Examples updated, minor bug fixes

fjosw · Oct 11, 2021 · 1d74e8c · 1d74e8c
1 parent e7ea0df
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Showing 12 changed files with 1,886 additions and 1,717 deletions.
diff --git a/examples/01_basic_example.ipynb b/examples/01_basic_example.ipynb
diff --git a/examples/02_correlators.ipynb b/examples/02_correlators.ipynb
diff --git a/examples/02_pcac_example.ipynb b/examples/02_pcac_example.ipynb
diff --git a/examples/03_fit_example.ipynb b/examples/03_fit_example.ipynb
diff --git a/examples/03_pcac_example.ipynb b/examples/03_pcac_example.ipynb
diff --git a/examples/04_fit_example.ipynb b/examples/04_fit_example.ipynb
diff --git a/examples/05_correlators.ipynb b/examples/05_correlators.ipynb
diff --git a/examples/04_matrix_operations.ipynb → examples/05_matrix_operations.ipynb b/examples/04_matrix_operations.ipynb → examples/05_matrix_operations.ipynb
@@ -6,8 +6,6 @@
  "metadata": {},
  "outputs": [],
  "source": [
- "import sys\n",
- "sys.path.append('..')\n",
  "import pyerrors as pe\n",
  "import numpy as np\n",
  "import scipy"
@@ -169,7 +167,7 @@
  "name": "stdout",
  "output_type": "stream",
  "text": [
- "[Obs[7.2(1.7)] Obs[-1.00(47)]]\n"
+ "[Obs[7.2(1.7)] Obs[-1.00(45)]]\n"
  ]
  }
  ],
@@ -229,7 +227,7 @@
  "name": "stdout",
  "output_type": "stream",
  "text": [
- "cond \t Obs[6.23(59)]\n",
+ "cond \t Obs[6.23(58)]\n",
  "expm_cond \t Obs[4.45(19)]\n"
  ]
  }
@@ -261,7 +259,7 @@
  "output_type": "stream",
  "text": [
  "[[Obs[2.025(49)] Obs[0.0]]\n",
- " [Obs[-0.494(50)] Obs[0.870(29)]]]\n"
+ " [Obs[-0.494(51)] Obs[0.870(29)]]]\n"
  ]
  }
  ],
@@ -349,20 +347,20 @@
  "output_type": "stream",
  "text": [
  "orth\n",
- "[[Obs[-0.9592(75)] Obs[0.283(25)]]\n",
- " [Obs[0.283(25)] Obs[0.9592(75)]]]\n",
+ "[[Obs[-0.9592(76)] Obs[0.283(26)]]\n",
+ " [Obs[0.283(26)] Obs[0.9592(76)]]]\n",
  "expm\n",
- "[[Obs[75(15)] Obs[-21.4(4.2)]]\n",
- " [Obs[-21.4(4.2)] Obs[8.3(1.4)]]]\n",
+ "[[Obs[75(15)] Obs[-21.4(4.1)]]\n",
+ " [Obs[-21.4(4.1)] Obs[8.3(1.4)]]]\n",
  "logm\n",
  "[[Obs[1.334(57)] Obs[-0.496(61)]]\n",
  " [Obs[-0.496(61)] Obs[-0.203(50)]]]\n",
  "sinhm\n",
  "[[Obs[37.3(7.4)] Obs[-10.8(2.1)]]\n",
- " [Obs[-10.8(2.1)] Obs[3.94(69)]]]\n",
+ " [Obs[-10.8(2.1)] Obs[3.94(68)]]]\n",
  "sqrtm\n",
  "[[Obs[1.996(51)] Obs[-0.341(37)]]\n",
- " [Obs[-0.341(37)] Obs[0.940(15)]]]\n"
+ " [Obs[-0.341(37)] Obs[0.940(14)]]]\n"
  ]
  }
  ],
@@ -397,8 +395,8 @@
  "Eigenvalues:\n",
  "[Obs[0.705(57)] Obs[4.39(19)]]\n",
  "Eigenvectors:\n",
- "[[Obs[-0.283(25)] Obs[-0.9592(75)]]\n",
- " [Obs[-0.9592(75)] Obs[0.283(25)]]]\n"
+ "[[Obs[-0.283(26)] Obs[-0.9592(76)]]\n",
+ " [Obs[-0.9592(76)] Obs[0.283(26)]]]\n"
  ]
  }
  ],
@@ -467,7 +465,7 @@
  "name": "python",
  "nbconvert_exporter": "python",
  "pygments_lexer": "ipython3",
- "version": "3.6.11"
+ "version": "3.6.9"
  }
  },
  "nbformat": 4,

diff --git a/examples/base_style.mplstyle b/examples/base_style.mplstyle
@@ -0,0 +1,30 @@
+# Base mplstyle, Fabian Joswig, 2021
+font.size: 12
+
+lines.marker : o
+lines.markersize : 6
+lines.linewidth : 1.0
+lines.linestyle : none
+
+font.family: serif
+
+axes.labelsize : 14
+
+xtick.labelsize : 12
+
+ytick.labelsize : 12
+
+figure.dpi : 100
+figure.figsize : 6.4, 3.9555 # figure size in inches, golden ratio
+figure.subplot.left : 0.125 # the left side of the subplots of the figure
+figure.subplot.right : 0.95 # the right side of the subplots of the figure
+figure.subplot.bottom : 0.125 # the bottom of the subplots of the figure
+figure.subplot.top : 0.95 # the top of the subplots of the figure
+
+errorbar.capsize : 3.4641016 # sqrt(markersize * 2)
+
+legend.fontsize : 12
+legend.frameon : False
+
+savefig.transparent : True
+savefig.dpi : 300
diff --git a/examples/data/correlator_test.p b/examples/data/correlator_test.p
diff --git a/pyerrors/correlators.py b/pyerrors/correlators.py
@@ -358,7 +358,7 @@ def set_prange(self, prange):
  return
 
  # Plotting routine for correlator
- def show(self, x_range=None, comp=None, logscale=False, plateau=None, fit_res=None, save=None, ylabel=None):
+ def show(self, x_range=None, comp=None, y_range=None, logscale=False, plateau=None, fit_res=None, save=None, ylabel=None):
  """Plots the correlator, uses tag as label if available.
 
  Parameters
@@ -371,7 +371,7 @@ def show(self, x_range=None, comp=None, logscale=False, plateau=None, fit_res=No
  if self.N!=1:
  raise Exception("Correlator must be projected before plotting")
  if x_range is None:
- x_range=[0, self.T]
+ x_range = [0, self.T]
 
  fig = plt.figure()
  ax1 = fig.add_subplot(111)
@@ -382,12 +382,15 @@ def show(self, x_range=None, comp=None, logscale=False, plateau=None, fit_res=No
  ax1.set_yscale('log')
  else:
  # we generate ylim instead of using autoscaling.
- try:
- y_min=min([(x[0].value - x[0].dvalue) for x in self.content[x_range[0]:x_range[1]] if (x is not None) and x[0].dvalue < 2 * np.abs(x[0].value)])
- y_max=max([(x[0].value + x[0].dvalue) for x in self.content[x_range[0]:x_range[1]] if (x is not None) and x[0].dvalue < 2 * np.abs(x[0].value)])
- ax1.set_ylim([y_min - 0.1 * (y_max - y_min), y_max + 0.1 * (y_max - y_min)])
- except:
- pass
+ if y_range is None:
+ try:
+ y_min=min([(x[0].value - x[0].dvalue) for x in self.content[x_range[0]:x_range[1]] if (x is not None) and x[0].dvalue < 2 * np.abs(x[0].value)])
+ y_max=max([(x[0].value + x[0].dvalue) for x in self.content[x_range[0]:x_range[1]] if (x is not None) and x[0].dvalue < 2 * np.abs(x[0].value)])
+ ax1.set_ylim([y_min - 0.1 * (y_max - y_min), y_max + 0.1 * (y_max - y_min)])
+ except:
+ pass
+ else:
+ ax1.set_ylim(y_range)
  if comp:
  if isinstance(comp, Corr) or isinstance(comp, list):
  for corr in comp if isinstance(comp, list) else [comp]:

diff --git a/pyerrors/fits.py b/pyerrors/fits.py
@@ -575,7 +575,7 @@ def residual_plot(x, y, func, fit_res):
  gs = gridspec.GridSpec(2, 1, height_ratios=[3, 1], wspace=0.0, hspace=0.0)
  ax0 = plt.subplot(gs[0])
  ax0.errorbar(x, [o.value for o in y], yerr=[o.dvalue for o in y], ls='none', fmt='o', capsize=3, markersize=5, label='Data')
- ax0.plot(x_samples, func([o.value for o in fit_res], x_samples), label='Fit', zorder=10)
+ ax0.plot(x_samples, func([o.value for o in fit_res], x_samples), label='Fit', zorder=10, ls='-', ms=0)
  ax0.set_xticklabels([])
  ax0.set_xlim([xstart, xstop])
  ax0.set_xticklabels([])