520 lines
No EOL
20 KiB
Python
520 lines
No EOL
20 KiB
Python
import nafuma.auxillary as aux
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import matplotlib.pyplot as plt
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from matplotlib.ticker import (MultipleLocator)
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from mpl_toolkits.axes_grid.inset_locator import (inset_axes, InsetPosition, BboxPatch, BboxConnector)
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from matplotlib.transforms import TransformedBbox
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from matplotlib.patches import Rectangle
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import importlib
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import matplotlib.patches as mpatches
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from matplotlib.lines import Line2D
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import matplotlib.lines as mlines
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import matplotlib.markers as mmarkers
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import itertools
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from PIL import Image
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import os
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import numpy as np
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def prepare_plot(options={}):
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''' A general function to prepare a plot based on contents of options['rc_params'] and options['format_params'].
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rc_params is a dictionary with keyval-pairs corresponding to rcParams in matplotlib, to give the user full control over this. Please consult the matplotlib-documentation
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format_params will determine the size, aspect ratio, resolution etc. of the figure. Should be modified to conform with any requirements from a journal.'''
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if 'rc_params' in options.keys():
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rc_params = options['rc_params']
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else:
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rc_params = {}
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if 'format_params' in options.keys():
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format_params = options['format_params']
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else:
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format_params = {}
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default_format_params = {
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'single_column_width': 8.3,
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'double_column_width': 17.1,
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'column_type': 'single',
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'width_ratio': '1:1',
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'aspect_ratio': '1:1',
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'width': None,
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'height': None,
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'compress_width': 1,
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'compress_height': 1,
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'upscaling_factor': 1.0,
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'dpi': 600,
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'nrows': 1,
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'ncols': 1,
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'grid_ratio_height': None,
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'grid_ratio_width': None
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}
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format_params = aux.update_options(options=format_params, default_options=default_format_params)
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# Reset run commands
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plt.rcdefaults()
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# Update run commands if any is passed (will pass an empty dictionary if not passed)
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update_rc_params(rc_params)
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if not format_params['width']:
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format_params['width'] = determine_width(format_params=format_params)
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if not format_params['height']:
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format_params['height'] = determine_height(format_params=format_params, width=format_params['width'])
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format_params['width'], format_params['height'] = scale_figure(format_params=format_params, width=format_params['width'], height=format_params['height'])
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if format_params['nrows'] == 1 and format_params['ncols'] == 1:
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fig, ax = plt.subplots(figsize=(format_params['width'], format_params['height']), dpi=format_params['dpi'])
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return fig, ax
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else:
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if not format_params['grid_ratio_height']:
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format_params['grid_ratio_height'] = [1 for i in range(format_params['nrows'])]
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if not format_params['grid_ratio_width']:
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format_params['grid-ratio_width'] = [1 for i in range(format_params['ncols'])]
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fig, axes = plt.subplots(nrows=format_params['nrows'], ncols=format_params['ncols'], figsize=(format_params['width'],format_params['height']),
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gridspec_kw={'height_ratios': format_params['grid_ratio_height'], 'width_ratios': format_params['grid_ratio_width']},
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facecolor='w', dpi=format_params['dpi'])
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return fig, axes
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def adjust_plot(fig, ax, options):
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''' A general function to adjust plot according to contents of the options-dictionary '''
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default_options = {
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'plot_kind': None, # defaults to None, but should be utilised when requiring special formatting for a particular plot
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'xlabel': None, 'ylabel': None,
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'xunit': None, 'yunit': None,
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'xlabel_pad': 4.0, 'ylabel_pad': 4.0,
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'hide_x_labels': False, 'hide_y_labels': False, # Whether the main labels on the x- and/or y-axes should be hidden
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'hide_x_ticklabels': False, 'hide_y_ticklabels': False, # Whether ticklabels on the x- and/or y-axes should be hidden
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'hide_x_ticks': False, 'hide_y_ticks': False, # Whether the ticks on the x- and/or y-axes should be hidden
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'x_tick_locators': None, 'y_tick_locators': None, # The major and minor tick locators for the x- and y-axes
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'rotation_x_ticks': 0, 'rotation_y_ticks': 0, # Degrees the x- and/or y-ticklabels should be rotated
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'xticks': None, 'yticks': None, # Custom definition of the xticks and yticks. This is not properly implemented now.
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'xlim': None, 'ylim': None, # Limits to the x- and y-axes
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'xlim_reset': False, 'ylim_reset': False, # For use in setting limits of backgrounds - forcing reset of xlim and ylim, useful when more axes
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'title': None, # Title of the plot
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'backgrounds': [],
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'legend': False, 'legend_position': ['lower center', (0.5, -0.1)], 'legend_ncol': 1, # Toggles on/off legend. Specifices legend position and the number of columns the legend should appear as.
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'subplots_adjust': {'left': None, 'right': None, 'top': None, 'bottom': None, 'wspace': None, 'hspace': None}, # Adjustment of the Axes-object within the Figure-object. Fraction of the Figure-object the left, bottom, right and top edges of the Axes-object will start.
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'marker_edges': None,
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'text': None # Text to show in the plot. Should be a list where the first element is the string, and the second is a tuple with x- and y-coordinates. Could also be a list of lists to show more strings of text.
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}
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options = aux.update_options(options=options, default_options=default_options)
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# Set labels on x- and y-axes
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if not options['hide_y_labels']:
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if not options['yunit']:
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ax.set_ylabel(f'{options["ylabel"]}', labelpad=options['ylabel_pad'])
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else:
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ax.set_ylabel(f'{options["ylabel"]} [{options["yunit"]}]', labelpad=options['ylabel_pad'])
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else:
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ax.set_ylabel('')
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if not options['hide_x_labels']:
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if not options['xunit']:
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ax.set_xlabel(f'{options["xlabel"]}', labelpad=options['xlabel_pad'])
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else:
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ax.set_xlabel(f'{options["xlabel"]} [{options["xunit"]}]', labelpad=options['xlabel_pad'])
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else:
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ax.set_xlabel('')
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# Set multiple locators
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if options['y_tick_locators']:
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ax.yaxis.set_major_locator(MultipleLocator(options['y_tick_locators'][0]))
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ax.yaxis.set_minor_locator(MultipleLocator(options['y_tick_locators'][1]))
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if options['x_tick_locators']:
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ax.xaxis.set_major_locator(MultipleLocator(options['x_tick_locators'][0]))
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ax.xaxis.set_minor_locator(MultipleLocator(options['x_tick_locators'][1]))
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# FIXME THIS NEEDS REWORK FOR IT TO FUNCTION PROPERLY!
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#if options['xticks']:
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# ax.set_xticks(np.arange(plot_data['start'], plot_data['end']+1))
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# ax.set_xticklabels(options['xticks'])
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# else:
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# ax.set_xticks(np.arange(plot_data['start'], plot_data['end']+1))
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# ax.set_xticklabels([x/2 for x in np.arange(plot_data['start'], plot_data['end']+1)])
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# Hide x- and y- ticklabels
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if options['hide_y_ticklabels']:
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ax.tick_params(axis='y', direction='in', which='both', labelleft=False, labelright=False)
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else:
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plt.xticks(rotation=options['rotation_x_ticks'])
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#ax.set_xticklabels(ax.get_xticks(), rotation = options['rotation_x_ticks'])
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if options['hide_x_ticklabels']:
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ax.tick_params(axis='x', direction='in', which='both', labelbottom=False, labeltop=False)
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else:
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pass
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#ax.set_yticklabels(ax.get_yticks(), rotation = options['rotation_y_ticks'])
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# Hide x- and y-ticks:
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if options['hide_y_ticks']:
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ax.tick_params(axis='y', direction='in', which='both', left=False, right=False)
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else:
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ax.tick_params(axis='y', direction='in', which='both', left=True, right=True)
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if options['hide_x_ticks']:
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ax.tick_params(axis='x', direction='in', which='both', bottom=False, top=False)
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else:
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ax.tick_params(axis='x', direction='in', which='both', bottom=True, top=True)
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# Set title
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if options['title']:
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ax.set_title(options['title'], fontsize=plt.rcParams['font.size'])
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#### DRAW/REMOVE LEGEND ####
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# Options:
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# 'legend_position': (default ['lower center', (0.5, -0.1)]) - Follows matplotlib's way of specifying legend position
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# 'legend_ncol': (default 1) # Number of columns to write the legend in
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# Also requires options to contain values in colours, markers and labels. (No defaults)
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if ax.get_legend():
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ax.get_legend().remove()
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if options['legend']:
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# Make palette and linestyles from original parameters
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if not options['colours']:
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colours = generate_colours(palettes=options['palettes'])
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else:
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colours = itertools.cycle(options['colours'])
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markers = itertools.cycle(options['markers'])
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# Create legend
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active_markers = []
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active_labels = []
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for label in options['labels']:
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# Discard next linestyle and colour if label is _
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if label == '_':
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_ = next(colours)
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_ = next(markers)
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else:
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marker = next(markers)
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if not marker:
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active_markers.append(mlines.Line2D([], [], color=next(colours)))
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else:
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active_markers.append(mlines.Line2D([], [], markerfacecolor=next(colours), markeredgecolor=options['marker_edges'], markersize=10, color=(1,1,1,0), marker=marker))
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active_labels.append(label)
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ax.legend(active_markers, active_labels, frameon=False, loc=options['legend_position'][0], bbox_to_anchor=options['legend_position'][1], ncol=options['legend_ncol'])
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#fig.legend(handles=patches, loc=options['legend_position'][0], bbox_to_anchor=options['legend_position'][1], frameon=False)
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# Adjust where the axes start within the figure. Default value is 10% in from the left and bottom edges. Used to make room for the plot within the figure size (to avoid using bbox_inches='tight' in the savefig-command, as this screws with plot dimensions)
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plt.subplots_adjust(**options['subplots_adjust'])
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# If limits for x- and y-axes is passed, sets these.
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if options['xlim'] is not None:
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ax.set_xlim(options['xlim'])
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if options['ylim'] is not None:
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ax.set_ylim(options['ylim'])
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#### DRAW BACKGROUNDS ####
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# options['backgrounds'] should contain a dictionary or a list of dictionaries. Options to be specified are listed below.
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if options['backgrounds']:
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if not isinstance(options['backgrounds'], list):
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options['backgrounds'] = [options['backgrounds']]
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for background in options['backgrounds']:
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default_background_options = {
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'colour': (0,0,0),
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'alpha': 0.2,
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'xlim': list(ax.get_xlim()),
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'ylim': list(ax.get_ylim()),
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'zorder': 0,
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'edgecolour': None,
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'linewidth': None
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}
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background = aux.update_options(options=background, default_options=default_background_options)
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if options['xlim_reset']:
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background['xlim'] = list(ax.get_xlim())
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if options['ylim_reset']:
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background['ylim'] = list(ax.get_ylim())
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if not background['xlim'][0]:
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background['xlim'][0] = ax.get_xlim()[0]
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if not background['xlim'][1]:
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background['xlim'][1] = ax.get_xlim()[1]
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if not background['ylim'][0]:
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background['ylim'][0] = ax.get_ylim()[0]
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if not background['ylim'][1]:
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background['ylim'][1] = ax.get_ylim()[1]
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ax.add_patch(Rectangle(
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xy=(background['xlim'][0], background['ylim'][0]), # Anchor point
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width=background['xlim'][1]-background['xlim'][0], # Width of background
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height=background['ylim'][1]-background['ylim'][0], # Height of background
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zorder=background['zorder'], # Placement in stack
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facecolor=(background['colour'][0], background['colour'][1], background['colour'][2], background['alpha']), # Colour
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edgecolor=background['edgecolour'], # Edgecolour
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linewidth=background['linewidth']) # Linewidth
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)
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# Add custom text
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if options['text']:
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# If only a single element, put it into a list so the below for-loop works.
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if isinstance(options['text'][0], str):
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options['text'] = [options['text']]
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# Plot all passed texts
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for text in options['text']:
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ax.text(x=text[1][0], y=text[1][1], s=text[0])
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return fig, ax
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def ipywidgets_update(func, data, options={}, **kwargs):
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''' A general ipywidgets update function that can be passed to ipywidgets.interactive. To use this, you can run:
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import ipywidgets as widgets
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import beamtime.plotting as btp
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w = widgets.interactive(btp.ipywidgets_update, func=widgets.fixed(my_func), plot_data=widgets.fixed(plot_data), options=widgets.fixed(options), key1=widget1, key2=widget2, key3=widget3)
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where key1, key2, key3 etc. are the values in the options-dictionary you want widget control of, and widget1, widget2, widget3 etc. are widgets to control these values, e.g. widgets.IntSlider(value=1, min=0, max=10)
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'''
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# Update the options-dictionary with the values from the widgets
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for key in kwargs:
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options[key] = kwargs[key]
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# Call the function with the plot_data and options-dictionaries
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func(data=data, options=options)
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def determine_width(format_params):
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''' '''
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conversion_cm_inch = 0.3937008 # cm to inch
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if format_params['column_type'] == 'single':
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column_width = format_params['single_column_width']
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elif format_params['column_type'] == 'double':
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column_width = format_params['double_column_width']
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column_width *= conversion_cm_inch
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width_ratio = [float(num) for num in format_params['width_ratio'].split(':')]
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width = column_width * width_ratio[0]/width_ratio[1]
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return width
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def determine_height(format_params, width):
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aspect_ratio = [float(num) for num in format_params['aspect_ratio'].split(':')]
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height = width/(aspect_ratio[0] / aspect_ratio[1])
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return height
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def scale_figure(format_params, width, height):
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width = width * format_params['upscaling_factor'] * format_params['compress_width']
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height = height * format_params['upscaling_factor'] * format_params['compress_height']
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return width, height
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def update_rc_params(rc_params):
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''' Update all passed run commands in matplotlib'''
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if rc_params:
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for key in rc_params.keys():
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plt.rcParams.update({key: rc_params[key]})
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def generate_colours(palettes, kind=None):
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if kind == 'single':
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colour_cycle = itertools.cycle(palettes)
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else:
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# Creates a list of all the colours that is passed in the colour_cycles argument. Then makes cyclic iterables of these.
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colour_collection = []
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for palette in palettes:
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mod = importlib.import_module("palettable.colorbrewer.%s" % palette[0])
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colour = getattr(mod, palette[1]).mpl_colors
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colour_collection = colour_collection + colour
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colour_cycle = itertools.cycle(colour_collection)
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return colour_cycle
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def prepare_inset_axes(parent_ax, options):
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default_options = {
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'hide_inset_x_labels': False, # Whether x labels should be hidden
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'hide_inset_x_ticklabels': False,
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'hide_inset_x_ticks': False,
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'rotation_inset_x_ticks': 0,
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'hide_inset_y_labels': False, # whether y labels should be hidden
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'hide_inset_y_ticklabels': False,
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'hide_inset_y_ticks': False,
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'rotation_inset_y_ticks': 0,
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'inset_x_tick_locators': [100, 50], # Major and minor tick locators
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'inset_y_tick_locators': [10, 5],
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'inset_position': [0.1,0.1,0.3,0.3],
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'inset_bounding_box': [0,0,0.1, 0.1],
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'inset_marks': [None, None],
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'legend_position': ['upper center', (0.20, 0.90)], # the position of the legend passed as arguments to loc and bbox_to_anchor respectively,
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'connecting_corners': [1,2]
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}
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options = aux.update_options(options=options, required_options=default_options.keys(), default_options=default_options)
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# Create a set of inset Axes: these should fill the bounding box allocated to
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# them.
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inset_ax = plt.axes(options["inset_bounding_box"])
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# Manually set the position and relative size of the inset axes within ax1
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ip = InsetPosition(parent_ax, options['inset_position'])
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inset_ax.set_axes_locator(ip)
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if options['connecting_corners'] and len(options["connecting_corners"]) == 2:
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connect_inset(parent_ax, inset_ax, loc1a=options['connecting_corners'][0], loc2a=options['connecting_corners'][1], loc1b=options['connecting_corners'][0], loc2b=options['connecting_corners'][1], fc='none', ec='black')
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elif options['connecting_corners'] and len(options['connecting_corners']) == 4:
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connect_inset(parent_ax, inset_ax, loc1a=options['connecting_corners'][0], loc2a=options['connecting_corners'][1], loc1b=options['connecting_corners'][2], loc2b=options['connecting_corners'][3], fc='none', ec='black', ls='--')
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inset_ax.xaxis.set_major_locator(MultipleLocator(options['inset_x_tick_locators'][0]))
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inset_ax.xaxis.set_minor_locator(MultipleLocator(options['inset_x_tick_locators'][1]))
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inset_ax.yaxis.set_major_locator(MultipleLocator(options['inset_y_tick_locators'][0]))
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inset_ax.yaxis.set_minor_locator(MultipleLocator(options['inset_y_tick_locators'][1]))
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return inset_ax
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def connect_inset(parent_axes, inset_axes, loc1a=1, loc1b=1, loc2a=2, loc2b=2, **kwargs):
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rect = TransformedBbox(inset_axes.viewLim, parent_axes.transData)
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pp = BboxPatch(rect, fill=False, **kwargs)
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parent_axes.add_patch(pp)
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|
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p1 = BboxConnector(inset_axes.bbox, rect, loc1=loc1a, loc2=loc1b, **kwargs)
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inset_axes.add_patch(p1)
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p1.set_clip_on(False)
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p2 = BboxConnector(inset_axes.bbox, rect, loc1=loc2a, loc2=loc2b, **kwargs)
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inset_axes.add_patch(p2)
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p2.set_clip_on(False)
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|
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return pp, p1, p2
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|
|
|
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|
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def make_animation(paths, options={}):
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|
|
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default_options = {
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'save_folder': '.',
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'save_filename': 'animation.gif',
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'fps': 5
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}
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|
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options = aux.update_options(options=options, default_options=default_options)
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|
|
|
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frames = []
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for path in paths:
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frame = Image.open(path)
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frames.append(frame)
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|
|
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frames[0].save(os.path.join(options['save_folder'], options['save_filename']), format='GIF', append_images=frames[1:], save_all=True, duration=(1/options['fps'])*1000, loop=0)
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|
|
|
|
|
|
|
|
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def mix_colours(colour1, colour2, options):
|
|
|
|
default_options = {
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'number_of_colours': 10,
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|
'weights': None
|
|
}
|
|
|
|
options = aux.update_options(options=options, default_options=default_options)
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|
|
|
if not options['weights']:
|
|
options['weights'] = [x/options['number_of_colours'] for x in range(options['number_of_colours'])]
|
|
|
|
colours = []
|
|
for weight in options['weights']:
|
|
colour = []
|
|
|
|
for c1, c2 in zip(colour1, colour2):
|
|
colour.append(np.round(((1-weight)*c1 + weight*c2), 5))
|
|
|
|
colours.append(colour)
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|
|
|
|
|
return colours
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|
|