-#!/usr/bin/env python
+# Copyright (C) 2008-2010 Alberto Gomez-Casado
+# Marco Brucale
+# 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/>.
-'''
-GENERALCLAMP.py
+"""Plugin regarding general force clamp measurements
+"""
-Plugin regarding general force clamp measurements
-'''
-from libhooke import WX_GOOD, ClickedPoint
-import wxversion\r
-import libhookecurve as lhc
+from hooke.libhooke import WX_GOOD, ClickedPoint
+
+import wxversion
wxversion.select(WX_GOOD)
-from wx import PostEvent\r
+from wx import PostEvent
+
+from .. import curve as lhc
+
+
+class generalclampCommands(object):
-class generalclampCommands:\r
-\r
def plotmanip_clamp(self, plot, current, customvalue=False):
'''
- Handles some viewing options for the "force clamp" data format, depending on the state of these configuration variables:\r
- (1) If self.config['fc_showphase'] != 0, the 'phase' data column (i.e. the 2nd) is shown in the 0th graph (else it isn't)\r
- (2) If self.config['fc_showimposed'] != 0, the 'imposed deflection' data column (i.e. the 5th) is shown in the 1st graph (else it isn't)\r
+ Handles some viewing options for the "force clamp" data format, depending on the state of these configuration variables:
+ (1) If self.config['fc_showphase'] != 0, the 'phase' data column (i.e. the 2nd) is shown in the 0th graph (else it isn't)
+ (2) If self.config['fc_showimposed'] != 0, the 'imposed deflection' data column (i.e. the 5th) is shown in the 1st graph (else it isn't)
(3) If self.config['fc_interesting'] == 0, the entire curve is shown in the graphs; if it has a non-zero value N, only phase N is shown.
-\r
- NOTE - my implementation of point(3) feels quite awkward - someone smarter than me plz polish that!\r
-\r
+
+ NOTE - my implementation of point(3) feels quite awkward - someone smarter than me plz polish that!
+
'''
-
+
#not a fclamp curve...
if current.curve.experiment != 'clamp':
- return plot\r
-\r
- if self.config['fc_interesting'] != 0 and plot.destination==0:\r
- lower = int((self.config['fc_interesting'])-1)\r
- upper = int((self.config['fc_interesting'])+1)\r
- trim = current.curve.trimindexes()[lower:upper]\r
- newtime = []\r
- newzpiezo = []\r
- newphase = []\r
- for x in range(trim[0],trim[1]):\r
- newtime.append(self.plots[0].vectors[0][0][x])\r
- newzpiezo.append(self.plots[0].vectors[0][1][x])\r
- newphase.append(self.plots[0].vectors[1][1][x])\r
- self.plots[0].vectors[0][0] = newtime\r
- self.plots[0].vectors[0][1] = newzpiezo\r
- self.plots[0].vectors[1][0] = newtime\r
- self.plots[0].vectors[1][1] = newphase\r
-\r
- if self.config['fc_interesting'] != 0 and plot.destination==1:\r
- lower = int((self.config['fc_interesting'])-1)\r
- upper = int((self.config['fc_interesting'])+1)\r
- trim = current.curve.trimindexes()[lower:upper]\r
- newtime = []\r
- newdefl = []\r
- newimposed = []\r
- for x in range(trim[0],trim[1]):\r
- newtime.append(self.plots[1].vectors[0][0][x])\r
- newdefl.append(self.plots[1].vectors[0][1][x])\r
- newimposed.append(self.plots[1].vectors[1][1][x])\r
- self.plots[1].vectors[0][0] = newtime\r
- self.plots[1].vectors[0][1] = newdefl\r
- self.plots[1].vectors[1][0] = newtime\r
- self.plots[1].vectors[1][1] = newimposed \r
- \r
- if self.config['fc_showphase'] == 0 and plot.destination==0:\r
- self.plots[0].remove_set(1)\r
- \r
- if self.config['fc_showimposed'] == 0 and plot.destination==1:\r
- self.plots[1].remove_set(1)\r
- \r
+ return plot
+
+ if self.config['fc_interesting'] != 0 and plot.destination==0:
+ lower = int((self.config['fc_interesting'])-1)
+ upper = int((self.config['fc_interesting'])+1)
+ trim = current.curve.trimindexes()[lower:upper]
+ newtime = []
+ newzpiezo = []
+ newphase = []
+ for x in range(trim[0],trim[1]):
+ newtime.append(self.plots[0].vectors[0][0][x])
+ newzpiezo.append(self.plots[0].vectors[0][1][x])
+ newphase.append(self.plots[0].vectors[1][1][x])
+ self.plots[0].vectors[0][0] = newtime
+ self.plots[0].vectors[0][1] = newzpiezo
+ self.plots[0].vectors[1][0] = newtime
+ self.plots[0].vectors[1][1] = newphase
+
+ if self.config['fc_interesting'] != 0 and plot.destination==1:
+ lower = int((self.config['fc_interesting'])-1)
+ upper = int((self.config['fc_interesting'])+1)
+ trim = current.curve.trimindexes()[lower:upper]
+ newtime = []
+ newdefl = []
+ newimposed = []
+ for x in range(trim[0],trim[1]):
+ newtime.append(self.plots[1].vectors[0][0][x])
+ newdefl.append(self.plots[1].vectors[0][1][x])
+ newimposed.append(self.plots[1].vectors[1][1][x])
+ self.plots[1].vectors[0][0] = newtime
+ self.plots[1].vectors[0][1] = newdefl
+ self.plots[1].vectors[1][0] = newtime
+ self.plots[1].vectors[1][1] = newimposed
+
+ if self.config['fc_showphase'] == 0 and plot.destination==0:
+ self.plots[0].remove_set(1)
+
+ if self.config['fc_showimposed'] == 0 and plot.destination==1:
+ self.plots[1].remove_set(1)
+
return plot
-
+
def do_time(self,args):
'''
Measures the time difference (in seconds) between two points
----
Syntax: time
'''
- if self.current.curve.experiment == 'clamp':\r
- time=self._delta(set=0)[0]\r
+ if self.current.curve.experiment == 'clamp':
+ time=self._delta(set=0)[0]
print str(time*1000)+' ms'
else:
print 'This command makes no sense for a non-force clamp experiment.'
-
+
def do_zpiezo(self,args):
'''
Measures the zpiezo difference (in nm) between two points
Syntax: zpiezo
'''
if self.current.curve.experiment == 'clamp':
- zpiezo=self._delta(set=0)[2]\r
+ zpiezo=self._delta(set=0)[2]
print str(zpiezo*(10**9))+' nm'
else:
print 'This command makes no sense for a non-force clamp experiment.'
-
+
def do_defl(self,args):
'''
Measures the deflection difference (in nm) between two points
print str(defl*(10**12))+' pN'
else:
print 'This command makes no sense for a non-force clamp experiment.'
-
+
def do_step(self,args):
'''
Measures the length and time duration of a time-Z step
dt=abs(points[1].graph_coords[0]-points[0].graph_coords[0])
print 'dZ: ',dz,' nm'
print 'dT: ',dt,' s'
-
+
+ else:
+ print 'This command makes no sense for a non-force clamp experiment.'
+
+ def do_fcfilt(self,args):
+ '''
+ Filters out featureless force clamp curves of the current playlist.
+ It's very similar to 'flatfilt' for velocity clamp curves.
+ Creates a new playlist only containing non-empty curves.
+
+ WARNING - Only works if you set an appropriate fc_interesting config variable!
+ WARNING - arguments are NOT optional at the moment!
+
+ Syntax: fcfilt maxretraction(nm) mindeviation (pN)
+
+ Suggested values for an (i27)8 experiment with our setup are 200nm and 10-15 pN
+ '''
+
+ if self.config['fc_interesting'] == 0:
+ print 'You must specify the phase of interest (using set fc_interesing X) prior to running fcfilt!'
+ return
+
+ maxretraction=0
+ threshold=0
+ args=args.split(' ')
+ if len(args)==2:
+ maxretraction=int(args[0])
+ threshold=int(args[1])
+ else:
+ print 'Arguments are not optional for fcfilt. You should pass two numbers:'
+ print '(1) the maximum plausible piezo retraction in NANOMETERS (e.g. the length of the protein)'
+ print "(2) the threshold, in PICONEWTONS. If signal deviates from imposed more than this, it's an event"
+ return
+
+
+ print 'Processing playlist... go get yourself a cup of coffee.'
+ notflat_list=[]
+
+ c=0
+
+ for item in self.current_list:
+ c+=1
+ try:
+ notflat=self.has_stuff(item,maxretraction,threshold)
+ print 'Curve',item.path,'is',c,'of',len(self.current_list),'--->Has Stuff =',notflat
+ except:
+ notflat=False
+ print 'Curve',item.path,'is',c,'of',len(self.current_list),'--->could not be processed'
+ if notflat:
+ item.features=notflat
+ item.curve=None
+ notflat_list.append(item)
+
+ if len(notflat_list)==0:
+ print 'Nothing interesting here. Reconsider either your filtering criteria or your experimental data'
+ return
else:
- print 'This command makes no sense for a non-force clamp experiment.'\r
-\r
- def do_fcfilt(self,args):\r
- '''\r
- Filters out featureless force clamp curves of the current playlist.\r
- It's very similar to 'flatfilt' for velocity clamp curves.\r
- Creates a new playlist only containing non-empty curves.\r
-\r
- WARNING - Only works if you set an appropriate fc_interesting config variable!\r
- WARNING - arguments are NOT optional at the moment!\r
-\r
- Syntax: fcfilt maxretraction(nm) mindeviation (pN)\r
-\r
- Suggested values for an (i27)8 experiment with our setup are 200nm and 10-15 pN\r
- '''\r
-\r
- if self.config['fc_interesting'] == 0:\r
- print 'You must specify the phase of interest (using set fc_interesing X) prior to running fcfilt!'\r
- return\r
- \r
- maxretraction=0\r
- threshold=0\r
- args=args.split(' ')\r
- if len(args)==2:\r
- maxretraction=int(args[0])\r
- threshold=int(args[1])\r
- else:\r
- print 'Arguments are not optional for fcfilt. You should pass two numbers:'\r
- print '(1) the maximum plausible piezo retraction in NANOMETERS (e.g. the length of the protein)'\r
- print "(2) the threshold, in PICONEWTONS. If signal deviates from imposed more than this, it's an event"\r
- return\r
- \r
-\r
- print 'Processing playlist... go get yourself a cup of coffee.'\r
- notflat_list=[]\r
-\r
- c=0\r
-\r
- for item in self.current_list:\r
- c+=1\r
- try:\r
- notflat=self.has_stuff(item,maxretraction,threshold)\r
- print 'Curve',item.path,'is',c,'of',len(self.current_list),'--->Has Stuff =',notflat\r
- except:\r
- notflat=False\r
- print 'Curve',item.path,'is',c,'of',len(self.current_list),'--->could not be processed'\r
- if notflat:\r
- item.features=notflat\r
- item.curve=None\r
- notflat_list.append(item)\r
-\r
- if len(notflat_list)==0:\r
- print 'Nothing interesting here. Reconsider either your filtering criteria or your experimental data'\r
- return\r
- else:\r
- print 'Found',len(notflat_list),'potentially interesting curves.'\r
- print 'Regenerating Playlist...'\r
- self.pointer=0\r
- self.current_list=notflat_list\r
- self.current=self.current_list[self.pointer]\r
- self.do_plot(0)\r
-\r
- def has_stuff(self,item,maxretraction,threshold):\r
- '''\r
- Decides whether a curve has some features in the interesting phase.\r
- Algorithm:\r
- - clip the interesting phase portion of the curve.\r
- - discard the first 20 milliseconds (this is due to a quirk of our hardware).\r
- - look at the zpiezo plot and note down when (if) retratcs more than [maxretraction] nm away from the first point.\r
- - clip off any data after this point, with an excess of 100 points (again, an hardware quirk)\r
- - if the remainder is less than 100 points, ditch the curve.\r
- - now look at the deflection plot and check if there are points more than [threshold] pN over the 'flat zone'.\r
- - if you find such points, bingo! \r
- '''\r
-\r
- item.identify(self.drivers)\r
- \r
- lower = int((self.config['fc_interesting'])-1)\r
- upper = int((self.config['fc_interesting'])+1)\r
- trim_idxs = item.curve.trimindexes()[lower:upper]\r
- lo=trim_idxs[0]+20 #clipping the first 20 points off...\r
- hi=trim_idxs[1]\r
- trimmed_zpiezo=item.curve.default_plots()[0].vectors[0][1][lo:hi]\r
- trimmed_defl=item.curve.default_plots()[1].vectors[0][1][lo:hi]\r
- trimmed_imposed=item.curve.default_plots()[1].vectors[1][1][lo:hi]\r
- imposed=trimmed_imposed[21] #just to match the 20-pts clipping...\r
- \r
- item.curve.close_all()\r
- del item.curve\r
- del item\r
-\r
- starting_z=trimmed_zpiezo[0]\r
- plausible=starting_z-(maxretraction*1e-9)\r
- det_trim=0\r
- while trimmed_zpiezo[det_trim]>plausible:\r
- det_trim+=1\r
- if det_trim >= len(trimmed_zpiezo): #breaking cycles makes me shiver...\r
- det_trim=len(trimmed_zpiezo) #but I cannot think of anything better now.\r
- break\r
- further_trim=det_trim-100\r
- if further_trim<100:\r
- return False\r
- trimmed_defl=trimmed_defl[:further_trim]\r
-\r
- trimmed_defl.sort()\r
- ninetypercent=int(0.9*len(trimmed_defl))\r
- j=0\r
- sum=0\r
- for j in trimmed_defl[:ninetypercent]:\r
- sum+=j\r
- avg=float(sum/ninetypercent)\r
- sweetspot=float(avg+(threshold*1e-12))\r
- if trimmed_defl[-1]>sweetspot:\r
- flag=True\r
- else:\r
- flag=False\r
-\r
- del trimmed_defl,trimmed_zpiezo,trimmed_imposed \r
-\r
- return flag \r
-
\ No newline at end of file
+ print 'Found',len(notflat_list),'potentially interesting curves.'
+ print 'Regenerating playlist...'
+ self.pointer=0
+ self.current_list=notflat_list
+ self.current=self.current_list[self.pointer]
+ self.do_plot(0)
+
+ def has_stuff(self,item,maxretraction,threshold):
+ '''
+ Decides whether a curve has some features in the interesting phase.
+ Algorithm:
+ - clip the interesting phase portion of the curve.
+ - discard the first 20 milliseconds (this is due to a quirk of our hardware).
+ - look at the zpiezo plot and note down when (if) retratcs more than [maxretraction] nm away from the first point.
+ - clip off any data after this point, with an excess of 100 points (again, an hardware quirk)
+ - if the remainder is less than 100 points, ditch the curve.
+ - now look at the deflection plot and check if there are points more than [threshold] pN over the 'flat zone'.
+ - if you find such points, bingo!
+ '''
+
+ item.identify(self.drivers)
+
+ lower = int((self.config['fc_interesting'])-1)
+ upper = int((self.config['fc_interesting'])+1)
+ trim_idxs = item.curve.trimindexes()[lower:upper]
+ lo=trim_idxs[0]+20 #clipping the first 20 points off...
+ hi=trim_idxs[1]
+ trimmed_zpiezo=item.curve.default_plots()[0].vectors[0][1][lo:hi]
+ trimmed_defl=item.curve.default_plots()[1].vectors[0][1][lo:hi]
+ trimmed_imposed=item.curve.default_plots()[1].vectors[1][1][lo:hi]
+ imposed=trimmed_imposed[21] #just to match the 20-pts clipping...
+
+ item.curve.close_all()
+ del item.curve
+ del item
+
+ starting_z=trimmed_zpiezo[0]
+ plausible=starting_z-(maxretraction*1e-9)
+ det_trim=0
+ while trimmed_zpiezo[det_trim]>plausible:
+ det_trim+=1
+ if det_trim >= len(trimmed_zpiezo): #breaking cycles makes me shiver...
+ det_trim=len(trimmed_zpiezo) #but I cannot think of anything better now.
+ break
+ further_trim=det_trim-100
+ if further_trim<100:
+ return False
+ trimmed_defl=trimmed_defl[:further_trim]
+
+ trimmed_defl.sort()
+ ninetypercent=int(0.9*len(trimmed_defl))
+ j=0
+ sum=0
+ for j in trimmed_defl[:ninetypercent]:
+ sum+=j
+ avg=float(sum/ninetypercent)
+ sweetspot=float(avg+(threshold*1e-12))
+ if trimmed_defl[-1]>sweetspot:
+ flag=True
+ else:
+ flag=False
+
+ del trimmed_defl,trimmed_zpiezo,trimmed_imposed
+
+ return flag
+
projects / hooke.git / blobdiff