load:[5,10,11,26,27],load_local_plugins_thread:3,load_ui:26,local:[31,34],locat:[20,24,26,31,38,39],log:[2,17,28],logger:1,logically_combin:12,loglogpreview:17,look:[29,31,32,37,39],loop:[10,38],love:31,low:17,lower:20,made:32,mai:14,mail:29,main:[2,11],mainloop:8,maintain:[31,37],major:31,make:[24,31,33,34,39],makeroi:24,manag:[31,36,37,39],mani:[14,31,32,34,37],manual:36,mask:24,master:[31,39],match:38,match_multilin:7,math_:12,matplotlib:33,matrix:14,max:37,maximum:17,maxit:17,maxnfram:17,mean:27,mean_filt:12,measur:[12,34,37],meausr:12,median_filt:12,menu_layout:39,merchant:35,merg:[31,35],messag:[2,11,31],metadata:[27,39],method:[18,23,24,26,37],micro:31,micron:20,microscop:37,microscopi:37,microscopist:37,might:[31,32],minnfram:17,minor:31,miss:37,missingwindowerror:12,mit:[34,35],mix:37,mode:37,modern:37,modif:31,modifi:[31,35],modul:[0,5,9,39],modular:37,molecul:37,molecular:37,more:[31,32,33,34,37,39],most:[18,33,37],motion:37,mous:[25,27],mouseclickev:27,mousemov:27,mousepressev:27,move:36,movement:27,movi:[16,18,20,34,37],mp4:16,msg:[11,21],multi:[7,37],multipl:37,multipli:12,must:[14,17,31,39],mynam:39,name:[19,26,27,31,33,34,39],namespac:[5,8],narrow:31,nation:34,natur:37,nchannel:23,ncore:21,nd2:[16,34],nd2reader:33,nearest:19,necessari:[3,31],need:[31,32,38],neglig:37,neighbor:14,neighborhood:14,neuron:37,never:31,newwidth:24,newwindow:[14,16,17,18,22,23],nframe:[17,18,23],nih:37,non:37,none:[2,4,11,16,20,21,24,26,27],noninfring:35,nonparti:26,norm_edg:17,note:16,notic:35,now:[31,37],npixel:23,number:[14,16,17,18,20,23,27,31,37],numer:34,numpi:[27,33],nx3:27,nyquist:17,object:[3,5,8,10,11,24,26,27,37],obtain:[35,37],odd:[14,17],off:[20,31],offlin:37,often:32,onc:[8,16,31,33],one:[17,24,26,27,32,37],onli:[8,22,27,31,33,37],onlin:3,opacity_slid:20,open:[11,16,24,26,33,34,36,37,38],open_fil:[12,24],open_file_gui:26,open_image_sequ:12,open_image_sequencefilenam:16,open_point:12,open_roi:[9,24],oper:[14,18,21,23,27,31,37],optic:37,option:10,orang:37,order:[9,14,16,17,19],org:[31,39],organ:31,origin:[16,27],orin:27,osx:34,other:[26,27,35,37],otherwis:[14,27,35],our:34,out:[19,31,35],outerfunc:21,output:[16,19,27],over:25,overlai:12,overlap:37,overrid:8,overview:31,own:[31,34,36,39],packag:[5,33,37],page:34,panda:33,paramet:[8,10,11,14,16,17,18,19,20,22,23,24,26,27],parent:[2,4,8,20,21,26],parker:34,parti:36,partial:26,partialthreadupdatedsign:25,particular:35,pass:[24,26,31],past:[24,27],path:[3,24,26,27,38],pen:24,pencilbutton:6,pencilset:6,per:[20,27],perform:[14,21,23,27,37],perhap:31,perman:8,permiss:[35,37],permit:35,permut:16,persist:16,person:35,phenotyp:37,php:31,pip:[33,38],pixel:[14,17,18,20,23,24,27,37],pixel_bin:12,place:[3,24],planck:37,platform:[33,37],pleas:[31,32,34,36,37,39],plot:[17,18,19,24,25],plotwidget:25,plugin:[3,28,30,33,34,37],plugin_manag:1,plugin_nam:3,pluginmanag:3,png:[16,26],point:[6,16,17,19,24,27],pointbutton:6,pointset:6,popul:11,popular:[31,37],popup:11,portion:35,pos:24,posit:24,possibl:[31,37],post:[29,31],potenti:31,power:[12,17],practic:37,preceed:17,prepar:37,press:[25,27,36],prevent:8,prior:18,privat:29,probabl:37,problem:37,process:[0,5,8,14,15,16,17,18,19,20,21,22,23,26,27,33,37],processlaunch:12,progessbar:12,program:37,progress_bar:12,progressbar:21,project:[30,31],projection_typ:23,prompt:26,proposit:31,protocol:37,provid:[16,35],pts:24,pub_socket:8,publish:35,pull:29,purpos:[35,37],push:31,put:[8,39],pyopengl:33,pypi:33,pyqtgraph:[24,25,33],python:[7,31,33,34,38,39],pythonhighlight:7,qapplic:26,qcloseev:[3,4,27],qcolor:[24,26],qdragenterev:[2,4],qdropev:[2,4],qevent:25,qgraphicsobject:24,qkeyev:[4,27],qlabel:2,qmainwindow:4,qmouseev:27,qobject:26,qregexp:7,qresizeev:27,qtconsol:[8,33],qtcore:[7,25,26],qtextcharformat:7,qtgui:[2,7,24,26],qtkernelmanag:8,qtpy:33,qtwidget:[24,26],quantit:37,question:[29,32],quick:[31,34,37],quickli:29,quickstart:31,quot:7,qwidget:[8,26],rais:18,ran:33,random:33,random_color:26,randomli:26,rang:[14,17,25],rank:14,rare:37,rasband:37,rate:[16,17],rather:38,ratio:12,ratio_typ:18,realm:37,realtim:25,recent:18,record:[34,37],rect:6,rect_lin:24,rectangl:24,rectbutton:6,rectset:6,redirect_output:8,reduc:[17,23],refer:[25,30,36],region:[14,24,25,37],releas:31,remot:37,remov:[14,24],remove_small_blob:12,repeat:14,report:29,repositori:31,repres:[2,7],represent:24,reproduc:31,request:[28,29],requir:[16,33,37],resiz:[12,24],resizeev:27,rest:[17,28],restart:[11,36],restrict:35,restricttooutsid:22,restricttoroi:22,result:[14,16,37],review:31,rich:34,rich_jupyter_widget:8,richjupyterwidget:8,right:[20,27,35],roi2:24,roi:[0,12,25,27,28,37],rst:31,run:[3,4,8,9,10,11,16,31,34,38,39],same:[17,27,33],sampl:30,save:[11,16,19,26,27],save_fil:12,save_file_gui:26,save_movi:12,save_point:12,save_roi:27,scale:[23,37],scale_bar:12,scan:37,scatter:27,scientif:37,scikit:[14,33],scipi:33,scope:31,script:[4,5,31,33,34,38],script_editor:1,script_namespac:1,scripteditor:4,scriptfil:4,search:29,second:[20,23,27],section:[36,37],see:[17,26,32,34,37],seen:29,segment:[24,37],select:[11,19,24,25,26,36],selector:25,self:[2,3,4,6,11,24,27],sell:35,semi:37,send:[29,31],sensit:29,separ:[26,37],seper:19,sequenc:16,sequenti:37,seri:[16,34,37],server:[31,37],session:[8,10],set:[11,16,17,18,22,24,26,27,38],set_valu:12,setascurrentwindow:27,setindex:27,setnam:27,settings_editor:1,settingseditor:6,settl:34,setup:31,setwidth:24,sever:37,shall:35,share:31,shell:8,shift:19,shortcom:37,should:[7,31,39],show:[3,4,6,20,24],showcheckbox:12,sigma1:17,sigma2:17,sigma:[14,17,33],signal:[25,34,37],sigpluginload:3,similar:30,simon:37,simpl:[31,37],simpli:11,singl:[7,37],size:[6,14,20,23,24],sliderlabelodd:12,slow:17,small:[31,37],smith:34,snippet:32,soft:17,softwar:[34,35,37],some:31,someth:[31,37,39],soon:39,sourc:[34,37],spatial:17,specif:[27,31,37],specifi:[14,16,19,23,24,26,39],specimen:37,spectral:37,spectrum:17,spike:37,split:15,split_channel:12,src:16,stack:[12,17,27,33,37],stackoverflow:[29,32],stamp:20,stand:[37,39],standalon:26,standard:[17,18,26],start:[8,17,27,30,31,32,34,36,39],start_flika:[9,10,33,38],state:7,statu:2,status_light:2,stderr:8,stdout:8,steeper:17,step:[8,31,34],still:[7,37],stitch:16,stk:[16,34],stoptol:17,store:[2,11,27,31],str2func:3,str:[11,14,16,18,19,23,24,26,27],straight:24,stream:8,string:[7,20,23,24,26],studi:34,style:7,subclass:8,subject:35,sublicens:35,submit:[29,30,34,36],submodul:[1,9,12],substanti:35,subtract:[12,17],subtract_trac:12,subvolum:37,suggest:[29,31,33],suit:37,supervis:37,support:[34,37],sure:[31,33],syntax:1,sys:[2,38],system:[31,37],tab:[4,19],tag:[29,37],take:[3,17,18,32,37],talk:[31,36,37],target:37,tarhan:34,teh:17,templat:[24,31,39],term:34,termin:[1,33,38],test:31,test_imag:28,text:[4,7,16],than:[14,37],thei:[17,19,23,31],them:[18,24,27,31,37],thi:[5,7,8,11,14,15,17,18,19,22,23,24,26,27,31,35,36,37,38,39],thing:33,think:37,third:36,those:7,thousand:37,threshold:12,threshold_loc:14,through:[5,31,34],tif:[16,27,34],tiff:16,tifffil:28,tile:37,time:[14,17,20,37],time_stamp:12,titl:11,togeth:16,toler:17,too:31,tool:[34,37],toolbox:37,top:[9,20,25,26],tort:35,trace:[2,17,18,19,24,25],tracefig:[0,11,19,24,28],tracewindow:[11,24,25],track:37,tracker:[29,31,34],train:37,translat:31,treat:14,tree:37,trim:12,tripl:7,troubleshoot:31,tupl:[16,26],turku:37,turn:20,tutori:[31,34],twitter:31,two:[14,23,24,36],txt:[16,24],type:[16,24,26,27,33,34,37,38],uint8:27,unclear:31,under:[31,34],uniqu:7,univers:37,unlik:26,unlink:[24,27],unmix:37,unplot:24,unsur:31,updat:[24,25,28],update_flika:28,url:39,usag:[30,33],use:[26,31,32,33,34,35,39],used:[14,16,17,18,23,24,27,37],useful:[9,31],user:[4,11,25,29,31,37,39],usernam:39,using:[11,14,27,31,33,34,36,37,38],usual:[29,31,39],util:[0,28],valu:[11,14,17,18,22,23,24,26],variabl:[3,5,8,9,11,27,33,38],varianc:17,variance_filt:12,variat:37,varieti:34,variou:32,veri:[31,37],version:[28,31,33,34,39],via:[27,31],video:16,vision:37,visual:37,volum:37,volumetr:37,wai:[27,36],want:[16,29,31,33,38],warn:17,warranti:35,wavelet_filt:12,wayn:37,web:[31,37],websit:31,welcom:31,well:[31,32,37],were:19,what:31,when:[3,7,11,16,25,26,27,31,34],where:[17,19,27,37,38,39],wherea:31,whether:[17,20,22,35],which:[8,11,14,26,32,37],white:[20,26],who:22,whom:35,wide:[23,27,34],widefield:37,widget:[2,8,25,26],width:[6,17,20,24],width_micron:20,width_pixel:20,wiki:31,win2:24,win:[11,27],windo:26,window1:[14,23],window2:[14,23],window:[0,2,9,11,14,15,16,17,18,23,24,26,34,39],windowselector:12,within:[24,36,37,38],without:[31,35,37],work:[8,31],workflow:37,world:37,worldwid:37,would:[32,34,39],write:[2,30,33,34,36],written:[36,37],xml:39,xstream:1,yet:[11,31,32],you:[2,16,17,18,22,27,29,31,32,33,34,36,37,38,39],your:[17,31,34,36,37,39],your_github_usernam:31,yourself:31,zero:17,zip:39,zproject:12},titles:["API Reference","Module: app","Submodule: application","Submodule: plugin_manager","Submodule: script_editor","Submodule: script_namespace","Submodule: settings_editor","Submodule: syntax","Submodule: terminal","flika","Module: flika","Module: global_vars","Module: process","Submodule: BaseProcess","Submodule: binary","Submodule: color","Submodule: file_","Submodule: filters","Submodule: math_","Submodule: measure","Submodule: overlay","Submodule: progress_bar","Submodule: roi","Submodule: stacks","Module: roi","Module: tracefig","Module: utils","Module: window","Changelog history","Contact channels","Full flika documentation","Contributions","Usages and Examples","Installation and Getting Started","flika: image processing for biologists","License","Installing and Using plugins","Similar Projects","Starting flika","Writing plugins"],titleterms:{"class":24,"function":24,Using:36,adapative_threshold:14,aka:37,api:0,app:[1,26],applic:2,author:34,basedialog:13,baseprocess:13,baseprocess_nopriorwindow:13,bilateral_filt:17,binari:14,binary_dil:14,bioimagexd:37,biologist:34,blocksizeslid:14,boxcar_differential_filt:17,brain:37,bug:[31,34],butterworth_filt:17,caiman:37,canny_edge_detector:14,cellprofil:37,change_datatyp:23,changelog:[28,34],channel:29,checkbox:13,chip:37,citat:34,clickablelabel:2,close:16,color:15,colorselector:13,combobox:13,concatenate_stack:23,contact:29,contribut:31,deinterleav:23,difference_filt:17,difference_of_gaussian:17,divid:18,divide_trac:18,document:[30,31,34],endrov:37,exampl:32,explor:37,farsight:37,featur:[31,34],feedback:31,fiji:37,file_:16,fileselector:13,filter:17,first:33,fix:31,flika:[9,10,30,31,33,34,38],flikaappl:2,fourier_filt:17,frame_bin:23,from:38,full:30,gaussian_blur:17,gemid:37,get:33,get_permutation_tupl:16,git:38,github:31,global_var:11,histori:28,ilastik:37,imag:34,image_calcul:23,imagej:37,implement:31,instal:[33,34,36],ipython:38,java:37,licens:[34,35],link:31,linux:33,logger:2,logically_combin:14,mac:33,main:9,math_:18,matlab:37,mean_filt:17,measur:19,meausr:19,median_filt:17,mesoscal:37,misc:26,missingwindowerror:13,modul:[1,10,11,12,24,25,26,27],multipli:18,next:33,object:9,omero:37,open_fil:16,open_image_sequ:16,open_point:16,osx:33,our:33,overlai:20,pixel_bin:23,plugin:[31,36,39],plugin_manag:3,power:18,prepar:31,process:[12,34],processlaunch:21,progessbar:21,progress_bar:21,project:37,publish:37,pull:31,pycharm:38,python:37,ratio:18,refer:0,remove_small_blob:14,report:31,request:[31,34],resiz:23,roi:[22,24],roi_bas:24,roi_lin:24,roi_rect_lin:24,roi_rectangl:24,run:33,sampl:39,save_fil:16,save_movi:16,save_point:16,scale_bar:20,script_editor:4,script_namespac:5,set_valu:22,settings_editor:6,showcheckbox:20,sima:37,similar:37,sliderlabelodd:13,split_channel:15,stack:23,start:[33,38],submit:[31,39],submodul:[2,3,4,5,6,7,8,13,14,15,16,17,18,19,20,21,22,23,26],subtract:18,subtract_trac:18,syntax:7,termin:8,test:33,threshold:14,time_stamp:20,todo:24,tracefig:25,trim:23,usag:32,util:26,variance_filt:17,via:37,wavelet_filt:17,where:33,window:[27,33],windowselector:13,write:[31,39],xstream:2,yet:37,zproject:23}})