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added example/vertex_coordinate_stats.ipynb

Fabian Peter Hammerle 5 years ago
parent
commit
8b9f3ec191
4 changed files with 666 additions and 0 deletions
  1. 15 0
      examples/Pipfile
  2. 411 0
      examples/Pipfile.lock
  3. 240 0
      examples/vertex_coordinate_stats.ipynb
  4. BIN
      tests/subjects/fabian/surf/lh.pial

+ 15 - 0
examples/Pipfile

@@ -0,0 +1,15 @@
+[[source]]
+url = "https://pypi.org/simple"
+verify_ssl = true
+name = "pypi"
+
+[packages]
+freesurfer-surface = {editable = true, path = "./.."}
+pandas = "<1"
+notebook = "<6"
+"ed0a5ba" = {editable = true, path = "./.."}
+
+[dev-packages]
+
+[requires]
+python_version = "3"

+ 411 - 0
examples/Pipfile.lock

@@ -0,0 +1,411 @@
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+                "sha256:ba2578f0ae582452c02ed9fac2dc477b08e80ce05d2c0885becf5fff6651ccb0",
+                "sha256:c69b0055c55702f5b0b6b354133e8325b9a56dbc80e1be2d240bead253fb9825",
+                "sha256:ca434e1858fe222380221ddeb81e86f45522773344c9da63c311d17161df5e06",
+                "sha256:d4b8ecfc3d92f114f04d5c40f60a65e5196198b827503341521dda12d8b14939",
+                "sha256:d706025c47b09a54f005953ebe206f6d07a22516776faa4f509aaff681cc5468",
+                "sha256:d8f27e958f8a2c0c8ffd4d8855c3ce8ac3fa1e105f0491ce31729aa2b3229740",
+                "sha256:dbd264298f76b9060ce537008eb989317ca787c857e23cbd1b3ddf89f190a9b1",
+                "sha256:e926d66f0df8fdbf03ba20583af0f215e475c667fb033d45fd031c66c63e34c9",
+                "sha256:efc3bd48237f973a749f7312f68062f1b4ca5c2032a0673ca3ea8e46aa77187b",
+                "sha256:f59bc782228777cbfe04555707a9c56d269c787ed25d6d28ed9d0fbb41cb1ad2",
+                "sha256:f8da5322f4ff5f667a0d5a27e871b560c6637153c81e318b35cb012b2a98835c"
+            ],
+            "version": "==18.0.1"
+        },
+        "send2trash": {
+            "hashes": [
+                "sha256:60001cc07d707fe247c94f74ca6ac0d3255aabcb930529690897ca2a39db28b2",
+                "sha256:f1691922577b6fa12821234aeb57599d887c4900b9ca537948d2dac34aea888b"
+            ],
+            "version": "==1.5.0"
+        },
+        "six": {
+            "hashes": [
+                "sha256:3350809f0555b11f552448330d0b52d5f24c91a322ea4a15ef22629740f3761c",
+                "sha256:d16a0141ec1a18405cd4ce8b4613101da75da0e9a7aec5bdd4fa804d0e0eba73"
+            ],
+            "version": "==1.12.0"
+        },
+        "terminado": {
+            "hashes": [
+                "sha256:d9d012de63acb8223ac969c17c3043337c2fcfd28f3aea1ee429b345d01ef460",
+                "sha256:de08e141f83c3a0798b050ecb097ab6259c3f0331b2f7b7750c9075ced2c20c2"
+            ],
+            "version": "==0.8.2"
+        },
+        "testpath": {
+            "hashes": [
+                "sha256:46c89ebb683f473ffe2aab0ed9f12581d4d078308a3cb3765d79c6b2317b0109",
+                "sha256:b694b3d9288dbd81685c5d2e7140b81365d46c29f5db4bc659de5aa6b98780f8"
+            ],
+            "version": "==0.4.2"
+        },
+        "tornado": {
+            "hashes": [
+                "sha256:1174dcb84d08887b55defb2cda1986faeeea715fff189ef3dc44cce99f5fca6b",
+                "sha256:2613fab506bd2aedb3722c8c64c17f8f74f4070afed6eea17f20b2115e445aec",
+                "sha256:44b82bc1146a24e5b9853d04c142576b4e8fa7a92f2e30bc364a85d1f75c4de2",
+                "sha256:457fcbee4df737d2defc181b9073758d73f54a6cfc1f280533ff48831b39f4a8",
+                "sha256:49603e1a6e24104961497ad0c07c799aec1caac7400a6762b687e74c8206677d",
+                "sha256:8c2f40b99a8153893793559919a355d7b74649a11e59f411b0b0a1793e160bc0",
+                "sha256:e1d897889c3b5a829426b7d52828fb37b28bc181cd598624e65c8be40ee3f7fa"
+            ],
+            "version": "==6.0.2"
+        },
+        "traitlets": {
+            "hashes": [
+                "sha256:9c4bd2d267b7153df9152698efb1050a5d84982d3384a37b2c1f7723ba3e7835",
+                "sha256:c6cb5e6f57c5a9bdaa40fa71ce7b4af30298fbab9ece9815b5d995ab6217c7d9"
+            ],
+            "version": "==4.3.2"
+        },
+        "wcwidth": {
+            "hashes": [
+                "sha256:3df37372226d6e63e1b1e1eda15c594bca98a22d33a23832a90998faa96bc65e",
+                "sha256:f4ebe71925af7b40a864553f761ed559b43544f8f71746c2d756c7fe788ade7c"
+            ],
+            "version": "==0.1.7"
+        },
+        "webencodings": {
+            "hashes": [
+                "sha256:a0af1213f3c2226497a97e2b3aa01a7e4bee4f403f95be16fc9acd2947514a78",
+                "sha256:b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923"
+            ],
+            "version": "==0.5.1"
+        }
+    },
+    "develop": {}
+}

+ 240 - 0
examples/vertex_coordinate_stats.ipynb

@@ -0,0 +1,240 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "155622"
+      ]
+     },
+     "execution_count": 1,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "from freesurfer_surface import Surface\n",
+    "\n",
+    "surface = Surface.read_triangular('../tests/subjects/fabian/surf/lh.pial')\n",
+    "len(surface.vertices)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<div>\n",
+       "<style scoped>\n",
+       "    .dataframe tbody tr th:only-of-type {\n",
+       "        vertical-align: middle;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe tbody tr th {\n",
+       "        vertical-align: top;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe thead th {\n",
+       "        text-align: right;\n",
+       "    }\n",
+       "</style>\n",
+       "<table border=\"1\" class=\"dataframe\">\n",
+       "  <thead>\n",
+       "    <tr style=\"text-align: right;\">\n",
+       "      <th></th>\n",
+       "      <th>right</th>\n",
+       "      <th>anterior</th>\n",
+       "      <th>superior</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>0</th>\n",
+       "      <td>-2.126251</td>\n",
+       "      <td>-93.136818</td>\n",
+       "      <td>-8.335812</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1</th>\n",
+       "      <td>-2.696686</td>\n",
+       "      <td>-93.194458</td>\n",
+       "      <td>-8.206024</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>2</th>\n",
+       "      <td>-3.738874</td>\n",
+       "      <td>-93.369530</td>\n",
+       "      <td>-8.548558</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>3</th>\n",
+       "      <td>-4.594223</td>\n",
+       "      <td>-93.183983</td>\n",
+       "      <td>-8.173017</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>4</th>\n",
+       "      <td>-2.160212</td>\n",
+       "      <td>-93.190521</td>\n",
+       "      <td>-8.865552</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "      right   anterior  superior\n",
+       "0 -2.126251 -93.136818 -8.335812\n",
+       "1 -2.696686 -93.194458 -8.206024\n",
+       "2 -3.738874 -93.369530 -8.548558\n",
+       "3 -4.594223 -93.183983 -8.173017\n",
+       "4 -2.160212 -93.190521 -8.865552"
+      ]
+     },
+     "execution_count": 2,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "import pandas\n",
+    "\n",
+    "vertex_frame = pandas.DataFrame(surface.vertices)\n",
+    "vertex_frame.head()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<div>\n",
+       "<style scoped>\n",
+       "    .dataframe tbody tr th:only-of-type {\n",
+       "        vertical-align: middle;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe tbody tr th {\n",
+       "        vertical-align: top;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe thead th {\n",
+       "        text-align: right;\n",
+       "    }\n",
+       "</style>\n",
+       "<table border=\"1\" class=\"dataframe\">\n",
+       "  <thead>\n",
+       "    <tr style=\"text-align: right;\">\n",
+       "      <th></th>\n",
+       "      <th>right</th>\n",
+       "      <th>anterior</th>\n",
+       "      <th>superior</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>count</th>\n",
+       "      <td>155622.000000</td>\n",
+       "      <td>155622.000000</td>\n",
+       "      <td>155622.000000</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>mean</th>\n",
+       "      <td>-26.856146</td>\n",
+       "      <td>-20.509144</td>\n",
+       "      <td>24.335409</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>std</th>\n",
+       "      <td>18.796259</td>\n",
+       "      <td>39.092622</td>\n",
+       "      <td>28.195845</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>min</th>\n",
+       "      <td>-68.530327</td>\n",
+       "      <td>-93.548004</td>\n",
+       "      <td>-39.114269</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>25%</th>\n",
+       "      <td>-41.877634</td>\n",
+       "      <td>-53.572824</td>\n",
+       "      <td>1.600599</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>50%</th>\n",
+       "      <td>-26.917927</td>\n",
+       "      <td>-23.102324</td>\n",
+       "      <td>24.000984</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>75%</th>\n",
+       "      <td>-9.776343</td>\n",
+       "      <td>10.147226</td>\n",
+       "      <td>47.299869</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>max</th>\n",
+       "      <td>7.291560</td>\n",
+       "      <td>70.085968</td>\n",
+       "      <td>86.737892</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "               right       anterior       superior\n",
+       "count  155622.000000  155622.000000  155622.000000\n",
+       "mean      -26.856146     -20.509144      24.335409\n",
+       "std        18.796259      39.092622      28.195845\n",
+       "min       -68.530327     -93.548004     -39.114269\n",
+       "25%       -41.877634     -53.572824       1.600599\n",
+       "50%       -26.917927     -23.102324      24.000984\n",
+       "75%        -9.776343      10.147226      47.299869\n",
+       "max         7.291560      70.085968      86.737892"
+      ]
+     },
+     "execution_count": 3,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "vertex_frame.describe()"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.6.7"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

BIN
tests/subjects/fabian/surf/lh.pial