class procplotsCommands:
- def _plug_init(self):
- pass
-
- def do_convplot(self):
- '''
- CONVPLOT
- (procplots.py)
- Plots the convolution data of the currently displayed force curve retraction.
- ------------
- Syntax:
- convplot
- '''
-
- #need to convert the string that contains the list into a list
- column = self.GetIntFromConfig('procplots', 'convplot', 'column')
- convolution = eval(self.GetStringFromConfig('procplots', 'convplot', 'convolution'))
- row = self.GetIntFromConfig('procplots', 'convplot', 'row')
- whatset_str = self.GetStringFromConfig('procplots', 'convplot', 'whatset')
- whatset = []
- if whatset_str == 'extension':
- whatset = [lh.EXTENSION]
- if whatset_str == 'retraction':
- whatset = [lh.RETRACTION]
- if whatset_str == 'both':
- whatset = [lh.EXTENSION, lh.RETRACTION]
-
- #TODO: add option to keep previous derivplot
- plot = self.GetDisplayedPlotCorrected()
-
- for index in whatset:
- conv_curve = copy.deepcopy(plot.curves[index])
- #Calculate convolution
- conv_curve.y = conv_dx(plot.curves[index].y, convolution)
-
- conv_curve.destination.column = column
- conv_curve.destination.row = row
- conv_curve.title = 'Convolution'
- plot.curves.append(conv_curve)
-
- #warn if no flattening has been done.
- if not self.AppliesPlotmanipulator('flatten'):
- self.AppendToOutput('Flatten manipulator was not applied. Processing was done without flattening.')
- self.AppendToOutput('Enable the flatten plotmanipulator for better results.')
-
- self.UpdatePlot(plot)
-
- def do_derivplot(self):
- '''
- Plots the discrete differentiation of the currently displayed force curve.
- '''
- column = self.GetIntFromConfig('procplots', 'derivplot', 'column')
- row = self.GetIntFromConfig('procplots', 'derivplot', 'row')
- #TODO: what os select good for?
- select = self.GetBoolFromConfig('procplots', 'derivplot', 'select')
- whatset_str = self.GetStringFromConfig('procplots', 'derivplot', 'whatset')
- whatset = []
- if whatset_str == 'extension':
- whatset = [lh.EXTENSION]
- if whatset_str == 'retraction':
- whatset = [lh.RETRACTION]
- if whatset_str == 'both':
- whatset = [lh.EXTENSION, lh.RETRACTION]
-
- #TODO: add option to keep previous derivplot
- plot = self.GetDisplayedPlotCorrected()
-
- for index in whatset:
- deriv_curve = copy.deepcopy(plot.curves[index])
- deriv_curve.x = deriv_curve.x[:-1]
- deriv_curve.y = diff(deriv_curve.y).tolist()
-
- deriv_curve.destination.column = column
- deriv_curve.destination.row = row
- deriv_curve.title = 'Discrete differentiation'
- deriv_curve.units.y += ' ' + deriv_curve.units.x + '-1'
- plot.curves.append(deriv_curve)
-
- self.UpdatePlot(plot)
-
- def do_replot(self):
- '''
- Replots the current force curve from scratch eliminating any secondary plots.
- '''
- self.UpdatePlot()
-
- def do_subtplot(self):
- '''
- SUBTPLOT
- (procplots.py plugin)
- Plots the difference between retraction and extension of the currently displayed curve
- -------
- Syntax: subtplot
- '''
-
- #TODO: add option to keep previous subtplot
- plot = self.GetDisplayedPlotCorrected()
-
- extension = plot.curves[lh.EXTENSION]
- retraction = plot.curves[lh.RETRACTION]
-
- extension, retraction = self.subtract_curves(extension, retraction)
-
- self.UpdatePlot(plot)
-
- def subtract_curves(self, minuend, subtrahend):
- '''
- calculates: difference = minuend - subtrahend
- (usually: extension - retraction
- '''
-
- #we want the same number of points for minuend and subtrahend
- #TODO: is this not already done when normalizing in the driver?
- maxpoints_tot = min(len(minuend.x), len(subtrahend.x))
- minuend.x = minuend.x[0:maxpoints_tot]
- minuend.y = minuend.y[0:maxpoints_tot]
- subtrahend.x = subtrahend.x[0:maxpoints_tot]
- subtrahend.y = subtrahend.y[0:maxpoints_tot]
-
- subtrahend.y = [y_subtrahend - y_minuend for y_subtrahend, y_minuend in zip(subtrahend.y, minuend.y)]
- minuend.y = [0] * len(minuend.x)
-
- return minuend, subtrahend
-
#-----PLOT MANIPULATORS
def plotmanip_median(self, plot, current, customvalue=False):
'''
plot.curves[lh.RETRACTION].x = [(zpoint - deflpoint) for zpoint,deflpoint in zip(plot.curves[lh.RETRACTION].x, defl_ret)]
return plot
-
- def plotmanip_centerzero(self, plot, current, customvalue=False):
- '''
- Centers the force curve so the median (the free level) corresponds to 0 N
- '''
- #use only for force spectroscopy experiments!
- if current.driver.experiment != 'smfs':
- return plot
-
- if not customvalue:
- customvalue = self.GetBoolFromConfig('procplots', 'centerzero')
- if not customvalue:
- return plot
-
- levelapp = float(median(plot.curves[lh.EXTENSION].y))
- levelret = float(median(plot.curves[lh.RETRACTION].y))
-
- level = (levelapp + levelret)/2
-
- plot.curves[lh.EXTENSION].y = [i-level for i in plot.curves[lh.EXTENSION].y]
- plot.curves[lh.RETRACTION].y = [i-level for i in plot.curves[lh.RETRACTION].y]
-
- return plot
-
-#FFT---------------------------
- def fft_plot(self, curve, boundaries=[0, -1]):
- '''
- calculates the fast Fourier transform for the selected vector in the plot
- '''
-
- fftlen = len(curve.y[boundaries[0]:boundaries[1]]) / 2 #need just 1/2 of length
- curve.x = arange(1, fftlen).tolist()
-
- try:
- curve.y = abs(fft(curve.y[boundaries[0]:boundaries[1]])[1:fftlen]).tolist()
- except TypeError: #we take care of newer NumPy (1.0.x)
- curve.y = abs(fft.fft(curve.y[boundaries[0]:boundaries[1]])[1:fftlen]).tolist()
-
- return curve
-
- def do_fft(self):
- '''
- 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)
- '''
-
- column = self.GetIntFromConfig('procplots', 'fft', 'column')
- row = self.GetIntFromConfig('procplots', 'fft', 'row')
- select = self.GetBoolFromConfig('procplots', 'fft', 'select')
- whatset_str = self.GetStringFromConfig('procplots', 'fft', 'whatset')
- whatset = []
- if whatset_str == 'extension':
- whatset = [lh.EXTENSION]
- if whatset_str == 'retraction':
- whatset = [lh.RETRACTION]
- if whatset_str == 'both':
- whatset = [lh.EXTENSION, lh.RETRACTION]
-
- if select:
- points = self._measure_N_points(N=2, message='Please select a region by clicking on the start and the end point.', whatset=lh.RETRACTION)
- boundaries = [points[0].index, points[1].index]
- boundaries.sort()
- else:
- boundaries = [0, -1]
-
- #TODO: add option to keep previous FFT
- plot = self.GetDisplayedPlotCorrected()
-
- for index in whatset:
- fft_curve = self.fft_plot(copy.deepcopy(plot.curves[index]), boundaries)
-
- fft_curve.decimals.x = 3
- fft_curve.decimals.y = 0
- fft_curve.destination.column = column
- fft_curve.destination.row = row
- fft_curve.label = plot.curves[index].label
- fft_curve.legend = True
- fft_curve.prefix.x = lib.prettyformat.get_prefix(max(fft_curve.x))
- fft_curve.prefix.y = lib.prettyformat.get_prefix(max(fft_curve.y))
- fft_curve.title = 'FFT'
- fft_curve.units.x = 'Hz'
- fft_curve.units.y = 'power'
- plot.curves.append(fft_curve)
-
- self.UpdatePlot(plot)
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