Source code for glue.core.util

import logging
from itertools import count
from functools import partial
from fractions import Fraction

import numpy as np

from matplotlib.ticker import AutoLocator, MaxNLocator, LogLocator
from matplotlib.ticker import LogFormatterMathtext, ScalarFormatter, FuncFormatter
from matplotlib.dates import AutoDateLocator, AutoDateFormatter
from matplotlib.projections.polar import ThetaFormatter, ThetaLocator
import matplotlib.ticker as mticker

from glue.utils import nanmin, nanmax

__all__ = ["ThetaRadianFormatter", "relim", "split_component_view", "join_component_view",
           "facet_subsets", "colorize_subsets", "disambiguate",
           'small_view', 'small_view_array', 'visible_limits',
           'tick_linker', 'update_ticks']

[docs]class ThetaRadianFormatter(mticker.Formatter): """ Used to format the *theta* tick labels in radians """ max_num = 20 max_den = 20 limit_den = 10000 @classmethod def _check_valid(cls, num, den): return den != 0 and abs(num) < cls.max_num and den < cls.max_den @classmethod def _numerator_denominator(cls, x): f = Fraction(x / np.pi).limit_denominator(cls.limit_den) n, d = f.numerator, f.denominator if cls._check_valid(n, d): return n, d f = Fraction(np.pi / x).limit_denominator(cls.limit_den) d, n = f.numerator, f.denominator d = d if n >= 0 else -d n = abs(n) if cls._check_valid(n, d): return n, d return None, None
[docs] @classmethod def rad_fn(cls, x, digits=2): n, d = cls._numerator_denominator(x) if n is None or d is None: return "{value:0.{digits}f}".format(value=x, digits=digits) ns = "" if n == 1 else str(n) if n == 0: return "0" elif d == 1: return r'${0}\pi$'.format(ns) elif abs(n) < cls.max_num and d < cls.max_den: sgn = "-" if n < 0 else "" return r"${0}{1}\pi/{2}$".format(sgn, ns, d)
[docs] def __call__(self, x, pos=None): vmin, vmax = self.axis.get_view_interval() d = abs(vmax - vmin) digits = max(-int(np.log10(d) - 1.5), 0) return ThetaRadianFormatter.rad_fn(x, digits=digits)
[docs]def relim(lo, hi, log=False): logging.getLogger(__name__).debug("Inputs to relim: %r %r", lo, hi) x, y = lo, hi if log: if lo < 0: x = 1e-5 if hi < 0: y = 1e5 return x * .95, y * 1.05 delta = y - x return (x - .02 * delta, y + .02 * delta)
[docs]def split_component_view(arg): """ Split the input to data or subset.__getitem__ into its pieces. Parameters ---------- arg The input passed to ``data`` or ``subset.__getitem__``. Assumed to be either a scalar or tuple Returns ------- selection The Component selection (a ComponentID or string) view Tuple of slices, slice scalar, or view """ if isinstance(arg, tuple): if len(arg) == 1: raise TypeError("Expected a scalar or >length-1 tuple, " "got length-1 tuple") if len(arg) == 2: return arg[0], arg[1] return arg[0], arg[1:] else: return arg, None
[docs]def join_component_view(component, view): """ Pack a ComponentID and optional view into single tuple. Returns an object compatible with ``data.__getitem__`` and related methods. Handles edge cases of when view is None, a scalar, a tuple, etc. Parameters ---------- component : `~glue.core.component_id.ComponentID` The ComponentID to pack view The view into the data, or `None` """ if view is None: return component result = [component] try: result.extend(view) except TypeError: # view is a scalar result = [component, view] return tuple(result)
[docs]def facet_subsets(data_collection, cid, lo=None, hi=None, steps=5, prefix='', log=False): """ Create a series of subsets that partition the values of a particular attribute into several bins This creates `steps` new subset groups, adds them to the data collection, and returns the list of newly created subset groups. Parameters ---------- data : :class:`~glue.core.data_collection.DataCollection` The DataCollection object to use cid : :class:`~glue.core.component_id.ComponentID` The ComponentID to facet on lo : float, optional The lower bound for the faceting. Defaults to minimum value in data hi : float, optional The upper bound for the faceting. Defaults to maximum value in data steps : int, optional The number of subsets to create. Defaults to 5 prefix : str, optional If present, the new subset labels will begin with `prefix` log : bool, optional If `True`, space divisions logarithmically. Default is `False` Returns ------- subset_groups : iterable List of :class:`~glue.core.subset_group.SubsetGroup` instances added to `data` Examples -------- :: facet_subset(data,['mass'], lo=0, hi=10, steps=2) creates 2 new subsets. The first represents the constraint 0 <= mass < 5. The second represents 5 <= mass <= 10:: facet_subset(data,['mass'], lo=10, hi=0, steps=2) Creates 2 new subsets. The first represents the constraint 10 >= x > 5 The second represents 5 >= mass >= 0:: facet_subset(data,['mass'], lo=0, hi=10, steps=2, prefix='m') Labels the subsets ``m_1`` and ``m_2``. Note that the last range is inclusive on both sides. For example, if ``lo`` is 0 and ``hi`` is 5, and ``steps`` is 5, then the intervals for the subsets are [0,1), [1,2), [2,3), [3,4), and [4,5]. """ from glue.core.exceptions import IncompatibleAttribute if lo is None or hi is None: for data in data_collection: try: vals = data[cid] break except IncompatibleAttribute: continue else: raise ValueError("Cannot infer data limits for ComponentID %s" % cid) if lo is None: lo = nanmin(vals) if hi is None: hi = nanmax(vals) reverse = lo > hi if log: rng = np.logspace(np.log10(lo), np.log10(hi), steps + 1) else: rng = np.linspace(lo, hi, steps + 1) states = [] labels = [] for i in range(steps): # The if i < steps - 1 clauses are needed because the last interval # has to be inclusive on both sides. if reverse: if i < steps - 1: states.append((cid <= rng[i]) & (cid > rng[i + 1])) labels.append(prefix + '{0}<{1}<={2}'.format(rng[i + 1], cid, rng[i])) else: states.append((cid <= rng[i]) & (cid >= rng[i + 1])) labels.append(prefix + '{0}<={1}<={2}'.format(rng[i + 1], cid, rng[i])) else: if i < steps - 1: states.append((cid >= rng[i]) & (cid < rng[i + 1])) labels.append(prefix + '{0}<={1}<{2}'.format(rng[i], cid, rng[i + 1])) else: states.append((cid >= rng[i]) & (cid <= rng[i + 1])) labels.append(prefix + '{0}<={1}<={2}'.format(rng[i], cid, rng[i + 1])) result = [] for lbl, s in zip(labels, states): sg = data_collection.new_subset_group(label=lbl, subset_state=s) result.append(sg) return result
[docs]def colorize_subsets(subsets, cmap, lo=0, hi=1): """ Re-color a list of subsets according to a colormap. The colormap will be sampled at `len(subsets)` even intervals between `lo` and `hi`. The color at the `ith` interval will be applied to `subsets[i]` Parameters ---------- subsets : list List of subsets cmap : `~matplotlib.colors.Colormap` Matplotlib colormap instance lo : float, optional Start location in colormap. 0-1. Defaults to 0 hi : float, optional End location in colormap. 0-1. Defaults to 1 """ from matplotlib import cm sm = cm.ScalarMappable(cmap=cmap) sm.norm.vmin = 0 sm.norm.vmax = 1 vals = np.linspace(lo, hi, len(subsets)) rgbas = sm.to_rgba(vals) for color, subset in zip(rgbas, subsets): r, g, b, a = color r = int(255 * r) g = int(255 * g) b = int(255 * b) = '#%2.2x%2.2x%2.2x' % (r, g, b)
[docs]def disambiguate(label, taken): """ If necessary, add a suffix to label to avoid name conflicts Returns label if it is not in the taken set. Otherwise, returns label_NN where NN is the lowest integer such that label_NN not in taken. Parameters ---------- label : str Desired label taken : iterable The set of already taken names """ if label not in taken: return label suffix = "_%2.2i" label = str(label) for i in count(1): candidate = label + (suffix % i) if candidate not in taken: return candidate
[docs]def small_view(data, attribute): """ Extract a downsampled view from a dataset, for quick statistical summaries """ shp = data.shape view = tuple([slice(None, None, np.intp(max(s / 50, 1))) for s in shp]) return data[attribute, view]
[docs]def small_view_array(data): """ Same as small_view, except using a numpy array as input """ shp = data.shape view = tuple([slice(None, None, np.intp(max(s / 50, 1))) for s in shp]) return np.asarray(data)[view]
[docs]def visible_limits(artists, axis): """ Determines the data limits for the data in a set of artists. Ignores non-visible artists Assumes each artist as a get_data method which returns a tuple of x,y Returns a tuple of min, max for the requested axis, or None if no data present Parameters ---------- artists : iterable An iterable collection of artists axis : int Which axis to compute. 0=xaxis, 1=yaxis """ data = [] for art in artists: if not art.visible: continue xy = art.get_data() assert isinstance(xy, tuple) val = xy[axis] if val.size > 0: data.append(xy[axis]) if len(data) == 0: return data = np.hstack(data) if data.size == 0: return data = data[np.isfinite(data)] if data.size == 0: return lo, hi = nanmin(data), nanmax(data) if not np.isfinite(lo): return return lo, hi
[docs]def tick_linker(all_categories, pos, *args): # We need to take care to ignore negative indices since these would actually # 'work' 'when accessing all_categories, but we need to avoid that. if pos < 0 or pos >= len(all_categories): return '' else: try: pos = np.round(pos) label = all_categories[int(pos)] if isinstance(label, bytes): return label.decode('ascii') else: return label except IndexError: return ''
[docs]def update_ticks(axes, coord, kinds, is_log, categories, projection='rectilinear', radians=True): """ Changes the axes to have the proper tick formatting based on the type of component. Returns `None` or the number of categories if components is Categorical. Parameters ---------- axes : `~matplotlib.axes.Axes` A matplotlib axis object to alter coord : { 'x' | 'y' } The coordinate axis on which to update the ticks components : iterable A list of components that are plotted along this axis if_log : boolean Whether the axis has a log-scale projection: str The name of the matplotlib projection for the axes object. Defaults to 'rectilinear'. Currently only the scatter viewer supports different projections. """ # Short circuit the full-sphere projections if projection in ['aitoff', 'hammer', 'mollweide', 'lambert']: return if coord == 'x': axis = axes.xaxis elif coord == 'y': axis = axes.yaxis else: raise TypeError("coord must be one of x,y") is_cat = 'categorical' in kinds is_date = 'datetime' in kinds if is_date: loc = AutoDateLocator() fmt = AutoDateFormatter(loc) axis.set_major_locator(loc) axis.set_major_formatter(fmt) elif is_log: axis.set_major_locator(LogLocator()) axis.set_major_formatter(LogFormatterMathtext()) elif is_cat: locator = MaxNLocator(10, integer=True) locator.view_limits(0, categories.shape[0]) format_func = partial(tick_linker, categories) formatter = FuncFormatter(format_func) axis.set_major_locator(locator) axis.set_major_formatter(formatter) # Have to treat the theta axis of polar plots differently elif projection == 'polar' and coord == 'x': axis.set_major_locator(ThetaLocator(AutoLocator())) formatter = ThetaRadianFormatter if radians else ThetaFormatter axis.set_major_formatter(formatter()) else: axis.set_major_locator(AutoLocator()) axis.set_major_formatter(ScalarFormatter())