From: W. Trevor King <wking@drexel.edu>
Date: Mon, 17 May 2010 14:29:41 +0000 (-0400)
Subject: Moving hooke.plugin.procplots to .curve in preparation for merge
X-Git-Url: http://git.tremily.us/?a=commitdiff_plain;h=bff2e146f66541f8935c634b93aa4bf4d74b04ca;p=hooke.git

Moving hooke.plugin.procplots to .curve in preparation for merge
---

diff --git a/hooke/plugin/curve.py b/hooke/plugin/curve.py
index 1e0ad06..3868a83 100644
--- a/hooke/plugin/curve.py
+++ b/hooke/plugin/curve.py
@@ -1,5 +1,6 @@
-# Copyright (C) 2010 Fibrin's Benedetti
-#                    W. Trevor King <wking@drexel.edu>
+# Copyright (C) 2008-2010 Alberto Gomez-Casado
+#                         Massimo Sandal <devicerandom@gmail.com>
+#                         W. Trevor King <wking@drexel.edu>
 #
 # This file is part of Hooke.
 #
@@ -17,133 +18,285 @@
 # License along with Hooke.  If not, see
 # <http://www.gnu.org/licenses/>.
 
-"""The ``curve`` module provides :class:`CurvePlugin` and several
-associated :class:`hooke.command.Command`\s for handling
-:mod:`hooke.curve` classes.
+"""Processed plots plugin for force curves.
 """
 
-from ..command import Command, Argument, Failure
-from ..plugin import Builtin
-from ..plugin.playlist import current_playlist_callback
-
-
-class CurvePlugin (Builtin):
-    def __init__(self):
-        super(CurvePlugin, self).__init__(name='curve')
-
-    def commands(self):
-        return [InfoCommand(), ]
-
-
-# Define common or complicated arguments
-
-def current_curve_callback(hooke, command, argument, value):
-    if value != None:
-        return value
-    playlist = current_playlist_callback(hooke, command, argument, value)
-    curve = playlist.current()
-    if curve == None:
-        raise Failure('No curves in %s' % playlist)
-    return curve
-
-CurveArgument = Argument(
-    name='curve', type='curve', callback=current_curve_callback,
-    help="""
-:class:`hooke.curve.Curve` to act on.  Defaults to the current curve
-of the current playlist.
-""".strip())
-
-
-# Define commands
-
-class InfoCommand (Command):
-    """Print selected information about a :class:`hooke.curve.Curve`.
-    """
-    def __init__(self):
-        args = [
-            CurveArgument,                    
-            Argument(name='all', type='bool', default=False, count=1,
-                     help='Print all curve information.'),
-            ]
-        self.fields = ['name', 'path', 'experiment', 'driver', 'filetype', 'note',
-                       'blocks', 'block sizes']
-        for field in self.fields:
-            args.append(Argument(
-                    name=field, type='bool', default=False, count=1,
-                    help='Print curve %s' % field))
-        super(InfoCommand, self).__init__(
-            name='curve info', arguments=args, help=self.__doc__)
-
-    def _run(self, hooke, inqueue, outqueue, params):
-        fields = {}
-        for key in self.fields:
-            fields[key] = params[key]
-        if reduce(lambda x,y: x and y, fields.values()) == False:
-            params['all'] = True # No specific fields set, default to 'all'
-        if params['all'] == True:
-            for key in self.fields:
-                fields[key] = True
-        lines = []
-        for key in self.fields:
-            if fields[key] == True:
-                get = getattr(self, '_get_%s' % key.replace(' ', '_'))
-                lines.append('%s: %s' % (key, get(params['curve'])))
-        outqueue.put('\n'.join(lines))
-
-    def _get_name(self, curve):
-        return curve.name
-
-    def _get_path(self, curve):
-        return curve.path
-
-    def _get_experiment(self, curve):
-        return curve.info.get('experiment', None)
-
-    def _get_driver(self, curve):
-        return curve.driver
-
-    def _get_filetype(self, curve):
-        return curve.info.get('filetype', None)
-
-    def _get_note(self, curve):
-        return curve.info.get('note', None)
-                              
-    def _get_blocks(self, curve):
-        return len(curve.data)
-
-    def _get_block_sizes(self, curve):
-        return [block.shape for block in curve.data]
-
-
-class ExportCommand (Command):
-    """Export a :class:`hooke.curve.Curve` data block as TAB-delimeted
-    ASCII text.
-    """
-    def __init__(self):
-        self.fields = ['name', 'path', 'experiment', 'driver', 'filetype', 'note',
-                       'blocks', 'block sizes']
-        for field in self.fields:
-            args.append(Argument(
-                    name=field, type='bool', default=False, count=1,
-                    help='Print curve %s' % field))
-        super(InfoCommand, self).__init__(
-            name='curve info',
-            arguments=[
-                CurveArgument,
-                Argument(name='block', aliases=['set'], type='int', default=0,
-                    help="""
-Data block to save.  For an approach/retract force curve, `0` selects
-the approacing curve and `1` selects the retracting curve.
-""".strip()),
-                Argument(name='output', type='file', default='curve.dat',
-                         help="""
-File name for the output data.  Defaults to 'curve.dat'
-""".strip()),
-                ],
-            help=self.__doc__)
-
-    def _run(self, hooke, inqueue, outqueue, params):
-        data = params['curve'].data[params['index']]
-        f = open(params['output'], 'w')
-        data.tofile(f, sep='\t')
-        f.close()
+from ..libhooke import WX_GOOD
+import wxversion
+wxversion.select(WX_GOOD)
+
+import wx
+import numpy as np
+import scipy as sp
+import scipy.signal
+import copy
+
+from .. import curve as lhc
+
+
+class procplotsCommands(object):
+
+    def _plug_init(self):
+        pass
+
+    def do_derivplot(self,args):
+        '''
+        DERIVPLOT
+        (procplots.py plugin)
+        Plots the derivate (actually, the discrete differentiation) of the current force curve
+        ---------
+        Syntax: derivplot
+        '''
+        dplot=self.derivplot_curves()
+        plot_graph=self.list_of_events['plot_graph']
+        wx.PostEvent(self.frame,plot_graph(plots=[dplot]))
+
+    def derivplot_curves(self):
+        '''
+        do_derivplot helper function
+
+        create derivate plot curves for force curves.
+        '''
+        dplot=lhc.PlotObject()
+        dplot.vectors=[]
+
+        for vector in self.plots[0].vectors:
+            dplot.vectors.append([])
+            dplot.vectors[-1].append(vector[0][:-1])
+            dplot.vectors[-1].append(np.diff(vector[1]))
+
+        dplot.destination=1
+        dplot.units=self.plots[0].units
+
+        return dplot
+
+    def do_subtplot(self, args):
+        '''
+        SUBTPLOT
+        (procplots.py plugin)
+        Plots the difference between ret and ext current curve
+        -------
+        Syntax: subtplot
+        '''
+        #FIXME: sub_filter and sub_order must be args
+
+        if len(self.plots[0].vectors) != 2:
+            print 'This command only works on a curve with two different plots.'
+            pass
+
+        outplot=self.subtract_curves(sub_order=1)
+
+        plot_graph=self.list_of_events['plot_graph']
+        wx.PostEvent(self.frame,plot_graph(plots=[outplot]))
+
+    def subtract_curves(self, sub_order):
+        '''
+        subtracts the extension from the retraction
+        '''
+        xext=self.plots[0].vectors[0][0]
+        yext=self.plots[0].vectors[0][1]
+        xret=self.plots[0].vectors[1][0]
+        yret=self.plots[0].vectors[1][1]
+
+        #we want the same number of points
+        maxpoints_tot=min(len(xext),len(xret))
+        xext=xext[0:maxpoints_tot]
+        yext=yext[0:maxpoints_tot]
+        xret=xret[0:maxpoints_tot]
+        yret=yret[0:maxpoints_tot]
+
+        if sub_order:
+            ydiff=[yretval-yextval for yretval,yextval in zip(yret,yext)]
+        else: #reverse subtraction (not sure it's useful, but...)
+            ydiff=[yextval-yretval for yextval,yretval in zip(yext,yret)]
+
+        outplot=copy.deepcopy(self.plots[0])
+        outplot.vectors[0][0], outplot.vectors[1][0] = xext,xret #FIXME: if I use xret, it is not correct!
+        outplot.vectors[1][1]=ydiff
+        outplot.vectors[0][1]=[0 for item in outplot.vectors[1][0]]
+
+        return outplot
+
+
+#-----PLOT MANIPULATORS
+    def plotmanip_median(self, plot, current, customvalue=None):
+        '''
+        does the median of the y values of a plot
+        '''
+        if customvalue:
+            median_filter=customvalue
+        else:
+            median_filter=self.config['medfilt']
+
+        if median_filter==0:
+            return plot
+
+        if float(median_filter)/2 == int(median_filter)/2:
+            median_filter+=1
+
+        nplots=len(plot.vectors)
+        c=0
+        while c<nplots:
+            plot.vectors[c][1]=scipy.signal.medfilt(plot.vectors[c][1],median_filter)
+            c+=1
+
+        return plot
+
+
+    def plotmanip_correct(self, plot, current, customvalue=None):
+        '''
+        does the correction for the deflection for a force spectroscopy curve.
+        Assumes that:
+        - the current plot has a deflection() method that returns a vector of values
+        - the deflection() vector is as long as the X of extension + the X of retraction
+        - plot.vectors[0][0] is the X of extension curve
+        - plot.vectors[1][0] is the X of retraction curve
+
+        FIXME: both this method and the picoforce driver have to be updated, deflection() must return
+        a more senseful data structure!
+        '''
+        #use only for force spectroscopy experiments!
+        if current.curve.experiment != 'smfs':
+            return plot
+
+        if customvalue != None:
+            execute_me=customvalue
+        else:
+            execute_me=self.config['correct']
+        if not execute_me:
+            return plot
+
+        defl_ext,defl_ret=current.curve.deflection()
+        #halflen=len(deflall)/2
+
+        plot.vectors[0][0]=[(zpoint-deflpoint) for zpoint,deflpoint in zip(plot.vectors[0][0],defl_ext)]
+        plot.vectors[1][0]=[(zpoint-deflpoint) for zpoint,deflpoint in zip(plot.vectors[1][0],defl_ret)]
+
+        return plot
+
+
+    def plotmanip_centerzero(self, plot, current, customvalue=None):
+        '''
+        Centers the force curve so the median (the free level) corresponds to 0 N
+        Assumes that:
+        - plot.vectors[0][1] is the Y of extension curve
+        - plot.vectors[1][1] is the Y of retraction curve
+        
+       
+        '''
+        #use only for force spectroscopy experiments!
+        if current.curve.experiment != 'smfs':
+            return plot
+    
+        if customvalue != None:
+            execute_me=customvalue
+        else:
+            execute_me=self.config['centerzero']
+        if not execute_me:
+            return plot
+     
+        
+	
+	#levelapp=float(np.median(plot.vectors[0][1]))
+	levelret=float(np.median(plot.vectors[1][1][-300:-1]))
+
+	level=levelret	
+
+	approach=[i-level for i in plot.vectors[0][1]]
+	retract=[i-level for i in plot.vectors[1][1]]
+	
+	plot.vectors[0][1]=approach	
+	plot.vectors[1][1]=retract	
+        return plot
+    
+    '''
+    def plotmanip_detriggerize(self, plot, current, customvalue=None):
+        #DEPRECATED
+        if self.config['detrigger']==0:
+            return plot
+
+        cutindex=2
+        startvalue=plot.vectors[0][0][0]
+
+        for index in range(len(plot.vectors[0][0])-1,2,-2):
+           if plot.vectors[0][0][index]>startvalue:
+                cutindex=index
+           else:
+                break
+
+        plot.vectors[0][0]=plot.vectors[0][0][:cutindex]
+        plot.vectors[0][1]=plot.vectors[0][1][:cutindex]
+
+        return plot
+    '''
+
+
+
+#FFT---------------------------
+    def fft_plot(self, vector):
+        '''
+        calculates the fast Fourier transform for the selected vector in the plot
+        '''
+        fftplot=lhc.PlotObject()
+        fftplot.vectors=[[]]
+
+        fftlen=len(vector)/2 #need just 1/2 of length
+        fftplot.vectors[-1].append(np.arange(1,fftlen).tolist())
+
+        try:
+            fftplot.vectors[-1].append(abs(np.fft(vector)[1:fftlen]).tolist())
+        except TypeError: #we take care of newer NumPy (1.0.x)
+            fftplot.vectors[-1].append(abs(np.fft.fft(vector)[1:fftlen]).tolist())
+
+
+        fftplot.destination=1
+
+
+        return fftplot
+
+
+    def do_fft(self,args):
+        '''
+        FFT
+        (procplots.py plugin)
+        Plots the fast Fourier transform of the selected plot
+        ---
+        Syntax: fft [top,bottom] [select] [0,1...]
+
+        By default, fft performs the Fourier transform on all the 0-th data set on the
+        top plot.
+
+        [top,bottom]: which plot is the data set to fft (default: top)
+        [select]: you pick up two points on the plot and fft only the segment between
+        [0,1,...]: which data set on the selected plot you want to fft (default: 0)
+        '''
+
+        #args parsing
+        #whatplot = plot to fft
+        #whatset = set to fft in the plot
+        select=('select' in args)
+        if 'top' in args:
+            whatplot=0
+        elif 'bottom' in args:
+            whatplot=1
+        else:
+            whatplot=0
+        whatset=0
+        for arg in args:
+            try:
+                whatset=int(arg)
+            except ValueError:
+                pass
+
+        if select:
+            points=self._measure_N_points(N=2, whatset=whatset)
+            boundaries=[points[0].index, points[1].index]
+            boundaries.sort()
+            y_to_fft=self.plots[whatplot].vectors[whatset][1][boundaries[0]:boundaries[1]] #y
+        else:
+            y_to_fft=self.plots[whatplot].vectors[whatset][1] #y
+
+        fftplot=self.fft_plot(y_to_fft)
+        fftplot.units=['frequency', 'power']
+        plot_graph=self.list_of_events['plot_graph']
+        wx.PostEvent(self.frame,plot_graph(plots=[fftplot]))
diff --git a/hooke/plugin/procplots.py b/hooke/plugin/procplots.py
deleted file mode 100644
index 3868a83..0000000
--- a/hooke/plugin/procplots.py
+++ /dev/null
@@ -1,302 +0,0 @@
-# Copyright (C) 2008-2010 Alberto Gomez-Casado
-#                         Massimo Sandal <devicerandom@gmail.com>
-#                         W. Trevor King <wking@drexel.edu>
-#
-# This file is part of Hooke.
-#
-# Hooke is free software: you can redistribute it and/or
-# modify it under the terms of the GNU Lesser General Public
-# License as published by the Free Software Foundation, either
-# version 3 of the License, or (at your option) any later version.
-#
-# Hooke is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with Hooke.  If not, see
-# <http://www.gnu.org/licenses/>.
-
-"""Processed plots plugin for force curves.
-"""
-
-from ..libhooke import WX_GOOD
-import wxversion
-wxversion.select(WX_GOOD)
-
-import wx
-import numpy as np
-import scipy as sp
-import scipy.signal
-import copy
-
-from .. import curve as lhc
-
-
-class procplotsCommands(object):
-
-    def _plug_init(self):
-        pass
-
-    def do_derivplot(self,args):
-        '''
-        DERIVPLOT
-        (procplots.py plugin)
-        Plots the derivate (actually, the discrete differentiation) of the current force curve
-        ---------
-        Syntax: derivplot
-        '''
-        dplot=self.derivplot_curves()
-        plot_graph=self.list_of_events['plot_graph']
-        wx.PostEvent(self.frame,plot_graph(plots=[dplot]))
-
-    def derivplot_curves(self):
-        '''
-        do_derivplot helper function
-
-        create derivate plot curves for force curves.
-        '''
-        dplot=lhc.PlotObject()
-        dplot.vectors=[]
-
-        for vector in self.plots[0].vectors:
-            dplot.vectors.append([])
-            dplot.vectors[-1].append(vector[0][:-1])
-            dplot.vectors[-1].append(np.diff(vector[1]))
-
-        dplot.destination=1
-        dplot.units=self.plots[0].units
-
-        return dplot
-
-    def do_subtplot(self, args):
-        '''
-        SUBTPLOT
-        (procplots.py plugin)
-        Plots the difference between ret and ext current curve
-        -------
-        Syntax: subtplot
-        '''
-        #FIXME: sub_filter and sub_order must be args
-
-        if len(self.plots[0].vectors) != 2:
-            print 'This command only works on a curve with two different plots.'
-            pass
-
-        outplot=self.subtract_curves(sub_order=1)
-
-        plot_graph=self.list_of_events['plot_graph']
-        wx.PostEvent(self.frame,plot_graph(plots=[outplot]))
-
-    def subtract_curves(self, sub_order):
-        '''
-        subtracts the extension from the retraction
-        '''
-        xext=self.plots[0].vectors[0][0]
-        yext=self.plots[0].vectors[0][1]
-        xret=self.plots[0].vectors[1][0]
-        yret=self.plots[0].vectors[1][1]
-
-        #we want the same number of points
-        maxpoints_tot=min(len(xext),len(xret))
-        xext=xext[0:maxpoints_tot]
-        yext=yext[0:maxpoints_tot]
-        xret=xret[0:maxpoints_tot]
-        yret=yret[0:maxpoints_tot]
-
-        if sub_order:
-            ydiff=[yretval-yextval for yretval,yextval in zip(yret,yext)]
-        else: #reverse subtraction (not sure it's useful, but...)
-            ydiff=[yextval-yretval for yextval,yretval in zip(yext,yret)]
-
-        outplot=copy.deepcopy(self.plots[0])
-        outplot.vectors[0][0], outplot.vectors[1][0] = xext,xret #FIXME: if I use xret, it is not correct!
-        outplot.vectors[1][1]=ydiff
-        outplot.vectors[0][1]=[0 for item in outplot.vectors[1][0]]
-
-        return outplot
-
-
-#-----PLOT MANIPULATORS
-    def plotmanip_median(self, plot, current, customvalue=None):
-        '''
-        does the median of the y values of a plot
-        '''
-        if customvalue:
-            median_filter=customvalue
-        else:
-            median_filter=self.config['medfilt']
-
-        if median_filter==0:
-            return plot
-
-        if float(median_filter)/2 == int(median_filter)/2:
-            median_filter+=1
-
-        nplots=len(plot.vectors)
-        c=0
-        while c<nplots:
-            plot.vectors[c][1]=scipy.signal.medfilt(plot.vectors[c][1],median_filter)
-            c+=1
-
-        return plot
-
-
-    def plotmanip_correct(self, plot, current, customvalue=None):
-        '''
-        does the correction for the deflection for a force spectroscopy curve.
-        Assumes that:
-        - the current plot has a deflection() method that returns a vector of values
-        - the deflection() vector is as long as the X of extension + the X of retraction
-        - plot.vectors[0][0] is the X of extension curve
-        - plot.vectors[1][0] is the X of retraction curve
-
-        FIXME: both this method and the picoforce driver have to be updated, deflection() must return
-        a more senseful data structure!
-        '''
-        #use only for force spectroscopy experiments!
-        if current.curve.experiment != 'smfs':
-            return plot
-
-        if customvalue != None:
-            execute_me=customvalue
-        else:
-            execute_me=self.config['correct']
-        if not execute_me:
-            return plot
-
-        defl_ext,defl_ret=current.curve.deflection()
-        #halflen=len(deflall)/2
-
-        plot.vectors[0][0]=[(zpoint-deflpoint) for zpoint,deflpoint in zip(plot.vectors[0][0],defl_ext)]
-        plot.vectors[1][0]=[(zpoint-deflpoint) for zpoint,deflpoint in zip(plot.vectors[1][0],defl_ret)]
-
-        return plot
-
-
-    def plotmanip_centerzero(self, plot, current, customvalue=None):
-        '''
-        Centers the force curve so the median (the free level) corresponds to 0 N
-        Assumes that:
-        - plot.vectors[0][1] is the Y of extension curve
-        - plot.vectors[1][1] is the Y of retraction curve
-        
-       
-        '''
-        #use only for force spectroscopy experiments!
-        if current.curve.experiment != 'smfs':
-            return plot
-    
-        if customvalue != None:
-            execute_me=customvalue
-        else:
-            execute_me=self.config['centerzero']
-        if not execute_me:
-            return plot
-     
-        
-	
-	#levelapp=float(np.median(plot.vectors[0][1]))
-	levelret=float(np.median(plot.vectors[1][1][-300:-1]))
-
-	level=levelret	
-
-	approach=[i-level for i in plot.vectors[0][1]]
-	retract=[i-level for i in plot.vectors[1][1]]
-	
-	plot.vectors[0][1]=approach	
-	plot.vectors[1][1]=retract	
-        return plot
-    
-    '''
-    def plotmanip_detriggerize(self, plot, current, customvalue=None):
-        #DEPRECATED
-        if self.config['detrigger']==0:
-            return plot
-
-        cutindex=2
-        startvalue=plot.vectors[0][0][0]
-
-        for index in range(len(plot.vectors[0][0])-1,2,-2):
-           if plot.vectors[0][0][index]>startvalue:
-                cutindex=index
-           else:
-                break
-
-        plot.vectors[0][0]=plot.vectors[0][0][:cutindex]
-        plot.vectors[0][1]=plot.vectors[0][1][:cutindex]
-
-        return plot
-    '''
-
-
-
-#FFT---------------------------
-    def fft_plot(self, vector):
-        '''
-        calculates the fast Fourier transform for the selected vector in the plot
-        '''
-        fftplot=lhc.PlotObject()
-        fftplot.vectors=[[]]
-
-        fftlen=len(vector)/2 #need just 1/2 of length
-        fftplot.vectors[-1].append(np.arange(1,fftlen).tolist())
-
-        try:
-            fftplot.vectors[-1].append(abs(np.fft(vector)[1:fftlen]).tolist())
-        except TypeError: #we take care of newer NumPy (1.0.x)
-            fftplot.vectors[-1].append(abs(np.fft.fft(vector)[1:fftlen]).tolist())
-
-
-        fftplot.destination=1
-
-
-        return fftplot
-
-
-    def do_fft(self,args):
-        '''
-        FFT
-        (procplots.py plugin)
-        Plots the fast Fourier transform of the selected plot
-        ---
-        Syntax: fft [top,bottom] [select] [0,1...]
-
-        By default, fft performs the Fourier transform on all the 0-th data set on the
-        top plot.
-
-        [top,bottom]: which plot is the data set to fft (default: top)
-        [select]: you pick up two points on the plot and fft only the segment between
-        [0,1,...]: which data set on the selected plot you want to fft (default: 0)
-        '''
-
-        #args parsing
-        #whatplot = plot to fft
-        #whatset = set to fft in the plot
-        select=('select' in args)
-        if 'top' in args:
-            whatplot=0
-        elif 'bottom' in args:
-            whatplot=1
-        else:
-            whatplot=0
-        whatset=0
-        for arg in args:
-            try:
-                whatset=int(arg)
-            except ValueError:
-                pass
-
-        if select:
-            points=self._measure_N_points(N=2, whatset=whatset)
-            boundaries=[points[0].index, points[1].index]
-            boundaries.sort()
-            y_to_fft=self.plots[whatplot].vectors[whatset][1][boundaries[0]:boundaries[1]] #y
-        else:
-            y_to_fft=self.plots[whatplot].vectors[whatset][1] #y
-
-        fftplot=self.fft_plot(y_to_fft)
-        fftplot.units=['frequency', 'power']
-        plot_graph=self.list_of_events['plot_graph']
-        wx.PostEvent(self.frame,plot_graph(plots=[fftplot]))