def __init__(self,
parent=None,
title='',
dstack=None,
log=None,
filename=None,
filedir=""):
wx.Frame.__init__(self, parent, -1, title)
self.ds = dstack
self.log = log
self.saved = False
self.filedir = filedir
if (dstack is None):
if (filename is None):
fdialog = wx.FileDialog(None,
'Please select Data Stack to open ...',
wildcard='*.kdf',
style=wx.FD_OPEN | wx.HIDE_READONLY)
succ = fdialog.ShowModal()
if (succ == wx.ID_OK):
self.ds = example.CDataStack(fdialog.GetPath())
self.SetTitle(fdialog.GetFilename())
self.saved = True
#fn =
else:
self.ds = example.CDataStack(filename)
self.SetTitle(filename)
self.saved = True
self.vp = MyViewPanel(self, self.ds)
sizer = wx.BoxSizer(wx.VERTICAL)
sizer.Add(self.vp, 1, wx.EXPAND, 0)
self.SetAutoLayout(1)
self.SetSizer(sizer)
sizer.Fit(self)
#sizer.SetSizeHints(self)
# Menu Bar
self.menubar = wx.MenuBar()
self.SetMenuBar(self.menubar)
tmp_menu = wx.Menu()
#F_SAVE = wx.NewId()
#F_CLOSE = wx.NewId()
tmp_menu.Append(wx.ID_SAVEAS, "Save As", "", wx.ITEM_NORMAL)
tmp_menu.Append(wx.ID_CLOSE, "Close", "", wx.ITEM_NORMAL)
self.menubar.Append(tmp_menu, "File")
mEdit = wx.Menu()
EDIT_CLEAR_SEL = wx.NewId()
EDIT_CROP = wx.NewId()
mEdit.Append(EDIT_CLEAR_SEL, "Reset Selection", "", wx.ITEM_NORMAL)
mEdit.Append(EDIT_CROP, "Crop", "", wx.ITEM_NORMAL)
self.menubar.Append(mEdit, "Edit")
# Menu Bar end
wx.EVT_MENU(self, wx.ID_SAVEAS, self.saveStack)
wx.EVT_MENU(self, wx.ID_CLOSE, self.menuClose)
wx.EVT_MENU(self, EDIT_CLEAR_SEL, self.clearSel)
wx.EVT_MENU(self, EDIT_CROP, self.crop)
wx.EVT_CLOSE(self, self.OnCloseWindow)
self.statusbar = self.CreateStatusBar(1, wx.STB_SIZEGRIP)
self.Layout()
self.update()
def crop(self, event):
cd = dCrop.dCrop(self, self.vp)
if cd.ShowModal():
ds2 = example.CDataStack(self.ds, cd.x1, cd.y1, cd.z1, cd.x2,
cd.y2, cd.z2, cd.chs)
dvf = DSViewFrame(self.GetParent(), '--cropped--', ds2)
dvf.Show()
def __init__(self, parent, dstack=None):
wx.ScrolledWindow.__init__(self, parent, -1)
if (dstack == None):
self.ds = example.CDataStack("test.kdf")
else:
self.ds = dstack
self.imagepanel = self
self.selecting = False
self.SetScrollRate(10, 10)
self.SetVirtualSize(wx.Size(self.ds.getWidth(), self.ds.getHeight()))
self.SetSize((self.ds.getWidth(), self.ds.getHeight()))
self.do = example.CDisplayOpts()
self.do.setDisp1Chan(0)
self.do.setDisp2Chan(0)
self.do.setDisp3Chan(0)
if (self.ds.getNumChannels() >= 2):
self.do.setDisp2Chan(1)
if (self.ds.getNumChannels() >= 3):
self.do.setDisp1Chan(2)
self.do.Optimise(self.ds)
self.rend = example.CLUT_RGBRenderer()
self.rend.setDispOpts(self.do)
self.scale = 0
self.updating = 0
self.selection = True
self.ResetSelection()
wx.EVT_PAINT(self, self.OnPaint)
wx.EVT_SIZE(self, self.OnSize)
wx.EVT_RIGHT_DOWN(self, self.OnRightDown)
wx.EVT_RIGHT_UP(self, self.OnRightUp)
wx.EVT_LEFT_DOWN(self.imagepanel, self.OnRightDown)
wx.EVT_LEFT_UP(self.imagepanel, self.OnRightUp)
wx.EVT_MOTION(self.imagepanel, self.OnMotion)
wx.EVT_ERASE_BACKGROUND(self, self.DoNix)
def generateThumbnail(inputFile, thumbSize):
global size
im = cSMI.CDataStack_AsArray(cSMI.CDataStack(inputFile.encode()),
0).mean(2).squeeze()
xsize = im.shape[0]
ysize = im.shape[1]
if xsize > ysize:
zoom = float(thumbSize) / xsize
else:
zoom = float(thumbSize) / ysize
size = (int(xsize * zoom), int(ysize * zoom))
im = im - im.min()
im = maximum(minimum(1 * (255 * im) / im.max(), 255), 0)
return im.astype('uint8')
def LoadKdf(self, filename):
'''load khorus formatted data - pretty much deprecated by now'''
import PYME.cSMI as cSMI
self.data = cSMI.CDataStack_AsArray(cSMI.CDataStack(filename),
0).squeeze()
self.mdh = MetaData.TIRFDefault
try: #try and get metadata from the .log file
lf = open(os.path.splitext(filename)[0] + '.log')
from PYME.DSView import logparser
lp = logparser.logparser()
log = lp.parse(lf.read())
lf.close()
self.mdh.setEntry('voxelsize.z', log['PIEZOS']['Stepsize'])
except:
pass
from PYME.ParallelTasks.relativeFiles import getRelFilename
self.seriesName = getRelFilename(filename)
self.mode = 'psf'
def __init__(self, parent, dstack=None):
viewpanel.ViewPanel.__init__(self, parent, -1)
if (dstack is None):
self.ds = example.CDataStack("test.kdf")
else:
self.ds = dstack
self.imagepanel.SetVirtualSize(
wx.Size(self.ds.getWidth(), self.ds.getHeight()))
self.imagepanel.SetSize((self.ds.getWidth(), self.ds.getHeight()))
self.do = example.CDisplayOpts()
self.do.setDisp1Chan(0)
self.do.setDisp2Chan(0)
self.do.setDisp3Chan(0)
if (self.ds.getNumChannels() >= 2):
self.do.setDisp2Chan(1)
if (self.ds.getNumChannels() >= 3):
self.do.setDisp1Chan(2)
self.do.Optimise(self.ds)
self.rend = example.CLUT_RGBRenderer()
self.rend.setDispOpts(self.do)
self.cbRedChan.Append("<none>")
self.cbGreenChan.Append("<none>")
self.cbBlueChan.Append("<none>")
for i in range(self.ds.getNumChannels()):
self.cbRedChan.Append(self.ds.getChannelName(i))
self.cbGreenChan.Append(self.ds.getChannelName(i))
self.cbBlueChan.Append(self.ds.getChannelName(i))
self.scale = 2
self.crosshairs = True
self.selection = True
self.ResetSelection()
self.SetOpts()
self.updating = 0
self.showOptsPanel = 1
wx.EVT_PAINT(self.imagepanel, self.OnPaint)
wx.EVT_MOUSEWHEEL(self, self.OnWheel)
wx.EVT_KEY_DOWN(self.imagepanel, self.OnKeyPress)
wx.EVT_LEFT_UP(self.imagepanel, self.OnLeftClick)
wx.EVT_RIGHT_DOWN(self.imagepanel, self.OnRightDown)
wx.EVT_RIGHT_UP(self.imagepanel, self.OnRightUp)
wx.EVT_COMBOBOX(self, self.cbRedChan.GetId(), self.GetOpts)
wx.EVT_COMBOBOX(self, self.cbGreenChan.GetId(), self.GetOpts)
wx.EVT_COMBOBOX(self, self.cbBlueChan.GetId(), self.GetOpts)
wx.EVT_COMBOBOX(self, self.cbSlice.GetId(), self.GetOpts)
wx.EVT_COMBOBOX(self, self.cbScale.GetId(), self.GetOpts)
wx.EVT_TEXT(self, self.tRedGain.GetId(), self.GetOpts)
wx.EVT_TEXT(self, self.tRedOff.GetId(), self.GetOpts)
wx.EVT_TEXT(self, self.tGreenGain.GetId(), self.GetOpts)
wx.EVT_TEXT(self, self.tGreenOff.GetId(), self.GetOpts)
wx.EVT_TEXT(self, self.tBlueGain.GetId(), self.GetOpts)
wx.EVT_TEXT(self, self.tBlueOff.GetId(), self.GetOpts)
wx.EVT_BUTTON(self, self.bOptimise.GetId(), self.Optim)
wx.EVT_BUTTON(self, self.bShowOpts.GetId(), self.ShowOpts)
wx.EVT_ERASE_BACKGROUND(self.imagepanel, self.DoNix)
wx.EVT_ERASE_BACKGROUND(self, self.DoNix)