def __init__(self, parent, sourceImage, destImage):
from PYME.Deconv import wiener
wx.Panel.__init__(self, parent)
self.dw = wiener.dec_wiener()
self.sourceImage = sourceImage
self.destImage = destImage
self.havePSF = False
self.decT = None
#GUI stuff
sizer2 = wx.BoxSizer(wx.VERTICAL)
sizer3 = wx.BoxSizer(wx.HORIZONTAL)
sizer3.Add(wx.StaticText(self, -1, 'PSF:'), 0, wx.ALIGN_CENTER_VERTICAL | wx.ALL, 5)
self.fpPSF = wx.FilePickerCtrl(self, -1, wildcard='*.psf', style=wx.FLP_OPEN|wx.FLP_FILE_MUST_EXIST)
self.fpPSF.Bind(wx.EVT_FILEPICKER_CHANGED, self.OnPSFFileChanged)
sizer3.Add(self.fpPSF, 1, wx.ALIGN_CENTER_VERTICAL | wx.ALL, 5)
sizer2.Add(sizer3, 0, wx.EXPAND|wx.ALIGN_CENTER_VERTICAL | wx.ALL, 0)
sizer3 = wx.BoxSizer(wx.HORIZONTAL)
sizer3.Add(wx.StaticText(self, -1, 'Offset:'), 0, wx.ALIGN_CENTER_VERTICAL | wx.ALL, 5)
self.tOffset = wx.TextCtrl(self, -1, '0')
sizer3.Add(self.tOffset, 1, wx.ALIGN_CENTER_VERTICAL | wx.ALL, 5)
sizer2.Add(sizer3, 0, wx.EXPAND|wx.ALIGN_CENTER_VERTICAL | wx.ALL, 0)
sizer3 = wx.BoxSizer(wx.HORIZONTAL)
sizer3.Add(wx.StaticText(self, -1, u'Regularisation \u03BB:'), 0, wx.ALIGN_CENTER_VERTICAL | wx.ALL, 5)
self.tRegLambda = wx.TextCtrl(self, -1, '1e-8')
sizer3.Add(self.tRegLambda, 1, wx.ALIGN_CENTER_VERTICAL | wx.ALL, 5)
sizer2.Add(sizer3, 0, wx.EXPAND|wx.ALIGN_CENTER_VERTICAL | wx.ALL, 0)
sizer3 = wx.BoxSizer(wx.HORIZONTAL)
sizer3.AddSpacer(10)
self.bCalculate = wx.Button(self, -1, 'Apply')
self.bCalculate.Bind(wx.EVT_BUTTON, self.OnCalculate)
self.bCalculate.Enable(False)
sizer3.Add(self.bCalculate, 1, wx.ALIGN_CENTER_VERTICAL | wx.ALL, 5)
sizer2.Add(sizer3, 0, wx.EXPAND|wx.ALIGN_CENTER_VERTICAL | wx.ALL, 0)
self.SetSizerAndFit(sizer2)
self.deconTimer = mytimer()
self.deconTimer.WantNotification.append(self.OnDeconTimer)
self.deconTimer.Start(500)
def __init__(self, parent, dsviewer):
wx.Panel.__init__(self,parent, -1)
dirname = os.path.dirname(__file__)
self.do = dsviewer.do
self.dsviewer = dsviewer
self.bmStartSeek = wx.Bitmap(os.path.join(dirname, '../icons/media-skip-backward.png'))
self.bmPlay = wx.Bitmap(os.path.join(dirname,'../icons/media-playback-start.png'))
self.bmPause = wx.Bitmap(os.path.join(dirname,'../icons/media-playback-pause.png'))
self.mode = 'HORIZ'
self.moving= False
#timer for playback
self.tPlay = mytimer()
self.tPlay.WantNotification.append(self.OnFrame)
self.do.WantChangeNotification.append(self.update)
self.genContents(self.mode)
self.Bind(wx.EVT_SIZE, self.OnSize)
def OnDeconvICTM(self, event, beadMode=False):
from PYME.Deconv.deconvDialogs import DeconvSettingsDialog,DeconvProgressDialog,DeconvProgressPanel
dlg = DeconvSettingsDialog(self.dsviewer, beadMode, self.image.data.shape[3])
if dlg.ShowModal() == wx.ID_OK:
from PYME.Deconv import dec, decThread, richardsonLucy
nIter = dlg.GetNumIterationss()
regLambda = dlg.GetRegularisationLambda()
decMDH = MetaDataHandler.NestedClassMDHandler(self.image.mdh)
decMDH['Deconvolution.NumIterations'] = nIter
decMDH['Deconvolution.OriginalFile'] = self.image.filename
#self.dlgDeconProg = DeconvProgressDialog(self.dsviewer, nIter)
#self.dlgDeconProg.Show()
vx = self.image.mdh.getEntry('voxelsize.x')
vy = self.image.mdh.getEntry('voxelsize.y')
vz = self.image.mdh.getEntry('voxelsize.z')
if beadMode:
from PYME.Deconv import beadGen
psf = beadGen.genBeadImage(dlg.GetBeadRadius(), (1e3*vx, 1e3*vy, 1e3*vz))
decMDH['Deconvolution.BeadRadius'] = dlg.GetBeadRadius()
else:
#psf, vs = numpy.load(dlg.GetPSFFilename())
#psf = numpy.atleast_3d(psf)
psfFilename, psf, vs = dlg.GetPSF(vshint = vx)
decMDH['Deconvolution.PSFFile'] = dlg.GetPSFFilename()
if not (vs.x == vx and vs.y == vy and vs.z ==vz):
#rescale psf to match data voxel size
psf = ndimage.zoom(psf, [vs.x/vx, vs.y/vy, vs.z/vz])
data = self.image.data[:,:,:, dlg.GetChannel()].astype('f') - dlg.GetOffset()
decMDH['Deconvolution.Offset'] = dlg.GetOffset()
bg = dlg.GetBackground()
decMDH['Deconvolution.Background'] = bg
#crop PSF in z if bigger than stack
print psf.shape, data.shape
if psf.shape[2] > data.shape[2]:
dz = psf.shape[2] - data.shape[2]
psf = psf[:,:,numpy.floor(dz/2):(psf.shape[2]-numpy.ceil(dz/2))]
print((data.shape, psf.shape))
if dlg.GetPadding():
padsize = numpy.array(dlg.GetPadSize())
decMDH['Deconvolution.Padding'] = padsize
dp = numpy.ones(numpy.array(data.shape) + 2*padsize, 'f')*data.mean()
weights = numpy.zeros_like(dp)
px, py, pz = padsize
#print data.shape, dp[px:-(px+1), py:-(py+1), pz:-(pz+1)].shape
dp[px:-px, py:-py, pz:-pz] = data
#if dlg.GetRemovePadding():
# data = dp[px:-px, py:-py, pz:-pz]#should be a slice
#else:
# data = dp
weights[px:-px, py:-py, pz:-pz] = 1.
weights = weights.ravel()
else:
dp = data
weights = 1
if dlg.GetBlocking():
decMDH['Deconvolution.Method'] = 'Blocked ICTM'
self.checkTQ()
from PYME.Deconv import tq_block_dec
bs = dlg.GetBlockSize()
self.decT = tq_block_dec.blocking_deconv(self.tq, data, psf, self.image.seriesName, blocksize={'y': bs, 'x': bs, 'z': 256})
self.decT.go()
else:
decMDH['Deconvolution.Method'] = dlg.GetMethod()
if dlg.GetMethod() == 'ICTM':
decMDH['Deconvolution.RegularisationParameter'] = regLambda
if beadMode:
self.dec = dec.dec_bead()
else:
self.dec = dec.dec_conv()
else:
if beadMode:
self.dec = richardsonLucy.rlbead()
else:
self.dec = richardsonLucy.dec_conv()
self.dec.psf_calc(psf, dp.shape)
self.decT = decThread.decThread(self.dec, dp, regLambda, nIter, weights, bg = bg)
self.decT.start()
tries = 0
while tries < 10 and not hasattr(self.dec, 'fs'):
time.sleep(1)
tries += 1
if dlg.GetPadding() and dlg.GetRemovePadding():
fs = self.dec.fs[px:-px, py:-py, pz:-pz]
else:
fs = self.dec.fs
im = ImageStack(data = fs, mdh = decMDH, titleStub = 'Deconvolution Result')
mode = 'lite'
if beadMode:
mode = 'psf'
im.defaultExt = '*.psf' #we want to save as PSF by default
self.res = ViewIm3D(im, mode=mode, parent=wx.GetTopLevelParent(self.dsviewer))
#self.res = View3D(fs, 'Deconvolution Result', mdh=decMDH, parent=wx.GetTopLevelParent(self.dsviewer), mode=mode)
self.dlgDeconProg = DeconvProgressPanel(self.res, nIter)
self.pinfo1 = aui.AuiPaneInfo().Name("deconvPanel").Top().Caption('Deconvolution Progress').DestroyOnClose(True).CloseButton(False)#.MinimizeButton(True).MinimizeMode(aui.AUI_MINIMIZE_CAPT_SMART|aui.AUI_MINIMIZE_POS_RIGHT)#.CaptionVisible(False)
self.res._mgr.AddPane(self.dlgDeconProg, self.pinfo1)
self.res._mgr.Update()
self.deconTimer = mytimer()
self.deconTimer.WantNotification.append(self.OnDeconTimer)
self.deconTimer.Start(500)
def OnDeconvICTM(self, event, beadMode=False):
from PYME.Deconv.deconvDialogs import DeconvSettingsDialog, DeconvProgressDialog, DeconvProgressPanel
dlg = DeconvSettingsDialog(self.dsviewer, beadMode,
self.image.data.shape[3])
if dlg.ShowModal() == wx.ID_OK:
from PYME.Deconv import dec, decThread, richardsonLucy
nIter = dlg.GetNumIterationss()
regLambda = dlg.GetRegularisationLambda()
decMDH = MetaDataHandler.NestedClassMDHandler(self.image.mdh)
decMDH['Deconvolution.NumIterations'] = nIter
decMDH['Deconvolution.OriginalFile'] = self.image.filename
#self.dlgDeconProg = DeconvProgressDialog(self.dsviewer, nIter)
#self.dlgDeconProg.Show()
vx = self.image.mdh.getEntry('voxelsize.x')
vy = self.image.mdh.getEntry('voxelsize.y')
vz = self.image.mdh.getEntry('voxelsize.z')
if beadMode:
from PYME.Deconv import beadGen
psf = beadGen.genBeadImage(dlg.GetBeadRadius(),
(1e3 * vx, 1e3 * vy, 1e3 * vz))
decMDH['Deconvolution.BeadRadius'] = dlg.GetBeadRadius()
else:
#psf, vs = numpy.load(dlg.GetPSFFilename())
#psf = numpy.atleast_3d(psf)
psfFilename, psf, vs = dlg.GetPSF(vshint=vx)
decMDH['Deconvolution.PSFFile'] = dlg.GetPSFFilename()
if not (vs.x == vx and vs.y == vy and vs.z == vz):
#rescale psf to match data voxel size
psf = ndimage.zoom(psf, [vs.x / vx, vs.y / vy, vs.z / vz])
data = self.image.data[:, :, :, dlg.GetChannel()].astype(
'f') - dlg.GetOffset()
decMDH['Deconvolution.Offset'] = dlg.GetOffset()
bg = dlg.GetBackground()
decMDH['Deconvolution.Background'] = bg
#crop PSF in z if bigger than stack
print psf.shape, data.shape
if psf.shape[2] > data.shape[2]:
dz = psf.shape[2] - data.shape[2]
psf = psf[:, :,
numpy.floor(dz / 2):(psf.shape[2] -
numpy.ceil(dz / 2))]
print((data.shape, psf.shape))
if dlg.GetPadding():
padsize = numpy.array(dlg.GetPadSize())
decMDH['Deconvolution.Padding'] = padsize
dp = numpy.ones(numpy.array(data.shape) + 2 * padsize,
'f') * data.mean()
weights = numpy.zeros_like(dp)
px, py, pz = padsize
#print data.shape, dp[px:-(px+1), py:-(py+1), pz:-(pz+1)].shape
dp[px:-px, py:-py, pz:-pz] = data
#if dlg.GetRemovePadding():
# data = dp[px:-px, py:-py, pz:-pz]#should be a slice
#else:
# data = dp
weights[px:-px, py:-py, pz:-pz] = 1.
weights = weights.ravel()
else:
dp = data
weights = 1
if dlg.GetBlocking():
decMDH['Deconvolution.Method'] = 'Blocked ICTM'
self.checkTQ()
from PYME.Deconv import tq_block_dec
bs = dlg.GetBlockSize()
self.decT = tq_block_dec.blocking_deconv(self.tq,
data,
psf,
self.image.seriesName,
blocksize={
'y': bs,
'x': bs,
'z': 256
})
self.decT.go()
else:
decMDH['Deconvolution.Method'] = dlg.GetMethod()
if dlg.GetMethod() == 'ICTM':
decMDH['Deconvolution.RegularisationParameter'] = regLambda
if beadMode:
self.dec = dec.dec_bead()
else:
self.dec = dec.dec_conv()
else:
if beadMode:
self.dec = richardsonLucy.rlbead()
else:
self.dec = richardsonLucy.dec_conv()
self.dec.psf_calc(psf, dp.shape)
self.decT = decThread.decThread(self.dec,
dp,
regLambda,
nIter,
weights,
bg=bg)
self.decT.start()
tries = 0
while tries < 10 and not hasattr(self.dec, 'fs'):
time.sleep(1)
tries += 1
if dlg.GetPadding() and dlg.GetRemovePadding():
fs = self.dec.fs[px:-px, py:-py, pz:-pz]
else:
fs = self.dec.fs
im = ImageStack(data=fs,
mdh=decMDH,
titleStub='Deconvolution Result')
mode = 'lite'
if beadMode:
mode = 'psf'
im.defaultExt = '*.psf' #we want to save as PSF by default
self.res = ViewIm3D(im,
mode=mode,
parent=wx.GetTopLevelParent(self.dsviewer))
#self.res = View3D(fs, 'Deconvolution Result', mdh=decMDH, parent=wx.GetTopLevelParent(self.dsviewer), mode=mode)
self.dlgDeconProg = DeconvProgressPanel(self.res, nIter)
self.pinfo1 = aui.AuiPaneInfo().Name("deconvPanel").Top(
).Caption('Deconvolution Progress').DestroyOnClose(
True
).CloseButton(
False
) #.MinimizeButton(True).MinimizeMode(aui.AUI_MINIMIZE_CAPT_SMART|aui.AUI_MINIMIZE_POS_RIGHT)#.CaptionVisible(False)
self.res._mgr.AddPane(self.dlgDeconProg, self.pinfo1)
self.res._mgr.Update()
self.deconTimer = mytimer()
self.deconTimer.WantNotification.append(self.OnDeconTimer)
self.deconTimer.Start(500)
def __init__(self, parent, options=None):
self._init_ctrls(parent)
self.options = options
self._mgr = aui.AuiManager(agwFlags=aui.AUI_MGR_DEFAULT
| aui.AUI_MGR_AUTONB_NO_CAPTION)
atabstyle = self._mgr.GetAutoNotebookStyle()
self._mgr.SetAutoNotebookStyle((atabstyle ^ aui.AUI_NB_BOTTOM)
| aui.AUI_NB_TOP)
# tell AuiManager to manage this frame
self._mgr.SetManagedWindow(self)
self.snapNum = 0
wx.EVT_CLOSE(self, self.OnCloseWindow)
self.MainFrame = self #reference to this window for use in scripts etc...
self.MainMenu = self.menuBar1
protocol.MainFrame = self
self.toolPanels = []
self.camPanels = []
self.postInit = []
self.initDone = False
self.scope = microscope.microscope()
self.splash = splashScreen.SplashScreen(self, self.scope)
self.splash.Show()
# self.sh = wx.py.shell.Shell(id=-1,
# parent=self.notebook1, size=wx.Size(-1, -1), style=0, locals=self.__dict__,
# introText='Python SMI bindings - note that help, license etc below is for Python, not PySMI\n\n')
#
self.sh = wx.py.shell.Shell(
id=-1,
parent=self,
size=wx.Size(-1, -1),
style=0,
locals=self.__dict__,
introText=
'Python SMI bindings - note that help, license etc below is for Python, not PySMI\n\n'
)
#self.notebook1.AddPage(imageId=-1, page=self.sh, select=True, text='Console')
#self.notebook1.AddPage(imageId=-1, page=self.panel1, select=False, text='About')
#self.notebook1.AddPage(page=self.sh, select=True, caption='Console')
self._mgr.AddPane(
self.sh,
aui.AuiPaneInfo().Name("shell").Caption(
"Console").Centre().CloseButton(False))
# self.notebook1.AddPage( page=self.panel1, select=False, caption='About')
#self.SetSize((400, 800))
self.CreateToolPanel()
#self.SetSize((1000, 800))
#self.sizer = wx.BoxSizer()
#self.sizer.Add(self.notebook1, 1, wx.EXPAND)
#self.SetSizer(self.Sizer)
self.SetSize((1030, 895))
#self._mgr.Update()
self.roi_on = False
self.bin_on = False
self.time1 = mytimer.mytimer()
self.time1.Start(500)
self.time1.WantNotification.append(self.runInitScript)
self.time1.WantNotification.append(self.checkInitDone)
self.time1.WantNotification.append(self.splash.Tick)
def __init__(self, parent, sourceImage, destImage):
from PYME.Deconv import wiener
wx.Panel.__init__(self, parent)
self.dw = wiener.dec_wiener()
self.sourceImage = sourceImage
self.destImage = destImage
self.havePSF = False
self.decT = None
#GUI stuff
sizer2 = wx.BoxSizer(wx.VERTICAL)
sizer3 = wx.BoxSizer(wx.HORIZONTAL)
sizer3.Add(wx.StaticText(self, -1, 'PSF:'), 0,
wx.ALIGN_CENTER_VERTICAL | wx.ALL, 5)
self.fpPSF = wx.FilePickerCtrl(self,
-1,
wildcard='*.psf',
style=wx.FLP_OPEN
| wx.FLP_FILE_MUST_EXIST)
self.fpPSF.Bind(wx.EVT_FILEPICKER_CHANGED, self.OnPSFFileChanged)
sizer3.Add(self.fpPSF, 1, wx.ALIGN_CENTER_VERTICAL | wx.ALL, 5)
sizer2.Add(sizer3, 0, wx.EXPAND | wx.ALIGN_CENTER_VERTICAL | wx.ALL, 0)
sizer3 = wx.BoxSizer(wx.HORIZONTAL)
sizer3.Add(wx.StaticText(self, -1, 'Offset:'), 0,
wx.ALIGN_CENTER_VERTICAL | wx.ALL, 5)
self.tOffset = wx.TextCtrl(self, -1, '0')
sizer3.Add(self.tOffset, 1, wx.ALIGN_CENTER_VERTICAL | wx.ALL, 5)
sizer2.Add(sizer3, 0, wx.EXPAND | wx.ALIGN_CENTER_VERTICAL | wx.ALL, 0)
sizer3 = wx.BoxSizer(wx.HORIZONTAL)
sizer3.Add(wx.StaticText(self, -1, u'Regularisation \u03BB:'), 0,
wx.ALIGN_CENTER_VERTICAL | wx.ALL, 5)
self.tRegLambda = wx.TextCtrl(self, -1, '1e-8')
sizer3.Add(self.tRegLambda, 1, wx.ALIGN_CENTER_VERTICAL | wx.ALL, 5)
sizer2.Add(sizer3, 0, wx.EXPAND | wx.ALIGN_CENTER_VERTICAL | wx.ALL, 0)
sizer3 = wx.BoxSizer(wx.HORIZONTAL)
sizer3.AddSpacer(10)
self.bCalculate = wx.Button(self, -1, 'Apply')
self.bCalculate.Bind(wx.EVT_BUTTON, self.OnCalculate)
self.bCalculate.Enable(False)
sizer3.Add(self.bCalculate, 1, wx.ALIGN_CENTER_VERTICAL | wx.ALL, 5)
sizer2.Add(sizer3, 0, wx.EXPAND | wx.ALIGN_CENTER_VERTICAL | wx.ALL, 0)
self.SetSizerAndFit(sizer2)
self.deconTimer = mytimer()
self.deconTimer.WantNotification.append(self.OnDeconTimer)
self.deconTimer.Start(500)
def __init__(self, dsviewer):
self.dsviewer = dsviewer
if 'tq' in dir(dsviewer):
self.tq = dsviewer.tq
else:
self.tq = None
self.image = dsviewer.image
self.view = dsviewer.view
self.do = dsviewer.do
#this should only occur for files types which we weren't expecting to process
#as LM data (eg tiffs)
if not 'EstimatedLaserOnFrameNo' in self.image.mdh.getEntryNames():
from PYME.Analysis import MetaData
#try:
MetaData.fillInBlanks(self.image.mdh, self.image.dataSource)
#except IndexError:
# pass
if 'fitResults' in dir(self.image):
self.fitResults = self.image.fitResults
else:
self.fitResults = []
if 'resultsMdh' in dir(self.image):
self.resultsMdh = self.image.resultsMdh
mTasks = wx.Menu()
TASKS_STANDARD_2D = wx.NewId()
TASKS_CALIBRATE_SPLITTER = wx.NewId()
TASKS_2D_SPLITTER = wx.NewId()
TASKS_3D = wx.NewId()
TASKS_3D_SPLITTER = wx.NewId()
TASKS_PRI = wx.NewId()
mTasks.Append(TASKS_STANDARD_2D, "Normal 2D analysis", "", wx.ITEM_NORMAL)
mTasks.Append(TASKS_CALIBRATE_SPLITTER, "Calibrating the splitter", "", wx.ITEM_NORMAL)
mTasks.Append(TASKS_2D_SPLITTER, "2D with splitter", "", wx.ITEM_NORMAL)
mTasks.Append(TASKS_3D, "3D analysis", "", wx.ITEM_NORMAL)
mTasks.Append(TASKS_3D_SPLITTER, "3D with splitter", "", wx.ITEM_NORMAL)
mTasks.Append(TASKS_PRI, "PRI", "", wx.ITEM_NORMAL)
self.dsviewer.menubar.Append(mTasks, "Set defaults for")
wx.EVT_MENU(self.dsviewer, TASKS_CALIBRATE_SPLITTER, self.OnCalibrateSplitter)
wx.EVT_MENU(self.dsviewer, TASKS_STANDARD_2D, self.OnStandard2D)
wx.EVT_MENU(self.dsviewer, TASKS_2D_SPLITTER, self.OnSpitter2D)
wx.EVT_MENU(self.dsviewer, TASKS_3D, self.OnStandard3D)
wx.EVT_MENU(self.dsviewer, TASKS_3D_SPLITTER, self.OnSpliter3D)
wx.EVT_MENU(self.dsviewer, TASKS_PRI, self.OnPRI3D)
BG_SUBTRACT = wx.NewId()
self.dsviewer.view_menu.AppendCheckItem(BG_SUBTRACT, 'Subtract Background')
wx.EVT_MENU(self.dsviewer, BG_SUBTRACT, self.OnToggleBackground)
#a timer object to update for us
self.timer = mytimer()
self.timer.Start(10000)
self.analDispMode = 'z'
self.numAnalysed = 0
self.numEvents = 0
dsviewer.pipeline = pipeline.Pipeline()
self.ds = None
dsviewer.paneHooks.append(self.GenPointFindingPanel)
dsviewer.paneHooks.append(self.GenAnalysisPanel)
dsviewer.paneHooks.append(self.GenFitStatusPanel)
dsviewer.updateHooks.append(self.update)
dsviewer.statusHooks.append(self.GetStatusText)
if 'Protocol.DataStartsAt' in self.image.mdh.getEntryNames():
self.do.zp = self.image.mdh.getEntry('Protocol.DataStartsAt')
else:
self.do.zp = self.image.mdh.getEntry('EstimatedLaserOnFrameNo')
def __init__(self, parent, options = None):
self._init_ctrls(parent)
self.options = options
self._mgr = aui.AuiManager(agwFlags = aui.AUI_MGR_DEFAULT | aui.AUI_MGR_AUTONB_NO_CAPTION)
atabstyle = self._mgr.GetAutoNotebookStyle()
self._mgr.SetAutoNotebookStyle((atabstyle ^ aui.AUI_NB_BOTTOM) | aui.AUI_NB_TOP)
# tell AuiManager to manage this frame
self._mgr.SetManagedWindow(self)
self.snapNum = 0
wx.EVT_CLOSE(self, self.OnCloseWindow)
self.MainFrame = self #reference to this window for use in scripts etc...
self.MainMenu = self.menuBar1
protocol.MainFrame = self
self.toolPanels = []
self.camPanels = []
self.postInit = []
self.initDone = False
self.scope = microscope.microscope()
self.splash = splashScreen.SplashScreen(self, self.scope)
self.splash.Show()
# self.sh = wx.py.shell.Shell(id=-1,
# parent=self.notebook1, size=wx.Size(-1, -1), style=0, locals=self.__dict__,
# introText='Python SMI bindings - note that help, license etc below is for Python, not PySMI\n\n')
#
self.sh = wx.py.shell.Shell(id=-1,
parent=self, size=wx.Size(-1, -1), style=0, locals=self.__dict__,
introText='Python SMI bindings - note that help, license etc below is for Python, not PySMI\n\n')
#self.notebook1.AddPage(imageId=-1, page=self.sh, select=True, text='Console')
#self.notebook1.AddPage(imageId=-1, page=self.panel1, select=False, text='About')
#self.notebook1.AddPage(page=self.sh, select=True, caption='Console')
self._mgr.AddPane(self.sh, aui.AuiPaneInfo().
Name("shell").Caption("Console").Centre().CloseButton(False))
# self.notebook1.AddPage( page=self.panel1, select=False, caption='About')
#self.SetSize((400, 800))
self.CreateToolPanel()
#self.SetSize((1000, 800))
#self.sizer = wx.BoxSizer()
#self.sizer.Add(self.notebook1, 1, wx.EXPAND)
#self.SetSizer(self.Sizer)
self.SetSize((1030, 895))
#self._mgr.Update()
self.roi_on = False
self.bin_on = False
self.time1 = mytimer.mytimer()
self.time1.Start(500)
self.time1.WantNotification.append(self.runInitScript)
self.time1.WantNotification.append(self.checkInitDone)
self.time1.WantNotification.append(self.splash.Tick)
def __init__(self, dsviewer):
self.dsviewer = dsviewer
if 'tq' in dir(dsviewer):
self.tq = dsviewer.tq
else:
self.tq = None
self.image = dsviewer.image
self.view = dsviewer.view
self.do = dsviewer.do
#this should only occur for files types which we weren't expecting to process
#as LM data (eg tiffs)
if not 'EstimatedLaserOnFrameNo' in self.image.mdh.getEntryNames():
from PYME.Analysis import MetaData
#try:
MetaData.fillInBlanks(self.image.mdh, self.image.dataSource)
#except IndexError:
# pass
if 'fitResults' in dir(self.image):
self.fitResults = self.image.fitResults
else:
self.fitResults = []
if 'resultsMdh' in dir(self.image):
self.resultsMdh = self.image.resultsMdh
mTasks = wx.Menu()
TASKS_STANDARD_2D = wx.NewId()
TASKS_CALIBRATE_SPLITTER = wx.NewId()
TASKS_2D_SPLITTER = wx.NewId()
TASKS_3D = wx.NewId()
TASKS_3D_SPLITTER = wx.NewId()
TASKS_PRI = wx.NewId()
mTasks.Append(TASKS_STANDARD_2D, "Normal 2D analysis", "",
wx.ITEM_NORMAL)
mTasks.Append(TASKS_CALIBRATE_SPLITTER, "Calibrating the splitter", "",
wx.ITEM_NORMAL)
mTasks.Append(TASKS_2D_SPLITTER, "2D with splitter", "",
wx.ITEM_NORMAL)
mTasks.Append(TASKS_3D, "3D analysis", "", wx.ITEM_NORMAL)
mTasks.Append(TASKS_3D_SPLITTER, "3D with splitter", "",
wx.ITEM_NORMAL)
mTasks.Append(TASKS_PRI, "PRI", "", wx.ITEM_NORMAL)
self.dsviewer.menubar.Append(mTasks, "Set defaults for")
wx.EVT_MENU(self.dsviewer, TASKS_CALIBRATE_SPLITTER,
self.OnCalibrateSplitter)
wx.EVT_MENU(self.dsviewer, TASKS_STANDARD_2D, self.OnStandard2D)
wx.EVT_MENU(self.dsviewer, TASKS_2D_SPLITTER, self.OnSpitter2D)
wx.EVT_MENU(self.dsviewer, TASKS_3D, self.OnStandard3D)
wx.EVT_MENU(self.dsviewer, TASKS_3D_SPLITTER, self.OnSpliter3D)
wx.EVT_MENU(self.dsviewer, TASKS_PRI, self.OnPRI3D)
BG_SUBTRACT = wx.NewId()
self.dsviewer.view_menu.AppendCheckItem(BG_SUBTRACT,
'Subtract Background')
wx.EVT_MENU(self.dsviewer, BG_SUBTRACT, self.OnToggleBackground)
#a timer object to update for us
self.timer = mytimer()
self.timer.Start(10000)
self.analDispMode = 'z'
self.numAnalysed = 0
self.numEvents = 0
dsviewer.pipeline = pipeline.Pipeline()
self.ds = None
dsviewer.paneHooks.append(self.GenPointFindingPanel)
dsviewer.paneHooks.append(self.GenAnalysisPanel)
dsviewer.paneHooks.append(self.GenFitStatusPanel)
dsviewer.updateHooks.append(self.update)
dsviewer.statusHooks.append(self.GetStatusText)
if 'Protocol.DataStartsAt' in self.image.mdh.getEntryNames():
self.do.zp = self.image.mdh.getEntry('Protocol.DataStartsAt')
else:
self.do.zp = self.image.mdh.getEntry('EstimatedLaserOnFrameNo')
def __init__(self, image, parent=None, title='', mode='LM',
size = (800,700), glCanvas=None):
wx.Frame.__init__(self,parent, -1, title,size=size, pos=(1100, 300))
self.SetAutoLayout(True)
self.mode = mode
self.glCanvas = glCanvas
self.paneHooks = []
self.updateHooks = []
self.statusHooks = []
self.installedModules = []
self.dataChangeHooks = []
self.updating = False
if glCanvas:
self.glCanvas.wantViewChangeNotification.add(self)
self.pane0 = None
self.timer = mytimer()
self.timer.Start(10000)
self.image = image
#self.image = ImageStack(data = dstack, mdh = mdh, filename = filename, queueURI = queueURI, events = None)
if not self.image.filename == None and title == '':
self.SetTitle(self.image.filename)
self._mgr = aui.AuiManager(agwFlags = aui.AUI_MGR_DEFAULT | aui.AUI_MGR_AUTONB_NO_CAPTION)
atabstyle = self._mgr.GetAutoNotebookStyle()
self._mgr.SetAutoNotebookStyle((atabstyle ^ aui.AUI_NB_BOTTOM) | aui.AUI_NB_TOP)
# tell AuiManager to manage this frame
self._mgr.SetManagedWindow(self)
self.do = DisplayOpts(self.image.data)
if self.image.data.shape[1] == 1:
self.do.slice = self.do.SLICE_XZ
self.do.Optimise()
if self.image.mdh and 'ChannelNames' in self.image.mdh.getEntryNames():
self.do.names = self.image.mdh.getEntry('ChannelNames')
#self.vp = ArraySettingsAndViewPanel(self, self.image.data, wantUpdates=[self.update], mdh=self.image.mdh)
#self.view = ArrayViewPanel(self, do=self.do)
#self.AddPage(self.view, True, 'Data')
#self._mgr.AddPane(self.vp, aui.AuiPaneInfo().
# Name("Data").Caption("Data").Centre().CloseButton(False).CaptionVisible(False))
self.mainFrame = weakref.ref(self)
#self.do = self.vp.do
self._menus = {}
# Menu Bar
self.menubar = wx.MenuBar()
self.SetMenuBar(self.menubar)
tmp_menu = wx.Menu()
tmp_menu.Append(wx.ID_OPEN, '&Open', "", wx.ITEM_NORMAL)
tmp_menu.Append(wx.ID_SAVE, "&Save As", "", wx.ITEM_NORMAL)
tmp_menu.Append(wx.ID_SAVEAS, "&Export Cropped", "", wx.ITEM_NORMAL)
#a submenu for modules to hook and install saving functions into
self.save_menu = wx.Menu()
self._menus['Save'] = self.save_menu
tmp_menu.AppendMenu(-1, 'Save &Results', self.save_menu)
tmp_menu.AppendSeparator()
tmp_menu.Append(wx.ID_CLOSE, "Close", "", wx.ITEM_NORMAL)
self.menubar.Append(tmp_menu, "File")
self.view_menu = wx.Menu()
self.menubar.Append(self.view_menu, "&View")
self._menus['View'] = self.view_menu
#'extras' menu for modules to install stuff into
self.mProcessing = wx.Menu()
self.menubar.Append(self.mProcessing, "&Processing")
self._menus['Processing'] = self.mProcessing
# Menu Bar end
wx.EVT_MENU(self, wx.ID_OPEN, self.OnOpen)
wx.EVT_MENU(self, wx.ID_SAVE, self.OnSave)
wx.EVT_MENU(self, wx.ID_SAVEAS, self.OnExport)
wx.EVT_CLOSE(self, self.OnCloseWindow)
wx.EVT_SIZE(self, self.OnSize)
self.statusbar = self.CreateStatusBar(1, wx.ST_SIZEGRIP)
self.panesToMinimise = []
modules.loadMode(self.mode, self)
self.CreateModuleMenu()
self.optionspanel = OptionsPanel(self, self.do, thresholdControls=True)
self.optionspanel.SetSize(self.optionspanel.GetBestSize())
pinfo = aui.AuiPaneInfo().Name("optionsPanel").Right().Caption('Display Settings').CloseButton(False).MinimizeButton(True).MinimizeMode(aui.AUI_MINIMIZE_CAPT_SMART|aui.AUI_MINIMIZE_POS_RIGHT)#.CaptionVisible(False)
self._mgr.AddPane(self.optionspanel, pinfo)
self.panesToMinimise.append(pinfo)
self._mgr.AddPane(self.optionspanel.CreateToolBar(self), aui.AuiPaneInfo().Name("ViewTools").Caption("View Tools").CloseButton(False).
ToolbarPane().Right().GripperTop())
if self.do.ds.shape[2] > 1:
from PYME.DSView.modules import playback
self.playbackpanel = playback.PlayPanel(self, self)
self.playbackpanel.SetSize(self.playbackpanel.GetBestSize())
pinfo1 = aui.AuiPaneInfo().Name("playbackPanel").Bottom().Caption('Playback').CloseButton(False).MinimizeButton(True).MinimizeMode(aui.AUI_MINIMIZE_CAPT_SMART|aui.AUI_MINIMIZE_POS_RIGHT)#.CaptionVisible(False)
self._mgr.AddPane(self.playbackpanel, pinfo1)
self.do.WantChangeNotification.append(self.playbackpanel.update)
#self.mWindows = wx.Menu()
#self.menubar.append(self.mWindows, '&Composite With')
self.do.WantChangeNotification.append(self.update)
self.CreateFoldPanel()
self._mgr.Update()
for pn in self.panesToMinimise:
self._mgr.MinimizePane(pn)
#self._mgr.MinimizePane(pinfo2)
self.Layout()
if 'view' in dir(self):
sc = pylab.floor(pylab.log2(1.0*self.view.Size[0]/self.do.ds.shape[0]))
#print self.view.Size[0], self.do.ds.shape[0], sc
self.do.SetScale(sc)
self.view.Refresh()
self.update()
self.drop = dt()
self.SetDropTarget(self.drop)
openViewers[self.image.filename] = self
