fix CI errors (#104)

Author: kdw503

.github/workflows/CI.yml

@@ -13,7 +13,7 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1.1'
+          - '1.10'
           - '1'
         os:
           - ubuntu-latest
@@ -25,7 +25,7 @@ jobs:
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
-      - uses: actions/cache@v1
+      - uses: actions/cache@v4
         env:
           cache-name: cache-artifacts
         with:

Project.toml

@@ -1,6 +1,6 @@
 name = "ImagineInterface"
 uuid = "a9d8408c-0fb1-11e9-0067-cb067474114e"
-version = "0.1.7"
+version = "0.1.8"
 
 [deps]
 AxisArrays = "39de3d68-74b9-583c-8d2d-e117c070f3a9"
@@ -23,12 +23,12 @@ AxisArrays = "0.4"
 DSP = "0.6, 0.7, 0.8"
 DataStructures = "0.17, 0.18"
 ImagineFormat = "1"
-ImagineHardware = "0.0.1"
+ImagineHardware = "0.0.1, 0.1"
 IntervalSets = "0.4, 0.5, 0.6, 0.7"
 JSON = "0.21"
 MappedArrays = "0.2, 0.3, 0.4"
 Statistics = "1"
-UnitAliases = "0.0.1"
+UnitAliases = "0.0.1, 0.1"
 Unitful = "1"
 julia = "0.7, 1"
 

src/ImagineInterface.jl

@@ -7,6 +7,7 @@ using MappedArrays, IntervalSets, DataStructures, DSP
 using ImagineFormat, ImagineHardware
 import ImagineHardware:samprate
 using AxisArrays
+using DSP.Filters: normalize_freq
 const axes = Base.axes
 
 import Base: convert, show, length, size, isempty, ==, append!, prepend!, pop!, empty!, replace!#, scale

src/hardware_templates.jl

@@ -16,16 +16,16 @@ function default_samplemapper(rig::AbstractString, daq_chan_name::String; sample
     end
 end
 
-function generic_ao_samplemapper(r::AbstractInterval{Traw},v::AbstractInterval{TV};
+function generic_ao_samplemapper(r::AbstractInterval{Traw},v::AbstractInterval{TV}; rawtype=Int16,
                                 sample_rate::HasInverseTimeUnits{Int, TU}=10000s^-1) where{Traw<:Integer,TV<:HasVoltageUnits, TU}
-    return SampleMapper(minimum(r), maximum(r), minimum(v), maximum(v), minimum(v), maximum(v), sample_rate)
+    return SampleMapper(rawtype(minimum(r)), rawtype(maximum(r)), minimum(v), maximum(v), minimum(v), maximum(v), sample_rate)
 end
 
 generic_ai_samplemapper = generic_ao_samplemapper
 
-function piezo_samplemapper(r::AbstractInterval{Traw},p::AbstractInterval{TL}, v::AbstractInterval{TV};
+function piezo_samplemapper(r::AbstractInterval{Traw},p::AbstractInterval{TL}, v::AbstractInterval{TV}; rawtype=Int16,
                             sample_rate::HasInverseTimeUnits{Int, TU}=10000s^-1) where{Traw<:Integer,TL<:HasLengthUnits,TV<:HasVoltageUnits, TU}
-    return SampleMapper(minimum(r), maximum(r), minimum(v), maximum(v), minimum(p), maximum(p), sample_rate)
+    return SampleMapper(rawtype(minimum(r)), rawtype(maximum(r)), minimum(v), maximum(v), minimum(p), maximum(p), sample_rate)
 end
 
 function galvo_ctrl_samplemapper(rawtype=Int16, sample_rate::HasInverseTimeUnits{Int, TU}=10000s^-1) where TU

src/stack.jl

@@ -7,7 +7,7 @@ function apply_lp(mod_samps::AbstractVector, sampr::HasInverseTimeUnits, cutoff:
     mod_samps3 = repeat(mod_samps, 11)
     fs = ustrip(uconvert(Unitful.Hz, sampr))
     cutoff = ustrip(uconvert(Unitful.Hz, cutoff))
-    responsetype = Lowpass(cutoff; fs=fs)
+    responsetype = Lowpass(normalize_freq(cutoff, fs))
     designmethod = Butterworth(4)
     filtd = filtfilt(digitalfilter(responsetype, designmethod), ustrip.(mod_samps3)).*unit(mod_samps[1])
     return filtd[5*length(mod_samps)+1:(6*length(mod_samps))]

src/validate_single.jl

@@ -26,7 +26,7 @@ function check_piezo(pos::ImagineSignal; window_sz = 100, val_state::ValidationS
     max_sp = PIEZO_MAX_SPEED[rig_name(pos)]
     window_dur = window_sz / samprate(pos)
     max_dist = max_sp * window_dur #length units
-    max_dist_raw = ceil(Int, (max_dist/width(interval_world(pos))) * width(interval_raw(pos)))
+    max_dist_raw = ceil(Int, (max_dist/width(interval_world(pos))) * width(convert(Int64,interval_raw(pos))))
     val_func = (samps, win_sz) -> check_max_speed(samps, max_dist_raw, win_sz)
     if length(pos) < window_sz #should this throw an error?
         @warn "Insufficient samples to check this signal with a window size setting of $window_sz"
@@ -40,6 +40,12 @@ function check_piezo(pos::ImagineSignal; window_sz = 100, val_state::ValidationS
     return val_state
 end
 
+function convert(::Type{T1}, i::AbstractInterval{T2}) where {T1,T2}
+    l = convert(T1,i.left)
+    r = convert(T1,i.right)
+    Interval{:closed,:closed,T1}(l,r)
+end
+
 function check_max_speed(raw_samps::Vector, raw_change::Int, in_n_samps::Int)
     @assert length(raw_samps) >= in_n_samps
     niter = length(raw_samps) - in_n_samps + 1

test/validate.jl

@@ -217,6 +217,8 @@ replace!(sigs[1], "test3", samps)
     ############STACK PARAMETERS#################
     pmin = 0.0*μm #Piezo start position in microns
     pmax = 200.0*μm #Piezo stop position in microns
+    pms = ImagineInterface.PIEZO_MAX_SPEED[rig]
+    mn_stack_img_time = abs(pmax - pmin)/pms
     stack_img_time = 0.26s #Time to complete the imaging sweep with the piezo (remember we also need to reset it to its starting position)
     reset_time = 0.001s #Time to reset piezo to starting position.  This time plus "stack_img_time" determines how long it takes to complete an entire stack and be ready to start a new stack
     z_spacing = 3.1μm #The space between slices in the z-stack.