Commit 54861567 authored by Pauline Pommeret's avatar Pauline Pommeret

Merge branch 'master' of gitlab.crans.org:senizergues-pommeret/itpp

Merging new features and documentation
parents 0cce9521 7dff8e46
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# -*- coding: utf-8 -*-
#
# xylok documentation build configuration file, created by
# sphinx-quickstart on Tue Dec 2 20:33:27 2014.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All configuration values have a default; values that are commented out
# serve to show the default.
import sys
import os
# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
sys.path.insert(0, os.path.abspath('../../'))
# -- General configuration ------------------------------------------------
# If your documentation needs a minimal Sphinx version, state it here.
#needs_sphinx = '1.0'
# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = ['sphinx.ext.autodoc', 'sphinx.ext.todo', 'sphinx.ext.coverage', 'sphinx.ext.viewcode']
# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']
# The suffix of source filenames.
source_suffix = '.rst'
# The encoding of source files.
#source_encoding = 'utf-8-sig'
# The master toctree document.
master_doc = 'index'
# General information about the project.
project = u'xylok'
copyright = u'2014, Pauline Pommeret, Jonas Sénizergues'
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
# built documents.
#
# The short X.Y version.
version = '0.9'
# The full version, including alpha/beta/rc tags.
release = '0.9'
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
#language = None
# There are two options for replacing |today|: either, you set today to some
# non-false value, then it is used:
#today = ''
# Else, today_fmt is used as the format for a strftime call.
#today_fmt = '%B %d, %Y'
# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
exclude_patterns = []
# The reST default role (used for this markup: `text`) to use for all
# documents.
#default_role = None
# If true, '()' will be appended to :func: etc. cross-reference text.
#add_function_parentheses = True
# If true, the current module name will be prepended to all description
# unit titles (such as .. function::).
#add_module_names = True
# If true, sectionauthor and moduleauthor directives will be shown in the
# output. They are ignored by default.
#show_authors = False
# The name of the Pygments (syntax highlighting) style to use.
pygments_style = 'sphinx'
# A list of ignored prefixes for module index sorting.
#modindex_common_prefix = []
# If true, keep warnings as "system message" paragraphs in the built documents.
#keep_warnings = False
# -- Options for HTML output ----------------------------------------------
# The theme to use for HTML and HTML Help pages. See the documentation for
# a list of builtin themes.
html_theme = 'default'
# Theme options are theme-specific and customize the look and feel of a theme
# further. For a list of options available for each theme, see the
# documentation.
#html_theme_options = {}
# Add any paths that contain custom themes here, relative to this directory.
#html_theme_path = []
# The name for this set of Sphinx documents. If None, it defaults to
# "<project> v<release> documentation".
#html_title = None
# A shorter title for the navigation bar. Default is the same as html_title.
#html_short_title = None
# The name of an image file (relative to this directory) to place at the top
# of the sidebar.
#html_logo = None
# The name of an image file (within the static path) to use as favicon of the
# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
# pixels large.
#html_favicon = None
# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
html_static_path = ['_static']
# Add any extra paths that contain custom files (such as robots.txt or
# .htaccess) here, relative to this directory. These files are copied
# directly to the root of the documentation.
#html_extra_path = []
# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
# using the given strftime format.
#html_last_updated_fmt = '%b %d, %Y'
# If true, SmartyPants will be used to convert quotes and dashes to
# typographically correct entities.
#html_use_smartypants = True
# Custom sidebar templates, maps document names to template names.
#html_sidebars = {}
# Additional templates that should be rendered to pages, maps page names to
# template names.
#html_additional_pages = {}
# If false, no module index is generated.
#html_domain_indices = True
# If false, no index is generated.
#html_use_index = True
# If true, the index is split into individual pages for each letter.
#html_split_index = False
# If true, links to the reST sources are added to the pages.
#html_show_sourcelink = True
# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
#html_show_sphinx = True
# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
#html_show_copyright = True
# If true, an OpenSearch description file will be output, and all pages will
# contain a <link> tag referring to it. The value of this option must be the
# base URL from which the finished HTML is served.
#html_use_opensearch = ''
# This is the file name suffix for HTML files (e.g. ".xhtml").
#html_file_suffix = None
# Output file base name for HTML help builder.
htmlhelp_basename = 'xylokdoc'
# -- Options for LaTeX output ---------------------------------------------
latex_elements = {
# The paper size ('letterpaper' or 'a4paper').
#'papersize': 'letterpaper',
# The font size ('10pt', '11pt' or '12pt').
#'pointsize': '10pt',
# Additional stuff for the LaTeX preamble.
#'preamble': '',
}
# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title,
# author, documentclass [howto, manual, or own class]).
latex_documents = [
('index', 'xylok.tex', u'xylok Documentation',
u'Pauline Pommeret, Jonas Sénizergues', 'manual'),
]
# The name of an image file (relative to this directory) to place at the top of
# the title page.
#latex_logo = None
# For "manual" documents, if this is true, then toplevel headings are parts,
# not chapters.
#latex_use_parts = False
# If true, show page references after internal links.
#latex_show_pagerefs = False
# If true, show URL addresses after external links.
#latex_show_urls = False
# Documents to append as an appendix to all manuals.
#latex_appendices = []
# If false, no module index is generated.
#latex_domain_indices = True
# -- Options for manual page output ---------------------------------------
# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
('index', 'xylok', u'xylok Documentation',
[u'Pauline Pommeret, Jonas Sénizergues'], 1)
]
# If true, show URL addresses after external links.
#man_show_urls = False
# -- Options for Texinfo output -------------------------------------------
# Grouping the document tree into Texinfo files. List of tuples
# (source start file, target name, title, author,
# dir menu entry, description, category)
texinfo_documents = [
('index', 'xylok', u'xylok Documentation',
u'Pauline Pommeret, Jonas Sénizergues', 'xylok', 'One line description of project.',
'Miscellaneous'),
]
# Documents to append as an appendix to all manuals.
#texinfo_appendices = []
# If false, no module index is generated.
#texinfo_domain_indices = True
# How to display URL addresses: 'footnote', 'no', or 'inline'.
#texinfo_show_urls = 'footnote'
# If true, do not generate a @detailmenu in the "Top" node's menu.
#texinfo_no_detailmenu = False
Welcome to Xylok's documentation!
=================================
Contents:
.. toctree::
:maxdepth: 3
xylok/sequence
xylok/lib/fft_tools
xylok/lib/trx
xylok/lib/file_tools
xylok/lib/database
xylok/lib/xylokexceptions
xylok/lib/correlation
Indices and tables
==================
* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`
Xylok lib/correlation -- Xylok own error objects
================================================
.. automodule:: lib.correlation
:members:
:private-members:
:special-members:
:show-inheritance:
Xylok lib/database -- PostGreSQL database tool for Xylok
========================================================
.. automodule:: lib.database
:members:
:private-members:
:special-members:
:show-inheritance:
Xylok lib/fft_tools -- Fast Fourier Transform tools for Xylok
=============================================================
.. automodule:: lib.fft_tools
:members:
:private-members:
:special-members:
:show-inheritance:
Xylok lib/file_tools -- File Management Tools
=============================================
.. automodule:: lib.file_tools
:members:
:private-members:
:special-members:
:show-inheritance:
Xylok lib/trx -- TRX tools for Xylok
====================================
.. automodule:: lib.trx
:members:
:private-members:
:special-members:
:show-inheritance:
Xylok lib/XylokExceptions -- Xylok own error objects
====================================================
.. automodule:: lib.XylokExceptions
:members:
:private-members:
:special-members:
:show-inheritance:
Xylok sequences -- sequence handling tools
==========================================
.. automodule:: sequence
:members:
:private-members:
:special-members:
:show-inheritance:
......@@ -5,6 +5,151 @@
import psycopg2
import psycopg2.extras
import itertools
class LearningPGCursor(object):
"""
A PG Cursor dedicated to learning functionalities (we use
standard Cursor instead of DictCursor, which order of result
is not guaranteed.
"""
def __init__(self):
"""
Starts a psycopg2 cursor and populates:
- ``self._conn``
- ``self._cur``
Parameters:
- ``self``
Returns:
- nothing
"""
self._conn = psycopg2.connect(database='itpp')
self._cur = self._conn.cursor()
def fetch_averaged_specific_sequence(self, seq_id):
# XXX meh.
data_list = []
data_list.extend(self.fetch_trx_data(seq_id))
data_list.extend(self.fetch_averaged_md_data(seq_id))
data_list.extend(self.fetch_averaged_correlations(seq_id))
return data_list
def fetch_averaged_sequence_data(self):
"""
"""
seq_query = """SELECT
id, label, name
FROM
sequences
ORDER BY
id
ASC;"""
self._cur.execute(seq_query)
sequences = self._cur.fetchall()
possible_answers = list(set([seq[1] for seq in sequences]))
answers = [possible_answers.index(seq[1]) for seq in sequences]
data_list = []
i = 0
for sequence in sequences:
seq_id = sequence[0]
data_list.append([])
data_list[i].extend(self.fetch_trx_data(seq_id))
data_list[i].extend(self.fetch_averaged_md_data(seq_id))
data_list[i].extend(self.fetch_averaged_correlations(seq_id))
i += 1
return data_list, answers, possible_answers
def fetch_averaged_md_data(self, seq_id):
"""
"""
data_list = []
for md_type in ["rise", "roll", "shift", "slide", "tilt", "twist"]:
md_query = """SELECT
avg(complete_peak_freq), avg(complete_peak), avg(complete_size), avg(center_peak_freq),\
avg(center_peak), avg(center_size), avg(sliding_peak_freq), avg(sliding_peak), avg(sliding_size)
FROM
md_%s
WHERE
seq_id = %s
GROUP BY
seq_id;""" % (md_type, seq_id)
self._cur.execute(md_query)
t = self._cur.fetchone()
if not t:
t = [0.0]*9
data_list.append(t)
return [elem for elem in itertools.chain(*data_list)]
def fetch_averaged_correlations(self, seq_id):
"""
Fetches data from correlation table, if some values are missing,
set values to 0.0
"""
data_dict = {}
types_a = ["rise", "roll", "shift", "slide", "tilt", "twist"]
types_b = ["roll", "shift", "slide", "tilt", "twist"]
couples = []
for type_a in types_a:
if type_a in types_b:
types_b.remove(type_a)
for type_b in types_b:
couples.append("%s/%s" % (type_a, type_b))
del types_a, types_b
for couple in couples:
data_dict[couple] = []
corr_query="""SELECT
type_a, type_b, avg(spearman_complete::int::float), avg(spearman_center::int::float), avg(pearson_complete::int::float), avg(pearson_center::int::float)
FROM
correlations
WHERE
seq_id = %s
GROUP BY
type_a, type_b
ORDER BY
type_a, type_b
ASC;""" % (seq_id, )
self._cur.execute(corr_query)
data = self._cur.fetchall()
for tpl in data:
data_dict["%s/%s" % (tpl[0], tpl[1])].extend(tpl[2:])
del data
data = []
for couple in couples:
if not data_dict[couple]:
data.extend([0.0]*4)
else:
data.extend(data_dict[couple])
return data
def fetch_trx_data(self, seq_id):
"""
Fetch trx data from DB
"""
trx_query = """SELECT
complete_peak_freq, complete_peak, complete_size, center_peak_freq, center_peak, center_size, sliding_peak_freq, sliding_peak, sliding_size
FROM
trx
WHERE
seq_id = %s;""" % (seq_id,)
self._cur.execute(trx_query)
return list(self._cur.fetchone())
class PGCursor(object):
"""
PostGreSQL Python Cursor.
......@@ -26,6 +171,23 @@ class PGCursor(object):
self._conn.set_session(autocommit=True)
self._cur = self._conn.cursor(cursor_factory=psycopg2.extras.DictCursor)
def check_sequence(self, seq):
"""
Checks if seq is already recorded in database.
"""
verif_query = """SELECT
id
FROM
sequences
WHERE
sequence=%s;"""
self._cur.execute(verif_query, (seq.sequence,))
ret = self._cur.fetchone()
if ret:
return ret[0]
else:
return False
def store_sequence(self, seq):
"""
Stores the sequence data in database
......@@ -38,6 +200,7 @@ class PGCursor(object):
- nothing
"""
# This query is designed to add the sequence metadata in the database.
# We give explicitly the columns of the table we want to fill, and we also give the dict keys for the VALUES,
# so we only have to give seq to cur.execute() as if seq was a dict.
......@@ -101,3 +264,15 @@ class PGCursor(object):
"type_b": type_b,
})
self._cur.execute(corr_query, dic_to_sql)
return seq_id
def remove_seq(self, seq_id):
"""
Removes a sequence from database
"""
for md_type in ["rise", "roll", "shift", "slide", "tilt", "twist"]:
self._cur.execute("DELETE FROM md_%s WHERE seq_id=%s" % (md_type, seq_id))
self._cur.execute('DELETE FROM trx WHERE seq_id=%s', (seq_id,))
self._cur.execute('DELETE FROM correlations WHERE seq_id=%s', (seq_id,))
self._cur.execute('DELETE FROM sequences WHERE id=%s', (seq_id,))
......@@ -90,6 +90,9 @@ def fft(frame, centering=None):
# Retrieves data
frame_number, (x_values, y_values) = split_frame(frame)
# Computes max of positive fft freqs
m_fft = (y_values.size + 1)/2
# Specific to centering
if centering is not None:
offset = int((len(x_values) - centering)/2)
......@@ -98,10 +101,10 @@ def fft(frame, centering=None):
# Creates frequency space, x_values[1] - x_values[0] is the typical delta
# in x_values.
freqs = numpy.fft.fftfreq(y_values.