reogranise into a python package

1 files changed, 583 insertions, 0 deletions

diff --git a/ipynbs/testing.py b/ipynbs/testing.py
new file mode 100644
index 0000000..5577f4b
--- /dev/null
+++ b/ipynbs/testing.py
@@ -0,0 +1,583 @@
+
+# coding: utf-8
+
+# In[1]:
+
+
+get_ipython().magic(u'matplotlib inline')
+get_ipython().magic(u'load_ext autoreload')
+get_ipython().magic(u'autoreload 2')
+
+
+# In[2]:
+
+
+import numpy as np
+
+
+# In[3]:
+
+
+sm_010 = np.load('./mcmc_DIM3_sfr_0_1_0_mfr_3.29685E+15_7.88411E+15_6.83344E+15_fix_scale_0.1_sigma_100000_proc.npy')
+sm_100 = np.load('./mcmc_DIM3_sfr_1_0_0_mfr_1.98171E+16_6.59371E+15_9.61795E+15_fix_scale_0.1_sigma_100000_proc.npy')
+
+bsm_010 = np.load('./mcmc_chains_DIM3_sfr_0_1_0_mfr_0_1_0_MixingScenario.T13_sigma_010.npy')
+bsm_100 = np.load('./mcmc_chains_DIM3_sfr_1_0_0_mfr_1_0_0_MixingScenario.T23_sigma_010.npy')
+
+
+# In[81]:
+
+
+import matplotlib as mpl
+import matplotlib.pyplot as plt
+from matplotlib.patches import Circle
+from matplotlib.legend_handler import HandlerPatch
+
+from scipy import interpolate
+
+import ternary
+
+
+# In[105]:
+
+
+bc = np.genfromtxt('./bayes_contours.csv', delimiter=',', skip_header=2)
+print bc
+
+def swap(x):
+    y = x.T
+    return np.vstack([y[1], y[-1], y[0]]).T
+
+def interp(i):
+    x, y, z = i.T
+    p = np.linspace(0, 1, len(x))
+    q = np.linspace(0, 1, 100)
+    s = 0.2
+    x_ = interpolate.splev(q, interpolate.splrep(p, x, s=s))
+    y_ = interpolate.splev(q, interpolate.splrep(p, y, s=s))
+    z_ = interpolate.splev(q, interpolate.splrep(p, z, s=s))
+    return np.vstack([x_, y_, z_]).T
+
+contour_68_upper = interp(swap(bc[:,:3]))
+contour_68_lower = interp(swap(bc[:,3:6]))
+contour_90_upper = interp(swap(bc[:,6:9]))
+contour_90_lower = interp(swap(bc[:,9:]))
+
+
+# In[67]:
+
+
+plt.style.use('./paper.mplstyle')
+
+
+# In[68]:
+
+
+class HandlerCircle(HandlerPatch):
+    def create_artists(self, legend, orig_handle,
+                       xdescent, ydescent, width, height,
+                       fontsize, trans):
+        r = 10
+        x = r + width//2 + 10
+        y = height//2 - 3
+
+        # create 
+        p = Circle(xy=(x, y), radius=r)
+
+        # update with data from oryginal object
+        self.update_prop(p, orig_handle, legend)
+
+        # move xy to legend
+        p.set_transform(trans)
+
+        return [p]
+
+
+# In[116]:
+
+
+# Figure
+fig = plt.figure(figsize=(12, 12))
+ax = fig.add_subplot(111)
+ax.set_aspect('equal')
+
+# Boundary and Gridlines
+scale = 1
+fig, tax = ternary.figure(ax=ax, scale=scale)
+
+# Draw Boundary and Gridlines
+tax.boundary(linewidth=2.0)
+tax.gridlines(color='grey', multiple=scale/5., linewidth=1.0, alpha=0.4, ls='--')
+tax.gridlines(color='grey', multiple=scale/10., linewidth=0.5, alpha=0.4, ls=':')
+
+# Set Axis labels and Title
+fontsize = 23
+tax.left_axis_label(r"$f_{\tau}^{\oplus}$", fontsize=fontsize+8, offset=0.2, rotation=0)
+tax.right_axis_label(r"$f_{\mu}^{\oplus}$", fontsize=fontsize+8, offset=0.2, rotation=0)
+tax.bottom_axis_label(r"$f_{e}^{\oplus}$", fontsize=fontsize+8, position=(0.55, -0.20/2, 0.5), rotation=0)
+
+# Remove default Matplotlib axis
+tax.get_axes().axis('off')
+tax.clear_matplotlib_ticks()
+
+# Plot
+tax.scatter(sm_010, marker='.', s=0.2, alpha=0.2, color='green')
+tax.scatter(sm_100, marker='.', s=0.2, alpha=0.2, color='blue')
+tax.scatter(bsm_010, marker='.', s=0.2, alpha=0.2, color='green')
+tax.scatter(bsm_100, marker='.', s=0.2, alpha=0.2, color='blue')
+
+# Contour
+tax.plot(contour_68_upper, linewidth=2.3, color='grey', zorder=0, alpha=0.6)
+tax.plot(contour_68_lower, linewidth=2.3, color='grey', zorder=0, alpha=0.6)
+tax.plot(contour_90_upper, linewidth=2.3, color='darkgrey', zorder=0, alpha=0.6)
+tax.plot(contour_90_lower, linewidth=2.3, color='darkgrey', zorder=0, alpha=0.6)
+
+# Lines
+marker_style = dict(
+    linestyle=' ', color='darkorange', linewidth=1.2,
+    markersize=14, zorder=0
+)
+
+p1 = (0.18301213, 0.43765598, 0.37933189)
+p2 = (0, 1, 0)
+divisions = 46
+x_d = np.linspace(p1[0], p2[0], divisions+1)
+y_d = np.linspace(p1[1], p2[1], divisions+1)
+z_d = np.linspace(p1[2], p2[2], divisions+1)
+for n in xrange(divisions-2):
+    p = (x_d[n], y_d[n], z_d[n])
+    q = (x_d[n+1], y_d[n+1], z_d[n+1])
+    tax.line(p, q, marker=(3, 2, 180+46.5), **marker_style)
+
+p1 = (0.55003613, 0.18301213, 0.26695174)
+p2 = (1, 0, 0)
+divisions = 35
+x_d = np.linspace(p1[0], p2[0], divisions+1)
+y_d = np.linspace(p1[1], p2[1], divisions+1)
+z_d = np.linspace(p1[2], p2[2], divisions+1)
+for n in xrange(divisions-2):
+    p = (x_d[n], y_d[n], z_d[n])
+    q = (x_d[n+1], y_d[n+1], z_d[n+1])
+    tax.line(p, q, marker=(3, 2, 180+63), **marker_style)
+
+# Text
+ax.text(0.36, 0.53, r'$\mathcal{O}_{e\tau}$', fontsize=fontsize,
+       rotation=0, verticalalignment='center')
+ax.text(0.445, 0.54, r'$\Lambda_d\Longrightarrow$', fontsize=fontsize+5,
+       rotation=80, verticalalignment='center')
+ax.text(0.68, 0.09, r'$\mathcal{O}_{\mu\tau}$', fontsize=fontsize,
+       rotation=0, verticalalignment='center')
+ax.text(0.7, 0.14, r'$\Lambda_d\Longrightarrow$', fontsize=fontsize+5,
+       rotation=-23, verticalalignment='center')
+ax.text(0.34, 0.2, r'$68\%$', fontsize=fontsize, rotation=5)
+ax.text(0.34, 0.1, r'$90\%$', fontsize=fontsize, rotation=5)
+
+# Legend
+l_size = fontsize
+legend_elements = []
+legend_elements.append(
+    Circle((0., 0.), 0.1, facecolor='green', alpha=0.7, edgecolor='k',
+           linewidth=2., label=r'$\left (0:1:0\right )$')
+)
+legend_elements.append(
+    Circle((0., 0.), 0.1, facecolor='blue', alpha=0.7, edgecolor='k',
+           linewidth=2., label=r'$\left (1:0:0\right )$')
+)
+legend = plt.legend(handles=legend_elements, loc=(0.65, 0.8),
+                    title='Source composition',
+                    fontsize=l_size,
+                    handler_map={Circle: HandlerCircle()})
+plt.setp(legend.get_title(), fontsize=l_size)
+legend.get_frame().set_linestyle('-')
+
+# Set ticks
+tax.ticks(axis='blr', multiple=scale/5., linewidth=1, offset=0.03,
+          fontsize=fontsize, tick_formats='%.1f')
+
+tax._redraw_labels()
+
+
+# In[10]:
+
+
+import sys
+sys.path.extend(['.', '..'])
+
+
+# In[35]:
+
+
+from utils import fr as fr_utils
+from utils import misc as misc_utils
+from utils.enums import MixingScenario
+
+
+# In[19]:
+
+
+s = [1, 0, 0]
+print s, '->', fr_utils.u_to_fr(s, np.array(fr_utils.NUFIT_U, dtype=np.complex128))
+s = [0, 1, 0]
+print s, '->', fr_utils.u_to_fr(s, np.array(fr_utils.NUFIT_U, dtype=np.complex128))
+
+
+# In[47]:
+
+
+sc = np.linspace(-60, -20, 4000)
+
+s = [1, 0, 0]
+frs_100 = []
+for x in sc:
+    u = fr_utils.params_to_BSMu(x, fix_mixing=MixingScenario.T23, dim=6, energy=1e6)
+    frs_100.append(fr_utils.u_to_fr(s, np.array(u, dtype=np.complex128)))
+frs_100 = np.vstack(frs_100)
+    
+s = [0, 1, 0]
+frs_010 = []
+for x in sc:
+    u = fr_utils.params_to_BSMu(x, fix_mixing=MixingScenario.T13, dim=6, energy=1e6)
+    frs_010.append(fr_utils.u_to_fr(s, np.array(u, dtype=np.complex128)))
+frs_010 = np.vstack(frs_010)
+
+s = [1, 2, 0]
+frs_120 = []
+for x in sc:
+    u = fr_utils.params_to_BSMu(x, fix_mixing=MixingScenario.T12, dim=6, energy=1e6)
+    frs_120.append(fr_utils.u_to_fr(s, np.array(u, dtype=np.complex128)))
+frs_120 = np.vstack(frs_120)
+
+
+# In[50]:
+
+
+# Figure
+fig = plt.figure(figsize=(12, 12))
+ax = fig.add_subplot(111)
+ax.set_aspect('equal')
+
+# Boundary and Gridlines
+scale = 1
+fig, tax = ternary.figure(ax=ax, scale=scale)
+
+# Draw Boundary and Gridlines
+tax.boundary(linewidth=2.0)
+tax.gridlines(color='grey', multiple=scale/5., linewidth=1.0, alpha=0.4, ls='--')
+tax.gridlines(color='grey', multiple=scale/10., linewidth=0.5, alpha=0.4, ls=':')
+
+# Set Axis labels and Title
+fontsize = 23
+tax.left_axis_label(r"$f_{\tau}^{\oplus}$", fontsize=fontsize+8, offset=0.2, rotation=0)
+tax.right_axis_label(r"$f_{\mu}^{\oplus}$", fontsize=fontsize+8, offset=0.2, rotation=0)
+tax.bottom_axis_label(r"$f_{e}^{\oplus}$", fontsize=fontsize+8, position=(0.55, -0.20/2, 0.5), rotation=0)
+
+# Remove default Matplotlib axis
+tax.get_axes().axis('off')
+tax.clear_matplotlib_ticks()
+
+# Plot
+tax.scatter(frs_010, marker='o', s=2, alpha=1, color='green')
+tax.scatter(frs_100, marker='o', s=2, alpha=1, color='blue')
+tax.scatter(frs_120, marker='o', s=2, alpha=1, color='red')
+
+# Legend
+l_size = fontsize
+legend_elements = []
+legend_elements.append(
+    Circle((0., 0.), 0.1, facecolor='red', alpha=0.7, edgecolor='k',
+           linewidth=2., label=r'$\left (1:2:0\right )$')
+)
+legend_elements.append(
+    Circle((0., 0.), 0.1, facecolor='green', alpha=0.7, edgecolor='k',
+           linewidth=2., label=r'$\left (0:1:0\right )$')
+)
+legend_elements.append(
+    Circle((0., 0.), 0.1, facecolor='blue', alpha=0.7, edgecolor='k',
+           linewidth=2., label=r'$\left (1:0:0\right )$')
+)
+legend = plt.legend(handles=legend_elements, loc=(0.65, 0.8),
+                    title='Source composition',
+                    fontsize=l_size,
+                    handler_map={Circle: HandlerCircle()})
+plt.setp(legend.get_title(), fontsize=l_size)
+legend.get_frame().set_linestyle('-')
+
+# Set ticks
+tax.ticks(axis='blr', multiple=scale/5., linewidth=1, offset=0.03,
+          fontsize=fontsize, tick_formats='%.1f')
+
+tax._redraw_labels()
+
+
+# In[69]:
+
+
+sc = np.linspace(-60, -20, 4000)
+
+scen = MixingScenario.T12
+
+s = [1, 0, 0]
+frs_100 = []
+for x in sc:
+    u = fr_utils.params_to_BSMu(x, fix_mixing=scen, dim=6, energy=1e6)
+    frs_100.append(fr_utils.u_to_fr(s, np.array(u, dtype=np.complex128)))
+frs_100 = np.vstack(frs_100)
+    
+s = [0, 1, 0]
+frs_010 = []
+for x in sc:
+    u = fr_utils.params_to_BSMu(x, fix_mixing=scen, dim=6, energy=1e6)
+    frs_010.append(fr_utils.u_to_fr(s, np.array(u, dtype=np.complex128)))
+frs_010 = np.vstack(frs_010)
+
+s = [1, 2, 0]
+frs_120 = []
+for x in sc:
+    u = fr_utils.params_to_BSMu(x, fix_mixing=scen, dim=6, energy=1e6)
+    frs_120.append(fr_utils.u_to_fr(s, np.array(u, dtype=np.complex128)))
+frs_120 = np.vstack(frs_120)
+
+
+# In[70]:
+
+
+# Figure
+fig = plt.figure(figsize=(12, 12))
+ax = fig.add_subplot(111)
+ax.set_aspect('equal')
+
+# Boundary and Gridlines
+scale = 1
+fig, tax = ternary.figure(ax=ax, scale=scale)
+
+# Draw Boundary and Gridlines
+tax.boundary(linewidth=2.0)
+tax.gridlines(color='grey', multiple=scale/5., linewidth=1.0, alpha=0.4, ls='--')
+tax.gridlines(color='grey', multiple=scale/10., linewidth=0.5, alpha=0.4, ls=':')
+
+# Set Axis labels and Title
+fontsize = 23
+tax.set_title(r'$\mathcal{O}_{e\mu}\:operator$', fontsize=fontsize+10, pad=35)
+tax.left_axis_label(r"$f_{\tau}^{\oplus}$", fontsize=fontsize+8, offset=0.2, rotation=0)
+tax.right_axis_label(r"$f_{\mu}^{\oplus}$", fontsize=fontsize+8, offset=0.2, rotation=0)
+tax.bottom_axis_label(r"$f_{e}^{\oplus}$", fontsize=fontsize+8, position=(0.55, -0.20/2, 0.5), rotation=0)
+
+# Remove default Matplotlib axis
+tax.get_axes().axis('off')
+tax.clear_matplotlib_ticks()
+
+# Plot
+tax.scatter(frs_010, marker='o', s=2, alpha=1, color='green')
+tax.scatter(frs_100, marker='o', s=2, alpha=1, color='blue')
+tax.scatter(frs_120, marker='o', s=2, alpha=1, color='red')
+
+# Legend
+l_size = fontsize
+legend_elements = []
+legend_elements.append(
+    Circle((0., 0.), 0.1, facecolor='red', alpha=0.7, edgecolor='k',
+           linewidth=2., label=r'$\left (1:2:0\right )$')
+)
+legend_elements.append(
+    Circle((0., 0.), 0.1, facecolor='green', alpha=0.7, edgecolor='k',
+           linewidth=2., label=r'$\left (0:1:0\right )$')
+)
+legend_elements.append(
+    Circle((0., 0.), 0.1, facecolor='blue', alpha=0.7, edgecolor='k',
+           linewidth=2., label=r'$\left (1:0:0\right )$')
+)
+legend = plt.legend(handles=legend_elements, loc=(0.65, 0.8),
+                    title='Source composition',
+                    fontsize=l_size,
+                    handler_map={Circle: HandlerCircle()})
+plt.setp(legend.get_title(), fontsize=l_size)
+legend.get_frame().set_linestyle('-')
+
+# Set ticks
+tax.ticks(axis='blr', multiple=scale/5., linewidth=1, offset=0.03,
+          fontsize=fontsize, tick_formats='%.1f')
+
+tax._redraw_labels()
+
+
+# In[64]:
+
+
+sc = np.linspace(-60, -20, 4000)
+
+scen = MixingScenario.T23
+
+s = [1, 0, 0]
+frs_100 = []
+for x in sc:
+    u = fr_utils.params_to_BSMu(x, fix_mixing=scen, dim=6, energy=1e6)
+    frs_100.append(fr_utils.u_to_fr(s, np.array(u, dtype=np.complex128)))
+frs_100 = np.vstack(frs_100)
+    
+s = [0, 1, 0]
+frs_010 = []
+for x in sc:
+    u = fr_utils.params_to_BSMu(x, fix_mixing=scen, dim=6, energy=1e6)
+    frs_010.append(fr_utils.u_to_fr(s, np.array(u, dtype=np.complex128)))
+frs_010 = np.vstack(frs_010)
+
+s = [1, 2, 0]
+frs_120 = []
+for x in sc:
+    u = fr_utils.params_to_BSMu(x, fix_mixing=scen, dim=6, energy=1e6)
+    frs_120.append(fr_utils.u_to_fr(s, np.array(u, dtype=np.complex128)))
+frs_120 = np.vstack(frs_120)
+
+
+# In[65]:
+
+
+# Figure
+fig = plt.figure(figsize=(12, 12))
+ax = fig.add_subplot(111)
+ax.set_aspect('equal')
+
+# Boundary and Gridlines
+scale = 1
+fig, tax = ternary.figure(ax=ax, scale=scale)
+
+# Draw Boundary and Gridlines
+tax.boundary(linewidth=2.0)
+tax.gridlines(color='grey', multiple=scale/5., linewidth=1.0, alpha=0.4, ls='--')
+tax.gridlines(color='grey', multiple=scale/10., linewidth=0.5, alpha=0.4, ls=':')
+
+# Set Axis labels and Title
+fontsize = 23
+tax.set_title(r'$\mathcal{O}_{\mu\tau}\:operator$', fontsize=fontsize+10, pad=35)
+tax.left_axis_label(r"$f_{\tau}^{\oplus}$", fontsize=fontsize+8, offset=0.2, rotation=0)
+tax.right_axis_label(r"$f_{\mu}^{\oplus}$", fontsize=fontsize+8, offset=0.2, rotation=0)
+tax.bottom_axis_label(r"$f_{e}^{\oplus}$", fontsize=fontsize+8, position=(0.55, -0.20/2, 0.5), rotation=0)
+
+# Remove default Matplotlib axis
+tax.get_axes().axis('off')
+tax.clear_matplotlib_ticks()
+
+# Plot
+tax.scatter(frs_010, marker='o', s=2, alpha=1, color='green')
+tax.scatter(frs_100, marker='o', s=2, alpha=1, color='blue')
+tax.scatter(frs_120, marker='o', s=2, alpha=1, color='red')
+
+# Legend
+l_size = fontsize
+legend_elements = []
+legend_elements.append(
+    Circle((0., 0.), 0.1, facecolor='red', alpha=0.7, edgecolor='k',
+           linewidth=2., label=r'$\left (1:2:0\right )$')
+)
+legend_elements.append(
+    Circle((0., 0.), 0.1, facecolor='green', alpha=0.7, edgecolor='k',
+           linewidth=2., label=r'$\left (0:1:0\right )$')
+)
+legend_elements.append(
+    Circle((0., 0.), 0.1, facecolor='blue', alpha=0.7, edgecolor='k',
+           linewidth=2., label=r'$\left (1:0:0\right )$')
+)
+legend = plt.legend(handles=legend_elements, loc=(0.65, 0.8),
+                    title='Source composition',
+                    fontsize=l_size,
+                    handler_map={Circle: HandlerCircle()})
+plt.setp(legend.get_title(), fontsize=l_size)
+legend.get_frame().set_linestyle('-')
+
+# Set ticks
+tax.ticks(axis='blr', multiple=scale/5., linewidth=1, offset=0.03,
+          fontsize=fontsize, tick_formats='%.1f')
+
+tax._redraw_labels()
+
+
+# In[66]:
+
+
+sc = np.linspace(-60, -20, 4000)
+
+scen = MixingScenario.T13
+
+s = [1, 0, 0]
+frs_100 = []
+for x in sc:
+    u = fr_utils.params_to_BSMu(x, fix_mixing=scen, dim=6, energy=1e6)
+    frs_100.append(fr_utils.u_to_fr(s, np.array(u, dtype=np.complex128)))
+frs_100 = np.vstack(frs_100)
+    
+s = [0, 1, 0]
+frs_010 = []
+for x in sc:
+    u = fr_utils.params_to_BSMu(x, fix_mixing=scen, dim=6, energy=1e6)
+    frs_010.append(fr_utils.u_to_fr(s, np.array(u, dtype=np.complex128)))
+frs_010 = np.vstack(frs_010)
+
+s = [1, 2, 0]
+frs_120 = []
+for x in sc:
+    u = fr_utils.params_to_BSMu(x, fix_mixing=scen, dim=6, energy=1e6)
+    frs_120.append(fr_utils.u_to_fr(s, np.array(u, dtype=np.complex128)))
+frs_120 = np.vstack(frs_120)
+
+
+# In[68]:
+
+
+# Figure
+fig = plt.figure(figsize=(12, 12))
+ax = fig.add_subplot(111)
+ax.set_aspect('equal')
+
+# Boundary and Gridlines
+scale = 1
+fig, tax = ternary.figure(ax=ax, scale=scale)
+
+# Draw Boundary and Gridlines
+tax.boundary(linewidth=2.0)
+tax.gridlines(color='grey', multiple=scale/5., linewidth=1.0, alpha=0.4, ls='--')
+tax.gridlines(color='grey', multiple=scale/10., linewidth=0.5, alpha=0.4, ls=':')
+
+# Set Axis labels and Title
+fontsize = 23
+tax.set_title(r'$\mathcal{O}_{e\tau}\:operator$', fontsize=fontsize+10, pad=35)
+tax.left_axis_label(r"$f_{\tau}^{\oplus}$", fontsize=fontsize+8, offset=0.2, rotation=0)
+tax.right_axis_label(r"$f_{\mu}^{\oplus}$", fontsize=fontsize+8, offset=0.2, rotation=0)
+tax.bottom_axis_label(r"$f_{e}^{\oplus}$", fontsize=fontsize+8, position=(0.55, -0.20/2, 0.5), rotation=0)
+
+# Remove default Matplotlib axis
+tax.get_axes().axis('off')
+tax.clear_matplotlib_ticks()
+
+# Plot
+tax.scatter(frs_010, marker='o', s=2, alpha=1, color='green')
+tax.scatter(frs_100, marker='o', s=2, alpha=1, color='blue')
+tax.scatter(frs_120, marker='o', s=2, alpha=1, color='red')
+
+# Legend
+l_size = fontsize
+legend_elements = []
+legend_elements.append(
+    Circle((0., 0.), 0.1, facecolor='red', alpha=0.7, edgecolor='k',
+           linewidth=2., label=r'$\left (1:2:0\right )$')
+)
+legend_elements.append(
+    Circle((0., 0.), 0.1, facecolor='green', alpha=0.7, edgecolor='k',
+           linewidth=2., label=r'$\left (0:1:0\right )$')
+)
+legend_elements.append(
+    Circle((0., 0.), 0.1, facecolor='blue', alpha=0.7, edgecolor='k',
+           linewidth=2., label=r'$\left (1:0:0\right )$')
+)
+legend = plt.legend(handles=legend_elements, loc=(0.65, 0.8),
+                    title='Source composition',
+                    fontsize=l_size,
+                    handler_map={Circle: HandlerCircle()})
+plt.setp(legend.get_title(), fontsize=l_size)
+legend.get_frame().set_linestyle('-')
+
+# Set ticks
+tax.ticks(axis='blr', multiple=scale/5., linewidth=1, offset=0.03,
+          fontsize=fontsize, tick_formats='%.1f')
+
+tax._redraw_labels()
+