Merge pull request #6 from CougPhenomics/fix-video-rootdir

find .here to establish root dir for paths. also define column types and label gifs with treatment

Author: dschneiderch

scripts/makeVideos.R

@@ -7,7 +7,7 @@
 
 # Get command line arguments
 args = commandArgs(trailingOnly = T)
-# args  = c('output/from_diy_data', 'diy_data')
+# args  = c('output/from_diy_data', 'diy_data/genotype_map.csv')
 
 # test if there are two arguments: if not, return an error
 if (length(args)<2) {
@@ -23,22 +23,24 @@ load_install = function(pkg){
 }
 
 # load all packages
-libs = c('magick','tidyverse','lubridate','av')
+libs = c('magick','tidyverse','lubridate','av','rprojroot')
 tmp = sapply(libs, FUN = load_install)
 
 
 # setup directories
+root = rprojroot::find_root('.here')
 datadir = args[1]
-indir = file.path(datadir, 'pseudocolor_images')
-outdir = file.path(datadir, 'timelapse')
+indir = file.path(root, datadir, 'pseudocolor_images')
+outdir = file.path(root, datadir, 'timelapse')
 dir.create(outdir, show = F, rec = T)
 
 # get genotype info
-gmap = read_csv(args[2])
+gmap = read_csv(file.path(root,args[2]))
 
 # get data processed
-output = read_csv(file.path(datadir,'output_psII_level0.csv')) %>% 
-  select(treatment, sampleid, roi, gtype)
+output = read_csv(file.path(root, datadir,'output_psII_level0.csv'),
+                  col_types = cols(treatment = col_character(), gtype = col_character())) %>% 
+  dplyr::select(treatment, sampleid, roi, gtype)
 
 # filter gmap for available output files
 gmap = inner_join(gmap, output) %>% distinct(treatment, sampleid, roi, gtype)
@@ -75,24 +77,26 @@ cntrl_ids = unique(gmap %>% filter(treatment == 'control') %>% pull(sampleid))
 l =  cross2(fluc_ids, cntrl_ids)
 
 # test values
-# sampleid0 = 'tray2'
-# sampleid1 = 'tray5'
+# sampleid_c = 'tray2'
+# sampleid_t = 'tray5'
 # parameter_string = 'FvFm_YII'#'FvFm_YII' #'t300_ALon_YII'
 # il = l[[1]]
 
 # define gif making function
 arrange_gif = function(il, parameter_string) {
   uil = unlist(il, rec = F)
-  sampleid1 = uil[1]
-  sampleid0 = uil[2]
-  print(paste(sampleid0, sampleid1, sep = ' x '))
+  sampleid_t = uil[1]
+  sampleid_c = uil[2]
+  gtype_treatment_label_t = get_treatment(sampleid_t)
+  print(paste(sampleid_c, sampleid_t, sep = ' x '))
+  print(gtype_treatment_label_t)
   print(parameter_string)
 
   # get images
-  fns0 = dir(file.path(indir, sampleid0),
+  fns0 = dir(file.path(indir, sampleid_c),
              pattern = parameter_string,
              full.names = T)
-  fns1 = dir(file.path(indir, sampleid1),
+  fns1 = dir(file.path(indir, sampleid_t),
              pattern = parameter_string,
              full.names = T)
 
@@ -110,8 +114,8 @@ arrange_gif = function(il, parameter_string) {
   fns1 <- fns1[elements1]
 
   # get genotypes
-  g0 = gmap %>% filter(sampleid == sampleid0) %>% pull(gtype)
-  g1 = gmap %>% filter(sampleid == sampleid1) %>% pull(gtype)
+  g0 = gmap %>% filter(sampleid == sampleid_c) %>% pull(gtype)
+  g1 = gmap %>% filter(sampleid == sampleid_t) %>% pull(gtype)
   # crossing(dtes0,dtes1) #TODO: filter dates and filenames for common dates
 
   stopifnot(all(dtes0 == dtes1))
@@ -123,7 +127,7 @@ arrange_gif = function(il, parameter_string) {
   # annotate with genotype
   imgs0a = image_annotate(
     imgs0,
-    get_treatment(sampleid0),
+    get_treatment(sampleid_c),
     size = 24,
     font = 'Arial',
     weight = 700,
@@ -144,7 +148,7 @@ arrange_gif = function(il, parameter_string) {
   )
 
   coords %>%
-    filter(sampleid == sampleid0) %>%
+    filter(sampleid == sampleid_c) %>%
     group_by(xpos, ypos, roi) %>%
     group_walk(
       keep = T,
@@ -178,7 +182,7 @@ arrange_gif = function(il, parameter_string) {
 
   imgs1a = image_annotate(
     imgs1,
-    get_treatment(sampleid1),
+    gtype_treatment_label_t,
     size = 24,
     font = 'Arial',
     weight = 700,
@@ -198,7 +202,7 @@ arrange_gif = function(il, parameter_string) {
   )
 
   coords %>%
-    filter(sampleid == sampleid1) %>%
+    filter(sampleid == sampleid_t) %>%
     group_by(xpos, ypos, roi) %>%
     group_walk(
       keep = T,
@@ -240,7 +244,8 @@ arrange_gif = function(il, parameter_string) {
     }
   }
   # newgif
-  outfn = paste0(parameter_string, '_', sampleid0, '_x_', sampleid1, '.gif')
+  treatmentlabel = strsplit(gtype_treatment_label_t,' ')[[1]][2]
+  outfn = paste0(parameter_string, '_', sampleid_c, '_x_', sampleid_t, '_',treatmentlabel,'.gif')
   image_write_video(newgif, file.path(outdir, outfn), framerate = 2)
   # image_write_gif(newgif,file.path(outdir, outfn), delay=0.5)
 }