diff --git a/pykat/utilities/plotting/tools.py b/pykat/utilities/plotting/tools.py
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+# ------------------------------------------------------
+# This file is very much in flux at the moment and will
+# undergo many significant changes without notice.
+# Don't use this for anything but playing/testing yet.
+# Andreas 06.03.2014
+# ------------------------------------------------------
+
+import numpy as np
+import matplotlib
+BACKEND = 'Qt4Agg'
+matplotlib.use(BACKEND)
+from matplotlib import rc
+import matplotlib.pyplot as plt
+
+formatter = matplotlib.ticker.EngFormatter(unit='', places=0)
+formatter.ENG_PREFIXES[-6] = 'u'
+
+
+def printPDF(fig, filename):
+ if filename !='' and filename != None:
+ if not filename.lower().endswith(('.pdf')):
+ filename=filename+'.pdf'
+ pdfp = matplotlib.backends.backend_pdf.PdfPages(filename)
+ pdfp.savefig(fig, dpi=300,bbox_inches='tight')
+ pdfp.close()
+
+def plot_power_contour(x,y,z,xlabel, ylabel, clabel, title='', filename=''):
+ ax,fig=plot_setup()
+ xm,ym=np.meshgrid(x,y)
+ extent = [x[0], x[-1], y[0], y[-1] ]
+ mycm='YlOrRd_r'
+ mycm='hot'
+ #im = ax.imshow(z,origin='lower',extent=extent,cmap=mycm, aspect='auto', interpolation='nearest')
+ im = ax.imshow(z,origin='lower',extent=extent,cmap=mycm, aspect='auto')
+ cb = fig.colorbar(im, format="%.4g")
+ #cb.set_clim(-1.0*zlimit, zlimit)
+ ax.autoscale(False)
+ #ct = ax.contour(xm,ym,z, zdir='z', levels = [0])
+ #ax.clabel(ct,inline=1,fontsize=10)
+ ax.set_xlabel(xlabel)
+ ax.set_ylabel(ylabel)
+ cb.set_label(clabel)
+ ax.xaxis.set_major_formatter(formatter)
+ ax.yaxis.set_major_formatter(formatter)
+ fig.canvas.manager.set_window_title(title)
+ plt.show()
+ printPDF(fig, filename)
+
+
+def plot_error_contour(x,y,z,xlabel, ylabel, clabel, title='', filename=''):
+ global fig, ax, cb, ct, data
+ rc('font',**pp.font)
+ rc('xtick',labelsize=pp.TICK_SIZE)
+ rc('ytick',labelsize=pp.TICK_SIZE)
+ rc('text', usetex=pp.USETEX)
+ rc('axes', labelsize = pp.LABEL_SIZE)
+ fig, ax =plt.subplots()
+ fig.set_size_inches(pp.fig_size)
+ fig.set_dpi(pp.FIG_DPI)
+ xm,ym=np.meshgrid(x,y)
+ RGB1 = 255*np.array([0.23, 0.299, 0.754])
+ RGB2 = 255*np.array([0.706,0.016, 0.15])
+ cm1 = CM(RGB1, RGB2)
+ cm_values = cm1.getMap()
+ #cm1.showMap()
+ mycm = matplotlib.colors.ListedColormap(cm_values)
+ extent = [x[0], x[-1], y[0], y[-1] ]
+ data=z
+ # make symmetric color display
+ zlimit=np.max([abs(data.max()),abs(data.min())])
+ im = ax.imshow(data,origin='lower',extent=extent,cmap=mycm, aspect='auto', interpolation='nearest')
+ #im = ax.imshow(z[:,:,4],origin='lower',extent=extent,cmap=mycm, aspect='auto')
+ cb = fig.colorbar(im, format="%.4g")
+ cb.set_clim(-1.0*zlimit, zlimit)
+ ax.autoscale(False)
+ ct = ax.contour(xm,ym,data, zdir='z', levels = [0])
+ ax.clabel(ct,inline=1,fontsize=10)
+ ax.set_xlabel(xlabel)
+ ax.set_ylabel(ylabel)
+ cb.set_label(clabel)
+ ax.xaxis.set_major_formatter(formatter)
+ fig.canvas.manager.set_window_title(title)
+ plt.show()
+ printPDF(fig, filename)
+
+def plot_setup():
+ rc('font',**pp.font)
+ rc('xtick',labelsize=pp.TICK_SIZE)
+ rc('ytick',labelsize=pp.TICK_SIZE)
+ rc('text', usetex=pp.USETEX)
+ rc('axes', labelsize = pp.LABEL_SIZE)
+ fig, ax =plt.subplots()
+ fig.set_size_inches(pp.fig_size)
+ fig.set_dpi(pp.FIG_DPI)
+ return ax,fig
+
+class pp():
+ # set some gobal settings first
+ BACKEND = 'Qt4Agg' # matplotlib backend
+ FIG_DPI=90 # DPI of on sceen plot
+ # Some help in calculating good figure size for Latex
+ # documents. Starting with plot size in pt,
+ # get this from LaTeX using \showthe\columnwidth
+ fig_width_pt = 484.0
+ inches_per_pt = 1.0/72.27 # Convert TeX pt to inches
+ golden_mean = (np.sqrt(5)-1.0)/2.0 # Aesthetic ratio
+ fig_width = fig_width_pt*inches_per_pt # width in inches
+ fig_height = fig_width*golden_mean # height in inches
+ fig_size = [fig_width,fig_height]
+ # some plot options:
+ LINEWIDTH = 1 # linewidths of traces in plot
+ AA = True # antialiasing of traces
+ USETEX = False # use Latex encoding in text
+ SHADOW = False # shadow of legend box
+ GRID = True # grid on or off
+ # font sizes for normal text, tick labels and legend
+ FONT_SIZE = 10 # size of normal text
+ TICK_SIZE = 10 # size of tick labels
+ LABEL_SIZE = 10 # size of axes labels
+ LEGEND_SIZE = 10 # size of legend
+ # font family and type
+ font = {'family':'sans-serif','sans-serif':['Helvetica'],'size':FONT_SIZE}
+ DPI=300 # DPI for saving via savefig
+ # print options given to savefig command:
+ print_options = {'dpi':DPI, 'transparent':True, 'bbox_inches':'tight', 'pad_inches':0.1}
+ # for Palatino and other serif fonts use:
+ #font = {'family':'serif','serif':['Palatino']}
+ SCREEN_TITLE = True # show title on screen?
+ PRINT_TITLE = False # show title in saved file?
+
+# =============================================================================
+# ====================== The Class ColorMapCreator ============================
+# =============================================================================
+
+class CM:
+ """
+ Class ColorMapCreator:
+ Create diverging colormaps from RGB1 to RGB2 using the method of Moreland
+ or a simple CIELAB-interpolation. numColors controls the number of color
+ values to output (odd number) and divide gives the possibility to output
+ RGB-values from 0.0-1.0 instead of 0-255. If a filename different than
+ "" is given, the colormap will be saved to this file, otherwise a simple
+ output using print will be given.
+ """
+
+ # ======================== Global Variables ===============================
+
+ # Reference white-point D65
+ Xn, Yn, Zn = [95.047, 100.0, 108.883] # from Adobe Cookbook
+
+ # Transfer-matrix for the conversion of RGB to XYZ color space
+ transM = np.array([[0.4124564, 0.2126729, 0.0193339],
+ [0.3575761, 0.7151522, 0.1191920],
+ [0.1804375, 0.0721750, 0.9503041]])
+
+
+ # ============================= Functions =================================
+
+
+ def __init__(self, RGB1, RGB2, numColors = 257., divide = 255.,
+ method = "moreland", filename = ""):
+
+ # create a class variable for the number of colors
+ self.numColors = numColors
+
+ # assert an odd number of points
+ assert np.mod(numColors,2) == 1, \
+ "For diverging colormaps odd numbers of colors are desireable!"
+
+ # assert a known method was specified
+ knownMethods = ["moreland", "lab"]
+ assert method in knownMethods, "Unknown method was specified!"
+
+ if method == knownMethods[0]:
+ #generate the Msh diverging colormap
+ self.colorMap = self.generateColorMap(RGB1, RGB2, divide)
+ elif method == knownMethods[1]:
+ # generate the Lab diverging colormap
+ self.colorMap = self.generateColorMapLab(RGB1, RGB2, divide)
+
+ def getMap(self):
+ return self.colorMap
+
+ def showMap(self):
+ #rc('text', usetex=False)
+ a=np.outer(np.arange(0,1,0.01),np.ones(10))
+ fig=plt.figure(99,figsize=(10,2))
+ plt.axis("off")
+ cm = matplotlib.colors.ListedColormap(self.colorMap)
+ pm=plt.imshow(a,aspect='auto',cmap=cm,origin="lower")
+ plt.clim(0,1)
+ fig.colorbar(pm)
+ plt.draw()
+
+
+ def rgblinear(self, RGB):
+ """
+ Conversion from the sRGB components to RGB components with physically
+ linear properties.
+ """
+
+ # initialize the linear RGB array
+ RGBlinear = np.zeros((3,))
+
+ # calculate the linear RGB values
+ for i,value in enumerate(RGB):
+ value = float(value) / 255.
+ if value > 0.04045 :
+ value = ( ( value + 0.055 ) / 1.055 ) ** 2.4
+ else :
+ value = value / 12.92
+ RGBlinear[i] = value * 100.
+ return RGBlinear
+ #-
+
+ def sRGB(self, RGBlinear):
+ """
+ Back conversion from linear RGB to sRGB.
+ """
+
+ # initialize the sRGB array
+ RGB = np.zeros((3,))
+
+ # calculate the sRGB values
+ for i,value in enumerate(RGBlinear):
+ value = float(value) / 100.
+
+ if value > 0.00313080495356037152:
+ value = (1.055 * np.power(value,1./2.4) ) - 0.055
+ else :
+ value = value * 12.92
+
+ RGB[i] = round(value * 255.)
+ return RGB
+ #-
+
+ def rgb2xyz(self, RGB):
+ """
+ Conversion of RGB to XYZ using the transfer-matrix
+ """
+ return np.dot(self.rgblinear(RGB), self.transM)
+ #-
+
+ def xyz2rgb(self, XYZ):
+ """
+ Conversion of RGB to XYZ using the transfer-matrix
+ """
+ #return np.round(np.dot(XYZ, np.array(np.matrix(transM).I)))
+ return self.sRGB(np.dot(XYZ, np.array(np.matrix(self.transM).I)))
+ #-
+
+ def rgb2Lab(self, RGB):
+ """
+ Conversion of RGB to CIELAB
+ """
+
+ # convert RGB to XYZ
+ X, Y, Z = (self.rgb2xyz(RGB)).tolist()
+
+ # helper function
+ def f(x):
+ limit = 0.008856
+ if x> limit:
+ return np.power(x, 1./3.)
+ else:
+ return 7.787*x + 16./116.
+
+ # calculation of L, a and b
+ L = 116. * ( f(Y/self.Yn) - (16./116.) )
+ a = 500. * ( f(X/self.Xn) - f(Y/self.Yn) )
+ b = 200. * ( f(Y/self.Yn) - f(Z/self.Zn) )
+ return np.array([L, a, b])
+ #-
+
+ def Lab2rgb(self, Lab):
+ """
+ Conversion of CIELAB to RGB
+ """
+
+ # unpack the Lab-array
+ L, a, b = Lab.tolist()
+
+ # helper function
+ def finverse(x):
+ xlim = 0.008856
+ a = 7.787
+ b = 16./116.
+ ylim = a*xlim+b
+ if x > ylim:
+ return np.power(x, 3)
+ else:
+ return ( x - b ) / a
+
+ # calculation of X, Y and Z
+ X = self.Xn * finverse( (a/500.) + (L+16.)/116. )
+ Y = self.Yn * finverse( (L+16.)/116. )
+ Z = self.Zn * finverse( (L+16.)/116. - (b/200.) )
+
+ # conversion of XYZ to RGB
+ return self.xyz2rgb(np.array([X,Y,Z]))
+ #-
+
+ def Lab2Msh(self, Lab):
+ """
+ Conversion of CIELAB to Msh
+ """
+
+ # unpack the Lab-array
+ L, a, b = Lab.tolist()
+
+ # calculation of M, s and h
+ M = np.sqrt(np.sum(np.power(Lab, 2)))
+ s = np.arccos(L/M)
+ h = np.arctan2(b,a)
+ return np.array([M,s,h])
+ #-
+
+ def Msh2Lab(self, Msh):
+ """
+ Conversion of Msh to CIELAB
+ """
+
+ # unpack the Msh-array
+ M, s, h = Msh.tolist()
+
+ # calculation of L, a and b
+ L = M*np.cos(s)
+ a = M*np.sin(s)*np.cos(h)
+ b = M*np.sin(s)*np.sin(h)
+ return np.array([L,a,b])
+ #-
+
+ def rgb2Msh(self, RGB):
+ """ Direct conversion of RGB to Msh. """
+ return self.Lab2Msh(self.rgb2Lab(RGB))
+ #-
+
+ def Msh2rgb(self, Msh):
+ """ Direct conversion of Msh to RGB. """
+ return self.Lab2rgb(self.Msh2Lab(Msh))
+ #-
+
+ def adjustHue(self, MshSat, Munsat):
+ """
+ Function to provide an adjusted hue when interpolating to an
+ unsaturated color in Msh space.
+ """
+
+ # unpack the saturated Msh-array
+ Msat, ssat, hsat = MshSat.tolist()
+
+ if Msat >= Munsat:
+ return hsat
+ else:
+ hSpin = ssat * np.sqrt(Munsat**2 - Msat**2) / \
+ (Msat * np.sin(ssat))
+ if hsat > -np.pi/3:
+ return hsat + hSpin
+ else:
+ return hsat - hSpin
+ #-
+
+ def interpolateColor(self, RGB1, RGB2, interp):
+ """
+ Interpolation algorithm to automatically create continuous diverging
+ color maps.
+ """
+
+ # convert RGB to Msh and unpack
+ Msh1 = self.rgb2Msh(RGB1)
+ M1, s1, h1 = Msh1.tolist()
+ Msh2 = self.rgb2Msh(RGB2)
+ M2, s2, h2 = Msh2.tolist()
+
+ # If points saturated and distinct, place white in middle
+ if (s1>0.05) and (s2>0.05) and ( np.abs(h1-h2) > np.pi/3. ):
+ Mmid = max([M1, M2, 88.])
+ if interp < 0.5:
+ M2 = Mmid
+ s2 = 0.
+ h2 = 0.
+ interp = 2*interp
+ else:
+ M1 = Mmid
+ s1 = 0.
+ h1 = 0.
+ interp = 2*interp-1.
+
+ # Adjust hue of unsaturated colors
+ if (s1 < 0.05) and (s2 > 0.05):
+ h1 = self.adjustHue(np.array([M2,s2,h2]), M1)
+ elif (s2 < 0.05) and (s1 > 0.05):
+ h2 = self.adjustHue(np.array([M1,s1,h1]), M2)
+
+ # Linear interpolation on adjusted control points
+ MshMid = (1-interp)*np.array([M1,s1,h1]) + \
+ interp*np.array([M2,s2,h2])
+
+ return self.Msh2rgb(MshMid)
+ #-
+
+ def generateColorMap(self, RGB1, RGB2, divide):
+ """
+ Generate the complete diverging color map using the Moreland-technique
+ from RGB1 to RGB2, placing "white" in the middle. The number of points
+ given by "numPoints" controls the resolution of the colormap. The
+ optional parameter "divide" gives the possibility to scale the whole
+ colormap, for example to have float values from 0 to 1.
+ """
+
+ # calculate
+ scalars = np.linspace(0., 1., self.numColors)
+ RGBs = np.zeros((self.numColors, 3))
+ for i,s in enumerate(scalars):
+ RGBs[i,:] = self.interpolateColor(RGB1, RGB2, s)
+ return RGBs/divide
+ #-
+
+ def generateColorMapLab(self, RGB1, RGB2, divide):
+ """
+ Generate the complete diverging color map using a transition from
+ Lab1 to Lab2, transitioning true RGB-white. The number of points
+ given by "numPoints" controls the resolution of the colormap. The
+ optional parameter "divide" gives the possibility to scale the whole
+ colormap, for example to have float values from 0 to 1.
+ """
+
+ # convert to Lab-space
+ Lab1 = self.rgb2Lab(RGB1)
+ Lab2 = self.rgb2Lab(RGB2)
+ LabWhite = np.array([100., 0., 0.])
+
+ # initialize the resulting arrays
+ Lab = np.zeros((self.numColors ,3))
+ RGBs = np.zeros((self.numColors ,3))
+ N2 = np.floor(self.numColors/2.)
+
+ # calculate
+ for i in range(3):
+ Lab[0:N2+1, i] = np.linspace(Lab1[i], LabWhite[i], N2+1)
+ Lab[N2:, i] = np.linspace(LabWhite[i], Lab2[i], N2+1)
+ for i,l in enumerate(Lab):
+ RGBs[i,:] = self.Lab2rgb(l)
+ return RGBs/divide
+ #-
+