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Commit 89287be0 authored by Baptiste Bauvin's avatar Baptiste Bauvin
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Merge branch 'develop' into private_algos

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......@@ -22,8 +22,8 @@ nb_folds: 2
nb_class: 3
classes:
type: ["multiview"]
algos_monoview: ["decision_tree", "adaboost", ]
algos_multiview: ["weighted_linear_late_fusion"]
algos_monoview: ["decision_tree", ]
algos_multiview: ["early_fusion_adaboost"]
stats_iter: 3
metrics:
accuracy_score: {}
......@@ -33,6 +33,11 @@ hps_type: "Random"
hps_args:
n_iter: 10
equivalent_draws: False
decision_tree:
max_depth:
Randint:
low: 1
high: 10
weighted_linear_early_fusion:
......
# -*- coding: utf-8 -*-
from __future__ import print_function, division
import time
import os
import sys
import fileinput
def findFiles(directory, files=[]):
"""scan a directory for py, pyx, pxd extension files."""
for filename in os.listdir(directory):
path = os.path.join(directory, filename)
if os.path.isfile(path) and (path.endswith(".py") or
path.endswith(".pyx") or
path.endswith(".pxd")):
if filename != "__init__.py" and filename != "version.py":
files.append(path)
elif os.path.isdir(path):
findFiles(path, files)
return files
def fileUnStamping(filename):
""" Remove stamp from a file """
is_stamp = False
for line in fileinput.input(filename, inplace=1):
if line.find("# COPYRIGHT #") != -1:
is_stamp = not is_stamp
elif not is_stamp:
print(line, end="")
def fileStamping(filename, stamp):
""" Write a stamp on a file
WARNING : The stamping must be done on an default utf8 machine !
"""
old_stamp = False # If a copyright already exist over write it.
for line in fileinput.input(filename, inplace=1):
if line.find("# COPYRIGHT #") != -1:
old_stamp = not old_stamp
elif line.startswith("# -*- coding: utf-8 -*-"):
print(line, end="")
print(stamp)
elif not old_stamp:
print(line, end="")
def getStamp(date, multimodal_version):
""" Return the corrected formated stamp """
stamp = open("copyrightstamp.txt").read()
stamp = stamp.replace("DATE", date)
stamp = stamp.replace("MULTIMODAL_VERSION", multimodal_version)
stamp = stamp.replace('\n', '\n# ')
stamp = "# " + stamp
stamp = stamp.replace("# \n", "#\n")
return stamp.strip()
def getVersionsAndDate():
""" Return (date, multimodal_version..
) """
v_text = open('VERSION').read().strip()
v_text_formted = '{"' + v_text.replace('\n', '","').replace(':', '":"')
v_text_formted += '"}'
v_dict = eval(v_text_formted)
return (time.strftime("%Y"), v_dict['multimodal'])
def writeStamp():
""" Write a copyright stamp on all files """
stamp = getStamp(*getVersionsAndDate())
files = findFiles(os.path.join(os.path.dirname(os.path.abspath(__file__)),
"multimodal"))
for filename in files:
fileStamping(filename, stamp)
fileStamping("setup.py", stamp)
def eraseStamp():
""" Erase a copyright stamp from all files """
files = findFiles(os.path.join(os.path.dirname(os.path.abspath(__file__)),
"multimodal"))
for filename in files:
fileUnStamping(filename)
fileUnStamping("setup.py")
def usage(arg):
print("Usage :")
print("\tpython %s stamping" % arg)
print("\tpython %s unstamping" % arg)
if __name__ == "__main__":
if len(sys.argv) == 1:
usage(sys.argv[0])
elif len(sys.argv) == 2:
if sys.argv[1].startswith("unstamping"):
eraseStamp()
elif sys.argv[1].startswith("stamping"):
writeStamp()
else:
usage(sys.argv[0])
else:
usage(sys.argv[0])
######### COPYRIGHT #########
Copyright(c) DATE
-----------------
* Université d'Aix Marseille (AMU) -
* Centre National de la Recherche Scientifique (CNRS) -
* Université de Toulon (UTLN).
* Copyright © 2019-2020 AMU, CNRS, UTLN
Contributors:
------------
* Sokol Koço <sokol.koco_AT_lis-lab.fr>
* Cécile Capponi <cecile.capponi_AT_univ-amu.fr>
* Dominique Benielli <dominique.benielli_AT_univ-amu.fr>
* Baptiste Bauvin <baptiste.bauvin_AT_univ-amu.fr>
Description:
-----------
Version:
-------
* multiview_generator version = MULTIMODAL_VERSION
Licence:
-------
License: New BSD License
######### COPYRIGHT #########
# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
config: 50408771402db3b72187e770c685f635
config: 4c918d26bc1f4b19df960586760ccaa9
tags: 645f666f9bcd5a90fca523b33c5a78b7
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<p><img alt="Pipeline status" src="https://gitlab.lis-lab.fr/baptiste.bauvin/summit/badges/master/pipeline.svg" /> <a class="reference external" href="http://www.gnu.org/licenses/gpl-3.0"><img alt="License: GPL v3" src="https://img.shields.io/badge/License-GPL%20v3-blue.svg" /></a> <a class="reference external" href="http://baptiste.bauvin.pages.lis-lab.fr/summit/coverage/index.html"><img alt="Coverage" src="https://gitlab.lis-lab.fr/baptiste.bauvin/summit/badges/master/coverage.svg" /></a></p>
<div class="section" id="supervised-multimodal-integration-tool-s-readme">
<h1>Supervised MultiModal Integration Tool’s Readme<a class="headerlink" href="#supervised-multimodal-integration-tool-s-readme" title="Permalink to this headline"></a></h1>
<p>This project aims to be an easy-to-use solution to run a prior benchmark on a dataset and evaluate mono- &amp; multi-view algorithms capacity to classify it correctly.</p>
<div class="section" id="getting-started">
<h2>Getting Started<a class="headerlink" href="#getting-started" title="Permalink to this headline"></a></h2>
<p>SuMMIT has been designed and uses continuous integration for Linux platforms (ubuntu 18.04), but we try to keep it as compatible as possible with Mac and Windows.</p>
<table border="1" class="docutils">
<colgroup>
<col width="34%" />
<col width="66%" />
</colgroup>
<thead valign="bottom">
<tr class="row-odd"><th class="head">Platform</th>
<th class="head">Last positive test</th>
</tr>
</thead>
<tbody valign="top">
<tr class="row-even"><td>Linux</td>
<td><img alt="Pipeline status" src="https://gitlab.lis-lab.fr/baptiste.bauvin/summit/badges/master/pipeline.svg" /></td>
</tr>
<tr class="row-odd"><td>Mac</td>
<td>1st of May, 2020</td>
</tr>
<tr class="row-even"><td>Windows</td>
<td>1st of May, 2020</td>
</tr>
</tbody>
</table>
<div class="section" id="prerequisites">
<h3>Prerequisites<a class="headerlink" href="#prerequisites" title="Permalink to this headline"></a></h3>
<p>To be able to use this project, you’ll need :</p>
<ul class="simple">
<li><a class="reference external" href="https://docs.python.org/3/">Python 3</a></li>
</ul>
<p>And the following python modules will be automatically installed :</p>
<ul class="simple">
<li><a class="reference external" href="http://www.numpy.org/">numpy</a>, <a class="reference external" href="https://scipy.org/">scipy</a>,</li>
<li><a class="reference external" href="http://matplotlib.org/">matplotlib</a> - Used to plot results,</li>
<li><a class="reference external" href="http://scikit-learn.org/stable/">sklearn</a> - Used for the monoview classifiers,</li>
<li><a class="reference external" href="https://pypi.python.org/pypi/joblib">joblib</a> - Used to compute on multiple threads,</li>
<li><a class="reference external" href="https://www.h5py.org">h5py</a> - Used to generate HDF5 datasets on hard drive and use them to spare RAM,</li>
<li><a class="reference external" href="https://docs.python.org/3/library/pickle.html">pickle</a> - Used to store some results,</li>
<li><a class="reference external" href="https://pandas.pydata.org/">pandas</a> - Used to manipulate data efficiently,</li>
<li><a class="reference external" href="https://pypi.org/project/six/">six</a> -</li>
<li><a class="reference external" href="https://pypi.org/project/m2r/">m2r</a> - Used to generate documentation from the readme,</li>
<li><a class="reference external" href="https://pypi.org/project/docutils/">docutils</a> - Used to generate documentation,</li>
<li><a class="reference external" href="https://pypi.org/project/PyYAML/">pyyaml</a> - Used to read the config files,</li>
<li><a class="reference external" href="https://plot.ly/">plotly</a> - Used to generate interactive HTML visuals,</li>
<li><a class="reference external" href="https://pypi.org/project/tabulate/">tabulate</a> - Used to generated the confusion matrix.</li>
</ul>
</div>
<div class="section" id="installing">
<h3>Installing<a class="headerlink" href="#installing" title="Permalink to this headline"></a></h3>
<p>Once you cloned the project from the <a class="reference external" href="https://gitlab.lis-lab.fr/baptiste.bauvin/summit/">gitlab repository</a>, you just have to use :</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">cd</span> path/to/summit/
pip install -e .
</pre></div>
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<p>In the <cite>summit</cite> directory to install SuMMIT and its dependencies.</p>
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<div class="section" id="running-the-tests">
<h3>Running the tests<a class="headerlink" href="#running-the-tests" title="Permalink to this headline"></a></h3>
<p>To run the test suite of SuMMIT, run :</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">cd</span> path/to/summit
pip install -e .<span class="o">[</span>dev<span class="o">]</span>
pytest
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<div class="section" id="building-the-documentation">
<h3>Building the documentation<a class="headerlink" href="#building-the-documentation" title="Permalink to this headline"></a></h3>
<p>To locally build the <a class="reference external" href="http://baptiste.bauvin.pages.lis-lab.fr/summit/index.html">documentation</a> run :</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">cd</span> path/to/summit
pip install -e .<span class="o">[</span>doc<span class="o">]</span>
python setup.py build_sphinx
</pre></div>
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<p>The built html files will be stored in <code class="docutils literal notranslate"><span class="pre">path/to/summit/build/sphinx/html</span></code></p>
</div>
<div class="clearer"></div>
<div class="section" id="running-on-simulated-data">
<h3>Running on simulated data<a class="headerlink" href="#running-on-simulated-data" title="Permalink to this headline"></a></h3>
<p>For your first go with SuMMIT, you can run it on simulated data with</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>python
&gt;&gt;&gt; from summit.execute import execute
&gt;&gt;&gt; execute<span class="o">(</span><span class="s2">&quot;example 1&quot;</span><span class="o">)</span>
</pre></div>
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<p>This will run the benchmark of <a class="reference external" href="http://baptiste.bauvin.pages.lis-lab.fr/summit/tutorials/example1.html">documentation’s Example 1</a>.</p>
<p>For more information about the examples, see the <a class="reference external" href="http://baptiste.bauvin.pages.lis-lab.fr/summit/index.html">documentation</a>.
Results will, by default, be stored in the results directory of the installation path :
<code class="docutils literal notranslate"><span class="pre">path/to/summit/multiview_platform/examples/results</span></code>.</p>
<p>The documentation proposes a detailed interpretation of the results and arguments of SuMMIT through <a class="reference external" href="http://baptiste.bauvin.pages.lis-lab.fr/summit/">6 tutorials</a>.</p>
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<div class="section" id="dataset-compatibility">
<h3>Dataset compatibility<a class="headerlink" href="#dataset-compatibility" title="Permalink to this headline"></a></h3>
<p>In order to start a benchmark on your own dataset, you need to format it so SuMMIT can use it. To do so, a <a class="reference external" href="https://gitlab.lis-lab.fr/baptiste.bauvin/summit/-/blob/master/format_dataset.py">python script</a> is provided.</p>
<p>For more information, see <a class="reference external" href="http://baptiste.bauvin.pages.lis-lab.fr/summit/tutorials/example5.html">Example 5</a></p>
<div class="section" id="running-on-your-dataset">
<h4>Running on your dataset<a class="headerlink" href="#running-on-your-dataset" title="Permalink to this headline"></a></h4>
<p>Once you have formatted your dataset, to run SuMMIT on it you need to modify the config file as</p>
<div class="highlight-yaml notranslate"><div class="highlight"><pre><span></span><span class="nt">name</span><span class="p">:</span> <span class="p p-Indicator">[</span><span class="s">&quot;your_file_name&quot;</span><span class="p p-Indicator">]</span>
<span class="nt">pathf</span><span class="p">:</span> <span class="s">&quot;path/to/your/dataset&quot;</span>
</pre></div>
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<p>It is however highly recommended to follow the documentation’s <a class="reference external" href="http://baptiste.bauvin.pages.lis-lab.fr/summit/tutorials/index.html">tutorials</a> to learn the use of each parameter.</p>
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<div class="section" id="authors">
<h2>Authors<a class="headerlink" href="#authors" title="Permalink to this headline"></a></h2>
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<li><strong>Baptiste BAUVIN</strong></li>
<li><strong>Dominique BENIELLI</strong></li>
<li><strong>Alexis PROD’HOMME</strong></li>
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