Source code for ccsgp_get_started.ccsgp.myplot

import os, re, sys
import Gnuplot, Gnuplot.funcutils
from subprocess import call
from utils import zip_flat, colorscale
from config import basic_setup, supported_styles, ureg, default_size
import numpy as np
from collections import deque

os.environ['GNUPLOT_PS_DIR'] = os.path.dirname(__file__)

[docs]class MyPlot(object): """base class - basic gnuplot setup (bars, grid, title, key, terminal, multiplot) - utility functions for general plotting :param title: image title :type title: str :param name: basename used for output files :type name: str :param debug: debug flag for verbose gnuplot output :type debug: bool :ivar name: basename for output files :ivar epsname: basename + '.eps' :ivar gp: Gnuplot.Gnuplot instance :ivar nPanels: number of panels in a multiplot :ivar nVertLines: number of vertical lines :ivar nLabels: number of labels :ivar nArrows: number of arrows :ivar axisLog: flags for logarithmic axes :ivar axisRange: axis range for respective axis (set in setAxisRange) """ def __init__(self, name = 'test', title = '', debug = 0): = name self.epsname = name + '.ps' = Gnuplot.Gnuplot(debug = debug) self.nPanels = 0 self.nVertLines = 0 self.nLabels = 0 self.nArrows = 0 self.axisLog = { 'x': False, 'y': False } self.axisRange = { 'x': [], 'y': [] } self.arrow_offset = 0.85 self.arrow_length = 0.2 self.arrow_bar = 0.005 self.dataSets = {} self.size = None self._setter(['title "%s"' % title] + basic_setup)
[docs] def _get_style_mod_prop(self, prop): """get style and modified property string""" m = re.compile('^with \w+').search(prop) style =[5:] if m else 'points' mod_prop = re.sub(, '', prop) if m else prop return style, mod_prop
[docs] def _using(self, data, prop = None): """determine string with columns to use :param data: one dataset :type data: numpy.array :param prop: property string of a dataset :type prop: str :returns: '1:2:3', '1:2:4' or '1:2:3:4' """ if not prop: # primary errors return ':'.join([ '%d' % (i+1) for i in xrange(4) if i < 2 or (i >= 2 and self.error_sums[i-2] > 0) ]) else: # secondary errors # filledcurves or candlesticka style, mod_prop = self._get_style_mod_prop(prop) if style == 'filledcurves': return '1:($2-$5):($2+$5)' else: low_lim = '(($2-$5)>0)?($2-$5):1e-20' \ if self.axisLog['y'] else '($2-$5)' return '1:%s:2:2:($2+$5)' % low_lim
[docs] def _with_main(self, prop): """get the correct property string for main data""" style, mod_prop = self._get_style_mod_prop(prop) if style not in supported_styles: raise Exception('gnuplot style %s not yet supported!' % style) style = 'linespoints' if style == 'filledcurves' else style return ' '.join([style, mod_prop])
[docs] def _sum_errs(self, data, i): """convenience function to calculate sum of i-th column""" return data[:, i].sum()
[docs] def _plot_errs(self, data): """determine whether to plot primary errors separately plot errorbars if data has more than two columns which are not all zero :param data: one dataset :type data: numpy.array :var error_sums: sum of x and y errors :returns: True or False """ if data.shape[1] > 5 or data.shape[1] == 3: raise Exception( '%d columns not allowed, use either 2, 4 or 5!' % data.shape[1] ) if data.shape[1] < 3: return False self.error_sums = [ self._sum_errs(data, i+2) for i in xrange(2) ] return (sum(self.error_sums) > 0)
[docs] def _plot_syserrs(self, data): """determine whether to plot secondary errors :param data: one dataset :type data: numpy.array :returns: True or False """ return data.shape[1] == 5 and self._sum_errs(data, 4) > 0
[docs] def _with_errs(self, data, prop): """generate special property string for primary errors * currently error bars are drawn in black * use same linewidth as for points * TODO: give user the option to draw error bars in lighter color according to the respective data points :param data: one dataset :type data: numpy.array :param prop: property string of a dataset :type prop: str :returns: property string for primary errors """ m = re.compile('lw \d').search(prop) lw =[-1] if m else '1' xy = ''.join([ axis for axis in ['x', 'y'] if self.error_sums[int(axis=='y')] > 0 ]) # TODO: get linewidth for errorbar arrows? return '%serrorbars pt 0 lt 1 lc 0 lw %s' % (xy, lw)
[docs] def _with_syserrs(self, prop): """generate special property string for secondary errors * draw box in lighter color than point/line color * does not support integer line colors, only hex :param prop: property string of a dataset :type prop: str :returns: property string for secondary errors """ m = re.compile('lc \d').search(prop) if m: raise Exception( '"%s" not supported! use default_colors or hex specification' % ) m_lc = re.compile('lc rgb "#[A-Fa-f0-9]{6}"').search(prop) lc = colorscale([-7:-1]) if m_lc else '0' m_lw = re.compile('lw \d').search(prop) lw =[-1] if m_lw else '1' style, mod_prop = self._get_style_mod_prop(prop) style = 'filledcurves' if style == 'filledcurves' else 'candlesticks' return '%s fs solid lw %s lt 1 lc %s' % (style, lw, lc)
[docs] def _prettify(self, str): """prettify string, remove special symbols""" return re.compile(ur'[\W]+',re.UNICODE).sub('_',str.strip())
[docs] def initData(self, data, properties, titles, subplot_title = None): """initialize the data - all lists given as parameters must have the same length. - each data set is drawn twice to allow for different colors for the errorbars - error bars use the same linewidth as data points and line color black - use 'boxwidth 0.03 absolute' in gp_calls to set the width of the uncertainty boxes - use alternative gnuplot style if ``properties`` contains a style specification in the form ``with <style>`` and if the style is in ccsgp.config.supported_styles (style specification has to be at the beginning of the property string!) :param data: data points w/ format [x, y, dx, dy] for each dataset :type data: list of numpy arrays :param properties: plot properties for each dataset (pt/lw/ps/lc...) :type properties: list of str :param titles: key/legend titles for each dataset :type titles: list of strings :param subplot_title: subplot title for panel plot case :type subplot_title: str :var dataSets: zipped titles and data for hdf5/ascii output and setAxisRange :var data: list of Gnuplot.Data including extra data sets for error plotting """ # dataSets used in _hdf5/_ascii and setAxisRange for i, (k, v) in enumerate(zip(titles, data)): key = k if k else 'graph' + str(i) if subplot_title is not None: # multiplot key = '_'.join([subplot_title, key]) if key in self.dataSets: raise ValueError("duplicate key '{0}'!".format(k)) else: self.dataSets[key] = v # plot arrows for data points with error bars larger than resp. value # TODO: lw/lt/lc are hardcoded! same for arrow length and offset. arr_upp_prop = 'head size screen %g,90 lw 4 lt 1 lc 0 front' % self.arrow_bar arr_low_prop = 'head empty lw 4 lt 1 lc 0 front' if self.axisLog['y']: for d in data: mask = d[:,1] - d[:,3] < 0 for dp in d[mask]: arr_start = [ dp[0], dp[1] + dp[3] ] if dp[1] > 0: self.setArrow( [ dp[0], dp[1] / self.arrow_offset ], arr_start, arr_upp_prop ) self.setArrow( [ dp[0], dp[1] * self.arrow_offset ], [ dp[0], self.arrow_length * dp[1] ], arr_low_prop ) elif arr_start[1] > 0: self.setArrow( [dp[0], (self.arrow_length + 0.1) * arr_start[1]], arr_start, arr_upp_prop ) self.setArrow( arr_start, [dp[0], self.arrow_length * arr_start[1]], arr_low_prop ) else: print 'point omitted:', dp d[:,3][mask] = 0 # zip all input parameters for easier looping zipped = zip(data, properties, titles) # main data points drawn last main_data = [ Gnuplot.Data( d, inline = 1, title = t, using = '1:2', with_ = self._with_main(p) ) for d, p, t in zipped ] # extra data set to plot "primary" errors separately prim_errs = [ Gnuplot.Data( d, inline = 1, using = self._using(d), with_ = self._with_errs(d, p) ) if self._plot_errs(d) else None for d, p, t in zipped ] # extra data set for "secondary" errors (systematic uncertainties) sec_errs = [ Gnuplot.Data( d, inline = 1, using = self._using(d, p), with_ = self._with_syserrs(p) ) if self._plot_syserrs(d) else None for d, p, t in zipped ] # zip main & secondary data and filter out None's = deque(filter(None, zip_flat(sec_errs, prim_errs, main_data)))
[docs] def _setter(self, list): """convenience function to set a list of gnuplot options :param list: list of strings given to gnuplot's set command :type list: list """ for s in list:'set %s' % s)
[docs] def setMargins(self, **kwargs): """set the margins * keys other than l(b,t,r)margin are ignored * if margin not given leave to gnuplot """ order = ['l', 'b', 'r', 't'] margins = dict((k, kwargs.get(k+'margin')) for k in order) self._setter([ '%smargin at screen %f' % (k,v) for k,v in margins.items() if v is not None ])
[docs] def setKeyOptions(self, key_opts): """set key options :param key_opts: strings for key/legend options :type key_opts: list """ self._setter(['key %s' % s for s in key_opts])
[docs] def setAxisRange(self, rng, axis = 'x', reverse = False): """set range for specified axis * automatically determines axis range to include all data points if range is not given. * logscale and secondary errors taken into account * y-axis range determined for points within given x-axis range :param rng: lower and upper range limits :type rng: list :param axis: axis to which to apply range :type axis: str :param reverse: reverse axis range :type reverse: bool """ if rng is None: col = int(axis == 'y') all_data = self.dataSets.values() vals = np.array([ n for v in all_data for n in v[:, col] ]) evals = np.zeros(len(vals)) if axis == 'y': evals = np.array([ max(n) if v.shape[1] >= 4 else 0. for v in all_data for n in v[:, 3:] ]) xvals = np.array([n for v in all_data for n in v[:, 0]]) mask = (xvals > self.axisRange['x'][0]) & (xvals < self.axisRange['x'][1]) vals = vals[mask] evals = evals[mask] axMin = (vals-evals).min() if self.axisLog[axis] and not axMin > 0: axMin = vals.min() axMax = (vals+evals).max() add_rng = 0.1 * (axMax - axMin) rng = [ axMin - add_rng if not self.axisLog[axis] else 0.9 * axMin, axMax + add_rng if not self.axisLog[axis] else 1.1 * axMax, ] self.axisRange[axis] = rng'set %srange [%e:%e] %s' % (axis, rng[0], rng[1], 'reverse' if reverse else ''))
[docs] def setAxisLabel(self, label, axis = 'x'): """set label for specified axis :param label: label :type label: str :param axis: axis which to label :type axis: str """'set %slabel "%s"' % (axis, label))
[docs] def setAxisLog(self, log, axis = 'x'): """set logarithmic scale for specified axis :param log: whether to set logarithmic :type log: bool :param axis: axis which to set logarithmic :type axis: str """ self.axisLog[axis] = log if log: self._setter([ 'logscale %s' % axis, 'grid m%stics' % axis, 'format {0} "10^{{%L}}"'.format(axis) ]) else:'unset logscale %s' % axis)'set format {0} "%g"'.format(axis))
[docs] def setAxisLogs(self, **kwargs): """set axes logarithmic if requested""" for axis in ['x', 'y']: self.setAxisLog(kwargs.get(axis + 'log'), axis = axis)
[docs] def setVerticalLine(self, x, opts): """draw a vertical line :param x: position on x-axis :type x: float :param opts: line draw options :type opts: str """ self.nVertLines += 1 'set arrow %d from %f,graph(0,0) to %f,graph(1,1) nohead %s' % ( self.nVertLines, x, x, opts ) )
[docs] def addHorizontalLine(self, y, opts): """draw horizontal line :param y: y-position :type y: float :param opts: line draw options :type opts: str """ d = np.array([ [self.axisRange['x'][i], y] for i in xrange(2) ]) d, inline = 1, title = '', using = '1:2', with_ = ' '.join(['lines', opts]) ))
[docs] def setLabel(self, label, pos, abs_place = False): """draw a label into the figure :param label: label :type label: str :param pos: x,y - position :type pos: list :param abs_place: absolute or relative placement :type abs_place: bool """ self.nLabels += 1 place = 'at' if abs_place else 'at graph' 'set label %d "%s" %s %f, %f' % ( self.nLabels, label, place, pos[0], pos[1] ) )
[docs] def setArrow(self, p0, p1, prop): """draw an arrow into the figure :param p0: start point [x, y] :type p0: list :param p1: end point [x, y] :type p1: list :param prop: gnuplot property string for the arrow :type prop: str """ self.nArrows += 1 'set arrow %d from %g,%g to %g,%g %s' % ( self.nArrows, p0[0], p0[1], p1[0], p1[1], prop ) )
[docs] def setErrorArrows(self, **kwargs): """reset properties of arrows used to plot special errors""" self.arrow_offset = kwargs.get('arrow_offset', self.arrow_offset) self.arrow_length = kwargs.get('arrow_length', self.arrow_length) self.arrow_bar = kwargs.get('arrow_bar', self.arrow_bar)
[docs] def prepare_plot(self, margins=True, **kwargs): """prepare for plotting (calls all members of MyPlot)""" if self.size is None: self.size = kwargs.get('size', default_size) if margins: self.setMargins(**kwargs) self.setKeyOptions(kwargs.get('key', [])) for axis in ['x', 'y']: self.setAxisLabel(kwargs.get(axis + 'label', ''), axis = axis) self.setAxisRange( kwargs.get(axis + 'r'), axis = axis, reverse = kwargs.get(axis + 'reverse', False) ) for k, v in kwargs.get('lines', {}).iteritems(): axis, pos = k.split('=') if axis == 'y': self.setVerticalLine(float(pos), v) else: self.addHorizontalLine(float(pos), v) for k, v in kwargs.get('labels', {}).iteritems(): self.setLabel(k, v[:2], v[-1]) for a in kwargs.get('arrows', []): self.setArrow(*a)
[docs] def _convert(self): """convert eps/ps original into pdf, png and jpg format""" pdf_dims = [ int(ureg.parse_expression(s).to('point').magnitude) for s in self.size.split(',') ] call(' '.join([ 'gs', '-dBATCH', '-dNOPAUSE', '-sOutputFile=%s.pdf' % (, '-sDEVICE=pdfwrite', '-dDEVICEWIDTHPOINTS=%d' % (pdf_dims[1]), '-dDEVICEHEIGHTPOINTS=%d' % (pdf_dims[0]), '-c "<</PageOffset [-50 -50]>> setpagedevice"', '-f', self.epsname ]), shell = True) for ext in ['.png', '.jpg']: call(' '.join([ 'convert -density 150', + '.pdf', + ext ]), shell = True)
[docs] def _hdf5(self): """write data contained in plot to HDF5 file - easy numpy import -> (savetxt) -> gnuplot - export to ROOT objects h5py howto (see - open file: `f = h5py.File(name, 'r')` - list datasets: `list(f)` - load entire dataset as np array: `arr = f['dset_name'][...]` - NOTE: literally type the 3 dots, replace dset_name - np.savetxt format: `fmt = '%.4f %.3e %.3e %.3e %.3e'` - save array to txt file: `np.savetxt('arr.dat', arr, fmt=fmt)` :raises: ImportError """ try: import h5py f = h5py.File( + '.hdf5', 'w') for k, v in self.dataSets.iteritems(): f.create_dataset(k, data = v) f.close() except ImportError: print 'install h5py to also save an hdf5 file of your plot!' except: print 'h5py imported but error raised!' raise
[docs] def _ascii(self): """write ascii file(s) w/ data contained in plot""" if not os.path.exists( os.makedirs( for k, v in self.dataSets.iteritems(): np.savetxt( + '/' + self._prettify(k) + '.dat', v, fmt='%.4e' )
[docs] def _hardcopy(self): """generate eps, convert to other formats and write data to hdf5""" if self.nPanels < 1: # self.epsname, enhanced = 1, color = 1, mode = 'landscape', fontsize = 24 #) self._setter([ 'terminal postscript landscape enhanced color 24 size %s' % self.size, 'output "%s"' % self.epsname, ]) self._convert() self._hdf5() self._ascii()
[docs] def plot(self, hardcopy = True): """plot and generate output files"""* if hardcopy: self._hardcopy()