Convert DAQ from NIDAQ.jl to DAQmx.jl

CLAUDE.md

@@ -87,6 +87,25 @@ Hardware implementations use `ccall` for vendor SDKs:
 - `mcl_stage/*.jl` - Mad City Labs NanoDrive
 - Serial devices (CrystaLaser, Vortran, Triggerscope) use `LibSerialPort`
 
+### Camera Image Data Convention
+
+**Convention:** Image data is stored and displayed as column-major `(H, W, N)` arrays where `data[row, col]` = `data[y, x]`.
+
+**At DLL boundary (getdata):** C SDKs return row-major buffers. Must permute after reshape:
+```julia
+# WRONG: reshape(buffer, (W, H)) - Julia reads column-first, data is transposed
+# CORRECT: permutedims(reshape(buffer, (W, H)), (2, 1)) -> (H, W)
+```
+
+**Display (Makie image/heatmap):** Both `image()` and `heatmap()` map dim1→x, dim2→y. For `(H, W)` data:
+```julia
+# Both work the same way:
+image(permutedims(data); axis=(yreversed=true,))    # W→x, H→y, origin top-left
+heatmap(permutedims(data); axis=(yreversed=true,))  # W→x, H→y, origin top-left
+```
+
+**Saving (HDF5):** No transform needed if getdata follows convention. Save `(H, W, N)` directly.
+
 ### Work in Progress
 
 Some hardware modules are commented out in `MicroscopeControl.jl` while under development:

Project.toml

@@ -1,11 +1,12 @@
 name = "MicroscopeControl"
 uuid = "aa70d9ae-4a1e-49fd-870a-8ccfd99f4c3e"
-authors = ["klidke@unm.edu"]
 version = "1.0.0-DEV"
+authors = ["klidke@unm.edu"]
 
 [deps]
 CEnum = "fa961155-64e5-5f13-b03f-caf6b980ea82"
 CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
+DAQmx = "bc903ccc-f951-4f60-9748-ff64248ad6aa"
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
 FFTW = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341"
 GLMakie = "e9467ef8-e4e7-5192-8a1a-b1aee30e663a"
@@ -14,23 +15,26 @@ ImageView = "86fae568-95e7-573e-a6b2-d8a6b900c9ef"
 Images = "916415d5-f1e6-5110-898d-aaa5f9f070e0"
 JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
 LibSerialPort = "a05a14c7-6e3b-5ba9-90a2-45558833e1df"
-NIDAQ = "66b72792-1abf-55ab-8064-6e9051317175"
+Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 Revise = "295af30f-e4ad-537b-8983-00126c2a3abe"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 
+[sources]
+DAQmx = {url = "https://github.com/LidkeLab/DAQmx.jl.git"}
+
 [compat]
-CairoMakie = "0.12, 0.13, 0.14, 0.15"
 CEnum = "0.5.0"
+CairoMakie = "0.12, 0.13, 0.14, 0.15"
 FFTW = "1"
 GLMakie = "0.10, 0.11, 0.12, 0.13"
 HDF5 = "0.17"
 ImageView = "0.12, 0.13"
 Images = "0.26"
 JLD2 = "0.5, 0.6"
-NIDAQ = "0.6"
+Reexport = "1.2.2"
 Revise = "3"
 Statistics = "1"
-julia = "1.10"
+julia = "1.11"
 
 [extras]
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

src/MicroscopeControl.jl

@@ -1,78 +1,32 @@
 """
-MicroscopeControl is the main module for the MicroscopeControl package. It exports all the abstract types and methods for the instrument, as well as the implementations for the hardware interfaces. It also exports the methods for saving data to an HDF5 file, and the methods for controlling the camera, stage, light source, DAQ, and FPGA. Finally, it re-exports the GUI method for the user interface.
+MicroscopeControl is the main module for the MicroscopeControl package.
+It exports all abstract types and methods for instruments, as well as the
+implementations for all hardware interfaces. It also provides methods for
+saving data to HDF5 files, and the GUI methods for user interfaces.
+
+Uses Reexport.jl to cleanly propagate exports from submodules.
 """
 module MicroscopeControl
 
 using HDF5
+using Reexport
 
-# To export the abstract types and methods for all the instruments
+# Core instrument abstraction
 include("instrument.jl")
 export AbstractInstrument
-export export_state, initialize, shutdown
+export AbstractSystem, AbstractSystemState
+export export_state, initialize, shutdown, get_state, set_state
 
-# Including the hardware interfaces and implementations and the HDF5 file saving methods
+# Hardware interfaces (abstract types + method signatures)
 include("hardware_interfaces/HardwareInterfaces.jl")
-include("hardware_implementations/HardwareImplementations.jl")
-include("h5_file_saving.jl")
-
-using .HardwareImplementations.SimulatedCamera
-using .HardwareImplementations.DCAM4
-using .HardwareImplementations.PI
-using .HardwareImplementations.SimulatedStage
-using .HardwareImplementations.MadCityLabs
-using .HardwareImplementations.PI_N472
-using .HardwareImplementations.ThorCamCSC
-using .HardwareImplementations.SimulatedLight
-using .HardwareImplementations.NIDAQcard
-using .HardwareImplementations.TCubeLaserControl
-using .HardwareImplementations.TransmissionDaqControl
-using .HardwareImplementations.CrystaLaserControl
-using .HardwareImplementations.VortranLaserControl
-using .HardwareImplementations.OK_XEM
-using .HardwareImplementations.ThorCamDCx
-# using .HardwareImplementations.Triggerscope
-# using .HardwareImplementations.MCLMicroPositioner
+@reexport using .HardwareInterfaces
 
-# # Export all HardwareImplementations modules
-# export DCAM4, SimulatedCamera, SimulatedStage, PI, MadCityLabs, PI_N472, ThorCamCSC
-# export SimulatedLight, NIDAQcard, TCubeLaserControl, TransmissionDaqControl
-# export CrystaLaserControl, VortranLaserControl, OK_XEM
+# Hardware implementations (concrete device drivers)
+include("hardware_implementations/HardwareImplementations.jl")
+@reexport using .HardwareImplementations
 
-# Export h5 file saving methods
+# HDF5 file saving utilities
+include("h5_file_saving.jl")
 export save_h5, save_attributes_and_data
 
-# Re-export camera implementations
-export SimCamera, DCAM4Camera, ThorCamCSCCamera, ThorCamDCXCamera
-export start_sequence, start_live
-export getlastframe, capture, live, sequence, abort, getdata
-export setexposuretime, settriggermode, setroi!, setexposuretime!
-export dcamprop_getvalue, DCAM_IDPROP_INTERNALFRAMERATE, CameraROI, dcamapi_uninit
-
-# Re-export stage implementations
-export PIStage, MCLStage, SimStage, N472
-export move, getposition, stopmotion, getrange
-export setvel, reference, servoxy, movexy, servo
-export move_to_z, get_z_position
-
-# Re-export light source implementations
-export SimLight, TCubeLaser, DaqTrLight, CrystaLaser, VortranLaser
-export light_on, light_off, setpower
-
-# Re-export DAQ implementations
-export NIdaq
-export showdevices, showchannels, createtask, setvoltage, readvoltage, deletetask
-
-# Re-export FPGA implementations
-export XEM
-export setexposure, enable, setupIO
-
-# Re-export triggerscope implementations
-# export Triggerscope4
-
-#re-export objective positioner implementations
-# export MclZPositioner
-
-# Re-export common GUI methods
-export gui
-
 end

src/h5_file_saving.jl

@@ -39,6 +39,13 @@ function save_group_recursive(h5parent, group_name::String, attributes::Dict, da
     # Save data
     if !isnothing(data)
         write(h5group, "data", data)
+        # Add dimension convention metadata for image data
+        if ndims(data) >= 2
+            dset = h5group["data"]
+            attrs(dset)["dimension_order"] = ndims(data) == 2 ? "HW" : "HWN"
+            attrs(dset)["dimension_labels"] = ndims(data) == 2 ? ["height", "width"] : ["height", "width", "frames"]
+            attrs(dset)["memory_layout"] = "column_major_julia"
+        end
     end
 
     # Save attributes

src/hardware_implementations/HardwareImplementations.jl

@@ -1,28 +1,71 @@
 """
-HardwareImplementations module is a container for all hardware implementations
+HardwareImplementations module is a container for all hardware implementations.
+Uses Reexport.jl to automatically propagate exports from submodules.
 """
 module HardwareImplementations
 
+using Reexport
 using ..MicroscopeControl
 
+# Camera implementations
 include("simulated_camera/SimulatedCamera.jl")
+@reexport using .SimulatedCamera
+
 include("dcam4_camera/DCAM4.jl")
+@reexport using .DCAM4
+
+include("thorcam_csc/ThorCamCSC.jl")
+@reexport using .ThorCamCSC
+
+include("thorcam_dcx/ThorCamDCx.jl")
+@reexport using .ThorCamDCx
+
+# Stage implementations
 include("pi_stage/PI.jl")
+@reexport using .PI
+
 include("simulated_stage/SimulatedStage.jl")
+@reexport using .SimulatedStage
+
 include("mcl_stage/MadCityLabs.jl")
+@reexport using .MadCityLabs
+
 include("pi_N472/PI_N472.jl")
+@reexport using .PI_N472
 
-include("thorcam_csc/ThorCamCSC.jl")
-include("thorcam_dcx/ThorCamDCx.jl")
-include("simulated_light/SimulatedLight.jl")
+# DAQ implementation (must come before modules that depend on it)
 include("nidaq/NIDAQcard.jl")
+@reexport using .NIDAQcard
+
+# Light source implementations
+include("simulated_light/SimulatedLight.jl")
+@reexport using .SimulatedLight
+
 include("tcube_laser/TCubeLaserControl.jl")
+@reexport using .TCubeLaserControl
+
 include("daq_transmission_light/TransmissionDaqControl.jl")
+@reexport using .TransmissionDaqControl
+
 include("crysta_laser_561/CrystaLaserControl.jl")
+@reexport using .CrystaLaserControl
+
 include("vortran_laser_488/VortranLaserControl.jl")
+@reexport using .VortranLaserControl
+
+# FPGA implementation (depends on NIDAQcard)
 include("ok_xem/OK_XEM.jl")
+@reexport using .OK_XEM
+
+# SLM implementation
 include("meadowlark_slm/Meadowlark.jl")
+@reexport using .Meadowlark
+
+# Work in progress - uncomment when ready
 # include("triggerscope/Triggerscope.jl")
+# @reexport using .Triggerscope
+
 # include("mcl_micro_positioner/MCLMicroPositioner.jl")
+# @reexport using .MCLMicroPositioner
 
-end
+end

src/hardware_implementations/crysta_laser_561/CrystaLaserControl.jl

@@ -5,7 +5,7 @@ A Module for controlling a laser through a NIDAQ card.
 """
 module CrystaLaserControl
 
-using NIDAQ
+using DAQmx
 
 using ...MicroscopeControl.HardwareInterfaces.LightSourceInterface
 using ...MicroscopeControl.HardwareImplementations.NIDAQcard

src/hardware_implementations/crysta_laser_561/interface_methods.jl

@@ -3,9 +3,6 @@
 """
 function initialize(light::CrystaLaser)
     light.properties.is_on = false
-    daq = light.daq
-    channelsAO = light.channelsAO
-    channelsDO = light.channelsDO
     return nothing
 end
 
@@ -19,63 +16,74 @@ Set the power of the laser by setting the voltage of the NIDAQ card.
 - `voltage::Float64`: The voltage to set the laser to.
 """
 function LightSourceInterface.setpower(light::CrystaLaser, voltage::Float64)
-    daq = light.daq
-    min_voltage = light.min_voltage
-    max_voltage = light.max_voltage
-    channelsAO = light.channelsAO
-    channelsDO = light.channelsDO
+    if isempty(light.channelsAO)
+        @warn "CrystaLaser: no AO channels available for setpower"
+        return
+    end
     if voltage < light.min_voltage || voltage > light.max_voltage
         @error "The voltage should be between $(light.min_voltage) and $(light.max_voltage)"
         return
     end
-    t = NIDAQcard.createtask(daq,"AO",channelsAO[1])
-    NIDAQcard.setvoltage(daq,t, voltage)
-    NIDAQcard.deletetask(daq,t)
+    try
+        t = NIDAQcard.createtask(light.daq, "AO", light.channelsAO[1])
+        NIDAQcard.setvoltage(light.daq, t, voltage)
+        NIDAQcard.deletetask(light.daq, t)
+    catch e
+        @warn "CrystaLaser setpower failed: $e"
+    end
 end
 
 """
     light_on(light::CrystaLaser)
 """
 function LightSourceInterface.light_on(light::CrystaLaser)
     light.properties.is_on = true
-    # power = 20.0
-    channelsAO = light.channelsAO
-    channelsDO = light.channelsDO
-    # voltage = (power-10)/90*(light.max_voltage-light.min_voltage)+light.min_voltage
-    # light.properties.power = power
-    voltage = 1.0
-    daq = light.daq
-    t = NIDAQcard.createtask(daq,"AO",light.channelsAO[1])
-    NIDAQcard.setvoltage(daq,t, voltage)
-    NIDAQcard.deletetask(daq,t)
+    if isempty(light.channelsAO)
+        @warn "CrystaLaser: no AO channels available for light_on"
+        return
+    end
+    try
+        t = NIDAQcard.createtask(light.daq, "AO", light.channelsAO[1])
+        NIDAQcard.setvoltage(light.daq, t, 1.0)
+        NIDAQcard.deletetask(light.daq, t)
+    catch e
+        @warn "CrystaLaser light_on failed: $e"
+    end
 end
 
 """
     light_off(light::CrystaLaser)
 """
 function LightSourceInterface.light_off(light::CrystaLaser)
     light.properties.is_on = false
-    daq = light.daq
-    channelsAO = light.channelsAO
-    channelsDO = light.channelsDO
-    voltage::Float64 = 0.0
-    t = NIDAQcard.createtask(daq,"AO",light.channelsAO[1])
-    NIDAQcard.setvoltage(daq,t, voltage)
-    NIDAQcard.deletetask(daq,t)
+    if isempty(light.channelsAO)
+        @warn "CrystaLaser: no AO channels available for light_off"
+        return
+    end
+    try
+        t = NIDAQcard.createtask(light.daq, "AO", light.channelsAO[1])
+        NIDAQcard.setvoltage(light.daq, t, 0.0)
+        NIDAQcard.deletetask(light.daq, t)
+    catch e
+        @warn "CrystaLaser light_off failed: $e"
+    end
 end
 
 """
     shutdown(light::CrystaLaser)
 """
 function shutdown(light::CrystaLaser)
     light.properties.is_on = false
-    daq = light.daq
-    channelsAO = light.channelsAO
-    channelsDO = light.channelsDO
-    voltage::Float64 = 0.0
-    t = NIDAQcard.createtask(daq,"AO",light.channelsAO[1])
-    NIDAQcard.setvoltage(daq,t, voltage)
-    NIDAQcard.deletetask(daq,t)
+    if isempty(light.channelsAO)
+        return
+    end
+    try
+        t = NIDAQcard.createtask(light.daq, "AO", light.channelsAO[1])
+        NIDAQcard.setvoltage(light.daq, t, 0.0)
+        NIDAQcard.deletetask(light.daq, t)
+    catch e
+        @warn "CrystaLaser shutdown failed: $e"
+    end
 end
 
 """