Python matplotlib.pylab() Examples

def drawMapqHistogram(self):
        """ From matplot lib plots a Mappping qualty histogram
        """
        #1. PLOT BUILDING
        readsMapq = self.mapping_stats.mapping_quality_reads
       
        mapqList = list(range(len(readsMapq)))
     
        matplotlib.pyplot.ioff()
        figure = plt.figure()
        plt.bar(mapqList,readsMapq,width=1,align='center',facecolor='blue', alpha=0.75)
        plt.xlabel('MapQ')
        plt.ylabel('Fragments')
        plt.title('MapQ Histogram')
        plt.axis([0, 60,min(readsMapq), max(readsMapq)])
        plt.grid(True)
        
        pylab.savefig(self.png_mapq_histogram)
        
        plt.close(figure) 

def show(*args, **kw):
    """
    Display a figure.

    When running in ipython with its pylab mode, display all
    figures and return to the ipython prompt.

    In non-interactive mode, display all figures and block until
    the figures have been closed; in interactive mode it has no
    effect unless figures were created prior to a change from
    non-interactive to interactive mode (not recommended).  In
    that case it displays the figures but does not block.

    A single experimental keyword argument, *block*, may be
    set to True or False to override the blocking behavior
    described above.
    """
    global _show
    _show(*args, **kw) 

def activate_matplotlib(backend):
    """Activate the given backend and set interactive to True."""

    import matplotlib
    matplotlib.interactive(True)
    
    # Matplotlib had a bug where even switch_backend could not force
    # the rcParam to update. This needs to be set *before* the module
    # magic of switch_backend().
    matplotlib.rcParams['backend'] = backend

    import matplotlib.pyplot
    matplotlib.pyplot.switch_backend(backend)

    # This must be imported last in the matplotlib series, after
    # backend/interactivity choices have been made
    import matplotlib.pylab as pylab

    pylab.show._needmain = False
    # We need to detect at runtime whether show() is called by the user.
    # For this, we wrap it into a decorator which adds a 'called' flag.
    pylab.draw_if_interactive = flag_calls(pylab.draw_if_interactive) 

def _plot_to_string():
    try:
        from StringIO import StringIO
        make_bytes = lambda x: x.buf
    except ImportError:
        from io import BytesIO as StringIO
        make_bytes = lambda x: x.getbuffer()
    try:
        from urllib import quote
    except:
        from urllib.parse import quote
    import base64
    import matplotlib.pylab as plt
    imgdata = StringIO()
    plt.savefig(imgdata)
    plt.close()
    imgdata.seek(0) 
    image = base64.encodestring(make_bytes(imgdata))
    return str(quote(image)) 

def update_current_task(task):
        # make sure we have a default vale
        if PatchedMatplotlib._global_image_counter_limit is None:
            from ..config import config
            PatchedMatplotlib._global_image_counter_limit = config.get('metric.matplotlib_untitled_history_size', 100)

        # if we already patched it, just update the current task
        if PatchedMatplotlib._patched_original_plot is not None:
            PatchedMatplotlib._current_task = task
        # if matplotlib is not loaded yet, get a callback hook
        elif not running_remotely() and \
                ('matplotlib.pyplot' not in sys.modules and 'matplotlib.pylab' not in sys.modules):
            PatchedMatplotlib._current_task = task
            PostImportHookPatching.add_on_import('matplotlib.pyplot', PatchedMatplotlib.patch_matplotlib)
            PostImportHookPatching.add_on_import('matplotlib.pylab', PatchedMatplotlib.patch_matplotlib)
        elif PatchedMatplotlib.patch_matplotlib():
            PatchedMatplotlib._current_task = task 

def _show_video(video, fps=10):
    # Import matplotlib/pylab only if needed
    import matplotlib
    matplotlib.use('TkAgg')
    import matplotlib.pylab as pl
    pl.style.use('ggplot')
    pl.axis('off')

    if fps < 0:
        fps = 25
    video /= 255.  # Pylab works in [0, 1] range
    img = None
    pause_length = 1. / fps
    try:
        for f in range(video.shape[0]):
            im = video[f, :, :, :]
            if img is None:
                img = pl.imshow(im)
            else:
                img.set_data(im)
            pl.pause(pause_length)
            pl.draw()
    except:
        pass 

def show(*args, **kw):
    """
    Display a figure.
    When running in ipython with its pylab mode, display all
    figures and return to the ipython prompt.

    In non-interactive mode, display all figures and block until
    the figures have been closed; in interactive mode it has no
    effect unless figures were created prior to a change from
    non-interactive to interactive mode (not recommended).  In
    that case it displays the figures but does not block.

    A single experimental keyword argument, *block*, may be
    set to True or False to override the blocking behavior
    described above.
    """
    global _show
    return _show(*args, **kw) 

def show(*args, **kw):
    """
    Display a figure.

    When running in ipython with its pylab mode, display all
    figures and return to the ipython prompt.

    In non-interactive mode, display all figures and block until
    the figures have been closed; in interactive mode it has no
    effect unless figures were created prior to a change from
    non-interactive to interactive mode (not recommended).  In
    that case it displays the figures but does not block.

    A single experimental keyword argument, *block*, may be
    set to True or False to override the blocking behavior
    described above.
    """
    global _show
    _show(*args, **kw) 

def _onEnter(self, evt):
        """Mouse has entered the window."""
        FigureCanvasBase.enter_notify_event(self, guiEvent = evt)


########################################################################
#
# The following functions and classes are for pylab compatibility
# mode (matplotlib.pylab) and implement figure managers, etc...
#
######################################################################## 

def drawMultipleInsertSizePlot(self):
        """ From matplot lib plots a Insert Size Plot
        """ 
        iSizeList = []
        readsList = []
        readsYaxis = []
        sizeXaxis = []
        lanesNames = []
        
        #1. PLOT BUILDING
        for laneStats in self.mapping_stats.list_lane_stats:
            lanesNames.append(laneStats.name)
            histogram_template_len = laneStats.read_insert_size_histogram
            sizeList  = []
            readList = []
            for insert_size_length,reads in histogram_template_len.items():
                sizeList.append(int(insert_size_length))
                readList.append(int(reads))
                
            readsYaxis.extend(readList)
            sizeXaxis.extend(sizeList)
            iSizeList.append(sizeList)
            readsList.append(readList)
            
        matplotlib.pyplot.ioff()            
        figure = plt.figure()

        for iSize, readList in zip(iSizeList, readsList):        
            plt.plot(iSize, readList,'.')
        
        plt.xlabel('Insert Size (bp)')
        plt.ylabel('Reads')
        plt.title('Insert Size Histogram Per Lane')
        plt.axis([min(sizeXaxis), 800,min(readsYaxis), max(readsYaxis)])
        plt.legend(lanesNames,loc='upper right')        
        
        plt.grid(True)
       
        pylab.savefig(self.png_insert_size_histogram)
        
        plt.close(figure) 

def drawInsertSizePlot(self):
        """ From matplot lib plots a Insert Size Plot
        """
        iSizeList = []
        readsList = []
        
        #1. PLOT BUILDING
        histogram_template_len = self.mapping_stats.read_insert_size_histogram
        
        for insert_size_length,reads in histogram_template_len.items():
            iSizeList.append(int(insert_size_length))
            readsList.append(int(reads))
            
        matplotlib.pyplot.ioff()            
        figure = plt.figure()

        plt.plot(iSizeList, readsList, '.',color="r")
        plt.xlabel('Insert Size (bp)')
        plt.ylabel('Reads')
        plt.title('Insert Size Histogram')
        plt.axis([min(iSizeList), 800,min(readsList), max(readsList)])
        plt.grid(True)
        
        pylab.savefig(self.png_insert_size_histogram)
        
        plt.close(figure) 

def saveAndClose(self):
        """Save the figure and close it"""
        pylab.savefig(self.pngFile)
        plt.close(self.figure) 

def new_figure_manager(num, *args, **kwargs):
    """
    Create a new figure manager instance
    """
    # in order to expose the Figure constructor to the pylab
    # interface we need to create the figure here
    DEBUG_MSG("new_figure_manager()", 3, None)
    _create_wx_app()

    FigureClass = kwargs.pop('FigureClass', Figure)
    fig = FigureClass(*args, **kwargs)
    return new_figure_manager_given_figure(num, fig) 

def _onEnter(self, evt):
        """Mouse has entered the window."""
        FigureCanvasBase.enter_notify_event(self, guiEvent = evt)


########################################################################
#
# The following functions and classes are for pylab compatibility
# mode (matplotlib.pylab) and implement figure managers, etc...
#
######################################################################## 

def new_figure_manager(num, *args, **kwargs):
    """
    Create a new figure manager instance
    """
    # in order to expose the Figure constructor to the pylab
    # interface we need to create the figure here
    DEBUG_MSG("new_figure_manager()", 3, None)
    _create_wx_app()

    FigureClass = kwargs.pop('FigureClass', Figure)
    fig = FigureClass(*args, **kwargs)
    return new_figure_manager_given_figure(num, fig) 

def _onEnter(self, evt):
        """Mouse has entered the window."""
        FigureCanvasBase.enter_notify_event(self, guiEvent = evt)


########################################################################
#
# The following functions and classes are for pylab compatibility
# mode (matplotlib.pylab) and implement figure managers, etc...
#
######################################################################## 

def new_figure_manager(num, *args, **kwargs):
    """
    Create a new figure manager instance
    """
    # in order to expose the Figure constructor to the pylab
    # interface we need to create the figure here
    DEBUG_MSG("new_figure_manager()", 3, None)
    _create_wx_app()

    FigureClass = kwargs.pop('FigureClass', Figure)
    fig = FigureClass(*args, **kwargs)
    return new_figure_manager_given_figure(num, fig) 

def drawMultipleMapqHistogram(self):
        """ From matplot lib plots a Mappping qualty histogram
        """  
        mapqFragmentsLanes = []
              
        for laneStats in self.mapping_stats.list_lane_stats:
            mapqFragmentsLanes.append(laneStats.mapping_quality_reads)
    
        matplotlib.pyplot.ioff()
        figure = plt.figure()
        ax = figure.add_subplot(111,projection='3d')
                       
        lane = 0
        for fragmentsQuality in mapqFragmentsLanes:
            qualityRange = list(range(len(fragmentsQuality)))            
            ax.bar(qualityRange,fragmentsQuality, zs=lane, zdir='y', color='b', alpha=0.8)
            lane = lane + 1
            
        ax.set_xlabel('MapQ')
        ax.set_ylabel('Lanes')
        ax.set_zlabel('Fragments')        
                
        #http://people.duke.edu/~ccc14/pcfb/numpympl/MatplotlibBarPlots.html
        pylab.savefig(self.png_mapq_histogram)
        
        plt.close(figure) 

def import_pylab(user_ns, import_all=True):
    """Populate the namespace with pylab-related values.
    
    Imports matplotlib, pylab, numpy, and everything from pylab and numpy.
    
    Also imports a few names from IPython (figsize, display, getfigs)
    
    """

    # Import numpy as np/pyplot as plt are conventions we're trying to
    # somewhat standardize on.  Making them available to users by default
    # will greatly help this.
    s = ("import numpy\n"
          "import matplotlib\n"
          "from matplotlib import pylab, mlab, pyplot\n"
          "np = numpy\n"
          "plt = pyplot\n"
          )
    exec s in user_ns
    
    if import_all:
        s = ("from matplotlib.pylab import *\n"
             "from numpy import *\n")
        exec s in user_ns
    
    # IPython symbols to add
    user_ns['figsize'] = figsize
    from IPython.core.display import display
    # Add display and getfigs to the user's namespace
    user_ns['display'] = display
    user_ns['getfigs'] = getfigs 

def select_figure_format(shell, fmt):
    """Select figure format for inline backend, can be 'png', 'retina', or 'svg'.

    Using this method ensures only one figure format is active at a time.
    """
    from matplotlib.figure import Figure
    from IPython.kernel.zmq.pylab import backend_inline

    svg_formatter = shell.display_formatter.formatters['image/svg+xml']
    png_formatter = shell.display_formatter.formatters['image/png']

    if fmt == 'png':
        svg_formatter.type_printers.pop(Figure, None)
        png_formatter.for_type(Figure, lambda fig: print_figure(fig, 'png'))
    elif fmt in ('png2x', 'retina'):
        svg_formatter.type_printers.pop(Figure, None)
        png_formatter.for_type(Figure, retina_figure)
    elif fmt == 'svg':
        png_formatter.type_printers.pop(Figure, None)
        svg_formatter.for_type(Figure, lambda fig: print_figure(fig, 'svg'))
    else:
        raise ValueError("supported formats are: 'png', 'retina', 'svg', not %r" % fmt)

    # set the format to be used in the backend()
    backend_inline._figure_format = fmt

#-----------------------------------------------------------------------------
# Code for initializing matplotlib and importing pylab
#----------------------------------------------------------------------------- 

def mpl_runner(safe_execfile):
    """Factory to return a matplotlib-enabled runner for %run.

    Parameters
    ----------
    safe_execfile : function
      This must be a function with the same interface as the
      :meth:`safe_execfile` method of IPython.

    Returns
    -------
    A function suitable for use as the ``runner`` argument of the %run magic
    function.
    """
    
    def mpl_execfile(fname,*where,**kw):
        """matplotlib-aware wrapper around safe_execfile.

        Its interface is identical to that of the :func:`execfile` builtin.

        This is ultimately a call to execfile(), but wrapped in safeties to
        properly handle interactive rendering."""

        import matplotlib
        import matplotlib.pylab as pylab

        #print '*** Matplotlib runner ***' # dbg
        # turn off rendering until end of script
        is_interactive = matplotlib.rcParams['interactive']
        matplotlib.interactive(False)
        safe_execfile(fname,*where,**kw)
        matplotlib.interactive(is_interactive)
        # make rendering call now, if the user tried to do it
        if pylab.draw_if_interactive.called:
            pylab.draw()
            pylab.draw_if_interactive.called = False

    return mpl_execfile 

def new_figure_manager(num, *args, **kwargs):
    """
    Create a new figure manager instance
    """
    # in order to expose the Figure constructor to the pylab
    # interface we need to create the figure here
    DEBUG_MSG("new_figure_manager()", 3, None)
    _create_wx_app()

    FigureClass = kwargs.pop('FigureClass', Figure)
    fig = FigureClass(*args, **kwargs)
    return new_figure_manager_given_figure(num, fig) 

def _onEnter(self, evt):
        """Mouse has entered the window."""
        FigureCanvasBase.enter_notify_event(self, guiEvent = evt)


########################################################################
#
# The following functions and classes are for pylab compatibility
# mode (matplotlib.pylab) and implement figure managers, etc...
#
######################################################################## 

def _print_image(self, filename, filetype, *args, **kwargs):
        origBitmap = self.bitmap

        l, b, width, height = self.figure.bbox.bounds
        width = math.ceil(width)
        height = math.ceil(height)

        self.bitmap = wx.Bitmap(width, height)

        renderer = RendererWx(self.bitmap, self.figure.dpi)

        gc = renderer.new_gc()

        self.figure.draw(renderer)

        # image is the object that we call SaveFile on.
        image = self.bitmap
        # set the JPEG quality appropriately.  Unfortunately, it is only
        # possible to set the quality on a wx.Image object.  So if we
        # are saving a JPEG, convert the wx.Bitmap to a wx.Image,
        # and set the quality.
        if filetype == wx.BITMAP_TYPE_JPEG:
            jpeg_quality = kwargs.get('quality',
                                      rcParams['savefig.jpeg_quality'])
            image = self.bitmap.ConvertToImage()
            image.SetOption(wx.IMAGE_OPTION_QUALITY, str(jpeg_quality))

        # Now that we have rendered into the bitmap, save it to the appropriate
        # file type and clean up.
        if isinstance(filename, str):
            if not image.SaveFile(filename, filetype):
                raise RuntimeError(f'Could not save figure to {filename}')
        elif cbook.is_writable_file_like(filename):
            if not isinstance(image, wx.Image):
                image = image.ConvertToImage()
            if not image.SaveStream(filename, filetype):
                raise RuntimeError(f'Could not save figure to {filename}')

        # Restore everything to normal
        self.bitmap = origBitmap

        # Note: draw is required here since bits of state about the
        # last renderer are strewn about the artist draw methods.  Do
        # not remove the draw without first verifying that these have
        # been cleaned up.  The artist contains() methods will fail
        # otherwise.
        if self._isDrawn:
            self.draw()
        self.Refresh()


########################################################################
#
# The following functions and classes are for pylab compatibility
# mode (matplotlib.pylab) and implement figure managers, etc...
#
######################################################################## 

def backtest_plot(self):
        """
==== OTCmd2 backtest plot

Plot the servings the chef has cooked, using matplotlib.
{{{
back plot show      - show the current plot
back plot trades    - plot the trades
back plot equity    - plot the cumulative equity
}}}
        """
        lArgs = self.lArgs
        sDo = 'plot'
        #!WTF local variable '__doc__' referenced before assignment
        self.dhelp['plot'] = __doc__
        lArgs = self.lArgs

        __doc__ = sBACplot__doc__
        _lCmds = ['show', 'trades', 'equity']
        if not hasattr(oOm, 'oBt') or not oOm.oBt:
            self.vError("You must use \"chef cook\" before you can plot")
            return
        # FixMe:
        oBt = oOm.oBt

        assert len(lArgs) > 1, "ERROR: " +sDo +str(_lCmds)
        sCmd = lArgs[1]
        assert sCmd in _lCmds, "ERROR: " +sDo +str(_lCmds)

        import matplotlib
        import matplotlib.pylab as pylab
        if sCmd == 'show':
            pylab.show()
            return

        # FixMe:
        matplotlib.rcParams['figure.figsize'] = (10, 5)

        if sCmd == 'equity':
            # FixMe: derive the period from the sTimeFrame
            sPeriod = 'W'
            close_label = 'C'
            mOhlc = oRecipe.dIngredients['mOhlc']
            oChefModule.vPlotEquity(oBt.equity, mOhlc, sTitle="%s\nEquity" % repr(oBt),
                                    sPeriod=sPeriod,
                                    close_label=close_label,
                                    )
            pylab.show()
            return

        if sCmd == 'trades':
            oBt.vPlotTrades()
            pylab.legend(loc='lower left')
            pylab.show()

            return
        self.vError("Unrecognized plot command: " + str(lArgs))
        return 

def _print_image(self, filename, filetype, *args, **kwargs):
        origBitmap = self.bitmap

        l, b, width, height = self.figure.bbox.bounds
        width = math.ceil(width)
        height = math.ceil(height)

        self.bitmap = wx.Bitmap(width, height)

        renderer = RendererWx(self.bitmap, self.figure.dpi)

        gc = renderer.new_gc()

        self.figure.draw(renderer)

        # image is the object that we call SaveFile on.
        image = self.bitmap
        # set the JPEG quality appropriately.  Unfortunately, it is only
        # possible to set the quality on a wx.Image object.  So if we
        # are saving a JPEG, convert the wx.Bitmap to a wx.Image,
        # and set the quality.
        if filetype == wx.BITMAP_TYPE_JPEG:
            jpeg_quality = kwargs.get('quality',
                                      rcParams['savefig.jpeg_quality'])
            image = self.bitmap.ConvertToImage()
            image.SetOption(wx.IMAGE_OPTION_QUALITY, str(jpeg_quality))

        # Now that we have rendered into the bitmap, save it to the appropriate
        # file type and clean up.
        if isinstance(filename, str):
            if not image.SaveFile(filename, filetype):
                raise RuntimeError(f'Could not save figure to {filename}')
        elif cbook.is_writable_file_like(filename):
            if not isinstance(image, wx.Image):
                image = image.ConvertToImage()
            if not image.SaveStream(filename, filetype):
                raise RuntimeError(f'Could not save figure to {filename}')

        # Restore everything to normal
        self.bitmap = origBitmap

        # Note: draw is required here since bits of state about the
        # last renderer are strewn about the artist draw methods.  Do
        # not remove the draw without first verifying that these have
        # been cleaned up.  The artist contains() methods will fail
        # otherwise.
        if self._isDrawn:
            self.draw()
        self.Refresh()


########################################################################
#
# The following functions and classes are for pylab compatibility
# mode (matplotlib.pylab) and implement figure managers, etc...
#
######################################################################## 

def pylab(self, line=''):
        """Load numpy and matplotlib to work interactively.

        This function lets you activate pylab (matplotlib, numpy and
        interactive support) at any point during an IPython session.
        
        %pylab makes the following imports::
        
            import numpy
            import matplotlib
            from matplotlib import pylab, mlab, pyplot
            np = numpy
            plt = pyplot
            
            from IPython.display import display
            from IPython.core.pylabtools import figsize, getfigs
            
            from pylab import *
            from numpy import *

        If you pass `--no-import-all`, the last two `*` imports will be excluded.
        
        See the %matplotlib magic for more details about activating matplotlib
        without affecting the interactive namespace.
        """
        args = magic_arguments.parse_argstring(self.pylab, line)
        if args.no_import_all is None:
            # get default from Application
            if Application.initialized():
                app = Application.instance()
                try:
                    import_all = app.pylab_import_all
                except AttributeError:
                    import_all = True
            else:
                # nothing specified, no app - default True
                import_all = True
        else:
            # invert no-import flag
            import_all = not args.no_import_all

        gui, backend, clobbered = self.shell.enable_pylab(args.gui, import_all=import_all)
        self._show_matplotlib_backend(args.gui, backend)
        print ("Populating the interactive namespace from numpy and matplotlib")
        if clobbered:
            warn("pylab import has clobbered these variables: %s"  % clobbered +
            "\n`%pylab --no-import-all` prevents importing * from pylab and numpy"
            ) 

def configure_inline_support(shell, backend):
    """Configure an IPython shell object for matplotlib use.

    Parameters
    ----------
    shell : InteractiveShell instance

    backend : matplotlib backend
    """
    # If using our svg payload backend, register the post-execution
    # function that will pick up the results for display.  This can only be
    # done with access to the real shell object.

    # Note: if we can't load the inline backend, then there's no point
    # continuing (such as in terminal-only shells in environments without
    # zeromq available).
    try:
        from IPython.kernel.zmq.pylab.backend_inline import InlineBackend
    except ImportError:
        return
    from matplotlib import pyplot

    cfg = InlineBackend.instance(parent=shell)
    cfg.shell = shell
    if cfg not in shell.configurables:
        shell.configurables.append(cfg)

    if backend == backends['inline']:
        from IPython.kernel.zmq.pylab.backend_inline import flush_figures
        shell.register_post_execute(flush_figures)

        # Save rcParams that will be overwrittern
        shell._saved_rcParams = dict()
        for k in cfg.rc:
            shell._saved_rcParams[k] = pyplot.rcParams[k]
        # load inline_rc
        pyplot.rcParams.update(cfg.rc)
    else:
        from IPython.kernel.zmq.pylab.backend_inline import flush_figures
        if flush_figures in shell._post_execute:
            shell._post_execute.pop(flush_figures)
        if hasattr(shell, '_saved_rcParams'):
            pyplot.rcParams.update(shell._saved_rcParams)
            del shell._saved_rcParams

    # Setup the default figure format
    select_figure_format(shell, cfg.figure_format) 

def vPlotEquityCurves(oBt, mOhlc, oChefModule,
                      sPeriod='W',
                      close_label='C',):
    import matplotlib
    import matplotlib.pylab as pylab
    # FixMe:
    matplotlib.rcParams['figure.figsize'] = (10, 5)

    # FixMe: derive the period from the sTimeFrame
    oChefModule.vPlotEquity(oBt.equity, mOhlc, sTitle="%s\nEquity" % repr(oBt),
                            sPeriod=sPeriod,
                            close_label=close_label,
                            )
    pylab.show()

    oBt.vPlotTrades()
    pylab.legend(loc='lower left')
    pylab.show()

    ## oBt.vPlotTrades(subset=slice(sYear+'-05-01', sYear+'-09-01'))
    ## pylab.legend(loc='lower left')
    ## pylab.show()