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[04/2020] add juxta settings

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efish
2020-04-30 14:54:13 +02:00
parent 3acc4fa942
commit a2a6d8312b
16 changed files with 1185 additions and 98 deletions
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16
torus/code/multisensory_stimuli.py
View File

@@ -33,12 +33,12 @@ class MultichannelStimulus(object):
def create_contrast_stim(self):
t = np.arange(0, self._contrast_sweep_duration, self._dt)
sweep_up = np.linspace(0., 1.0, len(t))
am = np.sin((self._eod_freq + self._df) * 2 * np.pi * t)
dc = np.sin(2*np.pi*self._dcf*t)
am = np.sin((self._eod_freq + self._df) * 2 * np.pi * t) * 0.5
dc = np.sin(2*np.pi*self._dcf*t) * 0.5
am_sweep = am * sweep_up
dc_sweep = dc * sweep_up
self._contrast_stimulus = np.hstack((am_sweep, dc_sweep, am + dc_sweep, dc + am_sweep))
self._contrast_stimulus = np.hstack((am_sweep, dc_sweep, (am + dc_sweep), (dc + am_sweep)))
header = {" ": "Contrast sweeps for ampullary and tuberous pathways",
"sd": 1.0,
"deltat": "%.5f s" % self._dt,
@@ -55,7 +55,7 @@ class MultichannelStimulus(object):
am = np.sin((self._eod_freq + self._df) * 2 * np.pi * t)
dc = np.sin(2*np.pi*self._df*t + phase_sweep)
self._phase_stimulus = am + dc
self._phase_stimulus = (am + dc)/2.
header = {" ": "Phase sweep stimulating ampullary and tuberous pathways",
"sd": 1.0,
"deltat": "%.5f s" % self._dt,
@@ -68,9 +68,9 @@ class MultichannelStimulus(object):
t = np.arange(0, self._zap_duration, self._dt)
m = self._maxfreq/self._zap_duration
dc = np.sin(2*np.pi*m*t*t)
am = np.sin(2*np.pi*(m*t + self._eod_freq)*t)
self._zap_stimulus = np.hstack((dc, am, dc+am))
dc = np.sin(2*np.pi*m*t*t) * 0.5
am = np.sin(2*np.pi*(m*t + self._eod_freq)*t) * 0.5
self._zap_stimulus = np.hstack((dc, am, (dc + am)))
header = {" ": "Zap stimulus for ampullary and tuberous pathways",
"sd": 1.0,
"deltat": "%.5f s" % self._dt,
@@ -112,7 +112,7 @@ if __name__ == "__main__":
help=args.dt_help)
parser.add_argument('-mf', '--maxfreq', type=float, default=100.,
help=args.maxfreq_help)
parser.add_argument('outfile prefix', help="name of the output file may include the path")
parser.add_argument('outfile', help="prefix name of the output file may include the path")
args = parser.parse_args()

5
torus/macros.cfg
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@@ -15,6 +15,11 @@ SAM: deltaf=20; contrast=20; duration=400ms; pause=100ms; repeats=0; am=true; fr
SAM: deltaf=20; contrast=20; duration=400ms; pause=100ms; repeats=0; am=false; freqsel=absolute; sinewave=true;
#############################################################################
$Noise AM: contrast=10%
Pause: duration=200ms
FileStimulus: file=/home/efish/stimuli/whitenoise/gwn300Hz10s0.3.dat; sigstdev=0.3; am=true; contrast=10%; repeats=5
FileStimulus: file=/home/efish/stimuli/whitenoise/gwn300Hz10s0.3.dat; sigstdev=0.3; am=true; contrast=5%; repeats=5
!FileStimulus: file=/home/efish/stimuli/whitenoise/gwn300Hz10s0.3.dat; sigstdev=0.3; am=true; contrast=20%
$Calib direct
CalibEField: am=0;

8
torus/macrotorus.cfg
View File

@@ -9,13 +9,15 @@ $FICurve DC: trials=5
FICurve: nints=10; am=false; blockrepeats=$trials
$SAMs AM
SAM: deltaf=(5,10,20)Hz; am=true; freqsel="relative to EOD"; duration=1s; repeats=5; contrast=10; name="SAM AM";
SAM: deltaf=(5,10,20,40,60,80,100)Hz; am=true; freqsel="relative to EOD"; duration=1s; repeats=5; contrast=10; name="SAM AM";
$SAMs DC
SAM: deltaf=(5,10,20)Hz; am=false; freqsel=absolute; duration=1s; repeats=5; contrast=10; name="SAM DC";
SAM: deltaf=(5,10,20,40,60,80,100)Hz; am=false; freqsel=absolute; duration=1s; repeats=5; contrast=10; name="SAM DC";
$Multisensory
FileStimulus: file=/home/efish/stimuli/torus/multisams.dat; sigstdev=0.3; am=false; contrast=$contrast; repeats=10; noisetype="none"; name="multisensory";
FileStimulus: file=/home/efish/stimuli/torus/zap.dat; am=false; contrast=10%; repeats=2; noisetype="none"; name="zap";
FileStimulus: file=/home/efish/stimuli/torus/contrast_sweep.dat; am=false; contrast=10%; repeats=2; noisetype="none"; name="contrast_sweep";
FileStimulus: file=/home/efish/stimuli/torus/phase_sweep.dat; am=false; contrast=10%; repeats=2; noisetype="none"; name="phase_sweep";
$Noise
FileStimulus: file=/home/efish/stimuli/whitenoise/gwn250Hz50s0.3.dat; duration=10000ms; sigstdev=0.3; am=true; contrast=10; repeats=10; noisetype="none"; name="noise AM";

8
torus/relacs.cfg
View File

@@ -45,12 +45,12 @@
inputtracecapacity : 600s
inputunipolar : false
inputtraceid : [ V-1, EOD, LocalEOD-1, GlobalEFieldStimulus ]
inputtracescale : [ 100, 1, 20, 5 ]
inputtracescale : [ 100, 1, 10, 5 ]
inputtraceunit : [ mV, mV, mV, mV ]
inputtracedevice : [ ai-1, ai-1, ai-1, ai-1 ]
inputtracechannel : [ 6, 0, 2, 4 ]
inputtracereference: [ ground, ground, ground, ground ]
inputtracemaxvalue : [ 100, 5, 3, 1 ]
inputtracemaxvalue : [ 200, 5, 2, 1 ]
inputtracecenter : [ true, true, true, true ]
output data:
outputtraceid : [ GlobalEField, GlobalEFieldAM, V, I ]
@@ -62,7 +62,7 @@
outputtracemodality: [ voltage, voltage, voltage, current ]
*Macros
file : [ macros.cfg, macrotorus.cfg, macrosdc.cfg, macrosam.cfg, macro_ELL_MS.cfg, macros_fakefish.cfg, macro_ELL_AM.cfg, /home/efish/data/ephys/pyramidals/macros.cfg ]
file : [ macrotorus.cfg, macros.cfg, macrosdc.cfg, macrosam.cfg, macro_ELL_MS.cfg, macros_fakefish.cfg, macro_ELL_AM.cfg, /home/efish/data/ephys/pyramidals/macros.cfg ]
mainfile : macros.cfg
fallbackonreload: true
@@ -176,7 +176,7 @@
bridgepin : 10
cclamppin : 9
vclamppin : 8
dclamppin : 13
dclamppin : -1
syncpin : 7
buzzerpulse : 500

61
torus/relacsplugins.cfg
View File

@@ -1,24 +1,24 @@
*Metadata
Recording:
Recording quality: [ Good, ~, good, poor, Poor, Fair, Good ]
Comment : ~
Experimenter : [ Jan Grewe, Dennis Huben, Janez Presern, Fabian Sinz, Juan Sehuanes, Carolin Sachgau, Jie Zhang, Jan Grewe, Jan Benda ]
WaterTemperature : 24.5°C
WaterConductivity: 330uS/cm
Recording quality: [ Fair, ~, good, poor, Poor, Fair, Good ]
Comment : strange cell
Experimenter : [ Lisa Vial, Lisa Vial, Dennis Huben, Janez Presern, Fabian Sinz, Juan Sehuanes, Carolin Sachgau, Jie Zhang, Jan Grewe, Jan Benda ]
WaterTemperature : 23.4°C
WaterConductivity: 289uS/cm
Cell:
CellType (Cell type) : [ unkown, Pyramidal, E-cell, E-cell deep, unknow, E-Cell, unkown, E-cell superficial, I-Cell, P-unit, Ampullary, T-unit ]
Structure (Recording location): [ Brain, Nerve, Brain ]
BrainRegion : [ TSd, TSd, Torus, n.A., ELL ]
BrainSubRegion : [ ~, ~, LS, CLS, CMS, MS ]
Depth : 535.7um
Lateral position : -1.4mm
Transverse section : 7
Depth : 1212.3um
Lateral position : -0.6mm
Transverse section : 18
Subject:
Species : [ Apteronotus leptorhynchus, Apteronotus albifrons, Apteronotus leptorhynchus ]
Gender (Sex): [ unknown, unknown, Male, Female ]
Size : 17cm
Weight : 13.6g
Identifier : "2018lepto24"
Size : 16.2cm
Weight : 10g
Identifier : "2018lepto89"
-Preparation-:
Type : [ in vivo, in vivo, slice ]
Anaesthesia : true
@@ -51,7 +51,7 @@
vctau : 1ms
*Control: SpectrumAnalyzer
intrace : [ LocalEOD-1, V-1, EOD, LocalEOD-1, GlobalEFieldStimulus ]
intrace : [ V-1, EOD, LocalEOD-1, GlobalEFieldStimulus ]
origin : [ before end of data, before signal, after signal ]
offset : 0ms
duration : 1000ms
@@ -194,9 +194,9 @@
*Event Detector: Spikes-1
Detector:
minthresh: 8.4mV
minthresh: 20.0mV
decay : 1sec
ratio : 12%
ratio : 5%
testwidth: false
maxwidth : 2.0ms
Indicators:
@@ -205,7 +205,7 @@
trendtime : 2.0sec
*Event Detector: EOD
threshold : 0.26mV
threshold : 0.051mV
interpolation: [ linear interpolation, closest datapoint, linear interpolation, linear fit, quadratic fit ]
*Event Detector: Chirps
@@ -216,10 +216,10 @@
interpolation: [ linear interpolation, closest datapoint, linear interpolation, linear fit, quadratic fit ]
*Event Detector: LocalBeat-1
minthresh: 0.022mV
minthresh: 0.028mV
*Event Detector: GlobalEFieldStimulus
threshold : 0.044256mV
threshold : 0.10465mV
interpolation: [ linear interpolation, closest datapoint, linear interpolation, linear fit, quadratic fit ]
*RePro: Pause
@@ -418,9 +418,9 @@
*RePro: CalibEField
General:
reset : false
resetval : 0.1
am : false
reset : true
resetval : 0.24
am : true
beatfreq : 20Hz
frequency: 600Hz
duration : 600ms
@@ -428,7 +428,7 @@
Range:
amplsel : [ contrast, amplitude ]
targetcontrast : 20%
mincontrast : 10%
mincontrast : 5%
maxcontrast : 40%
targetamplitude: 1mV/cm
minamplitude : 0.5mV/cm
@@ -617,18 +617,17 @@
adjust : false
*RePro: FileStimulus
General:
name: ~
Stimulus:
file : [ /home/efish/stimuli/whitenoise/dennis/InputArr_400hz_30s.dat, /home/efish/stimuli/whitenoise/dennis/InputArr_400hz_30s.dat, /home/efish/stimuli/whitenoise/dennis/InputArr_350to400hz_30s.dat, /home/efish/stimuli/whitenoise/gwn300Hz50s0.3.dat, ~, /home/efish/stimuli/whitenoise/gwn50Hz50s0.3.dat, /home/efish/stimuli/whitenoise/dennis/InputArr_250hz_30s.dat, /home/efish/stimuli/whitenoise/dennis/InputArr_50to100hz_30s.dat ]
sigstdev : 0.25
duration : 20000ms
file : [ /home/efish/stimuli/torus/zap.dat, ~, /home/efish/stimuli/whitenoise/dennis/InputArr_400hz_30s.dat, /home/efish/stimuli/whitenoise/dennis/InputArr_350to400hz_30s.dat, /home/efish/stimuli/whitenoise/gwn300Hz50s0.3.dat, /home/efish/stimuli/whitenoise/gwn50Hz50s0.3.dat, /home/efish/stimuli/whitenoise/dennis/InputArr_250hz_30s.dat, /home/efish/stimuli/whitenoise/dennis/InputArr_50to100hz_30s.dat, /home/efish/stimuli/torus/zap.dat, /home/efish/stimuli/torus/phase_sweep.dat ]
name : zap
sigstdev : 1
duration : 30000ms
pause : 1000ms
amplsel : [ contrast, absolute ]
contrast : 20%
contrast : 10%
amplitude: 1mV/cm
am : true
repeats : 5
am : false
repeats : 2
Additional noise:
noisetype : [ none, Gaussian-White, Ornstein-Uhlenbeck ]
uppercutoff : 600Hz
@@ -750,7 +749,7 @@
frequencyname : ~
frequencyunit : Hz
frequencyformat: %7.0f
gain : 0.91411
gain : 0.71863
offset : 0
*Attenuator-1
@@ -766,6 +765,6 @@
frequencyname : ~
frequencyunit : Hz
frequencyformat: %7.0f
gain : 0.059032
gain : 0.12211
offset : 0