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[plotting] library is unfolding and should be working tonight
This commit is contained in:
parent
a6c0d82ef7
commit
c3afb4eaaf
13 changed files with 648 additions and 263 deletions
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@ -2,14 +2,23 @@
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# Licensed under the BSD 3-clause license (see LICENSE.txt)
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try:
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#===========================================================================
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# Load in your plotting library here and
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# save it under the name plotting_library!
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# This is hooking the library in
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# for the usage in GPy:
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from ..util.config import config
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lib = config.get('plotting', 'library')
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if lib == 'matplotlib':
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import matplotlib
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from . import matplot_dep as plotting_library
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from .matplot_dep import plot_definitions
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plotting_library = plot_definitions.MatplotlibPlots()
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#===========================================================================
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except (ImportError, NameError):
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raise
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import warnings
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warnings.warn(ImportWarning("{} not available, install newest version of {} for plotting").format(lib, lib))
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warnings.warn(ImportWarning("{} not available, install newest version of {} for plotting".format(lib, lib)))
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config.set('plotting', 'library', 'none')
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if config.get('plotting', 'library') is not 'none':
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@ -20,12 +29,15 @@ if config.get('plotting', 'library') is not 'none':
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from ..core import GP
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GP.plot_data = gpy_plot.data_plots.plot_data
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GP.plot_mean = gpy_plot.gp_plots.plot_mean
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GP.plot_confidence = gpy_plot.gp_plots.plot_confidence
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from . import matplot_dep
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# Still to convert to new style:
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GP.plot = plotting_library.models_plots.plot_fit
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GP.plot_f = plotting_library.models_plots.plot_fit_f
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GP.plot_density = plotting_library.models_plots.plot_density
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GP.plot = matplot_dep.models_plots.plot_fit
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GP.plot_f = matplot_dep.models_plots.plot_fit_f
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GP.plot_density = matplot_dep.models_plots.plot_density
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GP.plot_errorbars_trainset = plotting_library.models_plots.plot_errorbars_trainset
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GP.plot_magnification = plotting_library.dim_reduction_plots.plot_magnification
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GP.plot_errorbars_trainset = matplot_dep.models_plots.plot_errorbars_trainset
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GP.plot_magnification = matplot_dep.dim_reduction_plots.plot_magnification
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145
GPy/plotting/abstract_plotting_library.py
Normal file
145
GPy/plotting/abstract_plotting_library.py
Normal file
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@ -0,0 +1,145 @@
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#===============================================================================
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# Copyright (c) 2015, Max Zwiessele
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# All rights reserved.
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#
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# Redistribution and use in source and binary forms, with or without
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# modification, are permitted provided that the following conditions are met:
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#
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# * Redistributions of source code must retain the above copyright notice, this
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# list of conditions and the following disclaimer.
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#
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# * Redistributions in binary form must reproduce the above copyright notice,
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# this list of conditions and the following disclaimer in the documentation
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# and/or other materials provided with the distribution.
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#
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# * Neither the name of GPy.plotting.abstract_plotting_library nor the names of its
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# contributors may be used to endorse or promote products derived from
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# this software without specific prior written permission.
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#
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# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
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# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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#===============================================================================
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#===============================================================================
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# Make sure that the necessary files and functions are
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# defined in the plotting library:
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class AbstractPlottingLibrary(object):
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def __init__(self):
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"""
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Set the defaults dictionary in the _defaults variable:
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E.g. for matplotlib we define a file defaults.py and
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set the dictionary of it here:
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from . import defaults
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_defaults = defaults.__dict__
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"""
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self._defaults = {}
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self.__defaults = None
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@property
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def defaults(self):
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#===============================================================================
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if self.__defaults is None:
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from collections import defaultdict
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class defaultdict(defaultdict):
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def __getattr__(self, *args, **kwargs):
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return defaultdict.__getitem__(self, *args, **kwargs)
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self.__defaults = defaultdict(dict, self._defaults)
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return self.__defaults
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#===============================================================================
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def get_new_canvas(self, **kwargs):
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"""
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Return a canvas, kwargupdate for your plotting library.
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This method does two things, it creates an empty canvas
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and updates the kwargs (deletes the unnecessary kwargs)
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for further usage in normal plotting.
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E.g. in matplotlib this means it deletes references to ax, as
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plotting is done on the axis itself and is not a kwarg.
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"""
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raise NotImplementedError("Implement all plot functions in AbstractPlottingLibrary in order to use your own plotting library")
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def show_canvas(self, canvas, plots):
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"""
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Show the canvas given.
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plots is either a list of plots or a dictionary with the plots
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as the items.
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E.g. in matplotlib this does not have to do anything, we make the tight plot, though.
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"""
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raise NotImplementedError("Implement all plot functions in AbstractPlottingLibrary in order to use your own plotting library")
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def plot(self, cavas, X, Y, **kwargs):
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"""
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Make a line plot from for Y on X (Y = f(X)) on the canvas.
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the kwargs are plotting library specific kwargs!
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"""
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raise NotImplementedError("Implement all plot functions in AbstractPlottingLibrary in order to use your own plotting library")
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def scatter(self, canvas, X, Y, **kwargs):
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"""
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Make a scatter plot between X and Y on the canvas given.
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the kwargs are plotting library specific kwargs!
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"""
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raise NotImplementedError("Implement all plot functions in AbstractPlottingLibrary in order to use your own plotting library")
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def xerrorbar(self, canvas, X, Y, error, **kwargs):
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"""
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Make an errorbar along the xaxis for points at (X,Y) on the canvas.
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the kwargs are plotting library specific kwargs!
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"""
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raise NotImplementedError("Implement all plot functions in AbstractPlottingLibrary in order to use your own plotting library")
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def yerrorbar(self, canvas, X, Y, error, **kwargs):
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"""
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Make errorbars along the yaxis on the canvas given.
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the kwargs are plotting library specific kwargs!
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"""
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raise NotImplementedError("Implement all plot functions in AbstractPlottingLibrary in order to use your own plotting library")
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def imshow(self, canvas, X, **kwargs):
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"""
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Show the image stored in X on the canvas/
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the kwargs are plotting library specific kwargs!
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"""
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raise NotImplementedError("Implement all plot functions in AbstractPlottingLibrary in order to use your own plotting library")
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def contour(self, canvas, X, Y, C, **kwargs):
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"""
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Make a contour plot at (X, Y) with heights stored in C on the canvas.
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the kwargs are plotting library specific kwargs!
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"""
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raise NotImplementedError("Implement all plot functions in AbstractPlottingLibrary in order to use your own plotting library")
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def fill_between(self, canvas, X, lower, upper, **kwargs):
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"""
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Fill along the xaxis between lower and upper.
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the kwargs are plotting library specific kwargs!
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"""
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raise NotImplementedError("Implement all plot functions in AbstractPlottingLibrary in order to use your own plotting library")
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def fill_gradient(self, canvas, X, percentiles, **kwargs):
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"""
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Plot a gradient (in alpha values) for the given percentiles.
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the kwargs are plotting library specific kwargs!
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"""
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raise NotImplementedError("Implement all plot functions in AbstractPlottingLibrary in order to use your own plotting library")
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@ -1,29 +1,3 @@
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def update_not_existing_kwargs(to_update, update_from):
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return to_update.update({k:v for k,v in update_from.items() if k not in to_update})
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#===============================================================================
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# Implement library specific defaults in the specific plotting librarys defaults.py file.
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# The following lines ensure, that an empty kwarg gets returned, when accessing a not
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# existing default
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from .. import plotting_library as pl
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from collections import defaultdict
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class defaultdict(defaultdict):
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def __getattr__(self, *args, **kwargs):
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return defaultdict.__getitem__(self, *args, **kwargs)
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defaults = defaultdict(dict, **pl.defaults.__dict__)
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pl.defaults = defaults
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#===============================================================================
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#===============================================================================
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# Make sure that the necessary files and functions are
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# defined in the plotting library:
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assert hasattr(pl, 'get_new_canvas'), "Please implement a function to get a new canvas for the specific library in plotting_library.get_new_canvas(**kwargs)"
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assert hasattr(pl, 'plot'), "Please implement a function to plot a simple line"
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assert hasattr(pl, 'scatter'), "Please implement a function to plot a simple scatterplot"
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#assert hasattr(pl, 'xerrorbar'), "Please implement a function to plot an errorbar along the xaxis"
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#assert hasattr(pl, 'xerrorbar'), "Please implement a function to plot an errorbar along the yaxis"
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#assert hasattr(pl, 'fill'), "Please implement a function to fill a section between points"
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#assert hasattr(pl, 'imshow'), "Please implement a function to plot an image in the given boundaries"
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#===============================================================================
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from . import data_plots, gp_plots
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@ -27,16 +27,51 @@
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# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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#===============================================================================
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from . import pl
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from . import update_not_existing_kwargs
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from . import defaults
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from functools import wraps
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from . import pl
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import numpy as np
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from .plot_util import get_x_y_var, get_free_dims, get_which_data_ycols,\
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get_which_data_rows, update_not_existing_kwargs
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def _plot_data(self, canvas, which_data_rows='all',
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which_data_ycols='all', visible_dims=None,
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error_kwargs=None, **plot_kwargs):
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if error_kwargs is None:
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error_kwargs = {}
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ycols = get_which_data_ycols(self, which_data_ycols)
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rows = get_which_data_rows(self, which_data_rows)
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X, X_variance, Y = get_x_y_var(self)
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free_dims = get_free_dims(self, visible_dims, None)
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plots = {}
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plots['dataplot'] = []
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plots['xerrorplot'] = []
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#one dimensional plotting
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if len(free_dims) == 1:
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for d in ycols:
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update_not_existing_kwargs(plot_kwargs, pl.defaults.data_1d)
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plots['dataplot'].append(pl.scatter(canvas, X[rows, free_dims], Y[rows, d], **plot_kwargs))
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if X_variance is not None:
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update_not_existing_kwargs(error_kwargs, pl.defaults.xerrorbar)
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plots['xerrorplot'].append(pl.xerrorbar(canvas, X[rows, free_dims].flatten(), Y[rows, d].flatten(),
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2 * np.sqrt(X_variance[rows, free_dims].flatten()),
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**error_kwargs))
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#2D plotting
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elif len(free_dims) == 2:
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for d in ycols:
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update_not_existing_kwargs(plot_kwargs, pl.defaults.data_2d)
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plots['dataplot'].append(pl.scatter(canvas, X[rows, free_dims[0]], X[rows, free_dims[1]],
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c=Y[rows, d], vmin=Y.min(), vmax=Y.max(), **plot_kwargs))
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else:
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raise NotImplementedError("Cannot plot in more then two dimensions")
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return plots
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def plot_data(self, which_data_rows='all',
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which_data_ycols='all', visible_dims=None,
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error_kwargs=None, **plot_kwargs):
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"""
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Plot the training data
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- For higher dimensions than two, use fixed_inputs to plot the data points with some of the inputs fixed.
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@ -52,53 +87,9 @@ def _plot_data(self, canvas, which_data_rows='all',
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:type visible_dims: a numpy array
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:param dict error_kwargs: kwargs for the error plot for the plotting library you are using
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:param kwargs plot_kwargs: kwargs for the data plot for the plotting library you are using
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"""
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#deal with optional arguments
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if which_data_rows == 'all':
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which_data_rows = slice(None)
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if which_data_ycols == 'all':
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which_data_ycols = np.arange(self.output_dim)
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if error_kwargs is None:
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error_kwargs = {}
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if hasattr(self, 'has_uncertain_inputs') and self.has_uncertain_inputs():
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X = self.X.mean
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X_variance = self.X.variance
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else:
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X = self.X
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X_variance = None
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Y = self.Y
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#work out what the inputs are for plotting (1D or 2D)
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if visible_dims is None:
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visible_dims = np.arange(self.input_dim)
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assert visible_dims.size <= 2, "Visible inputs cannot be larger than two"
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free_dims = visible_dims
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#one dimensional plotting
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if len(free_dims) == 1:
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for d in which_data_ycols:
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update_not_existing_kwargs(plot_kwargs, defaults.data_1d)
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canvas.append(pl.scatter(canvas, X[which_data_rows, free_dims], Y[which_data_rows, d], **plot_kwargs))
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if X_variance is not None:
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update_not_existing_kwargs(error_kwargs, defaults.xerrorbar)
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canvas.append(pl.xerrorbar(canvas, X[which_data_rows, free_dims].flatten(), Y[which_data_rows, d].flatten(),
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2 * np.sqrt(X_variance[which_data_rows, free_dims].flatten()),
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**error_kwargs))
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#2D plotting
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elif len(free_dims) == 2:
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for d in which_data_ycols:
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update_not_existing_kwargs(plot_kwargs, defaults.data_2d)
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canvas = pl.scatter(canvas, X[which_data_rows, free_dims[0]], X[which_data_rows, free_dims[1]],
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c=Y[which_data_rows, d], vmin=Y.min(), vmax=Y.max(), **plot_kwargs)
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else:
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raise NotImplementedError("Cannot plot in more then two dimensions")
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return canvas
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@wraps(_plot_data)
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def plot_data(self, which_data_rows='all',
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which_data_ycols='all', visible_dims=None,
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error_kwargs=None, **plot_kwargs):
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:returns list: of plots created.
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"""
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canvas, kwargs = pl.get_new_canvas(plot_kwargs)
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_plot_data(self, canvas, which_data_rows, which_data_ycols, visible_dims, error_kwargs, **kwargs)
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return pl.show_canvas(canvas)
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plots = _plot_data(self, canvas, which_data_rows, which_data_ycols, visible_dims, error_kwargs, **kwargs)
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return pl.show_canvas(canvas, plots)
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|
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@ -28,78 +28,140 @@
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# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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#===============================================================================
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from . import pl
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from . import update_not_existing_kwargs, defaults
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from .util import x_frame1D
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from scipy import sparse
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import numpy as np
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from functools import wraps
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def plot_mean(self, plot_limits=None, fixed_inputs=[],
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from . import pl
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from .plot_util import get_x_y_var, get_fixed_dims, get_free_dims, \
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x_frame1D, x_frame2D, update_not_existing_kwargs, \
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helper_predict_with_model
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def _helper_for_plots(self, plot_limits, fixed_inputs, resolution):
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"""
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Figure out the data, free_dims and create an Xgrid for
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the prediction.
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"""
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X, Xvar, Y = get_x_y_var(self)
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#work out what the inputs are for plotting (1D or 2D)
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fixed_dims = get_fixed_dims(self, fixed_inputs)
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free_dims = get_free_dims(self, None, fixed_dims)
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if len(free_dims) == 1:
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#define the frame on which to plot
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resolution = resolution or 200
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Xnew, xmin, xmax = x_frame1D(X[:,free_dims], plot_limits=plot_limits, resolution=resolution)
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Xgrid = np.empty((Xnew.shape[0],self.input_dim))
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Xgrid[:,free_dims] = Xnew
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for i,v in fixed_dims:
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Xgrid[:,i] = v
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x = Xgrid
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y = None
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elif len(free_dims) == 2:
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#define the frame for plotting on
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resolution = resolution or 50
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Xnew, x, y, xmin, xmax = x_frame2D(X[:,free_dims], plot_limits, resolution)
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Xgrid = np.empty((Xnew.shape[0],self.input_dim))
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Xgrid[:,free_dims] = Xnew
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for i,v in fixed_dims:
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Xgrid[:,i] = v
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return X, Xvar, Y, fixed_dims, free_dims, Xgrid, x, y, xmin, xmax, resolution
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def plot_mean(self, plot_limits=None, fixed_inputs=None,
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resolution=None, plot_raw=False,
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Y_metadata=None, apply_link=False,
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plot_uncertain_inputs=True, predict_kw=None,
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which_data_ycols='all',
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levels=20,
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predict_kw=None,
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**kwargs):
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"""
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Plot the mean of a GP.
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Plot the mean of the GP.
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:param plot_limits: The limits of the plot. If 1D [xmin,xmax], if 2D [[xmin,ymin],[xmax,ymax]]. Defaluts to data limits
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:type plot_limits: np.array
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:param fixed_inputs: a list of tuple [(i,v), (i,v)...], specifying that input index i should be set to value v.
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:param fixed_inputs: a list of tuple [(i,v), (i,v)...], specifying that input dimension i should be set to value v.
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:type fixed_inputs: a list of tuples
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:param levels: for 2D plotting, the number of contour levels to use is ax is None, create a new figure
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:type levels: int
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:param int resolution: The resolution of the prediction [defaults are 1D:200, 2D:50]
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:param bool plot_raw: plot the latent function (usually denoted f) only?
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:param dict Y_metadata: the Y_metadata (for e.g. heteroscedastic GPs)
|
||||
:param bool apply_link: whether to apply the link function of the GP to the raw prediction.
|
||||
:param array-like which_data_ycols: which columns of y to plot (array-like or list of ints)
|
||||
:param dict predict_kw: the keyword arguments for the prediction. If you want to plot a specific kernel give dict(kern=<specific kernel>) in here
|
||||
:param int levels: for 2D plotting, the number of contour levels to use is
|
||||
"""
|
||||
if hasattr(self, 'has_uncertain_inputs') and self.has_uncertain_inputs():
|
||||
X = self.X.mean
|
||||
X_variance = self.X.variance
|
||||
else:
|
||||
X = self.X
|
||||
|
||||
Y = self.Y
|
||||
|
||||
if sparse.issparse(Y): Y = Y.todense().view(np.ndarray)
|
||||
canvas, kwargs = pl.get_new_canvas(kwargs)
|
||||
plots = _plot_mean(self, canvas, plot_limits, fixed_inputs, resolution, plot_raw, Y_metadata, apply_link, which_data_ycols, levels, predict_kw, **kwargs)
|
||||
return pl.show_canvas(canvas, plots)
|
||||
|
||||
@wraps(plot_mean)
|
||||
def _plot_mean(self, canvas, plot_limits=None, fixed_inputs=None,
|
||||
resolution=None, plot_raw=False,
|
||||
Y_metadata=None, apply_link=False,
|
||||
which_data_ycols=None,
|
||||
levels=20,
|
||||
predict_kw=None, **kwargs):
|
||||
if predict_kw is None:
|
||||
predict_kw = {}
|
||||
|
||||
#work out what the inputs are for plotting (1D or 2D)
|
||||
fixed_dims = np.array([i for i,v in fixed_inputs])
|
||||
free_dims = np.setdiff1d(np.arange(self.input_dim),fixed_dims)
|
||||
_, _, _, _, free_dims, Xgrid, x, y, _, _, resolution = _helper_for_plots(self, plot_limits, fixed_inputs, resolution)
|
||||
|
||||
if len(free_dims<=2):
|
||||
which_data_ycols = get_which_data_ycols(self, which_data_ycols)
|
||||
mu, _ = helper_predict_with_model(self, Xgrid, plot_raw, apply_link, None, which_data_ycols, **predict_kw)
|
||||
if len(free_dims)==1:
|
||||
# 1D plotting:
|
||||
update_not_existing_kwargs(kwargs, pl.defaults.meanplot_1d)
|
||||
return dict(gpmean=[pl.plot(canvas, Xgrid, mu, **kwargs)])
|
||||
else:
|
||||
update_not_existing_kwargs(kwargs, pl.defaults.meanplot_2d)
|
||||
return dict(gpmean=[pl.contour(canvas, x, y,
|
||||
mu.reshape(resolution, resolution),
|
||||
levels=levels, **kwargs)])
|
||||
|
||||
def plot_confidence(self, lower=2.5, upper=97.5, plot_limits=None, fixed_inputs=None,
|
||||
resolution=None, plot_raw=False,
|
||||
Y_metadata=None, apply_link=False,
|
||||
which_data_ycols='all',
|
||||
predict_kw=None,
|
||||
**kwargs):
|
||||
"""
|
||||
Plot the confidence interval between the percentiles lower and upper.
|
||||
E.g. the 95% confidence interval is $2.5, 97.5$.
|
||||
Note: Only implemented for one dimension!
|
||||
|
||||
#define the frame on which to plot
|
||||
Xnew, xmin, xmax = x_frame1D(X[:,free_dims], plot_limits=plot_limits, resolution=resolution or 200)
|
||||
Xgrid = np.empty((Xnew.shape[0],self.input_dim))
|
||||
Xgrid[:,free_dims] = Xnew
|
||||
for i,v in fixed_inputs:
|
||||
Xgrid[:,i] = v
|
||||
:param plot_limits: The limits of the plot. If 1D [xmin,xmax], if 2D [[xmin,ymin],[xmax,ymax]]. Defaluts to data limits
|
||||
:type plot_limits: np.array
|
||||
:param fixed_inputs: a list of tuple [(i,v), (i,v)...], specifying that input dimension i should be set to value v.
|
||||
:type fixed_inputs: a list of tuples
|
||||
:param int resolution: The resolution of the prediction [default:200]
|
||||
:param bool plot_raw: plot the latent function (usually denoted f) only?
|
||||
:param dict Y_metadata: the Y_metadata (for e.g. heteroscedastic GPs)
|
||||
:param bool apply_link: whether to apply the link function of the GP to the raw prediction.
|
||||
:param array-like which_data_ycols: which columns of y to plot (array-like or list of ints)
|
||||
:param dict predict_kw: the keyword arguments for the prediction. If you want to plot a specific kernel give dict(kern=<specific kernel>) in here
|
||||
"""
|
||||
canvas, kwargs = pl.get_new_canvas(kwargs)
|
||||
plots = _plot_confidence(self, canvas, lower, upper, plot_limits,
|
||||
fixed_inputs, resolution, plot_raw, Y_metadata,
|
||||
apply_link, which_data_ycols,
|
||||
predict_kw, **kwargs)
|
||||
return pl.show_canvas(canvas, plots)
|
||||
|
||||
if plot_raw:
|
||||
mu = self._raw_predict(Xgrid)[0]
|
||||
|
||||
update_not_existing_kwargs(kwargs, defaults.meanplot)
|
||||
return pl.plot(Xgrid, mu, **kwargs)
|
||||
def _plot_confidence(self, canvas, lower, upper, plot_limits=None, fixed_inputs=None,
|
||||
resolution=None, plot_raw=False,
|
||||
Y_metadata=None, apply_link=False,
|
||||
which_data_ycols=None,
|
||||
predict_kw=None,
|
||||
**kwargs):
|
||||
if predict_kw is None:
|
||||
predict_kw = {}
|
||||
|
||||
_, _, _, _, _, Xgrid, _, _, _, _, _ = _helper_for_plots(self, plot_limits, fixed_inputs, resolution)
|
||||
|
||||
def gpplot(x, mu, lower, upper, edgecol='#3300FF', fillcol='#33CCFF', ax=None, fignum=None, **kwargs):
|
||||
_, axes = ax_default(fignum, ax)
|
||||
update_not_existing_kwargs(kwargs, pl.defaults.confidence_interval)
|
||||
_, percs = helper_predict_with_model(self, Xgrid, plot_raw, apply_link, (lower, upper), which_data_ycols, **predict_kw)
|
||||
|
||||
mu = mu.flatten()
|
||||
x = x.flatten()
|
||||
lower = lower.flatten()
|
||||
upper = upper.flatten()
|
||||
return dict(gpconfidence=pl.fill_between(canvas, Xgrid, percs[0], percs[1], **kwargs))
|
||||
|
||||
plots = []
|
||||
|
||||
#here's the mean
|
||||
plots.append(meanplot(x, mu, edgecol, axes))
|
||||
|
||||
#here's the box
|
||||
kwargs['linewidth']=0.5
|
||||
if not 'alpha' in kwargs.keys():
|
||||
kwargs['alpha'] = 0.3
|
||||
plots.append(axes.fill(np.hstack((x,x[::-1])),np.hstack((upper,lower[::-1])),color=fillcol,**kwargs))
|
||||
|
||||
#this is the edge:
|
||||
plots.append(meanplot(x, upper,color=edgecol, linewidth=0.2, ax=axes))
|
||||
plots.append(meanplot(x, lower,color=edgecol, linewidth=0.2, ax=axes))
|
||||
|
||||
return plots
|
||||
|
||||
|
||||
|
|
@ -27,3 +27,145 @@
|
|||
# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
|
||||
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
|
||||
#===============================================================================
|
||||
|
||||
import numpy as np
|
||||
from scipy import sparse
|
||||
|
||||
def helper_predict_with_model(self, Xgrid, plot_raw, apply_link, which_data_ycols, percentiles, **predict_kw):
|
||||
"""
|
||||
Make the right decisions for prediction with a model
|
||||
based on the standard arguments of plotting.
|
||||
|
||||
This is quite complex and will take a while to understand,
|
||||
so do not change anything in here lightly!!!
|
||||
"""
|
||||
if 'likelihood' not in predict_kw:
|
||||
if plot_raw:
|
||||
from ...likelihoods import Gaussian
|
||||
lik = Gaussian(0) # Make the likelihood not add any noise
|
||||
else:
|
||||
lik = None
|
||||
predict_kw['likelihood'] = lik
|
||||
|
||||
mu, _ = self.predict(Xgrid, **predict_kw)
|
||||
|
||||
if percentiles is not None:
|
||||
percentiles = self.predict_quantiles(Xgrid, quantiles=percentiles, **predict_kw)
|
||||
else: percentiles = {}
|
||||
|
||||
retmu = np.empty((Xgrid.shape[0], len(ycols)))
|
||||
|
||||
if plot_raw and apply_link:
|
||||
for i, d in enumerate(ycols):
|
||||
retmu = self.likelihood.gp_link.transf(mu[:, [i]])
|
||||
for perc in percentiles:
|
||||
perc[:, [i]] = self.likelihood.gp_link.transf(perc[:, [i]])
|
||||
|
||||
return mu, percentiles
|
||||
|
||||
def update_not_existing_kwargs(to_update, update_from):
|
||||
"""
|
||||
This function updates the keyword aguments from update_from in
|
||||
to_update, only if the keys are not set in to_update.
|
||||
|
||||
This is used for updated kwargs from the default dicts.
|
||||
"""
|
||||
return to_update.update({k:v for k,v in update_from.items() if k not in to_update})
|
||||
|
||||
def get_x_y_var(model):
|
||||
"""
|
||||
The the data from a model as
|
||||
X the inputs,
|
||||
X_variance the variance of the inputs ([default: None])
|
||||
and Y the outputs
|
||||
|
||||
:returns: (X, X_variance, Y)
|
||||
"""
|
||||
if hasattr(model, 'has_uncertain_inputs') and model.has_uncertain_inputs():
|
||||
X = model.X.mean
|
||||
X_variance = model.X.variance
|
||||
else:
|
||||
X = model.X
|
||||
X_variance = None
|
||||
Y = model.Y
|
||||
if sparse.issparse(Y): Y = Y.todense().view(np.ndarray)
|
||||
return X, X_variance, Y
|
||||
|
||||
def get_free_dims(model, visible_dims, fixed_dims):
|
||||
"""
|
||||
work out what the inputs are for plotting (1D or 2D)
|
||||
|
||||
The visible dimensions are the dimensions, which are visible.
|
||||
the fixed_dims are the fixed dimensions for this.
|
||||
|
||||
The free_dims are then the visible dims without the fixed dims.
|
||||
"""
|
||||
if visible_dims is None:
|
||||
visible_dims = np.arange(model.input_dim)
|
||||
assert visible_dims.size <= 2, "Visible inputs cannot be larger than two"
|
||||
if fixed_dims is None:
|
||||
return visible_dims
|
||||
else:
|
||||
return np.setdiff1d(visible_dims, fixed_dims)
|
||||
|
||||
def get_fixed_dims(model, fixed_inputs):
|
||||
"""
|
||||
Work out the fixed dimensions from the fixed_inputs list of tuples.
|
||||
"""
|
||||
if fixed_inputs is None:
|
||||
fixed_inputs = []
|
||||
return np.array([i for i,_ in fixed_inputs])
|
||||
|
||||
def get_which_data_ycols(model, which_data_ycols):
|
||||
"""
|
||||
Helper to get the data columns to plot.
|
||||
"""
|
||||
if which_data_ycols == 'all' or which_data_ycols is None:
|
||||
return np.arange(model.output_dim)
|
||||
return which_data_ycols
|
||||
|
||||
def get_which_data_rows(model, which_data_rows):
|
||||
"""
|
||||
Helper to get the data rows to plot.
|
||||
"""
|
||||
if which_data_rows == 'all' or which_data_rows is None:
|
||||
return slice(None)
|
||||
return which_data_rows
|
||||
|
||||
def x_frame1D(X,plot_limits=None,resolution=None):
|
||||
"""
|
||||
Internal helper function for making plots, returns a set of input values to plot as well as lower and upper limits
|
||||
"""
|
||||
assert X.shape[1] ==1, "x_frame1D is defined for one-dimensional inputs"
|
||||
if plot_limits is None:
|
||||
from ...core.parameterization.variational import VariationalPosterior
|
||||
if isinstance(X, VariationalPosterior):
|
||||
xmin,xmax = X.mean.min(0),X.mean.max(0)
|
||||
else:
|
||||
xmin,xmax = X.min(0),X.max(0)
|
||||
xmin, xmax = xmin-0.2*(xmax-xmin), xmax+0.2*(xmax-xmin)
|
||||
elif len(plot_limits)==2:
|
||||
xmin, xmax = plot_limits
|
||||
else:
|
||||
raise ValueError("Bad limits for plotting")
|
||||
|
||||
Xnew = np.linspace(xmin,xmax,resolution or 200)[:,None]
|
||||
return Xnew, xmin, xmax
|
||||
|
||||
def x_frame2D(X,plot_limits=None,resolution=None):
|
||||
"""
|
||||
Internal helper function for making plots, returns a set of input values to plot as well as lower and upper limits
|
||||
"""
|
||||
assert X.shape[1] ==2, "x_frame2D is defined for two-dimensional inputs"
|
||||
if plot_limits is None:
|
||||
xmin,xmax = X.min(0),X.max(0)
|
||||
xmin, xmax = xmin-0.2*(xmax-xmin), xmax+0.2*(xmax-xmin)
|
||||
elif len(plot_limits)==2:
|
||||
xmin, xmax = plot_limits
|
||||
else:
|
||||
raise ValueError("Bad limits for plotting")
|
||||
|
||||
resolution = resolution or 50
|
||||
xx, yy = np.mgrid[xmin[0]:xmax[0]:1j*resolution,xmin[1]:xmax[1]:1j*resolution]
|
||||
Xnew = np.vstack((xx.flatten(),yy.flatten())).T
|
||||
return Xnew, xx, yy, xmin, xmax
|
||||
|
|
@ -1,68 +0,0 @@
|
|||
#===============================================================================
|
||||
# Copyright (c) 2012-2015 GPy Authors
|
||||
# All rights reserved.
|
||||
#
|
||||
# Redistribution and use in source and binary forms, with or without
|
||||
# modification, are permitted provided that the following conditions are met:
|
||||
#
|
||||
# * Redistributions of source code must retain the above copyright notice, this
|
||||
# list of conditions and the following disclaimer.
|
||||
#
|
||||
# * Redistributions in binary form must reproduce the above copyright notice,
|
||||
# this list of conditions and the following disclaimer in the documentation
|
||||
# and/or other materials provided with the distribution.
|
||||
#
|
||||
# * Neither the name of GPy nor the names of its
|
||||
# contributors may be used to endorse or promote products derived from
|
||||
# this software without specific prior written permission.
|
||||
#
|
||||
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
|
||||
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
|
||||
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
|
||||
# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
|
||||
# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
|
||||
# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
|
||||
# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
|
||||
# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
|
||||
# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
|
||||
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
|
||||
#===============================================================================
|
||||
import numpy as np
|
||||
|
||||
def x_frame1D(X,plot_limits=None,resolution=None):
|
||||
"""
|
||||
Internal helper function for making plots, returns a set of input values to plot as well as lower and upper limits
|
||||
"""
|
||||
assert X.shape[1] ==1, "x_frame1D is defined for one-dimensional inputs"
|
||||
if plot_limits is None:
|
||||
from ...core.parameterization.variational import VariationalPosterior
|
||||
if isinstance(X, VariationalPosterior):
|
||||
xmin,xmax = X.mean.min(0),X.mean.max(0)
|
||||
else:
|
||||
xmin,xmax = X.min(0),X.max(0)
|
||||
xmin, xmax = xmin-0.2*(xmax-xmin), xmax+0.2*(xmax-xmin)
|
||||
elif len(plot_limits)==2:
|
||||
xmin, xmax = plot_limits
|
||||
else:
|
||||
raise ValueError("Bad limits for plotting")
|
||||
|
||||
Xnew = np.linspace(xmin,xmax,resolution or 200)[:,None]
|
||||
return Xnew, xmin, xmax
|
||||
|
||||
def x_frame2D(X,plot_limits=None,resolution=None):
|
||||
"""
|
||||
Internal helper function for making plots, returns a set of input values to plot as well as lower and upper limits
|
||||
"""
|
||||
assert X.shape[1] ==2, "x_frame2D is defined for two-dimensional inputs"
|
||||
if plot_limits is None:
|
||||
xmin,xmax = X.min(0),X.max(0)
|
||||
xmin, xmax = xmin-0.2*(xmax-xmin), xmax+0.2*(xmax-xmin)
|
||||
elif len(plot_limits)==2:
|
||||
xmin, xmax = plot_limits
|
||||
else:
|
||||
raise ValueError("Bad limits for plotting")
|
||||
|
||||
resolution = resolution or 50
|
||||
xx,yy = np.mgrid[xmin[0]:xmax[0]:1j*resolution,xmin[1]:xmax[1]:1j*resolution]
|
||||
Xnew = np.vstack((xx.flatten(),yy.flatten())).T
|
||||
return Xnew, xx, yy, xmin, xmax
|
||||
|
|
@ -1,54 +1,6 @@
|
|||
# Copyright (c) 2014, GPy authors (see AUTHORS.txt).
|
||||
# Licensed under the BSD 3-clause license (see LICENSE.txt)
|
||||
|
||||
from matplotlib import pyplot as plt
|
||||
from . import defaults
|
||||
|
||||
def get_new_canvas(kwargs):
|
||||
"""
|
||||
Return a canvas, kwargupdate for matplotlib. This just a
|
||||
dictionary for the collection and we add the an axis to kwarg.
|
||||
|
||||
This method does two things, it creates an empty canvas
|
||||
and updates the kwargs (deletes the unnecessary kwargs)
|
||||
for further usage in normal plotting.
|
||||
|
||||
in matplotlib this means it deletes references to ax, as
|
||||
plotting is done on the axis itself and is not a kwarg.
|
||||
"""
|
||||
if 'ax' in kwargs:
|
||||
ax = kwargs.pop('ax')
|
||||
elif 'num' in kwargs and 'figsize' in kwargs:
|
||||
ax = plt.figure(num=kwargs.pop('num'), figsize=kwargs.pop('figsize')).add_subplot(111)
|
||||
elif 'num' in kwargs:
|
||||
ax = plt.figure(num=kwargs.pop('num')).add_subplot(111)
|
||||
elif 'figsize' in kwargs:
|
||||
ax = plt.figure(figsize=kwargs.pop('figsize')).add_subplot(111)
|
||||
else:
|
||||
ax = plt.figure().add_subplot(111)
|
||||
# Add ax to kwargs to add all subsequent plots to this axis:
|
||||
#kwargs['ax'] = ax
|
||||
return ax, kwargs
|
||||
|
||||
def show_canvas(canvas):
|
||||
try:
|
||||
canvas.figure.canvas.draw()
|
||||
canvas.figure.tight_layout()
|
||||
except:
|
||||
pass
|
||||
return canvas
|
||||
|
||||
|
||||
def scatter(ax, *args, **kwargs):
|
||||
ax.scatter(*args, **kwargs)
|
||||
|
||||
def plot(ax, *args, **kwargs):
|
||||
ax.plot(*args, **kwargs)
|
||||
|
||||
def imshow(ax, *args, **kwargs):
|
||||
ax.imshow(*args, **kwargs)
|
||||
|
||||
|
||||
from . import base_plots
|
||||
from . import models_plots
|
||||
from . import priors_plots
|
||||
|
|
|
|||
|
|
@ -39,12 +39,15 @@ it gives back an empty default, when defaults are not defined.
|
|||
'''
|
||||
|
||||
from matplotlib import cm
|
||||
from . import Tango
|
||||
|
||||
# Data:
|
||||
data_1d = dict(lw=1.5, marker='x', edgecolor='k')
|
||||
data_2d = dict(s=35, edgecolors='none', linewidth=0., cmap=cm.get_cmap('hot'))
|
||||
xerrorbar = dict(ecolor='k', fmt='none', elinewidth=.5, alpha=.5)
|
||||
yerrorbar = dict(ecolor='darkred', fmt='none', elinewidth=.5, alpha=.5)
|
||||
yerrorbar = dict(ecolor=Tango.colorsHex['darkBlue'], fmt='none', elinewidth=.5, alpha=.5)
|
||||
|
||||
# GP plots
|
||||
meanplot = dict(color='#3300FF', linewidth=2)
|
||||
meanplot_1d = dict(color=Tango.colorsHex['mediumBlue'], linewidth=2)
|
||||
meanplot_2d = dict(cmap='hot', linewidth=.5)
|
||||
confidence_interval = dict(linecolor=Tango.colorsHex['darkBlue'],fillcolor=Tango.colorsHex['lightBlue'])
|
||||
|
|
@ -259,12 +259,12 @@ def plot_fit(self, plot_limits=None, which_data_rows='all',
|
|||
|
||||
#define the frame for plotting on
|
||||
resolution = resolution or 50
|
||||
Xnew, _, _, xmin, xmax = x_frame2D(X[:,free_dims], plot_limits, resolution)
|
||||
Xnew, x, y, xmin, xmax = x_frame2D(X[:,free_dims], plot_limits, resolution)
|
||||
Xgrid = np.empty((Xnew.shape[0],self.input_dim))
|
||||
Xgrid[:,free_dims] = Xnew
|
||||
for i,v in fixed_inputs:
|
||||
Xgrid[:,i] = v
|
||||
x, y = np.linspace(xmin[0], xmax[0], resolution), np.linspace(xmin[1], xmax[1], resolution)
|
||||
#x, y = np.linspace(xmin[0], xmax[0], resolution), np.linspace(xmin[1], xmax[1], resolution)
|
||||
|
||||
#predict on the frame and plot
|
||||
if plot_raw:
|
||||
|
|
|
|||
166
GPy/plotting/matplot_dep/plot_definitions.py
Normal file
166
GPy/plotting/matplot_dep/plot_definitions.py
Normal file
|
|
@ -0,0 +1,166 @@
|
|||
#===============================================================================
|
||||
# Copyright (c) 2015, Max Zwiessele
|
||||
# All rights reserved.
|
||||
#
|
||||
# Redistribution and use in source and binary forms, with or without
|
||||
# modification, are permitted provided that the following conditions are met:
|
||||
#
|
||||
# * Redistributions of source code must retain the above copyright notice, this
|
||||
# list of conditions and the following disclaimer.
|
||||
#
|
||||
# * Redistributions in binary form must reproduce the above copyright notice,
|
||||
# this list of conditions and the following disclaimer in the documentation
|
||||
# and/or other materials provided with the distribution.
|
||||
#
|
||||
# * Neither the name of GPy.plotting.matplot_dep.plot_definitions nor the names of its
|
||||
# contributors may be used to endorse or promote products derived from
|
||||
# this software without specific prior written permission.
|
||||
#
|
||||
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
|
||||
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
|
||||
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
|
||||
# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
|
||||
# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
|
||||
# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
|
||||
# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
|
||||
# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
|
||||
# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
|
||||
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
|
||||
#===============================================================================
|
||||
import numpy as np
|
||||
from matplotlib import pyplot as plt
|
||||
from ..abstract_plotting_library import AbstractPlottingLibrary
|
||||
from . import defaults
|
||||
|
||||
class MatplotlibPlots(AbstractPlottingLibrary):
|
||||
def __init__(self):
|
||||
super(MatplotlibPlots, self).__init__()
|
||||
self._defaults = defaults.__dict__
|
||||
|
||||
def get_new_canvas(self, kwargs):
|
||||
if 'ax' in kwargs:
|
||||
ax = kwargs.pop('ax')
|
||||
elif 'num' in kwargs and 'figsize' in kwargs:
|
||||
ax = plt.figure(num=kwargs.pop('num'), figsize=kwargs.pop('figsize')).add_subplot(111)
|
||||
elif 'num' in kwargs:
|
||||
ax = plt.figure(num=kwargs.pop('num')).add_subplot(111)
|
||||
elif 'figsize' in kwargs:
|
||||
ax = plt.figure(figsize=kwargs.pop('figsize')).add_subplot(111)
|
||||
else:
|
||||
ax = plt.figure().add_subplot(111)
|
||||
# Add ax to kwargs to add all subsequent plots to this axis:
|
||||
#kwargs['ax'] = ax
|
||||
return ax, kwargs
|
||||
|
||||
def show_canvas(self, ax, plots):
|
||||
try:
|
||||
ax.autoscale_view()
|
||||
ax.figure.canvas.draw()
|
||||
ax.figure.tight_layout()
|
||||
except:
|
||||
pass
|
||||
return ax
|
||||
|
||||
def scatter(self, ax, X, Y, **kwargs):
|
||||
return ax.scatter(X, Y, **kwargs)
|
||||
|
||||
def plot(self, ax, X, Y, **kwargs):
|
||||
return ax.plot(X, Y, **kwargs)
|
||||
|
||||
def xerrorbar(self, ax, X, Y, error, **kwargs):
|
||||
if not('linestyle' in kwargs or 'ls' in kwargs):
|
||||
kwargs['ls'] = 'none'
|
||||
return ax.errorbar(X, Y, xerr=error, **kwargs)
|
||||
|
||||
def yerrorbar(self, ax, X, Y, error, **kwargs):
|
||||
if not('linestyle' in kwargs or 'ls' in kwargs):
|
||||
kwargs['ls'] = 'none'
|
||||
return ax.errorbar(X, Y, yerr=error, **kwargs)
|
||||
|
||||
def imshow(self, ax, X, **kwargs):
|
||||
return ax.imshow(**kwargs)
|
||||
|
||||
def contour(self, ax, X, Y, C, levels=20, **kwargs):
|
||||
return ax.contour(X, Y, C, levels=np.linspace(C.min(), C.max(), levels), **kwargs)
|
||||
|
||||
def fill_between(self, ax, X, lower, upper, **kwargs):
|
||||
return ax.fill_between(X.flatten(), lower.flatten(), upper.flatten(), **kwargs)
|
||||
|
||||
def fill_gradient(self, canvas, X, percentiles, **kwargs):
|
||||
ax = canvas
|
||||
plots = []
|
||||
if not 'alpha' in kwargs.keys():
|
||||
kwargs['alpha'] = 1./(len(percentiles))
|
||||
|
||||
# pop where from kwargs
|
||||
where = kwargs.pop('where') if 'where' in kwargs else None
|
||||
# pop interpolate, which we actually do not do here!
|
||||
if 'interpolate' in kwargs: kwargs.pop('interpolate')
|
||||
|
||||
def pairwise(inlist):
|
||||
l = len(inlist)
|
||||
for i in range(int(np.ceil(l/2.))):
|
||||
yield inlist[:][i], inlist[:][(l-1)-i]
|
||||
|
||||
polycol = []
|
||||
for y1, y2 in pairwise(percentiles):
|
||||
import matplotlib.mlab as mlab
|
||||
# Handle united data, such as dates
|
||||
ax._process_unit_info(xdata=X, ydata=y1)
|
||||
ax._process_unit_info(ydata=y2)
|
||||
# Convert the arrays so we can work with them
|
||||
from numpy import ma
|
||||
x = ma.masked_invalid(ax.convert_xunits(X))
|
||||
y1 = ma.masked_invalid(ax.convert_yunits(y1))
|
||||
y2 = ma.masked_invalid(ax.convert_yunits(y2))
|
||||
|
||||
if y1.ndim == 0:
|
||||
y1 = np.ones_like(x) * y1
|
||||
if y2.ndim == 0:
|
||||
y2 = np.ones_like(x) * y2
|
||||
|
||||
if where is None:
|
||||
where = np.ones(len(x), np.bool)
|
||||
else:
|
||||
where = np.asarray(where, np.bool)
|
||||
|
||||
if not (x.shape == y1.shape == y2.shape == where.shape):
|
||||
raise ValueError("Argument dimensions are incompatible")
|
||||
|
||||
mask = reduce(ma.mask_or, [ma.getmask(a) for a in (x, y1, y2)])
|
||||
if mask is not ma.nomask:
|
||||
where &= ~mask
|
||||
|
||||
polys = []
|
||||
for ind0, ind1 in mlab.contiguous_regions(where):
|
||||
xslice = x[ind0:ind1]
|
||||
y1slice = y1[ind0:ind1]
|
||||
y2slice = y2[ind0:ind1]
|
||||
|
||||
if not len(xslice):
|
||||
continue
|
||||
|
||||
N = len(xslice)
|
||||
X = np.zeros((2 * N + 2, 2), np.float)
|
||||
|
||||
# the purpose of the next two lines is for when y2 is a
|
||||
# scalar like 0 and we want the fill to go all the way
|
||||
# down to 0 even if none of the y1 sample points do
|
||||
start = xslice[0], y2slice[0]
|
||||
end = xslice[-1], y2slice[-1]
|
||||
|
||||
X[0] = start
|
||||
X[N + 1] = end
|
||||
|
||||
X[1:N + 1, 0] = xslice
|
||||
X[1:N + 1, 1] = y1slice
|
||||
X[N + 2:, 0] = xslice[::-1]
|
||||
X[N + 2:, 1] = y2slice[::-1]
|
||||
|
||||
polys.append(X)
|
||||
polycol.extend(polys)
|
||||
from matplotlib.collections import PolyCollection
|
||||
plots.append(PolyCollection(polycol, **kwargs))
|
||||
ax.add_collection(plots[-1], autolim=True)
|
||||
ax.autoscale_view()
|
||||
return plots
|
||||
Loading…
Add table
Add a link
Reference in a new issue