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Merged
Cody-G merged 11 commits into from
Jul 21, 2017
Merged

Cjg/read inputs #23

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850ead2
Move these functions into the hardware constants file.
Cody-G Jun 28, 2017
4105540
Add function for extracting daq channel number from string
Cody-G Jun 28, 2017
833be02
Make the ImagineCommand type parametric, and enforce that output comm…
Cody-G Jun 28, 2017
fcd6574
Read .ai and .di files as ImagineCommands.
Cody-G Jun 29, 2017
45643cb
Export more functions, improve tests.
Cody-G Jul 5, 2017
912ee1f
Consider the jitter time of the camera when used in external triggeri…
Cody-G Jul 5, 2017
f6684a3
Update example files and parsing code for new conventions. Use Ordere…
Cody-G Jul 11, 2017
b2a1206
Generalize pulse finding and counting, add tests for new input functi…
Cody-G Jul 11, 2017
de94bac
Default to keeping laser on when frac is set greater than OR equal to…
Cody-G Jul 11, 2017
4028b63
Split rig-specific hardware constants into separate files in a rigs f…
Cody-G Jul 20, 2017
353a458
Drop support for julia 0.5
Cody-G Jul 21, 2017
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1 change: 0 additions & 1 deletion .travis.yml
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Expand Up @@ -4,7 +4,6 @@ os:
- linux
- osx
julia:
- 0.5
- 0.6
notifications:
email: false
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3 changes: 2 additions & 1 deletion REQUIRE
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Expand Up @@ -3,4 +3,5 @@ AxisArrays
IntervalSets
Unitful
MappedArrays
Compat 0.18
ImagineFormat
DataStructures
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55 changes: 55 additions & 0 deletions examples/t.imagine
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IMAGINE
[general]
header version=7
app version=2.0, build (Jul 5 2017, 10:40:58)
date and time=2017-07-05T11:13:58
byte order=l
rig=ocpi-2

[misc params]
stimulus file content=
comment=
ai data file=t.ai
di data file=t.di
image data file=d:t.cam
command file=t.json
piezo=start position: NA;stop position: NA;output scan rate: 50000;bidirection: 0

[ai]
nscans=-1
channel list=0 2
label list=axial piezo monitor$camera1 analog monitor
scan rate=50000
min sample=-32768
max sample=32767
min input=-10
max input=10

[di]
di nscans=-1
di channel list=24 25 26 27 28 29 30 31
di label list=camera1 frame monitor$camera2 frame monitor$laser monitor$unused$unused$unused$unused$unused
di scan rate=50000

[camera]
original image depth=16
saved image depth=16
image width=2060
image height=2048
number of frames requested=650
nStacks=10
idle time between stacks=NA
pre amp gain=
gain=0
exposure time=0.011 s
vertical shift speed=
vertical clock vol amp=-1
readout rate=
pixel order=x y z
frame index offset=0
frames per stack=65
pixel data type=uint16
camera=edge.main
um per pixel=-1
binning=hbin:1;vbin:1;hstart:1;hend:2060;vstart:1;vend:2048
angle from horizontal (deg)=-1
43 changes: 43 additions & 0 deletions examples/t.json
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59 changes: 59 additions & 0 deletions rigs/ocpi1.jl
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push!(RIGS, "ocpi-1")
#Mappings from DAQ channel to friendlier default names
const ocpi1_mappings = Dict("AO0"=>"axial piezo",
"AO1"=>"analogout1",
"AI0"=>"axial piezo monitor",
"AI2"=>"analogin1",
"AI3"=>"analogin2",
"AI4"=>"analogin3",
"AI5"=>"analogin4",
"AI6"=>"analogin5",
"AI7"=>"analogin6",
"AI8"=>"analogin7",
"AI9"=>"analogin8",
"AI10"=>"analogin9",
"AI11"=>"analogin10",
"AI12"=>"analogin11",
"AI13"=>"analogin12",
"AI14"=>"analogin13",
"AI15"=>"analogin14",
"P0.0"=>"stimulus1",
"P0.1"=>"stimulus2",
"P0.2"=>"stimulus3",
"P0.3"=>"stimulus4",
"P0.4"=>"488nm laser shutter",
"P0.5"=>"camera1",
"P0.6"=>"stimulus5",
"P0.7"=>"camera1 frame monitor")

DEFAULT_DAQCHANS_TO_NAMES["ocpi-1"] = ocpi1_mappings
DEFAULT_NAMES_TO_DAQCHANS["ocpi-1"] = map(reverse, ocpi1_mappings)

const ocpi1_aochans = map(x->"AO$(x)", 0:1)
const ocpi1_aichans = map(x->"AI$(x)", vcat([0;], [2:15...])) #currently AI1 is unused
const ocpi1_dochans = map(x->"P0.$(x)", 0:6)
const ocpi1_dichans = ["P0.7";]
const ocpi1_pos_ctrl_chans = map(x->DEFAULT_NAMES_TO_DAQCHANS["ocpi-1"][x], ["axial piezo"])
const ocpi1_pos_mon_chans = map(x->DEFAULT_NAMES_TO_DAQCHANS["ocpi-1"][x], ["axial piezo monitor"])
const ocpi1_cam_ctrl_chans = map(x->DEFAULT_NAMES_TO_DAQCHANS["ocpi-1"][x], ["camera1"])
const ocpi1_cam_mon_chans = map(x->DEFAULT_NAMES_TO_DAQCHANS["ocpi-1"][x], ["camera1 frame monitor"])
const ocpi1_laschans = map(x->DEFAULT_NAMES_TO_DAQCHANS["ocpi-1"][x], ["488nm laser shutter"])
const ocpi1_stimchans = map(x->DEFAULT_NAMES_TO_DAQCHANS["ocpi-1"][x], ["stimulus$x" for x = 1:5])
const ocpi1_fixed_names = ["axial piezo", "axial piezo monitor", "488nm laser shutter", "camera1", "camera1 frame monitor"]
const ocpi1_fixed_daqchans = map(x->DEFAULT_NAMES_TO_DAQCHANS["ocpi-1"][x], ocpi1_fixed_names)

AO_CHANS["ocpi-1"] = OrderedSet(ocpi1_aochans)
AI_CHANS["ocpi-1"] = OrderedSet(ocpi1_aichans)
DO_CHANS["ocpi-1"] = OrderedSet(ocpi1_dochans)
DI_CHANS["ocpi-1"] = OrderedSet(ocpi1_dichans)
POS_CONTROL_CHANS["ocpi-1"] = ocpi1_pos_ctrl_chans
POS_MONITOR_CHANS["ocpi-1"] = ocpi1_pos_mon_chans
CAM_CONTROL_CHANS["ocpi-1"] = ocpi1_cam_ctrl_chans
CAM_MONITOR_CHANS["ocpi-1"] = ocpi1_cam_mon_chans
LAS_CONTROL_CHANS["ocpi-1"] = ocpi1_laschans
STIM_CHANS["ocpi-1"] =OrderedSet(ocpi1_stimchans)
FIXED_NAMES["ocpi-1"] = ocpi1_fixed_names
FIXED_DAQ_CHANS["ocpi-1"] = ocpi1_fixed_daqchans

RIG_CHIP_SIZES["ocpi-1"] = PCO_EDGE_5_5_CHIP_SIZE
RIG_FRAMERATE_FUNCS["ocpi-1"] = PCO_EDGE_5_5_FRAMERATE_FUNC
102 changes: 102 additions & 0 deletions rigs/ocpi2.jl
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push!(RIGS, "ocpi-2")

const ocpi2_mappings = Dict("AO0"=>"axial piezo",
"AO1"=>"horizontal piezo",
"AO2"=>"analogout3",
"AO3"=>"analogout4",
"AI0"=>"axial piezo monitor",
"AI1"=>"horizontal piezo monitor",
"AI2"=>"analogin1",
"AI3"=>"analogin2",
"AI4"=>"analogin3",
"AI5"=>"analogin4",
"AI6"=>"analogin5",
"AI7"=>"analogin6",
"AI8"=>"analogin7",
"AI9"=>"analogin8",
"AI10"=>"analogin9",
"AI11"=>"analogin10",
"AI12"=>"analogin11",
"AI13"=>"analogin12",
"AI14"=>"analogin13",
"AI15"=>"analogin14",
"AI16"=>"analogin15",
"AI17"=>"analogin16",
"AI18"=>"analogin17",
"AI19"=>"analogin18",
"AI20"=>"analogin19",
"AI21"=>"analogin20",
"AI22"=>"analogin21",
"AI23"=>"analogin22",
"AI24"=>"analogin23",
"AI25"=>"analogin24",
"AI26"=>"analogin25",
"AI27"=>"analogin26",
"AI28"=>"analogin27",
"AI29"=>"analogin28",
"AI30"=>"analogin29",
"AI31"=>"analogin30",
"P0.0"=>"stimulus1",
"P0.1"=>"stimulus2",
"P0.2"=>"stimulus3",
"P0.3"=>"stimulus4",
"P0.4"=>"all lasers",
"P0.5"=>"camera1",
"P0.6"=>"camera2",
# "P0.7"=>"reserved",
"P0.8"=>"405nm laser",
"P0.9"=>"445nm laser",
"P0.10"=>"488nm laser",
"P0.11"=>"514nm laser",
"P0.12"=>"561nm laser",
"P0.13"=>"stimulus5",
"P0.14"=>"stimulus6",
"P0.15"=>"stimulus7",
"P0.16"=>"stimulus8",
"P0.17"=>"stimulus9",
"P0.18"=>"stimulus10",
"P0.19"=>"stimulus11",
"P0.20"=>"stimulus12",
"P0.21"=>"stimulus13",
"P0.22"=>"stimulus14",
"P0.23"=>"stimulus15",
"P0.24"=>"camera1 frame monitor",
"P0.25"=>"camera2 frame monitor",
"P0.26"=>"diginput1",
"P0.27"=>"diginput2",
"P0.28"=>"diginput3",
"P0.29"=>"diginput4",
"P0.30"=>"diginput5",
"P0.31"=>"diginput6",)

DEFAULT_DAQCHANS_TO_NAMES["ocpi-2"] = ocpi2_mappings
DEFAULT_NAMES_TO_DAQCHANS["ocpi-2"] = map(reverse, ocpi2_mappings)

const ocpi2_aochans = map(x->"AO$(x)", 0:3)
const ocpi2_aichans = map(x->"AI$(x)", 0:31)
const ocpi2_dochans = map(x->"P0.$(x)", vcat([0:6...], [8:23...]))
const ocpi2_dichans = map(x->"P0.$(x)", 24:31)
const ocpi2_pos_ctrl_chans = map(x->DEFAULT_NAMES_TO_DAQCHANS["ocpi-2"][x], ["axial piezo"; "horizontal piezo"])
const ocpi2_pos_mon_chans = map(x->DEFAULT_NAMES_TO_DAQCHANS["ocpi-2"][x], ["axial piezo monitor"; "horizontal piezo monitor"])
const ocpi2_cam_ctrl_chans = map(x->DEFAULT_NAMES_TO_DAQCHANS["ocpi-2"][x], ["camera1"; "camera2"])
const ocpi2_cam_mon_chans = map(x->DEFAULT_NAMES_TO_DAQCHANS["ocpi-2"][x], ["camera1 frame monitor"; "camera2 frame monitor"])
const ocpi2_laschans = map(x->DEFAULT_NAMES_TO_DAQCHANS["ocpi-2"][x], ["405nm laser"; "445nm laser"; "488nm laser"; "514nm laser"; "561nm laser"; "all lasers"])
const ocpi2_stimchans = map(x->DEFAULT_NAMES_TO_DAQCHANS["ocpi-2"][x], ["stimulus$x" for x = 1:15])
const ocpi2_fixed_names = ["axial piezo", "axial piezo monitor", "horizontal piezo", "horizontal piezo monitor", "camera1", "camera1 frame monitor", "camera2", "camera2 frame monitor", "405nm laser", "445nm laser", "488nm laser", "514nm laser", "561nm laser"]
const ocpi2_fixed_daqchans = map(x->DEFAULT_NAMES_TO_DAQCHANS["ocpi-2"][x], ocpi2_fixed_names)

AO_CHANS["ocpi-2"] = OrderedSet(ocpi2_aochans)
AI_CHANS["ocpi-2"] = OrderedSet(ocpi2_aichans)
DO_CHANS["ocpi-2"] = OrderedSet(ocpi2_dochans)
DI_CHANS["ocpi-2"] = OrderedSet(ocpi2_dichans)
POS_CONTROL_CHANS["ocpi-2"] = ocpi2_pos_ctrl_chans
POS_MONITOR_CHANS["ocpi-2"] = ocpi2_pos_mon_chans
CAM_CONTROL_CHANS["ocpi-2"] = ocpi2_cam_ctrl_chans
CAM_MONITOR_CHANS["ocpi-2"] = ocpi2_cam_mon_chans
LAS_CONTROL_CHANS["ocpi-2"] = ocpi2_laschans
STIM_CHANS["ocpi-2"] =OrderedSet(ocpi2_stimchans)
FIXED_NAMES["ocpi-2"] = ocpi2_fixed_names
FIXED_DAQ_CHANS["ocpi-2"] = ocpi2_fixed_daqchans

RIG_CHIP_SIZES["ocpi-2"] = PCO_EDGE_4_2_CHIP_SIZE
RIG_FRAMERATE_FUNCS["ocpi-2"] = PCO_EDGE_4_2_FRAMERATE_FUNC
104 changes: 104 additions & 0 deletions rigs/ocpi_lsk.jl
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push!(RIGS, "ocpi-lsk")

#Much like OCPI2, but with missing channels for missing hardware
const ocpi_lsk_mappings = Dict("AO0"=>"axial piezo",
# "AO1"=>"reserved",
"AO2"=>"analogout3",
"AO3"=>"analogout4",
"AI0"=>"axial piezo monitor",
# "AI1"=>"reserved",
"AI2"=>"analogin1",
"AI3"=>"analogin2",
"AI4"=>"analogin3",
"AI5"=>"analogin4",
"AI6"=>"analogin5",
"AI7"=>"analogin6",
"AI8"=>"analogin7",
"AI9"=>"analogin8",
"AI10"=>"analogin9",
"AI11"=>"analogin10",
"AI12"=>"analogin11",
"AI13"=>"analogin12",
"AI14"=>"analogin13",
"AI15"=>"analogin14",
"AI16"=>"analogin15",
"AI17"=>"analogin16",
"AI18"=>"analogin17",
"AI19"=>"analogin18",
"AI20"=>"analogin19",
"AI21"=>"analogin20",
"AI22"=>"analogin21",
"AI23"=>"analogin22",
"AI24"=>"analogin23",
"AI25"=>"analogin24",
"AI26"=>"analogin25",
"AI27"=>"analogin26",
"AI28"=>"analogin27",
"AI29"=>"analogin28",
"AI30"=>"analogin29",
"AI31"=>"analogin30",
"P0.0"=>"stimulus1",
"P0.1"=>"stimulus2",
"P0.2"=>"stimulus3",
"P0.3"=>"stimulus4",
"P0.4"=>"all lasers",
"P0.5"=>"camera1",
# "P0.6"=>"reserved",
# "P0.7"=>"reserved",
# "P0.8"=>"reserved",
# "P0.9"=>"reserved",
# "P0.10"=>"reserved",
# "P0.11"=>"reserved",
# "P0.12"=>"reserved",
"P0.13"=>"stimulus5",
"P0.14"=>"stimulus6",
"P0.15"=>"stimulus7",
"P0.16"=>"stimulus8",
"P0.17"=>"stimulus9",
"P0.18"=>"stimulus10",
"P0.19"=>"stimulus11",
"P0.20"=>"stimulus12",
"P0.21"=>"stimulus13",
"P0.22"=>"stimulus14",
"P0.23"=>"stimulus15",
"P0.24"=>"camera1 frame monitor",
# "P0.25"=>"reserved",
"P0.26"=>"diginput1",
"P0.27"=>"diginput2",
"P0.28"=>"diginput3",
"P0.29"=>"diginput4",
"P0.30"=>"diginput5",
"P0.31"=>"diginput6",)

DEFAULT_DAQCHANS_TO_NAMES["ocpi-lsk"] = ocpi_lsk_mappings
DEFAULT_NAMES_TO_DAQCHANS["ocpi-lsk"] = map(reverse, ocpi_lsk_mappings)

const ocpi_lsk_pos_ctrl_chans = map(x->DEFAULT_NAMES_TO_DAQCHANS["ocpi-lsk"][x], ["axial piezo"])
const ocpi_lsk_aochans = map(x->"AO$(x)", [0;2;3])
const ocpi_lsk_aichans = map(x->"AI$(x)", vcat([0;], [2:15...])) #currently AI1 is unused
const ocpi_lsk_dochans = map(x->"P0.$(x)", vcat([0:5...], [13:23...]))
const ocpi_lsk_dichans = map(x->"P0.$(x)", vcat([24;], [26:31...]))
const ocpi_lsk_pos_mon_chans = map(x->DEFAULT_NAMES_TO_DAQCHANS["ocpi-lsk"][x], ["axial piezo monitor"])
const ocpi_lsk_cam_ctrl_chans = map(x->DEFAULT_NAMES_TO_DAQCHANS["ocpi-lsk"][x], ["camera1"])
const ocpi_lsk_cam_mon_chans = map(x->DEFAULT_NAMES_TO_DAQCHANS["ocpi-lsk"][x], ["camera1 frame monitor"])
const ocpi_lsk_laschans = map(x->DEFAULT_NAMES_TO_DAQCHANS["ocpi-lsk"][x], ["all lasers"])
const ocpi_lsk_stimchans = map(x->DEFAULT_NAMES_TO_DAQCHANS["ocpi-lsk"][x], ["stimulus$x" for x = 1:15])
const ocpi_lsk_fixed_names = ["axial piezo", "axial piezo monitor", "all lasers", "camera1", "camera1 frame monitor"]
const ocpi_lsk_fixed_daqchans = map(x->DEFAULT_NAMES_TO_DAQCHANS["ocpi-lsk"][x], ocpi_lsk_fixed_names)

AO_CHANS["ocpi-lsk"] = OrderedSet(ocpi_lsk_aochans)
AI_CHANS["ocpi-lsk"] = OrderedSet(ocpi_lsk_aichans)
DO_CHANS["ocpi-lsk"] = OrderedSet(ocpi_lsk_dochans)
DI_CHANS["ocpi-lsk"] = OrderedSet(ocpi_lsk_dichans)
POS_CONTROL_CHANS["ocpi-lsk"] = ocpi_lsk_pos_ctrl_chans
POS_MONITOR_CHANS["ocpi-lsk"] = ocpi_lsk_pos_mon_chans
CAM_CONTROL_CHANS["ocpi-lsk"] = ocpi_lsk_cam_ctrl_chans
CAM_MONITOR_CHANS["ocpi-lsk"] = ocpi_lsk_cam_mon_chans
LAS_CONTROL_CHANS["ocpi-lsk"] = ocpi_lsk_laschans
STIM_CHANS["ocpi-lsk"] =OrderedSet(ocpi_lsk_stimchans)
FIXED_NAMES["ocpi-lsk"] = ocpi_lsk_fixed_names
FIXED_DAQ_CHANS["ocpi-lsk"] = ocpi_lsk_fixed_daqchans

#TODO: check these
#RIG_CHIP_SIZES["ocpi-lsk"] = PCO_EDGE_5_5_CHIP_SIZE
#RIG_FRAMERATE_FUNCS["ocpi-lsk"] = PCO_EDGE_5_5_FRAMERATE_FUNC
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