class Dialog(wx.Dialog): def __init__(self, parent, title, target=None, targetname='Relative target'): wx.Dialog.__init__(self, parent, -1, title) sbsztarget = wx.StaticBoxSizer(wx.StaticBox(self, -1, 'Target'), wx.VERTICAL) self.targetname = targetname self.iex = IntEntry(self, -1, chars=4) self.iey = IntEntry(self, -1, chars=4) if target is not None: if not parent.validate(target): raise ValueError x, y = target self.iex.SetValue(x) self.iey.SetValue(y) sztarget = wx.GridBagSizer(5, 5) label = wx.StaticText(self, -1, 'x') sztarget.Add(label, (0, 1), (1, 1), wx.ALIGN_CENTER) label = wx.StaticText(self, -1, 'y') sztarget.Add(label, (0, 2), (1, 1), wx.ALIGN_CENTER) label = wx.StaticText(self, -1, self.targetname) sztarget.Add(label, (1, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL) sztarget.Add(self.iex, (1, 1), (1, 1), wx.ALIGN_CENTER|wx.FIXED_MINSIZE) sztarget.Add(self.iey, (1, 2), (1, 1), wx.ALIGN_CENTER|wx.FIXED_MINSIZE) label = wx.StaticText(self, -1, 'pixels') sztarget.Add(label, (1, 3), (1, 1), wx.ALIGN_CENTER_VERTICAL) sbsztarget.Add(sztarget, 1, wx.EXPAND|wx.ALL, 5) self.bok = wx.Button(self, wx.ID_OK, 'OK') self.bcancel = wx.Button(self, wx.ID_CANCEL, 'Cancel') szbutton = wx.GridBagSizer(5, 5) szbutton.Add(self.bok, (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(sbsztarget, (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.onOK, self.bok) def onOK(self, evt): target = (self.iex.GetValue(), self.iey.GetValue()) if not self.GetParent().validate(target): dialog = wx.MessageDialog(self, 'Invalid target dimensions', 'Error', wx.OK|wx.ICON_ERROR) dialog.ShowModal() dialog.Destroy() else: self.target = target evt.Skip()
class Dialog(wx.Dialog):
def __init__(self, parent, title, ring=None):
wx.Dialog.__init__(self, parent, -1, title)
sbszring = wx.StaticBoxSizer(wx.StaticBox(self, -1, 'Ring'),
wx.VERTICAL)
self.ieinside = IntEntry(self, -1, min=0, chars=4)
self.ieoutside = IntEntry(self, -1, min=0, chars=4)
if ring is not None:
if not parent.validate(ring):
raise ValueError
inside, outside = ring
self.ieinside.SetValue(inside)
self.ieoutside.SetValue(outside)
szring = wx.GridBagSizer(5, 5)
label = wx.StaticText(self, -1, 'Inside')
szring.Add(label, (0, 1), (1, 1), wx.ALIGN_CENTER)
label = wx.StaticText(self, -1, 'Outside')
szring.Add(label, (0, 2), (1, 1), wx.ALIGN_CENTER)
label = wx.StaticText(self, -1, 'Diameter')
szring.Add(label, (1, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szring.Add(self.ieinside, (1, 1), (1, 1),
wx.ALIGN_CENTER | wx.FIXED_MINSIZE)
szring.Add(self.ieoutside, (1, 2), (1, 1),
wx.ALIGN_CENTER | wx.FIXED_MINSIZE)
label = wx.StaticText(self, -1, 'pixels')
szring.Add(label, (1, 3), (1, 1), wx.ALIGN_CENTER_VERTICAL)
sbszring.Add(szring, 1, wx.EXPAND | wx.ALL, 5)
self.bok = wx.Button(self, wx.ID_OK, 'OK')
self.bcancel = wx.Button(self, wx.ID_CANCEL, 'Cancel')
szbutton = wx.GridBagSizer(5, 5)
szbutton.Add(self.bok, (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(sbszring, (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.onOK, self.bok)
def onOK(self, evt):
ring = (self.ieinside.GetValue(), self.ieoutside.GetValue())
if not self.GetParent().validate(ring):
dialog = wx.MessageDialog(self, 'Invalid ring dimensions', 'Error',
wx.OK | wx.ICON_ERROR)
dialog.ShowModal()
dialog.Destroy()
else:
self.ring = ring
evt.Skip()
class ReproTestDialog(wx.Dialog):
def __init__(self, parent):
self.node = parent.node
wx.Dialog.__init__(self, parent, -1, 'Test Reproducibiltiy')
self.measure = wx.Button(self, -1, 'Run')
self.Bind(wx.EVT_BUTTON, self.onMeasureButton, self.measure)
szbutton = wx.GridBagSizer(5, 5)
szbutton.Add(self.measure, (0, 0), (1, 1), wx.EXPAND)
sbsz = wx.GridBagSizer(5, 5)
label = wx.StaticText(self, -1, 'Label:')
self.labvalue = Entry(self, -1, chars=20, value='test1')
sbsz.Add(label, (0, 0), (1, 1))
sbsz.Add(self.labvalue, (0, 1), (1, 1))
label = wx.StaticText(self, -1, 'Moves:')
self.movesvalue = IntEntry(self,
-1,
allownone=False,
chars=5,
value='10')
sbsz.Add(label, (1, 0), (1, 1))
sbsz.Add(self.movesvalue, (1, 1), (1, 1))
label = wx.StaticText(self, -1, 'Distance:')
self.distvalue = FloatEntry(self,
-1,
allownone=False,
chars=5,
value='1e-5')
sbsz.Add(label, (2, 0), (1, 1))
sbsz.Add(self.distvalue, (2, 1), (1, 1))
label = wx.StaticText(self, -1, 'Angle:')
self.angvalue = FloatEntry(self, -1, allownone=True, chars=5, value='')
sbsz.Add(label, (3, 0), (1, 1))
sbsz.Add(self.angvalue, (3, 1), (1, 1))
self.sizer = wx.GridBagSizer(5, 5)
self.sizer.Add(sbsz, (0, 0), (1, 1), wx.EXPAND | wx.ALL, 10)
self.sizer.Add(self.measure, (1, 0), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_RIGHT | wx.ALL, 10)
self.SetSizerAndFit(self.sizer)
def onMeasureButton(self, evt):
self.Close()
label = self.labvalue.GetValue()
moves = self.movesvalue.GetValue()
distance = self.distvalue.GetValue()
angle = self.angvalue.GetValue()
threading.Thread(target=self.node.move_away_move_back,
args=(label, moves, distance, angle)).start()
class C2SizeDialog(leginon.gui.wx.Dialog.Dialog): def __init__(self, parent, title): self.node = parent.node leginon.gui.wx.Dialog.Dialog.__init__(self, parent, title, style=wx.DEFAULT_DIALOG_STYLE) def onInitialize(self): c2sizer = wx.GridBagSizer(5, 5) label = wx.StaticText(self, -1, 'C2 size: ') c2sizer.Add(label, (0, 0), (1, 1), wx.ALIGN_LEFT) self.c2sizectrl = IntEntry(self, -1, chars=6) c2sizer.Add(self.c2sizectrl, (0, 1), (1, 1), wx.ALIGN_RIGHT) label = wx.StaticText(self, -1, 'um') c2sizer.Add(label, (0, 2), (1, 1), wx.ALIGN_LEFT) self.sz.Add(c2sizer, (0, 0), (1, 1), wx.EXPAND|wx.ALL,10) savebtn = wx.Button(self, -1, 'Save') self.sz.Add(savebtn, (1, 0), (1, 1), wx.EXPAND|wx.ALL,5) self.sz.AddGrowableCol(0) self.Bind(wx.EVT_BUTTON, self.onSave, savebtn) def onSave(self,evt): args = (self.c2sizectrl.GetValue(),) threading.Thread(target=self.node.uiSetC2Size,args=args).start()
class CustomDialog(wx.Dialog):
def __init__(self, parent, geometry):
wx.Dialog.__init__(self, parent, -1, 'Custom')
sb = wx.StaticBox(self, -1, 'Camera Configuration')
self.sbsz = wx.StaticBoxSizer(sb, wx.VERTICAL)
stx = wx.StaticText(self, -1, 'x')
sty = wx.StaticText(self, -1, 'y')
stdimension = wx.StaticText(self, -1, 'Dimension:')
self.iexdimension = IntEntry(self,
-1,
min=1,
max=parent.size['x'],
chars=len(str(parent.size['x'])))
self.ieydimension = IntEntry(self,
-1,
min=1,
max=parent.size['y'],
chars=len(str(parent.size['y'])))
stbinning = wx.StaticText(self, -1, 'Binning:')
self.cxbinning = wx.Choice(self,
-1,
choices=map(str, parent.binnings['x']))
self.cybinning = wx.Choice(self,
-1,
choices=map(str, parent.binnings['y']))
stoffset = wx.StaticText(self, -1, 'Offset:')
self.iexoffset = IntEntry(self,
-1,
min=0,
max=parent.size['x'],
chars=len(str(parent.size['x'])))
self.ieyoffset = IntEntry(self,
-1,
min=0,
max=parent.size['y'],
chars=len(str(parent.size['y'])))
self.szxy = wx.GridBagSizer(5, 5)
self.szxy.Add(stx, (0, 1), (1, 1), wx.ALIGN_CENTER)
self.szxy.Add(sty, (0, 2), (1, 1), wx.ALIGN_CENTER)
self.szxy.Add(stdimension, (1, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
self.szxy.Add(self.iexdimension, (1, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE | wx.ALL)
self.szxy.Add(self.ieydimension, (1, 2), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE | wx.ALL)
self.szxy.Add(stbinning, (2, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
self.szxy.Add(self.cxbinning, (2, 1), (1, 1), wx.ALIGN_CENTER | wx.ALL)
self.szxy.Add(self.cybinning, (2, 2), (1, 1), wx.ALIGN_CENTER | wx.ALL)
self.szxy.Add(stoffset, (3, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
self.szxy.Add(self.iexoffset, (3, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE | wx.ALL)
self.szxy.Add(self.ieyoffset, (3, 2), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE | wx.ALL)
bok = wx.Button(self, wx.ID_OK, 'OK')
bcancel = wx.Button(self, wx.ID_CANCEL, 'Cancel')
szbutton = wx.GridBagSizer(5, 5)
szbutton.Add(bok, (0, 0), (1, 1), wx.ALIGN_CENTER)
szbutton.Add(bcancel, (0, 1), (1, 1), wx.ALIGN_CENTER)
self.sbsz.Add(self.szxy, 0, wx.ALIGN_CENTER)
sz = wx.GridBagSizer(5, 5)
sz.Add(self.sbsz, (0, 0), (1, 1), wx.ALIGN_CENTER | wx.ALL, border=5)
sz.Add(szbutton, (1, 0), (1, 1), wx.ALIGN_RIGHT | wx.ALL, border=5)
if geometry is not None:
self.iexdimension.SetValue(int(geometry['dimension']['x']))
self.ieydimension.SetValue(int(geometry['dimension']['y']))
self.cxbinning.SetStringSelection(str(geometry['binning']['x']))
self.cybinning.SetStringSelection(str(geometry['binning']['y']))
self.iexoffset.SetValue(int(geometry['offset']['x']))
self.ieyoffset.SetValue(int(geometry['offset']['y']))
self.SetSizerAndFit(sz)
self.Bind(wx.EVT_BUTTON, self.onOK, bok)
def getGeometry(self):
geometry = {'dimension': {}, 'binning': {}, 'offset': {}}
geometry['dimension']['x'] = self.iexdimension.GetValue()
geometry['dimension']['y'] = self.ieydimension.GetValue()
geometry['binning']['x'] = int(self.cxbinning.GetStringSelection())
geometry['binning']['y'] = int(self.cybinning.GetStringSelection())
geometry['offset']['x'] = self.iexoffset.GetValue()
geometry['offset']['y'] = self.ieyoffset.GetValue()
return geometry
def onOK(self, evt):
geometry = self.getGeometry()
if geometry is not None and self.GetParent().validateGeometry(
geometry):
evt.Skip()
else:
dialog = wx.MessageDialog(self, 'Invalid camera geometry', 'Error',
wx.OK | wx.ICON_ERROR)
dialog.ShowModal()
dialog.Destroy()
class CameraPanel(wx.Panel):
def __init__(self, parent):
wx.Panel.__init__(self, parent, -1)
sb = wx.StaticBox(self, -1, 'Camera Configuration')
self.sbsz = wx.StaticBoxSizer(sb, wx.VERTICAL)
self.size = None
self.binmethod = 'exact'
self.geometry = None
self.binnings = {'x': [1, 2, 3, 4, 6, 8], 'y': [1, 2, 3, 4, 6, 8]}
self.defaultexptime = 1000.0
self.defaultsaveframes = False
self.defaultframetime = 200
self.defaultalignframes = False
self.defaultalignfilter = 'None'
self.defaultuseframes = ''
self.defaultreadoutdelay = 0
self.common = {}
self.setfuncs = {
'exposure time': self._setExposureTime,
'save frames': self._setSaveFrames,
'frame time': self._setFrameTime,
'align frames': self._setAlignFrames,
'align filter': self._setAlignFilter,
'use frames': self._setUseFrames,
'readout delay': self._setReadoutDelay,
}
self.getfuncs = {
'exposure time': self._getExposureTime,
'save frames': self._getSaveFrames,
'frame time': self._getFrameTime,
'align frames': self._getAlignFrames,
'align filter': self._getAlignFilter,
'use frames': self._getUseFrames,
'readout delay': self._getReadoutDelay,
}
# geometry
self.ccommon = wx.Choice(self, -1, choices=['(None)'])
self.ccommon.SetSelection(0)
bcustom = wx.Button(self, -1, 'Custom...')
std = wx.StaticText(self, -1, 'Dimension:')
self.stdimension = wx.StaticText(self, -1, '')
sto = wx.StaticText(self, -1, 'Offset:')
self.stoffset = wx.StaticText(self, -1, '')
stb = wx.StaticText(self, -1, 'Binning:')
self.stbinning = wx.StaticText(self, -1, '')
self.szmain = wx.GridBagSizer(3, 3)
sz = wx.GridBagSizer(5, 5)
sz.Add(self.ccommon, (0, 0), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_RIGHT)
sz.Add(bcustom, (0, 1), (1, 1), wx.ALIGN_CENTER_VERTICAL)
sz.AddGrowableRow(0)
sz.AddGrowableCol(0)
sz.AddGrowableCol(1)
self.szmain.Add(sz, (0, 0), (1, 2), wx.EXPAND)
self.szmain.Add(std, (1, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
self.szmain.Add(self.stdimension, (1, 1), (1, 1), wx.ALIGN_CENTER)
self.szmain.Add(sto, (2, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
self.szmain.Add(self.stoffset, (2, 1), (1, 1), wx.ALIGN_CENTER)
self.szmain.Add(stb, (3, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
self.szmain.Add(self.stbinning, (3, 1), (1, 1), wx.ALIGN_CENTER)
# exposure time
stet = wx.StaticText(self, -1, 'Exposure time:')
self.feexposuretime = FloatEntry(self, -1, min=0.0, chars=7)
stms = wx.StaticText(self, -1, 'ms')
self.szmain.Add(stet, (4, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
sz = wx.GridBagSizer(0, 3)
sz.Add(self.feexposuretime, (0, 0), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE)
sz.Add(stms, (0, 1), (1, 1), wx.ALIGN_CENTER_VERTICAL)
self.szmain.Add(sz, (4, 1), (1, 2), wx.ALIGN_CENTER | wx.EXPAND)
sb = wx.StaticBox(self, -1, 'Camera with Movie Mode')
ddsb = wx.StaticBoxSizer(sb, wx.VERTICAL)
ddsz = wx.GridBagSizer(5, 5)
# save frames
self.saveframes = wx.CheckBox(self, -1, 'Save frames')
ddsz.Add(self.saveframes, (0, 0), (1, 2), wx.ALIGN_CENTER | wx.EXPAND)
# frame time
stet = wx.StaticText(self, -1, 'Exposure time per Frame:')
self.frametime = FloatEntry(self, -1, min=0.01, chars=7)
stms = wx.StaticText(self, -1, 'ms')
ddsz.Add(stet, (1, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
ftsz = wx.GridBagSizer(0, 3)
ftsz.Add(self.frametime, (0, 0), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE)
ftsz.Add(stms, (0, 1), (1, 1), wx.ALIGN_CENTER_VERTICAL)
ddsz.Add(ftsz, (1, 1), (1, 2), wx.ALIGN_CENTER | wx.EXPAND)
# use raw frames
label = wx.StaticText(self, -1, 'Frames to use:')
self.useframes = Entry(self, -1)
ddsz.Add(label, (2, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
ddsz.Add(self.useframes, (2, 1), (1, 1), wx.ALIGN_CENTER | wx.EXPAND)
# readout delay
strd = wx.StaticText(self, -1, 'Readout delay:')
self.readoutdelay = IntEntry(self, -1, chars=7)
stms = wx.StaticText(self, -1, 'ms')
sz = wx.BoxSizer(wx.HORIZONTAL)
sz.Add(strd)
sz.Add(self.readoutdelay)
sz.Add(stms)
ddsz.Add(sz, (3, 0), (1, 2), wx.ALIGN_CENTER | wx.EXPAND)
# align frames box
sb = wx.StaticBox(self, -1, 'Frame-Aligning Camera Only')
afsb = wx.StaticBoxSizer(sb, wx.VERTICAL)
afsz = wx.GridBagSizer(3, 3)
# align frames
self.alignframes = wx.CheckBox(self, -1, 'Align frames')
afsz.Add(self.alignframes, (0, 0), (1, 2), wx.ALIGN_CENTER | wx.EXPAND)
# align frame filter
label = wx.StaticText(self, -1, 'c-correlation filter:')
self.alignfilter = wx.Choice(self, -1, choices=self.getAlignFilters())
self.alignfilter.SetSelection(0)
afsz.Add(label, (1, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
afsz.Add(self.alignfilter, (1, 1), (1, 1), wx.ALIGN_CENTER | wx.EXPAND)
afsb.Add(afsz, 0, wx.EXPAND | wx.ALL, 2)
ddsz.Add(afsb, (4, 0), (3, 2), wx.ALIGN_CENTER | wx.EXPAND)
ddsb.Add(ddsz, 0, wx.EXPAND | wx.ALL, 2)
self.szmain.Add(ddsb, (7, 0), (1, 3), wx.ALIGN_CENTER | wx.EXPAND)
ddsz.AddGrowableCol(1)
self.szmain.AddGrowableCol(1)
self.szmain.AddGrowableCol(2)
self.sbsz.Add(self.szmain, 0, wx.EXPAND | wx.ALL, 2)
self.SetSizerAndFit(self.sbsz)
self.Bind(wx.EVT_CHOICE, self.onCommonChoice, self.ccommon)
self.Bind(wx.EVT_BUTTON, self.onCustomButton, bcustom)
self.Bind(EVT_ENTRY, self.onExposureTime, self.feexposuretime)
self.Bind(wx.EVT_CHECKBOX, self.onSaveFrames, self.saveframes)
self.Bind(EVT_ENTRY, self.onFrameTime, self.frametime)
self.Bind(EVT_ENTRY, self.onUseFrames, self.useframes)
self.Bind(EVT_ENTRY, self.onReadoutDelay, self.readoutdelay)
self.Bind(EVT_SET_CONFIGURATION, self.onSetConfiguration)
#self.Enable(False)
def setGeometryLimits(self, limitdict):
if limitdict is None:
self.setSize(None)
if 'binnings' in limitdict.keys():
self.binnings['x'] = limitdict['binnings']
self.binnings['y'] = limitdict['binnings']
if 'binmethod' in limitdict.keys():
self.binmethod = limitdict['binmethod']
if 'size' in limitdict.keys():
self.setSize(limitdict['size'])
else:
self.setSize(None)
def setSize(self, size):
if size is None:
self.size = None
self.Freeze()
self.choices, self.common = None, None
self.ccommon.Clear()
self.ccommon.Append('(None)')
self.szmain.Layout()
#self.Enable(False)
self.Thaw()
else:
self.size = dict(size)
self.Freeze()
self.choices, self.common = self.getCenteredGeometries()
self.ccommon.Clear()
self.ccommon.AppendItems(self.choices)
if self.geometry is None or not self.validateGeometry():
self.ccommon.SetSelection(len(self.choices) - 1)
self.setGeometry(
self.common[self.ccommon.GetStringSelection()])
else:
self.setCommonChoice()
if self.feexposuretime.GetValue() is None:
self.feexposuretime.SetValue(self.defaultexptime)
#self.Enable(True)
self.szmain.Layout()
self.Thaw()
def clear(self):
if self.size is None:
return
self.Freeze()
self.ccommon.SetSelection(len(self.choices) - 1)
self.setGeometry(self.common[self.ccommon.GetStringSelection()])
self.feexposuretime.SetValue(self.defaultexptime)
self.saveframes.SetValue(self.defaultsaveframes)
self.frametime.SetValue(self.defaultframetime)
self.alignframes.SetValue(self.defaultalignframes)
self.alignfilter.SetValue(self.defaultalignfilter)
self.useframes.SetValue(self.defaultuseframes)
self.readoutdelay.SetValue(self.defaultreadoutdelay)
#self.Enable(False)
self.Thaw()
def onConfigurationChanged(self):
evt = ConfigurationChangedEvent(self.getConfiguration(), self)
self.GetEventHandler().AddPendingEvent(evt)
def onExposureTime(self, evt):
self.onConfigurationChanged()
def onSaveFrames(self, evt):
self.onConfigurationChanged()
def onFrameTime(self, evt):
self.onConfigurationChanged()
def onUseFrames(self, evt):
self.onConfigurationChanged()
def onReadoutDelay(self, evt):
self.onConfigurationChanged()
def setCommonChoice(self):
for key, geometry in self.common.items():
flag = True
for i in ['dimension', 'offset', 'binning']:
if self.geometry[i] != geometry[i]:
flag = False
break
if flag:
self.ccommon.SetStringSelection(key)
return
if self.ccommon.FindString('(Custom)') is wx.NOT_FOUND:
self.ccommon.Insert('(Custom)', 0)
self.ccommon.SetSelection(0)
def _getDimension(self):
return self.geometry['dimension']
def _setDimension(self, value):
self.geometry['dimension'] = value
self.setCommonChoice()
def _getOffset(self):
return self.geometry['offset']
def _setOffset(self, value):
self.geometry['offset'] = value
self.setCommonChoice()
def _getBinning(self):
return self.geometry['binning']
def _setBinning(self, value):
self.geometry['binning'] = value
self.setCommonChoice()
def _getExposureTime(self):
return self.feexposuretime.GetValue()
def _setExposureTime(self, value):
self.feexposuretime.SetValue(value)
def _getSaveFrames(self):
return self.saveframes.GetValue()
def _setSaveFrames(self, value):
value = bool(value)
self.saveframes.SetValue(value)
def _getFrameTime(self):
return self.frametime.GetValue()
def _setFrameTime(self, value):
self.frametime.SetValue(value)
def _getAlignFrames(self):
return self.alignframes.GetValue()
def _setAlignFrames(self, value):
value = bool(value)
self.alignframes.SetValue(value)
def getAlignFilters(self):
return [
'None', 'Hanning Window (default)', 'Bandpass Filter (default)',
'Sobel Filter (default)', 'Combined Filter (default)'
]
def _getAlignFilter(self):
return self.alignfilter.GetStringSelection()
def _setAlignFilter(self, value):
if value:
value = str(value)
else:
value = 'None'
self.alignfilter.SetStringSelection(value)
def _getUseFrames(self):
frames_str = self.useframes.GetValue()
numbers = re.split('\D+', frames_str)
numbers = filter(None, numbers)
if numbers:
numbers = map(int, numbers)
numbers = tuple(numbers)
else:
numbers = ()
return numbers
def _setUseFrames(self, value):
if value:
value = str(value)
else:
value = ''
self.useframes.SetValue(value)
def _getReadoutDelay(self):
return self.readoutdelay.GetValue()
def _setReadoutDelay(self, value):
return self.readoutdelay.SetValue(value)
def onCommonChoice(self, evt):
key = evt.GetString()
if key == '(Custom)' or key.startswith('-'):
return
if self.setGeometry(self.common[key]):
self.onConfigurationChanged()
n = self.ccommon.FindString('(Custom)')
if n is not wx.NOT_FOUND:
self.ccommon.Delete(n)
def onCustomButton(self, evt):
dialog = CustomDialog(self, self.getGeometry())
if dialog.ShowModal() == wx.ID_OK:
if self.setGeometry(dialog.getGeometry()):
self.onConfigurationChanged()
self.setCommonChoice()
dialog.Destroy()
def getCenteredGeometry(self, dimension, binning):
offset = {}
for axis in ['x', 'y']:
offset[axis] = int((self.size[axis] / binning - dimension) / 2)
geometry = {
'dimension': {
'x': dimension,
'y': dimension
},
'offset': {
'x': offset['x'],
'y': offset['y']
},
'binning': {
'x': binning,
'y': binning
}
}
return geometry
def getFullGeometry(self, binning):
if self.binmethod == 'exact' and ((self.size['x'] % binning) or
(self.size['y'] % binning)):
return None
dimx = self.size['x'] / binning
dimy = self.size['y'] / binning
geometry = {
'dimension': {
'x': dimx,
'y': dimy
},
'offset': {
'x': 0,
'y': 0
},
'binning': {
'x': binning,
'y': binning
}
}
return geometry
def getCenteredGeometries(self):
geometries = {}
keys = []
show_sections = False
if self.size['x'] != self.size['y']:
show_sections = True
keys.append('--- Full ---')
for binning in self.binnings['x']:
dimx = self.size['x'] / binning
dimy = self.size['y'] / binning
key = '%d x %d bin %d' % (dimx, dimy, binning)
geo = self.getFullGeometry(binning)
if geo is not None:
geometries[key] = geo
keys.append(key)
if self.binnings['x'] != self.binnings['y']:
return geometries
self.minsize = min(self.size['x'], self.size['y'])
dimensions = [int(self.minsize / float(b)) for b in self.binnings['x']]
def good(dim):
return not bool(numpy.modf(dim)[1] - dim)
def filtergood(input, mask):
result = []
for i, inval in enumerate(input):
if mask[i]:
result.append(inval)
return result
if self.binmethod == 'exact':
mask = [good(dim) for dim in dimensions]
else:
mask = [True for dim in dimensions]
dimensions = filtergood(dimensions, mask)
def minsize(size):
return size >= self.minsize / max(self.binnings['x'])
dimensions = filter(minsize, dimensions)
dimensions = map((lambda x: primefactor.getAllEvenPrimes(x)[-1]),
dimensions)
binnings = filtergood(self.binnings['x'], mask)
dimensions.reverse()
if show_sections:
keys.append('--- Center ---')
for d in dimensions:
for b in self.binnings['x']:
if d * b <= self.minsize:
key = '%d x %d bin %d' % (d, d, b)
geometries[key] = self.getCenteredGeometry(d, b)
keys.append(key)
else:
break
return keys, geometries
def validateGeometry(self, geometry=None):
if geometry is None:
geometry = self.geometry
for a in ['x', 'y']:
try:
if geometry['dimension'][a] < 1 or geometry['offset'][a] < 0:
return False
if geometry['binning'][a] not in self.binnings[a]:
return False
size = geometry['dimension'][a] + geometry['offset'][a]
size *= geometry['binning'][a]
if size > self.size[a]:
return False
except:
return False
return True
def cmpGeometry(self, geometry):
if self.geometry == geometry:
return True
for g in ['dimension', 'offset', 'binning']:
try:
for a in ['x', 'y']:
if self.geometry[g][a] != geometry[g][a]:
return False
except (KeyError, TypeError):
return False
return True
def setGeometry(self, geometry):
if self.cmpGeometry(geometry):
return False
if self.size is not None and not self.validateGeometry(geometry):
raise ValueError
self._setGeometry(geometry)
return True
def getGeometry(self):
return self.geometry
def getConfiguration(self):
g = self.getGeometry()
if g is None:
return None
c = copy.deepcopy(g)
for key, func in self.getfuncs.items():
c[key] = func()
return c
def _setGeometry(self, geometry):
if self.geometry is None:
self.geometry = {}
else:
self.geometry = copy.deepcopy(self.geometry)
self.Freeze()
for g in ['dimension', 'offset', 'binning']:
if g not in self.geometry:
self.geometry[g] = {}
try:
self.geometry[g].update(dict(geometry[g]))
if g == 'offset':
label = '(%d, %d)'
else:
#label = '%d × %d'
label = '%d x %d'
label = label % (self.geometry[g]['x'], self.geometry[g]['y'])
getattr(self, 'st' + g).SetLabel(label)
except:
pass
self.szmain.Layout()
self.Thaw()
return True
def _setConfiguration(self, value):
for key, func in self.setfuncs.items():
if key in value:
func(value[key])
self._setGeometry(value)
self.setCommonChoice()
def setConfiguration(self, value):
for key, func in self.setfuncs.items():
if key in value:
func(value[key])
self.setGeometry(value)
if self.size is not None:
self.setCommonChoice()
#if not self.IsEnabled():
# self.Enable(True)
def onSetConfiguration(self, evt):
self.setConfiguration(evt.configuration)
class AutoFillTargets(wx.Dialog):
def __init__(self, parent, title, targetname='Relative target'):
wx.Dialog.__init__(self, parent, -1, title)
self.targetname = targetname
self.numtargets = IntEntry(self, -1, chars=4, value='1')
self.radius = IntEntry(self, -1, chars=4, value='100')
self.angleoffset = IntEntry(self, -1, chars=4, value='0')
self.targets = []
valueentry = wx.GridBagSizer(5, 5)
label = wx.StaticText(self, -1, 'number of targets')
valueentry.Add(label, (0, 0), (1, 1), wx.ALIGN_LEFT | wx.ALL, 3)
valueentry.Add(self.numtargets, (0, 1), (1, 1),
wx.ALIGN_CENTER | wx.FIXED_MINSIZE | wx.ALL, 3)
label = wx.StaticText(self, -1, 'radius (pixels)')
valueentry.Add(label, (1, 0), (1, 1), wx.ALIGN_LEFT | wx.ALL, 3)
valueentry.Add(self.radius, (1, 1), (1, 1),
wx.ALIGN_CENTER | wx.FIXED_MINSIZE | wx.ALL, 3)
label = wx.StaticText(self, -1, 'angle offset (degrees)')
valueentry.Add(label, (2, 0), (1, 1), wx.ALIGN_LEFT | wx.ALL, 3)
valueentry.Add(self.angleoffset, (2, 1), (1, 1),
wx.ALIGN_CENTER | wx.FIXED_MINSIZE | wx.ALL, 3)
self.bok = wx.Button(self, wx.ID_OK, 'OK')
self.Bind(wx.EVT_BUTTON, self.onOK, self.bok)
self.bcancel = wx.Button(self, wx.ID_CANCEL, 'Cancel')
szbutton = wx.GridBagSizer(5, 5)
szbutton.Add(self.bok, (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(valueentry, (0, 0), (1, 1), wx.EXPAND | wx.ALL, 10)
sz.Add(szbutton, (1, 0), (1, 1), wx.EXPAND | wx.ALL, 10)
self.SetSizerAndFit(sz)
def onOK(self, evt):
numtargets = float(self.numtargets.GetValue())
if numtargets > 7:
self.Close()
dialog = wx.MessageDialog(
self, "Too many targets:\n'%d' is greater than 7" % numtargets,
'Error', wx.OK | wx.ICON_ERROR)
dialog.ShowModal()
dialog.Destroy()
evt.Skip()
return
radius = float(self.radius.GetValue())
degoffset = float(self.angleoffset.GetValue())
deg = 0.0
degincr = 360.0 / numtargets
while (deg < 359.9):
rad = (deg + degoffset) * math.pi / 180.0
x = int(math.cos(rad) * radius)
y = int(math.sin(rad) * radius)
target = (x, y)
if not self.GetParent().validate(target):
dialog = wx.MessageDialog(
self, 'Invalid target dimensions (%d,%d)' % x, y, 'Error',
wx.OK | wx.ICON_ERROR)
dialog.ShowModal()
dialog.Destroy()
self.targets.append(target)
deg += degincr
evt.Skip()
return
class FitThetaDialog(wx.Dialog):
#==================
def __init__(self, parent):
self.parent = parent
self.theta = self.parent.data['theta']
wx.Dialog.__init__(self, self.parent.frame, -1,
"Measure Tilt Angle, Theta")
inforow = wx.FlexGridSizer(3, 3, 15, 15)
thetastr = ("****** %3.3f ******" % self.theta)
label = wx.StaticText(self,
-1,
"Current tilt angle: ",
style=wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
self.tiltvalue = wx.StaticText(self,
-1,
thetastr,
style=wx.ALIGN_CENTER
| wx.ALIGN_CENTER_VERTICAL)
#self.tiltvalue = FloatEntry(self, -1, allownone=True, chars=5, value=thetastr)
label3 = wx.StaticText(self,
-1,
"degrees",
style=wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
inforow.Add(label, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
inforow.Add(
self.tiltvalue, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL | wx.ALL, 3)
inforow.Add(label3, 0,
wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL | wx.ALL, 3)
arealimstr = str(int(self.parent.data['arealim']))
label = wx.StaticText(self,
-1,
"Minimum Triangle Area: ",
style=wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
self.arealimit = IntEntry(self,
-1,
allownone=False,
chars=8,
value=arealimstr)
label2 = wx.StaticText(self,
-1,
"square pixels",
style=wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
inforow.Add(label, 0, wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
inforow.Add(
self.arealimit, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL | wx.ALL, 3)
inforow.Add(label2, 0,
wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL | wx.ALL, 3)
label = wx.StaticText(self,
-1,
"Triangles Used: ",
style=wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL)
self.trilabel1 = wx.StaticText(self,
-1,
" ",
style=wx.ALIGN_LEFT
| wx.ALIGN_CENTER_VERTICAL)
self.trilabel2 = wx.StaticText(self,
-1,
" ",
style=wx.ALIGN_LEFT
| wx.ALIGN_CENTER_VERTICAL)
inforow.Add(label, 0,
wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL | wx.ALL, 3)
inforow.Add(self.trilabel1, 0,
wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL | wx.ALL, 3)
inforow.Add(self.trilabel2, 0,
wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL | wx.ALL, 3)
self.canceltiltang = wx.Button(self, wx.ID_CANCEL, '&Cancel')
self.applytiltang = wx.Button(self, wx.ID_APPLY, '&Apply')
self.runtiltang = wx.Button(self, -1, '&Run')
self.Bind(wx.EVT_BUTTON, self.onRunTiltAng, self.runtiltang)
self.Bind(wx.EVT_BUTTON, self.onApplyTiltAng, self.applytiltang)
buttonrow = wx.GridSizer(1, 3)
buttonrow.Add(self.canceltiltang, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL, 0)
buttonrow.Add(self.applytiltang, 0,
wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_CENTER_VERTICAL, 0)
buttonrow.Add(self.runtiltang, 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 onRunTiltAng(self, evt):
arealim = self.arealimit.GetValue()
self.parent.data['arealim'] = arealim
targets1 = self.parent.panel1.getTargets('Picked')
a1 = self.parent.targetsToArray(targets1)
targets2 = self.parent.panel2.getTargets('Picked')
a2 = self.parent.targetsToArray(targets2)
na1 = numpy.array(a1, dtype=numpy.int32)
na2 = numpy.array(a2, dtype=numpy.int32)
self.fittheta = radermacher.tiltang(na1, na2, arealim)
#pprint.pprint(self.fittheta)
if self.fittheta and 'wtheta' in self.fittheta:
self.fittheta['point1'], self.fittheta['point2'] = \
apTiltTransform.getPointsFromArrays(a1, a2, self.parent.data['shiftx'], self.parent.data['shifty'])
self.theta = self.fittheta['wtheta']
self.thetadev = self.fittheta['wthetadev']
thetastr = ("%3.3f +/- %2.2f" % (self.theta, self.thetadev))
self.tiltvalue.SetLabel(label=thetastr)
tristr = apDisplay.orderOfMag(
self.fittheta['numtri']) + " of " + apDisplay.orderOfMag(
self.fittheta['tottri'])
self.trilabel1.SetLabel(label=tristr)
percent = str("%")
tristr = (" (%3.1f " % (100.0 * self.fittheta['numtri'] /
float(self.fittheta['tottri']))) + "%) "
self.trilabel2.SetLabel(label=tristr)
#==================
def onApplyTiltAng(self, evt):
self.Close()
self.parent.data['theta'] = self.theta
self.parent.data['tiltanglefitdata'] = self.fittheta
self.parent.data['point1'] = self.fittheta['point1']
self.parent.data['point2'] = self.fittheta['point2']
self.parent.data['thetarun'] = True
self.parent.onUpdate(evt)
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
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 PixelToPixelDialog(leginon.gui.wx.Dialog.Dialog):
def __init__(self, parent, title):
self.node = parent.node
leginon.gui.wx.Dialog.Dialog.__init__(self,
parent,
title,
style=wx.DEFAULT_DIALOG_STYLE)
def onInitialize(self):
mag1lab = wx.StaticText(self, -1, 'Mag 1:')
self.mag1 = IntEntry(self, -1, chars=8)
mag2lab = wx.StaticText(self, -1, 'Mag 2:')
self.mag2 = IntEntry(self, -1, chars=8)
p1lab = wx.StaticText(self, -1, 'Pixel 1:')
self.p1row = FloatEntry(self, -1, chars=4)
self.p1col = FloatEntry(self, -1, chars=4)
p2lab = wx.StaticText(self, -1, 'Pixel 2:')
self.p2row = FloatEntry(self, -1, chars=4)
self.p2col = FloatEntry(self, -1, chars=4)
angle1lab = wx.StaticText(self, -1, 'Angle 1')
self.angle1 = wx.StaticText(self, -1, '')
len1lab = wx.StaticText(self, -1, 'Length 1')
self.len1 = wx.StaticText(self, -1, '')
angle2lab = wx.StaticText(self, -1, 'Angle 2')
self.angle2 = wx.StaticText(self, -1, '')
len2lab = wx.StaticText(self, -1, 'Length 2')
self.len2 = wx.StaticText(self, -1, '')
calcp1 = wx.Button(self, -1, 'Calculate')
self.Bind(wx.EVT_BUTTON, self.calcp1, calcp1)
calcp2 = wx.Button(self, -1, 'Calculate')
self.Bind(wx.EVT_BUTTON, self.calcp2, calcp2)
self.sz.Add(mag1lab, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
self.sz.Add(self.mag1, (0, 1), (1, 2), wx.ALIGN_CENTER_VERTICAL)
self.sz.Add(mag2lab, (0, 3), (1, 1), wx.ALIGN_CENTER_VERTICAL)
self.sz.Add(self.mag2, (0, 4), (1, 2), wx.ALIGN_CENTER_VERTICAL)
self.sz.Add(p1lab, (1, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
self.sz.Add(self.p1row, (1, 1), (1, 1), wx.ALIGN_CENTER_VERTICAL)
self.sz.Add(self.p1col, (1, 2), (1, 1), wx.ALIGN_CENTER_VERTICAL)
self.sz.Add(p2lab, (1, 3), (1, 1), wx.ALIGN_CENTER_VERTICAL)
self.sz.Add(self.p2row, (1, 4), (1, 1), wx.ALIGN_CENTER_VERTICAL)
self.sz.Add(self.p2col, (1, 5), (1, 1), wx.ALIGN_CENTER_VERTICAL)
self.sz.Add(angle1lab, (2, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
self.sz.Add(self.angle1, (2, 1), (1, 1), wx.ALIGN_CENTER_VERTICAL)
self.sz.Add(angle2lab, (2, 3), (1, 1), wx.ALIGN_CENTER_VERTICAL)
self.sz.Add(self.angle2, (2, 4), (1, 1), wx.ALIGN_CENTER_VERTICAL)
self.sz.Add(len1lab, (3, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
self.sz.Add(self.len1, (3, 1), (1, 1), wx.ALIGN_CENTER_VERTICAL)
self.sz.Add(len2lab, (3, 3), (1, 1), wx.ALIGN_CENTER_VERTICAL)
self.sz.Add(self.len2, (3, 4), (1, 1), wx.ALIGN_CENTER_VERTICAL)
self.sz.Add(calcp1, (4, 0), (1, 3), wx.ALIGN_CENTER_VERTICAL)
self.sz.Add(calcp2, (4, 3), (1, 3), wx.ALIGN_CENTER_VERTICAL)
def calcp1(self, evt):
p2row = self.p2row.GetValue()
p2col = self.p2col.GetValue()
mag1 = self.mag1.GetValue()
mag2 = self.mag2.GetValue()
p2 = p2row, p2col
p1 = self.node.pixelToPixel(mag2, mag1, p2)
self.p1row.SetValue(p1[0])
self.p1col.SetValue(p1[1])
a, n = self.angle_len(p1)
self.angle1.SetLabel(str(a))
self.len1.SetLabel(str(n))
def calcp2(self, evt):
p1row = self.p1row.GetValue()
p1col = self.p1col.GetValue()
mag1 = self.mag1.GetValue()
mag2 = self.mag2.GetValue()
p1 = p1row, p1col
p2 = self.node.pixelToPixel(mag1, mag2, p1)
self.p2row.SetValue(p2[0])
self.p2col.SetValue(p2[1])
a, n = self.angle_len(p2)
self.angle2.SetLabel(str(a))
self.len2.SetLabel(str(n))
def angle_len(self, vect):
angle = numpy.arctan2(*tuple(vect))
angle = math.degrees(angle)
len = numpy.hypot(*tuple(vect))
return angle, len
class MeasureTiltAxisDialog(wx.Dialog):
def __init__(self, parent):
self.node = parent.node
wx.Dialog.__init__(self, parent, -1, "Measure Stage Tilt Axis Location")
sb = wx.StaticBox(self, -1, 'Tilt Axis Params')
sbsz2 = wx.StaticBoxSizer(sb, wx.VERTICAL)
sbsz = wx.GridBagSizer(3,6)
row = int(0)
label = wx.StaticText(self, -1, "Tilt angle: ", style=wx.ALIGN_LEFT|wx.ALIGN_CENTER_VERTICAL)
self.tiltvalue = FloatEntry(self, -1, allownone=False, chars=5, value='15.0')
label2 = wx.StaticText(self, -1, " degrees", style=wx.ALIGN_LEFT|wx.ALIGN_CENTER_VERTICAL)
sbsz.Add(label, (row,0), (1,1), wx.ALIGN_LEFT|wx.ALIGN_CENTER_VERTICAL)
sbsz.Add(self.tiltvalue, (row,1), (1,1), wx.ALIGN_CENTER_HORIZONTAL|wx.ALIGN_CENTER_VERTICAL)
sbsz.Add(label2, (row,2), (1,1), wx.ALIGN_LEFT|wx.ALIGN_CENTER_VERTICAL)
row += 1
self.tilttwice = wx.CheckBox(self, -1, "Tilt both directions")
sbsz.Add(self.tilttwice, (row,0), (1,3), wx.ALIGN_LEFT|wx.ALIGN_CENTER_VERTICAL)
row += 1
label = wx.StaticText(self, -1, "Average ", style=wx.ALIGN_LEFT|wx.ALIGN_CENTER_VERTICAL)
label2 = wx.StaticText(self, -1, " tilts", style=wx.ALIGN_LEFT|wx.ALIGN_CENTER_VERTICAL)
self.numtilts = IntEntry(self, -1, allownone=False, chars=1, value='1')
sbsz.Add(label, (row,0), (1,1), wx.ALIGN_LEFT|wx.ALIGN_CENTER_VERTICAL)
sbsz.Add(self.numtilts, (row,1), (1,1), wx.ALIGN_CENTER_HORIZONTAL|wx.ALIGN_CENTER_VERTICAL)
sbsz.Add(label2, (row,2), (1,1), wx.ALIGN_LEFT|wx.ALIGN_CENTER_VERTICAL)
row += 1
label = wx.StaticText(self, -1, "SNR cutoff: ", style=wx.ALIGN_LEFT|wx.ALIGN_CENTER_VERTICAL)
self.snrvalue = FloatEntry(self, -1, allownone=False, chars=5, value='10.0')
label2 = wx.StaticText(self, -1, " levels")
sbsz.Add(label, (row,0), (1,1), wx.ALIGN_LEFT|wx.ALIGN_CENTER_VERTICAL)
sbsz.Add(self.snrvalue, (row,1), (1,1), wx.ALIGN_CENTER_HORIZONTAL|wx.ALIGN_CENTER_VERTICAL)
sbsz.Add(label2, (row,2), (1,1), wx.ALIGN_LEFT|wx.ALIGN_CENTER_VERTICAL)
row += 1
label = wx.StaticText(self, -1, "Correlation: ", style=wx.ALIGN_LEFT|wx.ALIGN_CENTER_VERTICAL)
self.phasecorr = wx.RadioButton(self, -1, "Phase", style=wx.RB_GROUP|wx.ALIGN_CENTER_HORIZONTAL|wx.ALIGN_CENTER_VERTICAL)
self.crosscorr = wx.RadioButton(self, -1, "Cross", style=wx.ALIGN_CENTER_HORIZONTAL|wx.ALIGN_CENTER_VERTICAL)
sbsz.Add(label, (row,0), (1,1))
sbsz.Add(self.phasecorr, (row,1), (1,1))
sbsz.Add(self.crosscorr, (row,2), (1,1))
row += 1
self.medfilt = wx.CheckBox(self, -1, "Median filter phase correlation")
self.medfilt.SetValue(True)
sbsz.Add(self.medfilt, (row,0), (1,3), wx.EXPAND|wx.ALIGN_LEFT|wx.ALIGN_CENTER_VERTICAL)
self.measurecancel = wx.Button(self, wx.ID_CANCEL, 'Cancel')
self.measureinit = wx.Button(self, -1, 'Initial\nOffset')
self.Bind(wx.EVT_BUTTON, self.onMeasureButtonInit, self.measureinit)
self.measureupdate = wx.Button(self, -1, 'Update\nOffset')
self.Bind(wx.EVT_BUTTON, self.onMeasureButtonUpdate, self.measureupdate)
sbsz2.Add(sbsz, 0, wx.EXPAND|wx.ALIGN_CENTER_HORIZONTAL|wx.ALIGN_CENTER_VERTICAL|wx.ALL, 1)
buttonrow = wx.GridSizer(1,3)
self.measurecancel.SetMinSize((85, 46))
self.measureinit.SetMinSize((85, 46))
self.measureupdate.SetMinSize((85, 46))
buttonrow.Add(self.measurecancel, 0, wx.ALIGN_CENTER_HORIZONTAL|wx.ALIGN_CENTER_VERTICAL, 0)
buttonrow.Add(self.measureinit, 0, wx.ALIGN_CENTER_HORIZONTAL|wx.ALIGN_CENTER_VERTICAL|wx.ADJUST_MINSIZE, 0)
buttonrow.Add(self.measureupdate, 0, wx.ALIGN_CENTER_HORIZONTAL|wx.ALIGN_CENTER_VERTICAL|wx.ADJUST_MINSIZE, 0)
self.sizer = wx.FlexGridSizer(3,1)
sbsz2.SetMinSize((270, 200))
self.sizer.Add(sbsz2, 0, wx.EXPAND|wx.ALIGN_CENTER_HORIZONTAL|wx.ALIGN_CENTER_VERTICAL|wx.ALL, 3)
#self.sizer.Add((10, 10), 0, wx.ALIGN_CENTER_HORIZONTAL|wx.ALIGN_CENTER_VERTICAL|wx.ADJUST_MINSIZE|wx.ALL, 3)
self.sizer.Add(buttonrow, 0, wx.EXPAND|wx.ALIGN_CENTER_HORIZONTAL|wx.ALIGN_CENTER_VERTICAL|wx.ADJUST_MINSIZE|wx.ALL, 3)
self.SetSizerAndFit(self.sizer)
def onMeasureButtonInit(self, evt):
self.node.logger.info('Obtain new beam tilt axis')
self.onMeasure(evt, update=False)
def onMeasureButtonUpdate(self, evt):
self.node.logger.info('Updating beam tilt axis')
self.onMeasure(evt, update=True)
def onMeasure(self, evt, update):
self.Close()
atilt = self.tiltvalue.GetValue()
asnr = self.snrvalue.GetValue()
if asnr <= 0:
self.node.logger.error('SNR cannot be less than or equal to zero')
return
amedfilt = self.medfilt.GetValue()
anumtilts = self.numtilts.GetValue()
if(self.crosscorr.GetValue() and not self.phasecorr.GetValue()):
acorr = 'cross'
else:
acorr = 'phase'
atilttwice = self.tilttwice.GetValue()
#RUN THE Measurement
threading.Thread(target=self.node.measureTiltAxis, args=(atilt, anumtilts, atilttwice, update, asnr, acorr, amedfilt)).start()
