R/advGwlFunctions.R
In dcangst/rrobot: Useful R functions for the Tecan Freedom Evo
Defines functions
fwCommand
MCArelative
MCAvector
moveMCA
waitTimer
startTimer
moveLiHa
adv_mix
adv_wash
adv_gwl_comment
adv_dispense
adv_aspirate
Documented in
adv_aspirate
adv_dispense
adv_gwl_comment
adv_mix
adv_wash
fwCommand
MCArelative
MCAvector
moveLiHa
moveMCA
startTimer
waitTimer
#' Advanced Aspirate Command
#'
#' @param tipMask \code{vector("integer",8L)} containing 0, 1 indicating
#' selected tips (e.g. \code{c(1,0,1,0,0,0,0,0)} = pins 1 + 3)
#' @param liquidClass string, liquid class name
#' @param volumes \code{vector("integer",8L)} 8 integers which specify the
#' volume in µl for each tip. Specify 0 for tips which are not used or
#' not fitted.
#' @param Racklabel Max. 32 characters User-defined label (name) which is
#' assigned to the labware.
#' @param spacing integer 1 - .. tip spacing, must be 2 for 384 well plates
#' @param wellSelection vector containing the wells from which the LiHa should
#' aspirate (should be in one column!)
#' @param ncol integer, number of colums (left to right on worktable) of labware
#' @param nrow integer, number of rows (back to front on worktable) of labware
#' @param noOfLoopOptions integer 0 - 7 number of loop options required. If
#' non-zero, parameters \code{loopname, action, difference} are included
#' n times, where n = \code{noOfLoopOptions}
#' @param loopName loop name, \code{vector("character",noOfLoopOptions)}
#' @param action integer 0 - 3 loop action: 0 = vary the column,
#' 1=vary the row 2=vary the well 3=vary the rack,
#' \code{vector("character",noOfLoopOptions)}
#' @param difference integer number (“vary by”) which is used for the loop
#' action, \code{vector("character",noOfLoopOptions)}
#' @param arm integer 0 - 1 number of the LiHa performing the action:
#' 0 = LiHa 1=LiHa 2, should always be 0
#' @family advanced worklist commands
#' @export
adv_aspirate <- function(
tipMask = c(1, 0, 0, 0, 0, 0, 0, 0),
liquidClass = gwl$defaults$LiquidClass,
volumes = gwl$defaults$Volume,
RackLabel,
spacing=2,
wellSelection, ncol, nrow,
noOfLoopOptions = 0, loopName = "", action = 0, difference = 0,
arm = 0
){
tipMask_bin <- .binToDec(rev(tipMask))
volumes_str <- .advVolumeString(volumes, tipMask)
CMadd_warning <- volumes_str[[2]]
GridSite <- getGridSite(RackLabel)
wellSelection_string <- ANSIIFromWells(wellSelection, ncol, nrow)
if (noOfLoopOptions != 0){
loopString <- paste0(noOfLoopOptions)
for (i in 1:noOfLoopOptions){
loopString <- paste0(
loopString, ",",
paste0("\"", loopName[i], "\""), ",",
action[i], ",",
difference[i])
}
} else {
loopString <- "0"
}
asp_command <- str_c(
paste0("B;Aspirate(", tipMask_bin),
paste0("\"", liquidClass, "\""),
volumes_str[[1]],
GridSite$grid,
GridSite$site,
spacing,
wellSelection_string,
loopString,
paste0(arm, ");"),
sep = ",")
.updateVolume(volumes, RackLabel, direction = -1)
addToWorklist(asp_command, "advanced", CMadd_warning = CMadd_warning)
invisible(asp_command)
}
#' Advanced Dispense Command
#'
#' @param tipMask \code{vector("integer",8L)} containing 0, 1 indicating
#' selected tips (e.g. \code{c(1,0,1,0,0,0,0,0)} = pins 1 + 3)
#' @param liquidClass string1 liquid class name
#' @param volumes \code{vector("integer",12L)} 12 expressions which specify the
#' volume in µl for each tip. Specify 0 for tips which are not used or
#' not fitted.
#' @param RackLabel Max. 32 characters User-defined label (name) which is
#' assigned to the labware.
#' @param spacing integer 1 - .. tip spacing, must be 2 for 384 well plates
#' @param wellSelection vector containing the wells into which the LiHa should
#' dispense (should be in one column!)
#' @param ncol integer, number of colums (left to right on worktable) of labware
#' @param nrow integer, number of rows (back to front on worktable) of labware
#' @param noOfLoopOptions integer 0 - 7 number of loop options required. If
#' non-zero, parameters \code{loopname, action, difference} are included
#' n times, where n = \code{noOfLoopOptions}
#' @param loopName loop name, \code{vector("character",noOfLoopOptions)}
#' @param action integer 0 - 3 loop action: 0 = vary the column,
#' 1=vary the row 2=vary the well 3=vary the rack,
#' \code{vector("character",noOfLoopOptions)}
#' @param difference integer number (“vary by”) which is used for the loop
#' action, \code{vector("character",noOfLoopOptions)}
#' @param arm integer 0 - 1 number of the LiHa performing the action:
#' 0 = LiHa 1=LiHa 2, should always be 0
#' @family advanced worklist commands
#' @export
adv_dispense <- function(
tipMask = c(1, 0, 0, 0, 0, 0, 0, 0),
liquidClass = gwl$defaults$LiquidClass,
volumes = gwl$defaults$Volume,
RackLabel,
spacing = 2,
wellSelection, ncol, nrow,
noOfLoopOptions = 0, loopName = "", action = 0, difference = 0,
arm = 0
){
tipMask_bin <- .binToDec(rev(tipMask))
volumes_str <- .advVolumeString(volumes, tipMask)
CMadd_warning <- volumes_str[[2]]
GridSite <- getGridSite(RackLabel)
wellSelection_string <- ANSIIFromWells(wellSelection, ncol, nrow)
if (noOfLoopOptions != 0){
loopString <- paste0(noOfLoopOptions)
for (i in 1:noOfLoopOptions){
loopString <- paste0(
loopString, ",",
paste0("\"", loopName[i], "\""), ",",
action[i], ",", difference[i])
}
} else {
loopString <- "0"
}
disp_command <- str_c(
paste0("B;Dispense(", tipMask_bin),
paste0("\"", liquidClass, "\""),
volumes_str[[1]],
GridSite$grid,
GridSite$site,
spacing,
wellSelection_string,
loopString,
paste0(arm, ");"),
sep = ",")
.updateVolume(volumes, RackLabel, direction = 1)
addToWorklist(disp_command, "advanced", CMadd_warning = CMadd_warning)
invisible(disp_command)
}
#' Adv Comment Command
#'
#' insert a comment into the advanced worklist shows up in evoware running log
#' (as opposed to \code{gwl_comment} which only shows up in the .gwl file).
#' @family advanced worklist commands
#' @export
adv_gwl_comment <- function(comment){
comment <- str_c(d = "B;Comment(\"", comment, "\");", sep = "")
addToWorklist(comment, "advanced")
}
#' Adv Wash Command
#'
#' @param tipMask \code{vector("integer",8L)} containing 0, 1 indicating
#' selected tips (e.g. \code{c(1,0,1,0,0,0,0,0)} = pins 1 + 3)
#' @param RackLabel_waste Name of the waste rack
#' @param RackLabel_cleaner Name of the cleaner rack
#' @param wasteVol integer 0 - 100 volume in waste in ml
#' @param wasteDelay integer 0 - 1000 delay before closing valves in waste in ms
#' @param cleanerVol expression 0 - 100 volume in cleaner in ml
#' @param cleanerDelay integer 0 - 1000 delay before closing valves in cleaner
#' in ms
#' @param Airgap floating point 0 - 100 volume of airgap in µl which is
#' aspirated after washing the tips (system trailing airgap)
#' @param airgapSpeed integer 1 - 1000 speed of airgap aspiration in µl/s
#' @param retractSpeed integer 1 - 100 retract speed in mm/s
#' @param FastWash integer 0 - 1 1 = use fast-wash-module
#' @param lowVolume integer 0 - 1 1 = use pinch valves
#' @param arm integer 0 - 1 number of the LiHa performing the action:
#' 0 = LiHa 1=LiHa 2, should always be 0
#' @family advanced worklist commands
#' @export
adv_wash <- function(
tipMask = rep(1, 8),
RackLabel_waste = "wash1_waste",
RackLabel_cleaner = "wash1_shallow",
wasteVol = 3,
wasteDelay = 500,
cleanerVol = 4,
cleanerDelay = 500,
Airgap = 10,
airgapSpeed = 70,
retractSpeed = 30,
FastWash = 1,
lowVolume = 0,
arm = 0
){
CMadd_warning <- ""
tipMask_bin <- .binToDec(rev(tipMask))
GridSite_waste <- getGridSite(RackLabel_waste)
GridSite_cleaner <- getGridSite(RackLabel_cleaner)
wash_command <- str_c(
paste0("B;Wash(", tipMask_bin),
GridSite_waste$grid,
GridSite_waste$site,
GridSite_cleaner$grid,
GridSite_cleaner$site,
paste0("\"", wasteVol, "\""),
wasteDelay,
paste0("\"", cleanerVol, "\""),
cleanerDelay,
Airgap,
airgapSpeed,
retractSpeed,
FastWash,
lowVolume,
0,
paste0(arm, ");"),
sep = ",")
.updateVolume(wasteVol * 1000, RackLabel_waste, direction = -1)
.updateVolume(cleanerVol * 1000, RackLabel_cleaner, direction = -1)
addToWorklist(wash_command, "advanced", CMadd_warning = CMadd_warning)
invisible(wash_command)
}
#' Adv Mix Command
#'
#' @param tipMask \code{vector("integer",8L)} containing 0, 1 indicating
#' selected tips (e.g. \code{c(1,0,1,0,0,0,0,0)} = pins 1 + 3)
#' @param liquidClass string1 liquid class name
#' @param volumes \code{vector("integer",12L)} 12 expressions which specify the
#' volume for each tip. Specify 0 for tips which are not used or
#' not fitted.
#' @param p_RackLabel Max. 32 characters User-defined label (name) which is
#' assigned to the labware.
#' @param grid integer 1 - 67 labware location - carrier grid position
#' @param site integer 0 - 127 labware location - (site on carrier - 1)
#' @param spacing integer 1 - .. tip spacing, must be 2 for 384 well plates
#' @param wellSelection vector containing the wells from which the LiHa should
#' aspirate (should be in one column!)
#' @param ncol integer, number of colums (left to right on worktable) of labware
#' @param nrow integer, number of rows (back to front on worktable) of labware
#' @param cycles integer 0 .. 100 number of mixing cycles
#' @param noOfLoopOptions integer 0 - 7 number of loop options required. If
#' non-zero, parameters \code{loopname, action, difference} are included
#' n times, where n = \code{noOfLoopOptions}
#' @param loopName loop name, \code{vector("character",noOfLoopOptions)}
#' @param action integer 0 - 3 loop action: 0 = vary the column,
#' 1=vary the row 2=vary the well 3=vary the rack,
#' \code{vector("character",noOfLoopOptions)}
#' @param difference integer number (“vary by”) which is used for the loop
#' action, \code{vector("character",noOfLoopOptions)}
#' @param arm integer 0 - 1 number of the LiHa performing the action:
#' 0 = LiHa 1=LiHa 2, should always be 0
#' @family advanced worklist commands
#' @export
adv_mix <- function(
tipMask = c(1, 0, 0, 0, 0, 0, 0, 0),
liquidClass = gwl$defaults$LiquidClass,
volumes = gwl$defaults$Volume,
RackLabel,
spacing=2,
wellSelection,
ncol,
nrow,
cycles,
noOfLoopOptions = 0,
loopName = "",
action = 0,
difference = 0,
arm = 0
){
tipMask_bin <- .binToDec(rev(tipMask))
volumes_str <- .advVolumeString(volumes, tipMask)
CMadd_warning <- volumes_str[[2]]
GridSite <- getGridSite(RackLabel)
wellSelection_string <- ANSIIFromWells(wellSelection, ncol, nrow)
if (noOfLoopOptions != 0){
loopString <- paste0(noOfLoopOptions)
for (i in 1:noOfLoopOptions){
loopString <- paste0(loopString, ",",
paste0("\"", loopName[i], "\""), ",", action[i], ",",
difference[i])
}
} else {
loopString <- "0"
}
mix_command <- str_c(
paste0("B;Mix(", tipMask_bin),
paste0("\"", liquidClass, "\""),
volumes_str[[1]],
GridSite$grid,
GridSite$site,
spacing,
wellSelection_string,
cycles,
loopString,
paste0(arm, ");"),
sep = ",")
addToWorklist(mix_command, "advanced", CMadd_warning = CMadd_warning)
invisible(mix_command)
}
#' Move LiHa
#'
#' @param tipMask \code{vector("integer",8L)} containing 0, 1 indicating
#' selected tips (e.g. \code{c(1,0,1,0,0,0,0,0)} = pins 1 + 3)
#' @param RackLabel Max. 32 characters User-defined label (name) which is
#' assigned to the labware.
#' @param spacing integer 1 - .. tip spacing, must be 2 for 384 well plates
#' @param wellSelection vector containing the wells from which the LiHa should
#' aspirate (should be in one column!)
#' @param ncol integer, number of colums (left to right on worktable) of labware
#' @param nrow integer, number of rows (back to front on worktable) of labware
#' @param zMove integer 0 - 4 type of movement: 0 = positioning with global
#' z-travel 1 = positioning with local z-travel 2 = x-move 3 = y-move
#' 4 = z-move
#' @param zTarget integer 0 - 4 z-position after move: 0 = z-travel
#' 1 = z-dispense 2 = z-start 3 = z-max 4 = global z-travel
#' @param offset floating point [-1000,1000] offset in mm added to z-position
#' (zTarget)
#' @param speed floating point [0.1,400] move speed in mm/s if zMove is 2,3 or 4
#' @param noOfLoopOptions integer 0 - 7 number of loop options required. If
#' non-zero, parameters \code{loopname, action, difference} are included
#' n times, where n = \code{noOfLoopOptions}
#' @param loopName loop name, \code{vector("character",noOfLoopOptions)}
#' @param action integer 0 - 3 loop action: 0 = vary the column,
#' 1=vary the row, 2=vary the well 3=vary the rack,
#' \code{vector("character",noOfLoopOptions)}
#' @param difference integer number (“vary by”) which is used for the loop
#' action, \code{vector("character",noOfLoopOptions)}
#' @param arm integer 0 - 1 number of the LiHa performing the action:
#' 0 = LiHa 1=LiHa 2, should always be 0
#' @family advanced worklist commands
#' @export
moveLiHa <- function(
tipMask = c(1, 0, 0, 0, 0, 0, 0, 0),
RackLabel,
spacing = 1,
wellSelection,
ncol,
nrow,
zMove,
zTarget,
offset,
speed,
noOfLoopOptions = 0,
loopName = "",
action = 0,
difference = 0,
arm = 0
){
CMadd_warning <- ""
tipMask_bin <- .binToDec(rev(tipMask))
GridSite <- getGridSite(RackLabel)
wellSelection_string <- ANSIIFromWells(wellSelection, ncol, nrow)
if (noOfLoopOptions != 0){
loopString <- paste0(noOfLoopOptions)
for (i in 1:noOfLoopOptions){
loopString <- paste0(loopString, ",",
paste0("\"", loopName[i], "\""), ",",
action[i], ",", difference[i])
}
} else {
loopString <- "0"
}
moveLiHa_command <- str_c(
paste0("B;MoveLiha(", tipMask_bin),
GridSite$grid,
GridSite$site,
spacing,
wellSelection_string,
zMove,
zTarget,
offset,
speed,
loopString,
paste0(arm, ");"),
sep = ",")
addToWorklist(moveLiHa_command, "advanced", CMadd_warning = CMadd_warning)
invisible(moveLiHa_command)
}
#' Start Timer
#'
#' @param timer Number of Timer to (re-)start
#' @family advanced worklist commands
#' @export
startTimer <- function(timer){
startTimer_command <- str_c(d = "B;StartTimer(", timer, ");", sep = "")
addToWorklist(startTimer_command, "advanced")
}
#' Wait for Timer
#'
#' @param timer Number of Timer to (re-)start
#' @param timeSpan duration [0.02 - 86400]
#' @family advanced worklist commands
#' @export
waitTimer <- function(timer, timeSpan){
waitTimer_command <- str_c(d = "B;WaitTimer(", timer, ",",
timeSpan, ");", sep = "")
addToWorklist(waitTimer_command, "advanced")
}
#' MCA Move
#'
#' Move MCA to labware
#'
#' @param RackLabel Max. 32 characters User-defined label (name) which is
#' assigned to the labware.
#' @param quadrant integer 1-4, which quadrant?
#' @param ncol integer, number of colums (left to right on worktable) of labware
#' @param nrow integer, number of rows (back to front on worktable) of labware
#' @param zMove integer 0 - 5 type of movement: 0 = positioning with global
#' z-travel, 1 = positioning with local z-travel, 2 = x-move, 3 = y-move,
#' 4 = z-move, 5 = Positioning with advanced z-travel (undocumented & untested..)
#' @param zTarget integer 0 - 4 z-position after move: 0 = z-travel
#' 1 = z-dispense 2 = z-start 3 = z-max 4 = global z-travel
#' @param offset integer [-1000,1000] offset in mm added to z-position
#' (zTarget)
#' @param speed floating point [0.1,400] move speed in mm/s if zMove is 2,3 or 4
#' @param noOfLoopOptions integer 0 - 7 number of loop options required. If
#' non-zero, parameters \code{loopname, action, difference} are included
#' n times, where n = \code{noOfLoopOptions}
#' @param loopName loop name, \code{vector("character",noOfLoopOptions)}
#' @param action integer 0 - 3 loop action: 0 = vary the column,
#' 1=vary the row, 2=vary the well 3=vary the rack,
#' \code{vector("character",noOfLoopOptions)}
#' @param difference integer number (“vary by”) which is used for the loop
#' action, \code{vector("character",noOfLoopOptions)}
#' @param arm integer 0 - 1, number of the MCA96 performing the action:
#' 0 = MCA 1=MCA 2, should always be 0
#' @family advanced worklist commands
#' @export
moveMCA <- function(
RackLabel,
quadrant = 1,
ncol = 24,
nrow = 16,
zMove,
zTarget,
offset = 0,
speed,
noOfLoopOptions = 0,
loopName = "",
action = 0,
difference = 0,
arm = 0){
CMadd_warning <- ""
if (ncol == 12 & nrow == 8){
wellSelection <- 1:96
} else if (ncol == 24 & nrow == 16) {
wellSelection <- switch(quadrant,
as.vector(matrix(1:384, 24, 16)[c(T, F), c(T, F)]),
as.vector(matrix(1:384, 24, 16)[c(F, T), c(T, F)]),
as.vector(matrix(1:384, 24, 16)[c(T, F), c(F, T)]),
as.vector(matrix(1:384, 24, 16)[c(F, T), c(F, T)]))
} else {
rlang::abort("must target a 96 or a 384well plate!")
}
wellSelection_string <- ANSIIFromWells(wellSelection, ncol, nrow)
GridSite <- getGridSite(RackLabel)
if (noOfLoopOptions != 0){
loopString <- paste0(noOfLoopOptions)
for (i in 1:noOfLoopOptions){
loopString <- paste0(loopString, ",",
paste0("\"", loopName[i], "\""), ",",
action[i], ",", difference[i])
}
} else {
loopString <- "0"
}
moveMCA_command <- str_c(
"B;MCAMove(0",
GridSite$grid,
GridSite$site,
"1",
wellSelection_string,
zMove,
zTarget,
offset,
speed,
loopString,
paste0(arm, ");"),
sep = ",")
addToWorklist(moveMCA_command, "advanced", CMadd_warning = CMadd_warning)
invisible(moveMCA_command)
}
#' MCA96 Vector command
#'
#' execute MCA vector
#'
#' @param move_vector string, the name of the vector
#' @param grid integer, labware location grid
#' @param site integer, labware locatation site STARTING WITH 1 at the back NOT 0!
#' @param direction integer 0 or 1, 0 = from safe to end, 1 from end to safe
#' @param back integer 0 or 1, 0 = don't move back to safe, 1 = move back to safe
#' @param beginAction Gripper action at safe, O = open, 1 = close, 2 = do not move
#' @param endAction Gripper action at end, O = open, 1 = close, 2 = do not move
#' @param speed integer 0 or 1, 0 = max. speed, 1 = speed as defined in vector teaching
#' @param arm integer 0 - 1, number of the MCA96 performing the action:
#' 0 = MCA 1=MCA 2, should always be 0
#' @family advanced worklist commands
#' @export
MCAvector <- function(
move_vector,
grid,
site,
direction = 0,
back = 1,
beginAction = 2,
endAction = 2,
speed = 1,
arm = 0){
CMadd_warning <- ""
if (site == 0){
rlang::abort("MCAVector Sites start with 1 (from the back)!!!!")
}
MCAVector_command <- str_c(
str_c("B;MCAMoveVector(\"", move_vector, "\""),
grid,
site,
direction,
back,
beginAction,
endAction,
speed,
str_c(arm, ");"),
sep = ",")
addToWorklist(MCAVector_command, "advanced", CMadd_warning = CMadd_warning)
invisible(MCAVector_command)
}
#' MCA Relative movement
#'
#' Sets an offset to the MCA
#'
#' @param col_offset integer, [-23,23], positive numbers move the MCA to the
#' right, negative to the left. Defaults to 0 = reset offset.
#' @param row_offset integer, [-15,15], positive numbers move the MCA to the
#' front, negative to the back. Defaults to 0 = reset offset.
#' @param arm integer 0 - 1, number of the MCA96 performing the action:
#' 0 = MCA 1=MCA 2, should always be 0
#' @param verbose logical, print comments?
#' @family advanced worklist commands
#' @export
MCArelative <- function(
col_offset = 0,
row_offset = 0,
arm = 0,
verbose = FALSE){
CMadd_warning <- ""
if (col_offset == 0){
offsetMap_col <- "00"
} else {
offsetMap_col <- switch(as.integer(col_offset > 0) + 1,
"01", # col_offset < 0
"10") # col_offset > 0
}
if (row_offset == 0){
offsetMap_row <- "00"
} else {
offsetMap_row <- switch(as.integer(row_offset > 0) + 1,
"10", # row_offset < 0
"01") # row_offset > 0
}
offsetMap <- str_c(offsetMap_row, offsetMap_col)
if (verbose) {
gwl_comment(
str_c("offsetting MCA: col (X) = ", col_offset, "
/ row (Y) = ", row_offset)
)}
MCArelative_command <- str_c(
str_c("B;MCARelativeMovement(", offsetMap),
col_offset,
row_offset,
str_c(arm, ");"),
sep = ",")
addToWorklist(MCArelative_command, "advanced", CMadd_warning = CMadd_warning)
invisible(MCArelative_command)
}
#' Send Firmware command
#'
#' sends a firmware command
#'
#' @param command string, the command
#' @param options int 0-7, bit-coded options: 1 = wait for termination of
#' command, 2 = store error code in variable, 4 = store answer in variable
#' @param parameter int 1-16 number of the parameter in the response which is
#' stored in the variable “response”
#' @param response string, variable to store response, empty for no storage
#' @param error string, variable to store error, empty for no storage
#' @param errorScope int 0-2, scope of error variable: 0 = Run, 1 = Instance,
#' 2 = Script
#' @param responseScope int 0-2, scope of response variable: 0 = Run,
#' 1 = Instance, 2 = Script
#' @param responseType int 0-1, type of response variable. 0 = numeric,
#' 1 = string
#' @family advanced worklist commands
#' @export
fwCommand <- function(
command,
options = 1,
parameter = 1,
response = "",
error = "",
errorScope = 2,
responseScope = 2,
responseType = 0){
CMadd_warning <- ""
fwCommand_command <- str_c(
str_c("B;Command(\"", command, "\""),
options,
parameter,
response,
error,
errorScope,
responseScope,
str_c(responseType, ");"),
sep = ",")
addToWorklist(fwCommand_command, "advanced", CMadd_warning = CMadd_warning)
invisible(fwCommand_command)
}
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Defines functions fwCommand MCArelative MCAvector moveMCA waitTimer startTimer moveLiHa adv_mix adv_wash adv_gwl_comment adv_dispense adv_aspirate
Documented in adv_aspirate adv_dispense adv_gwl_comment adv_mix adv_wash fwCommand MCArelative MCAvector moveLiHa moveMCA startTimer waitTimer
#' Advanced Aspirate Command
#'
#' @param tipMask \code{vector("integer",8L)} containing 0, 1 indicating
#' selected tips (e.g. \code{c(1,0,1,0,0,0,0,0)} = pins 1 + 3)
#' @param liquidClass string, liquid class name
#' @param volumes \code{vector("integer",8L)} 8 integers which specify the
#' volume in µl for each tip. Specify 0 for tips which are not used or
#' not fitted.
#' @param Racklabel Max. 32 characters User-defined label (name) which is
#' assigned to the labware.
#' @param spacing integer 1 - .. tip spacing, must be 2 for 384 well plates
#' @param wellSelection vector containing the wells from which the LiHa should
#' aspirate (should be in one column!)
#' @param ncol integer, number of colums (left to right on worktable) of labware
#' @param nrow integer, number of rows (back to front on worktable) of labware
#' @param noOfLoopOptions integer 0 - 7 number of loop options required. If
#' non-zero, parameters \code{loopname, action, difference} are included
#' n times, where n = \code{noOfLoopOptions}
#' @param loopName loop name, \code{vector("character",noOfLoopOptions)}
#' @param action integer 0 - 3 loop action: 0 = vary the column,
#' 1=vary the row 2=vary the well 3=vary the rack,
#' \code{vector("character",noOfLoopOptions)}
#' @param difference integer number (“vary by”) which is used for the loop
#' action, \code{vector("character",noOfLoopOptions)}
#' @param arm integer 0 - 1 number of the LiHa performing the action:
#' 0 = LiHa 1=LiHa 2, should always be 0
#' @family advanced worklist commands
#' @export
adv_aspirate <- function(
tipMask = c(1, 0, 0, 0, 0, 0, 0, 0),
liquidClass = gwl$defaults$LiquidClass,
volumes = gwl$defaults$Volume,
RackLabel,
spacing=2,
wellSelection, ncol, nrow,
noOfLoopOptions = 0, loopName = "", action = 0, difference = 0,
arm = 0
){
tipMask_bin <- .binToDec(rev(tipMask))
volumes_str <- .advVolumeString(volumes, tipMask)
CMadd_warning <- volumes_str[[2]]
GridSite <- getGridSite(RackLabel)
wellSelection_string <- ANSIIFromWells(wellSelection, ncol, nrow)
if (noOfLoopOptions != 0){
loopString <- paste0(noOfLoopOptions)
for (i in 1:noOfLoopOptions){
loopString <- paste0(
loopString, ",",
paste0("\"", loopName[i], "\""), ",",
action[i], ",",
difference[i])
}
} else {
loopString <- "0"
}
asp_command <- str_c(
paste0("B;Aspirate(", tipMask_bin),
paste0("\"", liquidClass, "\""),
volumes_str[[1]],
GridSite$grid,
GridSite$site,
spacing,
wellSelection_string,
loopString,
paste0(arm, ");"),
sep = ",")
.updateVolume(volumes, RackLabel, direction = -1)
addToWorklist(asp_command, "advanced", CMadd_warning = CMadd_warning)
invisible(asp_command)
}
#' Advanced Dispense Command
#'
#' @param tipMask \code{vector("integer",8L)} containing 0, 1 indicating
#' selected tips (e.g. \code{c(1,0,1,0,0,0,0,0)} = pins 1 + 3)
#' @param liquidClass string1 liquid class name
#' @param volumes \code{vector("integer",12L)} 12 expressions which specify the
#' volume in µl for each tip. Specify 0 for tips which are not used or
#' not fitted.
#' @param RackLabel Max. 32 characters User-defined label (name) which is
#' assigned to the labware.
#' @param spacing integer 1 - .. tip spacing, must be 2 for 384 well plates
#' @param wellSelection vector containing the wells into which the LiHa should
#' dispense (should be in one column!)
#' @param ncol integer, number of colums (left to right on worktable) of labware
#' @param nrow integer, number of rows (back to front on worktable) of labware
#' @param noOfLoopOptions integer 0 - 7 number of loop options required. If
#' non-zero, parameters \code{loopname, action, difference} are included
#' n times, where n = \code{noOfLoopOptions}
#' @param loopName loop name, \code{vector("character",noOfLoopOptions)}
#' @param action integer 0 - 3 loop action: 0 = vary the column,
#' 1=vary the row 2=vary the well 3=vary the rack,
#' \code{vector("character",noOfLoopOptions)}
#' @param difference integer number (“vary by”) which is used for the loop
#' action, \code{vector("character",noOfLoopOptions)}
#' @param arm integer 0 - 1 number of the LiHa performing the action:
#' 0 = LiHa 1=LiHa 2, should always be 0
#' @family advanced worklist commands
#' @export
adv_dispense <- function(
tipMask = c(1, 0, 0, 0, 0, 0, 0, 0),
liquidClass = gwl$defaults$LiquidClass,
volumes = gwl$defaults$Volume,
RackLabel,
spacing = 2,
wellSelection, ncol, nrow,
noOfLoopOptions = 0, loopName = "", action = 0, difference = 0,
arm = 0
){
tipMask_bin <- .binToDec(rev(tipMask))
volumes_str <- .advVolumeString(volumes, tipMask)
CMadd_warning <- volumes_str[[2]]
GridSite <- getGridSite(RackLabel)
wellSelection_string <- ANSIIFromWells(wellSelection, ncol, nrow)
if (noOfLoopOptions != 0){
loopString <- paste0(noOfLoopOptions)
for (i in 1:noOfLoopOptions){
loopString <- paste0(
loopString, ",",
paste0("\"", loopName[i], "\""), ",",
action[i], ",", difference[i])
}
} else {
loopString <- "0"
}
disp_command <- str_c(
paste0("B;Dispense(", tipMask_bin),
paste0("\"", liquidClass, "\""),
volumes_str[[1]],
GridSite$grid,
GridSite$site,
spacing,
wellSelection_string,
loopString,
paste0(arm, ");"),
sep = ",")
.updateVolume(volumes, RackLabel, direction = 1)
addToWorklist(disp_command, "advanced", CMadd_warning = CMadd_warning)
invisible(disp_command)
}
#' Adv Comment Command
#'
#' insert a comment into the advanced worklist shows up in evoware running log
#' (as opposed to \code{gwl_comment} which only shows up in the .gwl file).
#' @family advanced worklist commands
#' @export
adv_gwl_comment <- function(comment){
comment <- str_c(d = "B;Comment(\"", comment, "\");", sep = "")
addToWorklist(comment, "advanced")
}
#' Adv Wash Command
#'
#' @param tipMask \code{vector("integer",8L)} containing 0, 1 indicating
#' selected tips (e.g. \code{c(1,0,1,0,0,0,0,0)} = pins 1 + 3)
#' @param RackLabel_waste Name of the waste rack
#' @param RackLabel_cleaner Name of the cleaner rack
#' @param wasteVol integer 0 - 100 volume in waste in ml
#' @param wasteDelay integer 0 - 1000 delay before closing valves in waste in ms
#' @param cleanerVol expression 0 - 100 volume in cleaner in ml
#' @param cleanerDelay integer 0 - 1000 delay before closing valves in cleaner
#' in ms
#' @param Airgap floating point 0 - 100 volume of airgap in µl which is
#' aspirated after washing the tips (system trailing airgap)
#' @param airgapSpeed integer 1 - 1000 speed of airgap aspiration in µl/s
#' @param retractSpeed integer 1 - 100 retract speed in mm/s
#' @param FastWash integer 0 - 1 1 = use fast-wash-module
#' @param lowVolume integer 0 - 1 1 = use pinch valves
#' @param arm integer 0 - 1 number of the LiHa performing the action:
#' 0 = LiHa 1=LiHa 2, should always be 0
#' @family advanced worklist commands
#' @export
adv_wash <- function(
tipMask = rep(1, 8),
RackLabel_waste = "wash1_waste",
RackLabel_cleaner = "wash1_shallow",
wasteVol = 3,
wasteDelay = 500,
cleanerVol = 4,
cleanerDelay = 500,
Airgap = 10,
airgapSpeed = 70,
retractSpeed = 30,
FastWash = 1,
lowVolume = 0,
arm = 0
){
CMadd_warning <- ""
tipMask_bin <- .binToDec(rev(tipMask))
GridSite_waste <- getGridSite(RackLabel_waste)
GridSite_cleaner <- getGridSite(RackLabel_cleaner)
wash_command <- str_c(
paste0("B;Wash(", tipMask_bin),
GridSite_waste$grid,
GridSite_waste$site,
GridSite_cleaner$grid,
GridSite_cleaner$site,
paste0("\"", wasteVol, "\""),
wasteDelay,
paste0("\"", cleanerVol, "\""),
cleanerDelay,
Airgap,
airgapSpeed,
retractSpeed,
FastWash,
lowVolume,
0,
paste0(arm, ");"),
sep = ",")
.updateVolume(wasteVol * 1000, RackLabel_waste, direction = -1)
.updateVolume(cleanerVol * 1000, RackLabel_cleaner, direction = -1)
addToWorklist(wash_command, "advanced", CMadd_warning = CMadd_warning)
invisible(wash_command)
}
#' Adv Mix Command
#'
#' @param tipMask \code{vector("integer",8L)} containing 0, 1 indicating
#' selected tips (e.g. \code{c(1,0,1,0,0,0,0,0)} = pins 1 + 3)
#' @param liquidClass string1 liquid class name
#' @param volumes \code{vector("integer",12L)} 12 expressions which specify the
#' volume for each tip. Specify 0 for tips which are not used or
#' not fitted.
#' @param p_RackLabel Max. 32 characters User-defined label (name) which is
#' assigned to the labware.
#' @param grid integer 1 - 67 labware location - carrier grid position
#' @param site integer 0 - 127 labware location - (site on carrier - 1)
#' @param spacing integer 1 - .. tip spacing, must be 2 for 384 well plates
#' @param wellSelection vector containing the wells from which the LiHa should
#' aspirate (should be in one column!)
#' @param ncol integer, number of colums (left to right on worktable) of labware
#' @param nrow integer, number of rows (back to front on worktable) of labware
#' @param cycles integer 0 .. 100 number of mixing cycles
#' @param noOfLoopOptions integer 0 - 7 number of loop options required. If
#' non-zero, parameters \code{loopname, action, difference} are included
#' n times, where n = \code{noOfLoopOptions}
#' @param loopName loop name, \code{vector("character",noOfLoopOptions)}
#' @param action integer 0 - 3 loop action: 0 = vary the column,
#' 1=vary the row 2=vary the well 3=vary the rack,
#' \code{vector("character",noOfLoopOptions)}
#' @param difference integer number (“vary by”) which is used for the loop
#' action, \code{vector("character",noOfLoopOptions)}
#' @param arm integer 0 - 1 number of the LiHa performing the action:
#' 0 = LiHa 1=LiHa 2, should always be 0
#' @family advanced worklist commands
#' @export
adv_mix <- function(
tipMask = c(1, 0, 0, 0, 0, 0, 0, 0),
liquidClass = gwl$defaults$LiquidClass,
volumes = gwl$defaults$Volume,
RackLabel,
spacing=2,
wellSelection,
ncol,
nrow,
cycles,
noOfLoopOptions = 0,
loopName = "",
action = 0,
difference = 0,
arm = 0
){
tipMask_bin <- .binToDec(rev(tipMask))
volumes_str <- .advVolumeString(volumes, tipMask)
CMadd_warning <- volumes_str[[2]]
GridSite <- getGridSite(RackLabel)
wellSelection_string <- ANSIIFromWells(wellSelection, ncol, nrow)
if (noOfLoopOptions != 0){
loopString <- paste0(noOfLoopOptions)
for (i in 1:noOfLoopOptions){
loopString <- paste0(loopString, ",",
paste0("\"", loopName[i], "\""), ",", action[i], ",",
difference[i])
}
} else {
loopString <- "0"
}
mix_command <- str_c(
paste0("B;Mix(", tipMask_bin),
paste0("\"", liquidClass, "\""),
volumes_str[[1]],
GridSite$grid,
GridSite$site,
spacing,
wellSelection_string,
cycles,
loopString,
paste0(arm, ");"),
sep = ",")
addToWorklist(mix_command, "advanced", CMadd_warning = CMadd_warning)
invisible(mix_command)
}
#' Move LiHa
#'
#' @param tipMask \code{vector("integer",8L)} containing 0, 1 indicating
#' selected tips (e.g. \code{c(1,0,1,0,0,0,0,0)} = pins 1 + 3)
#' @param RackLabel Max. 32 characters User-defined label (name) which is
#' assigned to the labware.
#' @param spacing integer 1 - .. tip spacing, must be 2 for 384 well plates
#' @param wellSelection vector containing the wells from which the LiHa should
#' aspirate (should be in one column!)
#' @param ncol integer, number of colums (left to right on worktable) of labware
#' @param nrow integer, number of rows (back to front on worktable) of labware
#' @param zMove integer 0 - 4 type of movement: 0 = positioning with global
#' z-travel 1 = positioning with local z-travel 2 = x-move 3 = y-move
#' 4 = z-move
#' @param zTarget integer 0 - 4 z-position after move: 0 = z-travel
#' 1 = z-dispense 2 = z-start 3 = z-max 4 = global z-travel
#' @param offset floating point [-1000,1000] offset in mm added to z-position
#' (zTarget)
#' @param speed floating point [0.1,400] move speed in mm/s if zMove is 2,3 or 4
#' @param noOfLoopOptions integer 0 - 7 number of loop options required. If
#' non-zero, parameters \code{loopname, action, difference} are included
#' n times, where n = \code{noOfLoopOptions}
#' @param loopName loop name, \code{vector("character",noOfLoopOptions)}
#' @param action integer 0 - 3 loop action: 0 = vary the column,
#' 1=vary the row, 2=vary the well 3=vary the rack,
#' \code{vector("character",noOfLoopOptions)}
#' @param difference integer number (“vary by”) which is used for the loop
#' action, \code{vector("character",noOfLoopOptions)}
#' @param arm integer 0 - 1 number of the LiHa performing the action:
#' 0 = LiHa 1=LiHa 2, should always be 0
#' @family advanced worklist commands
#' @export
moveLiHa <- function(
tipMask = c(1, 0, 0, 0, 0, 0, 0, 0),
RackLabel,
spacing = 1,
wellSelection,
ncol,
nrow,
zMove,
zTarget,
offset,
speed,
noOfLoopOptions = 0,
loopName = "",
action = 0,
difference = 0,
arm = 0
){
CMadd_warning <- ""
tipMask_bin <- .binToDec(rev(tipMask))
GridSite <- getGridSite(RackLabel)
wellSelection_string <- ANSIIFromWells(wellSelection, ncol, nrow)
if (noOfLoopOptions != 0){
loopString <- paste0(noOfLoopOptions)
for (i in 1:noOfLoopOptions){
loopString <- paste0(loopString, ",",
paste0("\"", loopName[i], "\""), ",",
action[i], ",", difference[i])
}
} else {
loopString <- "0"
}
moveLiHa_command <- str_c(
paste0("B;MoveLiha(", tipMask_bin),
GridSite$grid,
GridSite$site,
spacing,
wellSelection_string,
zMove,
zTarget,
offset,
speed,
loopString,
paste0(arm, ");"),
sep = ",")
addToWorklist(moveLiHa_command, "advanced", CMadd_warning = CMadd_warning)
invisible(moveLiHa_command)
}
#' Start Timer
#'
#' @param timer Number of Timer to (re-)start
#' @family advanced worklist commands
#' @export
startTimer <- function(timer){
startTimer_command <- str_c(d = "B;StartTimer(", timer, ");", sep = "")
addToWorklist(startTimer_command, "advanced")
}
#' Wait for Timer
#'
#' @param timer Number of Timer to (re-)start
#' @param timeSpan duration [0.02 - 86400]
#' @family advanced worklist commands
#' @export
waitTimer <- function(timer, timeSpan){
waitTimer_command <- str_c(d = "B;WaitTimer(", timer, ",",
timeSpan, ");", sep = "")
addToWorklist(waitTimer_command, "advanced")
}
#' MCA Move
#'
#' Move MCA to labware
#'
#' @param RackLabel Max. 32 characters User-defined label (name) which is
#' assigned to the labware.
#' @param quadrant integer 1-4, which quadrant?
#' @param ncol integer, number of colums (left to right on worktable) of labware
#' @param nrow integer, number of rows (back to front on worktable) of labware
#' @param zMove integer 0 - 5 type of movement: 0 = positioning with global
#' z-travel, 1 = positioning with local z-travel, 2 = x-move, 3 = y-move,
#' 4 = z-move, 5 = Positioning with advanced z-travel (undocumented & untested..)
#' @param zTarget integer 0 - 4 z-position after move: 0 = z-travel
#' 1 = z-dispense 2 = z-start 3 = z-max 4 = global z-travel
#' @param offset integer [-1000,1000] offset in mm added to z-position
#' (zTarget)
#' @param speed floating point [0.1,400] move speed in mm/s if zMove is 2,3 or 4
#' @param noOfLoopOptions integer 0 - 7 number of loop options required. If
#' non-zero, parameters \code{loopname, action, difference} are included
#' n times, where n = \code{noOfLoopOptions}
#' @param loopName loop name, \code{vector("character",noOfLoopOptions)}
#' @param action integer 0 - 3 loop action: 0 = vary the column,
#' 1=vary the row, 2=vary the well 3=vary the rack,
#' \code{vector("character",noOfLoopOptions)}
#' @param difference integer number (“vary by”) which is used for the loop
#' action, \code{vector("character",noOfLoopOptions)}
#' @param arm integer 0 - 1, number of the MCA96 performing the action:
#' 0 = MCA 1=MCA 2, should always be 0
#' @family advanced worklist commands
#' @export
moveMCA <- function(
RackLabel,
quadrant = 1,
ncol = 24,
nrow = 16,
zMove,
zTarget,
offset = 0,
speed,
noOfLoopOptions = 0,
loopName = "",
action = 0,
difference = 0,
arm = 0){
CMadd_warning <- ""
if (ncol == 12 & nrow == 8){
wellSelection <- 1:96
} else if (ncol == 24 & nrow == 16) {
wellSelection <- switch(quadrant,
as.vector(matrix(1:384, 24, 16)[c(T, F), c(T, F)]),
as.vector(matrix(1:384, 24, 16)[c(F, T), c(T, F)]),
as.vector(matrix(1:384, 24, 16)[c(T, F), c(F, T)]),
as.vector(matrix(1:384, 24, 16)[c(F, T), c(F, T)]))
} else {
rlang::abort("must target a 96 or a 384well plate!")
}
wellSelection_string <- ANSIIFromWells(wellSelection, ncol, nrow)
GridSite <- getGridSite(RackLabel)
if (noOfLoopOptions != 0){
loopString <- paste0(noOfLoopOptions)
for (i in 1:noOfLoopOptions){
loopString <- paste0(loopString, ",",
paste0("\"", loopName[i], "\""), ",",
action[i], ",", difference[i])
}
} else {
loopString <- "0"
}
moveMCA_command <- str_c(
"B;MCAMove(0",
GridSite$grid,
GridSite$site,
"1",
wellSelection_string,
zMove,
zTarget,
offset,
speed,
loopString,
paste0(arm, ");"),
sep = ",")
addToWorklist(moveMCA_command, "advanced", CMadd_warning = CMadd_warning)
invisible(moveMCA_command)
}
#' MCA96 Vector command
#'
#' execute MCA vector
#'
#' @param move_vector string, the name of the vector
#' @param grid integer, labware location grid
#' @param site integer, labware locatation site STARTING WITH 1 at the back NOT 0!
#' @param direction integer 0 or 1, 0 = from safe to end, 1 from end to safe
#' @param back integer 0 or 1, 0 = don't move back to safe, 1 = move back to safe
#' @param beginAction Gripper action at safe, O = open, 1 = close, 2 = do not move
#' @param endAction Gripper action at end, O = open, 1 = close, 2 = do not move
#' @param speed integer 0 or 1, 0 = max. speed, 1 = speed as defined in vector teaching
#' @param arm integer 0 - 1, number of the MCA96 performing the action:
#' 0 = MCA 1=MCA 2, should always be 0
#' @family advanced worklist commands
#' @export
MCAvector <- function(
move_vector,
grid,
site,
direction = 0,
back = 1,
beginAction = 2,
endAction = 2,
speed = 1,
arm = 0){
CMadd_warning <- ""
if (site == 0){
rlang::abort("MCAVector Sites start with 1 (from the back)!!!!")
}
MCAVector_command <- str_c(
str_c("B;MCAMoveVector(\"", move_vector, "\""),
grid,
site,
direction,
back,
beginAction,
endAction,
speed,
str_c(arm, ");"),
sep = ",")
addToWorklist(MCAVector_command, "advanced", CMadd_warning = CMadd_warning)
invisible(MCAVector_command)
}
#' MCA Relative movement
#'
#' Sets an offset to the MCA
#'
#' @param col_offset integer, [-23,23], positive numbers move the MCA to the
#' right, negative to the left. Defaults to 0 = reset offset.
#' @param row_offset integer, [-15,15], positive numbers move the MCA to the
#' front, negative to the back. Defaults to 0 = reset offset.
#' @param arm integer 0 - 1, number of the MCA96 performing the action:
#' 0 = MCA 1=MCA 2, should always be 0
#' @param verbose logical, print comments?
#' @family advanced worklist commands
#' @export
MCArelative <- function(
col_offset = 0,
row_offset = 0,
arm = 0,
verbose = FALSE){
CMadd_warning <- ""
if (col_offset == 0){
offsetMap_col <- "00"
} else {
offsetMap_col <- switch(as.integer(col_offset > 0) + 1,
"01", # col_offset < 0
"10") # col_offset > 0
}
if (row_offset == 0){
offsetMap_row <- "00"
} else {
offsetMap_row <- switch(as.integer(row_offset > 0) + 1,
"10", # row_offset < 0
"01") # row_offset > 0
}
offsetMap <- str_c(offsetMap_row, offsetMap_col)
if (verbose) {
gwl_comment(
str_c("offsetting MCA: col (X) = ", col_offset, "
/ row (Y) = ", row_offset)
)}
MCArelative_command <- str_c(
str_c("B;MCARelativeMovement(", offsetMap),
col_offset,
row_offset,
str_c(arm, ");"),
sep = ",")
addToWorklist(MCArelative_command, "advanced", CMadd_warning = CMadd_warning)
invisible(MCArelative_command)
}
#' Send Firmware command
#'
#' sends a firmware command
#'
#' @param command string, the command
#' @param options int 0-7, bit-coded options: 1 = wait for termination of
#' command, 2 = store error code in variable, 4 = store answer in variable
#' @param parameter int 1-16 number of the parameter in the response which is
#' stored in the variable “response”
#' @param response string, variable to store response, empty for no storage
#' @param error string, variable to store error, empty for no storage
#' @param errorScope int 0-2, scope of error variable: 0 = Run, 1 = Instance,
#' 2 = Script
#' @param responseScope int 0-2, scope of response variable: 0 = Run,
#' 1 = Instance, 2 = Script
#' @param responseType int 0-1, type of response variable. 0 = numeric,
#' 1 = string
#' @family advanced worklist commands
#' @export
fwCommand <- function(
command,
options = 1,
parameter = 1,
response = "",
error = "",
errorScope = 2,
responseScope = 2,
responseType = 0){
CMadd_warning <- ""
fwCommand_command <- str_c(
str_c("B;Command(\"", command, "\""),
options,
parameter,
response,
error,
errorScope,
responseScope,
str_c(responseType, ");"),
sep = ",")
addToWorklist(fwCommand_command, "advanced", CMadd_warning = CMadd_warning)
invisible(fwCommand_command)
}
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