--- /dev/null
+#!/usr/bin/env python\r
+# -*- coding: utf-8 -*-\r
+\r
+'''\r
+curvetools.py\r
+\r
+General library of peak detection related functions.\r
+\r
+Copyright ???? by ?\r
+with modifications by Dr. Rolf Schmidt (Concordia University, Canada)\r
+\r
+This program is released under the GNU General Public License version 2.\r
+'''\r
+\r
+class curvetoolsCommands:\r
+\r
+ def fit_interval_nm(self, start_index, x_vect, nm, backwards):\r
+ '''\r
+ Calculates the number of points to fit, given a fit interval in nm\r
+ start_index: index of point\r
+ plot: plot to use\r
+ backwards: if true, finds a point backwards.\r
+ '''\r
+\r
+ c = 0\r
+ i = start_index\r
+ maxlen=len(x_vect)\r
+ while abs(x_vect[i] - x_vect[start_index]) * (10**9) < nm:\r
+ if i == 0 or i == maxlen-1: #we reached boundaries of vector!\r
+ return c\r
+ if backwards:\r
+ i -= 1\r
+ else:\r
+ i += 1\r
+ c += 1\r
+ return c\r
+\r
+ def pickup_contact_point(self, filename=''):\r
+ '''\r
+ macro to pick up the contact point by clicking\r
+ '''\r
+\r
+ contact_point = self._measure_N_points(N=1, message='Please click on the contact point.')[0]\r
+ contact_point_index = contact_point.index\r
+ self.wlccontact_point = contact_point\r
+ self.wlccontact_index = contact_point.index\r
+ self.wlccurrent = filename\r
+ return contact_point, contact_point_index\r
--- /dev/null
+[multidistance]\r
+ [[apply_plotmanipulators]]\r
+ default = all\r
+ elements = all, flatten, none\r
+ type = enum\r
+ value = all\r
+ \r
+ [[blindwindow]]\r
+ default = 20\r
+ maximum = 10000\r
+ minimum = 0\r
+ type = float\r
+ value = 20\r
+ \r
+ [[color]]\r
+ default = black\r
+ type = color\r
+ value = "(0,0,0)"\r
+ \r
+ [[convolution]]\r
+ default = "[6.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0]"\r
+ type = string\r
+ value = "[6.0,-1.0,-1.0,-1.0,-1.0,-1.0,-1.0]"\r
+ \r
+ [[maxcut]]\r
+ default = 0.2\r
+ maximum = 1\r
+ minimum = 0\r
+ type = float\r
+ value = 0.2\r
+ visible = False\r
+ \r
+ [[medianfilter]]\r
+ default = 7\r
+ maximum = 100\r
+ minimum = 0\r
+ type = integer\r
+ value = 7\r
+ \r
+ [[mindeviation]]\r
+ default = 5\r
+ maximum = 100\r
+ minimum = 0\r
+ type = float\r
+ value = 5\r
+ \r
+ [[minpeaks]]\r
+ default = 5\r
+ maximum = 20\r
+ minimum = 0\r
+ type = integer\r
+ value = 5\r
+ \r
+ [[positive]]\r
+ default = False\r
+ type = boolean\r
+ value = False\r
+ \r
+ [[seedouble]]\r
+ default = 10\r
+ maximum = 1000\r
+ minimum = 0\r
+ type = integer\r
+ value = 10\r
+ \r
+ [[size]]\r
+ default = 20\r
+ maximum = 10000\r
+ minimum = 1\r
+ type = integer\r
+ value = 20\r
+ \r
+ [[stable]]\r
+ default = 0.005\r
+ maximum = 1\r
+ minimum = 0\r
+ type = float\r
+ value = 0.005\r
+ \r
+ [[use_convfilt]]\r
+ default = False\r
+ type = boolean\r
+ value = False\r
--- /dev/null
+#!/usr/bin/env python\r
+# -*- coding: utf-8 -*-\r
+\r
+'''\r
+multidistance.py\r
+\r
+Calculates the distances between peaks.\r
+\r
+Copyright 2010 by Fabrizio Benedetti\r
+with modifications by Dr. Rolf Schmidt (Concordia University, Canada)\r
+\r
+This program is released under the GNU General Public License version 2.\r
+'''\r
+\r
+import lib.libhooke as lh\r
+import wxversion\r
+wxversion.select(lh.WX_GOOD)\r
+\r
+import copy\r
+from numpy import RankWarning\r
+import os.path\r
+import time\r
+\r
+import warnings\r
+warnings.simplefilter('ignore', RankWarning)\r
+\r
+import lib.plugin\r
+import lib.results\r
+\r
+class multidistanceCommands:\r
+\r
+ def do_multidistance(self):\r
+ '''\r
+ MULTIDISTANCE\r
+ multidistance.py\r
+ Based on the convolution recognition automatically gives the distances between the peaks found.\r
+ The command allows also to remove the unwanted peaks that can be due to interference.\r
+ When you first issue the command, it will ask for a filename. If you are giving a filename\r
+ of an existing file, autopeak will resume it and append measurements to it. If you are giving\r
+ a new filename, it will create the file and append to it until you close Hooke.\r
+ You can also define a minimun deviation of the peaks.\r
+\r
+ Syntax:\r
+ multidistance [deviation]\r
+ deviation = number of times the convolution signal is above the noise absolute deviation.\r
+ '''\r
+\r
+ color = self.GetColorFromConfig('multidistance', 'color')\r
+ size = self.GetIntFromConfig('multidistance', 'size')\r
+ use_convfilt = self.GetBoolFromConfig('multidistance', 'use_convfilt')\r
+\r
+ plot = self.GetDisplayedPlotCorrected()\r
+ if use_convfilt:\r
+ peak_location, peak_size = self.has_peaks(plot)\r
+ else:\r
+ plugin = lib.plugin.Plugin()\r
+ plugin.name = 'multidistance'\r
+ plugin.section = 'multidistance'\r
+ peak_location, peak_size = self.has_peaks(plot, plugin)\r
+\r
+ #if no peaks, we have nothing to plot. exit.\r
+ if len(peak_location) == 0:\r
+ self.AppendToOutput('No peaks found.')\r
+ return\r
+\r
+ retraction = plot.curves[lh.RETRACTION]\r
+ results = lib.results.ResultsMultiDistance()\r
+\r
+ for peak in peak_location:\r
+ result = lib.results.Result()\r
+ result.result['Distance'] = retraction.x[peak]\r
+ result.color = color\r
+ result.size = size\r
+ result.x = retraction.x[peak]\r
+ result.y = retraction.y[peak]\r
+ results.results.append(result)\r
+\r
+ results.update()\r
+\r
+ self.results_str = 'multidistance'\r
+\r
+ results.set_multipliers(-1)\r
+ plot = self.GetActivePlot()\r
+ plot.results['multidistance'] = results\r
+ self.UpdatePlot()\r
projects / hooke.git / commitdiff