Merge pull request #398 from LinkedEarth/stripe_fix

Stripe fix

pyleoclim/core/multipleseries.py

@@ -2024,8 +2024,9 @@ def stackplot(self, figsize=None, savefig_settings=None, time_unit = None, xlim=
         else:
             return ax
 
-    def stripes(self, ref_period=None, figsize=None, savefig_settings=None,  time_unit=None,
-                LIM = 2.8, thickness=1.0, labels='auto',  label_color = 'gray',
+    def stripes(self, cmap = 'RdBu_r', sat=1.0, ref_period=None,
+                figsize=None, savefig_settings=None,  time_unit=None,
+                labels='auto',  label_color = 'gray', show_xaxis=False,
                 common_time_kwargs=None, xlim=None, font_scale=0.8, x_offset = 0.05):
         '''
         Represents a MultipleSeries object as a quilt of Ed Hawkins' "stripes" patterns
@@ -2039,21 +2040,24 @@ def stripes(self, ref_period=None, figsize=None, savefig_settings=None,  time_un
 
         Parameters
         ----------
-
+        cmap: str
+            colormap name (https://matplotlib.org/stable/tutorials/colors/colormaps.html)
+            Default is 'RdBu_r'
+            
         ref_period : TYPE, optional
             dates of the reference period, in the form "(first, last)".
             The default is None, which will pick the beginning and end of the common time axis.
         
-        LIM : float
-            scaling factor for color saturation. default is 2.8. 
-            The higher the LIM, the more compressed the color range (milder hues)
-        
-        thickness : float, optional
-            vertical thickness of the stripe . The default is 1.0
-            
         figsize : list
+            a list of two integers indicating the figure size (in inches)
         
-            Size of the figure.
+        
+        sat : float > 0
+            Controls the saturation of the colormap normalization by scaling the vmin, vmax in https://matplotlib.org/stable/tutorials/colors/colormapnorms.html
+            default = 1.0
+            
+        show_xaxis : bool
+            flag indicating whether or not the x-axis should be shown (default = False) 
             
         savefig_settings : dictionary
         
@@ -2126,12 +2130,11 @@ def stripes(self, ref_period=None, figsize=None, savefig_settings=None,  time_un
             :okexcept:
 
             import pyleoclim as pyleo
-            url = 'http://wiki.linked.earth/wiki/index.php/Special:WTLiPD?op=export&lipdid=MD982176.Stott.2004'
-            d = pyleo.Lipd(usr_path = url)
-            tslist = d.to_LipdSeriesList()
-            tslist = tslist[2:] # drop the first two series which only concerns age and depth
-            ms = pyleo.MultipleSeries(tslist)
-            @savefig md76_stripes.png
+            co2ts = pyleo.utils.load_dataset('AACO2')
+            lr04 = pyleo.utils.load_dataset('LR04')
+            edc = pyleo.utils.load_dataset('EDC-dD')
+            ms = lr04.flip() & edc & co2ts # create MS object
+            @savefig ms_stripes.png
             fig, ax = ms.stripes()
             pyleo.closefig(fig)
              
@@ -2144,23 +2147,25 @@ def stripes(self, ref_period=None, figsize=None, savefig_settings=None,  time_un
             :okwarning:
             :okexcept:
 
-            import pyleoclim as pyleo
-            url = 'http://wiki.linked.earth/wiki/index.php/Special:WTLiPD?op=export&lipdid=MD982176.Stott.2004'
-            d = pyleo.Lipd(usr_path = url)
-            tslist = d.to_LipdSeriesList()
-            tslist = tslist[2:] # drop the first two series which only concerns age and depth
-            ms = pyleo.MultipleSeries(tslist)
-            @savefig md76_stripes2.png
-            fig, ax = ms.stripes(common_time_kwargs={'step': 0.5}, x_offset = 200, 
-                                 LIM=4, figsize=[8,3])
-            pyleo.closefig(fig)     
+             import pyleoclim as pyleo
+             co2ts = pyleo.utils.load_dataset('AACO2')
+             lr04 = pyleo.utils.load_dataset('LR04')
+             edc = pyleo.utils.load_dataset('EDC-dD')
+             ms = lr04.flip() & edc & co2ts # create MS object
+             @savefig ms_stripes2.png
+             fig, ax = ms.stripes(figsize=(8,2.5),show_xaxis=True, sat = 0.8)
+             pyleo.closefig(fig)
             
         '''
         current_style = deepcopy(mpl.rcParams)
         plotting.set_style('journal', font_scale=font_scale)
         savefig_settings = {} if savefig_settings is None else savefig_settings.copy()
         common_time_kwargs = {} if common_time_kwargs is None else common_time_kwargs.copy()
 
+        if len(self.series_list)>20:
+            warnings.warn("You are trying to plot over 20 series; results will be hard to see",
+                          UserWarning, stacklevel=2)
+
         # deal with time units
         self = self.convert_time_unit(time_unit=time_unit)
 
@@ -2188,20 +2193,23 @@ def stripes(self, ref_period=None, figsize=None, savefig_settings=None,  time_un
         fig, axs = plt.subplots(n_ts, 1, sharex=True, figsize=figsize, layout = 'tight')
         ax = axs.flatten()
 
-        if xlim is None:
-            xlim = [time.min(), time.max()]
-
         for idx in range(n_ts-1):  # loop over series
-            ts = msc.series_list[idx].gaussianize()
-            ts.stripes(ref_period, LIM = LIM, label_color = label_color,
+            ts = msc.series_list[idx]
+            ts.stripes(ref_period, sat=sat, cmap= cmap,
+                       label_color = label_color,
                        ax=ax[idx], x_offset=x_offset) 
 
         # handle bottom plot
-        ts = msc.series_list[last].gaussianize()
-        ts.stripes(ref_period, LIM = LIM, label_color = label_color, 
-                   ax=ax[last], x_offset=x_offset, show_xaxis=True) 
-        ax[last].set_xlabel(time_label)
+        ts = msc.series_list[last]
+        ts.stripes(ref_period, sat=sat, cmap=cmap,
+                   label_color = label_color, show_xaxis=show_xaxis,
+                   ax=ax[last], x_offset=x_offset) 
+
+        if xlim is None:
+            xlim = [time.min(), time.max()]
         ax[last].set_xlim(xlim)
+
+        fig.tight_layout()
 
         if 'fig' in locals():
             if 'path' in savefig_settings:

pyleoclim/core/psds.py

@@ -324,7 +324,7 @@ def signif_test(self, method='ar1sim', number=None, seed=None, qs=[0.95],
         elif method == 'ar1asym':
             std = self.timeseries.stats()['std'] # assess standard deviation 
             if np.abs(std-1) > 0.1: 
-                warnings.warn("Asymptoics are only defined for a standard deviation of unity. Please apply to a standardized series only")
+                warnings.warn("Asymptotics are only defined for a standard deviation of unity. Please apply to a standardized series only")
 
             new=self.copy()
 

pyleoclim/core/series.py

@@ -964,10 +964,11 @@ def plot(self, figsize=[10, 4],
 
         return res
 
-    def stripes(self, ref_period, LIM = 2.8, thickness=1.0, figsize=[8, 1], xlim=None,
-              top_label=None, bottom_label=None, label_color = 'gray', label_size = None,
-              xlabel=None, savefig_settings=None, ax=None, invert_xaxis=False,
-              show_xaxis=False, x_offset = 0.05):
+    def stripes(self, figsize=[8, 1], cmap = 'RdBu_r', ref_period=None,  
+                sat=1.0, top_label=None, bottom_label=None, 
+                label_color = 'gray', label_size = None, xlim=None, 
+                xlabel=None, savefig_settings=None, ax=None, invert_xaxis=False,
+                show_xaxis=False, x_offset = 0.03):
         '''Represents the Series as an Ed Hawkins "stripes" pattern
 
         Credit: https://matplotlib.org/matplotblog/posts/warming-stripes/
@@ -977,14 +978,15 @@ def stripes(self, ref_period, LIM = 2.8, thickness=1.0, figsize=[8, 1], xlim=Non
         ref_period : array-like (2-elements)
             dates of the reference period, in the form "(first, last)"
 
-        thickness : float, optional
-            vertical thickness of the stripe . The default is 1.0
-
-        LIM : float
-            scaling factor for color saturation. default is 2.8
-
         figsize : list
             a list of two integers indicating the figure size (in inches)
+        
+        cmap: str
+            colormap name (https://matplotlib.org/stable/tutorials/colors/colormaps.html)
+            
+        sat : float > 0
+            Controls the saturation of the colormap normalization by scaling the vmin, vmax in https://matplotlib.org/stable/tutorials/colors/colormapnorms.html
+            default = 0.9
 
         xlim : list
             time axis limits
@@ -1032,48 +1034,56 @@ def stripes(self, ref_period, LIM = 2.8, thickness=1.0, figsize=[8, 1], xlim=Non
 
         See also
         --------
-
         pyleoclim.utils.plotting.stripes : stripes representation of a timeseries
-
         pyleoclim.utils.plotting.savefig : saving a figure in Pyleoclim
-
+        
+        
         Examples
         --------
 
         Plot the HadCRUT5 Global Mean Surface Temperature
-        
         >>> gmst = pyleo.utils.load_dataset('HadCRUT5')
         >>> fig, ax = gmst.stripes(ref_period=(1971,2000))
-        >>> pyleo.closefig(fig)
-
-        If you wanted to show the time axis:
+        
+        For a more pastel tone, dial down saturation:
+        >>>  fig, ax = gmst.stripes(ref_period=(1971,2000), sat = 0.8)
 
-         >>> gmst = pyleo.utils.load_dataset('HadCRUT5')
-         >>> fig, ax = gmst.stripes(ref_period=(1971,2000), show_xaxis=True, figsize=[8, 1.2])
-         >>> pyleo.closefig(fig)
+        To change the colormap:    
+        >>> fig, ax = gmst.stripes(ref_period=(1971,2000), cmap='Spectral_r')
+        >>> fig, ax = gmst.stripes(ref_period=(1971,2000), cmap='magma_r')
+        
+        To show the time axis: 
+        >>> fig, ax = gmst.stripes(ref_period=(1971,2000), show_xaxis=True)
 
-        Note that we had to increase the figure height to make space for the extra text.
         '''
 
         if top_label is None:
             top_label = self.label
 
         if bottom_label is None:
             bottom_label = self.value_name
-
-        idx0 = (np.abs(self.time - ref_period[0])).argmin()
-        idx1 = (np.abs(self.time - ref_period[1])).argmin()
-
-        LIMs = self.value.std()*LIM
+
+        if ref_period is None:
+            ref_period = [self.time.min(), self.time.max()]
+
+        if sat <= 0:
+            raise ValueError('sat must be a strictly positive number, ideally close to unity.')
+
         # Ed Hawkins says: Currently I use HadCRUT5 with a 1971-2000 baseline
         # and a colour scaling of +/- 0.75K (which is probably similar to LIM).
         # It should be relatively simple to duplicate the stripes exactly
+
+        # center and normalize values for proper display
+        yc =  self.center(timespan=ref_period).value
+        vmax = np.abs(yc).max()/sat
+
+        time_label, _ = self.make_labels()
 
-        res = plotting.stripes_xy(
-            x=self.time, y=self.value, ref_period=(idx0,idx1), LIM = LIMs, thickness = thickness,
+        res = plotting.stripes_xy(x=self.time, y=yc, cmap=cmap, vmin=-vmax, vmax=vmax,
             top_label = top_label, bottom_label = bottom_label, label_color = label_color,
-            figsize=figsize, ax=ax,  xlim=xlim, invert_xaxis=invert_xaxis,  label_size=label_size,
-            savefig_settings=savefig_settings, show_xaxis=show_xaxis, x_offset = x_offset,
+            figsize=figsize, ax=ax,  xlim=xlim, invert_xaxis=invert_xaxis,  
+            label_size=label_size, xlabel = time_label, x_offset = x_offset,
+            savefig_settings=savefig_settings, show_xaxis=show_xaxis, 
         )
 
         return res

pyleoclim/tests/test_core_MultipleSeries.py

@@ -127,6 +127,7 @@ def test_plot(self):
         assert_allclose(t_1, x_plot_1)
         assert_allclose(v_0, y_plot_0)
         assert_allclose(v_1, y_plot_1)
+        pyleo.closefig(fig)
 
 class TestMultipleSeriesStripes:
     '''Test for MultipleSeries.stripes()
@@ -140,17 +141,14 @@ def test_stripes(self):
         t_1, v_1 = gen_normal()
 
         #Create series objects
-        ts_0 = pyleo.Series(time = t_0, value = v_0)
-        ts_1 = pyleo.Series(time = t_1, value = v_1)
-
-        #Create a list of series objects
-        serieslist = [ts_0, ts_1]
+        ts_0 = pyleo.Series(time = t_0, value = v_0, label='series 1')
+        ts_1 = pyleo.Series(time = t_1, value = v_1, label='series 2')
 
         #Turn this list into a multiple series object
-        ts_M = pyleo.MultipleSeries(serieslist)
-
-        fig, ax = ts_M.stripes(LIM=4, x_offset=2, label_color = 'red')
+        ts_M = ts_0 &  ts_1
 
+        fig, ax = ts_M.stripes(sat=0.9, label_color = 'red', cmap='cividis_r')
+        pyleo.closefig(fig)
 
 class TestMultipleSeriesStandardize:
     '''Test for MultipleSeries.standardize()

pyleoclim/tests/test_core_Series.py

@@ -1037,22 +1037,17 @@ def test_plot(self):
 
         x_plot = line.get_xdata()
         y_plot = line.get_ydata()
-
-
         pyleo.closefig(fig)
 
 class TestUiSeriesStripes:
-    '''Test for Series.stripes()
-
-    Series.stripes outputs a matplotlib figure and axis object, so we will compare the time axis
-    of the axis object to the time array.'''
-
-    def test_stripes(self):
+    '''Test for Series.stripes()'''
+    @pytest.mark.parametrize('show_xaxis', [True, False])
+    def test_stripes(self, show_xaxis):
 
         ts = gen_normal()
 
-        fig, ax = ts.stripes(ref_period=[61,90],x_offset=2)
-
+        fig, ax = ts.stripes(ref_period=[61,90], show_xaxis=show_xaxis)
+        assert ax.xaxis.get_ticklabels() != []
         pyleo.closefig(fig)