Merge pull request #11 from Cody-G/cjg/waveform_mode

Cjg/waveform mode
timholy · Jul 21, 2017 · 2657497 · 2657497
2 parents db2ca07 + 88bb12e
commit 2657497
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Showing 3 changed files with 20 additions and 2 deletions.
diff --git a/src/ImagineFormat.jl b/src/ImagineFormat.jl
@@ -126,6 +126,9 @@ end
 
 _unit_string_dict = Dict("um" => μm, "s" => s, "us" => μs, "MHz" => MHz)
 function parse_quantity(s::AbstractString, strict::Bool = true)
+    if s == "NA"
+        return Float64(NaN)
+    end
     # Find the last character of the numeric component
     m = match(r"[0-9\.\+-](?![0-9\.\+-])", s)
     if m == nothing
@@ -155,14 +158,20 @@ const field_key_dict = Dict{AbstractString,Function}(
     "comment"                      => identity,
     "ai data file"                 => identity,
     "image data file"              => identity,
+    "di data file"                 => identity,
+    "command file"                 => identity,
     "start position"               => parse_quantity,
     "stop position"                => parse_quantity,
     "bidirection"                  => x->parse(Int,x) != 0,
     "output scan rate"             => x->parse_quantity(x, false),
     "nscans"                       => x->parse(Int,x),
+    "di nscans"                    => x->parse(Int,x),
     "channel list"                 => parse_vector_int,
+    "di channel list"              => parse_vector_int,
     "label list"                   => identity,
+    "di label list"                => identity,
     "scan rate"                    => x->parse_quantity(x, false),
+    "di scan rate"                 => x->parse_quantity(x, false),
     "min sample"                   => x->parse(Int,x),
     "max sample"                   => x->parse(Int,x),
     "min input"                    => x->parse(Float64,x),

diff --git a/test/runtests.jl b/test/runtests.jl
@@ -33,7 +33,7 @@ str = String(take!(io))
 # Optional fields
 MHz = u"MHz"
 μs = u"μs"
-@test img["imagineheader"]["readout rate"] == img2["imagineheader"]["readout rate"] == 35.0MHz
+@test isnan(img["imagineheader"]["readout rate"]) && isnan(img2["imagineheader"]["readout rate"]) #marked as NA in test.imagine
 @test img["imagineheader"]["vertical shift speed"] == img2["imagineheader"]["vertical shift speed"] == 1.9176μs
 
 h = ImagineFormat.parse_header("test_noshift.imagine")

diff --git a/test/test.imagine b/test/test.imagine
@@ -4,12 +4,15 @@ header version=5.1
 app version=0.9, build (Sep  4 2007, 14:11:42)
 date and time=2009-12-29T13:16:39
 byte order=l
+rig=ocpi-1
 
 [misc params]
 stimulus file content=STIMSEQ\nheader size=9 lines\nversion=3.0\napp version=3.0\ndatetime=2009-12-29T11:20:22\npost seq valve=0\nunit=stack\nunit offset=0\ncomment=\n0 	0 	Flush (leading)\n1 	5 	K+\n0 	10 	Flush (inter-stim)\n5 	20 	A7864\n0 	25 	Flush (inter-stim)\n14 	35 	Q3910\n0 	40 	Flush (inter-stim)\n8 	50 	E4105\n0 	55 	Flush (inter-stim)\n3 	65 	A6940\n0 	70 	Flush (inter-stim)\n10 	80 	P3865\n0 	85 	Flush (inter-stim)\n11 	95 	P8200\n0 	100 	Flush (inter-stim)\n4 	110 	A7010\n0 	115 	Flush (inter-stim)\n6 	125 	E0893\n0 	130 	Flush (inter-stim)\n13 	140 	Q3383\n0 	145 	Flush (inter-stim)\n12 	155 	Q1570\n0 	160 	Flush (inter-stim)\n9 	170 	P3817\n0 	175 	Flush (inter-stim)\n2 	185 	Ringers\n0 	190 	Flush (inter-stim)\n7 	200 	E1050\n0 	205 	Flush (inter-stim)\n13 	215 	Q3383\n0 	220 	Flush (inter-stim)\n9 	230 	P3817\n0 	235 	Flush (inter-stim)\n10 	245 	P3865\n0 	250 	Flush (inter-stim)\n12 	260 	Q1570\n0 	265 	Flush (inter-stim)\n1 	275 	K+\n0 	280 	Flush (inter-stim)\n14 	290 	Q3910\n0 	295 	Flush (inter-stim)\n11 	305 	P8200\n0 	310 	Flush (inter-stim)\n3 	320 	A6940\n0 	325 	Flush (inter-stim)\n6 	335 	E0893\n0 	340 	Flush (inter-stim)\n5 	350 	A7864\n0 	355 	Flush (inter-stim)\n2 	365 	Ringers\n0 	370 	Flush (inter-stim)\n8 	380 	E4105\n0 	385 	Flush (inter-stim)\n4 	395 	A7010\n0 	400 	Flush (inter-stim)\n7 	410 	E1050\n0 	415 	Flush (inter-stim)\n11 	425 	P8200\n0 	430 	Flush (inter-stim)\n5 	440 	A7864\n0 	445 	Flush (inter-stim)\n10 	455 	P3865\n0 	460 	Flush (inter-stim)\n9 	470 	P3817\n0 	475 	Flush (inter-stim)\n8 	485 	E4105\n0 	490 	Flush (inter-stim)\n4 	500 	A7010\n0 	505 	Flush (inter-stim)\n13 	515 	Q3383\n0 	520 	Flush (inter-stim)\n6 	530 	E0893\n0 	535 	Flush (inter-stim)\n12 	545 	Q1570\n0 	550 	Flush (inter-stim)\n2 	560 	Ringers\n0 	565 	Flush (inter-stim)\n7 	575 	E1050\n0 	580 	Flush (inter-stim)\n3 	590 	A6940\n0 	595 	Flush (inter-stim)\n1 	605 	K+\n0 	610 	Flush (inter-stim)\n14 	620 	Q3910\n0 	625 	Flush (inter-stim)\n7 	635 	E1050\n0 	640 	Flush (inter-stim)\n14 	650 	Q3910\n0 	655 	Flush (inter-stim)\n4 	665 	A7010\n0 	670 	Flush (inter-stim)\n2 	680 	Ringers\n0 	685 	Flush (inter-stim)\n10 	695 	P3865\n0 	700 	Flush (inter-stim)\n3 	710 	A6940\n0 	715 	Flush (inter-stim)\n1 	725 	K+\n0 	730 	Flush (inter-stim)\n8 	740 	E4105\n0 	745 	Flush (inter-stim)\n11 	755 	P8200\n0 	760 	Flush (inter-stim)\n13 	770 	Q3383\n0 	775 	Flush (inter-stim)\n5 	785 	A7864\n0 	790 	Flush (inter-stim)\n12 	800 	Q1570\n0 	805 	Flush (inter-stim)\n6 	815 	E0893\n0 	820 	Flush (inter-stim)\n9 	830 	P3817\n0 	835 	Flush (inter-stim)\n5 	845 	A7864\n0 	850 	Flush (inter-stim)\n2 	860 	Ringers\n0 	865 	Flush (inter-stim)\n10 	875 	P3865\n0 	880 	Flush (inter-stim)\n6 	890 	E0893\n0 	895 	Flush (inter-stim)\n14 	905 	Q3910\n0 	910 	Flush (inter-stim)\n12 	920 	Q1570\n0 	925 	Flush (inter-stim)\n3 	935 	A6940\n0 	940 	Flush (inter-stim)\n4 	950 	A7010\n0 	955 	Flush (inter-stim)\n13 	965 	Q3383\n0 	970 	Flush (inter-stim)\n8 	980 	E4105\n0 	985 	Flush (inter-stim)\n7 	995 	E1050\n0 	1000 	Flush (inter-stim)\n11 	1010 	P8200\n0 	1015 	Flush (inter-stim)\n9 	1025 	P3817\n0 	1030 	Flush (inter-stim)\n1 	1040 	K+\n0 	1045 	Flush (post-seq)\n
 comment=
 ai data file=F:/VNO/2009_12_29/vno_2009_12_29_2.ai
+di data file=F:/VNO/2009_12_29/vno_2009_12_29_2.di
 image data file=F:/VNO/2009_12_29/vno_2009_12_29_2.stacks\stack_%1_
+command file=F:/VNO/2009_12_29/vno_2009_12_29_2.stacks\stack_%1_.json
 piezo=start position: 0 um;stop position: 200 um;output scan rate: 10000
 
 [ai]
@@ -22,6 +25,12 @@ max sample=2047
 min input=-10
 max input=10
 
+[di]
+di nscans=-1
+di channel list=7 -1 -1 -1 -1 -1 -1 -1
+di label list=camera1 frame monitor$unused$unused$unused$unused$unused$unused$unused
+di scan rate=10000
+
 [camera]
 original image depth=14
 saved image depth=14
@@ -35,7 +44,7 @@ EM gain=25
 exposure time=0.05 s
 vertical shift speed=1.9176 us
 vertical clock vol amp=0
-readout rate=35 MHz
+readout rate=NA
 pixel order=x y z
 frame index offset=0
 frames per stack=3