@@ -2,6 +2,10 @@ from numpy import * import unittest import scipy.optimize as opt import copy as cp +import matplotlib.pyplot as plt +from matplotlib import scale as mscale +from matplotlib import transforms as mtransforms +from pylab import * class SasData(object): """A data object for holding 1-d Q versus I SAS data. @@ -88,11 +92,12 @@ class SasData(object): out.i[j] = self.i[j] * other return out - ######### + + ################################################# # # SasTrim Routines for Trimming and Masking SasData # - ######### + ################################################# def make_mask(self, mask_ranges): """Generates a mask list of 0's and 1's to remove data in mask_ranges @@ -148,6 +153,115 @@ class SasData(object): ################################################### # +# Definition of plotting routines +# +################################################### + +class SasPlot(object): + """Class for generating and handling data plots. + + Uses the pylab module of matplotlib to generate and + manipulate plots and provide some easy routines for + modifying them, adding data, etc. + """ + + def __init__(self, data_to_plot=None, format='rO'): + """__init__ routine creates a plot with default features. + + """ + + plt.plot(data.q, data.i, format) + plt.ylabel('I') + plt.xlabel('Q') + # plt.title(name of data_to_plot) - how do I do this? + plt.show() + + # setup a list for holding the data for this plot + # self.data.append(name of data_to_plot) + + # a place to hold the figure and plot number + self.figure = plt.gcf() + self.axes = plt.gca() + + def guinier(self): + """Routine to convert to a Guinier plot. + + Converts plot to show data on the coordinates of ln(I) + versus Q^2. First we need to get the correct figure + number and then change the axes. The actual data file + remains unchanged. + """ + + ax = self.axes + ax.set_yscale('log', basey=e) + ax.set_xscale('q_squared') + + +class SquaredScale(mscale.ScaleBase): + """ScaleBase class for generating x axis of Guinier plots. + + Uses the built in scalebase to generate a transformed axis type + called SquaredScale which can be called using ax.set_xscale('q_squared'). + Currently uses the default ticker and scale setup which will need + to be changed in the future. + + The class requires the import of pylab (AutoLocator, ScalarFormatter + NullLocator and NullFormatter) matplotlib.transforms (imported as + mtransforms, required for the mtransforms.Transform class) and + matplotlib.scale (imported as mscale, required for the mscale.ScaleBase + class for inheritance of the scale). + """ + + name = 'q_squared' + + def __init__(self, axis, **kwargs): + mscale.ScaleBase.__init__(self) # what does this do? + + + def set_default_locators_and_formatters(self, axis): + """ + Set the locators and formatters to reasonable defaults for + scaling. Not really too sure what these do at the moment. + """ + axis.set_major_locator(AutoLocator()) + axis.set_major_formatter(ScalarFormatter()) + axis.set_minor_locator(NullLocator()) + axis.set_minor_formatter(NullFormatter()) + + class SquaredTransform(mtransforms.Transform): + input_dims = 1 + output_dims = 1 + is_separable = True + + def transform(self, a): return a**2 + + def inverted(self): + return SquaredScale.InvertedSquaredTransform() + + class InvertedSquaredTransform(mtransforms.Transform): + input_dims = 1 + output_dims = 1 + is_separable = True + + def transform(self, a): return a**0.5 + + def inverted(self): + return SquaredScale.SquaredTransform() + + def get_transform(self): + """Set the actual transform for the axis coordinates. + + """ + return self.SquaredTransform() + +mscale.register_scale(SquaredScale) + + + + + +################################################### +# # Definition of data fitting models # ################################################### sas.py 945b97f8754309c46fa311c6e9bdb5d037b0e841 Cameron Neylon cameron.neylon@stfc.ac.uk http://github.com/cameronneylon/sas/commit/4967b68c0268ecca7573eaad80900b2ae833b46f 4967b68c0268ecca7573eaad80900b2ae833b46f 2009-03-08T10:49:22-07:00 2009-03-08T10:49:22-07:00 added plotting routines and new squared scale for guinier plots - unsure how to write tests for this at moment f0fb5aa999c0e89714cf8f8845c24a57c726bfd5 Cameron Neylon cameron.neylon@stfc.ac.uk