Merge pull request #34 from tmelorc/master

Updated doc

Author: Nathaniel Saul

docs/notebooks/distances.ipynb

@@ -20,7 +20,6 @@
    "source": [
     "import numpy as np\n",
     "import persim\n",
-    "import persim.plot\n",
     "import tadasets\n",
     "import ripser\n",
     "import matplotlib.pyplot as plt"
@@ -98,7 +97,8 @@
     }
    ],
    "source": [
-    "ripser.plot_dgms([dgm_clean, dgm_noisy] , labels=['Clean $H_1$', 'Noisy $H_1$'])"
+    "persim.plot_diagrams([dgm_clean, dgm_noisy] , labels=['Clean $H_1$', 'Noisy $H_1$'])\n"
+    "plt.show()"
    ]
   },
   {
@@ -136,7 +136,8 @@
     }
    ],
    "source": [
-    "persim.plot.bottleneck_matching(dgm_clean, dgm_noisy, matching, D, labels=['Clean $H_1$', 'Noisy $H_1$'])"
+    "persim.bottleneck_matching(dgm_clean, dgm_noisy, matching, D, labels=['Clean $H_1$', 'Noisy $H_1$'])\n"
+    "plt.show()"
    ]
   },
   {
@@ -198,7 +199,7 @@
     "    matching=True\n",
     ")\n",
     "\n",
-    "persim.plot.bottleneck_matching(dgm1, dgm2, matching, D, labels=['Clean $H_1$', 'Noisy $H_1$'])\n",
+    "persim.bottleneck_matching(dgm1, dgm2, matching, D, labels=['Clean $H_1$', 'Noisy $H_1$'])\n",
     "plt.title(\"Distance {:.3f}\".format(d))\n",
     "plt.show()"
    ]
@@ -450,7 +451,8 @@
    "source": [
     "plt.scatter(dists_bottleneck[:,0], dists_bottleneck[:,1], label=\"Bottleneck\", alpha=0.3)\n",
     "plt.scatter(dists_sliced[:,0], dists_sliced[:,1], label=\"Sliced Wasserstein\", alpha=0.3)\n",
-    "plt.legend()"
+    "plt.legend()\n"
+    "plt.show()"
    ]
   },
   {
@@ -493,11 +495,12 @@
     "        matching=True\n",
     "    )\n",
     "    \n",
-    "    persim.plot.bottleneck_matching(dgm_clean, dgm, matching, D, labels=['Clean $H_1$', 'Noisy $H_1$'])\n",
+    "    persim.bottleneck_matching(dgm_clean, dgm, matching, D, labels=['Clean $H_1$', 'Noisy $H_1$'])\n",
     "\n",
     "    plt.title(\"Noise:{} Distance:{:.3f}\".format(n, d))\n",
     "\n",
-    "plt.tight_layout()"
+    "plt.tight_layout()\n"
+    "plt.show()"
    ]
   }
  ],

persim/visuals.py

@@ -175,6 +175,8 @@ def plot_diagrams(
     if show is True:
         plt.show()
 
+def plot_a_bar(p, q, c='b', linestyle='-'):
+    plt.plot([p[0], q[0]], [p[1], q[1]], c=c, linestyle=linestyle, linewidth=1)
 
 def bottleneck_matching(I1, I2, matchidx, D, labels=["dgm1", "dgm2"], ax=None):
     """ Visualize bottleneck matching between two diagrams
@@ -279,4 +281,4 @@ def wasserstein_matching(I1, I2, matchidx, palette=None, labels=["dgm1", "dgm2"]
         else:
             plt.plot([I1[i, 0], I2[j, 0]], [I1[i, 1], I2[j, 1]], "g")
 
-    plot_diagrams([I1, I2], labels=labels, ax=ax)
+    plot_diagrams([I1, I2], labels=labels, ax=ax)