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matlab-session_2012-04-03_class-materials.log
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matlab-session_2012-04-03_class-materials.log
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< M A T L A B (R) >
Copyright 1984-2010 The MathWorks, Inc.
Version 7.11.0.584 (R2010b) 64-bit (glnxa64)
August 16, 2010
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
Destroying 1 pre-existing parallel job(s) created by matlabpool that were in the
finished or failed state.
Starting matlabpool using the 'local' configuration ... connected to 4 labs.
>> pwd
ans =
/home/cengiz/work/pandora
>> cd ~/Documents/writings/brute-force/database-analysis-lecture/GunayEdgertonJaeger2008/runs/run_sample/data/
>> ls
brute_1.save data1_0_pAcip.bin data20_0_pAcip.bin
brute_20.save data1_100_pAcip.bin data20_100_pAcip.bin
>> t = trace('data1_0_pAcip.bin', 1e-4, 1e-3, 'GP sim1', struct('trace_time_start', 1000, 'scale_y', 1e3))
readgenesis: data1_0_pAcip.bin, trace 1 of 1 (20000 points @ 10 kHz)
trace, id=GP sim1
ans =
data: [19001x1 double]
dt: 1.0000e-04
dy: 1.0000e-03
id: 'GP sim1'
props: [1x1 struct]
>> plot(t)
ans =
1
>> res = getResults(t)
{??? Input argument "a_spikes" is undefined.
Error in ==> trace.getResults at 33
results = mergeStructs(getRateResults(a_trace, a_spikes), ...
}
>> s = spikes(t)
spikes, id=GP sim1
ans =
times: [1329 3357 5392 7433 9479 11530 13586 15645 17708]
num_samples: 19001
dt: 1.0000e-04
id: 'GP sim1'
>> res = getResults(t, s)
res =
ISICV: 0.0059
SpikeRate: 4.7368
SpikeRateISI: 4.8843
avg: -64.1681
max: 38.5472
min: -70.0721
>> plot(s)
ans =
2
>> a_prof = getPro
{??? Undefined function or variable 'getPro'.
}
>> methods trace
Methods for class trace:
analyzeSpikesInPeriod getSpike set
avgTraces lowpassfilt setProp
binary_op medianfilt spike_shape
calcAvg minus spikes
calcMax mtimes sqrt
calcMin periodWhole subsasgn
display plot subsref
findFilteredSpikes plotData times
get plot_abstract trace
getDy plus uminus
getPotResults power unary_op
getProfileAllSpikes rdivide withinPeriod
getRateResults runAvg
getResults saveAsNeuronVecAscii
>> a_prof = getProfileAllSpikes(t)
{Warning: Error in GP sim1 ( spike#1): Error using ==>
spike_shape.calcInitVmMaxCurvPhasePlane>findMax at 323
No local maxima found!}
> In spike_shape.calcInitVmMaxCurvPhasePlane at 179
In spike_shape.calcInitVm at 117
In spike_shape.getResults at 81
In trace.analyzeSpikesInPeriod at 61
In trace.getProfileAllSpikes at 36
{Warning: vPP curvature ignored, v' > 15 for GP sim1 ( spike#1)}
> In spike_shape.calcInitVmMaxCurvPhasePlane at 253
In spike_shape.calcInitVm at 117
In spike_shape.getResults at 81
In trace.analyzeSpikesInPeriod at 61
In trace.getProfileAllSpikes at 36
{Warning: Warning: Max curv phase plane method signal failure, falling back to
supersampled threshold method.}
> In spike_shape.calcInitVm at 123
In spike_shape.getResults at 81
In trace.analyzeSpikesInPeriod at 61
In trace.getProfileAllSpikes at 36
{Warning: Error in GP sim1 ( spike#2): Error using ==>
spike_shape.calcInitVmMaxCurvPhasePlane>findMax at 323
No local maxima found!}
> In spike_shape.calcInitVmMaxCurvPhasePlane at 179
In spike_shape.calcInitVm at 117
In spike_shape.getResults at 81
In trace.analyzeSpikesInPeriod at 61
In trace.getProfileAllSpikes at 36
{Warning: vPP curvature ignored, v' > 15 for GP sim1 ( spike#2)}
> In spike_shape.calcInitVmMaxCurvPhasePlane at 253
In spike_shape.calcInitVm at 117
In spike_shape.getResults at 81
In trace.analyzeSpikesInPeriod at 61
In trace.getProfileAllSpikes at 36
{Warning: Warning: Max curv phase plane method signal failure, falling back to
supersampled threshold method.}
> In spike_shape.calcInitVm at 123
In spike_shape.getResults at 81
In trace.analyzeSpikesInPeriod at 61
In trace.getProfileAllSpikes at 36
{Warning: Error in GP sim1 ( spike#3): Error using ==>
spike_shape.calcInitVmMaxCurvPhasePlane>findMax at 323
No local maxima found!}
> In spike_shape.calcInitVmMaxCurvPhasePlane at 179
In spike_shape.calcInitVm at 117
In spike_shape.getResults at 81
In trace.analyzeSpikesInPeriod at 61
In trace.getProfileAllSpikes at 36
{Warning: vPP curvature ignored, v' > 15 for GP sim1 ( spike#3)}
> In spike_shape.calcInitVmMaxCurvPhasePlane at 253
In spike_shape.calcInitVm at 117
In spike_shape.getResults at 81
In trace.analyzeSpikesInPeriod at 61
In trace.getProfileAllSpikes at 36
{Warning: Warning: Max curv phase plane method signal failure, falling back to
supersampled threshold method.}
> In spike_shape.calcInitVm at 123
In spike_shape.getResults at 81
In trace.analyzeSpikesInPeriod at 61
In trace.getProfileAllSpikes at 36
{Warning: Error in GP sim1 ( spike#4): Error using ==>
spike_shape.calcInitVmMaxCurvPhasePlane>findMax at 323
No local maxima found!}
> In spike_shape.calcInitVmMaxCurvPhasePlane at 179
In spike_shape.calcInitVm at 117
In spike_shape.getResults at 81
In trace.analyzeSpikesInPeriod at 61
In trace.getProfileAllSpikes at 36
{Warning: vPP curvature ignored, v' > 15 for GP sim1 ( spike#4)}
> In spike_shape.calcInitVmMaxCurvPhasePlane at 253
In spike_shape.calcInitVm at 117
In spike_shape.getResults at 81
In trace.analyzeSpikesInPeriod at 61
In trace.getProfileAllSpikes at 36
{Warning: Warning: Max curv phase plane method signal failure, falling back to
supersampled threshold method.}
> In spike_shape.calcInitVm at 123
In spike_shape.getResults at 81
In trace.analyzeSpikesInPeriod at 61
In trace.getProfileAllSpikes at 36
{Warning: Error in GP sim1 ( spike#5): Error using ==>
spike_shape.calcInitVmMaxCurvPhasePlane>findMax at 323
No local maxima found!}
> In spike_shape.calcInitVmMaxCurvPhasePlane at 179
In spike_shape.calcInitVm at 117
In spike_shape.getResults at 81
In trace.analyzeSpikesInPeriod at 61
In trace.getProfileAllSpikes at 36
{Warning: vPP curvature ignored, v' > 15 for GP sim1 ( spike#5)}
> In spike_shape.calcInitVmMaxCurvPhasePlane at 253
In spike_shape.calcInitVm at 117
In spike_shape.getResults at 81
In trace.analyzeSpikesInPeriod at 61
In trace.getProfileAllSpikes at 36
{Warning: Warning: Max curv phase plane method signal failure, falling back to
supersampled threshold method.}
> In spike_shape.calcInitVm at 123
In spike_shape.getResults at 81
In trace.analyzeSpikesInPeriod at 61
In trace.getProfileAllSpikes at 36
{Warning: vPP curvature ignored, v' > 15 for GP sim1 ( spike#6)}
> In spike_shape.calcInitVmMaxCurvPhasePlane at 253
In spike_shape.calcInitVm at 117
In spike_shape.getResults at 81
In trace.analyzeSpikesInPeriod at 61
In trace.getProfileAllSpikes at 36
{Warning: Warning: Max curv phase plane method signal failure, falling back to
supersampled threshold method.}
> In spike_shape.calcInitVm at 123
In spike_shape.getResults at 81
In trace.analyzeSpikesInPeriod at 61
In trace.getProfileAllSpikes at 36
{Warning: Error in GP sim1 ( spike#8): Error using ==>
spike_shape.calcInitVmMaxCurvPhasePlane>findMax at 323
No local maxima found!}
> In spike_shape.calcInitVmMaxCurvPhasePlane at 179
In spike_shape.calcInitVm at 117
In spike_shape.getResults at 81
In trace.analyzeSpikesInPeriod at 61
In trace.getProfileAllSpikes at 36
{Warning: vPP curvature ignored, v' > 15 for GP sim1 ( spike#8)}
> In spike_shape.calcInitVmMaxCurvPhasePlane at 253
In spike_shape.calcInitVm at 117
In spike_shape.getResults at 81
In trace.analyzeSpikesInPeriod at 61
In trace.getProfileAllSpikes at 36
{Warning: Warning: Max curv phase plane method signal failure, falling back to
supersampled threshold method.}
> In spike_shape.calcInitVm at 123
In spike_shape.getResults at 81
In trace.analyzeSpikesInPeriod at 61
In trace.getProfileAllSpikes at 36
{??? Reference to non-existent field 'id'.
Error in ==> getfield at 38
f = s.(deblank(strField)); % deblank field name
Error in ==> results_profile.get at 12
b = getfield(struct(a), attr);
Error in ==> results_profile.display at 12
disp(sprintf('%s, %s', class(t), get(t, 'id')));
}
>> help trace/getProfileAllSpikes
getProfileAllSpikes - Creates a trace_allspikes_profile object by collecting test results of a trace, analyzing each individual spike.
Usage:
profile_obj = getProfileAllSpikes(a_trace)
Parameters:
a_trace: A trace object.
Returns:
profile_obj: A trace_allspikes_profile object.
Description:
Analyzes the spontaneous (periodIniSpont), pulse (periodPulse) and the
recovery (periodRecSpont) periods separately and produces spike shape
distribution results. Rate and CIP measurements are added to these.
See also: trace, trace_allspikes_profile
$Id: getProfileAllSpikes.m 896 2007-12-17 18:48:55Z cengiz $
Author: Cengiz Gunay <[email protected]>, 2005/04/26
>> size(a_prof)
ans =
1 1
>> a_prof
{??? Reference to non-existent field 'id'.
Error in ==> getfield at 38
f = s.(deblank(strField)); % deblank field name
Error in ==> results_profile.get at 12
b = getfield(struct(a), attr);
Error in ==> trace_allspikes_profile.display at 12
disp(sprintf('%s, %s', class(t), get(t, 'id')));
}
>> a_prof
trace_allspikes_profile, GP sim1
ans =
trace: [1x1 trace]
spikes: [1x1 spikes]
spikes_db: [1x1 spikes_db]
props: [1x1 struct]
results_profile: [1x1 results_profile]
results_profile, GP sim1
ans =
results: [1x1 struct]
id: 'GP sim1'
props: [0x0 struct]
ISICV: 0.0059
SpikeRate: 4.7368
SpikeRateISI: 4.8843
avg: -64.1681
max: 38.5472
min: -70.0721
SpikeAmplitudeMean: 88.7882
SpikeAmplitudeMode: 88.5418
SpikeAmplitudeSTD: 0.6131
SpikeBaseWidthMean: 2.1973
SpikeBaseWidthMode: 2.1194
SpikeBaseWidthSTD: 0.1450
SpikeDAHPMagMean: NaN
SpikeDAHPMagMode: 0
SpikeDAHPMagSTD: NaN
SpikeFallTimeMean: 1.7333
SpikeFallTimeMode: 1.7010
SpikeFallTimeSTD: 0.0707
SpikeFixVWidthMean: 1.1370
SpikeFixVWidthMode: 1.1325
SpikeFixVWidthSTD: 0.0037
plot SpikeHalfVmMean: -6.0533
SpikeHalfVmMode: -5.9603
SpikeHalfVmSTD: 0.3675
SpikeHalfWidthMean: 1.0712
SpikeHalfWidthMode: 1.0644
SpikeHalfWidthSTD: 0.0062
SpikeInitTimeMean: 6.6382
SpikeInitTimeMode: 6.6986
SpikeInitTimeSTD: 0.0955
SpikeInitVmBySlopeMean: -50.2910
SpikeInitVmBySlopeMode: -50.8911
SpikeInitVmBySlopeSTD: 0.3699
SpikeInitVmMean: -50.4473
SpikeInitVmMode: -51.8002
SpikeInitVmSTD: 0.6665
SpikeMaxAHPMean: 19.6204
SpikeMaxAHPMode: 19.7919
SpikeMaxAHPSTD: 0.6646
SpikeMaxVmSlopeMean: 362.9439
SpikeMaxVmSlopeMode: 338.2374
SpikeMaxVmSlopeSTD: 19.5736
SpikeMinTimeMean: 35.6889
SpikeMinTimeMode: 35.6995
SpikeMinTimeSTD: 0.0333
SpikeMinVmMean: -70.0678
SpikeMinVmMode: -70.0719
SpikeMinVmSTD: 0.0028
SpikePeakVmMean: 38.3408
SpikePeakVmMode: 38.2260
SpikePeakVmSTD: 0.1176
SpikeRiseTimeMean: 0.4640
SpikeRiseTimeMode: 0.4197
SpikeRiseTimeSTD: 0.0758
Spikes: 9
>> plot(a_prof)
{??? Cell contents reference from a non-cell array object.
Error in ==> results_profile.subsref at 24
b = a{index.subs{:}};
Error in ==> plot_abstract.plot at 81
ph = feval(a_plot.command, a_plot.data{:});
Error in ==> plot_abstract.plotFigure at 99
plot(a_plot);
Error in ==> results_profile.plot at 34
h = plotFigure(plot_abstract(a_tests_db, title_str));
}
>> plot(a_prof.a_spikes_db)
{??? Reference to non-existent field 'a_spikes_db'.
Error in ==> getfield at 38
f = s.(deblank(strField)); % deblank field name
Error in ==> results_profile.get at 12
b = getfield(struct(a), attr);
Error in ==> trace_allspikes_profile.get at 17
b = get(a.results_profile, attr);
Error in ==> results_profile.subsref at 21
b = get(a, index.subs);
}
>> plot(a_prof.spikes_db)
ans =
3
>> a_prof = getProfileAllSpikes(t)
{Warning: Error in GP sim1 ( spike#1): Error using ==>
spike_shape.calcInitVmMaxCurvPhasePlane>findMax at 323
No local maxima found!}
> In spike_shape.calcInitVmMaxCurvPhasePlane at 179
In spike_shape.calcInitVm at 117
In spike_shape.getResults at 81
In trace.analyzeSpikesInPeriod at 61
In trace.getProfileAllSpikes at 36
{Warning: vPP curvature ignored, v' > 15 for GP sim1 ( spike#1)}
> In spike_shape.calcInitVmMaxCurvPhasePlane at 253
In spike_shape.calcInitVm at 117
In spike_shape.getResults at 81
In trace.analyzeSpikesInPeriod at 61
In trace.getProfileAllSpikes at 36
{Warning: Warning: Max curv phase plane method signal failure, falling back to
supersampled threshold method.}
> In spike_shape.calcInitVm at 123
In spike_shape.getResults at 81
In trace.analyzeSpikesInPeriod at 61
In trace.getProfileAllSpikes at 36
{Warning: Error in GP sim1 ( spike#2): Error using ==>
spike_shape.calcInitVmMaxCurvPhasePlane>findMax at 323
No local maxima found!}
> In spike_shape.calcInitVmMaxCurvPhasePlane at 179
In spike_shape.calcInitVm at 117
In spike_shape.getResults at 81
In trace.analyzeSpikesInPeriod at 61
In trace.getProfileAllSpikes at 36
{Warning: vPP curvature ignored, v' > 15 for GP sim1 ( spike#2)}
> In spike_shape.calcInitVmMaxCurvPhasePlane at 253
In spike_shape.calcInitVm at 117
In spike_shape.getResults at 81
In trace.analyzeSpikesInPeriod at 61
In trace.getProfileAllSpikes at 36
{Warning: Warning: Max curv phase plane method signal failure, falling back to
supersampled threshold method.}
> In spike_shape.calcInitVm at 123
In spike_shape.getResults at 81
In trace.analyzeSpikesInPeriod at 61
In trace.getProfileAllSpikes at 36
{Warning: Error in GP sim1 ( spike#3): Error using ==>
spike_shape.calcInitVmMaxCurvPhasePlane>findMax at 323
No local maxima found!}
> In spike_shape.calcInitVmMaxCurvPhasePlane at 179
In spike_shape.calcInitVm at 117
In spike_shape.getResults at 81
In trace.analyzeSpikesInPeriod at 61
In trace.getProfileAllSpikes at 36
{Warning: vPP curvature ignored, v' > 15 for GP sim1 ( spike#3)}
> In spike_shape.calcInitVmMaxCurvPhasePlane at 253
In spike_shape.calcInitVm at 117
In spike_shape.getResults at 81
In trace.analyzeSpikesInPeriod at 61
In trace.getProfileAllSpikes at 36
{Warning: Warning: Max curv phase plane method signal failure, falling back to
supersampled threshold method.}
> In spike_shape.calcInitVm at 123
In spike_shape.getResults at 81
In trace.analyzeSpikesInPeriod at 61
In trace.getProfileAllSpikes at 36
{Warning: Error in GP sim1 ( spike#4): Error using ==>
spike_shape.calcInitVmMaxCurvPhasePlane>findMax at 323
No local maxima found!}
> In spike_shape.calcInitVmMaxCurvPhasePlane at 179
In spike_shape.calcInitVm at 117
In spike_shape.getResults at 81
In trace.analyzeSpikesInPeriod at 61
In trace.getProfileAllSpikes at 36
{Warning: vPP curvature ignored, v' > 15 for GP sim1 ( spike#4)}
> In spike_shape.calcInitVmMaxCurvPhasePlane at 253
In spike_shape.calcInitVm at 117
In spike_shape.getResults at 81
In trace.analyzeSpikesInPeriod at 61
In trace.getProfileAllSpikes at 36
{Warning: Warning: Max curv phase plane method signal failure, falling back to
supersampled threshold method.}
> In spike_shape.calcInitVm at 123
In spike_shape.getResults at 81
In trace.analyzeSpikesInPeriod at 61
In trace.getProfileAllSpikes at 36
{Warning: Error in GP sim1 ( spike#5): Error using ==>
spike_shape.calcInitVmMaxCurvPhasePlane>findMax at 323
No local maxima found!}
> In spike_shape.calcInitVmMaxCurvPhasePlane at 179
In spike_shape.calcInitVm at 117
In spike_shape.getResults at 81
In trace.analyzeSpikesInPeriod at 61
In trace.getProfileAllSpikes at 36
{Warning: vPP curvature ignored, v' > 15 for GP sim1 ( spike#5)}
> In spike_shape.calcInitVmMaxCurvPhasePlane at 253
In spike_shape.calcInitVm at 117
In spike_shape.getResults at 81
In trace.analyzeSpikesInPeriod at 61
In trace.getProfileAllSpikes at 36
{Warning: Warning: Max curv phase plane method signal failure, falling back to
supersampled threshold method.}
> In spike_shape.calcInitVm at 123
In spike_shape.getResults at 81
In trace.analyzeSpikesInPeriod at 61
In trace.getProfileAllSpikes at 36
{Warning: vPP curvature ignored, v' > 15 for GP sim1 ( spike#6)}
> In spike_shape.calcInitVmMaxCurvPhasePlane at 253
In spike_shape.calcInitVm at 117
In spike_shape.getResults at 81
In trace.analyzeSpikesInPeriod at 61
In trace.getProfileAllSpikes at 36
{Warning: Warning: Max curv phase plane method signal failure, falling back to
supersampled threshold method.}
> In spike_shape.calcInitVm at 123
In spike_shape.getResults at 81
In trace.analyzeSpikesInPeriod at 61
In trace.getProfileAllSpikes at 36
{Warning: Error in GP sim1 ( spike#8): Error using ==>
spike_shape.calcInitVmMaxCurvPhasePlane>findMax at 323
No local maxima found!}
> In spike_shape.calcInitVmMaxCurvPhasePlane at 179
In spike_shape.calcInitVm at 117
In spike_shape.getResults at 81
In trace.analyzeSpikesInPeriod at 61
In trace.getProfileAllSpikes at 36
{Warning: vPP curvature ignored, v' > 15 for GP sim1 ( spike#8)}
> In spike_shape.calcInitVmMaxCurvPhasePlane at 253
In spike_shape.calcInitVm at 117
In spike_shape.getResults at 81
In trace.analyzeSpikesInPeriod at 61
In trace.getProfileAllSpikes at 36
{Warning: Warning: Max curv phase plane method signal failure, falling back to
supersampled threshold method.}
> In spike_shape.calcInitVm at 123
In spike_shape.getResults at 81
In trace.analyzeSpikesInPeriod at 61
In trace.getProfileAllSpikes at 36
trace_allspikes_profile, GP sim1
ans =
trace: [1x1 trace]
spikes: [1x1 spikes]
spikes_db: [1x1 spikes_db]
props: [1x1 struct]
results_profile: [1x1 results_profile]
results_profile, GP sim1
ans =
results: [1x1 struct]
id: 'GP sim1'
props: [0x0 struct]
ISICV: 0.0059
SpikeRate: 4.7368
SpikeRateISI: 4.8843
avg: -64.1681
max: 38.5472
min: -70.0721
SpikeAmplitudeMean: 88.7882
SpikeAmplitudeMode: 88.5418
SpikeAmplitudeSTD: 0.6131
SpikeBaseWidthMean: 2.1973
SpikeBaseWidthMode: 2.1194
SpikeBaseWidthSTD: 0.1450
SpikeDAHPMagMean: NaN
SpikeDAHPMagMode: 0
SpikeDAHPMagSTD: NaN
SpikeFallTimeMean: 1.7333
SpikeFallTimeMode: 1.7010
SpikeFallTimeSTD: 0.0707
SpikeFixVWidthMean: 1.1370
SpikeFixVWidthMode: 1.1325
SpikeFixVWidthSTD: 0.0037
SpikeHalfVmMean: -6.0533
SpikeHalfVmMode: -5.9603
SpikeHalfVmSTD: 0.3675
SpikeHalfWidthMean: 1.0712
SpikeHalfWidthMode: 1.0644
SpikeHalfWidthSTD: 0.0062
SpikeInitTimeMean: 6.6382
SpikeInitTimeMode: 6.6986
SpikeInitTimeSTD: 0.0955
SpikeInitVmBySlopeMean: -50.2910
SpikeInitVmBySlopeMode: -50.8911
SpikeInitVmBySlopeSTD: 0.3699
SpikeInitVmMean: -50.4473
SpikeInitVmMode: -51.8002
SpikeInitVmSTD: 0.6665
SpikeMaxAHPMean: 19.6204
SpikeMaxAHPMode: 19.7919
SpikeMaxAHPSTD: 0.6646
SpikeMaxVmSlopeMean: 362.9439
SpikeMaxVmSlopeMode: 338.2374
SpikeMaxVmSlopeSTD: 19.5736
SpikeMinTimeMean: 35.6889
SpikeMinTimeMode: 35.6995
SpikeMinTimeSTD: 0.0333
SpikeMinVmMean: -70.0678
SpikeMinVmMode: -70.0719
SpikeMinVmSTD: 0.0028
SpikePeakVmMean: 38.3408
SpikePeakVmMode: 38.2260
SpikePeakVmSTD: 0.1176
SpikeRiseTimeMean: 0.4640
SpikeRiseTimeMode: 0.4197
SpikeRiseTimeSTD: 0.0758
Spikes: 9
>> help classes
DJLAB General Purpose Matlab Classes
The following classes are designed as generic templates that can be
subclassed to take specific tasks. They should not be modified for
more specialized tasks.
Basic data wrapper classes that define the measurements:
trace - A voltage/current trace.
spikes - Spike times of a trace.
spike_shape - Averaged spike shape from a trace.
period - Defines time periods to operate on trace or spikes objects.
Classes specialized for CIP experiments tests:
cip_trace - A voltage trace with a CIP applied.
Profile classes that hold test results:
result_profile - Base class that holds a results structure.
trace_profile - Generic example class for holding a trace profile.
cip_trace_profile - Holds cip_trace results. Template class designed
only for subclassing.
cip_trace_allspikes_profile
- Created by cip_trace/getProfileAllSpikes, contains statistics
of spike shape measures from individual spikes.
params_tests_profile- Collects both intermediate and result data structures
from analysis of a params_tests_db.
Dataset classes that point to or hold raw data:
params_tests_dataset - Base class for datasets.
params_tests_fileset - Holds a list of filenames and associated information,
capable of creating a params_tests_db.
params_cip_trace_fileset - Fileset from which cip_trace objects can be created.
physiol_cip_traceset - Dataset of a traceset from a single file.
physiol_cip_traceset_fileset - Dataset of a tracesets from many files.
Database classes created from datasets:
tests_db - Base class for databases. Contains many utilities.
params_tests_db - DB extended to hold parameter values
associated with results.
spikes_db - Holds measures from each individual spike in a trace.
test_3D_db - 3D database of tests that vary with a third variable.
corrcoefs_db - Holds correlation coefficients.
histogram_db - Holds histogram bins.
stats_db - Holds statistical measurements.
ranked_db - Database ranked for a criterion, holds error values or distances.
Bundle classes that bridge the gap between database and it's ancestral dataset:
dataset_db_bundle - Base class of bundles. Puts a processed and raw DBs with datasets.
model_ct_bundle - Bundle for model databases.
physiol_bundle - Bundle for physiology databases.
Plotting classes:
plot_abstract - Base class that holds information sufficient to generate any plot.
plot_simple - Simple extension that works for most simple plots.
plot_stack - Holds horizontal or vertical stack of plot_abstract objects.
plot_inset - Places multiple plots at absolute locations in a figure. Good for insets, etc.
plot_superpose - Allows superposing different plot_abstract's in the same axis.
plot_bars - Multi-axis bar plot with extended errorbars.
plot_errorbar - Errorbar plot.
plot_errorbars - Multi-axis errorbar plot.
Classes for generating formatted printable or presentable documents:
doc_generate - Base class for all document classes.
doc_plot - Holds a plot_abstract and captions, etc.
doc_multi - Combines multiple doc_generate objects.
Script control classes for cluster computing:
script_factory - Generates a set of scripts based on a recipe.
script_array - Designed to execute an array job serially on a computer.
script_array_for_cluster - Executes an array job on a cluster computer.
Notes:
See also: subclasses under classes/cengiz
$Id: Contents.m 806 2007-08-02 18:18:16Z cengiz $
Author: Cengiz Gunay <[email protected]>, 2004/09/14
>> help params_cip_trace_fileset
params_cip_trace_fileset -
Description of a raw dataset consisting of cip_trace files varying
with parameter values.
Usage:
obj = params_cip_trace_fileset(file_pattern, dt, dy,
pulse_time_start, pulse_time_width, id, props)
Description:
This is a subclass of params_tests_fileset.
Parameters:
file_pattern: File pattern mathing all files to be loaded.
dt: Time resolution [s]
dy: y-axis resolution [ISI (V, A, etc.)]
pulse_time_start, pulse_time_width:
Start and width of the pulse [dt]
id: An identification string
props: A structure with any optional properties.
profile_method_name: Use this profile method that takes a
cip_trace object and returns a results_profile class. It
can be 'cip_trace_profile' (default, but outdated) or
'getProfileAllSpikes' (more current).
(All other props are passed to cip_trace objects)
Returns a structure object with the following fields:
params_tests_fileset,
pulse_time_start, pulse_time_width.
General operations on params_cip_trace_fileset objects:
params_cip_trace_fileset - Construct a new object.
display - Returns and displays the identification string.
get - Gets attributes of this object and parents.
subsref - Allows usage of . operator.
loadItemProfile - Builds a cip_trace_profile for a file in the set.
cip_trace - Load a cip_trace corresponding to fileset entry.
cip_trace_profile - Load a cip_trace_profile corresponding to fileset entry.
Example:
>> fileset = params_cip_trace_fileset('/home/abc/data/*.bin', 1e-4, 1e-3, 20001, 10000, 'sim dataset gpsc0501', struct('trace_time_start', 10001, 'type', 'sim', 'scale_y', 1e3))
Additional methods:
See methods('params_cip_trace_fileset'), and
methods('params_tests_fileset').
See also: params_tests_fileset, params_tests_db
$Id: params_cip_trace_fileset.m 1316 2012-02-14 01:00:14Z cengiz $
Author: Cengiz Gunay <[email protected]>, 2004/09/14
>> help params_tests_fileset
params_tests_fileset - Description of a set of data files of raw data varying with parameter values.
Usage:
obj = params_tests_fileset(file_pattern, dt, dy, id, props)
Description:
This is a subclass of params_tests_dataset. This class is used to generate
params_tests_db objects and keep
a connection to the raw data files. This class only keeps names of
files and loads raw data files whenever it's requested. A database
object can easily be generated using the convertion methods.
Most methods defined here can
be used as-is, however some should be overloaded in subclasses.
The specific methods are loadItemProfile.
Parameters:
file_pattern: File pattern, or cell array of patterns, matching all
files to be loaded.
dt: Time resolution [s]
dy: y-axis resolution [ISI (V, A, etc.)]
id: An identification string
props: A structure with any optional properties.
num_params: Number of parameters that appear in filenames.
param_trial_name: Use this name on the filename as the 'trial' parameter.
param_row_filename: If given, the 'trial' parameter will be used
to address rows from this file and acquire parameters.
param_desc_filename: Contains the parameter range descriptions one per
each row. The parameter names are acquired from this file.
param_names: Cell array of parameter names corresponding to the
param_row_filename columns can be specified as an alternative to
specifying param_desc_filename. These names are not for the
parameters present in the data filename.
profile_method_name: It can be one of the profile-creating methods in this
class. E.g., 'trace_profile', 'srp_trace_profile', etc.
(See parent classes and cip_trace object for more props)
Returns a structure object with the following fields:
params_tests_dataset,
path: The pathname to files.
General operations on params_tests_fileset objects:
params_tests_fileset - Construct a new object.
loadItemProfile - Implements the specific way to load raw data
traces for this fileset.
testNames - Returns test names for this fileset. Uses
loadItemProfile to load the raw data.
paramNames - Returns parameter names for this fileset.
itemResultsRow - Uses loadItemProfile to load raw data and
queries it to get parameters and results.
trace - Load a trace corresponding to fileset entry.
trace_profile - Load a trace_profile corresponding to fileset entry.
display - Returns and displays the identification string.
get - Gets attributes of this object and parents.
subsref - Allows usage of . operator.
Additional methods:
See methods('params_tests_fileset')
See also: params_tests_db, tests_db, test_variable_db (N/I)
$Id: params_tests_fileset.m 1317 2012-02-14 01:02:19Z cengiz $
Author: Cengiz Gunay <[email protected]>, 2004/09/09
>> pwd
ans =
/home/cengiz/Documents/writings/brute-force/database-analysis-lecture/GunayEdgertonJaeger2008/runs/run_sample/data
>> ls
brute_1.save data1_0_pAcip.bin data20_0_pAcip.bin
brute_20.save data1_100_pAcip.bin data20_100_pAcip.bin
>> 4^2*3^7*5
ans =
174960
>> 100602*5
ans =
503010
>> methods tests_db
Methods for class tests_db:
addColumns plot
addLastRow plotBox
addRow plotCovar
allocateRows plotImage
anyRows plotScatter
approxMappingLIBSVM plotScatter3D
approxMappingNNet plotTestsHistsMatrix
approxMappingSVM plotUniquesStats2D
assignRowsTests plotUniquesStatsBars
checkConsistentCols plotUniquesStatsStacked3D
compareRows plotXRows
corrcoef plotYTests
cov plot_abstract
crossProd plot_bars
dbsize plotrow
delColumns plotrows
diff plus
display princomp
displayRows processDimNonNaNInf
displayRowsCSV rankMatching
displayRowsTeX rdivide
end renameColumns
enumerateColumns rop
eq rows2Struct
factoran set
fillMissingColumns setProp
ge setRows
get shufflerows
getColNames sortrows
groupBy sqrt
gt statsAll
hist3 statsBounds
histogram statsMeanSE
invarValues statsMeanStd
isinf std
isnan subsasgn
isnanrows subsref
joinRows sum
kmeansCluster swapRowsPages
le tests2cols
lt tests2idx
matchingRow tests2log
max testsHists
mean tests_db
meanDuplicateRows times
minus transpose
mtimes uminus
ne unique
noNaNRows uop
onlyRowsTests vertcat
physiol_bundle
>> t_100pA = trace('data1_100_pAcip.bin', 1e-4, 1e-3, 'GP sim1', struct('trace_time_start', 1000, 'scale_y', 1e3))
readgenesis: data1_100_pAcip.bin, trace 1 of 1 (20000 points @ 10 kHz)
trace, id=GP sim1
ans =
data: [19001x1 double]
dt: 1.0000e-04
dy: 1.0000e-03
id: 'GP sim1'
props: [1x1 struct]
>> plot(t_100pA)
ans =
4
>> whos
Name Size Bytes Class Attributes
a_plot 1x1 305904 plot_abstract
a_prof 1x1 326716 trace_allspikes_profile
ans 1x1 8 double
res 1x1 1104 struct
s 1x1 806 spikes
t 1x1 153476 trace
t_100pA 1x1 153476 trace
>> methods params_tests_db
Methods for class params_tests_db:
addParams joinRows rankVsAllDB
crossProd makeGenesisParFile rankVsDB
delColumns matchingRow reIndexNeurons
display meanDuplicateParams scaleParamsOneRow
displayRankingsTeX mergeMultipleCIPsInOne scanParamAllRows
fillMissingParams onlyRowsTests set
get paramsCoefs subsref
getDualCIPdb paramsHists testsHists
getParamNames paramsParamsCoefs unionCat
getParamRowIndices paramsTestsCoefsHists unionCatTwo
getProfile params_tests_db
invarParam plotParamsHists
invarParams plotVarBoxMatrix
>> help makeGenesisParFile
--- help for params_tests_db/makeGenesisParFile ---
makeGenesisParFile - Creates a Genesis parameter file with all the parameter values in a_db.
Usage:
makeGenesisParFile(a_db, filename, props)
Description:
For each a_db row, print the parameter names in a
file formatted for Genesis.
Parameters:
a_db: A params_tests_db object.
filename: Genesis parameter file to be created.
props: A structure with any optional properties.
trialStart: If given, adds/replaces the trial parameter and counts forward.
makeParamDesc: If 1, put the parameter names in a parameter description file with
with a .txt extension.
Returns:
nothing.
Example:
>> blocked_rows_db = makeModifiedParamDB(ranked_for_gps0501a_db, 1, [1, 2], 10, [-100 100]);
>> makeGenesisParFile(blocked_rows_db, 'blocked_gps0501-03.par')
See also: makeModifiedParamDB, scanParamAllRows, scaleParamsOneRow
$Id: makeGenesisParFile.m 1174 2009-03-31 03:14:21Z cengiz $
Author: Cengiz Gunay <[email protected]>, 2005/03/13
>> help makeModifiedParamDB
makeModifiedParamDB not found.
Use the Help browser search field to search the documentation, or
type "help help" for help command options, such as help for methods.
>> help scaleParamsOneRow
--- help for params_tests_db/scaleParamsOneRow ---
scaleParamsOneRow - Scales chosen parameters in a row by multiplying with levels to create a new parameter db with as many rows as values in levels.
Usage:
a_params_db = scaleParamsOneRow(a_db, params, levels)
Description:
Produces rows by multiplying desired params, in the first row of DB,
with each value in levels. Then, makeGenesisParFile can be used to generate
a parameter file from this DB to drive new simulations.
Parameters:
a_db: A params_tests_db object whose first row is subject to modifications.
params: Parameters to be varied (see tests2cols for param description).
levels: Column vector of parameter value multipliers (1=unity).
Returns:
a_params_db: A db only with params.
Example:
Blocks NaF from 0%-100% with 10% increments.
>> naf_rows_db = scanOneParam(a_db(desired_row, :), 'NaF', 0:0.1:1);
See also: ranked_db/blockedDistances, getParamRowIndices, makeGenesisParFile
$Id: scaleParamsOneRow.m 896 2007-12-17 18:48:55Z cengiz $
Author: Cengiz Gunay <[email protected]>, 2006/02/16
>> help params_tests_db
params_tests_db - A generic database of test results varying with parameter values, organized in a matrix format.
Usage 1:
obj = params_tests_db(params, param_names, a_test_results,
test_names, id, props)