diff options
Diffstat (limited to 'inst/GUI/gmkin.R')
| -rw-r--r-- | inst/GUI/gmkin.R | 220 |
1 files changed, 161 insertions, 59 deletions
diff --git a/inst/GUI/gmkin.R b/inst/GUI/gmkin.R index 4d33b35a..7588183b 100644 --- a/inst/GUI/gmkin.R +++ b/inst/GUI/gmkin.R @@ -23,9 +23,9 @@ require(mkin) # {{{1 # Set the GUI title and create the basic widget layout {{{1
w <- gwindow("gmkin - Browser based GUI for kinetic evaluations using mkin")
sb <- gstatusbar(paste("Powered by gWidgetsWWW2, ExtJS, Rook, FME, deSolve and minpack.lm --- Working directory is", getwd()), cont = w)
-pg <- gpanedgroup(cont = w, default.size = 300)
+pg <- gpanedgroup(cont = w, default.size = 260)
center <- gnotebook(cont = pg)
-left <- gvbox(cont = pg)
+left <- gvbox(cont = pg, use.scrollwindow = TRUE)
# Helper functions {{{1
# Override function for making it possible to override original data in the GUI {{{2
override <- function(d) {
@@ -122,6 +122,8 @@ update_f.df <- function() { ftmp <- f[[fit.index]]
f.df[f.count, ] <<- c(as.character(f.count), ftmp$ds.index, ftmp$mkinmod$name)
}
+ delete(f.gg.buttons, get.initials.gc)
+ get.initials.gc <<- gcombobox(paste("Fit", f.df$Fit), cont = f.gg.buttons)
}
f.df.empty <- f.df <- data.frame(Fit = "0",
Dataset = "",
@@ -137,10 +139,10 @@ upload_file_handler <- function(h, ...) project_file <<- pr.gf$filename
project_name <<- try(load(tmpfile))
if (inherits(project_name, "try-error")) {
- galert(paste("Failed to load", project_file, "from", getwd()), parent = w)
+ galert(paste("Failed to load", project_file), parent = w)
}
- svalue(sb) <- paste("Loaded project file", project_file, "from working directory", getwd())
+ svalue(sb) <- paste("Loaded project file", project_file)
svalue(pr.ge) <- project_name
workspace <- get(project_name)
@@ -208,7 +210,7 @@ change_project_name_handler = function(h, ...) { # Project data management GUI elements {{{2
pr.gf <- gfile(text = "Select project file", cont = prg,
handler = upload_file_handler)
-pr.ge <- gedit(project_name, cont = prg, label = "Project", width = 240,
+pr.ge <- gedit(project_name, cont = prg, label = "Project",
handler = change_project_name_handler)
# The save button is always visible {{{1
gbutton("Save current project contents", cont = left,
@@ -223,9 +225,9 @@ update_study_selector <- function(h, ...) { svalue(ds.study.gc, index = TRUE) <- ds[[ds.cur]]$study_nr
}
studies.gdf <- gdf(studies.df, name = "Edit studies in the project",
- width = 290, height = 200, cont = stg)
+ width = 235,
+ height = 180, cont = stg)
studies.gdf$set_column_width(1, 40)
-studies.gdf$set_column_width(2, 240)
addHandlerChanged(studies.gdf, update_study_selector)
# Datasets and models {{{1
dsm <- gframe("Datasets and models", cont = left, horizontal = FALSE)
@@ -235,9 +237,9 @@ ds.switcher <- function(h, ...) { update_ds_editor()
svalue(center) <- 1
}
-ds.gtable <- gtable(ds.df, width = 290, cont = dsm)
+ds.gtable <- gtable(ds.df, cont = dsm)
addHandlerDoubleClick(ds.gtable, ds.switcher)
-size(ds.gtable) <- list(columnWidths = c(40, 200, 40))
+size(ds.gtable) <- list(columnWidths = c(40, 150, 30))
ds.gtable$value <- 1
# Model table with handler {{{2
@@ -246,9 +248,9 @@ m.switcher <- function(h, ...) { update_m_editor()
svalue(center) <- 2
}
-m.gtable <- gtable(m.df, width = 290, cont = dsm)
+m.gtable <- gtable(m.df, cont = dsm)
addHandlerDoubleClick(m.gtable, m.switcher)
-size(m.gtable) <- list(columnWidths = c(40, 240))
+m.gtable$set_column_width(1, 40)
m.gtable$value <- 1
# Button for setting up a fit for the selected dataset and model
@@ -278,7 +280,10 @@ gbutton("Configure fit for selected model and dataset", cont = dsm, f.gg.po.obssel <<- gcheckboxgroup(names(ftmp$mkinmod$spec), cont = f.gg.plotopts,
checked = TRUE)
show_plot("Initial", default = TRUE)
+ oldwidth <<- options()$width
+ options(width = 90)
svalue(f.gg.summary) <- c("<pre>", capture.output(stmp), "</pre>")
+ options(width = oldwidth)
svalue(center) <- 3
})
@@ -295,13 +300,14 @@ f.switcher <- function(h, ...) { }
svalue(center) <- 3
}
-f.gtable <- gtable(f.df, width = 290, cont = f.gf)
+f.gtable <- gtable(f.df, cont = f.gf)
addHandlerDoubleClick(f.gtable, f.switcher)
-size(f.gtable) <- list(columnWidths = c(40, 60, 180))
+f.gtable$set_column_width(1, 40)
+f.gtable$set_column_width(2, 60)
# Dataset editor {{{1
ds.editor <- gframe("Dataset 1", horizontal = FALSE, cont = center, label = "Dataset editor")
-# Handler functions {{{3
+# # Handler functions {{{3
copy_dataset_handler <- function(h, ...) {
ds.old <- ds.cur
ds.cur <<- as.character(1 + length(ds))
@@ -344,10 +350,40 @@ new_dataset_handler <- function(h, ...) { update_ds_editor()
}
+load_text_file_with_data <- function(h, ...) {
+ tmptextfile <<- normalizePath(svalue(h$obj), winslash = "/")
+ tmptext <- readLines(tmptextfile, warn = FALSE)
+ tmptextskip <<- 0
+ for (tmptextline in tmptext) {
+ if (grepl(":|#|/", tmptextline)) tmptextskip <<- tmptextskip + 1
+ else break()
+ }
+ svalue(ds.e.up.skip) <- tmptextskip
+ if (svalue(ds.e.up.header)) {
+ tmptextheader <<- strsplit(tmptext[tmptextskip + 1],
+ " |\t|;|,")[[1]]
+ }
+ svalue(ds.e.up.wide.time) <- tmptextheader[[1]]
+ svalue(ds.e.up.long.time) <- tmptextheader[[2]]
+ svalue(ds.e.up.text) <- c("<pre>", tmptext, "</pre>")
+ svalue(ds.e.stack) <- 2
+}
+
new_ds_from_csv_handler <- function(h, ...) {
- tmpfile <- normalizePath(svalue(h$obj), winslash = "/")
- tmpd <- try(read.table(tmpfile, sep = "\t", header = TRUE, stringsAsFactors = FALSE))
- tmpdw <- mkin_wide_to_long(tmpd)
+ tmpd <- try(read.table(tmptextfile,
+ skip = as.numeric(svalue(ds.e.up.skip)),
+ dec = svalue(ds.e.up.dec),
+ sep = switch(svalue(ds.e.up.sep),
+ whitespace = "",
+ ";" = ";",
+ "," = ","),
+ header = svalue(ds.e.up.header),
+ stringsAsFactors = FALSE))
+ if(svalue(ds.e.up.widelong) == "wide") {
+ tmpdl <- mkin_wide_to_long(tmpd, time = as.character(svalue(ds.e.up.wide.time)))
+ } else {
+ tmpdl <- tmpd
+ }
if (class(tmpd) != "try-error") {
ds.cur <<- as.character(1 + length(ds))
ds[[ds.cur]] <<- list(
@@ -355,13 +391,13 @@ new_ds_from_csv_handler <- function(h, ...) { title = "New upload",
sampling_times = sort(unique(tmpd$t)),
time_unit = "",
- observed = unique(tmpdw$name),
+ observed = unique(tmpdl$name),
unit = "",
- replicates = max(aggregate(tmpdw$time,
- list(tmpdw$time,
- tmpdw$name),
+ replicates = max(aggregate(tmpdl$time,
+ list(tmpdl$time,
+ tmpdl$name),
length)$x),
- data = tmpdw)
+ data = tmpdl)
ds[[ds.cur]]$data$override <<- as.numeric(NA)
ds[[ds.cur]]$data$err <<- 1
update_ds.df()
@@ -371,7 +407,7 @@ new_ds_from_csv_handler <- function(h, ...) { galert("Uploading failed", parent = "w")
}
}
-
+
empty_grid_handler <- function(h, ...) {
obs <- strsplit(svalue(ds.e.obs), ", ")[[1]]
sampling_times <- strsplit(svalue(ds.e.st), ", ")[[1]]
@@ -402,6 +438,7 @@ keep_ds_changes_handler <- function(h, ...) { list(tmpd$time, tmpd$name), length)$x)
update_ds_editor()
observed.all <<- union(observed.all, ds[[ds.cur]]$observed)
+ update_m_editor()
}
# Widget setup {{{3
@@ -420,13 +457,18 @@ gbutton("Delete dataset", cont = ds.e.2a, handler = delete_dataset_handler) gbutton("New dataset", cont = ds.e.2a, handler = new_dataset_handler)
ds.e.2b <- ggroup(cont = ds.e.2)
+tmptextfile <- "" # Initialize file name for imported data
+tmptextskip <- 0 # Initialize number of lines to be skipped
+tmptexttime <- "V1" # Initialize name of time variable if no header row
upload_dataset.gf <- gfile(text = "Upload text file", cont = ds.e.2b,
- handler = new_ds_from_csv_handler)
+ handler = load_text_file_with_data)
gbutton("Keep changes", cont = ds.e.2, handler = keep_ds_changes_handler)
-# Line 3 with forms {{{4
-ds.e.forms <- ggroup(cont= ds.editor, horizontal = TRUE)
+# Line 3 with forms or upload area {{{4
+ds.e.stack <- gstackwidget(cont = ds.editor)
+# Forms for meta data {{{5
+ds.e.forms <- ggroup(cont = ds.e.stack, horizontal = TRUE)
ds.e.3a <- gvbox(cont = ds.e.forms)
ds.e.3a.gfl <- gformlayout(cont = ds.e.3a)
@@ -452,6 +494,36 @@ ds.e.obu <- gedit(ds[[ds.cur]]$unit, generate_grid.gb <- gbutton("Generate empty grid for kinetic data", cont = ds.e.3b,
handler = empty_grid_handler)
tooltip(generate_grid.gb) <- "Overwrites the kinetic data shown below"
+# Data upload area {{{5
+ds.e.upload <- ggroup(cont = ds.e.stack, horizontal = TRUE)
+ds.e.up.text <- ghtml("<pre></pre>", cont = ds.e.upload, width = 400, height = 400)
+ds.e.up.options <- ggroup(cont = ds.e.upload, horizontal = FALSE)
+ds.e.up.import <- gbutton("Import using options specified below", cont = ds.e.up.options,
+ handler = new_ds_from_csv_handler)
+ds.e.up.skip <- gedit(tmptextskip, label = "Comment lines", cont = ds.e.up.options)
+ds.e.up.header <- gcheckbox(cont = ds.e.up.options, label = "Column names",
+ checked = TRUE)
+ds.e.up.sep <- gcombobox(c("whitespace", ";", ","), cont = ds.e.up.options,
+ selected = 1, label = "Separator")
+ds.e.up.dec <- gcombobox(c(".", ","), cont = ds.e.up.options,
+ selected = 1, label = "Decimal")
+ds.e.up.widelong <- gradio(c("wide", "long"), horizontal = TRUE,
+ label = "Format", cont = ds.e.up.options,
+ handler = function(h, ...) {
+ widelong = svalue(h$obj, index = TRUE)
+ svalue(ds.e.up.wlstack) <- widelong
+ })
+ds.e.up.wlstack <- gstackwidget(cont = ds.e.up.options)
+ds.e.up.wide <- ggroup(cont = ds.e.up.wlstack, horizontal = FALSE, width = 300)
+ds.e.up.wide.time <- gedit(tmptexttime, cont = ds.e.up.wide, label = "Time column")
+ds.e.up.long <- ggroup(cont = ds.e.up.wlstack, horizontal = FALSE, width = 300)
+ds.e.up.long.name <- gedit("name", cont = ds.e.up.long, label = "Observed variables")
+ds.e.up.long.time <- gedit(tmptexttime, cont = ds.e.up.long, label = "Time column")
+ds.e.up.long.value <- gedit("value", cont = ds.e.up.long, label = "Value column")
+ds.e.up.long.err <- gedit("err", cont = ds.e.up.long, label = "Relative errors")
+svalue(ds.e.up.wlstack) <- 1
+
+svalue(ds.e.stack) <- 1
# Kinetic Data {{{4
@@ -470,7 +542,7 @@ update_ds_editor <- function() { svalue(ds.e.obs) <- paste(ds[[ds.cur]]$observed, collapse = ", ")
svalue(ds.e.obu) <- ds[[ds.cur]]$unit
svalue(ds.e.rep) <- ds[[ds.cur]]$replicates
-
+ svalue(ds.e.stack) <- 1
ds.e.gdf[,] <- ds[[ds.cur]]$data
}
# Model editor {{{1
@@ -604,8 +676,10 @@ show_plot <- function(type, default = FALSE) { if (type == "Initial" & default == FALSE) {
ftmp <<- suppressWarnings(mkinfit(ftmp$mkinmod,
override(ds[[ds.i]]$data),
- state.ini = stateparms,
parms.ini = deparms,
+ state.ini = stateparms,
+ fixed_parms = names(deparms),
+ fixed_initials = names(stateparms),
err = "err",
control.modFit = list(maxiter = 0)))
ftmp$ds.index <<- ds.i
@@ -659,6 +733,8 @@ run_fit <- function() { solution_type = svalue(f.gg.opts.st),
atol = as.numeric(svalue(f.gg.opts.atol)),
rtol = as.numeric(svalue(f.gg.opts.rtol)),
+ transform_rates = svalue(f.gg.opts.transform_rates),
+ transform_fractions = svalue(f.gg.opts.transform_fractions),
weight = weight,
err = err,
reweight.method = reweight.method,
@@ -697,7 +773,7 @@ plot_ftmp_png <- function() { } else {
obs_vars_plot = names(ftmp$mkinmod$spec)
}
- png(tf, width = 525, height = 600)
+ png(tf, width = 400, height = 500)
plot(ftmp, main = ftmp$ds$title, obs_vars = obs_vars_plot,
xlab = ifelse(ftmp$ds$time_unit == "", "Time",
paste("Time in", ftmp$ds$time_unit)),
@@ -708,20 +784,17 @@ plot_ftmp_png <- function() { return(tf)
}
-plot.gi <- gimage(plot_ftmp_png(), container = pf, width = 525, height = 600)
+plot.gi <- gimage(plot_ftmp_png(), container = pf, width = 400, height = 500)
# Buttons and notebook area to the left {{{3
p.gg <- ggroup(cont = pf, horizontal = FALSE)
# Row with buttons {{{4
f.gg.buttons <- ggroup(cont = p.gg)
-show.initial.gb <- gbutton("Show initial",
- handler = function(h, ...) show_plot("Initial"),
- cont = f.gg.buttons)
-tooltip(show.initial.gb) <- "Show model with current inital settings for current dataset"
-run.fit.gb <- gbutton("Run",
+run.fit.gb <- gbutton("Run", width = 100,
handler = function(h, ...) run_fit(), cont =
f.gg.buttons)
tooltip(run.fit.gb) <- "Fit with current settings on the current dataset, with the original model"
+
keep.fit.gb <- gbutton("Keep",
handler = function(h, ...) {
f.cur <<- as.character(length(f) + 1)
@@ -732,12 +805,53 @@ keep.fit.gb <- gbutton("Keep", }, cont = f.gg.buttons)
tooltip(keep.fit.gb) <- "Store the optimised model with all settings and the current dataset in the fit list"
+delete.fit.gb <- gbutton("Delete fit", handler = function(h, ...) {
+ if (length(f) > 0) {
+ f[[f.cur]] <<- NULL
+ s[[f.cur]] <<- NULL
+ }
+ if (length(f) > 0) {
+ names(f) <<- as.character(1:length(f))
+ names(s) <<- as.character(1:length(f))
+ update_f.df()
+ f.cur <<- "1"
+ ftmp <<- f[[f.cur]]
+ stmp <<- s[[f.cur]]
+ ds.i <<- ftmp$ds.index
+ update_plotting_and_fitting()
+ } else {
+ f.df <<- f.df.empty
+ f.cur <<- "0"
+ }
+ f.gtable[,] <<- f.df
+ }, cont = f.gg.buttons)
+tooltip(delete.fit.gb) <- "Delete the currently loaded fit from the fit list"
+
+show.initial.gb <- gbutton("Show initial",
+ handler = function(h, ...) show_plot("Initial"),
+ cont = f.gg.buttons)
+tooltip(show.initial.gb) <- "Show model with current inital settings for current dataset"
+
+get_initials_handler <- function(h, ...)
+{
+ f.i <- svalue(get.initials.gc, index = TRUE)
+ if (length(f) > 0) {
+ got_initials <- c(f[[f.i]]$bparms.fixed, f[[f.i]]$bparms.optim)
+ parnames <- f.gg.parms[,"Name"]
+ newparnames <- names(got_initials)
+ commonparnames <- intersect(parnames, newparnames)
+ f.gg.parms[commonparnames, "Initial"] <<- got_initials[commonparnames]
+ }
+}
+get.initials.gb <- gbutton("Get initials from", cont = f.gg.buttons,
+ handler = get_initials_handler)
+get.initials.gc <- gcombobox(paste("Fit", f.df$Fit), cont = f.gg.buttons)
# Notebook to the right {{{3
-f.gn <- gnotebook(cont = p.gg, width = 700, height = 700)
+f.gn <- gnotebook(cont = p.gg, width = 680, height = 790)
# Dataframe with initial and optimised parameters {{{4
f.gg.parms <- gdf(Parameters, cont = f.gn,
- width = 690, height = 660,
+ width = 670, height = 750,
do_add_remove_buttons = FALSE, label = "Parameters")
f.gg.parms$set_column_width(1, 200)
f.gg.parms$set_column_width(2, 50)
@@ -755,6 +869,10 @@ f.gg.opts.atol <- gedit(ftmp$atol, label = "atol", width = 20, cont = f.gg.opts)
f.gg.opts.rtol <- gedit(ftmp$rtol, label = "rtol", width = 20,
cont = f.gg.opts)
+f.gg.opts.transform_rates <- gcheckbox("transform_rates",
+ cont = f.gg.opts, checked = TRUE)
+f.gg.opts.transform_fractions <- gcheckbox("transform_fractions",
+ cont = f.gg.opts, checked = TRUE)
weights <- c("manual", "none", "std", "mean")
f.gg.opts.weight <- gcombobox(weights, selected = 1, label = "weight",
width = 200, cont = f.gg.opts)
@@ -768,30 +886,11 @@ f.gg.opts.reweight.max.iter <- gedit(10, label = "reweight.max.iter", width = 20, cont = f.gg.opts)
# Summary {{{3
+oldwidth <- options()$width
+options(width = 90)
f.gg.summary <- ghtml(c("<pre>", capture.output(stmp), "</pre>"),
cont = f.gn, label = "Summary")
-
-delete.fit.gb <- gbutton("Delete", handler = function(h, ...) {
- if (length(f) > 0) {
- f[[f.cur]] <<- NULL
- s[[f.cur]] <<- NULL
- }
- if (length(f) > 0) {
- names(f) <<- as.character(1:length(f))
- names(s) <<- as.character(1:length(f))
- update_f.df()
- f.cur <<- "1"
- ftmp <<- f[[f.cur]]
- stmp <<- s[[f.cur]]
- ds.i <<- ftmp$ds.index
- update_plotting_and_fitting()
- } else {
- f.df <<- f.df.empty
- f.cur <<- "0"
- }
- f.gtable[,] <<- f.df
- }, cont = f.gg.buttons)
-tooltip(delete.fit.gb) <- "Delete the currently loaded fit from the fit list"
+options(width = oldwidth)
# Plot options {{{4
f.gg.plotopts <- ggroup(cont = f.gn, label = "Plot options", horizontal = FALSE)
@@ -818,6 +917,9 @@ update_plotting_and_fitting <- function() { delete(f.gg.plotopts, f.gg.po.obssel)
f.gg.po.obssel <<- gcheckboxgroup(names(m[[m.cur]]$spec), cont = f.gg.plotopts,
checked = TRUE)
+ oldwidth <<- options()$width
+ options(width = 90)
svalue(f.gg.summary) <- c("<pre>", capture.output(stmp), "</pre>")
+ options(width = oldwidth)
}
# vim: set foldmethod=marker ts=2 sw=2 expandtab: {{{1
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