text: Search.setIndex({docnames:["index","rst/changelog","rst/modules","rst/spmap","rst/tutorial"],envversion:{"sphinx.domains.c":2,"sphinx.domains.changeset":1,"sphinx.domains.citation":1,"sphinx.domains.cpp":4,"sphinx.domains.index":1,"sphinx.domains.javascript":2,"sphinx.domains.math":2,"sphinx.domains.python":3,"sphinx.domains.rst":2,"sphinx.domains.std":2,"sphinx.ext.intersphinx":1,"sphinx.ext.todo":2,sphinx:56},filenames:["index.rst","rst\\changelog.rst","rst\\modules.rst","rst\\spmap.rst","rst\\tutorial.rst"],objects:{"":{spmap:[3,0,0,"-"]},"spmap.hyper_object":{abundance:[3,3,1,""],add_peaks:[3,3,1,""],airpls:[3,3,1,""],append:[3,3,1,""],clean_data:[3,3,1,""],clean_label:[3,3,1,""],clean_position:[3,3,1,""],cluster_cluster:[3,3,1,""],combine_label:[3,3,1,""],concat:[3,3,1,""],copy:[3,3,1,""],covariance:[3,3,1,""],dbscan:[3,3,1,""],diff:[3,3,1,""],gaussian:[3,3,1,""],get_area:[3,3,1,""],get_data:[3,3,1,""],get_intensity:[3,3,1,""],get_intensity_3D:[3,3,1,""],get_label:[3,3,1,""],get_name:[3,3,1,""],get_number:[3,3,1,""],get_pixel:[3,3,1,""],get_position:[3,3,1,""],get_resolution:[3,3,1,""],get_wavenumber:[3,3,1,""],gol:[3,3,1,""],hca:[3,3,1,""],hdbscan:[3,3,1,""],interpolate:[3,3,1,""],keep:[3,3,1,""],kmeans:[3,3,1,""],label_spikes:[3,3,1,""],mean:[3,3,1,""],norm:[3,3,1,""],norm_peak:[3,3,1,""],pca:[3,3,1,""],pls_lda:[3,3,1,""],read_1064_3D:[3,3,1,""],read_csv:[3,3,1,""],read_csv_3D:[3,3,1,""],read_csv_xz:[3,3,1,""],read_map2_1064:[3,3,1,""],read_map_1064:[3,3,1,""],read_mat:[3,3,1,""],read_multi_spc:[3,3,1,""],read_point_1064:[3,3,1,""],read_single_spc:[3,3,1,""],read_spc_holo:[3,3,1,""],remove:[3,3,1,""],remove_label:[3,3,1,""],remove_spectrum:[3,3,1,""],rename_label:[3,3,1,""],reset_index:[3,3,1,""],rubber:[3,3,1,""],save_data:[3,3,1,""],save_data_xz:[3,3,1,""],scatter_3D:[3,3,1,""],select_index:[3,3,1,""],select_label:[3,3,1,""],set_data:[3,3,1,""],set_label:[3,3,1,""],set_name:[3,3,1,""],set_original:[3,3,1,""],set_position:[3,3,1,""],set_position_3d:[3,3,1,""],set_resolution:[3,3,1,""],set_resolutionz:[3,3,1,""],set_wavenumber:[3,3,1,""],show:[3,3,1,""],show_intensity:[3,3,1,""],show_intensity_3d:[3,3,1,""],show_map:[3,3,1,""],show_profile:[3,3,1,""],show_scatter:[3,3,1,""],show_scatter_3d:[3,3,1,""],show_spectra:[3,3,1,""],show_stack:[3,3,1,""],snip:[3,3,1,""],spikes:[3,3,1,""],threshold:[3,3,1,""],vca:[3,3,1,""],vector:[3,3,1,""]},spmap:{NNLS:[3,1,1,""],OLS:[3,1,1,""],WhittakerSmooth:[3,1,1,""],airPLS:[3,1,1,""],estimate_snr:[3,1,1,""],find_pixel:[3,1,1,""],fixer:[3,1,1,""],hyper_object:[3,2,1,""],modified_z_score:[3,1,1,""],peak_finder:[3,1,1,""],pearson_affinity:[3,1,1,""],plot_conditions:[3,1,1,""],plot_dendrogram:[3,1,1,""],read_mat:[3,1,1,""],read_spc:[3,1,1,""],rubberband:[3,1,1,""],save_data:[3,1,1,""],snake_table:[3,1,1,""],snip:[3,1,1,""],vca:[3,1,1,""]}},objnames:{"0":["py","module","Python module"],"1":["py","function","Python function"],"2":["py","class","Python class"],"3":["py","method","Python method"]},objtypes:{"0":"py:module","1":"py:function","2":"py:class","3":"py:method"},terms:{"0":3,"1":3,"10":3,"1000":3,"1064":3,"11":3,"1997":3,"1d":3,"2":3,"2d":3,"3":3,"393":3,"3d":3,"4":3,"401":3,"50":3,"7":3,"class":3,"float":3,"function":3,"import":1,"int":3,"long":3,"new":3,"return":3,"true":3,It:3,The:3,abu:3,abud:3,abund:3,activaiton:3,adapt:3,add:3,add_peak:3,adjust:3,advanc:3,after:3,airpl:3,algoirthm:3,algorithm:3,all:3,alogrithm:3,among:3,an:3,analysi:3,anc:3,apli:3,append:3,appli:3,ar:3,area:3,arrai:3,author:3,auto:3,automat:3,aux:3,averag:3,ax:3,axi:3,background:3,band:3,base:3,baselin:3,befor:3,belong:3,between:3,betwen:3,bicub:3,binari:3,bolano:3,bool:3,branc:3,bro:3,calcul:3,calibr:3,calibraiton:3,can:3,categor:3,center:3,certain:3,cevik:3,changelog:0,chemometr:3,chosen:3,chromatogram:3,clean:3,clean_data:3,clean_label:3,clean_posit:3,clusteinrg:3,cluster:3,cluster_clust:3,clustr:3,cmap:3,col:3,color:3,column:3,combin:3,combine_label:3,complet:3,compon:3,componenet:3,componet:3,comput:3,concat:3,concatanet:3,concataneta:3,concentr:3,consid:3,constrain:3,constraint:3,contain:3,contamin:3,convert:3,coordiant:3,coordin:3,coovari:3,copi:3,correct:3,covari:3,creat:3,csv:3,current:3,curv:3,cut:3,dark:3,data:3,datafram:3,dataset:3,datetim:1,david:3,dbscan:3,de:3,debbug:3,debug:3,dedir:3,defect:3,defin:3,delta_int:3,dendogram:3,densiti:3,depend:3,deriv:3,descript:3,desir:3,determinat:3,deviat:3,diff:3,differ:3,directori:3,dist:3,distanc:3,distiguisbl:3,dr:3,draw:3,e:3,each:3,ecehan:3,element:3,enabl:3,end:3,endmemb:3,ep:3,estimate_snr:3,expand:3,expect:3,fals:3,fast:3,file:3,file_path:3,filenam:3,filter:3,find:3,find_pixel:3,first:3,fit:3,fixer:3,frame:3,from:[1,3],full:3,gaussian:3,get:3,get_area:3,get_data:3,get_intens:3,get_intensity_3d:3,get_label:3,get_nam:3,get_numb:3,get_pixel:3,get_posit:3,get_resolut:3,get_wavenumb:3,gol:3,golai:3,good:3,grai:3,ha:3,hca:3,hdbscan:3,hierchic:3,holomap:3,how:3,hyper:3,hyper_object:3,hyperobject:3,i:3,index:[0,3],indic:3,individu:3,inferno:3,input:3,instrument:3,integ:3,intenisti:3,intens:3,intensii:3,inter:3,interpol:3,iter:3,itermax:3,jong:3,journal:3,juan:3,kaiser:3,keep:3,kind:3,kmean:3,kwarg:3,label:3,label_spik:3,lambda:3,lambda_:3,landa:3,larger:3,lda:3,least:3,limit:3,line:3,linear:3,linkag:3,list:3,list_hyp:3,lista:3,load:3,low:3,lower:3,m:3,mai:3,main_contributor:3,mani:3,manual:3,map:3,mask:3,mat:3,matrix:3,max:3,mean:3,method:3,min_clust:3,min_sampl:3,minimum:3,mm:3,model:3,modified_z_scor:3,modul:[0,2],more:3,motor:3,munoz:3,n:3,name:3,nearest:3,neg:3,neighbor:3,niter:3,nnl:3,non:3,none:3,nonneg:3,nor:3,norm:3,norm_peak:3,normal:3,normalized_avg:3,now:1,num:3,num_clust:3,num_compon:3,num_components_pl:3,number:3,numi:3,numpi:3,numx:3,object:3,offset:3,ol:3,one:3,onto:3,order:3,other:3,otherwis:3,out:3,outlier:3,output:3,p:3,page:0,pairwis:3,panda:3,param:3,paramet:3,path:3,path_calibr:3,path_fil:3,pb:3,pbd:3,pca:3,peak:3,peak_find:3,pearson_affin:3,penal:3,penalti:3,percentag:3,perform:3,pixel:3,pl:3,place:3,plasma:3,plot:3,plot_condit:3,plot_dendrogram:3,pls_lda:3,point:3,polynomi:3,porcentag:3,porder:3,posit:3,possibl:3,possit:3,print:[1,3],profil:3,promin:3,proport:3,provi:3,q:3,r:3,r_m:3,radiou:3,raman_spectra:3,rang:3,ratio:3,raw:3,read:3,read_1064_3d:3,read_csv:3,read_csv_3d:3,read_csv_xz:3,read_map2_1064:3,read_map_1064:3,read_mat:3,read_multi_spc:3,read_point_1064:3,read_single_spc:3,read_spc:3,read_spc_holo:3,refer:3,region:3,remov:3,remove_label:3,remove_spectrum:3,renam:3,rename_label:3,repres:3,reset:3,reset_index:3,resolut:3,resolutionz:3,result:3,retun:3,reweight:3,row:3,rubber:3,rubberband:3,s:3,same:3,save:3,save_data:3,save_data_xz:3,savitki:3,scale:3,scatter:3,scatter_3d:3,score:3,search:0,select:3,select_index:3,select_label:3,seri:3,set:3,set_data:3,set_label:3,set_nam:3,set_origin:3,set_posit:3,set_position_3d:3,set_resolut:3,set_resolutionz:3,set_wavenumb:3,sever:3,shaik:3,shape:3,show:3,show_intens:3,show_intensity_3d:3,show_map:3,show_profil:3,show_scatt:3,show_scatter_3d:3,show_spectra:3,show_stack:3,sigma:3,signatur:3,sillout:3,singl:3,size:3,smooth:3,smoother:3,snake:3,snake_t:3,snip:3,snr_input:3,sourc:0,spatial:3,spc:3,special:3,specifi:3,spectra:3,spectral:3,spectrum:3,spike:3,spmap:[0,2],squar:3,stack:3,stage:3,standard:3,state:3,step:3,still:3,strig:3,string:3,strong:3,structur:3,substract:3,tabl:3,tanveer:3,temp:3,than:3,three:3,threshold:3,through:3,time:3,tune:3,tutori:0,txt:3,type:3,u:3,um:3,under:3,unit_in:3,unmix:3,up:3,upper:3,us:3,user:3,util:3,valu:3,varianc:3,vca:3,vector:3,verbos:3,vertex:3,vertic:3,viridi:3,visual:3,w:3,ward:3,wave:3,wavenumb:3,well:3,where:3,whittakersmooth:3,whole:3,wide:3,wider:3,window:3,x:3,x_resolut:3,xy:3,xz:3,y:3,z:3,z_resolut:3,zero:3},titles:["Welcome to SpectraMap\u2019s documentation!","Changelog","source","spmap module","Tutorial"],titleterms:{changelog:1,content:0,document:0,indic:0,modul:3,s:0,sourc:2,spectramap:0,spmap:3,tabl:0,tutori:4,welcom:0}})