def initialize(self):
leginon.gui.wx.Settings.ScrolledDialog.initialize(self)
sb = wx.StaticBox(self, -1, 'Spacing/Angle Calculator')
sbszauto = wx.StaticBoxSizer(sb, wx.VERTICAL)
szoptions = wx.GridBagSizer(5, 5)
## auto raster
self.widgets['raster preset'] = PresetChoice(self, -1)
presets = self.node.presetsclient.getPresetNames()
self.widgets['raster preset'].setChoices(presets)
self.widgets['raster overlap'] = FloatEntry(self, -1, chars=8)
movetypes = self.node.calclients.keys()
self.widgets['raster movetype'] = Choice(self, -1, choices=movetypes)
self.autobut = wx.Button(
self, -1,
'Calculate spacing and angle using the following parameters:')
szauto = wx.GridBagSizer(5, 5)
szauto.Add(self.autobut, (0, 0), (1, 2), wx.ALIGN_CENTER_VERTICAL)
label = wx.StaticText(self, -1, 'Raster Preset')
szauto.Add(label, (1, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szauto.Add(self.widgets['raster preset'], (1, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL)
label = wx.StaticText(self, -1, 'Overlap percent')
szauto.Add(label, (2, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szauto.Add(self.widgets['raster overlap'], (2, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL)
label = wx.StaticText(self, -1, 'Move Type')
szauto.Add(label, (3, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szauto.Add(self.widgets['raster movetype'], (3, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL)
sbszauto.Add(szauto, 1, wx.EXPAND | wx.ALL, 5)
self.Bind(wx.EVT_BUTTON, self.onAutoButton, self.autobut)
## end of auto raster
szoptions.Add(sbszauto, (0, 0), (1, 2), wx.ALIGN_CENTER_VERTICAL)
label = wx.StaticText(self, -1, 'Raster Spacing')
self.widgets['raster spacing'] = FloatEntry(self, -1, chars=8)
szoptions.Add(label, (1, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szoptions.Add(self.widgets['raster spacing'], (1, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL)
label = wx.StaticText(self, -1, 'Raster Angle')
self.widgets['raster angle'] = FloatEntry(self, -1, chars=8)
szoptions.Add(label, (2, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szoptions.Add(self.widgets['raster angle'], (2, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL)
szbutton = wx.GridBagSizer(5, 5)
self.bclear = wx.Button(self, -1, 'Clear Targets')
szbutton.Add(self.bclear, (0, 0), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_LEFT)
szbutton.AddGrowableCol(0)
self.Bind(wx.EVT_BUTTON, self.onClearButton, self.bclear)
self.btest = wx.Button(self, -1, 'Test')
szbutton.Add(self.btest, (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_RIGHT)
szbutton.AddGrowableCol(1)
self.Bind(wx.EVT_BUTTON, self.onTestButton, self.btest)
return [szoptions, szbutton]
def initialize(self):
leginon.gui.wx.Settings.ScrolledDialog.initialize(self)
sb = wx.StaticBox(self, -1, 'Stuff')
sbsz= wx.StaticBoxSizer(sb, wx.VERTICAL)
sz = wx.GridBagSizer(5, 5)
self.gobut = wx.Button(self, -1, 'Go')
sz.Add(self.gobut, (0, 0), (1, 1), wx.ALIGN_CENTER)
self.testbut = wx.Button(self, -1, 'Test')
sz.Add(self.testbut, (0, 1), (1, 1), wx.ALIGN_CENTER)
lab = wx.StaticText(self, -1, 'minsize')
self.widgets['minsize'] = FloatEntry(self, -1)
sz.Add(lab, (1,0), (1,1))
sz.Add(self.widgets['minsize'], (1,1), (1,1))
lab = wx.StaticText(self, -1, 'maxsize')
self.widgets['maxsize'] = FloatEntry(self, -1)
sz.Add(lab, (2,0), (1,1))
sz.Add(self.widgets['maxsize'], (2,1), (1,1))
lab = wx.StaticText(self, -1, 'pause')
self.widgets['pause'] = FloatEntry(self, -1)
sz.Add(lab, (3,0), (1,1))
sz.Add(self.widgets['pause'], (3,1), (1,1))
lab = wx.StaticText(self, -1, 'label')
self.widgets['label'] = Entry(self, -1)
sz.Add(lab, (4,0), (1,1))
sz.Add(self.widgets['label'], (4,1), (1,1))
lab = wx.StaticText(self, -1, 'threshold')
self.widgets['threshold'] = FloatEntry(self, -1)
sz.Add(lab, (5,0), (1,1))
sz.Add(self.widgets['threshold'], (5,1), (1,1))
lab = wx.StaticText(self, -1, 'maxcount')
self.widgets['maxcount'] = IntEntry(self, -1)
sz.Add(lab, (6,0), (1,1))
sz.Add(self.widgets['maxcount'], (6,1), (1,1))
lab = wx.StaticText(self, -1, 'minbright')
self.widgets['minbright'] = FloatEntry(self, -1)
sz.Add(lab, (7,0), (1,1))
sz.Add(self.widgets['minbright'], (7,1), (1,1))
lab = wx.StaticText(self, -1, 'maxbright')
self.widgets['maxbright'] = FloatEntry(self, -1)
sz.Add(lab, (8,0), (1,1))
sz.Add(self.widgets['maxbright'], (8,1), (1,1))
lab = wx.StaticText(self, -1, 'cutoffpercent')
self.widgets['cutoffpercent'] = FloatEntry(self, -1)
sz.Add(lab, (9,0), (1,1))
sz.Add(self.widgets['cutoffpercent'], (9,1), (1,1))
lab = wx.StaticText(self, -1, 'magsteps')
self.widgets['magsteps'] = IntEntry(self, -1)
sz.Add(lab, (10,0), (1,1))
sz.Add(self.widgets['magsteps'], (10,1), (1,1))
lab = wx.StaticText(self, -1, 'mag1')
self.widgets['mag1'] = IntEntry(self, -1)
sz.Add(lab, (11,0), (1,1))
sz.Add(self.widgets['mag1'], (11,1), (1,1))
lab = wx.StaticText(self, -1, 'mag2')
self.widgets['mag2'] = IntEntry(self, -1)
sz.Add(lab, (12,0), (1,1))
sz.Add(self.widgets['mag2'], (12,1), (1,1))
sbsz.Add(sz, 0, wx.EXPAND|wx.ALL, 5)
self.Bind(wx.EVT_BUTTON, self.onGo, self.gobut)
self.Bind(wx.EVT_BUTTON, self.onTest, self.testbut)
return [sbsz,]
def addTiltSettings(self):
sb = wx.StaticBox(self, -1, 'Tilt Options')
sbsz = wx.StaticBoxSizer(sb, wx.VERTICAL)
sizer = wx.GridBagSizer(5, 4)
bordersize = 3
label = wx.StaticText(self, -1, 'Activation Interval')
sizer.Add(label, (0, 0), (1, 2), wx.ALIGN_CENTER_VERTICAL)
self.widgets['activation interval'] = IntEntry(self, -1, chars=5, style=wx.ALIGN_RIGHT)
sizer.Add(self.widgets['activation interval'], (0,2), (1,2), wx.ALL|wx.EXPAND|wx.ALIGN_CENTER_VERTICAL, bordersize)
label = wx.StaticText(self, -1, 'List of Tilts to Collect (in degrees)')
sizer.Add(label, (1, 0), (1, 2), wx.ALIGN_CENTER_VERTICAL)
self.widgets['tilts'] = Entry(self, -1, chars=15, style=wx.ALIGN_RIGHT)
sizer.Add(self.widgets['tilts'], (1,2), (1,2), wx.ALL|wx.EXPAND|wx.ALIGN_CENTER_VERTICAL, bordersize)
label = wx.StaticText(self, -1, 'Maximum Tilt Stepsize (in degrees)')
sizer.Add(label, (2, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
self.widgets['stepsize'] = IntEntry(self, -1, chars=2, value='15')
sizer.Add(self.widgets['stepsize'], (2,1), (1,1), wx.ALL|wx.ALIGN_CENTER_VERTICAL, bordersize)
label = wx.StaticText(self, -1, 'Pause Between Steps')
sizer.Add(label, (2, 2), (1, 1), wx.ALIGN_CENTER_VERTICAL)
self.widgets['pause'] = FloatEntry(self, -1, chars=2, value='1')
sizer.Add(self.widgets['pause'], (2,3), (1,1), wx.ALL|wx.ALIGN_CENTER_VERTICAL, bordersize)
label = wx.StaticText(self, -1, 'Min Feature Size')
sizer.Add(label, (3,0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
self.widgets['minsize'] = FloatEntry(self, -1, chars=6, value='0.0')
sizer.Add(self.widgets['minsize'], (3,1), (1,1), wx.ALL|wx.ALIGN_CENTER_VERTICAL, bordersize)
label = wx.StaticText(self, -1, 'Max Feature Size')
sizer.Add(label, (3, 2), (1, 1), wx.ALIGN_CENTER_VERTICAL)
self.widgets['maxsize'] = FloatEntry(self, -1, chars=6, value='0.0')
sizer.Add(self.widgets['maxsize'], (3,3), (1,1), wx.ALL|wx.ALIGN_CENTER_VERTICAL, bordersize)
label = wx.StaticText(self, -1, 'Median Filter (pixels)')
sizer.Add(label, (4, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
self.widgets['medfilt'] = IntEntry(self, -1, chars=2, value='0')
sizer.Add(self.widgets['medfilt'], (4,1), (1,1), wx.ALL|wx.ALIGN_CENTER_VERTICAL, bordersize)
label = wx.StaticText(self, -1, 'LowPass Filter (pixels)')
sizer.Add(label, (4, 2), (1, 1), wx.ALIGN_CENTER_VERTICAL)
self.widgets['lowfilt'] = FloatEntry(self, -1, chars=2, value='0.0')
sizer.Add(self.widgets['lowfilt'], (4,3), (1,1), wx.ALL|wx.ALIGN_CENTER_VERTICAL, bordersize)
label = wx.StaticText(self, -1, 'Drift threshold')
sizer.Add(label, (5, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
self.widgets['drift threshold'] = FloatEntry(self, -1, chars=6, value='0.0')
sizer.Add(self.widgets['drift threshold'], (5,1), (1,1), wx.ALL|wx.ALIGN_CENTER_VERTICAL, bordersize)
label = wx.StaticText(self, -1, 'Drift preset')
sizer.Add(label, (5, 2), (1, 1), wx.ALIGN_CENTER_VERTICAL)
presets = self.node.presetsclient.getPresetNames()
self.widgets['drift preset'] = PresetChoice(self, -1)
self.widgets['drift preset'].setChoices(presets)
sizer.Add(self.widgets['drift preset'], (5,3), (1,1), wx.ALL|wx.ALIGN_CENTER_VERTICAL, bordersize)
sbsz.Add(sizer, 0, wx.ALIGN_CENTER|wx.ALL, 2)
return sbsz
def initialize(self):
leginon.gui.wx.Settings.ScrolledDialog.initialize(self)
sb = wx.StaticBox(self, -1, 'Ice Thickness Threshold')
sbszice = wx.StaticBoxSizer(sb, wx.VERTICAL)
sb = wx.StaticBox(self, -1, 'Focus Template Thickness')
sbszftt = wx.StaticBoxSizer(sb, wx.VERTICAL)
sb = wx.StaticBox(self, -1, 'Target Template')
sbsztt = wx.StaticBoxSizer(sb, wx.VERTICAL)
self.widgets['ice min mean'] = FloatEntry(self, -1, chars=6)
self.widgets['ice max mean'] = FloatEntry(self, -1, chars=6)
self.widgets['ice max std'] = FloatEntry(self, -1, chars=6)
self.widgets['focus hole'] = Choice(self, -1, choices=self.node.focustypes)
self.widgets['target template'] = wx.CheckBox(self, -1,
'Use target template')
self.widgets['focus template'] = leginon.gui.wx.TargetTemplate.Panel(self,
'Focus Target Template', autofill=True)
self.widgets['acquisition template'] = leginon.gui.wx.TargetTemplate.Panel(self,
'Acquisition Target Template', autofill=True)
self.widgets['focus template thickness'] = wx.CheckBox(self, -1,
'Use focus template thickness and limit to one focus target')
self.widgets['focus stats radius'] = IntEntry(self, -1, chars=6)
self.widgets['focus min mean thickness'] = FloatEntry(self, -1, chars=6)
self.widgets['focus max mean thickness'] = FloatEntry(self, -1, chars=6)
self.widgets['focus max stdev thickness'] = FloatEntry(self, -1, chars=6)
szice = wx.GridBagSizer(5, 5)
label = wx.StaticText(self, -1, 'Min. mean:')
szice.Add(label, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szice.Add(self.widgets['ice min mean'], (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL|wx.FIXED_MINSIZE|wx.ALIGN_RIGHT)
label = wx.StaticText(self, -1, 'Max. mean:')
szice.Add(label, (1, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szice.Add(self.widgets['ice max mean'], (1, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL|wx.FIXED_MINSIZE|wx.ALIGN_RIGHT)
label = wx.StaticText(self, -1, 'Max. stdev.:')
szice.Add(label, (2, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szice.Add(self.widgets['ice max std'], (2, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL|wx.FIXED_MINSIZE|wx.ALIGN_RIGHT)
label = wx.StaticText(self, -1, 'Focus hole selection:')
szice.Add(label, (3, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szice.Add(self.widgets['focus hole'], (3, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL|wx.ALIGN_RIGHT)
szice.AddGrowableCol(1)
sbszice.Add(szice, 1, wx.EXPAND|wx.ALL, 5)
szftt = wx.GridBagSizer(5, 5)
szftt.Add(self.widgets['focus template thickness'], (0, 0), (1, 2),
wx.ALIGN_CENTER_VERTICAL)
label = wx.StaticText(self, -1, 'Stats. radius:')
szftt.Add(label, (1, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szftt.Add(self.widgets['focus stats radius'], (1, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL|wx.FIXED_MINSIZE|wx.ALIGN_RIGHT)
label = wx.StaticText(self, -1, 'Min. mean thickness:')
szftt.Add(label, (2, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szftt.Add(self.widgets['focus min mean thickness'], (2, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL|wx.FIXED_MINSIZE|wx.ALIGN_RIGHT)
label = wx.StaticText(self, -1, 'Max. mean thickness:')
szftt.Add(label, (3, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szftt.Add(self.widgets['focus max mean thickness'], (3, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL|wx.FIXED_MINSIZE|wx.ALIGN_RIGHT)
label = wx.StaticText(self, -1, 'Max. std. thickness:')
szftt.Add(label, (4, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szftt.Add(self.widgets['focus max stdev thickness'], (4, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL|wx.FIXED_MINSIZE|wx.ALIGN_RIGHT)
szftt.AddGrowableCol(1)
sbszftt.Add(szftt, 1, wx.EXPAND|wx.ALL, 5)
sztt = wx.GridBagSizer(5, 5)
sztt.Add(self.widgets['target template'], (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
sztt.Add(sbszftt, (1, 0), (3, 1), wx.ALIGN_CENTER)
sztt.Add(self.widgets['focus template'], (0, 1), (2, 1), wx.ALIGN_CENTER|wx.EXPAND)
sztt.Add(self.widgets['acquisition template'], (2, 1), (2, 1), wx.ALIGN_CENTER|wx.EXPAND)
sztt.AddGrowableCol(1)
sztt.AddGrowableRow(0)
sztt.AddGrowableRow(2)
sbsztt.Add(sztt, 1, wx.EXPAND|wx.ALL, 5)
self.bice = wx.Button(self, -1, '&Test targeting')
self.cice = wx.Button(self, -1, '&Clear targets')
szbutton = wx.GridBagSizer(5, 5)
szbutton.Add(self.cice, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL|wx.ALIGN_LEFT)
szbutton.Add(self.bice, (0, 1), (1, 1), wx.ALIGN_CENTER_VERTICAL|wx.ALIGN_RIGHT)
szbutton.AddGrowableCol(1)
self.Bind(wx.EVT_BUTTON, self.onTestButton, self.bice)
self.Bind(wx.EVT_BUTTON, self.onClearButton, self.cice)
self.growrows = [False, True, False,]
return [sbszice, sbsztt, szbutton]
def addTomoBasicSettings(self):
tiltsb = wx.StaticBox(self, -1, 'Tilt')
tiltsbsz = wx.StaticBoxSizer(tiltsb, wx.VERTICAL)
expsb = wx.StaticBox(self, -1, 'Exposure')
expsbsz = wx.StaticBoxSizer(expsb, wx.VERTICAL)
miscsb = wx.StaticBox(self, -1, 'Misc.')
miscsbsz = wx.StaticBoxSizer(miscsb, wx.VERTICAL)
# tiltsbsz
self.widgets['tilt min'] = FloatEntry(self,
-1,
allownone=False,
chars=7,
value='0.0')
self.widgets['tilt max'] = FloatEntry(self,
-1,
allownone=False,
chars=7,
value='0.0')
self.widgets['tilt start'] = FloatEntry(self,
-1,
allownone=False,
chars=7,
value='0.0')
self.widgets['tilt step'] = FloatEntry(self,
-1,
allownone=False,
chars=7,
value='0.0')
tiltsz = wx.GridBagSizer(5, 5)
label = wx.StaticText(self, -1, 'Min.')
tiltsz.Add(label, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL | wx.LEFT,
10)
tiltsz.Add(self.widgets['tilt min'], (0, 1), (1, 1),
wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE)
label = wx.StaticText(self, -1, 'Max.')
tiltsz.Add(label, (0, 2), (1, 1),
wx.ALIGN_RIGHT | wx.ALIGN_CENTER_VERTICAL | wx.LEFT, 10)
tiltsz.Add(self.widgets['tilt max'], (0, 3), (1, 1),
wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE)
label = wx.StaticText(self, -1, 'Start')
tiltsz.Add(label, (0, 4), (1, 1),
wx.ALIGN_RIGHT | wx.ALIGN_CENTER_VERTICAL | wx.LEFT, 10)
tiltsz.Add(self.widgets['tilt start'], (0, 5), (1, 1),
wx.ALIGN_LEFT | wx.FIXED_MINSIZE)
label = wx.StaticText(self, -1, 'Step')
tiltsz.Add(label, (0, 6), (1, 1),
wx.ALIGN_RIGHT | wx.ALIGN_CENTER_VERTICAL | wx.LEFT, 10)
tiltsz.Add(self.widgets['tilt step'], (0, 7), (1, 1),
wx.ALIGN_LEFT | wx.FIXED_MINSIZE)
label = wx.StaticText(self, -1, 'degree(s)')
tiltsz.Add(label, (0, 8), (1, 1), wx.ALIGN_CENTER_VERTICAL)
tiltsbsz.Add(tiltsz, 0, wx.EXPAND | wx.ALL, 5)
#expsz
self.widgets['dose'] = FloatEntry(self,
-1,
min=0.0,
allownone=False,
chars=7,
value='200.0')
expsz = wx.GridBagSizer(5, 10)
label = wx.StaticText(self, -1, 'Total dose')
expsz.Add(label, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
expsz.Add(self.widgets['dose'], (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_RIGHT | wx.FIXED_MINSIZE)
label = wx.StaticText(self, -1, 'e-/A^2')
expsz.Add(label, (0, 2), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE)
expsz.AddGrowableCol(0)
expsz.AddGrowableRow(0)
expsbsz.Add(expsz, 1, wx.EXPAND | wx.ALL, 5)
#misc
self.widgets['integer'] = wx.CheckBox(self, -1, 'Scale by')
self.widgets['intscale'] = FloatEntry(self,
-1,
min=0.0,
allownone=False,
chars=5,
value='10.0')
self.widgets['mean threshold'] = FloatEntry(self,
-1,
min=0.0,
allownone=False,
chars=5,
value='100.0')
intsz = wx.GridBagSizer(5, 5)
intsz.Add(self.widgets['integer'], (0, 0), (1, 1),
wx.ALIGN_CENTER_VERTICAL)
intsz.Add(self.widgets['intscale'], (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL)
label = wx.StaticText(self, -1, 'to convert to integer')
intsz.Add(label, (0, 2), (1, 1), wx.ALIGN_CENTER_VERTICAL)
mtsz = wx.GridBagSizer(5, 5)
label = wx.StaticText(self, -1, 'Consider images with less than')
mtsz.Add(label, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
mtsz.Add(self.widgets['mean threshold'], (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE)
label = wx.StaticText(self, -1, 'counts as obstructed')
mtsz.Add(label, (0, 2), (1, 1), wx.ALIGN_CENTER_VERTICAL)
miscsz = wx.GridBagSizer(5, 10)
miscsz.Add(intsz, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
miscsz.Add(mtsz, (1, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
miscsbsz.Add(miscsz, 1, wx.ALL | wx.ALIGN_CENTER, 5)
# overall
sz = wx.GridBagSizer(5, 5)
sz.Add(tiltsbsz, (0, 0), (1, 2), wx.EXPAND)
sz.Add(expsbsz, (1, 0), (1, 1), wx.EXPAND)
sz.Add(miscsbsz, (1, 1), (1, 1), wx.EXPAND)
sz.AddGrowableRow(0)
sz.AddGrowableRow(1)
sz.AddGrowableCol(0)
sz.AddGrowableCol(1)
return sz
def addSettings(self):
overridebox = wx.StaticBox(self, -1, "Override Preset during Testing")
overridesz = wx.StaticBoxSizer(overridebox, wx.VERTICAL)
errbox = wx.StaticBox(self, -1,
"Error Checking and Correction during Testing")
errsz = wx.StaticBoxSizer(errbox, wx.VERTICAL)
# pause time
self.widgets['pause time'] = FloatEntry(self,
-1,
min=0.0,
allownone=False,
chars=4,
value='0.0')
szpausetime = wx.GridBagSizer(5, 5)
szpausetime.Add(wx.StaticText(self, -1, 'Wait'), (0, 0), (1, 1),
wx.ALIGN_CENTER_VERTICAL)
szpausetime.Add(self.widgets['pause time'], (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE)
szpausetime.Add(
wx.StaticText(self, -1, 'seconds before acquiring image'), (0, 2),
(1, 1), wx.ALIGN_CENTER_VERTICAL)
# override preset
self.widgets['override preset'] = wx.CheckBox(self, -1,
'Override Preset')
self.widgets['instruments'] = leginon.gui.wx.Instrument.SelectionPanel(
self, passive=True)
self.panel.setInstrumentSelection(self.widgets['instruments'])
self.widgets['camera settings'] = leginon.gui.wx.Camera.CameraPanel(
self)
self.widgets['camera settings'].setGeometryLimits({
'size':
self.node.instrument.camerasize,
'binnings':
self.node.instrument.camerabinnings,
'binmethod':
self.node.instrument.camerabinmethod
})
self.widgets['background readout'] = wx.CheckBox(
self, -1, 'Background Readout')
sz = wx.GridBagSizer(5, 10)
sz.Add(self.widgets['override preset'], (0, 0), (1, 1),
wx.ALIGN_CENTER_VERTICAL)
sz.Add(self.widgets['instruments'], (1, 0), (1, 1), wx.EXPAND)
sz.Add(self.widgets['camera settings'], (2, 0), (1, 1), wx.EXPAND)
sz.Add(self.widgets['background readout'], (3, 0), (1, 1), wx.EXPAND)
overridesz.Add(sz, 0, wx.ALIGN_CENTER | wx.ALL, 5)
# error checking and correction
self.widgets['check calibration'] = wx.CheckBox(
self, -1, 'Measure move error')
precsz = wx.GridBagSizer(5, 5)
label1 = wx.StaticText(self, -1, 'Move to within')
self.widgets['precision'] = FloatEntry(self,
-1,
min=0.0,
allownone=False,
chars=6,
value='0.0')
label2 = wx.StaticText(self, -1, 'm of clicked position')
precsz.Add(label1, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
precsz.Add(self.widgets['precision'], (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE)
precsz.Add(label2, (0, 2), (1, 1), wx.ALIGN_CENTER_VERTICAL)
label1 = wx.StaticText(self, -1, 'Acceptable distance:')
self.widgets['accept precision'] = FloatEntry(self,
-1,
min=0.0,
allownone=False,
chars=6,
value='1e-3')
label2 = wx.StaticText(self, -1, '(m) if move error get worse')
precsz.Add(label1, (1, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
precsz.Add(self.widgets['accept precision'], (1, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE)
precsz.Add(label2, (1, 2), (1, 1), wx.ALIGN_CENTER_VERTICAL)
self.widgets['final image shift'] = wx.CheckBox(
self, -1, 'Final Image Shift')
precsz.Add(self.widgets['final image shift'], (2, 0), (1, 2))
#maxerrsz = wx.GridBagSizer(5, 5)
#label = wx.StaticText(self, -1, 'Local Correlation Size (pixels)')
#self.widgets['max error'] = FloatEntry(self, -1, min=0.0, allownone=False, chars=6, value='0.0')
#maxerrsz.Add(label, (0, 0), (1, 1))
#maxerrsz.Add(self.widgets['max error'], (0, 1), (1, 1),
# wx.ALIGN_CENTER_VERTICAL)
hysfixsz = wx.GridBagSizer(5, 5)
label = wx.StaticText(self, -1, '')
self.widgets['cycle after'] = wx.CheckBox(
self, -1, 'Preset cycle after final move')
self.widgets['cycle each'] = wx.CheckBox(
self, -1, 'Preset cycle after each move')
hysfixsz.Add(self.widgets['cycle after'], (0, 0), (1, 1))
hysfixsz.Add(self.widgets['cycle each'], (1, 0), (1, 1))
##
ccsz = wx.GridBagSizer(5, 5)
ccsz.Add(self.widgets['check calibration'], (0, 0), (1, 1),
wx.ALIGN_CENTER_VERTICAL)
#sz.Add(maxerrsz, (1, 0), (1, 1),
# wx.ALIGN_CENTER_VERTICAL)
ccsz.Add(precsz, (2, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
ccsz.Add(hysfixsz, (3, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
errsz.Add(ccsz, 0, wx.ALIGN_CENTER | wx.ALL, 5)
# settings sizer
sz = wx.GridBagSizer(5, 10)
sz.Add(overridesz, (0, 0), (6, 1))
sz.Add(szpausetime, (1, 1), (1, 1), wx.ALIGN_CENTER_VERTICAL)
sz.Add(errsz, (3, 1), (1, 1))
#sz.AddGrowableRow(2)
return sz
def initialize(self):
leginon.gui.wx.Settings.ScrolledDialog.initialize(self)
sb = wx.StaticBox(self, -1, 'Robot')
sbsz = wx.StaticBoxSizer(sb, wx.VERTICAL)
self.widgets['column pressure threshold'] = FloatEntry(self,
-1,
min=0.0,
chars=6)
self.widgets['default Z position'] = FloatEntry(self,
-1,
min=-2.0,
chars=8)
self.widgets['simulate'] = wx.CheckBox(
self, -1, 'Simulate Robot Insert/Extraction')
self.widgets['turbo on'] = wx.CheckBox(self, -1,
'Turbo Pump Always On')
self.widgets['grid clear wait'] = wx.CheckBox(
self, -1, 'Wait for User Confirmation of Grid Clearing')
self.widgets['pause'] = wx.CheckBox(self, -1,
'Pause before Extraction')
szcolumnpressure = wx.GridBagSizer(5, 5)
label = wx.StaticText(self, -1, 'Column pressure threshold:')
szcolumnpressure.Add(label, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szcolumnpressure.Add(self.widgets['column pressure threshold'], (0, 1),
(1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE)
szdefzposition = wx.GridBagSizer(5, 5)
label = wx.StaticText(self, -1, 'Default Z Position:')
szdefzposition.Add(label, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szdefzposition.Add(self.widgets['default Z position'], (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE)
szsimu = wx.GridBagSizer(5, 5)
szsimu.Add(self.widgets['simulate'], (0, 0), (1, 1),
wx.ALIGN_CENTER_VERTICAL)
szpump = wx.GridBagSizer(5, 5)
szpump.Add(self.widgets['turbo on'], (0, 0), (1, 1),
wx.ALIGN_CENTER_VERTICAL)
sz = wx.GridBagSizer(5, 5)
szgridclear = wx.GridBagSizer(5, 5)
szgridclear.Add(self.widgets['grid clear wait'], (0, 0), (1, 1),
wx.ALIGN_CENTER_VERTICAL)
sz = wx.GridBagSizer(5, 5)
szpause = wx.GridBagSizer(5, 5)
szpause.Add(self.widgets['pause'], (0, 0), (1, 1),
wx.ALIGN_CENTER_VERTICAL)
sz.Add(szcolumnpressure, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
sz.Add(szdefzposition, (1, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
sz.Add(szsimu, (2, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
sz.Add(szpump, (3, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
sz.Add(szgridclear, (4, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
sz.Add(szpause, (5, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
sbsz.Add(sz, 0, wx.ALIGN_CENTER | wx.ALL, 5)
return [sbsz]
class PartCutoffDialog(wx.Dialog):
#==================
def __init__(self, parent):
self.parent = parent
### get stats
rmsd = self.parent.getRmsdArray()
worstvalstr = "%.3f" % (rmsd.max())
meanvalstr = "%.3f +/- %.3f" % (rmsd.mean(), rmsd.std())
minworsterrstr = "%.3f" % (self.parent.minworsterr)
### create dialog
wx.Dialog.__init__(self, self.parent.frame, -1,
"Particle Cutoff Removal")
### create input area
inforow = wx.FlexGridSizer(3, 2, 15, 15)
meanlabel = wx.StaticText(self,
-1,
"Current mean RMSD: ",
style=wx.ALIGN_LEFT
| wx.ALIGN_CENTER_VERTICAL)
meanvalue = wx.StaticText(self,
-1,
meanvalstr,
style=wx.ALIGN_CENTER
| wx.ALIGN_CENTER_VERTICAL)
inforow.Add(meanlabel, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
inforow.Add(
meanvalue, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL | wx.ALL, 3)
worstlabel = wx.StaticText(self,
-1,
"Current worst RMSD: ",
style=wx.ALIGN_LEFT
| wx.ALIGN_CENTER_VERTICAL)
worstvalue = wx.StaticText(self,
-1,
worstvalstr,
style=wx.ALIGN_CENTER
| wx.ALIGN_CENTER_VERTICAL)
inforow.Add(worstlabel, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
inforow.Add(
worstvalue, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL | wx.ALL, 3)
cutofflabel = wx.StaticText(self,
-1,
"RMSD cutoff: ",
style=wx.ALIGN_LEFT
| wx.ALIGN_CENTER_VERTICAL)
self.cutoffvalue = FloatEntry(self,
-1,
allownone=False,
chars=8,
value=minworsterrstr)
inforow.Add(cutofflabel, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
inforow.Add(
self.cutoffvalue, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL | wx.ALL, 3)
### create button area
cancelcutoff = wx.Button(self, wx.ID_CANCEL, '&Cancel')
self.applycutoff = wx.Button(self, wx.ID_APPLY, '&Apply')
self.Bind(wx.EVT_BUTTON, self.onApplyCutoff, self.applycutoff)
buttonrow = wx.GridSizer(1, 2)
buttonrow.Add(cancelcutoff, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL, 0)
buttonrow.Add(self.applycutoff, 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 onApplyCutoff(self, evt):
### get values
cutoff = self.cutoffvalue.GetValue()
a1 = self.parent.getArray1()
a2 = self.parent.getArray2()
rmsd = self.parent.getRmsdArray()
### must set a lower bound
if cutoff < rmsd.mean():
self.Destroy()
dialog = wx.MessageDialog(
self.parent.frame,
"Particle Cutoff must be greater than the mean error", 'Error',
wx.OK | wx.ICON_ERROR)
dialog.ShowModal()
dialog.Destroy()
return
### find good particles
g1 = []
g2 = []
for i, val in enumerate(rmsd):
if val < cutoff:
g1.append(a1[i])
g2.append(a2[i])
### replace existing particles with only good ones
apDisplay.printMsg("Eliminated " + str(len(a1) - len(g1)) +
" particles")
self.parent.panel1.setTargets('Worst', [])
self.parent.panel2.setTargets('Worst', [])
self.parent.panel1.setTargets('Picked', g1)
self.parent.panel2.setTargets('Picked', g2)
self.parent.onUpdate(None)
self.parent.statbar.PushStatusText(
"Removed " + str(len(a1) - len(g1)) + " particles", 0)
self.Destroy()
return
def __init__(self, parent):
self.parent = parent
### get stats
rmsd = self.parent.getRmsdArray()
worstvalstr = "%.3f" % (rmsd.max())
meanvalstr = "%.3f +/- %.3f" % (rmsd.mean(), rmsd.std())
minworsterrstr = "%.3f" % (self.parent.minworsterr)
### create dialog
wx.Dialog.__init__(self, self.parent.frame, -1,
"Particle Cutoff Removal")
### create input area
inforow = wx.FlexGridSizer(3, 2, 15, 15)
meanlabel = wx.StaticText(self,
-1,
"Current mean RMSD: ",
style=wx.ALIGN_LEFT
| wx.ALIGN_CENTER_VERTICAL)
meanvalue = wx.StaticText(self,
-1,
meanvalstr,
style=wx.ALIGN_CENTER
| wx.ALIGN_CENTER_VERTICAL)
inforow.Add(meanlabel, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
inforow.Add(
meanvalue, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL | wx.ALL, 3)
worstlabel = wx.StaticText(self,
-1,
"Current worst RMSD: ",
style=wx.ALIGN_LEFT
| wx.ALIGN_CENTER_VERTICAL)
worstvalue = wx.StaticText(self,
-1,
worstvalstr,
style=wx.ALIGN_CENTER
| wx.ALIGN_CENTER_VERTICAL)
inforow.Add(worstlabel, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
inforow.Add(
worstvalue, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL | wx.ALL, 3)
cutofflabel = wx.StaticText(self,
-1,
"RMSD cutoff: ",
style=wx.ALIGN_LEFT
| wx.ALIGN_CENTER_VERTICAL)
self.cutoffvalue = FloatEntry(self,
-1,
allownone=False,
chars=8,
value=minworsterrstr)
inforow.Add(cutofflabel, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
inforow.Add(
self.cutoffvalue, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL | wx.ALL, 3)
### create button area
cancelcutoff = wx.Button(self, wx.ID_CANCEL, '&Cancel')
self.applycutoff = wx.Button(self, wx.ID_APPLY, '&Apply')
self.Bind(wx.EVT_BUTTON, self.onApplyCutoff, self.applycutoff)
buttonrow = wx.GridSizer(1, 2)
buttonrow.Add(cancelcutoff, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL, 0)
buttonrow.Add(self.applycutoff, 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)
class EditPlanDialog(wx.Dialog):
def __init__(self, parent):
wx.Dialog.__init__(self, parent.GetParent(), -1, 'Edit Plan')
self.parent = parent
self.plan = parent.plan
strows = wx.StaticText(self, -1, 'Bad rows:')
stcolumns = wx.StaticText(self, -1, 'Bad columns:')
stpixels = wx.StaticText(self, -1, 'Bad Pixel (x,y):')
pixels = ', '.join(map(str, self.plan['pixels']))
rows = ', '.join(map(str, self.plan['rows']))
columns = ', '.join(map(str, self.plan['columns']))
self.tcrows = wx.TextCtrl(self, -1, rows)
self.tccolumns = wx.TextCtrl(self, -1, columns)
self.tcpixels = wx.TextCtrl(self, -1, pixels)
self.cdespike = wx.CheckBox(self, -1, 'Despike images')
self.cdespike_size = IntEntry(self, -1, min=1, chars=4)
self.cdespike_threshold = FloatEntry(self, -1, min=0, chars=4)
self.cdespike.SetValue(self.plan['despike'])
self.cdespike_size.SetValue(self.plan['despike size'])
self.cdespike_threshold.SetValue(self.plan['despike threshold'])
szdespike = wx.GridBagSizer(5, 5)
szdespike.Add(self.cdespike, (0, 0), (1, 2), wx.ALIGN_CENTER_VERTICAL)
label = wx.StaticText(self, -1, 'Neighborhood size:')
szdespike.Add(label, (1, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szdespike.Add(
self.cdespike_size, (1, 1), (1, 1),
wx.ALIGN_RIGHT | wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE)
label = wx.StaticText(self, -1, 'Threshold:')
szdespike.Add(label, (2, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szdespike.Add(
self.cdespike_threshold, (2, 1), (1, 1),
wx.ALIGN_RIGHT | wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE)
szdespike.AddGrowableCol(1)
bsave = wx.Button(self, wx.ID_OK, 'Save')
bcancel = wx.Button(self, wx.ID_CANCEL, 'Cancel')
szbutton = wx.GridBagSizer(5, 5)
szbutton.Add(bsave, (0, 0), (1, 1), wx.ALIGN_CENTER)
szbutton.Add(bcancel, (0, 1), (1, 1), wx.ALIGN_CENTER)
szplan = wx.GridBagSizer(5, 5)
szplan.Add(strows, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szplan.Add(self.tcrows, (0, 1), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szplan.Add(stcolumns, (1, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szplan.Add(self.tccolumns, (1, 1), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szplan.Add(stpixels, (2, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szplan.Add(self.tcpixels, (2, 1), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szplan.Add(szdespike, (3, 0), (1, 2), wx.EXPAND)
sz = wx.GridBagSizer(5, 5)
sz.Add(szplan, (0, 0), (1, 1), wx.ALIGN_RIGHT | wx.ALL, border=5)
sz.Add(szbutton, (1, 0), (1, 1), wx.ALIGN_RIGHT | wx.ALL, border=5)
self.SetSizerAndFit(sz)
self.Bind(wx.EVT_BUTTON, self.onSave, bsave)
def onSave(self, evt):
try:
rows = str2plan(self.tcrows.GetValue())
columns = str2plan(self.tccolumns.GetValue())
pixels = str2pixels(self.tcpixels.GetValue())
except ValueError:
dialog = wx.MessageDialog(self, 'Invalid plan', 'Error',
wx.OK | wx.ICON_ERROR)
dialog.ShowModal()
dialog.Destroy()
else:
self.plan = {
'rows': rows,
'columns': columns,
'pixels': pixels,
'despike': self.cdespike.GetValue(),
'despike size': self.cdespike_size.GetValue(),
'despike threshold': self.cdespike_threshold.GetValue()
}
evt.Skip()
class MeasureComafreeDialog(wx.Dialog):
def __init__(self, parent):
self.node = parent.node
self.panel = parent
wx.Dialog.__init__(self, parent, -1, 'Measure Coma-free Beam Tilt')
self.measure = wx.Button(self, -1, 'Measure')
self.correctshift = wx.CheckBox(self, -1, 'Correct image-shift-induced beam tilt')
self.correct = wx.Button(self, -1, 'Correct Beam Tilt')
self.correct.Enable(False)
self.Bind(wx.EVT_BUTTON, self.onMeasureButton, self.measure)
self.Bind(wx.EVT_BUTTON, self.onCorrectButton, self.correct)
szbutton = wx.GridBagSizer(5, 5)
szbutton.Add(self.correctshift, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL|wx.EXPAND)
szbutton.Add(self.measure, (1, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL|wx.EXPAND)
szbutton.Add(self.correct, (2, 0), (1, 1), wx.EXPAND)
sbsz = wx.GridBagSizer(5, 5)
tiltlabel = wx.StaticText(self, -1, 'Tilt (radian):')
self.tiltvalue = FloatEntry(self, -1, allownone=False, chars=5, value='0.005')
sbsz.Add(tiltlabel, (0,0), (1,1))
sbsz.Add(self.tiltvalue, (0,1), (1,1))
self.labels = {}
self.labels['comatilt'] = {}
for axis in ('x', 'y'):
self.labels['comatilt'][axis] = wx.StaticText(self, -1, '(Not measured)')
szresult = wx.GridBagSizer(5, 5)
label = wx.StaticText(self, -1, 'Beam Tilt Adjustment')
szresult.Add(label, (0, 0), (1, 2), wx.ALIGN_CENTER_VERTICAL)
label = wx.StaticText(self, -1, 'x')
szresult.Add(label, (1, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szresult.Add(self.labels['comatilt']['x'], (1, 1), (1, 1), wx.ALIGN_CENTER_VERTICAL)
label = wx.StaticText(self, -1, 'y')
szresult.Add(label, (2, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szresult.Add(self.labels['comatilt']['y'], (2, 1), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szresult.AddGrowableRow(0)
szresult.AddGrowableRow(1)
szresult.AddGrowableRow(2)
szresult.AddGrowableCol(1)
self.sizer = wx.GridBagSizer(5, 5)
self.sizer.Add(sbsz, (0, 0), (1, 2), wx.EXPAND|wx.ALL, 10)
self.sizer.Add(szresult, (1, 0), (2, 2), wx.EXPAND|wx.ALL, 10)
self.sizer.Add(szbutton, (3, 0), (2, 2), wx.ALIGN_CENTER_VERTICAL|wx.EXPAND|wx.ALL, 10)
self.SetSizerAndFit(self.sizer)
def onMeasureButton(self, evt):
btilt = self.tiltvalue.GetValue()
correctshift = self.correctshift.GetValue()
self.panel._calibrationEnable(False)
threading.Thread(target=self.node.measureComaFree, args=(btilt,correctshift)).start()
def onCorrectButton(self, evt):
self.panel.instrumentEnable(False)
threading.Thread(target=self.node.correctComaTilt).start()
def addSettings(self):
presets = self.node.presetsclient.getPresetNames()
self.widgets['preset'] = PresetChoice(self, -1)
self.widgets['preset'].setChoices(presets)
self.widgets['label'] = Entry(self, -1, allowspaces=False)
self.widgets['radius'] = FloatEntry(self, -1, min=0.0, chars=6)
self.widgets['max size'] = IntEntry(self, -1, chars=6)
self.widgets['max targets'] = IntEntry(self, -1, chars=6)
self.widgets['overlap'] = FloatEntry(self, -1, max=100.0, chars=6)
self.widgets['mosaic center'] = Choice(
self, -1, choices=['stage center', 'current position'])
self.widgets['ignore request'] = wx.CheckBox(
self, -1, 'Ignore Request to Make Targets from Others')
#szradius = wx.GridBagSizer(5, 5)
#szradius.Add(self.widgets['radius'], (0, 0), (1, 1),
# wx.ALIGN_CENTER_VERTICAL|wx.FIXED_MINSIZE)
#label = wx.StaticText(self, -1, 'meters')
#szradius.Add(label, (0, 1), (1, 1), wx.ALIGN_CENTER_VERTICAL)
sz = wx.GridBagSizer(5, 10)
label = wx.StaticText(self, -1, 'Preset:')
sz.Add(label, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
sz.Add(self.widgets['preset'], (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.EXPAND)
label = wx.StaticText(self, -1, 'Label:')
sz.Add(label, (1, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
sz.Add(self.widgets['label'], (1, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.EXPAND)
label = wx.StaticText(self, -1, 'Radius:')
sz.Add(label, (2, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
#sz.Add(szradius, (2, 1), (1, 1), wx.ALIGN_CENTER_VERTICAL|wx.ALIGN_RIGHT)
sz.Add(self.widgets['radius'], (2, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE | wx.ALIGN_RIGHT)
label = wx.StaticText(self, -1, 'm')
sz.Add(label, (2, 2), (1, 1), wx.ALIGN_CENTER_VERTICAL)
label = wx.StaticText(self, -1, 'Max size:')
sz.Add(label, (3, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
sz.Add(self.widgets['max size'], (3, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.EXPAND)
label = wx.StaticText(self, -1, 'Max targets:')
sz.Add(label, (4, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
sz.Add(self.widgets['max targets'], (4, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.EXPAND)
label = wx.StaticText(self, -1, 'Overlap:')
sz.Add(label, (5, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
sz.Add(self.widgets['overlap'], (5, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE | wx.ALIGN_RIGHT)
label = wx.StaticText(self, -1, '%')
sz.Add(label, (5, 2), (1, 1), wx.ALIGN_CENTER_VERTICAL)
label = wx.StaticText(self, -1, 'Mosaic Center:')
sz.Add(label, (6, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
sz.Add(self.widgets['mosaic center'], (6, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE | wx.ALIGN_RIGHT)
sz.Add(self.widgets['ignore request'], (7, 0), (1, 3),
wx.ALIGN_CENTER_VERTICAL)
sz.AddGrowableCol(1)
return sz
def initialize(self):
sizers = leginon.gui.wx.Acquisition.ScrolledSettings.initialize(self)
sb = wx.StaticBox(self, -1, 'Tilt Imaging and Correlation')
sbsz = wx.StaticBoxSizer(sb, wx.VERTICAL)
sizer = wx.GridBagSizer(5, 5)
self.widgets['tableau type'] = Choice(self,
-1,
choices=self.node.tableau_types)
label = wx.StaticText(self, -1, 'Tableau Type (method-display):')
sizer.Add(label, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
sizer.Add(self.widgets['tableau type'], (0, 1), (1, 1),
wx.ALIGN_CENTER)
self.widgets['beam tilt'] = FloatEntry(self,
-1,
min=0.0,
allownone=False,
chars=6,
value='0.005')
bt_sizer = wx.GridBagSizer(5, 5)
bt_sizer.Add(self.widgets['beam tilt'], (0, 0), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE)
bt_sizer.Add(wx.StaticText(self, -1, 'radian'), (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL)
label = wx.StaticText(self, -1, 'Beam Tilt:')
sizer.Add(label, (1, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
sizer.Add(bt_sizer, (1, 1), (1, 1), wx.ALIGN_CENTER)
self.widgets['sites'] = IntEntry(self,
-1,
min=0,
allownone=False,
chars=4,
value='0')
label = wx.StaticText(self, -1, 'Number of tilt directions:')
sizer.Add(label, (2, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
sizer.Add(self.widgets['sites'], (2, 1), (1, 1), wx.ALIGN_CENTER)
self.widgets['startangle'] = FloatEntry(self,
-1,
min=0,
allownone=False,
chars=4,
value='0')
label = wx.StaticText(self, -1, 'Start Angle:')
sizer.Add(label, (3, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
sizer.Add(self.widgets['startangle'], (3, 1), (1, 1), wx.ALIGN_CENTER)
label = wx.StaticText(self, -1, 'degrees')
sizer.Add(label, (3, 2), (1, 1), wx.ALIGN_CENTER_VERTICAL)
self.widgets['correlation type'] = Choice(
self, -1, choices=self.node.correlation_types)
label = wx.StaticText(self, -1, 'Correlation Type:')
sizer.Add(label, (4, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
sizer.Add(self.widgets['correlation type'], (4, 1), (1, 1),
wx.ALIGN_CENTER)
self.widgets['tableau binning'] = IntEntry(self,
-1,
min=1,
allownone=False,
chars=4,
value='2')
label = wx.StaticText(self, -1, 'Tableau Binning:')
sizer.Add(label, (5, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
sizer.Add(self.widgets['tableau binning'], (5, 1), (1, 1),
wx.ALIGN_CENTER)
self.widgets['beam tilt count'] = IntEntry(self,
-1,
min=1,
allownone=False,
chars=4,
value='1')
label = wx.StaticText(self, -1, 'Beam Tilt Count:')
sizer.Add(label, (6, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
sizer.Add(self.widgets['beam tilt count'], (6, 1), (1, 1),
wx.ALIGN_CENTER)
self.widgets['tableau split'] = IntEntry(self,
-1,
min=1,
allownone=False,
chars=4,
value='8')
label = wx.StaticText(self, -1, 'Tableau Split:')
sizer.Add(label, (7, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
sizer.Add(self.widgets['tableau split'], (7, 1), (1, 1),
wx.ALIGN_CENTER)
sbsz.Add(sizer, 0, wx.ALIGN_CENTER_HORIZONTAL | wx.ALL, 5)
self.widgets['tableau type'].Bind(wx.EVT_CHOICE,
self.onTableauTypeChoice)
return sizers + [sbsz]
def initialize(self):
leginon.gui.wx.Settings.ScrolledDialog.initialize(self)
szoptions = wx.GridBagSizer(5, 5)
self.widgets['autofinder'] = wx.CheckBox(self, -1,
'Enable auto targeting')
szoptions.Add(self.widgets['autofinder'], (0, 0), (1, 2),
wx.ALIGN_CENTER_VERTICAL)
choices = [
'Limit by Sections', 'Sections Only', 'Tissue only',
'Regions from Centers'
]
self.widgets['find section options'] = Choice(self,
-1,
choices=choices)
label = wx.StaticText(self, -1, 'Finding Mode')
szoptions.Add(label, (1, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szoptions.Add(self.widgets['find section options'], (1, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL)
label = wx.StaticText(self, -1,
'Initial Minimum Region Area (% of tile area)')
self.widgets['min region area'] = FloatEntry(self, -1, chars=8)
szoptions.Add(label, (2, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szoptions.Add(self.widgets['min region area'], (2, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL)
label = wx.StaticText(self, -1, 'Maximum Region Area (% of tile area)')
self.widgets['max region area'] = FloatEntry(self, -1, chars=8)
szoptions.Add(label, (3, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szoptions.Add(self.widgets['max region area'], (3, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL)
label = wx.StaticText(self, -1, 'Vertex Evolution Limit')
self.widgets['ve limit'] = FloatEntry(self, -1, chars=8)
szoptions.Add(label, (4, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szoptions.Add(self.widgets['ve limit'], (4, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL)
label = wx.StaticText(self, -1, 'Region Min Threshold')
self.widgets['min threshold'] = FloatEntry(self, -1, chars=8)
szoptions.Add(label, (5, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szoptions.Add(self.widgets['min threshold'], (5, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL)
label = wx.StaticText(self, -1, 'Section/Background Threshold')
self.widgets['max threshold'] = FloatEntry(self, -1, chars=8)
szoptions.Add(label, (6, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szoptions.Add(self.widgets['max threshold'], (6, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL)
label = wx.StaticText(self, -1, 'Max Ellipse Axis Ratio')
self.widgets['axis ratio'] = FloatEntry(self, -1, chars=8)
szoptions.Add(label, (7, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szoptions.Add(self.widgets['axis ratio'], (7, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL)
szsections = wx.GridBagSizer(6, 6)
label = wx.StaticText(self, -1, 'Per-Section Area (% of tile area)')
self.widgets['section area'] = FloatEntry(self, -1, chars=8)
szsections.Add(label, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szsections.Add(self.widgets['section area'], (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL)
label = wx.StaticText(self, -1, 'Maximum Number of Section per Grid')
self.widgets['max sections'] = IntEntry(self, -1, min=1, chars=4)
szsections.Add(label, (1, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szsections.Add(self.widgets['max sections'], (1, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL)
label = wx.StaticText(
self, -1, 'Per-Section Area Modification Thershold (% of current)')
self.widgets['adjust section area'] = FloatEntry(self, -1, chars=8)
szsections.Add(label, (2, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szsections.Add(self.widgets['adjust section area'], (2, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL)
szbutton = wx.GridBagSizer(7, 7)
self.bclear = wx.Button(self, -1, 'Clear Regions')
szbutton.Add(self.bclear, (0, 0), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_LEFT)
szbutton.AddGrowableCol(0)
self.Bind(wx.EVT_BUTTON, self.onClearButton, self.bclear)
self.btest = wx.Button(self, -1, 'Test')
szbutton.Add(self.btest, (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_RIGHT)
szbutton.AddGrowableCol(1)
self.Bind(wx.EVT_BUTTON, self.onTestButton, self.btest)
return [szoptions, szsections, szbutton]
def __init__(self, parent, mag, ps, comment):
wx.Dialog.__init__(self, parent, -1, 'Edit Pixel Size')
sb = wx.StaticBox(self, -1, 'Pixel Size')
sbsz = wx.StaticBoxSizer(sb, wx.VERTICAL)
self.stmag = wx.StaticText(self, -1)
self.stmag.SetLabel(str(mag))
self.feps = FloatEntry(self, -1, min=0.0, chars=9)
self.feps.SetValue(ps)
self.tccomment = wx.TextCtrl(self,
-1,
'Manual entry',
style=wx.TE_MULTILINE)
self.tccomment.SetValue(comment)
szedit = wx.GridBagSizer(5, 5)
label = wx.StaticText(self, -1, 'Magnification:')
szedit.Add(label, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szedit.Add(self.stmag, (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_RIGHT)
label = wx.StaticText(self, -1, 'Pixel size:')
szedit.Add(label, (1, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szedit.Add(
self.feps, (1, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_RIGHT | wx.FIXED_MINSIZE)
label = wx.StaticText(self, -1, 'm/pixel')
szedit.Add(label, (1, 2), (1, 1), wx.ALIGN_CENTER_VERTICAL)
label = wx.StaticText(self, -1, 'Comment:')
szedit.Add(label, (2, 0), (1, 3), wx.ALIGN_CENTER_VERTICAL)
szedit.Add(self.tccomment, (3, 0), (1, 3), wx.EXPAND)
szedit.AddGrowableRow(3)
szedit.AddGrowableRow(0)
szedit.AddGrowableCol(0)
szedit.AddGrowableCol(1)
szedit.AddGrowableCol(2)
sbsz.Add(szedit, 1, wx.EXPAND | wx.ALL, 5)
self.bsave = wx.Button(self, wx.ID_OK, 'Save')
self.bcancel = wx.Button(self, wx.ID_CANCEL, 'Cancel')
if ps is None:
self.bsave.Enable(False)
else:
self.bsave.Enable(True)
szbutton = wx.GridBagSizer(5, 5)
szbutton.Add(self.bsave, (0, 0), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_RIGHT)
szbutton.Add(self.bcancel, (0, 1), (1, 1), wx.ALIGN_CENTER)
szbutton.AddGrowableCol(0)
sz = wx.GridBagSizer(5, 5)
sz.Add(sbsz, (0, 0), (1, 1), wx.EXPAND | wx.ALL, 10)
sz.Add(szbutton, (1, 0), (1, 1), wx.EXPAND | wx.ALL, 10)
self.SetSizerAndFit(sz)
self.Bind(wx.EVT_BUTTON, self.validate, self.bsave)
self.Bind(leginon.gui.wx.Entry.EVT_ENTRY, self.onPixelSizeEntry,
self.feps)
class FitAllDialog(wx.Dialog):
#==================
def __init__(self, parent):
self.parent = parent
wx.Dialog.__init__(self, self.parent.frame, -1,
"Least Squares Optimization")
self.lsfit = None
inforow = wx.FlexGridSizer(5, 4, 15, 15)
thetastr = "%3.3f" % self.parent.data['theta']
label = wx.StaticText(self,
-1,
"Tilt angle (theta): ",
style=wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
#self.tiltvalue = wx.StaticText(self, -1, thetastr, style=wx.ALIGN_CENTER|wx.ALIGN_CENTER_VERTICAL)
self.thetavalue = FloatEntry(self,
-1,
allownone=False,
chars=8,
value=thetastr)
label2 = wx.StaticText(self,
-1,
"degrees",
style=wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
self.thetatog = wx.ToggleButton(self, -1, "Refine")
self.Bind(wx.EVT_TOGGLEBUTTON, self.onToggleTheta, self.thetatog)
#self.thetavalue.Enable(False)
#self.thetatog.SetValue(1)
inforow.Add(label, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
inforow.Add(
self.thetavalue, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL | wx.ALL, 3)
inforow.Add(label2, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
inforow.Add(self.thetatog, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
gammastr = "%3.3f" % self.parent.data['gamma']
label = wx.StaticText(self,
-1,
"Image 1 Rotation (gamma): ",
style=wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
self.gammavalue = FloatEntry(self,
-1,
allownone=False,
chars=8,
value=gammastr)
label2 = wx.StaticText(self,
-1,
"degrees",
style=wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
self.gammatog = wx.ToggleButton(self, -1, "Refine")
self.Bind(wx.EVT_TOGGLEBUTTON, self.onToggleGamma, self.gammatog)
inforow.Add(label, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
inforow.Add(self.gammavalue, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL)
inforow.Add(label2, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
inforow.Add(self.gammatog, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
phistr = "%3.3f" % self.parent.data['phi']
label = wx.StaticText(self,
-1,
"Image 2 Rotation (phi): ",
style=wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
self.phivalue = FloatEntry(self,
-1,
allownone=False,
chars=8,
value=phistr)
label2 = wx.StaticText(self,
-1,
"degrees",
style=wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
self.phitog = wx.ToggleButton(self, -1, "Refine")
self.Bind(wx.EVT_TOGGLEBUTTON, self.onTogglePhi, self.phitog)
inforow.Add(label, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
inforow.Add(self.phivalue, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL)
inforow.Add(label2, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
inforow.Add(self.phitog, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
scalestr = "%3.3f" % self.parent.data['scale']
label = wx.StaticText(self,
-1,
"Scaling factor: ",
style=wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
self.scalevalue = FloatEntry(self,
-1,
allownone=False,
chars=8,
value=scalestr)
label2 = wx.StaticText(self,
-1,
" ",
style=wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
self.scaletog = wx.ToggleButton(self, -1, "Locked")
self.Bind(wx.EVT_TOGGLEBUTTON, self.onToggleScale, self.scaletog)
self.scalevalue.Enable(False)
self.scaletog.SetValue(1)
inforow.Add(label, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
inforow.Add(self.scalevalue, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL)
inforow.Add(label2, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
inforow.Add(self.scaletog, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
shiftxstr = "%3.3f" % self.parent.data['shiftx']
shiftystr = "%3.3f" % self.parent.data['shifty']
label = wx.StaticText(self,
-1,
"Shift (x,y) pixels: ",
style=wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
self.shiftxvalue = FloatEntry(self,
-1,
allownone=False,
chars=8,
value=shiftxstr)
self.shiftyvalue = FloatEntry(self,
-1,
allownone=False,
chars=8,
value=shiftystr)
self.shifttog = wx.ToggleButton(self, -1, "Refine")
self.Bind(wx.EVT_TOGGLEBUTTON, self.onToggleShift, self.shifttog)
#self.shiftxvalue.Enable(False)
#self.shiftyvalue.Enable(False)
#self.shifttog.SetValue(1)
inforow.Add(label, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
inforow.Add(self.shiftxvalue, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL)
inforow.Add(self.shiftyvalue, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL)
inforow.Add(self.shifttog, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
summaryrow = wx.GridSizer(1, 4)
label = wx.StaticText(self,
-1,
"RMSD (pixels): ",
style=wx.ALIGN_RIGHT | wx.ALIGN_CENTER_VERTICAL)
self.rmsdlabel = wx.StaticText(self,
-1,
" unknown ",
style=wx.ALIGN_LEFT
| wx.ALIGN_CENTER_VERTICAL)
summaryrow.Add(label, 0, wx.ALIGN_RIGHT | wx.ALIGN_CENTER_VERTICAL)
summaryrow.Add(self.rmsdlabel, 0,
wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
label = wx.StaticText(self,
-1,
"Iterations: ",
style=wx.ALIGN_RIGHT | wx.ALIGN_CENTER_VERTICAL)
self.iterlabel = wx.StaticText(self,
-1,
" none ",
style=wx.ALIGN_LEFT
| wx.ALIGN_CENTER_VERTICAL)
summaryrow.Add(label, 0, wx.ALIGN_RIGHT | wx.ALIGN_CENTER_VERTICAL)
summaryrow.Add(self.iterlabel, 0,
wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
self.cancelfitall = wx.Button(self, wx.ID_CANCEL, '&Cancel')
self.applyfitall = wx.Button(self, wx.ID_APPLY, '&Apply')
self.runfitall = wx.Button(self, -1, '&Run')
self.Bind(wx.EVT_BUTTON, self.onRunLeastSquares, self.runfitall)
self.Bind(wx.EVT_BUTTON, self.onApplyLeastSquares, self.applyfitall)
buttonrow = wx.GridSizer(1, 3)
buttonrow.Add(self.cancelfitall, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL, 0)
buttonrow.Add(self.applyfitall, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL, 0)
buttonrow.Add(self.runfitall, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL, 0)
self.sizer = wx.FlexGridSizer(3, 1)
self.sizer.Add(inforow, 0, wx.EXPAND | wx.ALL, 10)
self.sizer.Add(summaryrow, 0, wx.EXPAND | wx.ALL, 5)
self.sizer.Add(buttonrow, 0, wx.EXPAND | wx.ALL, 5)
self.SetSizerAndFit(self.sizer)
self.onToggleScale(True)
#==================
def onToggleTheta(self, evt):
if self.thetatog.GetValue() is True:
self.thetavalue.Enable(False)
self.thetatog.SetLabel("Locked")
else:
self.thetavalue.Enable(True)
self.thetatog.SetLabel("Refine")
#==================
def onToggleGamma(self, evt):
if self.gammatog.GetValue() is True:
self.gammavalue.Enable(False)
self.gammatog.SetLabel("Locked")
else:
self.gammavalue.Enable(True)
self.gammatog.SetLabel("Refine")
#==================
def onTogglePhi(self, evt):
if self.phitog.GetValue() is True:
self.phivalue.Enable(False)
self.phitog.SetLabel("Locked")
else:
self.phivalue.Enable(True)
self.phitog.SetLabel("Refine")
#==================
def onTogglePhi(self, evt):
if self.phitog.GetValue() is True:
self.phivalue.Enable(False)
self.phitog.SetLabel("Locked")
else:
self.phivalue.Enable(True)
self.phitog.SetLabel("Refine")
#==================
def onToggleScale(self, evt):
if self.scaletog.GetValue() is True:
self.scalevalue.Enable(False)
self.scaletog.SetLabel("Locked")
else:
self.scalevalue.Enable(True)
self.scaletog.SetLabel("Refine")
#==================
def onToggleShift(self, evt):
if self.shifttog.GetValue() is True:
self.shiftxvalue.Enable(False)
self.shiftyvalue.Enable(False)
self.shifttog.SetLabel("Locked")
else:
self.shiftxvalue.Enable(True)
self.shiftyvalue.Enable(True)
self.shifttog.SetLabel("Refine")
#==================
def onRunLeastSquares(self, evt):
theta = self.thetavalue.GetValue()
gamma = self.gammavalue.GetValue()
phi = self.phivalue.GetValue()
scale = self.scalevalue.GetValue()
shiftx = self.shiftxvalue.GetValue()
shifty = self.shiftyvalue.GetValue()
#SET XSCALE
xscale = numpy.array((
not self.thetatog.GetValue(),
not self.gammatog.GetValue(),
not self.phitog.GetValue(),
not self.scaletog.GetValue(),
not self.shifttog.GetValue(),
not self.shifttog.GetValue(),
),
dtype=numpy.float32)
#GET TARGETS
targets1 = self.parent.panel1.getTargets('Picked')
a1 = self.parent.targetsToArray(targets1)
targets2 = self.parent.panel2.getTargets('Picked')
a2 = self.parent.targetsToArray(targets2)
if len(a1) > len(a2):
print "shorten a1"
a1 = a1[0:len(a2), :]
elif len(a2) > len(a1):
print "shorten a2"
a2 = a2[0:len(a1), :]
self.lsfit = apTiltTransform.willsq(a1, a2, theta, gamma, phi, scale,
shiftx, shifty, xscale)
#pprint.pprint(self.lsfit)
self.thetavalue.SetValue(round(self.lsfit['theta'], 5))
self.gammavalue.SetValue(round(self.lsfit['gamma'], 5))
self.phivalue.SetValue(round(self.lsfit['phi'], 5))
self.scalevalue.SetValue(round(self.lsfit['scale'], 5))
self.shiftxvalue.SetValue(round(self.lsfit['shiftx'], 5))
self.shiftyvalue.SetValue(round(self.lsfit['shifty'], 5))
self.rmsdlabel.SetLabel(str(round(self.lsfit['rmsd'], 5)))
self.iterlabel.SetLabel(str(self.lsfit['iter']))
#==================
def onApplyLeastSquares(self, evt):
self.Close()
self.parent.data['leastsqfitdata'] = self.lsfit
self.parent.data['theta'] = self.thetavalue.GetValue()
self.parent.data['gamma'] = self.gammavalue.GetValue()
self.parent.data['phi'] = self.phivalue.GetValue()
self.parent.data['scale'] = self.scalevalue.GetValue()
self.parent.data['shiftx'] = self.shiftxvalue.GetValue()
self.parent.data['shifty'] = self.shiftyvalue.GetValue()
self.parent.data['rmsd'] = self.lsfit['rmsd']
self.parent.data['point1'] = self.lsfit['point1']
self.parent.data['point2'] = self.lsfit['point2']
self.parent.data['optimrun'] = True
self.parent.onUpdate(evt)
def initialize(self):
leginon.gui.wx.Settings.ScrolledDialog.initialize(self)
sb = wx.StaticBox(self, -1, 'Pixel Size Measurement')
sbsz = wx.StaticBoxSizer(sb, wx.VERTICAL)
sbl = wx.StaticBox(self, -1, 'Lattice Parameters')
sblsz = wx.StaticBoxSizer(sbl, wx.VERTICAL)
sbm = wx.StaticBox(self, -1, 'Distance Measured Between reflections')
sbmsz = wx.StaticBoxSizer(sbm, wx.VERTICAL)
sbp = wx.StaticBox(self, -1, 'Pixel Size Results')
sbpsz = wx.StaticBoxSizer(sbp, wx.VERTICAL)
self.calculate = wx.Button(self, -1, 'Calculate Pixel Size')
self.measurements = MeasurementListCtrl(self, -1)
self.save = wx.Button(self, -1,
'Save Averaged Pixel Size From Selected')
self.widgets['lattice a'] = FloatEntry(self, -1, chars=9)
self.widgets['lattice b'] = FloatEntry(self, -1, chars=9)
self.widgets['lattice gamma'] = FloatEntry(self, -1, chars=9)
self.widgets['distance'] = FloatEntry(self, -1, chars=9)
self.widgets['h1'] = IntEntry(self, -1, chars=9)
self.widgets['k1'] = IntEntry(self, -1, chars=9)
self.widgets['h2'] = IntEntry(self, -1, chars=9)
self.widgets['k2'] = IntEntry(self, -1, chars=9)
sz = wx.GridBagSizer(5, 5)
label = wx.StaticText(self, -1, 'a:')
sz.Add(label, (0, 0), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_RIGHT)
sz.Add(self.widgets['lattice a'], (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE | wx.ALIGN_RIGHT)
label = wx.StaticText(self, -1, 'Angstrum')
sz.Add(label, (0, 2), (1, 1), wx.ALIGN_CENTER_VERTICAL)
label = wx.StaticText(self, -1, 'b:')
sz.Add(label, (1, 0), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_RIGHT)
sz.Add(self.widgets['lattice b'], (1, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE | wx.ALIGN_RIGHT)
label = wx.StaticText(self, -1, 'Angstrum')
sz.Add(label, (1, 2), (1, 1), wx.ALIGN_CENTER_VERTICAL)
label = wx.StaticText(self, -1, 'gamma')
sz.Add(label, (2, 0), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_RIGHT)
sz.Add(self.widgets['lattice gamma'], (2, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE | wx.ALIGN_RIGHT)
label = wx.StaticText(self, -1, 'deg')
sz.Add(label, (2, 2), (1, 1), wx.ALIGN_CENTER_VERTICAL)
sblsz.Add(sz, 0, wx.ALIGN_CENTER_VERTICAL)
sz = wx.GridBagSizer(5, 5)
label = wx.StaticText(self, -1, 'Between Index h:')
sz.Add(label, (0, 0), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_RIGHT)
sz.Add(self.widgets['h1'], (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE | wx.ALIGN_CENTER)
label = wx.StaticText(self, -1, 'k:')
sz.Add(label, (0, 2), (1, 1), wx.ALIGN_CENTER_VERTICAL)
sz.Add(self.widgets['k1'], (0, 3), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE | wx.ALIGN_CENTER)
label = wx.StaticText(self, -1, 'and Index h:')
sz.Add(label, (1, 0), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_RIGHT)
sz.Add(self.widgets['h2'], (1, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE | wx.ALIGN_CENTER)
label = wx.StaticText(self, -1, 'k:')
sz.Add(label, (1, 2), (1, 1), wx.ALIGN_CENTER_VERTICAL)
sz.Add(self.widgets['k2'], (1, 3), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE | wx.ALIGN_CENTER)
sbmsz.Add(sz, 0, wx.ALIGN_CENTER)
sbmsz.AddSpacer((20, 20))
sz = wx.GridBagSizer(5, 5)
label = wx.StaticText(self, -1, 'Measured Distance on Power Spectrum:')
sz.Add(label, (0, 0), (2, 1), wx.ALIGN_CENTER_VERTICAL | wx.EXPAND)
sz.Add(self.widgets['distance'], (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE | wx.ALIGN_CENTER)
label = wx.StaticText(self, -1, '(pixels)')
sz.Add(label, (0, 2), (1, 1), wx.ALIGN_CENTER_VERTICAL)
sz.Add(self.calculate, (2, 0), (1, 3),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE | wx.ALIGN_CENTER)
sbmsz.Add(sz, 0, wx.ALIGN_CENTER)
label = ' need image to find saved pixel size'
self.currentimagepixelsize = wx.StaticText(self, -1, label)
sbpsz.Add(self.currentimagepixelsize, 0, wx.ALIGN_CENTER | wx.EXPAND)
sbpsz.SetItemMinSize(self.measurements,
self.measurements.getBestSize())
sbpsz.Add(self.measurements, 1, wx.EXPAND)
sbpsz.Add(self.save, 0, wx.ALIGN_CENTER)
sbsz.Add(sblsz, 0, wx.ALIGN_CENTER_VERTICAL | wx.EXPAND)
sbsz.Add(sbmsz, 0, wx.ALIGN_CENTER_VERTICAL | wx.EXPAND)
sbsz.Add(sbpsz, 1, wx.ALIGN_CENTER_VERTICAL | wx.EXPAND)
self.Bind(wx.EVT_BUTTON, self.onCalculateButton, self.calculate)
self.Bind(wx.EVT_BUTTON, self.onSaveButton, self.save)
return [sbsz]
def __init__(self, parent):
self.parent = parent
wx.Dialog.__init__(self, self.parent.frame, -1,
"Least Squares Optimization")
self.lsfit = None
inforow = wx.FlexGridSizer(5, 4, 15, 15)
thetastr = "%3.3f" % self.parent.data['theta']
label = wx.StaticText(self,
-1,
"Tilt angle (theta): ",
style=wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
#self.tiltvalue = wx.StaticText(self, -1, thetastr, style=wx.ALIGN_CENTER|wx.ALIGN_CENTER_VERTICAL)
self.thetavalue = FloatEntry(self,
-1,
allownone=False,
chars=8,
value=thetastr)
label2 = wx.StaticText(self,
-1,
"degrees",
style=wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
self.thetatog = wx.ToggleButton(self, -1, "Refine")
self.Bind(wx.EVT_TOGGLEBUTTON, self.onToggleTheta, self.thetatog)
#self.thetavalue.Enable(False)
#self.thetatog.SetValue(1)
inforow.Add(label, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
inforow.Add(
self.thetavalue, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL | wx.ALL, 3)
inforow.Add(label2, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
inforow.Add(self.thetatog, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
gammastr = "%3.3f" % self.parent.data['gamma']
label = wx.StaticText(self,
-1,
"Image 1 Rotation (gamma): ",
style=wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
self.gammavalue = FloatEntry(self,
-1,
allownone=False,
chars=8,
value=gammastr)
label2 = wx.StaticText(self,
-1,
"degrees",
style=wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
self.gammatog = wx.ToggleButton(self, -1, "Refine")
self.Bind(wx.EVT_TOGGLEBUTTON, self.onToggleGamma, self.gammatog)
inforow.Add(label, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
inforow.Add(self.gammavalue, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL)
inforow.Add(label2, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
inforow.Add(self.gammatog, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
phistr = "%3.3f" % self.parent.data['phi']
label = wx.StaticText(self,
-1,
"Image 2 Rotation (phi): ",
style=wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
self.phivalue = FloatEntry(self,
-1,
allownone=False,
chars=8,
value=phistr)
label2 = wx.StaticText(self,
-1,
"degrees",
style=wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
self.phitog = wx.ToggleButton(self, -1, "Refine")
self.Bind(wx.EVT_TOGGLEBUTTON, self.onTogglePhi, self.phitog)
inforow.Add(label, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
inforow.Add(self.phivalue, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL)
inforow.Add(label2, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
inforow.Add(self.phitog, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
scalestr = "%3.3f" % self.parent.data['scale']
label = wx.StaticText(self,
-1,
"Scaling factor: ",
style=wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
self.scalevalue = FloatEntry(self,
-1,
allownone=False,
chars=8,
value=scalestr)
label2 = wx.StaticText(self,
-1,
" ",
style=wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
self.scaletog = wx.ToggleButton(self, -1, "Locked")
self.Bind(wx.EVT_TOGGLEBUTTON, self.onToggleScale, self.scaletog)
self.scalevalue.Enable(False)
self.scaletog.SetValue(1)
inforow.Add(label, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
inforow.Add(self.scalevalue, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL)
inforow.Add(label2, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
inforow.Add(self.scaletog, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
shiftxstr = "%3.3f" % self.parent.data['shiftx']
shiftystr = "%3.3f" % self.parent.data['shifty']
label = wx.StaticText(self,
-1,
"Shift (x,y) pixels: ",
style=wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
self.shiftxvalue = FloatEntry(self,
-1,
allownone=False,
chars=8,
value=shiftxstr)
self.shiftyvalue = FloatEntry(self,
-1,
allownone=False,
chars=8,
value=shiftystr)
self.shifttog = wx.ToggleButton(self, -1, "Refine")
self.Bind(wx.EVT_TOGGLEBUTTON, self.onToggleShift, self.shifttog)
#self.shiftxvalue.Enable(False)
#self.shiftyvalue.Enable(False)
#self.shifttog.SetValue(1)
inforow.Add(label, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
inforow.Add(self.shiftxvalue, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL)
inforow.Add(self.shiftyvalue, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL)
inforow.Add(self.shifttog, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
summaryrow = wx.GridSizer(1, 4)
label = wx.StaticText(self,
-1,
"RMSD (pixels): ",
style=wx.ALIGN_RIGHT | wx.ALIGN_CENTER_VERTICAL)
self.rmsdlabel = wx.StaticText(self,
-1,
" unknown ",
style=wx.ALIGN_LEFT
| wx.ALIGN_CENTER_VERTICAL)
summaryrow.Add(label, 0, wx.ALIGN_RIGHT | wx.ALIGN_CENTER_VERTICAL)
summaryrow.Add(self.rmsdlabel, 0,
wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
label = wx.StaticText(self,
-1,
"Iterations: ",
style=wx.ALIGN_RIGHT | wx.ALIGN_CENTER_VERTICAL)
self.iterlabel = wx.StaticText(self,
-1,
" none ",
style=wx.ALIGN_LEFT
| wx.ALIGN_CENTER_VERTICAL)
summaryrow.Add(label, 0, wx.ALIGN_RIGHT | wx.ALIGN_CENTER_VERTICAL)
summaryrow.Add(self.iterlabel, 0,
wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
self.cancelfitall = wx.Button(self, wx.ID_CANCEL, '&Cancel')
self.applyfitall = wx.Button(self, wx.ID_APPLY, '&Apply')
self.runfitall = wx.Button(self, -1, '&Run')
self.Bind(wx.EVT_BUTTON, self.onRunLeastSquares, self.runfitall)
self.Bind(wx.EVT_BUTTON, self.onApplyLeastSquares, self.applyfitall)
buttonrow = wx.GridSizer(1, 3)
buttonrow.Add(self.cancelfitall, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL, 0)
buttonrow.Add(self.applyfitall, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL, 0)
buttonrow.Add(self.runfitall, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL, 0)
self.sizer = wx.FlexGridSizer(3, 1)
self.sizer.Add(inforow, 0, wx.EXPAND | wx.ALL, 10)
self.sizer.Add(summaryrow, 0, wx.EXPAND | wx.ALL, 5)
self.sizer.Add(buttonrow, 0, wx.EXPAND | wx.ALL, 5)
self.SetSizerAndFit(self.sizer)
self.onToggleScale(True)
def initialize(self):
leginon.gui.wx.Settings.ScrolledDialog.initialize(self)
sb = wx.StaticBox(self, -1, 'Lattice Fitting')
sbszlattice = wx.StaticBoxSizer(sb, wx.VERTICAL)
sb = wx.StaticBox(self, -1, 'Hole Statistics')
sbszstats = wx.StaticBoxSizer(sb, wx.VERTICAL)
self.widgets['lattice spacing'] = FloatEntry(self, -1, chars=6)
self.widgets['lattice tolerance'] = FloatEntry(self, -1, chars=6)
self.widgets['lattice hole radius'] = FloatEntry(self, -1, chars=6)
self.widgets['lattice zero thickness'] = FloatEntry(self, -1, chars=6)
extendlabel = wx.StaticText(self, -1, 'Extend Lattice')
self.widgets['lattice extend'] = Choice(self,
-1,
choices=self.node.extendtypes)
szlattice = wx.GridBagSizer(5, 5)
label = wx.StaticText(self, -1, 'Spacing:')
szlattice.Add(label, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szlattice.Add(
self.widgets['lattice spacing'], (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE | wx.ALIGN_RIGHT)
label = wx.StaticText(self, -1, 'Tolerance:')
szlattice.Add(label, (1, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szlattice.Add(
self.widgets['lattice tolerance'], (1, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE | wx.ALIGN_RIGHT)
szlattice.Add(extendlabel, (2, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szlattice.Add(self.widgets['lattice extend'], (2, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE)
szlattice.AddGrowableCol(1)
sbszlattice.Add(szlattice, 1, wx.EXPAND | wx.ALL, 5)
szstats = wx.GridBagSizer(5, 5)
label = wx.StaticText(self, -1, 'Radius:')
szstats.Add(label, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szstats.Add(
self.widgets['lattice hole radius'], (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE | wx.ALIGN_RIGHT)
label = wx.StaticText(self, -1, 'Reference Intensity:')
szstats.Add(label, (1, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szstats.Add(
self.widgets['lattice zero thickness'], (1, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE | wx.ALIGN_RIGHT)
szstats.AddGrowableCol(1)
sbszstats.Add(szstats, 1, wx.EXPAND | wx.ALL, 5)
self.btest = wx.Button(self, -1, 'Test')
szbutton = wx.GridBagSizer(5, 5)
szbutton.Add(self.btest, (0, 0), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_RIGHT)
szbutton.AddGrowableCol(0)
self.Bind(wx.EVT_BUTTON, self.onTestButton, self.btest)
return [sbszlattice, sbszstats, szbutton]
class DogPickerDialog(wx.Dialog):
#==================
def __init__(self, parent):
self.parent = parent
wx.Dialog.__init__(self, self.parent.frame, -1,
"DoG Auto Particle Picker")
inforow = wx.FlexGridSizer(3, 3, 10, 10)
inforow.Add((1, 1), 0, 3)
inforow.Add((1, 1), 0, 3)
inforow.Add((1, 1), 0, 3)
### standard options
box = wx.StaticBox(self, -1, 'Standard Options')
boxrow = wx.StaticBoxSizer(box, wx.VERTICAL)
hbox1 = wx.FlexGridSizer(1, 2, 10, 10)
label = wx.StaticText(self,
-1,
"Particle diameter (pixels): ",
style=wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
self.diam = FloatEntry(self,
-1,
allownone=False,
chars=5,
value="100.0")
hbox1.Add(label, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
hbox1.Add(
self.diam, 0, wx.ALIGN_RIGHT | wx.ALIGN_CENTER_HORIZONTAL
| wx.ALIGN_CENTER_VERTICAL, 3)
hbox1.AddGrowableCol(0)
boxrow.Add(hbox1, 0, wx.ALIGN_CENTER_VERTICAL | wx.EXPAND)
boxrow.Add((3, 3), 0)
hbox2 = wx.FlexGridSizer(1, 2, 10, 10)
label = wx.StaticText(self,
-1,
"Min Threshold: ",
style=wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
self.minthresh = FloatEntry(self,
-1,
allownone=False,
chars=5,
value="0.7")
hbox2.Add(label, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
hbox2.Add(self.minthresh, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL, 3)
hbox2.AddGrowableCol(0)
boxrow.Add(hbox2, 0, wx.ALIGN_CENTER_VERTICAL | wx.EXPAND)
boxrow.Add((3, 3), 0)
label = wx.StaticText(self,
-1,
"Particle contrast: ",
style=wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
boxrow.Add(label, 0,
wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL | wx.EXPAND, 3)
hbox8 = wx.FlexGridSizer(1, 2, 10, 10)
self.whitePart = wx.RadioButton(self,
-1,
'Light on Dark (stain)', (10, 10),
style=wx.RB_GROUP)
self.blackPart = wx.RadioButton(self, -1, 'Dark on Light (ice)',
(10, 30))
self.Bind(wx.EVT_RADIOBUTTON,
self.partContrast,
id=self.whitePart.GetId())
self.Bind(wx.EVT_RADIOBUTTON,
self.partContrast,
id=self.blackPart.GetId())
self.partContrast(True)
hbox8.Add(self.whitePart, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
hbox8.Add(self.blackPart, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
boxrow.Add(hbox8, 0, wx.ALIGN_CENTER_VERTICAL | wx.EXPAND)
boxrow.Add((3, 3), 0)
inforow.Add((1, 1), 0, 3)
inforow.Add(
boxrow, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL | wx.EXPAND,
3)
inforow.Add((1, 1), 0, 3)
### end standard options
### advanced options
box = wx.StaticBox(self, -1, 'Advanded Options')
boxrow = wx.StaticBoxSizer(box, wx.VERTICAL)
hbox3 = wx.FlexGridSizer(1, 2, 10, 10)
label = wx.StaticText(self,
-1,
"Diameter range (pixels): ",
style=wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
self.srange = FloatEntry(self,
-1,
allownone=False,
chars=5,
value="20.0")
hbox3.Add(label, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
hbox3.Add(self.srange, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL, 3)
hbox3.AddGrowableCol(0)
boxrow.Add(hbox3, 0, wx.ALIGN_CENTER_VERTICAL | wx.EXPAND)
hbox4 = wx.FlexGridSizer(1, 2, 10, 10)
label = wx.StaticText(self,
-1,
"Number of sizes: ",
style=wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
self.numslices = IntEntry(self,
-1,
allownone=False,
chars=3,
value="2")
hbox4.Add(label, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
hbox4.Add(self.numslices, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL, 3)
hbox4.AddGrowableCol(0)
boxrow.Add(hbox4, 0, wx.ALIGN_CENTER_VERTICAL | wx.EXPAND)
hbox5 = wx.FlexGridSizer(1, 2, 10, 10)
label = wx.StaticText(self,
-1,
"Max threshold: ",
style=wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
self.maxthresh = FloatEntry(self,
-1,
allownone=False,
chars=5,
value="1.5")
hbox5.Add(label, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
hbox5.Add(self.maxthresh, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL, 3)
hbox5.AddGrowableCol(0)
boxrow.Add(hbox5, 0, wx.ALIGN_CENTER_VERTICAL | wx.EXPAND)
hbox6 = wx.FlexGridSizer(1, 2, 10, 10)
label = wx.StaticText(self,
-1,
"Max peak area (% πr^2): ",
style=wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
self.peakarea = FloatEntry(self,
-1,
allownone=False,
chars=5,
value="0.3")
hbox6.Add(label, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
hbox6.Add(self.peakarea, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL, 3)
hbox6.AddGrowableCol(0)
boxrow.Add(hbox6, 0, wx.ALIGN_CENTER_VERTICAL | wx.EXPAND)
hbox9 = wx.FlexGridSizer(1, 2, 10, 10)
label = wx.StaticText(self,
-1,
"Max peaks: ",
style=wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
self.maxpeaks = IntEntry(self,
-1,
allownone=False,
chars=5,
value="500")
hbox9.Add(label, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
hbox9.Add(self.maxpeaks, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL, 3)
hbox9.AddGrowableCol(0)
boxrow.Add(hbox9, 0, wx.ALIGN_CENTER_VERTICAL | wx.EXPAND)
boxrow.Add((3, 3), 0)
inforow.Add((1, 1), 0, 3)
inforow.Add(
boxrow, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL | wx.EXPAND,
3)
inforow.Add((1, 1), 0, 3)
### end advanced options
self.canceldog = wx.Button(self, wx.ID_CANCEL, '&Cancel')
self.rundog = wx.Button(self, wx.ID_OK, '&Run')
self.Bind(wx.EVT_BUTTON, self.onRunDogPicker, self.rundog)
buttonrow = wx.FlexGridSizer(1, 2, 10, 10)
buttonrow.Add(self.canceldog, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL,
10)
buttonrow.Add(self.rundog, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL,
10)
self.sizer = wx.FlexGridSizer(3, 1, 10, 10)
self.sizer.Add(inforow, 0, wx.ALIGN_CENTER_HORIZONTAL, border=10)
self.sizer.Add(buttonrow, 0, wx.ALIGN_CENTER_HORIZONTAL, border=10)
label = wx.StaticText(self,
-1,
"Check command line after running",
style=wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
self.sizer.Add(label, 0, wx.EXPAND, 5)
self.SetSizerAndFit(self.sizer)
#==================
def partContrast(self, evt):
if self.whitePart.GetValue() is True:
return False
return True
#==================
def onRunDogPicker(self, evt):
apDisplay.printColor("===============\nRunning experimental DoGPicker",
"cyan")
### remove existing maps
lefts = glob.glob("maps/leftimage.dogmap*.jpg")
for imgname in lefts:
apFile.removeFile(imgname, warn=False)
rights = glob.glob("maps/rightimage.dogmap*.jpg")
for imgname in rights:
apFile.removeFile(imgname, warn=False)
pixdiam = self.diam.GetValue()
sizerange = self.srange.GetValue()
minthresh = self.minthresh.GetValue()
maxthresh = self.maxthresh.GetValue()
peakarea = self.peakarea.GetValue()
invert = self.partContrast(None)
maxpeaks = self.maxpeaks.GetValue()
numslices = self.numslices.GetValue()
if invert is True:
apDisplay.printMsg(
"Picking dark particles on light backgound, i.e. ice")
else:
apDisplay.printMsg(
"Picking light particles on dark backgound, i.e. stain")
self.Close()
apParam.createDirectory("maps")
#1. set DoG parameters / hack to use existing pipeline function
dogparams = {
'apix': 1.0, # set to 1 because we are using pixels
'bin': 1.0, # set to 1 because we are using pixels
'diam': pixdiam, # diameter of particles
'sizerange': sizerange, # diameter range of particles
'numslices': numslices, # number of slices to perform
'kfactor': 1.2, # does not matter
'overlapmult': 1.5,
'rundir': os.getcwd(),
'maxpeaks': maxpeaks,
'maxthresh': maxthresh,
'thresh': minthresh,
'maxsize': peakarea,
'peaktype': 'maximum',
'background': False,
'doubles': False,
}
#2a. get image 1
img1 = numpy.asarray(self.parent.panel1.imagedata, dtype=numpy.float32)
if invert is True:
img1 = apImage.invertImage(img1)
#3a. run DoG picker on image 1
dogarrays1 = apDog.diffOfGaussParam(img1, dogparams)
#4a: threshold & find peaks image 1
imgdict1 = {
'filename': 'leftimage',
'image': img1,
}
peaktree1 = apPeaks.findPeaks(imgdict1,
dogarrays1,
dogparams,
maptype="dogmap",
pikfile=False)
#5a: insert into self.parent.picks1
self.parent.picks1 = self.peaktreeToPicks(peaktree1)
#===
#2b: get image 2
img2 = numpy.asarray(self.parent.panel2.imagedata, dtype=numpy.float32)
if invert is True:
img2 = apImage.invertImage(img2)
#3b. run DoG picker on image 2
dogarrays2 = apDog.diffOfGaussParam(img2, dogparams)
#4b: threshold & find peaks image 2
imgdict2 = {
'filename': 'rightimage',
'image': img2,
}
peaktree2 = apPeaks.findPeaks(imgdict2,
dogarrays2,
dogparams,
maptype="dogmap",
pikfile=False)
#5b: insert into self.parent.picks2
self.parent.picks2 = self.peaktreeToPicks(peaktree2)
self.parent.onImportPicks(None, pixdiam, showmaps=True)
apDisplay.printColor("Finished DoGPicker\n===================", "cyan")
#==================
def peaktreeToPicks(self, peaktree):
picks = []
for p in peaktree:
picks.append((p['xcoord'], p['ycoord']))
npicks = numpy.asarray(picks, dtype=numpy.float32)
return npicks
def initialize(self):
leginon.gui.wx.Settings.ScrolledDialog.initialize(self)
sb = wx.StaticBox(self, -1, 'Low Pass Filter (Phase Correlation)')
sbszlpf = wx.StaticBoxSizer(sb, wx.VERTICAL)
sb = wx.StaticBox(self, -1, 'Template Correlation')
sbsztemplate = wx.StaticBoxSizer(sb, wx.VERTICAL)
self.widgets['template lpf'] = {}
self.widgets['template lpf']['sigma'] = FloatEntry(self, -1,
min=0.0, chars=4)
szlpf = wx.GridBagSizer(5, 5)
label = wx.StaticText(self, -1, 'Sigma:')
szlpf.Add(label, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szlpf.Add(self.widgets['template lpf']['sigma'], (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL|wx.FIXED_MINSIZE|wx.ALIGN_RIGHT)
szlpf.AddGrowableCol(1)
sbszlpf.Add(szlpf, 1, wx.EXPAND|wx.ALL, 5)
self.widgets['template filename'] = Entry(self, -1, chars=12)
self.widgets['file diameter'] = IntEntry(self, -1, chars=4)
self.widgets['template diameter'] = IntEntry(self, -1, chars=4)
self.widgets['template type'] = Choice(self, -1, choices=self.node.cortypes)
szcor = wx.GridBagSizer(5, 5)
label = wx.StaticText(self, -1, 'Use')
szcor.Add(label, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szcor.Add(self.widgets['template type'], (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL)
label = wx.StaticText(self, -1, 'correlation')
szcor.Add(label, (0, 2), (1, 1), wx.ALIGN_CENTER_VERTICAL)
sztemplate = wx.GridBagSizer(5, 5)
sztemplate.Add(szcor, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
label = wx.StaticText(self, -1, 'Template Filename')
sztemplate.Add(label, (1, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
sztemplate.Add(self.widgets['template filename'], (1, 1), (1, 1),
wx.ALIGN_CENTER|wx.FIXED_MINSIZE)
label = wx.StaticText(self, -1, 'Original Template Diameter')
sztemplate.Add(label, (2, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
sztemplate.Add(self.widgets['file diameter'], (2, 1), (1, 1),
wx.ALIGN_CENTER|wx.FIXED_MINSIZE)
label = wx.StaticText(self, -1, 'Final Template Diameter')
sztemplate.Add(label, (3, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
sztemplate.Add(self.widgets['template diameter'], (3, 1), (1, 1),
wx.ALIGN_CENTER|wx.FIXED_MINSIZE)
sbsztemplate.Add(sztemplate, 1, wx.EXPAND|wx.ALL, 5)
self.btest = wx.Button(self, -1, 'Test')
szbutton = wx.GridBagSizer(5, 5)
szbutton.Add(self.btest, (0, 0), (1, 1),
wx.ALIGN_CENTER_VERTICAL|wx.ALIGN_RIGHT)
szbutton.AddGrowableCol(0)
self.Bind(wx.EVT_BUTTON, self.onTestButton, self.btest)
return [sbsztemplate, sbszlpf, szbutton]
def __init__(self, parent):
self.parent = parent
wx.Dialog.__init__(self, self.parent.frame, -1,
"DoG Auto Particle Picker")
inforow = wx.FlexGridSizer(3, 3, 10, 10)
inforow.Add((1, 1), 0, 3)
inforow.Add((1, 1), 0, 3)
inforow.Add((1, 1), 0, 3)
### standard options
box = wx.StaticBox(self, -1, 'Standard Options')
boxrow = wx.StaticBoxSizer(box, wx.VERTICAL)
hbox1 = wx.FlexGridSizer(1, 2, 10, 10)
label = wx.StaticText(self,
-1,
"Particle diameter (pixels): ",
style=wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
self.diam = FloatEntry(self,
-1,
allownone=False,
chars=5,
value="100.0")
hbox1.Add(label, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
hbox1.Add(
self.diam, 0, wx.ALIGN_RIGHT | wx.ALIGN_CENTER_HORIZONTAL
| wx.ALIGN_CENTER_VERTICAL, 3)
hbox1.AddGrowableCol(0)
boxrow.Add(hbox1, 0, wx.ALIGN_CENTER_VERTICAL | wx.EXPAND)
boxrow.Add((3, 3), 0)
hbox2 = wx.FlexGridSizer(1, 2, 10, 10)
label = wx.StaticText(self,
-1,
"Min Threshold: ",
style=wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
self.minthresh = FloatEntry(self,
-1,
allownone=False,
chars=5,
value="0.7")
hbox2.Add(label, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
hbox2.Add(self.minthresh, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL, 3)
hbox2.AddGrowableCol(0)
boxrow.Add(hbox2, 0, wx.ALIGN_CENTER_VERTICAL | wx.EXPAND)
boxrow.Add((3, 3), 0)
label = wx.StaticText(self,
-1,
"Particle contrast: ",
style=wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
boxrow.Add(label, 0,
wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL | wx.EXPAND, 3)
hbox8 = wx.FlexGridSizer(1, 2, 10, 10)
self.whitePart = wx.RadioButton(self,
-1,
'Light on Dark (stain)', (10, 10),
style=wx.RB_GROUP)
self.blackPart = wx.RadioButton(self, -1, 'Dark on Light (ice)',
(10, 30))
self.Bind(wx.EVT_RADIOBUTTON,
self.partContrast,
id=self.whitePart.GetId())
self.Bind(wx.EVT_RADIOBUTTON,
self.partContrast,
id=self.blackPart.GetId())
self.partContrast(True)
hbox8.Add(self.whitePart, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
hbox8.Add(self.blackPart, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
boxrow.Add(hbox8, 0, wx.ALIGN_CENTER_VERTICAL | wx.EXPAND)
boxrow.Add((3, 3), 0)
inforow.Add((1, 1), 0, 3)
inforow.Add(
boxrow, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL | wx.EXPAND,
3)
inforow.Add((1, 1), 0, 3)
### end standard options
### advanced options
box = wx.StaticBox(self, -1, 'Advanded Options')
boxrow = wx.StaticBoxSizer(box, wx.VERTICAL)
hbox3 = wx.FlexGridSizer(1, 2, 10, 10)
label = wx.StaticText(self,
-1,
"Diameter range (pixels): ",
style=wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
self.srange = FloatEntry(self,
-1,
allownone=False,
chars=5,
value="20.0")
hbox3.Add(label, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
hbox3.Add(self.srange, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL, 3)
hbox3.AddGrowableCol(0)
boxrow.Add(hbox3, 0, wx.ALIGN_CENTER_VERTICAL | wx.EXPAND)
hbox4 = wx.FlexGridSizer(1, 2, 10, 10)
label = wx.StaticText(self,
-1,
"Number of sizes: ",
style=wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
self.numslices = IntEntry(self,
-1,
allownone=False,
chars=3,
value="2")
hbox4.Add(label, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
hbox4.Add(self.numslices, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL, 3)
hbox4.AddGrowableCol(0)
boxrow.Add(hbox4, 0, wx.ALIGN_CENTER_VERTICAL | wx.EXPAND)
hbox5 = wx.FlexGridSizer(1, 2, 10, 10)
label = wx.StaticText(self,
-1,
"Max threshold: ",
style=wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
self.maxthresh = FloatEntry(self,
-1,
allownone=False,
chars=5,
value="1.5")
hbox5.Add(label, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
hbox5.Add(self.maxthresh, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL, 3)
hbox5.AddGrowableCol(0)
boxrow.Add(hbox5, 0, wx.ALIGN_CENTER_VERTICAL | wx.EXPAND)
hbox6 = wx.FlexGridSizer(1, 2, 10, 10)
label = wx.StaticText(self,
-1,
"Max peak area (% πr^2): ",
style=wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
self.peakarea = FloatEntry(self,
-1,
allownone=False,
chars=5,
value="0.3")
hbox6.Add(label, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
hbox6.Add(self.peakarea, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL, 3)
hbox6.AddGrowableCol(0)
boxrow.Add(hbox6, 0, wx.ALIGN_CENTER_VERTICAL | wx.EXPAND)
hbox9 = wx.FlexGridSizer(1, 2, 10, 10)
label = wx.StaticText(self,
-1,
"Max peaks: ",
style=wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
self.maxpeaks = IntEntry(self,
-1,
allownone=False,
chars=5,
value="500")
hbox9.Add(label, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
hbox9.Add(self.maxpeaks, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL, 3)
hbox9.AddGrowableCol(0)
boxrow.Add(hbox9, 0, wx.ALIGN_CENTER_VERTICAL | wx.EXPAND)
boxrow.Add((3, 3), 0)
inforow.Add((1, 1), 0, 3)
inforow.Add(
boxrow, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL | wx.EXPAND,
3)
inforow.Add((1, 1), 0, 3)
### end advanced options
self.canceldog = wx.Button(self, wx.ID_CANCEL, '&Cancel')
self.rundog = wx.Button(self, wx.ID_OK, '&Run')
self.Bind(wx.EVT_BUTTON, self.onRunDogPicker, self.rundog)
buttonrow = wx.FlexGridSizer(1, 2, 10, 10)
buttonrow.Add(self.canceldog, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL,
10)
buttonrow.Add(self.rundog, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL,
10)
self.sizer = wx.FlexGridSizer(3, 1, 10, 10)
self.sizer.Add(inforow, 0, wx.ALIGN_CENTER_HORIZONTAL, border=10)
self.sizer.Add(buttonrow, 0, wx.ALIGN_CENTER_HORIZONTAL, border=10)
label = wx.StaticText(self,
-1,
"Check command line after running",
style=wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
self.sizer.Add(label, 0, wx.EXPAND, 5)
self.SetSizerAndFit(self.sizer)
def addTomoSettings(self):
tiltsb = wx.StaticBox(self, -1, 'Tilt')
tiltsbsz = wx.StaticBoxSizer(tiltsb, wx.VERTICAL)
equalslopesb = wx.StaticBox(self, -1, 'Cosine Rule Tilting')
equalslopesbsz = wx.StaticBoxSizer(equalslopesb, wx.VERTICAL)
expsb = wx.StaticBox(self, -1, 'Exposure')
expsbsz = wx.StaticBoxSizer(expsb, wx.VERTICAL)
bcsb = wx.StaticBox(self, -1, 'Before Collection')
bcsbsz = wx.StaticBoxSizer(bcsb, wx.VERTICAL)
miscsb = wx.StaticBox(self, -1, 'Misc.')
miscsbsz = wx.StaticBoxSizer(miscsb, wx.VERTICAL)
modelb = wx.StaticBox(self, -1, 'Model')
modelbsz = wx.StaticBoxSizer(modelb, wx.VERTICAL)
optb = wx.StaticBox(self, -1,
'Custom Tilt Axis Model in +/- Directions(d)')
optbsz = wx.StaticBoxSizer(optb, wx.VERTICAL)
self.widgets['tilt min'] = FloatEntry(self,
-1,
allownone=False,
chars=7,
value='0.0')
self.widgets['tilt max'] = FloatEntry(self,
-1,
allownone=False,
chars=7,
value='0.0')
self.widgets['tilt start'] = FloatEntry(self,
-1,
allownone=False,
chars=7,
value='0.0')
self.widgets['tilt step'] = FloatEntry(self,
-1,
allownone=False,
chars=7,
value='0.0')
self.widgets['equally sloped'] = wx.CheckBox(self, -1,
'Use cosine rule')
self.widgets['equally sloped n'] = IntEntry(self,
-1,
min=1,
allownone=False,
chars=5,
value='30')
tiltoptsz = wx.GridBagSizer(5, 5)
tiltsz = wx.GridBagSizer(5, 5)
label = wx.StaticText(self, -1, 'Min.')
tiltsz.Add(label, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL | wx.LEFT,
10)
tiltsz.Add(self.widgets['tilt min'], (0, 1), (1, 1),
wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE)
label = wx.StaticText(self, -1, 'Max.')
tiltsz.Add(label, (0, 2), (1, 1),
wx.ALIGN_RIGHT | wx.ALIGN_CENTER_VERTICAL | wx.LEFT, 10)
tiltsz.Add(self.widgets['tilt max'], (0, 3), (1, 1),
wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE)
label = wx.StaticText(self, -1, 'Start')
tiltsz.Add(label, (0, 4), (1, 1),
wx.ALIGN_RIGHT | wx.ALIGN_CENTER_VERTICAL | wx.LEFT, 10)
tiltsz.Add(self.widgets['tilt start'], (0, 5), (1, 1),
wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE)
label = wx.StaticText(self, -1, 'Step')
tiltsz.Add(label, (0, 6), (1, 1),
wx.ALIGN_RIGHT | wx.ALIGN_CENTER_VERTICAL | wx.LEFT, 10)
tiltsz.Add(self.widgets['tilt step'], (0, 7), (1, 1),
wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE)
label = wx.StaticText(self, -1, 'degree(s)')
tiltsz.Add(label, (0, 8), (1, 1), wx.ALIGN_CENTER_VERTICAL)
addonsizer = wx.GridBagSizer(5, 5)
label = wx.StaticText(self, -1,
'List of Extra Tilts to Collect (in degrees)')
addonsizer.Add(label, (0, 0), (1, 2), wx.ALIGN_CENTER_VERTICAL)
self.widgets['addon tilts'] = Entry(self,
-1,
chars=45,
style=wx.ALIGN_RIGHT | wx.EXPAND)
addonsizer.Add(self.widgets['addon tilts'], (0, 2), (1, 7), wx.EXPAND)
addonsizer.AddGrowableCol(2)
tiltsz.Add(addonsizer, (1, 0), (1, 9), wx.EXPAND)
tiltoptsz.Add(tiltsz, (1, 0), (2, 9),
wx.ALIGN_CENTER_VERTICAL | wx.EXPAND)
equalslopesz = wx.GridBagSizer(0, 5)
equalslopesz.Add(self.widgets['equally sloped'], (0, 0), (1, 2),
wx.ALIGN_LEFT | wx.FIXED_MINSIZE)
equalslopesz.Add(self.widgets['equally sloped n'], (1, 0), (1, 1),
wx.ALIGN_LEFT | wx.FIXED_MINSIZE)
label = wx.StaticText(
self, -1, 'Number of tilts in the maximal tilting direction')
equalslopesz.Add(label, (1, 1), (1, 1), wx.ALIGN_CENTER_VERTICAL)
equalslopesbsz.Add(equalslopesz, 0, wx.EXPAND)
tiltoptsz.Add(equalslopesbsz, (0, 9), (3, 2),
wx.EXPAND | wx.ALIGN_CENTER_VERTICAL)
tiltsbsz.Add(tiltoptsz, 0, wx.EXPAND | wx.ALL, 5)
self.widgets['dose'] = FloatEntry(self,
-1,
min=0.0,
allownone=False,
chars=7,
value='200.0')
self.widgets['min exposure'] = FloatEntry(self,
-1,
min=0.0,
allownone=False,
chars=5,
value='0.25')
self.widgets['max exposure'] = FloatEntry(self,
-1,
min=0.0,
allownone=False,
chars=5,
value='2.0')
expsz = wx.GridBagSizer(5, 10)
label = wx.StaticText(self, -1, 'Total dose')
expsz.Add(label, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
expsz.Add(self.widgets['dose'], (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_RIGHT | wx.FIXED_MINSIZE)
label = wx.StaticText(self, -1, 'e-/A^2')
expsz.Add(label, (0, 2), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE)
label = wx.StaticText(self, -1, 'Exposure time')
expsz.Add(label, (1, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
exptsz = wx.GridBagSizer(0, 0)
label = wx.StaticText(self, -1, 'Min.')
exptsz.Add(label, (0, 0), (1, 1),
wx.ALIGN_RIGHT | wx.ALIGN_CENTER_VERTICAL)
exptsz.Add(self.widgets['min exposure'], (0, 1), (1, 1),
wx.ALIGN_LEFT | wx.FIXED_MINSIZE)
label = wx.StaticText(self, -1, 'Max.')
exptsz.Add(label, (0, 2), (1, 1),
wx.ALIGN_RIGHT | wx.ALIGN_CENTER_VERTICAL)
exptsz.Add(self.widgets['max exposure'], (0, 3), (1, 1),
wx.ALIGN_LEFT | wx.FIXED_MINSIZE)
label = wx.StaticText(self, -1, 'seconds')
exptsz.Add(label, (0, 4), (1, 1), wx.ALIGN_CENTER_VERTICAL)
expsz.Add(exptsz, (1, 1), (1, 2),
wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_RIGHT)
expsz.AddGrowableCol(0)
expsz.AddGrowableRow(0)
expsz.AddGrowableRow(1)
expsbsz.Add(expsz, 1, wx.EXPAND | wx.ALL, 5)
self.widgets['run buffer cycle'] = wx.CheckBox(self, -1,
'Run buffer cycle')
self.widgets['align zero loss peak'] = wx.CheckBox(
self, -1, 'Align zero loss peak')
self.widgets['measure dose'] = wx.CheckBox(self, -1, 'Measure dose')
bcsz = wx.GridBagSizer(5, 10)
bcsz.Add(self.widgets['run buffer cycle'], (0, 0), (1, 1),
wx.ALIGN_CENTER_VERTICAL)
bcsz.Add(self.widgets['align zero loss peak'], (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL)
bcsz.Add(self.widgets['measure dose'], (1, 0), (1, 1),
wx.ALIGN_CENTER_VERTICAL)
bcsbsz.Add(bcsz, 1, wx.ALL | wx.ALIGN_CENTER, 5)
self.widgets['integer'] = wx.CheckBox(self, -1, 'Scale by')
self.widgets['intscale'] = FloatEntry(self,
-1,
min=0.0,
allownone=False,
chars=5,
value='10.0')
self.widgets['mean threshold'] = FloatEntry(self,
-1,
min=0.0,
allownone=False,
chars=5,
value='100.0')
self.widgets['collection threshold'] = FloatEntry(self,
-1,
min=0.0,
allownone=False,
chars=5,
value='90.0')
self.widgets['tilt pause time'] = FloatEntry(self,
-1,
min=0.0,
allownone=False,
chars=5,
value='1.0')
# self.widgets['measure defocus'] = wx.CheckBox(self, -1, 'Measure defocus')
self.widgets['use lpf'] = wx.CheckBox(
self, -1, 'Use lpf in peak finding of tilt image correlation')
self.widgets['use tilt'] = wx.CheckBox(
self, -1,
'Stretch images according to the tilt before correlation')
# tapersz = wx.GridBagSizer(5,5)
# lab = wx.StaticText(self, -1, 'edge tapered upto')
# tapersz.Add(lab, (0,0), (1,1))
# tapersz.Add(self.widgets['taper size'], (0,1), (1,1))
# lab = wx.StaticText(self, -1, '% image length')
# tapersz.Add(lab, (0,2), (1,1))
intsz = wx.GridBagSizer(5, 5)
intsz.Add(self.widgets['integer'], (0, 0), (1, 1),
wx.ALIGN_CENTER_VERTICAL)
intsz.Add(self.widgets['intscale'], (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL)
label = wx.StaticText(self, -1, 'to convert to integer')
intsz.Add(label, (0, 2), (1, 1), wx.ALIGN_CENTER_VERTICAL)
mtsz = wx.GridBagSizer(5, 5)
label = wx.StaticText(self, -1, 'Consider images with less than')
mtsz.Add(label, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
mtsz.Add(self.widgets['mean threshold'], (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE)
label = wx.StaticText(self, -1, 'counts as obstructed')
mtsz.Add(label, (0, 2), (1, 1), wx.ALIGN_CENTER_VERTICAL)
ctsz = wx.GridBagSizer(5, 5)
label = wx.StaticText(self, -1,
'Abort if first half collected less than')
ctsz.Add(label, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
ctsz.Add(self.widgets['collection threshold'], (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE)
label = wx.StaticText(self, -1, '% of images')
ctsz.Add(label, (0, 2), (1, 1), wx.ALIGN_CENTER_VERTICAL)
tptsz = wx.GridBagSizer(5, 5)
label = wx.StaticText(self, -1, 'Pause')
tptsz.Add(label, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
tptsz.Add(self.widgets['tilt pause time'], (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE)
label = wx.StaticText(self, -1, 'seconds before each tilt image.')
tptsz.Add(label, (0, 2), (1, 1), wx.ALIGN_CENTER_VERTICAL)
miscsz = wx.GridBagSizer(5, 10)
miscsz.Add(intsz, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
miscsz.Add(mtsz, (1, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
miscsz.Add(ctsz, (2, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
miscsz.Add(tptsz, (3, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
miscsz.Add(self.widgets['use lpf'], (4, 0), (1, 1), wx.ALIGN_CENTER)
miscsz.Add(self.widgets['use tilt'], (5, 0), (1, 1), wx.ALIGN_CENTER)
#miscsz.Add(tapersz, (7, 0), (1, 1), wx.ALIGN_CENTER)
#miscsz.Add(self.widgets['measure defocus'], (5, 0), (1, 1), wx.ALIGN_CENTER)
miscsbsz.Add(miscsz, 1, wx.ALL | wx.ALIGN_CENTER, 5)
modelmags = self.getMagChoices()
self.widgets['model mag'] = wx.Choice(self, -1, choices=modelmags)
self.widgets['phi'] = FloatEntry(self,
-1,
allownone=False,
chars=4,
value='0.0')
self.widgets['phi2'] = FloatEntry(self,
-1,
allownone=False,
chars=4,
value='0.0')
self.widgets['offset'] = FloatEntry(self,
-1,
allownone=False,
chars=6,
value='0.0')
self.widgets['offset2'] = FloatEntry(self,
-1,
allownone=False,
chars=6,
value='0.0')
self.widgets['z0'] = FloatEntry(self,
-1,
allownone=False,
chars=6,
value='0.0')
self.widgets['z02'] = FloatEntry(self,
-1,
allownone=False,
chars=6,
value='0.0')
self.widgets['z0 error'] = FloatEntry(self,
-1,
min=0.0,
allownone=False,
chars=6,
value='2e-6')
self.widgets['fixed model'] = wx.CheckBox(
self, -1, 'Keep the tilt axis parameters fixed')
self.widgets['use z0'] = wx.CheckBox(
self, -1, 'Initialize z0 with current model')
self.widgets['fit data points'] = IntEntry(self,
-1,
min=4,
allownone=False,
chars=5,
value='4')
magsz = wx.GridBagSizer(5, 5)
label = wx.StaticText(self, -1, 'Initialize with the model of')
magsz.Add(label, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
magsz.Add(self.widgets['model mag'], (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL)
phisz = wx.GridBagSizer(2, 2)
phisz.AddGrowableCol(0)
label = wx.StaticText(self, -1, 'Tilt Axis from Y')
phisz.Add(label, (0, 0), (2, 1), wx.ALIGN_CENTER_VERTICAL)
label = wx.StaticText(self, -1, '+d')
phisz.Add(label, (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_RIGHT)
phisz.Add(self.widgets['phi'], (0, 2), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE)
label = wx.StaticText(self, -1, '-d')
phisz.Add(label, (1, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_RIGHT)
phisz.Add(self.widgets['phi2'], (1, 2), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE)
label = wx.StaticText(self, -1, 'degs')
phisz.Add(label, (0, 3), (2, 1), wx.ALIGN_CENTER_VERTICAL)
offsetsz = wx.GridBagSizer(2, 2)
label = wx.StaticText(self, -1, 'Offset:')
offsetsz.Add(label, (0, 0), (2, 1), wx.ALIGN_CENTER_VERTICAL)
label = wx.StaticText(self, -1, '+d')
offsetsz.Add(label, (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_RIGHT)
offsetsz.Add(self.widgets['offset'], (0, 2), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE)
label = wx.StaticText(self, -1, 'um')
offsetsz.Add(label, (0, 3), (2, 1), wx.ALIGN_CENTER_VERTICAL)
label = wx.StaticText(self, -1, '-d')
offsetsz.Add(label, (1, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_RIGHT)
offsetsz.Add(self.widgets['offset2'], (1, 2), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE)
z0sz = wx.GridBagSizer(2, 2)
label = wx.StaticText(self, -1, 'Z0:')
z0sz.Add(label, (0, 0), (2, 1), wx.ALIGN_CENTER_VERTICAL)
label = wx.StaticText(self, -1, '+d')
z0sz.Add(label, (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_RIGHT)
z0sz.Add(self.widgets['z0'], (0, 2), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE)
label = wx.StaticText(self, -1, 'um')
z0sz.Add(label, (0, 3), (1, 1), wx.ALIGN_CENTER_VERTICAL)
label = wx.StaticText(self, -1, '-d')
z0sz.Add(label, (1, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_RIGHT)
z0sz.Add(self.widgets['z02'], (1, 2), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE)
label = wx.StaticText(self, -1, 'um')
z0sz.Add(label, (1, 3), (2, 1), wx.ALIGN_CENTER_VERTICAL)
optsz = wx.GridBagSizer(5, 10)
optsz.Add(phisz, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
optsz.Add(offsetsz, (0, 1), (1, 1), wx.ALIGN_CENTER_VERTICAL)
optsz.Add(z0sz, (1, 0), (1, 2), wx.ALIGN_CENTER_VERTICAL)
optbsz.Add(optsz, 1, wx.ALL | wx.ALIGN_CENTER, 5)
optsz.AddGrowableCol(0)
zsz = wx.GridBagSizer(5, 5)
label = wx.StaticText(self, -1, 'Allow')
zsz.Add(label, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
zsz.Add(self.widgets['z0 error'], (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE)
label = wx.StaticText(self, -1, 'um of z0 jump between models')
zsz.Add(label, (0, 2), (1, 1), wx.ALIGN_CENTER_VERTICAL)
fsz = wx.GridBagSizer(5, 5)
label = wx.StaticText(self, -1, 'Smooth')
fsz.Add(label, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
fsz.Add(self.widgets['fit data points'], (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE)
label = wx.StaticText(self, -1, 'tilts (>=4) for defocus prediction')
fsz.Add(label, (0, 2), (1, 1), wx.ALIGN_CENTER_VERTICAL)
modelsz = wx.GridBagSizer(5, 5)
modelsz.Add(magsz, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
modelsz.Add(optbsz, (1, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
modelsz.Add(zsz, (2, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
modelsz.Add(self.widgets['fixed model'], (3, 0), (1, 1),
wx.ALIGN_CENTER_VERTICAL)
modelsz.Add(self.widgets['use z0'], (4, 0), (1, 1),
wx.ALIGN_CENTER_VERTICAL)
modelsz.Add(fsz, (5, 0), (1, 1), wx.ALIGN_RIGHT)
modelbsz.Add(modelsz, 1, wx.ALL | wx.ALIGN_CENTER, 5)
modelsz.AddGrowableCol(0)
sz = wx.GridBagSizer(5, 5)
sz.Add(tiltsbsz, (0, 0), (1, 2), wx.EXPAND)
sz.Add(expsbsz, (1, 0), (1, 1), wx.EXPAND)
sz.Add(bcsbsz, (1, 1), (1, 1), wx.EXPAND)
sz.Add(miscsbsz, (2, 0), (1, 1), wx.EXPAND)
sz.Add(modelbsz, (2, 1), (1, 1), wx.EXPAND)
sz.AddGrowableRow(0)
sz.AddGrowableRow(1)
sz.AddGrowableRow(2)
sz.AddGrowableCol(0)
sz.AddGrowableCol(1)
self.Bind(wx.EVT_CHECKBOX, self.onFixedModel,
self.widgets['fixed model'])
return sz
def __init__(self, parent):
self.parent = parent
wx.Dialog.__init__(self, self.parent.frame, -1, "Guess Initial Shift")
inforow = wx.FlexGridSizer(3, 2, 15, 15)
gammastr = "%3.3f" % self.parent.data['gamma']
label = wx.StaticText(self,
-1,
"Tilt axis angle (degrees): ",
style=wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
self.tiltaxis = FloatEntry(self,
-1,
allownone=False,
chars=5,
value=gammastr)
inforow.Add(label, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
inforow.Add(
self.tiltaxis, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL | wx.ALL, 3)
label = wx.StaticText(self,
-1,
"Vertical is 0 degrees",
style=wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
inforow.Add(label, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
inforow.Add((1, 1), 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
thetastr = "%3.3f" % self.parent.data['theta']
label = wx.StaticText(self,
-1,
"Tilt angle: ",
style=wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
self.tiltangle = FloatEntry(self,
-1,
allownone=False,
chars=5,
value=thetastr)
inforow.Add(label, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
inforow.Add(
self.tiltangle, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL | wx.ALL, 3)
label = wx.StaticText(
self,
-1,
"negative tilted on left, positive tilted or right",
style=wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
inforow.Add(label, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
inforow.Add((1, 1), 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
self.cancelguess = wx.Button(self, wx.ID_CANCEL, '&Cancel')
self.runguess = wx.Button(self, wx.ID_OK, '&Run')
self.Bind(wx.EVT_BUTTON, self.onRunGuessShift, self.runguess)
buttonrow = wx.GridSizer(1, 2)
buttonrow.Add(self.cancelguess, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL, 0)
buttonrow.Add(self.runguess, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL, 0)
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 addSettings(self):
sb = wx.StaticBox(self, -1, 'Main Screen')
sbszscreen = wx.StaticBoxSizer(sb, wx.VERTICAL)
sb = wx.StaticBox(self, -1, 'Low Dose')
sbszlowdose = wx.StaticBoxSizer(sb, wx.VERTICAL)
sb = wx.StaticBox(self, -1, 'Defocus Pair')
sbszdefocus = wx.StaticBoxSizer(sb, wx.VERTICAL)
self.instrumentselection = leginon.gui.wx.Instrument.SelectionPanel(self)
self.panel.setInstrumentSelection(self.instrumentselection)
self.widgets['camera settings'] = leginon.gui.wx.Camera.CameraPanel(self)
self.widgets['camera settings'].setGeometryLimits({'size':self.node.instrument.camerasize,'binnings':self.node.instrument.camerabinnings,'binmethod':self.node.instrument.camerabinmethod})
self.widgets['screen up'] = wx.CheckBox(self, -1, 'Up before acquire')
self.widgets['screen down'] = wx.CheckBox(self, -1, 'Down after acquired')
self.widgets['beam blank'] = wx.CheckBox(self, -1, 'Force beam blank after acquired')
self.widgets['correct image'] = wx.CheckBox(self, -1, 'Correct image')
self.widgets['save image'] = wx.CheckBox(self, -1,
'Save image to the database')
self.widgets['image label'] = Entry(self, -1, chars=12)
self.widgets['loop pause time'] = FloatEntry(self, -1, min=0.0, chars=4)
self.widgets['low dose'] = wx.CheckBox(self, -1, 'Use low dose')
self.widgets['low dose pause time'] = FloatEntry(self, -1, min=0.0, chars=4)
szscreen = wx.GridBagSizer(5, 5)
szscreen.Add(self.widgets['screen up'], (0, 0), (1, 1),
wx.ALIGN_CENTER_VERTICAL)
szscreen.Add(self.widgets['screen down'], (1, 0), (1, 1),
wx.ALIGN_CENTER_VERTICAL)
sbszscreen.Add(szscreen, 1, wx.EXPAND|wx.ALL, 5)
szlowdose = wx.GridBagSizer(5, 5)
szlowdose.Add(self.widgets['low dose'], (0, 0), (1, 1),
wx.ALIGN_CENTER_VERTICAL)
szlowdose.Add(self.widgets['beam blank'], (1, 0), (1, 1),
wx.ALIGN_CENTER_VERTICAL)
label = wx.StaticText(self, -1, 'Low dose pause')
szlowdose.Add(label, (2, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szlowdose.Add(self.widgets['low dose pause time'], (2, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL|wx.ALIGN_RIGHT|wx.FIXED_MINSIZE)
label = wx.StaticText(self, -1, 'seconds')
szlowdose.Add(label, (2, 2), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szlowdose.AddGrowableCol(1)
sbszlowdose.Add(szlowdose, 1, wx.EXPAND|wx.ALL, 5)
sz = wx.GridBagSizer(5, 5)
sz.Add(self.instrumentselection, (0, 0), (1, 3), wx.EXPAND)
sz.Add(self.widgets['camera settings'], (1, 0), (1, 3), wx.EXPAND)
sz.Add(self.widgets['correct image'], (2, 0), (1, 3),
wx.ALIGN_CENTER_VERTICAL)
sz.Add(self.widgets['save image'], (3, 0), (1, 3),
wx.ALIGN_CENTER_VERTICAL)
sb2 = wx.GridBagSizer(5,5)
szdefocus= wx.GridBagSizer(5, 5)
label = wx.StaticText(self, -1,'(leave both unchecked to use current defocus)')
szdefocus.Add(label, (0,0), (1,2))
self.widgets['defocus1switch'] = wx.CheckBox(self, -1, 'Defocus 1')
szdefocus.Add(self.widgets['defocus1switch'], (1,0), (1,1))
self.widgets['defocus1'] = FloatEntry(self, -1, chars=6)
szdefocus.Add(self.widgets['defocus1'], (1,1), (1,1))
self.widgets['defocus2switch'] = wx.CheckBox(self, -1, 'Defocus 2')
szdefocus.Add(self.widgets['defocus2switch'], (2,0), (1,1))
self.widgets['defocus2'] = FloatEntry(self, -1, chars=6)
szdefocus.Add(self.widgets['defocus2'], (2,1), (1,1))
sbszdefocus.Add(szdefocus, 1, wx.EXPAND|wx.ALL, 5)
sb2.Add(sbszscreen,(0,0),(1,3), wx.EXPAND)
sb2.Add(sbszlowdose,(1,0),(1,3), wx.EXPAND)
sb2.Add(sbszdefocus,(2,0),(1,3), wx.EXPAND)
label = wx.StaticText(self, -1, 'Loop pause')
sb2.Add(label, (3, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
sb2.Add(self.widgets['loop pause time'], (3, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL|wx.ALIGN_RIGHT|wx.FIXED_MINSIZE)
label = wx.StaticText(self, -1, 'seconds')
sb2.Add(label, (3, 2), (1, 1), wx.ALIGN_CENTER_VERTICAL)
label = wx.StaticText(self, -1, 'Label')
sb2.Add(label, (4, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
sb2.Add(self.widgets['image label'], (4, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL|wx.ALIGN_RIGHT|wx.FIXED_MINSIZE)
sb2.AddGrowableCol(1)
self.widgets['dark'] = wx.CheckBox(self, -1, 'Dark Exposure')
sb2.Add(self.widgets['dark'], (5,0), (1,1))
self.widgets['force annotate'] = wx.CheckBox(self, -1, 'Always Annotate Saved Images')
sb2.Add(self.widgets['force annotate'], (6,0), (1,1))
self.widgets['reduced params'] = wx.CheckBox(self, -1, 'Reduced EM Parameter Set (for slow TEMs)')
sb2.Add(self.widgets['reduced params'], (7,0), (1,1))
sba = wx.GridBagSizer(5,5)
# put the two sizers in columns
sba.Add(sz,(0,0),(1,1))
sba.Add(sb2,(0,1),(1,1))
return sba
def initialize(self):
#szs = leginon.gui.wx.Acquisition.ScrolledSettings.initialize(self)
simusb = wx.StaticBox(self, -1, 'Simulation')
simusbsz = wx.StaticBoxSizer(simusb, wx.VERTICAL)
miscsb = wx.StaticBox(self, -1, 'Misc.')
miscsbsz = wx.StaticBoxSizer(miscsb, wx.VERTICAL)
modelb = wx.StaticBox(self, -1, 'Model')
modelbsz = wx.StaticBoxSizer(modelb, wx.VERTICAL)
optb = wx.StaticBox(self, -1,
'Custom Tilt Axis Model in +/- Directions(d)')
optbsz = wx.StaticBoxSizer(optb, wx.VERTICAL)
alltiltseries = self.getTiltSeriesChoices()
self.widgets['simu tilt series'] = wx.Choice(self,
-1,
choices=alltiltseries)
simusz = wx.GridBagSizer(5, 5)
label = wx.StaticText(self, -1,
'Simulate Data Collection and Prediction of')
simusz.Add(label, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
simusz.Add(self.widgets['simu tilt series'], (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL)
simusbsz.Add(simusz, 1, wx.ALL | wx.ALIGN_CENTER, 5)
self.widgets['use lpf'] = wx.CheckBox(
self, -1, 'Use lpf in peak finding of tilt image correlation')
self.widgets['use tilt'] = wx.CheckBox(
self, -1, 'Use tilt info to stretch images')
self.widgets['taper size'] = IntEntry(self,
-1,
min=0,
allownone=False,
chars=3,
value='10')
tapersz = wx.GridBagSizer(5, 5)
lab = wx.StaticText(self, -1, 'edge tapered upto')
tapersz.Add(lab, (0, 0), (1, 1))
tapersz.Add(self.widgets['taper size'], (0, 1), (1, 1))
lab = wx.StaticText(self, -1, '% image length')
tapersz.Add(lab, (0, 2), (1, 1))
miscsz = wx.GridBagSizer(5, 10)
miscsz.Add(self.widgets['use lpf'], (0, 0), (1, 1), wx.ALIGN_CENTER)
miscsz.Add(self.widgets['use tilt'], (1, 0), (1, 1), wx.ALIGN_CENTER)
miscsz.Add(tapersz, (2, 0), (1, 1), wx.ALIGN_CENTER)
#miscsz.Add(self.widgets['measure defocus'], (5, 0), (1, 1), wx.ALIGN_CENTER)
miscsz.AddGrowableRow(0)
miscsz.AddGrowableRow(1)
miscsz.AddGrowableCol(0)
miscsbsz.Add(miscsz, 1, wx.ALL | wx.ALIGN_CENTER, 5)
modelmags = self.getMagChoices()
self.widgets['model mag'] = wx.Choice(self, -1, choices=modelmags)
self.widgets['phi'] = FloatEntry(self,
-1,
allownone=False,
chars=4,
value='0.0')
self.widgets['phi2'] = FloatEntry(self,
-1,
allownone=False,
chars=4,
value='0.0')
self.widgets['offset'] = FloatEntry(self,
-1,
allownone=False,
chars=6,
value='0.0')
self.widgets['offset2'] = FloatEntry(self,
-1,
allownone=False,
chars=6,
value='0.0')
self.widgets['z0 error'] = FloatEntry(self,
-1,
min=0.0,
allownone=False,
chars=6,
value='2e-6')
self.widgets['fixed model'] = wx.CheckBox(
self, -1, 'Keep the tilt axis parameters fixed')
self.widgets['fit data points'] = IntEntry(self,
-1,
min=4,
allownone=False,
chars=5,
value='4')
magsz = wx.GridBagSizer(5, 5)
label = wx.StaticText(self, -1, 'Initialize with the model of')
magsz.Add(label, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
magsz.Add(self.widgets['model mag'], (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL)
phisz = wx.GridBagSizer(2, 2)
phisz.AddGrowableCol(0)
label = wx.StaticText(self, -1, 'Tilt Axis from Y')
phisz.Add(label, (0, 0), (2, 1), wx.ALIGN_CENTER_VERTICAL)
label = wx.StaticText(self, -1, '+d')
phisz.Add(label, (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_RIGHT)
phisz.Add(self.widgets['phi'], (0, 2), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE)
label = wx.StaticText(self, -1, '-d')
phisz.Add(label, (1, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_RIGHT)
phisz.Add(self.widgets['phi2'], (1, 2), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE)
label = wx.StaticText(self, -1, 'degs')
phisz.Add(label, (0, 3), (2, 1), wx.ALIGN_CENTER_VERTICAL)
offsetsz = wx.GridBagSizer(2, 2)
label = wx.StaticText(self, -1, 'Offset:')
offsetsz.Add(label, (0, 0), (2, 1), wx.ALIGN_CENTER_VERTICAL)
label = wx.StaticText(self, -1, '+d')
offsetsz.Add(label, (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_RIGHT)
offsetsz.Add(self.widgets['offset'], (0, 2), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE)
label = wx.StaticText(self, -1, 'um')
offsetsz.Add(label, (0, 3), (2, 1), wx.ALIGN_CENTER_VERTICAL)
label = wx.StaticText(self, -1, '-d')
offsetsz.Add(label, (1, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_RIGHT)
offsetsz.Add(self.widgets['offset2'], (1, 2), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE)
optsz = wx.GridBagSizer(5, 10)
optsz.Add(phisz, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
optsz.Add(offsetsz, (0, 1), (1, 1), wx.ALIGN_CENTER_VERTICAL)
optbsz.Add(optsz, 1, wx.ALL | wx.ALIGN_CENTER, 5)
optsz.AddGrowableCol(0)
zsz = wx.GridBagSizer(5, 5)
label = wx.StaticText(self, -1, 'Allow')
zsz.Add(label, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
zsz.Add(self.widgets['z0 error'], (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE)
label = wx.StaticText(self, -1, 'um of z0 jump between models')
zsz.Add(label, (0, 2), (1, 1), wx.ALIGN_CENTER_VERTICAL)
fsz = wx.GridBagSizer(5, 5)
label = wx.StaticText(self, -1, 'Smooth')
fsz.Add(label, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
fsz.Add(self.widgets['fit data points'], (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE)
label = wx.StaticText(self, -1, 'tilts (>=4) for defocus prediction')
fsz.Add(label, (0, 2), (1, 1), wx.ALIGN_CENTER_VERTICAL)
modelsz = wx.GridBagSizer(5, 5)
modelsz.Add(magsz, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
modelsz.Add(optbsz, (1, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
modelsz.Add(zsz, (2, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
modelsz.Add(self.widgets['fixed model'], (3, 0), (1, 1),
wx.ALIGN_CENTER_VERTICAL)
modelsz.Add(fsz, (4, 0), (1, 1), wx.ALIGN_RIGHT)
modelbsz.Add(modelsz, 1, wx.ALL | wx.ALIGN_CENTER, 5)
modelsz.AddGrowableCol(0)
sz = wx.GridBagSizer(5, 5)
sz.Add(simusbsz, (0, 0), (1, 2), wx.EXPAND)
sz.Add(miscsbsz, (1, 0), (1, 1), wx.EXPAND)
sz.Add(modelbsz, (1, 1), (1, 1), wx.EXPAND)
sz.AddGrowableRow(0)
sz.AddGrowableRow(1)
sz.AddGrowableCol(0)
sz.AddGrowableCol(1)
self.Bind(wx.EVT_CHECKBOX, self.onFixedModel,
self.widgets['fixed model'])
return [sz]
def initialize(self):
leginon.gui.wx.Settings.ScrolledDialog.initialize(self)
sb = wx.StaticBox(self, -1, 'Raster')
sbszraster = wx.StaticBoxSizer(sb, wx.VERTICAL)
sb = wx.StaticBox(self, -1, 'Spacing/Angle Calculator')
sbszauto = wx.StaticBoxSizer(sb, wx.VERTICAL)
self.widgets['raster spacing'] = IntEntry(self, -1, chars=4, min=1)
self.widgets['raster spacing asymm'] = IntEntry(self, -1, chars=4)
self.widgets['raster limit'] = IntEntry(self, -1, chars=4, min=1)
self.widgets['raster limit asymm'] = IntEntry(self, -1, chars=4)
self.widgets['raster angle'] = FloatEntry(self, -1, chars=4)
self.widgets['raster center on image'] = wx.CheckBox(self, -1, 'Center on image')
self.widgets['raster center x'] = IntEntry(self, -1, chars=4)
self.widgets['raster center y'] = IntEntry(self, -1, chars=4)
self.widgets['raster symmetric'] = wx.CheckBox(self, -1, '&Symmetric')
## auto raster
self.autobut = wx.Button(self, -1, 'Calculate spacing and angle using the following parameters:')
self.Bind(wx.EVT_BUTTON, self.onAutoButton, self.autobut)
self.widgets['raster preset'] = PresetChoice(self, -1)
presets = self.node.presetsclient.getPresetNames()
self.widgets['raster preset'].setChoices(presets)
self.widgets['raster overlap'] = FloatEntry(self, -1, chars=8)
szauto = wx.GridBagSizer(5, 5)
szauto.Add(self.autobut, (0, 0), (1, 2), wx.ALIGN_CENTER_VERTICAL)
label = wx.StaticText(self, -1, 'Raster Preset')
szauto.Add(label, (1, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szauto.Add(self.widgets['raster preset'], (1, 1), (1, 1), wx.ALIGN_CENTER_VERTICAL)
label = wx.StaticText(self, -1, 'Overlap percent')
szauto.Add(label, (2, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szauto.Add(self.widgets['raster overlap'], (2, 1), (1, 1), wx.ALIGN_CENTER_VERTICAL)
movetypes = self.node.calclients.keys()
self.widgets['raster movetype'] = Choice(self, -1, choices=movetypes)
label = wx.StaticText(self, -1, 'Move Type')
szauto.Add(label, (3, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szauto.Add(self.widgets['raster movetype'], (3, 1), (1, 1), wx.ALIGN_CENTER_VERTICAL)
sbszauto.Add(szauto, 1, wx.EXPAND|wx.ALL,5)
szraster = wx.GridBagSizer(5, 5)
label = wx.StaticText(self, -1, 'XY symmetry:')
szraster.Add(label, (0,0), (1,1) , wx.ALIGN_CENTER_VERTICAL)
self.Bind(wx.EVT_CHECKBOX, self.onToggleSymm, self.widgets['raster symmetric'])
szraster.Add(self.widgets['raster symmetric'], (0,1), (1,2) , wx.ALIGN_CENTER_VERTICAL|wx.ALIGN_RIGHT)
self.widgets['raster symmetric'].SetMinSize((120,30))
label = wx.StaticText(self, -1, 'Spacing (x,y):')
szraster.Add(label, (1,0), (1,1), wx.ALIGN_CENTER_VERTICAL)
szraster.Add(self.widgets['raster spacing'], (1,1), (1,1),
wx.ALIGN_CENTER_VERTICAL|wx.ALIGN_RIGHT)
szraster.Add(self.widgets['raster spacing asymm'], (1,2), (1,1),
wx.ALIGN_CENTER_VERTICAL|wx.ALIGN_RIGHT)
label = wx.StaticText(self, -1, 'Num points (x,y):')
szraster.Add(label, (2,0), (1,1), wx.ALIGN_CENTER_VERTICAL)
szraster.Add(self.widgets['raster limit'], (2,1), (1,1),
wx.ALIGN_CENTER_VERTICAL|wx.ALIGN_RIGHT)
szraster.Add(self.widgets['raster limit asymm'], (2,2), (1,1),
wx.ALIGN_CENTER_VERTICAL|wx.ALIGN_RIGHT)
szraster.AddGrowableCol(1)
label = wx.StaticText(self, -1, 'Angle:')
szraster.Add(label, (3,0), (1,1), wx.ALIGN_CENTER_VERTICAL)
szraster.Add(self.widgets['raster angle'], (3,1), (1,2),
wx.ALIGN_CENTER_VERTICAL|wx.ALIGN_CENTER_HORIZONTAL)
szraster.Add(self.widgets['raster center on image'], (4,0), (1,3),
wx.ALIGN_CENTER_VERTICAL|wx.ALIGN_CENTER_HORIZONTAL)
self.Bind(wx.EVT_CHECKBOX, self.onCheckBox, self.widgets['raster center on image'])
label = wx.StaticText(self, -1, 'Center on x,y:')
szraster.Add(label, (5,0), (1,1), wx.ALIGN_CENTER_VERTICAL)
szraster.Add(self.widgets['raster center x'], (5,1), (1,1), wx.ALIGN_CENTER_VERTICAL)
szraster.Add(self.widgets['raster center y'], (5,2), (1,1), wx.ALIGN_CENTER_VERTICAL)
if self.widgets['raster center on image'].GetValue():
self.widgets['raster center x'].Enable(False)
self.widgets['raster center y'].Enable(False)
if self.widgets['raster symmetric'].GetValue():
self.widgets['raster spacing asymm'].Enable(False)
self.widgets['raster limit asymm'].Enable(False)
self.widgets['raster spacing asymm'].SetValue(None)
self.widgets['raster limit asymm'].SetValue(None)
else:
self.widgets['raster spacing asymm'].Enable(True)
self.widgets['raster limit asymm'].Enable(True)
sbszraster.Add(szraster, 1, wx.EXPAND|wx.ALL, 5)
self.btest = wx.Button(self, -1, 'Test')
szbutton = wx.GridBagSizer(5, 5)
szbutton.Add(self.btest, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL|wx.ALIGN_RIGHT)
szbutton.AddGrowableCol(0)
self.Bind(wx.EVT_BUTTON, self.onTestButton, self.btest)
return [sbszauto,sbszraster, szbutton]
def initialize(self):
leginon.gui.wx.Settings.ScrolledDialog.initialize(self)
sb = wx.StaticBox(self, -1, 'Low Pass Filter')
sbszlpf = wx.StaticBoxSizer(sb, wx.VERTICAL)
self.widgets['edge lpf'] = {}
self.widgets['edge lpf']['sigma'] = FloatEntry(self,
-1,
min=0.0,
chars=4)
szlpf = wx.GridBagSizer(5, 5)
label = wx.StaticText(self, -1, 'Sigma:')
szlpf.Add(label, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szlpf.Add(self.widgets['edge lpf']['sigma'], (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE | wx.ALIGN_RIGHT)
szlpf.AddGrowableCol(1)
sbszlpf.Add(szlpf, 1, wx.EXPAND | wx.ALL, 5)
# self.widgets['edge'] = wx.CheckBox(self, -1, 'Use edge finding')
# self.widgets['edge type'] = Choice(self, -1, choices=self.node.filtertypes)
# self.widgets['edge log size'] = IntEntry(self, -1, min=1, chars=4)
# self.widgets['edge log sigma'] = FloatEntry(self, -1, min=0.0, chars=4)
# self.widgets['edge absolute'] = wx.CheckBox(self, -1,
# 'Take absolute value of edge values')
sb = wx.StaticBox(self, -1, 'Edge Finding')
sbszedge = wx.StaticBoxSizer(sb, wx.VERTICAL)
self.widgets['edge threshold'] = FloatEntry(self, -1, chars=9)
szedge = wx.GridBagSizer(5, 5)
# szedge.Add(self.widgets['edge'], (0, 0), (1, 2), wx.ALIGN_CENTER_VERTICAL)
# label = wx.StaticText(self, -1, 'Type:')
# szedge.Add(label, (1, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
# szedge.Add(self.widgets['edge type'], (1, 1), (1, 1),
# wx.ALIGN_CENTER_VERTICAL)
# label = wx.StaticText(self, -1, 'LoG Size:')
# szedge.Add(label, (2, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
# szedge.Add(self.widgets['edge log size'], (2, 1), (1, 1),
# wx.ALIGN_CENTER_VERTICAL|wx.FIXED_MINSIZE|wx.ALIGN_RIGHT)
# label = wx.StaticText(self, -1, 'LoG Sigma:')
# szedge.Add(label, (3, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
# szedge.Add(self.widgets['edge log sigma'], (3, 1), (1, 1),
# wx.ALIGN_CENTER_VERTICAL|wx.FIXED_MINSIZE|wx.ALIGN_RIGHT)
# szedge.Add(self.widgets['edge absolute'], (4, 0), (1, 2),
# wx.ALIGN_CENTER_VERTICAL)
label = wx.StaticText(self, -1, 'Threshold:')
szedge.Add(label, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szedge.Add(
self.widgets['edge threshold'], (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE | wx.ALIGN_RIGHT)
szedge.AddGrowableCol(1)
sbszedge.Add(szedge, 1, wx.EXPAND | wx.ALL, 5)
self.btest = wx.Button(self, -1, 'Test')
szbutton = wx.GridBagSizer(5, 5)
szbutton.Add(self.btest, (0, 0), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_RIGHT)
szbutton.AddGrowableCol(0)
self.Bind(wx.EVT_BUTTON, self.onTestButton, self.btest)
return [sbszlpf, sbszedge, szbutton]
def initialize(self):
leginon.gui.wx.Settings.ScrolledDialog.initialize(self)
sb = wx.StaticBox(self, -1, 'Ice Analysis')
sbszice = wx.StaticBoxSizer(sb, wx.VERTICAL)
sb = wx.StaticBox(self, -1, 'Focus Targets')
sbszft = wx.StaticBoxSizer(sb, wx.VERTICAL)
sb = wx.StaticBox(self, -1, 'Acquisition Targets')
sbszat = wx.StaticBoxSizer(sb, wx.VERTICAL)
self.widgets['ice box size'] = FloatEntry(self, -1, chars=8)
self.widgets['ice thickness'] = FloatEntry(self, -1, chars=8)
self.widgets['ice min mean'] = FloatEntry(self, -1, chars=8)
self.widgets['ice max mean'] = FloatEntry(self, -1, chars=8)
self.widgets['ice max std'] = FloatEntry(self, -1, chars=8)
self.widgets['focus convolve'] = wx.CheckBox(self, -1, 'Convolve')
self.widgets['focus convolve template'] = \
leginon.gui.wx.TargetTemplate.Panel(self, 'Convolve Template')
self.widgets['focus constant template'] = \
leginon.gui.wx.TargetTemplate.Panel(self, 'Constant Template',
targetname='Constant target')
self.widgets['acquisition convolve'] = wx.CheckBox(
self, -1, 'Convolve')
self.widgets['acquisition convolve template'] = \
leginon.gui.wx.TargetTemplate.Panel(self, 'Convolve Template')
self.widgets['acquisition constant template'] = \
leginon.gui.wx.TargetTemplate.Panel(self, 'Constant Template',
targetname='Constant target')
szice = wx.GridBagSizer(5, 5)
label = wx.StaticText(self, -1, 'Box size:')
szice.Add(label, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szice.Add(self.widgets['ice box size'], (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE | wx.ALIGN_RIGHT)
label = wx.StaticText(self, -1, 'Reference Intensity:')
szice.Add(label, (1, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szice.Add(self.widgets['ice thickness'], (1, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE | wx.ALIGN_RIGHT)
label = wx.StaticText(self, -1, 'Min. mean:')
szice.Add(label, (2, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szice.Add(self.widgets['ice min mean'], (2, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE | wx.ALIGN_RIGHT)
label = wx.StaticText(self, -1, 'Max. mean:')
szice.Add(label, (3, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szice.Add(self.widgets['ice max mean'], (3, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE | wx.ALIGN_RIGHT)
label = wx.StaticText(self, -1, 'Max. stdev.:')
szice.Add(label, (4, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szice.Add(self.widgets['ice max std'], (4, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE | wx.ALIGN_RIGHT)
szice.AddGrowableCol(1)
sbszice.Add(szice, 1, wx.EXPAND | wx.ALL, 5)
szft = wx.GridBagSizer(5, 5)
szft.Add(self.widgets['focus convolve'], (0, 0), (1, 2),
wx.ALIGN_CENTER_VERTICAL)
szft.Add(self.widgets['focus convolve template'], (1, 0), (1, 1),
wx.ALIGN_CENTER | wx.FIXED_MINSIZE)
szft.Add(self.widgets['focus constant template'], (2, 0), (1, 1),
wx.ALIGN_CENTER | wx.FIXED_MINSIZE)
szft.AddGrowableCol(0)
sbszft.Add(szft, 1, wx.EXPAND | wx.ALL, 5)
szat = wx.GridBagSizer(5, 5)
szat.Add(self.widgets['acquisition convolve'], (0, 0), (1, 2),
wx.ALIGN_CENTER_VERTICAL)
szat.Add(self.widgets['acquisition convolve template'], (1, 0), (1, 1),
wx.ALIGN_CENTER | wx.FIXED_MINSIZE)
szat.Add(self.widgets['acquisition constant template'], (2, 0), (1, 1),
wx.ALIGN_CENTER | wx.FIXED_MINSIZE)
szat.AddGrowableCol(0)
sbszat.Add(szat, 1, wx.EXPAND | wx.ALL, 5)
self.bice = wx.Button(self, -1, 'Analyze Ice')
szbutton = wx.GridBagSizer(5, 5)
szbutton.Add(self.bice, (0, 0), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_RIGHT)
szbutton.AddGrowableCol(0)
szt = wx.GridBagSizer(5, 5)
szt.Add(sbszft, (0, 0), (1, 1), wx.EXPAND | wx.ALL)
szt.Add(sbszat, (0, 1), (1, 1), wx.EXPAND | wx.ALL)
self.Bind(wx.EVT_BUTTON, self.onAnalyzeIceButton, self.bice)
return [sbszice, szt, szbutton]
def initialize(self):
leginon.gui.wx.Settings.ScrolledDialog.initialize(self)
sb = wx.StaticBox(self, -1, 'Parameters')
sbsz = wx.StaticBoxSizer(sb, wx.VERTICAL)
self.widgets['measure beam tilt'] = FloatEntry(self, -1, chars=7)
self.labels = {}
self.labels['defocus'] = wx.StaticText(self, -1, '(Not measured)')
self.labels['stigmator'] = {}
for axis in ('x', 'y'):
self.labels['stigmator'][axis] = wx.StaticText(
self, -1, '(Not measured)')
szresult = wx.GridBagSizer(5, 5)
label = wx.StaticText(self, -1, 'beam tilt (+/-)')
szresult.Add(label, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szresult.Add(self.widgets['measure beam tilt'], (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE)
label = wx.StaticText(self, -1, 'Defocus')
szresult.Add(label, (1, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szresult.Add(self.labels['defocus'], (1, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL)
label = wx.StaticText(self, -1, 'Stig. x')
szresult.Add(label, (2, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szresult.Add(self.labels['stigmator']['x'], (2, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL)
label = wx.StaticText(self, -1, 'Stig. y')
szresult.Add(label, (3, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szresult.Add(self.labels['stigmator']['y'], (3, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL)
szresult.AddGrowableRow(0)
szresult.AddGrowableRow(1)
szresult.AddGrowableRow(2)
szresult.AddGrowableRow(3)
szresult.AddGrowableCol(0)
self.measure = wx.Button(self, -1, 'Measure')
self.correctdefocus = wx.Button(self, -1, 'Correct Defocus')
self.correctstig = wx.Button(self, -1, 'Correct Stig.')
self.resetdefocus = wx.Button(self, -1, 'Reset Defocus')
self.correctdefocus.Enable(False)
self.correctstig.Enable(False)
szbutton = wx.GridBagSizer(5, 5)
szbutton.Add(self.measure, (0, 0), (1, 1), wx.EXPAND)
szbutton.Add(self.correctdefocus, (1, 0), (1, 1), wx.EXPAND)
szbutton.Add(self.correctstig, (2, 0), (1, 1), wx.EXPAND)
szbutton.Add(self.resetdefocus, (3, 0), (1, 1), wx.EXPAND)
sz = wx.GridBagSizer(5, 20)
sz.Add(szresult, (0, 0), (1, 1), wx.ALIGN_CENTER)
sz.Add(szbutton, (0, 1), (1, 1), wx.ALIGN_CENTER)
sbsz.Add(sz, 0, wx.ALIGN_CENTER | wx.ALL, 5)
self.Bind(wx.EVT_BUTTON, self.onMeasureButton, self.measure)
self.Bind(wx.EVT_BUTTON, self.onCorrectDefocusButton,
self.correctdefocus)
self.Bind(wx.EVT_BUTTON, self.onCorrectStigButton, self.correctstig)
self.Bind(wx.EVT_BUTTON, self.onResetDefocusButton, self.resetdefocus)
return [sbsz]
