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Remove custom path specifcation in example notebook #29

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Remove custom path specifcation in example notebook #29

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123 changes: 32 additions & 91 deletions brainx/notebooks/detect_partition_degeneracy.ipynb
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Original file line number Diff line number Diff line change
@@ -1,7 +1,16 @@
{
"metadata": {
"kernelspec": {
"codemirror_mode": {
"name": "ipython",
"version": 2
},
"display_name": "IPython (Python 2)",
"language": "python",
"name": "python2"
},
"name": "",
"signature": "sha256:a279c98a0412414b9c96041884cdbed8d963c45cbdc2d0208f2a84a5f0f09451"
"signature": "sha256:1b5afc6e5122b380a91d4eb08d65d1493d39af6d846e87f1e8a8ca3656a13d90"
},
"nbformat": 3,
"nbformat_minor": 0,
Expand Down Expand Up @@ -57,28 +66,23 @@
"import numpy as np\n",
"import networkx as nx\n",
"from glob import glob\n",
"from matplotlib import pyplot as plt"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 2
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"# user-specific imports\n",
"import json\n",
"from matplotlib import pyplot as plt\n",
"\n",
"brainxdir = '/home/jagust/graph/scripts/brainx/brainx/' ## EDIT ME! ##\n",
"os.chdir(brainxdir)\n",
"from util import threshold_adjacency_matrix"
"from brainx.util import threshold_adjacency_matrix"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 3
"outputs": [
{
"output_type": "stream",
"stream": "stderr",
"text": [
"/home/stefan/src/brainx/brainx/__init__.py:30: UserWarning: Monkeypatching NetworkX's Watts-Strogatz routine\n",
" warnings.warn(\"Monkeypatching NetworkX's Watts-Strogatz routine\")\n"
]
}
],
"prompt_number": 2
},
{
"cell_type": "heading",
Expand Down Expand Up @@ -232,14 +236,7 @@
"[[2, 3, 5, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 64, 65, 66, 71, 72, 73, 83, 84, 85, 86], [76, 77], [70], [74], [75], [87]]\n",
"1006_gbsm cost: 0.25\n",
"[[1, 10, 11, 16, 17, 18, 19, 20, 21, 28, 29, 32, 33, 36, 37, 39, 56, 57, 59, 60, 62, 63, 67, 78, 79, 80, 81, 82, 83, 85, 89], [87]]\n",
"1007_base"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
" cost: 0.25\n",
"1007_base cost: 0.25\n",
"[[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 18, 19, 22, 23, 24, 25, 26, 27, 33, 34, 35, 56, 57, 58, 59, 60, 61, 64, 65, 66, 67, 68, 69, 85], [20], [21]]\n",
"[[42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 54, 55, 88], [52, 53]]\n",
"1007_gbsm cost: 0.25\n",
Expand All @@ -248,53 +245,25 @@
"[[1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 13, 18, 19, 22, 23, 24, 25, 31, 32, 33, 34, 35, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 84, 85, 88], [27]]\n",
"1008_base cost: 0.25\n",
"[[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 30, 31, 34, 35, 51, 55, 58, 59, 60, 61, 64, 65, 66, 67, 76, 77, 84, 85, 86, 87, 89], [20], [21]]\n",
"1008_edu"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
" cost: 0.25\n",
"1008_edu cost: 0.25\n",
"[[2, 3, 4, 5, 6, 7, 8, 9, 12, 14, 15, 22, 23, 24, 25, 32, 34, 35, 64, 65, 66, 67, 70, 71, 84, 85, 86], [76, 77]]\n",
"[[0, 11, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 33, 36, 37, 38, 40, 56, 57, 68, 69, 78, 79, 80, 81, 82, 83, 87], [72, 73, 74, 75], [39], [41]]\n",
"1008_gbsm cost: 0.25\n",
"[[64, 2, 70, 6, 8, 9, 10, 12, 13, 14, 77, 76, 84, 86, 55, 88, 89, 60], [41]]\n",
"[[3, 4, 5, 7, 15, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 65, 66, 67, 71, 72, 74, 85, 87], [45]]\n",
"1009_edu cost: 0.25\n",
"[[0, 1, 21, 23, 24, 25, 26, 27, 37, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 68, 69, 80, 84, 85], [20]]\n",
"1009_gbsm"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
" cost: 0.25\n",
"1009_gbsm cost: 0.25\n",
"1010_edu cost: 0.25\n",
"[[3, 5, 7, 9, 13, 14, 15, 16, 17, 22, 23, 25, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 54, 55, 59, 63, 65, 67, 68, 69, 70, 72, 73, 74, 75, 76, 77, 78, 79, 81, 82, 83, 87, 89], [27, 20, 21, 71]]\n",
"1010_gbsm cost: 0.25\n",
"[[3, 5, 15, 20, 21, 22, 23, 25, 27, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 64, 65, 75, 82, 83, 85, 86, 87, 89], [26], [71]]\n",
"[[0, 1, 2, 6, 7, 10, 11, 12, 13, 16, 17, 18, 19, 28, 29, 32, 56, 57, 60, 61, 62, 68, 69, 72, 73, 74, 76, 77, 79, 80, 81], [24], [70]]\n",
"[[33, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 58, 59, 63, 66, 67, 78, 84, 88], [4], [8], [9], [14]]\n",
"1011_edu"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
" cost: 0.25\n",
"1011_edu cost: 0.25\n",
"1011_gbsm cost: 0.25\n",
"1015_base cost: 0.25\n",
"1015_edu"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
" cost: 0.25\n",
"1015_edu cost: 0.25\n",
"[[0, 4, 8, 24, 25, 26, 27, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 66, 67, 68, 69, 88], [20, 21], [86], [87]]\n",
"1015_gbsm cost: 0.25\n",
"[[16, 17, 28, 29, 36, 37, 38, 39, 40, 41, 62, 63, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87], [21]]\n",
Expand All @@ -303,55 +272,27 @@
"1016_base cost: 0.25\n",
"[[4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 26, 27, 28, 29, 36, 37, 38, 40, 41, 60, 61, 62, 63, 64, 65, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 85, 86, 87, 89], [20], [70]]\n",
"[[0, 1, 2, 3, 18, 19, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 66, 67, 68, 69, 84, 88], [39], [71]]\n",
"1016_gbsm"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
" cost: 0.25\n",
"1016_gbsm cost: 0.25\n",
"[[32, 36, 38, 72, 73, 74, 75, 76, 77, 82, 83, 21, 28, 29, 62], [41, 37, 86, 87], [20], [39], [40]]\n",
"1017_base cost: 0.25\n",
"[[6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 32, 36, 37, 38, 39, 40, 41, 62, 63, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 86, 87, 88, 89], [70]]\n",
"[[42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 66, 67, 68, 69, 84, 85], [71]]\n",
"1017_edu cost: 0.25\n",
"1017_gbsm"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
" cost: 0.25\n",
"1017_gbsm cost: 0.25\n",
"[[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 59, 60, 61, 62, 69], [70], [71]]\n",
"[[16, 17, 28, 29, 36, 37, 38, 39, 40, 41, 63, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89], [64, 65]]\n",
"1018_base cost: 0.25\n",
"[[2, 3, 4, 5, 6, 7, 8, 9, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 30, 31, 34, 35, 64, 65, 66, 67, 82, 84, 85, 86, 87, 89], [20, 21], [70, 71]]\n",
"1018_edu cost: 0.25\n",
"[[1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 30, 31, 35, 52, 56, 57, 60, 61, 63, 64, 65, 69, 84, 85, 89], [5], [20], [70], [71]]\n",
"[[0, 16, 17, 18, 19, 28, 29, 32, 33, 34, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 53, 54, 55, 58, 59, 62, 66, 67, 68, 76, 77, 78, 79, 80, 81, 82, 83, 86, 88], [72, 73, 74, 75], [40, 41], [87]]\n",
"1018_gbsm"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
" cost: 0.25\n",
"1018_gbsm cost: 0.25\n",
"[[1, 6, 16, 17, 18, 19, 28, 29, 32, 33, 41, 57, 59, 60, 61, 62, 63, 69, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 83, 87], [70, 71]]\n",
"1020_base cost: 0.25\n",
"[[0, 1, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 68, 69, 82, 88, 89], [38]]\n",
"1020_edu cost: 0.25\n",
"[[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 38, 39, 57, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 71, 76, 77, 78, 79, 80, 81, 82, 83, 86, 89], [70]]\n",
"1020_gbsm"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
" cost: 0.25\n",
"1020_gbsm cost: 0.25\n",
"[[2, 3, 4, 5, 6, 8, 9, 10, 11, 13, 14, 15, 20, 22, 23, 24, 25, 26, 27, 30, 31, 34, 35, 60, 64, 65, 89], [70, 71]]\n",
"[[7, 16, 17, 18, 19, 28, 29, 32, 33, 40, 62, 63, 66, 67, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83], [21]]\n"
]
Expand Down