├── test.txt ├── doc ├── source │ ├── actions.rst │ ├── exceptions.rst │ ├── utilities.rst │ ├── Classes.rst │ ├── FileSet.rst.bkg │ ├── index.rst │ └── tutorial │ │ ├── simpleapplicationpipeline.rst │ │ ├── simpletrainingpipeline.rst │ │ └── usingthescripts.rst ├── numpydoc │ ├── MANIFEST.in │ ├── numpydoc │ │ ├── __init__.py │ │ ├── tests │ │ │ ├── test_linkcode.py │ │ │ ├── test_traitsdoc.py │ │ │ ├── test_phantom_import.py │ │ │ └── test_plot_directive.py │ │ ├── linkcode.py │ │ └── traitsdoc.py │ ├── .travis.yml │ ├── setup.py │ └── README.rst ├── scipy-sphinx-theme │ ├── test_autodoc.rst │ ├── _static │ │ └── scipyshiny_small.png │ ├── _theme │ │ └── scipy │ │ │ ├── static │ │ │ ├── img │ │ │ │ ├── contents.png │ │ │ │ ├── navigation.png │ │ │ │ ├── scipy-logo.png │ │ │ │ ├── flags │ │ │ │ │ ├── flag-ad.png │ │ │ │ │ ├── flag-ae.png │ │ │ │ │ ├── flag-af.png │ │ │ │ │ ├── flag-ag.png │ │ │ │ │ ├── flag-ai.png │ │ │ │ │ ├── flag-al.png │ │ │ │ │ ├── flag-am.png │ │ │ │ │ ├── flag-ao.png │ │ │ │ │ ├── flag-aq.png │ │ │ │ │ ├── flag-ar.png │ │ │ │ │ ├── flag-as.png │ │ │ │ │ ├── flag-at.png │ │ │ │ │ ├── flag-au.png │ │ │ │ │ ├── flag-aw.png │ │ │ │ │ ├── flag-az.png │ │ │ │ │ ├── flag-ba.png │ │ │ │ │ ├── flag-bb.png │ │ │ │ │ ├── flag-bd.png │ │ │ │ │ ├── flag-be.png │ │ │ │ │ ├── flag-bf.png │ │ │ │ │ ├── flag-bg.png │ │ │ │ │ ├── flag-bh.png │ │ │ │ │ ├── flag-bi.png │ │ │ │ │ ├── flag-bj.png │ │ │ │ │ ├── flag-bl.png │ │ │ │ │ ├── flag-bm.png │ │ │ │ │ ├── flag-bn.png │ │ │ │ │ ├── flag-bo.png │ │ │ │ │ ├── flag-br.png │ │ │ │ │ ├── flag-bs.png │ │ │ │ │ ├── flag-bt.png │ │ │ │ │ ├── flag-bw.png │ │ │ │ │ ├── flag-by.png │ │ │ │ │ ├── flag-bz.png │ │ │ │ │ ├── flag-ca.png │ │ │ │ │ ├── flag-cc.png │ │ │ │ │ ├── flag-cd.png │ │ │ │ │ ├── flag-cf.png │ │ │ │ │ ├── flag-cg.png │ │ │ │ │ ├── flag-ch.png │ │ │ │ │ ├── flag-ci.png │ │ │ │ │ ├── flag-ck.png │ │ │ │ │ ├── flag-cl.png │ │ │ │ │ ├── flag-cm.png │ │ │ │ │ ├── flag-cn.png │ │ │ │ │ ├── flag-co.png │ │ │ │ │ ├── flag-cr.png │ │ │ │ │ ├── flag-cu.png │ │ │ │ │ ├── flag-cv.png │ │ │ │ │ ├── flag-cw.png │ │ │ │ │ ├── flag-cx.png │ │ │ │ │ ├── flag-cy.png │ │ │ │ │ ├── flag-cz.png │ │ │ │ │ ├── flag-de.png │ │ │ │ │ ├── flag-dj.png │ │ │ │ │ ├── flag-dk.png │ │ │ │ │ ├── flag-dm.png │ │ │ │ │ ├── flag-do.png │ │ │ │ │ ├── flag-dz.png │ │ │ │ │ ├── flag-ec.png │ │ │ │ │ ├── flag-ee.png │ │ │ │ │ ├── flag-eg.png │ │ │ │ │ ├── flag-er.png │ │ │ │ │ ├── flag-es.png │ │ │ │ │ ├── flag-et.png │ │ │ │ │ ├── flag-fi.png │ │ │ │ │ ├── flag-fj.png │ │ │ │ │ ├── flag-fk.png │ │ │ │ │ ├── flag-fm.png │ │ │ │ │ ├── flag-fo.png │ │ │ │ │ ├── flag-fr.png │ │ │ │ │ ├── flag-ga.png │ │ │ │ │ ├── flag-gb.png │ │ │ │ │ ├── flag-gd.png │ │ │ │ │ ├── flag-ge.png │ │ │ │ │ ├── flag-gf.png │ │ │ │ │ ├── flag-gg.png │ │ │ │ │ ├── flag-gh.png │ │ │ │ │ ├── flag-gi.png │ │ │ │ │ ├── flag-gl.png │ │ │ │ │ ├── flag-gm.png │ │ │ │ │ ├── flag-gn.png │ │ │ │ │ ├── flag-gq.png │ │ │ │ │ ├── flag-gr.png │ │ │ │ │ ├── flag-gs.png │ │ │ │ │ ├── flag-gt.png │ │ │ │ │ ├── flag-gu.png │ │ │ │ │ ├── flag-gw.png │ │ │ │ │ ├── flag-gy.png │ │ │ │ │ ├── flag-hk.png │ │ │ │ │ ├── flag-hm.png │ │ │ │ │ ├── flag-hn.png │ │ │ │ │ ├── flag-hr.png │ │ │ │ │ ├── flag-ht.png │ │ │ │ │ ├── flag-hu.png │ │ │ │ │ ├── flag-id.png │ │ │ │ │ ├── flag-ie.png │ │ │ │ │ ├── flag-il.png │ │ │ │ │ ├── flag-im.png │ │ │ │ │ ├── flag-in.png │ │ │ │ │ ├── flag-io.png │ │ │ │ │ ├── flag-iq.png │ │ │ │ │ ├── flag-ir.png │ │ │ │ │ ├── flag-is.png │ │ │ │ │ ├── flag-it.png │ │ │ │ │ ├── flag-je.png │ │ │ │ │ ├── flag-jm.png │ │ │ │ │ ├── flag-jo.png │ │ │ │ │ ├── flag-jp.png │ │ │ │ │ ├── flag-ke.png │ │ │ │ │ ├── flag-kg.png │ │ │ │ │ ├── flag-kh.png │ │ │ │ │ ├── flag-ki.png │ │ │ │ │ ├── flag-km.png │ │ │ │ │ ├── flag-kn.png │ │ │ │ │ ├── flag-kp.png │ │ │ │ │ ├── flag-kr.png │ │ │ │ │ ├── flag-kw.png │ │ │ │ │ ├── flag-ky.png │ │ │ │ │ ├── flag-kz.png │ │ │ │ │ ├── flag-la.png │ │ │ │ │ ├── flag-lb.png │ │ │ │ │ ├── flag-lc.png │ │ │ │ │ ├── flag-li.png │ │ │ │ │ ├── flag-lk.png │ │ │ │ │ ├── flag-lr.png │ │ │ │ │ ├── flag-ls.png │ │ │ │ │ ├── flag-lt.png │ │ │ │ │ ├── flag-lu.png │ │ │ │ │ ├── flag-lv.png │ │ │ │ │ ├── flag-ly.png │ │ │ │ │ ├── flag-ma.png │ │ │ │ │ ├── flag-mc.png │ │ │ │ │ ├── flag-md.png │ │ │ │ │ ├── flag-me.png │ │ │ │ │ ├── flag-mf.png │ │ │ │ │ ├── flag-mg.png │ │ │ │ │ ├── flag-mh.png │ │ │ │ │ ├── flag-mk.png │ │ │ │ │ ├── flag-ml.png │ │ │ │ │ ├── flag-mm.png │ │ │ │ │ ├── flag-mn.png │ │ │ │ │ ├── flag-mo.png │ │ │ │ │ ├── flag-mp.png │ │ │ │ │ ├── flag-mq.png │ │ │ │ │ ├── flag-mr.png │ │ │ │ │ ├── flag-ms.png │ │ │ │ │ ├── flag-mt.png │ │ │ │ │ ├── flag-mu.png │ │ │ │ │ ├── flag-mv.png │ │ │ │ │ ├── flag-mw.png │ │ │ │ │ ├── flag-mx.png │ │ │ │ │ ├── flag-my.png │ │ │ │ │ ├── flag-mz.png │ │ │ │ │ ├── flag-na.png │ │ │ │ │ ├── flag-nc.png │ │ │ │ │ ├── flag-ne.png │ │ │ │ │ ├── flag-nf.png │ │ │ │ │ ├── flag-ng.png │ │ │ │ │ ├── flag-ni.png │ │ │ │ │ ├── flag-nl.png │ │ │ │ │ ├── flag-no.png │ │ │ │ │ ├── flag-np.png │ │ │ │ │ ├── flag-nr.png │ │ │ │ │ ├── flag-nu.png │ │ │ │ │ ├── flag-nz.png │ │ │ │ │ ├── flag-om.png │ │ │ │ │ ├── flag-pa.png │ │ │ │ │ ├── flag-pe.png │ │ │ │ │ ├── flag-pf.png │ │ │ │ │ ├── flag-pg.png │ │ │ │ │ ├── flag-ph.png │ │ │ │ │ ├── flag-pk.png │ │ │ │ │ ├── flag-pl.png │ │ │ │ │ ├── flag-pm.png │ │ │ │ │ ├── flag-pn.png │ │ │ │ │ ├── flag-pr.png │ │ │ │ │ ├── flag-ps.png │ │ │ │ │ ├── flag-pt.png │ │ │ │ │ ├── flag-pw.png │ │ │ │ │ ├── flag-py.png │ │ │ │ │ ├── flag-qa.png │ │ │ │ │ ├── flag-re.png │ │ │ │ │ ├── flag-ro.png │ │ │ │ │ ├── flag-rs.png │ │ │ │ │ ├── flag-ru.png │ │ │ │ │ ├── flag-rw.png │ │ │ │ │ ├── flag-sa.png │ │ │ │ │ ├── flag-sb.png │ │ │ │ │ ├── flag-sc.png │ │ │ │ │ ├── flag-sd.png │ │ │ │ │ ├── flag-se.png │ │ │ │ │ ├── flag-sg.png │ │ │ │ │ ├── flag-sh.png │ │ │ │ │ ├── flag-si.png │ │ │ │ │ ├── flag-sj.png │ │ │ │ │ ├── flag-sk.png │ │ │ │ │ ├── flag-sl.png │ │ │ │ │ ├── flag-sm.png │ │ │ │ │ ├── flag-sn.png │ │ │ │ │ ├── flag-so.png │ │ │ │ │ ├── flag-sr.png │ │ │ │ │ ├── flag-st.png │ │ │ │ │ ├── flag-sv.png │ │ │ │ │ ├── flag-sy.png │ │ │ │ │ ├── flag-sz.png │ │ │ │ │ ├── flag-tc.png │ │ │ │ │ ├── flag-td.png │ │ │ │ │ ├── flag-tf.png │ │ │ │ │ ├── flag-tg.png │ │ │ │ │ ├── flag-th.png │ │ │ │ │ ├── flag-tj.png │ │ │ │ │ ├── flag-tk.png │ │ │ │ │ ├── flag-tl.png │ │ │ │ │ ├── flag-tm.png │ │ │ │ │ ├── flag-tn.png │ │ │ │ │ ├── flag-to.png │ │ │ │ │ ├── flag-tr.png │ │ │ │ │ ├── flag-tt.png │ │ │ │ │ ├── flag-tv.png │ │ │ │ │ ├── flag-tw.png │ │ │ │ │ ├── flag-tz.png │ │ │ │ │ ├── flag-ua.png │ │ │ │ │ ├── flag-ug.png │ │ │ │ │ ├── flag-um.png │ │ │ │ │ ├── flag-us.png │ │ │ │ │ ├── flag-uy.png │ │ │ │ │ ├── flag-uz.png │ │ │ │ │ ├── flag-va.png │ │ │ │ │ ├── flag-vc.png │ │ │ │ │ ├── flag-ve.png │ │ │ │ │ ├── flag-vg.png │ │ │ │ │ ├── flag-vi.png │ │ │ │ │ ├── flag-vn.png │ │ │ │ │ ├── flag-vu.png │ │ │ │ │ ├── flag-wf.png │ │ │ │ │ ├── flag-ws.png │ │ │ │ │ ├── flag-ye.png │ │ │ │ │ ├── flag-za.png │ │ │ │ │ ├── flag-zm.png │ │ │ │ │ └── flag-zw.png │ │ │ │ ├── important-icon.png │ │ │ │ ├── scipy_org_logo.gif │ │ │ │ ├── information-icon.png │ │ │ │ ├── person-list-icon.png │ │ │ │ ├── scipycentral_logo.png │ │ │ │ ├── scipyshiny_small.png │ │ │ │ ├── send-email-icon.png │ │ │ │ ├── single-file-icon.png │ │ │ │ ├── transparent-pixel.gif │ │ │ │ ├── external-link-icon.png │ │ │ │ ├── multiple-file-icon.png │ │ │ │ ├── ui-anim_basic_16x16.gif │ │ │ │ ├── glyphicons-halflings.png │ │ │ │ ├── internet-web-browser.png │ │ │ │ ├── person-list-icon-tiny.png │ │ │ │ ├── single-file-list-icon.png │ │ │ │ ├── create-new-account-icon.png │ │ │ │ ├── external-link-list-icon.png │ │ │ │ ├── multiple-file-list-icon.png │ │ │ │ ├── single-file-icon-shrunk.png │ │ │ │ ├── external-link-icon-shrunk.png │ │ │ │ ├── glyphicons-halflings-white.png │ │ │ │ ├── multiple-file-icon-shrunk.png │ │ │ │ ├── single-file-list-icon-tiny.png │ │ │ │ ├── external-link-list-icon-tiny.png │ │ │ │ ├── multiple-file-list-icon-tiny.png │ │ │ │ ├── single-file-list-icon-tiniest.png │ │ │ │ └── external-link-list-icon-tiniest.png │ │ │ ├── less │ │ │ │ ├── spc-footer.less │ │ │ │ ├── spc-rightsidebar.less │ │ │ │ ├── bootstrap │ │ │ │ │ ├── layouts.less │ │ │ │ │ ├── component-animations.less │ │ │ │ │ ├── utilities.less │ │ │ │ │ ├── grid.less │ │ │ │ │ ├── breadcrumbs.less │ │ │ │ │ ├── responsive-768px-979px.less │ │ │ │ │ ├── hero-unit.less │ │ │ │ │ ├── wells.less │ │ │ │ │ ├── responsive-1200px-min.less │ │ │ │ │ ├── close.less │ │ │ │ │ ├── accordion.less │ │ │ │ │ ├── pager.less │ │ │ │ │ ├── media.less │ │ │ │ │ ├── scaffolding.less │ │ │ │ │ ├── responsive.less │ │ │ │ │ ├── thumbnails.less │ │ │ │ │ ├── code.less │ │ │ │ │ ├── alerts.less │ │ │ │ │ ├── bootstrap.less │ │ │ │ │ ├── responsive-utilities.less │ │ │ │ │ ├── tooltip.less │ │ │ │ │ ├── labels-badges.less │ │ │ │ │ ├── modals.less │ │ │ │ │ ├── pagination.less │ │ │ │ │ ├── carousel.less │ │ │ │ │ ├── progress-bars.less │ │ │ │ │ ├── popovers.less │ │ │ │ │ └── responsive-767px-max.less │ │ │ │ ├── spc-extend.less │ │ │ │ ├── spc-utils.less │ │ │ │ ├── spc-bootstrap.less │ │ │ │ ├── spc-header.less │ │ │ │ └── spc-content.less │ │ │ ├── css │ │ │ │ ├── spc-extend.css │ │ │ │ ├── extend.css │ │ │ │ └── pygments.css │ │ │ └── js │ │ │ │ └── copybutton.js │ │ │ ├── theme.conf │ │ │ └── sourcelink.html │ ├── test_autodoc_3.rst │ ├── test_autodoc_2.rst │ ├── test_autodoc_4.rst │ ├── index.rst │ ├── README.rst │ ├── conf.py │ └── Makefile └── README ├── neuroless ├── shell.pyc ├── utilities.pyc ├── __init__.py ├── utilities.py ├── actions │ ├── training.py │ ├── postprocessing.py │ ├── biasfieldcorrection.py │ ├── application.py │ ├── __init__.py │ └── skullstripping.py └── exceptions.py ├── .pydevproject ├── .project ├── test.py~ ├── test.py └── .gitignore /test.txt: -------------------------------------------------------------------------------- 1 | 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5px; 6 | font-size: small; 7 | } 8 | 9 | //footer inside yet to be done (may be not required). -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/theme.conf: -------------------------------------------------------------------------------- 1 | [theme] 2 | inherit = basic 3 | stylesheet = scipy.css 4 | pygments_style = friendly 5 | 6 | [options] 7 | edit_link = false 8 | rootlinks = [] 9 | sidebar = left 10 | scipy_org_logo = 11 | navigation_links = true 12 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/sourcelink.html: -------------------------------------------------------------------------------- 1 | {%- if show_source and has_source and sourcename %} 2 |

{{ _('This Page') }}

3 |
4 | {{ _('Show Source') }} 6 |
7 | {%- endif %} 8 | -------------------------------------------------------------------------------- /doc/numpydoc/numpydoc/tests/test_traitsdoc.py: -------------------------------------------------------------------------------- 1 | from __future__ import division, absolute_import, print_function 2 | 3 | import sys 4 | from nose import SkipTest 5 | 6 | def test_import(): 7 | if sys.version_info[0] >= 3: 8 | raise SkipTest("traitsdoc not ported to Python3") 9 | import numpydoc.traitsdoc 10 | 11 | # No tests at the moment... 12 | -------------------------------------------------------------------------------- /doc/numpydoc/numpydoc/tests/test_phantom_import.py: -------------------------------------------------------------------------------- 1 | from __future__ import division, absolute_import, print_function 2 | 3 | import sys 4 | from nose import SkipTest 5 | 6 | def test_import(): 7 | if sys.version_info[0] >= 3: 8 | raise SkipTest("phantom_import not ported to Py3") 9 | 10 | import numpydoc.phantom_import 11 | 12 | # No tests at the moment... 13 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/spc-rightsidebar.less: -------------------------------------------------------------------------------- 1 | @import "bootstrap/variables.less"; 2 | 3 | .spc-rightsidebar { 4 | color: @gray; 5 | .navigation { 6 | padding: @paddingSmall; 7 | font-size: @fontSizeSmall; 8 | } 9 | .navigation .nav-title { 10 | font-weight: bold; 11 | text-transform: uppercase; 12 | } 13 | .navigation li { margin: 5px; } 14 | } -------------------------------------------------------------------------------- /doc/source/FileSet.rst.bkg: -------------------------------------------------------------------------------- 1 | ======= 2 | FileSet 3 | ======= 4 | 5 | .. currentmodule:: neuroless 6 | 7 | .. autoclass:: FileSet 8 | 9 | 10 | .. rubric:: Methods 11 | 12 | .. autosummary:: 13 | :toctree: generated/ 14 | 15 | ~Fileset.__init__ 16 | ~Fileset.fromfileset 17 | ~Fileset.fromdirectory 18 | ~Fileset.getfiles 19 | ~Fileset.getfile 20 | -------------------------------------------------------------------------------- /doc/numpydoc/numpydoc/tests/test_plot_directive.py: -------------------------------------------------------------------------------- 1 | from __future__ import division, absolute_import, print_function 2 | 3 | import sys 4 | from nose import SkipTest 5 | 6 | def test_import(): 7 | if sys.version_info[0] >= 3: 8 | raise SkipTest("plot_directive not ported to Python 3 (use the one from Matplotlib instead)") 9 | import numpydoc.plot_directive 10 | 11 | # No tests at the moment... 12 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/layouts.less: -------------------------------------------------------------------------------- 1 | // 2 | // Layouts 3 | // -------------------------------------------------- 4 | 5 | 6 | // Container (centered, fixed-width layouts) 7 | .container { 8 | .container-fixed(); 9 | } 10 | 11 | // Fluid layouts (left aligned, with sidebar, min- & max-width content) 12 | .container-fluid { 13 | padding-right: @gridGutterWidth; 14 | padding-left: @gridGutterWidth; 15 | .clearfix(); 16 | } -------------------------------------------------------------------------------- /.pydevproject: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | /neuroless 7 | 8 | python 2.7 9 | Default 10 | 11 | -------------------------------------------------------------------------------- /.project: -------------------------------------------------------------------------------- 1 | 2 | 3 | neuroless 4 | 5 | 6 | medpy 7 | 8 | 9 | 10 | org.python.pydev.PyDevBuilder 11 | 12 | 13 | 14 | 15 | 16 | org.python.pydev.pythonNature 17 | 18 | 19 | -------------------------------------------------------------------------------- /doc/numpydoc/.travis.yml: -------------------------------------------------------------------------------- 1 | # After changing this file, check it on: 2 | # http://lint.travis-ci.org/ 3 | language: python 4 | python: 5 | - 3.3 6 | - 2.7 7 | before_install: 8 | - pip install --upgrade pip setuptools # Upgrade pip and setuptools to get ones with `wheel` support 9 | - pip install --find-links http://wheels.astropy.org/ --find-links http://wheels2.astropy.org/ --use-wheel --use-mirrors nose numpy matplotlib Sphinx 10 | script: 11 | - python setup.py test 12 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/component-animations.less: -------------------------------------------------------------------------------- 1 | // 2 | // Component animations 3 | // -------------------------------------------------- 4 | 5 | 6 | .fade { 7 | opacity: 0; 8 | .transition(opacity .15s linear); 9 | &.in { 10 | opacity: 1; 11 | } 12 | } 13 | 14 | .collapse { 15 | position: relative; 16 | height: 0; 17 | overflow: hidden; 18 | .transition(height .35s ease); 19 | &.in { 20 | height: auto; 21 | } 22 | } 23 | -------------------------------------------------------------------------------- /doc/source/index.rst: -------------------------------------------------------------------------------- 1 | NeuroLess 2 | ========= 3 | 4 | :Release: |release| 5 | :Date: |today| 6 | 7 | NeuroLess is a simple, modular pipeline to train a brain lesion segmentation decision forest and apply it. 8 | 9 | Tutorials 10 | --------- 11 | 12 | .. toctree:: 13 | :glob: 14 | :maxdepth: 1 15 | 16 | tutorial/* 17 | 18 | Reference 19 | --------- 20 | 21 | .. toctree:: 22 | :maxdepth: 1 23 | 24 | Classes 25 | actions 26 | utilities 27 | exceptions 28 | 29 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/spc-extend.less: -------------------------------------------------------------------------------- 1 | //spc extend settings 2 | 3 | body { 4 | background-color: rgb(249,250,245); 5 | } 6 | 7 | .container { 8 | width: 80%; 9 | } 10 | 11 | .main { 12 | background-color: white; 13 | padding: 18px; 14 | -moz-box-shadow: 0 0 3px #888; 15 | -webkit-box-shadow: 0 0 3px #888; 16 | box-shadow: 0 0 3px #888; 17 | } 18 | 19 | @import "spc-header.less"; 20 | @import "spc-content.less"; 21 | @import "spc-rightsidebar.less"; 22 | @import "spc-footer.less"; -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/utilities.less: -------------------------------------------------------------------------------- 1 | // 2 | // Utility classes 3 | // -------------------------------------------------- 4 | 5 | 6 | // Quick floats 7 | .pull-right { 8 | float: right; 9 | } 10 | .pull-left { 11 | float: left; 12 | } 13 | 14 | // Toggling content 15 | .hide { 16 | display: none; 17 | } 18 | .show { 19 | display: block; 20 | } 21 | 22 | // Visibility 23 | .invisible { 24 | visibility: hidden; 25 | } 26 | 27 | // For Affix plugin 28 | .affix { 29 | position: fixed; 30 | } 31 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/spc-utils.less: -------------------------------------------------------------------------------- 1 | // LESS Utilities for spc 2 | @import "bootstrap/variables.less"; 3 | 4 | .padding (@top: 0px, @bottom: 0px, @left: 0px, @right: 0px) { 5 | padding-top: @top; 6 | padding-bottom: @bottom; 7 | padding-left: @left; 8 | padding-right: @right; 9 | } 10 | 11 | .margin (@top: 0px, @bottom: 0px, @left: 0px, @right: 0px) { 12 | margin-top: @top; 13 | margin-bottom: @bottom; 14 | margin-left: @left; 15 | margin-right:@right; 16 | } 17 | 18 | .underline { 19 | border-bottom: 1.5px solid @hrBorder; 20 | } 21 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/grid.less: -------------------------------------------------------------------------------- 1 | // 2 | // Grid system 3 | // -------------------------------------------------- 4 | 5 | 6 | // Fixed (940px) 7 | #grid > .core(@gridColumnWidth, @gridGutterWidth); 8 | 9 | // Fluid (940px) 10 | #grid > .fluid(@fluidGridColumnWidth, @fluidGridGutterWidth); 11 | 12 | // Reset utility classes due to specificity 13 | [class*="span"].hide, 14 | .row-fluid [class*="span"].hide { 15 | display: none; 16 | } 17 | 18 | [class*="span"].pull-right, 19 | .row-fluid [class*="span"].pull-right { 20 | float: right; 21 | } 22 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/spc-bootstrap.less: -------------------------------------------------------------------------------- 1 | // spc bootstrap settings 2 | @import "bootstrap/bootstrap.less"; 3 | @import "bootstrap/responsive.less"; 4 | 5 | // google webfont 6 | @import url(http://fonts.googleapis.com/css?family=Open+Sans); 7 | 8 | //Typography 9 | @sansFontFamily: 'Open Sans', sans-serif !important; 10 | @baseFontSize: 13px; 11 | @baseLineHeight: 19px; 12 | 13 | //Colors 14 | @blue: #12567D; 15 | 16 | //Sprites 17 | @iconSpritePath: '../../img/glyphicons-halflings.png'; 18 | @iconWhiteSpritePath: '../../img/glyphicons-halflings-white.png'; -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/breadcrumbs.less: -------------------------------------------------------------------------------- 1 | // 2 | // Breadcrumbs 3 | // -------------------------------------------------- 4 | 5 | 6 | .breadcrumb { 7 | padding: 8px 15px; 8 | margin: 0 0 @baseLineHeight; 9 | list-style: none; 10 | background-color: #f5f5f5; 11 | .border-radius(@baseBorderRadius); 12 | > li { 13 | display: inline-block; 14 | .ie7-inline-block(); 15 | text-shadow: 0 1px 0 @white; 16 | > .divider { 17 | padding: 0 5px; 18 | color: #ccc; 19 | } 20 | } 21 | > .active { 22 | color: @grayLight; 23 | } 24 | } 25 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/spc-header.less: -------------------------------------------------------------------------------- 1 | // settings for 2 | // 1) .header 3 | // header block is found on the top of the website 4 | // spc-navbar, spc-header-searchbar found inside .header 5 | // 2) .spc-navbar 6 | // 3) .spc-header-searchbar 7 | 8 | @import "spc-utils.less"; 9 | 10 | .header { 11 | .margin(@top: 15px, @bottom: 15px); 12 | } 13 | 14 | .spc-navbar { 15 | .margin (@top: 15px, @bottom: 5px); 16 | .nav-pills { 17 | margin-bottom: 0px; 18 | font-size: 12px; 19 | 20 | >li >a { 21 | padding-top: 2.5px; 22 | padding-bottom: 2.5px; 23 | } 24 | } 25 | } -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/responsive-768px-979px.less: -------------------------------------------------------------------------------- 1 | // 2 | // Responsive: Tablet to desktop 3 | // -------------------------------------------------- 4 | 5 | 6 | @media (min-width: 768px) and (max-width: 979px) { 7 | 8 | // Fixed grid 9 | #grid > .core(@gridColumnWidth768, @gridGutterWidth768); 10 | 11 | // Fluid grid 12 | #grid > .fluid(@fluidGridColumnWidth768, @fluidGridGutterWidth768); 13 | 14 | // Input grid 15 | #grid > .input(@gridColumnWidth768, @gridGutterWidth768); 16 | 17 | // No need to reset .thumbnails here since it's the same @gridGutterWidth 18 | 19 | } 20 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/hero-unit.less: -------------------------------------------------------------------------------- 1 | // 2 | // Hero unit 3 | // -------------------------------------------------- 4 | 5 | 6 | .hero-unit { 7 | padding: 60px; 8 | margin-bottom: 30px; 9 | font-size: 18px; 10 | font-weight: 200; 11 | line-height: @baseLineHeight * 1.5; 12 | color: @heroUnitLeadColor; 13 | background-color: @heroUnitBackground; 14 | .border-radius(6px); 15 | h1 { 16 | margin-bottom: 0; 17 | font-size: 60px; 18 | line-height: 1; 19 | color: @heroUnitHeadingColor; 20 | letter-spacing: -1px; 21 | } 22 | li { 23 | line-height: @baseLineHeight * 1.5; // Reset since we specify in type.less 24 | } 25 | } 26 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/wells.less: -------------------------------------------------------------------------------- 1 | // 2 | // Wells 3 | // -------------------------------------------------- 4 | 5 | 6 | // Base class 7 | .well { 8 | min-height: 20px; 9 | padding: 19px; 10 | margin-bottom: 20px; 11 | background-color: @wellBackground; 12 | border: 1px solid darken(@wellBackground, 7%); 13 | .border-radius(@baseBorderRadius); 14 | .box-shadow(inset 0 1px 1px rgba(0,0,0,.05)); 15 | blockquote { 16 | border-color: #ddd; 17 | border-color: rgba(0,0,0,.15); 18 | } 19 | } 20 | 21 | // Sizes 22 | .well-large { 23 | padding: 24px; 24 | .border-radius(@borderRadiusLarge); 25 | } 26 | .well-small { 27 | padding: 9px; 28 | .border-radius(@borderRadiusSmall); 29 | } 30 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/responsive-1200px-min.less: -------------------------------------------------------------------------------- 1 | // 2 | // Responsive: Large desktop and up 3 | // -------------------------------------------------- 4 | 5 | 6 | @media (min-width: 1200px) { 7 | 8 | // Fixed grid 9 | #grid > .core(@gridColumnWidth1200, @gridGutterWidth1200); 10 | 11 | // Fluid grid 12 | #grid > .fluid(@fluidGridColumnWidth1200, @fluidGridGutterWidth1200); 13 | 14 | // Input grid 15 | #grid > .input(@gridColumnWidth1200, @gridGutterWidth1200); 16 | 17 | // Thumbnails 18 | .thumbnails { 19 | margin-left: -@gridGutterWidth1200; 20 | } 21 | .thumbnails > li { 22 | margin-left: @gridGutterWidth1200; 23 | } 24 | .row-fluid .thumbnails { 25 | margin-left: 0; 26 | } 27 | 28 | } 29 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/index.rst: -------------------------------------------------------------------------------- 1 | .. scipy-sphinx-theme documentation master file, created by 2 | sphinx-quickstart on Sun Apr 21 11:22:24 2013. 3 | You can adapt this file completely to your liking, but it should at least 4 | contain the root `toctree` directive. 5 | 6 | Welcome to scipy-sphinx-theme's documentation! 7 | ============================================== 8 | 9 | The theme is under `_theme`, this document contains various test 10 | pages. 11 | 12 | Contents: 13 | 14 | .. toctree:: 15 | :maxdepth: 2 16 | 17 | README 18 | test_optimize 19 | test_autodoc 20 | test_autodoc_2 21 | test_autodoc_3 22 | test_autodoc_4 23 | 24 | Indices and tables 25 | ================== 26 | 27 | * :ref:`genindex` 28 | * :ref:`modindex` 29 | * :ref:`search` 30 | 31 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/close.less: -------------------------------------------------------------------------------- 1 | // 2 | // Close icons 3 | // -------------------------------------------------- 4 | 5 | 6 | .close { 7 | float: right; 8 | font-size: 20px; 9 | font-weight: bold; 10 | line-height: @baseLineHeight; 11 | color: @black; 12 | text-shadow: 0 1px 0 rgba(255,255,255,1); 13 | .opacity(20); 14 | &:hover, 15 | &:focus { 16 | color: @black; 17 | text-decoration: none; 18 | cursor: pointer; 19 | .opacity(40); 20 | } 21 | } 22 | 23 | // Additional properties for button version 24 | // iOS requires the button element instead of an anchor tag. 25 | // If you want the anchor version, it requires `href="#"`. 26 | button.close { 27 | padding: 0; 28 | cursor: pointer; 29 | background: transparent; 30 | border: 0; 31 | -webkit-appearance: none; 32 | } -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/accordion.less: -------------------------------------------------------------------------------- 1 | // 2 | // Accordion 3 | // -------------------------------------------------- 4 | 5 | 6 | // Parent container 7 | .accordion { 8 | margin-bottom: @baseLineHeight; 9 | } 10 | 11 | // Group == heading + body 12 | .accordion-group { 13 | margin-bottom: 2px; 14 | border: 1px solid #e5e5e5; 15 | .border-radius(@baseBorderRadius); 16 | } 17 | .accordion-heading { 18 | border-bottom: 0; 19 | } 20 | .accordion-heading .accordion-toggle { 21 | display: block; 22 | padding: 8px 15px; 23 | } 24 | 25 | // General toggle styles 26 | .accordion-toggle { 27 | cursor: pointer; 28 | } 29 | 30 | // Inner needs the styles because you can't animate properly with any styles on the element 31 | .accordion-inner { 32 | padding: 9px 15px; 33 | border-top: 1px solid #e5e5e5; 34 | } 35 | -------------------------------------------------------------------------------- /neuroless/__init__.py: -------------------------------------------------------------------------------- 1 | """ 2 | Neuro lesion segmentation pipeline in Python. 3 | 4 | Copyright (C) 2013 Oskar Maier, 5 | 6 | This library is free software: you can redistribute it and/or modify 7 | it under the terms of the GNU General Public License as published by 8 | the Free Software Foundation, either version 3 of the License, or 9 | (at your option) any later version. 10 | 11 | This program is distributed in the hope that it will be useful, 12 | but WITHOUT ANY WARRANTY; without even the implied warranty of 13 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 14 | GNU General Public License for more details. 15 | 16 | You should have received a copy of the GNU General Public License 17 | along with this program. If not, see . 18 | """ 19 | from .FileSet import FileSet 20 | from .TaskMachine import TaskMachine 21 | from .TrainedForest import TrainedForest -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/pager.less: -------------------------------------------------------------------------------- 1 | // 2 | // Pager pagination 3 | // -------------------------------------------------- 4 | 5 | 6 | .pager { 7 | margin: @baseLineHeight 0; 8 | list-style: none; 9 | text-align: center; 10 | .clearfix(); 11 | } 12 | .pager li { 13 | display: inline; 14 | } 15 | .pager li > a, 16 | .pager li > span { 17 | display: inline-block; 18 | padding: 5px 14px; 19 | background-color: #fff; 20 | border: 1px solid #ddd; 21 | .border-radius(15px); 22 | } 23 | .pager li > a:hover, 24 | .pager li > a:focus { 25 | text-decoration: none; 26 | background-color: #f5f5f5; 27 | } 28 | .pager .next > a, 29 | .pager .next > span { 30 | float: right; 31 | } 32 | .pager .previous > a, 33 | .pager .previous > span { 34 | float: left; 35 | } 36 | .pager .disabled > a, 37 | .pager .disabled > a:hover, 38 | .pager .disabled > a:focus, 39 | .pager .disabled > span { 40 | color: @grayLight; 41 | background-color: #fff; 42 | cursor: default; 43 | } -------------------------------------------------------------------------------- /test.py~: -------------------------------------------------------------------------------- 1 | #!/usr/bin/python 2 | 3 | import os 4 | from neuroless.shell import tmpdir, scp, cp, mv, smv, mkdircond, emptydircond,\ 5 | rmdircond 6 | from neuroless.exceptions import FileSystemOperationError 7 | 8 | with tmpdir() as t: 9 | print t 10 | 11 | cp('test.txt', os.path.join(t, 'test2.txt')) 12 | scp('test.txt', os.path.join(t, 'test3.txt')) 13 | try: 14 | scp('test.txt', os.path.join(t, 'test2.txt')) 15 | except FileSystemOperationError as e: 16 | print e 17 | mv(os.path.join(t, 'test2.txt'), os.path.join(t, 'test3.txt')) 18 | smv(os.path.join(t, 'test3.txt'), os.path.join(t, 'test4.txt')) 19 | try: 20 | smv('test.txt', os.path.join(t, 'test4.txt')) 21 | except FileSystemOperationError as e: 22 | print e 23 | mkdircond(os.path.join(t, 'test')) 24 | 25 | cp('test.txt', os.path.join(t, 'test', 'test2.txt')) 26 | 27 | for r, d, f in os.walk(t): 28 | print r, d 29 | print r, f 30 | 31 | emptydircond(os.path.join(t, 'test')) 32 | rmdircond(os.path.join(t, 'test')) 33 | 34 | 35 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/spc-content.less: -------------------------------------------------------------------------------- 1 | @import "spc-utils.less"; 2 | @import "bootstrap/variables.less"; 3 | 4 | .spc-page-title { 5 | h1, h2, h3, h4 { 6 | font-weight: normal; 7 | .underline; 8 | } 9 | } 10 | 11 | //tags -- depricated 12 | // need to design 13 | .tags .btn { 14 | border: none; 15 | font-size: 9.5px; 16 | font-weight: bold; 17 | } 18 | 19 | // search item specific settings 20 | .spc-search-result { 21 | &-title { 22 | h1, h2, h3, h4 { font-weight: normal; } 23 | } 24 | } 25 | 26 | // snippet specific settings 27 | .spc-snippet-header { 28 | margin-bottom: 5px; 29 | } 30 | 31 | .spc-snippet-info { 32 | padding-top: 10px; 33 | 34 | .dl-horizontal { 35 | margin: 5px; 36 | dt { font-weight: normal; } 37 | } 38 | } 39 | 40 | .spc-snippet-body { 41 | padding: 10px; 42 | 43 | .accordion-group { 44 | border: none; 45 | } 46 | 47 | .accordion-heading { 48 | text-transform: uppercase; 49 | font-size: 14px; 50 | border-bottom: 1px solid #e5e5e5; 51 | } 52 | 53 | .accordion-heading .accordion-toggle { 54 | padding-top: 10px; 55 | padding-bottom: 5px; 56 | } 57 | } 58 | -------------------------------------------------------------------------------- /doc/numpydoc/setup.py: -------------------------------------------------------------------------------- 1 | from __future__ import division, print_function 2 | 3 | import sys 4 | import setuptools 5 | from distutils.core import setup 6 | 7 | if sys.version_info[:2] < (2, 6) or (3, 0) <= sys.version_info[0:2] < (3, 3): 8 | raise RuntimeError("Python version 2.6, 2.7 or >= 3.3 required.") 9 | 10 | version = "0.6.dev" 11 | 12 | setup( 13 | name="numpydoc", 14 | packages=["numpydoc"], 15 | version=version, 16 | description="Sphinx extension to support docstrings in Numpy format", 17 | # classifiers from http://pypi.python.org/pypi?%3Aaction=list_classifiers 18 | classifiers=["Development Status :: 3 - Alpha", 19 | "Environment :: Plugins", 20 | "License :: OSI Approved :: BSD License", 21 | "Topic :: Documentation"], 22 | keywords="sphinx numpy", 23 | author="Pauli Virtanen and others", 24 | author_email="pav@iki.fi", 25 | url="https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt", 26 | license="BSD", 27 | requires=["sphinx (>= 1.0.1)"], 28 | package_data={'numpydoc': ['tests/test_*.py']}, 29 | test_suite = 'nose.collector', 30 | ) 31 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/media.less: -------------------------------------------------------------------------------- 1 | // Media objects 2 | // Source: http://stubbornella.org/content/?p=497 3 | // -------------------------------------------------- 4 | 5 | 6 | // Common styles 7 | // ------------------------- 8 | 9 | // Clear the floats 10 | .media, 11 | .media-body { 12 | overflow: hidden; 13 | *overflow: visible; 14 | zoom: 1; 15 | } 16 | 17 | // Proper spacing between instances of .media 18 | .media, 19 | .media .media { 20 | margin-top: 15px; 21 | } 22 | .media:first-child { 23 | margin-top: 0; 24 | } 25 | 26 | // For images and videos, set to block 27 | .media-object { 28 | display: block; 29 | } 30 | 31 | // Reset margins on headings for tighter default spacing 32 | .media-heading { 33 | margin: 0 0 5px; 34 | } 35 | 36 | 37 | // Media image alignment 38 | // ------------------------- 39 | 40 | .media > .pull-left { 41 | margin-right: 10px; 42 | } 43 | .media > .pull-right { 44 | margin-left: 10px; 45 | } 46 | 47 | 48 | // Media list variation 49 | // ------------------------- 50 | 51 | // Undo default ul/ol styles 52 | .media-list { 53 | margin-left: 0; 54 | list-style: none; 55 | } 56 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/scaffolding.less: -------------------------------------------------------------------------------- 1 | // 2 | // Scaffolding 3 | // -------------------------------------------------- 4 | 5 | 6 | // Body reset 7 | // ------------------------- 8 | 9 | body { 10 | margin: 0; 11 | font-family: @baseFontFamily; 12 | font-size: @baseFontSize; 13 | line-height: @baseLineHeight; 14 | color: @textColor; 15 | background-color: @bodyBackground; 16 | } 17 | 18 | 19 | // Links 20 | // ------------------------- 21 | 22 | a { 23 | color: @linkColor; 24 | text-decoration: none; 25 | } 26 | a:hover, 27 | a:focus { 28 | color: @linkColorHover; 29 | text-decoration: underline; 30 | } 31 | 32 | 33 | // Images 34 | // ------------------------- 35 | 36 | // Rounded corners 37 | .img-rounded { 38 | .border-radius(6px); 39 | } 40 | 41 | // Add polaroid-esque trim 42 | .img-polaroid { 43 | padding: 4px; 44 | background-color: #fff; 45 | border: 1px solid #ccc; 46 | border: 1px solid rgba(0,0,0,.2); 47 | .box-shadow(0 1px 3px rgba(0,0,0,.1)); 48 | } 49 | 50 | // Perfect circle 51 | .img-circle { 52 | .border-radius(500px); // crank the border-radius so it works with most reasonably sized images 53 | } 54 | -------------------------------------------------------------------------------- /test.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/python 2 | 3 | import os 4 | from neuroless.shell import tmpdir, scp, cp, mv, smv, mkdircond, emptydircond,\ 5 | rmdircond 6 | from neuroless.exceptions import FileSystemOperationError 7 | 8 | with tmpdir() as t: 9 | print t 10 | 11 | cp('test.txt', os.path.join(t, 'test2.txt')) 12 | scp('test.txt', os.path.join(t, 'test3.txt')) 13 | try: 14 | scp('test.txt', os.path.join(t, 'test2.txt')) 15 | except FileSystemOperationError as e: 16 | print e 17 | mv(os.path.join(t, 'test2.txt'), os.path.join(t, 'test3.txt')) 18 | smv(os.path.join(t, 'test3.txt'), os.path.join(t, 'test4.txt')) 19 | try: 20 | smv('test.txt', os.path.join(t, 'test4.txt')) 21 | except FileSystemOperationError as e: 22 | print e 23 | mkdircond(os.path.join(t, 'test')) 24 | 25 | cp('test.txt', os.path.join(t, 'test', 'test2.txt')) 26 | 27 | for r, d, f in os.walk(t): 28 | print r, d 29 | print r, f 30 | 31 | emptydircond(os.path.join(t, 'test')) 32 | rmdircond(os.path.join(t, 'test')) 33 | 34 | with tmpdir() as t: 35 | print t 36 | raise Exception() 37 | 38 | 39 | -------------------------------------------------------------------------------- /doc/README: -------------------------------------------------------------------------------- 1 | Building the HTML documentation 2 | ############################### 3 | 4 | Run 5 | 6 | sphinx-build -aE -b html source/ build/ 7 | 8 | , then edit .rst files belong to Python classes 9 | 10 | source/generated/neuroless.FileSet.rst 11 | source/generated/neuroless.TaskMachine.rst 12 | source/generated/neuroless.TrainedForest.rst 13 | 14 | by removing the line 15 | 16 | .. automethod:: __init__ 17 | 18 | and adding the line 19 | 20 | :toctree: generated/ 21 | 22 | beneath each ".. autosummary::" command. 23 | 24 | Additionally change all entries like 25 | 26 | ~TaskMachine.[...] 27 | 28 | to 29 | 30 | ~TaskMachine.TaskMachine.[...] 31 | 32 | Finally rerun the build 33 | 34 | sphinx-build -aE -b html source/ build/ 35 | 36 | 37 | Enabling the search box 38 | ####################### 39 | 40 | Remove 41 | 42 | scipy-sphinx-theme/_theme/scipy/searchbox.html 43 | 44 | from the scipy template, as it somehow overrides the search box with a custom link to edit the .rst files in-place online. 45 | 46 | 47 | Generate the API documentation files 48 | #################################### 49 | 50 | Run 51 | 52 | sphinx-apidoc -efF -H MedPy -A "Oskar Maier" -V 0.2 -R 1 -o generated/ ../../medpy/medpy/ 53 | 54 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/responsive.less: -------------------------------------------------------------------------------- 1 | /*! 2 | * Bootstrap Responsive v2.3.1 3 | * 4 | * Copyright 2012 Twitter, Inc 5 | * Licensed under the Apache License v2.0 6 | * http://www.apache.org/licenses/LICENSE-2.0 7 | * 8 | * Designed and built with all the love in the world @twitter by @mdo and @fat. 9 | */ 10 | 11 | 12 | // Responsive.less 13 | // For phone and tablet devices 14 | // ------------------------------------------------------------- 15 | 16 | 17 | // REPEAT VARIABLES & MIXINS 18 | // ------------------------- 19 | // Required since we compile the responsive stuff separately 20 | 21 | @import "variables.less"; // Modify this for custom colors, font-sizes, etc 22 | @import "mixins.less"; 23 | 24 | 25 | // RESPONSIVE CLASSES 26 | // ------------------ 27 | 28 | @import "responsive-utilities.less"; 29 | 30 | 31 | // MEDIA QUERIES 32 | // ------------------ 33 | 34 | // Large desktops 35 | @import "responsive-1200px-min.less"; 36 | 37 | // Tablets to regular desktops 38 | @import "responsive-768px-979px.less"; 39 | 40 | // Phones to portrait tablets and narrow desktops 41 | @import "responsive-767px-max.less"; 42 | 43 | 44 | // RESPONSIVE NAVBAR 45 | // ------------------ 46 | 47 | // From 979px and below, show a button to toggle navbar contents 48 | @import "responsive-navbar.less"; 49 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/README.rst: -------------------------------------------------------------------------------- 1 | scipy-sphinx-theme 2 | ================== 3 | 4 | `Sphinx `__ theme for `Scipy `__. 5 | 6 | 7 | Theme options 8 | ------------- 9 | 10 | The theme takes the followin options in the `html_options` 11 | configuration variable: 12 | 13 | - ``edit_link`` 14 | 15 | ``True`` or ``False``. Determines if an "edit this page" link is displayed 16 | in the left sidebar. 17 | 18 | - ``rootlinks`` 19 | 20 | List of tuples ``(url, link_name)`` to show in the beginning of the 21 | breadcrumb list on the top left. You can override it by defining an 22 | `edit_link` block in ``searchbox.html``. 23 | 24 | - ``sidebar`` 25 | 26 | One of ``"left"``, ``"right"``, ``"none"``. Defines where the sidebar 27 | should appear. 28 | 29 | - ``scipy_org_logo`` 30 | 31 | ``True`` or ``False``. Whether to plaster the scipy.org logo on top. 32 | 33 | You can use your own logo by overriding the :attr:`layout.html:header` 34 | block. 35 | 36 | - ``navigation_links`` 37 | 38 | ``True`` or ``False``. Whether to display "next", "prev", "index", etc. 39 | links. 40 | 41 | The following blocks are defined: 42 | 43 | - ``layout.html:header`` 44 | 45 | Block at the top of the page, for logo etc. 46 | 47 | - ``searchbox.html:edit_link`` 48 | 49 | Edit link HTML code to paste in the left sidebar, if `edit_link` is enabled. 50 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/thumbnails.less: -------------------------------------------------------------------------------- 1 | // 2 | // Thumbnails 3 | // -------------------------------------------------- 4 | 5 | 6 | // Note: `.thumbnails` and `.thumbnails > li` are overriden in responsive files 7 | 8 | // Make wrapper ul behave like the grid 9 | .thumbnails { 10 | margin-left: -@gridGutterWidth; 11 | list-style: none; 12 | .clearfix(); 13 | } 14 | // Fluid rows have no left margin 15 | .row-fluid .thumbnails { 16 | margin-left: 0; 17 | } 18 | 19 | // Float li to make thumbnails appear in a row 20 | .thumbnails > li { 21 | float: left; // Explicity set the float since we don't require .span* classes 22 | margin-bottom: @baseLineHeight; 23 | margin-left: @gridGutterWidth; 24 | } 25 | 26 | // The actual thumbnail (can be `a` or `div`) 27 | .thumbnail { 28 | display: block; 29 | padding: 4px; 30 | line-height: @baseLineHeight; 31 | border: 1px solid #ddd; 32 | .border-radius(@baseBorderRadius); 33 | .box-shadow(0 1px 3px rgba(0,0,0,.055)); 34 | .transition(all .2s ease-in-out); 35 | } 36 | // Add a hover/focus state for linked versions only 37 | a.thumbnail:hover, 38 | a.thumbnail:focus { 39 | border-color: @linkColor; 40 | .box-shadow(0 1px 4px rgba(0,105,214,.25)); 41 | } 42 | 43 | // Images and captions 44 | .thumbnail > img { 45 | display: block; 46 | max-width: 100%; 47 | margin-left: auto; 48 | margin-right: auto; 49 | } 50 | .thumbnail .caption { 51 | padding: 9px; 52 | color: @gray; 53 | } 54 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | TODO.txt 2 | 3 | # Images # 4 | ########## 5 | *.nii 6 | *.mhd 7 | *.raw 8 | 9 | # DOC dirs # 10 | ############ 11 | doc/build/ 12 | doc/generated/ 13 | doc/source/generated/ 14 | 15 | # BUILD dirs # 16 | ############## 17 | build/ 18 | dist/ 19 | NeuroLess.egg-info/ 20 | 21 | # Only locally used, temporary .py scripts. # 22 | ############################################# 23 | _*.py 24 | !__init__.py 25 | 26 | # Compiled source # 27 | ################### 28 | *.com 29 | *.class 30 | *.dll 31 | *.exe 32 | *.o 33 | *.so 34 | *.pyc 35 | *.pyo 36 | 37 | # Packages # 38 | ############ 39 | # it's better to unpack these files and commit the raw source 40 | # git has its own built in compression methods 41 | *.7z 42 | *.dmg 43 | *.gz 44 | *.iso 45 | *.jar 46 | *.rar 47 | *.tar 48 | *.zip 49 | 50 | # Logs and databases # 51 | ###################### 52 | *.log 53 | *.sql 54 | *.sqlite 55 | 56 | # OS generated files # 57 | ###################### 58 | .DS_Store* 59 | ehthumbs.db 60 | Icon? 61 | Thumbs.db 62 | *~ 63 | 64 | # Eclipse and PyDev project files # 65 | ################################### 66 | .project 67 | .pydevproject 68 | .settings/ 69 | .metadata/ 70 | 71 | # Suggestions by GitHub for Python projects # 72 | ############################################# 73 | # Packages 74 | *.egg 75 | *.egg-info 76 | dist 77 | build 78 | eggs 79 | parts 80 | var 81 | sdist 82 | develop-eggs 83 | .installed.cfg 84 | 85 | # Installer logs 86 | pip-log.txt 87 | 88 | # Unit test / coverage reports 89 | .coverage 90 | .tox 91 | 92 | #Translations 93 | *.mo 94 | 95 | #Mr Developer 96 | .mr.developer.cfg 97 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/code.less: -------------------------------------------------------------------------------- 1 | // 2 | // Code (inline and blocK) 3 | // -------------------------------------------------- 4 | 5 | 6 | // Inline and block code styles 7 | code, 8 | pre { 9 | padding: 0 3px 2px; 10 | #font > #family > .monospace; 11 | font-size: @baseFontSize - 2; 12 | color: @grayDark; 13 | .border-radius(3px); 14 | } 15 | 16 | // Inline code 17 | code { 18 | padding: 2px 4px; 19 | color: #d14; 20 | background-color: #f7f7f9; 21 | border: 1px solid #e1e1e8; 22 | white-space: nowrap; 23 | } 24 | 25 | // Blocks of code 26 | pre { 27 | display: block; 28 | padding: (@baseLineHeight - 1) / 2; 29 | margin: 0 0 @baseLineHeight / 2; 30 | font-size: @baseFontSize - 1; // 14px to 13px 31 | line-height: @baseLineHeight; 32 | word-break: break-all; 33 | word-wrap: break-word; 34 | white-space: pre; 35 | white-space: pre-wrap; 36 | background-color: #f5f5f5; 37 | border: 1px solid #ccc; // fallback for IE7-8 38 | border: 1px solid rgba(0,0,0,.15); 39 | .border-radius(@baseBorderRadius); 40 | 41 | // Make prettyprint styles more spaced out for readability 42 | &.prettyprint { 43 | margin-bottom: @baseLineHeight; 44 | } 45 | 46 | // Account for some code outputs that place code tags in pre tags 47 | code { 48 | padding: 0; 49 | color: inherit; 50 | white-space: pre; 51 | white-space: pre-wrap; 52 | background-color: transparent; 53 | border: 0; 54 | } 55 | } 56 | 57 | // Enable scrollable blocks of code 58 | .pre-scrollable { 59 | max-height: 340px; 60 | overflow-y: scroll; 61 | } -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/alerts.less: -------------------------------------------------------------------------------- 1 | // 2 | // Alerts 3 | // -------------------------------------------------- 4 | 5 | 6 | // Base styles 7 | // ------------------------- 8 | 9 | .alert { 10 | padding: 8px 35px 8px 14px; 11 | margin-bottom: @baseLineHeight; 12 | text-shadow: 0 1px 0 rgba(255,255,255,.5); 13 | background-color: @warningBackground; 14 | border: 1px solid @warningBorder; 15 | .border-radius(@baseBorderRadius); 16 | } 17 | .alert, 18 | .alert h4 { 19 | // Specified for the h4 to prevent conflicts of changing @headingsColor 20 | color: @warningText; 21 | } 22 | .alert h4 { 23 | margin: 0; 24 | } 25 | 26 | // Adjust close link position 27 | .alert .close { 28 | position: relative; 29 | top: -2px; 30 | right: -21px; 31 | line-height: @baseLineHeight; 32 | } 33 | 34 | 35 | // Alternate styles 36 | // ------------------------- 37 | 38 | .alert-success { 39 | background-color: @successBackground; 40 | border-color: @successBorder; 41 | color: @successText; 42 | } 43 | .alert-success h4 { 44 | color: @successText; 45 | } 46 | .alert-danger, 47 | .alert-error { 48 | background-color: @errorBackground; 49 | border-color: @errorBorder; 50 | color: @errorText; 51 | } 52 | .alert-danger h4, 53 | .alert-error h4 { 54 | color: @errorText; 55 | } 56 | .alert-info { 57 | background-color: @infoBackground; 58 | border-color: @infoBorder; 59 | color: @infoText; 60 | } 61 | .alert-info h4 { 62 | color: @infoText; 63 | } 64 | 65 | 66 | // Block alerts 67 | // ------------------------- 68 | 69 | .alert-block { 70 | padding-top: 14px; 71 | padding-bottom: 14px; 72 | } 73 | .alert-block > p, 74 | .alert-block > ul { 75 | margin-bottom: 0; 76 | } 77 | .alert-block p + p { 78 | margin-top: 5px; 79 | } 80 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/bootstrap.less: -------------------------------------------------------------------------------- 1 | /*! 2 | * Bootstrap v2.3.1 3 | * 4 | * Copyright 2012 Twitter, Inc 5 | * Licensed under the Apache License v2.0 6 | * http://www.apache.org/licenses/LICENSE-2.0 7 | * 8 | * Designed and built with all the love in the world @twitter by @mdo and @fat. 9 | */ 10 | 11 | // Core variables and mixins 12 | @import "variables.less"; // Modify this for custom colors, font-sizes, etc 13 | @import "mixins.less"; 14 | 15 | // CSS Reset 16 | @import "reset.less"; 17 | 18 | // Grid system and page structure 19 | @import "scaffolding.less"; 20 | @import "grid.less"; 21 | @import "layouts.less"; 22 | 23 | // Base CSS 24 | @import "type.less"; 25 | @import "code.less"; 26 | @import "forms.less"; 27 | @import "tables.less"; 28 | 29 | // Components: common 30 | @import "sprites.less"; 31 | @import "dropdowns.less"; 32 | @import "wells.less"; 33 | @import "component-animations.less"; 34 | @import "close.less"; 35 | 36 | // Components: Buttons & Alerts 37 | @import "buttons.less"; 38 | @import "button-groups.less"; 39 | @import "alerts.less"; // Note: alerts share common CSS with buttons and thus have styles in buttons.less 40 | 41 | // Components: Nav 42 | @import "navs.less"; 43 | @import "navbar.less"; 44 | @import "breadcrumbs.less"; 45 | @import "pagination.less"; 46 | @import "pager.less"; 47 | 48 | // Components: Popovers 49 | @import "modals.less"; 50 | @import "tooltip.less"; 51 | @import "popovers.less"; 52 | 53 | // Components: Misc 54 | @import "thumbnails.less"; 55 | @import "media.less"; 56 | @import "labels-badges.less"; 57 | @import "progress-bars.less"; 58 | @import "accordion.less"; 59 | @import "carousel.less"; 60 | @import "hero-unit.less"; 61 | 62 | // Utility classes 63 | @import "utilities.less"; // Has to be last to override when necessary 64 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/responsive-utilities.less: -------------------------------------------------------------------------------- 1 | // 2 | // Responsive: Utility classes 3 | // -------------------------------------------------- 4 | 5 | 6 | // IE10 Metro responsive 7 | // Required for Windows 8 Metro split-screen snapping with IE10 8 | // Source: http://timkadlec.com/2012/10/ie10-snap-mode-and-responsive-design/ 9 | @-ms-viewport{ 10 | width: device-width; 11 | } 12 | 13 | // Hide from screenreaders and browsers 14 | // Credit: HTML5 Boilerplate 15 | .hidden { 16 | display: none; 17 | visibility: hidden; 18 | } 19 | 20 | // Visibility utilities 21 | 22 | // For desktops 23 | .visible-phone { display: none !important; } 24 | .visible-tablet { display: none !important; } 25 | .hidden-phone { } 26 | .hidden-tablet { } 27 | .hidden-desktop { display: none !important; } 28 | .visible-desktop { display: inherit !important; } 29 | 30 | // Tablets & small desktops only 31 | @media (min-width: 768px) and (max-width: 979px) { 32 | // Hide everything else 33 | .hidden-desktop { display: inherit !important; } 34 | .visible-desktop { display: none !important ; } 35 | // Show 36 | .visible-tablet { display: inherit !important; } 37 | // Hide 38 | .hidden-tablet { display: none !important; } 39 | } 40 | 41 | // Phones only 42 | @media (max-width: 767px) { 43 | // Hide everything else 44 | .hidden-desktop { display: inherit !important; } 45 | .visible-desktop { display: none !important; } 46 | // Show 47 | .visible-phone { display: inherit !important; } // Use inherit to restore previous behavior 48 | // Hide 49 | .hidden-phone { display: none !important; } 50 | } 51 | 52 | // Print utilities 53 | .visible-print { display: none !important; } 54 | .hidden-print { } 55 | 56 | @media print { 57 | .visible-print { display: inherit !important; } 58 | .hidden-print { display: none !important; } 59 | } 60 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/tooltip.less: -------------------------------------------------------------------------------- 1 | // 2 | // Tooltips 3 | // -------------------------------------------------- 4 | 5 | 6 | // Base class 7 | .tooltip { 8 | position: absolute; 9 | z-index: @zindexTooltip; 10 | display: block; 11 | visibility: visible; 12 | font-size: 11px; 13 | line-height: 1.4; 14 | .opacity(0); 15 | &.in { .opacity(80); } 16 | &.top { margin-top: -3px; padding: 5px 0; } 17 | &.right { margin-left: 3px; padding: 0 5px; } 18 | &.bottom { margin-top: 3px; padding: 5px 0; } 19 | &.left { margin-left: -3px; padding: 0 5px; } 20 | } 21 | 22 | // Wrapper for the tooltip content 23 | .tooltip-inner { 24 | max-width: 200px; 25 | padding: 8px; 26 | color: @tooltipColor; 27 | text-align: center; 28 | text-decoration: none; 29 | background-color: @tooltipBackground; 30 | .border-radius(@baseBorderRadius); 31 | } 32 | 33 | // Arrows 34 | .tooltip-arrow { 35 | position: absolute; 36 | width: 0; 37 | height: 0; 38 | border-color: transparent; 39 | border-style: solid; 40 | } 41 | .tooltip { 42 | &.top .tooltip-arrow { 43 | bottom: 0; 44 | left: 50%; 45 | margin-left: -@tooltipArrowWidth; 46 | border-width: @tooltipArrowWidth @tooltipArrowWidth 0; 47 | border-top-color: @tooltipArrowColor; 48 | } 49 | &.right .tooltip-arrow { 50 | top: 50%; 51 | left: 0; 52 | margin-top: -@tooltipArrowWidth; 53 | border-width: @tooltipArrowWidth @tooltipArrowWidth @tooltipArrowWidth 0; 54 | border-right-color: @tooltipArrowColor; 55 | } 56 | &.left .tooltip-arrow { 57 | top: 50%; 58 | right: 0; 59 | margin-top: -@tooltipArrowWidth; 60 | border-width: @tooltipArrowWidth 0 @tooltipArrowWidth @tooltipArrowWidth; 61 | border-left-color: @tooltipArrowColor; 62 | } 63 | &.bottom .tooltip-arrow { 64 | top: 0; 65 | left: 50%; 66 | margin-left: -@tooltipArrowWidth; 67 | border-width: 0 @tooltipArrowWidth @tooltipArrowWidth; 68 | border-bottom-color: @tooltipArrowColor; 69 | } 70 | } 71 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/conf.py: -------------------------------------------------------------------------------- 1 | needs_sphinx = '1.1' 2 | 3 | extensions = ['sphinx.ext.autodoc', 'sphinx.ext.pngmath', 'numpydoc', 4 | 'sphinx.ext.intersphinx', 'sphinx.ext.coverage', 5 | 'sphinx.ext.autosummary', 'matplotlib.sphinxext.plot_directive'] 6 | 7 | templates_path = ['_templates'] 8 | source_suffix = '.rst' 9 | master_doc = 'index' 10 | project = u'scipy-sphinx-theme' 11 | copyright = u'2013, Surya Kasturi and Pauli Virtanen' 12 | version = '0.1' 13 | release = '0.1' 14 | exclude_patterns = ['_build'] 15 | pygments_style = 'sphinx' 16 | 17 | # -- Options for HTML output --------------------------------------------------- 18 | 19 | html_theme = 'scipy' 20 | html_theme_path = ['_theme'] 21 | #html_logo = '_static/scipyshiny_small.png' 22 | html_static_path = ['_static'] 23 | html_theme_options = { 24 | "edit_link": "true", 25 | "sidebar": "right", 26 | "scipy_org_logo": "false", 27 | "rootlinks": [("http://scipy.org/", "Scipy.org"), 28 | ("http://docs.scipy.org/", "Docs")] 29 | } 30 | 31 | pngmath_latex_preamble = r""" 32 | \usepackage{color} 33 | \definecolor{textgray}{RGB}{51,51,51} 34 | \color{textgray} 35 | """ 36 | pngmath_use_preview = True 37 | pngmath_dvipng_args = ['-gamma 1.5', '-D 96', '-bg Transparent'] 38 | 39 | #------------------------------------------------------------------------------ 40 | # Plot style 41 | #------------------------------------------------------------------------------ 42 | 43 | plot_pre_code = """ 44 | import numpy as np 45 | import scipy as sp 46 | np.random.seed(123) 47 | """ 48 | plot_include_source = True 49 | plot_formats = [('png', 96), 'pdf'] 50 | plot_html_show_formats = False 51 | 52 | import math 53 | phi = (math.sqrt(5) + 1)/2 54 | 55 | font_size = 13*72/96.0 # 13 px 56 | 57 | plot_rcparams = { 58 | 'font.size': font_size, 59 | 'axes.titlesize': font_size, 60 | 'axes.labelsize': font_size, 61 | 'xtick.labelsize': font_size, 62 | 'ytick.labelsize': font_size, 63 | 'legend.fontsize': font_size, 64 | 'figure.figsize': (3*phi, 3), 65 | 'figure.subplot.bottom': 0.2, 66 | 'figure.subplot.left': 0.2, 67 | 'figure.subplot.right': 0.9, 68 | 'figure.subplot.top': 0.85, 69 | 'figure.subplot.wspace': 0.4, 70 | 'text.usetex': False, 71 | } 72 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/labels-badges.less: -------------------------------------------------------------------------------- 1 | // 2 | // Labels and badges 3 | // -------------------------------------------------- 4 | 5 | 6 | // Base classes 7 | .label, 8 | .badge { 9 | display: inline-block; 10 | padding: 2px 4px; 11 | font-size: @baseFontSize * .846; 12 | font-weight: bold; 13 | line-height: 14px; // ensure proper line-height if floated 14 | color: @white; 15 | vertical-align: baseline; 16 | white-space: nowrap; 17 | text-shadow: 0 -1px 0 rgba(0,0,0,.25); 18 | background-color: @grayLight; 19 | } 20 | // Set unique padding and border-radii 21 | .label { 22 | .border-radius(3px); 23 | } 24 | .badge { 25 | padding-left: 9px; 26 | padding-right: 9px; 27 | .border-radius(9px); 28 | } 29 | 30 | // Empty labels/badges collapse 31 | .label, 32 | .badge { 33 | &:empty { 34 | display: none; 35 | } 36 | } 37 | 38 | // Hover/focus state, but only for links 39 | a { 40 | &.label:hover, 41 | &.label:focus, 42 | &.badge:hover, 43 | &.badge:focus { 44 | color: @white; 45 | text-decoration: none; 46 | cursor: pointer; 47 | } 48 | } 49 | 50 | // Colors 51 | // Only give background-color difference to links (and to simplify, we don't qualifty with `a` but [href] attribute) 52 | .label, 53 | .badge { 54 | // Important (red) 55 | &-important { background-color: @errorText; } 56 | &-important[href] { background-color: darken(@errorText, 10%); } 57 | // Warnings (orange) 58 | &-warning { background-color: @orange; } 59 | &-warning[href] { background-color: darken(@orange, 10%); } 60 | // Success (green) 61 | &-success { background-color: @successText; } 62 | &-success[href] { background-color: darken(@successText, 10%); } 63 | // Info (turquoise) 64 | &-info { background-color: @infoText; } 65 | &-info[href] { background-color: darken(@infoText, 10%); } 66 | // Inverse (black) 67 | &-inverse { background-color: @grayDark; } 68 | &-inverse[href] { background-color: darken(@grayDark, 10%); } 69 | } 70 | 71 | // Quick fix for labels/badges in buttons 72 | .btn { 73 | .label, 74 | .badge { 75 | position: relative; 76 | top: -1px; 77 | } 78 | } 79 | .btn-mini { 80 | .label, 81 | .badge { 82 | top: 0; 83 | } 84 | } 85 | -------------------------------------------------------------------------------- /neuroless/utilities.py: -------------------------------------------------------------------------------- 1 | """ 2 | ====================================== 3 | Utilities (:mod:`neuroless.utilities`) 4 | ====================================== 5 | .. currentmodule:: neuroless.utilities 6 | 7 | A number of small, internal utilities used by the NeuroLess package. 8 | 9 | .. module:: neuroless.utilities 10 | .. autosummary:: 11 | :toctree: generated/ 12 | 13 | set_qform_code 14 | set_sform_code 15 | set_qform 16 | set_sform 17 | get_qform_code 18 | get_sform_code 19 | get_affine 20 | get_qform 21 | get_sform 22 | get_diagonal 23 | 24 | """ 25 | 26 | # Copyright (C) 2013 Oskar Maier 27 | # 28 | # This program is free software: you can redistribute it and/or modify 29 | # it under the terms of the GNU General Public License as published by 30 | # the Free Software Foundation, either version 3 of the License, or 31 | # (at your option) any later version. 32 | # 33 | # This program is distributed in the hope that it will be useful, 34 | # but WITHOUT ANY WARRANTY; without even the implied warranty of 35 | # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 36 | # GNU General Public License for more details. 37 | # 38 | # You should have received a copy of the GNU General Public License 39 | # along with this program. If not, see . 40 | # 41 | # author Oskar Maier 42 | # version r0.1 43 | # since 2014-09-26 44 | # status Development 45 | 46 | # build-in module 47 | 48 | # third-party modules 49 | import numpy 50 | from medpy.io import header 51 | 52 | # own modules 53 | 54 | # constants 55 | 56 | # documentation templates 57 | 58 | # code 59 | def set_qform_code(h, v): 60 | h.get_header()['qform_code'] = v 61 | 62 | def set_sform_code(h, v): 63 | h.get_header()['sform_code'] = v 64 | 65 | def set_qform(h, v): 66 | h.set_qform(v) 67 | 68 | def set_sform(h, v): 69 | h.set_sform(v) 70 | 71 | def get_qform_code(h): 72 | return h.get_header()['qform_code'] 73 | 74 | def get_sform_code(h): 75 | return h.get_header()['sform_code'] 76 | 77 | def get_affine(h): 78 | return h.get_affine() 79 | 80 | def get_qform(h): 81 | return h.get_qform() 82 | 83 | def get_sform(h): 84 | return h.get_sform() 85 | 86 | def get_diagonal(h): 87 | return numpy.diag(list(header.get_pixel_spacing(h)) + [1]) -------------------------------------------------------------------------------- /neuroless/actions/training.py: -------------------------------------------------------------------------------- 1 | # Copyright (C) 2013 Oskar Maier 2 | # 3 | # This program is free software: you can redistribute it and/or modify 4 | # it under the terms of the GNU General Public License as published by 5 | # the Free Software Foundation, either version 3 of the License, or 6 | # (at your option) any later version. 7 | # 8 | # This program is distributed in the hope that it will be useful, 9 | # but WITHOUT ANY WARRANTY; without even the implied warranty of 10 | # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 11 | # GNU General Public License for more details. 12 | # 13 | # You should have received a copy of the GNU General Public License 14 | # along with this program. If not, see . 15 | # 16 | # author Oskar Maier 17 | # version r0.1 18 | # since 2014-10-02 19 | # status Development 20 | 21 | # build-in module 22 | import multiprocessing 23 | 24 | # third-party modules 25 | import numpy 26 | from sklearn.ensemble.forest import ExtraTreesClassifier 27 | 28 | # own modules 29 | 30 | # constants 31 | 32 | # code 33 | def trainet(trainingset, **kwargs): 34 | r""" 35 | Train an ExtraTree decision forest. 36 | 37 | Note 38 | ---- 39 | This function does not use a ``TaskMachine``. 40 | 41 | Parameters 42 | ---------- 43 | trainingset : FileSet 44 | The training set file set. 45 | **kwargs 46 | Keyword arguments to pass to the forest. 47 | 48 | Returns 49 | ------- 50 | forest : ExtraTreesClassifier 51 | A trained forest instance. 52 | """ 53 | trainingfeaturesfile = trainingset.getfile(identifier='features') 54 | trainingclassesfile = trainingset.getfile(identifier='classes') 55 | 56 | # loading training features 57 | with open(trainingfeaturesfile, 'r') as f: 58 | training_feature_vector = numpy.load(f) 59 | if 1 == training_feature_vector.ndim: 60 | training_feature_vector = numpy.expand_dims(training_feature_vector, -1) 61 | with open(trainingclassesfile , 'r') as f: 62 | training_class_vector = numpy.load(f) 63 | 64 | # prepare and train the decision forest 65 | forest = ExtraTreesClassifier(n_jobs=multiprocessing.cpu_count(), random_state=None, **kwargs) 66 | forest.fit(training_feature_vector, training_class_vector) 67 | 68 | return forest 69 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/Makefile: -------------------------------------------------------------------------------- 1 | # Makefile for Sphinx documentation 2 | # 3 | 4 | # You can set these variables from the command line. 5 | SPHINXOPTS = 6 | SPHINXBUILD = sphinx-build 7 | PAPER = 8 | BUILDDIR = _build 9 | 10 | # Internal variables. 11 | PAPEROPT_a4 = -D latex_paper_size=a4 12 | PAPEROPT_letter = -D latex_paper_size=letter 13 | ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . 14 | # the i18n builder cannot share the environment and doctrees with the others 15 | I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . 16 | 17 | .PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext all css 18 | 19 | all: html 20 | 21 | css: $(wildcard _theme/scipy/static/css/*.css) 22 | 23 | _theme/scipy/static/css/%.css: _theme/scipy/static/less/%.less 24 | lessc $^ > $@.new 25 | mv -f $@.new $@ 26 | 27 | help: 28 | @echo "Please use \`make ' where is one of" 29 | @echo " html to make standalone HTML files" 30 | @echo " dirhtml to make HTML files named index.html in directories" 31 | @echo " singlehtml to make a single large HTML file" 32 | @echo " pickle to make pickle files" 33 | @echo " json to make JSON files" 34 | @echo " htmlhelp to make HTML files and a HTML help project" 35 | @echo " qthelp to make HTML files and a qthelp project" 36 | @echo " devhelp to make HTML files and a Devhelp project" 37 | @echo " epub to make an epub" 38 | @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter" 39 | @echo " latexpdf to make LaTeX files and run them through pdflatex" 40 | @echo " text to make text files" 41 | @echo " man to make manual pages" 42 | @echo " texinfo to make Texinfo files" 43 | @echo " info to make Texinfo files and run them through makeinfo" 44 | @echo " gettext to make PO message catalogs" 45 | @echo " changes to make an overview of all changed/added/deprecated items" 46 | @echo " linkcheck to check all external links for integrity" 47 | @echo " doctest to run all doctests embedded in the documentation (if enabled)" 48 | 49 | clean: 50 | -rm -rf $(BUILDDIR)/* 51 | 52 | html: 53 | $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html 54 | @echo 55 | @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." 56 | -------------------------------------------------------------------------------- /doc/source/tutorial/simpleapplicationpipeline.rst: -------------------------------------------------------------------------------- 1 | =========================== 2 | Simple application pipeline 3 | =========================== 4 | 5 | Read in the images to segment 6 | 7 | >>> casedb = FileSet.fromdirectory(images-directory, list-of-MRI-sequences, filesource='identifiers') 8 | 9 | Check if the mapping of MRI sequence type to file name is correct 10 | 11 | >>> print 'Deducted sequence to file mapping:', traindb.filenamemapping 12 | 13 | Load a trained forest instance 14 | 15 | >>> TrainedForest.fromdirectory('directory-with-trained-forest-instance') 16 | 17 | Exdecute the pre-processing of the images are denoted by the forest instance, starting with unifying the MRI sequences 18 | 19 | >>> unified = unify('/tmp/training-workingdir/00unification', casedb, fixedsequence=forestinstance.fixedsequence, targetspacing=forestinstance.workingresolution) 20 | 21 | Compute brain masks 22 | 23 | >>> brainmasks, _ = stripskull('/tmp/training-workingdir/02skullstrip', unified, stripsequence=forestinstance.skullstripsequence) 24 | 25 | Correct the bias fields 26 | 27 | >>> biascorrected = correctbiasfields('/tmp/training-workingdir/03biasfield', unified, brainmasks) 28 | 29 | Applying intensity range models 30 | 31 | >>> standarised = percentilemodelapplication('/tmp/training-workingdir/04intensitystd', biascorrected, brainmasks, forestinstance.getintensitymodels()) 32 | 33 | Extract features 34 | 35 | >>> features, _, fnames = extractfeatures('/tmp/training-workingdir/05features', standarised, brainmasks) 36 | 37 | Segment the cases 38 | 39 | >>> segmentations, probabilities = applyforest('/tmp/training-workingdir/05segmentations', forestinstance.forest, features, brainmasks) 40 | 41 | Post-processing segmentations 42 | 43 | >>> postprocessed = postprocess('/tmp/training-workingdir/06postprocessed', segmentations, objectthreshold=1500) 44 | 45 | Re-sampling segmentations, probability maps and brain masks to original space 46 | 47 | >>> origsegmentations = resamplebyexample('directory-to-place-segmentations', postprocessed, casedb, forestinstance.fixedsequence, binary=True) 48 | >>> origprobabilities = resamplebyexample('directory-to-place-segmentations', probabilities, casedb, forestinstance.fixedsequence) 49 | >>> origbrainmasks = resamplebyexample('directory-to-place-segmentations/brainmasks', brainmasks, casedb, forestinstance.fixedsequence, binary=True) 50 | 51 | ... and it is done. 52 | 53 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/modals.less: -------------------------------------------------------------------------------- 1 | // 2 | // Modals 3 | // -------------------------------------------------- 4 | 5 | // Background 6 | .modal-backdrop { 7 | position: fixed; 8 | top: 0; 9 | right: 0; 10 | bottom: 0; 11 | left: 0; 12 | z-index: @zindexModalBackdrop; 13 | background-color: @black; 14 | // Fade for backdrop 15 | &.fade { opacity: 0; } 16 | } 17 | 18 | .modal-backdrop, 19 | .modal-backdrop.fade.in { 20 | .opacity(80); 21 | } 22 | 23 | // Base modal 24 | .modal { 25 | position: fixed; 26 | top: 10%; 27 | left: 50%; 28 | z-index: @zindexModal; 29 | width: 560px; 30 | margin-left: -280px; 31 | background-color: @white; 32 | border: 1px solid #999; 33 | border: 1px solid rgba(0,0,0,.3); 34 | *border: 1px solid #999; /* IE6-7 */ 35 | .border-radius(6px); 36 | .box-shadow(0 3px 7px rgba(0,0,0,0.3)); 37 | .background-clip(padding-box); 38 | // Remove focus outline from opened modal 39 | outline: none; 40 | 41 | &.fade { 42 | .transition(e('opacity .3s linear, top .3s ease-out')); 43 | top: -25%; 44 | } 45 | &.fade.in { top: 10%; } 46 | } 47 | .modal-header { 48 | padding: 9px 15px; 49 | border-bottom: 1px solid #eee; 50 | // Close icon 51 | .close { margin-top: 2px; } 52 | // Heading 53 | h3 { 54 | margin: 0; 55 | line-height: 30px; 56 | } 57 | } 58 | 59 | // Body (where all modal content resides) 60 | .modal-body { 61 | position: relative; 62 | overflow-y: auto; 63 | max-height: 400px; 64 | padding: 15px; 65 | } 66 | // Remove bottom margin if need be 67 | .modal-form { 68 | margin-bottom: 0; 69 | } 70 | 71 | // Footer (for actions) 72 | .modal-footer { 73 | padding: 14px 15px 15px; 74 | margin-bottom: 0; 75 | text-align: right; // right align buttons 76 | background-color: #f5f5f5; 77 | border-top: 1px solid #ddd; 78 | .border-radius(0 0 6px 6px); 79 | .box-shadow(inset 0 1px 0 @white); 80 | .clearfix(); // clear it in case folks use .pull-* classes on buttons 81 | 82 | // Properly space out buttons 83 | .btn + .btn { 84 | margin-left: 5px; 85 | margin-bottom: 0; // account for input[type="submit"] which gets the bottom margin like all other inputs 86 | } 87 | // but override that for button groups 88 | .btn-group .btn + .btn { 89 | margin-left: -1px; 90 | } 91 | // and override it for block buttons as well 92 | .btn-block + .btn-block { 93 | margin-left: 0; 94 | } 95 | } 96 | -------------------------------------------------------------------------------- /doc/numpydoc/README.rst: -------------------------------------------------------------------------------- 1 | .. image:: https://travis-ci.org/numpy/numpydoc.png?branch=master 2 | :target: https://travis-ci.org/numpy/numpydoc/ 3 | 4 | ===================================== 5 | numpydoc -- Numpy's Sphinx extensions 6 | ===================================== 7 | 8 | Numpy's documentation uses several custom extensions to Sphinx. These 9 | are shipped in this ``numpydoc`` package, in case you want to make use 10 | of them in third-party projects. 11 | 12 | The following extensions are available: 13 | 14 | - ``numpydoc``: support for the Numpy docstring format in Sphinx, and add 15 | the code description directives ``np:function``, ``np-c:function``, etc. 16 | that support the Numpy docstring syntax. 17 | 18 | - ``numpydoc.traitsdoc``: For gathering documentation about Traits attributes. 19 | 20 | - ``numpydoc.plot_directive``: Adaptation of Matplotlib's ``plot::`` 21 | directive. Note that this implementation may still undergo severe 22 | changes or eventually be deprecated. 23 | 24 | See `A Guide to NumPy/SciPy Documentation `_ 25 | for how to write docs that use this extension. 26 | 27 | 28 | numpydoc 29 | ======== 30 | 31 | Numpydoc inserts a hook into Sphinx's autodoc that converts docstrings 32 | following the Numpy/Scipy format to a form palatable to Sphinx. 33 | 34 | Options 35 | ------- 36 | 37 | The following options can be set in conf.py: 38 | 39 | - numpydoc_use_plots: bool 40 | 41 | Whether to produce ``plot::`` directives for Examples sections that 42 | contain ``import matplotlib``. 43 | 44 | - numpydoc_show_class_members: bool 45 | 46 | Whether to show all members of a class in the Methods and Attributes 47 | sections automatically. 48 | ``True`` by default. 49 | 50 | - numpydoc_show_inherited_class_members: bool 51 | 52 | Whether to show all inherited members of a class in the Methods and Attributes 53 | sections automatically. If it's false, inherited members won't shown. 54 | ``True`` by default. 55 | 56 | - numpydoc_class_members_toctree: bool 57 | 58 | Whether to create a Sphinx table of contents for the lists of class 59 | methods and attributes. If a table of contents is made, Sphinx expects 60 | each entry to have a separate page. 61 | ``True`` by default. 62 | 63 | - numpydoc_edit_link: bool (DEPRECATED -- edit your HTML template instead) 64 | 65 | Whether to insert an edit link after docstrings. 66 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/css/spc-extend.css: -------------------------------------------------------------------------------- 1 | body { 2 | background-color: #f9faf5; 3 | } 4 | .container { 5 | width: 80%; 6 | } 7 | .main { 8 | background-color: white; 9 | padding: 18px; 10 | -moz-box-shadow: 0 0 3px #888; 11 | -webkit-box-shadow: 0 0 3px #888; 12 | box-shadow: 0 0 3px #888; 13 | } 14 | .underline { 15 | border-bottom: 1.5px solid #eeeeee; 16 | } 17 | .header { 18 | margin-top: 15px; 19 | margin-bottom: 15px; 20 | margin-left: 0px; 21 | margin-right: 0px; 22 | } 23 | .spc-navbar { 24 | margin-top: 15px; 25 | margin-bottom: 5px; 26 | margin-left: 0px; 27 | margin-right: 0px; 28 | } 29 | .spc-navbar .nav-pills { 30 | margin-bottom: 0px; 31 | font-size: 12px; 32 | } 33 | .spc-navbar .nav-pills > li > a { 34 | padding-top: 2.5px; 35 | padding-bottom: 2.5px; 36 | } 37 | .underline { 38 | border-bottom: 1.5px solid #eeeeee; 39 | } 40 | .spc-page-title h1, 41 | .spc-page-title h2, 42 | .spc-page-title h3, 43 | .spc-page-title h4 { 44 | font-weight: normal; 45 | border-bottom: 1.5px solid #eeeeee; 46 | } 47 | .tags .btn { 48 | border: none; 49 | font-size: 9.5px; 50 | font-weight: bold; 51 | } 52 | .spc-search-result-title h1, 53 | .spc-search-result-title h2, 54 | .spc-search-result-title h3, 55 | .spc-search-result-title h4 { 56 | font-weight: normal; 57 | } 58 | .spc-snippet-header { 59 | margin-bottom: 5px; 60 | } 61 | .spc-snippet-info { 62 | padding-top: 10px; 63 | } 64 | .spc-snippet-info .dl-horizontal { 65 | margin: 5px; 66 | } 67 | .spc-snippet-info .dl-horizontal dt { 68 | font-weight: normal; 69 | } 70 | .spc-snippet-body { 71 | padding: 10px; 72 | } 73 | .spc-snippet-body .accordion-group { 74 | border: none; 75 | } 76 | .spc-snippet-body .accordion-heading { 77 | text-transform: uppercase; 78 | font-size: 14px; 79 | border-bottom: 1px solid #e5e5e5; 80 | } 81 | .spc-snippet-body .accordion-heading .accordion-toggle { 82 | padding-top: 10px; 83 | padding-bottom: 5px; 84 | } 85 | .spc-rightsidebar { 86 | color: #555555; 87 | } 88 | .spc-rightsidebar .navigation { 89 | padding: 2px 10px; 90 | font-size: 11.9px; 91 | } 92 | .spc-rightsidebar .navigation .nav-title { 93 | font-weight: bold; 94 | text-transform: uppercase; 95 | } 96 | .spc-rightsidebar .navigation li { 97 | margin: 5px; 98 | } 99 | .footer { 100 | padding: 5px; 101 | font-size: small; 102 | } 103 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/css/extend.css: -------------------------------------------------------------------------------- 1 | .container { 2 | width: 80%; 3 | } 4 | .navbar1 { 5 | padding-bottom: 10px; 6 | } 7 | .navbar1 .nav-pills { 8 | margin-bottom: 0px; 9 | font-size: 12px; 10 | } 11 | .navbar1 .nav-pills > li > a { 12 | padding-top: 2.5px; 13 | padding-bottom: 2.5px; 14 | } 15 | .navbar1 .dropdown.dropdown-menu { 16 | padding: 0px; 17 | } 18 | .header { 19 | padding-top: 30px; 20 | padding-bottom: 18px; 21 | } 22 | .SearchBar .form-search { 23 | margin-bottom: 0px; 24 | } 25 | .SearchBar .input-append input { 26 | height: 12px; 27 | } 28 | body { 29 | font-family: Segoe UI; 30 | background-color: #f9faf7; 31 | } 32 | .main { 33 | background-color: white; 34 | padding: 18px; 35 | -moz-box-shadow: 0 0 3px #888; 36 | -webkit-box-shadow: 0 0 3px #888; 37 | box-shadow: 0 0 3px #888; 38 | } 39 | .MainHeader h1 { 40 | font-weight: normal; 41 | } 42 | .content .contentTitle h4 { 43 | font-size: 18px; 44 | font-weight: normal; 45 | } 46 | .content .meta { 47 | font-size: small; 48 | } 49 | .tags .btn { 50 | border: none; 51 | font-size: 10px; 52 | font-weight: bold; 53 | } 54 | .navigation { 55 | font-size: 12px; 56 | padding-bottom: 12px; 57 | } 58 | .navigation .nav-title { 59 | color: #333333; 60 | font-family: "Segoe UI semibold"; 61 | font-size: 16px; 62 | text-transform: uppercase; 63 | } 64 | .navigation li { 65 | margin: 5px; 66 | } 67 | .snippetHeader { 68 | margin-bottom: 5px; 69 | } 70 | .snippetHeader .snippetTitle { 71 | font-size: 21px; 72 | line-height: 40px; 73 | border-bottom: 1px solid #e5e5e5; 74 | display: block; 75 | color: #333333; 76 | } 77 | .snippetInfo { 78 | padding-top: 10px; 79 | } 80 | .snippetInfo .dl-horizontal { 81 | margin: 5px; 82 | } 83 | .snippet-body { 84 | padding: 10px; 85 | } 86 | .snippet-body .accordion-group { 87 | border: none; 88 | } 89 | .snippet-body .accordion-heading { 90 | text-transform: uppercase; 91 | font-size: 14px; 92 | border-bottom: 1px solid #e5e5e5; 93 | } 94 | .snippet-body .accordion-heading .accordion-toggle { 95 | padding-top: 10px; 96 | padding-bottom: 5px; 97 | } 98 | .SearchResult { 99 | padding: 10px; 100 | padding-top: 0px; 101 | } 102 | .SearchResult .PageTitle { 103 | font-size: 21px; 104 | line-height: 40px; 105 | border-bottom: 1px solid #e5e5e5; 106 | padding-bottom: 5px; 107 | display: block; 108 | color: #333333; 109 | } 110 | .footer { 111 | padding: 10px; 112 | } 113 | .footer-inside { 114 | border-top: 1px solid #e5e5e5; 115 | padding: 10px; 116 | } 117 | -------------------------------------------------------------------------------- /doc/source/tutorial/simpletrainingpipeline.rst: -------------------------------------------------------------------------------- 1 | ======================== 2 | Simple training pipeline 3 | ======================== 4 | 5 | Read in the training images 6 | 7 | >>> traindb = FileSet.fromdirectory(training-images-directory, list-of-MRI-sequences, filesource='identifiers') 8 | 9 | Check if the mapping of MRI sequence type to file name is correct 10 | 11 | >>> print 'Deducted sequence to file mapping:', traindb.filenamemapping 12 | 13 | Read in the ground-truth images for each case 14 | 15 | >>> gtset = FileSet.fromdirectory(ground-truth-directory, traindb.cases, filesource='cases') 16 | 17 | Unifying MRI sequences 18 | 19 | >>> unified = unify('/tmp/training-workingdir/00unification', traindb, fixedsequence='flair') 20 | 21 | Re-sample the ground-truth accordingly 22 | 23 | >>> gtunified = resample('/tmp/training-workingdir/01gtunification', gtset, order=1) 24 | 25 | Compute brain masks 26 | 27 | >>> brainmasks, stripsequence = stripskull('/tmp/training-workingdir/02skullstrip', unified) 28 | 29 | Correct the bias fields 30 | 31 | >>> biascorrected = correctbiasfields('/tmp/training-workingdir/03biasfield', unified, brainmasks) 32 | 33 | Computing and applying intensity range models 34 | 35 | >>> standarised, intstdmodels = percentilemodelstandardisation('/tmp/training-workingdir/04intensitystd', biascorrected, brainmasks) 36 | 37 | Extract features 38 | 39 | >>> features, classes, fnames = extractfeatures('/tmp/training-workingdir/05features', standarised, brainmasks, gtunified) 40 | 41 | Sampling training-set 42 | 43 | >>> trainingset, samplepointset = sample('/tmp/training-workingdir/06samplingset', features, classes, brainmasks, sampler='stratifiedrandomsampling', nsamples=100000) 44 | 45 | Training decision forest 46 | 47 | >>> forest = trainet(trainingset, n_estimators = 200) 48 | 49 | Creating and setting forest instance 50 | 51 | >>> forestinstance = TrainedForest('directory-to-place-forest', list-of-MRI-sequences) 52 | >>> forestinstance.forest = forest 53 | >>> forestinstance.trainingimages = traindb 54 | >>> forestinstance.samplingparameters = ['stratifiedrandomsampling', 100000] 55 | >>> forestinstance.forestparameters = {'n_estimators': 200} 56 | >>> forestinstance.fixedsequence = 'flair' 57 | >>> forestinstance.workingresolution = 1 58 | >>> forestinstance.skullstripsequence = stripsequence 59 | >>> for sequence in intstdmodels.identifiers: 60 | model = intstdmodels.getfile(identifier=sequence) 61 | with open(model, 'rb') as f: 62 | forestinstance.setintensitystdmodel(sequence, pickle.load(f)) 63 | 64 | Persist forest instance 65 | 66 | >>> forestinstance.persist() 67 | 68 | ... and it is done. 69 | 70 | -------------------------------------------------------------------------------- /doc/numpydoc/numpydoc/linkcode.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | """ 3 | linkcode 4 | ~~~~~~~~ 5 | 6 | Add external links to module code in Python object descriptions. 7 | 8 | :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS. 9 | :license: BSD, see LICENSE for details. 10 | 11 | """ 12 | from __future__ import division, absolute_import, print_function 13 | 14 | import warnings 15 | import collections 16 | 17 | warnings.warn("This extension has been accepted to Sphinx upstream. " 18 | "Use the version from there (Sphinx >= 1.2) " 19 | "https://bitbucket.org/birkenfeld/sphinx/pull-request/47/sphinxextlinkcode", 20 | FutureWarning, stacklevel=1) 21 | 22 | 23 | from docutils import nodes 24 | 25 | from sphinx import addnodes 26 | from sphinx.locale import _ 27 | from sphinx.errors import SphinxError 28 | 29 | class LinkcodeError(SphinxError): 30 | category = "linkcode error" 31 | 32 | def doctree_read(app, doctree): 33 | env = app.builder.env 34 | 35 | resolve_target = getattr(env.config, 'linkcode_resolve', None) 36 | if not isinstance(env.config.linkcode_resolve, collections.Callable): 37 | raise LinkcodeError( 38 | "Function `linkcode_resolve` is not given in conf.py") 39 | 40 | domain_keys = dict( 41 | py=['module', 'fullname'], 42 | c=['names'], 43 | cpp=['names'], 44 | js=['object', 'fullname'], 45 | ) 46 | 47 | for objnode in doctree.traverse(addnodes.desc): 48 | domain = objnode.get('domain') 49 | uris = set() 50 | for signode in objnode: 51 | if not isinstance(signode, addnodes.desc_signature): 52 | continue 53 | 54 | # Convert signode to a specified format 55 | info = {} 56 | for key in domain_keys.get(domain, []): 57 | value = signode.get(key) 58 | if not value: 59 | value = '' 60 | info[key] = value 61 | if not info: 62 | continue 63 | 64 | # Call user code to resolve the link 65 | uri = resolve_target(domain, info) 66 | if not uri: 67 | # no source 68 | continue 69 | 70 | if uri in uris or not uri: 71 | # only one link per name, please 72 | continue 73 | uris.add(uri) 74 | 75 | onlynode = addnodes.only(expr='html') 76 | onlynode += nodes.reference('', '', internal=False, refuri=uri) 77 | onlynode[0] += nodes.inline('', _('[source]'), 78 | classes=['viewcode-link']) 79 | signode += onlynode 80 | 81 | def setup(app): 82 | app.connect('doctree-read', doctree_read) 83 | app.add_config_value('linkcode_resolve', None, '') 84 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/js/copybutton.js: -------------------------------------------------------------------------------- 1 | // Copyright 2014 PSF. Licensed under the PYTHON SOFTWARE FOUNDATION LICENSE VERSION 2 2 | // File originates from the cpython source found in Doc/tools/sphinxext/static/copybutton.js 3 | 4 | $(document).ready(function() { 5 | /* Add a [>>>] button on the top-right corner of code samples to hide 6 | * the >>> and ... prompts and the output and thus make the code 7 | * copyable. */ 8 | var div = $('.highlight-python .highlight,' + 9 | '.highlight-python3 .highlight') 10 | var pre = div.find('pre'); 11 | 12 | // get the styles from the current theme 13 | pre.parent().parent().css('position', 'relative'); 14 | var hide_text = 'Hide the prompts and output'; 15 | var show_text = 'Show the prompts and output'; 16 | var border_width = pre.css('border-top-width'); 17 | var border_style = pre.css('border-top-style'); 18 | var border_color = pre.css('border-top-color'); 19 | var button_styles = { 20 | 'cursor':'pointer', 'position': 'absolute', 'top': '0', 'right': '0', 21 | 'border-color': border_color, 'border-style': border_style, 22 | 'border-width': border_width, 'color': border_color, 'text-size': '75%', 23 | 'font-family': 'monospace', 'padding-left': '0.2em', 'padding-right': '0.2em', 24 | 'border-radius': '0 3px 0 0' 25 | } 26 | 27 | // create and add the button to all the code blocks that contain >>> 28 | div.each(function(index) { 29 | var jthis = $(this); 30 | if (jthis.find('.gp').length > 0) { 31 | var button = $('>>>'); 32 | button.css(button_styles) 33 | button.attr('title', hide_text); 34 | jthis.prepend(button); 35 | } 36 | // tracebacks (.gt) contain bare text elements that need to be 37 | // wrapped in a span to work with .nextUntil() (see later) 38 | jthis.find('pre:has(.gt)').contents().filter(function() { 39 | return ((this.nodeType == 3) && (this.data.trim().length > 0)); 40 | }).wrap(''); 41 | }); 42 | 43 | // define the behavior of the button when it's clicked 44 | $('.copybutton').toggle( 45 | function() { 46 | var button = $(this); 47 | button.parent().find('.go, .gp, .gt').hide(); 48 | button.next('pre').find('.gt').nextUntil('.gp, .go').css('visibility', 'hidden'); 49 | button.css('text-decoration', 'line-through'); 50 | button.attr('title', show_text); 51 | }, 52 | function() { 53 | var button = $(this); 54 | button.parent().find('.go, .gp, .gt').show(); 55 | button.next('pre').find('.gt').nextUntil('.gp, .go').css('visibility', 'visible'); 56 | button.css('text-decoration', 'none'); 57 | button.attr('title', hide_text); 58 | }); 59 | }); 60 | 61 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/pagination.less: -------------------------------------------------------------------------------- 1 | // 2 | // Pagination (multiple pages) 3 | // -------------------------------------------------- 4 | 5 | // Space out pagination from surrounding content 6 | .pagination { 7 | margin: @baseLineHeight 0; 8 | } 9 | 10 | .pagination ul { 11 | // Allow for text-based alignment 12 | display: inline-block; 13 | .ie7-inline-block(); 14 | // Reset default ul styles 15 | margin-left: 0; 16 | margin-bottom: 0; 17 | // Visuals 18 | .border-radius(@baseBorderRadius); 19 | .box-shadow(0 1px 2px rgba(0,0,0,.05)); 20 | } 21 | .pagination ul > li { 22 | display: inline; // Remove list-style and block-level defaults 23 | } 24 | .pagination ul > li > a, 25 | .pagination ul > li > span { 26 | float: left; // Collapse white-space 27 | padding: 4px 12px; 28 | line-height: @baseLineHeight; 29 | text-decoration: none; 30 | background-color: @paginationBackground; 31 | border: 1px solid @paginationBorder; 32 | border-left-width: 0; 33 | } 34 | .pagination ul > li > a:hover, 35 | .pagination ul > li > a:focus, 36 | .pagination ul > .active > a, 37 | .pagination ul > .active > span { 38 | background-color: @paginationActiveBackground; 39 | } 40 | .pagination ul > .active > a, 41 | .pagination ul > .active > span { 42 | color: @grayLight; 43 | cursor: default; 44 | } 45 | .pagination ul > .disabled > span, 46 | .pagination ul > .disabled > a, 47 | .pagination ul > .disabled > a:hover, 48 | .pagination ul > .disabled > a:focus { 49 | color: @grayLight; 50 | background-color: transparent; 51 | cursor: default; 52 | } 53 | .pagination ul > li:first-child > a, 54 | .pagination ul > li:first-child > span { 55 | border-left-width: 1px; 56 | .border-left-radius(@baseBorderRadius); 57 | } 58 | .pagination ul > li:last-child > a, 59 | .pagination ul > li:last-child > span { 60 | .border-right-radius(@baseBorderRadius); 61 | } 62 | 63 | 64 | // Alignment 65 | // -------------------------------------------------- 66 | 67 | .pagination-centered { 68 | text-align: center; 69 | } 70 | .pagination-right { 71 | text-align: right; 72 | } 73 | 74 | 75 | // Sizing 76 | // -------------------------------------------------- 77 | 78 | // Large 79 | .pagination-large { 80 | ul > li > a, 81 | ul > li > span { 82 | padding: @paddingLarge; 83 | font-size: @fontSizeLarge; 84 | } 85 | ul > li:first-child > a, 86 | ul > li:first-child > span { 87 | .border-left-radius(@borderRadiusLarge); 88 | } 89 | ul > li:last-child > a, 90 | ul > li:last-child > span { 91 | .border-right-radius(@borderRadiusLarge); 92 | } 93 | } 94 | 95 | // Small and mini 96 | .pagination-mini, 97 | .pagination-small { 98 | ul > li:first-child > a, 99 | ul > li:first-child > span { 100 | .border-left-radius(@borderRadiusSmall); 101 | } 102 | ul > li:last-child > a, 103 | ul > li:last-child > span { 104 | .border-right-radius(@borderRadiusSmall); 105 | } 106 | } 107 | 108 | // Small 109 | .pagination-small { 110 | ul > li > a, 111 | ul > li > span { 112 | padding: @paddingSmall; 113 | font-size: @fontSizeSmall; 114 | } 115 | } 116 | // Mini 117 | .pagination-mini { 118 | ul > li > a, 119 | ul > li > span { 120 | padding: @paddingMini; 121 | font-size: @fontSizeMini; 122 | } 123 | } 124 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/carousel.less: -------------------------------------------------------------------------------- 1 | // 2 | // Carousel 3 | // -------------------------------------------------- 4 | 5 | 6 | .carousel { 7 | position: relative; 8 | margin-bottom: @baseLineHeight; 9 | line-height: 1; 10 | } 11 | 12 | .carousel-inner { 13 | overflow: hidden; 14 | width: 100%; 15 | position: relative; 16 | } 17 | 18 | .carousel-inner { 19 | 20 | > .item { 21 | display: none; 22 | position: relative; 23 | .transition(.6s ease-in-out left); 24 | 25 | // Account for jankitude on images 26 | > img, 27 | > a > img { 28 | display: block; 29 | line-height: 1; 30 | } 31 | } 32 | 33 | > .active, 34 | > .next, 35 | > .prev { display: block; } 36 | 37 | > .active { 38 | left: 0; 39 | } 40 | 41 | > .next, 42 | > .prev { 43 | position: absolute; 44 | top: 0; 45 | width: 100%; 46 | } 47 | 48 | > .next { 49 | left: 100%; 50 | } 51 | > .prev { 52 | left: -100%; 53 | } 54 | > .next.left, 55 | > .prev.right { 56 | left: 0; 57 | } 58 | 59 | > .active.left { 60 | left: -100%; 61 | } 62 | > .active.right { 63 | left: 100%; 64 | } 65 | 66 | } 67 | 68 | // Left/right controls for nav 69 | // --------------------------- 70 | 71 | .carousel-control { 72 | position: absolute; 73 | top: 40%; 74 | left: 15px; 75 | width: 40px; 76 | height: 40px; 77 | margin-top: -20px; 78 | font-size: 60px; 79 | font-weight: 100; 80 | line-height: 30px; 81 | color: @white; 82 | text-align: center; 83 | background: @grayDarker; 84 | border: 3px solid @white; 85 | .border-radius(23px); 86 | .opacity(50); 87 | 88 | // we can't have this transition here 89 | // because webkit cancels the carousel 90 | // animation if you trip this while 91 | // in the middle of another animation 92 | // ;_; 93 | // .transition(opacity .2s linear); 94 | 95 | // Reposition the right one 96 | &.right { 97 | left: auto; 98 | right: 15px; 99 | } 100 | 101 | // Hover/focus state 102 | &:hover, 103 | &:focus { 104 | color: @white; 105 | text-decoration: none; 106 | .opacity(90); 107 | } 108 | } 109 | 110 | // Carousel indicator pips 111 | // ----------------------------- 112 | .carousel-indicators { 113 | position: absolute; 114 | top: 15px; 115 | right: 15px; 116 | z-index: 5; 117 | margin: 0; 118 | list-style: none; 119 | 120 | li { 121 | display: block; 122 | float: left; 123 | width: 10px; 124 | height: 10px; 125 | margin-left: 5px; 126 | text-indent: -999px; 127 | background-color: #ccc; 128 | background-color: rgba(255,255,255,.25); 129 | border-radius: 5px; 130 | } 131 | .active { 132 | background-color: #fff; 133 | } 134 | } 135 | 136 | // Caption for text below images 137 | // ----------------------------- 138 | 139 | .carousel-caption { 140 | position: absolute; 141 | left: 0; 142 | right: 0; 143 | bottom: 0; 144 | padding: 15px; 145 | background: @grayDark; 146 | background: rgba(0,0,0,.75); 147 | } 148 | .carousel-caption h4, 149 | .carousel-caption p { 150 | color: @white; 151 | line-height: @baseLineHeight; 152 | } 153 | .carousel-caption h4 { 154 | margin: 0 0 5px; 155 | } 156 | .carousel-caption p { 157 | margin-bottom: 0; 158 | } 159 | -------------------------------------------------------------------------------- /neuroless/actions/postprocessing.py: -------------------------------------------------------------------------------- 1 | # Copyright (C) 2013 Oskar Maier 2 | # 3 | # This program is free software: you can redistribute it and/or modify 4 | # it under the terms of the GNU General Public License as published by 5 | # the Free Software Foundation, either version 3 of the License, or 6 | # (at your option) any later version. 7 | # 8 | # This program is distributed in the hope that it will be useful, 9 | # but WITHOUT ANY WARRANTY; without even the implied warranty of 10 | # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 11 | # GNU General Public License for more details. 12 | # 13 | # You should have received a copy of the GNU General Public License 14 | # along with this program. If not, see . 15 | # 16 | # author Oskar Maier 17 | # version r0.1 18 | # since 2014-10-08 19 | # status Development 20 | 21 | # build-in module 22 | 23 | # third-party modules 24 | import numpy 25 | from scipy.ndimage.morphology import binary_fill_holes 26 | from medpy.io import load, header, save 27 | from medpy.filter.binary import size_threshold 28 | 29 | # own modules 30 | from .. import FileSet, TaskMachine 31 | 32 | # constants 33 | 34 | # code 35 | def postprocess(directory, inset, threshold): 36 | r""" 37 | Post-process segmentation results. 38 | 39 | Parameters 40 | ---------- 41 | directory : string 42 | Where to place the results. 43 | inset : FileSet 44 | The input file set. 45 | threshold : float 46 | All unconnected binary objects whose size in *ml* is smaller than this value are 47 | removed. 48 | 49 | Returns 50 | ------- 51 | resultset : FileSet 52 | A FilSet centered on ``directory`` and representing the post-processed segmentations. 53 | """ 54 | # prepare the task machine 55 | tm = TaskMachine(multiprocessing=True) 56 | 57 | # prepare output 58 | resultset = FileSet.fromfileset(directory, inset) 59 | 60 | # prepare and register skull-stripping tasks 61 | for case in inset.cases: 62 | src = inset.getfile(case=case) 63 | dest = resultset.getfile(case=case) 64 | tm.register([src], [dest], _postprocess, [src, dest, threshold], dict(), 'post-processing') 65 | 66 | # run 67 | tm.run() 68 | 69 | return resultset 70 | 71 | def _postprocess(src, dest, threshold): 72 | r""" 73 | Execute post-processing on a segmentation. 74 | """ 75 | # load source image 76 | img, hdr = load(src) 77 | img = img.astype(numpy.bool) 78 | 79 | # fill holes in 3D 80 | img = binary_fill_holes(img) 81 | # adapt threshold by voxel spacing 82 | threshold /= numpy.prod(header.get_pixel_spacing(hdr)) 83 | # threshold binary objects 84 | out = size_threshold(img, threshold, 'lt') 85 | # reset if last object has been removed 86 | if 0 == numpy.count_nonzero(out): 87 | out = img 88 | # fill holes in 2d 89 | out = _fill2d(out) 90 | 91 | # save 92 | save(out, dest, hdr, True) 93 | 94 | def _fill2d(arr, structure = None, dimension = 2): 95 | r""" 96 | Fill holes along a certain dimension only. 97 | """ 98 | res = numpy.zeros(arr.shape, numpy.bool) 99 | for sl in range(arr.shape[dimension]): 100 | res[:,:,sl] = binary_fill_holes(arr[:,:,sl], structure) 101 | return res 102 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/progress-bars.less: -------------------------------------------------------------------------------- 1 | // 2 | // Progress bars 3 | // -------------------------------------------------- 4 | 5 | 6 | // ANIMATIONS 7 | // ---------- 8 | 9 | // Webkit 10 | @-webkit-keyframes progress-bar-stripes { 11 | from { background-position: 40px 0; } 12 | to { background-position: 0 0; } 13 | } 14 | 15 | // Firefox 16 | @-moz-keyframes progress-bar-stripes { 17 | from { background-position: 40px 0; } 18 | to { background-position: 0 0; } 19 | } 20 | 21 | // IE9 22 | @-ms-keyframes progress-bar-stripes { 23 | from { background-position: 40px 0; } 24 | to { background-position: 0 0; } 25 | } 26 | 27 | // Opera 28 | @-o-keyframes progress-bar-stripes { 29 | from { background-position: 0 0; } 30 | to { background-position: 40px 0; } 31 | } 32 | 33 | // Spec 34 | @keyframes progress-bar-stripes { 35 | from { background-position: 40px 0; } 36 | to { background-position: 0 0; } 37 | } 38 | 39 | 40 | 41 | // THE BARS 42 | // -------- 43 | 44 | // Outer container 45 | .progress { 46 | overflow: hidden; 47 | height: @baseLineHeight; 48 | margin-bottom: @baseLineHeight; 49 | #gradient > .vertical(#f5f5f5, #f9f9f9); 50 | .box-shadow(inset 0 1px 2px rgba(0,0,0,.1)); 51 | .border-radius(@baseBorderRadius); 52 | } 53 | 54 | // Bar of progress 55 | .progress .bar { 56 | width: 0%; 57 | height: 100%; 58 | color: @white; 59 | float: left; 60 | font-size: 12px; 61 | text-align: center; 62 | text-shadow: 0 -1px 0 rgba(0,0,0,.25); 63 | #gradient > .vertical(#149bdf, #0480be); 64 | .box-shadow(inset 0 -1px 0 rgba(0,0,0,.15)); 65 | .box-sizing(border-box); 66 | .transition(width .6s ease); 67 | } 68 | .progress .bar + .bar { 69 | .box-shadow(~"inset 1px 0 0 rgba(0,0,0,.15), inset 0 -1px 0 rgba(0,0,0,.15)"); 70 | } 71 | 72 | // Striped bars 73 | .progress-striped .bar { 74 | #gradient > .striped(#149bdf); 75 | .background-size(40px 40px); 76 | } 77 | 78 | // Call animation for the active one 79 | .progress.active .bar { 80 | -webkit-animation: progress-bar-stripes 2s linear infinite; 81 | -moz-animation: progress-bar-stripes 2s linear infinite; 82 | -ms-animation: progress-bar-stripes 2s linear infinite; 83 | -o-animation: progress-bar-stripes 2s linear infinite; 84 | animation: progress-bar-stripes 2s linear infinite; 85 | } 86 | 87 | 88 | 89 | // COLORS 90 | // ------ 91 | 92 | // Danger (red) 93 | .progress-danger .bar, .progress .bar-danger { 94 | #gradient > .vertical(#ee5f5b, #c43c35); 95 | } 96 | .progress-danger.progress-striped .bar, .progress-striped .bar-danger { 97 | #gradient > .striped(#ee5f5b); 98 | } 99 | 100 | // Success (green) 101 | .progress-success .bar, .progress .bar-success { 102 | #gradient > .vertical(#62c462, #57a957); 103 | } 104 | .progress-success.progress-striped .bar, .progress-striped .bar-success { 105 | #gradient > .striped(#62c462); 106 | } 107 | 108 | // Info (teal) 109 | .progress-info .bar, .progress .bar-info { 110 | #gradient > .vertical(#5bc0de, #339bb9); 111 | } 112 | .progress-info.progress-striped .bar, .progress-striped .bar-info { 113 | #gradient > .striped(#5bc0de); 114 | } 115 | 116 | // Warning (orange) 117 | .progress-warning .bar, .progress .bar-warning { 118 | #gradient > .vertical(lighten(@orange, 15%), @orange); 119 | } 120 | .progress-warning.progress-striped .bar, .progress-striped .bar-warning { 121 | #gradient > .striped(lighten(@orange, 15%)); 122 | } 123 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/popovers.less: -------------------------------------------------------------------------------- 1 | // 2 | // Popovers 3 | // -------------------------------------------------- 4 | 5 | 6 | .popover { 7 | position: absolute; 8 | top: 0; 9 | left: 0; 10 | z-index: @zindexPopover; 11 | display: none; 12 | max-width: 276px; 13 | padding: 1px; 14 | text-align: left; // Reset given new insertion method 15 | background-color: @popoverBackground; 16 | -webkit-background-clip: padding-box; 17 | -moz-background-clip: padding; 18 | background-clip: padding-box; 19 | border: 1px solid #ccc; 20 | border: 1px solid rgba(0,0,0,.2); 21 | .border-radius(6px); 22 | .box-shadow(0 5px 10px rgba(0,0,0,.2)); 23 | 24 | // Overrides for proper insertion 25 | white-space: normal; 26 | 27 | // Offset the popover to account for the popover arrow 28 | &.top { margin-top: -10px; } 29 | &.right { margin-left: 10px; } 30 | &.bottom { margin-top: 10px; } 31 | &.left { margin-left: -10px; } 32 | } 33 | 34 | .popover-title { 35 | margin: 0; // reset heading margin 36 | padding: 8px 14px; 37 | font-size: 14px; 38 | font-weight: normal; 39 | line-height: 18px; 40 | background-color: @popoverTitleBackground; 41 | border-bottom: 1px solid darken(@popoverTitleBackground, 5%); 42 | .border-radius(5px 5px 0 0); 43 | 44 | &:empty { 45 | display: none; 46 | } 47 | } 48 | 49 | .popover-content { 50 | padding: 9px 14px; 51 | } 52 | 53 | // Arrows 54 | // 55 | // .arrow is outer, .arrow:after is inner 56 | 57 | .popover .arrow, 58 | .popover .arrow:after { 59 | position: absolute; 60 | display: block; 61 | width: 0; 62 | height: 0; 63 | border-color: transparent; 64 | border-style: solid; 65 | } 66 | .popover .arrow { 67 | border-width: @popoverArrowOuterWidth; 68 | } 69 | .popover .arrow:after { 70 | border-width: @popoverArrowWidth; 71 | content: ""; 72 | } 73 | 74 | .popover { 75 | &.top .arrow { 76 | left: 50%; 77 | margin-left: -@popoverArrowOuterWidth; 78 | border-bottom-width: 0; 79 | border-top-color: #999; // IE8 fallback 80 | border-top-color: @popoverArrowOuterColor; 81 | bottom: -@popoverArrowOuterWidth; 82 | &:after { 83 | bottom: 1px; 84 | margin-left: -@popoverArrowWidth; 85 | border-bottom-width: 0; 86 | border-top-color: @popoverArrowColor; 87 | } 88 | } 89 | &.right .arrow { 90 | top: 50%; 91 | left: -@popoverArrowOuterWidth; 92 | margin-top: -@popoverArrowOuterWidth; 93 | border-left-width: 0; 94 | border-right-color: #999; // IE8 fallback 95 | border-right-color: @popoverArrowOuterColor; 96 | &:after { 97 | left: 1px; 98 | bottom: -@popoverArrowWidth; 99 | border-left-width: 0; 100 | border-right-color: @popoverArrowColor; 101 | } 102 | } 103 | &.bottom .arrow { 104 | left: 50%; 105 | margin-left: -@popoverArrowOuterWidth; 106 | border-top-width: 0; 107 | border-bottom-color: #999; // IE8 fallback 108 | border-bottom-color: @popoverArrowOuterColor; 109 | top: -@popoverArrowOuterWidth; 110 | &:after { 111 | top: 1px; 112 | margin-left: -@popoverArrowWidth; 113 | border-top-width: 0; 114 | border-bottom-color: @popoverArrowColor; 115 | } 116 | } 117 | 118 | &.left .arrow { 119 | top: 50%; 120 | right: -@popoverArrowOuterWidth; 121 | margin-top: -@popoverArrowOuterWidth; 122 | border-right-width: 0; 123 | border-left-color: #999; // IE8 fallback 124 | border-left-color: @popoverArrowOuterColor; 125 | &:after { 126 | right: 1px; 127 | border-right-width: 0; 128 | border-left-color: @popoverArrowColor; 129 | bottom: -@popoverArrowWidth; 130 | } 131 | } 132 | 133 | } 134 | -------------------------------------------------------------------------------- /neuroless/actions/biasfieldcorrection.py: -------------------------------------------------------------------------------- 1 | # Copyright (C) 2013 Oskar Maier 2 | # 3 | # This program is free software: you can redistribute it and/or modify 4 | # it under the terms of the GNU General Public License as published by 5 | # the Free Software Foundation, either version 3 of the License, or 6 | # (at your option) any later version. 7 | # 8 | # This program is distributed in the hope that it will be useful, 9 | # but WITHOUT ANY WARRANTY; without even the implied warranty of 10 | # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 11 | # GNU General Public License for more details. 12 | # 13 | # You should have received a copy of the GNU General Public License 14 | # along with this program. If not, see . 15 | # 16 | # author Oskar Maier 17 | # version r0.1 18 | # since 2014-10-02 19 | # status Development 20 | 21 | # build-in module 22 | import itertools 23 | import os 24 | 25 | # third-party modules 26 | from medpy.io import save, load 27 | 28 | # own modules 29 | from .. import FileSet, TaskMachine 30 | from ..shell import call 31 | from ..exceptions import CommandExecutionError 32 | from ..utilities import get_affine, set_qform, set_sform, set_qform_code,\ 33 | set_sform_code 34 | 35 | # constants 36 | 37 | # code 38 | def correctbiasfields(directory, inset, brainmasks): 39 | r""" 40 | Compute and correct the bias fields of MR images. 41 | 42 | Parameters 43 | ---------- 44 | directory : string 45 | Where to place the results. 46 | inset : FileSet 47 | The input file set. 48 | brainmasks : FileSet 49 | The associated brain masks file set. 50 | 51 | Returns 52 | ------- 53 | resultset : FileSet 54 | A FileSet centered on ``directory`` and containing the bias field corrected 55 | images. 56 | """ 57 | # prepare the task machine 58 | tm = TaskMachine(multiprocessing=True) 59 | 60 | # prepare output 61 | resultset = FileSet.fromfileset(directory, inset) 62 | 63 | # register bias-field correction tasks 64 | for case, identifier in itertools.product(inset.cases, inset.identifiers): 65 | src = inset.getfile(case=case, identifier=identifier) 66 | dest = resultset.getfile(case=case, identifier=identifier) 67 | brainmaskfile = brainmasks.getfile(case=case) 68 | tm.register([src, brainmaskfile], [dest], _correctbiasfield, [src, dest, brainmaskfile], dict(), 'bias-field') 69 | 70 | # run 71 | tm.run() 72 | 73 | return resultset 74 | 75 | def _correctbiasfield(src, dest, bmask): 76 | r""" 77 | Correct the bias field of an image. 78 | 79 | Parameters 80 | ---------- 81 | src : string 82 | Path to the image to correct. 83 | dest : string 84 | Target location for the bias-field corrected image. 85 | bmask : string 86 | A binary image where the non-zero values denote the area over which to 87 | compute the bias field. 88 | """ 89 | # prepare and run skull-stripping command 90 | cmd = ['cmtk', 'mrbias', '--mask', bmask, src, dest] 91 | rtcode, stdout, stderr = call(cmd) 92 | 93 | # check if successful 94 | if not os.path.isfile(dest): 95 | raise CommandExecutionError(cmd, rtcode, stdout, stderr, 'Bias-corrected image not created.') 96 | 97 | _correctniftiheader(dest) 98 | 99 | def _correctniftiheader(image): 100 | r""" 101 | Correct the NIfTI header meta-data of a file in-place. 102 | This is usually required after an application of CMTK, as this screwes up the header. 103 | """ 104 | # correct the NIfTI header meta-data (it gets screwed up by cmtk) 105 | i, h = load(image) 106 | aff = get_affine(h) 107 | set_qform(h, aff) 108 | set_sform(h, aff) 109 | set_qform_code(h, 1) 110 | set_sform_code(h, 1) 111 | save(i, image, h, force=True) 112 | -------------------------------------------------------------------------------- /neuroless/exceptions.py: -------------------------------------------------------------------------------- 1 | """ 2 | ======================================== 3 | Exceptions (:mod:`neuroless.exceptions`) 4 | ======================================== 5 | .. currentmodule:: neuroless.exceptions 6 | 7 | Custom exceptions used by the NeuroLess package. 8 | 9 | .. module:: neuroless.exceptions 10 | .. autosummary:: 11 | :toctree: generated/ 12 | 13 | NeurolessException 14 | ConsistencyError 15 | InvalidConfigurationError 16 | TaskExecutionError 17 | FileSetExecption 18 | UnsupportedCombinationError 19 | FileSystemOperationError 20 | CommandExecutionError 21 | 22 | """ 23 | # Copyright (C) 2013 Oskar Maier 24 | # 25 | # This program is free software: you can redistribute it and/or modify 26 | # it under the terms of the GNU General Public License as published by 27 | # the Free Software Foundation, either version 3 of the License, or 28 | # (at your option) any later version. 29 | # 30 | # This program is distributed in the hope that it will be useful, 31 | # but WITHOUT ANY WARRANTY; without even the implied warranty of 32 | # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 33 | # GNU General Public License for more details. 34 | # 35 | # You should have received a copy of the GNU General Public License 36 | # along with this program. If not, see . 37 | # 38 | # author Oskar Maier 39 | # version r0.1 40 | # since 2014-10-02 41 | # status Development 42 | 43 | # build-in module 44 | 45 | # third-party modules 46 | 47 | # own modules 48 | 49 | # constants 50 | 51 | # code 52 | 53 | ######################################## 54 | 55 | class NeurolessException(BaseException): 56 | r"""Base class for all exceptions raised in the neuroless package.""" 57 | pass 58 | 59 | ######################################## 60 | 61 | class ConsistencyError(NeurolessException): 62 | r"""Raised when the structure of an object is violated.""" 63 | pass 64 | 65 | class InvalidConfigurationError(NeurolessException): 66 | r"""Raises when an invalid configuration occured in an object.""" 67 | 68 | class TaskExecutionError(NeurolessException): 69 | r"""Raises when The execution of a task failed.""" 70 | 71 | ######################################## 72 | 73 | class FileSetExecption(NeurolessException): 74 | r"""Base class for all exceptions raised by the `FileSet` class.""" 75 | pass 76 | 77 | class UnsupportedCombinationError(FileSetExecption): 78 | r"""Raise whenever an unsuported combination of case and identifier is passed to a FileSet.""" 79 | pass 80 | 81 | ######################################## 82 | 83 | class FileSystemOperationError(NeurolessException): 84 | r"""Raised when a file-system level operation failed.""" 85 | pass 86 | 87 | ######################################## 88 | 89 | class CommandExecutionError(NeurolessException): 90 | r"""Raised when the execution of a command failed to produce the expected results.""" 91 | 92 | def __init__(self, cmd, rtcode, stdout, stderr, info = ""): 93 | r""" 94 | Parameters 95 | ---------- 96 | cmd : sequence of strings 97 | The command execute as sequence of strings. 98 | rtcode : integer 99 | The return-code from the command execution. 100 | stdout : string 101 | The STDOUT message. 102 | stderr : string 103 | The STDERR message 104 | info : string 105 | Additional information string describing the error in more detail. 106 | """ 107 | message = """ 108 | Running "{}" did not produce the expected results: {} 109 | Return-code:\t{} 110 | Stdout: 111 | ------- 112 | {} 113 | ------- 114 | Stderr: 115 | ------- 116 | {} 117 | ------- 118 | """.format(' '.join(cmd), info, rtcode, stdout, stderr) 119 | super(CommandExecutionError, self).__init__(message) 120 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/css/pygments.css: -------------------------------------------------------------------------------- 1 | /* Styling for the source code listings: (mostly from pygments)*/ 2 | 3 | .highlight pre{ 4 | overflow: auto; 5 | padding: 5px; 6 | background-color: #ffffff; 7 | color: #333333; 8 | border: 1px solid #ac9; 9 | border-left: none; 10 | border-right: none; 11 | } 12 | 13 | /* Styling for pre elements: from http://perishablepress.com/press/2009/11/09/perfect-pre-tags/ */ 14 | /* no vertical scrollbars for IE 6 */ 15 | * html pre { 16 | padding-bottom:25px; 17 | overflow-y:hidden; 18 | overflow:visible; 19 | overflow-x:auto 20 | } 21 | /* no vertical scrollbars for IE 7 */ 22 | *:first-child+html pre { 23 | padding-bottom:25px; 24 | overflow-y:hidden; 25 | overflow:visible; 26 | overflow-x:auto 27 | } 28 | 29 | div#spc-section-body td.linenos pre { 30 | padding: 5px 0px; 31 | border: 0; 32 | background-color: transparent; 33 | color: #aaa; 34 | } 35 | .highlight .hll { background-color: #ffffcc } 36 | .highlight { background: #ffffff; } 37 | .highlight .c { color: #008000 } /* Comment */ 38 | .highlight .k { color: #000080; font-weight: bold } /* Keyword */ 39 | .highlight .n { color: #000000 } /* Name */ 40 | .highlight .o { color: #000000 } /* Operator */ 41 | .highlight .cm { color: #008000 } /* Comment.Multiline */ 42 | .highlight .cp { color: #008000 } /* Comment.Preproc */ 43 | .highlight .c1 { color: #008000 } /* Comment.Single */ 44 | .highlight .cs { color: #008000 } /* Comment.Special */ 45 | .highlight .kc { color: #000080; font-weight: bold } /* Keyword.Constant */ 46 | .highlight .kd { color: #000080; font-weight: bold } /* Keyword.Declaration */ 47 | .highlight .kn { color: #000080; font-weight: bold } /* Keyword.Namespace */ 48 | .highlight .kp { color: #000080; font-weight: bold } /* Keyword.Pseudo */ 49 | .highlight .kr { color: #000080; font-weight: bold } /* Keyword.Reserved */ 50 | .highlight .kt { color: #000080; font-weight: bold } /* Keyword.Type */ 51 | .highlight .m { color: #008080 } /* Literal.Number */ 52 | .highlight .s { color: #800080 } /* Literal.String */ 53 | .highlight .na { color: #000000 } /* Name.Attribute */ 54 | .highlight .nb { color: #407090 } /* Name.Builtin */ 55 | .highlight .nc { color: #0000F0; font-weight: bold } /* Name.Class */ 56 | .highlight .no { color: #000000 } /* Name.Constant */ 57 | .highlight .nd { color: #000000 } /* Name.Decorator */ 58 | .highlight .ni { color: #000000 } /* Name.Entity */ 59 | .highlight .ne { color: #000000 } /* Name.Exception */ 60 | .highlight .nf { color: #008080; font-weight: bold } /* Name.Function */ 61 | .highlight .nl { color: #000000 } /* Name.Label */ 62 | .highlight .nn { color: #000000 } /* Name.Namespace */ 63 | .highlight .nx { color: #000000 } /* Name.Other */ 64 | .highlight .py { color: #000000 } /* Name.Property */ 65 | .highlight .nt { color: #000000 } /* Name.Tag */ 66 | .highlight .nv { color: #000000 } /* Name.Variable */ 67 | .highlight .ow { color: #AA22FF; font-weight: bold } /* Operator.Word */ 68 | .highlight .mf { color: #008080 } /* Literal.Number.Float */ 69 | .highlight .mh { color: #008080 } /* Literal.Number.Hex */ 70 | .highlight .mi { color: #008080 } /* Literal.Number.Integer */ 71 | .highlight .mo { color: #008080 } /* Literal.Number.Oct */ 72 | .highlight .sb { color: #800080 } /* Literal.String.Backtick */ 73 | .highlight .sc { color: #800080 } /* Literal.String.Char */ 74 | .highlight .sd { color: #800000 } /* Literal.String.Doc */ 75 | .highlight .s2 { color: #800080 } /* Literal.String.Double */ 76 | .highlight .se { color: #800080 } /* Literal.String.Escape */ 77 | .highlight .sh { color: #800080 } /* Literal.String.Heredoc */ 78 | .highlight .si { color: #800080 } /* Literal.String.Interpol */ 79 | .highlight .sx { color: #800080 } /* Literal.String.Other */ 80 | .highlight .sr { color: #800080 } /* Literal.String.Regex */ 81 | .highlight .s1 { color: #800080 } /* Literal.String.Single */ 82 | .highlight .ss { color: #800080 } /* Literal.String.Symbol */ 83 | .highlight .bp { color: #407090 } /* Name.Builtin.Pseudo */ 84 | .highlight .vc { color: #000000 } /* Name.Variable.Class */ 85 | .highlight .vg { color: #000000 } /* Name.Variable.Global */ 86 | .highlight .vi { color: #000000 } /* Name.Variable.Instance */ 87 | .highlight .il { color: #008080 } /* Literal.Number.Integer.Long */ 88 | -------------------------------------------------------------------------------- /neuroless/actions/application.py: -------------------------------------------------------------------------------- 1 | # Copyright (C) 2013 Oskar Maier 2 | # 3 | # This program is free software: you can redistribute it and/or modify 4 | # it under the terms of the GNU General Public License as published by 5 | # the Free Software Foundation, either version 3 of the License, or 6 | # (at your option) any later version. 7 | # 8 | # This program is distributed in the hope that it will be useful, 9 | # but WITHOUT ANY WARRANTY; without even the implied warranty of 10 | # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 11 | # GNU General Public License for more details. 12 | # 13 | # You should have received a copy of the GNU General Public License 14 | # along with this program. If not, see . 15 | # 16 | # author Oskar Maier 17 | # version r0.1 18 | # since 2014-10-06 19 | # status Development 20 | 21 | # build-in module 22 | 23 | # third-party modules 24 | import numpy 25 | from medpy.io import load, save 26 | from medpy.features.utilities import join 27 | 28 | # own modules 29 | from .. import TaskMachine, FileSet 30 | 31 | # constants 32 | PROBABILITY_THRESHOLD = 0.5 33 | """The probability of belonging to the foreground a voxel must reach to be considered object.""" 34 | 35 | # code 36 | def applyforest(directory, forest, featureset, brainmasks): 37 | r""" 38 | Apply a forest to images to segment objects. 39 | 40 | Parameters 41 | ---------- 42 | directory : string 43 | Where to place the results. 44 | forest : "ForestInstance" 45 | An instance of a trained forest from ``scikit.learn``. 46 | featureset : FileSet 47 | The features of the images. 48 | brainmasks : FileSet 49 | The associated brain masks. 50 | 51 | Returns 52 | ------- 53 | segmentationset : FileSet 54 | A FileSet centered on ``directory`` and containing the segmentation masks. 55 | probabilityset : FileSet 56 | A FileSet centered on ``directory`` and containing the segmentation probabilities. 57 | """ 58 | # prepare the task machine 59 | tm = TaskMachine(multiprocessing=True) 60 | 61 | # prepare output 62 | segmentationset = FileSet(directory, featureset.cases, None, ['{}_segmentation.nii.gz'.format(c) for c in featureset.cases], 'cases', False) 63 | probabilityset = FileSet(directory, featureset.cases, None, ['{}_probability.nii.gz'.format(c) for c in featureset.cases], 'cases', False) 64 | 65 | # register forest application tasks tasks 66 | for case in featureset.cases: 67 | featurefiles = featureset.getfiles(case=case) 68 | brainmaskfile = brainmasks.getfile(case=case) 69 | segmentationfile = segmentationset.getfile(case=case) 70 | probabilityfile = probabilityset.getfile(case=case) 71 | tm.register(featurefiles + [brainmaskfile], 72 | [segmentationfile, probabilityfile], 73 | __applyforest, 74 | [forest, featurefiles, brainmaskfile, segmentationfile, probabilityfile], 75 | dict(), 76 | 'forest-application') 77 | 78 | # run 79 | tm.run() 80 | 81 | return segmentationset, probabilityset 82 | 83 | def __applyforest(forest, featurefiles, brainmaskfile, segmentationfile, probabilityfile): 84 | r"""Apply a forest using the features and save the results.""" 85 | # memory-efficient loading of the features for this case 86 | features = join(*[numpy.load(featurefile, mmap_mode='r') for featurefile in featurefiles]) 87 | if 1 == features.ndim: 88 | features = numpy.expand_dims(features, -1) 89 | 90 | # apply forest 91 | probability_results = forest.predict_proba(features)[:,1] 92 | classification_results = probability_results > PROBABILITY_THRESHOLD # equivalent to forest.predict 93 | 94 | # create result image 95 | m, h = load(brainmaskfile) 96 | m = m.astype(numpy.bool) 97 | oc = numpy.zeros(m.shape, numpy.uint8) 98 | op = numpy.zeros(m.shape, numpy.float32) 99 | oc[m] = numpy.squeeze(classification_results).ravel() 100 | op[m] = numpy.squeeze(probability_results).ravel() 101 | 102 | # saving the results 103 | save(oc, segmentationfile, h) 104 | save(op, probabilityfile, h) 105 | -------------------------------------------------------------------------------- /neuroless/actions/__init__.py: -------------------------------------------------------------------------------- 1 | """ 2 | =========================================== 3 | Pipeline actions (:mod:`neuroless.actions`) 4 | =========================================== 5 | .. currentmodule:: neuroless.actions 6 | 7 | This package contains various actions that can be used to build up a pipeline for 8 | neuroscientific image processing. Most of the actions make use of the ``TaskMachine``, 9 | and thus allow for parallel batch execution. 10 | 11 | Unify and re-sample images :mod:`neuroless.actions.unification` 12 | =============================================================== 13 | 14 | .. module:: neuroless.actions.unification 15 | .. autosummary:: 16 | :toctree: generated/ 17 | 18 | unify 19 | resample 20 | resamplebyexample 21 | 22 | Skull-stripping :mod:`neuroless.actions.skullstripping` 23 | ======================================================= 24 | 25 | .. module:: neuroless.actions.skullstripping 26 | .. autosummary:: 27 | :toctree: generated/ 28 | 29 | stripskull 30 | 31 | Bias-filed correction :mod:`neuroless.actions.biasfieldcorrection` 32 | ================================================================== 33 | 34 | .. module:: neuroless.actions.biasfieldcorrection 35 | .. autosummary:: 36 | :toctree: generated/ 37 | 38 | correctbiasfields 39 | 40 | Image intensity range standardisation :mod:`neuroless.actions.intensityrangestandardisation` 41 | ============================================================================================ 42 | 43 | .. module:: neuroless.actions.intensityrangestandardisation 44 | .. autosummary:: 45 | :toctree: generated/ 46 | 47 | percentilemodelstandardisation 48 | percentilemodelapplication 49 | 50 | 51 | Feature extraction and sampling :mod:`neuroless.actions.features` 52 | ================================================================= 53 | 54 | .. module:: neuroless.actions.features 55 | .. autosummary:: 56 | :toctree: generated/ 57 | 58 | extractfeatures 59 | sample 60 | stratifiedrandomsampling 61 | 62 | 63 | Decision forest training :mod:`neuroless.actions.training` 64 | ========================================================== 65 | 66 | .. module:: neuroless.actions.training 67 | .. autosummary:: 68 | :toctree: generated/ 69 | 70 | trainet 71 | 72 | Decision forest application :mod:`neuroless.actions.application` 73 | ================================================================ 74 | 75 | .. module:: neuroless.actions.application 76 | .. autosummary:: 77 | :toctree: generated/ 78 | 79 | applyforest 80 | 81 | Post-process segmentation results :mod:`neuroless.actions.postprocessing` 82 | ========================================================================= 83 | 84 | .. module:: neuroless.actions.postprocessing 85 | .. autosummary:: 86 | :toctree: generated/ 87 | 88 | postprocess 89 | 90 | """ 91 | 92 | # Copyright (C) 2013 Oskar Maier 93 | # 94 | # This program is free software: you can redistribute it and/or modify 95 | # it under the terms of the GNU General Public License as published by 96 | # the Free Software Foundation, either version 3 of the License, or 97 | # (at your option) any later version. 98 | # 99 | # This program is distributed in the hope that it will be useful, 100 | # but WITHOUT ANY WARRANTY; without even the implied warranty of 101 | # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 102 | # GNU General Public License for more details. 103 | # 104 | # You should have received a copy of the GNU General Public License 105 | # along with this program. If not, see . 106 | 107 | # if __all__ is not set, only the following, explicit import statements are executed 108 | from unification import unify, resample, resamplebyexample 109 | from skullstripping import stripskull 110 | from biasfieldcorrection import correctbiasfields 111 | from intensityrangestandardisation import percentilemodelstandardisation, percentilemodelapplication 112 | from features import extractfeatures, sample 113 | from training import trainet 114 | from application import applyforest 115 | from postprocessing import postprocess 116 | 117 | # import all sub-modules in the __all__ variable 118 | __all__ = [s for s in dir() if not s.startswith('_')] 119 | 120 | 121 | -------------------------------------------------------------------------------- /neuroless/actions/skullstripping.py: -------------------------------------------------------------------------------- 1 | # Copyright (C) 2013 Oskar Maier 2 | # 3 | # This program is free software: you can redistribute it and/or modify 4 | # it under the terms of the GNU General Public License as published by 5 | # the Free Software Foundation, either version 3 of the License, or 6 | # (at your option) any later version. 7 | # 8 | # This program is distributed in the hope that it will be useful, 9 | # but WITHOUT ANY WARRANTY; without even the implied warranty of 10 | # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 11 | # GNU General Public License for more details. 12 | # 13 | # You should have received a copy of the GNU General Public License 14 | # along with this program. If not, see . 15 | # 16 | # author Oskar Maier 17 | # version r0.1 18 | # since 2014-10-02 19 | # status Development 20 | 21 | # build-in module 22 | import os 23 | 24 | # third-party modules 25 | from medpy.core.logger import Logger 26 | 27 | # own modules 28 | from .. import FileSet, TaskMachine 29 | from ..shell import call, mv 30 | from ..exceptions import CommandExecutionError 31 | 32 | # constants 33 | SEQUENCE_PREFERENCES = ['t1', 't2', 'flair'] 34 | PREFERRED_FILE_SUFFIX = 'nii.gz' 35 | 36 | # code 37 | def stripskull(directory, inset, stripsequence = False): 38 | r""" 39 | Compute a brain mask for MR brain images. 40 | 41 | Parameters 42 | ---------- 43 | directory : string 44 | Where to place the results. 45 | inset : FileSet 46 | The input file set. 47 | stripsequence : False or string 48 | The sequence to use for computing the brain mask. If none supplied, the order 49 | in `~skullstripping.SEQUENCE_PREFERENCES` is respected. 50 | 51 | Returns 52 | ------- 53 | resultset : FileSet 54 | A FilSet centered on ``directory`` and representing the binary brain masks. 55 | stripsequence : string 56 | The sequence employed for the skull-stripping. 57 | """ 58 | logger = Logger.getInstance() 59 | 60 | # decide on strip-sequence 61 | if not stripsequence: 62 | for sequence in SEQUENCE_PREFERENCES: 63 | if sequence in inset.identifiers: 64 | stripsequence = sequence 65 | break 66 | if not stripsequence: 67 | stripsequence = inset.identifiers[0] 68 | logger.warning('None of the preferred sequences for skull-stripping "{}" available. Falling back to "{}"'.format(SEQUENCE_PREFERENCES, stripsequence)) 69 | elif not stripsequence in inset.identifiers: 70 | raise ValueError('The chosen skull-strip sequence "{}" is not available in the input image set.'.format(stripsequence)) 71 | 72 | # prepare the task machine 73 | tm = TaskMachine(multiprocessing=True) 74 | 75 | # prepare output 76 | resultset = FileSet(directory, inset.cases, False, ['{}.{}'.format(cid, PREFERRED_FILE_SUFFIX) for cid in inset.cases], 'cases', False) 77 | 78 | # prepare and register skull-stripping tasks 79 | for case in inset.cases: 80 | src = inset.getfile(case=case, identifier=stripsequence) 81 | dest = resultset.getfile(case=case) 82 | rfile = dest.replace('.{}'.format(PREFERRED_FILE_SUFFIX), '_mask.{}'.format(PREFERRED_FILE_SUFFIX)) 83 | tm.register([src], [dest], brainmask, [src, dest, rfile], dict(), 'skull-strip') 84 | 85 | # run 86 | tm.run() 87 | 88 | return resultset, stripsequence 89 | 90 | def brainmask(src, dest, resultfile): 91 | r""" 92 | Computes a brain mask. 93 | 94 | Parameters 95 | ---------- 96 | src : string 97 | Path to the image on which to compute the brain mask. 98 | dest : string 99 | Target location for the brain mask. 100 | resultfile : string 101 | The actual result file created by the external call. 102 | """ 103 | # prepare and run skull-stripping command 104 | cmd = ['fsl5.0-bet', src, dest, '-n', '-m', '-R'] 105 | rtcode, stdout, stderr = call(cmd) 106 | 107 | # check if successful 108 | if not os.path.isfile(resultfile): 109 | raise CommandExecutionError(cmd, rtcode, stdout, stderr, 'Brain mask image not created.') 110 | 111 | # copy 112 | mv(resultfile, dest) 113 | -------------------------------------------------------------------------------- /doc/source/tutorial/usingthescripts.rst: -------------------------------------------------------------------------------- 1 | ================= 2 | Using the scripts 3 | ================= 4 | 5 | NeuroLess comes with a number of Python command-line scripts with pre-made processing pipelines. They facilitate training a classifier to segment pathologies in brain MRI. The following example ist for ischemic stroke lesions. 6 | 7 | 8 | Preparations 9 | ------------ 10 | You will need a number of training cases with associated ground truth (20+ should do). Place the images in a folder of the following layout:: 11 | 12 | [..]//. 13 | 14 | e.g.:: 15 | 16 | path-to-training-images/01/flair.nii.gz 17 | path-to-training-images/01/t1.nii.gz 18 | path-to-training-images/02/flair.nii.gz 19 | path-to-training-images/02/t1.nii.gz 20 | path-to-training-images/03/flair.nii.gz 21 | ... 22 | 23 | The associated ground-truth is placed in its own folder:: 24 | 25 | [..]/. 26 | 27 | e.g.:: 28 | 29 | path-to-ground-truth-images/01.nii.gz 30 | path-to-ground-truth-images/02.nii.gz 31 | ... 32 | 33 | Then you'll need a directory, where you want to place your trained decision forest classifiers, lets call it ``forests``. And finally, you'll require a working directory, in which the intermediate results are placed and which will allow you to re-start the process from any pipeline-step. Note that you will need quite some disc space, depending on the file-format and the amount of training cases (with 20 cases à 2 sequences each e.g. ~1GB). 34 | 35 | 36 | Training 37 | -------- 38 | Now lets commence with the training by calling:: 39 | 40 | neuroless_train.py path-to-training-images/ path-to-ground-truth-images/ forests/mynewforest/ /tmp/workingdir/ FLAIR,T1 --fixedsequence=flair --nsamples=250000 --workingresolution=3 41 | 42 | Note here that the supplied MR sequence identifiers have to be in the same order as the files in the case folders. Simply run:: 43 | 44 | ls path-to-training-images/01/* 45 | 46 | to check the native ordering. After starting the script, you'll get an additional message along the lines of:: 47 | 48 | Deducted sequence to file mapping: {'t1': 't1.nii.gz', 'flair': 'flair.nii.gz'} 49 | 50 | to confirm the order. Kill the script when the ordering is wrong and supply it correctly. (Note: since the script uses multi-processing you might need to call ``killall neuroless_train.py``) 51 | 52 | The *neuroless_train.py* offers a wide range of settings. You can see them all when calling:: 53 | 54 | neuroless_train.py -h 55 | 56 | Here we just used ``--fixedsequence=flair`` to declare the sequence on which the ground-truth has been painted, ``--nsamples=250000`` to denote the number of samples we would like to use to the classifier training, and ``--workingresolution=3`` to define a common spacing for all sequences. 57 | 58 | Now wait (sometimes quite some time), until the neuro pipeline is finished. If everything worked out, you will find a couple of files in ``forests/mynewforest/``. If something failed, try to figure out what the error message means, correct the problem and run the command again. All successfully finished steps (identified by their respective files in ``/tmp/workingdir/``) are not execute again. 59 | 60 | In ``/tmp/workingdir/`` you can find the different intermediate results and observe the progress of the pipeline execution. 61 | 62 | 63 | Application 64 | ----------- 65 | Now we have a trained classifier for our case and want to apply it to some (formerly unseen) cases. These we place in the same layout as the training images:: 66 | 67 | [..]//. 68 | 69 | and call 70 | 71 | neuroless_apply.py path-to-images-to-segment/ forests/ directory-to-place-the-segmentations/ /tmp/workingdirapplyication/ FLAIR,T1 72 | 73 | as you can see, we need again a working directory and the sequences. Probably you have noted, that not the trained forest itself (``forests/mynewforest/``), but the parent directory is supplied. This is because the application script intelligently selects from all trained forests the best fitting for the cases at hand (according to their MRI sequences). 74 | 75 | After termination, you'll find in ``directory-to-place-the-segmentations/`` for each case the three files:: 76 | 77 | directory-to-place-the-segmentations/_segmentation.nii.gz 78 | directory-to-place-the-segmentations/_proabilities.nii.gz 79 | directory-to-place-the-segmentations/brainmasks/.nii.gz 80 | 81 | The first is the binary lesion segmentation, the second the lesion probabilities (range [0, 1]) and the third the computed brain masks. 82 | 83 | Have fun :) 84 | 85 | -------------------------------------------------------------------------------- /doc/numpydoc/numpydoc/traitsdoc.py: -------------------------------------------------------------------------------- 1 | """ 2 | ========= 3 | traitsdoc 4 | ========= 5 | 6 | Sphinx extension that handles docstrings in the Numpy standard format, [1] 7 | and support Traits [2]. 8 | 9 | This extension can be used as a replacement for ``numpydoc`` when support 10 | for Traits is required. 11 | 12 | .. [1] http://projects.scipy.org/numpy/wiki/CodingStyleGuidelines#docstring-standard 13 | .. [2] http://code.enthought.com/projects/traits/ 14 | 15 | """ 16 | from __future__ import division, absolute_import, print_function 17 | 18 | import inspect 19 | import os 20 | import pydoc 21 | import collections 22 | 23 | from . import docscrape 24 | from . import docscrape_sphinx 25 | from .docscrape_sphinx import SphinxClassDoc, SphinxFunctionDoc, SphinxDocString 26 | 27 | from . import numpydoc 28 | 29 | from . import comment_eater 30 | 31 | class SphinxTraitsDoc(SphinxClassDoc): 32 | def __init__(self, cls, modulename='', func_doc=SphinxFunctionDoc): 33 | if not inspect.isclass(cls): 34 | raise ValueError("Initialise using a class. Got %r" % cls) 35 | self._cls = cls 36 | 37 | if modulename and not modulename.endswith('.'): 38 | modulename += '.' 39 | self._mod = modulename 40 | self._name = cls.__name__ 41 | self._func_doc = func_doc 42 | 43 | docstring = pydoc.getdoc(cls) 44 | docstring = docstring.split('\n') 45 | 46 | # De-indent paragraph 47 | try: 48 | indent = min(len(s) - len(s.lstrip()) for s in docstring 49 | if s.strip()) 50 | except ValueError: 51 | indent = 0 52 | 53 | for n,line in enumerate(docstring): 54 | docstring[n] = docstring[n][indent:] 55 | 56 | self._doc = docscrape.Reader(docstring) 57 | self._parsed_data = { 58 | 'Signature': '', 59 | 'Summary': '', 60 | 'Description': [], 61 | 'Extended Summary': [], 62 | 'Parameters': [], 63 | 'Returns': [], 64 | 'Raises': [], 65 | 'Warns': [], 66 | 'Other Parameters': [], 67 | 'Traits': [], 68 | 'Methods': [], 69 | 'See Also': [], 70 | 'Notes': [], 71 | 'References': '', 72 | 'Example': '', 73 | 'Examples': '', 74 | 'index': {} 75 | } 76 | 77 | self._parse() 78 | 79 | def _str_summary(self): 80 | return self['Summary'] + [''] 81 | 82 | def _str_extended_summary(self): 83 | return self['Description'] + self['Extended Summary'] + [''] 84 | 85 | def __str__(self, indent=0, func_role="func"): 86 | out = [] 87 | out += self._str_signature() 88 | out += self._str_index() + [''] 89 | out += self._str_summary() 90 | out += self._str_extended_summary() 91 | for param_list in ('Parameters', 'Traits', 'Methods', 92 | 'Returns','Raises'): 93 | out += self._str_param_list(param_list) 94 | out += self._str_see_also("obj") 95 | out += self._str_section('Notes') 96 | out += self._str_references() 97 | out += self._str_section('Example') 98 | out += self._str_section('Examples') 99 | out = self._str_indent(out,indent) 100 | return '\n'.join(out) 101 | 102 | def looks_like_issubclass(obj, classname): 103 | """ Return True if the object has a class or superclass with the given class 104 | name. 105 | 106 | Ignores old-style classes. 107 | """ 108 | t = obj 109 | if t.__name__ == classname: 110 | return True 111 | for klass in t.__mro__: 112 | if klass.__name__ == classname: 113 | return True 114 | return False 115 | 116 | def get_doc_object(obj, what=None, config=None): 117 | if what is None: 118 | if inspect.isclass(obj): 119 | what = 'class' 120 | elif inspect.ismodule(obj): 121 | what = 'module' 122 | elif isinstance(obj, collections.Callable): 123 | what = 'function' 124 | else: 125 | what = 'object' 126 | if what == 'class': 127 | doc = SphinxTraitsDoc(obj, '', func_doc=SphinxFunctionDoc, config=config) 128 | if looks_like_issubclass(obj, 'HasTraits'): 129 | for name, trait, comment in comment_eater.get_class_traits(obj): 130 | # Exclude private traits. 131 | if not name.startswith('_'): 132 | doc['Traits'].append((name, trait, comment.splitlines())) 133 | return doc 134 | elif what in ('function', 'method'): 135 | return SphinxFunctionDoc(obj, '', config=config) 136 | else: 137 | return SphinxDocString(pydoc.getdoc(obj), config=config) 138 | 139 | def setup(app): 140 | # init numpydoc 141 | numpydoc.setup(app, get_doc_object) 142 | 143 | -------------------------------------------------------------------------------- /doc/scipy-sphinx-theme/_theme/scipy/static/less/bootstrap/responsive-767px-max.less: -------------------------------------------------------------------------------- 1 | // 2 | // Responsive: Landscape phone to desktop/tablet 3 | // -------------------------------------------------- 4 | 5 | 6 | @media (max-width: 767px) { 7 | 8 | // Padding to set content in a bit 9 | body { 10 | padding-left: 20px; 11 | padding-right: 20px; 12 | } 13 | // Negative indent the now static "fixed" navbar 14 | .navbar-fixed-top, 15 | .navbar-fixed-bottom, 16 | .navbar-static-top { 17 | margin-left: -20px; 18 | margin-right: -20px; 19 | } 20 | // Remove padding on container given explicit padding set on body 21 | .container-fluid { 22 | padding: 0; 23 | } 24 | 25 | // TYPOGRAPHY 26 | // ---------- 27 | // Reset horizontal dl 28 | .dl-horizontal { 29 | dt { 30 | float: none; 31 | clear: none; 32 | width: auto; 33 | text-align: left; 34 | } 35 | dd { 36 | margin-left: 0; 37 | } 38 | } 39 | 40 | // GRID & CONTAINERS 41 | // ----------------- 42 | // Remove width from containers 43 | .container { 44 | width: auto; 45 | } 46 | // Fluid rows 47 | .row-fluid { 48 | width: 100%; 49 | } 50 | // Undo negative margin on rows and thumbnails 51 | .row, 52 | .thumbnails { 53 | margin-left: 0; 54 | } 55 | .thumbnails > li { 56 | float: none; 57 | margin-left: 0; // Reset the default margin for all li elements when no .span* classes are present 58 | } 59 | // Make all grid-sized elements block level again 60 | [class*="span"], 61 | .uneditable-input[class*="span"], // Makes uneditable inputs full-width when using grid sizing 62 | .row-fluid [class*="span"] { 63 | float: none; 64 | display: block; 65 | width: 100%; 66 | margin-left: 0; 67 | .box-sizing(border-box); 68 | } 69 | .span12, 70 | .row-fluid .span12 { 71 | width: 100%; 72 | .box-sizing(border-box); 73 | } 74 | .row-fluid [class*="offset"]:first-child { 75 | margin-left: 0; 76 | } 77 | 78 | // FORM FIELDS 79 | // ----------- 80 | // Make span* classes full width 81 | .input-large, 82 | .input-xlarge, 83 | .input-xxlarge, 84 | input[class*="span"], 85 | select[class*="span"], 86 | textarea[class*="span"], 87 | .uneditable-input { 88 | .input-block-level(); 89 | } 90 | // But don't let it screw up prepend/append inputs 91 | .input-prepend input, 92 | .input-append input, 93 | .input-prepend input[class*="span"], 94 | .input-append input[class*="span"] { 95 | display: inline-block; // redeclare so they don't wrap to new lines 96 | width: auto; 97 | } 98 | .controls-row [class*="span"] + [class*="span"] { 99 | margin-left: 0; 100 | } 101 | 102 | // Modals 103 | .modal { 104 | position: fixed; 105 | top: 20px; 106 | left: 20px; 107 | right: 20px; 108 | width: auto; 109 | margin: 0; 110 | &.fade { top: -100px; } 111 | &.fade.in { top: 20px; } 112 | } 113 | 114 | } 115 | 116 | 117 | 118 | // UP TO LANDSCAPE PHONE 119 | // --------------------- 120 | 121 | @media (max-width: 480px) { 122 | 123 | // Smooth out the collapsing/expanding nav 124 | .nav-collapse { 125 | -webkit-transform: translate3d(0, 0, 0); // activate the GPU 126 | } 127 | 128 | // Block level the page header small tag for readability 129 | .page-header h1 small { 130 | display: block; 131 | line-height: @baseLineHeight; 132 | } 133 | 134 | // Update checkboxes for iOS 135 | input[type="checkbox"], 136 | input[type="radio"] { 137 | border: 1px solid #ccc; 138 | } 139 | 140 | // Remove the horizontal form styles 141 | .form-horizontal { 142 | .control-label { 143 | float: none; 144 | width: auto; 145 | padding-top: 0; 146 | text-align: left; 147 | } 148 | // Move over all input controls and content 149 | .controls { 150 | margin-left: 0; 151 | } 152 | // Move the options list down to align with labels 153 | .control-list { 154 | padding-top: 0; // has to be padding because margin collaspes 155 | } 156 | // Move over buttons in .form-actions to align with .controls 157 | .form-actions { 158 | padding-left: 10px; 159 | padding-right: 10px; 160 | } 161 | } 162 | 163 | // Medias 164 | // Reset float and spacing to stack 165 | .media .pull-left, 166 | .media .pull-right { 167 | float: none; 168 | display: block; 169 | margin-bottom: 10px; 170 | } 171 | // Remove side margins since we stack instead of indent 172 | .media-object { 173 | margin-right: 0; 174 | margin-left: 0; 175 | } 176 | 177 | // Modals 178 | .modal { 179 | top: 10px; 180 | left: 10px; 181 | right: 10px; 182 | } 183 | .modal-header .close { 184 | padding: 10px; 185 | margin: -10px; 186 | } 187 | 188 | // Carousel 189 | .carousel-caption { 190 | position: static; 191 | } 192 | 193 | } 194 | --------------------------------------------------------------------------------