From 05c60e0288f980b4d42106342834e6ad7a0b9576 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?hinzhao=28=E8=B5=B5=E8=BD=A9=29?= <hinzhao@tencent.com>
Date: Wed, 1 Sep 2021 10:36:50 +0800
Subject: [PATCH 1/7] fix the bug of calling vaa3d plugin

---
 shiny_app/server.R | 48 +++++++++++++++++++++++++++-------------------
 1 file changed, 28 insertions(+), 20 deletions(-)

diff --git a/shiny_app/server.R b/shiny_app/server.R
index 86c6824..ff52de6 100644
--- a/shiny_app/server.R
+++ b/shiny_app/server.R
@@ -79,30 +79,38 @@ shinyServer(function(input, output, session) {
       for(i in 1:length(inFile$datapath)){
         #Xvfb :100 -ac &
         #export DISPLAY=:100.0
-        log0 <- system('Xvfb :100 -ac & export DISPLAY=:100.0', intern=T)
-        output$console <- renderPrint({
-          return(print(log0))
-        })
+        # log0 <- system('Xvfb :100 -ac & export DISPLAY=:100.0', intern=T)
+        # output$console <- renderPrint({
+        #   return(print(log0))
+        # })
         # log0 <- system('xhost local:allencenter', intern=T)
         # output$console <- renderPrint({
         #   return(print(log0))
         # })
-        log0 <- system('ls', intern=T)
-        output$console <- renderPrint({
-          return(print(log0))
-        })
-        log <- system(paste0('Vaa3D/vaa3d -x blastneuron -f pre_processing -p "#i ',inFile$datapath[i],' #o "',inFile$datapath[i],'"_prep.swc #l 3 #s 2 #r 1"'),
-                      intern=T)
-        output$console <- renderPrint({
-          return(print(log))
-        })
-        pathswc <- data.frame(file=paste0("SWCFILE=",inFile$datapath[i],"_prep.swc"))
-        write.table(pathswc,file="mydatabase.ano",col.names=F,row.names=F,quote=F)
-        log2 <- system('Vaa3D/vaa3d -x blastneuron -f batch_compute -p \"#i mydatabase.ano #o features.csv"',
-                      intern=T)
+        # log0 <- system('ls', intern=T)
+        # output$console <- renderPrint({
+        #   return(print(log0))
+        # })
+        # log <- system(paste0('Vaa3D/vaa3d -x blastneuron -f pre_processing -p "#i ',inFile$datapath[i],' #o "',inFile$datapath[i],'"_prep.swc #l 3 #s 2 #r 1"'),
+        #               intern=T)
+        # output$console <- renderPrint({
+        #   return(print(log))
+        # })
+        # pathswc <- data.frame(file=paste0("SWCFILE=",inFile$datapath[i],"_prep.swc"))
+        # write.table(pathswc,file="mydatabase.ano",col.names=F,row.names=F,quote=F)
+        # log2 <- system('Vaa3D/vaa3d -x blastneuron -f batch_compute -p \"#i mydatabase.ano #o features.csv"',
+        #               intern=T)
         # output$console <- renderPrint({
         #   return(print(log2))
         # })
+
+        # zx output the system command to "tmp.txt" for debug 
+        sink("tmp.txt")
+        cat(paste0('export DISPLAY=:8463; Xvfb :8463 -auth /dev/null  > xvfblog.txt 2>&1 & Vaa3D/vaa3d -x blastneuron -f pre_processing -p "#i ',inFile$datapath[i],' #o ',inFile$datapath[i],'_prep.swc #l 3 #s 2 #r 1"; cat "SWCFILE=',inFile$datapath[i],'_prep.swc" > mydatabase.ano; Vaa3D/vaa3d -x blastneuron -f batch_compute -p "#i mydatabase.ano #o features.csv"; Vaa3D/vaa3d -x neuron_distance -f neuron_distance -i ',Sys.glob(file.path(paste0("gold_163_all_soma_sort_s1_onlyswc/",strsplit(inFile$name[i],"[.]")[[1]][1]), "*.swc")),' ',inFile$datapath[i],' -o dists/',i,'.txt -p 2'))
+        sink()
+        # zx merge all call system to one call
+        system(paste0('export DISPLAY=:8463; Xvfb :8463 -auth /dev/null  > xvfblog.txt 2>&1 & Vaa3D/vaa3d -x blastneuron -f pre_processing -p "#i ',inFile$datapath[i],' #o ',inFile$datapath[i],'_prep.swc #l 3 #s 2 #r 1"; echo "SWCFILE=',inFile$datapath[i],'_prep.swc" > mydatabase.ano; Vaa3D/vaa3d -x blastneuron -f batch_compute -p "#i mydatabase.ano #o features.csv"; Vaa3D/vaa3d -x /home/vaa3d/v3d_external/bin/plugins/neuron_utilities/neuron_distance/libneuron_dist.so -f neuron_distance -i ',Sys.glob(file.path(paste0("gold_163_all_soma_sort_s1_onlyswc/",strsplit(inFile$name[i],"[.]")[[1]][1]), "*.swc")),' ',inFile$datapath[i],' -o dists/',i,'.txt -p 2'))
+
         try(nbdata <-  read.csv("features.csv"))
         try(print(nbdata))
         nbdata <- nbdata[c(3:22,36)]
@@ -111,9 +119,9 @@ shinyServer(function(input, output, session) {
         # })
         
         # Add distance metrics
-        gspath <- Sys.glob(file.path(paste0("gold_163_all_soma_sort_s1_onlyswc/",strsplit(inFile$name[i],"[.]")[[1]][1]), "*.swc")) 
-        log3 <- system(paste0('Vaa3D/vaa3d -x neuron_distance -f neuron_distance -i ',gspath,' ',inFile$datapath[i],' -p 2 -o dists/',i,'.txt'),
-                       intern=T)
+        # gspath <- Sys.glob(file.path(paste0("gold_163_all_soma_sort_s1_onlyswc/",strsplit(inFile$name[i],"[.]")[[1]][1]), "*.swc")) 
+        # log3 <- system(paste0('Vaa3D/vaa3d -x neuron_distance -f neuron_distance -i ',gspath,' ',inFile$datapath[i],' -p 2 -o dists/',i,'.txt'),
+        #                intern=T)
         dataFile <- readLines(paste0("dists/",i,".txt"))
         
         dfdist <- data.frame(esa1t2=NA,esa2t1=NA,ab_esa=NA,dsa=NA,pds1t2=NA,pds2t1=NA,a_pds=NA)

From 9f7f7016413a06bf6bccb8156b89986b08075d08 Mon Sep 17 00:00:00 2001
From: ZX003 <1320435719@qq.com>
Date: Wed, 1 Sep 2021 12:27:52 +0800
Subject: [PATCH 2/7] fix the bug of call vaa3d plugin

---
 shiny_app/server.R | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/shiny_app/server.R b/shiny_app/server.R
index ff52de6..d51b887 100644
--- a/shiny_app/server.R
+++ b/shiny_app/server.R
@@ -109,8 +109,8 @@ shinyServer(function(input, output, session) {
         cat(paste0('export DISPLAY=:8463; Xvfb :8463 -auth /dev/null  > xvfblog.txt 2>&1 & Vaa3D/vaa3d -x blastneuron -f pre_processing -p "#i ',inFile$datapath[i],' #o ',inFile$datapath[i],'_prep.swc #l 3 #s 2 #r 1"; cat "SWCFILE=',inFile$datapath[i],'_prep.swc" > mydatabase.ano; Vaa3D/vaa3d -x blastneuron -f batch_compute -p "#i mydatabase.ano #o features.csv"; Vaa3D/vaa3d -x neuron_distance -f neuron_distance -i ',Sys.glob(file.path(paste0("gold_163_all_soma_sort_s1_onlyswc/",strsplit(inFile$name[i],"[.]")[[1]][1]), "*.swc")),' ',inFile$datapath[i],' -o dists/',i,'.txt -p 2'))
         sink()
         # zx merge all call system to one call
-        system(paste0('export DISPLAY=:8463; Xvfb :8463 -auth /dev/null  > xvfblog.txt 2>&1 & Vaa3D/vaa3d -x blastneuron -f pre_processing -p "#i ',inFile$datapath[i],' #o ',inFile$datapath[i],'_prep.swc #l 3 #s 2 #r 1"; echo "SWCFILE=',inFile$datapath[i],'_prep.swc" > mydatabase.ano; Vaa3D/vaa3d -x blastneuron -f batch_compute -p "#i mydatabase.ano #o features.csv"; Vaa3D/vaa3d -x /home/vaa3d/v3d_external/bin/plugins/neuron_utilities/neuron_distance/libneuron_dist.so -f neuron_distance -i ',Sys.glob(file.path(paste0("gold_163_all_soma_sort_s1_onlyswc/",strsplit(inFile$name[i],"[.]")[[1]][1]), "*.swc")),' ',inFile$datapath[i],' -o dists/',i,'.txt -p 2'))
-
+        # zx It seems that the dists folder cannot be written in shinyapp, so change path to i._dists_tmp.txt
+        system(paste0('export DISPLAY=:8463; Xvfb :8463 -auth /dev/null  > xvfblog.txt 2>&1 & Vaa3D/vaa3d -x blastneuron -f pre_processing -p "#i ',inFile$datapath[i],' #o ',inFile$datapath[i],'_prep.swc #l 3 #s 2 #r 1"; echo "SWCFILE=',inFile$datapath[i],'_prep.swc" > mydatabase.ano; Vaa3D/vaa3d -x blastneuron -f batch_compute -p "#i mydatabase.ano #o features.csv"; Vaa3D/vaa3d -x /home/vaa3d/v3d_external/bin/plugins/neuron_utilities/neuron_distance/libneuron_dist.so -f neuron_distance -i ',Sys.glob(file.path(paste0("gold_163_all_soma_sort_s1_onlyswc/",strsplit(inFile$name[i],"[.]")[[1]][1]), "*.swc")),' ',inFile$datapath[i],' -o ',i,'_dists_tmp.txt -p 2; echo test > dists/',i,'_dists_tmp.txt'))
         try(nbdata <-  read.csv("features.csv"))
         try(print(nbdata))
         nbdata <- nbdata[c(3:22,36)]
@@ -122,7 +122,9 @@ shinyServer(function(input, output, session) {
         # gspath <- Sys.glob(file.path(paste0("gold_163_all_soma_sort_s1_onlyswc/",strsplit(inFile$name[i],"[.]")[[1]][1]), "*.swc")) 
         # log3 <- system(paste0('Vaa3D/vaa3d -x neuron_distance -f neuron_distance -i ',gspath,' ',inFile$datapath[i],' -p 2 -o dists/',i,'.txt'),
         #                intern=T)
-        dataFile <- readLines(paste0("dists/",i,".txt"))
+        
+        #zx change path to i._dists_tmp.txt
+        dataFile <- readLines(paste0(i,"_dists_tmp.txt"))
         
         dfdist <- data.frame(esa1t2=NA,esa2t1=NA,ab_esa=NA,dsa=NA,pds1t2=NA,pds2t1=NA,a_pds=NA)
         dfdist$esa1t2 <- as.numeric(strsplit(dataFile[3],'=')[[1]][2])

From 56add68064b75d9bf99c3b2eeeedc09421049b8f Mon Sep 17 00:00:00 2001
From: ZX003 <1320435719@qq.com>
Date: Wed, 1 Sep 2021 20:24:19 +0800
Subject: [PATCH 3/7] merge main branch to docker branch

---
 shiny_app/server.R | 62 ++++++++++++++++++++++++++++++++++++++--------
 shiny_app/ui.R     |  8 ++++--
 2 files changed, 58 insertions(+), 12 deletions(-)

diff --git a/shiny_app/server.R b/shiny_app/server.R
index d51b887..d4588a5 100644
--- a/shiny_app/server.R
+++ b/shiny_app/server.R
@@ -75,8 +75,14 @@ shinyServer(function(input, output, session) {
     {
       # Run blastneuron for each uploaded reconstruction
       inFile <- input$file1
+
+      #zx linus changed
+      IQpaths <- inFile$datapath[grepl(".csv",inFile$datapath)]
+      SWCpaths <- inFile$datapath[grepl(".swc",inFile$datapath)]
+      SWCnames <- inFile$name[grepl(".swc",inFile$datapath)]
       
-      for(i in 1:length(inFile$datapath)){
+      #zx change inFile$datapath to SWCpaths
+      for(i in 1:length(SWCpaths)){
         #Xvfb :100 -ac &
         #export DISPLAY=:100.0
         # log0 <- system('Xvfb :100 -ac & export DISPLAY=:100.0', intern=T)
@@ -110,7 +116,7 @@ shinyServer(function(input, output, session) {
         sink()
         # zx merge all call system to one call
         # zx It seems that the dists folder cannot be written in shinyapp, so change path to i._dists_tmp.txt
-        system(paste0('export DISPLAY=:8463; Xvfb :8463 -auth /dev/null  > xvfblog.txt 2>&1 & Vaa3D/vaa3d -x blastneuron -f pre_processing -p "#i ',inFile$datapath[i],' #o ',inFile$datapath[i],'_prep.swc #l 3 #s 2 #r 1"; echo "SWCFILE=',inFile$datapath[i],'_prep.swc" > mydatabase.ano; Vaa3D/vaa3d -x blastneuron -f batch_compute -p "#i mydatabase.ano #o features.csv"; Vaa3D/vaa3d -x /home/vaa3d/v3d_external/bin/plugins/neuron_utilities/neuron_distance/libneuron_dist.so -f neuron_distance -i ',Sys.glob(file.path(paste0("gold_163_all_soma_sort_s1_onlyswc/",strsplit(inFile$name[i],"[.]")[[1]][1]), "*.swc")),' ',inFile$datapath[i],' -o ',i,'_dists_tmp.txt -p 2; echo test > dists/',i,'_dists_tmp.txt'))
+        system(paste0('export DISPLAY=:8463; Xvfb :8463 -auth /dev/null  > xvfblog.txt 2>&1 & Vaa3D/vaa3d -x blastneuron -f pre_processing -p "#i ',SWCpaths[i],' #o ',SWCpaths[i],'_prep.swc #l 3 #s 2 #r 1"; echo "SWCFILE=',SWCpaths[i],'_prep.swc" > mydatabase.ano; Vaa3D/vaa3d -x blastneuron -f batch_compute -p "#i mydatabase.ano #o features.csv"; Vaa3D/vaa3d -x /home/vaa3d/v3d_external/bin/plugins/neuron_utilities/neuron_distance/libneuron_dist.so -f neuron_distance -i ',Sys.glob(file.path(paste0("gold_163_all_soma_sort_s1_onlyswc/",strsplit(SWCnames[i],"[.]")[[1]][1]), "*.swc")),' ',SWCpaths[i],' -o ',i,'_dists_tmp.txt -p 2; echo test > dists/',i,'_dists_tmp.txt'))
         try(nbdata <-  read.csv("features.csv"))
         try(print(nbdata))
         nbdata <- nbdata[c(3:22,36)]
@@ -137,7 +143,29 @@ shinyServer(function(input, output, session) {
         
         # Add image metrics
         # which(ids=="5") this is index for data to get image metrics
-        dfim <- data[which(ids==strsplit(inFile$name[i],"[.]")[[1]][1])[1],29:43]
+
+        #zx change 43 to 60 because the column number of data and the column number of idata is different
+        #zx but I don't know if it is right
+        #dfim <- data[which(ids==strsplit(inFile$name[i],"[.]")[[1]][1])[1],29:60]
+
+        #zx linus here change to it
+        dfim <- data[which(ids==strsplit(SWCnames[i],"[.]")[[1]][1])[1],c(29:54)]
+
+        IQ <- read.csv(paste0(IQpaths[i]),header=T)
+        dfim$FocusScore_swc <- IQ$FocusScore
+        dfim$MADIntensity_swc <- IQ$MADIntensity
+        dfim$MaxIntensity_swc <- IQ$MaxIntensity
+        dfim$MeanIntensity_swc <- IQ$MeanIntensity
+        dfim$MedianIntensity_swc <- IQ$MedianIntensity
+        dfim$MinIntensity_swc <- IQ$MinIntensity
+        dfim$PercentMaximal_swc <- IQ$PercentMaximal
+        dfim$PercentMinimal_swc <- IQ$PercentMinimal
+        dfim$StdIntensity_swc <- IQ$StdIntensity
+        dfim$SNR_mean_swc <- IQ$SNR_mean
+        dfim$CNR_mean_swc <- IQ$CNR_mean
+        dfim$ThresholdOtsu_swc <- IQ$ThresholdOtsu
+        dfim$SNR_otsu_swc <- IQ$SNR_otsu
+        dfim$CNR_otsu_swc <- IQ$CNR_otsu
         
         # Add row to data for each uploaded reconstruction
         idata = c(as.numeric(nbdata),as.numeric(dfdist),as.numeric(dfim))
@@ -242,16 +270,30 @@ shinyServer(function(input, output, session) {
     {
       inFile <- input$file1
 
-      for(i in 1:length(inFile$datapath)){
+      #zx linus changed
+      SWCpaths <- inFile$datapath[grepl(".swc",inFile$datapath)]
+      SWCnames <- inFile$name[grepl(".swc",inFile$datapath)]
+
+      #zx change inFile$datapath to SWCpaths
+      for(i in 1:length(SWCpaths)){
         # Get dataset, and define group, algorithm and paths
-        idataset <- groupsdf[which(ids==strsplit(inFile$name[i],"[.]")[[1]][1])[1],1]
-        igroup <- input$inputalg
-        ialgorithm <- input$inputalg
-        ipaths <- paste0("/x/x/x/x/x/x/",strsplit(inFile$name[i],"[.]")[[1]][1])
-        iids <- strsplit(inFile$name[i],"[.]")[[1]][1]
+        # idataset <- groupsdf[which(ids==strsplit(inFile$name[i],"[.]")[[1]][1])[1],1]
+        # igroup <- input$inputalg
+        # ialgorithm <- input$inputalg
+        # ipaths <- paste0("/x/x/x/x/x/x/",strsplit(inFile$name[i],"[.]")[[1]][1])
+        # iids <- strsplit(inFile$name[i],"[.]")[[1]][1]
+        
+        #zx this sentence make igroupsdf to same column numbers with groupsdf 
+        igroupsdf <- groupsdf[1,]
+        igroupsdf$dataset <- groupsdf[which(ids==strsplit(SWCnames[i],"[.]")[[1]][1])[1],1]
+        igroupsdf$group <- input$inputalg
+        igroupsdf$algorithm <- input$inputalg
+        igroupsdf$paths <- paste0("/x/x/x/x/x/x/",strsplit(SWCnames[i],"[.]")[[1]][1])
+        igroupsdf$ids <- strsplit(SWCnames[i],"[.]")[[1]][1]
 
         # Merge with groupsdf data
-        igroupsdf <- data.frame(dataset=idataset,group=igroup,algorithm=ialgorithm,paths=ipaths,ids=iids)
+        #igroupsdf <- data.frame(dataset=idataset,group=igroup,algorithm=ialgorithm,paths=ipaths,ids=iids)
+        
         groupsdf <- rbind(groupsdf,igroupsdf)
       }
     }
diff --git a/shiny_app/ui.R b/shiny_app/ui.R
index 798527c..13958db 100644
--- a/shiny_app/ui.R
+++ b/shiny_app/ui.R
@@ -130,9 +130,13 @@ shinyUI(fluidPage(
           # Horizontal line ----
           tags$hr(),
           # Input: Select a file ----
-          fileInput("file1", "Choose SWC Files",
+
+          #zx linus changed
+          #fileInput("file1", "Choose SWC Files",
+          fileInput("file1", "Choose SWC and their associated IQ files",
               multiple = TRUE,
-              accept = c(".swc",".eswc"))),
+              #accept = c(".swc",".eswc"))),
+              accept = c(".swc",".eswc",".txt"))),
 
           # # Input: Checkbox 
           # checkboxGroupInput("variableinpdat", "Choose images of uploaded reconstructions","",selected="variableinpdat",inline=TRUE),

From 959792c6d0c2312de2cafff7b3dc26de5cf53bc7 Mon Sep 17 00:00:00 2001
From: ZX003 <1320435719@qq.com>
Date: Thu, 2 Sep 2021 09:57:16 +0800
Subject: [PATCH 4/7] change txt to csv in ui.R and delete the vaa3d plugin
 output files

---
 shiny_app/server.R | 22 +++++++++++++---------
 shiny_app/ui.R     |  3 ++-
 2 files changed, 15 insertions(+), 10 deletions(-)

diff --git a/shiny_app/server.R b/shiny_app/server.R
index d4588a5..4eb655a 100644
--- a/shiny_app/server.R
+++ b/shiny_app/server.R
@@ -111,9 +111,10 @@ shinyServer(function(input, output, session) {
         # })
 
         # zx output the system command to "tmp.txt" for debug 
-        sink("tmp.txt")
-        cat(paste0('export DISPLAY=:8463; Xvfb :8463 -auth /dev/null  > xvfblog.txt 2>&1 & Vaa3D/vaa3d -x blastneuron -f pre_processing -p "#i ',inFile$datapath[i],' #o ',inFile$datapath[i],'_prep.swc #l 3 #s 2 #r 1"; cat "SWCFILE=',inFile$datapath[i],'_prep.swc" > mydatabase.ano; Vaa3D/vaa3d -x blastneuron -f batch_compute -p "#i mydatabase.ano #o features.csv"; Vaa3D/vaa3d -x neuron_distance -f neuron_distance -i ',Sys.glob(file.path(paste0("gold_163_all_soma_sort_s1_onlyswc/",strsplit(inFile$name[i],"[.]")[[1]][1]), "*.swc")),' ',inFile$datapath[i],' -o dists/',i,'.txt -p 2'))
-        sink()
+        # sink("tmp.txt")
+        # cat(paste0('export DISPLAY=:8463; Xvfb :8463 -auth /dev/null  > xvfblog.txt 2>&1 & Vaa3D/vaa3d -x blastneuron -f pre_processing -p "#i ',inFile$datapath[i],' #o ',inFile$datapath[i],'_prep.swc #l 3 #s 2 #r 1"; cat "SWCFILE=',inFile$datapath[i],'_prep.swc" > mydatabase.ano; Vaa3D/vaa3d -x blastneuron -f batch_compute -p "#i mydatabase.ano #o features.csv"; Vaa3D/vaa3d -x neuron_distance -f neuron_distance -i ',Sys.glob(file.path(paste0("gold_163_all_soma_sort_s1_onlyswc/",strsplit(inFile$name[i],"[.]")[[1]][1]), "*.swc")),' ',inFile$datapath[i],' -o dists/',i,'.txt -p 2'))
+        # sink()
+        
         # zx merge all call system to one call
         # zx It seems that the dists folder cannot be written in shinyapp, so change path to i._dists_tmp.txt
         system(paste0('export DISPLAY=:8463; Xvfb :8463 -auth /dev/null  > xvfblog.txt 2>&1 & Vaa3D/vaa3d -x blastneuron -f pre_processing -p "#i ',SWCpaths[i],' #o ',SWCpaths[i],'_prep.swc #l 3 #s 2 #r 1"; echo "SWCFILE=',SWCpaths[i],'_prep.swc" > mydatabase.ano; Vaa3D/vaa3d -x blastneuron -f batch_compute -p "#i mydatabase.ano #o features.csv"; Vaa3D/vaa3d -x /home/vaa3d/v3d_external/bin/plugins/neuron_utilities/neuron_distance/libneuron_dist.so -f neuron_distance -i ',Sys.glob(file.path(paste0("gold_163_all_soma_sort_s1_onlyswc/",strsplit(SWCnames[i],"[.]")[[1]][1]), "*.swc")),' ',SWCpaths[i],' -o ',i,'_dists_tmp.txt -p 2; echo test > dists/',i,'_dists_tmp.txt'))
@@ -171,13 +172,16 @@ shinyServer(function(input, output, session) {
         idata = c(as.numeric(nbdata),as.numeric(dfdist),as.numeric(dfim))
         data <- rbind(data,idata)
         
+        #zx remove vaa3d plugins output files
+        system("rm *_dists_tmp.txt features.csv mydatabase.ano") 
+
         # Remove remote files
-        system("rm dists/*",
-               intern=T)
-        system("rm features.csv",
-               intern=T)
-        system("rm mydatabase.ano",
-               intern=T)
+        # system("rm dists/*",
+        #        intern=T)
+        # system("rm features.csv",
+        #        intern=T)
+        # system("rm mydatabase.ano",
+        #        intern=T)
       }
       
     }
diff --git a/shiny_app/ui.R b/shiny_app/ui.R
index 13958db..bb29136 100644
--- a/shiny_app/ui.R
+++ b/shiny_app/ui.R
@@ -136,7 +136,8 @@ shinyUI(fluidPage(
           fileInput("file1", "Choose SWC and their associated IQ files",
               multiple = TRUE,
               #accept = c(".swc",".eswc"))),
-              accept = c(".swc",".eswc",".txt"))),
+              #zx change .txt to .csv
+              accept = c(".swc",".eswc",".csv"))),
 
           # # Input: Checkbox 
           # checkboxGroupInput("variableinpdat", "Choose images of uploaded reconstructions","",selected="variableinpdat",inline=TRUE),

From c43846fe5fd7e67293cd5c3ad895779a55924837 Mon Sep 17 00:00:00 2001
From: ZX003 <1320435719@qq.com>
Date: Thu, 12 May 2022 08:55:48 +0800
Subject: [PATCH 5/7] fix upload

---
 shiny_app/server.R | 2 +-
 shiny_app/ui.R     | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/shiny_app/server.R b/shiny_app/server.R
index 4eb655a..0779fb9 100644
--- a/shiny_app/server.R
+++ b/shiny_app/server.R
@@ -117,7 +117,7 @@ shinyServer(function(input, output, session) {
         
         # zx merge all call system to one call
         # zx It seems that the dists folder cannot be written in shinyapp, so change path to i._dists_tmp.txt
-        system(paste0('export DISPLAY=:8463; Xvfb :8463 -auth /dev/null  > xvfblog.txt 2>&1 & Vaa3D/vaa3d -x blastneuron -f pre_processing -p "#i ',SWCpaths[i],' #o ',SWCpaths[i],'_prep.swc #l 3 #s 2 #r 1"; echo "SWCFILE=',SWCpaths[i],'_prep.swc" > mydatabase.ano; Vaa3D/vaa3d -x blastneuron -f batch_compute -p "#i mydatabase.ano #o features.csv"; Vaa3D/vaa3d -x /home/vaa3d/v3d_external/bin/plugins/neuron_utilities/neuron_distance/libneuron_dist.so -f neuron_distance -i ',Sys.glob(file.path(paste0("gold_163_all_soma_sort_s1_onlyswc/",strsplit(SWCnames[i],"[.]")[[1]][1]), "*.swc")),' ',SWCpaths[i],' -o ',i,'_dists_tmp.txt -p 2; echo test > dists/',i,'_dists_tmp.txt'))
+        system(paste0('export DISPLAY=:8463; Xvfb :8463 -auth /dev/null  > xvfblog.txt 2>&1 & Vaa3D/vaa3d -x blastneuron -f pre_processing -p "#i ',SWCpaths[i],' #o ',SWCpaths[i],'_prep.swc #l 3 #s 2 #r 1"; echo "SWCFILE=',SWCpaths[i],'_prep.swc" > mydatabase.ano; Vaa3D/vaa3d -x blastneuron -f batch_compute -p "#i mydatabase.ano #o features.csv"; Vaa3D/vaa3d -x /home/vaa3d/v3d_external/bin/plugins/neuron_utilities/neuron_distance/libneuron_dist.so -f neuron_distance -i ',Sys.glob(file.path(paste0("gold_163_all_soma_sort_s1_onlyswc/",strsplit(SWCnames[i],"[.]")[[1]][1]), "*.swc")),' ',SWCpaths[i],' -o ',i,'_dists_tmp.txt -p 2'))
         try(nbdata <-  read.csv("features.csv"))
         try(print(nbdata))
         nbdata <- nbdata[c(3:22,36)]
diff --git a/shiny_app/ui.R b/shiny_app/ui.R
index bb29136..a4cfd23 100644
--- a/shiny_app/ui.R
+++ b/shiny_app/ui.R
@@ -136,8 +136,8 @@ shinyUI(fluidPage(
           fileInput("file1", "Choose SWC and their associated IQ files",
               multiple = TRUE,
               #accept = c(".swc",".eswc"))),
-              #zx change .txt to .csv
-              accept = c(".swc",".eswc",".csv"))),
+              #zx add .csv
+              accept = c(".swc",".eswc",".txt",".csv"))),
 
           # # Input: Checkbox 
           # checkboxGroupInput("variableinpdat", "Choose images of uploaded reconstructions","",selected="variableinpdat",inline=TRUE),

From 4c7a9f3c15d0da299e8b453df729f33e840eed75 Mon Sep 17 00:00:00 2001
From: ZX003 <1320435719@qq.com>
Date: Thu, 12 May 2022 09:20:51 +0800
Subject: [PATCH 6/7] merger file

---
 shiny_app/server.R | 23 -----------------------
 1 file changed, 23 deletions(-)

diff --git a/shiny_app/server.R b/shiny_app/server.R
index 6cead0b..b3b46af 100644
--- a/shiny_app/server.R
+++ b/shiny_app/server.R
@@ -291,27 +291,9 @@ shinyServer(function(input, output, session) {
       SWCpaths <- inFile$datapath[grepl(".swc",inFile$datapath)]
       SWCnames <- inFile$name[grepl(".swc",inFile$datapath)]
 
-<<<<<<< HEAD
-      #zx linus changed
-      SWCpaths <- inFile$datapath[grepl(".swc",inFile$datapath)]
-      SWCnames <- inFile$name[grepl(".swc",inFile$datapath)]
-
-      #zx change inFile$datapath to SWCpaths
-      for(i in 1:length(SWCpaths)){
-        # Get dataset, and define group, algorithm and paths
-        # idataset <- groupsdf[which(ids==strsplit(inFile$name[i],"[.]")[[1]][1])[1],1]
-        # igroup <- input$inputalg
-        # ialgorithm <- input$inputalg
-        # ipaths <- paste0("/x/x/x/x/x/x/",strsplit(inFile$name[i],"[.]")[[1]][1])
-        # iids <- strsplit(inFile$name[i],"[.]")[[1]][1]
-        
-        #zx this sentence make igroupsdf to same column numbers with groupsdf 
-        igroupsdf <- groupsdf[1,]
-=======
       for(i in 1:length(SWCpaths)){
         igroupsdf <- groupsdf[1,]
         # Get dataset, and define group, algorithm and paths
->>>>>>> origin/main
         igroupsdf$dataset <- groupsdf[which(ids==strsplit(SWCnames[i],"[.]")[[1]][1])[1],1]
         igroupsdf$group <- input$inputalg
         igroupsdf$algorithm <- input$inputalg
@@ -319,14 +301,9 @@ shinyServer(function(input, output, session) {
         igroupsdf$ids <- strsplit(SWCnames[i],"[.]")[[1]][1]
 
         # Merge with groupsdf data
-<<<<<<< HEAD
-        #igroupsdf <- data.frame(dataset=idataset,group=igroup,algorithm=ialgorithm,paths=ipaths,ids=iids)
-        
-=======
         # igroupsdf <- data.frame(dataset=idataset,group=igroup,algorithm=ialgorithm,paths=ipaths,ids=iids)
         # print(names(groupsdf))
         # print(names(igroupsdf))
->>>>>>> origin/main
         groupsdf <- rbind(groupsdf,igroupsdf)
       }
     }

From cae55c119ae87ed61843a5f98213ab5e046f5e98 Mon Sep 17 00:00:00 2001
From: ZX003 <1320435719@qq.com>
Date: Fri, 13 May 2022 15:37:19 +0800
Subject: [PATCH 7/7] change neuron_distance

---
 shiny_app/server.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/shiny_app/server.R b/shiny_app/server.R
index b3b46af..b7b8377 100644
--- a/shiny_app/server.R
+++ b/shiny_app/server.R
@@ -123,7 +123,7 @@ shinyServer(function(input, output, session) {
         #})
         # zx merge all call system to one call
         # zx It seems that the dists folder cannot be written in shinyapp, so change path to i._dists_tmp.txt
-        system(paste0('export DISPLAY=:8463; Xvfb :8463 -auth /dev/null  > xvfblog.txt 2>&1 & Vaa3D/vaa3d -x blastneuron -f pre_processing -p "#i ',SWCpaths[i],' #o ',SWCpaths[i],'_prep.swc #l 3 #s 2 #r 1"; echo "SWCFILE=',SWCpaths[i],'_prep.swc" > mydatabase.ano; Vaa3D/vaa3d -x blastneuron -f batch_compute -p "#i mydatabase.ano #o features.csv"; Vaa3D/vaa3d -x /home/vaa3d/v3d_external/bin/plugins/neuron_utilities/neuron_distance/libneuron_dist.so -f neuron_distance -i ',Sys.glob(file.path(paste0("gold_163_all_soma_sort_s1_onlyswc/",strsplit(SWCnames[i],"[.]")[[1]][1]), "*.swc")),' ',SWCpaths[i],' -o ',i,'_dists_tmp.txt -p 2'))
+        system(paste0('export DISPLAY=:8463; Xvfb :8463 -auth /dev/null  > xvfblog.txt 2>&1 & Vaa3D/vaa3d -x blastneuron -f pre_processing -p "#i ',SWCpaths[i],' #o ',SWCpaths[i],'_prep.swc #l 3 #s 2 #r 1"; echo "SWCFILE=',SWCpaths[i],'_prep.swc" > mydatabase.ano; Vaa3D/vaa3d -x blastneuron -f batch_compute -p "#i mydatabase.ano #o features.csv"; Vaa3D/vaa3d -x neuron_distance -f neuron_distance -i ',Sys.glob(file.path(paste0("gold_163_all_soma_sort_s1_onlyswc/",strsplit(SWCnames[i],"[.]")[[1]][1]), "*.swc")),' ',SWCpaths[i],' -o ',i,'_dists_tmp.txt -p 2'))
         try(nbdata <-  read.csv("features.csv"))
         try(print(nbdata))
         nbdata <- nbdata[c(3:22,36)]