def GenPointFindingPanel(self, _pnl):
item = afp.foldingPane(_pnl, -1, caption="Point Finding", pinned = True)
# item = _pnl.AddFoldPanel("Point Finding", collapsed=False,
# foldIcons=self.Images)
pan = wx.Panel(item, -1)
vsizer = wx.BoxSizer(wx.VERTICAL)
hsizer = wx.BoxSizer(wx.HORIZONTAL)
hsizer.Add(wx.StaticText(pan, -1, 'Threshold:'), 1,wx.RIGHT|wx.ALIGN_CENTER_VERTICAL, 5)
self.tThreshold = wx.TextCtrl(pan, -1, value='0.6', size=(40, -1))
hsizer.Add(self.tThreshold, 0,wx.RIGHT|wx.ALIGN_CENTER_VERTICAL, 5)
vsizer.Add(hsizer, 0,wx.BOTTOM|wx.EXPAND, 2)
#load any additional point finding settings
self._populateFindOptionsPanel(pan, vsizer)
hsizer = wx.BoxSizer(wx.HORIZONTAL)
bTest = wx.Button(pan, -1, 'Test', style=wx.BU_EXACTFIT)
bTest.Bind(wx.EVT_BUTTON, self.OnTest)
hsizer.Add(bTest, 0,wx.LEFT|wx.ALIGN_CENTER_VERTICAL, 5)
bTestF = wx.Button(pan, -1, 'Test This Frame', style=wx.BU_EXACTFIT)
bTestF.Bind(wx.EVT_BUTTON, self.OnTestFrame)
hsizer.Add(bTestF, 0,wx.LEFT|wx.ALIGN_CENTER_VERTICAL, 5)
vsizer.Add(hsizer, 0,wx.BOTTOM|wx.EXPAND, 2)
pan.SetSizerAndFit(vsizer)
item.AddNewElement(pan)
_pnl.AddPane(item)
def GenBlobFitPanel(self, _pnl):
item = afp.foldingPane(_pnl, -1, caption="Object Fitting", pinned=True)
# item = _pnl.AddFoldPanel("Object Fitting", collapsed=False,
# foldIcons=self.Images)
bFitObjects = wx.Button(item, -1, 'Fit')
bFitObjects.Bind(wx.EVT_BUTTON, self.OnFitObjects)
#_pnl.AddFoldPanelWindow(item, bFitObjects, fpb.FPB_ALIGN_WIDTH, fpb.FPB_DEFAULT_SPACING, 10)
item.AddNewElement(bFitObjects)
pan = wx.Panel(item, -1)
hsizer = wx.BoxSizer(wx.HORIZONTAL)
hsizer.Add(wx.StaticText(pan, -1, 'Bead wxy:'), 0,
wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5)
self.tBeadWXY = wx.TextCtrl(pan, -1, value='125', size=(40, -1))
hsizer.Add(self.tBeadWXY, 0, wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5)
pan.SetSizer(hsizer)
hsizer.Fit(pan)
item.AddNewElement(pan)
bCalcShiftMap = wx.Button(item, -1, 'Shiftmap')
bCalcShiftMap.Bind(wx.EVT_BUTTON, self.OnCalcShiftmap)
#_pnl.AddFoldPanelWindow(item, bFitObjects, fpb.FPB_ALIGN_WIDTH, fpb.FPB_DEFAULT_SPACING, 10)
item.AddNewElement(bCalcShiftMap)
_pnl.AddPane(item)
def GenBlobFitPanel(self, _pnl):
item = afp.foldingPane(_pnl, -1, caption="Object Fitting", pinned = True)
# item = _pnl.AddFoldPanel("Object Fitting", collapsed=False,
# foldIcons=self.Images)
bFitObjects = wx.Button(item, -1, 'Fit')
bFitObjects.Bind(wx.EVT_BUTTON, self.OnFitObjects)
#_pnl.AddFoldPanelWindow(item, bFitObjects, fpb.FPB_ALIGN_WIDTH, fpb.FPB_DEFAULT_SPACING, 10)
item.AddNewElement(bFitObjects)
pan = wx.Panel(item, -1)
hsizer = wx.BoxSizer(wx.HORIZONTAL)
hsizer.Add(wx.StaticText(pan, -1, 'Bead wxy:'), 0,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
self.tBeadWXY = wx.TextCtrl(pan, -1, value='125', size=(40, -1))
hsizer.Add(self.tBeadWXY, 0,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
pan.SetSizer(hsizer)
hsizer.Fit(pan)
item.AddNewElement(pan)
bCalcShiftMap = wx.Button(item, -1, 'Shiftmap')
bCalcShiftMap.Bind(wx.EVT_BUTTON, self.OnCalcShiftmap)
#_pnl.AddFoldPanelWindow(item, bFitObjects, fpb.FPB_ALIGN_WIDTH, fpb.FPB_DEFAULT_SPACING, 10)
item.AddNewElement(bCalcShiftMap)
_pnl.AddPane(item)
def GenPointFindingPanel(self, _pnl):
item = afp.foldingPane(_pnl, -1, caption="Point Finding", pinned=True)
# item = _pnl.AddFoldPanel("Point Finding", collapsed=False,
# foldIcons=self.Images)
pan = wx.Panel(item, -1)
vsizer = wx.BoxSizer(wx.VERTICAL)
hsizer = wx.BoxSizer(wx.HORIZONTAL)
hsizer.Add(wx.StaticText(pan, -1, 'Threshold:'), 1,
wx.RIGHT | wx.ALIGN_CENTER_VERTICAL, 5)
self.tThreshold = wx.TextCtrl(pan, -1, value='0.6', size=(40, -1))
hsizer.Add(self.tThreshold, 0, wx.RIGHT | wx.ALIGN_CENTER_VERTICAL, 5)
vsizer.Add(hsizer, 0, wx.BOTTOM | wx.EXPAND, 2)
#load any additional point finding settings
self._populateFindOptionsPanel(pan, vsizer)
hsizer = wx.BoxSizer(wx.HORIZONTAL)
bTest = wx.Button(pan, -1, 'Test', style=wx.BU_EXACTFIT)
bTest.Bind(wx.EVT_BUTTON, self.OnTest)
hsizer.Add(bTest, 0, wx.LEFT | wx.ALIGN_CENTER_VERTICAL, 5)
bTestF = wx.Button(pan, -1, 'Test This Frame', style=wx.BU_EXACTFIT)
bTestF.Bind(wx.EVT_BUTTON, self.OnTestFrame)
hsizer.Add(bTestF, 0, wx.LEFT | wx.ALIGN_CENTER_VERTICAL, 5)
vsizer.Add(hsizer, 0, wx.BOTTOM | wx.EXPAND, 2)
pan.SetSizerAndFit(vsizer)
item.AddNewElement(pan)
_pnl.AddPane(item)
def GenBlobPanel(self, pnl):
# item = self._pnl.AddFoldPanel("Objects", collapsed=False,
# foldIcons=self.Images)
item = afp.foldingPane(pnl, -1, caption="Objects", pinned = True)
pan = wx.Panel(item, -1)
bsizer = wx.BoxSizer(wx.VERTICAL)
hsizer = wx.BoxSizer(wx.HORIZONTAL)
hsizer.Add(wx.StaticText(pan, -1, 'Threshold [nm]:'), 0,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
self.tBlobDist = wx.TextCtrl(pan, -1, '%3.0f' % self.pipeline.objThreshold,size=(40,-1))
hsizer.Add(self.tBlobDist, 1,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
bsizer.Add(hsizer, 0, wx.ALL|wx.EXPAND, 0)
hsizer = wx.BoxSizer(wx.HORIZONTAL)
hsizer.Add(wx.StaticText(pan, -1, 'Min Size [events]:'), 0,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
self.tMinObjSize = wx.TextCtrl(pan, -1, '%d' % self.pipeline.objMinSize, size=(40, -1))
hsizer.Add(self.tMinObjSize, 1,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
bsizer.Add(hsizer, 0, wx.ALL|wx.EXPAND, 0)
hsizer = wx.BoxSizer(wx.HORIZONTAL)
hsizer.Add(wx.StaticText(pan, -1, 'Jittering:'), 0,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
self.tObjJitter = wx.TextCtrl(pan, -1, '%d' % self.pipeline.blobJitter, size=(40, -1))
hsizer.Add(self.tObjJitter, 1,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
bsizer.Add(hsizer, 0, wx.ALL|wx.EXPAND, 0)
self.bApplyThreshold = wx.Button(pan, -1, 'Apply')
bsizer.Add(self.bApplyThreshold, 0, wx.ALL|wx.ALIGN_CENTER_HORIZONTAL, 5)
self.bObjMeasure = wx.Button(pan, -1, 'Measure')
#self.bObjMeasure.Enable(False)
bsizer.Add(self.bObjMeasure, 0, wx.ALL|wx.ALIGN_CENTER_HORIZONTAL, 5)
hsizer = wx.BoxSizer(wx.HORIZONTAL)
hsizer.Add(wx.StaticText(pan, -1, 'Object Colour:'), 0,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
self.cBlobColour = wx.Choice(pan, -1, choices=['Index', 'Random'])
self.cBlobColour.SetSelection(0)
self.cBlobColour.Bind(wx.EVT_CHOICE, self.OnSetBlobColour)
hsizer.Add(self.cBlobColour, 1,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
bsizer.Add(hsizer, 0, wx.ALL|wx.EXPAND, 0)
pan.SetSizer(bsizer)
bsizer.Fit(pan)
#self._pnl.AddFoldPanelWindow(item, pan, fpb.FPB_ALIGN_WIDTH, fpb.FPB_DEFAULT_SPACING, 5)
item.AddNewElement(pan)
self.bApplyThreshold.Bind(wx.EVT_BUTTON, self.OnObjApplyThreshold)
self.bObjMeasure.Bind(wx.EVT_BUTTON, self.OnObjMeasure)
pnl.AddPane(item)
def GenPlayPanel(self, _pnl):
item = afp.foldingPane(_pnl, -1, caption="Playback", pinned = True)
self.playPan = PlayPanel(item, self.dsviewer)
item.AddNewElement(self.playPan)
_pnl.AddPane(item)
def AddAqTool(self, panel, title):
'''Adds a pane to the Acquisition section of the GUI
Parameters
----------
panel : an instance of a wx.Window derived class
The pane to add
title : string
The caption for the panel.
'''
item = afp.foldingPane(self.aqPanel, -1, caption=title, pinned=True)
panel.Reparent(item)
item.AddNewElement(panel)
self.aqPanel.AddPane(item)
def AddAqTool(self, panel, title):
'''Adds a pane to the Acquisition section of the GUI
Parameters
----------
panel : an instance of a wx.Window derived class
The pane to add
title : string
The caption for the panel.
'''
item = afp.foldingPane(self.aqPanel, -1, caption=title, pinned = True)
panel.Reparent(item)
item.AddNewElement(panel)
self.aqPanel.AddPane(item)
def GenDataSourcePanel(self, pnl):
item = afp.foldingPane(pnl, -1, caption="Data Source", pinned = False)
self.dsRadioIds = []
for ds in self.pipeline.dataSources:
rbid = wx.NewId()
self.dsRadioIds.append(rbid)
rb = wx.RadioButton(item, rbid, ds._name)
rb.SetValue(ds == self.pipeline.selectedDataSource)
rb.Bind(wx.EVT_RADIOBUTTON, self.OnSourceChange)
item.AddNewElement(rb)
pnl.AddPane(item)
def GenPointsPanel(self, title='Points'):
item = afp.foldingPane(self._pnl, -1, caption=title, pinned=True)
# item = self._pnl.AddFoldPanel(title, collapsed=False,
# foldIcons=self.Images)
pan = wx.Panel(item, -1)
bsizer = wx.BoxSizer(wx.VERTICAL)
hsizer = wx.BoxSizer(wx.HORIZONTAL)
hsizer.Add(wx.StaticText(pan, -1, 'Size [nm]:'), 0,
wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5)
self.tPointSize = wx.TextCtrl(pan, -1,
'%3.2f' % self.glCanvas.pointSize)
hsizer.Add(self.tPointSize, 0, wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5)
bsizer.Add(hsizer, 0, wx.ALL, 0)
colData = ['<None>']
if not self.pipeline.colourFilter == None:
colData += list(self.pipeline.keys())
colData += list(self.pipeline.GeneratedMeasures.keys())
hsizer = wx.BoxSizer(wx.HORIZONTAL)
hsizer.Add(wx.StaticText(pan, -1, 'Colour:'), 0,
wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5)
self.chPointColour = wx.Choice(pan,
-1,
choices=colData,
size=(100, -1))
if self.colData in colData:
self.chPointColour.SetSelection(colData.index(self.colData))
hsizer.Add(self.chPointColour, 0, wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5)
bsizer.Add(hsizer, 0, wx.ALL, 0)
pan.SetSizer(bsizer)
bsizer.Fit(pan)
item.AddNewElement(pan)
#self._pnl.AddFoldPanelWindow(item, pan, fpb.FPB_ALIGN_WIDTH, fpb.FPB_DEFAULT_SPACING, 5)
self.tPointSize.Bind(wx.EVT_TEXT, self.OnPointSizeChange)
self.chPointColour.Bind(wx.EVT_CHOICE, self.OnChangePointColour)
self._pnl.AddPane(item)
def GenFitStatusPanel(self, _pnl):
item = afp.foldingPane(_pnl, -1, caption="Fit Status", pinned=True)
pan = wx.Panel(item, -1, size=(160, 300))
vsizer = wx.BoxSizer(wx.VERTICAL)
hsizer = wx.BoxSizer(wx.HORIZONTAL)
hsizer.Add(wx.StaticText(pan, -1, 'Colour:'), 0,
wx.LEFT | wx.RIGHT | wx.ALIGN_CENTER_VERTICAL, 5)
self.chProgDispColour = wx.Choice(pan,
-1,
choices=['z', 'gFrac', 't'],
size=(60, -1))
self.chProgDispColour.Bind(wx.EVT_CHOICE, self.OnProgDispColourChange)
hsizer.Add(self.chProgDispColour, 1, wx.ALL | wx.ALIGN_CENTER_VERTICAL,
0)
vsizer.Add(hsizer, 0, wx.BOTTOM | wx.EXPAND, 2)
hsizer = wx.BoxSizer(wx.HORIZONTAL)
hsizer.Add(wx.StaticText(pan, -1, 'CMap:'), 0,
wx.LEFT | wx.RIGHT | wx.ALIGN_CENTER_VERTICAL, 5)
self.chProgDispCMap = wx.Choice(pan,
-1,
choices=['gist_rainbow', 'RdYlGn'],
size=(60, -1))
self.chProgDispCMap.Bind(wx.EVT_CHOICE, self.OnProgDispCMapChange)
hsizer.Add(self.chProgDispCMap, 1, wx.ALL | wx.ALIGN_CENTER_VERTICAL,
0)
vsizer.Add(hsizer, 0, wx.BOTTOM | wx.EXPAND, 7)
self.progPan = progGraph.progPanel(pan,
self.fitResults,
size=(220, 250))
self.progPan.draw()
vsizer.Add(self.progPan, 1,
wx.ALL | wx.ALIGN_CENTER_HORIZONTAL | wx.EXPAND, 0)
pan.SetSizer(vsizer)
vsizer.Fit(pan)
#_pnl.AddFoldPanelWindow(item, pan, fpb.FPB_ALIGN_WIDTH, fpb.FPB_DEFAULT_SPACING, 0)
item.AddNewElement(pan)
_pnl.AddPane(item)
def AddCamTool(self, panel, title):
'''Adds a pane to the Camera section of the GUI
Parameters
----------
panel : an instance of a wx.Window derived class
The pane to add
title : string
The caption for the panel.
'''
#item = self.camPanel.AddFoldPanel(title, collapsed=False, foldIcons=self.Images)
item = afp.foldingPane(self.camPanel, -1, caption=title, pinned=True)
panel.Reparent(item)
item.AddNewElement(panel)
self.camPanel.AddPane(item)
def AddCamTool(self, panel, title):
'''Adds a pane to the Camera section of the GUI
Parameters
----------
panel : an instance of a wx.Window derived class
The pane to add
title : string
The caption for the panel.
'''
#item = self.camPanel.AddFoldPanel(title, collapsed=False, foldIcons=self.Images)
item = afp.foldingPane(self.camPanel, -1, caption=title, pinned = True)
panel.Reparent(item)
item.AddNewElement(panel)
self.camPanel.AddPane(item)
def GenPointsPanel(self, pnl, title='Points'):
item = afp.foldingPane(pnl, -1, caption=title, pinned = True)
# item = self._pnl.AddFoldPanel(title, collapsed=False,
# foldIcons=self.Images)
pan = wx.Panel(item, -1)
bsizer = wx.BoxSizer(wx.VERTICAL)
hsizer = wx.BoxSizer(wx.HORIZONTAL)
hsizer.Add(wx.StaticText(pan, -1, 'Size [nm]:'), 0,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
self.tPointSize = wx.TextCtrl(pan, -1, '%3.2f' % self.glCanvas.pointSize)
hsizer.Add(self.tPointSize, 0,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
bsizer.Add(hsizer, 0, wx.ALL, 0)
colData = ['<None>']
if not self.pipeline.colourFilter == None:
colData += list(self.pipeline.keys())
colData += list(self.pipeline.GeneratedMeasures.keys())
hsizer = wx.BoxSizer(wx.HORIZONTAL)
hsizer.Add(wx.StaticText(pan, -1, 'Colour:'), 0,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
self.chPointColour = wx.Choice(pan, -1, choices=colData, size=(100, -1))
if self.colData in colData:
self.chPointColour.SetSelection(colData.index(self.colData))
hsizer.Add(self.chPointColour, 0,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
bsizer.Add(hsizer, 0, wx.ALL, 0)
pan.SetSizer(bsizer)
bsizer.Fit(pan)
item.AddNewElement(pan)
#self._pnl.AddFoldPanelWindow(item, pan, fpb.FPB_ALIGN_WIDTH, fpb.FPB_DEFAULT_SPACING, 5)
self.tPointSize.Bind(wx.EVT_TEXT, self.OnPointSizeChange)
self.chPointColour.Bind(wx.EVT_CHOICE, self.OnChangePointColour)
pnl.AddPane(item)
def GenQuadTreePanel(self):
from PYME.Analysis.QuadTree import pointQT
item = afp.foldingPane(self._pnl, -1, caption="QuadTree", pinned=True)
# item = self._pnl.AddFoldPanel("QuadTree", collapsed=False,
# foldIcons=self.Images)
pan = wx.Panel(item, -1)
bsizer = wx.BoxSizer(wx.VERTICAL)
hsizer = wx.BoxSizer(wx.HORIZONTAL)
hsizer.Add(wx.StaticText(pan, -1, 'Leaf Size:'), 0,
wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5)
self.tQTLeafSize = wx.TextCtrl(pan, -1, '%d' % pointQT.QT_MAXRECORDS)
hsizer.Add(self.tQTLeafSize, 0, wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5)
bsizer.Add(hsizer, 0, wx.ALL, 0)
self.stQTSNR = wx.StaticText(
pan, -1,
'Effective SNR = %3.2f' % pylab.sqrt(pointQT.QT_MAXRECORDS / 2.0))
bsizer.Add(self.stQTSNR, 0, wx.ALL, 5)
#hsizer = wx.BoxSizer(wx.HORIZONTAL)
#hsizer.Add(wx.StaticText(pan, -1, 'Goal pixel size [nm]:'), 0,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
#self.tQTSize = wx.TextCtrl(pan, -1, '20000')
#hsizer.Add(self.tQTLeafSize, 0,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
#bsizer.Add(hsizer, 0, wx.ALL, 0)
pan.SetSizer(bsizer)
bsizer.Fit(pan)
item.AddNewElement(pan)
#self._pnl.AddFoldPanelWindow(item, pan, fpb.FPB_ALIGN_WIDTH, fpb.FPB_DEFAULT_SPACING, 5)
self.tQTLeafSize.Bind(wx.EVT_TEXT, self.OnQTLeafChange)
self._pnl.AddPane(item)
def GenQuadTreePanel(self, pnl):
from PYME.Analysis.QuadTree import pointQT
item = afp.foldingPane(pnl, -1, caption="QuadTree", pinned = True)
# item = self._pnl.AddFoldPanel("QuadTree", collapsed=False,
# foldIcons=self.Images)
pan = wx.Panel(item, -1)
bsizer = wx.BoxSizer(wx.VERTICAL)
hsizer = wx.BoxSizer(wx.HORIZONTAL)
hsizer.Add(wx.StaticText(pan, -1, 'Leaf Size:'), 0,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
self.tQTLeafSize = wx.TextCtrl(pan, -1, '%d' % pointQT.QT_MAXRECORDS)
hsizer.Add(self.tQTLeafSize, 0,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
bsizer.Add(hsizer, 0, wx.ALL, 0)
self.stQTSNR = wx.StaticText(pan, -1, 'Effective SNR = %3.2f' % pylab.sqrt(pointQT.QT_MAXRECORDS/2.0))
bsizer.Add(self.stQTSNR, 0, wx.ALL, 5)
#hsizer = wx.BoxSizer(wx.HORIZONTAL)
#hsizer.Add(wx.StaticText(pan, -1, 'Goal pixel size [nm]:'), 0,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
#self.tQTSize = wx.TextCtrl(pan, -1, '20000')
#hsizer.Add(self.tQTLeafSize, 0,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
#bsizer.Add(hsizer, 0, wx.ALL, 0)
pan.SetSizer(bsizer)
bsizer.Fit(pan)
item.AddNewElement(pan)
#self._pnl.AddFoldPanelWindow(item, pan, fpb.FPB_ALIGN_WIDTH, fpb.FPB_DEFAULT_SPACING, 5)
self.tQTLeafSize.Bind(wx.EVT_TEXT, self.OnQTLeafChange)
pnl.AddPane(item)
def GenTrackingPanel(self, _pnl):
item = afp.foldingPane(_pnl,
-1,
caption="Particle Tracking",
pinned=True)
pan = self.edit_traits(parent=item, kind='panel')
item.AddNewElement(pan.control)
#pan = wx.Panel(item, -1)
# vsizer = wx.BoxSizer(wx.VERTICAL)
#
## #if self.multiChannel: #we have channels
# hsizer = wx.BoxSizer(wx.HORIZONTAL)
# hsizer.Add(wx.StaticText(pan, -1, 'Features:'), 0,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
#
# self.tFeatures = wx.Text(pan, -1, 'x, y')
#
# hsizer.Add(self.tFeatures, 1,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
#
# vsizer.Add(hsizer, 0,wx.EXPAND|wx.ALL|wx.ALIGN_CENTER_HORIZONTAL, 0)
#
# hsizer = wx.BoxSizer(wx.HORIZONTAL)
#
#
#
# vsizer.Add(hsizer, 0,wx.ALL|wx.ALIGN_RIGHT, 5)
#
#
# pan.SetSizer(vsizer)
# vsizer.Fit(pan)
#item.AddNewElement(pan)
bTrack = wx.Button(item, -1, 'Track')
bTrack.Bind(wx.EVT_BUTTON, self.OnTrack)
item.AddNewElement(bTrack)
_pnl.AddPane(item)
def GenTrackingPanel(self, _pnl):
item = afp.foldingPane(_pnl, -1, caption="Particle Tracking", pinned = True)
pan = self.edit_traits(parent=item, kind='panel')
item.AddNewElement(pan.control)
#pan = wx.Panel(item, -1)
# vsizer = wx.BoxSizer(wx.VERTICAL)
#
## #if self.multiChannel: #we have channels
# hsizer = wx.BoxSizer(wx.HORIZONTAL)
# hsizer.Add(wx.StaticText(pan, -1, 'Features:'), 0,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
#
# self.tFeatures = wx.Text(pan, -1, 'x, y')
#
# hsizer.Add(self.tFeatures, 1,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
#
# vsizer.Add(hsizer, 0,wx.EXPAND|wx.ALL|wx.ALIGN_CENTER_HORIZONTAL, 0)
#
# hsizer = wx.BoxSizer(wx.HORIZONTAL)
#
#
#
# vsizer.Add(hsizer, 0,wx.ALL|wx.ALIGN_RIGHT, 5)
#
#
# pan.SetSizer(vsizer)
# vsizer.Fit(pan)
#item.AddNewElement(pan)
bTrack = wx.Button(item, -1, 'Track')
bTrack.Bind(wx.EVT_BUTTON, self.OnTrack)
item.AddNewElement(bTrack)
_pnl.AddPane(item)
def GenFitStatusPanel(self, _pnl):
item = afp.foldingPane(_pnl, -1, caption="Fit Status", pinned = True)
pan = wx.Panel(item, -1, size = (160, 300))
vsizer = wx.BoxSizer(wx.VERTICAL)
hsizer = wx.BoxSizer(wx.HORIZONTAL)
hsizer.Add(wx.StaticText(pan, -1, 'Colour:'), 0, wx.LEFT|wx.RIGHT|wx.ALIGN_CENTER_VERTICAL, 5)
self.chProgDispColour = wx.Choice(pan, -1, choices = ['z', 'gFrac', 't'], size=(60, -1))
self.chProgDispColour.Bind(wx.EVT_CHOICE, self.OnProgDispColourChange)
hsizer.Add(self.chProgDispColour, 1, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 0)
vsizer.Add(hsizer, 0,wx.BOTTOM|wx.EXPAND, 2)
hsizer = wx.BoxSizer(wx.HORIZONTAL)
hsizer.Add(wx.StaticText(pan, -1, 'CMap:'), 0, wx.LEFT|wx.RIGHT|wx.ALIGN_CENTER_VERTICAL, 5)
self.chProgDispCMap = wx.Choice(pan, -1, choices = ['gist_rainbow', 'RdYlGn'], size=(60, -1))
self.chProgDispCMap.Bind(wx.EVT_CHOICE, self.OnProgDispCMapChange)
hsizer.Add(self.chProgDispCMap, 1, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 0)
vsizer.Add(hsizer, 0,wx.BOTTOM|wx.EXPAND, 7)
self.progPan = progGraph.progPanel(pan, self.fitResults, size=(220, 250))
self.progPan.draw()
vsizer.Add(self.progPan, 1,wx.ALL|wx.ALIGN_CENTER_HORIZONTAL|wx.EXPAND, 0)
pan.SetSizer(vsizer)
vsizer.Fit(pan)
#_pnl.AddFoldPanelWindow(item, pan, fpb.FPB_ALIGN_WIDTH, fpb.FPB_DEFAULT_SPACING, 0)
item.AddNewElement(pan)
_pnl.AddPane(item)
def GenPSFPanel(self, _pnl):
item = afp.foldingPane(_pnl, -1, caption="PSF Extraction", pinned = True)
pan = wx.Panel(item, -1)
vsizer = wx.BoxSizer(wx.VERTICAL)
#if self.multiChannel: #we have channels
hsizer = wx.BoxSizer(wx.HORIZONTAL)
hsizer.Add(wx.StaticText(pan, -1, 'Channel:'), 0,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
self.chChannel = wx.Choice(pan, -1, choices=self.do.names)
hsizer.Add(self.chChannel, 1,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
vsizer.Add(hsizer, 0,wx.EXPAND|wx.ALL|wx.ALIGN_CENTER_HORIZONTAL, 0)
hsizer = wx.BoxSizer(wx.HORIZONTAL)
#
# hsizer.Add(wx.StaticText(pan, -1, 'Threshold:'), 0,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
# self.tThreshold = wx.TextCtrl(pan, -1, value='50', size=(40, -1))
#
bTagPSF = wx.Button(pan, -1, 'Tag', style=wx.BU_EXACTFIT)
bTagPSF.Bind(wx.EVT_BUTTON, self.OnTagPSF)
hsizer.Add(bTagPSF, 0,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
bTagPoints = wx.Button(pan, -1, 'Tag Points', style=wx.BU_EXACTFIT)
bTagPoints.Bind(wx.EVT_BUTTON, self.OnTagPoints)
hsizer.Add(bTagPoints, 0,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
bClearTagged = wx.Button(pan, -1, 'Clear', style=wx.BU_EXACTFIT)
bClearTagged.Bind(wx.EVT_BUTTON, self.OnClearTags)
hsizer.Add(bClearTagged, 0,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
vsizer.Add(hsizer, 0,wx.ALL|wx.ALIGN_CENTER_HORIZONTAL, 5)
hsizer = wx.BoxSizer(wx.HORIZONTAL)
hsizer.Add(wx.StaticText(pan, -1, 'ROI Size:'), 0,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
self.tPSFROI = wx.TextCtrl(pan, -1, value='30,30,30', size=(40, -1))
hsizer.Add(self.tPSFROI, 1,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
self.tPSFROI.Bind(wx.EVT_TEXT, self.OnPSFROI)
vsizer.Add(hsizer, 0,wx.EXPAND|wx.ALL|wx.ALIGN_CENTER_HORIZONTAL, 0)
hsizer = wx.BoxSizer(wx.HORIZONTAL)
hsizer.Add(wx.StaticText(pan, -1, 'Blur:'), 0,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
self.tPSFBlur = wx.TextCtrl(pan, -1, value='.5,.5,1', size=(40, -1))
hsizer.Add(self.tPSFBlur, 1,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
vsizer.Add(hsizer, 0,wx.EXPAND|wx.ALL|wx.ALIGN_CENTER_HORIZONTAL, 0)
hsizer = wx.BoxSizer(wx.HORIZONTAL)
hsizer.Add(wx.StaticText(pan, -1, 'PSF Type:'), 0,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
self.chType = wx.Choice(pan, -1, choices=['Widefield', 'Confocal'], size=(40, -1))
hsizer.Add(self.chType, 1,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
if 'Camera.IntegrationTime' in self.image.mdh.getEntryNames():
#most likely widefield
self.chType.SetSelection(0)
else:
#most likely confocal
#confocal is a safe default as widefield just does some fancy extra
#background correction
self.chType.SetSelection(1)
vsizer.Add(hsizer, 0,wx.EXPAND|wx.ALL|wx.ALIGN_CENTER_HORIZONTAL, 0)
hsizer = wx.BoxSizer(wx.HORIZONTAL)
bExtract = wx.Button(pan, -1, 'Extract', style=wx.BU_EXACTFIT)
bExtract.Bind(wx.EVT_BUTTON, self.OnExtractPSF)
hsizer.Add(bExtract, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
bExtractSplit = wx.Button(pan, -1, 'Extract Split', style=wx.BU_EXACTFIT)
bExtractSplit.Bind(wx.EVT_BUTTON, self.OnExtractSplitPSF)
hsizer.Add(bExtractSplit, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
vsizer.Add(hsizer, 0,wx.ALL|wx.ALIGN_RIGHT, 5)
bAxialShift = wx.Button(pan, -1, 'Estimate axial shift', style=wx.BU_EXACTFIT)
bAxialShift.Bind(wx.EVT_BUTTON, self.OnCalcShift)
vsizer.Add(bAxialShift, 0,wx.ALL|wx.ALIGN_RIGHT, 5)
pan.SetSizer(vsizer)
vsizer.Fit(pan)
#_pnl.AddFoldPanelWindow(item, pan, fpb.FPB_ALIGN_WIDTH, fpb.FPB_DEFAULT_SPACING, 5)
item.AddNewElement(pan)
_pnl.AddPane(item)
def GenBlobFindingPanel(self, _pnl):
item = afp.foldingPane(_pnl, -1, caption="Object Finding", pinned=True)
pan = wx.Panel(item, -1)
hsizer = wx.BoxSizer(wx.HORIZONTAL)
hsizer.Add(wx.StaticText(pan, -1, 'Threshold:'), 0,
wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5)
self.tThreshold = wx.TextCtrl(pan, -1, value='50', size=(40, -1))
hsizer.Add(self.tThreshold, 0, wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5)
pan.SetSizer(hsizer)
hsizer.Fit(pan)
#_pnl.AddFoldPanelWindow(item, pan, fpb.FPB_ALIGN_WIDTH, fpb.FPB_DEFAULT_SPACING, 5)
item.AddNewElement(pan)
pan = wx.Panel(item, -1)
hsizer = wx.BoxSizer(wx.HORIZONTAL)
#hsizer.Add(wx.StaticText(pan, -1, 'Method:'), 0,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
self.chMethod = wx.Choice(
pan,
-1,
choices=['Simple Threshold', 'SNR Threshold', 'Multi-threshold'])
self.chMethod.SetSelection(0)
self.chMethod.Bind(wx.EVT_CHOICE, self.OnChangeMethod)
hsizer.Add(self.chMethod, 0, wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5)
pan.SetSizer(hsizer)
hsizer.Fit(pan)
#_pnl.AddFoldPanelWindow(item, pan, fpb.FPB_ALIGN_WIDTH, fpb.FPB_DEFAULT_SPACING, 5)
item.AddNewElement(pan)
pan = wx.Panel(item, -1)
hsizer = wx.BoxSizer(wx.HORIZONTAL)
hsizer.Add(wx.StaticText(pan, -1, 'Channel:'), 0,
wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5)
self.chChannel = wx.Choice(pan, -1, choices=self.do.names)
hsizer.Add(self.chChannel, 1, wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5)
pan.SetSizer(hsizer)
hsizer.Fit(pan)
item.AddNewElement(pan)
pan = wx.Panel(item, -1)
hsizer = wx.BoxSizer(wx.HORIZONTAL)
hsizer.Add(wx.StaticText(pan, -1, 'Blur size:'), 0,
wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5)
self.tBlurSize = wx.TextCtrl(pan, -1, value='1.5', size=(40, -1))
self.tBlurSize.Disable()
hsizer.Add(self.tBlurSize, 0, wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5)
pan.SetSizer(hsizer)
hsizer.Fit(pan)
#_pnl.AddFoldPanelWindow(item, pan, fpb.FPB_ALIGN_WIDTH, fpb.FPB_DEFAULT_SPACING, 5)
item.AddNewElement(pan)
#self.cbSNThreshold = wx.CheckBox(item, -1, 'SNR Threshold')
#self.cbSNThreshold.SetValue(False)
#_pnl.AddFoldPanelWindow(item, self.cbSNThreshold, fpb.FPB_ALIGN_WIDTH, fpb.FPB_DEFAULT_SPACING, 5)
#item.AddNewElement(self.cbSNThreshold)
#self.cbThresholdRange = wx.CheckBox(item, -1, 'Multi-thresholds')
#self.cbThresholdRange.SetValue(False)
#_pnl.AddFoldPanelWindow(item, self.cbSNThreshold, fpb.FPB_ALIGN_WIDTH, fpb.FPB_DEFAULT_SPACING, 5)
#item.AddNewElement(self.cbThresholdRange)
bFindObjects = wx.Button(item, -1, 'Find')
bFindObjects.Bind(wx.EVT_BUTTON, self.OnFindObjects)
#_pnl.AddFoldPanelWindow(item, bFindObjects, fpb.FPB_ALIGN_WIDTH, fpb.FPB_DEFAULT_SPACING, 10)
item.AddNewElement(bFindObjects)
_pnl.AddPane(item)
def GenBlobFindingPanel(self, _pnl):
item = afp.foldingPane(_pnl, -1, caption="Object Finding", pinned = True)
pan = wx.Panel(item, -1)
hsizer = wx.BoxSizer(wx.HORIZONTAL)
hsizer.Add(wx.StaticText(pan, -1, 'Threshold:'), 0,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
self.tThreshold = wx.TextCtrl(pan, -1, value='50', size=(40, -1))
hsizer.Add(self.tThreshold, 0,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
pan.SetSizer(hsizer)
hsizer.Fit(pan)
#_pnl.AddFoldPanelWindow(item, pan, fpb.FPB_ALIGN_WIDTH, fpb.FPB_DEFAULT_SPACING, 5)
item.AddNewElement(pan)
pan = wx.Panel(item, -1)
hsizer = wx.BoxSizer(wx.HORIZONTAL)
#hsizer.Add(wx.StaticText(pan, -1, 'Method:'), 0,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
self.chMethod = wx.Choice(pan, -1, choices=['Simple Threshold', 'SNR Threshold', 'Multi-threshold'])
self.chMethod.SetSelection(0)
self.chMethod.Bind(wx.EVT_CHOICE, self.OnChangeMethod)
hsizer.Add(self.chMethod, 0,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
pan.SetSizer(hsizer)
hsizer.Fit(pan)
#_pnl.AddFoldPanelWindow(item, pan, fpb.FPB_ALIGN_WIDTH, fpb.FPB_DEFAULT_SPACING, 5)
item.AddNewElement(pan)
pan = wx.Panel(item, -1)
hsizer = wx.BoxSizer(wx.HORIZONTAL)
hsizer.Add(wx.StaticText(pan, -1, 'Channel:'), 0,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
self.chChannel = wx.Choice(pan, -1, choices=self.do.names)
hsizer.Add(self.chChannel, 1,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
pan.SetSizer(hsizer)
hsizer.Fit(pan)
item.AddNewElement(pan)
pan = wx.Panel(item, -1)
hsizer = wx.BoxSizer(wx.HORIZONTAL)
hsizer.Add(wx.StaticText(pan, -1, 'Blur size:'), 0,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
self.tBlurSize = wx.TextCtrl(pan, -1, value='1.5', size=(40, -1))
self.tBlurSize.Disable()
hsizer.Add(self.tBlurSize, 0,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
pan.SetSizer(hsizer)
hsizer.Fit(pan)
#_pnl.AddFoldPanelWindow(item, pan, fpb.FPB_ALIGN_WIDTH, fpb.FPB_DEFAULT_SPACING, 5)
item.AddNewElement(pan)
#self.cbSNThreshold = wx.CheckBox(item, -1, 'SNR Threshold')
#self.cbSNThreshold.SetValue(False)
#_pnl.AddFoldPanelWindow(item, self.cbSNThreshold, fpb.FPB_ALIGN_WIDTH, fpb.FPB_DEFAULT_SPACING, 5)
#item.AddNewElement(self.cbSNThreshold)
#self.cbThresholdRange = wx.CheckBox(item, -1, 'Multi-thresholds')
#self.cbThresholdRange.SetValue(False)
#_pnl.AddFoldPanelWindow(item, self.cbSNThreshold, fpb.FPB_ALIGN_WIDTH, fpb.FPB_DEFAULT_SPACING, 5)
#item.AddNewElement(self.cbThresholdRange)
bFindObjects = wx.Button(item, -1, 'Find')
bFindObjects.Bind(wx.EVT_BUTTON, self.OnFindObjects)
#_pnl.AddFoldPanelWindow(item, bFindObjects, fpb.FPB_ALIGN_WIDTH, fpb.FPB_DEFAULT_SPACING, 10)
item.AddNewElement(bFindObjects)
_pnl.AddPane(item)
def GenAnalysisPanel(self, _pnl):
item = afp.foldingPane(_pnl, -1, caption="Analysis", pinned = True)
##############################
pan = wx.Panel(item, -1)
vsizer = wx.BoxSizer(wx.VERTICAL)
hsizer = wx.BoxSizer(wx.HORIZONTAL)
hsizer.Add(wx.StaticText(pan, -1, 'Start at:'), 1,wx.RIGHT|wx.ALIGN_CENTER_VERTICAL, 5)
if 'Protocol.DataStartsAt' in self.image.mdh.getEntryNames():
startAt = self.image.mdh.getEntry('Protocol.DataStartsAt')
else:
startAt = self.do.zp
self.tStartAt = wx.TextCtrl(pan, -1, value='%d' % startAt, size=(50, -1))
hsizer.Add(self.tStartAt, 0,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 0)
vsizer.Add(hsizer, 0,wx.BOTTOM|wx.EXPAND, 2)
hsizer = wx.BoxSizer(wx.HORIZONTAL)
hsizer.Add(wx.StaticText(pan, -1, 'Background:'), 1,wx.RIGHT|wx.ALIGN_CENTER_VERTICAL, 5)
self.tBackgroundFrames = wx.TextCtrl(pan, -1, value='-30:0', size=(50, -1))
hsizer.Add(self.tBackgroundFrames, 0,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 0)
vsizer.Add(hsizer, 0,wx.BOTTOM|wx.EXPAND, 2)
pan.SetSizer(vsizer)
vsizer.Fit(pan)
item.AddNewElement(pan)
self.cbSubtractBackground = wx.CheckBox(item, -1, 'Subtract background in fit')
self.cbSubtractBackground.SetValue(True)
item.AddNewElement(self.cbSubtractBackground)
#############################
#std options
pan = wx.Panel(item, -1)
vsizer = wx.BoxSizer(wx.VERTICAL)
pan.SetSizer(vsizer)
self._populateStdOptionsPanel(pan, vsizer)
item.AddNewElement(pan)
#######################
#Fit factory selection
pan = wx.Panel(item, -1)
#find out what fit factories we have
self.fitFactories = PYME.Analysis.FitFactories.resFitFactories
print((self.fitFactories))
vsizer = wx.BoxSizer(wx.VERTICAL)
hsizer = wx.BoxSizer(wx.HORIZONTAL)
hsizer.Add(wx.StaticText(pan, -1, 'Type:'), 0,wx.RIGHT|wx.ALIGN_CENTER_VERTICAL, 5)
self.cFitType = wx.Choice(pan, -1, choices = ['{:<35} \t- {:} '.format(f, PYME.Analysis.FitFactories.useFor[f]) for f in self.fitFactories], size=(110, -1))
if 'Analysis.FitModule' in self.image.mdh.getEntryNames():
#has already been analysed - most likely to want the same method again
self.cFitType.SetSelection(self.fitFactories.index(self.image.mdh['Analysis.FitModule']))
self.tThreshold.SetValue('%s' % self.image.mdh['Analysis.DetectionThreshold'])
#elif 'Camera.ROIPosY' in self.image.mdh.getEntryNames() and (self.image.mdh.getEntry('Camera.ROIHeight') + 1 + 2*(self.image.mdh.getEntry('Camera.ROIPosY')-1)) == 512:
# #we have a symetrical ROI about the centre - most likely want to analyse using splitter
# self.cFitType.SetSelection(self.fitFactories.index('SplitterFitQR'))
# self.tThreshold.SetValue('0.5')
else:
self.cFitType.SetSelection(self.fitFactories.index('LatGaussFitFR'))
self.cFitType.Bind(wx.EVT_CHOICE, self.OnFitModuleChanged)
hsizer.Add(self.cFitType, 1,wx.ALIGN_CENTER_VERTICAL, 0)
vsizer.Add(hsizer, 0,wx.BOTTOM|wx.EXPAND, 2)
pan.SetSizer(vsizer)
vsizer.Fit(pan)
item.AddNewElement(pan)
# self.cbDrift = wx.CheckBox(item, -1, 'Estimate Drift')
# self.cbDrift.SetValue(False)
#
# #_pnl.AddFoldPanelWindow(item, self.cbDrift, fpb.FPB_ALIGN_WIDTH, 7, 5)
# item.AddNewElement(self.cbDrift)
########################################
#custom (fit factory dependant) options
self.customOptionsPan = wx.Panel(item, -1)
self.customOptionsSizer = wx.BoxSizer(wx.VERTICAL)
self.customOptionsPan.SetSizer(self.customOptionsSizer)
self._populateCustomAnalysisPanel(self.customOptionsPan, self.customOptionsSizer)
item.AddNewElement(self.customOptionsPan)
######################
#Go
self.bGo = wx.Button(item, -1, 'Go')
self.bGo.Bind(wx.EVT_BUTTON, self.OnGo)
item.AddNewElement(self.bGo)
_pnl.AddPane(item)
self.analysisPanel = item
def GenAnalysisPanel(self, _pnl):
item = afp.foldingPane(_pnl, -1, caption="Analysis", pinned=True)
##############################
pan = wx.Panel(item, -1)
vsizer = wx.BoxSizer(wx.VERTICAL)
hsizer = wx.BoxSizer(wx.HORIZONTAL)
hsizer.Add(wx.StaticText(pan, -1, 'Start at:'), 1,
wx.RIGHT | wx.ALIGN_CENTER_VERTICAL, 5)
if 'Protocol.DataStartsAt' in self.image.mdh.getEntryNames():
startAt = self.image.mdh.getEntry('Protocol.DataStartsAt')
else:
startAt = self.do.zp
self.tStartAt = wx.TextCtrl(pan,
-1,
value='%d' % startAt,
size=(50, -1))
hsizer.Add(self.tStartAt, 0, wx.ALL | wx.ALIGN_CENTER_VERTICAL, 0)
vsizer.Add(hsizer, 0, wx.BOTTOM | wx.EXPAND, 2)
hsizer = wx.BoxSizer(wx.HORIZONTAL)
hsizer.Add(wx.StaticText(pan, -1, 'Background:'), 1,
wx.RIGHT | wx.ALIGN_CENTER_VERTICAL, 5)
self.tBackgroundFrames = wx.TextCtrl(pan,
-1,
value='-30:0',
size=(50, -1))
hsizer.Add(self.tBackgroundFrames, 0,
wx.ALL | wx.ALIGN_CENTER_VERTICAL, 0)
vsizer.Add(hsizer, 0, wx.BOTTOM | wx.EXPAND, 2)
pan.SetSizer(vsizer)
vsizer.Fit(pan)
item.AddNewElement(pan)
self.cbSubtractBackground = wx.CheckBox(item, -1,
'Subtract background in fit')
self.cbSubtractBackground.SetValue(True)
item.AddNewElement(self.cbSubtractBackground)
#############################
#std options
pan = wx.Panel(item, -1)
vsizer = wx.BoxSizer(wx.VERTICAL)
pan.SetSizer(vsizer)
self._populateStdOptionsPanel(pan, vsizer)
item.AddNewElement(pan)
#######################
#Fit factory selection
pan = wx.Panel(item, -1)
#find out what fit factories we have
self.fitFactories = PYME.Analysis.FitFactories.resFitFactories
print((self.fitFactories))
vsizer = wx.BoxSizer(wx.VERTICAL)
hsizer = wx.BoxSizer(wx.HORIZONTAL)
hsizer.Add(wx.StaticText(pan, -1, 'Type:'), 0,
wx.RIGHT | wx.ALIGN_CENTER_VERTICAL, 5)
self.cFitType = wx.Choice(pan,
-1,
choices=[
'{:<35} \t- {:} '.format(
f,
PYME.Analysis.FitFactories.useFor[f])
for f in self.fitFactories
],
size=(110, -1))
if 'Analysis.FitModule' in self.image.mdh.getEntryNames():
#has already been analysed - most likely to want the same method again
self.cFitType.SetSelection(
self.fitFactories.index(self.image.mdh['Analysis.FitModule']))
self.tThreshold.SetValue(
'%s' % self.image.mdh['Analysis.DetectionThreshold'])
#elif 'Camera.ROIPosY' in self.image.mdh.getEntryNames() and (self.image.mdh.getEntry('Camera.ROIHeight') + 1 + 2*(self.image.mdh.getEntry('Camera.ROIPosY')-1)) == 512:
# #we have a symetrical ROI about the centre - most likely want to analyse using splitter
# self.cFitType.SetSelection(self.fitFactories.index('SplitterFitQR'))
# self.tThreshold.SetValue('0.5')
else:
self.cFitType.SetSelection(
self.fitFactories.index('LatGaussFitFR'))
self.cFitType.Bind(wx.EVT_CHOICE, self.OnFitModuleChanged)
hsizer.Add(self.cFitType, 1, wx.ALIGN_CENTER_VERTICAL, 0)
vsizer.Add(hsizer, 0, wx.BOTTOM | wx.EXPAND, 2)
pan.SetSizer(vsizer)
vsizer.Fit(pan)
item.AddNewElement(pan)
# self.cbDrift = wx.CheckBox(item, -1, 'Estimate Drift')
# self.cbDrift.SetValue(False)
#
# #_pnl.AddFoldPanelWindow(item, self.cbDrift, fpb.FPB_ALIGN_WIDTH, 7, 5)
# item.AddNewElement(self.cbDrift)
########################################
#custom (fit factory dependant) options
self.customOptionsPan = wx.Panel(item, -1)
self.customOptionsSizer = wx.BoxSizer(wx.VERTICAL)
self.customOptionsPan.SetSizer(self.customOptionsSizer)
self._populateCustomAnalysisPanel(self.customOptionsPan,
self.customOptionsSizer)
item.AddNewElement(self.customOptionsPan)
######################
#Go
self.bGo = wx.Button(item, -1, 'Go')
self.bGo.Bind(wx.EVT_BUTTON, self.OnGo)
item.AddNewElement(self.bGo)
_pnl.AddPane(item)
self.analysisPanel = item
def GenPSFPanel(self, _pnl):
item = afp.foldingPane(_pnl, -1, caption="PSF Extraction", pinned=True)
pan = wx.Panel(item, -1)
vsizer = wx.BoxSizer(wx.VERTICAL)
#if self.multiChannel: #we have channels
hsizer = wx.BoxSizer(wx.HORIZONTAL)
hsizer.Add(wx.StaticText(pan, -1, 'Channel:'), 0,
wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5)
self.chChannel = wx.Choice(pan, -1, choices=self.do.names)
hsizer.Add(self.chChannel, 1, wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5)
vsizer.Add(hsizer, 0, wx.EXPAND | wx.ALL | wx.ALIGN_CENTER_HORIZONTAL,
0)
hsizer = wx.BoxSizer(wx.HORIZONTAL)
#
# hsizer.Add(wx.StaticText(pan, -1, 'Threshold:'), 0,wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5)
# self.tThreshold = wx.TextCtrl(pan, -1, value='50', size=(40, -1))
#
bTagPSF = wx.Button(pan, -1, 'Tag', style=wx.BU_EXACTFIT)
bTagPSF.Bind(wx.EVT_BUTTON, self.OnTagPSF)
hsizer.Add(bTagPSF, 0, wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5)
bTagPoints = wx.Button(pan, -1, 'Tag Points', style=wx.BU_EXACTFIT)
bTagPoints.Bind(wx.EVT_BUTTON, self.OnTagPoints)
hsizer.Add(bTagPoints, 0, wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5)
bClearTagged = wx.Button(pan, -1, 'Clear', style=wx.BU_EXACTFIT)
bClearTagged.Bind(wx.EVT_BUTTON, self.OnClearTags)
hsizer.Add(bClearTagged, 0, wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5)
vsizer.Add(hsizer, 0, wx.ALL | wx.ALIGN_CENTER_HORIZONTAL, 5)
hsizer = wx.BoxSizer(wx.HORIZONTAL)
hsizer.Add(wx.StaticText(pan, -1, 'ROI Size:'), 0,
wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5)
self.tPSFROI = wx.TextCtrl(pan, -1, value='30,30,30', size=(40, -1))
hsizer.Add(self.tPSFROI, 1, wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5)
self.tPSFROI.Bind(wx.EVT_TEXT, self.OnPSFROI)
vsizer.Add(hsizer, 0, wx.EXPAND | wx.ALL | wx.ALIGN_CENTER_HORIZONTAL,
0)
hsizer = wx.BoxSizer(wx.HORIZONTAL)
hsizer.Add(wx.StaticText(pan, -1, 'Blur:'), 0,
wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5)
self.tPSFBlur = wx.TextCtrl(pan, -1, value='.5,.5,1', size=(40, -1))
hsizer.Add(self.tPSFBlur, 1, wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5)
vsizer.Add(hsizer, 0, wx.EXPAND | wx.ALL | wx.ALIGN_CENTER_HORIZONTAL,
0)
hsizer = wx.BoxSizer(wx.HORIZONTAL)
hsizer.Add(wx.StaticText(pan, -1, 'PSF Type:'), 0,
wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5)
self.chType = wx.Choice(pan,
-1,
choices=['Widefield', 'Confocal'],
size=(40, -1))
hsizer.Add(self.chType, 1, wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5)
if 'Camera.IntegrationTime' in self.image.mdh.getEntryNames():
#most likely widefield
self.chType.SetSelection(0)
else:
#most likely confocal
#confocal is a safe default as widefield just does some fancy extra
#background correction
self.chType.SetSelection(1)
vsizer.Add(hsizer, 0, wx.EXPAND | wx.ALL | wx.ALIGN_CENTER_HORIZONTAL,
0)
hsizer = wx.BoxSizer(wx.HORIZONTAL)
bExtract = wx.Button(pan, -1, 'Extract', style=wx.BU_EXACTFIT)
bExtract.Bind(wx.EVT_BUTTON, self.OnExtractPSF)
hsizer.Add(bExtract, 0, wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5)
bExtractSplit = wx.Button(pan,
-1,
'Extract Split',
style=wx.BU_EXACTFIT)
bExtractSplit.Bind(wx.EVT_BUTTON, self.OnExtractSplitPSF)
hsizer.Add(bExtractSplit, 0, wx.ALL | wx.ALIGN_CENTER_VERTICAL, 5)
vsizer.Add(hsizer, 0, wx.ALL | wx.ALIGN_RIGHT, 5)
bAxialShift = wx.Button(pan,
-1,
'Estimate axial shift',
style=wx.BU_EXACTFIT)
bAxialShift.Bind(wx.EVT_BUTTON, self.OnCalcShift)
vsizer.Add(bAxialShift, 0, wx.ALL | wx.ALIGN_RIGHT, 5)
pan.SetSizer(vsizer)
vsizer.Fit(pan)
#_pnl.AddFoldPanelWindow(item, pan, fpb.FPB_ALIGN_WIDTH, fpb.FPB_DEFAULT_SPACING, 5)
item.AddNewElement(pan)
_pnl.AddPane(item)
