See Section 1.6 on how to get online help about the software within MATLAB.
tests_db, channel_info, props.
![[*]](crossref.png)
), chanTables2DB (p. )names.
(rest passed to plot_abstract.)
a_plot: A plot_abstract object that can be visualized.
), trace/plot (p. ), plot_abstract (p. )(rest passed to matrixPlots.)
a_plot: A plot_abstract object that can be visualized.
), trace/plot (p. ), plot_abstract (p. )(rest passed to plot_abstract.)
a_plot: A plot_abstract object that can be visualized.
), trace/plot (p. ), plot_abstract (p. )names.
(rest passed to plot_abstract.)
a_plot: A plot_abstract object that can be visualized.
), trace/plot (p. ), plot_abstract (p. )Start and width of the pulse [dt]
(see trace for more)
trace, pulse_time_start, pulse_time_width, props.
), spikes (p. ), spike_shape (p. ), period (p. )calculated automatically if given as [].
), trace/getSpike (p. )(rest passed to trace/plotData)
a_plot: A plot_abstract object that can be visualized.
), trace/plot (p. ), plot_abstract (p. )the_period: A period object.
), cip_trace (p. ), trace (p. )the time is kept
the_period: A period object.
), cip_trace (p. ), trace (p. )the_period: A period object.
), cip_trace (p. ), trace (p. )results: A structure associating test names with result values.
), spikes (p. ), spike_shape (p. )the_period: A period object.
), cip_trace (p. ), trace (p. )the_period: A period object.
), cip_trace (p. ), trace (p. )the_period: A period object.
), cip_trace (p. ), trace (p. )results: A structure associating test names with result values.
), spikes (p. ), spike_shape (p. )the_period: A period object.
), cip_trace (p. ), trace (p. )the_period: A period object.
), cip_trace (p. ), trace (p. )results: A structure associating test names with result values.
), spikes (p. ), spike_shape (p. )the_period: A period object.
), cip_trace (p. ), trace (p. )measures: A structure with cell arrays of types of measures, and measure names inside.
), getProfileAllSpikes (p. ), mergeMultipleCIPsInOne (p. )avg_val: The avg value [dy].
), trace (p. ), trace/calcAvg (p. )results: A structure associating test names with result values.
), spikes (p. ), spike_shape (p. )avg_val: The avg value [dy].
), trace (p. ), trace/calcAvg (p. )the time is ignored.
the_period: A period object.
), cip_trace (p. ), trace (p. )the_period: A period object.
), cip_trace (p. ), trace (p. ))(optional).
), period (p. )the_period: A period object.
), cip_trace (p. ), trace (p. )the_period: A period object.
), cip_trace (p. ), trace (p. )min_val: The min value [dy]. min_idx: The index of the min value [dt]. sag_val: The sag amount [dy].
), trace (p. ), trace/calcMin (p. )the_period: A period object.
), cip_trace (p. ), trace (p. )(rest passed to plot_abstract.)
a_plot: A plot_abstract object that can be visualized.
), trace/plot (p. ), plot_abstract (p. )profile_obj: A cip_trace_allspikes_profile object.
), cip_trace_allspikes_profile (p. )tests_dbs with spontaneous, pulse and recovery period spike info.
trace, spikes, spont_spikes_db, pulse_spikes_db, recov_spikes_db, props
), spikes (p. ), tests_db (p. )a_plot: A plot_abstract object that can be visualized.
), cip_trace (p. ), spike_shape/plotCompareMethodsSimple (p. ), plot_abstract (p. )Start and width of the pulse [dt]
trace, spikes, spont_spike_shape, results, id, props.
), spikes (p. ), spike_shape (p. )h: Plot handle(s).
params_tests_dataset, cipmag, props (see above).
), params_tests_fileset (p. ), params_tests_db (p. )params_row: Parameter values in the same order of paramNames
), params_tests_dataset (p. ), paramNames (p. ), testNames (p. )a_cip_trace_profile: A cip_trace_profile object.
), params_tests_dataset (p. )a_profile: A profile object that implements the getResults method.
), params_tests_dataset (p. ), paramNames (p. ), testNames (p. )params_names: Cell array with ordered parameter names.
), paramNames (p. ), testNames (p. )params_tests_dataset, ct, props (see above).
), params_tests_fileset (p. ), params_tests_db (p. )params_row: Parameter values in the same order of paramNames
), params_tests_dataset (p. ), paramNames (p. ), testNames (p. )a_cip_trace_profile: A cip_trace_profile object.
), params_tests_dataset (p. )a_profile: A profile object that implements the getResults method.
), params_tests_dataset (p. ), paramNames (p. ), testNames (p. )params_names: Cell array with ordered parameter names.
), paramNames (p. ), testNames (p. )params_tests_dataset, cip_mags
), params_tests_dataset (p. ), params_tests_db (p. )params, param_names, tests, test_names: See params_tests_db.
), params_tests_fileset (p. ), itemResultsRow
testNames (p. ), paramNames (p. ), physiol_cip_traceset_fileset (p. )a_profile: A profile object that implements the getResults method.
), params_tests_fileset (p. ), paramNames (p. ), testNames (p. )tests_db, orig_db: original DB from which clusters were obtained, cluster_idx: Array associating rows of orig_db to each cluster here. props.
), tests_db/kmeansCluster (p. )a_plot: A plot_abstract object that can be plotted.
), plotFigure (p. ), histogram_db (p. ), histogram_db/plot_abstract (p. )a_plot: A plot_abstract object that can be plotted.
), plotFigure (p. ), silhouette (p. )a_plot: A plot_abstract object that can be plotted.
), cluster_db/plotHist (p. )tests_db.
), plot_simple (p. ), tests_db/histogram (p. )dataset, db, joined_db, props.
), params_tests_dataset (p. )crit_db: A tests_db with two rows for values and STDs.
), tests_db (p. ), tests2cols (p. )a_row_index: A row index of neuron in a_bundle.joined_db.
)(passed to a_bundle.dataset/cip_trace)
a_cip_trace: One or more cip_trace objects that hold the raw data.
), physiol_bundle/ctFromRows (p. )1a/b: Either one of the +/- 100 pA traces in one plot.
a_doc: A doc_generate object, or a subclass, that can be plotted, or printed as a PS or PDF file.
), doc_generate (p. ), doc_generate/printTeXFile (p. )a_bundle: Modified bundle.
)obj: The new tests_db object.
), tests_db (p. )(passed to plot_superpose)
a_plot: A plot_superpose that contains a f-I curve plot.
), plot_superpose (p. )which can be created with matchingRow.
tex_string: LaTeX document string.
)text, id, props.
), doc_multi (p. )tex_string: A string that contains TeX commands, which upon writing to a file, can be interpreted by the TeX engine to produce a document.
), doc_plot (p. ), string2File (p. ), properFilename (p. )tex_string: A string that contains TeX commands, which upon writing to a file, can be interpreted by the TeX engine to produce a document.
), doc_plot (p. )docs, doc_generate.
), getTeXString (p. ), doc_generate/printTeXFile (p. )tex_string: A string that contains TeX commands, which upon writing to a file, can be interpreted by the TeX engine to produce a document.
), doc_plot (p. )plot, caption, plot_filename, float_props, doc_generate.
), TeXtable (p. )figure_handle: Handle of newly opened figure.
), doc_generate (p. ), doc_plot (p. )(rest passed to plot_abstract.)
a_plot: A plot_abstract object or vector that can be visualized.
), plot_abstract (p. )tex_string: A string that contains TeX commands, which upon writing to a file, can be interpreted by the TeX engine to produce a document.
), doc_plot (p. )tests_db, props.
), plot_simple (p. ), tests_db/histogram (p. )a_plot: A object of plot_abstract or one of its subclasses.
), plot_simple (p. )mode_val: The center of the bin that has most members. mode_mag: The value of the histogram bin.
)(rest passed to histogram_db/plot_abstract)
a_plot: A object of plot_abstract or one of its subclasses.
)a_plot: A object of plot_abstract or one of its subclasses.
), plot_simple (p. )a_plot: A object of plot_abstract or one of its subclasses.
), plot_simple (p. )to have the pAcip, trial, and ItemIndex columns.
dataset_db_bundle.
), tests_db (p. ), params_tests_dataset (p. ), params_tests_db/mergeMultipleCIPsInOne (p. )(others passed to rankMatching)
tex_filename: Name of LaTeX file generated.
), physiol_cip_traceset/cip_trace (p. ), physiol_bundle/matchingRow (p. )(passed to plot_superpose)
a_plot: A plot_superpose that contains a f-I curve plot.
), plot_superpose (p. )a_row_index: A row index of neuron in a_bundle.joined_db.
)(passed to a_mbundle.dataset/cip_trace)
a_cip_trace: One or more cip_trace objects that hold the raw data.
)a_label: A string label identifying selected neuron in bundle.
)a_mbundle: a model_ct_bundle object containing the added DB.
), multi_fileset_gpsim_cns2005/addFileDir (p. )a_doc_multi: A doc_multi object that can be printed as a PS or PDF file.
), doc_generate (p. ), doc_generate/printTeXFile (p. )(passed to tests_db/rankMatching)
a_ranked_db: a ranked_db object containing the rankings.
), ranked_db (p. )row_index: Row indices of best matching models.
trial_num: The trial number(s) identifying selected neuron(s) in bundle.
)plots: A structure that contains the joined_db, and the plot vectors trace_d100_plots and trace_h100_plots.
to have the pAcip, trial, and ItemIndex columns.
crit_bundle, model_ct_bundle.
), ranked_db (p. ), params_tests_dataset (p. )a_doc: A doc_plot that contains a f-I curve plot and associated captions.
), doc_plot (p. )plots: A structure that contains the joined_db, and the plot vectors trace_d100_plots and trace_h100_plots.
which can be created with matchingRow.
tex_string: LaTeX document string.
)Start and width of the pulse [dt]
(All other props are passed to cip_trace objects)
params_tests_fileset, pulse_time_start, pulse_time_width.
), params_tests_db (p. )(passed to params_cip_trace_fileset/cip_trace)
a_cip_trace: One or more cip_trace objects that hold the raw data.
), physiol_cip_traceset/cip_trace (p. )a_cip_trace_profile: A cip_trace_profile object.
), params_tests_fileset (p. )a_cip_trace: A cip_trace object.
), params_tests_fileset (p. )a_profile: A profile object that implements the getResults method.
), params_tests_fileset (p. ), paramNames (p. ), testNames (p. )list, dt, dy, id, props (see above).
), params_tests_fileset (p. ), cip_traces_dataset (p. )dataset: With the added item.
), params_tests_dataset (p. ), paramNames (p. ), testNames (p. )params, param_names, tests, test_names: See params_tests_db.
), params_tests_fileset (p. ), itemResultsRow
testNames (p. ), paramNames (p. )params_row: Parameter values in the same order of paramNames
), params_tests_dataset (p. ), paramNames (p. ), testNames (p. )params_names: Cell array with ordered parameter names. item: (Optional) If given, read names by loading item at this index.
), paramNames (p. ), testNames (p. )db_obj: A params_tests_db object.
), params_tests_db (p. ), params_tests_dataset (p. ), itemResultsRow
testNames (p. ), paramNames (p. )params_row: Parameter values in the same order of paramNames tests_row: Test values in the same order with testNames
), params_tests_dataset (p. ), paramNames (p. ), testNames (p. )item: Object, filename, etc.
), params_tests_dataset (p. ), paramNames (p. ), testNames (p. )tests_db num_params: Number of variable parameters in simulations.
), test_variable_db (N/I) (p. )col_names: A cell array of strings.
), tests_db (p. )crit_db: A tests_db with two rows for values and STDs.
), rankMatching (p. ), tests_db (p. ), tests2cols (p. )a_db: A params_tests_db object.
)which can be created with matchingRow.
a_ranked_db: The created DB with original rows and a distance measure, in ascending order.
), rankMatching (p. ), joinRows (p. )a_ps: A horizontal plot_stack of plots
), paramsHists (p. ), plotEqSpaced (p. )feval(levelFunc, min_val, max_val, num_levels). Example: 'logLevels'
a_params_db: A db only with params.
), scaleParamsOneRow (p. ), ranked_db/blockedDistances (p. ), getParamRowIndices (p. ), logLevels (p. )a_plot_stack: A plot_stack with the plots organized in matrix form
), plotVar (p. )a_params_tests_db: The db object of with the means on page 1 and standard deviations on page 2.
), tests_db/mean (p. ), tests_db/std (p. ), sortedUniqueValues (p. )names of rows. If ':', all rows. For names, regular expressions are supported if quoted with slashes (e.g., '/a.*/'). See tests2idx.
obj: The new tests_db object.
), tests_db (p. ), test2idx (p. )p_coefs: A cell array of corrcoefs_dbs for each param in a_db.
)which can be created with matchingRow.
tex_string: LaTeX document string.
), displayRowsTeX (p. )obj: The tests_db object that includes the new columns.
), tests_db (p. )with a .txt extension.
nothing.
), scanParamAllRows (p. ), scaleParamsOneRow (p. )new_db: a new database with new neuron index.
), tests_db/physiol_bundle (p. )ranked_dbs: Array of created DBs with original rows and a distance measure, in ascending order. tex_string: A LaTeX string for all tables created.
), matchingRow (p. ), rankMatching (p. ), joinRows (p. )pp_coefs: A cell array of corrcoefs_dbs for each param combination in a_db.
)The order of names correspond to each unique CIP level in db, with increasing order.
(default is 'RowIndex' suffixed with the first field name).
cip levels that correspond to names_tests_cell db. Missing levels are replaced with NaN values. DB is filtered to remove other CIP levels.
a_db: A params_tests_db object of organized values.
), tests_3D_db (p. ), corrCoefs (p. ), tests_3D_db/plotVarBox (p. )row_indices: Array of row indices.
), scanParamAllRows (p. ), scaleParamsOneRow (p. ), makeGenesisParFile (p. )vector of histogram bin centers.
t_hists: An array of histograms for each test in a_db.
)a_db: A params_tests_db object of organized values.
), tests_3D_db (p. ), corrCoefs (p. ), tests_3D_db/plotPair (p. )a_3D_db: A tests_3D_db object of organized values.
), tests_3D_db (p. ), corrCoefs (p. ), tests_3D_db/plotPair (p. )
), results_profile (p. ), params_tests_db (p. ), params_tests_fileset (p. ), tests_db (p. ), tests_3D_db (p. ), histogram_db (p. ), stats_db (p. ), corrcoefs_db (p. )obj: The tests_db object that is missing the columns.
)a_params_db: A db only with params.
), getParamRowIndices (p. ), makeGenesisParFile (p. )p_hists: An array of histograms for each parameter in a_db.
)pt_coefs_hists: A cell array of corrcoefs_dbs for each param in a_db.
)cross_db: The tests_db object with all combinations of rows.
)p_t3ds: An array of tests_3D_dbs for each param in a_db.
)files to be loaded.
to address rows from this file and acquire parameters.
each row. The parameter names are acquired from this file.
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.
class. E.g., 'trace_profile', 'srp_trace_profile', etc. (See parent classes and cip_trace object for more props)
params_tests_dataset, path: The pathname to files.
), tests_db (p. ), test_variable_db (N/I) (p. )a_trace_profile: A trace_profile object.
), params_tests_fileset (p. )params_row: Parameter values in the same order of paramNames
), params_tests_dataset (p. ), paramNames (p. ), testNames (p. )to address rows from this file and acquire parameters.
a_fileset: The augmented fileset object. index_list: The vector of index numbers of the new files added. Can be used to selectively load the new files into a DB using params_test_db.
), params_tests_dataset/params_test_db. (p. )a_profile: A profile object that implements the getResults method.
), params_tests_fileset (p. ), paramNames (p. ), testNames (p. )params_names: Cell array with ordered parameter names.
), paramNames (p. ), testNames (p. )a_trace: A trace object.
), params_tests_fileset (p. )results_profile: Contains results of tests. db: The params_tests_db. props.
), params_tests_db/params_tests_profile (p. )(see below for the rest)
start_time, end_time: Inclusive period [dt].
), spikes (p. ), spike_shape (p. )the_period: The cropped set of spike times that fall within a period.
), cip_trace (p. ), trace (p. ), spikes (p. )It only needs to have the pAcip, pAbias, TracesetIndex, and ItemIndex columns.
dataset_db_bundle, joined_control_db: DB of control neurons (no pharmacological applications).
), tests_db (p. ), params_tests_dataset (p. )a_crit_bundle: A tests_db with two rows for values and STDs.
), tests_db (p. ), tests2cols (p. )a_crit_db: A tests_db with two rows for values and STDs.
), tests_db/matchingRow (p. )a_row_index: A row index of neuron in a_bundle.joined_db.
)a_cip_trace: One or more cip_trace object that holds the raw data.
), physiol_cip_traceset/cip_trace (p. )a_label: A string label identifying selected neuron in bundle.
)(passed to plot_superpose)
a_plot: An f-I curve plot.
), plot_abstract (p. ), plot_superpose (p. )a_pbundle: One or more cip_trace object that holds the raw data.
), physiol_cip_traceset/cip_trace (p. )neurons.
(passed to rankMatching)
all_ranks_db: DB of best matching from joined_db. Each row corresponds to p_bundle.joined_control_db rows.
), tests_db/matchingRow (p. )channel (vgain does NOT include the 10X amplification from the Axoclamp, so vgain = 1 would mean no additional amplification beyond the 10X.)
of compounds.
of ns_open_file is given here. Must be defined to allow special NeuroSAGE processing.
profile (Default: 'getProfileAllSpikes').
(All other props are passed to cip_trace objects)
params_tests_dataset, data_src, ichan, vchan, vgain, igain, treatments.
), params_tests_dataset (p. ), params_tests_db (p. )obj: The new object with the updated properties.
), params_tests_dataset (p. ), params_tests_db (p. )params_row: Parameter values in the same order of paramNames
), params_tests_dataset (p. ), paramNames (p. ), testNames (p. )a_profile: A profile object that implements the getResults method.
), params_tests_fileset (p. ), paramNames (p. ), testNames (p. )a_cip_trace: A cip_trace object that holds the raw data.
), params_tests_fileset (p. ), paramNames (p. ), testNames (p. )a_profile: A profile object that implements the getResults method.
), params_tests_fileset (p. ), paramNames (p. ), testNames (p. )params_row: Parameter values in the same order of paramNames tests_row: Test values in the same order with testNames
), params_tests_dataset (p. ), paramNames (p. ), testNames (p. )param_names: Cell array with ordered parameter names.
), paramNames (p. ), testNames (p. )string. Function should return a cell array of physiol_cip_traceset items. Alternatively a preconstructed cell array can be provided directly. If it is an ASCII filename, then it should contain the following tab-delimited items: 1. Neuron ID (name to associate with the neuron). If left blank, use the filename with the '.all' extension removed. 2. The absolute path of the data file 3. The trace numbers to load, space-delimited (e.g. 1-21 24 26 27) 4. Vchan: voltage channel number 5. Ichan: current channel number 6. Vgain: external gain on voltage channel IN ADDITION to the 10X that automatically comes from the Axoclamp 2B. 7. Igain: external gain on current channel. 8. Pairs of condition names and molar concentrations in any order e.g.: TTX 1e-8 apamin 2e-7 picrotoxin 1e-4
neuron_idx: A structure that points from neuron names to NeuronId numbers. params_tests_dataset
), params_tests_dataset (p. ), params_tests_db (p. )obj: The new object with the updated properties.
(Passed to tests_db/physiol_bundle)
a_physiol_bundle: One or more physiol_bundle object that holds the raw data.
)params, param_names, tests, test_names: See params_tests_db.
), params_tests_fileset (p. ), itemResultsRow (p. )overlapping neuron_id items.
obj: The new object with combined contents.
)to row in cells_filename) to find the cell information.
a_cip_trace: One or more cip_trace object that holds the raw data.
), physiol_cip_traceset/cip_trace (p. )to row in cells_filename) to use grab the cell information.
a_profile: A profile object that implements the getResults method.
), params_tests_fileset (p. ), paramNames (p. ), testNames (p. )name_strs: Cell array of neuron names corresponding to the ids given.
)fed to plot commands.
If a scalar, equal border on all sides, give a four-element vector [left bottom right top] to define borders for each side.
function handle, its output is passed instead.
size, if 1 (default), redraws figure after each resize event and prints at PaperPosition size.
PaperPosition property. Implies resizeControl=0.
data, axis_labels, title, legend, command, props
), plot_abstract/plotFigure (p. )If NaN, doesn't open a new axis.
handles: Handles of graphical objects drawn.
)obj: The new object with the updated properties.
ranges: The ranges as a vector in the same way 'axis' would return.
), plot_abstract/plot (p. )corresponding dimension.
a_plot: A plot_abstract object.
), plot_abstract/plot (p. ), plot_abstract/plotFigure (p. )a_plot: A plot_abstract object.
), plot_abstract/plot (p. ), plot_abstract/plotFigure (p. )handles: Handles of graphical objects drawn.
), plot_abstract/plot (p. )handle: Handle of new figure.
), plot_abstract/plot (p. ), plot_abstract/decorate (p. )If NaN, doesn't open a new axis.
handles: Handles of graphical objects drawn.
)(default=1).
instead of just a sequence of numbers.
plot_abstract
), plot_abstract/plot (p. )plot_abstract.
), plot_abstract/plot (p. )ranges: The ranges as a vector in the same way 'axis' would return.
), plot_abstract/plot (p. )plot_abstract, labels.
), plot_abstract/plot (p. )it will be a monocolor gradient (e.g., gray-level); if 2, it will be a dual-color gradient (e.g., blue to red) with a black crossing point. This point is determined by the minValue (below). Default numGrads=2, if negative values exist in image_data after scaling.
(image_data - minValue) / (maxValue - minValue). Otherwise, its min and max is used.
(Rest passed to plotImage.)
plot_abstract.
), plot_abstract/plot (p. )ranges: The ranges as a vector in the same way 'axis' would return.
), plot_abstract/plot (p. ), axis (p. )'relative' to the 1st plot (default='absolute'). Relative positioning doesn't work well.
plot_abstract, plots, axis_locations.
), plot_abstract/plotFigure (p. )handles: Handles of graphical objects drawn.
)plot_abstract.
), plot_abstract/plot (p. )limits. In this vector, NaNs are untouched, Infs are replaced by minimal and maximal ranges of the stacked plots.
(Example: relativeSizes=[1 2] makes second plot twice wider than first.)
plot_abstract, plots, axis_limits, orient.
), plot_abstract/plotFigure (p. )handles: Handles of graphical objects drawn.
), plot_abstract (p. )a_plot: A plot_stack object.
), plot_abstract/plot (p. ), plot_abstract/plotFigure (p. )handles: Handles of graphical objects drawn.
), plot_abstract/plot (p. )plot_abstract, plots
), plot_superpose/plot (p. )handles: Handles of graphical objects drawn.
)ranges: The ranges as a vector in the same way 'axis' would return.
), plot_abstract/plot (p. )a_plot: A plot_superpose object.
), plot_stack/superposePlots (p. )handles: Handles of graphical objects drawn.
), plot_abstract/plot (p. )tests_db, orig_db, crit_db, props.
), tests_db/rankMatching (p. ), tests_db/matchingRow (p. )overall distance.
(rest passed to plot_abstract)
a_plot: A plot_abstract object.
), tests_db/rankMatching (p. ), plot_abstract (p. ), plotImage (p. )a_db: A params_tests_db object (same type as a_ranked_db.orig_db) containing the desired rows in ascending order of distance.
)(also passed to plot_abstract)
a_plot: A plot_abstract object.
), plot_abstract (p. ), getDistMatrix (p. ), plotCompareDistMatx (p. )a_db: The ranked_db object that includes the new columns.
)(also passed to plot_abstract)
a_plot: A plot_abstract object.
), plot_abstract (p. )s: A structure of column name and value pairs.
)a_plot: A plot_abstract object.
), plot_abstract (p. )a_db: A tests_db object with the matrix of distances. ranked_dbs: A cell array of ranked_dbs for each row.
), getParamRowIndices (p. )results, id, props.
), cip_trace_profile (p. )h: The figure handle created.
), plotFigure (p. )results: A structure associating test names to values.
)num_runs, id, props.
), runLast (p. ), runJob (p. )job_result: Any output produced by the job.
), runFirst (p. )job_results: Any output produced by the job.
), runFirst (p. )job_results: A cell array of results collected from each item of the vector jobs.
), runJob (p. )Matlab commands on the cluster nodes. It can have qsub options prepended to it such as '-p -100 -q all.q <abs_path_to>/sge_matlab.sh'.
(others passed to script_array)
num_runs, id, props.
), runLast (p. ), runJob (p. ), script_array (p. )job_results: A cell array of results collected from each item of the vector jobs.
)filename corresponds to the script number.
num_scripts, out_name, id, props.
)1- maximum acceleration point 2- threshold crossing of acceleration (needs threshold) 3- threshold crossing of slope (needs threshold) 4- maximum acceleration in phase space (optionally specify maximal threshold as init_threshold) 5- point of maximum curvature, when slope is between init_lo_thr and init_hi_thr 6- local maximum of second derivative in the phase space nearest slope crossing init_threshold 7- threshold crossing of interpolated slope (needs threshold) 8- maximum curvature in phase-plane 9- Combined curvature and inflection method in time-domain.
(see above methods and implementation in calcInitVm)
trace, props.
), trace/analyzeSpikesInPeriod (p. ), trace (p. ), spikes (p. ), period (p. )(optional).
init_idx: Its index in the spike_shape [dt]. a_plot: plot_abstract, if requested.
)min_val: The min value [dy]. min_idx: Its index in the spike_shape [dt]. max_min_time: Time from max to min [dt].
), spike_shape (p. ), trace/calcMin (p. )(optional).
init_idx: Its index in the spike_shape [dt]. a_plot: plot_abstract, if requested.
)(optional).
init_idx: AP threshold index in the spike_shape [dt]. a_plot: plot_abstract, if requested.
)max_val: The max value. max_idx: Its index in the spike_shape [dt].
), spike_shape (p. ), trace/calcMax (p. )(optional).
results: A structure associating test names to values in ms and mV. a_plot: plot_abstract, if requested.
)a_plot: A plot_abstract object that can be visualized.
), plot_abstract (p. )a_plot: A plot_abstract object that can be visualized.
), plot_abstract (p. )(optional).
init_idx: AP threshold index in the spike_shape [dt]. a_plot: plot_abstract, if requested.
)(optional).
init_idx: Indices of threshold candidates in the spike_shape [dt]. a_plot: plot_abstract, if requested.
)a_plot: A plot_abstract object that can be visualized.
), plot_abstract (p. )a_plot: A plot_abstract object that can be visualized. title_str: (Optional) String to append to plot title. props: A structure with any optional properties, passed to trace/plotData.
), plot_abstract (p. )(optional).
init_idx: AP threshold index in the spike_shape [dt]. a_plot: plot_abstract, if requested.
)(optional).
init_idx: AP threshold index in the spike_shape [dt]. max_d1o: Maximal value of first voltage derivative [dy]. a_plot: plot_abstract, if requested. fail_cond: True if this algorithm fails to be trustable.
)a_plot: A plot_abstract object that can be visualized.
), plot_abstract (p. ), diffT (p. )(optional).
init_val: The potential value [dy]. init_idx: Its index in the spike_shape [dt]. rise_time: Time from initiation to maximum [dt]. amplitude: Magnitude from initiation to max [dy]. peak_mag: Peak value [dy]. peak_idx: Extrapolated spike peak index [dt]. max_d1o: Maximal value of first voltage derivative [dy]. a_plot: plot_abstract, if requested.
)base_width: Width of spike at base [dt] half_width: Width of spike at half_Vm [dt] half_Vm: Half height of spike [dy] fall_time: Time from peak to initialization level [dt]. min_idx: The index of the minimal point of the spike_shape [dt]. max_ahp: Magnitude from initiation to minimum [dy]. ahp_decay_constant: Approximation to refractory decay after maxAHP [dt]. dahp_mag: Magnitude of the double AHP peak dahp_mag: Index of the double AHP peak
)(optional).
init_idx: AP threshold index in the spike_shape [dt]. a_plot: plot_abstract, if requested.
)results_profile: Contains results of tests. spike_shape: The spike_shape object from which results were obtained. props.
)a_plot: A plot_abstract object that can be visualized.
), plot_abstract (p. )times, num_samples, dt, id.
), trace (p. ), spike_shape (p. ), period (p. )a_plot: A plot_abstract object that can be visualized. title_str: (Optional) String to append to plot title.
), plot_abstract (p. )h: Handle to figure object.
), plot_abstract (p. )cv: Coefficient of variation.
), period (p. )results: A structure associating test names to values in ms and mV (or mA).
)a_plot: A plot_abstract object that can be visualized. title_str: (Optional) String to append to plot title.
), plot_abstract (p. )), spikes (p. )isi: Inter-spike-interval vector [dt]
), spikes (p. ), period (p. )freq: Firing rate [Hz]
), spikes (p. ), period (p. )freq: Firing rate [Hz]
), period (p. )obj: A spikes object
), period (p. )a_tau: Approximate amplitude decay constant. da_inf: Delta change in final spike peak value from initial.
), spikes (p. ), trace (p. )a_spikes, with_spikes, ...: Spikes objects.
a_spikes: A tests_spikes that contains times of all given spikes objects.
), spikes (p. )obj: A spikes object
), period (p. )obj: A spikes object
), period (p. )s: The updated object.
)'manhattan' uses flat lines of 1/isi height between spike times (default). (others passed to plot_abstract)
a_plot: A plot_abstract object that can be visualized. title_str: (Optional) String to append to plot title.
), plot_abstract (p. )sfa: Spike frequency accommodation.
), period (p. )tests_db, trace, period, props.
), trace (p. ), period (p. ), trace/analyzeSpikesInPeriod (p. )a_pm: A trace plot.
), tests_db/plot_abstract (p. ), plotFigure (p. )db_conn: The DB Toolbox connection object. id, props.
), database (p. )
), database (p. ), sql_portal/tests_db (p. )response_str: Response string from the SQL engine.
), database (p. )into the tests_db object.
a_db: A tests_db object.
), database (p. )(e.g., a different invariant parameter).
for errorbar axes.
tests_3D_db.
), plot_abstract (p. )a_mult_stats_db: A multi-page stats_db.
), plot_simple (p. )calling tests_3D_db/paramsTestsHistsStats.
'plot_bars' uses stats_db/plot_bars
a_plot_stack: A plot_stack with the plots organized in matrix form
), params_tests_profile (p. ), plotVar. (p. )calling tests_3D_db/paramsTestsHistsStats.
'plot_bars' uses stats_db/plot_bars
a_plot: A plot_abstract with the color plot
), params_tests_profile (p. ), plotVar. (p. )obj: The new tests_db object.
), tests_db (p. )(rest passed to plot_abstract)
a_plot: A plot_abstract object or one of its subclasses.
), plot_simple (p. )a_plot: A plot_abstract object that can be plotted.
), plotFigure (p. ), stats_db/plot_bars (p. )a_p: A plot_abstract.
)(passed to plot_bars/plot_bars)
a_plot: A object of plot_bars or one of its subclasses.
), plot_bars/plot_bars (p. )a_plot: A object of plot_abstract or one of its subclasses.
), plot_simple (p. )tests_db, page_idx.
), tests_db/invarValues (p. )a_plot: A plot_abstract object or one of its subclasses.
), plotImage (p. ), plot_abstract. (p. )a_db: A tests_db object.
), tests_3D_db (p. )a_tests_db: A tests_db that holds the requested differences of parameter values.
), plot_abstract (p. )a_histogram_db: A histogram_db object containing the histogram.
), tests_db (p. )a_plot: A plot_abstract object or one of its subclasses.
), plot_abstract (p. )a_db: A tests_db object.
)will be skipped. (default=1)
a_coefs_db: A corrcoefs_db of the coefficients and page indices.
), corrcoefs_db (p. )calling the params_tests_db/invarParams method.
pt_hists: An array of 3D histograms for each pair of param and test. p_stats: An array of stats_dbs for each param.
), params_tests_profile (p. )a_3D_db: A tests_3D_db object.
)tests and rows for separate observations.
data: The data matrix. row_idx, col_idx: Structure associating row/column names to indices. id, props.
), params_db (p. ), test_variable_db (N/I) (p. )obj: The tests_db object with the new rows.
), addRow (p. ), tests_db (p. )will be skipped. (default=1)
a_coefs_db: A tests_3D_db of the coefficients.
), corrcoefs_db (p. )obj: The new tests_db object.
), addRow (p. ), setRows (p. ), tests_db (p. )crit_db: A tests_db with two rows for values and STDs.
), tests_db (p. ), tests2cols (p. )test name or a cell array of test names. If ':', all tests. For name strings, regular expressions are supported if quoted with slashes (e.g., '/a.*/')
idx: Array of column indices.
), tests2cols (p. ), regexp (p. )invariant. Include result columns here.
(Optional; used only if database is not symmetric, to ignore missing values of in_page_unique_cols)
a_tests_3D_db: A tests_3D_db object of organized values.
), tests_3D_db/corrCoefs (p. ), tests_3D_db/plotPair (p. ), joinRows (p. ), tests_3D_db/swapRowsPages (p. ), tests_3D_db/mergePages (p. )if 0 shuffle each test separately.
a_db: The shuffled db.
)h: The figure handle created.
), plotFigure (p. )obj: The new object with the updated properties.
that are same w.r.t other parameters. (default='pulseOn', 'pulseOff', 'traceEnd', 'pAbias', 'ItemIndex').
control db (default='TTX', 'Apamin', 'EBIO', 'XE991', 'Cadmium', 'drug_4AP').
others), default is an empty array, which means to choose all.
eliminated. (default=30)
phys_joined_db: Final one row per cip and neuron db. phys_joined_control_db: Rows where all drug treatments are zero. phys_db: Original db only with parameter and including the weedCols.
), params_tests_db (p. )a_db: The resulting tests_db.
), mtimes (p. )obj: The tests_db object that includes the new columns.
), tests_db (p. )and the other can be a scalar or tests_db.
a_db: The resulting tests_db.
)test name or a cell array of test names. If ':', all tests. For name strings, regular expressions are supported if quoted with slashes (e.g., '/a.*/')
a_log: Array of column indices.
), tests2cols (p. ), regexp (p. )a_db: The transposed tests_db.
)(default='RowIndex').
(default=1, for multi-page DBs; 0, otherwise).
indices with NaN values. It will fail if all indices are NaNs. (default=0)
a_db: A tests_db object.
)vector of histogram bin centers.
a_histogram_db: A histogram_db object containing the histogram.
), tests_db (p. ), hist (p. )when checking for uniqueness.
a_db: The modified DB.
)returned id.
a_db: The resulting tests_db.
), uminus (p. )(see tests2cols for accept column specifications).
inputs and outputs.
prior class probabilities.
(Rest passed to balanceInputProbs and tests_db)
an_approx_db: A tests_db object containing the original inputs and the approximated outputs. a_nnet: The Matlab neural network approximator object.
), newff (p. )rows: A logical column vector of rows.
), tests_db (p. )and the other can be a scalar.
a_db: The resulting tests_db.
)tex_string: LaTeX string for table float.
), TeXtable (p. ), cell2TeX (p. )plotScatter.
a_p: A plot_abstract.
this many iterations. (rest passed to plot_image.)
a_plot: A plot_abstract object or one of its subclasses.
), plotImage (p. ), tests_db/matchingRow (p. ), corrcoefs. (p. )a_db: DB with missing rows.
)a_pca_db: A tests_db where each row is a principal component.
), zscore (p. )(others passed to tests_db)
a_cov_db: A tests_db which contains the covariance matrix.
)a_plot: A plot_abstract object that can be plotted.
), plotFigure (p. )the common columns.
col_names, with_col_names: list of column names of each DB.
), tests_db (p. )rows: A logical or index vector to be used in indexing db objects.
), tests_db (p. )a_db: The DB with std values. n: (Optional) Numbers of non-NaN rows included in calculating each column.
), tests_db (p. )sorted_db: The sorted tests_db. idx: The row index permutation vector, such that sorted_db = db(idx, :).
), tests_db (p. )takes the data as the first argument and dimension to work as second.
a_db: The DB with one row of max values, with selected dimension replaced by the output of the given function. n: (Optional) Numbers of used values in each call of a_func.
), mean (p. ), feval (p. ), tests_db (p. )a_factors_db: A corrcoefs_db of the coefficients and page indices.
), corrcoefs_db (p. )a_plot: A plot_stack object that can be plotted.
), plotFigure (p. )a_db: The DB with one row of mean values. n: (Optional) Numbers of non-NaN rows included in calculating each column.
), tests_db (p. ), if 1, NaN values are given a fixed 3xSTD penalty (default=1).
calculating distances.
matrix in crit_db.
a_ranked_db: A ranked_db object.
), tests_db (p. )names of rows. If ':', all rows. For names, regular expressions are supported if quoted with slashes (e.g., '/a.*/'). See tests2idx.
obj: The new tests_db object.
), tests_db (p. ), tests2idx (p. ), regexp (p. )a_db: The resulting tests_db.
), mtimes (p. )a_db: The tests_db object that includes the new columns.
), tests_db (p. )a_stats_db: A stats_db object.
)col_names: A cell array of strings.
), tests_db (p. )obj: The tests_db object that includes the new row.
), addRow (p. ), tests_db (p. )rows: A logical column vector of rows.
), tests_db (p. )obj: The new tests_db object.
), tests_db (p. )rows: A logical or index vector to be used in indexing db objects.
), tests_db (p. )a_plot: A plot_abstract object that can be plotted.
), plotFigure (p. ), boxplotp (p. )a_db: The resulting tests_db.
), uop (p. )s: The size values.
), tests_db (p. )a_db: The resulting tests_db.
)a_pm: A plot_stack with the plots organized in matrix form
), plotVar (p. )idx: A logical column vector of matching db row indices. rows_idx: Indices of rows entries corresponding to each db row. Non-matching entries were left as NaN.
), eq (p. ), tests_db (p. )rows: A logical or index vector to be used in indexing db objects.
), tests_db (p. )Two-element cell of histogram bin centers vectors.
a_histogram_db: A histogram_db object containing the 2D histogram.
), tests_db (p. ), hist3 (p. )a_cluster_db: A tests_db where each row is a cluster center. a_hist_db: histogram_db showing cluster membership from original db. idx: Cluster indices of each row or original db. sum_distances: Quality of clustering indicated by total distance from centroid for each cluster.
), histogram_db (p. )idx: A inverted logical column vector of comparison results. (false if db == rows, true otherwise) compared: A column vector of differences of each DB row to the given row (i.e., compared = db - rows).
), anyRows (p. ), ge (p. ), gt (p. ), le (p. ), lt (p. ), tests_db (p. )a_stats_db: A stats_db object.
)for column representation).
a_tests_3D_db: A tests_3D_db object of organized values.
), tests_3D_db (p. ), tests_3D_db/corrCoefs (p. ), tests_3D_db/plotPair (p. ), joinRows (p. ), tests_3D_db/swapRowsPages (p. ), tests_3D_db/mergePages (p. )a_stats_db: A stats_db object.
)s: The size.
), tests_db (p. )rows: A logical vector to be used in indexing db objects or passed through other logical operators.
), tests_db (p. )rows: A logical or index vector to be used in indexing db objects.
), tests_db (p. )& Y of the 2D image plot.
unique value.
(rest passed to plotUniquesStats2D and plot_stack).
a_stacked_plot: A plot_abstract object to be plotted.
), sortedUniqueValues (p. ), statsMeanStd (p. ), plot_abstract (p. ), plotImage (p. )a_p: A plot_abstract.
and the other can be a scalar or tests_db.
returned id.
a_db: The resulting tests_db.
), tests_db/minus (p. ), tests_db/mtimes (p. ), tests_db/rdivide (p. )a_db: A tests_db that contains rows of db and with_db.
), tests_db (p. )rows: A logical or index vector to be used in indexing db objects.
), tests_db (p. )a_db: The resulting tests_db.
)obj: The tests_db object that includes the new row.
), allocateRows (p. ), tests_db (p. )a_p: A plot_abstract.
)population mean. If NaN, calculated from a_db.
interesting part of the bar plot.
(rest passed to plot_bars [and plot_superpose if popMean]).
a_bar_plot: A plot_abstract object to be plotted.
), sortedUniqueValues (p. ), statsMeanStd (p. ), plot_bars (p. )a_p: A plot_abstract.
obj: The new tests_db object.
), tests_db (p. )and the other can be a scalar or tests_db.
a_db: The resulting tests_db.
)s: A cell array of trasposed database contents, prefixed with column names on each row. Meant to be displayed on the screen.
)vector of histogram bin centers.
t_hists: An array of histograms for each test in a_db.
)rows: A logical or index vector to be used in indexing db objects.
), tests_db (p. )a_db: A tests_db object.
)& Y of the 2D image plot.
unique value.
population mean. If NaN, calculate from given a_db.
(default=.3 or 2*STD if popMean=NaN).
unique_test1,unique_test2.
(rest passed to plotImage and plot_abstract).
an_image_plot: A plot_abstract object to be plotted.
), sortedUniqueValues (p. ), statsMeanStd (p. ), plot_abstract (p. ), plotImage (p. )a_plot: A object of plot_bars or one of its subclasses.
), plot_simple (p. )a_db: The resulting tests_db.
), tests_3D_db/getDiff2DDB (p. )obj: The tests_db object that is missing the columns.
), tests_db (p. )a_tests_db: The db object of with the means on page 1 and standard deviations on page 2.
), tests_db/std (p. ), sortedUniqueValues (p. )a_stats_db: A stats_db object.
)a_db: The resulting tests_db.
)a_pm: A plot_stack with the plots organized in matrix form
), plotTestsHistsMatrix (p. ), plotFigure (p. )cross_db: The tests_db object with all combinations of rows.
), tests_db (p. )test name or a cell array of test names. If ':', all tests. For name strings, regular expressions are supported if quoted with slashes (e.g., '/a.*/'). See tests2idx for more.
cols: Array of column indices.
), tests2idx (p. )s: A structure of column name and value pairs.
)a_db: The DB with one row of max values. n: (Optional) Numbers of non-NaN rows included in calculating each column.
), tests_db (p. )Genesis (.bin, .gbin, .genflac), PCDX (.all), or Matlab (.mat).
'genesis': Raw binary files created with Genesis disk_out method. 'genesis_flac': Compressed Genesis binary files. 'neuron': Binary files created with Neuron's Vector.vwrite method. 'pcdx': .ALL data acquisition files from PCDX program. 'matlab': Matlab .MAT binary files with matrix data.
(1 for findFilteredSpikes, 2 for findspikes).
shape calculation (see spike_shape/spike_shape).
(see above methods and implementation in calcInitVm)
If custom_filter == 1, a filter with custom lowpass and highpass cutoffs can be specified. This allows for fast and accurate spike discrimination. The filter type used is a 2-pole butterworth, different than the default high-order Cheby2. Creates new prop called 'butterWorth' to hold the filter.
data: The trace column matrix. dt, dy, id, props (see above)
), spike_shape (p. ), cip_trace (p. ), period (p. )(rest passed to plot_abstract.)
a_plot: A plot_abstract object that can be visualized.
), trace/plot (p. ), plot_abstract (p. )h: Handle to figure object.
), plot_abstract (p. )obj: The new object with the updated properties.
max_val: The max value. max_idx: Its index in the trace.
), trace (p. )results: A structure associating test names to values in ms and mV (or mA).
)), trace (p. )results: Results structure names prefixed with prefix_str. period_spikes: Corrected spikes object for this period. a_spikes_db: A mini spikes database of results from each spike in period. spikes_stats_db: Statistics from the mini spikes database. spikes_hists_dbs: Cell array of histograms from the mini spikes database.
), spikes (p. ), period (p. ), spike_shape (p. ), getProfileAllSpikes (p. )), trace (p. )min_val: The min value. min_idx: Its index in the trace.
), trace (p. )avg_t: A trace object that contains the running average of this trace.
)dy: The dy value.
)minamp (optional): minimum amplitude above baseline that must be reached. -> adjust as necessary to discriminate spikes from EPSPs.
), period (p. )obj: A trace object
), period (p. )(optional, if empty vector, taken as wholePeriod).
(optional).
-> adjust as needed to discriminate spikes from EPSPs. (optional)
)calculated automatically if given as [].
)(rest passed to plot_abstract.)
a_plot: A plot_abstract object that can be visualized.
), trace/plot (p. ), plot_abstract (p. ))trace, spikes, spike_shape, results, id, props.
), spikes (p. ), spike_shape (p. )tex_string: LaTeX string for table float.
levels: A column vector of logarithmic series between min_val and max_val.
names_vals: A two-column cell array with names and values.
)a_label: The corrected proper a_label.
_day'
deriv3: Estimate of the derivative.
filename: The corrected proper filename.
struct(n): A structure.
results: The merged structure.
(see errorbar)
handles: Handles to graphics objects.
a_tests_db: A tests_db object.
x_idx: Indices of maxima.
(rest passed to tests_db.)
a_chans_db: A tests_db object containing channel tables.
), trace/plot (p. ), plot_abstract (p. ), GP/common/dump_chans.g (Genesis) (p. )new_struct: The new structure.
tex_string: LaTeX formatted table string.
new_axis: Modified axis.
)deriv2: Estimate of the derivative.
colors: RGB color matrix to be passed to colormap function.
)deriv2: Estimate of the derivative.
this string (e.g., 'Amp1 Vm'). If numeric, use as channel number. Added to the neuron_id to distinguish multiple neurons recorded in same file. If not specified, the first voltage channel is used.
trace. Does not affect neuron_id.
when the gains are not specified in the file.
sequence name to look for.
sequence name to avoid searching.
values for this traceset to keep consistent accross tracesets. Use only lowercase in treatment names.
these. Same format as addTreats.
are skipped. (All other props are passed to physiol_cip_traceset)
a_tss: Cell array of physiol_cip_traceset objects.
), physiol_cip_traceset (p. ), params_tests_dataset (p. )
)rows: A matrix or column vector of unique rows. idx: Indices of the unique rows in the original data matrix.
), unique (p. )
inter-spike-interval of the given spike train and the
time resolution dt.
deriv2: Estimate of the derivative.
range: The maximal range obtained that includes all given axes.
colors: RGB color matrix to be passed to colormap function.
)deriv: Estimate of the first derivative.
val: the value taken from the nearest integer indices of data and interpolated.
)handle: Text object handle.
ratio_x, ratio_y: Normalized to points ratio for axis width and height, respectively.
each class if used. If 0, prior class probabilities are followed.
with larger class. Otherwise, takes the minimal number of samples to avoid repetitions (default=1).
new_inputs, new_outputs: New input and output vectors.
), tests_db (p. )
rows: A matrix or column vector of unique rows. idx: Indices of the unique rows in the original data matrix.
)idx: Structure associating names to array indices.
)