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  44. <h1>Python Scientific Lecture Notes<a class="headerlink" href="#python-scientific-lecture-notes" title="Permalink to this headline">ΒΆ</a></h1>
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  133. <p class="topic-title first">This document</p>
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  134. <p>Teaching material on the scientific Python ecosystem, a quick
    135. 

  135. introduction to central tools and technics. The different chapters
    136. 

  136. each correspond to a 1 to 2 hours course with increasing level of
    137. 

  137. expertise, from beginner to expert.</p>
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  140. <li class="toctree-l1"><a class="reference internal" href="AUTHORS.html">Authors</a></li>
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  141. <li class="toctree-l1"><a class="reference internal" href="LICENSE.html">License</a></li>
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    147. 

  147. <ul>
    148. 

  148. <li class="toctree-l1"><a class="reference internal" href="intro/index.html">1. Getting started with Python for science</a><ul>
    149. 

  149. <li class="toctree-l2"><a class="reference internal" href="intro/intro.html">1.1. Scientific computing with tools and workflow</a><ul>
    150. 

  150. <li class="toctree-l3"><a class="reference internal" href="intro/intro.html#why-python">1.1.1. Why Python?</a></li>
    151. 

  151. <li class="toctree-l3"><a class="reference internal" href="intro/intro.html#scientific-python-building-blocks">1.1.2. Scientific Python building blocks</a></li>
    152. 

  152. <li class="toctree-l3"><a class="reference internal" href="intro/intro.html#the-interactive-workflow-ipython-and-a-text-editor">1.1.3. The interactive workflow: IPython and a text editor</a></li>
    153. 

  153. </ul>
    154. 

  154. </li>
    155. 

  155. <li class="toctree-l2"><a class="reference internal" href="intro/language/python_language.html">1.2. The Python language</a><ul>
    156. 

  156. <li class="toctree-l3"><a class="reference internal" href="intro/language/first_steps.html">1.2.1. First steps</a></li>
    157. 

  157. <li class="toctree-l3"><a class="reference internal" href="intro/language/basic_types.html">1.2.2. Basic types</a></li>
    158. 

  158. <li class="toctree-l3"><a class="reference internal" href="intro/language/assignment.html">1.2.3. Assignment operator</a></li>
    159. 

  159. <li class="toctree-l3"><a class="reference internal" href="intro/language/control_flow.html">1.2.4. Control Flow</a></li>
    160. 

  160. <li class="toctree-l3"><a class="reference internal" href="intro/language/functions.html">1.2.5. Defining functions</a></li>
    161. 

  161. <li class="toctree-l3"><a class="reference internal" href="intro/language/reusing_code.html">1.2.6. Reusing code: scripts and modules</a></li>
    162. 

  162. <li class="toctree-l3"><a class="reference internal" href="intro/language/io.html">1.2.7. Input and Output</a></li>
    163. 

  163. <li class="toctree-l3"><a class="reference internal" href="intro/language/standard_library.html">1.2.8. Standard Library</a></li>
    164. 

  164. <li class="toctree-l3"><a class="reference internal" href="intro/language/exceptions.html">1.2.9. Exceptions handling in Python</a></li>
    165. 

  165. <li class="toctree-l3"><a class="reference internal" href="intro/language/oop.html">1.2.10. Object-oriented programming (OOP)</a></li>
    166. 

  166. </ul>
    167. 

  167. </li>
    168. 

  168. <li class="toctree-l2"><a class="reference internal" href="intro/numpy/numpy.html">1.3. NumPy: creating and manipulating numerical data</a><ul>
    169. 

  169. <li class="toctree-l3"><a class="reference internal" href="intro/numpy/numpy.html#intro">1.3.1. Intro</a></li>
    170. 

  170. <li class="toctree-l3"><a class="reference internal" href="intro/numpy/numpy.html#basics-i">1.3.2. 1. Basics I</a></li>
    171. 

  171. <li class="toctree-l3"><a class="reference internal" href="intro/numpy/numpy.html#basics-ii">1.3.3. 2. Basics II</a></li>
    172. 

  172. <li class="toctree-l3"><a class="reference internal" href="intro/numpy/numpy.html#moving-on">1.3.4. 3. Moving on</a></li>
    173. 

  173. <li class="toctree-l3"><a class="reference internal" href="intro/numpy/numpy.html#under-the-hood">1.3.5. 4. Under the hood</a></li>
    174. 

  174. </ul>
    175. 

  175. </li>
    176. 

  176. <li class="toctree-l2"><a class="reference internal" href="intro/help/help.html">1.4. Getting help and finding documentation</a></li>
    177. 

  177. <li class="toctree-l2"><a class="reference internal" href="intro/matplotlib/matplotlib.html">1.5. Matplotlib</a><ul>
    178. 

  178. <li class="toctree-l3"><a class="reference internal" href="intro/matplotlib/matplotlib.html#introduction">1.5.1. Introduction</a></li>
    179. 

  179. <li class="toctree-l3"><a class="reference internal" href="intro/matplotlib/matplotlib.html#ipython">1.5.2. IPython</a></li>
    180. 

  180. <li class="toctree-l3"><a class="reference internal" href="intro/matplotlib/matplotlib.html#pylab">1.5.3. pylab</a></li>
    181. 

  181. <li class="toctree-l3"><a class="reference internal" href="intro/matplotlib/matplotlib.html#simple-plots">1.5.4. Simple Plots</a></li>
    182. 

  182. <li class="toctree-l3"><a class="reference internal" href="intro/matplotlib/matplotlib.html#properties">1.5.5. Properties</a></li>
    183. 

  183. <li class="toctree-l3"><a class="reference internal" href="intro/matplotlib/matplotlib.html#text">1.5.6. Text</a></li>
    184. 

  184. <li class="toctree-l3"><a class="reference internal" href="intro/matplotlib/matplotlib.html#ticks">1.5.7. Ticks</a></li>
    185. 

  185. <li class="toctree-l3"><a class="reference internal" href="intro/matplotlib/matplotlib.html#figures-subplots-and-axes">1.5.8. Figures, Subplots, and Axes</a></li>
    186. 

  186. <li class="toctree-l3"><a class="reference internal" href="intro/matplotlib/matplotlib.html#other-types-of-plots">1.5.9. Other Types of Plots</a></li>
    187. 

  187. <li class="toctree-l3"><a class="reference internal" href="intro/matplotlib/matplotlib.html#the-class-library">1.5.10. The Class Library</a></li>
    188. 

  188. </ul>
    189. 

  189. </li>
    190. 

  190. <li class="toctree-l2"><a class="reference internal" href="intro/scipy.html">1.6. Scipy : high-level scientific computing</a><ul>
    191. 

  191. <li class="toctree-l3"><a class="reference internal" href="intro/scipy.html#scipy-builds-upon-numpy">1.6.1. Scipy builds upon Numpy</a></li>
    192. 

  192. <li class="toctree-l3"><a class="reference internal" href="intro/scipy.html#file-input-output-scipy-io">1.6.2. File input/output: <tt class="docutils literal"><span class="pre">scipy.io</span></tt></a></li>
    193. 

  193. <li class="toctree-l3"><a class="reference internal" href="intro/scipy.html#signal-processing-scipy-signal">1.6.3. Signal processing: <tt class="docutils literal"><span class="pre">scipy.signal</span></tt></a></li>
    194. 

  194. <li class="toctree-l3"><a class="reference internal" href="intro/scipy.html#special-functions-scipy-special">1.6.4. Special functions: <tt class="docutils literal"><span class="pre">scipy.special</span></tt></a></li>
    195. 

  195. <li class="toctree-l3"><a class="reference internal" href="intro/scipy.html#statistics-and-random-numbers-scipy-stats">1.6.5. Statistics and random numbers: <tt class="docutils literal"><span class="pre">scipy.stats</span></tt></a></li>
    196. 

  196. <li class="toctree-l3"><a class="reference internal" href="intro/scipy.html#linear-algebra-operations-scipy-linalg">1.6.6. Linear algebra operations: <tt class="docutils literal"><span class="pre">scipy.linalg</span></tt></a></li>
    197. 

  197. <li class="toctree-l3"><a class="reference internal" href="intro/scipy.html#numerical-integration-scipy-integrate">1.6.7. Numerical integration: <tt class="docutils literal"><span class="pre">scipy.integrate</span></tt></a></li>
    198. 

  198. <li class="toctree-l3"><a class="reference internal" href="intro/scipy.html#fast-fourier-transforms-scipy-fftpack">1.6.8. Fast Fourier transforms: <tt class="docutils literal"><span class="pre">scipy.fftpack</span></tt></a></li>
    199. 

  199. <li class="toctree-l3"><a class="reference internal" href="intro/scipy.html#interpolation-scipy-interpolate">1.6.9. Interpolation: <tt class="docutils literal"><span class="pre">scipy.interpolate</span></tt></a></li>
    200. 

  200. <li class="toctree-l3"><a class="reference internal" href="intro/scipy.html#optimization-and-fit-scipy-optimize">1.6.10. Optimization and fit: <tt class="docutils literal"><span class="pre">scipy.optimize</span></tt></a></li>
    201. 

  201. <li class="toctree-l3"><a class="reference internal" href="intro/scipy.html#image-processing-scipy-ndimage">1.6.11. Image processing: <tt class="docutils literal"><span class="pre">scipy.ndimage</span></tt></a></li>
    202. 

  202. <li class="toctree-l3"><a class="reference internal" href="intro/scipy.html#summary-exercises-on-scientific-computing">1.6.12. Summary exercises on scientific computing</a></li>
    203. 

  203. </ul>
    204. 

  204. </li>
    205. 

  205. </ul>
    206. 

  206. </li>
    207. 

  207. <li class="toctree-l1"><a class="reference internal" href="advanced/index.html">2. Advanced topics</a><ul>
    208. 

  208. <li class="toctree-l2"><a class="reference internal" href="advanced/advanced_python/index.html">2.1. Advanced Python Constructs</a><ul>
    209. 

  209. <li class="toctree-l3"><a class="reference internal" href="advanced/advanced_python/index.html#iterators-generator-expressions-and-generators">2.1.1. Iterators, generator expressions and generators</a></li>
    210. 

  210. <li class="toctree-l3"><a class="reference internal" href="advanced/advanced_python/index.html#decorators">2.1.2. Decorators</a></li>
    211. 

  211. <li class="toctree-l3"><a class="reference internal" href="advanced/advanced_python/index.html#context-managers">2.1.3. Context managers</a></li>
    212. 

  212. </ul>
    213. 

  213. </li>
    214. 

  214. <li class="toctree-l2"><a class="reference internal" href="advanced/advanced_numpy/index.html">2.2. Advanced Numpy</a><ul>
    215. 

  215. <li class="toctree-l3"><a class="reference internal" href="advanced/advanced_numpy/index.html#life-of-ndarray">2.2.1. Life of ndarray</a></li>
    216. 

  216. <li class="toctree-l3"><a class="reference internal" href="advanced/advanced_numpy/index.html#universal-functions">2.2.2. Universal functions</a></li>
    217. 

  217. <li class="toctree-l3"><a class="reference internal" href="advanced/advanced_numpy/index.html#interoperability-features">2.2.3. Interoperability features</a></li>
    218. 

  218. <li class="toctree-l3"><a class="reference internal" href="advanced/advanced_numpy/index.html#siblings-chararray-maskedarray-matrix">2.2.4. Siblings: <tt class="docutils literal"><span class="pre">chararray</span></tt>, <tt class="docutils literal"><span class="pre">maskedarray</span></tt>, <tt class="docutils literal"><span class="pre">matrix</span></tt></a></li>
    219. 

  219. <li class="toctree-l3"><a class="reference internal" href="advanced/advanced_numpy/index.html#summary">2.2.5. Summary</a></li>
    220. 

  220. <li class="toctree-l3"><a class="reference internal" href="advanced/advanced_numpy/index.html#contributing-to-numpy-scipy">2.2.6. Contributing to Numpy/Scipy</a></li>
    221. 

  221. </ul>
    222. 

  222. </li>
    223. 

  223. <li class="toctree-l2"><a class="reference internal" href="advanced/debugging/index.html">2.3. Debugging code</a><ul>
    224. 

  224. <li class="toctree-l3"><a class="reference internal" href="advanced/debugging/index.html#avoiding-bugs">2.3.1. Avoiding bugs</a></li>
    225. 

  225. <li class="toctree-l3"><a class="reference internal" href="advanced/debugging/index.html#debugging-workflow">2.3.2. Debugging workflow</a></li>
    226. 

  226. <li class="toctree-l3"><a class="reference internal" href="advanced/debugging/index.html#using-the-python-debugger">2.3.3. Using the Python debugger</a></li>
    227. 

  227. <li class="toctree-l3"><a class="reference internal" href="advanced/debugging/index.html#debugging-segmentation-faults-using-gdb">2.3.4. Debugging segmentation faults using gdb</a></li>
    228. 

  228. </ul>
    229. 

  229. </li>
    230. 

  230. <li class="toctree-l2"><a class="reference internal" href="advanced/optimizing/index.html">2.4. Optimizing code</a><ul>
    231. 

  231. <li class="toctree-l3"><a class="reference internal" href="advanced/optimizing/index.html#optimization-workflow">2.4.1. Optimization workflow</a></li>
    232. 

  232. <li class="toctree-l3"><a class="reference internal" href="advanced/optimizing/index.html#profiling-python-code">2.4.2. Profiling Python code</a></li>
    233. 

  233. <li class="toctree-l3"><a class="reference internal" href="advanced/optimizing/index.html#making-code-go-faster">2.4.3. Making code go faster</a></li>
    234. 

  234. <li class="toctree-l3"><a class="reference internal" href="advanced/optimizing/index.html#writing-faster-numerical-code">2.4.4. Writing faster numerical code</a></li>
    235. 

  235. </ul>
    236. 

  236. </li>
    237. 

  237. <li class="toctree-l2"><a class="reference internal" href="advanced/scipy_sparse/index.html">2.5. Sparse Matrices in SciPy</a><ul>
    238. 

  238. <li class="toctree-l3"><a class="reference internal" href="advanced/scipy_sparse/introduction.html">2.5.1. Introduction</a></li>
    239. 

  239. <li class="toctree-l3"><a class="reference internal" href="advanced/scipy_sparse/storage_schemes.html">2.5.2. Storage Schemes</a></li>
    240. 

  240. <li class="toctree-l3"><a class="reference internal" href="advanced/scipy_sparse/solvers.html">2.5.3. Linear System Solvers</a></li>
    241. 

  241. <li class="toctree-l3"><a class="reference internal" href="advanced/scipy_sparse/other_packages.html">2.5.4. Other Interesting Packages</a></li>
    242. 

  242. </ul>
    243. 

  243. </li>
    244. 

  244. <li class="toctree-l2"><a class="reference internal" href="advanced/image_processing/index.html">2.6. Image manipulation and processing using Numpy and Scipy</a><ul>
    245. 

  245. <li class="toctree-l3"><a class="reference internal" href="advanced/image_processing/index.html#opening-and-writing-to-image-files">2.6.1. Opening and writing to image files</a></li>
    246. 

  246. <li class="toctree-l3"><a class="reference internal" href="advanced/image_processing/index.html#displaying-images">2.6.2. Displaying images</a></li>
    247. 

  247. <li class="toctree-l3"><a class="reference internal" href="advanced/image_processing/index.html#basic-manipulations">2.6.3. Basic manipulations</a></li>
    248. 

  248. <li class="toctree-l3"><a class="reference internal" href="advanced/image_processing/index.html#image-filtering">2.6.4. Image filtering</a></li>
    249. 

  249. <li class="toctree-l3"><a class="reference internal" href="advanced/image_processing/index.html#feature-extraction">2.6.5. Feature extraction</a></li>
    250. 

  250. <li class="toctree-l3"><a class="reference internal" href="advanced/image_processing/index.html#measuring-objects-properties">2.6.6. Measuring objects properties</a></li>
    251. 

  251. </ul>
    252. 

  252. </li>
    253. 

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    254. 

  254. <li class="toctree-l3"><a class="reference internal" href="advanced/3d_plotting/simple_example.html">2.7.1. A simple example</a></li>
    255. 

  255. <li class="toctree-l3"><a class="reference internal" href="advanced/3d_plotting/3d_plotting_functions.html">2.7.2. 3D plotting functions</a></li>
    256. 

  256. <li class="toctree-l3"><a class="reference internal" href="advanced/3d_plotting/figures_and_decorations.html">2.7.3. Figures and decorations</a></li>
    257. 

  257. <li class="toctree-l3"><a class="reference internal" href="advanced/3d_plotting/interaction.html">2.7.4. Interaction</a></li>
    258. 

  258. </ul>
    259. 

  259. </li>
    260. 

  260. <li class="toctree-l2"><a class="reference internal" href="advanced/sympy.html">2.8. Sympy : Symbolic Mathematics in Python</a><ul>
    261. 

  261. <li class="toctree-l3"><a class="reference internal" href="advanced/sympy.html#first-steps-with-sympy">2.8.1. First Steps with SymPy</a></li>
    262. 

  262. <li class="toctree-l3"><a class="reference internal" href="advanced/sympy.html#algebraic-manipulations">2.8.2. Algebraic manipulations</a></li>
    263. 

  263. <li class="toctree-l3"><a class="reference internal" href="advanced/sympy.html#calculus">2.8.3. Calculus</a></li>
    264. 

  264. <li class="toctree-l3"><a class="reference internal" href="advanced/sympy.html#equation-solving">2.8.4. Equation solving</a></li>
    265. 

  265. <li class="toctree-l3"><a class="reference internal" href="advanced/sympy.html#linear-algebra">2.8.5. Linear Algebra</a></li>
    266. 

  266. </ul>
    267. 

  267. </li>
    268. 

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    269. 

  269. <li class="toctree-l3"><a class="reference internal" href="advanced/scikit-learn/index.html#loading-an-example-dataset">2.9.1. Loading an example dataset</a></li>
    270. 

  270. <li class="toctree-l3"><a class="reference internal" href="advanced/scikit-learn/index.html#supervised-learning">2.9.2. Supervised learning</a></li>
    271. 

  271. <li class="toctree-l3"><a class="reference internal" href="advanced/scikit-learn/index.html#clustering-grouping-observations-together">2.9.3. Clustering: grouping observations together</a></li>
    272. 

  272. <li class="toctree-l3"><a class="reference internal" href="advanced/scikit-learn/index.html#putting-it-all-together-face-recognition-with-support-vector-machines">2.9.4. Putting it all together : face recognition with Support Vector Machines</a></li>
    273. 

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