Work at SourceForge, help us to make it a better place! We have an immediate need for a Support Technician in our San Francisco or Denver office.

Close

[r282]: trunk / gnuplot-py / PlotItems.py Maximize Restore History

Download this file

PlotItems.py    754 lines (579 with data), 26.2 kB

  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
# $Id: PlotItems.py 282 2005-12-18 13:19:43Z mhagger $
# Copyright (C) 1998-2003 Michael Haggerty <mhagger@alum.mit.edu>
#
# This file is licensed under the GNU Lesser General Public License
# (LGPL). See LICENSE.txt for details.
"""PlotItems.py -- Objects that can be plotted by Gnuplot.
This module contains several types of PlotItems. PlotItems can be
plotted by passing them to a Gnuplot.Gnuplot object. You can derive
your own classes from the PlotItem hierarchy to customize their
behavior.
"""
__cvs_version__ = '$Revision: 282 $'
import os, string, tempfile, types
try:
from cStringIO import StringIO
except ImportError:
from StringIO import StringIO
import Numeric
import gp, utils, Errors
class _unset:
"""Used to represent unset keyword arguments."""
pass
class PlotItem:
"""Plotitem represents an item that can be plotted by gnuplot.
For the finest control over the output, you can create 'PlotItems'
yourself with additional keyword options, or derive new classes
from 'PlotItem'.
The handling of options is complicated by the attempt to allow
options and their setting mechanism to be inherited conveniently.
Note first that there are some options that can only be set in the
constructor then never modified, and others that can be set in the
constructor and/or modified using the 'set_option()' member
function. The former are always processed within '__init__'. The
latter are always processed within 'set_option', which is called
by the constructor.
'set_option' is driven by a class-wide dictionary called
'_option_list', which is a mapping '{ <option> : <setter> }' from
option name to the function object used to set or change the
option. <setter> is a function object that takes two parameters:
'self' (the 'PlotItem' instance) and the new value requested for
the option. If <setter> is 'None', then the option is not allowed
to be changed after construction and an exception is raised.
Any 'PlotItem' that needs to add options can add to this
dictionary within its class definition. Follow one of the
examples in this file. Alternatively it could override the
'set_option' member function if it needs to do wilder things.
Members:
'_basecommand' -- a string holding the elementary argument that
must be passed to gnuplot's `plot' command for this item;
e.g., 'sin(x)' or '"filename.dat"'.
'_options' -- a dictionary of (<option>,<string>) tuples
corresponding to the plot options that have been set for
this instance of the PlotItem. <option> is the option as
specified by the user; <string> is the string that needs to
be set in the command line to set that option (or None if no
string is needed). Example::
{'title' : ('Data', 'title "Data"'),
'with' : ('linespoints', 'with linespoints')}
"""
# For _option_list explanation, see docstring for PlotItem.
_option_list = {
'axes' : lambda self, axes: self.set_string_option(
'axes', axes, None, 'axes %s'),
'with' : lambda self, with: self.set_string_option(
'with', with, None, 'with %s'),
'title' : lambda self, title: self.set_string_option(
'title', title, 'notitle', 'title "%s"'),
}
# order in which options need to be passed to gnuplot:
_option_sequence = [
'binary',
'index', 'every', 'thru', 'using', 'smooth',
'axes', 'title', 'with'
]
def __init__(self, **keyw):
"""Construct a 'PlotItem'.
Keyword options:
'with=<string>' -- choose how item will be plotted, e.g.,
with='points 3 3'.
'title=<string>' -- set the title to be associated with the item
in the plot legend.
'title=None' -- choose 'notitle' option (omit item from legend).
Note that omitting the title option is different than setting
'title=None'; the former chooses gnuplot's default whereas the
latter chooses 'notitle'.
"""
self._options = {}
self.set_option(**keyw)
def get_option(self, name):
"""Return the setting of an option. May be overridden."""
try:
return self._options[name][0]
except:
raise KeyError('option %s is not set!' % name)
def set_option(self, **keyw):
"""Set or change a plot option for this PlotItem.
See documentation for '__init__' for information about allowed
options. This function can be overridden by derived classes
to allow additional options, in which case those options will
also be allowed by '__init__' for the derived class. However,
it is easier to define a new '_option_list' variable for the
derived class.
"""
for (option, value) in keyw.items():
try:
setter = self._option_list[option]
except KeyError:
raise Errors.OptionError('%s=%s' % (option,value))
if setter is None:
raise Errors.OptionError(
'Cannot modify %s option after construction!', option)
else:
setter(self, value)
def set_string_option(self, option, value, default, fmt):
"""Set an option that takes a string value."""
if value is None:
self._options[option] = (value, default)
elif type(value) is types.StringType:
self._options[option] = (value, fmt % value)
else:
Errors.OptionError('%s=%s' % (option, value,))
def clear_option(self, name):
"""Clear (unset) a plot option. No error if option was not set."""
try:
del self._options[name]
except KeyError:
pass
def get_base_command_string(self):
raise NotImplementedError()
def get_command_option_string(self):
cmd = []
for opt in self._option_sequence:
(val,str) = self._options.get(opt, (None,None))
if str is not None:
cmd.append(str)
return string.join(cmd)
def command(self):
"""Build the plot command to be sent to gnuplot.
Build and return the plot command, with options, necessary to
display this item. If anything else needs to be done once per
plot, it can be done here too.
"""
return string.join([
self.get_base_command_string(),
self.get_command_option_string(),
])
def pipein(self, f):
"""Pipe necessary inline data to gnuplot.
If the plot command requires data to be put on stdin (i.e.,
'plot "-"'), this method should put that data there. Can be
overridden in derived classes.
"""
pass
class Func(PlotItem):
"""Represents a mathematical expression to plot.
Func represents a mathematical expression that is to be computed by
gnuplot itself, as if you would type for example::
gnuplot> plot sin(x)
into gnuplot itself. The argument to the contructor is a string
that should be a mathematical expression. Example::
g.plot(Func('sin(x)', with='line 3'))
As shorthand, a string passed to the plot method of a Gnuplot
object is also treated as a Func::
g.plot('sin(x)')
"""
def __init__(self, function, **keyw):
PlotItem.__init__(self, **keyw)
self.function = function
def get_base_command_string(self):
return self.function
class _FileItem(PlotItem):
"""A PlotItem representing a file that contains gnuplot data.
This class is not meant for users but rather as a base class for
other types of FileItem.
"""
_option_list = PlotItem._option_list.copy()
_option_list.update({
'binary' : lambda self, binary: self.set_option_binary(binary),
'index' : lambda self, value: self.set_option_colonsep('index', value),
'every' : lambda self, value: self.set_option_colonsep('every', value),
'using' : lambda self, value: self.set_option_colonsep('using', value),
'smooth' : lambda self, smooth: self.set_string_option(
'smooth', smooth, None, 'smooth %s'
),
})
def __init__(self, filename, **keyw):
"""Represent a PlotItem that gnuplot treates as a file.
This class holds the information that is needed to construct
the plot command line, including options that are specific to
file-like gnuplot input.
<filename> is a string representing the filename to be passed
to gnuplot within quotes. It may be the name of an existing
file, '-' for inline data, or the name of a named pipe.
Keyword arguments:
'using=<int>' -- plot that column against line number
'using=<tuple>' -- plot using a:b:c:d etc. Elements in
the tuple that are None are output as the empty
string.
'using=<string>' -- plot `using <string>' (allows gnuplot's
arbitrary column arithmetic)
'every=<value>' -- plot 'every <value>'. <value> is
formatted as for 'using' option.
'index=<value>' -- plot 'index <value>'. <value> is
formatted as for 'using' option.
'binary=<boolean>' -- data in the file is in binary format
(this option is only allowed for grid data for splot).
'smooth=<string>' -- smooth the data. Option should be
'unique', 'csplines', 'acsplines', 'bezier', or
'sbezier'.
The keyword arguments recognized by 'PlotItem' can also be
used here.
Note that the 'using' option is interpreted by gnuplot, so
columns must be numbered starting with 1.
By default, gnuplot uses the name of the file plus any 'using'
option as the dataset title. If you want another title, set
it explicitly using the 'title' option.
"""
self.filename = filename
PlotItem.__init__(self, **keyw)
def get_base_command_string(self):
return gp.double_quote_string(self.filename)
def set_option_colonsep(self, name, value):
if value is None:
self.clear_option(name)
elif type(value) in [types.StringType, types.IntType]:
self._options[name] = (value, '%s %s' % (name, value,))
elif type(value) is types.TupleType:
subopts = []
for subopt in value:
if subopt is None:
subopts.append('')
else:
subopts.append(str(subopt))
self._options[name] = (
value,
'%s %s' % (name, string.join(subopts, ':'),),
)
else:
raise Errors.OptionError('%s=%s' % (name, value,))
def set_option_binary(self, binary):
if binary:
if not gp.GnuplotOpts.recognizes_binary_splot:
raise Errors.OptionError(
'Gnuplot.py is currently configured to reject binary data')
self._options['binary'] = (1, 'binary')
else:
self._options['binary'] = (0, None)
class _NewFileItem(_FileItem):
def __init__(self, content, filename=None, **keyw):
binary = keyw.get('binary', 0)
if binary:
mode = 'wb'
else:
mode = 'w'
if filename:
# This is a permanent file
self.temp = False
f = open(filename, mode)
else:
self.temp = True
if hasattr(tempfile, 'mkstemp'):
# Use the new secure method of creating temporary files:
(fd, filename,) = tempfile.mkstemp(
suffix='.gnuplot', text=(not binary)
)
f = os.fdopen(fd, mode)
else:
# for backwards compatibility to pre-2.3:
filename = tempfile.mktemp()
f = open(filename, mode)
f.write(content)
f.close()
# If the user hasn't specified a title, set it to None so
# that the name of the temporary file is not used:
if self.temp and 'title' not in keyw:
keyw['title'] = None
_FileItem.__init__(self, filename, **keyw)
def __del__(self):
if self.temp:
os.unlink(self.filename)
class _InlineFileItem(_FileItem):
"""A _FileItem that actually indicates inline data.
"""
def __init__(self, content, **keyw):
# If the user hasn't specified a title, set it to None so that
# '-' is not used:
if 'title' not in keyw:
keyw['title'] = None
if keyw.get('binary', 0):
raise Errors.OptionError('binary inline data is not supported')
_FileItem.__init__(self, '-', **keyw)
if content[-1] == '\n':
self.content = content
else:
self.content = content + '\n'
def pipein(self, f):
f.write(self.content + 'e\n')
if gp.GnuplotOpts.support_fifo:
import threading
class _FIFOWriter(threading.Thread):
"""Create a FIFO (named pipe), write to it, then delete it.
The writing takes place in a separate thread so that the main
thread is not blocked. The idea is that once the writing is
finished we know that gnuplot is done with the data that were in
the file so we can delete the file. This technique removes the
ambiguity about when the temporary files should be deleted.
Since the tempfile module does not provide an easy, secure way
to create a FIFO without race conditions, we instead create a
temporary directory using mkdtemp() then create the FIFO
within that directory. When the writer thread has written the
full information to the FIFO, it deletes both the FIFO and the
temporary directory that contained it.
"""
def __init__(self, content, mode='w'):
self.content = content
self.mode = mode
if hasattr(tempfile, 'mkdtemp'):
# Make the file within a temporary directory that is
# created securely:
self.dirname = tempfile.mkdtemp(suffix='.gnuplot')
self.filename = os.path.join(self.dirname, 'fifo')
else:
# For backwards compatibility pre-2.3, just use
# mktemp() to create filename:
self.dirname = None
self.filename = tempfile.mktemp()
threading.Thread.__init__(
self,
name=('FIFO Writer for %s' % (self.filename,)),
)
os.mkfifo(self.filename)
self.start()
def run(self):
f = open(self.filename, self.mode)
f.write(self.content)
f.close()
os.unlink(self.filename)
if self.dirname is not None:
os.rmdir(self.dirname)
class _FIFOFileItem(_FileItem):
"""A _FileItem based on a FIFO (named pipe).
This class depends on the availablity of os.mkfifo(), which only
exists under Unix.
"""
def __init__(self, content, **keyw):
# If the user hasn't specified a title, set it to None so that
# the name of the temporary FIFO is not used:
if 'title' not in keyw:
keyw['title'] = None
_FileItem.__init__(self, '', **keyw)
self.content = content
if keyw.get('binary', 0):
self.mode = 'wb'
else:
self.mode = 'w'
def get_base_command_string(self):
"""Create the gnuplot command for plotting this item.
The basecommand is different each time because each FIFOWriter
creates a new FIFO.
"""
# Create a new FIFO and a thread to write to it. Retrieve the
# filename of the FIFO to be used in the basecommand.
fifo = _FIFOWriter(self.content, self.mode)
return gp.double_quote_string(fifo.filename)
def File(filename, **keyw):
"""Construct a _FileItem object referring to an existing file.
This is a convenience function that just returns a _FileItem that
wraps the filename.
<filename> is a string holding the filename of an existing file.
The keyword arguments are the same as those of the _FileItem
constructor.
"""
if type(filename) is not types.StringType:
raise Errors.OptionError(
'Argument (%s) must be a filename' % (filename,)
)
return _FileItem(filename, **keyw)
def Data(*set, **keyw):
"""Create and return a _FileItem representing the data from *set.
Create a '_FileItem' object (which is a type of 'PlotItem') out of
one or more Float Python Numeric arrays (or objects that can be
converted to a Float Numeric array). If the routine is passed a
single with multiple dimensions, then the last index ranges over
the values comprising a single data point (e.g., [<x>, <y>,
<sigma>]) and the rest of the indices select the data point. If
passed a single array with 1 dimension, then each point is
considered to have only one value (i.e., by default the values
will be plotted against their indices). If the routine is passed
more than one array, they must have identical shapes, and then
each data point is composed of one point from each array. E.g.,
'Data(x,x**2)' is a 'PlotItem' that represents x squared as a
function of x. For the output format, see the comments for
'write_array()'.
How the data are written to gnuplot depends on the 'inline'
argument and preference settings for the platform in use.
Keyword arguments:
'cols=<tuple>' -- write only the specified columns from each
data point to the file. Since cols is used by python, the
columns should be numbered in the python style (starting
from 0), not the gnuplot style (starting from 1).
'inline=<bool>' -- transmit the data to gnuplot 'inline'
rather than through a temporary file. The default is the
value of gp.GnuplotOpts.prefer_inline_data.
'filename=<string>' -- save data to a permanent file.
The keyword arguments recognized by '_FileItem' can also be used
here.
"""
if len(set) == 1:
# set was passed as a single structure
set = utils.float_array(set[0])
# As a special case, if passed a single 1-D array, then it is
# treated as one value per point (by default, plotted against
# its index):
if len(set.shape) == 1:
set = set[:,Numeric.NewAxis]
else:
# set was passed column by column (for example,
# Data(x,y)); pack it into one big array (this will test
# that sizes are all the same):
set = utils.float_array(set)
dims = len(set.shape)
# transpose so that the last index selects x vs. y:
set = Numeric.transpose(set, (dims-1,) + tuple(range(dims-1)))
if 'cols' in keyw:
cols = keyw['cols']
del keyw['cols']
if type(cols) is types.IntType:
cols = (cols,)
set = Numeric.take(set, cols, -1)
if 'filename' in keyw:
filename = keyw['filename'] or None
del keyw['filename']
else:
filename = None
if 'inline' in keyw:
inline = keyw['inline']
del keyw['inline']
if inline and filename:
raise Errors.OptionError(
'cannot pass data both inline and via a file'
)
else:
inline = (not filename) and gp.GnuplotOpts.prefer_inline_data
# Output the content into a string:
f = StringIO()
utils.write_array(f, set)
content = f.getvalue()
if inline:
return _InlineFileItem(content, **keyw)
elif filename:
return _NewFileItem(content, filename=filename, **keyw)
elif gp.GnuplotOpts.prefer_fifo_data:
return _FIFOFileItem(content, **keyw)
else:
return _NewFileItem(content, **keyw)
def GridData(
data, xvals=None, yvals=None, inline=_unset, filename=None, **keyw
):
"""Return a _FileItem representing a function of two variables.
'GridData' represents a function that has been tabulated on a
rectangular grid. The data are written to a file; no copy is kept
in memory.
Arguments:
'data' -- the data to plot: a 2-d array with dimensions
(numx,numy).
'xvals' -- a 1-d array with dimension 'numx'
'yvals' -- a 1-d array with dimension 'numy'
'binary=<bool>' -- send data to gnuplot in binary format?
'inline=<bool>' -- send data to gnuplot "inline"?
'filename=<string>' -- save data to a permanent file.
Note the unusual argument order! The data are specified *before*
the x and y values. (This inconsistency was probably a mistake;
after all, the default xvals and yvals are not very useful.)
'data' must be a data array holding the values of a function
f(x,y) tabulated on a grid of points, such that 'data[i,j] ==
f(xvals[i], yvals[j])'. If 'xvals' and/or 'yvals' are omitted,
integers (starting with 0) are used for that coordinate. The data
are written to a temporary file; no copy of the data is kept in
memory.
If 'binary=0' then the data are written to a datafile as 'x y
f(x,y)' triplets (y changes most rapidly) that can be used by
gnuplot's 'splot' command. Blank lines are included each time the
value of x changes so that gnuplot knows to plot a surface through
the data.
If 'binary=1' then the data are written to a file in a binary
format that 'splot' can understand. Binary format is faster and
usually saves disk space but is not human-readable. If your
version of gnuplot doesn't support binary format (it is a
recently-added feature), this behavior can be disabled by setting
the configuration variable
'gp.GnuplotOpts.recognizes_binary_splot=0' in the appropriate
gp*.py file.
Thus if you have three arrays in the above format and a Gnuplot
instance called g, you can plot your data by typing
'g.splot(Gnuplot.GridData(data,xvals,yvals))'.
"""
# Try to interpret data as an array:
data = utils.float_array(data)
try:
(numx, numy) = data.shape
except ValueError:
raise Errors.DataError('data array must be two-dimensional')
if xvals is None:
xvals = Numeric.arange(numx)
else:
xvals = utils.float_array(xvals)
if xvals.shape != (numx,):
raise Errors.DataError(
'The size of xvals must be the same as the size of '
'the first dimension of the data array')
if yvals is None:
yvals = Numeric.arange(numy)
else:
yvals = utils.float_array(yvals)
if yvals.shape != (numy,):
raise Errors.DataError(
'The size of yvals must be the same as the size of '
'the second dimension of the data array')
# Binary defaults to true if recognizes_binary_plot is set;
# otherwise it is forced to false.
binary = keyw.get('binary', 1) and gp.GnuplotOpts.recognizes_binary_splot
keyw['binary'] = binary
if inline is _unset:
inline = (
(not binary) and (not filename)
and gp.GnuplotOpts.prefer_inline_data
)
elif inline and filename:
raise Errors.OptionError(
'cannot pass data both inline and via a file'
)
# xvals, yvals, and data are now all filled with arrays of data.
if binary:
if inline:
raise Errors.OptionError('binary inline data not supported')
# write file in binary format
# It seems that the gnuplot documentation for binary mode
# disagrees with its actual behavior (as of v. 3.7). The
# documentation has the roles of x and y exchanged. We ignore
# the documentation and go with the code.
mout = Numeric.zeros((numy + 1, numx + 1), Numeric.Float32)
mout[0,0] = numx
mout[0,1:] = xvals.astype(Numeric.Float32)
mout[1:,0] = yvals.astype(Numeric.Float32)
try:
# try copying without the additional copy implied by astype():
mout[1:,1:] = Numeric.transpose(data)
except:
# if that didn't work then downcasting from double
# must be necessary:
mout[1:,1:] = Numeric.transpose(data.astype(Numeric.Float32))
content = mout.tostring()
if (not filename) and gp.GnuplotOpts.prefer_fifo_data:
return _FIFOFileItem(content, **keyw)
else:
return _NewFileItem(content, filename=filename, **keyw)
else:
# output data to file as "x y f(x)" triplets. This
# requires numy copies of each x value and numx copies of
# each y value. First reformat the data:
set = Numeric.transpose(
Numeric.array(
(Numeric.transpose(Numeric.resize(xvals, (numy, numx))),
Numeric.resize(yvals, (numx, numy)),
data)), (1,2,0))
# Now output the data with the usual routine. This will
# produce data properly formatted in blocks separated by blank
# lines so that gnuplot can connect the points into a grid.
f = StringIO()
utils.write_array(f, set)
content = f.getvalue()
if inline:
return _InlineFileItem(content, **keyw)
elif filename:
return _NewFileItem(content, filename=filename, **keyw)
elif gp.GnuplotOpts.prefer_fifo_data:
return _FIFOFileItem(content, **keyw)
else:
return _NewFileItem(content, **keyw)