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generate Chromeleon program files #17

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generate Chromeleon program files #17

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6468bfc
add way to programmatically generate .pgm files
tmcgrath325 Jun 29, 2023
313d378
fix omissions, add clarity to output .pgm
tmcgrath325 Jun 30, 2023
10e07b7
fix quotes/comments in generated .pgm
tmcgrath325 Jun 30, 2023
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102 changes: 4 additions & 98 deletions src/Autosampler.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -4,103 +4,9 @@ using CSV, DataFrames, ImagineFormat, ImagineInterface
using Random, Mmap

export stim_randomize, update_imagine
export chromeleon_program

"""
stim_randomize(filein, trials::Int, fileout=insertfilename(filein, "_sequence"))
include("seqfile.jl")
include("progfile.jl")

Generate a randomize sequence of stimuli. `filein` is a string containing the name
of a CSV file that describes the unique stimuli (see format described in the README).
`trials` specifies the number of pseudo-random sequences used to generate the
final stimulus sequence.
`fileout` is an optional argument used to control the name of the output file;
the default is to insert "_sequence" right before the extension of `filein`.
"""
function stim_randomize(filein::AbstractString, trials::Int; fileout=insertfilename(filein, "_sequence"), kwargs...)
open(fileout, "w") do io
stim_randomize(io, filein, trials; kwargs...)
end
return fileout
end

function stim_randomize(io::IO, filein::AbstractString, trials::Int; header=false, kwargs...)
df = CSV.File(filein) |> DataFrame
println("Headers found: ", String.(names(df)))
n = size(df, 1)
println(n, " stimuli found")
# $ is a disallowed character since we will use it as a separator
for i = 1:n
occursin('\$', df[i,1]) && error("\$ is disallowed in stimulus names")
end
p = Int[]
for i = 1:trials
append!(p, randperm(n))
end
CSV.write(io, df[p, :]; header=header, kwargs...)
flush(io)
end

function update_imagine(imaginefile, sequencefile; um_per_pixel=nothing, aifile=replaceext(imaginefile, ".ai"), difile=replaceext(imaginefile, ".di"), updatedfile=imaginefile, csvheader=0, kwargs...)
header = ImagineFormat.parse_header(imaginefile)
haskey(header, "stimulus sequence") && error(imaginefile, " already has a `stimulus sequence` entry")
if um_per_pixel === nothing
um_per_pixel = header["um per pixel"]
end
um_per_pixel < 0 && error("must specify um_per_pixel")
header["um per pixel"] = um_per_pixel

df = CSV.File(sequencefile; header=csvheader, kwargs...) |> DataFrame
n = size(df, 1)

# Scan the AI file for stimulus triggers
ai = parse_ai(aifile, header)
aistim = getname(ai, "stimuli")
stimhi = find_pulse_starts(aistim; sampmap=:volts)
stimlo = find_pulse_stops(aistim; sampmap=:volts)
if occursin("camera frame TTL", header["label list"])
aiframe = getname(ai, "camera frame TTL")
framestarts = find_pulse_starts(aiframe; sampmap=:volts)
elseif occursin("camera1 frame monitor", header["di label list"])
di = parse_di(difile, header)
diframe = getname(di, "camera1 frame monitor")
framestarts = find_pulse_starts(diframe) #; sampmap=:volts)
end

# Record as frameidx after the stimulus trigger
fps = header["frames per stack"]
framehi, framelo = Int[], Int[]
for (frameidxs, scanidxs) in ((framehi, stimhi), (framelo, stimlo))
for i in scanidxs
idx = last(searchsorted(framestarts, i))
push!(frameidxs, idx)
end
end

# Add to header
header["stimulus sequence"] = join(df[:,1], '\$')
header["stimulus scan hi"] = stimhi
header["stimulus scan lo"] = stimlo
header["stimulus frame hi"] = framehi
header["stimulus frame lo"] = framelo

if updatedfile == imaginefile
mv(imaginefile, imaginefile*".orig")
sleep(0.25)
isfile(imaginefile) && error("failed to move the old file")
end
ImagineFormat.save_header(updatedfile, header; misc=(
"stimulus sequence", "stimulus scan hi", "stimulus scan lo",
"stimulus frame hi", "stimulus frame lo"))
return header
end

function insertfilename(filename, tail)
basename, ext = splitext(filename)
return basename*tail*ext
end

function replaceext(filename, ext)
basename, _ = splitext(filename)
return basename*ext
end

end # module
end
150 changes: 150 additions & 0 deletions src/progfile.jl
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# These parameters were chosen from .pgm files used by former Holy lab members
# Most parameters were kept the same between users, with the exception of the flowrate "Flow" and wait time "Delay"
# Some of these parameters may be extraneous when using "InjectMode = UserProg".
const default_params = Dict{String,String}(
"Flow" => "0.540", # mL/min
"Delay" => "0.500", # min

"PreflushVolume" => "5.0", # μL

"TempCtrl" => "On",
"TemperatureNominal" => "30.0", # [°C]
"TemperatureLowerLimit" => "27.0", # [°C]
"TemperatureUpperLimit" => "33.0", # [°C]
"ReadyTempDelta" => "2.0", # [°C]
"PressureLowerLimit" => "0", # [bar]
"PressureUpperLimit" => "350", # [bar]
"MaximumFlowRampDown" => "6.000", # [ml/min²]
"MaximumFlowRampUp" => "6.000", # [ml/min²]
"%A.Equate" => "\"%A\"",
"DrawSpeed" => "10.000", # [µl/s]
"DrawDelay" => "1000", # [ms]
"DispSpeed" => "20.000", # [µl/s]
"DispenseDelay" => "0",
"WasteSpeed" => "20.000", # [µl/s]
"SampleHeight" => "2.000", # [mm]
"InjectWash" => "AfterDraw",
"WashVolume" => "100.000", # [µl]
"WashSpeed" => "30.000", # [µl/s]
"LoopWashFactor" => "1.000",
"PunctureOffset" => "0.0", # [mm]
"PumpDevice" => "\"Pump\"",
"SyncWithPump" => "Off",
"Pump_Pressure.Step" => "0.01", # [s]
"Pump_Pressure.Average" => "Off",
"Curve" => "5",
)

"""
chromeleon_program(fileout::AbstractString, params::Dict{String,String}=default_params)

Generate a Chromeleon program file (.pgm) to be used for timing injections performed by the autosampler
with an external TTL input (e.g. one from Imagine).
`fileout` is a string containing the name of the program file to be written.
`params` specifies the parameters to be used in the program file. Default settings based on settings used
by current and former Holy lab members are provided in `default_params`.
For typical use, only the flowrate `params["Flow"]` and wait time `params["Delay"]` need to be changed between experiments.
"""
function chromeleon_program(fileout::AbstractString, params::Dict{String,String}=default_params)
split(fileout, ".")[end] == "pgm" || error("fileout must have .pgm extension")
open(fileout, "w") do io
chromeleon_program(io, params)
end
return fileout
end

function chromeleon_program(io::IO, params=default_params)
# Newlines use the \r\n convention for compatibility with Windows/Notepad
write(io,
"\tTempCtrl =\t$(params["TempCtrl"])\r\n",
"\tTemperature.Nominal =\t$(params["TemperatureNominal"]) [°C]\r\n",
"\tTemperature.LowerLimit =\t$(params["TemperatureLowerLimit"]) [°C]\r\n",
"\tTemperature.UpperLimit =\t$(params["TemperatureUpperLimit"]) [°C]\r\n",
"\tReadyTempDelta =\t$(params["ReadyTempDelta"]) [°C]\r\n",
"\tPressure.LowerLimit =\t$(params["PressureLowerLimit"]) [bar]\r\n",
"\tPressure.UpperLimit =\t$(params["PressureUpperLimit"]) [bar]\r\n",
"\tMaximumFlowRampDown =\t$(params["MaximumFlowRampDown"]) [ml/min²]\r\n",
"\tMaximumFlowRampUp =\t$(params["MaximumFlowRampUp"]) [ml/min²]\r\n",
"\t%A.Equate =\t$(params["%A.Equate"])\r\n",
"\tDrawSpeed =\t$(params["DrawSpeed"]) [µl/s]\r\n",
"\tDrawDelay =\t$(params["DrawDelay"]) [ms]\r\n",
"\tDispSpeed =\t$(params["DispSpeed"]) [µl/s]\r\n",
"\tDispenseDelay =\t$(params["DispenseDelay"]) [ms]\r\n",
"\tWasteSpeed =\t$(params["WasteSpeed"]) [µl/s]\r\n",
"\tSampleHeight =\t$(params["SampleHeight"]) [mm]\r\n",
"\tInjectWash =\t$(params["InjectWash"])\r\n",
"\tWashVolume =\t$(params["WashVolume"]) [µl]\r\n",
"\tWashSpeed =\t$(params["WashSpeed"]) [µl/s]\r\n",
"\tLoopWashFactor =\t$(params["LoopWashFactor"])\r\n",
"\tPunctureOffset =\t$(params["PunctureOffset"]) [mm]\r\n",
"\tPumpDevice =\t$(params["PumpDevice"])\r\n",
"\tSyncWithPump =\t$(params["SyncWithPump"])\r\n",
"\tPump_Pressure.Step =\t$(params["Pump_Pressure.Step"]) [s]\r\n",
"\tPump_Pressure.Average =\t$(params["Pump_Pressure.Average"])\r\n",
"\tCurve =\t$(params["Curve"])\r\n\r\n",

"\tFlow =\t$(params["Flow"]) [ml/min]\r\n\r\n",

"\t; Wait for the Ready signals from the pump and autsosampler\r\n",
" 0.000\tWait\tPump.Ready and Sampler.Ready and PumpModule.Ready\r\n\r\n",

"\tInjectMode =\tUserProg\r\n\r\n",

"\t; The following section of code (containing all beginning with 'Udp') is not evaluated by Chromeleon as it is read.\r\n",
"\t; Instead, the commands are carried out when the 'Inject' command is read.\r\n\r\n",

"\t; USER DEFINED INJECTION STARTS HERE\r\n\r\n",

"\t; Wait for the stimulus input to have a Low signal, to prevent trigger of two injections from a single signal\r\n",
"\tUdpWaitInput\tInput=Inp1, State=Low\r\n\r\n",

"\t; Preflush the injection needle\r\n",
"\tUdpInjectValve\tPosition=Inject\r\n",
"\tUdpSyringeValve\tPosition=Needle\r\n",
"\tUdpDraw\tFrom=SampleVial, Volume=$(params["PreflushVolume"]), SyringeSpeed=GlobalSpeed, SampleHeight=Globalheight\r\n",
"\tUdpMixWait\tDuration=$(parse(Float64, params["DrawDelay"])/1000) ; Pause to avoid air intake from aspirating the sample too quickly\r\n\r\n",

"\t; Fill the Sample Loop with the plate position and volume specified by the sequence file\r\n",
"\tUdpInjectValve\tPosition=Load\r\n",
"\tUdpDraw\tFrom=SampleVial, Volume=Volume, SyringeSpeed=GlobalSpeed, SampleHeight=Globalheight\r\n",
"\tUdpMixWait\tDuration=$(parse(Float64, params["DrawDelay"])/1000) ; Pause to avoid air intake from aspirating the sample too quickly\r\n\r\n",

"\t; Wait for the signal from Image before performing the injection\r\n",
"\tUdpWaitInput\tInput=Inp1, State=High\r\n\r\n",

"\t; Inject the sample and signal to Chromeleon that the injection has been performed\r\n",
"\tUdpInjectValve\tPosition=Inject\r\n",
"\tUdpInjectMarker\r\n\r\n",

"\t; Wash the needle\r\n",
"\tUdpSyringeValve\tPosition=Waste\r\n",
"\tUdpMoveSyringeHome\tSyringeSpeed=GlobalSpeed\r\n",
"\tUdpMixNeedleWash\tVolume=$(params["WashVolume"])\r\n\r\n",

"\t; USER DEFINED INJECTION ENDS HERE\r\n\r\n",

"\t; Perform the user-defined injection (see above)\r\n",
"\tInject\r\n\r\n",

"\t; Send timestamp signal to imagine\r\n",
"\tRelay_4.State\tOn\r\n\r\n",

"\t; Start recording the pump pressure (not used for optical records, but I'm not sure if it is safe to omit this step)\r\n",
"\tPump_Pressure.AcqOn\r\n\r\n",

" $(params["Delay"])\tPump_Pressure.AcqOff ; Stop pressure acquisition\r\n",
"\t; Note the time of the above command (in minutes).\r\n",
"\t; This time interval may be important for fully emptying/washing the Sample Loop.\r\n",
"\t; If set too long, it might also cause Chromeleon to \"miss\" a signal from Imagine.\r\n\r\n",

"\t; Check your flowrate for the pump (\"Flow\" above), sample volume in your sequence file,\r\n",
"\t; and inter-trial delay for your Imagine waveforms to avoid issues.\r\n\r\n",

"\t; Turn off Relay 4\r\n",
"\tRelay_4.State\tOff\r\n\r\n",

"\tEnd\r\n",
)
flush(io)
end

97 changes: 97 additions & 0 deletions src/seqfile.jl
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"""
stim_randomize(filein, trials::Int, fileout=insertfilename(filein, "_sequence"))

Generate a randomize sequence of stimuli. `filein` is a string containing the name
of a CSV file that describes the unique stimuli (see format described in the README).
`trials` specifies the number of pseudo-random sequences used to generate the
final stimulus sequence.
`fileout` is an optional argument used to control the name of the output file;
the default is to insert "_sequence" right before the extension of `filein`.
"""
function stim_randomize(filein::AbstractString, trials::Int; fileout=insertfilename(filein, "_sequence"), kwargs...)
open(fileout, "w") do io
stim_randomize(io, filein, trials; kwargs...)
end
return fileout
end

function stim_randomize(io::IO, filein::AbstractString, trials::Int; header=false, kwargs...)
df = CSV.File(filein) |> DataFrame
println("Headers found: ", String.(names(df)))
n = size(df, 1)
println(n, " stimuli found")
# $ is a disallowed character since we will use it as a separator
for i = 1:n
occursin('\$', df[i,1]) && error("\$ is disallowed in stimulus names")
end
p = Int[]
for i = 1:trials
append!(p, randperm(n))
end
CSV.write(io, df[p, :]; header=header, kwargs...)
flush(io)
end

function update_imagine(imaginefile, sequencefile; um_per_pixel=nothing, aifile=replaceext(imaginefile, ".ai"), difile=replaceext(imaginefile, ".di"), updatedfile=imaginefile, csvheader=0, kwargs...)
header = ImagineFormat.parse_header(imaginefile)
haskey(header, "stimulus sequence") && error(imaginefile, " already has a `stimulus sequence` entry")
if um_per_pixel === nothing
um_per_pixel = header["um per pixel"]
end
um_per_pixel < 0 && error("must specify um_per_pixel")
header["um per pixel"] = um_per_pixel

df = CSV.File(sequencefile; header=csvheader, kwargs...) |> DataFrame
n = size(df, 1)

# Scan the AI file for stimulus triggers
ai = parse_ai(aifile, header)
aistim = getname(ai, "stimuli")
stimhi = find_pulse_starts(aistim; sampmap=:volts)
stimlo = find_pulse_stops(aistim; sampmap=:volts)
if occursin("camera frame TTL", header["label list"])
aiframe = getname(ai, "camera frame TTL")
framestarts = find_pulse_starts(aiframe; sampmap=:volts)
elseif occursin("camera1 frame monitor", header["di label list"])
di = parse_di(difile, header)
diframe = getname(di, "camera1 frame monitor")
framestarts = find_pulse_starts(diframe) #; sampmap=:volts)
end

# Record as frameidx after the stimulus trigger
fps = header["frames per stack"]
framehi, framelo = Int[], Int[]
for (frameidxs, scanidxs) in ((framehi, stimhi), (framelo, stimlo))
for i in scanidxs
idx = last(searchsorted(framestarts, i))
push!(frameidxs, idx)
end
end

# Add to header
header["stimulus sequence"] = join(df[:,1], '\$')
header["stimulus scan hi"] = stimhi
header["stimulus scan lo"] = stimlo
header["stimulus frame hi"] = framehi
header["stimulus frame lo"] = framelo

if updatedfile == imaginefile
mv(imaginefile, imaginefile*".orig")
sleep(0.25)
isfile(imaginefile) && error("failed to move the old file")
end
ImagineFormat.save_header(updatedfile, header; misc=(
"stimulus sequence", "stimulus scan hi", "stimulus scan lo",
"stimulus frame hi", "stimulus frame lo"))
return header
end

function insertfilename(filename, tail)
basename, ext = splitext(filename)
return basename*tail*ext
end

function replaceext(filename, ext)
basename, _ = splitext(filename)
return basename*ext
end