Last active
December 31, 2015 11:29
-
-
Save kmader/7980071 to your computer and use it in GitHub Desktop.
Shiny Beamline Interface
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| library(tiff) | |
| library(gdata) | |
| # path paste | |
| pa.paste<-function(...) paste(...,sep="/") | |
| get.last<-function(in.list,offset=0) in.list[length(in.list)-offset] | |
| pa.getlast<-function(in.path,offset=0) get.last(strsplit(in.path,"/")[[1]],offset=offset) | |
| get.or.blank<-function(var,altval="") { | |
| if(is.null(var)) altval | |
| else var | |
| } | |
| read.dmp.vals<-function(path="/Users/mader/Dropbox/TIPL/test/io_tests/rec_DMP/pivoB04_0301.sin.DMP") { | |
| pprint("reading img",path) | |
| if(nchar(path)>1) { | |
| cdmp<-file(path,open="rb") | |
| dimx<-readBin(cdmp,"int",signed=F,endian="little",size=2) | |
| dimy<-readBin(cdmp,"int",signed=F,endian="little",size=2) | |
| dimz<-readBin(cdmp,"int",signed=F,endian="little",size=2) | |
| o.vals<-readBin(cdmp,"double",endian="little",size=4,n=dimx*dimy) | |
| close(cdmp) | |
| } else { | |
| print("image is empty") | |
| o.vals<-c(1,1,1,1) | |
| dimx<-2 | |
| dimy<-2 | |
| } | |
| list(vals=o.vals,dim=c(dimx,dimy)) | |
| } | |
| dmp.val.to.img<-function(dmp.val) { | |
| (array(dmp.val$vals,dim=dmp.val$dim)) | |
| } | |
| read.dmp<-function(path="/Users/mader/Dropbox/TIPL/test/io_tests/rec_DMP/pivoB04_0301.sin.DMP") { | |
| dmp.val<-read.dmp.vals(path) | |
| dmp.val.to.img(path) | |
| } | |
| pprint<-function(...) print(paste(...)) | |
| parse.log.lines<-function(log.lines) { | |
| get.clean<-function(c.arg) { # trim the leading and trailing whitespaces | |
| gsub(". $", "",gsub("^ .", "", c.arg)) | |
| } | |
| get.clean<-trim | |
| get.val<-function(c.in) { | |
| if(length(c.in)<2) "" | |
| else get.clean(get.last(c.in)) | |
| } | |
| # initially no category | |
| cur.category<<-"" | |
| o.df<-ldply(log.lines,function(c.item) { | |
| if(substring(c.item,1,3)=="---") { | |
| # new catagory | |
| invisible(cur.category<<-get.clean(gsub("-","",c.item))) | |
| data.frame() | |
| } else { | |
| if(nchar(c.item)>0) { | |
| c.split<-strsplit(c.item,":")[[1]] | |
| data.frame(Category=cur.category, | |
| Option=get.clean(c.split[1]), | |
| Value=get.val(c.split)) | |
| } else { | |
| data.frame() | |
| } | |
| } | |
| }) | |
| o.df$Value<-as.character(o.df$Value) | |
| o.df$Option<-as.character(o.df$Option) | |
| o.df | |
| } | |
| parse.scan.info<-function(in.df) { | |
| o.val<-list() | |
| o.val$Darks<-as.numeric(subset(in.df,Category=="Scan Settings" & Option=="Number of darks")$Value) | |
| o.val$Flats<-as.numeric(subset(in.df,Category=="Scan Settings" & Option=="Number of flats")$Value) | |
| o.val$Projections<-as.numeric(subset(in.df,Category=="Scan Settings" & Option=="Number of projections")$Value) | |
| o.val | |
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| library(shiny) | |
| library(ggplot2) | |
| library(ggthemes) | |
| library(plyr) | |
| source('recoTools.R') | |
| shinyServer(function(input, output) { | |
| ## path code for selecting the current measurement | |
| root.dir<-reactive({ | |
| if(!exists("old.wd")) old.wd<-getwd() | |
| old.wd | |
| }) | |
| get.drives<-reactive({ | |
| drv.list<-sapply(Sys.glob(pa.paste(root.dir(),"*/")), | |
| pa.getlast) | |
| as.vector(drv.list) | |
| }) | |
| get.disks<-reactive({ | |
| as.vector(sapply(Sys.glob(pa.paste(root.dir(), | |
| get.or.blank(input$drive_selected,"*"), | |
| "*/")), | |
| pa.getlast)) | |
| }) | |
| get.samples<-reactive({ | |
| as.vector(sapply(Sys.glob(pa.paste(root.dir(), | |
| get.or.blank(input$drive_selected,"*"), | |
| get.or.blank(input$disk_selected,"*"), | |
| "*/")), | |
| pa.getlast)) | |
| }) | |
| output$drive_selector<-renderUI({ | |
| selectInput("drive_selected","Drive Name",get.drives()) | |
| }) | |
| output$disk_selector<-renderUI({ | |
| selectInput("disk_selected","Disk Name",get.disks()) | |
| }) | |
| output$sample_selector<-renderUI({ | |
| selectInput("sample_selected","Sample Name",get.samples()) | |
| }) | |
| get.disk.path<-reactive({ | |
| pa.paste(root.dir(), | |
| get.or.blank(input$drive_selected,"*"), | |
| get.or.blank(input$disk_selected,"*")) | |
| }) | |
| # reading the log information and projections | |
| get.sample.path<-reactive({ | |
| if(!is.null(input$sample_selected)) pa.paste(get.disk.path(), | |
| get.or.blank(input$sample_selected,"*")) | |
| else "" | |
| }) | |
| get.log.lines<-reactive({ | |
| log.name<-Sys.glob(pa.paste(get.sample.path(),"tif/*.log"))[1] | |
| print(log.name) | |
| log.file<-file(log.name,"r") | |
| out.lines<-readLines(log.file) | |
| close(log.file) | |
| parse.log.lines(out.lines) | |
| }) | |
| get.scan.info<-reactive({ | |
| parse.scan.info(get.log.lines()) | |
| }) | |
| get.projections<-reactive({ | |
| as.vector(sapply(Sys.glob(pa.paste(get.sample.path(),"tif/*.tif")),pa.getlast)) | |
| }) | |
| output$projection_selector<-renderUI({ | |
| if (length(get.projections())>1) { | |
| wellPanel(selectInput('projection_selected', 'Projections', get.projections()), | |
| sliderInput('drk_sel', 'Select Dark', min=1, max=get.scan.info()$Darks,value=1,round=0), | |
| sliderInput('flt_sel', 'Select Flat', min=1, max=get.scan.info()$Flats,value=1,round=0), | |
| sliderInput('prj_sel', 'Select Projection', min=1, max=get.scan.info()$Projections,value=1,round=0)) | |
| } else h3("No Projections for Current Sample") | |
| }) | |
| ## read projections, scale, and perform flat-field correction | |
| read.cur.prj<-reactive({ | |
| tif.file<-pa.paste(get.sample.path(),"tif", | |
| get.or.blank(input$projection_selected)) | |
| readTIFF(tif.file) | |
| }) | |
| get.flt.prj<-reactive({ | |
| "/Users/mader/Dropbox/WorkRelated/BeamlineTools/Data10/disk1/01_/tif/01_0044.tif" | |
| }) | |
| read.flt.prj<-reactive({ | |
| readTIFF(get.flt.prj()) | |
| }) | |
| get.cor.prj<-reactive({ | |
| if(get.or.blank(input$flatfield_correction,F)) read.flt.prj()/read.cur.prj() | |
| else read.cur.prj() | |
| }) | |
| output$prj_histogram<-renderPlot({ | |
| hist(get.cor.prj()) | |
| }) | |
| output$minmax_selector<-renderUI({ | |
| gvals<-as.vector(get.cor.prj()) | |
| if (length(gvals)>1) { | |
| wellPanel(sliderInput('prj_min_val', 'Minimum Value', | |
| min=min(gvals), max=max(gvals), | |
| value=min(gvals)), | |
| sliderInput('prj_max_val', 'Maximum Value', | |
| min=min(gvals), max=max(gvals), | |
| value=max(gvals)), | |
| h4(paste("Cur Position",input$previewClick$x,", y",input$previewClick$y))) | |
| } else h3("No Image Loaded") | |
| }) | |
| get.min<-reactive({ | |
| get.or.blank(input$prj_min_val,0.00) | |
| }) | |
| get.max<-reactive({ | |
| get.or.blank(input$prj_max_val,1) | |
| }) | |
| ## code for rendering the projection | |
| get.colors<-reactive({ | |
| if (input$use_color) rainbow(80) | |
| else gray((0:80)/80) | |
| }) | |
| output$prj_preview<-renderPlot({ | |
| c.img<-t(get.cor.prj()) | |
| x.vals<-c(1:nrow(c.img)) | |
| y.vals<-c(1:ncol(c.img)) | |
| if(input$prj_crop) { | |
| imagefn<-function(...) image(...,xlim=c(input$prj_crop_minx,input$prj_crop_maxx), | |
| ylim=c(input$prj_crop_miny,input$prj_crop_maxy),asp=0,axes=T) # no aspect ratio | |
| } | |
| else { | |
| imagefn<-function(...) image(...,asp=1,axes=F) | |
| } | |
| imagefn(x.vals,y.vals,c.img, | |
| zlim=c(get.min(),get.max()), | |
| useRaster=T,col=get.colors()) | |
| }) | |
| ## reconstruction previewing and such | |
| get.reconstructions<-reactive({ | |
| as.vector(sapply(Sys.glob(pa.paste(get.sample.path(),"rec*/")),pa.getlast)) | |
| }) | |
| get.reco.slices<-reactive({ | |
| as.vector(sapply(Sys.glob(pa.paste(get.sample.path(), | |
| get.or.blank(input$reconstruction_selected), | |
| "/*.*")),pa.getlast)) | |
| }) | |
| output$reconstruction_selector<-renderUI({ | |
| if (length(get.reconstructions())>1) { | |
| wellPanel(selectInput('reconstruction_selected', 'Reconstruction', get.reconstructions()), | |
| selectInput('slice_selected','Slice',get.reco.slices())) | |
| } else h3("No Reconstructions for Current Sample") | |
| }) | |
| ## code for previewing folders | |
| output$log_file<-renderDataTable({ | |
| o.df<-(get.log.lines()) | |
| o.df | |
| }) | |
| output$folder_contents<-renderDataTable({ | |
| if(nchar(get.sample.path()>0)) { | |
| all.subfiles<-Sys.glob(pa.paste(get.sample.path(),"*/*.*")) | |
| subfiles<-ldply(all.subfiles,function(filename) { | |
| data.frame(folder=pa.getlast(filename,1), | |
| ext=get.last(strsplit(pa.getlast(filename),"[.]")[[1]]), | |
| size=file.info(filename)$size) | |
| }) | |
| ddply(subfiles,.(folder),function(c.folder) { | |
| data.frame(files=nrow(c.folder), | |
| size_gb=sum(c.folder$size)/1e9, | |
| exts=paste(unique(c.folder$ext),collapse=",")) | |
| }) | |
| } | |
| }) | |
| output$disk_contents<-renderDataTable({ | |
| if(nchar(get.disk.path()>0)) { | |
| all.subfiles<-Sys.glob(pa.paste(get.disk.path(),"*/*/*.*")) | |
| subfiles<-ldply(all.subfiles,function(filename) { | |
| data.frame(folder=pa.getlast(filename,3), | |
| ext=get.last(strsplit(pa.getlast(filename),"[.]")[[1]]), | |
| size=file.info(filename)$size) | |
| }) | |
| ddply(subfiles,.(folder),function(c.folder) { | |
| data.frame(files=nrow(c.folder), | |
| size_gb=sum(c.folder$size)/1e9, | |
| exts=paste(unique(c.folder$ext),collapse=",")) | |
| }) | |
| } | |
| }) | |
| }) |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| library(shiny) | |
| library(ggplot2) | |
| shinyUI(pageWithSidebar( | |
| headerPanel("Beamline Tools"), | |
| sidebarPanel( | |
| uiOutput("drive_selector"), | |
| uiOutput("disk_selector"), | |
| uiOutput("sample_selector") | |
| ), | |
| mainPanel( | |
| tabsetPanel( | |
| tabPanel("Projection Viewer", | |
| checkboxInput("flatfield_correction","Perform flat-field correction",F), | |
| uiOutput('projection_selector'), | |
| plotOutput('prj_preview',clickId='previewClick',height="600px"), | |
| checkboxInput("use_color","Color Projection",F), | |
| checkboxInput("prj_crop","Crop Projection (Zoom)",F), | |
| conditionalPanel( | |
| condition = "input.prj_crop == true", | |
| sliderInput('prj_crop_minx', 'Min X', min=1, max=2560,value=1,round=0), | |
| sliderInput('prj_crop_maxx', 'Max X', min=1, max=2560,value=2560,round=0), | |
| sliderInput('prj_crop_miny', 'Min Y', min=1, max=2160,value=1,round=0), | |
| sliderInput('prj_crop_maxy', 'Min Y', min=1, max=2160,value=2160,round=0) | |
| ), | |
| uiOutput('minmax_selector'), | |
| plotOutput('prj_histogram') | |
| ), | |
| tabPanel("Reconstruction Viewer", | |
| uiOutput('reconstruction_selector'), | |
| plotOutput('rec_preview',clickId='recoClick',height="600px"), | |
| plotOutput('rec_histogram') | |
| ), | |
| tabPanel("Log File",dataTableOutput("log_file")), | |
| tabPanel("Folder Contents",dataTableOutput("folder_contents")), | |
| tabPanel("Disk Contents",dataTableOutput("disk_contents")) | |
| ) | |
| ) | |
| )) |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Rscript -e "library(shiny);old.wd<-getwd();runGist(7980071)"