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slarson/Synapse positions work 8-22.ipynb

Created August 22, 2013 23:43
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iPython Notebook file for work done on synapse positions, 8/22
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Synapse positions work 8-22.ipynb
{
"metadata": {
"name": "Synapse positions work 8-22"
},
"nbformat": 3,
"nbformat_minor": 0,
"worksheets": [
{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": "Need to pull down the relevant repos to work with from GitHub"
},
{
"cell_type": "markdown",
"metadata": {},
"source": "LibNeuroML\n----------\n\nRather than pulling from the root repo, I have forked this into my own personal repository. When the root development branch is updated, I need to update my personal development branch with a pull request that I respond to, which got done.\n\nNow then what is needed is to clone my repo and switch to the development branch\n\n [email protected]:slarson/libNeuroML.git\n \nBut I haven't configured Git on this box yet so I still have to do that. I will use [GitHub's instructions](https://help.github.com/articles/set-up-git) to do so."
},
{
"cell_type": "markdown",
"metadata": {},
"source": "Setting up Git\n-------------\n\n"
},
{
"cell_type": "code",
"collapsed": false,
"input": "!git config --global user.name \"slarson\"",
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 3
},
{
"cell_type": "code",
"collapsed": false,
"input": "!git config --global user.email \"[email protected]\"",
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 4
},
{
"cell_type": "markdown",
"metadata": {},
"source": "fingers crossed...\n\nGrabbing the libNeuroML repo\n---------------------------\n\nFollowing [GitHub instructions](https://help.github.com/articles/fork-a-repo) for command line Git"
},
{
"cell_type": "code",
"collapsed": false,
"input": "!git clone https://github.com/slarson/libNeuroML.git",
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": "Cloning into 'libNeuroML'...\r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": "remote: Counting objects: 2465, done.\u001b[K\r\nremote: Compressing objects: 0% (1/1031) \u001b[K\rremote: Compressing objects: 1% (11/1031) \u001b[K\rremote: Compressing objects: 2% (21/1031) \u001b[K\rremote: Compressing objects: 3% (31/1031) \u001b[K\rremote: Compressing objects: 4% (42/1031) \u001b[K\rremote: Compressing objects: 5% (52/1031) \u001b[K\rremote: Compressing objects: 6% (62/1031) \u001b[K\rremote: Compressing objects: 7% (73/1031) \u001b[K\rremote: Compressing objects: 8% (83/1031) \u001b[K\rremote: Compressing objects: 9% (93/1031) \u001b[K\rremote: Compressing objects: 10% (104/1031) \u001b[K\rremote: Compressing objects: 11% (114/1031) \u001b[K\rremote: Compressing objects: 12% (124/1031) \u001b[K\rremote: Compressing objects: 13% (135/1031) \u001b[K\rremote: Compressing objects: 14% (145/1031) \u001b[K\rremote: Compressing objects: 15% (155/1031) \u001b[K\rremote: Compressing objects: 16% (165/1031) \u001b[K\rremote: Compressing objects: 17% (176/1031) 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},
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"text": "Resolving deltas: 51% (697/1355) \rResolving deltas: 52% (710/1355) \rResolving deltas: 54% (743/1355) \rResolving deltas: 55% (746/1355) \rResolving deltas: 56% (768/1355) \rResolving deltas: 57% (773/1355) \rResolving deltas: 58% (786/1355) \rResolving deltas: 59% (800/1355) \rResolving deltas: 60% (813/1355) \rResolving deltas: 61% (829/1355) \rResolving deltas: 62% (852/1355) \rResolving deltas: 63% (859/1355) \rResolving deltas: 65% (881/1355) \rResolving deltas: 66% (895/1355) \rResolving deltas: 67% (910/1355) \rResolving deltas: 68% (925/1355) \rResolving deltas: 69% (941/1355) \rResolving deltas: 70% (960/1355) \rResolving deltas: 76% (1037/1355) \rResolving deltas: 78% (1060/1355) \rResolving deltas: 79% (1083/1355) \rResolving deltas: 80% (1089/1355) \rResolving deltas: 81% (1100/1355) \rResolving deltas: 82% (1112/1355) \rResolving deltas: 83% (1128/1355) \rResolving deltas: 87% (1180/1355) \rResolving deltas: 88% (1196/1355) \rResolving deltas: 89% (1208/1355) \rResolving deltas: 91% (1237/1355) \rResolving deltas: 92% (1257/1355) \rResolving deltas: 93% (1261/1355) \rResolving deltas: 94% (1281/1355) \rResolving deltas: 95% (1288/1355) \rResolving deltas: 97% (1321/1355) \rResolving deltas: 98% (1328/1355) \rResolving deltas: 99% (1347/1355) \rResolving deltas: 100% (1355/1355) \rResolving deltas: 100% (1355/1355), done.\r\n"
}
],
"prompt_number": 6
},
{
"cell_type": "code",
"collapsed": false,
"input": "!cd libNeuroML; ls",
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": "AUTHORS doc LICENSE MANIFEST.in neuroml README requirements.txt setup.py\r\n"
}
],
"prompt_number": 7
},
{
"cell_type": "markdown",
"metadata": {},
"source": "success!\n\nSwitching into the development branch\n-------------------------------------"
},
{
"cell_type": "code",
"collapsed": false,
"input": "!cd libNeuroML",
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 1
},
{
"cell_type": "code",
"collapsed": false,
"input": "!git checkout development",
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": "error: pathspec 'development' did not match any file(s) known to git.\r\n"
}
],
"prompt_number": 2
},
{
"cell_type": "code",
"collapsed": false,
"input": "!git branch",
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": "* master\r\n"
}
],
"prompt_number": 3
},
{
"cell_type": "markdown",
"metadata": {},
"source": "WTF? There's no development branch [like there is on the website](https://github.com/slarson/libNeuroML/tree/development)\n\nTurns out, that's not a bug, its [a feature](http://stackoverflow.com/questions/2841373/github-repos-cloning-but-no-tags-branches-recreated)"
},
{
"cell_type": "code",
"collapsed": false,
"input": "!cd libNeuroML; git branch -a",
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": "* master\r\n remotes/origin/HEAD -> origin/master\r\n remotes/origin/dev\r\n remotes/origin/development\r\n remotes/origin/master\r\n"
}
],
"prompt_number": 9
},
{
"cell_type": "markdown",
"metadata": {},
"source": "Ah there it is."
},
{
"cell_type": "code",
"collapsed": false,
"input": "!cd libNeuroML; git checkout -b development origin/development",
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": "Branch development set up to track remote branch development from origin.\r\nSwitched to a new branch 'development'\r\n"
}
],
"prompt_number": 12
},
{
"cell_type": "markdown",
"metadata": {},
"source": "Now back to the [issue at hand](https://github.com/openworm/OpenWorm/issues/136)\n\nOh and rats, looks like I could have used the following from the start to simplify life.\n\n git clone -b development git://github.com/slarson/libNeuroML.git\n\nLesson learned"
},
{
"cell_type": "code",
"collapsed": false,
"input": "%cd libNeuroML",
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": "/home/ubuntu/ipython/libNeuroML\n"
}
],
"prompt_number": 16
},
{
"cell_type": "code",
"collapsed": false,
"input": "!python setup.py install",
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": "/usr/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'install_requires'\r\n warnings.warn(msg)\r\nrunning install\r\nrunning build\r\nrunning build_py\r\ncreating build\r\ncreating build/lib.linux-x86_64-2.7\r\ncreating build/lib.linux-x86_64-2.7/neuroml\r\ncopying neuroml/__init__.py -> build/lib.linux-x86_64-2.7/neuroml\r\ncopying neuroml/writers.py -> build/lib.linux-x86_64-2.7/neuroml\r\ncopying neuroml/loaders.py -> build/lib.linux-x86_64-2.7/neuroml\r\ncopying neuroml/arraymorph.py -> build/lib.linux-x86_64-2.7/neuroml\r\ncreating build/lib.linux-x86_64-2.7/neuroml/test\r\ncopying neuroml/test/test_arraymorph.py -> build/lib.linux-x86_64-2.7/neuroml/test\r\ncopying neuroml/test/__init__.py -> build/lib.linux-x86_64-2.7/neuroml/test\r\ncopying neuroml/test/test_integration.py -> build/lib.linux-x86_64-2.7/neuroml/test\r\ncopying neuroml/test/test_loaders.py -> build/lib.linux-x86_64-2.7/neuroml/test\r\ncopying neuroml/test/test_segment.py -> build/lib.linux-x86_64-2.7/neuroml/test\r\ncopying neuroml/test/misc_tests.py -> build/lib.linux-x86_64-2.7/neuroml/test\r\ncopying neuroml/test/test_writers.py -> build/lib.linux-x86_64-2.7/neuroml/test\r\ncopying neuroml/test/test_morphology.py -> build/lib.linux-x86_64-2.7/neuroml/test\r\ncreating build/lib.linux-x86_64-2.7/neuroml/nml\r\ncopying neuroml/nml/generateds_config.py -> build/lib.linux-x86_64-2.7/neuroml/nml\r\ncopying neuroml/nml/config.py -> build/lib.linux-x86_64-2.7/neuroml/nml\r\ncopying neuroml/nml/__init__.py -> build/lib.linux-x86_64-2.7/neuroml/nml\r\ncopying neuroml/nml/nml.py -> build/lib.linux-x86_64-2.7/neuroml/nml\r\ncopying neuroml/nml/helper_methods.py -> build/lib.linux-x86_64-2.7/neuroml/nml\r\ncopying neuroml/test/Purk2M9s.nml -> build/lib.linux-x86_64-2.7/neuroml/test\r\nrunning install_lib\r\ncreating /usr/local/lib/python2.7/dist-packages/neuroml\r\ncopying build/lib.linux-x86_64-2.7/neuroml/__init__.py -> /usr/local/lib/python2.7/dist-packages/neuroml\r\ncopying build/lib.linux-x86_64-2.7/neuroml/writers.py -> /usr/local/lib/python2.7/dist-packages/neuroml\r\ncreating /usr/local/lib/python2.7/dist-packages/neuroml/test\r\ncopying build/lib.linux-x86_64-2.7/neuroml/test/test_arraymorph.py -> /usr/local/lib/python2.7/dist-packages/neuroml/test\r\ncopying build/lib.linux-x86_64-2.7/neuroml/test/__init__.py -> /usr/local/lib/python2.7/dist-packages/neuroml/test\r\ncopying build/lib.linux-x86_64-2.7/neuroml/test/Purk2M9s.nml -> /usr/local/lib/python2.7/dist-packages/neuroml/test\r\ncopying build/lib.linux-x86_64-2.7/neuroml/test/test_integration.py -> /usr/local/lib/python2.7/dist-packages/neuroml/test\r\ncopying build/lib.linux-x86_64-2.7/neuroml/test/test_loaders.py -> /usr/local/lib/python2.7/dist-packages/neuroml/test\r\ncopying build/lib.linux-x86_64-2.7/neuroml/test/test_segment.py -> /usr/local/lib/python2.7/dist-packages/neuroml/test\r\ncopying build/lib.linux-x86_64-2.7/neuroml/test/misc_tests.py -> /usr/local/lib/python2.7/dist-packages/neuroml/test\r\ncopying build/lib.linux-x86_64-2.7/neuroml/test/test_writers.py -> /usr/local/lib/python2.7/dist-packages/neuroml/test\r\ncopying build/lib.linux-x86_64-2.7/neuroml/test/test_morphology.py -> /usr/local/lib/python2.7/dist-packages/neuroml/test\r\ncreating /usr/local/lib/python2.7/dist-packages/neuroml/nml\r\ncopying build/lib.linux-x86_64-2.7/neuroml/nml/generateds_config.py -> /usr/local/lib/python2.7/dist-packages/neuroml/nml\r\ncopying build/lib.linux-x86_64-2.7/neuroml/nml/config.py -> /usr/local/lib/python2.7/dist-packages/neuroml/nml\r\ncopying build/lib.linux-x86_64-2.7/neuroml/nml/__init__.py -> /usr/local/lib/python2.7/dist-packages/neuroml/nml\r\ncopying build/lib.linux-x86_64-2.7/neuroml/nml/nml.py -> /usr/local/lib/python2.7/dist-packages/neuroml/nml\r\ncopying build/lib.linux-x86_64-2.7/neuroml/nml/helper_methods.py -> /usr/local/lib/python2.7/dist-packages/neuroml/nml\r\ncopying build/lib.linux-x86_64-2.7/neuroml/loaders.py -> /usr/local/lib/python2.7/dist-packages/neuroml\r\ncopying build/lib.linux-x86_64-2.7/neuroml/arraymorph.py -> /usr/local/lib/python2.7/dist-packages/neuroml\r\nbyte-compiling /usr/local/lib/python2.7/dist-packages/neuroml/__init__.py to __init__.pyc\r\nbyte-compiling /usr/local/lib/python2.7/dist-packages/neuroml/writers.py to writers.pyc\r\nbyte-compiling /usr/local/lib/python2.7/dist-packages/neuroml/test/test_arraymorph.py to test_arraymorph.pyc\r\nbyte-compiling /usr/local/lib/python2.7/dist-packages/neuroml/test/__init__.py to __init__.pyc\r\nbyte-compiling /usr/local/lib/python2.7/dist-packages/neuroml/test/test_integration.py to test_integration.pyc\r\nbyte-compiling /usr/local/lib/python2.7/dist-packages/neuroml/test/test_loaders.py to test_loaders.pyc\r\nbyte-compiling /usr/local/lib/python2.7/dist-packages/neuroml/test/test_segment.py to test_segment.pyc\r\nbyte-compiling /usr/local/lib/python2.7/dist-packages/neuroml/test/misc_tests.py to misc_tests.pyc\r\nbyte-compiling /usr/local/lib/python2.7/dist-packages/neuroml/test/test_writers.py to test_writers.pyc\r\nbyte-compiling /usr/local/lib/python2.7/dist-packages/neuroml/test/test_morphology.py to test_morphology.pyc\r\nbyte-compiling /usr/local/lib/python2.7/dist-packages/neuroml/nml/generateds_config.py to generateds_config.pyc\r\nbyte-compiling /usr/local/lib/python2.7/dist-packages/neuroml/nml/config.py to config.pyc\r\nbyte-compiling /usr/local/lib/python2.7/dist-packages/neuroml/nml/__init__.py to __init__.pyc\r\nbyte-compiling /usr/local/lib/python2.7/dist-packages/neuroml/nml/nml.py to nml.pyc\r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": "byte-compiling /usr/local/lib/python2.7/dist-packages/neuroml/nml/helper_methods.py to helper_methods.pyc\r\nbyte-compiling /usr/local/lib/python2.7/dist-packages/neuroml/loaders.py to loaders.pyc\r\nbyte-compiling /usr/local/lib/python2.7/dist-packages/neuroml/arraymorph.py to arraymorph.pyc\r\nrunning install_data\r\ncopying neuroml/test/Purk2M9s.nml -> /usr/local/\r\nrunning install_egg_info\r\nWriting /usr/local/lib/python2.7/dist-packages/libNeuroML-0.1.7.egg-info\r\n"
}
],
"prompt_number": 17
},
{
"cell_type": "markdown",
"metadata": {},
"source": "Now [refreshing memory](https://groups.google.com/forum/?fromgroups#!topic/openworm-discuss/qKqJ-rv7eYg) on recent developments.\n\nRight now we need to:\n\nGrab the CElegansNeuroML repo\n-----------------------------\n\nHappily this one doesn't have a development branch, so it should just be:"
},
{
"cell_type": "code",
"collapsed": false,
"input": "%cd ..",
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 18
},
{
"cell_type": "code",
"collapsed": false,
"input": "!git clone https://github.com/slarson/CElegansNeuroML.git",
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 19
},
{
"cell_type": "code",
"collapsed": false,
"input": "%cd CElegansNeuroML",
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": "/home/ubuntu/ipython/CElegansNeuroML\n"
}
],
"prompt_number": 2
},
{
"cell_type": "code",
"collapsed": false,
"input": "!ls",
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": "CElegans CElegansNeuronTables.xls connectome\tREADME\tsqlConnections\r\n"
}
],
"prompt_number": 3
},
{
"cell_type": "markdown",
"metadata": {},
"source": "Now to [regenerate the connectome](https://github.com/openworm/OpenWorm/wiki/Regenerate-the-connectome-in-NeuroML-format#regenerate-the-connectome)"
},
{
"cell_type": "code",
"collapsed": false,
"input": "%cd CElegans/pythonScripts",
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": "/home/ubuntu/ipython/CElegansNeuroML/CElegans/pythonScripts\n"
}
],
"prompt_number": 4
},
{
"cell_type": "code",
"collapsed": false,
"input": "!python RegenerateConnectome.py",
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": "Traceback (most recent call last):\r\n File \"RegenerateConnectome.py\", line 11, in <module>\r\n import SpreadsheetDataReader\r\n File \"/home/ubuntu/ipython/CElegansNeuroML/CElegans/pythonScripts/SpreadsheetDataReader.py\", line 4, in <module>\r\n from xlrd import open_workbook\r\nImportError: No module named xlrd\r\n"
}
],
"prompt_number": 5
},
{
"cell_type": "markdown",
"metadata": {},
"source": "erg..."
},
{
"cell_type": "code",
"collapsed": false,
"input": "!ls",
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": "CheckProject.py NeuroMLUtilities.py RegenerateConnectome.py test.png\r\nGenerateNeuroML.py NeuroMLUtilities.pyc SpreadsheetDataReader.py\r\nmodify\t\t README\t\t SpreadsheetDataReader.pyc\r\n"
}
],
"prompt_number": 6
},
{
"cell_type": "code",
"collapsed": false,
"input": "!cat README",
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": "Some scripts to interact with, test and update the CElegans project\r\n\r\nPrerequisites: \r\n get pip (http://www.pip-installer.org/en/latest/installing.html)\r\n use pip to get libNeuroML (sudo pip install libNeuroML)\r\n use pip to get xlrd (sudo pip install xlrd)\r\n"
}
],
"prompt_number": 12
},
{
"cell_type": "code",
"collapsed": false,
"input": "!sudo pip install xlrd",
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": "Downloading/unpacking xlrd\r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": " Downloading xlrd-0.9.2.tar.gz (167Kb): \r Downloading xlrd-0.9.2.tar.gz (167Kb): 2% 4.1Kb"
},
{
"output_type": "stream",
"stream": "stdout",
"text": "\r Downloading xlrd-0.9.2.tar.gz (167Kb): 4% 8.2Kb\r Downloading xlrd-0.9.2.tar.gz (167Kb): 7% 12Kb \r Downloading xlrd-0.9.2.tar.gz (167Kb): 9% 16Kb\r Downloading xlrd-0.9.2.tar.gz (167Kb): 12% 20Kb\r Downloading xlrd-0.9.2.tar.gz (167Kb): 14% 24Kb\r Downloading xlrd-0.9.2.tar.gz (167Kb): 17% 28Kb\r Downloading xlrd-0.9.2.tar.gz (167Kb): 19% 32Kb\r Downloading xlrd-0.9.2.tar.gz (167Kb): 21% 36Kb\r Downloading xlrd-0.9.2.tar.gz (167Kb): 24% 40Kb\r Downloading xlrd-0.9.2.tar.gz (167Kb): 26% 45Kb\r Downloading xlrd-0.9.2.tar.gz (167Kb): 29% 49Kb\r Downloading xlrd-0.9.2.tar.gz (167Kb): 31% 53Kb\r Downloading xlrd-0.9.2.tar.gz (167Kb): 34% 57Kb\r Downloading xlrd-0.9.2.tar.gz (167Kb): 36% 61Kb\r Downloading xlrd-0.9.2.tar.gz (167Kb): 39% 65Kb\r Downloading xlrd-0.9.2.tar.gz (167Kb): 41% 69Kb\r Downloading xlrd-0.9.2.tar.gz (167Kb): 43% 73Kb\r Downloading xlrd-0.9.2.tar.gz (167Kb): 46% 77Kb\r Downloading xlrd-0.9.2.tar.gz (167Kb): 48% 81Kb\r Downloading xlrd-0.9.2.tar.gz (167Kb): 51% 86Kb\r Downloading xlrd-0.9.2.tar.gz (167Kb): 53% 90Kb\r Downloading xlrd-0.9.2.tar.gz (167Kb): 56% 94Kb\r Downloading xlrd-0.9.2.tar.gz (167Kb): 58% 98Kb\r Downloading xlrd-0.9.2.tar.gz (167Kb): 60% 102Kb\r Downloading xlrd-0.9.2.tar.gz (167Kb): 63% 106Kb\r Downloading xlrd-0.9.2.tar.gz (167Kb): 65% 110Kb\r Downloading xlrd-0.9.2.tar.gz (167Kb): 68% 114Kb\r Downloading xlrd-0.9.2.tar.gz (167Kb): 70% 118Kb\r Downloading xlrd-0.9.2.tar.gz (167Kb): 73% 122Kb\r Downloading xlrd-0.9.2.tar.gz (167Kb): 75% 126Kb\r Downloading xlrd-0.9.2.tar.gz (167Kb): 78% 131Kb\r Downloading xlrd-0.9.2.tar.gz (167Kb): 80% 135Kb\r Downloading xlrd-0.9.2.tar.gz (167Kb): 82% 139Kb\r Downloading xlrd-0.9.2.tar.gz (167Kb): 85% 143Kb\r Downloading xlrd-0.9.2.tar.gz (167Kb): 87% 147Kb\r Downloading xlrd-0.9.2.tar.gz (167Kb): 90% 151Kb\r Downloading xlrd-0.9.2.tar.gz (167Kb): 92% 155Kb\r Downloading xlrd-0.9.2.tar.gz (167Kb): 95% 159Kb\r Downloading xlrd-0.9.2.tar.gz (167Kb): 97% 163Kb\r Downloading xlrd-0.9.2.tar.gz (167Kb): 100% 167Kb\r Downloading xlrd-0.9.2.tar.gz (167Kb): \r Downloading xlrd-0.9.2.tar.gz (167Kb): 167Kb downloaded\r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": " Running setup.py egg_info for package xlrd\r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": " \r\nInstalling collected packages: xlrd\r\n Running setup.py install for xlrd\r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": " changing mode of build/scripts-2.7/runxlrd.py from 644 to 755\r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": " \r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": " changing mode of /usr/local/bin/runxlrd.py to 755\r\nSuccessfully installed xlrd\r\nCleaning up...\r\n"
}
],
"prompt_number": 8
},
{
"cell_type": "code",
"collapsed": false,
"input": "!python RegenerateConnectome.py",
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": "Traceback (most recent call last):\r\n File \"RegenerateConnectome.py\", line 20, in <module>\r\n import neuroml.writers as writers\r\n File \"/usr/local/lib/python2.7/dist-packages/neuroml/writers.py\", line 2, in <module>\r\n import numpy as np\r\nImportError: No module named numpy\r\n"
}
],
"prompt_number": 13
},
{
"cell_type": "markdown",
"metadata": {},
"source": "Oh gosh. I didn't install libNeuroML with pip because I wanted the development branch and obviously it didn't bring in its dependencies. Now time for some dependency hell... :(\n\nSuppressed the output, but kept the order of commands:\n\n !sudo pip install numpy"
},
{
"cell_type": "code",
"collapsed": false,
"input": "!python RegenerateConnectome.py",
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": "Traceback (most recent call last):\r\n File \"RegenerateConnectome.py\", line 20, in <module>\r\n import neuroml.writers as writers\r\n File \"/usr/local/lib/python2.7/dist-packages/neuroml/writers.py\", line 3, in <module>\r\n import tables\r\nImportError: No module named tables\r\n"
}
],
"prompt_number": 15
},
{
"cell_type": "markdown",
"metadata": {},
"source": " !sudo pip install tables"
},
{
"cell_type": "markdown",
"metadata": {},
"source": " !sudo pip install numexpr"
},
{
"cell_type": "markdown",
"metadata": {},
"source": " !sudo pip install tables"
},
{
"cell_type": "markdown",
"metadata": {},
"source": " !sudo pip install Cython"
},
{
"cell_type": "markdown",
"metadata": {},
"source": " !sudo pip install tables"
},
{
"cell_type": "markdown",
"metadata": {},
"source": " !sudo apt-get -y install libhdf5-serial-dev"
},
{
"cell_type": "markdown",
"metadata": {},
"source": " !sudo pip install tables"
},
{
"cell_type": "code",
"collapsed": false,
"input": "!python RegenerateConnectome.py",
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": "Traceback (most recent call last):\r\n File \"RegenerateConnectome.py\", line 20, in <module>\r\n import neuroml.writers as writers\r\n File \"/usr/local/lib/python2.7/dist-packages/neuroml/writers.py\", line 4, in <module>\r\n from jsonpickle import encode as json_encode\r\nImportError: No module named jsonpickle\r\n"
}
],
"prompt_number": 9
},
{
"cell_type": "markdown",
"metadata": {},
"source": " !sudo pip install jsonpickle"
},
{
"cell_type": "code",
"collapsed": false,
"input": "!python RegenerateConnectome.py",
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": "Opened Excel file: ../../CElegansNeuronTables.xls\r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": "Not a valid NeuroML 2 doc: (<type 'exceptions.AttributeError'>, AttributeError('nsmap',), <traceback object at 0x2933e60>)\r\nTraceback (most recent call last):\r\n File \"RegenerateConnectome.py\", line 76, in <module>\r\n all_cells[cell] = doc.cells[0]\r\nAttributeError: 'NoneType' object has no attribute 'cells'\r\n"
}
],
"prompt_number": 11
},
{
"cell_type": "markdown",
"metadata": {},
"source": "OK.. this problem was reported by me and Peter on [the thread](https://groups.google.com/forum/?fromgroups#!topic/openworm-discuss/qKqJ-rv7eYg).\n\nTime to put in [the fix](https://github.com/openworm/OpenWorm/issues/136#issuecomment-23040250)"
},
{
"cell_type": "markdown",
"metadata": {},
"source": " !sudo pip install lxml"
},
{
"cell_type": "markdown",
"metadata": {},
"source": " !sudo apt-get install -y libxml2-dev"
},
{
"cell_type": "markdown",
"metadata": {},
"source": " !sudo apt-get update"
},
{
"cell_type": "markdown",
"metadata": {},
"source": " !sudo apt-get install -y libxml2-dev"
},
{
"cell_type": "markdown",
"metadata": {},
"source": " !sudo apt-get install -y libxslt-dev"
},
{
"cell_type": "markdown",
"metadata": {},
"source": " !sudo pip install lxml"
},
{
"cell_type": "markdown",
"metadata": {},
"source": "Big picture here -- now I've tried to load the script but the amount of output coming back actually crashes iPython Notebook.\n\nInstead, I've had to load it up and reduce the amount of print statements. Turns out the script has a 'debug' boolean that I can set to false."
},
{
"cell_type": "code",
"collapsed": false,
"input": "%load RegenerateConnectome.py",
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 33
},
{
"cell_type": "code",
"collapsed": false,
"input": "%%file RegenerateConnectome.py\n############################################################\n\n# A simple script to regenerate the CElegans connectome in NeuroML2\n# Currently uses SpreadsheetDataReader to load connection info \n# from the CElegansNeuronTables.xls spreadsheet\n\n############################################################\n\nimport SpreadsheetDataReader\n\nfrom neuroml import NeuroMLDocument\nfrom neuroml import Network\nfrom neuroml import Population\nfrom neuroml import Instance\nfrom neuroml import Location\nfrom neuroml import Projection\nfrom neuroml import Connection\nimport neuroml.writers as writers\nimport neuroml.loaders as loaders\n\nfrom random import random\nfrom random import randint\n\nfrom NeuroMLUtilities import validateNeuroML2\nfrom NeuroMLUtilities import getSegmentIds\nfrom NeuroMLUtilities import get3DPosition\n\nimport math\nimport time\n\n# Get the standard name for a network connection as used in the neuroConstruct project\ndef get_projection_id(pre, post, syntype):\n\n proj_id = \"NCXLS_%s_%s\"%(pre, post)\n \n if \"GapJunction\" in syntype:\n proj_id += '_GJ'\n\n return proj_id\n\n\nif __name__ == \"__main__\":\n\n # Use the spreadsheet reader to give a list of all cells and a list of all connections\n # This could be replaced with a call to \"DatabaseReader\" or \"OpenWormNeuroLexReader\" in future...\n cell_names, conns = SpreadsheetDataReader.readDataFromSpreadsheet()\n\n net_id = \"CElegansConnectome\"\n\n nml_network_doc = NeuroMLDocument(id=net_id)\n\n # Create a NeuroML Network data structure to hold on to all the connection info.\n net = Network(id=net_id)\n nml_network_doc.networks.append(net)\n\n # To hold all Cell NeuroML objects vs. names\n all_cells = {}\n \n for cell in cell_names:\n \t# build a Population data structure out of the cell name\n pop0 = Population(id=cell, component=cell, size=1)\n inst = Instance(id=\"0\")\n # Each of these cells is at (0,0,0), i.e. segment 3D info in each cell is absolute\n inst.location = Location(x=\"0.0\", y=\"0.0\", z=\"0.0\")\n pop0.instances.append(inst)\n \n # put that Population into the Network data structure from above\n net.populations.append(pop0)\n \n # also use the cell name to grab the morphology file, as a NeuroML data structure\n # into the 'all_cells' dict\n cell_file = '../generatedNeuroML2/%s.nml'%cell\n doc = loaders.NeuroMLLoader.load(cell_file)\n all_cells[cell] = doc.cells[0]\n print(\"Loaded morphology file from: %s, with id: %s\"%(cell_file, all_cells[cell].id))\n\n dists = []\n start_time = time.time()\n for conn in conns:\n\t\t\n # take information about each connection and package it into a \n # NeuroML Projection data structure\n proj_id = get_projection_id(conn.pre_cell, conn.post_cell, conn.syntype)\n proj0 = Projection(id=proj_id, \\\n \t\t \t presynaptic_population=conn.pre_cell, \n \t\t \t postsynaptic_population=conn.post_cell, \n \t\t \t synapse=conn.synclass)\n\n # Get the corresponding Cell for each \n pre_cell = all_cells[conn.pre_cell]\n post_cell = all_cells[conn.post_cell]\n\n # Get lists of the valid segment ids\n pre_segs = getSegmentIds(pre_cell)\n post_segs = getSegmentIds(post_cell)\n\n debug = False\n #if \"VC5\" in conn.pre_cell: debug = True\n #debug = True\n if debug: print \"Projection between %s and %s has %i conns\"%(conn.pre_cell,conn.post_cell,conn.number)\n\n for conn_id in range(0,conn.number):\n\n use_substitute_connections = False\n\n if use_substitute_connections:\n\n print(\"Substituting a connection...\")\n ###########################################\n\n # This can be where alternate connections (e.g. extracted fromn Steve Cook's data) are added\n\n ###########################################\n\n else:\n\n #print \"--- Conn %i\"%conn_id\n best_dist = 1e6\n num_to_try = min(5000,int(0.5*len(pre_segs)*len(post_segs)))\n if debug: print(\"Trying %i possible random connections\"%num_to_try)\n \n # Try a number of times to get the shortest connection between pre & post cells\n for i in range(num_to_try):\n pre_segment_index = randint(0, len(pre_cell.morphology.segments)-1)\n pre_segment_id = pre_segs[pre_segment_index]\n pre_fraction_along = random()\n post_segment_index = randint(0, len(post_cell.morphology.segments)-1)\n post_segment_id = post_segs[post_segment_index]\n post_fraction_along = random()\n \n pre_x, pre_y,pre_z = get3DPosition(pre_cell, pre_segment_index, pre_fraction_along)\n post_x, post_y,post_z = get3DPosition(post_cell, post_segment_index, post_fraction_along)\n\n dist = math.sqrt(math.pow(pre_x-post_x,2)+math.pow(pre_y-post_y,2)+math.pow(pre_z-post_z,2))\n #print dist\n \n if dist < best_dist:\n best_dist = dist\n if debug: print \"Shortest length of connection: %f um\"%best_dist\n best_pre_seg = pre_segment_id\n best_pre_fract = pre_fraction_along\n best_post_seg = post_segment_id\n best_post_fract = post_fraction_along\n\n dists.append(best_dist)\n \n # Add a Connection with the closest locations\n conn0 = Connection(id=conn_id, \\\n\n pre_cell_id=\"../%s/0/%s\"%(conn.pre_cell, conn.pre_cell),\n pre_segment_id = best_pre_seg,\n pre_fraction_along = best_pre_fract,\n post_cell_id=\"../%s/0/%s\"%(conn.post_cell, conn.post_cell),\n post_segment_id = best_post_seg,\n post_fraction_along = best_post_fract)\n \n proj0.connections.append(conn0)\n\n net.projections.append(proj0)\n\n print (\"Connections generated in %f seconds, mean length: %f um\"%((time.time() - start_time), sum(dists)/len(dists)))\n nml_file = net_id+'.nml'\n writers.NeuroMLWriter.write(nml_network_doc, nml_file)\n\n print(\"Written network file to: \"+nml_file)\n\n ###### Validate the NeuroML ###### \n\n validateNeuroML2(nml_file)\n\n\n\n",
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": "Overwriting RegenerateConnectome.py\n"
}
],
"prompt_number": 34
},
{
"cell_type": "code",
"collapsed": false,
"input": "!python RegenerateConnectome.py",
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": "Opened Excel file: ../../CElegansNeuronTables.xls\r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": "Loaded morphology file from: ../generatedNeuroML2/ADAL.nml, with id: ADAL\r\nLoaded morphology file from: ../generatedNeuroML2/ADFL.nml, with id: ADFL\r\nLoaded morphology file from: ../generatedNeuroML2/AIBL.nml, with id: AIBL\r\nLoaded morphology file from: ../generatedNeuroML2/AIBR.nml, with id: AIBR\r\nLoaded morphology file from: ../generatedNeuroML2/ASHL.nml, with id: ASHL\r\nLoaded morphology file from: ../generatedNeuroML2/AVAR.nml, with id: AVAR\r\nLoaded morphology file from: ../generatedNeuroML2/AVBL.nml, with id: AVBL\r\nLoaded morphology file from: ../generatedNeuroML2/AVBR.nml, with id: AVBR\r\nLoaded morphology file from: ../generatedNeuroML2/AVDL.nml, with id: AVDL\r\nLoaded morphology file from: ../generatedNeuroML2/AVDR.nml, with id: AVDR\r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": "Loaded morphology file from: ../generatedNeuroML2/AVEL.nml, with id: AVEL\r\nLoaded morphology file from: ../generatedNeuroML2/AVJR.nml, with id: AVJR\r\nLoaded morphology file from: ../generatedNeuroML2/FLPR.nml, with id: FLPR\r\nLoaded morphology file from: ../generatedNeuroML2/PVQL.nml, with id: PVQL\r\nLoaded morphology file from: ../generatedNeuroML2/RICL.nml, with id: RICL\r\nLoaded morphology file from: ../generatedNeuroML2/RICR.nml, with id: RICR\r\nLoaded morphology file from: ../generatedNeuroML2/RIML.nml, with id: RIML\r\nLoaded morphology file from: ../generatedNeuroML2/RIPL.nml, with id: RIPL\r\nLoaded morphology file from: ../generatedNeuroML2/SMDVR.nml, with id: SMDVR\r\nLoaded morphology file from: ../generatedNeuroML2/ADAR.nml, with id: ADAR\r\nLoaded morphology file from: ../generatedNeuroML2/ADFR.nml, with id: ADFR\r\nLoaded morphology file from: ../generatedNeuroML2/ASHR.nml, with id: ASHR\r\nLoaded morphology file from: ../generatedNeuroML2/AVAL.nml, with id: AVAL\r\nLoaded morphology file from: ../generatedNeuroML2/AVJL.nml, with id: AVJL\r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": "Loaded morphology file from: ../generatedNeuroML2/PVQR.nml, with id: PVQR\r\nLoaded morphology file from: ../generatedNeuroML2/RIMR.nml, with id: RIMR\r\nLoaded morphology file from: ../generatedNeuroML2/RIPR.nml, with id: RIPR\r\nLoaded morphology file from: ../generatedNeuroML2/RIVR.nml, with id: RIVR\r\nLoaded morphology file from: ../generatedNeuroML2/SMDVL.nml, with id: SMDVL\r\nLoaded morphology file from: ../generatedNeuroML2/ADEL.nml, with id: ADEL\r\nLoaded morphology file from: ../generatedNeuroML2/ADER.nml, with id: ADER\r\nLoaded morphology file from: ../generatedNeuroML2/AINL.nml, with id: AINL\r\nLoaded morphology file from: ../generatedNeuroML2/AVKR.nml, with id: AVKR\r\nLoaded morphology file from: ../generatedNeuroML2/AVL.nml, with id: AVL\r\nLoaded morphology file from: ../generatedNeuroML2/BDUL.nml, with id: BDUL\r\nLoaded morphology file from: ../generatedNeuroML2/CEPDL.nml, with id: CEPDL\r\nLoaded morphology file from: ../generatedNeuroML2/FLPL.nml, with id: FLPL\r\nLoaded morphology file from: ../generatedNeuroML2/IL1L.nml, with id: IL1L\r\nLoaded morphology file from: ../generatedNeuroML2/IL2L.nml, with id: IL2L\r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": "Loaded morphology file from: ../generatedNeuroML2/OLLL.nml, with id: OLLL\r\nLoaded morphology file from: ../generatedNeuroML2/RIAL.nml, with id: RIAL\r\nLoaded morphology file from: ../generatedNeuroML2/RIFL.nml, with id: RIFL\r\nLoaded morphology file from: ../generatedNeuroML2/RIGL.nml, with id: RIGL\r\nLoaded morphology file from: ../generatedNeuroML2/RIGR.nml, with id: RIGR\r\nLoaded morphology file from: ../generatedNeuroML2/RIH.nml, with id: RIH\r\nLoaded morphology file from: ../generatedNeuroML2/RIVL.nml, with id: RIVL\r\nLoaded morphology file from: ../generatedNeuroML2/RMDL.nml, with id: RMDL\r\nLoaded morphology file from: ../generatedNeuroML2/RMGL.nml, with id: RMGL\r\nLoaded morphology file from: ../generatedNeuroML2/RMHL.nml, with id: RMHL\r\nLoaded morphology file from: ../generatedNeuroML2/SIADR.nml, with id: SIADR\r\nLoaded morphology file from: ../generatedNeuroML2/SIBDR.nml, with id: SIBDR\r\nLoaded morphology file from: ../generatedNeuroML2/SMBDR.nml, with id: SMBDR\r\nLoaded morphology file from: ../generatedNeuroML2/URBL.nml, with id: URBL\r\nLoaded morphology file from: ../generatedNeuroML2/ALA.nml, with id: ALA\r\nLoaded morphology file from: ../generatedNeuroML2/AVER.nml, with id: AVER\r\nLoaded morphology file from: ../generatedNeuroML2/AVKL.nml, with id: AVKL\r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": "Loaded morphology file from: ../generatedNeuroML2/CEPDR.nml, with id: CEPDR\r\nLoaded morphology file from: ../generatedNeuroML2/OLLR.nml, with id: OLLR\r\nLoaded morphology file from: ../generatedNeuroML2/PVR.nml, with id: PVR\r\nLoaded morphology file from: ../generatedNeuroML2/RMDR.nml, with id: RMDR\r\nLoaded morphology file from: ../generatedNeuroML2/SAAVR.nml, with id: SAAVR\r\nLoaded morphology file from: ../generatedNeuroML2/AIZL.nml, with id: AIZL\r\nLoaded morphology file from: ../generatedNeuroML2/AUAL.nml, with id: AUAL\r\nLoaded morphology file from: ../generatedNeuroML2/OLQVL.nml, with id: OLQVL\r\nLoaded morphology file from: ../generatedNeuroML2/RIR.nml, with id: RIR\r\nLoaded morphology file from: ../generatedNeuroML2/SMBVL.nml, with id: SMBVL\r\nLoaded morphology file from: ../generatedNeuroML2/AIAR.nml, with id: AIAR\r\nLoaded morphology file from: ../generatedNeuroML2/AIYR.nml, with id: AIYR\r\nLoaded morphology file from: ../generatedNeuroML2/AIZR.nml, with id: AIZR\r\nLoaded morphology file from: ../generatedNeuroML2/AUAR.nml, with id: AUAR\r\nLoaded morphology file from: ../generatedNeuroML2/AWBR.nml, with id: AWBR\r\nLoaded morphology file from: ../generatedNeuroML2/PVPR.nml, with id: PVPR\r\nLoaded morphology file from: ../generatedNeuroML2/RIAR.nml, with id: RIAR\r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": "Loaded morphology file from: ../generatedNeuroML2/SMBVR.nml, with id: SMBVR\r\nLoaded morphology file from: ../generatedNeuroML2/URXR.nml, with id: URXR\r\nLoaded morphology file from: ../generatedNeuroML2/ADLL.nml, with id: ADLL\r\nLoaded morphology file from: ../generatedNeuroML2/ADLR.nml, with id: ADLR\r\nLoaded morphology file from: ../generatedNeuroML2/AIAL.nml, with id: AIAL\r\nLoaded morphology file from: ../generatedNeuroML2/ASER.nml, with id: ASER\r\nLoaded morphology file from: ../generatedNeuroML2/AWBL.nml, with id: AWBL\r\nLoaded morphology file from: ../generatedNeuroML2/AWCR.nml, with id: AWCR\r\nLoaded morphology file from: ../generatedNeuroML2/PVCL.nml, with id: PVCL\r\nLoaded morphology file from: ../generatedNeuroML2/AFDL.nml, with id: AFDL\r\nLoaded morphology file from: ../generatedNeuroML2/AFDR.nml, with id: AFDR\r\nLoaded morphology file from: ../generatedNeuroML2/AINR.nml, with id: AINR\r\nLoaded morphology file from: ../generatedNeuroML2/AIYL.nml, with id: AIYL\r\nLoaded morphology file from: ../generatedNeuroML2/AIML.nml, with id: AIML\r\nLoaded morphology file from: ../generatedNeuroML2/ASGL.nml, with id: ASGL\r\nLoaded morphology file from: ../generatedNeuroML2/ASIL.nml, with id: ASIL\r\nLoaded morphology file from: ../generatedNeuroML2/ASKL.nml, with id: ASKL\r\nLoaded morphology file from: ../generatedNeuroML2/AWAL.nml, with id: AWAL\r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": "Loaded morphology file from: ../generatedNeuroML2/HSNL.nml, with id: HSNL\r\nLoaded morphology file from: ../generatedNeuroML2/ASGR.nml, with id: ASGR\r\nLoaded morphology file from: ../generatedNeuroML2/ASIR.nml, with id: ASIR\r\nLoaded morphology file from: ../generatedNeuroML2/AWAR.nml, with id: AWAR\r\nLoaded morphology file from: ../generatedNeuroML2/AWCL.nml, with id: AWCL\r\nLoaded morphology file from: ../generatedNeuroML2/RIFR.nml, with id: RIFR\r\nLoaded morphology file from: ../generatedNeuroML2/DVC.nml, with id: DVC\r\nLoaded morphology file from: ../generatedNeuroML2/PVT.nml, with id: PVT\r\nLoaded morphology file from: ../generatedNeuroML2/RIBR.nml, with id: RIBR\r\nLoaded morphology file from: ../generatedNeuroML2/SAADL.nml, with id: SAADL\r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": "Loaded morphology file from: ../generatedNeuroML2/SAADR.nml, with id: SAADR\r\nLoaded morphology file from: ../generatedNeuroML2/SMDDR.nml, with id: SMDDR\r\nLoaded morphology file from: ../generatedNeuroML2/DB1.nml, with id: DB1\r\nLoaded morphology file from: ../generatedNeuroML2/RIBL.nml, with id: RIBL\r\nLoaded morphology file from: ../generatedNeuroML2/RIS.nml, with id: RIS\r\nLoaded morphology file from: ../generatedNeuroML2/SMDDL.nml, with id: SMDDL\r\nLoaded morphology file from: ../generatedNeuroML2/VB1.nml, with id: VB1\r\nLoaded morphology file from: ../generatedNeuroML2/ALML.nml, with id: ALML\r\nLoaded morphology file from: ../generatedNeuroML2/AVFL.nml, with id: AVFL\r\nLoaded morphology file from: ../generatedNeuroML2/AVFR.nml, with id: AVFR\r\nLoaded morphology file from: ../generatedNeuroML2/AVHL.nml, with id: AVHL\r\nLoaded morphology file from: ../generatedNeuroML2/AVHR.nml, with id: AVHR\r\nLoaded morphology file from: ../generatedNeuroML2/AIMR.nml, with id: AIMR\r\nLoaded morphology file from: ../generatedNeuroML2/ASJR.nml, with id: ASJR\r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": "Loaded morphology file from: ../generatedNeuroML2/ASKR.nml, with id: ASKR\r\nLoaded morphology file from: ../generatedNeuroML2/HSNR.nml, with id: HSNR\r\nLoaded morphology file from: ../generatedNeuroML2/OLQDR.nml, with id: OLQDR\r\nLoaded morphology file from: ../generatedNeuroML2/PVNR.nml, with id: PVNR\r\nLoaded morphology file from: ../generatedNeuroML2/RMGR.nml, with id: RMGR\r\nLoaded morphology file from: ../generatedNeuroML2/ASEL.nml, with id: ASEL\r\nLoaded morphology file from: ../generatedNeuroML2/BAGL.nml, with id: BAGL\r\nLoaded morphology file from: ../generatedNeuroML2/BAGR.nml, with id: BAGR\r\nLoaded morphology file from: ../generatedNeuroML2/RID.nml, with id: RID\r\nLoaded morphology file from: ../generatedNeuroML2/DVA.nml, with id: DVA\r\nLoaded morphology file from: ../generatedNeuroML2/SMBDL.nml, with id: SMBDL\r\nLoaded morphology file from: ../generatedNeuroML2/VB2.nml, with id: VB2\r\nLoaded morphology file from: ../generatedNeuroML2/AVM.nml, with id: AVM\r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": "Loaded morphology file from: ../generatedNeuroML2/CEPVL.nml, with id: CEPVL\r\nLoaded morphology file from: ../generatedNeuroML2/PVCR.nml, with id: PVCR\r\nLoaded morphology file from: ../generatedNeuroML2/RMDDR.nml, with id: RMDDR\r\nLoaded morphology file from: ../generatedNeuroML2/SDQL.nml, with id: SDQL\r\nLoaded morphology file from: ../generatedNeuroML2/ALMR.nml, with id: ALMR\r\nLoaded morphology file from: ../generatedNeuroML2/BDUR.nml, with id: BDUR\r\nLoaded morphology file from: ../generatedNeuroML2/CEPVR.nml, with id: CEPVR\r\nLoaded morphology file from: ../generatedNeuroML2/RMDDL.nml, with id: RMDDL\r\nLoaded morphology file from: ../generatedNeuroML2/SIADL.nml, with id: SIADL\r\nLoaded morphology file from: ../generatedNeuroML2/ALNL.nml, with id: ALNL\r\nLoaded morphology file from: ../generatedNeuroML2/SAAVL.nml, with id: SAAVL\r\nLoaded morphology file from: ../generatedNeuroML2/ALNR.nml, with id: ALNR\r\nLoaded morphology file from: ../generatedNeuroML2/RMHR.nml, with id: RMHR\r\nLoaded morphology file from: ../generatedNeuroML2/AQR.nml, with id: AQR\r\nLoaded morphology file from: ../generatedNeuroML2/PVPL.nml, with id: PVPL\r\nLoaded morphology file from: ../generatedNeuroML2/URXL.nml, with id: URXL\r\nLoaded morphology file from: ../generatedNeuroML2/AS1.nml, with id: AS1\r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": "Loaded morphology file from: ../generatedNeuroML2/DA1.nml, with id: DA1\r\nLoaded morphology file from: ../generatedNeuroML2/VA3.nml, with id: VA3\r\nLoaded morphology file from: ../generatedNeuroML2/VD1.nml, with id: VD1\r\nLoaded morphology file from: ../generatedNeuroML2/VD2.nml, with id: VD2\r\nLoaded morphology file from: ../generatedNeuroML2/AS10.nml, with id: AS10\r\nLoaded morphology file from: ../generatedNeuroML2/AS11.nml, with id: AS11\r\nLoaded morphology file from: ../generatedNeuroML2/PDA.nml, with id: PDA\r\nLoaded morphology file from: ../generatedNeuroML2/PDB.nml, with id: PDB\r\nLoaded morphology file from: ../generatedNeuroML2/VD13.nml, with id: VD13\r\nLoaded morphology file from: ../generatedNeuroML2/AS2.nml, with id: AS2\r\nLoaded morphology file from: ../generatedNeuroML2/DA2.nml, with id: DA2\r\nLoaded morphology file from: ../generatedNeuroML2/DD1.nml, with id: DD1\r\nLoaded morphology file from: ../generatedNeuroML2/VA4.nml, with id: VA4\r\nLoaded morphology file from: ../generatedNeuroML2/AS3.nml, with id: AS3\r\nLoaded morphology file from: ../generatedNeuroML2/DA3.nml, with id: DA3\r\nLoaded morphology file from: ../generatedNeuroML2/VA5.nml, with id: VA5\r\nLoaded morphology file from: ../generatedNeuroML2/VD3.nml, with id: VD3\r\nLoaded morphology file from: ../generatedNeuroML2/AS4.nml, with id: AS4\r\nLoaded morphology file from: ../generatedNeuroML2/AS5.nml, with id: AS5\r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": "Loaded morphology file from: ../generatedNeuroML2/VD4.nml, with id: VD4\r\nLoaded morphology file from: ../generatedNeuroML2/DD2.nml, with id: DD2\r\nLoaded morphology file from: ../generatedNeuroML2/VA7.nml, with id: VA7\r\nLoaded morphology file from: ../generatedNeuroML2/VD5.nml, with id: VD5\r\nLoaded morphology file from: ../generatedNeuroML2/AS6.nml, with id: AS6\r\nLoaded morphology file from: ../generatedNeuroML2/DA5.nml, with id: DA5\r\nLoaded morphology file from: ../generatedNeuroML2/VA8.nml, with id: VA8\r\nLoaded morphology file from: ../generatedNeuroML2/VD6.nml, with id: VD6\r\nLoaded morphology file from: ../generatedNeuroML2/AS7.nml, with id: AS7\r\nLoaded morphology file from: ../generatedNeuroML2/AS8.nml, with id: AS8\r\nLoaded morphology file from: ../generatedNeuroML2/AS9.nml, with id: AS9\r\nLoaded morphology file from: ../generatedNeuroML2/DVB.nml, with id: DVB\r\nLoaded morphology file from: ../generatedNeuroML2/ASJL.nml, with id: ASJL\r\nLoaded morphology file from: ../generatedNeuroML2/DA4.nml, with id: DA4\r\nLoaded morphology file from: ../generatedNeuroML2/DA6.nml, with id: DA6\r\nLoaded morphology file from: ../generatedNeuroML2/DA7.nml, with id: DA7\r\nLoaded morphology file from: ../generatedNeuroML2/DA8.nml, with id: DA8\r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": "Loaded morphology file from: ../generatedNeuroML2/DA9.nml, with id: DA9\r\nLoaded morphology file from: ../generatedNeuroML2/DB5.nml, with id: DB5\r\nLoaded morphology file from: ../generatedNeuroML2/DB6.nml, with id: DB6\r\nLoaded morphology file from: ../generatedNeuroML2/LUAL.nml, with id: LUAL\r\nLoaded morphology file from: ../generatedNeuroML2/SABD.nml, with id: SABD\r\nLoaded morphology file from: ../generatedNeuroML2/SABVR.nml, with id: SABVR\r\nLoaded morphology file from: ../generatedNeuroML2/SDQR.nml, with id: SDQR\r\nLoaded morphology file from: ../generatedNeuroML2/URYDL.nml, with id: URYDL\r\nLoaded morphology file from: ../generatedNeuroML2/URYVR.nml, with id: URYVR\r\nLoaded morphology file from: ../generatedNeuroML2/VA1.nml, with id: VA1\r\nLoaded morphology file from: ../generatedNeuroML2/VA10.nml, with id: VA10\r\nLoaded morphology file from: ../generatedNeuroML2/VA11.nml, with id: VA11\r\nLoaded morphology file from: ../generatedNeuroML2/VA12.nml, with id: VA12\r\nLoaded morphology file from: ../generatedNeuroML2/VA2.nml, with id: VA2\r\nLoaded morphology file from: ../generatedNeuroML2/VA6.nml, with id: VA6\r\nLoaded morphology file from: ../generatedNeuroML2/VA9.nml, with id: VA9\r\nLoaded morphology file from: ../generatedNeuroML2/VB9.nml, with id: VB9\r\nLoaded morphology file from: ../generatedNeuroML2/DB3.nml, with id: DB3\r\nLoaded morphology file from: ../generatedNeuroML2/LUAR.nml, with id: LUAR\r\nLoaded morphology file from: ../generatedNeuroML2/PDEL.nml, with id: PDEL\r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": "Loaded morphology file from: ../generatedNeuroML2/PDER.nml, with id: PDER\r\nLoaded morphology file from: ../generatedNeuroML2/SABVL.nml, with id: SABVL\r\nLoaded morphology file from: ../generatedNeuroML2/URYDR.nml, with id: URYDR\r\nLoaded morphology file from: ../generatedNeuroML2/URYVL.nml, with id: URYVL\r\nLoaded morphology file from: ../generatedNeuroML2/DB4.nml, with id: DB4\r\nLoaded morphology file from: ../generatedNeuroML2/DB7.nml, with id: DB7\r\nLoaded morphology file from: ../generatedNeuroML2/SIBVL.nml, with id: SIBVL\r\nLoaded morphology file from: ../generatedNeuroML2/VB10.nml, with id: VB10\r\nLoaded morphology file from: ../generatedNeuroML2/VB11.nml, with id: VB11\r\nLoaded morphology file from: ../generatedNeuroML2/VB4.nml, with id: VB4\r\nLoaded morphology file from: ../generatedNeuroML2/VB5.nml, with id: VB5\r\nLoaded morphology file from: ../generatedNeuroML2/VB6.nml, with id: VB6\r\nLoaded morphology file from: ../generatedNeuroML2/VB7.nml, with id: VB7\r\nLoaded morphology file from: ../generatedNeuroML2/VB8.nml, with id: VB8\r\nLoaded morphology file from: ../generatedNeuroML2/VC3.nml, with id: VC3\r\nLoaded morphology file from: ../generatedNeuroML2/DB2.nml, with id: DB2\r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": "Loaded morphology file from: ../generatedNeuroML2/PVNL.nml, with id: PVNL\r\nLoaded morphology file from: ../generatedNeuroML2/VB3.nml, with id: VB3\r\nLoaded morphology file from: ../generatedNeuroML2/VD10.nml, with id: VD10\r\nLoaded morphology file from: ../generatedNeuroML2/PQR.nml, with id: PQR\r\nLoaded morphology file from: ../generatedNeuroML2/RMDVR.nml, with id: RMDVR\r\nLoaded morphology file from: ../generatedNeuroML2/RMEV.nml, with id: RMEV\r\nLoaded morphology file from: ../generatedNeuroML2/RMDVL.nml, with id: RMDVL\r\nLoaded morphology file from: ../generatedNeuroML2/AVG.nml, with id: AVG\r\nLoaded morphology file from: ../generatedNeuroML2/VC4.nml, with id: VC4\r\nLoaded morphology file from: ../generatedNeuroML2/VD11.nml, with id: VD11\r\nLoaded morphology file from: ../generatedNeuroML2/PHAL.nml, with id: PHAL\r\nLoaded morphology file from: ../generatedNeuroML2/PHBR.nml, with id: PHBR\r\nLoaded morphology file from: ../generatedNeuroML2/PLMR.nml, with id: PLMR\r\nLoaded morphology file from: ../generatedNeuroML2/PVM.nml, with id: PVM\r\nLoaded morphology file from: ../generatedNeuroML2/RMFR.nml, with id: RMFR\r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": "Loaded morphology file from: ../generatedNeuroML2/SIAVR.nml, with id: SIAVR\r\nLoaded morphology file from: ../generatedNeuroML2/RMFL.nml, with id: RMFL\r\nLoaded morphology file from: ../generatedNeuroML2/DD6.nml, with id: DD6\r\nLoaded morphology file from: ../generatedNeuroML2/PVWL.nml, with id: PVWL\r\nLoaded morphology file from: ../generatedNeuroML2/VD12.nml, with id: VD12\r\nLoaded morphology file from: ../generatedNeuroML2/URADL.nml, with id: URADL\r\nLoaded morphology file from: ../generatedNeuroML2/URADR.nml, with id: URADR\r\nLoaded morphology file from: ../generatedNeuroML2/IL1DL.nml, with id: IL1DL\r\nLoaded morphology file from: ../generatedNeuroML2/OLQDL.nml, with id: OLQDL\r\nLoaded morphology file from: ../generatedNeuroML2/IL1DR.nml, with id: IL1DR\r\nLoaded morphology file from: ../generatedNeuroML2/IL1R.nml, with id: IL1R\r\nLoaded morphology file from: ../generatedNeuroML2/URBR.nml, with id: URBR\r\nLoaded morphology file from: ../generatedNeuroML2/IL1VL.nml, with id: IL1VL\r\nLoaded morphology file from: ../generatedNeuroML2/SIAVL.nml, with id: SIAVL\r\nLoaded morphology file from: ../generatedNeuroML2/URAVL.nml, with id: URAVL\r\nLoaded morphology file from: ../generatedNeuroML2/IL1VR.nml, with id: IL1VR\r\nLoaded morphology file from: ../generatedNeuroML2/IL2VR.nml, with id: IL2VR\r\nLoaded morphology file from: ../generatedNeuroML2/OLQVR.nml, with id: OLQVR\r\nLoaded morphology file from: ../generatedNeuroML2/URAVR.nml, with id: URAVR\r\nLoaded morphology file from: ../generatedNeuroML2/PHCL.nml, with id: PHCL\r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": "Loaded morphology file from: ../generatedNeuroML2/DD3.nml, with id: DD3\r\nLoaded morphology file from: ../generatedNeuroML2/DD4.nml, with id: DD4\r\nLoaded morphology file from: ../generatedNeuroML2/VD8.nml, with id: VD8\r\nLoaded morphology file from: ../generatedNeuroML2/DD5.nml, with id: DD5\r\nLoaded morphology file from: ../generatedNeuroML2/VD9.nml, with id: VD9\r\nLoaded morphology file from: ../generatedNeuroML2/VC5.nml, with id: VC5\r\nLoaded morphology file from: ../generatedNeuroML2/VC2.nml, with id: VC2\r\nLoaded morphology file from: ../generatedNeuroML2/I1L.nml, with id: I1L\r\nLoaded morphology file from: ../generatedNeuroML2/I1R.nml, with id: I1R\r\nLoaded morphology file from: ../generatedNeuroML2/I3.nml, with id: I3\r\nLoaded morphology file from: ../generatedNeuroML2/I5.nml, with id: I5\r\nLoaded morphology file from: ../generatedNeuroML2/I2L.nml, with id: I2L\r\nLoaded morphology file from: ../generatedNeuroML2/M1.nml, with id: M1\r\nLoaded morphology file from: ../generatedNeuroML2/I2R.nml, with id: I2R\r\nLoaded morphology file from: ../generatedNeuroML2/M2L.nml, with id: M2L\r\nLoaded morphology file from: ../generatedNeuroML2/M2R.nml, with id: M2R\r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": "Loaded morphology file from: ../generatedNeuroML2/I4.nml, with id: I4\r\nLoaded morphology file from: ../generatedNeuroML2/M5.nml, with id: M5\r\nLoaded morphology file from: ../generatedNeuroML2/MI.nml, with id: MI\r\nLoaded morphology file from: ../generatedNeuroML2/I6.nml, with id: I6\r\nLoaded morphology file from: ../generatedNeuroML2/M4.nml, with id: M4\r\nLoaded morphology file from: ../generatedNeuroML2/NSML.nml, with id: NSML\r\nLoaded morphology file from: ../generatedNeuroML2/NSMR.nml, with id: NSMR\r\nLoaded morphology file from: ../generatedNeuroML2/RMER.nml, with id: RMER\r\nLoaded morphology file from: ../generatedNeuroML2/RMEL.nml, with id: RMEL\r\nLoaded morphology file from: ../generatedNeuroML2/RMED.nml, with id: RMED\r\nLoaded morphology file from: ../generatedNeuroML2/IL2R.nml, with id: IL2R\r\nLoaded morphology file from: ../generatedNeuroML2/IL2DL.nml, with id: IL2DL\r\nLoaded morphology file from: ../generatedNeuroML2/IL2DR.nml, with id: IL2DR\r\nLoaded morphology file from: ../generatedNeuroML2/VC1.nml, with id: VC1\r\nLoaded morphology file from: ../generatedNeuroML2/VD7.nml, with id: VD7\r\nLoaded morphology file from: ../generatedNeuroML2/IL2VL.nml, with id: IL2VL\r\nLoaded morphology file from: ../generatedNeuroML2/PHBL.nml, with id: PHBL\r\nLoaded morphology file from: ../generatedNeuroML2/PLML.nml, with id: PLML\r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": "Loaded morphology file from: ../generatedNeuroML2/M3L.nml, with id: M3L\r\nLoaded morphology file from: ../generatedNeuroML2/M3R.nml, with id: M3R\r\nLoaded morphology file from: ../generatedNeuroML2/MCL.nml, with id: MCL\r\nLoaded morphology file from: ../generatedNeuroML2/MCR.nml, with id: MCR\r\nLoaded morphology file from: ../generatedNeuroML2/SIBVR.nml, with id: SIBVR\r\nLoaded morphology file from: ../generatedNeuroML2/SIBDL.nml, with id: SIBDL\r\nLoaded morphology file from: ../generatedNeuroML2/PHAR.nml, with id: PHAR\r\nLoaded morphology file from: ../generatedNeuroML2/PHCR.nml, with id: PHCR\r\nLoaded morphology file from: ../generatedNeuroML2/PLNL.nml, with id: PLNL\r\nLoaded morphology file from: ../generatedNeuroML2/PLNR.nml, with id: PLNR\r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": "Loaded morphology file from: ../generatedNeuroML2/PVDL.nml, with id: PVDL\r\nLoaded morphology file from: ../generatedNeuroML2/PVWR.nml, with id: PVWR\r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": "Loaded morphology file from: ../generatedNeuroML2/PVDR.nml, with id: PVDR\r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": "Connections generated in 184.035447 seconds, mean length: 1.342035 um\r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": "Written network file to: CElegansConnectome.nml\r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": "Validating CElegansConnectome.nml against https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2beta1.xsd\r\n"
},
{
"output_type": "stream",
"stream": "stdout",
"text": "It's valid!\r\n"
}
],
"prompt_number": 35
},
{
"cell_type": "markdown",
"metadata": {},
"source": "Having set debug to false, I can see that the script can finish. Yay!\n\nNow I can address the real goal:\n\nIncorporating Steve Cook's data into the CElegansNeuroML\n--------------------------------------------------------\n\nThe data set was turned into [a google spreadsheet](https://docs.google.com/spreadsheet/ccc?key=0Avt3mQaA-HaMdGxoRE0wYURfYlBpM21Lb2VHOGxjQlE#gid=0). I went in and added an annotation on the 'post' cell to explain how to read out the muscle cells\n\nWe are now trying to follow [the procedure I mapped out earlier](http://nbviewer.ipython.org/5919352) this summer.\n\nThe first step has to be to incorporate that new Cook data into the [spreadsheet that is used by the script](https://github.com/openworm/CElegansNeuroML/blob/master/CElegansNeuronTables.xls)"
}
],
"metadata": {}
}
]
}
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