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# -*- coding: utf-8 -*-
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"""Improved replacement for the Gnuplot.Gnuplot class.
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This module imports Gnuplot and replaces some of its functionality with
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improved versions. They add better handling of arrays for plotting and more
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convenient PostScript generation, plus some fixes for hardcopy().
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It also adds a convenient plot2 method for plotting dictionaries and
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lists/tuples of arrays.
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This module is meant to be used as a drop-in replacement to the original
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Gnuplot, so it should be safe to do:
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import IPython.Gnuplot2 as Gnuplot
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"""
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import cStringIO
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import os
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import string
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import sys
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import tempfile
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import time
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import types
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import Gnuplot as Gnuplot_ori
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import Numeric
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from IPython.utils.genutils import popkey,xsys
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# needed by hardcopy():
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gp = Gnuplot_ori.gp
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# Patch for Gnuplot.py 1.6 compatibility.
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# Thanks to Hayden Callow <h.callow@elec.canterbury.ac.nz>
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try:
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OptionException = Gnuplot_ori.PlotItems.OptionException
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except AttributeError:
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OptionException = Gnuplot_ori.Errors.OptionError
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# exhibit a similar interface to Gnuplot so it can be somewhat drop-in
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Data = Gnuplot_ori.Data
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Func = Gnuplot_ori.Func
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GridData = Gnuplot_ori.GridData
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PlotItem = Gnuplot_ori.PlotItem
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PlotItems = Gnuplot_ori.PlotItems
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# Modify some of Gnuplot's functions with improved versions (or bugfixed, in
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# hardcopy's case). In order to preserve the docstrings at runtime, I've
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# copied them from the original code.
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# After some significant changes in v 1.7 of Gnuplot.py, we need to do a bit
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# of version checking.
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if Gnuplot_ori.__version__ <= '1.6':
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_BaseFileItem = PlotItems.File
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_BaseTempFileItem = PlotItems.TempFile
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# Fix the File class to add the 'index' option for Gnuplot versions < 1.7
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class File(_BaseFileItem):
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_option_list = _BaseFileItem._option_list.copy()
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_option_list.update({
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'index' : lambda self, index: self.set_option_index(index),
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})
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# A new initializer is needed b/c we want to add a modified
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# _option_sequence list which includes 'index' in the right place.
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def __init__(self,*args,**kw):
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self._option_sequence = ['binary', 'index', 'using', 'smooth', 'axes',
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'title', 'with']
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_BaseFileItem.__init__(self,*args,**kw)
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# Let's fix the constructor docstring
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__newdoc = \
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"""Additional Keyword arguments added by IPython:
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'index=<int>' -- similar to the `index` keyword in Gnuplot.
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This allows only some of the datasets in a file to be
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plotted. Datasets within a file are assumed to be separated
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by _pairs_ of blank lines, and the first one is numbered as
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0 (similar to C/Python usage)."""
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__init__.__doc__ = PlotItems.File.__init__.__doc__ + __newdoc
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def set_option_index(self, index):
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if index is None:
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self.clear_option('index')
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elif type(index) in [type(''), type(1)]:
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self._options['index'] = (index, 'index %s' % index)
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elif type(index) is type(()):
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self._options['index'] = (index,'index %s' %
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string.join(map(repr, index), ':'))
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else:
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raise OptionException('index=%s' % (index,))
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# We need a FileClass with a different name from 'File', which is a
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# factory function in 1.7, so that our String class can subclass FileClass
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# in any version.
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_FileClass = File
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elif Gnuplot_ori.__version__ =='1.7':
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_FileClass = _BaseFileItem = PlotItems._FileItem
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_BaseTempFileItem = PlotItems._TempFileItem
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File = PlotItems.File
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else: # changes in the newer version (svn as of March'06)
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_FileClass = _BaseFileItem = PlotItems._FileItem
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_BaseTempFileItem = PlotItems._NewFileItem
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File = PlotItems.File
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# Now, we can add our generic code which is version independent
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# First some useful utilities
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def eps_fix_bbox(fname):
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"""Fix the bounding box of an eps file by running ps2eps on it.
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If its name ends in .eps, the original file is removed.
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This is particularly useful for plots made by Gnuplot with square aspect
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ratio: there is a bug in Gnuplot which makes it generate a bounding box
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which is far wider than the actual plot.
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This function assumes that ps2eps is installed in your system."""
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# note: ps2ps and eps2eps do NOT work, ONLY ps2eps works correctly. The
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# others make output with bitmapped fonts, which looks horrible.
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print 'Fixing eps file: <%s>' % fname
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xsys('ps2eps -f -q -l %s' % fname)
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if fname.endswith('.eps'):
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os.rename(fname+'.eps',fname)
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def is_list1d(x,containers = [types.ListType,types.TupleType]):
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"""Returns true if x appears to be a 1d list/tuple/array.
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The heuristics are: identify Numeric arrays, or lists/tuples whose first
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element is not itself a list/tuple. This way zipped lists should work like
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the original Gnuplot. There's no inexpensive way to know if a list doesn't
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have a composite object after its first element, so that kind of input
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will produce an error. But it should work well in most cases.
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"""
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x_type = type(x)
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return x_type == Numeric.ArrayType and len(x.shape)==1 or \
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(x_type in containers and
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type(x[0]) not in containers + [Numeric.ArrayType])
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def zip_items(items,titles=None):
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"""zip together neighboring 1-d arrays, and zip standalone ones
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with their index. Leave other plot items alone."""
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class StandaloneItem(Exception): pass
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def get_titles(titles):
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"""Return the next title and the input titles array.
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The input array may be changed to None when no titles are left to
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prevent extra unnecessary calls to this function."""
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try:
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title = titles[tit_ct[0]] # tit_ct[0] is in zip_items'scope
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except IndexError:
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titles = None # so we don't enter again
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title = None
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else:
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tit_ct[0] += 1
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return title,titles
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new_items = []
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if titles:
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# Initialize counter. It was put in a list as a hack to allow the
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# nested get_titles to modify it without raising a NameError.
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tit_ct = [0]
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n = 0 # this loop needs to be done by hand
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while n < len(items):
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item = items[n]
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try:
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if is_list1d(item):
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if n==len(items)-1: # last in list
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raise StandaloneItem
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else: # check the next item and zip together if needed
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next_item = items[n+1]
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if next_item is None:
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n += 1
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raise StandaloneItem
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elif is_list1d(next_item):
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# this would be best done with an iterator
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if titles:
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title,titles = get_titles(titles)
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else:
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title = None
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new_items.append(Data(zip(item,next_item),
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title=title))
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n += 1 # avoid double-inclusion of next item
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else: # can't zip with next, zip with own index list
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raise StandaloneItem
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else: # not 1-d array
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new_items.append(item)
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except StandaloneItem:
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if titles:
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title,titles = get_titles(titles)
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else:
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title = None
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new_items.append(Data(zip(range(len(item)),item),title=title))
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except AttributeError:
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new_items.append(item)
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n+=1
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return new_items
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# And some classes with enhanced functionality.
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class String(_FileClass):
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"""Make a PlotItem from data in a string with the same format as a File.
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This allows writing data directly inside python scripts using the exact
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same format and manipulation options which would be used for external
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files."""
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def __init__(self, data_str, **keyw):
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"""Construct a String object.
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<data_str> is a string formatted exactly like a valid Gnuplot data
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file would be. All options from the File constructor are valid here.
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Warning: when used for interactive plotting in scripts which exit
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immediately, you may get an error because the temporary file used to
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hold the string data was deleted before Gnuplot had a chance to see
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it. You can work around this problem by putting a raw_input() call at
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the end of the script.
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This problem does not appear when generating PostScript output, only
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with Gnuplot windows."""
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self.tmpfile = _BaseTempFileItem()
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tmpfile = file(self.tmpfile.filename,'w')
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tmpfile.write(data_str)
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_BaseFileItem.__init__(self,self.tmpfile,**keyw)
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class Gnuplot(Gnuplot_ori.Gnuplot):
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"""Improved Gnuplot class.
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Enhancements: better plot,replot and hardcopy methods. New methods for
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quick range setting.
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"""
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def xrange(self,min='*',max='*'):
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"""Set xrange. If min/max is omitted, it is set to '*' (auto).
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Note that this is different from the regular Gnuplot behavior, where
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an unspecified limit means no change. Here any unspecified limit is
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set to autoscaling, allowing these functions to be used for full
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autoscaling when called with no arguments.
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To preserve one limit's current value while changing the other, an
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explicit '' argument must be given as the limit to be kept.
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Similar functions exist for [y{2}z{2}rtuv]range."""
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self('set xrange [%s:%s]' % (min,max))
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def yrange(self,min='*',max='*'):
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self('set yrange [%s:%s]' % (min,max))
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def zrange(self,min='*',max='*'):
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self('set zrange [%s:%s]' % (min,max))
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def x2range(self,min='*',max='*'):
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self('set xrange [%s:%s]' % (min,max))
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def y2range(self,min='*',max='*'):
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self('set yrange [%s:%s]' % (min,max))
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def z2range(self,min='*',max='*'):
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self('set zrange [%s:%s]' % (min,max))
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def rrange(self,min='*',max='*'):
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self('set rrange [%s:%s]' % (min,max))
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def trange(self,min='*',max='*'):
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self('set trange [%s:%s]' % (min,max))
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def urange(self,min='*',max='*'):
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self('set urange [%s:%s]' % (min,max))
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def vrange(self,min='*',max='*'):
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self('set vrange [%s:%s]' % (min,max))
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def set_ps(self,option):
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"""Set an option for the PostScript terminal and reset default term."""
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self('set terminal postscript %s ' % option)
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self('set terminal %s' % gp.GnuplotOpts.default_term)
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def __plot_ps(self, plot_method,*items, **keyw):
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"""Wrapper for plot/splot/replot, with processing of hardcopy options.
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For internal use only."""
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# Filter out PostScript options which will crash the normal plot/replot
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psargs = {'filename':None,
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'mode':None,
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'eps':None,
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'enhanced':None,
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'color':None,
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'solid':None,
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'duplexing':None,
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'fontname':None,
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'fontsize':None,
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'debug':0 }
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for k in psargs.keys():
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if keyw.has_key(k):
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psargs[k] = keyw[k]
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del keyw[k]
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# Filter out other options the original plot doesn't know
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hardcopy = popkey(keyw,'hardcopy',psargs['filename'] is not None)
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titles = popkey(keyw,'titles',0)
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# the filename keyword should control hardcopy generation, this is an
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# override switch only which needs to be explicitly set to zero
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if hardcopy:
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if psargs['filename'] is None:
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raise ValueError, \
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'If you request hardcopy, you must give a filename.'
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# set null output so nothing goes to screen. hardcopy() restores output
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self('set term dumb')
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# I don't know how to prevent screen output in Windows
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if os.name == 'posix':
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self('set output "/dev/null"')
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new_items = zip_items(items,titles)
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# plot_method is either plot or replot from the original Gnuplot class:
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plot_method(self,*new_items,**keyw)
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# Do hardcopy if requested
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if hardcopy:
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if psargs['filename'].endswith('.eps'):
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psargs['eps'] = 1
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self.hardcopy(**psargs)
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def plot(self, *items, **keyw):
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"""Draw a new plot.
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Clear the current plot and create a new 2-d plot containing
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the specified items. Each arguments should be of the
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following types:
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'PlotItem' (e.g., 'Data', 'File', 'Func') -- This is the most
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flexible way to call plot because the PlotItems can
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contain suboptions. Moreover, PlotItems can be saved to
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variables so that their lifetime is longer than one plot
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command; thus they can be replotted with minimal overhead.
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'string' (e.g., 'sin(x)') -- The string is interpreted as
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'Func(string)' (a function that is computed by gnuplot).
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Anything else -- The object, which should be convertible to an
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array, is passed to the 'Data' constructor, and thus
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plotted as data. If the conversion fails, an exception is
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raised.
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This is a modified version of plot(). Compared to the original in
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Gnuplot.py, this version has several enhancements, listed below.
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Modifications to the input arguments
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------------------------------------
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(1-d array means Numeric array, list or tuple):
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(i) Any 1-d array which is NOT followed by another 1-d array, is
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automatically zipped with range(len(array_1d)). Typing g.plot(y) will
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plot y against its indices.
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(ii) If two 1-d arrays are contiguous in the argument list, they are
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automatically zipped together. So g.plot(x,y) plots y vs. x, and
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g.plot(x1,y1,x2,y2) plots y1 vs. x1 and y2 vs. x2.
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(iii) Any 1-d array which is followed by None is automatically zipped
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with range(len(array_1d)). In this form, typing g.plot(y1,None,y2)
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will plot both y1 and y2 against their respective indices (and NOT
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versus one another). The None prevents zipping y1 and y2 together, and
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since y2 is unpaired it is automatically zipped to its indices by (i)
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(iv) Any other arguments which don't match these cases are left alone and
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passed to the code below.
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For lists or tuples, the heuristics used to determine whether they are
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in fact 1-d is fairly simplistic: their first element is checked, and
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if it is not a list or tuple itself, it is assumed that the whole
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object is one-dimensional.
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An additional optional keyword 'titles' has been added: it must be a
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list of strings to be used as labels for the individual plots which
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are NOT PlotItem objects (since those objects carry their own labels
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within).
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PostScript generation
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---------------------
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This version of plot() also handles automatically the production of
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PostScript output. The main options are (given as keyword arguments):
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- filename: a string, typically ending in .eps. If given, the plot is
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sent to this file in PostScript format.
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- hardcopy: this can be set to 0 to override 'filename'. It does not
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need to be given to produce PostScript, its purpose is to allow
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switching PostScript output off globally in scripts without having to
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manually change 'filename' values in multiple calls.
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All other keywords accepted by Gnuplot.hardcopy() are transparently
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passed, and safely ignored if output is sent to the screen instead of
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PostScript.
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For example:
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In [1]: x=frange(0,2*pi,npts=100)
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Generate a plot in file 'sin.eps':
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In [2]: plot(x,sin(x),filename = 'sin.eps')
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Plot to screen instead, without having to change the filename:
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In [3]: plot(x,sin(x),filename = 'sin.eps',hardcopy=0)
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Pass the 'color=0' option to hardcopy for monochrome output:
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In [4]: plot(x,sin(x),filename = 'sin.eps',color=0)
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PostScript generation through plot() is useful mainly for scripting
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uses where you are not interested in interactive plotting. For
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interactive use, the hardcopy() function is typically more convenient:
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In [5]: plot(x,sin(x))
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In [6]: hardcopy('sin.eps') """
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self.__plot_ps(Gnuplot_ori.Gnuplot.plot,*items,**keyw)
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def plot2(self,arg,**kw):
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"""Plot the entries of a dictionary or a list/tuple of arrays.
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This simple utility calls plot() with a list of Gnuplot.Data objects
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constructed either from the values of the input dictionary, or the entries
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in it if it is a tuple or list. Each item gets labeled with the key/index
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in the Gnuplot legend.
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Each item is plotted by zipping it with a list of its indices.
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Any keywords are passed directly to plot()."""
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if hasattr(arg,'keys'):
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keys = arg.keys()
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keys.sort()
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else:
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keys = range(len(arg))
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pitems = [Data(zip(range(len(arg[k])),arg[k]),title=`k`) for k in keys]
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self.plot(*pitems,**kw)
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def splot(self, *items, **keyw):
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"""Draw a new three-dimensional plot.
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Clear the current plot and create a new 3-d plot containing
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the specified items. Arguments can be of the following types:
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'PlotItem' (e.g., 'Data', 'File', 'Func', 'GridData' ) -- This
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is the most flexible way to call plot because the
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PlotItems can contain suboptions. Moreover, PlotItems can
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be saved to variables so that their lifetime is longer
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than one plot command--thus they can be replotted with
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minimal overhead.
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'string' (e.g., 'sin(x*y)') -- The string is interpreted as a
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'Func()' (a function that is computed by gnuplot).
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Anything else -- The object is converted to a Data() item, and
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thus plotted as data. Note that each data point should
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normally have at least three values associated with it
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(i.e., x, y, and z). If the conversion fails, an
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exception is raised.
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This is a modified version of splot(). Compared to the original in
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Gnuplot.py, this version has several enhancements, listed in the
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plot() documentation.
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"""
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self.__plot_ps(Gnuplot_ori.Gnuplot.splot,*items,**keyw)
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def replot(self, *items, **keyw):
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"""Replot the data, possibly adding new 'PlotItem's.
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Replot the existing graph, using the items in the current
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itemlist. If arguments are specified, they are interpreted as
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additional items to be plotted alongside the existing items on
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the same graph. See 'plot' for details.
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If you want to replot to a postscript file, you MUST give the
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'filename' keyword argument in each call to replot. The Gnuplot python
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interface has no way of knowing that your previous call to
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Gnuplot.plot() was meant for PostScript output."""
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self.__plot_ps(Gnuplot_ori.Gnuplot.replot,*items,**keyw)
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# The original hardcopy has a bug. See fix at the end. The rest of the code
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# was lifted verbatim from the original, so that people using IPython get the
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# benefits without having to manually patch Gnuplot.py
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def hardcopy(self, filename=None,
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mode=None,
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eps=None,
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enhanced=None,
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color=None,
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solid=None,
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duplexing=None,
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fontname=None,
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fontsize=None,
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debug = 0,
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):
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|
"""Create a hardcopy of the current plot.
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Create a postscript hardcopy of the current plot to the
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|
default printer (if configured) or to the specified filename.
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|
Note that gnuplot remembers the postscript suboptions across
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|
terminal changes. Therefore if you set, for example, color=1
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|
for one hardcopy then the next hardcopy will also be color
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|
unless you explicitly choose color=0. Alternately you can
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|
force all of the options to their defaults by setting
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|
mode='default'. I consider this to be a bug in gnuplot.
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|
Keyword arguments:
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|
'filename=<string>' -- if a filename is specified, save the
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|
output in that file; otherwise print it immediately
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|
using the 'default_lpr' configuration option. If the
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|
filename ends in '.eps', EPS mode is automatically
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|
selected (like manually specifying eps=1 or mode='eps').
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|
'mode=<string>' -- set the postscript submode ('landscape',
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|
'portrait', 'eps', or 'default'). The default is
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|
to leave this option unspecified.
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|
'eps=<bool>' -- shorthand for 'mode="eps"'; asks gnuplot to
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|
generate encapsulated postscript.
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|
'enhanced=<bool>' -- if set (the default), then generate
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|
enhanced postscript, which allows extra features like
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|
font-switching, superscripts, and subscripts in axis
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|
labels. (Some old gnuplot versions do not support
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|
enhanced postscript; if this is the case set
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|
gp.GnuplotOpts.prefer_enhanced_postscript=None.)
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|
'color=<bool>' -- if set, create a plot with color. Default
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|
is to leave this option unchanged.
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|
'solid=<bool>' -- if set, force lines to be solid (i.e., not
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|
dashed).
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|
'duplexing=<string>' -- set duplexing option ('defaultplex',
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|
'simplex', or 'duplex'). Only request double-sided
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|
printing if your printer can handle it. Actually this
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|
option is probably meaningless since hardcopy() can only
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|
print a single plot at a time.
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|
'fontname=<string>' -- set the default font to <string>,
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|
which must be a valid postscript font. The default is
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|
|
to leave this option unspecified.
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|
'fontsize=<double>' -- set the default font size, in
|
|
|
postscript points.
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|
|
'debug=<bool>' -- print extra debugging information (useful if
|
|
|
your PostScript files are misteriously not being created).
|
|
|
"""
|
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|
|
|
if filename is None:
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|
|
assert gp.GnuplotOpts.default_lpr is not None, \
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|
|
OptionException('default_lpr is not set, so you can only '
|
|
|
'print to a file.')
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|
|
filename = gp.GnuplotOpts.default_lpr
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|
|
lpr_output = 1
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|
|
else:
|
|
|
if filename.endswith('.eps'):
|
|
|
eps = 1
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|
|
lpr_output = 0
|
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|
|
|
|
# Be careful processing the options. If the user didn't
|
|
|
# request an option explicitly, do not specify it on the 'set
|
|
|
# terminal' line (don't even specify the default value for the
|
|
|
# option). This is to avoid confusing older versions of
|
|
|
# gnuplot that do not support all of these options. The
|
|
|
# exception is 'enhanced', which is just too useful to have to
|
|
|
# specify each time!
|
|
|
|
|
|
setterm = ['set', 'terminal', 'postscript']
|
|
|
if eps:
|
|
|
assert mode is None or mode=='eps', \
|
|
|
OptionException('eps option and mode are incompatible')
|
|
|
setterm.append('eps')
|
|
|
else:
|
|
|
if mode is not None:
|
|
|
assert mode in ['landscape', 'portrait', 'eps', 'default'], \
|
|
|
OptionException('illegal mode "%s"' % mode)
|
|
|
setterm.append(mode)
|
|
|
if enhanced is None:
|
|
|
enhanced = gp.GnuplotOpts.prefer_enhanced_postscript
|
|
|
if enhanced is not None:
|
|
|
if enhanced: setterm.append('enhanced')
|
|
|
else: setterm.append('noenhanced')
|
|
|
if color is not None:
|
|
|
if color: setterm.append('color')
|
|
|
else: setterm.append('monochrome')
|
|
|
if solid is not None:
|
|
|
if solid: setterm.append('solid')
|
|
|
else: setterm.append('dashed')
|
|
|
if duplexing is not None:
|
|
|
assert duplexing in ['defaultplex', 'simplex', 'duplex'], \
|
|
|
OptionException('illegal duplexing mode "%s"' % duplexing)
|
|
|
setterm.append(duplexing)
|
|
|
if fontname is not None:
|
|
|
setterm.append('"%s"' % fontname)
|
|
|
if fontsize is not None:
|
|
|
setterm.append('%s' % fontsize)
|
|
|
|
|
|
self(string.join(setterm))
|
|
|
self.set_string('output', filename)
|
|
|
# replot the current figure (to the printer):
|
|
|
self.refresh()
|
|
|
|
|
|
# fperez. Ugly kludge: often for some reason the file is NOT created
|
|
|
# and we must reissue the creation commands. I have no idea why!
|
|
|
if not lpr_output:
|
|
|
#print 'Hardcopy <%s>' % filename # dbg
|
|
|
maxtries = 20
|
|
|
delay = 0.1 # delay (in seconds) between print attempts
|
|
|
for i in range(maxtries):
|
|
|
time.sleep(0.05) # safety, very small delay
|
|
|
if os.path.isfile(filename):
|
|
|
if debug:
|
|
|
print 'Hardcopy to file <%s> success at attempt #%s.' \
|
|
|
% (filename,i+1)
|
|
|
break
|
|
|
time.sleep(delay)
|
|
|
# try again, issue all commands just in case
|
|
|
self(string.join(setterm))
|
|
|
self.set_string('output', filename)
|
|
|
self.refresh()
|
|
|
if not os.path.isfile(filename):
|
|
|
print >> sys.stderr,'ERROR: Tried %s times and failed to '\
|
|
|
'create hardcopy file `%s`' % (maxtries,filename)
|
|
|
|
|
|
# reset the terminal to its `default' setting:
|
|
|
self('set terminal %s' % gp.GnuplotOpts.default_term)
|
|
|
self.set_string('output')
|
|
|
|
|
|
#********************** End of file <Gnuplot2.py> ************************
|
|
|
|
