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Copy pathApTiltPicker_import.py
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ApTiltPicker_import.py
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#!/usr/bin/env python
## pythonlib
import os
import time
import math
from optparse import OptionParser
## wxPython
import wx
## PIL
from PIL import Image
## appion
from appionlib import apImage
from appionlib import apParam
from appionlib import apDisplay
from appionlib.apTilt import tiltDialog, apTiltTransform, apTiltShift, tiltfile, autotilt
## leginon
import leginon.gui.wx.TargetPanel
from leginon.gui.wx.Entry import FloatEntry, IntEntry, EVT_ENTRY
## numpy/scipy
import numpy
import pyami.quietscipy
from scipy import ndimage
class HelicalStepDialog(wx.Dialog):
#==================
def __init__(self, parent):
self.parent = parent
### create dialog
wx.Dialog.__init__(self, self.parent.frame, -1, "Helical Step Size")
### create input area
inforow = wx.FlexGridSizer(2, 2, 15, 15)
helicallabel = wx.StaticText(self, -1, "Helical Step Size (in Angstroms): ",
style=wx.ALIGN_LEFT|wx.ALIGN_CENTER_VERTICAL)
self.helicalvalue = FloatEntry(self, -1, allownone=False, chars=5, value="0")
inforow.Add(helicallabel, 0, wx.ALIGN_LEFT|wx.ALIGN_CENTER_VERTICAL)
inforow.Add(self.helicalvalue, 0, wx.ALIGN_CENTER_HORIZONTAL|wx.ALIGN_CENTER_VERTICAL|wx.ALL, 3)
### create button area
cancelhelical = wx.Button(self, wx.ID_CANCEL, '&Cancel')
self.applyhelical = wx.Button(self, wx.ID_APPLY, '&Set')
self.Bind(wx.EVT_BUTTON, self.onSetHelical, self.applyhelical)
buttonrow = wx.GridSizer(1,2)
buttonrow.Add(cancelhelical, 0, wx.ALIGN_CENTER_HORIZONTAL|wx.ALIGN_CENTER_VERTICAL, 0)
buttonrow.Add(self.applyhelical, 0, wx.ALIGN_CENTER_HORIZONTAL|wx.ALIGN_CENTER_VERTICAL, 0)
### merge input and button areas
self.sizer = wx.FlexGridSizer(2,1)
self.sizer.Add(inforow, 0, wx.EXPAND|wx.ALL, 10)
self.sizer.Add(buttonrow, 0, wx.EXPAND|wx.ALL, 5)
self.SetSizerAndFit(self.sizer)
#==================
def onSetHelical(self, evt):
### get values
self.parent.helicalstep = self.helicalvalue.GetValue()
self.Destroy()
return
class TiltTargetPanel(leginon.gui.wx.TargetPanel.TargetImagePanel):
def __init__(self, parent, id, callback=None, tool=True, name=None):
leginon.gui.wx.TargetPanel.TargetImagePanel.__init__(self, parent, id,
callback=callback, tool=tool, mode="vertical")
if name is not None:
self.outname = name
else:
self.outname="unknown"
#---------------------------------------
def setOtherPanel(self, panel):
self.other = panel
#---------------------------------------
def addTarget(self, name, x, y):
### check for out of bounds particles
if x < 2 or y < 2:
return
if x > self.imagedata.shape[1] or y > self.imagedata.shape[0]:
return
numtargets = len(self.getTargets(name))
numotargets = len(self.other.getTargets(name))
#self.parent.statbar.PushStatusText("Added %d target at location (%d,%d)" % numtargets, x, y)
if numtargets > 3 and numotargets > 3:
self.app.onFileSave(None)
return self._getSelectionTool().addTarget(name, x, y)
#---------------------------------------
def deleteTarget(self, target):
return self._getSelectionTool().deleteTarget(target)
#---------------------------------------
def openImageFile(self, filename):
self.filename = filename
if filename is None:
self.setImage(None)
elif filename[-4:] == '.spi':
image = apImage.spiderToArray(filename, msg=False)
self.setImage(image.astype(numpy.float32))
elif filename[-4:] == '.mrc':
image = apImage.mrcToArray(filename, msg=False)
self.setImage(image.astype(numpy.float32))
else:
image = Image.open(filename)
array = apImage.imageToArray(image, msg=False)
array = array.astype(numpy.float32)
self.setImage(array)
#---------------------------------------
class PickerApp(wx.App):
def __init__(self, mode='default',
pickshape="circle", pshapesize=24,
alignshape="square", ashapesize=6,
worstshape="square", wshapesize=28,
tiltangle=None, tiltaxis=None,
picks1="picks1", picks2="picks2",outfileout="outfile",doinit=True):
self.mode = mode
self.pshape = self.canonicalShape(pickshape)
self.pshapesize = int(pshapesize)
self.ashape = self.canonicalShape(alignshape)
self.ashapesize = int(ashapesize)
self.eshape = self.canonicalShape(worstshape)
self.wshapesize = int(wshapesize)
self.inittiltangle = tiltangle
self.inittiltaxis = tiltaxis
self.picks1=numpy.genfromtxt(picks1,delimiter="\t")
self.picks2=numpy.genfromtxt(picks2,delimiter="\t")
self.outfileout=outfileout
wx.App.__init__(self)
def OnInit(self):
self.data = {}
self.helicalstep = None
self.appionloop = None
self.onInitParams(None, False)
self.data['pixdiam'] = 20.0
self.data['outfile'] = self.outfileout
self.data['dirname'] = ""
if self.inittiltangle is not None:
self.data['theta'] = self.inittiltangle
if self.inittiltaxis is not None:
self.data['gamma'] = self.inittiltaxis
self.data['phi'] = self.inittiltaxis
self.appionloop = None
self.data['filetypeindex'] = None
self.data['thetarun'] = False
self.data['optimrun'] = False
#self.picks1 = numpy.genfromtxt("14mar28y_14mar28z_14mar27y_13feb14w_12aug01q_008u_dc4_convert_2cols.spi",delimiter="\t")
#self.picks2 = numpy.genfromtxt("14mar28y_14mar28z_14mar27y_13feb14w_12aug01q_008t_dc4_convert_2cols.spi",delimiter="\t")
self.buttonheight = 15
self.deselectcolor = wx.Color(240,240,240)
self.frame = wx.Frame(None, -1, 'Image Viewer')
splitter = wx.SplitterWindow(self.frame)
self.panel1 = TiltTargetPanel(splitter, -1, name="untilt")
self.panel1.parent = self.frame
self.panel1.app = self
self.panel1.addTargetTool('Picked', color=wx.Color(215, 32, 32),
shape=self.pshape, size=self.pshapesize, target=True, numbers=True)
self.panel1.setTargets('Picked', [])
self.panel1.selectiontool.setTargeting('Picked', True)
self.panel1.addTargetTool('Aligned', color=wx.Color(32, 128, 215),
shape=self.ashape, size=self.ashapesize, numbers=True)
self.panel1.setTargets('Aligned', [])
self.panel1.selectiontool.setDisplayed('Aligned', True)
self.panel1.addTargetTool('Worst', color=wx.Color(250, 160, 32),
shape=self.eshape, size=self.wshapesize)
self.panel1.setTargets('Worst', [])
self.panel1.selectiontool.setDisplayed('Worst', True)
self.panel1.addTargetTool('Polygon', color=wx.Color(32, 215, 32),
shape='polygon', target=True)
self.panel1.setTargets('Polygon', [])
self.panel1.selectiontool.setDisplayed('Polygon', True)
#self.panel1.SetMinSize((256,256))
#self.panel1.SetBackgroundColour("sky blue")
self.panel2 = TiltTargetPanel(splitter, -1, name="tilt")
self.panel2.parent = self.frame
self.panel2.app = self
self.panel2.addTargetTool('Picked', color=wx.Color(32, 128, 215),
shape=self.pshape, size=self.pshapesize, target=True, numbers=True)
self.panel2.setTargets('Picked', [])
self.panel2.selectiontool.setTargeting('Picked', True)
self.panel2.addTargetTool('Aligned', color=wx.Color(215, 32, 32),
shape=self.ashape, size=self.ashapesize, numbers=True)
self.panel2.setTargets('Aligned', [])
self.panel2.selectiontool.setDisplayed('Aligned', True)
self.panel2.addTargetTool('Worst', color=wx.Color(250, 160, 32),
shape=self.eshape, size=self.wshapesize)
self.panel2.setTargets('Worst', [])
self.panel2.selectiontool.setDisplayed('Worst', True)
self.panel2.addTargetTool('Polygon', color=wx.Color(32, 215, 32),
shape='polygon', target=True)
self.panel2.setTargets('Polygon', [])
self.panel2.selectiontool.setDisplayed('Polygon', True)
#self.panel2.SetMinSize((256,256))
#self.panel2.SetBackgroundColour("pink")
self.panel1.setOtherPanel(self.panel2)
self.panel2.setOtherPanel(self.panel1)
### create menu buttons
self.createMenuButtons()
if self.mode == 'default':
self.createStandAloneButtons()
else:
self.createLoopButtons()
self.sizer = wx.GridBagSizer(2,2)
#splitter.Initialize(self.panel1)
splitter.SplitVertically(self.panel1, self.panel2)
splitter.SetMinimumPaneSize(10)
self.sizer.Add(splitter, (0,0), (1,2), wx.EXPAND|wx.ALL, 3)
#self.sizer.Add(self.panel1, (0,0), (1,1), wx.EXPAND|wx.ALL, 3)
#self.sizer.Add(self.panel2, (0,1), (1,1), wx.EXPAND|wx.ALL, 3)
self.sizer.Add(self.buttonrow, (1,0), (1,2), wx.EXPAND|wx.ALL|wx.CENTER, 3)
self.sizer.AddGrowableRow(0)
self.sizer.AddGrowableCol(0)
self.sizer.AddGrowableCol(1)
self.statbar = self.frame.CreateStatusBar(3)
self.statbar.SetStatusWidths([-1, 65, 150])
self.statbar.PushStatusText("Ready", 0)
self.createMenuBar()
self.frame.SetSizer(self.sizer)
self.frame.SetMinSize((256,128))
self.SetTopWindow(self.frame)
self.frame.Show(True)
return True
#---------------------------------------
def createMenuButtons(self):
"""
These are buttons related to both the standalone and pipeline versions of TiltPicker
"""
self.buttonrow = wx.FlexGridSizer(1,20)
self.update = wx.Button(self.frame, wx.ID_APPLY, '&Apply')
self.frame.Bind(wx.EVT_BUTTON, self.onUpdate, self.update)
self.buttonrow.Add(self.update, 0, wx.ALIGN_CENTER_VERTICAL|wx.ALL, 1)
#spacer
self.buttonrow.Add((8,self.buttonheight), 0, wx.ALL, 1)
self.theta_dialog = tiltDialog.FitThetaDialog(self)
self.fittheta = wx.Button(self.frame, -1, '&Theta...')
self.frame.Bind(wx.EVT_BUTTON, self.onFitTheta, self.fittheta)
self.buttonrow.Add(self.fittheta, 0, wx.ALIGN_CENTER_VERTICAL|wx.ALL, 1)
self.fitall_dialog = tiltDialog.FitAllDialog(self)
self.fitall = wx.Button(self.frame, -1, '&Optimize...')
self.frame.Bind(wx.EVT_BUTTON, self.onFitAll, self.fitall)
self.buttonrow.Add(self.fitall, 0, wx.ALIGN_CENTER_VERTICAL|wx.ALL, 1)
self.maskregion = wx.Button(self.frame, -1, '&Mask')
self.frame.Bind(wx.EVT_BUTTON, self.onMaskRegion, self.maskregion)
self.buttonrow.Add(self.maskregion, 0, wx.ALIGN_CENTER_VERTICAL|wx.ALL, 1)
self.autooptim = wx.Button(self.frame, -1, 'Auto Optimi&ze')
self.frame.Bind(wx.EVT_BUTTON, self.onAutoOptim, self.autooptim)
self.buttonrow.Add(self.autooptim, 0, wx.ALIGN_CENTER_VERTICAL|wx.ALL, 1)
#spacer
self.buttonrow.Add((8,self.buttonheight), 0, wx.ALL, 1)
self.clear = wx.Button(self.frame, -1, 'Rm &Worst Picks')
self.frame.Bind(wx.EVT_BUTTON, self.onClearBadPicks, self.clear)
self.buttonrow.Add(self.clear, 0, wx.ALIGN_CENTER_VERTICAL|wx.ALL, 1)
self.particleCutoff = wx.Button(self.frame, -1, '&Cutoff...')
self.Bind(wx.EVT_BUTTON, self.onParticleCutoff, self.particleCutoff)
self.buttonrow.Add(self.particleCutoff, 0, wx.ALIGN_CENTER_VERTICAL|wx.ALL, 3)
self.xferpick = wx.Button(self.frame, -1, '&Xfer picks')
self.frame.Bind(wx.EVT_BUTTON, self.onXferPick, self.xferpick)
self.buttonrow.Add(self.xferpick, 0, wx.ALIGN_CENTER_VERTICAL|wx.ALL, 1)
self.clearPolygon = wx.Button(self.frame, wx.ID_REMOVE, 'Rm &Polygon')
self.Bind(wx.EVT_BUTTON, self.onClearPolygon, self.clearPolygon)
self.buttonrow.Add(self.clearPolygon, 0, wx.ALIGN_CENTER_VERTICAL|wx.ALL, 3)
self.reset = wx.Button(self.frame, wx.ID_RESET, 'Reset...')
self.frame.Bind(wx.EVT_BUTTON, self.onResetParams, self.reset)
self.buttonrow.Add(self.reset, 0, wx.ALIGN_CENTER_VERTICAL|wx.ALL, 1)
#---------------------------------------
def createStandAloneButtons(self):
"""
These are buttons related to the standalone version of TiltPicker
"""
#spacer
self.buttonrow.Add((8,self.buttonheight), 0, wx.ALL, 1)
self.importpicks = wx.Button(self.frame, -1, '&Import')
self.frame.Bind(wx.EVT_BUTTON, self.onImportPicks, self.importpicks)
self.buttonrow.Add(self.importpicks, 0, wx.ALIGN_CENTER_VERTICAL|wx.ALL, 1)
#spacer
self.buttonrow.Add((8,self.buttonheight), 0, wx.ALL, 1)
self.dogpick_dialog = tiltDialog.DogPickerDialog(self)
self.dogpick = wx.Button(self.frame, wx.ID_OPEN, '&DoG Pick...')
self.frame.Bind(wx.EVT_BUTTON, self.onAutoDogPick, self.dogpick)
self.buttonrow.Add(self.dogpick, 0, wx.ALIGN_CENTER_VERTICAL|wx.ALL, 1)
#spacer
self.buttonrow.Add((8,self.buttonheight), 0, wx.ALL, 1)
self.quit = wx.Button(self.frame, wx.ID_FORWARD, '&Forward')
self.frame.Bind(wx.EVT_BUTTON, self.onQuit, self.quit)
self.buttonrow.Add(self.quit, 0, wx.ALIGN_CENTER_VERTICAL|wx.ALL, 1)
#self.quit = wx.Button(self.frame, wx.ID_EXIT, '&Quit')
#self.frame.Bind(wx.EVT_BUTTON, self.onQuit, self.quit)
#self.buttonrow.Add(self.quit, 0, wx.ALIGN_CENTER_VERTICAL|wx.ALL, 1)
return
#---------------------------------------
def createLoopButtons(self):
"""
These are buttons related to the Appion pipeline version of TiltPicker
"""
#spacer
self.buttonrow.Add((8,self.buttonheight), 0, wx.ALL, 1)
self.shift = wx.Button(self.frame,-1, '&Get Shift')
self.frame.Bind(wx.EVT_BUTTON, self.onGuessShift, self.shift)
self.buttonrow.Add(self.shift, 0, wx.ALIGN_CENTER_VERTICAL|wx.ALL, 1)
self.importpicks = wx.Button(self.frame, -1, '&Import')
self.frame.Bind(wx.EVT_BUTTON, self.onImportPicks, self.importpicks)
self.buttonrow.Add(self.importpicks, 0, wx.ALIGN_CENTER_VERTICAL|wx.ALL, 1)
#spacer
self.buttonrow.Add((8,self.buttonheight), 0, wx.ALL, 1)
self.quit = wx.Button(self.frame, wx.ID_FORWARD, '&Forward')
self.frame.Bind(wx.EVT_BUTTON, self.onQuit, self.quit)
self.buttonrow.Add(self.quit, 0, wx.ALIGN_CENTER_VERTICAL|wx.ALL, 1)
#spacer
self.buttonrow.Add((8,self.buttonheight), 0, wx.ALL, 1)
self.assessnone = wx.ToggleButton(self.frame, -1, "None")
self.Bind(wx.EVT_TOGGLEBUTTON, self.onToggleNone, self.assessnone)
self.assessnone.SetValue(0)
self.assessnone.SetMinSize((70,self.buttonheight))
self.buttonrow.Add(self.assessnone, 0, wx.ALIGN_CENTER_VERTICAL|wx.ALL, 3)
self.assesskeep = wx.ToggleButton(self.frame, -1, "&Keep")
self.Bind(wx.EVT_TOGGLEBUTTON, self.onToggleKeep, self.assesskeep)
self.assesskeep.SetValue(0)
self.assesskeep.SetMinSize((70,self.buttonheight))
self.buttonrow.Add(self.assesskeep, 0, wx.ALIGN_CENTER_VERTICAL|wx.ALL, 3)
self.assessreject = wx.ToggleButton(self.frame, -1, "&Reject")
self.Bind(wx.EVT_TOGGLEBUTTON, self.onToggleReject, self.assessreject)
self.assessreject.SetValue(0)
#self.assessreject.SetMinSize((70,self.buttonheight))
self.buttonrow.Add(self.assessreject, 0, wx.ALIGN_CENTER_VERTICAL|wx.ALL, 3)
self.helicalinsert = wx.Button(self.frame, -1, '&Helical insert')
self.helicalinsert.SetMinSize((120,40))
self.Bind(wx.EVT_BUTTON, self.onHelicalInsert, self.helicalinsert)
self.buttonrow.Add(self.helicalinsert, 0, wx.ALIGN_CENTER_VERTICAL|wx.ALL, 3)
return
#---------------------------------------
def menuData(self):
if self.mode == 'default':
return [
("&File", (
( "&Open", "Open picked particles from file", self.onFileOpen, wx.ID_OPEN ),
( "Open new left image", "Open new left image and restart TiltPicker", self.selectLeftImageToOpen ),
( "Open new right image", "Open new right image and restart TiltPicker", self.selectRightImageToOpen ),
( 0, 0, 0),
( "&Save", "Save picked particles to file", self.onFileSave, wx.ID_SAVE ),
( "Save &As...", "Save picked particles to new file", self.onFileSaveAs, wx.ID_SAVEAS ),
( "Save file type", (
( "&Text", "Readable text file", self.onSetFileType, -1, wx.ITEM_RADIO),
( "&XML", "XML file", self.onSetFileType, -1, wx.ITEM_RADIO),
( "&Spider", "Spider format file", self.onSetFileType, -1, wx.ITEM_RADIO),
( "&Pickle", "Python pickle file", self.onSetFileType, -1, wx.ITEM_RADIO),
)),
( 0, 0, 0),
( "&Quit", "Exit the program / advance to next image", self.onQuit, wx.ID_EXIT ),
)),
("&Edit", (
( "&Clear", "Clear all picked particles", self.onClearPicks, wx.ID_CLEAR ),
( "&Init", "Initialize alignment parameters", self.onInitParams ),
( "&Reset", "Clear picks and reset parameters", self.onResetParams, wx.ID_RESET ),
( "Clear &Worst Picks", "Remove worst picked particles", self.onClearBadPicks ),
( "Clear &Polygon", "Clear particle with polygon", self.onClearPolygon ),
)),
("Refine", (
( "Auto Op&timize", "Find theta and optimize angles", self.onAutoOptim ),
( 0, 0, 0),
( "Find &Theta", "Calculate theta from picked particles", self.onFitTheta ),
( "&Optimize Angles", "Optimize angles with least squares", self.onFitAll ),
( "&Apply", "Apply picks", self.onUpdate, wx.ID_APPLY ),
( "&Mask Overlapping Region", "Mask overlapping region", self.onMaskRegion ),
( "&Calculate Percent Overlap", "Calculate percent overlap", self.onGetOverlap ),
)),
("Picking", (
( "Auto &DoG pick particles", "Run DoG picker program", self.onAutoDogPick ),
( "Tran&Xfer Picks", "Transfer picks from one image to another using fit parameters", self.onXferPick ),
( "Remove &Worst particle picks", "Remove picks that with the largest error", self.onClearBadPicks ),
( "Apply particle RMSD &Cutoff", "Remove picks with RMSD above a certain cutoff", self.onParticleCutoff ),
( "Remove picks within &Polygon", "Remove picks within Polygon", self.onClearPolygon ),
( "&Guess initial particle match", "Try to find an initial particle match using a cross-correlation search", self.onCheckGuessShift ),
( "Repair picks", "Attempt to repair your picks if you accidentally deleted a pick and forgot where", self.onRepairList ),
( 0, 0, 0),
( "&Clear picks", "Clear all picked particles", self.onClearPicks, wx.ID_CLEAR ),
( "&Reset TiltPicker", "Remove all picks and start over", self.onResetParams, wx.ID_RESET ),
)),
("&Help", (
( "&About TiltPicker", "Show product information", self.onShowAboutTiltPicker, wx.ID_HELP),
)),
]
else:
return [
("Pipeline", (
( "&Import picks", "Import picked particles from previous run", self.onImportPicks ),
( "&Forward", "Advance to next image", self.onQuit, wx.ID_FORWARD ),
)),
("&Edit", (
( "&Clear", "Clear all picked particles", self.onClearPicks, wx.ID_CLEAR ),
( "&Init", "Initialize alignment parameters", self.onInitParams ),
( "&Reset", "Clear picks and reset parameters", self.onResetParams, wx.ID_RESET ),
( "Clear &Worst Picks", "Remove worst picked particles", self.onClearBadPicks ),
( "Clear &Polygon", "Clear particle with polygon", self.onClearPolygon ),
)),
("Refine", (
( "Find &Theta", "Calculate theta from picked particles", self.onFitTheta ),
( "&Optimize Angles", "Optimize angles with least squares", self.onFitAll ),
( "Auto Op&timize", "Find theta and optimize angles", self.onAutoOptim ),
( "&Apply", "Apply picks", self.onUpdate, wx.ID_APPLY ),
( "&Mask Overlapping Region", "Mask overlapping region", self.onMaskRegion ),
( "&Calculate Percent Overlap", "Calculate percent overlap", self.onGetOverlap ),
)),
("Picking", (
( "Auto &DoG pick particles", "Run DoG picker program", self.onAutoDogPick ),
( "Tran&Xfer Picks", "Transfer picks from one image to another using fit parameters", self.onXferPick ),
( "Remove &Worst particle picks", "Remove picks that with the largest error", self.onClearBadPicks ),
( "Apply particle RMSD &Cutoff", "Remove picks with RMSD above a certain cutoff", self.onParticleCutoff ),
( "Remove picks within &Polygon", "Remove picks within Polygon", self.onClearPolygon ),
( "&Guess initial particle match", "Try to find an initial particle match using a cross-correlation search", self.onCheckGuessShift ),
( "Repair picks", "Attempt to repair your picks if you accidentally deleted a pick and forgot where", self.onRepairList ),
( 0, 0, 0),
( "&Clear picks", "Clear all picked particles", self.onClearPicks, wx.ID_CLEAR ),
( "&Reset TiltPicker", "Remove all picks and start over", self.onResetParams, wx.ID_RESET ),
)),
("Assess", (
( "&None", "Don't assess image pair", self.onToggleNone, -1, wx.ITEM_RADIO),
( "&Keep", "Keep this image pair", self.onToggleKeep, -1, wx.ITEM_RADIO),
( "&Reject", "Reject this image pair", self.onToggleReject, -1, wx.ITEM_RADIO),
)),
("&Help", (
( "&About TiltPicker", "Show product information", self.onShowAboutTiltPicker, wx.ID_HELP ),
)),
]
#---------------------------------------
def createMenuBar(self):
self.menubar = wx.MenuBar()
self.about_dialog = tiltDialog.AboutTiltPickerDialog(self)
for eachMenuData in self.menuData():
menuLabel = eachMenuData[0]
menuItems = eachMenuData[1]
self.menubar.Append(self.createMenu(menuItems), menuLabel)
self.frame.SetMenuBar(self.menubar)
#---------------------------------------
def createMenu(self, menudata):
menu = wx.Menu()
for eachItem in menudata:
if len(eachItem) == 2:
label = eachItem[0]
subMenu = self.createMenu(eachItem[1])
menu.AppendMenu(wx.NewId(), label, subMenu)
else:
self.createMenuItem(menu, *eachItem)
return menu
#---------------------------------------
def createMenuItem(self, menu, label, status, handler, wid=-1, kind=wx.ITEM_NORMAL):
if not label:
menu.AppendSeparator()
return
menuItem = menu.Append(wid, label, status, kind)
self.Bind(wx.EVT_MENU, handler, menuItem)
#---------------------------------------
def onHelicalInsert(self, evt):
"""
connect the last two targets by filling inbetween
copied from EMAN1 boxer
"""
### get last two targets
targets = self.panel1.getTargets('Picked')
if len(targets) < 2:
apDisplay.printWarning("not enough targets")
return
array = self.targetsToArray(targets)
### get pixelsize
apix = self.appionloop.params['apix']
if not apix or apix == 0.0:
apDisplay.printWarning("unknown pixel size")
return
### get helicalstep
if self.helicalstep is None:
helicaldialog = HelicalStepDialog(self)
helicaldialog.ShowModal()
helicaldialog.Destroy()
helicalstep = self.helicalstep
first = array[-2]
last = array[-1]
pixeldistance = math.hypot(first[0] - last[0], first[1] - last[1])
if pixeldistance == 0:
### this will probably never happen since mouse does not let you click same point twice
apDisplay.printWarning("points have zero distance")
return
stepsize = helicalstep/pixeldistance*apix
### parameterization of a line btw points (x1,y1) and (x2,y2):
# x = (1 - t)*x1 + t*x2,
# y = (1 - t)*y1 + t*y2,
# t { [0,1] ; t is a real number btw 0 and 1
points = list(array)
t = 0.0
while t < 1.0:
x = int(round( (1.0 - t)*first[0] + t*last[0], 0))
y = int(round( (1.0 - t)*first[1] + t*last[1], 0))
points.append((x,y))
t += stepsize
self.panel1.setTargets('Picked', points)
### transfer points to second panel
a2 = self.getArray2()
a1b = self.getAlignedArray1()
lastpick = a1b[len(a2):]
a2list = self.panel2.getTargets('Picked')
a2list.extend(lastpick)
self.panel2.setTargets('Picked', a2list )
self.onUpdate(evt)
#---------------------------------------
def setAssessStatus(self):
if self.appionloop.assess is True:
self.onToggleKeep(None)
elif self.appionloop.assess is False:
self.onToggleReject(None)
else:
self.onToggleNone(None)
#---------------------------------------
def onToggleNone(self, evt):
self.assessnone.SetValue(1)
self.assessnone.SetBackgroundColour(wx.Color(200,200,0))
self.assesskeep.SetValue(0)
self.assesskeep.SetBackgroundColour(self.deselectcolor)
self.assessreject.SetValue(0)
self.assessreject.SetBackgroundColour(self.deselectcolor)
self.assess = None
#---------------------------------------
def onToggleKeep(self, evt):
self.assessnone.SetValue(0)
self.assessnone.SetBackgroundColour(self.deselectcolor)
self.assesskeep.SetValue(1)
self.assesskeep.SetBackgroundColour(wx.Color(0,200,0))
self.assessreject.SetValue(0)
self.assessreject.SetBackgroundColour(self.deselectcolor)
self.assess = True
#---------------------------------------
def onToggleReject(self, evt):
self.assessnone.SetValue(0)
self.assessnone.SetBackgroundColour(self.deselectcolor)
self.assesskeep.SetValue(0)
self.assesskeep.SetBackgroundColour(self.deselectcolor)
self.assessreject.SetValue(1)
self.assessreject.SetBackgroundColour(wx.Color(200,0,0))
self.assess = False
#---------------------------------------
def onSetFileType(self, evt):
print dir(evt)
#---------------------------------------
def onClearPolygon(self, evt):
t0 = time.time()
### check particles
targets1 = self.getArray1()
targets2 = self.getArray2()
if len(targets1) == 0 or len(targets2) == 0:
self.statbar.PushStatusText("ERROR: Cannot remove polygon. There are no picks.", 0)
dialog = wx.MessageDialog(self.frame, "Cannot remove polygon.\nThere are no picks.",\
'Error', wx.OK|wx.ICON_ERROR)
dialog.ShowModal()
dialog.Destroy()
return False
### check polygon vertices
vert1 = self.panel1.getTargetPositions('Polygon')
vert2 = self.panel2.getTargetPositions('Polygon')
### check polygon vertices
if len(vert1) < 3 and len(vert2) < 3:
self.statbar.PushStatusText("ERROR: Could not create a closed polygon. Select more vertices.", 0)
dialog = wx.MessageDialog(self.frame,
"Could not create a closed polygon.\nSelect more vertices.",\
'Error', wx.OK|wx.ICON_ERROR)
dialog.ShowModal()
dialog.Destroy()
return False
elif len(vert1) >= 3 and len(vert2) >= 3:
self.statbar.PushStatusText("ERROR: Polygons on both images. Create a polygon on only one image.", 0)
dialog = wx.MessageDialog(self.frame,
"Polygons on both images.\nCreate a polygon on only one image.",\
'Error', wx.OK|wx.ICON_ERROR)
dialog.ShowModal()
dialog.Destroy()
self.panel2.setTargets('Polygon', [])
return False
if self.data['optimrun'] is False:
self.statbar.PushStatusText("ERROR: Cannot remove polygon. No alignment parameters.", 0)
dialog = wx.MessageDialog(self.frame, "Cannot remove polygon.\nNo alignment parameters.",\
'Error', wx.OK|wx.ICON_ERROR)
dialog.ShowModal()
dialog.Destroy()
return False
newpart1 = []
newpart2 = []
eliminated = 0
apDisplay.printMsg("Removing points inside polygon")
if len(vert1) > len(vert2):
#draw transformed polygon
v1 = numpy.asarray(vert1, dtype=numpy.float32)
v2 = apTiltTransform.a1Toa2Data(v1, self.data)
self.panel2.setTargets('Polygon', v2)
self.panel2.UpdateDrawing()
for i in range(targets1.shape[0]):
point = tuple((targets1[i,0], targets1[i,1]))
#print coord
if self.insidePolygon(point, v1):
eliminated += 1
else:
newpart1.append(targets1[i])
newpart2.append(targets2[i])
elif len(vert2) > len(vert1):
#draw transformed polygon
v2 = numpy.asarray(vert2, dtype=numpy.float32)
v1 = apTiltTransform.a2Toa1Data(v2, self.data)
self.panel1.setTargets('Polygon', v1)
self.panel1.UpdateDrawing()
for i in range(targets2.shape[0]):
point = tuple((targets2[i,0], targets2[i,1]))
if self.insidePolygon(point, v2):
eliminated += 1
else:
newpart1.append(targets1[i])
newpart2.append(targets2[i])
self.panel1.setTargets('Picked',newpart1)
self.panel2.setTargets('Picked',newpart2)
self.panel1.UpdateDrawing()
self.panel2.UpdateDrawing()
apDisplay.printMsg("Removed %d particles inside polygon in %s"%(eliminated, apDisplay.timeString(time.time()-t0)))
self.statbar.PushStatusText("Removed %d particles inside polygon"%(eliminated), 0)
dialog = wx.MessageDialog(self.frame,
"Removed %d particles inside polygon"%(eliminated), 'INFORMATION', wx.OK|wx.ICON_INFORMATION)
if dialog.ShowModal() == wx.ID_OK:
dialog.Destroy()
self.panel1.setTargets('Polygon', [])
self.panel2.setTargets('Polygon', [])
self.onUpdate(evt)
#---------------------------------------
def insidePolygon(self, point, verts):
"""Test whether the points are inside the specified polygon.
The shape is specified by 'verts'
Arguments:
points - (x,y) point
verts - (N,2) array of x,y vertices
Returns:
- True/False based on result of in/out test.
Uses the 'ray to infinity' even-odd test.
Let the ray be the horizontal ray starting at p and going to +inf in x.
"""
verts = numpy.asarray(verts)
x,y = point
### setup edge list
N = verts.shape[0]
### create edge pairs
edges = numpy.column_stack([range(N),range(1, N+1)])
### wrap last vertex
edges[N-1,1] = 0
inside = False
for e in edges:
v0,v1 = verts[e[0]], verts[e[1]]
# Check if both verts to the left of ray
if v0[0]<x and v1[0]<x:
continue
# check if both on the same side of ray
if (v0[1]<y and v1[1]<y) or (v0[1]>y and v1[1]>y):
continue
#check for horizontal line - another horz line can't intersect it
if (v0[1]==v1[1]):
continue
# compute x intersection value
xisect = v0[0] + (v1[0]-v0[0])*((y-v0[1])/(v1[1]-v0[1]))
if xisect >= x:
inside = not inside
return inside
#---------------------------------------
def onMaskRegion(self, evt):
#GET THE ARRAYS
targets1 = self.panel1.getTargets('Picked')
targets2 = self.panel2.getTargets('Picked')
a1 = self.targetsToArray(targets1)
a2 = self.targetsToArray(targets2)
#GET THE POINT VALUES
apTiltTransform.setPointsFromArrays(a1, a2, self.data)
#CHECK IF WE HAVE POINTS
if len(a1) == 0 or len(a2) == 0:
self.statbar.PushStatusText("ERROR: Cannot mask images. Not enough picks", 0)
dialog = wx.MessageDialog(self.frame, "Cannot mask images.\nThere are no picks.",\
'Error', wx.OK|wx.ICON_ERROR)
dialog.ShowModal()
dialog.Destroy()
return False
if self.data['optimrun'] is False:
self.statbar.PushStatusText("ERROR: Cannot mask images. No alignment parameters.", 0)
dialog = wx.MessageDialog(self.frame, "Cannot mask images.\nNo alignment parameters.",\
'Error', wx.OK|wx.ICON_ERROR)
dialog.ShowModal()
dialog.Destroy()
return False
#GET IMAGES
self.panel1.openImageFile(self.panel1.filename)
self.panel2.openImageFile(self.panel2.filename)
image1 = numpy.asarray(self.panel1.imagedata, dtype=numpy.float32)
image2 = numpy.asarray(self.panel2.imagedata, dtype=numpy.float32)
#DO THE MASKING
image1, image2 = apTiltTransform.maskOverlapRegion(image1, image2, self.data)
#SET IMAGES AND REFRESH SCREEN
self.panel1.setImage(image1)
self.panel2.setImage(image2)
self.panel1.setBitmap()
self.panel1.setVirtualSize()
self.panel1.setBuffer()
self.panel1.UpdateDrawing()
self.panel2.setBitmap()
self.panel2.setVirtualSize()
self.panel2.setBuffer()
self.panel2.UpdateDrawing()
#GET THE VALUE
bestOverlap, tiltOverlap = apTiltTransform.getOverlapPercent(image1, image2, self.data)
overlapStr = str(round(100*bestOverlap,2))+"% and "+str(round(100*tiltOverlap,2))+"%"
self.statbar.PushStatusText("Overlap percentage of "+overlapStr, 0)
self.data['overlap'] = round(bestOverlap,5)
#---------------------------------------
def onGetOverlap(self, evt):
"""
This function gets the overlap between the two images based on the alignment parameters
"""
#GET THE ARRAYS
targets1 = self.panel1.getTargets('Picked')
targets2 = self.panel2.getTargets('Picked')
a1 = self.targetsToArray(targets1)
a2 = self.targetsToArray(targets2)
#GET THE POINT VALUES
apTiltTransform.setPointsFromArrays(a1, a2, self.data)
#CHECK IF WE HAVE POINTS
if len(a1) == 0 or len(a2) == 0:
self.statbar.PushStatusText("ERROR: Cannot get overlap. Not enough picks", 0)
dialog = wx.MessageDialog(self.frame, "Cannot get overlap.\nThere are no picks.",\
'Error', wx.OK|wx.ICON_ERROR)
dialog.ShowModal()
dialog.Destroy()
return False
if self.data['optimrun'] is False:
self.statbar.PushStatusText("ERROR: Cannot get overlap. No alignment parameters.", 0)
dialog = wx.MessageDialog(self.frame, "Cannot get overlap.\nNo alignment parameters.",\
'Error', wx.OK|wx.ICON_ERROR)
dialog.ShowModal()
dialog.Destroy()
return False
#GET IMAGES
image1 = numpy.asarray(self.panel1.imagedata, dtype=numpy.float32)
image2 = numpy.asarray(self.panel2.imagedata, dtype=numpy.float32)
#GET THE VALUE
bestOverlap, tiltOverlap = apTiltTransform.getOverlapPercent(image1, image2, self.data)
overlapStr = str(round(100*bestOverlap,2))+"% and "+str(round(100*tiltOverlap,2))+"%"
self.statbar.PushStatusText("Overlap percentage of "+overlapStr, 0)
self.data['overlap'] = round(bestOverlap,5)
#---------------------------------------
def onUpdate(self, evt):
"""
This function updates the aligned particles to the picked particles
"""
#GET ARRAYS
a1 = self.getArray1()
a2 = self.getArray2()
#CHECK TO SEE IF IT OKAY TO PROCEED
if len(a1) == 0 or len(a2) == 0:
self.statbar.PushStatusText("ERROR: Cannot transfer picks. There are no picks.", 0)
dialog = wx.MessageDialog(self.frame, "Cannot transfer picks.\nThere are no picks.",\
'Error', wx.OK|wx.ICON_ERROR)
dialog.ShowModal()
dialog.Destroy()
return False
#SORT PARTICLES
#self.sortParticles(None)
#GET ARRAYS
a1b = self.getAlignedArray1()
a2b = self.getAlignedArray2()
#SET THE ALIGNED ARRAYS
self.panel2.setTargets('Aligned', a1b )
self.panel1.setTargets('Aligned', a2b )
#FIND PARTICLES WITH LARGE ERROR
(a1c, a2c) = self.getBadPicks()
if len(a1c) > 0:
self.panel1.setTargets('Worst', a1c )
if len(a2c) > 0:
self.panel2.setTargets('Worst', a2c )
#for target in targets1:
# target['stats']['RMSD'] = rmsd
#---------------------------------------
def onXferPick(self, evt):
"""
This function transfers any picked particles without a corresponding pair
to the other image using the alignment parameters
"""
#GET ARRAYS
a1 = self.getArray1()
a2 = self.getArray2()
#CHECK TO SEE IF IT OKAY TO PROCEED
if len(a1) == 0 or len(a2) == 0:
self.statbar.PushStatusText("ERROR: Cannot transfer picks. There are no picks.", 0)
dialog = wx.MessageDialog(self.frame, "Cannot transfer picks.\nThere are no picks.",\
'Error', wx.OK|wx.ICON_ERROR)
dialog.ShowModal()
dialog.Destroy()
return False
if self.data['optimrun'] is False:
self.statbar.PushStatusText("ERROR: Cannot transfer picks. No alignment parameters.", 0)
dialog = wx.MessageDialog(self.frame, "Cannot transfer picks.\nNo alignment parameters.",\
'Error', wx.OK|wx.ICON_ERROR)
dialog.ShowModal()
dialog.Destroy()
return False
if len(a1) - len(a2) == 0:
self.statbar.PushStatusText("ERROR: Cannot transfer picks. Same number picks for each panel.", 0)
dialog = wx.MessageDialog(self.frame, "Cannot transfer picks.\nSame number picks for each panel.",\
'Error', wx.OK|wx.ICON_ERROR)
dialog.ShowModal()
dialog.Destroy()
return False
### Case 1: left panel has more than right panel
if len(a1) > len(a2):
a1b = self.getAlignedArray1()
lastpick = a1b[len(a2):]
a2list = self.panel2.getTargets('Picked')
a2list.extend(lastpick)
self.panel2.setTargets('Picked', a2list )
elif len(a2) > len(a1):
a2b = self.getAlignedArray2()
lastpick = a2b[len(a1):]
a1list = self.panel1.getTargets('Picked')
a1list.extend(lastpick)
self.panel1.setTargets('Picked', a1list )
self.onUpdate(evt)
#---------------------------------------
def sortParticles(self, evt):
#GET ARRAYS
a1 = self.getArray1()
a2 = self.getArray2()
if len(a1) != len(a2):
return False
#MERGE INTO ONE
#a3 = numpy.hstack((a1, a2))
a3 = []
for i in range(len(a1)):
a3.append([a1[i,0], a1[i,1], a2[i,0], a2[i,1],])
#SORT PARTICLES
def _distSortFunc(a, b):
if 5*a[0]+a[1] > 5*b[0]+b[1]:
return 1
return -1
a3.sort(_distSortFunc)
a3b = numpy.asarray(a3)
#SPLIT BACK UP
a1b = a3b[:,0:2]
a2b = a3b[:,2:4]
#fix first particle???
#a1c = numpy.vstack(([[a1[0,0], a1[0,1]],a1b)
#a2c = numpy.vstack(([[a2[0,0], a2[0,1]],a2b)
#SET SORTED TARGETS
self.panel1.setTargets('Picked', a1b )
self.panel2.setTargets('Picked', a2b )
#---------------------------------------
def onCheckGuessShift(self, evt):
if ( self.data['theta'] == 0.0
or self.data['gamma'] == 0.0
or self.data['phi'] == 0.0 ):
self.shift_dialog.Show()
else:
self.onGuessShift(evt)
return
#---------------------------------------
def onGuessShift(self, evt):
targets1 = self.panel1.getTargets('Picked')
targets2 = self.panel2.getTargets('Picked')
if len(targets1) > 2 or len(targets2) > 2:
self.statbar.PushStatusText("ERROR: Abort guess shift; more than 2 particles", 0)
dialog = wx.MessageDialog(self.frame,
"Will not guess shift when you have more than 2 particles.",\
'Error', wx.OK|wx.ICON_ERROR)
dialog.ShowModal()
dialog.Destroy()
return False
#cross-corrlate to get shift
img1 = numpy.asarray(self.panel1.imagedata, dtype=numpy.float32)
tiltdiff = self.data['theta']
img2 = numpy.asarray(self.panel2.imagedata, dtype=numpy.float32)
tiltaxis = (self.data['phi'] + self.data['gamma'])/2.0
if tiltaxis == 0.0:
tiltaxis = -7.2
# snr > than arbitrary value run some other stuff
if len(self.picks1) > 10 and len(self.picks2) > 10:
### PIPELINE MODE
### set important parameters
imgfile1 = self.panel1.filename
imgfile2 = self.panel2.filename
outfile = self.data['outfile']
pixdiam = self.data['pixdiam']
if False:
### run old tilt automation scheme
origin, newpart, snr, ang = apTiltShift.getTiltedCoordinates(img1, img2, tiltdiff,
self.picks1, angsearch=True, inittiltaxis=tiltaxis)
self.panel1.setTargets('Picked', [origin])
self.panel2.setTargets('Picked', [newpart])
self.shift.SetBackgroundColour(self.deselectcolor)