From 418248bb44d7977e7fa21f367e62d544a4cba649 Mon Sep 17 00:00:00 2001
From: illysam <devnull@localhost>
Date: Mon, 22 Feb 2010 20:29:30 +0000
Subject: [PATCH] HookeGUI added curvetools.ini added curvetools.py added
 multidistance.ini added multidistance.py

---
 plugins/curvetools.ini    |  1 +
 plugins/curvetools.py     | 48 ++++++++++++++++++++++
 plugins/multidistance.ini | 83 ++++++++++++++++++++++++++++++++++++++
 plugins/multidistance.py  | 85 +++++++++++++++++++++++++++++++++++++++
 4 files changed, 217 insertions(+)
 create mode 100644 plugins/curvetools.ini
 create mode 100644 plugins/curvetools.py
 create mode 100644 plugins/multidistance.ini
 create mode 100644 plugins/multidistance.py

diff --git a/plugins/curvetools.ini b/plugins/curvetools.ini
new file mode 100644
index 0000000..d3f5a12
--- /dev/null
+++ b/plugins/curvetools.ini
@@ -0,0 +1 @@
+
diff --git a/plugins/curvetools.py b/plugins/curvetools.py
new file mode 100644
index 0000000..cd00fc6
--- /dev/null
+++ b/plugins/curvetools.py
@@ -0,0 +1,48 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+'''
+curvetools.py
+
+General library of peak detection related functions.
+
+Copyright ???? by ?
+with modifications by Dr. Rolf Schmidt (Concordia University, Canada)
+
+This program is released under the GNU General Public License version 2.
+'''
+
+class curvetoolsCommands:
+
+    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/multidistance.ini b/plugins/multidistance.ini
new file mode 100644
index 0000000..778aef4
--- /dev/null
+++ b/plugins/multidistance.ini
@@ -0,0 +1,83 @@
+[multidistance]
+    [[apply_plotmanipulators]]
+        default = all
+        elements = all, flatten, none
+        type = enum
+        value = all
+    
+    [[blindwindow]]
+        default = 20
+        maximum = 10000
+        minimum = 0
+        type = float
+        value = 20
+    
+    [[color]]
+        default = black
+        type = color
+        value = "(0,0,0)"
+    
+    [[convolution]]
+        default = "[6.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0]"
+        type = string
+        value = "[6.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0]"
+    
+    [[maxcut]]
+        default = 0.2
+        maximum = 1
+        minimum = 0
+        type = float
+        value = 0.2
+        visible = False
+    
+    [[medianfilter]]
+        default = 7
+        maximum = 100
+        minimum = 0
+        type = integer
+        value = 7
+    
+    [[mindeviation]]
+        default = 5
+        maximum = 100
+        minimum = 0
+        type = float
+        value = 5
+    
+    [[minpeaks]]
+        default = 5
+        maximum = 20
+        minimum = 0
+        type = integer
+        value = 5
+    
+    [[positive]]
+        default = False
+        type = boolean
+        value = False
+    
+    [[seedouble]]
+        default = 10
+        maximum = 1000
+        minimum = 0
+        type = integer
+        value = 10
+    
+    [[size]]
+        default = 20
+        maximum = 10000
+        minimum = 1
+        type = integer
+        value = 20
+    
+    [[stable]]
+        default = 0.005
+        maximum = 1
+        minimum = 0
+        type = float
+        value = 0.005
+    
+    [[use_convfilt]]
+        default = False
+        type = boolean
+        value = False
diff --git a/plugins/multidistance.py b/plugins/multidistance.py
new file mode 100644
index 0000000..77b08fa
--- /dev/null
+++ b/plugins/multidistance.py
@@ -0,0 +1,85 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+'''
+multidistance.py
+
+Calculates the distances between peaks.
+
+Copyright 2010 by Fabrizio Benedetti
+with modifications by Dr. Rolf Schmidt (Concordia University, Canada)
+
+This program is released under the GNU General Public License version 2.
+'''
+
+import lib.libhooke as lh
+import wxversion
+wxversion.select(lh.WX_GOOD)
+
+import copy
+from numpy import RankWarning
+import os.path
+import time
+
+import warnings
+warnings.simplefilter('ignore', RankWarning)
+
+import lib.plugin
+import lib.results
+
+class multidistanceCommands:
+
+    def do_multidistance(self):
+        '''
+        MULTIDISTANCE
+        multidistance.py
+        Based on the convolution recognition automatically gives the distances between the peaks found.
+        The command allows also to remove the unwanted peaks that can be due to interference.
+        When you first issue the command, it will ask for a filename. If you are giving a 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.
+        You can also define a minimun deviation of the peaks.
+
+        Syntax:
+        multidistance [deviation]
+        deviation = number of times the convolution signal is above the noise absolute deviation.
+        '''
+
+        color = self.GetColorFromConfig('multidistance', 'color')
+        size = self.GetIntFromConfig('multidistance', 'size')
+        use_convfilt = self.GetBoolFromConfig('multidistance', 'use_convfilt')
+
+        plot = self.GetDisplayedPlotCorrected()
+        if use_convfilt:
+            peak_location, peak_size = self.has_peaks(plot)
+        else:
+            plugin = lib.plugin.Plugin()
+            plugin.name = 'multidistance'
+            plugin.section = 'multidistance'
+            peak_location, peak_size = self.has_peaks(plot, plugin)
+
+        #if no peaks, we have nothing to plot. exit.
+        if len(peak_location) == 0:
+            self.AppendToOutput('No peaks found.')
+            return
+
+        retraction = plot.curves[lh.RETRACTION]
+        results = lib.results.ResultsMultiDistance()
+
+        for peak in peak_location:
+            result = lib.results.Result()
+            result.result['Distance'] = retraction.x[peak]
+            result.color = color
+            result.size = size
+            result.x = retraction.x[peak]
+            result.y = retraction.y[peak]
+            results.results.append(result)
+
+        results.update()
+
+        self.results_str = 'multidistance'
+
+        results.set_multipliers(-1)
+        plot = self.GetActivePlot()
+        plot.results['multidistance'] = results
+        self.UpdatePlot()
-- 
2.26.2