forked from ColinTalbert/sahm
-
Notifications
You must be signed in to change notification settings - Fork 0
/
SahmSpatialOutputViewer.py
1252 lines (1028 loc) · 49 KB
/
SahmSpatialOutputViewer.py
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
###############################################################################
##
## Copyright (C) 2010-2012, USGS Fort Collins Science Center.
## All rights reserved.
## Contact: talbertc@usgs.gov
##
## This file is part of the Software for Assisted Habitat Modeling package
## for VisTrails.
##
## "Redistribution and use in source and binary forms, with or without
## modification, are permitted provided that the following conditions are met:
##
## - Redistributions of source code must retain the above copyright notice,
## this list of conditions and the following disclaimer.
## - Redistributions in binary form must reproduce the above copyright
## notice, this list of conditions and the following disclaimer in the
## documentation and/or other materials provided with the distribution.
## - Neither the name of the University of Utah nor the names of its
## contributors may be used to endorse or promote products derived from
## this software without specific prior written permission.
##
## THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
## AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
## THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
## PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
## EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
## PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
## OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
## WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
## OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE."
##
## Although this program has been used by the U.S. Geological Survey (USGS),
## no warranty, expressed or implied, is made by the USGS or the
## U.S. Government as to the accuracy and functioning of the program and
## related program material nor shall the fact of distribution constitute
## any such warranty, and no responsibility is assumed by the USGS
## in connection therewith.
##
## Any use of trade, firm, or product names is for descriptive purposes only
## and does not imply endorsement by the U.S. Government.
###############################################################################
################################################################################
# ImageViewer widgets/toolbar implementation
################################################################################
import os
import csv
import gc
import itertools
import utils
import math
from PyQt4 import QtCore, QtGui
from core.modules.vistrails_module import Module
from packages.spreadsheet.basic_widgets import SpreadsheetCell, CellLocation
from packages.spreadsheet.spreadsheet_cell import QCellWidget, QCellToolBar
from packages.spreadsheet.spreadsheet_controller import spreadsheetController
from sahm_picklists import OutputRaster
from utils import map_ports
from utils import getRasterParams
from utils import print_timing
from pySAHM.utilities import dbfreader as dbfreader
import matplotlib
from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas
from matplotlib.backends.backend_qt4agg import NavigationToolbar2QTAgg as NavigationToolbar
#from matplotlib.backends.backend_qt4 import FigureCanvasQT as FigureCanvas
#from matplotlib.backends.backend_qt4 import NavigationToolbar2QT as NavigationToolbar
from matplotlib.figure import Figure
from matplotlib.offsetbox import AnchoredOffsetbox, TextArea
import matplotlib.colors as colors
import numpy as np
from osgeo import gdal, gdalconst
from core.packagemanager import get_package_manager
import utils
import pySAHM.utilities as utilities
import GenerateModuleDoc as GenModDoc
doc_file = os.path.abspath(os.path.join(os.path.dirname(__file__), "documentation.xml"))
GenModDoc.load_documentation(doc_file)
class SAHMSpatialOutputViewerCell(SpreadsheetCell):
"""
SAHMModelOutputViewerCell is a VisTrails Module that
displays the various output from a SAHM Model run in a single cell
"""
__doc__ = GenModDoc.construct_module_doc('SAHMSpatialOutputViewerCell')
_input_ports = [("row", "(edu.utah.sci.vistrails.basic:Integer)"),
("column", "(edu.utah.sci.vistrails.basic:Integer)"),
('display_presense_points', '(edu.utah.sci.vistrails.basic:Boolean)', {'defaults':'["False"]', 'optional':False}),
('display_absense_points', '(edu.utah.sci.vistrails.basic:Boolean)', {'defaults':'["False"]', 'optional':False}),
('display_background_points', '(edu.utah.sci.vistrails.basic:Boolean)', {'defaults':'["False"]', 'optional':False}),
('initial_raster_display', '(gov.usgs.sahm:OutputRaster:Other)', {'defaults':'["Probability"]'}),
('model_workspace', '(edu.utah.sci.vistrails.basic:Directory)')]
#all inputs are determined relative to the model_workspace
@classmethod
def provide_input_port_documentation(cls, port_name):
return GenModDoc.construct_port_doc(cls, port_name, 'in')
@classmethod
def provide_output_port_documentation(cls, port_name):
return GenModDoc.construct_port_doc(cls, port_name, 'out')
def __init__(self):
SpreadsheetCell.__init__(self)
self.port_map = {'display_presense_points': ("display_pres_points", None, True),
'display_absense_points': ("display_abs_points", None, True),
'display_background_points': ("display_backs_points", None, True),
'initial_raster_display': ("initial_raster", None, True),
"model_workspace": ("model_workspace", None, True)}
# @print_timing
def compute(self):
inputs = {}
inputs = map_ports(self, self.port_map)
# inputs["model_workspace"] = self.forceGetInputFromPort('model_workspace').name
#
# for port in ['display_presense_points', 'display_absense_points', 'display_background_points', 'initial-raster_display']:
# inputs[port] = self.forceGetInputFromPort(port)
# pm = get_package_manager()
# hasVisWall = pm.has_package('gov.usgs.VisWallServer')
# if hasVisWall:
# row = self.forceGetInputFromPort("row", -1)
# col = self.forceGetInputFromPort("column", -1)
# from packages.VisWallServer import display_sahm_output
# display_sahm_output(row, col, {"model_workspace": inputs["model_workspace"]}, 'SpatialOutput')
# return
inputs["model_dir"] = os.path.normcase(inputs["model_workspace"])
for model_output in ['prob', 'bin', 'resid', 'mess', 'MoD']:
try:
inputs[model_output +"_map"] = os.path.join(inputs["model_dir"],
utils.find_file(inputs["model_dir"], "_" + model_output + "_map.tif"))
except:
inputs[model_output + "_map"] = ""
try:
inputs["mds"] = self.find_mds(inputs["model_dir"])
except RuntimeError:
inputs["mds"] = ""
inputs["model_tag"] = os.path.split(inputs["model_dir"])[1]
if self.hasInputFromPort("row"):
if not self.location:
self.location = CellLocation()
self.location.row = self.getInputFromPort('row') - 1
if self.hasInputFromPort("column"):
if not self.location:
self.location = CellLocation()
self.location.col = self.getInputFromPort('column') - 1
if self.inputPorts.has_key('Location'):
self.location = self.inputPorts['Location'][0].obj
# if self.hasInputFromPort("max_cells_dimension"):
# inputs["max_cells_dimension"] = self.getInputFromPort('max_cells_dimension')
# else:
# inputs["max_cells_dimension"] = [item for item in self._input_ports if item[0] == 'max_cells_dimension'][0][2]['defaults']
if utils.checkIfModelFinished(inputs["model_dir"]):
self.local_displayAndWait(inputs)
# @print_timing
def local_displayAndWait(self, inputs):
self.displayAndWait(SAHMSpatialOutputViewerCellWidget,
inputs)
def find_mds(self, model_dir):
"""returns the path to the mds that was used to generate this
model output. While the text file that the R model produces
has an absolute path to the data this function assumes that
the mds file is in the session folder that this model output
folder is in. That is it looks for an mds with the same
file name in the parent folder of the model folder.
"""
model_text = os.path.join(model_dir,
utils.find_file(model_dir, "_output.txt"))
#assumed to be one level up from model folder.
session_folder = os.path.split(model_dir)[0]
f = open(model_text, 'rb')
lines = f.read().splitlines()
# grab the line after "Data:"
try:
originalMDS = [lines[i + 1] for i in range(len(lines))
if lines[i].startswith("Data:")][0].strip()
fname = os.path.split(originalMDS)[1]
mds_in_root = os.path.join(session_folder, fname)
if os.path.exists(originalMDS):
return originalMDS
elif os.path.exists(mds_in_root):
return mds_in_root
else:
raise RuntimeError('Valid input MDS file not found in Model text output.')
except IndexError:
raise RuntimeError('Valid input MDS file not found in Model text output.')
class SAHMSpatialOutputViewerCellWidget(QCellWidget):
"""
"""
def __init__(self, parent=None):
""" QGISCellWidget(parent: QWidget) -> QGISCellWidget
Initialize the widget with its central layout
"""
QCellWidget.__init__(self, parent)
self.displaylegend = True
centralLayout = QtGui.QVBoxLayout()
self.setLayout(centralLayout)
centralLayout.setMargin(0)
centralLayout.setSpacing(0)
self.create_main_frame()
self.fig.canvas.draw()
self.sync_changes = "all"
self.setAnimationEnabled(False)
self.displayTL = True
self.pointsLoaded = False
# @print_tming
def updateContents(self, inputs):
""" updateContents(inputs: dictionary) -> None
Update the widget contents based on the input data
"""
# print "SAHMSpatialOutputViewerCellWidget updateContents"
self.toolBarType = SAHMSpatialViewerToolBar
self.controlBarType = SAHMSpatialViewerToolBar
self.inputs = inputs
self.load_layers()
self.on_draw(UseMaxExt=True)
self.maxXlim, self.maxYlim = self.getMaxDisplayExtent()
self.axes.set_ylim(self.maxYlim, emit=False)
self.axes.set_xlim(self.maxXlim, emit=False)
self.fig.canvas.draw()
self.update()
# @print_timing
def create_main_frame(self):
self.setFocusPolicy(QtCore.Qt.ClickFocus)
self.dpi = 100
self.fig = Figure((5.0, 4.0), dpi=self.dpi)
# self.fig.subplots_adjust(left = 0.01, right=0.99, top=0.99, bottom=0.001)
self.fig.subplots_adjust(left = 0, right=1, top=1, bottom=0)
self.map_canvas = MyMapCanvas(self.fig)
self.map_canvas.mpl_connect('scroll_event', self.wheel_zoom)
# self.connect(self, QtCore.SIGNAL('keyPressEvent(QString)'),
# self.key_press)
self.map_canvas.mpl_connect('button_release_event', self.button_up)
self.map_canvas.mpl_connect('resize_event', self._resize)
self.add_axis()
self.mpl_toolbar = NavigationToolbar(self.map_canvas, None)
self.mpl_toolbar.pan()
# self.popMenu = popup_menu(self, self.mpl_toolbar)
self.popMenu = None
self.map_canvas.setContextMenuPolicy( QtCore.Qt.CustomContextMenu )
self.connect(self.map_canvas, QtCore.SIGNAL('customContextMenuRequested(const QPoint&)'), self.on_context_menu)
self.layout().addWidget(self.map_canvas)
def on_context_menu(self, point):
if self.popMenu is None:
self.popMenu = self.createPopupMenu()
self.popMenu.exec_(self.map_canvas.mapToGlobal(point))
def createPopupMenu(self):
sheet = self.findSheetTabWidget()
toolbar = SAHMSpatialViewerToolBar(sheet)
row, col = self.findCurrentCell()
toolbar.snapTo(row, col)
return toolbar.gen_popup_menu()
def getRasterParams(self, rasterfile):
return getRasterParams(rasterfile)
# @print_timing
def wheel_zoom(self, event):
#zoom in or out centered on the current cursor position
inv = self.axes.transData.inverted()
curX, curY = inv.transform((event.x, event.y))
curL, curR = self.axes.get_xlim()
curB, curT = self.axes.get_ylim()
width = curR - curL
height = curT - curB
steps = -1 * event.step / 0.25
factor = steps / 35
#sanity check
if factor > 0.5:
factor = 0.5
if factor < -0.5:
factor = -0.5
newWidth = width * (1.0 - factor)
newHeight = height * (1.0 - factor)
dWidth = width - newWidth
dHeight = height -newHeight
pcntLofX = 1 - (width - (curX - curL)) / width
pcntUnderTop = (height - (curT - curY)) / height
newL = curL + (dWidth * pcntLofX)
newR = curR - (dWidth*(1-pcntLofX))
newB = curB + (dHeight * pcntUnderTop)
newT = curT - (dWidth * (1 - pcntUnderTop))
self.axes.set_xlim((newL, newR))
self.axes.set_ylim((newB, newT))
self.sync_extents()
def button_up(self, event):
if event.button == 1:
# self.pull_pixels()
self.sync_extents()
# @print_timing
def _resize(self, event):
self.pull_pixels()
# @print_timing
def pull_pixels(self):
# print "SAHMSpatialOutputViewerCellWidget _pull_pixels"
try:
self.rasterlayer.ax_update(self.axes)
except AttributeError:
pass
# @print_timing
def keyPressEvent(self, event):
if type(event) == QtGui.QKeyEvent and event.key() == QtCore.Qt.Key_T:
active_cells = self.getSelectedCellWidgets()
displayed = not self.displayTL
for cell in active_cells:
cell.displayTL = displayed
cell.on_draw()
cell.fig.canvas.draw()
cell.update()
def deleteLater(self):
""" deleteLater() -> None
Overriding PyQt deleteLater to free up resources
"""
self.fig.clf()
self.map_canvas.close()
gc.collect()
QCellWidget.deleteLater(self)
# @print_timing
def load_layers(self):
# print "SAHMSpatialOutputViewerCellWidget load_layers"
self.all_layers = {"prob_map":{"type":"raster", "title":"Probability" ,"categorical":False, "min":0, "max":1, 'cmap':matplotlib.cm.jet, "displayorder":9999, "displayed":False, "enabled":False, "file":""},
"bin_map":{"type":"raster", "title":"Binary probability" , "categorical":False, "min":0, "max":1, 'cmap':matplotlib.cm.Greys, "displayorder":9999, "displayed":False, "enabled":False, "file":""},
"resid_map":{"type":"raster", "title":"Residuals" , "categorical":False, "min":"pullfromdata", "max":"pullfromdata", 'cmap':matplotlib.cm.Accent, "displayorder":9999, "displayed":False, "enabled":False, "file":""},
"mess_map":{"type":"raster", "title":"Mess" , "categorical":False, "min":0, "max":"pullfromdata", "categories":"pullfromdata", 'cmap':matplotlib.cm.jet, "displayorder":9999, "displayed":False, "enabled":False, "file":""},
"MoD_map":{"type":"raster", "title":"MoD" , "categorical":True, "min":0, "max":"pullfromdata", 'cmap':matplotlib.cm.prism, "displayorder":9999, "num_breaks":7, "displayed":False, "enabled":False, "file":""},
"pres_points":{"type":"Vector", "title":"Presence", "color":(1,0,0), "displayorder":3, "num_breaks":7, "displayed":False, "enabled":True, "file":""},
"abs_points":{"type":"Vector", "title":"Absence", "color":(0,1,0), "displayorder":2, "num_breaks":7, "displayed":False, "enabled":True, "file":""},
"backs_points":{"type":"Vector", "title":"Background", "color":(0,0,0), "displayorder":1, "num_breaks":7, "displayed":False, "enabled":True, "file":""}}
#set the inital layers to display passed on passed in inputs
for layer in ["display_pres_points", "display_abs_points", "display_backs_points"]:
self.all_layers[layer.replace("display_", "")]["displayed"] = self.inputs[layer]
initial_map_dict = {'Probability':"prob_map", 'Binary Probability':"bin_map",
'Residuals':"resid_map", 'Mess':"mess_map", 'MoD':"MoD_map"}
self.all_layers[initial_map_dict[self.inputs['initial_raster']]]["displayed"] = True
for k,v in self.all_layers.items():
if k in self.inputs:
if os.path.exists(self.inputs[k]):
self.all_layers[k]["file"] = self.inputs[k]
self.all_layers[k]["enabled"] = True
rasterparams = getRasterParams(self.all_layers[initial_map_dict[self.inputs['initial_raster']]]["file"])
self.maxExtent = [rasterparams["ulx"],rasterparams["lrx"],rasterparams["lry"],rasterparams["uly"]]
#make our specialty colormaps
if self.all_layers["resid_map"]['enabled']:
self.all_layers["resid_map"]["cmap"] = self.make_resid_cmap(self.all_layers["resid_map"])
if self.all_layers["MoD_map"]['enabled']:
self.all_layers["MoD_map"]["cmap"] = self.make_categorical_cmap(self.all_layers["MoD_map"])
# def set_maxExtent(self, width=1, height=1, portionRow=1, portionCol=1):
# rasterparams = getRasterParams(self.all_layers[self.initial_map_dict[self.inputs['initial_raster']]]["file"])
# cellWidth = (rasterparams["lrx"] - rasterparams["ulx"]) / width
# cellHeight = (rasterparams["uly"] - rasterparams["lry"]) / height
#
# ulx = rasterparams["ulx"] + ((portionCol) * cellWidth)
# lrx = rasterparams["ulx"] + ((portionCol + 1) * cellWidth)
# uly = rasterparams["uly"] - ((portionRow) * cellHeight)
# lry = rasterparams["uly"] - ((portionRow + 1) * cellHeight)
#
# self.maxExtent = [ulx, lrx, lry, uly]
# @print_timing
def loadPoints(self):
#initialize our arrays
for pointType in ['abs_points', 'pres_points', 'backs_points']:
self.all_layers[pointType]['x'] = []
self.all_layers[pointType]['y'] = []
if os.path.exists(self.inputs["mds"]):
mdsReader = csv.reader(open(self.inputs["mds"], 'r'))
header = mdsReader.next()
header2 = mdsReader.next()
header3 = mdsReader.next()
for row in mdsReader:
if int(row[2]) > 0:
self.all_layers['pres_points']['x'].append(float(row[0]))
self.all_layers['pres_points']['y'].append(float(row[1]))
elif int(row[2]) == 0:
self.all_layers['abs_points']['x'].append(float(row[0]))
self.all_layers['abs_points']['y'].append(float(row[1]))
else:
self.all_layers['backs_points']['x'].append(float(row[0]))
self.all_layers['backs_points']['y'].append(float(row[1]))
for pointType in ['abs_points', 'pres_points', 'backs_points']:
self.all_layers[pointType]["enabled"] = len(self.all_layers[pointType]['x']) > 0
def add_axis(self):
self.axes = self.fig.add_subplot(111, aspect='equal', adjustable='datalim')
self.axes.spines['right'].set_color('none')
self.axes.spines['top'].set_color('none')
self.axes.spines['bottom'].set_color('none')
self.axes.spines['left'].set_color('none')
self.axes.get_xaxis().set_visible(False)
self.axes.get_yaxis().set_visible(False)
def add_title(self, title):
at = AnchoredText(title,
loc=2, frameon=True, pad=.05, borderpad=0.2)
at.patch.set_boxstyle("round,rounding_size=0.2")
at.set_alpha(0.1)
self.axes.add_artist(at)
def make_resid_cmap(self, kwargs):
# vals = self.get_array_from_raster(kwargs['file'])
# vals = self.rasterlayer()
# vals_min = np.amin(vals)
# vals_max = np.amax(vals)
vals_min, vals_max = utils.getrasterminmax(kwargs['file'])
diff = vals_max - vals_min
zero_ratio = abs(vals_min) / diff
cdict = {'red': ((0.0, 1.0, 0.0),
(zero_ratio, 0.53, 1.0),
(1.0, 1.0, 1.0)),
'green': ((0.0, 1.0, 0.0),
(zero_ratio, 1, 1.0),
(1.0, 0.0, 1.0)),
'blue': ((0.0, 0.0, 1.0),
(zero_ratio, 1, 0.0),
(1.0, 0.0, 1.0))}
return matplotlib.colors.LinearSegmentedColormap('my_colormap',cdict,256)
def make_categorical_cmap(self, kwargs):
# vals = self.get_array_from_raster(kwargs['file'])
# vals = self.rasterlayer()
# uniques = np.unique(vals)
uniques = []
labels = []
vatdbf = kwargs['file'] + ".vat.dbf"
if os.path.exists(vatdbf):
#we'll pull labels from this file
f = open(vatdbf, 'rb')
db = list(dbfreader(f))
f.close()
for record in db[2:]:
uniques.append(record[0])
labels.append(record[1].strip())
kwargs['cbar_ticks'] = uniques
kwargs['cbar_labels'] = labels
return matplotlib.cm.get_cmap('Accent', len(uniques))
# @print_timing
def on_draw(self, UseMaxExt=False, passedExtent=None):
""" Completely clears then redraws the figure
There's probably a more efficient way to do this.
"""
# print "SAHMSpatialOutputViewerCellWidget _on_draw"
if passedExtent is not None:
curExtent = passedExtent
elif UseMaxExt:
curExtents = self.getMaxExtent()
else:
curExtents = self.get_extent()
# print "curExtents: ", curExtents
self.fig.clear()
self.add_axis()
displayed_keys = [key for key in self.all_layers.keys() if self.all_layers[key]['displayed']]
displayed_keys = sorted(displayed_keys, key=lambda disp_key: self.all_layers[disp_key]['displayorder'])
#loop through all_layers and display the enabled layers
#only displayed layers sorted by display order
title = self.inputs["model_tag"] + "\n"
for k in displayed_keys:
v = self.all_layers[k]
if v['enabled']:
if v['type'] == 'Vector':
self.add_vector(k)
else:
self.add_raster(v, curExtents)
title += self.all_layers[k]['title']
if self.displayTL:
self.add_title(title)
# @print_timing
def add_vector(self, layername):
kwargs = self.all_layers[layername]
if not self.pointsLoaded or not kwargs.has_key("x"):
self.loadPoints()
self.pointsLoaded = True
if self.all_layers[layername]['enabled']:
self.axes.scatter(kwargs['x'], kwargs['y'], s=10, c=kwargs['color'], linewidth=0.5, antialiased=True)
# @print_timing
def add_raster(self, kwargs, curExtents):
rasterfile = kwargs['file']
self.rasterlayer = RasterDisplay()
self.rasterlayer.setDims(self.axes)
self.rasterlayer.switch_raster(rasterfile)
# rasterparams = getRasterParams(rasterfile)
# map_extent = [rasterparams["ulx"],rasterparams["lrx"],rasterparams["lry"],rasterparams["uly"]]
#
#
## raster_array = self.get_array_from_raster(rasterfile)
# curXLim = self.axes.get_xlim()
# curYLim = self.axes.get_ylim()
# raster_array = self.rasterlayer(rasterparams["ulx"], rasterparams["lrx"], rasterparams["lry"], rasterparams["uly"])
# print "\n_addraster"
raster_array = self.rasterlayer(*curExtents)
#
# rmin = np.amin(raster_array)
# rmax = np.amax(raster_array)
if kwargs.get('categorical', False):
raster_plot = self.axes.imshow(raster_array, interpolation="nearest", cmap=kwargs['cmap'], origin='upper', extent=self.getDataExtent())
elif kwargs.get('threeband', False):
raster_plot = self.axes.imshow(raster_array, origin='upper', extent=self.getDataExtent())
else:
rmin = kwargs['min']
rmax = kwargs['max']
if kwargs["max"] == "pullfromdata" or \
kwargs["min"] == "pullfromdata":
min, max = utils.getrasterminmax(kwargs['file'])
if kwargs["max"] == "pullfromdata":
rmax = max
if kwargs["min"] == "pullfromdata":
rmin = min
norm = colors.Normalize(rmin, rmax)
# print "raster_array is None:", raster_array is None
# print "raster_array.size:", raster_array.size
# print "type(raster_array):", type(raster_array)
# print raster_array
if raster_array.size == 1:
print "raster_array is None!!!/n/n"
raster_array = np.empty([1960, 1080])
# print raster_array
raster_plot = self.axes.imshow(raster_array,interpolation="nearest", cmap=kwargs['cmap'], norm=norm, origin='upper', extent=self.getDataExtent())
if self.displayTL:
if kwargs['categorical']:
cb = self.fig.colorbar(raster_plot, ticks=kwargs['cbar_ticks'], orientation='vertical', pad=0.01, shrink=.9, fraction=.3, aspect=15)
cb.ax.set_yticklabels(kwargs['cbar_labels'])
else:
cb = self.fig.colorbar(raster_plot, orientation='horizontal', pad=0.01, fraction=.1, shrink=.9, aspect=30)
for t in cb.ax.get_xticklabels():
if kwargs['categorical']:
t.set_fontsize(5)
t.set_rotation(90)
else:
t.set_fontsize(7)
#
# def get_array_from_raster(self, raster_file):
# '''return a numpy array with the values from the raster_file
# if there are more than 10,000 rows or cols the data will be
# subsampled and self.map_ratio will be set.
# All nodata values will be removed
# '''
# ds = gdal.Open(raster_file, gdal.GA_ReadOnly)
# rasterparams = getRasterParams(raster_file)
# nrows = rasterparams["height"]
# ncols = rasterparams["width"]
# max_dimension = max([nrows, ncols])
# if max_dimension > self.inputs["max_cells_dimension"]:
# ratio = float(self.inputs["max_cells_dimension"]) / max_dimension
# nrows = int(ratio * nrows)
# ncols = int(ratio * ncols)
#
# try:
# ary = ds.GetRasterBand(1).ReadAsArray(buf_ysize=nrows, buf_xsize=ncols)
# ndval = ds.GetRasterBand(1).GetNoDataValue()
# except MemoryError:
# msgbox = QtGui.QMessageBox(self)
# msgbox.setText("This viewer cannot handle datasets this large.\nTry setting the max_cells_dimension to a smaller value.")
# msgbox.exec_()
# raise MemoryError
#
# return np.ma.masked_array(ary, mask=(ary==ndval))
def dumpToFile(self, filename):
pass
def saveToPDF(self, filename):
pass
def findSheetTabWidget(self):
""" findSheetTabWidget() -> QTabWidget
Find and return the sheet tab widget
"""
p = self.parent()
while p:
if hasattr(p, 'isSheetTabWidget'):
if p.isSheetTabWidget()==True:
return p
p = p.parent()
return None
def findCurrentCell(self):
sheet = self.findSheetTabWidget()
all_cells = list(itertools.product(range(sheet.getDimension()[0]), range(sheet.getDimension()[1])))
for row, col in all_cells:
cell = sheet.getCell(row, col)
if cell is self:
return row, col
return -1, -1
def getSAHMSpatialsInCellList(self, sheet, cells):
""" Get the list of SAHM spatial outputviewers
inside a list of (row, column) cells.
"""
SAHMspatials = []
for (row, col) in cells:
cell = sheet.getCell(row, col)
if hasattr(cell, 'make_resid_cmap'):
SAHMspatials.append(cell)
return SAHMspatials
def getSelectedCellWidgets(self):
sheet = self.findSheetTabWidget()
if sheet:
selected_cells = sheet.getSelectedLocations()
return self.getSAHMSpatialsInCellList(sheet, selected_cells)
return []
def get_allCellWidgets(self):
sheet = self.findSheetTabWidget()
if sheet:
all_cells = list(itertools.product(range(sheet.getDimension()[0]), range(sheet.getDimension()[1])))
return self.getSAHMSpatialsInCellList(sheet, all_cells)
return []
def get_active_cells(self):
if self.sync_changes == "all":
return self.get_allCellWidgets()
elif self.sync_changes == "sel":
return self.getSelectedCellWidgets()
else:
return [self]
def getActionByTag(self, tag):
if self.popMenu is None:
self.popMenu = self.createPopupMenu()
for action in self.popMenu.actions():
try:
if action.tag == tag:
return action
except AttributeError:
pass
return None
#Functions dealing with managing extents
# @print_timing
def set_extent(self, ylim, xlim):
# print "_set_extent"
self.axes.set_ylim(ylim, emit=False)
self.axes.set_xlim(xlim, emit=False)
self.pull_pixels()
self.fig.canvas.draw()
self.update()
# @print_timing
def get_extent(self):
# print "_get_extent"
return list(self.axes.get_xlim()) + list(self.axes.get_ylim())
def getMaxExtent(self):
return self.maxExtent
def getDataExtent(self):
return self.maxExtent
def getMaxDisplayExtent(self):
return self.axes.get_xlim(), self.axes.get_ylim()
def zoomFull(self):
self.axes.set_xlim(self.maxXlim)
self.axes.set_ylim(self.maxYlim)
self.sync_extents()
def sync_extents(self):
# print "_sync_extents"
for spatialViewer in self.get_active_cells():
spatialViewer.set_extent(self.axes.get_ylim(), self.axes.get_xlim())
spatialViewer.pull_pixels()
spatialViewer.map_canvas.draw()
class MyMapCanvas(FigureCanvas):
def __init__(self, fig):
FigureCanvas.__init__(self, fig)
# self._cursorx = None
# @print_timing
def resizeEvent(self, event):
if not event.size().height() == 0:
FigureCanvas.resizeEvent(self, event)
#these are not currently working so they will need to be commented out
# def enterEvent(self, event):
# FigureCanvas.enterEvent(self, event)
# if (self._cursorx is not None and
# QtGui.QApplication.overrideCursor() is None):
# QtGui.QApplication.setOverrideCursor(self._cursorx)
# def leaveEvent(self, event):
#
## FigureCanvas.leaveEvent(self, event)
# self._cursorx = QtGui.QCursor(QtGui.QApplication.overrideCursor())
# QtGui.QApplication.restoreOverrideCursor()
class RasterDisplay(object):
'''The idea behind this is from
http://matplotlib.sourceforge.net/examples/event_handling/viewlims.py
basically we want to only query as much data as we have screen pixels for.
When the user zooms, pans, resizes we'll go back to the original display
and get another set of pixels.
This object has a pointer to the original raster and functions
for switching the input file or getting an array of pixel values
'''
def __init__(self, threeBand=False, NoDataValue="ExtractFromFile", width=300, height=300):
self.height = height
self.width = width
self.threeBand = threeBand
self.NoDataValue = NoDataValue
# @prit_timing
def switch_raster(self, rasterfile):
self.rasterfile = rasterfile
self.rasterparams = getRasterParams(rasterfile)
# @print_timing
def __call__(self, xstart, xend, ystart, yend):
# print "RasterDisplay __call__"
self.x = np.linspace(xstart, xend, self.width)
self.y = np.linspace(ystart, yend, self.height).reshape(-1,1)
#pull the pixels we need, no more
ds = gdal.Open(self.rasterfile, gdal.GA_ReadOnly)
xform = ds.GetGeoTransform()
if xstart < xform[0]:
xstart = xform[0]
if xend > (xform[0] + (ds.RasterXSize * xform[1])):
xend = (xform[0] + (ds.RasterXSize * xform[1]))
if ystart < (xform[3] + (ds.RasterYSize * xform[5])):
ystart = (xform[3] + (ds.RasterYSize * xform[5]))
if yend > xform[3]:
yend = xform[3]
ncols = int((xend - xstart) / xform[1])
nrows = int((yend - ystart) / abs(xform[5]))
xOffset = int((xstart - xform[0]) / xform[1])
yOffset = int((yend- xform[3]) / xform[5])
if xOffset + ncols > ds.RasterXSize:
xOffset = max(0, ds.RasterXSize - xOffset)
if xOffset < 0:
xOffset = 0
if yOffset + nrows > ds.RasterYSize:
yOffset = 0
if yOffset < 0:
yOffset = 0
if ncols + xOffset > ds.RasterXSize:
ncols = ds.RasterXSize - xOffset
if ncols < 0:
ncols = ds.RasterXSize
if nrows + yOffset > ds.RasterYSize:
nrows = ds.RasterYSize - yOffset
if nrows < 0:
nrows = ds.RasterYSize
# print "rows, cols: ", ncols, nrows
# print "pixelspulled: ", self.height, self.width
if self.threeBand:
from PIL import Image
r = ds.GetRasterBand(1)
g = ds.GetRasterBand(2)
b = ds.GetRasterBand(3)
r1 = r.ReadAsArray(xoff=xOffset, yoff=yOffset,
win_xsize=ncols, win_ysize=nrows,
buf_ysize=self.height, buf_xsize=self.width)
b1 = b.ReadAsArray(xoff=xOffset, yoff=yOffset,
win_xsize=ncols, win_ysize=nrows,
buf_ysize=self.height, buf_xsize=self.width)
g1 = g.ReadAsArray(xoff=xOffset, yoff=yOffset,
win_xsize=ncols, win_ysize=nrows,
buf_ysize=self.height, buf_xsize=self.width)
imR = Image.fromarray(r1)
imG = Image.fromarray(g1)
imB = Image.fromarray(b1)
return Image.merge('RGB', (imR, imG, imB))
else:
ary = ds.GetRasterBand(1).ReadAsArray(xoff=xOffset, yoff=yOffset,
win_xsize=ncols, win_ysize=nrows,
buf_ysize=self.height, buf_xsize=self.width)
if self.NoDataValue == "ExtractFromFile":
ndval = utils.getNDVal(self.rasterfile)
else:
ndval = float(self.NoDataValue)
if ary is None or ary.size == 1:
print "raster_array is None!!!/n/n"
return np.empty([1960, 1080])
else:
return np.ma.masked_array(ary, mask=(ary==ndval))
# @print_timing
def setDims(self, ax):
#Get the number of points from the number of pixels in the window
dims = ax.axesPatch.get_window_extent().bounds
# print "RasterDisplay setDims: ", dims
self.width = int(dims[2] + 0.5)
self.height = int(dims[3] + 0.5)
# @print_timing
def ax_update(self, ax):
ax.set_autoscale_on(False) # Otherwise, infinite loop
self.setDims(ax)
# print "RasterDisplay ax_update"
#Get the range for the new area
xstart,ystart,xdelta,ydelta = ax.axes.viewLim.bounds
xend = xstart + xdelta
yend = ystart + ydelta
factor = 0.1 #we want to pull more pixels than we absolutely need
#so that we don't get white edges
xBuff = (xend - xstart) * factor
yBuff = (yend - ystart) * factor
xstart = xstart - xBuff
ystart = ystart - yBuff
xend = xend + xBuff
yend = yend + yBuff
# print " Before: "
# print " xlim: ", int(xstart), int(xend)
# print " ylim: ", int(ystart), int(yend)
#reel these values in if they are outside our bounds
for bound in ['xstart', 'xend']:
if eval(bound) < self.rasterparams["ulx"]:
exec(bound + " = " + str(self.rasterparams["ulx"]))
if eval(bound) > self.rasterparams["lrx"]:
exec(bound + " = " + str(self.rasterparams["lrx"]))
for bound in ['ystart', 'yend']:
if eval(bound) < self.rasterparams["lry"]:
exec(bound + " = " + str(self.rasterparams["lry"]))
if eval(bound) > self.rasterparams["uly"]:
exec(bound + " = " + str(self.rasterparams["uly"]))
# Update the image object with our new data and extent
im = ax.images[-1]
# print " After: "
# print " xlim: ", int(xstart), int(xend)
# print " ylim: ", int(ystart), int(yend)
im.set_data(self.__call__(xstart, xend, ystart, yend))
im.set_extent((xstart, xend, ystart, yend))
ax.figure.canvas.draw_idle()
class fullExtent(QtGui.QAction):
def __init__(self, parent=None):
icon = os.path.abspath(os.path.join(
os.path.dirname(__file__), "Images", "world.png"))
QtGui.QAction.__init__(self,
QtGui.QIcon(icon),
"Full Extent",
parent)
self.setCheckable(False)
def triggeredSlot(self):
cellWidget = self.toolBar.getSnappedWidget()
cellWidget.zoomFull()
class viewTitleLegend(QtGui.QAction):
def __init__(self, parent=None):
icon = os.path.abspath(os.path.join(
os.path.dirname(__file__), "Images", "titlelegend.png"))
QtGui.QAction.__init__(self,
QtGui.QIcon(icon),
"Show/Hide Title and Legend",
parent)
self.setCheckable(True)
self.setChecked(True)
def triggeredSlot(self):
cellWidget = self.toolBar.getSnappedWidget()
active_cells = cellWidget.get_active_cells()
for cell in active_cells:
xlim = cell.axes.get_xlim()
ylim = cell.axes.get_ylim()
cell.displayTL = self.isChecked()
cell.on_draw()
cell.fig.canvas.draw()
cell.update()
cell.axes.set_xlim(xlim)
cell.axes.set_ylim(ylim)
class sync_changes(QtGui.QAction):
def __init__(self, parent=None):