Hi Eric,
On 30/12/06, Eric Emsellem <[EMAIL PROTECTED]> wrote:
Hi,
I am writing a small module to easily load images and interact with
them.
Sorry for getting to this thread late - back from a quick holiday now.
I have written an image browser module that does what it sounds like
you're trying to do (and works with 3-D image stacks as well). It's
still quite rudimentary, and I hadn't really planned on sharing it in
its current state, but it may be that you can find some useful ideas
in the code. The image browser is a matplotlib canvas embedded in a wx
window, and I use the WxAgg backend - I've no idea how that will
change things from your setup. I run it interactively from ipython
-pylab as shown below.
Usage is pretty simple:
In [1]: import pyvis
In [2]: pv = pyvis.pyvis()
In [3]: pv.AddImg(arange(10000).reshape(100,100), 'my gradient')
then play around with the menus. More than one image can be loaded at
a time. I haven't had a close look at the memory usage, but it has
been working adequately for quite large image stacks
(1024x1024x250x8-bit). Feel free to use the code as you like.
Angus.
--
AJC McMorland, PhD Student
Physiology, University of Auckland
import numpy
import wx
import matplotlib
matplotlib.interactive(False)
matplotlib.use("WXAgg")
from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg, \
NavigationToolbar2WxAgg, FigureManager
from matplotlib.figure import Figure
from matplotlib.axes import Subplot
ID_FILE_EXIT = 101
ID_WINDOW_VIEWS = 102
ID_WINDOW_DATA = 103
ID_TOOLS_MAXPROJ = 104
ID_TOOLS_DELITEM = 105
ID_TOOLS_LOSEFOCUS = 106
ID_CMAP_GRAY = 107
ID_CMAP_JET = 108
version = 0.100
class MyNavToolbar2WxAgg(NavigationToolbar2WxAgg):
def __init__(self, canvas, parent):
self.parent = parent
return NavigationToolbar2WxAgg.__init__(self, canvas)
def home(self, *args):
self.parent.ResetLims()
NavigationToolbar2WxAgg.home(self, *args)
# '''rendered obsolete by use of toolbar.mode (which I didn''t
# realise existed).'''
# def __init__(self, canvas):
# self.zoomode = False
# self.panmode = False
# return NavigationToolbar2WxAgg.__init__(self, canvas)
# def zoom(self, *args):
# self.zoomode = not self.zoomode
# if self.panmode:
# self.panmode = False
# NavigationToolbar2WxAgg.zoom(self, *args)
# def pan(self, *args):
# self.panmode = not self.panmode
# if self.zoomode:
# self.zoomode = False
# NavigationToolbar2WxAgg.pan(self, *args)
# ---------------------------------------------------------------
class ViewsFrame(wx.Frame):
'''
frame for Views controls'''
def __init__(self,parent):
wx.Frame.__init__(self,None,-1,"Views")
self.parent = parent
wx.EVT_CLOSE(self, self.OnCloseViews)
self.sizerouter = wx.BoxSizer(wx.VERTICAL)
self.sizerinner = wx.BoxSizer(wx.HORIZONTAL)
self.sizerinner.Add((10,1))
self.zslider = \
wx.Slider( self, -1, 0, 0, 100, \
wx.DefaultPosition, wx.DefaultSize, \
wx.SL_HORIZONTAL | wx.SL_AUTOTICKS | \
wx.SL_LABELS )
self.sizerinner.Add( wx.StaticText( self, -1, 'z' ), 1, \
wx.ALIGN_CENTER )
self.sizerinner.Add( self.zslider, 9, wx.EXPAND )
self.sizerouter.Add( self.sizerinner, 1, wx.EXPAND )
self.Bind(wx.EVT_SLIDER, self.SliderUpdate)
self.SetSizer(self.sizerouter)
self.SetAutoLayout(1)
def OnCloseViews(self,evt):
if not evt.CanVeto():
self.Destroy()
else:
evt.Veto()
self.parent.mainframe.windowmenu.Check(ID_WINDOW_VIEWS, False)
self.Show(False)
def SliderUpdate(self,evt):
if self.zslider.GetValue() != self.parent.zpos:
self.parent.zpos = self.zslider.GetValue()
self.parent.UpdateImage(keepaxes=True)
# ---------------------------------------------------------------
class DataFrame(wx.Frame):
'''
frame for Data list'''
def __init__(self,parent):
wx.Frame.__init__(self,None,-1,"Data")
self.parent = parent
wx.EVT_CLOSE(self, self.OnCloseViews)
id = wx.NewId()
self.list = wx.ListCtrl(self,id,style=wx.LC_REPORT | wx.LC_SINGLE_SEL)
self.list.InsertColumn(0, "name")
self.list.InsertColumn(1, "shape")
self.sizer = wx.BoxSizer(wx.VERTICAL)
self.sizer.Add(self.list,1,wx.EXPAND)
self.Bind(wx.EVT_LIST_ITEM_SELECTED, self.OnSelectItem)
self.SetSizer(self.sizer)
self.SetAutoLayout(1)
def OnCloseViews(self,evt):
if not evt.CanVeto():
self.Destroy()
else:
evt.Veto()
self.parent.mainframe.windowmenu.Check(ID_WINDOW_DATA, False)
self.Show(False)
def ShapeString(self, id):
ndims = numpy.rank( self.parent.ims[id] )
str = ''
for i in range( ndims ):
dimsize = self.parent.ims[id].shape[i]
if dimsize > 1:
if i > 0:
str = str + ' x '
str = str + "%d" % dimsize
return str
def AddItem(self, name):
id = self.list.GetItemCount()
self.list.InsertStringItem(id, name)
self.list.SetStringItem(id, 1, self.ShapeString(name) )
def DelItem(self, name):
id = self.list.FindItem(-1, name)
self.list.DeleteItem(id)
# select last remaining item in list
self.list.Select(self.list.GetItemCount() - 1)
def OnSelectItem(self, evt):
self.parent._pdbg(3, '->dataframe.OnSelectItem')
if self.parent.curname != evt.GetText():
self.parent.SwitchToData(evt.GetText())
def SelectItem(self, name):
self.parent._pdbg(3, '->dataframe.SelectItem')
id = self.list.FindItem(-1, name)
self.list.Select(id)
def GetCurrentItemText(self):
sid = self.list.GetFirstSelected()
if sid > 0:
return self.list.GetItemText(sid)
else:
return None
# ---------------------------------------------------------------
class PlotFigure(wx.Frame):
def __init__(self, parent):
wx.Frame.__init__(self, None, -1, "PyVis")
self.parent = parent
self.fig = Figure((5,4), 75)
# canvas stuff
self.canvas = FigureCanvasWxAgg(self, -1, self.fig)
self.canvas.mpl_connect('motion_notify_event', self.SetMouseStatus)
self.toolbar = MyNavToolbar2WxAgg(self.canvas, self)
#self.toolbar = NavigationToolbar2WxAgg(self.canvas)
self.toolbar.Realize()
self.CreateStatusBar()
self.cmap = None
# file menu
filemenu = wx.Menu()
filemenu.Append(ID_FILE_EXIT, "E&xit", "Terminate the program")
self.Connect(ID_FILE_EXIT, -1, wx.wxEVT_COMMAND_MENU_SELECTED, \
self.OnMenuExit)
# window menu
self.windowmenu = wx.Menu()
self.windowmenu.AppendCheckItem(ID_WINDOW_DATA, "&Data",
"Open/close Data window")
self.windowmenu.AppendCheckItem(ID_WINDOW_VIEWS, "&Views",
"Toggle open state of Views window")
self.Connect(ID_WINDOW_VIEWS, -1, wx.wxEVT_COMMAND_MENU_SELECTED, \
self.ShowHideViews)
# tools menu
toolsmenu = wx.Menu()
toolsmenu.Append(ID_TOOLS_MAXPROJ, "&Maximum projection", \
"Show maximum projection over selected axes" )
toolsmenu.Append(ID_TOOLS_DELITEM, "&Delete", \
"Delete the currently selected item" )
self.Connect(ID_TOOLS_MAXPROJ, -1, wx.wxEVT_COMMAND_MENU_SELECTED, \
self.ShowMaxProj)
self.Connect(ID_TOOLS_DELITEM, -1, wx.wxEVT_COMMAND_MENU_SELECTED, \
self.DelCurItem)
# colourmap menu
self.cmapmenu = wx.Menu()
self.cmapmenu.AppendCheckItem(ID_CMAP_GRAY, "&Gray", \
"Use Gray colour map")
self.cmapmenu.AppendCheckItem(ID_CMAP_JET, "&Jet", \
"Use Jet colour map")
self.Connect(ID_CMAP_GRAY, -1, wx.wxEVT_COMMAND_MENU_SELECTED, \
self.CMapGray)
self.Connect(ID_CMAP_JET, -1, wx.wxEVT_COMMAND_MENU_SELECTED, \
self.CMapJet)
# menu bar
menuBar = wx.MenuBar()
menuBar.Append(filemenu, "&File")
menuBar.Append(self.windowmenu, "&Window")
menuBar.Append(toolsmenu, "&Tools")
menuBar.Append(self.cmapmenu, "&Colourmaps")
self.SetMenuBar(menuBar)
self.Bind(wx.EVT_CLOSE, self.OnCloseWindow)
wx.EVT_MENU(self, ID_WINDOW_DATA, self.ShowHideData)
self.figmgr = FigureManager(self.canvas, 1, self)
sizer = wx.BoxSizer(wx.VERTICAL)
sizer.Add(self.canvas, 1, wx.LEFT|wx.TOP|wx.GROW)
sizer.Add(self.toolbar, 0, wx.GROW)
self.SetSizer(sizer)
self.Fit()
def plot_data(self, array, vmin=None, vmax=None, keepaxes=False):
a = self.fig.add_subplot(111)
if keepaxes:
xlims = a.get_xlim()
ylims = a.get_ylim()
a.imshow(array, interpolation='nearest', vmin=vmin, vmax=vmax, cmap=self.cmap)
if keepaxes:
a.set_xlim(xlims)
a.set_ylim(ylims)
self.toolbar.update()
self.Refresh()
def GetLims(self):
a = self.fig.add_subplot(111)
xlims = a.get_xlim()
ylims = a.get_ylim()
return xlims, ylims
def ResetLims(self):
a = self.fig.add_subplot(111)
maxes = self.parent.ims[self.parent.curname].shape
a.set_xlim((0,maxes[0]))
a.set_ylim((0,maxes[1]))
self.Refresh()
def GetToolbar(self):
return self.toolbar
def OnCloseWindow(self, evt):
if not self.IsBeingDeleted():
self.parent.viewsframe.Close(True)
self.parent.dataframe.Close(True)
self.Destroy()
def OnMenuExit(self, evt):
self.parent.viewsframe.Close(True)
self.parent.dataframe.Close(True)
self.Destroy()
def ShowHideData(self, evt):
self.parent.dataframe.Show(not self.parent.dataframe.IsShown())
def ShowHideViews(self, evt):
self.parent.viewsframe.Show(not self.parent.viewsframe.IsShown())
def SetMouseStatus(self, evt):
a = self.fig.gca()
xpos, ypos = evt.xdata, evt.ydata
if xpos != None and ypos != None:
zpos = self.parent.zpos
# should probably do proper check that exact upper value isn't met
try:
val = self.parent.im[numpy.floor(xpos), numpy.floor(ypos)]
status_str = "x: %4.2f y: %4.2f z: %4.2f I:%4.2f" \
% (xpos, ypos, zpos, val)
self.SetStatusText(status_str)
except:
pass
def ShowMaxProj(self, evt):
self.parent.MaxProj(self.parent.curname)
def DelCurItem(self, evt):
self.parent.DelItem( self.parent.curname )
def CMapGray(self, evt):
self.cmap = matplotlib.cm.gray
self.cmapmenu.Check(ID_CMAP_GRAY, True)
self.cmapmenu.Check(ID_CMAP_JET, False)
self.parent.UpdateImage(keepaxes=True)
def CMapJet(self, evt):
self.cmap = matplotlib.cm.jet
self.cmapmenu.Check(ID_CMAP_GRAY, False)
self.cmapmenu.Check(ID_CMAP_JET, True)
self.parent.UpdateImage(keepaxes=True)
# ---------------------------------------------------------------
class pyvis(wx.App):
verbosity = 0
def OnInit(self):
'''Usage pv = pyvis.pyvis()
pv.AddImage(arr, 'arname')
PyVis array visualization tool, based loosely after the
excellent KVis by Richard Gooch, which connects to pdl'''
self._pdbg(3, '->init')
self.nextnum = 0
self.zpos = 0
self.ims = {}
self.mainframe = PlotFigure(self)
self.mainframe.Show(True)
self.dataframe = DataFrame(self)
self.viewsframe = ViewsFrame(self)
self.SetTopWindow(self.mainframe)
self.cid = []
self.curname = None
return True
def _pdbg(self, level, str):
if self.verbosity > level:
print str
def AddImg(self, stack, name=None):
'''Usage: AddImg(data, name=name)
Add an image (2 or 3-D) to PyVis stack, with an optional
name for reference.'''
self._pdbg(3, '->AddImg')
# set appropriate data name
if name == None:
name = "image %d" % self.nextnum
self.nextnum += 1
if name in self.ims.keys():
# ensure unique image name
name = name + '%d' % self.nextnum
self.nextnum += 1
# load data into memory
self.ims[name] = stack
self.dataframe.AddItem(name)
self.SwitchToData(name)
def UpdateImage(self, keepaxes=False):
'''Internal usage mainly. Used to redraw the current image
(2-D). Keepaxes is used when switching z-position to maintain
the axis position (zoom level).'''
self._pdbg(3, '->UpdateImage')
# for coding convenience
data = self.ims[self.curname]
# load data (plane if 3-D) into image
if numpy.rank(data) == 2:
self.im = data
elif numpy.rank(data) == 3:
self.im = data[:,:,self.zpos]
else:
raise TypeError("Data has too many dimensions")
# display image
self.mainframe.plot_data(self.im[:,::-1].transpose(), \
vmin=self.imin, vmax=self.imax, \
keepaxes=keepaxes)
def SwitchToData(self, name):
'''Usage: SwitchToData(name)
Switch to viewing the data named <name>.'''
self._pdbg(3, '->SwitchToData')
if name == None:
self.mainframe.fig.clf()
self.curname == None
else:
# working out if should keep same x-y position/zoom
# as long as some old image is present...
if not self.curname is None:
old_lims = self.mainframe.GetLims()
self._pdbg( 3, "in SwitchToData: old lims" + str( old_lims ) )
else:
self._pdbg(3, "in SwitchToData: no old lims")
old_lims = None
# for coding convenience
data = self.ims[name]
# for colour-table preservation throughout stack
self.imin = data.min()
self.imax = data.max()
# if 2-D set maximum z to be 0
if numpy.rank(data) == 2:
zmax = 0
# if 3-D go to same (current) plane or max available
elif numpy.rank(data) == 3:
if self.zpos > data.shape[2]:
self.zpos = data.shape[2] - 1
zmax = data.shape[2] - 1
# for later reference
self.curname = name
# make sure current item selected in Data window is correct
if self.dataframe.GetCurrentItemText() != name:
self.dataframe.SelectItem(name)
# update maximum for z-slider in Views window
self.viewsframe.zslider.SetMax( zmax )
# continue working out if old x-y position
# is appropriate for new data
keepaxes = False
if not old_lims is None:
if numpy.all( numpy.array(old_lims).max(1) < data.shape[0:2] ):
keepaxes = True
# update the screen image
self.UpdateImage(keepaxes)
def DelItem(self, name):
'''Usage: DelItem(name)
Deletes item <name> from stack (and switches to last item if
deleted item was the current one).'''
if self.curname == name:
lastname = self.ims.keys()[-1]
if lastname != name:
# if we're not deleting last (most recent) item
# - switch to that one
nextname = lastname
else:
# we are deleting last item
if len( self.ims ) > 1:
# there is another one to switch to
nextname = self.ims.keys()[-2]
else:
# we're deleting the only item
nextname = None
self.SwitchToData( nextname )
self.dataframe.DelItem(name)
del self.ims[name]
def MaxProj(self, name):
'''Usage: MaxProj(name)
Calculates a maximum z-projection of the data <name>
and switches to make it the current data.'''
maxprojx = self.ims[name].max(2)
self.AddImg(maxprojx, name + ' (max projection)')
def ClickHandler(self, evt):
#if not (self.mainframe.toolbar.panmode or \
# self.mainframe.toolbar.zoomode):
if self.mainframe.toolbar.mode == '':
x = evt.xdata
y = evt.ydata
z = self.zpos
if not self.clickcallback is None:
print "To callback."
self.clickcallback(x,y,z, *self.clickcallbackargs)
def ConnectClickCallback(self, func, *args):
'''Usage: ConnectClickCallback(func, *args)
Connects function <func> to respond to non-zoom, non-pan click
events in the current canvas. func must have the signature:
def <callbackfunc>(x,y,z, *args):
...
where x,y,z are the click co-ordinates when inside the
axes and None (x and y anyway) when click is outside and
args are any other parameters the callback needs.'''
print "Connecting", func.__name__
self.clickcallback = func
self.clickcallbackargs = args
self.cid.append( self.mainframe.canvas.mpl_connect(\
'button_press_event', self.ClickHandler) )
def DisconnectClickCallback(self):
'''Usage: DisconnectClickCallback()
Disconnects all connected callback routines from click event.'''
while len(self.cid) > 0:
i = self.cid.pop()
self.mainframe.canvas.mpl_disconnect(i)
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