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TarrySinghTarrySingh
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Updated for Python 3.6+
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‎neurophysics-neuroscience/python/todo/allie/allie_tutorial.ipynb

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"cells": [
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{
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"cell_type": "code",
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"execution_count": null,
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"execution_count": 1,
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"metadata": {
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"collapsed": true
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},
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},
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{
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"cell_type": "code",
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"execution_count": 86,
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"metadata": {
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"collapsed": true
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},
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"execution_count": 3,
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"metadata": {},
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"outputs": [],
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"source": [
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"import scipy.io as si\n",
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"execution_count": 5,
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"metadata": {
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"collapsed": true
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"scrolled": true
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},
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"outputs": [],
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"source": []
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"source": [
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"import numpy as np\n",
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"from nipy.core.api import Image, vox2mni"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 84,
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"metadata": {
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"collapsed": false,
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"scrolled": true
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},
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"execution_count": 6,
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"metadata": {},
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"outputs": [
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{
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"ename": "ImportError",
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"evalue": "No module named nipy.core.api",
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"ename": "FileNotFoundError",
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"evalue": "[Errno 2] No such file or directory: '../Allie/SfN_materials/Classification/code/fmriDat.mat'",
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"output_type": "error",
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"traceback": [
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"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
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"\u001b[0;31mImportError\u001b[0m Traceback (most recent call last)",
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"\u001b[0;32m<ipython-input-84-78da7e6cd696>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mnumpy\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0mnp\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 2\u001b[0;31m \u001b[0;32mfrom\u001b[0m \u001b[0mnipy\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcore\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mapi\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mImage\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mvox2mni\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
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"\u001b[0;31mImportError\u001b[0m: No module named nipy.core.api"
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"\u001b[0;31mFileNotFoundError\u001b[0m Traceback (most recent call last)",
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"\u001b[0;32m<ipython-input-6-01a24fb99e57>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[0;31m## Load the data\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 2\u001b[0;31m \u001b[0mdata\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msi\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mloadmat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'../Allie/SfN_materials/Classification/code/fmriDat.mat'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
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"\u001b[0;32m~/anaconda/lib/python3.6/site-packages/scipy/io/matlab/mio.py\u001b[0m in \u001b[0;36mloadmat\u001b[0;34m(file_name, mdict, appendmat, **kwargs)\u001b[0m\n\u001b[1;32m 133\u001b[0m \"\"\"\n\u001b[1;32m 134\u001b[0m \u001b[0mvariable_names\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mkwargs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpop\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'variable_names'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 135\u001b[0;31m \u001b[0mMR\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mmat_reader_factory\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfile_name\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mappendmat\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 136\u001b[0m \u001b[0mmatfile_dict\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mMR\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget_variables\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mvariable_names\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 137\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mmdict\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
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"\u001b[0;32m~/anaconda/lib/python3.6/site-packages/scipy/io/matlab/mio.py\u001b[0m in \u001b[0;36mmat_reader_factory\u001b[0;34m(file_name, appendmat, **kwargs)\u001b[0m\n\u001b[1;32m 56\u001b[0m \u001b[0mtype\u001b[0m \u001b[0mdetected\u001b[0m \u001b[0;32min\u001b[0m\u001b[0;31m \u001b[0m\u001b[0;31m`\u001b[0m\u001b[0mfilename\u001b[0m\u001b[0;31m`\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 57\u001b[0m \"\"\"\n\u001b[0;32m---> 58\u001b[0;31m \u001b[0mbyte_stream\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0m_open_file\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfile_name\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mappendmat\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 59\u001b[0m \u001b[0mmjv\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmnv\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mget_matfile_version\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mbyte_stream\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 60\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mmjv\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;36m0\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
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"\u001b[0;32m~/anaconda/lib/python3.6/site-packages/scipy/io/matlab/mio.py\u001b[0m in \u001b[0;36m_open_file\u001b[0;34m(file_like, appendmat)\u001b[0m\n\u001b[1;32m 21\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfile_like\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mstring_types\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 22\u001b[0m \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 23\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mopen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfile_like\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'rb'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 24\u001b[0m \u001b[0;32mexcept\u001b[0m \u001b[0mIOError\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0me\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 25\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mappendmat\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0mfile_like\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mendswith\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'.mat'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
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"\u001b[0;31mFileNotFoundError\u001b[0m: [Errno 2] No such file or directory: '../Allie/SfN_materials/Classification/code/fmriDat.mat'"
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]
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}
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],
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"source": [
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"import numpy as np\n",
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"from nipy.core.api import Image, vox2mni"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": true
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},
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"outputs": [],
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"source": []
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},
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{
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"cell_type": "code",
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"execution_count": 2,
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"metadata": {
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"collapsed": true
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},
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"outputs": [],
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"source": [
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"## Load the data\n",
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"data = si.loadmat('../../Allie/SfN_materials/Classification/code/fmriDat.mat')"
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"data = si.loadmat('../Allie/SfN_materials/Classification/code/fmriDat.mat')"
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]
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},
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{
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{
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"cell_type": "code",
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"execution_count": 77,
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"metadata": {},
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"outputs": [],
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"source": [
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"import nibabel as nb"
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"metadata": {},
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"outputs": [],
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"source": [
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"meta = data['metaDat'][0, 0][0]\n",
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{
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"cell_type": "code",
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"execution_count": 80,
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"metadata": {},
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"mask_z = meta[:, 2] == iz\n",
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"metadata": {},
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"ename": "IndexError",
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"metadata": {},
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"data": {
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"metadata": {
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"hide_input": false,
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"kernelspec": {
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"display_name": "Python 2",
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"display_name": "Python 3",
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"language": "python",
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"name": "python2"
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 2
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"version": 3
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython2",
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"version": "2.7.11"
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"pygments_lexer": "ipython3",
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"version": "3.6.1"
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}
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},
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"nbformat": 4,

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