def plot_some_shots(run, ax=None):
    file_name = h5_file_name_funk(run)
    h5 = load_file(file_name)
    spec_group = h5['spectral_properties']

    #####
    # Select region in the tree to get traces

#    centers = (spec_group['center_eV'].value -
#               h5['photoelectron_energy_prediction_eV'].value)
    widths = spec_group['width_eV'].value

    #I = np.abs(centers) < (center_max - center_min) / 10
#    I = ((np.nanmax(widths) - (np.nanmax(widths) - np.nanmin(widths)) / 5) <
#         widths)

    I = np.isfinite(widths)

    selected = np.random.choice(np.where(I)[0], 5)
    selected.sort()

    energy_scale_eV = h5['energy_scale_eV'].value
    traces = h5['energy_signal'].value

    if ax is None:
        plt.figure('energy traces ' + str(run))
        plt.clf()
    else:
        plt.sca(ax)

    for shot in selected:
        plt.plot(energy_scale_eV, traces[shot, :] * 1e3)

    plt.xlim(70, 130)

def demo_alternatinggraphcut():
    t = 12
    ## Simulate small image
    im, G = simulation.simulate_image(11,13,t,theta=0.4*np.pi )
    
    # Show grid overlaid image
    fig, ax = plt.subplots(1,2)
    plt.sca(ax[0])
    plt.imshow(im,cmap=plt.cm.gray)
    plt.title('True grid')
    plotgrid(G)
    
    # Add random, disturbing, points
    Nnew = 15
    x_new = np.random.uniform(np.min(G.xy[:,0]),np.max(G.xy[:,0]), Nnew)
    y_new = np.random.uniform(np.min(G.xy[:,1]),np.max(G.xy[:,1]), Nnew )
    xy_new = np.vstack((x_new,y_new)).T
    
    # Add to grid and make naive guess for edges
    G.xy = np.vstack((G.xy,xy_new))
    G.resolve_edges(remove_long=False)
    
    # Show this modified grid
    plt.sca(ax[1])
    plotgrid(G)
    plt.title('Modified/disturbed grid')
    plt.show()
    
    # Clean up using alternating graph cut
    xy_hat, simplices_hat = alternating_graphcut.cleanup(G.xy,im,alpha=3,beta=2)
    G_hat = grid.TriangularGrid.from_simplices(xy_hat,simplices_hat)
    plt.figure()
    plotgrid(G_hat)
    plt.show(block=True)

def plotBestFit(weights):
    m = shape(dataMat)[0]
    xcord1 = []
    ycord1 = []
    xcord2 = []
    ycord2 = []
    for i in range(m):
        if labelMat[i] == 1:
            xcord1.append(dataMat[i, 1])
            ycord1.append(dataMat[i, 2])
        else:
            xcord2.append(dataMat[i, 1])
            ycord2.append(dataMat[i, 2])
    plt.figure(1)
    ax = plt.subplot(111)
    ax.scatter(xcord1, ycord1, s=30, c='red', marker='s')
    ax.scatter(xcord2, ycord2, s=30, c='green')
    x = arange(0.2, 0.8, 0.1)
    y = array((-weights[0] - weights[1] * x) / weights[2])
    print shape(x)
    print shape(y)
    plt.sca(ax)
    plt.plot(x, y)  # ramdomgradAscent
    # plt.plot(x,y[0])   #gradAscent
    plt.xlabel('density')
    plt.ylabel('ratio_sugar')
    # plt.title('gradAscent logistic regression')
    plt.title('ramdom gradAscent logistic regression')
    plt.show()

    def plot_marginals(self, func, **kwargs):
        """Draw univariate plots for `x` and `y` separately.

        Parameters
        ----------
        func : plotting callable
            This must take a 1d array of data as the first positional
            argument, it must plot on the "current" axes, and it must
            accept a "vertical" keyword argument to orient the measure
            dimension of the plot vertically.
        kwargs : key, value mappings
            Keyword argument are passed to the plotting function.

        Returns
        -------
        self : JointGrid instance
            Returns `self`.

        """
        plt.sca(self.ax_marg_x)
        func(self.x, **kwargs)

        kwargs["vertical"] = True
        plt.sca(self.ax_marg_y)
        func(self.y, **kwargs)

        return self

    def map_upper(self, func, **kwargs):
        """Plot with a bivariate function on the upper diagonal subplots.

        Parameters
        ----------
        func : callable plotting function
            Must take x, y arrays as positional arguments and draw onto the
            "currently active" matplotlib Axes.

        """
        kw_color = kwargs.pop("color", None)
        for i, j in zip(*np.triu_indices_from(self.axes, 1)):

            hue_grouped = self.data.groupby(self.hue_vals)
            for k, (label_k, data_k) in enumerate(hue_grouped):

                ax = self.axes[i, j]
                plt.sca(ax)

                x_var = self.x_vars[j]
                y_var = self.y_vars[i]

                color = self.palette[k] if kw_color is None else kw_color
                func(data_k[x_var], data_k[y_var], label=label_k,
                     color=color, **kwargs)

            self._clean_axis(ax)
            self._update_legend_data(ax)

        if kw_color is not None:
            kwargs["color"] = kw_color

def niceplot(ax=None, axfs='12', lfs='14', tightlayout=True,
             mew=1.25, lw=2.0, ms=7.0, **kwargs):
    """Pretty up a plot for publication.

    Parameters
    ----------
    ax : matplotlib.axes.AxesSubplot, optional
      An axis to niceify.  Default is all axes in the current figure.
    axfs : string, float, or int, optional
      Axis tick label font size.
    lfs : string, float, or int, optional
      Axis label font size.
    tightlayout : bool, optional
      Run `plt.tight_layout`.
    **kwargs
      Any line or marker property keyword.

    """

    import matplotlib.pyplot as plt
    
    if ax is None:
        for ax in plt.gcf().get_axes():
            niceplot(ax, tightlayout=tightlayout, axfs=axfs, lfs=lfs, **kwargs)

    # for the axes
    plt.setp(ax.get_ymajorticklabels(), fontsize=axfs)
    plt.setp(ax.get_xmajorticklabels(), fontsize=axfs)

    # axis labes
    labels = (ax.xaxis.get_label(), ax.yaxis.get_label())
    plt.setp(labels, fontsize=lfs)

    # for plot markers, ticks
    lines = ax.get_lines()
    mew = kwargs.pop('markeredgewidth', kwargs.pop('mew', None))
    if mew is not None:
        plt.setp(lines, mew=mew)

    ms = kwargs.pop('markersize', kwargs.pop('ms', None))
    if ms is not None:
        plt.setp(lines, ms=ms)

    lw = kwargs.pop('linewidth', kwargs.pop('lw', None))
    if lw is not None:
        plt.setp(lines, lw=lw)

    if len(kwargs) > 0:
        plt.setp(lines, **kwargs)

    lines = ax.xaxis.get_minorticklines() + ax.xaxis.get_majorticklines() + \
        ax.yaxis.get_minorticklines() + ax.yaxis.get_majorticklines()
    plt.setp(lines, mew=1.25)

    # the frame
    plt.setp(ax.patch, lw=2.0)

    if hasattr(plt, "tight_layout") and tightlayout:
        plt.sca(ax)
        plt.tight_layout()

    def plot_locations(self, ax=None, lu=None):
        if self.annotations_loaded == False:
            return

        if ax is None:
            fig, ax = pl.subplots(1, 1, sharex=True, sharey=False, figsize=(20, 5))
        else:
            pl.sca(ax)

        if lu is None:
            lu = (self.meta['start'], self.meta['end'])

        palette = it.cycle(sns.husl_palette())

        offsets = self.get_offsets()
        for ai in xrange(self.num_annotators):
            col = next(palette)
            offset = offsets[ai]
            for index, rr in slice_df_start_stop(self.locations[ai], lu).iterrows():
                pl.plot([rr['start'], rr['end']], [self.location_targets.index(rr['name']) + offset * 2] * 2, color=col,
                        linewidth=5, alpha=0.5)

        pl.yticks(np.arange(len(self.location_targets)), self.location_targets)
        pl.ylim((-1, len(self.location_targets)))
        pl.xlim(lu)

    def update(self, t, alpha, beta, x_basis=False):
        from matplotlib import pyplot as pl
        ax = self.ax
        pl.sca(ax)
        pl.cla()
        x_basis = self.x_basis

        if x_basis:
            from sglib import ip, col
            from numpy import sqrt
            alpha_x = ip(col(1,1)/sqrt(2), col(alpha,beta))
            beta_x = ip(col(1,-1)/sqrt(2), col(alpha,beta))
            alpha = alpha_x; beta = beta_x

        prob_plus = alpha*alpha.conjugate()
        prob_minus = beta*beta.conjugate()
        pos_plus = self.pos_plus
        pos_minus = self.pos_minus
        width = self.width
        p1 = pl.bar([pos_plus], prob_plus, width, color='blue')
        p2 = pl.bar([pos_minus], prob_minus, width, color='red')

        pl.xticks(self.xticks, self.xlabels)
        pl.ylabel('Probability')
        pl.yticks(self.yticks)
        pl.xlim(0, 1.1)
        pl.ylim(0, 1.1)
        pl.draw()
        pl.show()

def visualize_predictions(prediction_seqs, label_seqs, num_classes,
                          fig_width=6.5, fig_height_per_seq=0.5):
    """ Visualize predictions vs. ground truth.

    Args:
        prediction_seqs: A list of int NumPy arrays, each with shape
            `[duration, 1]`.
        label_seqs: A list of int NumPy arrays, each with shape `[duration, 1]`.
        num_classes: An integer.
        fig_width: A float. Figure width (inches).
        fig_height_per_seq: A float. Figure height per sequence (inches).

    Returns:
        A tuple of the created figure, axes.
    """

    num_seqs = len(label_seqs)
    max_seq_length = max([seq.shape[0] for seq in label_seqs])
    figsize = (fig_width, num_seqs*fig_height_per_seq)
    fig, axes = plt.subplots(nrows=num_seqs, ncols=1,
                             sharex=True, figsize=figsize)

    for pred_seq, label_seq, ax in zip(prediction_seqs, label_seqs, axes):
        plt.sca(ax)
        plot_label_seq(label_seq, num_classes, 1)
        plot_label_seq(pred_seq, num_classes, -1)
        ax.get_xaxis().set_visible(False)
        ax.get_yaxis().set_visible(False)
        plt.xlim(0, max_seq_length)
        plt.ylim(-2.75, 2.75)
        plt.tight_layout()

    return fig, axes

    def draw_all(self):
        for i in range(0, len(self.cpustats)):
            ax = plt.subplot(2, len(self.cpustats)/2, i)
            plt.sca(ax)
            self.draw(self.cpustats[i], plt)

        plt.show()

	def updateImage(self):

		# clear plot
		plt.sca(self.ax)
		plt.cla()
		self.initImage()

		# Fetch data from SQL database
		# try:
		if   self.current_plot == 'time_stack':
			x,y = self.main_widget.imageAquisitionTab.stack.fetch_mologram_data()
		elif self.current_plot == 'post_processing':
			x,y = self.main_widget.postProcessingTab.get_time_and_molo_intensity()
		else:
			print('Current plot is empty')
			return
		# except Exception:
		# 	print('Couldn\'t get data to plot')
		# 	return
		
		# plot appearance
		plt.xlim([0,         np.amax(x)])
		plt.ylim([np.amin(y),np.amax(y)])
		self.figure.tight_layout()

		# add titles
		self.ax.set_xlabel('Time (s)')
		self.ax.set_ylabel('Mologram Intensity (arbitrary units)')		
		self.ax.ticklabel_format(style='sci', axis='y', scilimits=(0,0))

		# plot data and show canvas
		self.points = plt.plot(x,y)
		self.canvas.draw()

    def map(self, func, *args, **kwargs):
        """
        Apply a plotting function to each facet's subset of the data.

        Parameters
        ----------
        func : callable
            A plotting function that takes data and keyword arguments. It
            must plot to the currently active matplotlib Axes and take a
            `color` keyword argument. If faceting on the `hue` dimension,
            it must also take a `label` keyword argument.
        args : strings
            Column names in self.data that identify variables with data to
            plot. The data for each variable is passed to `func` in the
            order the variables are specified in the call.
        kwargs : keyword arguments
            All keyword arguments are passed to the plotting function.

        Returns
        -------
        self : FacetGrid object

        """
        import matplotlib.pyplot as plt

        for ax, namedict in zip(self.axes.flat, self.name_dicts.flat):
            if namedict is not None:
                data = self.data[namedict]
                plt.sca(ax)
                innerargs = [data[a].values for a in args]
                func(*innerargs, **kwargs)

        return self

def plot_confusion_matrix(cm, classes, ax,
                          normalize=False,
                          title='Confusion matrix',
                          cmap=plt.cm.Blues):
    """
    This function prints and plots the confusion matrix.
    Normalization can be applied by setting `normalize=True`.
    """
    print(cm)
    print('')

    ax.imshow(cm, interpolation='nearest', cmap=cmap)
    ax.set_title(title)
    tick_marks = np.arange(len(classes))
    plt.xticks(tick_marks, classes, rotation=45)
    plt.sca(ax)
    plt.yticks(tick_marks, classes)

    fmt = '.2f' if normalize else 'd'
    thresh = cm.max() / 2.
    for i, j in itertools.product(range(cm.shape[0]), range(cm.shape[1])):
        ax.text(j, i, format(cm[i, j], fmt),
                horizontalalignment="center",
                color="white" if cm[i, j] > thresh else "black")

    ax.set_ylabel('True label')
    ax.set_xlabel('Predicted label')

def visualize(model, filename):
    values = model.all_params()
    cols = OrderedDict()
    for key, value in values.items():
        if isinstance(value, np.ndarray):  # TODO group by prefix, showing W and b side by side
            cols.setdefault(key[:-2] + key[-1] if len(key) > 1 and key[-2] in "bW" else key, []).append((key, value))
    _, axes = plt.subplots(2, len(cols), figsize=(5*len(cols), 10))  # TODO https://stackoverflow.com/a/13784887/223267
    plt.tight_layout()
    for j, col in enumerate(tqdm(cols.values(), unit="param", desc=filename)):
        for i in range(2):
            axis = axes[i, j] if len(values) > 1 else axes
            if len(col) <= i:
                plt.delaxes(axis)
            else:
                plt.sca(axis)
                key, value = col[i]
                plt.colorbar(plt.pcolormesh(smooth(value)))
                for pattern, repl in REPLACEMENTS:  # TODO map 0123->ifoc
                    key = re.sub(pattern, repl, key)
                plt.title(key)
                for axis in (plt.gca().xaxis, plt.gca().yaxis):
                    axis.set_major_locator(MaxNLocator(integer=True))
    output_file = filename + ".png"
    plt.savefig(output_file)
    plt.clf()
    print("Saved '%s'." % output_file)

def plot(w):
    dataMat=np.array(df[['density','ratio_sugar']].values[:,:])
    labelMat=np.mat(df['good'].values[:]).transpose()
    m=np.shape(dataMat)[0]
    xcord1=[]
    ycord1=[]
    xcord2=[]
    ycord2=[]
    for i in range(m):
        if labelMat[i]==1:
            xcord1.append(dataMat[i,0])
            ycord1.append(dataMat[i,1])
        else:
            xcord2.append(dataMat[i,0])
            ycord2.append(dataMat[i,1])
    plt.figure(1)
    ax=plt.subplot(111)
    ax.scatter(xcord1,ycord1,s=30,c='red',marker='s')
    ax.scatter(xcord2,ycord2,s=30,c='green')
    x=np.arange(-0.2,0.8,0.1)
    y=np.array((-w[0,0]*x)/w[0,1])

    plt.sca(ax)
    plt.plot(x,y)   #gradAscent
    plt.xlabel('density')
    plt.ylabel('ratio_sugar')
    plt.title('LDA')
    plt.show()

def labeledDendrogram(dmat, labels, method='complete', cmap=None):
    """Perform hierarchical clustering on df columns and plot square heatmap of pairwise distances"""
    """TODO: add tick labels, with sparsity option"""

    Z = sch.linkage(dmat, method=method)
    den = sch.dendrogram(Z, color_threshold=np.inf, no_plot=True)

    figh = plt.gcf()
    figh.clf()

    denAX = figh.add_axes([0.32, 0.05, 0.6, 0.9])
    cbAX =  figh.add_axes([0.25, 0.05, 0.05, 0.9])

    plt.sca(denAX)
    denD = sch.dendrogram(Z, color_threshold=np.inf, orientation='left')
    ind = denD['leaves']
    clean_axis(denAX)
    
    cbSE, lookup = mapColors2Labels(labels, cmap=cmap, returnLookup=True)
    axi = cbAX.imshow([[x] for x in cbSE.iloc[ind].values],
                      interpolation='nearest',
                      aspect='auto',
                      origin='lower')
    clean_axis(cbAX)

    colorLegend(list(lookup.values()), list(lookup.keys()), axh=denAX)

    def plot_session_PSTH(self, session, tetrode, experiment=-1, site=-1, cluster = None, sortArray='currentFreq', timeRange = [-0.5, 1], replace=0, lw=3, colorEachCond=None):
        sessionObj = self.get_session_obj(session, experiment, site)
        sessionDir = sessionObj.ephys_dir()

        ephysData, bdata, info = self.load_session_data(session, experiment, site, tetrode, cluster)
        eventOnsetTimes = ephysData['events']['stimOn']
        spikeTimestamps = ephysData['spikeTimes']
        if bdata is not None:
            sortArray = bdata[sortArray]
            if colorEachCond is None:
                colorEachCond = self.get_colours(len(np.unique(sortArray)))
        else:
            sortArray = []
        plotTitle = info['sessionDir']

        ephysData = ephyscore.load_ephys(sessionObj.subject, sessionObj.paradigm, sessionDir, tetrode, cluster)
        eventOnsetTimes = ephysData['events']['stimOn']
        spikeTimestamps = ephysData['spikeTimes']

        if replace==1:
            plt.cla()
        elif replace==2:
            plt.sca(ax)
        else:
            plt.figure()
        plot_psth(spikeTimestamps, eventOnsetTimes, sortArray = sortArray, timeRange=timeRange, lw=lw, colorEachCond=colorEachCond, plotLegend=0)

def plotrfACC():
    #data = json.loads(open('rf_accs.json').read())
    data = json.loads(open('rf_accs_top3.json').read())
    data = json.loads(open('rf_accs_nowindow.json').read())
    nLetter = 3 #14
    data["texts/ADHD_various_half/"] = [data["texts/ADHD_various_half/"][i] for i in [1,2,3]]

    sns.set_style("dark")

    #f, (ax1, ax2) = plt.subplots(1, 2)
    f, ax1 = plt.subplots()
    bar1 = ax1.bar(range(nLetter),data["texts/ADHD_various_half/"])
    ax1.set_title('RF accs for half SAX')
    plt.sca(ax1)
    plt.xticks(np.arange(nLetter) + .4, range(3,nLetter+3))
    plt.xlabel('# of bins (letters)/word')
    ax1.set_ylim([0.6,0.9])

    #bar2 = ax2.bar(range(nLetter),data["texts/ADHD_various_full/"])
    #ax2.set_title('RF accs for full SAX')
    #plt.sca(ax2)
    #plt.xticks(np.arange(nLetter) + .4, range(2,nLetter+2))
    #plt.xlabel('# of bins (letters)/word')
    #ax2.set_ylim([0.6,0.9])

    plt.show()

def add_bovy_rix(axScatter,Rmin,Rmax,zmin,zmax):
    #Now calculate and plot our model
    fehs= numpy.linspace(-1.6,0.5,26)
    afes= numpy.linspace(-0.15,0.55,25)
    ourDist= numpy.zeros((len(fehs),len(afes)))
    for ii in range(len(fehs)):
        for jj in range(len(afes)):
            ourDist[ii,jj]= maps.abundanceDist(fehs[ii],afes[jj],
                                               z=[zmin*1000.,zmax*1000.],
                                               r=[Rmin,Rmax])
    _ADJUSTABUNDANCES= True
    _ADJUSTFEH= True
    if _ADJUSTABUNDANCES:
        if _ADJUSTFEH:
            fehs+= 0.15
        afes/= 1.5
        afes-= 0.025
    #Contour this in axScatter
    ourDist[numpy.isnan(ourDist)]= 0.
    sortindx= numpy.argsort(ourDist.flatten())[::-1]
    cumul= numpy.cumsum(numpy.sort(ourDist.flatten())[::-1])/numpy.sum(ourDist.flatten())
    cntrThis= numpy.zeros(numpy.prod(ourDist.shape))
    cntrThis[sortindx]= cumul
    cntrThis= numpy.reshape(cntrThis,ourDist.shape)
    pyplot.sca(axScatter)
    CS= pyplot.contour(fehs,afes,
                       cntrThis.T,levels=[0.68,0.95],
                       linewidths=3.,linestyles='dashed',
                       colors='r',zorder=10)

def plot_col_pos(cs_xzdf, cs_xydf, cs_xdf, colposperiod, colpostype):
    dat=pd.date_range(start=cs_xzdf.index[0],end=cs_xzdf.index[-1], freq=colposperiod)
    
    fig,ax=plt.subplots(nrows=1,ncols=2, sharex=True, sharey=True,figsize=fig_size)
    plt.suptitle(colname+"\n"+colpostype+" col pos")
    cm = plt.get_cmap('gist_rainbow')
    ax[0].set_color_cycle([cm(1.*(len(dat)-i-1)/len(dat)) for i in range(len(dat))])
    ax[1].set_color_cycle([cm(1.*(len(dat)-i-1)/len(dat)) for i in range(len(dat))])

    for d in range(len(dat)):
        curxz=cs_xzdf[(cs_xzdf.index==dat[d])]
        curxy=cs_xydf[(cs_xydf.index==dat[d])]
        curx=cs_xdf[(cs_xdf.index==dat[d])]

        if colpostype=='rel':
            curxz=curxz.sub(cs_xzdf.iloc[0,:],axis=1)    
            curxy=curxy.sub(cs_xydf.iloc[0,:],axis=1)    

        plt.sca(ax[0])
        plt.axis('equal')
        plt.plot([[0]]+curxz.values.T.tolist(),[[0.0]]+curx.values.T.tolist(), '.-')

        plt.sca(ax[1])
        plt.axis('equal')
        plt.plot([[0.0]]+curxy.values.T.tolist(),[[0.0]]+curx.values.T.tolist(), '.-',label=datetime.strftime(dat[d],'%Y-%m-%d'))
        

    ax[0].set_xlabel("XZ disp, m \n (+) downslope", fontsize='small',horizontalalignment='center')
    ax[0].set_ylabel("X disp, m \n (+) towards surface", fontsize='small', rotation='vertical',horizontalalignment='center')
    ax[1].set_xlabel("XY disp, m \n (+) to the right, facing downslope", fontsize='small', horizontalalignment='center')
    plt.legend(loc='lower right', fontsize='small')
    
    plt.tight_layout()
    plt.subplots_adjust(left=None, bottom=None, right=None, top=0.9,wspace=None, hspace=None)
    return fig,ax