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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 937 938 939 940 941 942 943 944 945 946 947 948 949 950 951 952 953 954 955 956 957 958 959 960 961 962 963 964 965 966 967 968 969 970 971 972 973 974 975 976 977 978 979 980 981 982 983 984 985 986 987 988 989 990 991 992 993 994 995 996 997 998 999 1000 1001 1002 1003 1004 1005 1006 1007 1008 1009 1010 1011 1012 1013 1014 1015 1016 1017 1018 1019 1020 1021 1022 1023 1024 1025 1026 1027 1028 1029 1030 1031 1032 1033 1034 1035 1036 1037 1038 1039 1040 1041 1042 1043 1044 1045 1046 1047 1048 1049 1050 1051 1052 1053 1054 1055 1056 1057 1058 1059 1060 1061 1062 1063 1064 1065 1066 1067 1068 1069 1070 1071 1072 1073 1074 1075 1076 1077 1078 1079 1080 1081 1082 1083 1084 1085 1086 1087 1088 1089 1090 1091 1092 1093 1094 1095 1096 1097 1098 1099 1100 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1111 1112 1113 1114 1115 1116 1117 1118 1119 1120 1121 1122 1123 1124 1125 1126 1127 1128 1129 1130 1131 1132 1133 1134 1135 1136 1137 1138 1139 1140 1141 1142 1143 1144 1145 1146 1147 1148 1149 1150 1151 1152 1153 1154 1155 1156 1157 1158 1159 1160 1161 1162 1163 1164 1165 1166 1167 1168 1169 1170 1171 1172 1173 1174 1175 1176 1177 1178 1179 1180 1181 1182 1183 1184 1185 1186 1187 1188 1189 1190 1191 1192 1193 1194 1195 1196 1197 1198 1199 1200 1201 1202 1203 1204 1205 1206 1207 1208 1209 1210 1211 1212 1213 1214 1215 1216 1217 1218 1219 1220 1221 1222 1223 1224 1225 1226 1227 1228 1229 1230 1231 1232 1233 1234 1235 1236 1237 1238 1239 1240 1241 1242 1243 1244 1245 1246 1247 1248 1249 1250 1251 1252 1253 1254 1255 1256 1257 1258 1259 1260 1261 1262 1263 1264 1265 1266 1267 1268 1269 1270 1271 1272 1273 1274 1275 1276 1277 1278 1279 1280 1281 1282 1283 1284 1285 1286 1287
|
'''
Code to use matplotlib for creating raster and spectral views.
'''
from __future__ import absolute_import, division, print_function, unicode_literals
__all__ = ['ImageView', 'imshow']
import numpy as np
import warnings
_mpl_callbacks_checked = False
def check_disable_mpl_callbacks():
'''Disables matplotlib key event handlers, if appropriate.'''
import matplotlib as mpl
from spectral import settings
global _mpl_callbacks_checked
if _mpl_callbacks_checked is True or \
settings.imshow_disable_mpl_callbacks is False:
return
_mpl_callbacks_checked = True
mpl.rcParams['keymap.back'] = ''
mpl.rcParams['keymap.xscale'] = ''
mpl.rcParams['keymap.yscale'] = ''
mpl.rcParams['keymap.home'] = 'r'
def xy_to_rowcol(x, y):
'''Converts image (x, y) coordinate to pixel (row, col).'''
return (int(y + 0.5), int(x + 0.5))
def rowcol_to_xy(r, c):
'''Converts pixel (row, col) coordinate to (x, y) of pixel center.'''
return (float(c), float(r))
class MplCallback(object):
'''Base class for callbacks using matplotlib's CallbackRegistry.
Behavior of MplCallback objects can be customized by providing a callable
object to the constructor (or `connect` method) or by defining a
`handle_event` method in a subclass.
'''
# If the following class attribute is False, callbacks will silently
# disconnect when an exception is encountered during event processing
# (e.g., if an associated window has been closed) . If it is True, the
# associated exception will be rethrown.
raise_event_exceptions = False
show_events = False
def __init__(self, registry=None, event=None, callback=None):
'''
Arguments:
registry (ImageView, CallbackRegistry, or FigureCanvas):
The object that will generate the callback. If the argument is
an ImageView, the callback will be bound to the associated
FigureCanvas.
event (str):
The event type for which callbacks should be generated.
callback (callable):
An optional callable object to handle the event. If not
provided, the `handle_event` method of the MplCallback will
be called to handle the event (this method must be defined by
a derived class if `callback` is not provided.
Note that these arguments can be deferred until `MplCallback.connect`
is called.
'''
self.set_registry(registry)
self.event = event
self.callback = callback
self.cid = None
self.is_connected = False
self.children = []
def set_registry(self, registry=None):
'''
Arguments:
registry (ImageView, CallbackRegistry, or FigureCanvas):
The object that will generate the callback. If the argument is
an ImageView, the callback will be bound to the associated
FigureCanvas.
'''
from matplotlib.cbook import CallbackRegistry
if isinstance(registry, CallbackRegistry):
self.registry = registry
elif isinstance(registry, ImageView):
self.registry = registry.axes.figure.canvas
else:
self.registry = registry
def connect(self, registry=None, event=None, callback=None):
'''Binds the callback to the registry and begins receiving event.
Arguments:
registry (ImageView, CallbackRegistry, or FigureCanvas):
The object that will generate the callback. If the argument is
an ImageView, the callback will be bound to the associated
FigureCanvas.
event (str):
The event type for which callbacks should be generated.
callback (callable):
An optional callable object to handle the event. If not
provided, the `handle_event` method of the MplCallback will
be called to handle the event (this method must be defined by
a derived class if `callback` is not provided.
Note that these arguments can also be provided to the constructor.
'''
from matplotlib.cbook import CallbackRegistry
if self.is_connected:
raise Exception('Callback is already connected.')
if registry is not None:
self.set_registry(registry)
if event is not None:
self.event = event
if callback is not None:
self.callback = callback
if self.callback is None:
cb = self
else:
cb = self.callback
if isinstance(self.registry, CallbackRegistry):
self.cid = self.registry.connect(self.event, self)
elif isinstance(self.registry, ImageView):
self.cid = self.registry.connect(self.event, self)
else:
# Assume registry is an MPL canvas
self.cid = self.registry.mpl_connect(self.event, self)
self.is_connected = True
for c in self.children:
c.connect()
def disconnect(self):
'''Stops the callback from receiving events.'''
from matplotlib.cbook import CallbackRegistry
if isinstance(self.registry, CallbackRegistry):
self.registry.disconnect(self.cid)
else:
# Assume registry is an MPL canvas
self.registry.mpl_disconnect(self.cid)
self.is_connected = False
self.cid = None
for c in self.children:
c.disconnect()
def __call__(self, *args, **kwargs):
if self.callback is not None:
try:
self.callback(*args, **kwargs)
except Exception as e:
self.disconnect()
if self.raise_event_exceptions:
raise e
else:
try:
self.handle_event(*args, **kwargs)
except Exception as e:
self.disconnect()
if self.raise_event_exceptions:
raise e
class ImageViewCallback(MplCallback):
'''Base class for callbacks that operate on ImageView objects.'''
def __init__(self, view, *args, **kwargs):
super(ImageViewCallback, self).__init__(*args, **kwargs)
self.view = view
class ParentViewPanCallback(ImageViewCallback):
'''A callback to pan an image based on a click in another image.'''
def __init__(self, child, parent, *args, **kwargs):
'''
Arguments:
`child` (ImageView):
The view that will be panned based on a parent click event.
`parent` (ImageView):
The view whose click location will cause the child to pan.
See ImageViewCallback and MplCallback for additional arguments.
'''
super(ParentViewPanCallback, self).__init__(parent, *args, **kwargs)
self.child = child
def handle_event(self, event):
if self.show_events:
print(event, 'key = %s' % event.key)
if event.inaxes is not self.view.axes:
return
(r, c) = xy_to_rowcol(event.xdata, event.ydata)
(nrows, ncols) = self.view._image_shape
if r < 0 or r >= nrows or c < 0 or c >= ncols:
return
kp = KeyParser(event.key)
if event.button == 1 and kp.mods_are('ctrl'):
self.child.pan_to(event.ydata, event.xdata)
def connect(self):
super(ParentViewPanCallback, self).connect(registry=self.view,
event='button_press_event')
class ImageViewKeyboardHandler(ImageViewCallback):
'''Default handler for keyboard events in an ImageView.'''
def __init__(self, view, *args, **kwargs):
super(ImageViewKeyboardHandler, self).__init__(view,
registry=view,
event='key_press_event',
*args, **kwargs)
self.cb_key_release = ImageViewCallback(view, registry=view,
event='key_release_event',
callback=self.on_key_release,
*args, **kwargs)
# Must add to children member to automatically connect/disconnect.
self.children.append(self.cb_key_release)
self.idstr = ''
def on_key_release(self, event):
if self.show_events:
print('key = %s' % event.key)
kp = KeyParser(event.key)
key = kp.key
if key is None and self.view.selector is not None and \
self.view.selector.get_active() and kp.mods_are('shift') \
and self.view.selector.eventpress is not None:
print('Resetting selection.')
self.view.selector.eventpress = None
self.view.selector.set_active(False)
self.view.selection = None
self.view.selector.to_draw.set_visible(False)
self.view.refresh()
def handle_event(self, event):
from spectral import settings
if self.show_events:
print('key = %s' % event.key)
kp = KeyParser(event.key)
key = kp.key
#-----------------------------------------------------------
# Handling for keyboard input related to class ID assignment
#-----------------------------------------------------------
if key is None and kp.mods_are('shift') and \
self.view.selector is not None:
# Rectangle selector is active while shift key is pressed
self.view.selector.set_active(True)
return
if key in [str(i) for i in range(10)] and self.view.selector is not None:
if self.view.selection is None:
print('Select an image region before assigning a class ID.')
return
if len(self.idstr) > 0 and self.idstr[-1] == '!':
print('Cancelled class ID assignment.')
self.idstr = ''
return
else:
self.idstr += key
return
if key == 'enter' and self.view.selector is not None:
if self.view.selection is None:
print('Select an image region before assigning a class ID.')
return
if len(self.idstr) == 0:
print('Enter a numeric class ID before assigning a class ID.')
return
if self.idstr[-1] != '!':
print('Press ENTER again to assign class %s to pixel ' \
'region [%d:%d, %d:%d]:' \
% ((self.idstr,) + tuple(self.view.selection)))
self.idstr += '!'
return
else:
i = int(self.idstr[:-1])
n = self.view.label_region(self.view.selection, i)
if n == 0:
print('No pixels reassigned.')
else:
print('%d pixels reassigned to class %d.' % (n, i))
self.idstr = ''
return
if len(self.idstr) > 0:
self.idstr = ''
print('Cancelled class ID assignment.')
#-----------------------------------------------------------
# General keybinds
#-----------------------------------------------------------
if key == 'a' and self.view.display_mode == 'overlay':
self.view.class_alpha = max(self.view.class_alpha - 0.05, 0)
elif key == 'A' and self.view.display_mode == 'overlay':
self.view.class_alpha = min(self.view.class_alpha + 0.05, 1)
elif key == 'c':
if self.view.classes is not None:
self.view.set_display_mode('classes')
elif key == 'C':
if self.view.classes is not None \
and self.view.data_axes is not None:
self.view.set_display_mode('overlay')
elif key == 'd':
if self.view.data_axes is not None:
self.view.set_display_mode('data')
elif key == 'h':
self.print_help()
elif key == 'i':
if self.view.interpolation == 'nearest':
self.view.interpolation = settings.imshow_interpolation
else:
self.view.interpolation = 'nearest'
elif key == 'z':
self.view.open_zoom()
def print_help(self):
print()
print('Mouse Functions:')
print('----------------')
print('ctrl+left-click -> pan zoom window to pixel')
print('shift+left-click&drag -> select rectangular image region')
print('left-dblclick -> plot pixel spectrum')
print()
print('Keybinds:')
print('---------')
print('0-9 -> enter class ID for image pixel labeling')
print('ENTER -> apply specified class ID to selected rectangular region')
print('a/A -> decrease/increase class overlay alpha value')
print('c -> set display mode to "classes" (if classes set)')
print('C -> set display mode to "overlay" (if data and ' \
'classes set)')
print('d -> set display mode to "data" (if data set)')
print('h -> print help message')
print('i -> toggle pixel interpolation between "nearest" and ' \
'SPy default.')
print('z -> open zoom window')
print()
print('See matplotlib imshow documentation for addition key binds.')
print()
class KeyParser(object):
'''Class to handle ambiguities in matplotlib event key values.'''
aliases = {'ctrl': ['ctrl', 'control'],
'alt': ['alt'],
'shift': ['shift'],
'super': ['super']}
def __init__(self, key_str=None):
self.reset()
if key_str is not None:
self.parse(key_str)
def reset(self):
self.key = None
self.modifiers = set()
def parse(self, key_str):
'''Extracts the key value and modifiers from a string.'''
self.reset()
if key_str is None:
return
tokens = key_str.split('+')
for token in tokens[:-1]:
mods = self.get_token_modifiers(token)
if len(mods) == 0:
raise ValueError('Unrecognized modifier: %s' % repr(token))
self.modifiers.update(mods)
# For the final token, need to determine if it is a key or modifier
mods = self.get_token_modifiers(tokens[-1])
if len(mods) > 0:
self.modifiers.update(mods)
else:
self.key = tokens[-1]
def has_mod(self, m):
'''Returns True if `m` is one of the modifiers.'''
return m in self.modifiers
def mods_are(self, *args):
'''Return True if modifiers are exactly the ones specified.'''
for a in args:
if a not in self.modifiers:
return False
return True
def get_token_modifiers(self, token):
mods = set()
for (modifier, aliases) in list(self.aliases.items()):
if token in aliases:
mods.add(modifier)
return mods
class ImageViewMouseHandler(ImageViewCallback):
def __init__(self, view, *args, **kwargs):
super(ImageViewMouseHandler, self).__init__(view,
registry=view,
event='button_press_event',
*args, **kwargs)
def handle_event(self, event):
'''Callback for click event in the image display.'''
if self.show_events:
print(event, ', key = %s' % event.key)
if event.inaxes is not self.view.axes:
return
(r, c) = (int(event.ydata + 0.5), int(event.xdata + 0.5))
(nrows, ncols) = self.view._image_shape
if r < 0 or r >= nrows or c < 0 or c >= ncols:
return
kp = KeyParser(event.key)
if event.button == 1:
if event.dblclick and kp.key is None:
if self.view.source is not None:
from spectral import settings
import matplotlib.pyplot as plt
if self.view.spectrum_plot_fig_id is None:
f = plt.figure()
self.view.spectrum_plot_fig_id = f.number
try:
f = plt.figure(self.view.spectrum_plot_fig_id)
except:
f = plt.figure()
self.view.spectrum_plot_fig_id = f.number
s = f.gca()
settings.plotter.plot(self.view.source[r, c],
self.view.source)
s.xaxis.axes.relim()
s.xaxis.axes.autoscale(True)
f.canvas.draw()
class SpyMplEvent(object):
def __init__(self, name):
self.name = name
class ImageView(object):
'''Class to manage events and data associated with image raster views.
In most cases, it is more convenient to simply call :func:`~spectral.graphics.spypylab.imshow`,
which creates, displays, and returns an :class:`ImageView` object. Creating
an :class:`ImageView` object directly (or creating an instance of a subclass)
enables additional customization of the image display (e.g., overriding
default event handlers). If the object is created directly, call the
:meth:`show` method to display the image. The underlying image display
functionality is implemented via :func:`matplotlib.pyplot.imshow`.
'''
selector_rectprops = dict(facecolor='red', edgecolor = 'black',
alpha=0.5, fill=True)
selector_lineprops = dict(color='black', linestyle='-',
linewidth = 2, alpha=0.5)
def __init__(self, data=None, bands=None, classes=None, source=None,
**kwargs):
'''
Arguments:
`data` (ndarray or :class:`SpyFile`):
The source of RGB bands to be displayed. with shape (R, C, B).
If the shape is (R, C, 3), the last dimension is assumed to
provide the red, green, and blue bands (unless the `bands`
argument is provided). If :math:`B > 3` and `bands` is not
provided, the first, middle, and last band will be used.
`bands` (triplet of integers):
Specifies which bands in `data` should be displayed as red,
green, and blue, respectively.
`classes` (ndarray of integers):
An array of integer-valued class labels with shape (R, C). If
the `data` argument is provided, the shape must match the first
two dimensions of `data`.
`source` (ndarray or :class:`SpyFile`):
The source of spectral data associated with the image display.
This optional argument is used to access spectral data (e.g., to
generate a spectrum plot when a user double-clicks on the image
display.
Keyword arguments:
Any keyword that can be provided to :func:`~spectral.graphics.graphics.get_rgb`
or :func:`matplotlib.imshow`.
'''
import spectral
from spectral import settings
self.is_shown = False
self.imshow_data_kwargs = {'cmap': settings.imshow_float_cmap}
self.rgb_kwargs = {}
self.imshow_class_kwargs = {'zorder': 1}
self.data = data
self.data_rgb = None
self.data_rgb_meta = {}
self.classes = None
self.class_rgb = None
self.source = None
self.bands = bands
self.data_axes = None
self.class_axes = None
self.axes = None
self._image_shape = None
self.display_mode = None
self._interpolation = None
self.selection = None
self.interpolation = kwargs.get('interpolation',
settings.imshow_interpolation)
if data is not None:
self.set_data(data, bands, **kwargs)
if classes is not None:
self.set_classes(classes, **kwargs)
if source is not None:
self.set_source(source)
self.class_colors = spectral.spy_colors
self.spectrum_plot_fig_id = None
self.parent = None
self.selector = None
self._on_parent_click_cid = None
self._class_alpha = settings.imshow_class_alpha
# Callbacks for events associated specifically with this window.
self.callbacks = None
# A sharable callback registry for related windows. If this
# CallbackRegistry is set prior to calling ImageView.show (e.g., by
# setting it equal to the `callbacks_common` member of another
# ImageView object), then the registry will be shared. Otherwise, a new
# callback registry will be created for this ImageView.
self.callbacks_common = None
check_disable_mpl_callbacks()
def set_data(self, data, bands=None, **kwargs):
'''Sets the data to be shown in the RGB channels.
Arguments:
`data` (ndarray or SpyImage):
If `data` has more than 3 bands, the `bands` argument can be
used to specify which 3 bands to display. `data` will be
passed to `get_rgb` prior to display.
`bands` (3-tuple of int):
Indices of the 3 bands to display from `data`.
Keyword Arguments:
Any valid keyword for `get_rgb` or `matplotlib.imshow` can be
given.
'''
from .graphics import _get_rgb_kwargs
self.data = data
self.bands = bands
rgb_kwargs = {}
for k in _get_rgb_kwargs:
if k in kwargs:
rgb_kwargs[k] = kwargs.pop(k)
self.set_rgb_options(**rgb_kwargs)
self._update_data_rgb()
if self._image_shape is None:
self._image_shape = data.shape[:2]
elif data.shape[:2] != self._image_shape:
raise ValueError('Image shape is inconsistent with previously ' \
'set data.')
self.imshow_data_kwargs.update(kwargs)
if 'interpolation' in self.imshow_data_kwargs:
self.interpolation = self.imshow_data_kwargs['interpolation']
self.imshow_data_kwargs.pop('interpolation')
if len(kwargs) > 0 and self.is_shown:
msg = 'Keyword args to set_data only have an effect if ' \
'given before the image is shown.'
warnings.warn(UserWarning(msg))
if self.is_shown:
self.refresh()
def set_rgb_options(self, **kwargs):
'''Sets parameters affecting RGB display of data.
Accepts any keyword supported by :func:`~spectral.graphics.graphics.get_rgb`.
'''
from .graphics import _get_rgb_kwargs
for k in kwargs:
if k not in _get_rgb_kwargs:
raise ValueError('Unexpected keyword: {0}'.format(k))
self.rgb_kwargs = kwargs.copy()
if self.is_shown:
self._update_data_rgb()
self.refresh()
def _update_data_rgb(self):
'''Regenerates the RGB values for display.'''
from .graphics import get_rgb_meta
(self.data_rgb, self.data_rgb_meta) = \
get_rgb_meta(self.data, self.bands, **self.rgb_kwargs)
# If it is a gray-scale image, only keep the first RGB component so
# matplotlib imshow's cmap can still be used.
if self.data_rgb_meta['mode'] == 'monochrome' and \
self.data_rgb.ndim == 3:
self.data_rgb = self.data_rgb[:, :, 0]
def set_classes(self, classes, colors=None, **kwargs):
'''Sets the array of class values associated with the image data.
Arguments:
`classes` (ndarray of int):
`classes` must be an integer-valued array with the same
number rows and columns as the display data (if set).
`colors`: (array or 3-tuples):
Color triplets (with values in the range [0, 255]) that
define the colors to be associatd with the integer indices
in `classes`.
Keyword Arguments:
Any valid keyword for `matplotlib.imshow` can be provided.
'''
from .graphics import _get_rgb_kwargs
self.classes = classes
if classes is None:
return
if self._image_shape is None:
self._image_shape = classes.shape[:2]
elif classes.shape[:2] != self._image_shape:
raise ValueError('Class data shape is inconsistent with ' \
'previously set data.')
if colors is not None:
self.class_colors = colors
kwargs = dict([item for item in list(kwargs.items()) if item[0] not in \
_get_rgb_kwargs])
self.imshow_class_kwargs.update(kwargs)
if 'interpolation' in self.imshow_class_kwargs:
self.interpolation = self.imshow_class_kwargs['interpolation']
self.imshow_class_kwargs.pop('interpolation')
if len(kwargs) > 0 and self.is_shown:
msg = 'Keyword args to set_classes only have an effect if ' \
'given before the image is shown.'
warnings.warn(UserWarning(msg))
if self.is_shown:
self.refresh()
def set_source(self, source):
'''Sets the image data source (used for accessing spectral data).
Arguments:
`source` (ndarray or :class:`SpyFile`):
The source for spectral data associated with the view.
'''
self.source = source
def show(self, mode=None, fignum=None):
'''Renders the image data.
Arguments:
`mode` (str):
Must be one of:
"data": Show the data RGB
"classes": Shows indexed color for `classes`
"overlay": Shows class colors overlaid on data RGB.
If `mode` is not provided, a mode will be automatically
selected, based on the data set in the ImageView.
`fignum` (int):
Figure number of the matplotlib figure in which to display
the ImageView. If not provided, a new figure will be created.
'''
import matplotlib.pyplot as plt
from spectral import settings
if self.is_shown:
msg = 'ImageView.show should only be called once.'
warnings.warn(UserWarning(msg))
return
set_mpl_interactive()
kwargs = {}
if fignum is not None:
kwargs['num'] = fignum
if settings.imshow_figure_size is not None:
kwargs['figsize'] = settings.imshow_figure_size
plt.figure(**kwargs)
if self.data_rgb is not None:
self.show_data()
if self.classes is not None:
self.show_classes()
if mode is None:
self._guess_mode()
else:
self.set_display_mode(mode)
self.axes.format_coord = self.format_coord
self.init_callbacks()
self.is_shown = True
def init_callbacks(self):
'''Creates the object's callback registry and default callbacks.'''
from spectral import settings
from matplotlib.cbook import CallbackRegistry
self.callbacks = CallbackRegistry()
# callbacks_common may have been set to a shared external registry
# (e.g., to the callbacks_common member of another ImageView object). So
# don't create it if it has already been set.
if self.callbacks_common is None:
self.callbacks_common = CallbackRegistry()
# Keyboard callback
self.cb_mouse = ImageViewMouseHandler(self)
self.cb_mouse.connect()
# Mouse callback
self.cb_keyboard = ImageViewKeyboardHandler(self)
self.cb_keyboard.connect()
# Class update event callback
def updater(*args, **kwargs):
if self.classes is None:
self.set_classes(args[0].classes)
self.refresh()
callback = MplCallback(registry=self.callbacks_common,
event='spy_classes_modified',
callback=updater)
callback.connect()
self.cb_classes_modified = callback
if settings.imshow_enable_rectangle_selector is False:
return
try:
from matplotlib.widgets import RectangleSelector
self.selector = RectangleSelector(self.axes,
self._select_rectangle,
button=1,
useblit=True,
spancoords='data',
drawtype='box',
rectprops = \
self.selector_rectprops)
self.selector.set_active(False)
except:
self.selector = None
msg = 'Failed to create RectangleSelector object. Interactive ' \
'pixel class labeling will be unavailable.'
warnings.warn(msg)
def label_region(self, rectangle, class_id):
'''Assigns all pixels in the rectangle to the specified class.
Arguments:
`rectangle` (4-tuple of integers):
Tuple or list defining the rectangle bounds. Should have the
form (row_start, row_stop, col_start, col_stop), where the
stop indices are not included (i.e., the effect is
`classes[row_start:row_stop, col_start:col_stop] = id`.
class_id (integer >= 0):
The class to which pixels will be assigned.
Returns the number of pixels reassigned (the number of pixels in the
rectangle whose class has *changed* to `class_id`.
'''
if self.classes is None:
self.classes = np.zeros(self.data_rgb.shape[:2], dtype=np.int16)
r = rectangle
n = np.sum(self.classes[r[0]:r[1], r[2]:r[3]] != class_id)
if n > 0:
self.classes[r[0]:r[1], r[2]:r[3]] = class_id
event = SpyMplEvent('spy_classes_modified')
event.classes = self.classes
event.nchanged = n
self.callbacks_common.process('spy_classes_modified', event)
# Make selection rectangle go away.
self.selector.to_draw.set_visible(False)
self.refresh()
return n
return 0
def _select_rectangle(self, event1, event2):
if event1.inaxes is not self.axes or event2.inaxes is not self.axes:
self.selection = None
return
(r1, c1) = xy_to_rowcol(event1.xdata, event1.ydata)
(r2, c2) = xy_to_rowcol(event2.xdata, event2.ydata)
(r1, r2) = sorted([r1, r2])
(c1, c2) = sorted([c1, c2])
if (r2 < 0) or (r1 >= self._image_shape[0]) or \
(c2 < 0) or (c1 >= self._image_shape[1]):
self.selection = None
return
r1 = max(r1, 0)
r2 = min(r2, self._image_shape[0] - 1)
c1 = max(c1, 0)
c2 = min(c2, self._image_shape[1] - 1)
print('Selected region: [%d: %d, %d: %d]' % (r1, r2 + 1, c1, c2 + 1))
self.selection = [r1, r2 + 1, c1, c2 + 1]
self.selector.set_active(False)
# Make the rectangle display until at least the next event
self.selector.to_draw.set_visible(True)
self.selector.update()
def _guess_mode(self):
'''Select an appropriate display mode, based on current data.'''
if self.data_rgb is not None:
self.set_display_mode('data')
elif self.classes is not None:
self.set_display_mode('classes')
else:
raise Exception('Unable to display image: no data set.')
def show_data(self):
'''Show the image data.'''
import matplotlib.pyplot as plt
if self.data_axes is not None:
msg = 'ImageView.show_data should only be called once.'
warnings.warn(UserWarning(msg))
return
elif self.data_rgb is None:
raise Exception('Unable to display data: data array not set.')
if self.axes is not None:
# A figure has already been created for the view. Make it current.
plt.figure(self.axes.figure.number)
self.imshow_data_kwargs['interpolation'] = self._interpolation
self.data_axes = plt.imshow(self.data_rgb, **self.imshow_data_kwargs)
if self.axes is None:
self.axes = self.data_axes.axes
def show_classes(self):
'''Show the class values.'''
import matplotlib.pyplot as plt
from matplotlib.colors import ListedColormap, NoNorm
from spectral import get_rgb
if self.class_axes is not None:
msg = 'ImageView.show_classes should only be called once.'
warnings.warn(UserWarning(msg))
return
elif self.classes is None:
raise Exception('Unable to display classes: class array not set.')
cm = ListedColormap(np.array(self.class_colors) / 255.)
self._update_class_rgb()
kwargs = self.imshow_class_kwargs.copy()
kwargs.update({'cmap': cm, 'norm':NoNorm(),
'interpolation': self._interpolation})
if self.axes is not None:
# A figure has already been created for the view. Make it current.
plt.figure(self.axes.figure.number)
self.class_axes = plt.imshow(self.class_rgb, **kwargs)
if self.axes is None:
self.axes = self.class_axes.axes
self.class_axes.set_zorder(1)
if self.display_mode == 'overlay':
self.class_axes.set_alpha(self._class_alpha)
else:
self.class_axes.set_alpha(1)
#self.class_axes.axes.set_axis_bgcolor('black')
def refresh(self):
'''Updates the displayed data (if it has been shown).'''
if self.is_shown:
self._update_class_rgb()
if self.class_axes is not None:
self.class_axes.set_data(self.class_rgb)
self.class_axes.set_interpolation(self._interpolation)
elif self.display_mode in ('classes', 'overlay'):
self.show_classes()
if self.data_axes is not None:
self.data_axes.set_data(self.data_rgb)
self.data_axes.set_interpolation(self._interpolation)
elif self.display_mode in ('data', 'overlay'):
self.show_data()
self.axes.figure.canvas.draw()
def _update_class_rgb(self):
if self.display_mode == 'overlay':
self.class_rgb = np.ma.array(self.classes, mask=(self.classes==0))
else:
self.class_rgb = np.array(self.classes)
def set_display_mode(self, mode):
'''`mode` must be one of ("data", "classes", "overlay").'''
if mode not in ('data', 'classes', 'overlay'):
raise ValueError('Invalid display mode: ' + repr(mode))
self.display_mode = mode
show_data = mode in ('data', 'overlay')
if self.data_axes is not None:
self.data_axes.set_visible(show_data)
show_classes = mode in ('classes', 'overlay')
if self.classes is not None and self.class_axes is None:
# Class data values were just set
self.show_classes()
if self.class_axes is not None:
self.class_axes.set_visible(show_classes)
if mode == 'classes':
self.class_axes.set_alpha(1)
else:
self.class_axes.set_alpha(self._class_alpha)
self.refresh()
@property
def class_alpha(self):
'''alpha transparency for the class overlay.'''
return self._class_alpha
@class_alpha.setter
def class_alpha(self, alpha):
if alpha < 0 or alpha > 1:
raise ValueError('Alpha value must be in range [0, 1].')
self._class_alpha = alpha
if self.class_axes is not None:
self.class_axes.set_alpha(alpha)
if self.is_shown:
self.refresh()
@property
def interpolation(self):
'''matplotlib pixel interpolation to use in the image display.'''
return self._interpolation
@interpolation.setter
def interpolation(self, interpolation):
if interpolation == self._interpolation:
return
self._interpolation = interpolation
if not self.is_shown:
return
if self.data_axes is not None:
self.data_axes.set_interpolation(interpolation)
if self.class_axes is not None:
self.class_axes.set_interpolation(interpolation)
self.refresh()
def set_title(self, s):
if self.is_shown:
self.axes.set_title(s)
self.refresh()
def open_zoom(self, center=None, size=None):
'''Opens a separate window with a zoomed view.
If a ctrl-lclick event occurs in the original view, the zoomed window
will pan to the location of the click event.
Arguments:
`center` (two-tuple of int):
Initial (row, col) of the zoomed view.
`size` (int):
Width and height (in source image pixels) of the initial
zoomed view.
Returns:
A new ImageView object for the zoomed view.
'''
from spectral import settings
import matplotlib.pyplot as plt
if size is None:
size = settings.imshow_zoom_pixel_width
(nrows, ncols) = self._image_shape
fig_kwargs = {}
if settings.imshow_zoom_figure_width is not None:
width = settings.imshow_zoom_figure_width
fig_kwargs['figsize'] = (width, width)
fig = plt.figure(**fig_kwargs)
view = ImageView(source=self.source)
view.set_data(self.data, self.bands, **self.rgb_kwargs)
view.set_classes(self.classes, self.class_colors)
view.imshow_data_kwargs = self.imshow_data_kwargs.copy()
kwargs = {'extent': (-0.5, ncols - 0.5, nrows - 0.5, -0.5)}
view.imshow_data_kwargs.update(kwargs)
view.imshow_class_kwargs = self.imshow_class_kwargs.copy()
view.imshow_class_kwargs.update(kwargs)
view.callbacks_common = self.callbacks_common
view.spectrum_plot_fig_id = self.spectrum_plot_fig_id
view.show(fignum=fig.number, mode=self.display_mode)
view.axes.set_xlim(0, size)
view.axes.set_ylim(size, 0)
view.interpolation = 'nearest'
if center is not None:
view.pan_to(*center)
view.cb_parent_pan = ParentViewPanCallback(view, self)
view.cb_parent_pan.connect()
return view
def pan_to(self, row, col):
'''Centers view on pixel coordinate (row, col).'''
if self.axes is None:
raise Exception('Cannot pan image until it is shown.')
(xmin, xmax) = self.axes.get_xlim()
(ymin, ymax) = self.axes.get_ylim()
xrange_2 = (xmax - xmin) / 2.0
yrange_2 = (ymax - ymin) / 2.0
self.axes.set_xlim(col - xrange_2, col + xrange_2)
self.axes.set_ylim(row - yrange_2, row + yrange_2)
self.axes.figure.canvas.draw()
def zoom(self, scale):
'''Zooms view in/out (`scale` > 1 zooms in).'''
(xmin, xmax) = self.axes.get_xlim()
(ymin, ymax) = self.axes.get_ylim()
x = (xmin + xmax) / 2.0
y = (ymin + ymax) / 2.0
dx = (xmax - xmin) / 2.0 / scale
dy = (ymax - ymin) / 2.0 / scale
self.axes.set_xlim(x - dx, x + dx)
self.axes.set_ylim(y - dy, y + dy)
self.refresh()
def format_coord(self, x, y):
'''Formats pixel coordinate string displayed in the window.'''
(nrows, ncols) = self._image_shape
if x < -0.5 or x > ncols - 0.5 or y < -0.5 or y > nrows - 0.5:
return ""
(r, c) = xy_to_rowcol(x, y)
s = 'pixel=[%d,%d]' % (r, c)
if self.classes is not None:
try:
s += ' class=%d' % self.classes[r, c]
except:
pass
return s
def __str__(self):
meta = self.data_rgb_meta
s = 'ImageView object:\n'
if 'bands' in meta:
s += ' {0:<20}: {1}\n'.format("Display bands", meta['bands'])
if self.interpolation == None:
interp = "<default>"
else:
interp = self.interpolation
s += ' {0:<20}: {1}\n'.format("Interpolation", interp)
if 'rgb range' in meta:
s += ' {0:<20}:\n'.format("RGB data limits")
for (c, r) in zip('RGB', meta['rgb range']):
s += ' {0}: {1}\n'.format(c, str(r))
return s
def __repr__(self):
return str(self)
def imshow(data=None, bands=None, classes=None, source=None, colors=None,
figsize=None, fignum=None, title=None, **kwargs):
'''A wrapper around matplotlib's imshow for multi-band images.
Arguments:
`data` (SpyFile or ndarray):
Can have shape (R, C) or (R, C, B).
`bands` (tuple of integers, optional)
If `bands` has 3 values, the bands specified are extracted from
`data` to be plotted as the red, green, and blue colors,
respectively. If it contains a single value, then a single band
will be extracted from the image.
`classes` (ndarray of integers):
An array of integer-valued class labels with shape (R, C). If
the `data` argument is provided, the shape must match the first
two dimensions of `data`. The returned `ImageView` object will use
a copy of this array. To access class values that were altered
after calling `imshow`, access the `classes` attribute of the
returned `ImageView` object.
`source` (optional, SpyImage or ndarray):
Object used for accessing image source data. If this argument is
not provided, events such as double-clicking will have no effect
(i.e., a spectral plot will not be created).
`colors` (optional, array of ints):
Custom colors to be used for class image view. If provided, this
argument should be an array of 3-element arrays, each of which
specifies an RGB triplet with integer color components in the
range [0, 256).
`figsize` (optional, 2-tuple of scalar):
Specifies the width and height (in inches) of the figure window
to be created. If this value is not provided, the value specified
in `spectral.settings.imshow_figure_size` will be used.
`fignum` (optional, integer):
Specifies the figure number of an existing matplotlib figure. If
this argument is None, a new figure will be created.
`title` (str):
The title to be displayed above the image.
Keywords:
Keywords accepted by :func:`~spectral.graphics.graphics.get_rgb` or
:func:`matplotlib.imshow` will be passed on to the appropriate
function.
This function defaults the color scale (imshow's "cmap" keyword) to
"gray". To use imshow's default color scale, call this function with
keyword `cmap=None`.
Returns:
An `ImageView` object, which can be subsequently used to refine the
image display.
See :class:`~spectral.graphics.spypylab.ImageView` for additional details.
Examples:
Show a true color image of a hyperspectral image:
>>> data = open_image('92AV3C.lan').load()
>>> view = imshow(data, bands=(30, 20, 10))
Show ground truth in a separate window:
>>> classes = open_image('92AV3GT.GIS').read_band(0)
>>> cview = imshow(classes=classes)
Overlay ground truth data on the data display:
>>> view.set_classes(classes)
>>> view.set_display_mode('overlay')
Show RX anomaly detector results in the view and a zoom window showing
true color data:
>>> x = rx(data)
>>> zoom = view.open_zoom()
>>> view.set_data(x)
Note that pressing ctrl-lclick with the mouse in the main window will
cause the zoom window to pan to the clicked location.
Opening zoom windows, changing display modes, and other functions can
also be achieved via keys mapped directly to the displayed image. Press
"h" with focus on the displayed image to print a summary of mouse/
keyboard commands accepted by the display.
'''
import matplotlib.pyplot as plt
from spectral import settings
from .graphics import get_rgb
set_mpl_interactive()
view = ImageView()
if data is not None:
view.set_data(data, bands, **kwargs)
if classes is not None:
view.set_classes(classes, colors, **kwargs)
if source is not None:
view.set_source(source)
elif data is not None and len(data.shape) == 3 and data.shape[2] > 3:
view.set_source(data)
if fignum is not None or figsize is not None:
fig = plt.figure(num=fignum, figsize=figsize)
view.show(fignum=fig.number)
else:
view.show()
if title is not None:
view.set_title(title)
return view
def plot(data, source=None):
'''
Creates an x-y plot.
USAGE: plot(data)
If data is a vector, all the values in data will be drawn in a
single series. If data is a 2D array, each column of data will
be drawn as a separate series.
'''
import matplotlib.pyplot as plt
import spectral
set_mpl_interactive()
if source is not None and hasattr(source, 'bands') and \
source.bands.centers is not None:
xvals = source.bands.centers
else:
xvals = list(range(data.shape[-1]))
if data.ndim == 1:
data = data[np.newaxis, :]
data = data.reshape(-1, data.shape[-1])
if source is not None and hasattr(source, 'metadata') and \
'bbl' in source.metadata:
# Do not plot bad bands
data = np.array(data)
data[:, np.array(source.metadata['bbl']) == 0] = None
for x in data:
p = plt.plot(xvals, x)
spectral._xyplot = p
plt.grid(1)
if source is not None and hasattr(source, 'bands'):
if source.bands.band_quantity is not None:
xlabel = source.bands.band_quantity
else:
xlabel = ''
if source.bands.band_unit is not None:
if len(xlabel) > 0:
xlabel += ' (%s)' % source.bands.band_unit
else:
xlabel = str(source.bands.band_unit)
plt.xlabel(xlabel)
return p
def set_mpl_interactive():
'''Ensure matplotlib is in interactive mode.'''
import matplotlib.pyplot as plt
if not plt.isinteractive():
plt.interactive(True)
|