Source code for brainbox.plot_base

import numpy as np
import matplotlib.pyplot as plt
from matplotlib.image import NonUniformImage
import matplotlib
from matplotlib import cm
from iblutil.util import Bunch


axis_dict = {'x': 0, 'y': 1, 'z': 2}


[docs]class DefaultPlot(object): def __init__(self, plot_type, data): """ Base class for organising data into a structure that can be easily used to create plots. The idea is that the dictionary is independent of plotting method and so can be fed into matplotlib, pyqtgraph, datoviz (or any plotting method of choice). :param plot_type: type of plot (just for reference) :type plot_type: string :param data: dict of data containing at least 'x', 'y', and may additionally contain 'z' for 3D plots and 'c' 2D (image or scatter plots) with third variable represented by colour :type data: dict """ self.plot_type = plot_type self.data = data self.hlines = [] self.vlines = [] self.set_labels()
[docs] def add_lines(self, pos, orientation, lim=None, style='--', width=3, color='k'): """ Method to specify position and style of horizontal or vertical reference lines :param pos: position of line :param orientation: either 'v' for vertical line or 'h' for horizontal line :param lim: extent of lines :param style: line style :param width: line width :param color: line colour :return: """ if orientation == 'v': lim = self._set_default(lim, self.ylim) self.vlines.append(Bunch({'pos': pos, 'lim': lim, 'style': style, 'width': width, 'color': color})) if orientation == 'h': lim = self._set_default(lim, self.xlim) self.hlines.append(Bunch({'pos': pos, 'lim': lim, 'style': style, 'width': width, 'color': color}))
[docs] def set_labels(self, title=None, xlabel=None, ylabel=None, zlabel=None, clabel=None): """ Set labels for plot :param title: title :param xlabel: x axis label :param ylabel: y axis label :param zlabel: z axis label :param clabel: cbar label :return: """ self.labels = Bunch({'title': title, 'xlabel': xlabel, 'ylabel': ylabel, 'zlabel': zlabel, 'clabel': clabel})
[docs] def set_xlim(self, xlim=None): """ Set xlim values :param xlim: xlim values (min, max) supports tuple, list or np.array of len(2). If not specified will compute as min, max of y data """ self.xlim = self._set_lim('x', lim=xlim)
[docs] def set_ylim(self, ylim=None): """ Set ylim values :param ylim: ylim values (min, max) supports tuple, list or np.array of len(2). If not specified will compute as min, max of y data """ self.ylim = self._set_lim('y', lim=ylim)
[docs] def set_zlim(self, zlim=None): """ Set zlim values :param zlim: zlim values (min, max) supports tuple, list or np.array of len(2). If not specified will compute as min, max of z data """ self.zlim = self._set_lim('z', lim=zlim)
[docs] def set_clim(self, clim=None): """ Set clim values :param clim: clim values (min, max) supports tuple, list or np.array of len(2). If not specified will compute as min, max of c data """ self.clim = self._set_lim('c', lim=clim)
def _set_lim(self, axis, lim=None): """ General function to set limits to either specified value if lim is not None or to nanmin, nanmin of data :param axis: x, y, z or c :param lim: lim values (min, max) supports tuple, list or np.array of len(2) :return: """ if lim is not None: assert(len(lim) == 2) else: lim = (np.nanmin(self.data[axis]), np.nanmax(self.data[axis])) return lim def _set_default(self, val, default): """ General function to set value of attribute. If val is not None, the value of val will be returned otherwise default value will be returned :param val: non-default value to set attribute to :param default: default value of attribute :return: """ if val is None: return default else: return val
[docs] def convert2dict(self): """ Convert class object to dictionary :return: dict with variables needed for plotting """ return vars(self)
[docs]class ImagePlot(DefaultPlot): def __init__(self, img, x=None, y=None, cmap=None): """ Class for organising data that will be used to create 2D image plots :param img: 2D image data :param x: x coordinate of each image voxel in x dimension :param y: y coordinate of each image voxel in y dimension :param cmap: name of colormap to use """ data = Bunch({'x': self._set_default(x, np.arange(img.shape[0])), 'y': self._set_default(y, np.arange(img.shape[1])), 'c': img}) # Make sure dimensions agree assert data['c'].shape[0] == data['x'].shape[0], 'dimensions must agree' assert data['c'].shape[1] == data['y'].shape[0], 'dimensions must agree' # Initialise default plot class with data super().__init__('image', data) self.scale = None self.offset = None self.cmap = self._set_default(cmap, 'viridis') self.set_xlim() self.set_ylim() self.set_clim()
[docs] def set_scale(self, scale=None): """ Set the scaling factor to apply to image (mainly for pyqtgraph implementation) :param scale: scale values (xscale, yscale), supports tuple, list or np.array of len(2). If not specified will automatically compute from xlims/ylims and shape of data :return: """ # For pyqtgraph implementation if scale is not None: assert(len(scale) == 2) self.scale = self._set_default(scale, (self._get_scale('x'), self._get_scale('y')))
def _get_scale(self, axis): """ Calculate scaling factor to apply along axis. Don't use directly, use set_scale() method :param axis: 'x' or 'y' :return: """ lim = self._set_lim(axis) scale = (lim[1] - lim[0]) / self.data['c'].shape[axis_dict[axis]] return scale
[docs] def set_offset(self, offset=None): """ Set the offset to apply to the image (mainly for pyqtgraph implementation) :param offset: offset values (xoffset, yoffset), supports tuple, list or np.array of len(2) If not specified will automatically compute from minimum of xlim and ylim :return: """ # For pyqtgraph implementation if offset is not None: assert(len(offset) == 2) self.offset = self._set_default(offset, (self._get_offset('x'), self._get_offset('y')))
def _get_offset(self, axis): """ Calculate offset to apply to axis. Don't use directly, use set_offset() method :param axis: 'x' or 'y' :return: """ offset = np.nanmin(self.data[axis]) return offset
[docs]class ProbePlot(DefaultPlot): def __init__(self, img, x, y, cmap=None): """ Class for organising data that will be used to create 2D probe plots. Use function plot_base.arrange_channels2bank to prepare data in correct format before using this class :param img: list of image data for each bank of probe :param x: list of x coordinate for each bank of probe :param y: list of y coordinate for each bank or probe :param cmap: name of cmap """ # Make sure we have inputs as lists, can get input from arrange_channels2banks assert(type(img) == list) assert(type(x) == list) assert(type(y) == list) data = Bunch({'x': x, 'y': y, 'c': img}) super().__init__('probe', data) self.cmap = self._set_default(cmap, 'viridis') self.set_xlim() self.set_ylim() self.set_clim() self.set_scale() self.set_offset()
[docs] def set_scale(self, idx=None, scale=None): if scale is not None: self.scale[idx] = scale else: self.scale = [(self._get_scale(i, 'x'), self._get_scale(i, 'y')) for i in range(len(self.data['x']))]
def _get_scale(self, idx, axis): lim = self._set_lim_list(axis, idx) scale = (lim[1] - lim[0]) / self.data['c'][idx].shape[axis_dict[axis]] return scale def _set_lim_list(self, axis, idx, lim=None): if lim is not None: assert(len(lim) == 2) else: lim = (np.nanmin(self.data[axis][idx]), np.nanmax(self.data[axis][idx])) return lim
[docs] def set_offset(self, idx=None, offset=None): if offset is not None: self.offset[idx] = offset else: self.offset = [(np.min(self.data['x'][i]), np.min(self.data['y'][i])) for i in range(len(self.data['x']))]
def _set_lim(self, axis, lim=None): if lim is not None: assert (len(lim) == 2) else: data = np.concatenate([np.squeeze(np.ravel(d)) for d in self.data[axis]]).ravel() lim = (np.nanmin(data), np.nanmax(data)) return lim
[docs]class ScatterPlot(DefaultPlot): def __init__(self, x, y, z=None, c=None, cmap=None, plot_type='scatter'): """ Class for organising data that will be used to create scatter plots. Can be 2D or 3D (if z given). Can also represent variable through color by specifying c :param x: x values for data :param y: y values for data :param z: z values for data :param c: values to use to represent color of scatter points :param cmap: name of colormap to use if c is given :param plot_type: """ data = Bunch({'x': x, 'y': y, 'z': z, 'c': c}) assert len(data['x']) == len(data['y']), 'dimensions must agree' if data['z'] is not None: assert len(data['z']) == len(data['x']), 'dimensions must agree' if data['c'] is not None: assert len(data['c']) == len(data['x']), 'dimensions must agree' super().__init__(plot_type, data) self._set_init_style() self.set_xlim() self.set_ylim() # If we have 3D data if data['z'] is not None: self.set_zlim() # If we want colorbar associated with scatter plot self.set_clim() self.cmap = self._set_default(cmap, 'viridis') def _set_init_style(self): """ Initialise defaults :return: """ self.set_color() self.set_marker_size() self.set_marker_type('o') self.set_opacity() self.set_line_color() self.set_line_width() self.set_line_style()
[docs] def set_color(self, color=None): """ Color of scatter points. :param color: string e.g 'k', single RGB e,g [0,0,0] or np.array of RGB. In the latter case must give same no. of colours as datapoints i.e. len(np.array(RGB)) == len(data['x']) :return: """ self.color = self._set_default(color, 'b')
[docs] def set_marker_size(self, marker_size=None): """ Size of each scatter point :param marker_size: int or np.array of int. In the latter case must give same no. of marker_size as datapoints i.e len(np.array(marker_size)) == len(data['x']) :return: """ self.marker_size = self._set_default(marker_size, None)
[docs] def set_marker_type(self, marker_type=None): """ Shape of each scatter point :param marker_type: :return: """ self.marker_type = self._set_default(marker_type, None)
[docs] def set_opacity(self, opacity=None): """ Opacity of each scatter point :param opacity: :return: """ self.opacity = self._set_default(opacity, 1)
[docs] def set_line_color(self, line_color=None): """ Colour of edge of scatter point :param line_color: string e.g 'k' or RGB e.g [0,0,0] :return: """ self.line_color = self._set_default(line_color, None)
[docs] def set_line_width(self, line_width=None): """ Width of line on edge of scatter point :param line_width: int :return: """ self.line_width = self._set_default(line_width, None)
[docs] def set_line_style(self, line_style=None): """ Style of line on edge of scatter point :param line_style: :return: """ self.line_style = self._set_default(line_style, '-')
[docs]class LinePlot(ScatterPlot): def __init__(self, x, y): """ Class for organising data that will be used to create line plots. :param x: x values for data :param y: y values for data """ super().__init__(x, y, plot_type='line') self._set_init_style() self.set_xlim() self.set_ylim() def _set_init_style(self): self.set_line_color('k') self.set_line_width(2) self.set_line_style() self.set_marker_size() self.set_marker_type()
[docs]def add_lines(ax, data, **kwargs): """ Function to add vertical and horizontal reference lines to matplotlib axis :param ax: matplotlib axis :param data: dict of plot data :param kwargs: matplotlib keywords arguments associated with vlines/hlines :return: """ for vline in data['vlines']: ax.vlines(vline['pos'], ymin=vline['lim'][0], ymax=vline['lim'][1], linestyles=vline['style'], linewidth=vline['width'], colors=vline['color'], **kwargs) for hline in data['hlines']: ax.hlines(hline['pos'], xmin=hline['lim'][0], xmax=hline['lim'][1], linestyles=hline['style'], linewidth=hline['width'], colors=hline['color'], **kwargs) return ax
[docs]def plot_image(data, ax=None, show_cbar=True, fig_kwargs=dict(), line_kwargs=dict(), img_kwargs=dict()): """ Function to create matplotlib plot from ImagePlot object :param data: ImagePlot object, either class or dict :param ax: matplotlib axis to plot on, if None, will create figure :param show_cbar: whether or not to display colour bar :param fig_kwargs: dict of matplotlib keywords associcated with plt.subplots e.g can be fig size, tight layout etc. :param line_kwargs: dict of matplotlib keywords associated with ax.hlines/ax.vlines :param img_kwargs: dict of matplotlib keywords associated with matplotlib.imshow :return: matplotlib axis and figure handles """ if not isinstance(data, dict): data = data.convert2dict() if not ax: fig, ax = plt.subplots(**fig_kwargs) else: fig = plt.gcf() img = ax.imshow(data['data']['c'].T, extent=np.r_[data['xlim'], data['ylim']], cmap=data['cmap'], vmin=data['clim'][0], vmax=data['clim'][1], origin='lower', aspect='auto', **img_kwargs) ax.set_xlim(data['xlim'][0], data['xlim'][1]) ax.set_ylim(data['ylim'][0], data['ylim'][1]) ax.set_xlabel(data['labels']['xlabel']) ax.set_ylabel(data['labels']['ylabel']) ax.set_title(data['labels']['title']) if show_cbar: cbar = fig.colorbar(img, ax=ax) cbar.set_label(data['labels']['clabel']) ax = add_lines(ax, data, **line_kwargs) plt.show() return ax, fig
[docs]def plot_scatter(data, ax=None, show_cbar=True, fig_kwargs=dict(), line_kwargs=dict(), scat_kwargs=dict()): """ Function to create matplotlib plot from ScatterPlot object. If data['colors'] is given for each data point it will override automatic colours that would be generated from data['data']['c'] :param data: ScatterPlot object, either class or dict :param ax: matplotlib axis to plot on, if None, will create figure :param show_cbar: whether or not to display colour bar :param fig_kwargs: dict of matplotlib keywords associcated with plt.subplots e.g can be fig size, tight layout etc. :param line_kwargs: dict of matplotlib keywords associated with ax.hlines/ax.vlines :param scat_kwargs: dict of matplotlib keywords associated with matplotlib.scatter :return: matplotlib axis and figure handles """ if not isinstance(data, dict): data = data.convert2dict() if not ax: fig, ax = plt.subplots(**fig_kwargs) else: fig = plt.gcf() # Single color for all points if data['data']['c'] is None: scat = ax.scatter(x=data['data']['x'], y=data['data']['y'], c=data['color'], s=data['marker_size'], marker=data['marker_type'], edgecolors=data['line_color'], linewidths=data['line_width'], **scat_kwargs) else: # Colour for each point specified if len(data['color']) == len(data['data']['x']): if np.max(data['color']) > 1: data['color'] = data['color'] / 255 scat = ax.scatter(x=data['data']['x'], y=data['data']['y'], c=data['color'], s=data['marker_size'], marker=data['marker_type'], edgecolors=data['line_color'], linewidths=data['line_width'], **scat_kwargs) if show_cbar: norm = matplotlib.colors.Normalize(vmin=data['clim'][0], vmax=data['clim'][1], clip=True) cbar = fig.colorbar(cm.ScalarMappable(norm=norm, cmap=data['cmap']), ax=ax) cbar.set_label(data['labels']['clabel']) # Automatically generate from c data else: scat = ax.scatter(x=data['data']['x'], y=data['data']['y'], c=data['data']['c'], s=data['marker_size'], marker=data['marker_type'], cmap=data['cmap'], vmin=data['clim'][0], vmax=data['clim'][1], edgecolors=data['line_color'], linewidths=data['line_width'], **scat_kwargs) if show_cbar: cbar = fig.colorbar(scat, ax=ax) cbar.set_label(data['labels']['clabel']) ax = add_lines(ax, data, **line_kwargs) ax.set_xlim(data['xlim'][0], data['xlim'][1]) ax.set_ylim(data['ylim'][0], data['ylim'][1]) ax.set_xlabel(data['labels']['xlabel']) ax.set_ylabel(data['labels']['ylabel']) ax.set_title(data['labels']['title']) plt.show() return ax, fig
[docs]def plot_probe(data, ax=None, show_cbar=True, make_pretty=True, fig_kwargs=dict(), line_kwargs=dict()): """ Function to create matplotlib plot from ProbePlot object :param data: ProbePlot object, either class or dict :param ax: matplotlib axis to plot on, if None, will create figure :param show_cbar: whether or not to display colour bar :param make_pretty: get rid of spines on axis :param fig_kwargs: dict of matplotlib keywords associcated with plt.subplots e.g can be fig size, tight layout etc. :param line_kwargs: dict of matplotlib keywords associated with ax.hlines/ax.vlines :return: matplotlib axis and figure handles """ if not isinstance(data, dict): data = data.convert2dict() if not ax: fig, ax = plt.subplots(figsize=(2, 8), **fig_kwargs) else: fig = plt.gcf() for (x, y, dat) in zip(data['data']['x'], data['data']['y'], data['data']['c']): im = NonUniformImage(ax, interpolation='nearest', cmap=data['cmap']) im.set_clim(data['clim'][0], data['clim'][1]) im.set_data(x, y, dat.T) ax.images.append(im) ax.set_xlim(data['xlim'][0], data['xlim'][1]) ax.set_ylim(data['ylim'][0], data['ylim'][1]) ax.set_xlabel(data['labels']['xlabel']) ax.set_ylabel(data['labels']['ylabel']) ax.set_title(data['labels']['title']) if make_pretty: ax.get_xaxis().set_visible(False) ax.spines['right'].set_visible(False) ax.spines['top'].set_visible(False) ax.spines['bottom'].set_visible(False) if show_cbar: cbar = fig.colorbar(im, orientation="horizontal", pad=0.02, ax=ax) cbar.set_label(data['labels']['clabel']) ax = add_lines(ax, data, **line_kwargs) plt.show() return ax, fig
[docs]def plot_line(data, ax=None, fig_kwargs=dict(), line_kwargs=dict()): """ Function to create matplotlib plot from LinePlot object :param data: LinePlot object either class or dict :param ax: matplotlib axis to plot on :param fig_kwargs: dict of matplotlib keywords associcated with plt.subplots e.g can be fig size, tight layout etc. :param line_kwargs: dict of matplotlib keywords associated with ax.hlines/ax.vlines :return: matplotlib axis and figure handles """ if not isinstance(data, dict): data = data.convert2dict() if not ax: fig, ax = plt.subplots(**fig_kwargs) else: fig = plt.gcf() ax.plot(data['data']['x'], data['data']['y'], color=data['line_color'], linestyle=data['line_style'], linewidth=data['line_width'], marker=data['marker_type'], markersize=data['marker_size']) ax = add_lines(ax, data, **line_kwargs) ax.set_xlim(data['xlim'][0], data['xlim'][1]) ax.set_ylim(data['ylim'][0], data['ylim'][1]) ax.set_xlabel(data['labels']['xlabel']) ax.set_ylabel(data['labels']['ylabel']) ax.set_title(data['labels']['title']) plt.show() return ax, fig
[docs]def scatter_xyc_plot(x, y, c, cmap=None, clim=None, rgb=False): """ General function for preparing x y scatter plot with third variable encoded by colour of points :param x: :param y: :param c: :param cmap: :param clim: :param rgb: Whether to compute rgb (set True when preparing pyqtgraph data) :return: """ data = ScatterPlot(x=x, y=y, c=c, cmap=cmap) data.set_clim(clim=clim) if rgb: norm = matplotlib.colors.Normalize(vmin=data.clim[0], vmax=data.clim[1], clip=True) mapper = cm.ScalarMappable(norm=norm, cmap=cm.get_cmap(cmap)) cluster_color = np.array([mapper.to_rgba(col) for col in c]) data.set_color(color=cluster_color) return data
[docs]def arrange_channels2banks(data, chn_coords, depth=None, pad=True, x_offset=1): """ Rearranges data on channels so it matches geometry of probe. e.g For Neuropixel 2.0 rearranges channels into 4 banks with checkerboard pattern :param data: data on channels :param chn_coords: local coordinates of channels on probe :param depth: depth location of electrode (for example could be relative to bregma). If none given will stay in probe local coordinates :param pad: for matplotlib implementation with NonUniformImage we need to surround our data with nans so that it shows as finite display :param x_offset: spacing between banks in x direction :return: list, data, x position and y position for each bank """ data_bank = [] x_bank = [] y_bank = [] if depth is None: depth = chn_coords[:, 1] for iX, x in enumerate(np.unique(chn_coords[:, 0])): bnk_idx = np.where(chn_coords[:, 0] == x)[0] bnk_data = data[bnk_idx, np.newaxis].T # This is a hack! Although data is 1D we give it two x coords so we can correctly set # scale and extent (compatible with pyqtgraph and matplotlib.imshow) # For matplotlib.image.Nonuniformimage must use pad=True option bnk_x = np.array((iX * x_offset, (iX + 1) * x_offset)) bnk_y = depth[bnk_idx] if pad: # pad data in y direction bnk_data = np.insert(bnk_data, 0, np.nan) bnk_data = np.append(bnk_data, np.nan) # pad data in x direction bnk_data = bnk_data[:, np.newaxis].T bnk_data = np.insert(bnk_data, 0, np.full(bnk_data.shape[1], np.nan), axis=0) bnk_data = np.append(bnk_data, np.full((1, bnk_data.shape[1]), np.nan), axis=0) # pad the x values bnk_x = np.arange(iX * x_offset, (iX + 3) * x_offset, x_offset) # pad the y values diff = np.diff(bnk_y) diff = diff[np.nonzero(diff)] bnk_y = np.insert(bnk_y, 0, bnk_y[0] - np.abs(diff[0])) bnk_y = np.append(bnk_y, bnk_y[-1] + np.abs(diff[-1])) data_bank.append(bnk_data) x_bank.append(bnk_x) y_bank.append(bnk_y) return data_bank, x_bank, y_bank