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1. Executes program with mpiexec when using oarsub that was missed before. 2. Adds notebooks to create mu images with different values.
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| results/ | ||
| diagnostics/ | ||
| build/ | ||
| buildNewNef/ | ||
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| /src/Makefile | ||
| /GPATH | ||
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notebooks/.ipynb_checkpoints/create_image_from_labels-checkpoint.ipynb
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| @@ -0,0 +1,6 @@ | ||
| { | ||
| "cells": [], | ||
| "metadata": {}, | ||
| "nbformat": 4, | ||
| "nbformat_minor": 0 | ||
| } |
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| { | ||
| "cells": [ | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "# Create images using label images and tables of desired values" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 1, | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "outputs": [], | ||
| "source": [ | ||
| "import sys\n", | ||
| "sys.path.insert(0, '../scripts')\n", | ||
| "\n", | ||
| "def create_table_file(fname, header, label_value_pairs):\n", | ||
| " '''\n", | ||
| " Write a new file which starts with header and then writes\n", | ||
| " in each line the label_value_pairs given as a list.\n", | ||
| " '''\n", | ||
| " with open(fname, 'w') as fil:\n", | ||
| " fil.write(header)\n", | ||
| " for pair in label_value_pairs:\n", | ||
| " fil.write('%s\\t%s\\n' % (pair[0], pair[1]))\n", | ||
| " return\n", | ||
| "\n", | ||
| "def create_image(img_file, label_value_pairs, label_img, modify_img=None):\n", | ||
| " '''\n", | ||
| " Creates image by putting values present in label_value_pairs in \n", | ||
| " the selected labels in corresponding ROIs present in label_img.\n", | ||
| " If modify_img is given update it instead of creating a new image\n", | ||
| " with zero in all regions where the asked label is not present.\n", | ||
| " '''\n", | ||
| " import bish_utils as bu\n", | ||
| " tbl_fl = 'tmp++table'\n", | ||
| " header = 'labels\\tnewValues\\n'\n", | ||
| " create_table_file(tbl_fl, header, label_value_pairs)\n", | ||
| " cmd = ('../build/src/createImageFromLabelImage -t %s -l %s -o %s'\n", | ||
| " % (tbl_fl, label_img, img_file))\n", | ||
| " if modify_img:\n", | ||
| " cmd += ' -m %s' % (modify_img)\n", | ||
| " bu.print_and_execute(cmd)\n", | ||
| " bu.print_and_execute('rm %s' % tbl_fl)\n", | ||
| " " | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "outputs": [], | ||
| "source": [ | ||
| "import os as os\n", | ||
| "import os.path as op\n", | ||
| "\n", | ||
| "in_img_dir = '/proj/asclepios/cluster/asclepios2/bkhanal/works/AdLemModel/results/patients/miriad_189_AD_M_10_MR_1'\n", | ||
| "#in_img_dir = '../results/patients/miriad_189_AD_M_10_MR_1'\n", | ||
| "\n", | ||
| "csf_model_label = op.join(in_img_dir, 'maskwithCsfD2R0.nii.gz')\n", | ||
| "#aseg_label = op.join(in_img_dir, 'aseg_cropped.nii.gz')\n", | ||
| "aseg_label = op.join(in_img_dir, 'labelsWithCsfD2R0.nii.gz')\n", | ||
| "\n", | ||
| "out_img_dir = in_img_dir\n", | ||
| "out_img = op.join(out_img_dir, 'muImageWmBstem10_GmCsf1.nii.gz')\n", | ||
| "\n", | ||
| "# make all tissue and CSF 1 first\n", | ||
| "lab_val = [(1, 1), (2, 1)]\n", | ||
| "create_image(out_img, lab_val, csf_model_label)\n", | ||
| "\n", | ||
| "# change labels of Brain stem and WM\n", | ||
| "h_val = 10\n", | ||
| "lab_val = [(16, h_val), (28, h_val), (60, h_val), (41, h_val), (2, h_val), (46, h_val), (7, h_val)]\n", | ||
| "create_image(out_img, lab_val, aseg_label, out_img)\n" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": { | ||
| "collapsed": true | ||
| }, | ||
| "outputs": [], | ||
| "source": [] | ||
| } | ||
| ], | ||
| "metadata": { | ||
| "kernelspec": { | ||
| "display_name": "Python 2", | ||
| "language": "python", | ||
| "name": "python2" | ||
| }, | ||
| "language_info": { | ||
| "codemirror_mode": { | ||
| "name": "ipython", | ||
| "version": 2 | ||
| }, | ||
| "file_extension": ".py", | ||
| "mimetype": "text/x-python", | ||
| "name": "python", | ||
| "nbconvert_exporter": "python", | ||
| "pygments_lexer": "ipython2", | ||
| "version": "2.7.10" | ||
| } | ||
| }, | ||
| "nbformat": 4, | ||
| "nbformat_minor": 0 | ||
| } |
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