def initialize(self):
leginon.gui.wx.Settings.ScrolledDialog.initialize(self)
sb = wx.StaticBox(self, -1, 'Settings')
sbsz = wx.StaticBoxSizer(sb, wx.VERTICAL)
sz = wx.GridBagSizer(5, 10)
label = wx.StaticText(self, -1, 'Mask Run Name:')
masknames = self.node.getMaskRunNames()
self.widgets['mask run'] = Choice(self, -1, choices=masknames)
sz.Add(label, (0, 0), (1, 1))
sz.Add(self.widgets['mask run'], (0, 1), (1, 1))
label = wx.StaticText(self, -1, 'Assessor Run Name:')
self.widgets['run'] = Entry(self, -1)
sz.Add(label, (1, 1), (1, 1))
sz.Add(self.widgets['run'], (1, 2), (1, 1))
self.widgets['continueon'] = wx.CheckBox(self, -1, 'Continue')
sz.Add(self.widgets['continueon'], (2, 0), (1, 1))
self.widgets['jump filename'] = Entry(self, -1, chars=12)
label = wx.StaticText(self, -1, 'Image to Jump to:')
sz.Add(label, (3, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
sz.Add(self.widgets['jump filename'], (3, 1), (1, 1),
wx.ALIGN_CENTER | wx.FIXED_MINSIZE)
sbsz.Add(sz, 0, wx.ALIGN_CENTER | wx.ALL, 5)
return [
sbsz,
]
def createNewPlateSelector(self, start_position):
sb = wx.StaticBox(self, -1, 'New Prep Plate')
sbsz = wx.StaticBoxSizer(sb, wx.VERTICAL)
szplate = wx.GridBagSizer(5, 5)
# plate format
label = wx.StaticText(self, -1, 'Plate Format:')
szplate.Add(label, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
self.cplateformat = wx.Choice(self, -1)
self.cplateformat.Enable(False)
szplate.Add(self.cplateformat, (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL)
# plate name
label = wx.StaticText(self, -1, 'New Plate Name:')
szplate.Add(label, (1, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
self.newplate = Entry(self, -1)
szplate.Add(self.newplate, (1, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.EXPAND)
self.savenewplate = wx.Button(self, wx.ID_SAVE)
szplate.Add(self.savenewplate, (2, 0), (1, 2),
wx.ALIGN_CENTER_VERTICAL)
szplate.AddGrowableCol(1)
sbsz.Add(szplate, 0, wx.EXPAND | wx.ALL, 5)
self.szmain.Add(sbsz, start_position, (1, 1),
wx.EXPAND | wx.ALL | wx.ALIGN_CENTER_VERTICAL)
class Panel(GridSelectionPanel):
def setDefaultGridSelection(self):
self.default_gridlabel = '--New Grid as Below--'
def addNew(self):
self.createNewGridEntry((1, 0))
def enableNew(self, gridlabel):
# enable entry of new grid
if gridlabel != self.default_gridlabel:
self.newgrid.Enable(False)
else:
self.newgrid.Enable(True)
def runNew(self):
self.onSaveNewGrid(None)
def createNewGridEntry(self, start_position):
sb = wx.StaticBox(self, -1, 'New Grid')
sbsz = wx.StaticBoxSizer(sb, wx.VERTICAL)
szgrid = wx.GridBagSizer(5, 5)
label = wx.StaticText(self, -1, 'New Grid Name:')
szgrid.Add(label, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
self.newgrid = Entry(self, -1)
szgrid.Add(self.newgrid, (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.EXPAND)
self.savenewgrid = wx.Button(self, wx.ID_APPLY)
szgrid.Add(self.savenewgrid, (2, 0), (1, 2), wx.ALIGN_CENTER_VERTICAL)
szgrid.AddGrowableCol(1)
sbsz.Add(szgrid, 0, wx.EXPAND | wx.ALL, 5)
self.szmain.Add(sbsz, start_position, (1, 1),
wx.EXPAND | wx.ALL | wx.ALIGN_CENTER_VERTICAL)
def onNodeInitialized(self):
super(Panel, self).onNodeInitialized()
self.Bind(wx.EVT_BUTTON, self.onSaveNewGrid, self.savenewgrid)
def onSaveNewGrid(self, evt=None):
choices = self.node.getGridNames()
newgrid = self.newgrid.Update()
newgrid = self.newgrid.GetValue()
if newgrid is None or newgrid == '':
self.node.onBadEMGridName('No Grid Name')
return
elif newgrid in choices:
self.node.onBadEMGridName('Grid Name Exists')
return
else:
self.node.publishNewEMGrid(newgrid)
self.refreshGrids()
def initialize(self):
leginon.gui.wx.Settings.ScrolledDialog.initialize(self)
sb = wx.StaticBox(self, -1, 'Settings')
sbsz = wx.StaticBoxSizer(sb, wx.VERTICAL)
sz = wx.GridBagSizer(5, 10)
#self.widgets['image directory'] = filebrowse.FileBrowseButton(self, -1)
presets = self.node.presetsclient.getPresetNames()
label = wx.StaticText(self, -1, 'Transform From:')
self.widgets['child preset'] = PresetChoice(self, -1)
self.widgets['child preset'].setChoices(presets)
sz.Add(label, (0, 0), (1, 1))
sz.Add(self.widgets['child preset'], (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.EXPAND)
label = wx.StaticText(self, -1, 'Transform To:')
self.widgets['ancestor preset'] = PresetChoice(self, -1)
self.widgets['ancestor preset'].setChoices(presets)
sz.Add(label, (1, 0), (1, 1))
sz.Add(self.widgets['ancestor preset'], (1, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.EXPAND)
self.widgets['jump filename'] = Entry(self, -1, chars=12)
label = wx.StaticText(self, -1, 'Image to Jump to:')
sz.Add(label, (2, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
sz.Add(self.widgets['jump filename'], (2, 1), (1, 1),
wx.ALIGN_CENTER | wx.FIXED_MINSIZE)
sbsz.Add(sz, 0, wx.ALIGN_CENTER | wx.ALL, 5)
return [
sbsz,
]
def initialize(self):
leginon.gui.wx.Settings.ScrolledDialog.initialize(self)
sb = wx.StaticBox(self, -1, 'ACE')
sbsz = wx.StaticBoxSizer(sb, wx.VERTICAL)
sb = wx.StaticBox(self, -1, 'Images in Database')
sbszdb = wx.StaticBoxSizer(sb, wx.VERTICAL)
self.widgets['process'] = wx.CheckBox(self, -1, 'Analyze CTF')
self.widgets['label'] = Entry(self, -1)
sz = wx.GridBagSizer(5, 10)
sz.Add(self.widgets['process'], (1, 0), (1, 1),
wx.ALIGN_CENTER_VERTICAL)
sbsz.Add(sz, 0, wx.ALIGN_CENTER | wx.ALL, 5)
sz = wx.GridBagSizer(5, 5)
label = wx.StaticText(self, -1,
'Find images in this session with label:')
sz.Add(label, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
sz.Add(self.widgets['label'], (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.EXPAND)
sbszdb.Add(sz, 0, wx.ALIGN_CENTER | wx.ALL, 5)
return [sbsz, sbszdb]
def addTiltSettings(self):
sb = wx.StaticBox(self, -1, 'Tilting')
sbsz = wx.StaticBoxSizer(sb, wx.VERTICAL)
sizer = wx.GridBagSizer(5, 4)
bordersize = 3
self.widgets['use tilts'] = \
wx.CheckBox(self, -1, 'Acquire each target at different tilt in the list')
sizer.Add(self.widgets['use tilts'], (0, 0), (1, 4),
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, 1), (1, 1), 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)
self.widgets['reset per targetlist'] = \
wx.CheckBox(self, -1, 'Reset to the first of the tilts for targets from new image')
sizer.Add(self.widgets['reset per targetlist'], (2, 1), (1, 3),
wx.ALL | wx.EXPAND | wx.ALIGN_CENTER_VERTICAL, bordersize)
sbsz.Add(sizer, 0, wx.ALIGN_CENTER_HORIZONTAL | wx.ALL, 5)
return sbsz
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 addRCTSettings(self): sb = wx.StaticBox(self, -1, 'RCT Options') sbsz = wx.StaticBoxSizer(sb, wx.VERTICAL) sizer = wx.GridBagSizer(5, 4) bordersize = 3 label = wx.StaticText(self, -1, 'List of Tilts to Collect (in degrees)') sizer.Add(label, (0, 0), (1, 2), wx.ALIGN_CENTER_VERTICAL) self.widgets['tilts'] = Entry(self, -1, chars=15, style=wx.ALIGN_RIGHT) sizer.Add(self.widgets['tilts'], (0,2), (1,2), wx.ALL|wx.EXPAND|wx.ALIGN_CENTER_VERTICAL, bordersize) label = wx.StaticText(self, -1, 'Maximum Tilt Stepsize (in degrees)') sizer.Add(label, (1, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL) self.widgets['stepsize'] = IntEntry(self, -1, chars=2, value='15') sizer.Add(self.widgets['stepsize'], (1,1), (1,1), wx.ALL|wx.ALIGN_CENTER_VERTICAL, bordersize) label = wx.StaticText(self, -1, 'Pause Between Steps') sizer.Add(label, (1, 2), (1, 1), wx.ALIGN_CENTER_VERTICAL) self.widgets['pause'] = FloatEntry(self, -1, chars=2, value='1') sizer.Add(self.widgets['pause'], (1,3), (1,1), wx.ALL|wx.ALIGN_CENTER_VERTICAL, bordersize) ''' label = wx.StaticText(self, -1, 'Min Feature Size') sizer.Add(label, (2,0), (1, 1), wx.ALIGN_CENTER_VERTICAL) self.widgets['minsize'] = FloatEntry(self, -1, chars=6, value='0.0') #sizer.Add(self.widgets['minsize'], (2,1), (1,1), wx.ALL|wx.ALIGN_CENTER_VERTICAL, bordersize) label = wx.StaticText(self, -1, 'Max Feature Size') sizer.Add(label, (2, 2), (1, 1), wx.ALIGN_CENTER_VERTICAL) self.widgets['maxsize'] = FloatEntry(self, -1, chars=6, value='0.0') sizer.Add(self.widgets['maxsize'], (2,3), (1,1), wx.ALL|wx.ALIGN_CENTER_VERTICAL, bordersize) label = wx.StaticText(self, -1, 'Median Filter (pixels)') sizer.Add(label, (3, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL) self.widgets['medfilt'] = IntEntry(self, -1, chars=2, value='0') sizer.Add(self.widgets['medfilt'], (3,1), (1,1), wx.ALL|wx.ALIGN_CENTER_VERTICAL, bordersize) ''' label = wx.StaticText(self, -1, 'LowPass Filter (pixels)') sizer.Add(label, (3, 2), (1, 1), wx.ALIGN_CENTER_VERTICAL) self.widgets['lowfilt'] = IntEntry(self, -1, chars=2, value='0') sizer.Add(self.widgets['lowfilt'], (3,3), (1,1), wx.ALL|wx.ALIGN_CENTER_VERTICAL, bordersize) label = wx.StaticText(self, -1, 'Drift threshold') sizer.Add(label, (4, 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'], (4,1), (1,1), wx.ALL|wx.ALIGN_CENTER_VERTICAL, bordersize) label = wx.StaticText(self, -1, 'Drift preset') sizer.Add(label, (4, 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'], (4,3), (1,1), wx.ALL|wx.ALIGN_CENTER_VERTICAL, bordersize) sbsz.Add(sizer, 0, wx.ALIGN_CENTER|wx.ALL, 2) return sbsz
def __init__(self, parent, title='Film'):
self.parent = parent
wx.StaticBoxSizer.__init__(self, wx.StaticBox(self.parent, -1, title),
wx.VERTICAL)
self.sz = wx.GridBagSizer(5, 5)
self.Add(self.sz, 1, wx.EXPAND|wx.ALL, 5)
parameterorder = [
'Stock',
'Exposure number',
'Exposure type',
'Automatic exposure time',
'Manual exposure time',
'User code',
'Date Type',
'Text',
'Shutter',
'External shutter',
]
self.parameters = {
'Stock': wx.StaticText(self.parent, -1, ''),
'Exposure number': IntEntry(self.parent, -1, chars=5, allownone=True),
'Exposure type': wx.Choice(self.parent, -1),
'Automatic exposure time': wx.StaticText(self.parent, -1, ''),
'Manual exposure time': FloatEntry(self.parent, -1, chars=5, allownone=True),
'User code': Entry(self.parent, -1, chars=3),
'Date Type': wx.Choice(self.parent, -1),
'Text': Entry(self.parent, -1, chars=20),
'Shutter': wx.Choice(self.parent, -1),
'External shutter': wx.Choice(self.parent, -1),
}
row = 0
for key in parameterorder:
st = wx.StaticText(self.parent, -1, key + ':')
self.sz.Add(st, (row, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
style = wx.ALIGN_CENTER
if isinstance(self.parameters[key], Entry):
style |= wx.FIXED_MINSIZE
self.sz.Add(self.parameters[key], (row, 1), (1, 1), style)
self.parameters[key].Enable(False)
self.parameters[key].Enable(False)
row += 1
self.sz.AddGrowableCol(1)
def createNewGridEntry(self, start_position):
sb = wx.StaticBox(self, -1, 'New Grid')
sbsz = wx.StaticBoxSizer(sb, wx.VERTICAL)
szgrid = wx.GridBagSizer(5, 5)
label = wx.StaticText(self, -1, 'New Grid Name:')
szgrid.Add(label, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
self.newgrid = Entry(self, -1)
szgrid.Add(self.newgrid, (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.EXPAND)
self.savenewgrid = wx.Button(self, wx.ID_APPLY)
szgrid.Add(self.savenewgrid, (2, 0), (1, 2), wx.ALIGN_CENTER_VERTICAL)
szgrid.AddGrowableCol(1)
sbsz.Add(szgrid, 0, wx.EXPAND | wx.ALL, 5)
self.szmain.Add(sbsz, start_position, (1, 1),
wx.EXPAND | wx.ALL | wx.ALIGN_CENTER_VERTICAL)
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()
def initialize(self): sizers = leginon.gui.wx.TargetRepeater.ScrolledSettings.initialize(self) sb = wx.StaticBox(self, -1, 'Tilts') sbsz = wx.StaticBoxSizer(sb, wx.VERTICAL) self.widgets['tilts'] = Entry(self, -1, chars=15, style=wx.ALIGN_RIGHT) sbsz.Add(self.widgets['tilts'], wx.EXPAND) return sizers + [sbsz]
def createTemplateFilenameEntry(self, sz, start_position):
# define widget
self.widgets['template filename'] = Entry(self, -1, chars=20)
label = wx.StaticText(self, -1, 'Template Filename')
# add to main
newrow, newcol = self.addToSizer(sz, label, start_position, (1, 1))
newrow, newcol = self.addToSizer(sz, self.widgets['template filename'],
(start_position[0], newcol), (1, 2),
wx.ALIGN_CENTER_VERTICAL | wx.EXPAND)
return newrow, newcol
def initialize(self):
leginon.gui.wx.Settings.ScrolledDialog.initialize(self)
sb = wx.StaticBox(self, -1, 'Settings')
sbsz = wx.StaticBoxSizer(sb, wx.VERTICAL)
sz = wx.GridBagSizer(5, 10)
#self.widgets['image directory'] = filebrowse.FileBrowseButton(self, -1)
#self.widgets['image directory'].SetMinSize((500,50))
label = wx.StaticText(self, -1, 'Image Directory:')
self.widgets['image directory'] = Entry(self, -1)
sz.Add(label, (0, 0), (1, 1))
sz.Add(self.widgets['image directory'], (0, 1), (1, 1))
label = wx.StaticText(self, -1, 'Image Format:')
self.widgets['format'] = leginon.gui.wx.Choice.Choice(
self, -1, choices=['mrc', 'jpg', 'png'])
sz.Add(label, (1, 0), (1, 1))
sz.Add(self.widgets['format'], (1, 1), (1, 1))
label = wx.StaticText(self, -1, 'Output Filename:')
self.widgets['outputfile'] = Entry(self, -1)
sz.Add(label, (2, 0), (1, 1))
sz.Add(self.widgets['outputfile'], (2, 1), (1, 1))
label = wx.StaticText(self, -1, 'Run Name:')
self.widgets['run'] = Entry(self, -1)
sz.Add(label, (3, 0), (1, 1))
sz.Add(self.widgets['run'], (3, 1), (1, 1))
self.widgets['jump filename'] = Entry(self, -1, chars=12)
label = wx.StaticText(self, -1, 'Image to Jump to:')
sz.Add(label, (4, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
sz.Add(self.widgets['jump filename'], (4, 1), (1, 1),
wx.ALIGN_CENTER | wx.FIXED_MINSIZE)
sbsz.Add(sz, 0, wx.ALIGN_CENTER | wx.ALL, 5)
return [
sbsz,
]
def initialize(self):
leginon.gui.wx.Settings.ScrolledDialog.initialize(self)
sb = wx.StaticBox(self, -1, 'Settings')
sbsz = wx.StaticBoxSizer(sb, wx.VERTICAL)
sz = wx.GridBagSizer(5, 10)
label = wx.StaticText(self, -1, 'Preset Name:')
self.widgets['preset'] = Entry(self, -1)
sz.Add(label, (0, 0), (1, 1))
sz.Add(self.widgets['preset'], (0, 1), (1, 1))
label = wx.StaticText(self, -1, 'Binning:')
self.widgets['bin'] = IntEntry(self, -1, min=1, chars=4)
sz.Add(label, (1, 0), (1, 1))
sz.Add(self.widgets['bin'], (1, 1), (1, 1))
label = wx.StaticText(self, -1, 'Mask Run Name:')
self.widgets['run'] = Entry(self, -1)
sz.Add(label, (2, 0), (1, 1))
sz.Add(self.widgets['run'], (2, 1), (1, 1))
self.widgets['continueon'] = wx.CheckBox(
self, -1, 'empty-mask-overwrite Not Allowed')
sz.Add(self.widgets['continueon'], (3, 0), (1, 1))
label = wx.StaticText(self, -1, 'Mask Run Path:')
self.widgets['path'] = Entry(self, -1)
sz.Add(label, (4, 0), (1, 1))
sz.Add(self.widgets['path'], (4, 1), (1, 1))
self.widgets['jump filename'] = Entry(self, -1, chars=12)
label = wx.StaticText(self, -1, 'Image to Jump to:')
sz.Add(label, (5, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
sz.Add(self.widgets['jump filename'], (5, 1), (1, 1),
wx.ALIGN_CENTER | wx.FIXED_MINSIZE)
sbsz.Add(sz, 0, wx.ALIGN_CENTER | wx.ALL, 5)
return [
sbsz,
]
def addBasicTiltSettings(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, 'Min Feature Size')
sizer.Add(label, (2, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
self.widgets['minsize'] = FloatEntry(self, -1, chars=6, value='0.0')
sizer.Add(self.widgets['minsize'], (2, 1), (1, 1),
wx.ALL | wx.ALIGN_CENTER_VERTICAL, bordersize)
label = wx.StaticText(self, -1, 'Max Feature Size')
sizer.Add(label, (2, 2), (1, 1), wx.ALIGN_CENTER_VERTICAL)
self.widgets['maxsize'] = FloatEntry(self, -1, chars=6, value='0.0')
sizer.Add(self.widgets['maxsize'], (2, 3), (1, 1),
wx.ALL | wx.ALIGN_CENTER_VERTICAL, bordersize)
label = wx.StaticText(self, -1, 'Median Filter (pixels)')
sizer.Add(label, (3, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
self.widgets['medfilt'] = IntEntry(self, -1, chars=2, value='0')
sizer.Add(self.widgets['medfilt'], (3, 1), (1, 1),
wx.ALL | wx.ALIGN_CENTER_VERTICAL, bordersize)
label = wx.StaticText(self, -1, 'LowPass Filter (pixels)')
sizer.Add(label, (3, 2), (1, 1), wx.ALIGN_CENTER_VERTICAL)
self.widgets['lowfilt'] = FloatEntry(self, -1, chars=2, value='0.0')
sizer.Add(self.widgets['lowfilt'], (3, 3), (1, 1),
wx.ALL | wx.ALIGN_CENTER_VERTICAL, bordersize)
sbsz.Add(sizer, 0, wx.ALIGN_CENTER | wx.ALL, 2)
return sbsz
def __init__(self, *args, **kwargs):
leginon.gui.wx.Node.Panel.__init__(self, *args, **kwargs)
self.toolbar.AddTool(leginon.gui.wx.ToolBar.ID_SETTINGS,
'settings',
shortHelpString='Start')
self.toolbar.AddSeparator()
self.toolbar.AddTool(leginon.gui.wx.ToolBar.ID_PLAY,
'play',
shortHelpString='Start')
self.toolbar.AddSeparator()
self.toolbar.AddTool(leginon.gui.wx.ToolBar.ID_REFRESH,
'refresh',
shortHelpString='Refresh Grid List')
self.cgrid = wx.Choice(self, -1)
self.cgrid.Enable(False)
szgrid = wx.GridBagSizer(5, 5)
label = wx.StaticText(self, -1, 'Grids in the project')
szgrid.Add(label, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szgrid.Add(self.cgrid, (0, 1), (1, 1), wx.ALIGN_CENTER_VERTICAL)
label = wx.StaticText(self, -1, 'New Grid Name:')
szgrid.Add(label, (1, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
self.newgrid = Entry(self, -1)
szgrid.Add(self.newgrid, (1, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.EXPAND)
self.savenewgrid = wx.Button(self, wx.ID_APPLY)
szgrid.Add(self.savenewgrid, (1, 2), (1, 1), wx.ALIGN_CENTER_VERTICAL)
self.szmain.Add(szgrid, (0, 0), (1, 1), wx.ALIGN_CENTER)
self.szmain.AddGrowableCol(0)
self.SetSizer(self.szmain)
self.SetAutoLayout(True)
self.SetupScrolling()
def addBasicRCTSettings(self):
sb = wx.StaticBox(self, -1, 'RCT Options')
sbsz = wx.StaticBoxSizer(sb, wx.VERTICAL)
sizer = wx.GridBagSizer(5, 4)
bordersize = 3
label = wx.StaticText(self, -1,
'List of Tilts to Collect (in degrees)')
sizer.Add(label, (0, 0), (1, 2), wx.ALIGN_CENTER_VERTICAL)
self.widgets['tilts'] = Entry(self, -1, chars=15, style=wx.ALIGN_RIGHT)
sizer.Add(self.widgets['tilts'], (0, 2), (1, 2),
wx.ALL | wx.EXPAND | 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, 'Raptor Settings')
sbsz = wx.StaticBoxSizer(sb, wx.VERTICAL)
self.widgets['process'] = wx.CheckBox(self, -1,
'Process images when event received')
self.widgets['path'] = Entry(self, -1)
self.widgets['time'] = IntEntry(self, -1)
self.widgets['binning'] = IntEntry(self, -1)
sbsz.Add(self.widgets['process'])
sbsz.Add(self.widgets['path'])
sbsz.Add(self.widgets['time'])
sbsz.Add(self.widgets['binning'])
return [sbsz]
def addBasicSettings(self): sz = wx.GridBagSizer(5, 10) # preset presets = self.node.presetsclient.getPresetNames() self.widgets['preset'] = PresetChoice(self, -1) self.widgets['preset'].setChoices(presets) 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) # atlas label self.widgets['label'] = Entry(self, -1, allowspaces=False) 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) # radius self.widgets['radius'] = FloatEntry(self, -1, min=0.0, chars=6) 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) ''' # atlas max size self.widgets['max size'] = IntEntry(self, -1) 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) # atlas max size self.widgets['max targets'] = IntEntry(self, -1) 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) ''' return sz
def initialize(self):
leginon.gui.wx.Settings.ScrolledDialog.initialize(self)
sb = wx.StaticBox(self, -1, 'FFT')
sbsz = wx.StaticBoxSizer(sb, wx.VERTICAL)
sb = wx.StaticBox(self, -1, 'Images in Database')
sbszdb = wx.StaticBoxSizer(sb, wx.VERTICAL)
self.widgets['process'] = wx.CheckBox(self, -1, 'Calculate FFT')
self.widgets['save'] = wx.CheckBox(self, -1, 'Save to the database')
self.widgets['reduced'] = wx.CheckBox(
self, -1, 'Truncate FFT to center 1024 pixels')
self.widgets['mask radius'] = FloatEntry(self, -1, min=0.0, chars=6)
self.widgets['label'] = Entry(self, -1)
szmaskradius = wx.GridBagSizer(5, 5)
label = wx.StaticText(self, -1, 'Mask radius:')
szmaskradius.Add(label, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szmaskradius.Add(self.widgets['mask radius'], (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.FIXED_MINSIZE)
label = wx.StaticText(self, -1, '% of image width')
szmaskradius.Add(label, (0, 2), (1, 1), wx.ALIGN_CENTER_VERTICAL)
sz = wx.GridBagSizer(5, 10)
sz.Add(self.widgets['reduced'], (0, 0), (1, 1),
wx.ALIGN_CENTER_VERTICAL)
sz.Add(self.widgets['process'], (1, 0), (1, 1),
wx.ALIGN_CENTER_VERTICAL)
sz.Add(self.widgets['save'], (2, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
sz.Add(szmaskradius, (3, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
sbsz.Add(sz, 0, wx.ALIGN_CENTER | wx.ALL, 5)
sz = wx.GridBagSizer(5, 5)
label = wx.StaticText(self, -1,
'Find images in this session with label:')
sz.Add(label, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
sz.Add(self.widgets['label'], (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.EXPAND)
sbszdb.Add(sz, 0, wx.ALIGN_CENTER | wx.ALL, 5)
return [sbsz, sbszdb]
def addGonModelerSettings(self):
sb = wx.StaticBox(self, -1, 'Measurement')
sbszmeasure = wx.StaticBoxSizer(sb, wx.VERTICAL)
sb = wx.StaticBox(self, -1, 'Modeling')
sbszmodel = wx.StaticBoxSizer(sb, wx.VERTICAL)
self.widgets['measure axis'] = Choice(self, -1, choices=self.node.axes)
self.widgets['measure points'] = IntEntry(self, -1, min=2, chars=5)
self.widgets['measure tolerance'] = FloatEntry(self,
-1,
min=0.0,
chars=5)
self.widgets['measure interval'] = FloatEntry(self, -1, chars=9)
self.widgets['measure label'] = Entry(self, -1, chars=12)
self.widgets['model label'] = Entry(self, -1, chars=12)
self.widgets['model axis'] = Choice(self, -1, choices=self.node.axes)
self.widgets['model magnification'] = FloatEntry(self, -1, chars=9)
self.widgets['model terms'] = IntEntry(self, -1, chars=2)
self.widgets['model mag only'] = wx.CheckBox(
self, -1, 'Scale and Rotation Adjustment Only')
szmeasure = wx.GridBagSizer(5, 5)
label = wx.StaticText(self, -1, 'Axis:')
szmeasure.Add(label, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szmeasure.Add(self.widgets['measure axis'], (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_RIGHT)
label = wx.StaticText(self, -1, 'Points:')
szmeasure.Add(label, (1, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szmeasure.Add(
self.widgets['measure points'], (1, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_RIGHT | wx.FIXED_MINSIZE)
label = wx.StaticText(self, -1, 'Tolerance:')
szmeasure.Add(label, (2, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szmeasure.Add(
self.widgets['measure tolerance'], (2, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_RIGHT | wx.FIXED_MINSIZE)
label = wx.StaticText(self, -1, '%')
szmeasure.Add(label, (2, 2), (1, 1), wx.ALIGN_CENTER_VERTICAL)
label = wx.StaticText(self, -1, 'Interval')
szmeasure.Add(label, (3, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szmeasure.Add(
self.widgets['measure interval'], (3, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_RIGHT | wx.FIXED_MINSIZE)
label = wx.StaticText(self, -1, 'Label')
szmeasure.Add(label, (4, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szmeasure.Add(
self.widgets['measure label'], (4, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_RIGHT | wx.FIXED_MINSIZE)
szmeasure.AddGrowableCol(1)
sbszmeasure.Add(szmeasure, 1, wx.EXPAND | wx.ALL, 5)
szmodel = wx.GridBagSizer(5, 5)
label = wx.StaticText(self, -1, 'Label:')
szmodel.Add(label, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szmodel.Add(
self.widgets['model label'], (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_RIGHT | wx.FIXED_MINSIZE)
label = wx.StaticText(self, -1, 'Axis:')
szmodel.Add(label, (1, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szmodel.Add(self.widgets['model axis'], (1, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_RIGHT)
label = wx.StaticText(self, -1, 'Magnification:')
szmodel.Add(label, (2, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szmodel.Add(
self.widgets['model magnification'], (2, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_RIGHT | wx.FIXED_MINSIZE)
label = wx.StaticText(self, -1, 'Terms:')
szmodel.Add(label, (3, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
szmodel.Add(
self.widgets['model terms'], (3, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_RIGHT | wx.FIXED_MINSIZE)
szmodel.Add(self.widgets['model mag only'], (4, 0), (1, 2),
wx.ALIGN_CENTER)
szmodel.AddGrowableCol(1)
sbszmodel.Add(szmodel, 1, wx.EXPAND | wx.ALL, 5)
return [sbszmeasure, sbszmodel]
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)
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)
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
class Panel(leginon.gui.wx.GridEntry.GridSelectionPanel):
#icon = 'robot'
def setDefaultGridSelection(self):
self.default_gridlabel = '--Not-specified--'
def addNew(self):
self.createNewGridFromPlate((2, 0))
self.createNewPlateSelector((4, 0))
def runNew(self):
self.node.onBadEMGridName('No Grid')
def createNewGridFromPlate(self, start_position):
sb = wx.StaticBox(self, -1, 'New Grid Batch')
sbsz = wx.StaticBoxSizer(sb, wx.VERTICAL)
szgrid = wx.GridBagSizer(5, 5)
label = wx.StaticText(self, -1, 'Select a Grid Format (r x c:skips):')
szgrid.Add(label, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL | wx.EXPAND)
self.cgridformat = wx.Choice(self, -1)
self.cgridformat.Enable(False)
szgrid.Add(self.cgridformat, (0, 1), (1, 1), wx.ALIGN_CENTER_VERTICAL)
label = wx.StaticText(self, -1, 'Select a plate in the project')
szgrid.Add(label, (1, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
self.cplate = wx.Choice(self, -1)
self.cplate.Enable(False)
szgrid.Add(self.cplate, (1, 1), (1, 1), wx.ALIGN_CENTER_VERTICAL)
self.savenewgrid = wx.Button(self, wx.ID_APPLY)
szgrid.Add(self.savenewgrid, (2, 0), (1, 2), wx.ALIGN_CENTER_VERTICAL)
szgrid.AddGrowableCol(1)
sbsz.Add(szgrid, 0, wx.EXPAND | wx.ALL, 5)
self.szmain.Add(sbsz, start_position, (1, 1),
wx.EXPAND | wx.ALL | wx.ALIGN_CENTER_VERTICAL)
def createNewPlateSelector(self, start_position):
sb = wx.StaticBox(self, -1, 'New Prep Plate')
sbsz = wx.StaticBoxSizer(sb, wx.VERTICAL)
szplate = wx.GridBagSizer(5, 5)
# plate format
label = wx.StaticText(self, -1, 'Plate Format:')
szplate.Add(label, (0, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
self.cplateformat = wx.Choice(self, -1)
self.cplateformat.Enable(False)
szplate.Add(self.cplateformat, (0, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL)
# plate name
label = wx.StaticText(self, -1, 'New Plate Name:')
szplate.Add(label, (1, 0), (1, 1), wx.ALIGN_CENTER_VERTICAL)
self.newplate = Entry(self, -1)
szplate.Add(self.newplate, (1, 1), (1, 1),
wx.ALIGN_CENTER_VERTICAL | wx.EXPAND)
self.savenewplate = wx.Button(self, wx.ID_SAVE)
szplate.Add(self.savenewplate, (2, 0), (1, 2),
wx.ALIGN_CENTER_VERTICAL)
szplate.AddGrowableCol(1)
sbsz.Add(szplate, 0, wx.EXPAND | wx.ALL, 5)
self.szmain.Add(sbsz, start_position, (1, 1),
wx.EXPAND | wx.ALL | wx.ALIGN_CENTER_VERTICAL)
def onNodeInitialized(self):
super(Panel, self).onNodeInitialized()
self.Bind(wx.EVT_BUTTON, self.onSaveNewGrids, self.savenewgrid)
self.Bind(wx.EVT_CHOICE, self.onGridFormatChoice, self.cgridformat)
self.Bind(wx.EVT_CHOICE, self.onPlateChoice, self.cplate)
self.Bind(wx.EVT_CHOICE, self.onPlateFormatChoice, self.cplateformat)
self.Bind(wx.EVT_BUTTON, self.onSaveNewPlate, self.savenewplate)
self.refreshNewGrids()
self.refreshPlates()
def onSaveNewGrids(self, evt=None):
self.cplate.Update()
plate = self.cplate.GetStringSelection()
if plate is None or plate == '':
self.node.onBadEMGridName('No Plate')
return
if plate == '--New Plate as Below--':
# save the new plate entry and then update the value
status = self.onSaveNewPlate()
if status is False:
return
plate = self.cplate.GetStringSelection()
self.cgridformat.Update()
gformat = self.cgridformat.GetStringSelection()
if gformat is None or gformat == '':
self.node.onBadEMGridName('No Grid Format')
return
else:
self.node.publishNewEMGrids(gformat, plate)
self.refreshGrids()
def onGridFormatChoice(self, evt=None):
if evt is None:
formatlabel = self.cgridformat.GetStringSelection()
else:
formatlabel = evt.GetString()
settings = self.node.getSettings()
settings['grid format name'] = formatlabel
self.node.setSettings(settings)
self.newplate.Enable(False)
def onPlateFormatChoice(self, evt=None):
if evt is None:
formatlabel = self.cplateformat.GetStringSelection()
else:
formatlabel = evt.GetString()
settings = self.node.getSettings()
settings['plate format name'] = formatlabel
self.node.setSettings(settings)
self.newplate.Enable(True)
def setGridFormatSelection(self, choices):
if choices:
self.cgridformat.Clear()
self.cgridformat.AppendItems(choices)
if self.node.settings['grid format name']:
n = self.cgridformat.FindString(
self.node.settings['grid format name'])
else:
n = wx.NOT_FOUND
if n == wx.NOT_FOUND:
self.cgridformat.SetSelection(0)
else:
self.cgridformat.SetSelection(n)
self.cgridformat.Enable(True)
self.onGridFormatChoice()
def setPlateFormatSelection(self, choices):
if choices:
self.cplateformat.Clear()
self.cplateformat.AppendItems(choices)
if self.node.settings['plate format name']:
n = self.cplateformat.FindString(
self.node.settings['plate format name'])
else:
n = wx.NOT_FOUND
if n == wx.NOT_FOUND:
self.cplateformat.SetSelection(0)
else:
self.cplateformat.SetSelection(n)
self.cplateformat.Enable(True)
self.onPlateFormatChoice()
def onSaveNewPlate(self, evt=None):
choices = self.node.getPlateNames()
self.newplate.Update()
newplate = self.newplate.GetValue()
if newplate is None or newplate == '':
self.node.onBadPlateName('No Plate Name')
return False
elif newplate in choices:
self.node.onBadPlateName('Plate Name Exists')
return False
choices = self.node.getPlateFormats()
self.cplateformat.Update()
pformat = self.cplateformat.GetStringSelection()
if pformat is None or pformat == '':
self.node.onBadPlateName('No Plate Format')
return False
else:
self.node.publishNewPlate(newplate, pformat)
self.refreshPlates()
def onPlateChoice(self, evt=None):
if evt is None:
platelabel = self.cplate.GetStringSelection()
else:
platelabel = evt.GetString()
settings = self.node.getSettings()
settings['plate name'] = platelabel
self.node.setSettings(settings)
if platelabel != '--New Plate as Below--':
self.newplate.Enable(False)
else:
self.newplate.Enable(True)
def setPlateSelection(self, choices):
if choices:
self.cplate.Clear()
self.cplate.AppendItems(choices)
if self.node.settings['plate name']:
n = self.cplate.FindString(self.node.settings['plate name'])
else:
n = wx.NOT_FOUND
if n == wx.NOT_FOUND:
self.cplate.SetSelection(0)
else:
self.cplate.SetSelection(n)
self.cplate.Enable(True)
self.onPlateChoice()
def onRefreshGridsButton(self, evt):
self.refreshGrids()
self.refreshNewGrids()
self.refreshPlates()
def refreshNewGrids(self):
choices = self.node.getGridFormats()
self.setGridFormatSelection(choices)
def refreshPlates(self):
choices = self.node.getPlateNames()
choices.insert(0, '--New Plate as Below--')
self.setPlateSelection(choices)
choices = self.node.getPlateFormats()
self.setPlateFormatSelection(choices)
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 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):
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 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