1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591
|
from __future__ import absolute_import, division, print_function
import logging
import operator
import warnings
import numpy as np
import pandas as pd
from glue.core.subset import (RoiSubsetState, RangeSubsetState,
CategoricalROISubsetState, AndState,
MultiRangeSubsetState,
CategoricalMultiRangeSubsetState,
CategoricalROISubsetState2D)
from glue.core.roi import (PolygonalROI, CategoricalROI, RangeROI, XRangeROI,
YRangeROI, RectangularROI)
from glue.core.util import row_lookup
from glue.utils import (unique, shape_to_string, coerce_numeric, check_sorted,
polygon_line_intersections)
__all__ = ['Component', 'DerivedComponent',
'CategoricalComponent', 'CoordinateComponent']
class Component(object):
""" Stores the actual, numerical information for a particular quantity
Data objects hold one or more components, accessed via
ComponentIDs. All Components in a data set must have the same
shape and number of dimensions
Notes
-----
Instead of instantiating Components directly, consider using
:meth:`Component.autotyped`, which chooses a subclass most appropriate
for the data type.
"""
def __init__(self, data, units=None):
"""
:param data: The data to store
:type data: :class:`numpy.ndarray`
:param units: Optional unit label
:type units: str
"""
# The physical units of the data
self.units = units
# The actual data
# subclasses may pass non-arrays here as placeholders.
if isinstance(data, np.ndarray):
data = coerce_numeric(data)
data.setflags(write=False) # data is read-only
self._data = data
@property
def units(self):
return self._units
@units.setter
def units(self, value):
if value is None:
self._units = ''
else:
self._units = str(value)
@property
def hidden(self):
"""Whether the Component is hidden by default"""
return False
@property
def data(self):
""" The underlying :class:`numpy.ndarray` """
return self._data
@property
def shape(self):
""" Tuple of array dimensions """
return self._data.shape
@property
def ndim(self):
""" The number of dimensions """
return len(self._data.shape)
def __getitem__(self, key):
logging.debug("Using %s to index data of shape %s", key, self.shape)
return self._data[key]
@property
def numeric(self):
"""
Whether or not the datatype is numeric
"""
return np.can_cast(self.data.dtype, np.complex)
@property
def categorical(self):
"""
Whether or not the datatype is categorical
"""
return False
def __str__(self):
return "Component with shape %s" % shape_to_string(self.shape)
def jitter(self, method=None):
raise NotImplementedError
def subset_from_roi(self, att, roi, other_comp=None, other_att=None, coord='x'):
"""
Create a SubsetState object from an ROI.
This encapsulates the logic for creating subset states with Components.
See the documentation for CategoricalComponents for caveats involved
with mixed-type plots.
:param att: attribute name of this Component
:param roi: an ROI object
:param other_comp: The other Component for 2D ROIs
:param other_att: The attribute name of the other Component
:param coord: The orientation of this Component
:param is_nested: True if this was passed from another Component.
:return: A SubsetState (or subclass) object
"""
if coord not in ('x', 'y'):
raise ValueError('coord should be one of x/y')
other_coord = 'y' if coord == 'x' else 'x'
if isinstance(roi, RangeROI):
# The selection is either an x range or a y range
if roi.ori == coord:
# The selection applies to the current component
lo, hi = roi.range()
subset_state = RangeSubsetState(lo, hi, att)
else:
# The selection applies to the other component, so we delegate
return other_comp.subset_from_roi(other_att, roi,
other_comp=self,
other_att=att,
coord=other_coord)
else:
# The selection is polygon-like. Categorical components require
# special care, so if the other component is categorical, we need to
# delegate to CategoricalComponent.subset_from_roi.
if isinstance(other_comp, CategoricalComponent):
return other_comp.subset_from_roi(other_att, roi,
other_comp=self,
other_att=att,
is_nested=True,
coord=other_coord)
else:
subset_state = RoiSubsetState()
subset_state.xatt = att
subset_state.yatt = other_att
x, y = roi.to_polygon()
subset_state.roi = PolygonalROI(x, y)
return subset_state
def to_series(self, **kwargs):
""" Convert into a pandas.Series object.
:param kwargs: All kwargs are passed to the Series constructor.
:return: pandas.Series
"""
return pd.Series(self.data.ravel(), **kwargs)
@classmethod
def autotyped(cls, data, units=None):
"""
Automatically choose between Component and CategoricalComponent,
based on the input data type.
:param data: The data to pack into a Component (array-like)
:param units: Optional units
:type units: str
:returns: A Component (or subclass)
"""
data = np.asarray(data)
if np.issubdtype(data.dtype, np.object_):
return CategoricalComponent(data, units=units)
n = coerce_numeric(data)
thresh = 0.5
try:
use_categorical = np.issubdtype(data.dtype, np.character) and \
np.isfinite(n).mean() <= thresh
except TypeError: # isfinite not supported. non-numeric dtype
use_categorical = True
if use_categorical:
return CategoricalComponent(data, units=units)
else:
return Component(n, units=units)
class DerivedComponent(Component):
""" A component which derives its data from a function """
def __init__(self, data, link, units=None):
"""
:param data: The data object to use for calculation
:type data: :class:`~glue.core.data.Data`
:param link: The link that carries out the function
:type link: :class:`~glue.core.component_link.ComponentLink`
:param units: Optional unit description
"""
super(DerivedComponent, self).__init__(data, units=units)
self._link = link
def set_parent(self, data):
""" Reassign the Data object that this DerivedComponent operates on """
self._data = data
@property
def hidden(self):
return self._link.hidden
@property
def data(self):
""" Return the numerical data as a numpy array """
return self._link.compute(self._data)
@property
def link(self):
""" Return the component link """
return self._link
def __getitem__(self, key):
return self._link.compute(self._data, key)
class CoordinateComponent(Component):
"""
Components associated with pixel or world coordinates
The numerical values are computed on the fly.
"""
def __init__(self, data, axis, world=False):
super(CoordinateComponent, self).__init__(None, None)
self.world = world
self._data = data
self.axis = axis
@property
def data(self):
return self._calculate()
def _calculate(self, view=None):
slices = [slice(0, s, 1) for s in self.shape]
grids = np.broadcast_arrays(*np.ogrid[slices])
if view is not None:
grids = [g[view] for g in grids]
if self.world:
world = self._data.coords.pixel2world(*grids[::-1])[::-1]
return world[self.axis]
else:
return grids[self.axis]
@property
def shape(self):
""" Tuple of array dimensions. """
return self._data.shape
@property
def ndim(self):
""" Number of dimensions """
return len(self._data.shape)
def __getitem__(self, key):
return self._calculate(key)
def __lt__(self, other):
if self.world == other.world:
return self.axis < other.axis
return self.world
def __gluestate__(self, context):
return dict(axis=self.axis, world=self.world)
@classmethod
def __setgluestate__(cls, rec, context):
return cls(None, rec['axis'], rec['world'])
class CategoricalComponent(Component):
"""
Container for categorical data.
"""
def __init__(self, categorical_data, categories=None, jitter=None, units=None):
"""
:param categorical_data: The underlying :class:`numpy.ndarray`
:param categories: List of unique values in the data
:jitter: Strategy for jittering the data
"""
super(CategoricalComponent, self).__init__(None, units)
self._categorical_data = np.asarray(categorical_data)
if self._categorical_data.ndim > 1:
raise ValueError("Categorical Data must be 1-dimensional")
# Disable changing of categories
self._categorical_data.setflags(write=False)
self._categories = categories
self._jitter_method = jitter
self._is_jittered = False
self._data = None
if self._categories is None:
self._update_categories()
else:
self._update_data()
@property
def codes(self):
"""
The index of the category for each value in the array.
"""
return self._data
@property
def labels(self):
"""
The original categorical data.
"""
return self._categorical_data
@property
def categories(self):
"""
The categories.
"""
return self._categories
@property
def data(self):
warnings.warn("The 'data' attribute is deprecated. Use 'codes' "
"instead to access the underlying index of the "
"categories")
return self.codes
@property
def numeric(self):
return False
@property
def categorical(self):
return True
def _update_categories(self, categories=None):
"""
:param categories: A sorted array of categories to find in the dataset.
If None the categories are the unique items in the data.
:return: None
"""
if categories is None:
categories, inv = unique(self._categorical_data)
self._categories = categories
self._data = inv.astype(np.float)
self._data.setflags(write=False)
self.jitter(method=self._jitter_method)
else:
if check_sorted(categories):
self._categories = categories
self._update_data()
else:
raise ValueError("Provided categories must be Sorted")
def _update_data(self):
"""
Converts the categorical data into the numeric representations given
self._categories
"""
self._is_jittered = False
self._data = row_lookup(self._categorical_data, self._categories)
self.jitter(method=self._jitter_method)
self._data.setflags(write=False)
def jitter(self, method=None):
"""
Jitter the data so the density of points can be easily seen in a
scatter plot.
:param method: None | 'uniform':
* None: No jittering is done (or any jittering is undone).
* uniform: A unformly distributed random variable (-0.5, 0.5)
is applied to each point.
:return: None
"""
if method not in set(['uniform', None]):
raise ValueError('%s jitter not supported' % method)
self._jitter_method = method
seed = 1234567890
rand_state = np.random.RandomState(seed)
if (self._jitter_method is None) and self._is_jittered:
self._update_data()
elif (self._jitter_method is 'uniform') and not self._is_jittered:
iswrite = self._data.flags['WRITEABLE']
self._data.setflags(write=True)
self._data += rand_state.uniform(-0.5, 0.5, size=self._data.shape)
self._is_jittered = True
self._data.setflags(write=iswrite)
def subset_from_roi(self, att, roi, other_comp=None, other_att=None,
coord='x', is_nested=False):
"""
Create a SubsetState object from an ROI.
This encapsulates the logic for creating subset states with
CategoricalComponents. There is an important caveat, only RangeROIs
and RectangularROIs make sense in mixed type plots. As such, polygons
are converted to their outer-most edges in this case.
:param att: attribute name of this Component
:param roi: an ROI object
:param other_comp: The other Component for 2D ROIs
:param other_att: The attribute name of the other Component
:param coord: The orientation of this Component
:param is_nested: True if this was passed from another Component.
:return: A SubsetState (or subclass) object
"""
if coord not in ('x', 'y'):
raise ValueError('coord should be one of x/y')
if isinstance(roi, RangeROI):
# The selection is either an x range or a y range
if roi.ori == coord:
# The selection applies to the current component
return CategoricalROISubsetState.from_range(self, att, roi.min, roi.max)
else:
# The selection applies to the other component, so we delegate
other_coord = 'y' if coord == 'x' else 'x'
return other_comp.subset_from_roi(other_att, roi,
other_comp=self,
other_att=att,
coord=other_coord)
elif isinstance(roi, RectangularROI):
# In this specific case, we can decompose the rectangular
# ROI into two RangeROIs that are combined with an 'and'
# logical operation.
other_coord = 'y' if coord == 'x' else 'x'
if coord == 'x':
range1 = XRangeROI(roi.xmin, roi.xmax)
range2 = YRangeROI(roi.ymin, roi.ymax)
else:
range2 = XRangeROI(roi.xmin, roi.xmax)
range1 = YRangeROI(roi.ymin, roi.ymax)
# We get the subset state for the current component
subset1 = self.subset_from_roi(att, range1,
other_comp=other_comp,
other_att=other_att,
coord=coord)
# We now get the subset state for the other component
subset2 = other_comp.subset_from_roi(other_att, range2,
other_comp=self,
other_att=att,
coord=other_coord)
return AndState(subset1, subset2)
elif isinstance(roi, CategoricalROI):
# The selection is categorical itself
return CategoricalROISubsetState(roi=roi, att=att)
else:
# The selection is polygon-like, which requires special care.
if isinstance(other_comp, CategoricalComponent):
# For each category, we check which categories along the other
# axis fall inside the polygon:
selection = {}
for code, label in enumerate(self.categories):
# Determine the coordinates of the points to check
n_other = len(other_comp.categories)
y = np.arange(n_other)
x = np.repeat(code, n_other)
if coord == 'y':
x, y = y, x
# Determine which points are in the polygon, and which
# categories these correspond to
in_poly = roi.contains(x, y)
categories = other_comp.categories[in_poly]
if len(categories) > 0:
selection[label] = set(categories)
return CategoricalROISubsetState2D(selection, att, other_att)
else:
# If the other component is not categorical, we treat this as if
# each categorical component was mapped to a numerical value,
# and at each value, we keep track of the polygon intersection
# with the component. This will result in zero, one, or
# multiple separate numerical ranges for each categorical value.
# TODO: if we ever allow the category order to be changed, we
# need to figure out how to update this!
x, y = roi.to_polygon()
if is_nested:
x, y = y, x
# We loop over each category and for each one we find the
# numerical ranges
selection = {}
for code, label in enumerate(self.categories):
# We determine all the numerical segments that represent the
# ensemble of points in y that fall in the polygon
# TODO: profile the following function
segments = polygon_line_intersections(x, y, xval=code)
if len(segments) > 0:
selection[label] = segments
return CategoricalMultiRangeSubsetState(selection, att, other_att)
def to_series(self, **kwargs):
""" Convert into a pandas.Series object.
This will be converted as a dtype=np.object!
:param kwargs: All kwargs are passed to the Series constructor.
:return: pandas.Series
"""
return pd.Series(self._categorical_data.ravel(),
dtype=np.object, **kwargs)
|