python-microscopy 25.11.20__cp313-cp313-win_amd64.whl

PYME/DSView/modules/composite.py

@@ -0,0 +1,715 @@
+#!/usr/bin/python
+##################
+# vis3D.py
+#
+# Copyright David Baddeley, 2011
+# d.baddeley@auckland.ac.nz
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+##################
+#import numpy
+from __future__ import print_function
+import wx
+import wx.lib.mixins.listctrl  as  listmix
+import os
+#import pylab
+from PYME.IO import MetaDataHandler
+from PYME.IO import image
+from PYME.DSView import View3D, ViewIm3D
+from PYME.IO import dataWrap
+
+import wx.lib.agw.aui as aui
+
+from PYME.Analysis.composite import common_prefix, make_composite
+
+class ShiftPanel(wx.Panel):
+    def __init__(self, dsviewer):
+        wx.Panel.__init__(self, dsviewer)
+        self.dsviewer = dsviewer
+        self.image = dsviewer.image
+        
+        vsizer = wx.BoxSizer(wx.VERTICAL)
+
+        self.xctls = []
+        self.yctls = []
+        self.zctls = [] 
+        
+        self.rbs = []
+        
+        chanList = self.image.data.dataList
+        
+        #iterate over colours
+        for i in range(self.image.data.shape[3]):
+            shifts = chanList[i].shifts
+            #vsizer.Add(wx.StaticText(self, -1, 'Chan %d:' % i), 0, wx.EXPAND|wx.ALL, 2)
+            rb = wx.RadioButton(self, -1, 'Chan %d:' % i)
+            if i == 0:
+                rb.SetValue(True)
+            vsizer.Add(rb, 0, wx.EXPAND|wx.ALL, 2)
+            self.rbs.append(rb)
+            hsizer = wx.BoxSizer(wx.HORIZONTAL)
+            #hsizer.Add(wx.StaticText(self, -1, 'dx'), 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 2)
+            iD = wx.NewIdRef()
+            x1 = wx.TextCtrl(self, iD, str(int(shifts[0])), size=[30,-1])
+            self.xctls.append(x1)
+            hsizer.Add(x1, 1, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 2)
+            
+            #hsizer.Add(wx.StaticText(self, -1, 'dy'), 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 2)
+            iD = wx.NewIdRef()
+            y1 = wx.TextCtrl(self, iD, str(int(shifts[1])), size=[30,-1])
+            self.yctls.append(y1)
+            hsizer.Add(y1, 1, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 2)
+            
+            #hsizer.Add(wx.StaticText(self, -1, 'dz'), 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 2)
+            iD = wx.NewIdRef()
+            y1 = wx.TextCtrl(self, iD, str(int(shifts[2])), size=[30,-1])
+            self.zctls.append(y1)
+            hsizer.Add(y1, 1, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 2)
+            
+            vsizer.Add(hsizer, 0, wx.EXPAND, 0)
+            
+        
+        hsizer = wx.BoxSizer(wx.HORIZONTAL)
+        bUpdate = wx.Button(self, -1, 'Update', size=[40, -1])
+        bUpdate.Bind(wx.EVT_BUTTON, self.OnApply)
+        hsizer.Add(bUpdate, 1, wx.ALL, 2)
+        bZero = wx.Button(self, -1, 'Zero', size=[40, -1])
+        bZero.Bind(wx.EVT_BUTTON, self.OnZero) 
+        hsizer.Add(bZero, 0, wx.ALL, 2)
+        
+        vsizer.Add(hsizer, 0, wx.ALL|wx.EXPAND, 0)
+        
+        
+        
+        bEstimate = wx.Button(self, -1, 'Estimate (slow)')
+        vsizer.Add(bEstimate, 0, wx.ALL|wx.EXPAND, 2)
+        
+        bEstimate.Bind(wx.EVT_BUTTON, self.OnCorrelate)
+        
+        self.SetSizerAndFit(vsizer)
+        
+    def OnApply(self, event):
+        chanList = self.image.data.dataList
+            
+        for i in range(self.image.data.shape[3]):
+            dx = float(self.xctls[i].GetValue())
+            dy = float(self.yctls[i].GetValue())
+            dz = float(self.zctls[i].GetValue())
+            
+            chanList[i].SetShifts([dx,dy,dz])
+            
+        self.dsviewer.do.OnChange()
+        
+    def OnCorrelate(self, event):
+        from numpy.fft import fftn, ifftn, fftshift, ifftshift
+        # from pylab import fftshift, ifftshift
+        import numpy as np
+        #ch0 = self.image.data[:,:,:,0]
+        chanList = self.image.data.dataList
+        
+        for i in range(len(self.rbs)):
+            if self.rbs[i].GetValue():
+                ch0 = self.image.data[:,:,:,i]
+                
+        ch0 = np.maximum(ch0 - ch0.mean(), 0)
+        
+        F0 = fftn(ch0)
+        
+        for i in range(self.image.data.shape[3]):
+            if not self.rbs[i].GetValue():
+                ch0 = self.image.data[:,:,:,i]
+                ch0 = np.maximum(ch0 - ch0.mean(), 0)
+                Fi = ifftn(ch0)
+                
+                corr = abs(fftshift(ifftn(F0*Fi)))
+                
+                corr -= corr.min()
+                
+                corr = np.maximum(corr - corr.max()*.75, 0)
+                
+                xi, yi, zi = np.where(corr)
+                
+                corr_s = corr[corr>0]
+                corr_s/= corr_s.sum()
+                
+                dxi =  ((xi*corr_s).sum() - corr.shape[0]/2.)*chanList[i].voxelsize[0]
+                dyi =  ((yi*corr_s).sum() - corr.shape[1]/2.)*chanList[i].voxelsize[1]
+                dzi =  ((zi*corr_s).sum() - corr.shape[2]/2.)*chanList[i].voxelsize[2]
+                
+                self.xctls[i].SetValue(str(int(dxi)))
+                self.yctls[i].SetValue(str(int(dyi)))
+                self.zctls[i].SetValue(str(int(dzi)))
+            
+        self.OnApply(None)
+        
+    def OnZero(self, event):
+        for i in range(self.image.data.shape[3]):
+            self.xctls[i].SetValue('0')
+            self.yctls[i].SetValue('0')
+            self.zctls[i].SetValue('0')
+            
+        self.OnApply(None)
+        #View3D(corr)
+        
+class ShiftmapSelectionDialog(wx.Dialog):
+    def __init__(self, parent, image):
+        wx.Dialog.__init__(self, parent, title='Deconvolution')
+        nChans = image.data.shape[3]
+
+        sizer1 = wx.BoxSizer(wx.VERTICAL)
+        
+        sizer2 = wx.GridSizer(nChans, 2, 5, 5)
+        
+        sizer2.Add(wx.StaticText(self, -1, 'Channel:'))
+        sizer2.Add(wx.StaticText(self, -1, 'Shiftmap:'))
+        
+        self.filectrls = {}
+        
+        for chan in range(nChans):
+            sizer2.Add(wx.StaticText(self, -1, image.names[chan]), 0, wx.ALIGN_CENTER_VERTICAL | wx.ALL, 5)
+            fp = wx.FilePickerCtrl(self, -1, wildcard='*.sm', style=wx.FLP_OPEN|wx.FLP_FILE_MUST_EXIST|wx.FLP_USE_TEXTCTRL)
+            sizer2.Add(fp, 1, wx.ALIGN_CENTER_VERTICAL | wx.ALL, 5)
+            self.filectrls[chan] = fp
+            
+        sizer1.Add(sizer2, 1, wx.ALL|wx.EXPAND, 5)
+            
+        btSizer = wx.StdDialogButtonSizer()
+
+        self.bOK = wx.Button(self, wx.ID_OK)
+        self.bOK.SetDefault()
+
+        btSizer.AddButton(self.bOK)
+
+        btn = wx.Button(self, wx.ID_CANCEL)
+
+        btSizer.AddButton(btn)
+
+        btSizer.Realize()
+
+        sizer1.Add(btSizer, 0, wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL|wx.ALL, 5)
+
+        self.SetSizer(sizer1)
+        sizer1.Fit(self)
+        
+    def GetChanFilename(self, chan):
+        return self.filectrls[chan].GetPath()
+        
+def _getImage(name):
+    if name in image.openImages.keys():
+        img = image.openImages[name]
+        chan = 0
+    else:
+        n_, chan_, cn_ = name.split('$')
+        img = image.openImages[n_]
+        chan = int(chan_)
+        
+    return img, chan
+        
+class ImageList(wx.ListCtrl):
+    def __init__(self, parent, id=-1, imageNames=[], size=(300,200)):
+        wx.ListCtrl.__init__(self, parent, id, 
+            style=wx.LC_REPORT|wx.LC_VIRTUAL|wx.LC_VRULES, size=size)
+        #listmix.ListCtrlAutoWidthMixin.__init__(self)
+            
+        self.imageNames = list(imageNames)
+        self.shiftmaps = {}
+        self.channelNames = {}
+        
+        self.InsertColumn(0, "Name")
+        self.InsertColumn(1, "dx")
+        self.InsertColumn(2, "dy")
+        
+        self.InsertColumn(3, "width")
+        self.InsertColumn(4, "height")
+        self.InsertColumn(5, "Shiftmap")
+        
+        self.SetColumnWidth(0, 300)
+        self.SetColumnWidth(1, 50)
+        self.SetColumnWidth(2, 50)
+        self.SetColumnWidth(3, 50)
+        self.SetColumnWidth(4, 50)
+        self.SetColumnWidth(5, 200)
+        #self.InsertColumn(5, "x0")
+        #self.InsertColumn(6, "y0")
+        
+        self.SetItemCount(len(self.imageNames))
+        
+   
+        
+    def OnGetItemText(self, item, col):
+        name = self.imageNames[item]
+        #print item, col, name
+        if col == 0:
+            #item name
+            return self.channelNames[name]
+        else:
+            img, chan = _getImage(name)
+            if col == 1:
+                return '%3.2f' % img.mdh['voxelsize.x']
+            elif col == 2:
+                return '%3.2f' % img.mdh['voxelsize.y']
+            elif col == 3:
+                return '%3.2f' % (img.imgBounds.width() / 1e3)
+            elif col == 4:
+                return '%3.2f' % (img.imgBounds.height() / 1e3)
+            elif col == 5:
+                try:
+                    return self.shiftmaps[name]
+                except KeyError:
+                    return ''
+                
+                
+    def Append(self, name):
+        self.imageNames.append(name)
+        self.channelNames[name] = os.path.split(name)[-1]
+        self.SetItemCount(len(self.imageNames))
+        #self.SetColumnWidth(0, wx.LIST_AUTOSIZE)
+        
+    def SetShiftmap(self, name):
+        filename = wx.FileSelector('Choose a shiftmap', default_extension='*.sm', wildcard="Shiftmaps (*.sm)|*.sm")
+        #if filename:
+        self.shiftmaps[name] = filename
+            
+        self.Refresh()
+        
+    def DeleteItem(self, index):
+        self.imageNames.pop(index)
+        self.SetItemCount(len(self.imageNames))
+        
+    def ShiftItem(self, index, direction='up'):
+        tmp = self.imageNames[index]
+        if direction == 'up':
+            if index > 0:
+                self.imageNames[index] = self.imageNames[index - 1]
+                self.imageNames[index -1] = tmp
+                self.SetItemState(-1, 0, wx.LIST_STATE_SELECTED)
+                self.Select(index-1)
+        else:
+            if index < (len(self.imageNames) - 1):
+                self.imageNames[index] = self.imageNames[index + 1]
+                self.imageNames[index +1] = tmp
+                self.SetItemState(-1, 0, wx.LIST_STATE_SELECTED)
+                self.Select(index+1)
+        self.Refresh()
+        
+    def GetName(self, index):
+        return self.imageNames[index]
+            
+        
+
+class CompositeDialog(wx.Dialog):
+    def __init__(self, parent, img):
+        wx.Dialog.__init__(self, parent, title='Composite')
+        #nChans = image.data.shape[3]
+        
+        self.imageNames =  image.openImages.keys()
+        
+        self.dispNames = []
+        
+        for iN in self.imageNames:
+            im = image.openImages[iN]
+            if im.data.shape[3] == 1: #single colour
+                self.dispNames.append(iN)
+            else:
+                for i in range(im.data.shape[3]):
+                    self.dispNames.append('%s$%d$%s' % (iN, i, im.names[i]))
+                    
+        #for testing
+        #self.dispNames = ['a', 'b', 'c']
+
+        sizer1 = wx.BoxSizer(wx.VERTICAL)
+        
+        hsizer = wx.BoxSizer(wx.HORIZONTAL)
+
+        vsizer = wx.BoxSizer(wx.VERTICAL)
+        
+        vsizer.Add(wx.StaticText(self, -1, 'Available Channels:'), 0, wx.ALL, 2)
+        self.lAvail = wx.ListBox(self, -1, choices=self.dispNames, size=(300, 200), style=wx.LB_SORT|wx.LB_NEEDED_SB|wx.LB_EXTENDED)
+        
+        vsizer.Add(self.lAvail, 0, wx.ALL|wx.EXPAND, 2)
+        hsizer.Add(vsizer, 0, wx.ALL|wx.EXPAND, 2)
+        
+        vsizer = wx.BoxSizer(wx.VERTICAL)
+        
+        bmp = wx.ArtProvider.GetBitmap(wx.ART_GO_FORWARD, wx.ART_TOOLBAR, (16,16))
+        self.bAddChan = wx.BitmapButton(self, -1, bmp)
+        self.bAddChan.Bind(wx.EVT_BUTTON, self.OnAddChan)
+        vsizer.Add(self.bAddChan, 0, wx.ALL, 2)
+        
+        bmp = wx.ArtProvider.GetBitmap(wx.ART_GO_BACK, wx.ART_TOOLBAR, (16,16))
+        self.bRemoveChan = wx.BitmapButton(self, -1, bmp)
+        self.bRemoveChan.Bind(wx.EVT_BUTTON, self.OnRemoveChan)
+        vsizer.Add(self.bRemoveChan, 0, wx.ALL, 2)
+        
+
+        hsizer.Add(vsizer, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 2)
+        
+        vsizer = wx.BoxSizer(wx.VERTICAL)
+        
+        vsizer.Add(wx.StaticText(self, -1, 'Selected Channels:'), 0, wx.ALL, 2)
+        self.lSelected = ImageList(self, -1, size=(600, 200))
+        
+        vsizer.Add(self.lSelected, 1, wx.ALL|wx.EXPAND, 2)
+        hsizer.Add(vsizer, 1, wx.ALL|wx.EXPAND, 2)
+        
+        vsizer = wx.BoxSizer(wx.VERTICAL) 
+        bmp = wx.ArtProvider.GetBitmap(wx.ART_GO_UP, wx.ART_TOOLBAR, (16,16))
+        self.bChanUp = wx.BitmapButton(self, -1, bmp)
+        self.bChanUp.Bind(wx.EVT_BUTTON, self.OnChanUp)
+        vsizer.Add(self.bChanUp, 0, wx.ALL, 2)
+        
+        bmp = wx.ArtProvider.GetBitmap(wx.ART_GO_DOWN, wx.ART_TOOLBAR, (16,16))
+        self.bChanDown = wx.BitmapButton(self, -1, bmp)
+        self.bChanDown.Bind(wx.EVT_BUTTON, self.OnChanDown)
+        vsizer.Add(self.bChanDown, 0, wx.ALL, 2)
+        
+        vsizer.AddSpacer(10)
+        
+        bmp = wx.ArtProvider.GetBitmap(wx.ART_HELP_SETTINGS, wx.ART_TOOLBAR, (16,16))
+        self.bSetShiftmap = wx.BitmapButton(self, -1, bmp)
+        self.bSetShiftmap.Bind(wx.EVT_BUTTON, self.OnSetShiftmap)
+        self.bSetShiftmap.SetToolTipString("Specify a shiftmap for the selected channel")
+        vsizer.Add(self.bSetShiftmap, 0, wx.ALL, 2)
+        
+        hsizer.Add(vsizer, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 2)
+        
+        sizer1.Add(hsizer, 1, wx.ALL|wx.EXPAND, 5)
+        
+        hsizer = wx.BoxSizer(wx.HORIZONTAL)
+        hsizer.Add(wx.StaticText(self, -1, 'Shape:'), 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 2)        
+        
+        self.tShapeX = wx.TextCtrl(self, -1)
+        hsizer.Add(self.tShapeX, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 2)
+        self.tShapeY = wx.TextCtrl(self, -1)
+        hsizer.Add(self.tShapeY, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 2)
+        self.tShapeZ = wx.TextCtrl(self, -1)
+        hsizer.Add(self.tShapeZ, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 2)
+        
+        hsizer.Add(wx.StaticText(self, -1, 'Voxelsize [nm]:'), 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 2)        
+        
+        self.tVoxX = wx.TextCtrl(self, -1)
+        hsizer.Add(self.tVoxX, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 2)
+        self.tVoxY = wx.TextCtrl(self, -1)
+        hsizer.Add(self.tVoxY, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 2)
+        self.tVoxZ = wx.TextCtrl(self, -1)
+        hsizer.Add(self.tVoxZ, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 2)
+        
+        hsizer.Add(wx.StaticText(self, -1, 'Origin [nm]:'), 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 2)        
+        
+        self.tOriginX = wx.TextCtrl(self, -1)
+        hsizer.Add(self.tOriginX, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 2)
+        self.tOriginY = wx.TextCtrl(self, -1)
+        hsizer.Add(self.tOriginY, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 2)
+        self.tOriginZ = wx.TextCtrl(self, -1)
+        hsizer.Add(self.tOriginZ, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 2)
+        
+        sizer1.Add(hsizer, 0, wx.ALL|wx.EXPAND, 5)
+                
+        
+        self.stOutput = wx.StaticText(self, -1, 'Pixel Size: 0,0\t Shape: 0,0')
+        sizer1.Add(self.stOutput, 0, wx.ALL, 2) 
+        
+        self.cbIgnoreZ = wx.CheckBox(self, -1, 'Ignore Z Origin')
+        self.cbIgnoreZ.SetValue(True)
+        sizer1.Add(self.cbIgnoreZ, 0, wx.ALL, 2) 
+        
+        self.cbInterp = wx.CheckBox(self, -1, 'Interpolate')
+        self.cbInterp.SetValue(True)
+        sizer1.Add(self.cbInterp, 0, wx.ALL, 2) 
+            
+        btSizer = wx.StdDialogButtonSizer()
+
+        self.bOK = wx.Button(self, wx.ID_OK)
+        self.bOK.SetDefault()
+
+        btSizer.AddButton(self.bOK)
+
+        btn = wx.Button(self, wx.ID_CANCEL)
+
+        btSizer.AddButton(btn)
+
+        btSizer.Realize()
+
+        sizer1.Add(btSizer, 0, wx.ALL, 5)
+
+        self.SetSizer(sizer1)
+        sizer1.Fit(self)
+        
+    def SetMaster(self, master):
+        self.master = master
+        
+        ms, ch = _getImage(master)
+        
+        #self.shape = list(ms.data.shape[:3])
+        #self.voxelsize = ms.voxelsize
+        #self.origin = ms.origin
+        
+        self.tShapeX.SetValue('%d' % ms.data.shape[0])
+        self.tShapeY.SetValue('%d' % ms.data.shape[1])
+        self.tShapeZ.SetValue('%d' % ms.data.shape[2])
+        
+        self.tVoxX.SetValue('%3.3f' % ms.voxelsize[0])
+        self.tVoxY.SetValue('%3.3f' % ms.voxelsize[1])
+        self.tVoxZ.SetValue('%3.3f' % ms.voxelsize[2])
+        
+        self.tOriginX.SetValue('%d' % ms.origin[0])
+        self.tOriginY.SetValue('%d' % ms.origin[1])
+        self.tOriginZ.SetValue('%d' % ms.origin[2])
+        
+        sh = self.shape + [self.lSelected.GetItemCount()]
+        
+        self.stOutput.SetLabel('Output Shape: %s\t Output Voxel Size: %s' % (sh, ms.voxelsize))
+        
+    @property
+    def voxelsize(self):
+        return float(self.tVoxX.GetValue()), float(self.tVoxY.GetValue()),float(self.tVoxZ.GetValue())
+        
+    @property
+    def origin(self):
+        return float(self.tOriginX.GetValue()), float(self.tOriginY.GetValue()),float(self.tOriginZ.GetValue())
+
+    @property
+    def shape(self):
+        return [int(self.tShapeX.GetValue()), int(self.tShapeY.GetValue()),int(self.tShapeZ.GetValue())]
+        
+    def OnAddChan(self, event):
+        chans = list(self.lAvail.GetSelections())
+        
+        for chan in chans:
+            self.lSelected.Append(self.lAvail.GetString(chan))
+            if self.lSelected.GetItemCount() == 1:
+                #first channel is master
+                self.SetMaster(self.lAvail.GetString(chan))
+        
+        chans.sort()
+        chans.reverse()
+        
+        for chan in chans:
+            #print chan
+            self.lAvail.Delete(chan)
+            
+    def OnRemoveChan(self, event):
+        chan = self.lSelected.GetFirstSelected()
+        
+        if not chan == wx.NOT_FOUND:
+            self.lAvail.Append(self.lSelected.GetName(chan))
+            self.lSelected.DeleteItem(chan)
+        
+    def OnChanUp(self, event):
+        chan = self.lSelected.GetFirstSelected()
+        
+        if not chan == wx.NOT_FOUND:
+            self.lSelected.ShiftItem(chan, 'up')
+#            if chan > 0: #chan is not already at top
+#                text = self.lSelected.GetName(chan)
+#                self.lSelected.DeleteItem(chan)
+#                self.lSelected.InsertStringItem(chan - 1, text)
+#                #self.lSelected.Insert(text, chan - 1)
+#                self.lSelected.Select(chan -1)
+                
+    def OnChanDown(self, event):
+        chan = self.lSelected.GetFirstSelected()
+        
+        if not chan == wx.NOT_FOUND:
+            self.lSelected.ShiftItem(chan, 'down')
+#            if chan < (self.lSelected.GetItemCount() - 1): #chan is not already at top
+#                text = self.lSelected.GetName(chan)
+#                self.lSelected.DeleteItem(chan)
+#                self.lSelected.InsertStringItem(chan + 1, text)
+#                #self.lSelected.Insert(text, chan + 1)
+#                #print ch
+#                self.lSelected.Select(chan + 1)
+                
+    def OnSetShiftmap(self, event):
+        chan = self.lSelected.GetFirstSelected()
+        if not chan == wx.NOT_FOUND:
+            text = self.lSelected.GetName(chan)
+            self.lSelected.SetShiftmap(text)
+                
+    def GetSelections(self):
+        return [self.lSelected.GetName(ch) for ch in range(self.lSelected.GetItemCount())]
+        
+    def GetMaster(self):
+        return self.master
+        
+    def GetShiftmap(self, chan):
+        try:
+            return self.lSelected.shiftmaps[chan]
+        except KeyError:
+            return ''
+        
+    def GetIgnoreZ(self):
+        return self.cbIgnoreZ.GetValue()
+        
+    def GetInterp(self):
+        return self.cbInterp.GetValue()
+        
+
+from ._base import Plugin
+class Compositor(Plugin):
+    def __init__(self, dsviewer):
+        Plugin.__init__(self, dsviewer)
+
+        #self.compMenu = wx.Menu()
+
+        dsviewer.mProcessing.AppendSeparator()
+        
+        dsviewer.AddMenuItem("Processing", "Make Composite", self.OnMakeComposites)
+        dsviewer.AddMenuItem("Processing", "Split Channels", self.OnSplitChannels)
+        dsviewer.AddMenuItem("Processing", "Apply vector shifts", self.OnApplyShiftmap)
+        dsviewer.AddMenuItem("Processing", "Align Channels", self.OnAlignChannels)
+        
+        dsviewer.mProcessing.AppendSeparator()
+
+        
+    def OnMakeComposites(self, event):
+        dlg = CompositeDialog(self.dsviewer, self.image)
+        
+        if dlg.ShowModal() == wx.ID_OK:
+            imgs = []
+            for im_name in dlg.GetSelections():
+                im, chan = _getImage(im_name)
+                shiftfield = dlg.GetShiftmap(im_name)
+                
+                imgs.append((im, chan, shiftfield))
+            
+            if len(imgs) > 0:
+                out = make_composite(imgs,
+                                     ignoreZ=dlg.GetIgnoreZ(),
+                                     interp=dlg.GetInterp(),
+                                     shape=dlg.shape,
+                                     origin=dlg.origin,
+                                     voxelsize=dlg.voxelsize)
+                
+                ViewIm3D(out, 'Composite', mode=self.dsviewer.mode,
+                       parent=wx.GetTopLevelParent(self.dsviewer), glCanvas=self.dsviewer.glCanvas)
+            
+        dlg.Destroy()
+    
+
+    def OnSplitChannels(self, event):
+        try:
+            names = self.image.mdh.getEntry('ChannelNames')
+        except:
+            names = ['%d' % d for d in range(self.image.data.shape[3])]
+
+        for i in range(self.image.data.shape[3]):
+            mdh = MetaDataHandler.NestedClassMDHandler(self.image.mdh)
+            mdh.setEntry('ChannelNames', [names[i]])
+
+            View3D(self.image.data[:,:,:,i], '%s - %s' % (self.image.filename, names[i]), mdh=mdh, parent=wx.GetTopLevelParent(self.dsviewer))
+        
+        
+    def OnApplyShiftmap(self, event):
+        """apply a vectorial correction for chromatic shift to an image - this
+        is a generic vectorial shift compensation, rather than the secial case 
+        correction used with the splitter."""
+        from scipy import ndimage
+        import numpy as np
+        from PYME.DSView import ImageStack, ViewIm3D
+        from PYME.IO.MetaDataHandler import get_camera_roi_origin
+        
+        dlg = ShiftmapSelectionDialog(self.dsviewer, self.image)
+        succ = dlg.ShowModal()
+        if (succ == wx.ID_OK):
+            #self.ds = example.CDataStack(fdialog.GetPath().encode())
+            #self.ds =
+            ds = []
+            shiftFiles = {}
+            X, Y, Z = np.mgrid[0:self.image.data.shape[0], 0:self.image.data.shape[1], 0:self.image.data.shape[2]]
+            
+            vx, vy, vz = self.image.voxelsize_nm
+            
+            roi_x0, roi_y0 = get_camera_roi_origin(self.image.mdh)
+            
+            for ch in range(self.image.data.shape[3]):
+                sfFilename = dlg.GetChanFilename(ch)
+                shiftFiles[ch] = sfFilename
+                
+                data = self.image.data[:,:,:, ch]
+                
+                if os.path.exists(sfFilename):
+                    spx, spy, dz = np.load(sfFilename)
+                    
+                    dx = spx.ev(vx*(X+roi_x0), vy*(Y+roi_y0))/vx
+                    dy = spy.ev(vx*(X+roi_x0), vy*(Y+roi_y0))/vy
+                    dz = dz/vz
+                    
+                    ds.append(ndimage.map_coordinates(data, [X+dx, Y+dy, Z+dz], mode='nearest'))
+                else:
+                    ds.append(data)
+                
+            
+            fns = os.path.split(self.image.filename)[1]
+            im = ImageStack(ds, titleStub = '%s - corrected' % fns)
+            im.mdh.copyEntriesFrom(self.image.mdh)
+            im.mdh['Parent'] = self.image.filename
+            im.mdh.setEntry('ChromaCorrection.ShiftFilenames', shiftFiles)
+            
+            if 'fitResults' in dir(self.image):
+                im.fitResults = self.image.fitResults
+            #im.mdh['Processing.GaussianFilter'] = sigmas
+    
+            if self.dsviewer.mode == 'visGUI':
+                mode = 'visGUI'
+            else:
+                mode = 'lite'
+    
+            dv = ViewIm3D(im, mode=mode, glCanvas=self.dsviewer.glCanvas, parent=wx.GetTopLevelParent(self.dsviewer))
+            
+        dlg.Destroy()
+            
+            
+            
+    def OnAlignChannels(self, event):
+        #try:
+        #    names = self.image.mdh.getEntry('ChannelNames')
+        #except:
+        #    names = ['%d' % d for d in range(self.image.data.shape[3])]
+        from PYME.IO.DataSources import AlignDataSource
+        from  PYME.IO import dataWrap
+        
+        if isinstance(self.image.data, dataWrap.ListWrapper):
+            nd = [AlignDataSource.DataSource(ds) for ds in self.image.data.wrapList]
+        else:
+            nd = [AlignDataSource.DataSource(dataWrap.Wrap(self.image.data[:,:,:,i])) for i in range(self.image.data.shape[3])]
+            
+        mdh = MetaDataHandler.NestedClassMDHandler(self.image.mdh)
+            
+
+        res = View3D(nd, '%s - %s' % (self.image.filename, 'align'), mdh=mdh, parent=wx.GetTopLevelParent(self.dsviewer))
+        
+        res.panAlign = ShiftPanel(res)
+
+        pinfo1 = aui.AuiPaneInfo().Name("shiftPanel").Right().Caption('Alignment').DestroyOnClose(True).CloseButton(False).MinimizeButton(True).MinimizeMode(aui.AUI_MINIMIZE_CAPT_SMART|aui.AUI_MINIMIZE_POS_RIGHT)#.MinimizeButton(True).MinimizeMode(aui.AUI_MINIMIZE_CAPT_SMART|aui.AUI_MINIMIZE_POS_RIGHT)#.CaptionVisible(False)
+        #pinfo2 = aui.AuiPaneInfo().Name("overlayPanel").Right().Caption('Overlays').CloseButton(False).MinimizeButton(True).MinimizeMode(aui.AUI_MINIMIZE_CAPT_SMART|aui.AUI_MINIMIZE_POS_RIGHT)#.CaptionVisible(False)
+        res._mgr.AddPane(res.panAlign, pinfo1)
+        res._mgr.Update()
+
+
+
+
+
+       
+    
+
+
+def Plug(dsviewer):
+    return Compositor(dsviewer)
+    #if 'chanList' in dir(dsviewer.image.data) and 'shifts' in dir(dsviewer.image.data.chanList[0]):
+        #we have shiftable channels
+        
+
+