py2ls 0.1.6.3__tar.gz → 0.1.6.4__tar.gz

{py2ls-0.1.6.3 → py2ls-0.1.6.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: py2ls
-Version: 0.1.6.3
+Version: 0.1.6.4
 Summary: py(thon)2(too)ls
 Author: Jianfeng
 Author-email: Jianfeng.Liu0413@gmail.com

{py2ls-0.1.6.3 → py2ls-0.1.6.4}/py2ls/__init__.py

@@ -2,5 +2,6 @@
     __init__ of the pyos module
 """
 from .ips import *
-from.translator import *
+from .translator import *
 from .netfinder import *
+from .plot import *

{py2ls-0.1.6.3 → py2ls-0.1.6.4}/py2ls/plot.py

@@ -33,19 +33,34 @@ def catplot(data, *args, **kwargs):
         if not isinstance(opt_e['MarkerEdgeColor'],list):
             opt_e['MarkerEdgeColor']=[opt_e['MarkerEdgeColor']]  
         for i, (x, y, err) in enumerate(zip(error_positions, data_m, errors)):
-            ax.errorbar(x, y, yerr=err, 
-                        fmt=opt_e['Marker'], 
-                        ecolor=opt_e['LineColor'], 
-                        elinewidth=opt_e['LineWidth'], 
-                        lw=opt_e['LineWidth'], 
-                        ls=opt_e['LineStyle'], 
-                        capsize=opt_e['CapSize'],
-                        capthick=opt_e['CapLineWidth'], 
-                        markersize=opt_e['MarkerSize'],
-                        mec=opt_e['MarkerEdgeColor'][i % len(opt_e['MarkerEdgeColor'])],
-                        mfc=opt_e['FaceColor'][i % len(opt_e['FaceColor'])],
-                        visible=opt_e['Visible']
-                        )
+            if opt_e['MarkerSize']=='auto':
+                ax.errorbar(x, y, yerr=err, 
+                            fmt=opt_e['Marker'], 
+                            ecolor=opt_e['LineColor'], 
+                            elinewidth=opt_e['LineWidth'], 
+                            lw=opt_e['LineWidth'], 
+                            ls=opt_e['LineStyle'], 
+                            capsize=opt_e['CapSize'],
+                            capthick=opt_e['CapLineWidth'],  
+                            mec=opt_e['MarkerEdgeColor'][i % len(opt_e['MarkerEdgeColor'])],
+                            mfc=opt_e['FaceColor'][i % len(opt_e['FaceColor'])],
+                            visible=opt_e['Visible']
+                            )
+            else:
+                ax.errorbar(x, y, yerr=err, 
+                            fmt=opt_e['Marker'], 
+                            ecolor=opt_e['LineColor'], 
+                            elinewidth=opt_e['LineWidth'], 
+                            lw=opt_e['LineWidth'], 
+                            ls=opt_e['LineStyle'], 
+                            capsize=opt_e['CapSize'],
+                            capthick=opt_e['CapLineWidth'], 
+                            markersize=opt_e['MarkerSize'],
+                            mec=opt_e['MarkerEdgeColor'][i % len(opt_e['MarkerEdgeColor'])],
+                            mfc=opt_e['FaceColor'][i % len(opt_e['FaceColor'])],
+                            visible=opt_e['Visible']
+                            )
+                
 
     def plot_scatter(data, opt_s, xloc, ax):
         scatter_positions = get_positions(xloc, opt_s['loc'], opt_s['x_width'], data.shape[0])
@@ -56,7 +71,9 @@ def catplot(data, *args, **kwargs):
                         alpha=opt_s['FaceAlpha'], 
                         edgecolor=opt_s['MarkerEdgeColor'], 
                         s=opt_s['MarkerSize'],
-                        marker=opt_s['Marker']
+                        marker=opt_s['Marker'],
+                        linewidths=opt_s['LineWidth'],
+                        cmap=opt_s['cmap']
                         )
 
     def plot_boxplot(data, bx_opt, xloc,ax):
@@ -198,7 +215,30 @@ def catplot(data, *args, **kwargs):
             return np.tile(np.concatenate([xloc[:1] - x_width, xloc[1:-1], xloc[-1:] + x_width]),(n_row,1))
         else:
             return np.tile(xloc,(n_row,1))
+    def sort_catplot_layers(custom_order, full_order= ['b', 'bx', 'e', 'v', 's', 'l']):
+        """
+        sort layers
+        """
+        # Ensure custom_order is a list of strings
+        custom_order = [str(layer) for layer in custom_order] 
+        j = 1
+        layers = list(range(len(full_order)))
+        for i in range(len(full_order)):
+            if full_order[i] not in custom_order:
+                layers[i] = i
+            else:
+                layers[i] = None
+        j = 0
+        for i in range(len(layers)):
+            if layers[i] is None:
+                full_order[i] = custom_order[j]
+                j += 1
+        return full_order
+        # # Example usage:
+        # custom_order = ['s', 'bx', 'e']
+        # full_order = sort_catplot_layers(custom_order)
     
+    # full_order
     opt = kwargs.get('opt',{}) 
     ax = kwargs.get('ax',None)
     if 'ax' not in locals() or ax is None:
@@ -223,26 +263,30 @@ def catplot(data, *args, **kwargs):
     opt['loc'].setdefault('xloc', np.arange(1, data.shape[1] + 1))
 
     # export setting
-    opt.setdefault('export', False)
+    opt.setdefault('export', {})
     opt['export'].setdefault('path', None)
     print(opt['export'])
 
+    # opt.setdefault('layer', {})
+    opt.setdefault('layer', ['b', 'bx', 'e', 'v', 's', 'l'])
+
     opt.setdefault('b', {})
-    opt['b'].setdefault('go', 0) 
+    opt['b'].setdefault('go', 1) 
+    opt['b'].setdefault('loc', 'c')
     opt['b'].setdefault('EdgeColor', 'k')
-    opt['b'].setdefault('FaceAlpha', 1)
+    opt['b'].setdefault('FaceAlpha', 0.65)
     opt['b'].setdefault('EdgeAlpha', 1)
     opt['b'].setdefault('LineStyle', '-')
     opt['b'].setdefault('x_width', 0.5)
     opt['b'].setdefault('ShowBaseLine', 'off')
-    opt['b'].setdefault('loc', 'c')
     opt['b'].setdefault('FaceColor', opt['c'])
 
     opt.setdefault('e', {})
     opt['e'].setdefault('go', 1) 
+    opt['e'].setdefault('loc', 'l')
     opt['e'].setdefault('LineWidth', 1)
     opt['e'].setdefault('CapLineWidth', 1)
-    opt['e'].setdefault('CapSize', opt['b']['x_width'] * 100 * 0.1)
+    opt['e'].setdefault('CapSize', 2)
     opt['e'].setdefault('Marker', 'none')
     opt['e'].setdefault('LineStyle', 'none')
     opt['e'].setdefault('LineColor', 'k')
@@ -253,63 +297,70 @@ def catplot(data, *args, **kwargs):
     opt['e'].setdefault('Visible', True)
     opt['e'].setdefault('Orientation', 'vertical')
     opt['e'].setdefault('error', 'sem')
-    opt['e'].setdefault('loc', 'c')
     opt['e'].setdefault('x_width', opt['b']['x_width'] / 5)
     opt['e'].setdefault('cap_dir', 'b')
 
     opt.setdefault('s', {})
     opt['s'].setdefault('go', 1) 
+    opt['s'].setdefault('loc', 'r')
+    opt['s'].setdefault('FaceColor', opt['c'])
+    opt['s'].setdefault('cmap', None)
+    opt['s'].setdefault('FaceAlpha', 1)
     opt['s'].setdefault('x_width', opt['b']['x_width'] / 5)
     opt['s'].setdefault('Marker', 'o')
-    opt['s'].setdefault('MarkerSize', 6)  # Set default size for markers
-    opt['s'].setdefault('LineWidth', 1)
-    opt['s'].setdefault('FaceColor', opt['c'])
-    opt['s'].setdefault('FaceAlpha', 0.6)
-    opt['s'].setdefault('loc', 'random')
-    opt['s'].setdefault('MarkerEdgeColor', None)
-
+    opt['s'].setdefault('MarkerSize', 10)  
+    opt['s'].setdefault('LineWidth', 0.5)
+    opt['s'].setdefault('MarkerEdgeColor', 'k')
+    
+    opt.setdefault('l', {})
+    opt['l'].setdefault('go', 1)
+    opt['l'].setdefault('LineStyle', '-')
+    opt['l'].setdefault('LineColor', 'k')
+    opt['l'].setdefault('LineWidth', 0.5)
+    opt['l'].setdefault('LineAlpha', 0.5) 
+    
     opt.setdefault('bx', {})
     opt['bx'].setdefault('go', 0)
+    opt['bx'].setdefault('loc', 'r')
+    opt['bx'].setdefault('FaceColor', opt['c'])
     opt['bx'].setdefault('EdgeColor', 'k')
-    opt['bx'].setdefault('FaceAlpha', 1)
+    opt['bx'].setdefault('FaceAlpha', 0.7)
     opt['bx'].setdefault('EdgeAlpha', 1)
     opt['bx'].setdefault('LineStyle', '-')
-    opt['bx'].setdefault('x_width', 0.5)
+    opt['bx'].setdefault('x_width', 0.2)
     opt['bx'].setdefault('ShowBaseLine', 'off')
-    opt['bx'].setdefault('loc', 'c')
-    opt['bx'].setdefault('FaceColor', opt['c'])
     opt['bx'].setdefault('Notch', False)
-    opt['bx'].setdefault('MedianStyle', 'line')
     opt['bx'].setdefault('Outliers', 'on')
     opt['bx'].setdefault('OutlierMarker', '+')
     opt['bx'].setdefault('OutlierColor', 'r')
     opt['bx'].setdefault('OutlierSize', 6)
-    opt['bx'].setdefault('PlotStyle', 'traditional')
-    opt['bx'].setdefault('FactorDirection', 'auto')
-    opt['bx'].setdefault('Whisker', 1.5)
+    # opt['bx'].setdefault('PlotStyle', 'traditional')
+    # opt['bx'].setdefault('FactorDirection', 'auto')
+    opt['bx'].setdefault('Whisker', 0.5)
     opt['bx'].setdefault('Orientation', 'vertical')
-    opt['bx'].setdefault('BoxLineWidth', 1.5)
+    opt['bx'].setdefault('BoxLineWidth', 0.5)
     opt['bx'].setdefault('FaceColor', 'k')
     opt['bx'].setdefault('WhiskerLineStyle', '-')
     opt['bx'].setdefault('WhiskerLineColor', 'k')
-    opt['bx'].setdefault('WhiskerLineWidth', 1.5)
+    opt['bx'].setdefault('WhiskerLineWidth', 0.5)
     opt['bx'].setdefault('Caps', True)
     opt['bx'].setdefault('CapLineColor', 'k')
-    opt['bx'].setdefault('CapLineWidth', 1.5)
-    opt['bx'].setdefault('CapSize', 0.35)
+    opt['bx'].setdefault('CapLineWidth', 0.5)
+    opt['bx'].setdefault('CapSize', 0.2)
     opt['bx'].setdefault('MedianLineStyle', '-')
+    opt['bx'].setdefault('MedianStyle', 'line')
     opt['bx'].setdefault('MedianLineColor', 'k')
-    opt['bx'].setdefault('MedianLineWidth', 1.5)
+    opt['bx'].setdefault('MedianLineWidth', 2)
     opt['bx'].setdefault('MedianLineTop', False)
     opt['bx'].setdefault('MeanLine', False)
     opt['bx'].setdefault('showmeans', opt['bx']['MeanLine'])
     opt['bx'].setdefault('MeanLineStyle', '-')
-    opt['bx'].setdefault('MeanLineColor', 'b')
-    opt['bx'].setdefault('MeanLineWidth', 1.5)
+    opt['bx'].setdefault('MeanLineColor', 'w')
+    opt['bx'].setdefault('MeanLineWidth', 2)
     
     # Violin plot options
     opt.setdefault('v', {})
-    opt['v'].setdefault('go', 1)
+    opt['v'].setdefault('go', 0)
     opt['v'].setdefault('x_width', 0.3)
     opt['v'].setdefault('loc', 'r')
     opt['v'].setdefault('EdgeColor', 'none')
@@ -321,35 +372,35 @@ def catplot(data, *args, **kwargs):
     opt['v'].setdefault('NumPoints', 500)
     opt['v'].setdefault('BoundaryCorrection', 'reflection')
     
-    # line plot options
-    opt.setdefault('l', {})
-    opt['l'].setdefault('go', 0)
-    opt['l'].setdefault('LineStyle', '-')
-    opt['l'].setdefault('LineColor', 'k')
-    opt['l'].setdefault('LineWidth', 0.5)
-    opt['l'].setdefault('LineAlpha', 0.5) 
 
     data_m = np.nanmean(data, axis=0)
     nr, nc = data.shape
-
-    xloc = opt['loc']['xloc']
-
-    if opt['b']['go']:
-        plot_bars(data_m, opt['b'], xloc, ax)
-
-    if opt['e']['go']:
-        plot_errors(data, data_m, opt['e'], xloc, ax)
-
-    if opt['s']['go']:
-        plot_scatter(data, opt['s'], xloc, ax)
-        
-    if opt['bx']['go']:
-        plot_boxplot(data, opt['bx'], xloc, ax)
-    if opt['v']['go']:
-        plot_violin(data, opt['v'], xloc, ax) 
-    if opt['l']['go'] and opt['s']['go']:
-        plot_lines(data, opt['l'], opt['s'], ax)
-
+ 
+    for key in kwargs.keys():
+        if key in opt:
+            if isinstance(kwargs[key], dict):
+                opt[key].update(kwargs[key])
+            else:
+                opt[key] = kwargs[key]
+    xloc = opt['loc']['xloc'] 
+    layers = sort_catplot_layers(opt['layer'])
+    for layer in layers: 
+        if layer== 'b' and opt['b']['go']: 
+            plot_bars(data_m, opt['b'], xloc, ax)
+        elif layer== 'e' and opt['e']['go']:
+            plot_errors(data, data_m, opt['e'], xloc, ax)
+        elif layer== 's' and opt['s']['go']:
+            plot_scatter(data, opt['s'], xloc, ax)
+        elif layer== 'bx' and opt['bx']['go']:
+            plot_boxplot(data, opt['bx'], xloc, ax)
+        elif layer== 'v' and opt['v']['go']:
+            plot_violin(data, opt['v'], xloc, ax) 
+        elif all([layer== 'l',opt['l']['go'],opt['s']['go']]):
+            plot_lines(data, opt['l'], opt['s'], ax)
+    # figsets
+    kw_figsets=kwargs.get('figsets',None)
+    if kw_figsets is not None:
+        figsets(ax=ax,**kw_figsets)
     return ax
 
 # from py2ls.ips import get_color,figsets
@@ -1036,7 +1087,7 @@ def stdshade(ax=None,*args, **kwargs):
     # line_kws = kwargs.get('line_kws', {})
 
     # setting form kwargs
-    lw = kwargs.get('lw', 1.5)
+    lw = kwargs.get('lw', 0.5)
     ls= kwargs.get('ls', plotStyle)
     marker=kwargs.get("marker",plotMarker)
     label=kwargs.get("label",None)
@@ -1075,6 +1126,12 @@ def stdshade(ax=None,*args, **kwargs):
 
     fill = ax.fill_between(x, yMean + wings, yMean - wings, **kws_fill)
     line = ax.plot(x, yMean, **kws_line)
+
+    # figsets
+    kw_figsets=kwargs.get('figsets',None)
+    if kw_figsets is not None:
+        figsets(ax=ax,**kw_figsets)
+
     return line[0], fill
 
 
@@ -1106,4 +1163,67 @@ plot.stdshade(data,
 plt.legend()
 
 """
- 
+
+
+def adjust_spines(ax=None, spines=['left', 'bottom'],distance=2):
+    if ax is None:
+        ax = plt.gca()
+    for loc, spine in ax.spines.items():
+        if loc in spines:
+            spine.set_position(('outward', distance))  # outward by 2 points
+            # spine.set_smart_bounds(True)
+        else:
+            spine.set_color('none')  # don't draw spine
+    # turn off ticks where there is no spine
+    if 'left' in spines:
+        ax.yaxis.set_ticks_position('left')
+    else:
+        ax.yaxis.set_ticks([])
+    if 'bottom' in spines:
+        ax.xaxis.set_ticks_position('bottom')
+    else:
+        # no xaxis ticks
+        ax.xaxis.set_ticks([])
+# And then plot the data:
+
+def add_colorbar(im, width=None, pad=None, **kwargs):
+    # usage: add_colorbar(im, width=0.01, pad=0.005, label="PSD (dB)", shrink=0.8)
+    l, b, w, h = im.axes.get_position().bounds  # get boundaries
+    width = width or 0.1 * w  # get width of the colorbar
+    pad = pad or width  # get pad between im and cbar
+    fig = im.axes.figure  # get figure of image
+    cax = fig.add_axes([l + w + pad, b, width, h])  # define cbar Axes
+    return fig.colorbar(im, cax=cax, **kwargs)  # draw cbar
+
+def padcat(*args, fill_value=np.nan, axis=1):
+    """
+    Concatenate vectors with padding.
+
+    Parameters:
+    *args : variable number of list or 1D arrays
+        Input arrays to concatenate.
+    fill_value : scalar, optional
+        The value to use for padding the shorter lists (default is np.nan).
+    axis : int, optional
+        The axis along which to concatenate (0 for rows, 1 for columns, default is 0).
+
+    Returns:
+    np.ndarray
+        A 2D array with the input arrays concatenated along the specified axis, padded with fill_value where necessary.
+    """
+    if axis == 0:
+        # Concatenate along rows
+        max_len = max(len(lst) for lst in args)
+        result = np.full((len(args), max_len), fill_value)
+        for i, lst in enumerate(args):
+            result[i, :len(lst)] = lst
+    elif axis == 1:
+        # Concatenate along columns
+        max_len = max(len(lst) for lst in args)
+        result = np.full((max_len, len(args)), fill_value)
+        for i, lst in enumerate(args):
+            result[:len(lst), i] = lst
+    else:
+        raise ValueError("axis must be 0 or 1")
+    
+    return result

{py2ls-0.1.6.3 → py2ls-0.1.6.4}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "py2ls"
-version = "0.1.6.3"
+version = "0.1.6.4"
 description = "py(thon)2(too)ls"
 authors = ["Jianfeng <Jianfeng.Liu0413@gmail.com>"]
 readme = "README.md"