From d30fbf5db48d369da4cdaeb97b9a0f1951b41ec8 Mon Sep 17 00:00:00 2001
From: illysam <devnull@localhost>
Date: Fri, 19 Feb 2010 21:07:57 +0000
Subject: [PATCH] hooke.py - added ApplyPlotmanipulators() - added
 configuration support to _delta() - added linewidth option to UpdatePlot() -
 'fixed' GetDisplayedPlot()

hooke configspec.ini
- added curvetools plugin

hooke.ini
- added curvetools plugin
- added multidistance plugin
- removed plot plugin (do_replot() was moved to procplots.py)

curve.py
- added linewidth

playlist.py
- fixed the way the filename is retrieved from the playlist file

plugin.py
- added option section
- removed option key
- added comments

prettyformat.py
- fixed pretty_format() for 0 and NaN

results.py
- added class ResultsMultiDistance()
- fixed set_multipliers()

autopeak.ini/autopeak.py
- renamed 'peak_color' option to 'color'
- removed options: peak_show and peak_size (now in flatfilts.py-do_peaks())
- renamed x_values/y_values to retraction.x/retraction.y, respectively
- removed flatten plotmanipulator option (now in convfilt)

export.ini/export.py
- added append option

flatfilts.ini/flatfilts.py
- added apply_plotmanipulators option
- added configuration support to has_peaks()
- removed exec_has_peaks() as it is no longer necessary

generalvclamp.ini/generalvclamp.py
- added options: color, size to [distance]
- renamed 'show_points' to 'show' in [distance]
- added options: color, show, size to [force]
- added options: color, show, size to [forcebase]
- added options: point_color, point_show, point_size, slope_color, slope_linewidth, slope_show to [slope]
- added configuration support to do_distance(), do_force()

procplots.ini/procplots.py
- added option centerzero
- moved do_replot() form plot.py to procplots.py

results.py
- fixed do_show_results() to work with configuration options
---
 config/hooke configspec.ini |   1 +
 config/hooke.ini            |   3 +-
 hooke.py                    | 130 +++++++++++++++-----------
 lib/curve.py                |   1 +
 lib/libhooke.py             |   3 +-
 lib/playlist.py             |   8 +-
 lib/plugin.py               |  13 ++-
 lib/prettyformat.py         |  32 ++++---
 lib/results.py              |  86 ++++++++++-------
 plugins/autopeak.ini        |  22 +----
 plugins/autopeak.py         | 179 +++++++++++++-----------------------
 plugins/export.ini          |   7 +-
 plugins/export.py           |  36 +++++---
 plugins/flatfilts.ini       |   8 +-
 plugins/flatfilts.py        |  97 ++++++++-----------
 plugins/generalvclamp.ini   |  96 ++++++++++++++++++-
 plugins/generalvclamp.py    | 127 ++++++++++++++++---------
 plugins/procplots.ini       |  15 ++-
 plugins/procplots.py        |  26 +++---
 plugins/results.py          |   3 +-
 20 files changed, 506 insertions(+), 387 deletions(-)

diff --git a/config/hooke configspec.ini b/config/hooke configspec.ini
index 3bb1cda..f1cd81e 100644
--- a/config/hooke configspec.ini	
+++ b/config/hooke configspec.ini	
@@ -27,6 +27,7 @@ active = string(default = Default)
 
 [plugins]
 autopeak = boolean(default = True)
+curvetools = boolean(default = True)
 export = boolean(default = True)
 fit = boolean(default = True)
 flatfilts = boolean(default = True)
diff --git a/config/hooke.ini b/config/hooke.ini
index b803753..6f96553 100644
--- a/config/hooke.ini
+++ b/config/hooke.ini
@@ -39,12 +39,13 @@ default = Default
 #this section defines which plugins have to be loaded by Hooke
 [plugins]
 autopeak = True
+curvetools = True
 export = True
 fit = True
 flatfilts = True
 generalvclamp = True
+multidistance = True
 playlist = True
-plot = True
 procplots = True
 results = True
 
diff --git a/hooke.py b/hooke.py
index 8be70d1..7c7a311 100644
--- a/hooke.py
+++ b/hooke.py
@@ -156,6 +156,8 @@ class HookeFrame(wx.Frame):
         self.plotmanipulators = []
         #self.plugins contains: {the name of the plugin: [caption, function]}
         self.plugins = {}
+        #self.results_str contains the type of results we want to display
+        self.results_str = 'wlc'
 
         #tell FrameManager to manage this frame
         self._mgr = aui.AuiManager()
@@ -440,11 +442,22 @@ class HookeFrame(wx.Frame):
 
     def AppliesPlotmanipulator(self, name):
         '''
-        returns True if the plotmanipulator 'name' is applied, False otherwise
+        Returns True if the plotmanipulator 'name' is applied, False otherwise
         name does not contain 'plotmanip_', just the name of the plotmanipulator (e.g. 'flatten')
         '''
         return self.GetBoolFromConfig('core', 'plotmanipulators', name)
 
+    def ApplyPlotmanipulators(self, plot, plot_file):
+        '''
+        Apply all active plotmanipulators.
+        '''
+        if plot is not None and plot_file is not None:
+            manipulated_plot = copy.deepcopy(plot)
+            for plotmanipulator in self.plotmanipulators:
+                if self.GetBoolFromConfig('core', 'plotmanipulators', plotmanipulator.name):
+                    manipulated_plot = plotmanipulator.method(manipulated_plot, plot_file)
+            return manipulated_plot
+
     def CreateApplicationIcon(self):
         iconFile = 'resources' + os.sep + 'microscope.ico'
         icon = wx.Icon(iconFile, wx.BITMAP_TYPE_ICO)
@@ -613,8 +626,8 @@ class HookeFrame(wx.Frame):
 
     def GetDisplayedPlot(self):
         plot = copy.deepcopy(self.displayed_plot)
-        plot.curves = []
-        plot.curves = copy.deepcopy(plot.curves)
+        #plot.curves = []
+        #plot.curves = copy.deepcopy(plot.curves)
         return plot
 
     def GetDisplayedPlotCorrected(self):
@@ -926,9 +939,10 @@ class HookeFrame(wx.Frame):
     def OnResultsCheck(self, index, flag):
         #TODO: fix for multiple results
         results = self.GetActivePlot().results
-        fit_function_str = self.GetStringFromConfig('results', 'show_results', 'fit_function')
-        results[fit_function_str].results[index].visible = flag
-        self.UpdatePlot()
+        if results.has_key(self.results_str):
+            results[self.results_str].results[index].visible = flag
+            results[self.results_str].update()
+            self.UpdatePlot()
 
     def OnSavePerspective(self, event):
 
@@ -1047,35 +1061,6 @@ class HookeFrame(wx.Frame):
             self.panelFolders.Fit()
         self._mgr.Update()
 
-    def _measure_N_points(self, N, message='', whatset=lh.RETRACTION):
-        '''
-        General helper function for N-points measurements
-        By default, measurements are done on the retraction
-        '''
-        if message != '':
-            dialog = wx.MessageDialog(None, message, 'Info', wx.OK)
-            dialog.ShowModal()
-
-        figure = self.GetActiveFigure()
-
-        xvector = self.displayed_plot.curves[whatset].x
-        yvector = self.displayed_plot.curves[whatset].y
-
-        clicked_points = figure.ginput(N, timeout=-1, show_clicks=True)
-
-        points = []
-        for clicked_point in clicked_points:
-            point = lh.ClickedPoint()
-            point.absolute_coords = clicked_point[0], clicked_point[1]
-            point.dest = 0
-            #TODO: make this optional?
-            #so far, the clicked point is taken, not the corresponding data point
-            point.find_graph_coords(xvector, yvector)
-            point.is_line_edge = True
-            point.is_marker = True
-            points.append(point)
-        return points
-
     def _clickize(self, xvector, yvector, index):
         '''
         returns a ClickedPoint() object from an index and vectors of x, y coordinates
@@ -1086,10 +1071,25 @@ class HookeFrame(wx.Frame):
         point.find_graph_coords(xvector, yvector)
         return point
 
-    def _delta(self, color='black', message='Click 2 points', show=True, whatset=1):
+    def _delta(self, message='Click 2 points', plugin=None):
         '''
         calculates the difference between two clicked points
         '''
+        if plugin is None:
+            color = 'black'
+            show_points = True
+            size = 20
+            whatset = lh.RETRACTION
+        else:
+            color = self.GetColorFromConfig(plugin.name, plugin.section, plugin.prefix + 'color')
+            show_points = self.GetBoolFromConfig(plugin.name, plugin.section, plugin.prefix + 'show_points')
+            size = self.GetIntFromConfig(plugin.name, plugin.section, plugin.prefix + 'size')
+            whatset_str = self.GetStringFromConfig(plugin.name, plugin.section, plugin.prefix + 'whatset')
+            if whatset_str == 'extension':
+                whatset = lh.EXTENSION
+            if whatset_str == 'retraction':
+                whatset = lh.RETRACTION
+
         clicked_points = self._measure_N_points(N=2, message=message, whatset=whatset)
         dx = abs(clicked_points[0].graph_coords[0] - clicked_points[1].graph_coords[0])
         dy = abs(clicked_points[0].graph_coords[1] - clicked_points[1].graph_coords[1])
@@ -1101,14 +1101,14 @@ class HookeFrame(wx.Frame):
         unity = curve.units.y
 
         #TODO: move this to clicked_points?
-        if show:
+        if show_points:
             for point in clicked_points:
                 points = copy.deepcopy(curve)
                 points.x = point.graph_coords[0]
                 points.y = point.graph_coords[1]
 
                 points.color = color
-                points.size = 20
+                points.size = size
                 points.style = 'scatter'
                 plot.curves.append(points)
 
@@ -1116,6 +1116,35 @@ class HookeFrame(wx.Frame):
 
         return dx, unitx, dy, unity
 
+    def _measure_N_points(self, N, message='', whatset=lh.RETRACTION):
+        '''
+        General helper function for N-points measurements
+        By default, measurements are done on the retraction
+        '''
+        if message != '':
+            dialog = wx.MessageDialog(None, message, 'Info', wx.OK)
+            dialog.ShowModal()
+
+        figure = self.GetActiveFigure()
+
+        xvector = self.displayed_plot.curves[whatset].x
+        yvector = self.displayed_plot.curves[whatset].y
+
+        clicked_points = figure.ginput(N, timeout=-1, show_clicks=True)
+
+        points = []
+        for clicked_point in clicked_points:
+            point = lh.ClickedPoint()
+            point.absolute_coords = clicked_point[0], clicked_point[1]
+            point.dest = 0
+            #TODO: make this optional?
+            #so far, the clicked point is taken, not the corresponding data point
+            point.find_graph_coords(xvector, yvector)
+            point.is_line_edge = True
+            point.is_marker = True
+            points.append(point)
+        return points
+
     def do_plotmanipulators(self):
         '''
         Please select the plotmanipulators you would like to use
@@ -1215,7 +1244,7 @@ class HookeFrame(wx.Frame):
                 axes_list[destination].set_xlabel(curve.units.x)
                 axes_list[destination].set_ylabel(curve.units.y)
                 if curve.style == 'plot':
-                    axes_list[destination].plot(curve.x, curve.y, color=curve.color, label=curve.label, zorder=1)
+                    axes_list[destination].plot(curve.x, curve.y, color=curve.color, label=curve.label, lw=curve.linewidth, zorder=1)
                 if curve.style == 'scatter':
                     axes_list[destination].scatter(curve.x, curve.y, color=curve.color, label=curve.label, s=curve.size, zorder=2)
 
@@ -1226,10 +1255,8 @@ class HookeFrame(wx.Frame):
             self.displayed_plot = copy.deepcopy(active_file.plot)
             #add raw curves to plot
             self.displayed_plot.raw_curves = copy.deepcopy(self.displayed_plot.curves)
-            #apply all active plotmanipulators and add the 'manipulated' data
-            for plotmanipulator in self.plotmanipulators:
-                if self.GetBoolFromConfig('core', 'plotmanipulators', plotmanipulator.name):
-                    self.displayed_plot = plotmanipulator.method(self.displayed_plot, active_file)
+            #apply all active plotmanipulators
+            self.displayed_plot = self.ApplyPlotmanipulators(self.displayed_plot, active_file)
             #add corrected curves to plot
             self.displayed_plot.corrected_curves = copy.deepcopy(self.displayed_plot.curves)
         else:
@@ -1256,17 +1283,14 @@ class HookeFrame(wx.Frame):
         figure.subplots_adjust(hspace=0.3)
 
         #TODO: add multiple results support to fit in curve.results:
-        #get the fit_function results to display
-        fit_function_str = self.GetStringFromConfig('results', 'show_results', 'fit_function')
+        #display results
         self.panelResults.ClearResults()
-        plot = self.GetActivePlot()
-        if plot is not None:
-            if plot.results.has_key(fit_function_str):
-                for curve in plot.results[fit_function_str].results:
-                    add_to_plot(curve)
-                self.panelResults.DisplayResults(plot.results[fit_function_str])
-            else:
-                self.panelResults.ClearResults()
+        if self.displayed_plot.results.has_key(self.results_str):
+            for curve in self.displayed_plot.results[self.results_str].results:
+                add_to_plot(curve)
+            self.panelResults.DisplayResults(self.displayed_plot.results[self.results_str])
+        else:
+            self.panelResults.ClearResults()
 
         figure.canvas.draw()
 
diff --git a/lib/curve.py b/lib/curve.py
index 176d7bf..0d81a96 100644
--- a/lib/curve.py
+++ b/lib/curve.py
@@ -16,6 +16,7 @@ class Curve(object):
         self.color = 'blue'
         self.destination = Destination()
         self.label = ''
+        self.linewidth = 1
         self.size = 0.5
         self.style = 'plot'
         self.title = ''
diff --git a/lib/libhooke.py b/lib/libhooke.py
index f69f2d2..11d8565 100644
--- a/lib/libhooke.py
+++ b/lib/libhooke.py
@@ -74,9 +74,8 @@ class ClickedPoint(object):
 
         self.index=dists.index(min(dists))
         self.graph_coords=(xvector[self.index], yvector[self.index])
-#-----------------------------------------
-#CSV-HELPING FUNCTIONS
 
+#CSV-HELPING FUNCTIONS
 def transposed2(lists, defval=0):
     '''
     transposes a list of lists, i.e. from [[a,b,c],[x,y,z]] to [[a,x],[b,y],[c,z]] without losing
diff --git a/lib/playlist.py b/lib/playlist.py
index c82e697..92b9629 100644
--- a/lib/playlist.py
+++ b/lib/playlist.py
@@ -24,7 +24,7 @@ class Playlist(object):
         self.figure = None
         self.files = []
         self.generics_dict = {}
-        self.hidden_attributes = ['curve', 'data', 'driver', 'fits', 'name', 'plots']
+        self.hidden_attributes = ['curve', 'data', 'driver', 'fits', 'name', 'plot', 'plots']
         self.index = -1
         self.name = None
         self.path = None
@@ -75,7 +75,7 @@ class Playlist(object):
 
     def load(self, filename):
         '''
-        loads a playlist file
+        Loads a playlist file
         '''
         self.filename = filename
         self.path, self.name = os.path.split(filename)
@@ -91,9 +91,9 @@ class Playlist(object):
             #rebuild a data structure from the xml attributes
             #the next two lines are here for backwards compatibility, newer playlist files use 'filename' instead of 'path'
             if element.hasAttribute('path'):
-                filename = lib.libhooke.get_file_path(element.getAttribute('path'))
+                filename = element.getAttribute('path')
             if element.hasAttribute('filename'):
-                filename = lib.libhooke.get_file_path(element.getAttribute('filename'))
+                filename = element.getAttribute('filename')
             if os.path.isfile(filename):
                 data_file = lib.file.File(filename)
                 self.files.append(data_file)
diff --git a/lib/plugin.py b/lib/plugin.py
index a4641a6..24364cb 100644
--- a/lib/plugin.py
+++ b/lib/plugin.py
@@ -11,8 +11,19 @@ This program is released under the GNU General Public License version 2.
 '''
 
 class Plugin(object):
+    '''
+    Plugin is a class that is used to facilitate accessing
+    configuration parameters in a ConfigObj from different plugins.
+    '''
 
     def __init__(self):
-        self.key = ''
         self.name = ''
+        #if the calling plugin uses a prefix, this can be added to the name
+        #e.g. autopeak.ini: [[peak_color]]
+        #flatfilts.ini [[color]]
+        #are both used to set the color of the peak plot (scatter plot)
+        #in order to access 'peak_color' rather than 'color', the prefix needs to
+        #be set to 'peak_'
+        #if the names are identical, set prefix to ''
         self.prefix = ''
+        self.section = ''
diff --git a/lib/prettyformat.py b/lib/prettyformat.py
index b346115..7297e66 100644
--- a/lib/prettyformat.py
+++ b/lib/prettyformat.py
@@ -19,22 +19,24 @@ import math
 from numpy import isnan
 
 def pretty_format(fValue, sUnit='', iDecimals=-1, iMultiplier=1, bLeadingSpaces=False):
-    if fValue != 0:
-        iLeadingSpaces = 0
-        if bLeadingSpaces:
-            iLeadingSpaces = 5
-        if iMultiplier == 1:
-            iMultiplier=get_multiplier(fValue)
-        sUnitString = ''
-        if sUnit != '':
-            sUnitString = ' ' + get_prefix(iMultiplier) + sUnit
-        if iDecimals >= 0:
-            formatString = '% ' + repr(iLeadingSpaces + iDecimals) + '.' + repr(iDecimals) + 'f'
-            return formatString % (fValue / iMultiplier) + sUnitString
-        else:
-            return str(fValue / iMultiplier) + sUnitString
-    else:
+    if fValue == 0:
         return '0'
+    if isnan(fValue):
+        return 'NaN'
+
+    iLeadingSpaces = 0
+    if bLeadingSpaces:
+        iLeadingSpaces = 5
+    if iMultiplier == 1:
+        iMultiplier=get_multiplier(fValue)
+    sUnitString = ''
+    if sUnit != '':
+        sUnitString = ' ' + get_prefix(iMultiplier) + sUnit
+    if iDecimals >= 0:
+        formatString = '% ' + repr(iLeadingSpaces + iDecimals) + '.' + repr(iDecimals) + 'f'
+        return formatString % (fValue / iMultiplier) + sUnitString
+    else:
+        return str(fValue / iMultiplier) + sUnitString
     return str(fValue / iMultiplier) + ' ' + get_prefix(fValue / iMultiplier) + sUnit
 
 def get_multiplier(fValue):
diff --git a/lib/results.py b/lib/results.py
index 7535ac9..644fc85 100644
--- a/lib/results.py
+++ b/lib/results.py
@@ -10,6 +10,8 @@ Copyright 2009 by Dr. Rolf Schmidt (Concordia University, Canada)
 This program is released under the GNU General Public License version 2.
 '''
 
+from numpy import nan
+
 import prettyformat
 import lib.curve
 
@@ -127,16 +129,18 @@ class Results(object):
 
     def set_multipliers(self, index=0):
         if self.has_results():
-            if index >= 0 and index < len(self.results):
-                for column in self.columns:
-                    #result will contain the results dictionary at 'index'
-                    result = self.results[index][0]
-                    #in position 0 of the result we find the value
-                    self.multipliers[column] = prettyformat.get_multiplier(result[column][0])
-                self.has_multipliers = True
+            for column in self.columns:
+                #result will contain the results dictionary at 'index'
+                result = self.results[index].result
+                #in position 0 of the result we find the value
+                self.multipliers[column] = prettyformat.get_multiplier(result[column])
+            self.has_multipliers = True
         else:
             self.has_multipliers = False
 
+    def update(self):
+        pass
+
 
 class ResultsFJC(Results):
     def __init__(self):
@@ -153,21 +157,42 @@ class ResultsFJC(Results):
 
     def set_multipliers(self, index=0):
         if self.has_results():
-            if index >= 0 and index < len(self.results):
-                for column in self.columns:
-                    #result will contain the results dictionary at 'index'
-                    result = self.results[index].result
-                    #in position 0 of the result we find the value
-                    if column == 'sigma contour length':
-                        self.multipliers[column] = self.multipliers['Contour length']
-                    elif column == 'sigma Kuhn length':
-                        self.multipliers[column] = self.multipliers['Kuhn length']
-                    else:
-                        self.multipliers[column] = prettyformat.get_multiplier(result[column])
-                self.has_multipliers = True
+            for column in self.columns:
+                #result will contain the results dictionary at 'index'
+                result = self.results[index].result
+                #in position 0 of the result we find the value
+                if column == 'sigma contour length':
+                    self.multipliers[column] = self.multipliers['Contour length']
+                elif column == 'sigma Kuhn length':
+                    self.multipliers[column] = self.multipliers['Kuhn length']
+                else:
+                    self.multipliers[column] = prettyformat.get_multiplier(result[column])
+            self.has_multipliers = True
         else:
             self.has_multipliers = False
 
+class ResultsMultiDistance(Results):
+    def __init__(self):
+        Results.__init__(self)
+        self.columns = ['Distance']
+        self.units['Distance'] = 'm'
+        self.set_decimals(2)
+
+    def update(self):
+        if (self.results) > 0:
+            for result in self.results:
+                if result.visible:
+                    reference_peak = result.x
+                    break
+
+            for result in self.results:
+                if result.visible:
+                    result.result['Distance'] = reference_peak - result.x
+                    reference_peak = result.x
+                else:
+                    result.result['Distance'] = nan
+
+
 class ResultsWLC(Results):
     def __init__(self):
         Results.__init__(self)
@@ -183,17 +208,16 @@ class ResultsWLC(Results):
 
     def set_multipliers(self, index=0):
         if self.has_results():
-            if index >= 0 and index < len(self.results):
-                for column in self.columns:
-                    #result will contain the results dictionary at 'index'
-                    result = self.results[index].result
-                    #in position 0 of the result we find the value
-                    if column == 'sigma contour length':
-                        self.multipliers[column] = self.multipliers['Contour length']
-                    elif column == 'sigma persistence length':
-                        self.multipliers[column] = self.multipliers['Persistence length']
-                    else:
-                        self.multipliers[column] = prettyformat.get_multiplier(result[column])
-                self.has_multipliers = True
+            for column in self.columns:
+                #result will contain the results dictionary at 'index'
+                result = self.results[index].result
+                #in position 0 of the result we find the value
+                if column == 'sigma contour length':
+                    self.multipliers[column] = self.multipliers['Contour length']
+                elif column == 'sigma persistence length':
+                    self.multipliers[column] = self.multipliers['Persistence length']
+                else:
+                    self.multipliers[column] = prettyformat.get_multiplier(result[column])
+            self.has_multipliers = True
         else:
             self.has_multipliers = False
diff --git a/plugins/autopeak.ini b/plugins/autopeak.ini
index d2c5b23..88fb6c0 100644
--- a/plugins/autopeak.ini
+++ b/plugins/autopeak.ini
@@ -47,6 +47,11 @@
         type = enum
         value = contact point
     
+    [[color]]
+        default = black
+        type = color
+        value = "(255,0,128)"
+    
     [[fit_function]]
         default = wlc
         elements = wlc, fjc, fjcPEG
@@ -63,23 +68,6 @@
         type = boolean
         value = False
     
-    [[peak_color]]
-        default = black
-        type = color
-        value = "(255,128,0)"
-    
-    [[peak_show]]
-        default = False
-        type = boolean
-        value = False
-    
-    [[peak_size]]
-        default = 20
-        maximum = 10000
-        minimum = 1
-        type = integer
-        value = 50
-    
     [[persistence_length]]
         default = 0.35e-9
         minimum = 0
diff --git a/plugins/autopeak.py b/plugins/autopeak.py
index 6e6d5a2..2951ca4 100644
--- a/plugins/autopeak.py
+++ b/plugins/autopeak.py
@@ -21,7 +21,6 @@ from numpy import mean, RankWarning
 import warnings
 warnings.simplefilter('ignore', RankWarning)
 
-#import config
 import lib.plugin
 import lib.results
 
@@ -69,49 +68,47 @@ class autopeakCommands:
 
         usepoints : fit interval by number of points instead than by nanometers
 
-        noflatten : does not use the "flatten" plot manipulator
-
-        When you first issue the command, it will ask for the filename. If you are giving the filename
-        of an existing file, autopeak will resume it and append measurements to it. If you are giving
-        a new filename, it will create the file and append to it until you close Hooke.
-
-
-        Useful variables (to set with SET command):
-        ---
-        fit_function = type of function to use for elasticity. If "wlc" worm-like chain is used, if "fjc" freely jointed
-                       chain is used
-
-        temperature= temperature of the system for wlc/fjc fit (in K)
-
-        auto_slope_span = number of points on which measure the slope, for slope
-
-        auto_fit_nm = number of nm to fit before the peak maximum, for WLC/FJC (if usepoints false)
-        auto_fit_points = number of points to fit before the peak maximum, for WLC/FJC (if usepoints true)
-
-        baseline_clicks = contact point: no baseline, f=0 at the contact point (whether hand-picked or automatically found)
-                          automatic:     automatic baseline
-                          1 point:       decide baseline with a single click and length defined in auto_left_baseline
-                          2 points:      let user click points of baseline
-        auto_left_baseline = length in nm to use as baseline from the right point (if baseline_clicks = automatic , 1 point)
-        auto_right_baseline = distance in nm of peak-most baseline point from last peak (if baseline_clicks = automatic)
-
-        auto_min_p ; auto_max_p = Minimum and maximum persistence length (if using WLC) or Kuhn length (if using FJC)
-                                  outside of which the peak is automatically discarded (in nm)
+        Configuration
+        -------------
+        apply_plotmanipulators:
+            - all (all selected plotmanipulators will be applied)
+            - flatten (only the flatten plotmanipulator will be applied)
+            - none (no plotmanipulators will be applied)
+        fit_function: type of function to use for elasticity. If "wlc" worm-like chain is used, if "fjc" freely jointed
+                      chain is used
+
+        temperature: temperature of the system for WLC/FJC fit (in K)
+
+        auto_slope_span: number of points on which measure the slope, for slope
+
+        auto_fit_nm: number of nm to fit before the peak maximum, for WLC/FJC (if usepoints false)
+        auto_fit_points: number of points to fit before the peak maximum, for WLC/FJC (if usepoints true)
+
+        baseline_clicks:
+            contact point: no baseline, f=0 at the contact point (whether hand-picked or automatically found)
+            automatic:     automatic baseline
+            1 point:       decide baseline with a single click and length defined in auto_left_baseline
+            2 points:      let user click points of baseline
+        auto_left_baseline: length in nm to use as baseline from the right point (if baseline_clicks = automatic , 1 point)
+        auto_right_baseline: distance in nm of peak-most baseline point from last peak (if baseline_clicks = automatic)
+
+        auto_max_p: Maximum persistence length (if using WLC) or Kuhn length (if using FJC)
+                    outside of which the peak is automatically discarded (in nm)
+        auto_min_p: Minimum persistence length (if using WLC) or Kuhn length (if using FJC)
+                    outside of which the peak is automatically discarded (in nm)
         '''
 
-        #default fit etc. variables
+        #default variables
         auto_fit_nm = self.GetFloatFromConfig('autopeak', 'auto_fit_nm')
         auto_left_baseline = self.GetFloatFromConfig('autopeak', 'auto_left_baseline')
         auto_max_p = self.GetFloatFromConfig('autopeak', 'auto_max_p')
         auto_min_p = self.GetFloatFromConfig('autopeak', 'auto_min_p')
         auto_right_baseline = self.GetFloatFromConfig('autopeak', 'auto_right_baseline')
         baseline_clicks = self.GetStringFromConfig('autopeak', 'baseline_clicks')
+        color = self.GetColorFromConfig('autopeak', 'color')
         fit_function = self.GetStringFromConfig('autopeak', 'fit_function')
         fit_points = self.GetIntFromConfig('autopeak', 'auto_fit_points')
         noauto = self.GetBoolFromConfig('autopeak', 'noauto')
-        #noflatten: if true we do not flatten the curve
-        noflatten = self.GetBoolFromConfig('autopeak', 'noflatten')
-        peak_show = self.GetBoolFromConfig('autopeak', 'peak_show')
         persistence_length = self.GetFloatFromConfig('autopeak', 'persistence_length')
         #rebase: redefine the baseline
         rebase = self.GetBoolFromConfig('autopeak', 'rebase')
@@ -154,24 +151,19 @@ class autopeakCommands:
         forces = []
         slopes = []
 
-        #pick up plot
+        #pick up plot and filename
         if plot is None:
-            plot = copy.deepcopy(self.GetActivePlot())
+            plot = self.GetDisplayedPlotCorrected()
         filename = self.GetActiveFile().name
 
-        #apply all active plotmanipulators and add the 'manipulated' data
-        for plotmanipulator in self.plotmanipulators:
-            if self.GetBoolFromConfig('core', 'plotmanipulators', plotmanipulator.name):
-                if plotmanipulator.name == 'flatten':
-                    if not noflatten:
-                        plot = plotmanipulator.method(plot, self.GetActiveFile())
-                else:
-                    plot = plotmanipulator.method(plot, self.GetActiveFile())
-
+        TODO: add convfilt option?
         #--Using points instead of nm interval
         if not usepoints:
             fit_points = None
 
+        extension = plot.curves[lh.EXTENSION]
+        retraction = plot.curves[lh.RETRACTION]
+
         #--Contact point arguments
         if reclick:
             contact_point, contact_point_index = self.pickup_contact_point(filename=filename)
@@ -184,10 +176,10 @@ class autopeakCommands:
         else:
             #Automatically find contact point
             cindex = self.find_contact_point(plot)
-            contact_point = self._clickize(plot.curves[lh.RETRACTION].x, plot.curves[lh.EXTENSION].y, cindex)
+            contact_point = self._clickize(retraction.x, extension.y, cindex)
 
         #peak_size comes from convolution curve
-        peak_location, peak_size = self.find_current_peaks(plot=plot, noflatten=noflatten)
+        peak_location, peak_size = self.has_peaks(plot)
 
         if len(peak_location) == 0:
             self.AppendToOutput('No peaks to fit.')
@@ -196,39 +188,37 @@ class autopeakCommands:
         #Pick up force baseline
         if baseline_clicks == 'contact point':
             try:
-                avg = plot.curves[lh.RETRACTION].y[contact_point_index]
+                avg = retraction.y[contact_point_index]
             except:
-                avg = plot.curves[lh.RETRACTION].y[cindex]
+                avg = retraction.y[cindex]
 
         if rebase or (self.basecurrent != filename) or self.basepoints is None:
             if baseline_clicks == 'automatic':
                 self.basepoints = []
-                base_index_0 = peak_location[-1] + self.fit_interval_nm(peak_location[-1], plot.curves[lh.RETRACTION].x, auto_right_baseline, False)
-                self.basepoints.append(self._clickize(plot.curves[lh.RETRACTION].x, plot.curves[lh.RETRACTION].y, base_index_0))
-                base_index_1 = self.basepoints[0].index + self.fit_interval_nm(self.basepoints[0].index, plot.curves[lh.RETRACTION].x, auto_left_baseline, False)
-                self.basepoints.append(self._clickize(plot.curves[lh.RETRACTION].x, plot.curves[lh.RETRACTION].y, base_index_1))
+                base_index_0 = peak_location[-1] + self.fit_interval_nm(peak_location[-1], retraction.x, auto_right_baseline, False)
+                self.basepoints.append(self._clickize(retraction.x, retraction.y, base_index_0))
+                base_index_1 = self.basepoints[0].index + self.fit_interval_nm(self.basepoints[0].index, retraction.x, auto_left_baseline, False)
+                self.basepoints.append(self._clickize(retraction.x, retraction.y, base_index_1))
             if baseline_clicks == '1 point':
                 self.basepoints=self._measure_N_points(N=1, message='Click on 1 point to select the baseline.', whatset=whatset)
-                base_index_1 = self.basepoints[0].index + self.fit_interval_nm(self.basepoints[0].index, plot.curves[lh.RETRACTION].x, auto_left_baseline, False)
-                self.basepoints.append(self._clickize(plot.curves[lh.RETRACTION].x, plot.curves[lh.RETRACTION].y, base_index_1))
+                base_index_1 = self.basepoints[0].index + self.fit_interval_nm(self.basepoints[0].index, retraction.x, auto_left_baseline, False)
+                self.basepoints.append(self._clickize(retraction.x, retraction.y, base_index_1))
             if baseline_clicks == '2 points':
                 self.basepoints=self._measure_N_points(N=2, message='Click on 2 points to select the baseline.', whatset=whatset)
         if baseline_clicks != 'contact point':
             boundaries=[self.basepoints[0].index, self.basepoints[1].index]
             boundaries.sort()
-            to_average = plot.curves[lh.RETRACTION].y[boundaries[0]:boundaries[1]] #y points to average
+            to_average = retraction.y[boundaries[0]:boundaries[1]] #y points to average
             avg = mean(to_average)
             self.basecurrent = filename
 
-        x_values = plot.curves[lh.RETRACTION].x
-        y_values = plot.curves[lh.RETRACTION].y
         for index, peak in enumerate(peak_location):
             #WLC FITTING
             #define fit interval
             if not usepoints:
-                fit_points = self.fit_interval_nm(peak, plot.curves[lh.RETRACTION].x, auto_fit_nm, True)
-            peak_point = self._clickize(x_values, y_values, peak)
-            other_fit_point=self._clickize(x_values, y_values, peak - fit_points)
+                fit_points = self.fit_interval_nm(peak, retraction.x, auto_fit_nm, True)
+            peak_point = self._clickize(retraction.x, retraction.y, peak)
+            other_fit_point=self._clickize(retraction.x, retraction.y, peak - fit_points)
 
             #points for the fit
             points = [contact_point, peak_point, other_fit_point]
@@ -237,18 +227,20 @@ class autopeakCommands:
                 continue
 
             if fit_function == 'wlc':
-                params, yfit, xfit, fit_errors = self.wlc_fit(points, x_values, y_values, pl_value, T, return_errors=True)
+                params, yfit, xfit, fit_errors = self.wlc_fit(points, retraction.x, retraction.y, pl_value, T, return_errors=True)
             elif fit_function == 'fjc':
-                params, yfit, xfit, fit_errors = self.fjc_fit(points, x_values, y_values, pl_value, T, return_errors=True)
+                params, yfit, xfit, fit_errors = self.fjc_fit(points, retraction.x, retraction.y, pl_value, T, return_errors=True)
             elif fit_function == 'fjcPEG':
-                params, yfit, xfit, fit_errors = self.fjcPEG_fit(points, x_values, y_values, pl_value, T, return_errors=True)
+                params, yfit, xfit, fit_errors = self.fjcPEG_fit(points, retraction.x, retraction.y, pl_value, T, return_errors=True)
+
+            self.results_str = fit_function
 
             #Measure forces
-            delta_to_measure = y_values[peak - delta_force:peak + delta_force]
+            delta_to_measure = retraction.y[peak - delta_force:peak + delta_force]
             y = min(delta_to_measure)
             #save force values (pN)
             #Measure slopes
-            slope = self.linefit_between(peak - slope_span, peak, whatset=lh.RETRACTION)[0]
+            slope = self.linefit_between(peak - slope_span, peak, whatset=whatset)[0]
 
             #check fitted data and, if right, add peak to the measurement
             fit_result = lib.results.Result()
@@ -289,10 +281,11 @@ class autopeakCommands:
                     fit_result.result = {}
 
             if len(fit_result.result) > 0:
+                fit_result.color = color
                 fit_result.label = fit_function + '_' + str(index)
-                fit_result.title = plot.curves[lh.RETRACTION].title
-                fit_result.units.x = plot.curves[lh.RETRACTION].units.x
-                fit_result.units.y = plot.curves[lh.RETRACTION].units.y
+                fit_result.title = retraction.title
+                fit_result.units.x = retraction.units.x
+                fit_result.units.y = retraction.units.y
                 fit_result.visible = True
                 fit_result.x = xfit
                 fit_result.y = yfit
@@ -302,57 +295,9 @@ class autopeakCommands:
             fit_results.set_multipliers(0)
             plot = self.GetActivePlot()
             plot.results[fit_function] = fit_results
-            if peak_show:
-                plugin = lib.plugin.Plugin()
-                plugin.name = 'autopeak'
-                plugin.section = 'autopeak'
-                plugin.prefix = 'peak_'
-                self.do_peaks(plugin=plugin, peak_location=peak_location, peak_size=peak_size)
-            else:
-                self.UpdatePlot()
-
+            self.UpdatePlot()
         else:
             self.AppendToOutput('No peaks found.')
 
         #TODO:
         #self.do_note('autopeak')
-
-    def find_current_peaks(self, plot=None, noflatten=True):
-        if not noflatten:
-            plot_temp = self.plotmanip_flatten(plot, self.GetActiveFile(), customvalue=1)
-        peak_location, peak_size = self.has_peaks(plot_temp)
-        return peak_location, peak_size
-
-    def fit_interval_nm(self, start_index, x_vect, nm, backwards):
-        '''
-        Calculates the number of points to fit, given a fit interval in nm
-        start_index: index of point
-        plot: plot to use
-        backwards: if true, finds a point backwards.
-        '''
-
-        c = 0
-        i = start_index
-        maxlen=len(x_vect)
-        while abs(x_vect[i] - x_vect[start_index]) * (10**9) < nm:
-            if i == 0 or i == maxlen-1: #we reached boundaries of vector!
-                return c
-            if backwards:
-                i -= 1
-            else:
-                i += 1
-            c += 1
-        return c
-
-    def pickup_contact_point(self, filename=''):
-        '''
-        macro to pick up the contact point by clicking
-        '''
-        contact_point = self._measure_N_points(N=1, message='Please click on the contact point.')[0]
-        contact_point_index = contact_point.index
-        self.wlccontact_point = contact_point
-        self.wlccontact_index = contact_point.index
-        self.wlccurrent = filename
-        return contact_point, contact_point_index
-
-
diff --git a/plugins/export.ini b/plugins/export.ini
index da8db68..a46f0bb 100644
--- a/plugins/export.ini
+++ b/plugins/export.ini
@@ -47,6 +47,11 @@
         value = _
 
 [results]
+    [[append]]
+        default = True
+        type = boolean
+        value = True
+    
     [[filename]]
         default = fit export.txt
         type = filename
@@ -56,5 +61,3 @@
         default = ","
         type = string
         value = ", "
-
-        
diff --git a/plugins/export.py b/plugins/export.py
index a111c0d..171f943 100644
--- a/plugins/export.py
+++ b/plugins/export.py
@@ -27,14 +27,9 @@ class exportCommands(object):
     def _plug_init(self):
         pass
 
-    def do_fits(self):#, ext='', folder='', prefix='', separator=''):
+    def do_fits(self):
         '''
-        Exports all approach and retraction files in a playlist and
-        all fitting results (if available) in a columnar ASCII format.
-        Please make sure that the number of points in the fit is smaller
-        or equal to the number of points in the approach/retraction.
-        For the time being, exports only one set of results (e.g. WLC
-        or FJC, not both).
+        Exports all fitting results (if available) in a columnar ASCII format.
         '''
 
         ext = self.GetStringFromConfig('export', 'fits', 'ext')
@@ -47,7 +42,6 @@ class exportCommands(object):
         active_file = self.GetActiveFile()
         plot = self.GetDisplayedPlot()
 
-        #TODO: fix for multiple results
         #add empty columns before adding new results if necessary
         if plot is not None:
             for results_str, results in plot.results.items():
@@ -88,18 +82,22 @@ class exportCommands(object):
         #add string for Other
 
         active_file = self.GetActiveFile()
-        plot = self.GetActivePlot()
-        extension = plot.curves[lh.EXTENSION]
-        retraction = plot.curves[lh.RETRACTION]
+        #create the header from the raw plot (i.e. only the force curve)
+        plot = self.GetDisplayedPlotRaw()
 
         output = []
         header_str = ''
         for index, curve in enumerate(plot.curves):
+            #TODO: only add labels for original curves (i.e. excluding anything added after the fact)
             header_str += curve.label + '_x (' + curve.units.x + ')' + separator + curve.label + '_y (' + curve.units.y + ')'
             if index < len(plot.curves) - 1:
                 header_str += separator
         output.append(header_str)
-        #TODO: add units
+
+        #export the displayed plot
+        plot = self.GetDisplayedPlot()
+        extension = plot.curves[lh.EXTENSION]
+        retraction = plot.curves[lh.RETRACTION]
         for index, row in enumerate(extension.x):
             output.append(separator.join([str(extension.x[index]), str(extension.y[index]), str(retraction.x[index]), str(retraction.y[index])]))
 
@@ -171,11 +169,15 @@ class exportCommands(object):
                 output_file.close
         progress_dialog.Destroy()
 
-    def do_results(self, filename='', separator=''):
+    def do_results(self, append=None, filename='', separator=''):
         '''
-        EXPORTFITS
         Exports all visible fit results in a playlist into a delimited text file
+        append: set append to True if you want to append to an existing results file
+        filename: the filename and path of the results file
+        separator: the separator between columns
         '''
+        if not append:
+            append = self.GetStringFromConfig('export', 'results', 'append')
         if filename == '':
             filename = self.GetStringFromConfig('export', 'results', 'filename')
         if separator == '':
@@ -203,7 +205,11 @@ class exportCommands(object):
                             output_str = ''.join([output_str, line_str, '\n'])
         if output_str != '':
             output_str = ''.join(['Analysis started ', time.asctime(), '\n', output_str])
-            output_file = open(filename, 'w')
+
+            if append and os.path.isfile(filename):
+		output_file = open(filename,'a')
+	    else:
+		output_file = open(filename, 'w')
             output_file.write(output_str)
             output_file.close
         else:
diff --git a/plugins/flatfilts.ini b/plugins/flatfilts.ini
index 3a6f604..3a0168b 100644
--- a/plugins/flatfilts.ini
+++ b/plugins/flatfilts.ini
@@ -1,4 +1,10 @@
 [convfilt]
+    [[apply_plotmanipulators]]
+        default = all
+        elements = all, flatten, none
+        type = enum
+        value = all
+    
     [[blindwindow]]
         default = 20
         maximum = 10000
@@ -86,7 +92,7 @@
     [[color]]
         default = black
         type = color
-        value = "(255,0,128)"
+        value = "(128,128,128)"
     
     [[size]]
         default = 20
diff --git a/plugins/flatfilts.py b/plugins/flatfilts.py
index 9ce8a93..d1814e1 100644
--- a/plugins/flatfilts.py
+++ b/plugins/flatfilts.py
@@ -129,35 +129,46 @@ class flatfiltsCommands:
     #-----Convolution-based peak recognition and filtering.
     #Requires the peakspot.py library
 
-    def has_peaks(self, plot=None):
+    def has_peaks(self, plot=None, plugin=None):
         '''
         Finds peak position in a force curve.
         FIXME: should be moved to peakspot.py
+        #TODO: should this really be moved? this is obviously tied into flatfilts/convfilt
+        #flatfilts.py is where 'has_peaks' belongs
         '''
 
-        blindwindow = self.GetFloatFromConfig('flatfilts', 'convfilt', 'blindwindow')
-        #need to convert the string that contains the list into a list
-        convolution = eval(self.GetStringFromConfig('flatfilts', 'convfilt', 'convolution'))
-        maxcut = self.GetFloatFromConfig('flatfilts', 'convfilt', 'maxcut')
-        mindeviation = self.GetFloatFromConfig('flatfilts', 'convfilt', 'mindeviation')
-        positive = self.GetBoolFromConfig('flatfilts', 'convfilt', 'positive')
-        seedouble = self.GetIntFromConfig('flatfilts', 'convfilt', 'seedouble')
-        stable = self.GetFloatFromConfig('flatfilts', 'convfilt', 'stable')
+        if plugin is None:
+            blindwindow = self.GetFloatFromConfig('flatfilts', 'convfilt', 'blindwindow')
+            #need to convert the string that contains the list into a list
+            convolution = eval(self.GetStringFromConfig('flatfilts', 'convfilt', 'convolution'))
+            maxcut = self.GetFloatFromConfig('flatfilts', 'convfilt', 'maxcut')
+            mindeviation = self.GetFloatFromConfig('flatfilts', 'convfilt', 'mindeviation')
+            positive = self.GetBoolFromConfig('flatfilts', 'convfilt', 'positive')
+            seedouble = self.GetIntFromConfig('flatfilts', 'convfilt', 'seedouble')
+            stable = self.GetFloatFromConfig('flatfilts', 'convfilt', 'stable')
+        else:
+            blindwindow = self.GetFloatFromConfig(plugin.name, plugin.section, plugin.prefix + 'blindwindow')
+            #need to convert the string that contains the list into a list
+            convolution = eval(self.GetStringFromConfig(plugin.name, plugin.section, plugin.prefix + 'convolution'))
+            maxcut = self.GetFloatFromConfig(plugin.name, plugin.section, plugin.prefix + 'maxcut')
+            mindeviation = self.GetFloatFromConfig(plugin.name, plugin.section, plugin.prefix + 'mindeviation')
+            positive = self.GetBoolFromConfig(plugin.name, plugin.section, plugin.prefix + 'positive')
+            seedouble = self.GetIntFromConfig(plugin.name, plugin.section, plugin.prefix + 'seedouble')
+            stable = self.GetFloatFromConfig(plugin.name, plugin.section, plugin.prefix + 'stable')
 
         if plot is None:
-            plot = self.GetActivePlot()
+            plot = self.GetDisplayedPlotCorrected()
 
-        xret = plot.curves[lh.RETRACTION].x
-        yret = plot.curves[lh.RETRACTION].y
+        retraction = plot.curves[lh.RETRACTION]
         #Calculate convolution
-        convoluted = lps.conv_dx(yret, convolution)
+        convoluted = lps.conv_dx(retraction.y, convolution)
 
         #surely cut everything before the contact point
         cut_index = self.find_contact_point(plot)
         #cut even more, before the blind window
-        start_x = xret[cut_index]
+        start_x = retraction.x[cut_index]
         blind_index = 0
-        for value in xret[cut_index:]:
+        for value in retraction.x[cut_index:]:
             if abs((value) - (start_x)) > blindwindow * (10 ** -9):
                 break
             blind_index += 1
@@ -169,32 +180,15 @@ class flatfiltsCommands:
         #take the maximum
         for i in range(len(peak_location)):
             peak = peak_location[i]
-            maxpk = min(yret[peak - 10:peak + 10])
-            index_maxpk = yret[peak - 10:peak + 10].index(maxpk) + (peak - 10)
+            maxpk = min(retraction.y[peak - 10:peak + 10])
+            index_maxpk = retraction.y[peak - 10:peak + 10].index(maxpk) + (peak - 10)
             peak_location[i] = index_maxpk
 
         return peak_location, peak_size
 
-    def exec_has_peaks(self, item):
-        '''
-        encapsulates has_peaks for the purpose of correctly treating the curve objects in the convfilt loop,
-        to avoid memory leaks
-        '''
-        #TODO: things have changed, check for the memory leak again
-
-        if self.HasPlotmanipulator('plotmanip_flatten'):
-            #If flatten is present, use it for better recognition of peaks...
-            flat_plot = self.plotmanip_flatten(item.plot, item, customvalue=1)
-
-        peak_location, peak_size = self.has_peaks(flat_plot)
-
-        return peak_location, peak_size
-
     def do_peaks(self, plugin=None, peak_location=None, peak_size=None):
         '''
-        PEAKS
-        (flatfilts.py)
-        Test command for convolution filter / test.
+        Test command for convolution filter.
         ----
         Syntax: peaks [deviations]
         absolute deviation = number of times the convolution signal is above the noise absolute deviation.
@@ -222,17 +216,15 @@ class flatfiltsCommands:
             self.AppendToOutput('Found ' + str(len(peak_location)) + peak_str)
 
         if peak_location:
-            xplotted_ret = plot.curves[lh.RETRACTION].x
-            yplotted_ret = plot.curves[lh.RETRACTION].y
-            xgood = [xplotted_ret[index] for index in peak_location]
-            ygood = [yplotted_ret[index] for index in peak_location]
+            retraction = plot.curves[lh.RETRACTION]
 
             peaks = lib.curve.Curve()
             peaks.color = color
             peaks.size = size
             peaks.style = 'scatter'
-            peaks.x = xgood
-            peaks.y = ygood
+            peaks.title = 'Peaks'
+            peaks.x = [retraction.x[index] for index in peak_location]
+            peaks.y = [retraction.y[index] for index in peak_location]
 
             plot.curves.append(peaks)
 
@@ -240,26 +232,17 @@ class flatfiltsCommands:
 
     def do_convfilt(self):
         '''
-        CONVFILT
-        (flatfilts.py)
         Filters out flat (featureless) files of the current playlist,
         creating a playlist containing only the files with potential
         features.
         ------------
-        Syntax:
-        convfilt [min_npks min_deviation]
-
-        min_npks = minmum number of peaks
-        (to set the default, see convfilt.conf file; CONVCONF and SETCONF commands)
-
-        min_deviation = minimum signal/noise ratio *in the convolution*
-        (to set the default, see convfilt.conf file; CONVCONF and SETCONF commands)
-
-        If called without arguments, it uses default values.
+        min_npks: minmum number of peaks
+        min_deviation: minimum signal/noise ratio *in the convolution*
         '''
 
         self.AppendToOutput('Processing playlist...')
         self.AppendToOutput('(Please wait)')
+        apply_plotmanipulators = self.GetStringFromConfig('flatfilts', 'convfilt', 'apply_plotmanipulators')
         minpeaks = self.GetIntFromConfig('flatfilts', 'convfilt', 'minpeaks')
         features = []
         playlist = self.GetActivePlaylist()
@@ -271,7 +254,8 @@ class flatfiltsCommands:
             file_index += 1
             try:
                 current_file.identify(self.drivers)
-                peak_location, peak_size = self.exec_has_peaks(copy.deepcopy(current_file))
+                plot = self.ApplyPlotmanipulators(current_file.plot, current_file)
+                peak_location, peak_size = self.has_peaks(plot)
                 number_of_peaks = len(peak_location)
                 if number_of_peaks != 1:
                     if number_of_peaks > 0:
@@ -293,10 +277,7 @@ class flatfiltsCommands:
                 current_file.peak_size = peak_size
                 features.append(file_index - 1)
 
-        #Warn that no flattening had been done.
-        if not self.HasPlotmanipulator('plotmanip_flatten'):
-            self.AppendToOutput('Flatten manipulator was not found. Processing was done without flattening.')
-            self.AppendToOutput('Try to enable it in the configuration file for better results.')
+        #TODO: warn when flatten is not applied?
         if not features:
             self.AppendToOutput('Found nothing interesting. Check the playlist, could be a bug or criteria could be too stringent.')
         else:
diff --git a/plugins/generalvclamp.ini b/plugins/generalvclamp.ini
index 3d930e9..5968d03 100644
--- a/plugins/generalvclamp.ini
+++ b/plugins/generalvclamp.ini
@@ -1,9 +1,21 @@
 [distance]
-    [[show_points]]
+    [[color]]
+        default = black
+        type = color
+        value = "(128,0,128)"
+    
+    [[show]]
         default = True
         type = boolean
         value = True
     
+    [[size]]
+        default = 20
+        maximum = 10000
+        minimum = 1
+        type = integer
+        value = 100
+    
     [[whatset]]
         default = retraction
         elements = extension, retraction
@@ -11,6 +23,23 @@
         value = retraction
 
 [force]
+    [[color]]
+        default = black
+        type = color
+        value = "(0,255,0)"
+    
+    [[show]]
+        default = True
+        type = boolean
+        value = False
+    
+    [[size]]
+        default = 20
+        maximum = 10000
+        minimum = 1
+        type = integer
+        value = 100
+    
     [[whatset]]
         default = retraction
         elements = extension, retraction
@@ -18,6 +47,15 @@
         value = retraction
 
 [forcebase]
+    [[baseline]]
+        type = none
+        value = 1
+    
+    [[color]]
+        default = black
+        type = color
+        value = "(255,0,128)"
+    
     [[max]]
         default = False
         type = boolean
@@ -28,15 +66,23 @@
         type = boolean
         value = False
     
+    [[show]]
+        default = True
+        type = boolean
+        value = True
+    
+    [[size]]
+        default = 20
+        maximum = 10000
+        minimum = 1
+        type = integer
+        value = 50
+    
     [[whatset]]
         default = retraction
         elements = extension, retraction
         type = enum
         value = retraction
-    
-    [[baseline]]
-        type = none
-        value = 1
 
 [generalvclamp]
     [[flatten]]
@@ -65,3 +111,43 @@
         minimum = 0
         type = integer
         value = 60
+    
+    [[point_color]]
+        default = black
+        type = color
+        value = "(0,255,0)"
+    
+    [[point_show]]
+        default = False
+        type = boolean
+        value = False
+    
+    [[point_size]]
+        default = 20
+        maximum = 10000
+        minimum = 1
+        type = integer
+        value = 10
+    
+    [[slope_color]]
+        default = black
+        type = color
+        value = "(255,0,128)"
+    
+    [[slope_linewidth]]
+        default = 1
+        maximum = 10000
+        minimum = 1
+        type = integer
+        value = 2
+    
+    [[slope_show]]
+        default = True
+        type = boolean
+        value = True
+    
+    [[whatset]]
+        default = retraction
+        elements = extension, retraction
+        type = enum
+        value = retraction
diff --git a/plugins/generalvclamp.py b/plugins/generalvclamp.py
index 9f97136..9425880 100644
--- a/plugins/generalvclamp.py
+++ b/plugins/generalvclamp.py
@@ -15,6 +15,7 @@ import lib.libhooke as lh
 import wxversion
 wxversion.select(lh.WX_GOOD)
 
+from copy import deepcopy
 import numpy as np
 import scipy as sp
 
@@ -42,20 +43,15 @@ class generalvclampCommands:
         -----------------
         Syntax: distance
         '''
-        show_points = self.GetBoolFromConfig('generalvclamp', 'distance', 'show_points')
-        whatset_str = self.GetStringFromConfig('generalvclamp', 'distance', 'whatset')
-        whatset = 'retraction'
-        if whatset_str == 'extension':
-            whatset = lh.EXTENSION
-        if whatset_str == 'retraction':
-            whatset = lh.RETRACTION
-
         active_file = self.GetActiveFile()
         plot = self.GetActivePlot()
         if active_file.driver.experiment == 'clamp':
             self.AppendToOutput('You wanted to use zpiezo perhaps?')
             return
-        dx, unitx, dy, unity = self._delta(message='Click 2 points to measure the distance.', show=show_points, whatset=whatset)
+        plugin = lib.plugin.Plugin()
+        plugin.name = 'generalvclamp'
+        plugin.section = 'distance'
+        dx, unitx, dy, unity = self._delta(message='Click 2 points to measure the distance.', plugin=plugin)
         #TODO: pretty format
         self.AppendToOutput(str(dx * (10 ** 9)) + ' nm')
 
@@ -67,19 +63,15 @@ class generalvclampCommands:
         ---------------
         Syntax: force
         '''
-        whatset_str = self.GetStringFromConfig('generalvclamp', 'force', 'whatset')
-        whatset = 'retraction'
-        if whatset_str == 'extension':
-            whatset = lh.EXTENSION
-        if whatset_str == 'retraction':
-            whatset = lh.RETRACTION
-
         active_file = self.GetActiveFile()
         plot = self.GetActivePlot()
         if active_file.driver.experiment == 'clamp':
             self.AppendToOutput('This command makes no sense for a force clamp experiment.')
             return
-        dx, unitx, dy, unity = self._delta(whatset=whatset, message='Click 2 points to measure the force.')
+        plugin = lib.plugin.Plugin()
+        plugin.name = 'generalvclamp'
+        plugin.section = 'force'
+        dx, unitx, dy, unity = self._delta(message='Click 2 points to measure the force.', plugin=plugin)
         #TODO: pretty format
         self.AppendToOutput(str(dy * (10 ** 12)) + ' pN')
 
@@ -98,33 +90,48 @@ class generalvclampCommands:
                 max: Instead of asking for a point to measure, asks for two points and use
                      the maximum peak in between
         '''
+        color =  self.GetColorFromConfig('generalvclamp', 'forcebase', 'color')
         maxpoint = self.GetBoolFromConfig('generalvclamp', 'forcebase', 'max')
         rebase = self.GetBoolFromConfig('generalvclamp', 'forcebase', 'rebase')
+        show_points = self.GetBoolFromConfig('generalvclamp', 'forcebase', 'show_points')
+        size = self.GetIntFromConfig('generalvclamp', 'forcebase', 'size')
         whatset_str = self.GetStringFromConfig('generalvclamp', 'forcebase', 'whatset')
         whatset = 'retraction'
         if whatset_str == 'extension':
             whatset = lh.EXTENSION
         if whatset_str == 'retraction':
             whatset = lh.RETRACTION
+
         plot = self.GetDisplayedPlotCorrected()
 
+        clicked_points = []
+
         filename = self.GetActiveFile().name
         if rebase or (self.basecurrent != filename):
             self.basepoints = self._measure_N_points(N=2, message='Click on 2 points to select the baseline.', whatset=whatset)
             self.basecurrent = filename
+            clicked_points = self.basepoints
 
+        #TODO: maxpoint does not seem to be picking up the 'real' minimum (at least not with test.hkp/default.000)
         if maxpoint:
             boundpoints = []
             points = self._measure_N_points(N=2, message='Click 2 points to select the range for maximum detection.', whatset=whatset)
             boundpoints = [points[0].index, points[1].index]
             boundpoints.sort()
+            clicked_points += points
             try:
-                y = min(plot.curves[whatset].y[boundpoints[0]:boundpoints[1]])
+                vector_x = plot.curves[whatset].x[boundpoints[0]:boundpoints[1]]
+                vector_y = plot.curves[whatset].y[boundpoints[0]:boundpoints[1]]
+                y = min(vector_y)
+                index = vector_y.index(y)
+                clicked_points += [self._clickize(vector_x, vector_y, index)]
             except ValueError:
                 self.AppendToOutput('Chosen interval not valid. Try picking it again. Did you pick the same point as begin and end of the interval?')
+                return
         else:
             points = self._measure_N_points(N=1, message='Click on the point to measure.', whatset=whatset)
             y = points[0].graph_coords[1]
+            clicked_points += [points[0]]
 
         boundaries = [self.basepoints[0].index, self.basepoints[1].index]
         boundaries.sort()
@@ -132,12 +139,26 @@ class generalvclampCommands:
 
         avg = np.mean(to_average)
         forcebase = abs(y - avg)
+
+        if show_points:
+            curve = plot.curves[whatset]
+            for point in clicked_points:
+                points = deepcopy(curve)
+                points.x = point.graph_coords[0]
+                points.y = point.graph_coords[1]
+
+                points.color = color
+                points.size = size
+                points.style = 'scatter'
+                plot.curves.append(points)
+
+        self.UpdatePlot(plot)
         #TODO: pretty format
         self.AppendToOutput(str(forcebase * (10 ** 12)) + ' pN')
-
+
     def plotmanip_multiplier(self, plot, current, customvalue=False):
         '''
-        Multiplies all the Y values of an SMFS curve by a value stored in the 'force_multiplier'
+        Multiplies all the Y values of an SMFS curve by a value stored in the 'force_multiplier'
         configuration variable. Useful for calibrations and other stuff.
         '''
 
@@ -147,12 +168,12 @@ class generalvclampCommands:
 
         force_multiplier = self.GetFloatFromConfig('generalvclamp', 'force_multiplier')
         if force_multiplier == 1:
-            return plot
+            return plot
 
         plot.curves[lh.EXTENSION].y = [element * force_multiplier for element in plot.curves[lh.EXTENSION].y]
         plot.curves[lh.RETRACTION].y = [element * force_multiplier for element in plot.curves[lh.RETRACTION].y]
-
-        return plot
+
+        return plot
 
     def plotmanip_flatten(self, plot, current, customvalue=0):
         '''
@@ -237,24 +258,36 @@ class generalvclampCommands:
         '''
 
         fitspan = self.GetIntFromConfig('generalvclamp', 'slope', 'fitspan')
+        point_color = self.GetColorFromConfig('generalvclamp', 'slope', 'point_color')
+        point_show = self.GetBoolFromConfig('generalvclamp', 'slope', 'point_show')
+        point_size = self.GetIntFromConfig('generalvclamp', 'slope', 'point_size')
+        slope_color = self.GetColorFromConfig('generalvclamp', 'slope', 'slope_color')
+        slope_linewidth = self.GetIntFromConfig('generalvclamp', 'slope', 'slope_linewidth')
+        slope_show = self.GetBoolFromConfig('generalvclamp', 'slope', 'slope_show')
+        whatset_str = self.GetStringFromConfig('generalvclamp', 'forcebase', 'whatset')
+        whatset = 'retraction'
+        if whatset_str == 'extension':
+            whatset = lh.EXTENSION
+        if whatset_str == 'retraction':
+            whatset = lh.RETRACTION
+
         # Decides between the two forms of user input
         #TODO: add an option 'mode' with options 'chunk' and 'point'
-        #TODO: add 'whatset' as option, too
         if fitspan == 0:
             # Gets the Xs of two clicked points as indexes on the curve curve vector
             clickedpoints = []
-            points = self._measure_N_points(N=2, message='Click 2 points to select the chunk.', whatset=1)
+            points = self._measure_N_points(N=2, message='Click 2 points to select the chunk.', whatset=whatset)
             clickedpoints = [points[0].index, points[1].index]
             clickedpoints.sort()
         else:
             clickedpoints = []
-            points = self._measure_N_points(N=1, message='Click on the leftmost point of the chunk (i.e.usually the peak).', whatset=1)
+            points = self._measure_N_points(N=1, message='Click on the leftmost point of the chunk (i.e.usually the peak).', whatset=whatset)
             clickedpoints = [points[0].index - fitspan, points[0].index]
 
         # Calls the function linefit_between
         parameters = [0, 0, [], []]
         try:
-            parameters = self.linefit_between(clickedpoints[0], clickedpoints[1])
+            parameters = self.linefit_between(clickedpoints[0], clickedpoints[1], whatset=whatset)
         except:
             self.AppendToOutput('Cannot fit. Did you click the same point twice?')
             return
@@ -279,25 +312,27 @@ class generalvclampCommands:
             clickvector_x.append(item.graph_coords[0])
             clickvector_y.append(item.graph_coords[1])
 
-        #add the slope to the plot
-        slope = lib.curve.Curve()
-        slope.color = 'red'
-        slope.label = 'slope'
-        slope.style = 'plot'
-        slope.x = xtoplot
-        slope.y = ytoplot
-
-        #add the clicked points to the plot
-        points = lib.curve.Curve()
-        points.color = 'black'
-        points.label = 'points'
-        points.size = 10
-        points.style = 'scatter'
-        points.x = clickvector_x
-        points.y = clickvector_y
-
-        plot.curves.append(slope)
-        plot.curves.append(points)
+        if slope_show:
+            #add the slope to the plot
+            slope = lib.curve.Curve()
+            slope.color = slope_color
+            slope.label = 'slope'
+            slope.linewidth = slope_linewidth
+            slope.style = 'plot'
+            slope.x = xtoplot
+            slope.y = ytoplot
+            plot.curves.append(slope)
+
+        if point_show:
+            #add the clicked points to the plot
+            points = lib.curve.Curve()
+            points.color = point_color
+            points.label = 'points'
+            points.size = point_size
+            points.style = 'scatter'
+            points.x = clickvector_x
+            points.y = clickvector_y
+            plot.curves.append(points)
 
         self.UpdatePlot(plot)
 
diff --git a/plugins/procplots.ini b/plugins/procplots.ini
index 842abb9..90c11e1 100644
--- a/plugins/procplots.ini
+++ b/plugins/procplots.ini
@@ -77,14 +77,19 @@
         value = both
 
 [procplots]
+    [[centerzero]]
+        default = True
+        type = boolean
+        value = True
+    
+    [[correct]]
+        default = True
+        type = boolean
+        value = True
+    
     [[median]]
         default = 0
         maximum = 100
         minimum = 0
         type = integer
         value = 7
-    
-    [[correct]]
-        default = True
-        type = boolean
-        value = True
diff --git a/plugins/procplots.py b/plugins/procplots.py
index b7dd12c..748c96c 100644
--- a/plugins/procplots.py
+++ b/plugins/procplots.py
@@ -72,11 +72,7 @@ class procplotsCommands:
 
     def do_derivplot(self):
         '''
-        DERIVPLOT
-        (procplots.py plugin)
-        Plots the discrete differentiation of the currently displayed force curve retraction
-        ---------
-        Syntax: derivplot
+        Plots the discrete differentiation of the currently displayed force curve.
         '''
         column = self.GetIntFromConfig('procplots', 'derivplot', 'column')
         row = self.GetIntFromConfig('procplots', 'derivplot', 'row')
@@ -107,6 +103,12 @@ class procplotsCommands:
 
         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
@@ -198,7 +200,7 @@ class procplotsCommands:
         #use only for force spectroscopy experiments!
         if current.driver.experiment != 'smfs':
             return plot
-    
+
         if not customvalue:
             customvalue = self.GetBoolFromConfig('procplots', 'centerzero')
         if not customvalue:
@@ -206,16 +208,14 @@ class procplotsCommands:
 
         levelapp = float(median(plot.curves[lh.EXTENSION].y))
         levelret = float(median(plot.curves[lh.RETRACTION].y))
-    
-        level = (levelapp + levelret)/2    
-    
+
+        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]
-        
-#        plot.vectors[0][1]=approach    
-#        plot.vectors[1][1]=retract    
+
         return plot
-    
+
 #FFT---------------------------
     def fft_plot(self, curve, boundaries=[0, -1]):
         '''
diff --git a/plugins/results.py b/plugins/results.py
index 10851bc..e7b67ce 100644
--- a/plugins/results.py
+++ b/plugins/results.py
@@ -30,6 +30,7 @@ class resultsCommands(object):
 
     def do_show_results(self):
         '''
-        Select which fitting results should be displayed on the plot.
+        Select which type of result should be displayed on the plot.
         '''
+        self.results_str = self.GetStringFromConfig('results', 'show_results', 'result_type')
         self.UpdatePlot()
-- 
2.26.2