Source code for netpyne.plotting.plotRaster

# Generate a raster plot

import matplotlib.patches as mpatches
from ..analysis.utils import exception #, loadData
from import loadData
from .plotter import ScatterPlotter

[docs]@exception def plotRaster( rasterData=None, popNumCells=None, popLabels=None, popColors=None, axis=None, legend=True, colorList=None, orderInverse=False, returnPlotter=False, **kwargs): """Function to produce a raster plot of cell spiking, grouped by population Parameters ---------- rasterData : list, tuple, dict, str the data necessary to plot the raster (spike times and spike indices, at minimum). *Default:* ``None`` uses ``analysis.prepareRaster`` to produce ``rasterData`` using the current NetPyNE sim object. *Options:* if a *list* or a *tuple*, the first item must be a *list* of spike times and the second item must be a *list* the same length of spike indices (the id of the cell corresponding to that spike time). Optionally, a third item may be a *list* of *ints* representing the number of cells in each population (in lieu of ``popNumCells``). Optionally, a fourth item may be a *list* of *strs* representing the population names (in lieu of ``popLabels``). If a *dict* it must have keys ``'spkTimes'`` and ``'spkInds'`` and may optionally include ``'popNumCells'`` and ``'popLabels'``. If a *str* it must represent a file path to previously saved data. popNumCells : list a *list* of *ints* representing the number of cells in each population. *Default:* ``None`` puts all cells into a single population. popLabels : list a *list* of *strs* of population names. Must be the same length as ``popNumCells``. *Default:* ``None`` uses generic names. popColors : dict a *dict* of ``popLabels`` and their desired color. *Default:* ``None`` draws from the NetPyNE default colorList. axis : matplotlib axis the axis to plot into, allowing overlaying of plots. *Default:* ``None`` produces a new figure and axis. legend : bool whether or not to add a legend to the plot. *Default:* ``True`` adds a legend. colorList : list a *list* of colors to draw from when plotting. *Default:* ``None`` uses the default NetPyNE colorList. orderInverse : bool whether or not to invert the y axis (useful if populations are defined top-down). *Default:* ``False`` does not invert the y-axis. returnPlotter : bool whether to return the figure or the NetPyNE Plotter object. *Default:* ``False`` returns the figure. Plot Options ------------ title : str the axis title. *Default:* ``'Raster Plot of Spiking'`` xlabel : str label for x-axis. *Default:* ``'Time (ms)'`` ylabel : str label for y-axis. *Default:* ``'Cells'`` s : int marker size. *Default:* ``5`` marker : str marker symbol. *Default:* ``'|'`` linewidth : int line width (affects other sizes). *Default:* ``2`` legendKwargs : dict a *dict* containing any or all legend kwargs. These include ``'title'``, ``'loc'``, ``'fontsize'``, ``'bbox_to_anchor'``, ``'borderaxespad'``, and ``'handlelength'``. rcParams : dict a *dict* containing any or all matplotlib rcParams. To see all options, execute ``import matplotlib; print(matplotlib.rcParams)`` in Python. Any options in this *dict* will be used for this current figure and then returned to their prior settings. overwrite : bool whether to overwrite existing figure files. *Default:* ``True`` overwrites the figure file *Options:* ``False`` adds a number to the file name to prevent overwriting NetPyNE Options --------------- include : str, int, list cells and/or NetStims to return information from *Default:* ``'allCells'`` includes all cells and no NetStims *Options:* (1) ``'all'`` includes all cells and all NetStims, (2) ``'allNetStims'`` includes all NetStims but no cells, (3) a *str* which matches a popLabel includes all cells in that pop, (4) a *str* which matches a NetStim name includes that NetStim, (5) an *int* includes the cell with that global identifier (GID), (6) a *list* of *ints* includes the cells with those GIDS, (7) a *list* with two items, the first of which is a *str* matching a popLabel and the second of which is an *int* (or a *list* of *ints*), includes the relative cell(s) from that population (e.g. (``['popName', [0, 1]]``) includes the first two cells in popName. timeRange : list time range to include in the raster: ``[min, max]``. *Default:* ``None`` uses the entire simulation maxSpikes : int the maximum number of spikes to include (by reducing the max time range). *Default:* ``1e8`` orderBy : str how to order the cells along the y-axis. *Default:* ``'gid'`` orders cells by their index *Options:* any NetPyNe cell tag, e.g. ``'pop'``, ``'x'``, ``'ynorm'`` . popRates : bool whether to include the spiking rates in the plot title and legend. *Default:* ``True`` includes detailed pop information on plot. *Options:* ``False`` only includes pop names. ``'minimal'`` includes minimal pop information. saveData : bool whether to save to a file the data used to create the figure. *Default:* ``False`` does not save the data to file fileName : str if ``saveData`` is ``True``, this is the name of the saved file. *Default:* ``None`` a file name is automatically generated. fileDesc : str an additional *str* to include in the file name just before the file extension. *Default:* ``None`` includes no extra text in the file name. fileType : str the type of file to save the data to. *Default:* ``json`` saves the file in JSON format. *Options:* ``pkl`` saves the file in Python Pickle format. fileDir : str the directory to save the data to. *Default:* ``None`` saves to the current directory. sim : NetPyNE sim object the *sim object* from which to get data. *Default:* ``None`` uses the current NetPyNE sim object Returns ------- rasterPlot : *matplotlib figure* By default, returns the *figure*. If ``returnPlotter`` is ``True``, instead returns the NetPyNE *Plotter object* used. Examples -------- There are many options available in plotRaster. To run a variety of examples, enter the following:: from netpyne.plotting import plotRaster from netpyne.plotting.examples import spikeSim sim = spikeSim() First, let's just use mostly the default settings, though we will save the figure and the data. If ``rasterData`` is ``None`` (default), NetPyNE uses ``analysis.prepareRaster`` to generate the ``rasterData`` used in the plot:: plot = plotRaster(showFig=True, saveData=True) Because we will just be looking at data from one example simulation, we don't need to reprocess the data every time. Let's save the output data, and then we can use that to generate more plots:: plot = plotRaster(showFig=True, saveFig=True overwrite=True, saveData=True) This will save a data file with the raster data. """ # If there is no input data, get the data from the NetPyNE sim object if rasterData is None: if 'sim' not in kwargs: from .. import sim else: sim = kwargs['sim'] rasterData = sim.analysis.prepareRaster(legend=legend, popLabels=popLabels, **kwargs) print('Plotting raster...') # If input is a file name, load data from the file if type(rasterData) == str: rasterData = loadData(rasterData) # If input is a dictionary, pull the data out of it if type(rasterData) == dict: spkTimes = rasterData['spkTimes'] spkInds = rasterData['spkInds'] if not popNumCells: popNumCells = rasterData.get('popNumCells') if not popLabels: popLabels = rasterData.get('popLabels') axisArgs = rasterData.get('axisArgs') legendLabels = rasterData.get('legendLabels') # If input is a list or tuple, the first item is spike times, the second is spike indices elif type(rasterData) == list or type(rasterData) == tuple: spkTimes = rasterData[0] spkInds = rasterData[1] axisArgs = None legendLabels = None # If there is a third item, it should be popNumCells if not popNumCells: try: popNumCells = rasterData[2] except: pass # If there is a fourth item, it should be popLabels if not popLabels: try: popLabels = rasterData[3] except: pass # If there is no info about pops, generate info for a single pop if not popNumCells: popNumCells = [max(spkInds)] if popLabels: popLabels = [str(popLabels[0])] else: popLabels = ['population'] # If there is info about pop numbers, but not labels, generate the labels elif not popLabels: popLabels = ['pop_' + str(index) for index, pop in enumerate(popNumCells)] # If there is info about pop numbers and labels, make sure they are the same size if len(popNumCells) != len(popLabels): raise Exception('In plotRaster, popNumCells (' + str(len(popNumCells)) + ') and popLabels (' + str(len(popLabels)) + ') must be the same size') # Create a dictionary with the color for each pop if not colorList: from .plotter import colorList popColorsTemp = {popLabel: colorList[ipop%len(colorList)] for ipop, popLabel in enumerate(popLabels)} if popColors: popColorsTemp.update(popColors) popColors = popColorsTemp # Create a list to link cells to their populations indPop = [] for popLabel, popNumCell in zip(popLabels, popNumCells): indPop.extend(int(popNumCell) * [popLabel]) # Create a dictionary to link cells to their population color cellGids = list(set(spkInds)) gidColors = {cellGid: popColors[indPop[cellGid]] for cellGid in cellGids} # Create a list of spkColors to be fed into the scatter plot spkColors = [gidColors[spkInd] for spkInd in spkInds] # Set the time range appropriately if 'timeRange' in kwargs: timeRange = kwargs['timeRange'] elif 'timeRange' in rasterData: timeRange = rasterData['timeRange'] else: timeRange = [0, np.ceil(max(spkTimes))] # Create a dictionary with the inputs for a scatter plot scatterData = {} scatterData['x'] = spkTimes scatterData['y'] = spkInds scatterData['c'] = spkColors scatterData['s'] = 5 scatterData['marker'] = '|' scatterData['linewidth'] = 2 scatterData['cmap'] = None scatterData['norm'] = None scatterData['alpha'] = None scatterData['linewidths'] = None # If we use a kwarg, we add it to the list to be removed from kwargs kwargDels = [] # If a kwarg matches a scatter input key, use the kwarg value instead of the default for kwarg in kwargs: if kwarg in scatterData: scatterData[kwarg] = kwargs[kwarg] kwargDels.append(kwarg) # Create a dictionary to hold axis inputs if not axisArgs: axisArgs = {} axisArgs['title'] = 'Raster Plot of Spiking' axisArgs['xlabel'] = 'Time (ms)' axisArgs['ylabel'] = 'Cells' # It is often useful to invert the ordering of cells, so positions match the legend if orderInverse: axisArgs['invert_yaxis'] = True # If a kwarg matches an axis input key, use the kwarg value instead of the default for kwarg in kwargs: if kwarg in axisArgs.keys(): axisArgs[kwarg] = kwargs[kwarg] kwargDels.append(kwarg) # Delete any kwargs that have been used for kwargDel in kwargDels: kwargs.pop(kwargDel) # create Plotter object rasterPlotter = ScatterPlotter(data=scatterData, kind='raster', axis=axis, **axisArgs, **kwargs) # add legend if legend: # Set up a dictionary of population colors if not popColors: colorList = colorList popColors = {popLabel: colorList[ipop % len(colorList)] for ipop, popLabel in enumerate(popLabels)} # Create the labels and handles for the legend # (use rectangles instead of markers because some markers don't show up well) labels = [] handles = [] for popIndex, popLabel in enumerate(popLabels): if legendLabels: labels.append(legendLabels[popIndex]) else: labels.append(popLabel) handles.append(mpatches.Rectangle((0, 0), 1, 1, fc=popColors[popLabel])) # Set up the default legend settings legendKwargs = {} legendKwargs['title'] = 'Populations' legendKwargs['bbox_to_anchor'] = (1.025, 1) legendKwargs['loc'] = 2 legendKwargs['borderaxespad'] = 0.0 legendKwargs['handlelength'] = 0.5 legendKwargs['fontsize'] = 'small' # If 'legendKwargs' is found in kwargs, use those values instead of the defaults if 'legendKwargs' in kwargs: legendKwargs_input = kwargs['legendKwargs'] kwargs.pop('legendKwargs') for key, value in legendKwargs_input: if key in legendKwargs: legendKwargs[key] = value # Add the legend rasterPlotter.addLegend(handles, labels, **legendKwargs) # Adjust the plot to make room for the legend rightOffset = 0.8 maxLabelLen = max([len(label) for label in popLabels]) rasterPlotter.fig.subplots_adjust(right=(rightOffset - 0.012 * maxLabelLen)) # Generate the figure rasterPlot = rasterPlotter.plot(**axisArgs, **kwargs) # Default is to return the figure, but you can also return the plotter if returnPlotter: return rasterPlotter else: return rasterPlot