This tag will be replaced by update_copyright.py with the full
copyright blurb for each file.
70 files changed:
Usage:
python FMjoin.py origindir destdir
Usage:
python FMjoin.py origindir destdir
-
-
-Alberto Gomez-Casado (c) 2010, University of Twente (The Netherlands)
-This program is released under the GNU General Public License version 2.
import h5py
import numpy
import os
import h5py
import numpy
import os
"""Auto-generate reStructuredText of the hooke module tree for Sphinx.
"""Auto-generate reStructuredText of the hooke module tree for Sphinx.
"""The hooke module does all the legwork for Hooke_.
"""The hooke module does all the legwork for Hooke_.
"""The `command` module provides :class:`Command`\s and
:class:`Argument`\s for defining commands.
"""The `command` module provides :class:`Command`\s and
:class:`Argument`\s for defining commands.
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-'''
-config.py
-
-Configuration defaults, read/write, and template file creation for Hooke.
-
-COPYRIGHT
-'''
+"""Configuration defaults, read/write, and template file creation for
+Hooke.
+"""
import ConfigParser as configparser
import os.path
import ConfigParser as configparser
import os.path
"""The `curve` module provides :class:`Curve` and :class:`Data` for
storing force curves.
"""
"""The `curve` module provides :class:`Curve` and :class:`Data` for
storing force curves.
"""
"""The driver module provides :class:`Driver`\s for identifying and
reading data files.
"""The driver module provides :class:`Driver`\s for identifying and
reading data files.
-Simple driver to read general comma-separated values in Hooke
+"""Simple driver to read general comma-separated values in Hooke
Columns are read this way:
X1 , Y1 , X2 , Y2 , X3 , Y3 ...
If the number of columns is odd, the last column is ignored.
Columns are read this way:
X1 , Y1 , X2 , Y2 , X3 , Y3 ...
If the number of columns is odd, the last column is ignored.
-
-(c)Massimo Sandal, 2008
-'''
from .. import curve as lhc
from .. import libhooke as lh
from .. import curve as lhc
from .. import libhooke as lh
-'''
-hdf5.py
-
-Driver for text-exported HDF5 files from Igor pro
-
-Alberto Gomez-Casado (c) 2010
-Massimo Sandal (c) 2009
-'''
+"""Driver for text-exported HDF5 files from Igor pro
+"""
from .. import curve as lhc
from .. import libhooke as lh
from .. import curve as lhc
from .. import libhooke as lh
-'''
-libhemingclamp.py
-
-Library for interpreting Hemingway force spectroscopy files.
-Copyright (C) 2008 Massimo Sandal, Marco Brucale (University of Bologna, Italy)
-
-This program is released under the GNU General Public License version 2.
-'''
+"""Library for interpreting Hemingway force spectroscopy files.
+"""
__version__='2007_02_15_devel'
__changelog__='''
__version__='2007_02_15_devel'
__changelog__='''
import string
from .. import curve as lhc
import string
from .. import curve as lhc
-driver for mcs fluorescence files
-
-Massimo Sandal, Allen Chen (c) 2009
-'''
+"""Driver for mcs fluorescence files
+"""
from .. import curve as lhc
from .. import libhooke as lh
from .. import curve as lhc
from .. import libhooke as lh
-Driver for text-exported MFP 1D files
-
-Massimo Sandal (c) 2009
-'''
+"""Driver for text-exported MFP 1D files
+"""
+"""Driver for MFP-3D files.
-Driver for MFP-3D files.
+This driver reads Igor binary waves.
-Copyright 2010 by Dr. Rolf Schmidt (Concordia University, Canada)
-This driver is based on the work of R. Naud and A. Seeholzer (see below)
-to read Igor binary waves. Code used with permission.
-
-Modified for usage with Hooke CLI by Alberto Gomez-Casado (University of Twente, The Netherlands)
-
-This program is released under the GNU General Public License version 2.
-'''
+AUTHORS:
+Matlab version: Richard Naud August 2008 (http://lcn.epfl.ch/~naud/)
+Python port: A. Seeholzer October 2008
+Hooke submission: Rolf Schmidt, Alberto Gomez-Casado 2009
+"""
# DEFINITION:
# Reads Igor's (Wavemetric) binary wave format, .ibw, files.
# DEFINITION:
# Reads Igor's (Wavemetric) binary wave format, .ibw, files.
# http://mirror.optus.net.au/pub/wavemetrics/IgorPro/Technical_Notes/) and data
# type 2 or 4 (non complex, single or double precision vector, real values).
#
# http://mirror.optus.net.au/pub/wavemetrics/IgorPro/Technical_Notes/) and data
# type 2 or 4 (non complex, single or double precision vector, real values).
#
-# AUTHORS:
-# Matlab version: R. Naud August 2008 (http://lcn.epfl.ch/~naud/Home.html)
-# Python port: A. Seeholzer October 2008
-#
# VERSION: 0.1
#
# COMMENTS:
# VERSION: 0.1
#
# COMMENTS:
-Library for interpreting Picoforce force spectroscopy files.
-
-Copyright (C) 2006 Massimo Sandal (University of Bologna, Italy).
-
-This program is released under the GNU General Public License version 2.
-'''
+"""Library for interpreting Picoforce force spectroscopy files.
+"""
-Library for interpreting Picoforce force spectroscopy files. Alternate version
+"""Library for interpreting Picoforce force spectroscopy files.
-Copyright (C) 2006 Massimo Sandal (University of Bologna, Italy).
-Copyright (C) 2008 Alberto Gomez-Casado (University of Twente, Netherlands).
-
-This program is released under the GNU General Public License version 2.
-'''
+An alternave implementation of :mod:`hooke.driver.picoforce`.
+"""
import re, struct
from scipy import arange
import re, struct
from scipy import arange
-# Copyright (c) 2008 Massimo Sandal
-# 2010 W. Trevor King
"""Tutorial driver for Hooke.
"""Tutorial driver for Hooke.
"""The `engine` module provides :class:`CommandEngine` for executing
:class:`hooke.command.Command`\s.
"""
"""The `engine` module provides :class:`CommandEngine` for executing
:class:`hooke.command.Command`\s.
"""
"""Define :class:`Experiment` and assorted subclasses.
This allows :class:`hooke.plugin.Plugin`\s to specify the types of
"""Define :class:`Experiment` and assorted subclasses.
This allows :class:`hooke.plugin.Plugin`\s to specify the types of
-'''
-Hooke - A force spectroscopy review & analysis tool.
-
-A free, open source data analysis platform
-
-COPYRIGHT
-'''
+"""Hooke - A force spectroscopy review & analysis tool.
+"""
import multiprocessing
import optparse
import multiprocessing
import optparse
"""The `interaction` module provides :class:`Request`,
:class:`Response`, an related classes for handling user interaction
through the
"""The `interaction` module provides :class:`Request`,
:class:`Response`, an related classes for handling user interaction
through the
"""The `playlist` module provides a :class:`Playlist` and its subclass
:class:`FilePlaylist` for manipulating lists of
:class:`hooke.curve.Curve`\s.
"""The `playlist` module provides a :class:`Playlist` and its subclass
:class:`FilePlaylist` for manipulating lists of
:class:`hooke.curve.Curve`\s.
"""The `plugin` module provides optional submodules that add new Hooke
commands.
"""The `plugin` module provides optional submodules that add new Hooke
commands.
-# -*- coding: utf-8 -*-
-# COPYRIGHT
"""The autopeak module provides :class:`Autopeak`, a
:class:`hooke.plugin.Plugin` for automatically extracting force peaks
"""The autopeak module provides :class:`Autopeak`, a
:class:`hooke.plugin.Plugin` for automatically extracting force peaks
"""The `config` module provides :class:`ConfigPlugin` and several
associated :class:`hooke.command.Command`\s for handling
:mod:`hooke.config` classes.
"""The `config` module provides :class:`ConfigPlugin` and several
associated :class:`hooke.command.Command`\s for handling
:mod:`hooke.config` classes.
from ..libhooke import WX_GOOD, ClickedPoint
import wxversion
from ..libhooke import WX_GOOD, ClickedPoint
import wxversion
"""The `cut` module provides :class:`CutPlugin` and
:class:`CutCommand`.
"""
"""The `cut` module provides :class:`CutPlugin` and
:class:`CutCommand`.
"""
"""The `debug` module provides :class:`DebugPlugin` and associated
:class:`hooke.command.Command`\s which provide useful debugging
information.
"""The `debug` module provides :class:`DebugPlugin` and associated
:class:`hooke.command.Command`\s which provide useful debugging
information.
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-'''
-FIT
-
-Force spectroscopy curves basic fitting plugin.
-Licensed under the GNU GPL version 2
+"""Force spectroscopy curves basic fitting plugin.
Non-standard Dependencies:
procplots.py (plot processing plugin)
Non-standard Dependencies:
procplots.py (plot processing plugin)
from ..libhooke import WX_GOOD, ClickedPoint
import wxversion
from ..libhooke import WX_GOOD, ClickedPoint
import wxversion
-'''
-FLATFILTS
-
-Force spectroscopy curves filtering of flat curves
-Licensed under the GNU LGPL version 2
+"""Force spectroscopy curves filtering of flat curves
Other plugin dependencies:
procplots.py (plot processing plugin)
Other plugin dependencies:
procplots.py (plot processing plugin)
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-'''
-FLATFILTS
-
-Force spectroscopy curves filtering of flat curves
-Licensed under the GNU LGPL version 2
+"""Force spectroscopy curves filtering of flat curves
Other plugin dependencies:
procplots.py (plot processing plugin)
Other plugin dependencies:
procplots.py (plot processing plugin)
from hooke.libhooke import WX_GOOD
from hooke.libhooke import WX_GOOD
+# Copyright
+
+"""Plugin regarding general force clamp measurements
+"""
-Plugin regarding general force clamp measurements
-'''
from hooke.libhooke import WX_GOOD, ClickedPoint
import wxversion
from hooke.libhooke import WX_GOOD, ClickedPoint
import wxversion
-General utilities for TCCD stuff
-'''
+"""General utilities for TCCD stuff
+"""
class generaltccdCommands(object):
class generaltccdCommands(object):
-#!/usr/bin/env python
-# -*- coding: iso-8859-1 -*-
-'''
-generalvclamp.py
-
-Plugin regarding general velocity clamp measurements
-'''
+"""Plugin regarding general velocity clamp measurements
+"""
from hooke.libhooke import WX_GOOD, ClickedPoint
import wxversion
from hooke.libhooke import WX_GOOD, ClickedPoint
import wxversion
from ..libhooke import WX_GOOD, ClickedPoint
import wxversion
wxversion.select(WX_GOOD)
from ..libhooke import WX_GOOD, ClickedPoint
import wxversion
wxversion.select(WX_GOOD)
-'''
-COMMAND MACRO PLUGIN FOR HOOKE
-Records, saves and executes batches of commands
-(c)Alberto Gomez-Casado 2008
-'''
+"""Records, saves and executes batches of commands
+"""
import os.path
import string
import os.path
import string
-Global analysis of force curves with various parameters
+"""Global analysis of force curves with various parameters
Requires:
libpeakspot.py
flatfilts.py
Requires:
libpeakspot.py
flatfilts.py
import numpy as np
import csv
import numpy as np
import csv
from hooke.libhooke import WX_GOOD, ClickedPoint
import wxversion
from hooke.libhooke import WX_GOOD, ClickedPoint
import wxversion
-#!/usr/bin/env python
-
-'''
-multifit.py
-
-Alberto Gomez-Casado, (c) 2010, University of Twente (The Netherlands)
-Licensed under GNU GPL v2
-'''
#FIXME clean this, probably some dependencies are not needed
#FIXME clean this, probably some dependencies are not needed
"""The `note` module provides :class:`NotePlugin` the associated
:class:`hooke.command.Command`\s for annotating several Hooke classes
(:mod:`hooke.playlist.Playlist`, :mod:`hooke.curve.Curve`, ...).
"""The `note` module provides :class:`NotePlugin` the associated
:class:`hooke.command.Command`\s for annotating several Hooke classes
(:mod:`hooke.playlist.Playlist`, :mod:`hooke.curve.Curve`, ...).
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
from ..libhooke import WX_GOOD, ClickedPoint, config_file_path
from mdp import pca
from ..libhooke import WX_GOOD, ClickedPoint, config_file_path
from mdp import pca
-'''
-a library of helping functions for spotting force spectroscopy peaks
+# Copyright
+
+"""a library of helping functions for spotting force spectroscopy peaks.
+"""
-(c)Fabrizio Benedetti and Massimo Sandal , 2007
-'''
import numpy as np
def conv_dx(data,vect):
import numpy as np
def conv_dx(data,vect):
"""The `playlist` module provides :class:`PlaylistPlugin` several
associated :class:`hooke.command.Command`\s for handling
:mod:`hooke.playlist` classes.
"""The `playlist` module provides :class:`PlaylistPlugin` several
associated :class:`hooke.command.Command`\s for handling
:mod:`hooke.playlist` classes.
-'''
-PROCPLOTS
-Processed plots plugin for force curves.
+# Copyright
+
+"""Processed plots plugin for force curves.
+"""
-Licensed under the GNU GPL version 2
-'''
from ..libhooke import WX_GOOD
import wxversion
wxversion.select(WX_GOOD)
from ..libhooke import WX_GOOD
import wxversion
wxversion.select(WX_GOOD)
-#!/usr/bin/env python
-
-'''review.py
-Alberto Gomez-Casado (c) 2010 University of Twente
-'''
from ..libhooke import WX_GOOD
import wxversion
from ..libhooke import WX_GOOD
import wxversion
-'''
-SHOW CONVOLUTED CURVE PLUGIN FOR HOOKE
-
-This plugin contains a plotmanipulator to show the convoluted curve.
-(c) Dr. Rolf Schmidt, 2009
-'''
+"""This plugin contains a plotmanipulator to show the convoluted curve.
+"""
from ..libhooke import WX_GOOD
import wxversion
wxversion.select(WX_GOOD)
from ..libhooke import WX_GOOD
import wxversion
wxversion.select(WX_GOOD)
"""The `system` module provides :class:`SystemPlugin` and several
associated :class:`hooke.command.Command`\s for interacting with the
operating system and execution environment.
"""The `system` module provides :class:`SystemPlugin` and several
associated :class:`hooke.command.Command`\s for interacting with the
operating system and execution environment.
-'''
-TUTORIAL PLUGIN FOR HOOKE
-This plugin contains example commands to teach how to write an Hooke plugin, including description of main Hooke
-internals.
-(c)Massimo Sandal 2007
-'''
+"""This plugin contains example commands to teach how to write an
+Hooke plugin, including description of main Hooke internals.
+"""
"""The `ui` module provides :class:`UserInterface` and various subclasses.
"""
"""The `ui` module provides :class:`UserInterface` and various subclasses.
"""
"""Defines :class:`CommandLine` for driving Hooke from the command
line.
"""
"""Defines :class:`CommandLine` for driving Hooke from the command
line.
"""
def _generate_vectors(self):
"""
def _generate_vectors(self):
"""
#PLOT EXPORT AND MANIPULATION COMMANDS
def help_export(self):
print '''
#PLOT EXPORT AND MANIPULATION COMMANDS
def help_export(self):
print '''
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-'''
-formatter.py
-
-Number formatting utilities for Hooke.
-
-Copyright (C) 2006 Massimo Sandal (University of Bologna, Italy).
-With algorithms contributed by Francesco Musiani (University of Bologna, Italy)
-
-This program is released under the GNU General Public License version 2.
-'''
+"""A number formatting utilities for Hooke.
+"""
from matplotlib.ticker import ScalarFormatter
from matplotlib.ticker import ScalarFormatter
#import os
#import os.path
import wx
#import os
#import os.path
import wx
import sys
import time
import math
import sys
import time
import math
class PlotObject(object):
def __init__(self):
class PlotObject(object):
def __init__(self):
#PLOT INTERACTION COMMANDS
#-------------------------------
def help_plot(self):
#PLOT INTERACTION COMMANDS
#-------------------------------
def help_plot(self):
class ClickedPoint(object):
'''
this class defines what a clicked point on the curve plot is
class ClickedPoint(object):
'''
this class defines what a clicked point on the curve plot is
-'''
-//
-// prettyformat.py - simple Python function to format values with nice prefixes
-// Version 1.0.1
-//
-// History
-// 2009 07 16: added negative number support
-// added decimal-formatted output
-//
-// Copyright (c) 2009 Rolf Schmidt, Montreal
-// rschmidt@alcor.concordia.ca
-//
-// This procedure is released under the GNU General Public License version 2
-//
-'''
+# Copyright
+
+"""Format values with nice prefixes.
+History:
+
+* 2009 07 16:
+
+ * added negative number support
+ * added decimal-formatted output
+"""
+__version__ = "1.0.1"
import math
from numpy import isnan
import math
from numpy import isnan
for aValue in scaleValues: print decimalFormat(aValue/iMultiplier, iDecimals),
#print the scale label using the value at iIndex
print '\n'+get_prefix(scaleValues[iIndex])+'N'
for aValue in scaleValues: print decimalFormat(aValue/iMultiplier, iDecimals),
#print the scale label using the value at iIndex
print '\n'+get_prefix(scaleValues[iIndex])+'N'
-'''
\ No newline at end of file
import prettyformat
DEFAULT_COLOR = 'orange'
import prettyformat
DEFAULT_COLOR = 'orange'
"""The util module contains assorted utilities not directly associated
with Hooke functionality.
"""The util module contains assorted utilities not directly associated
with Hooke functionality.
"""Define :class:`Graph`, a directed, acyclic graph structure.
:class:`Graph`\s are composed of :class:`Node`\s, also defined by this
"""Define :class:`Graph`, a directed, acyclic graph structure.
:class:`Graph`\s are composed of :class:`Node`\s, also defined by this
"""Hooke: tools for analyzing force spectroscopy data.
Mercurial repository:
"""Hooke: tools for analyzing force spectroscopy data.
Mercurial repository:
"""Hooke integration tests.
Besides the unittests embedded in the Hooke code, we also want to
"""Hooke integration tests.
Besides the unittests embedded in the Hooke code, we also want to
"""
>>> from hooke.hooke import Hooke
>>> h = Hooke()
"""
>>> from hooke.hooke import Hooke
>>> h = Hooke()