def Export(self,
data,
outFile,
xslice,
yslice,
zslice,
metadata=None,
events=None,
origName=None):
#xmd = None
if not metadata == None:
xmd = MetaDataHandler.XMLMDHandler(mdToCopy=metadata)
if data.shape[3] > 1: #have multiple colour channels
if data.shape[2] == 1: #2d image -> stack with chans
#d = numpy.concatenate([numpy.atleast_3d(data[xslice, yslice, 0, i].squeeze()) for i in range(data.shape[3])],2)
#saveTiffStack.saveTiffMultipage(d, outFile)
mpt = saveTiffStack.TiffMP(outFile)
for i in range(data.shape[3]):
mpt.AddSlice(data[xslice, yslice, 0, i].squeeze())
mpt.close()
else: #save each channel as it's own stack
if not metadata == None and 'ChannelNames' in metadata.getEntryNames(
):
chanNames = metadata['ChannelNames']
else:
chanNames = range(data.shape[3])
chanFiles = [
os.path.splitext(os.path.split(outFile)[1])[0] +
'__%s.tif' % chanNames[i] for i in range(data.shape[3])
]
if not metadata == None:
xmd['ChannelFiles'] = chanFiles
for i in range(data.shape[3]):
saveTiffStack.saveTiffMultipage(
data[xslice, yslice, zslice, i].squeeze(),
os.path.splitext(outFile)[0] +
'__%s.tif' % chanNames[i])
else:
saveTiffStack.saveTiffMultipage(data[xslice, yslice, zslice],
outFile)
if not metadata == None:
#xmd = MetaDataHandler.XMLMDHandler(mdToCopy=metadata)
if not origName == None:
xmd.setEntry('cropping.originalFile', origName)
xmd.setEntry('cropping.xslice', xslice.indices(data.shape[0]))
xmd.setEntry('cropping.yslice', yslice.indices(data.shape[1]))
xmd.setEntry('cropping.zslice', zslice.indices(data.shape[2]))
print((xslice.indices(data.shape[0])))
xmlFile = os.path.splitext(outFile)[0] + '.xml'
xmd.writeXML(xmlFile)
def saveDeconvolution(self, event=None):
fdialog = wx.FileDialog(None, 'Save Positions ...',
wildcard='TIFF Files|*.tif', defaultFile=os.path.splitext(self.seriesName)[0] + '_dec.tif', style=wx.SAVE|wx.HIDE_READONLY)
succ = fdialog.ShowModal()
if (succ == wx.ID_OK):
outFilename = fdialog.GetPath()
from PYME.FileUtils import saveTiffStack
saveTiffStack.saveTiffMultipage(self.dec.res, outFilename)
def saveDeconvolution(self, event=None):
fdialog = wx.FileDialog(
None,
'Save Positions ...',
wildcard='TIFF Files|*.tif',
defaultFile=os.path.splitext(self.seriesName)[0] + '_dec.tif',
style=wx.SAVE | wx.HIDE_READONLY)
succ = fdialog.ShowModal()
if (succ == wx.ID_OK):
outFilename = fdialog.GetPath()
from PYME.FileUtils import saveTiffStack
saveTiffStack.saveTiffMultipage(self.dec.res, outFilename)
def Export(self, data, outFile, xslice, yslice, zslice, metadata=None, events = None, origName=None):
#xmd = None
if not metadata == None:
xmd = MetaDataHandler.XMLMDHandler(mdToCopy=metadata)
if data.shape[3] > 1: #have multiple colour channels
if data.shape[2] == 1: #2d image -> stack with chans
#d = numpy.concatenate([numpy.atleast_3d(data[xslice, yslice, 0, i].squeeze()) for i in range(data.shape[3])],2)
#saveTiffStack.saveTiffMultipage(d, outFile)
mpt = saveTiffStack.TiffMP(outFile)
for i in range(data.shape[3]):
mpt.AddSlice(data[xslice, yslice, 0, i].squeeze())
mpt.close()
else: #save each channel as it's own stack
if not metadata == None and 'ChannelNames' in metadata.getEntryNames():
chanNames = metadata['ChannelNames']
else:
chanNames = range(data.shape[3])
chanFiles = [os.path.splitext(os.path.split(outFile)[1])[0] + '__%s.tif' % chanNames[i] for i in range(data.shape[3])]
if not metadata == None:
xmd['ChannelFiles'] = chanFiles
for i in range(data.shape[3]):
saveTiffStack.saveTiffMultipage(data[xslice, yslice, zslice, i].squeeze(), os.path.splitext(outFile)[0] + '__%s.tif' % chanNames[i])
else:
saveTiffStack.saveTiffMultipage(data[xslice, yslice, zslice], outFile)
if not metadata == None:
#xmd = MetaDataHandler.XMLMDHandler(mdToCopy=metadata)
if not origName == None:
xmd.setEntry('cropping.originalFile', origName)
xmd.setEntry('cropping.xslice', xslice.indices(data.shape[0]))
xmd.setEntry('cropping.yslice', yslice.indices(data.shape[1]))
xmd.setEntry('cropping.zslice', zslice.indices(data.shape[2]))
print((xslice.indices(data.shape[0])))
xmlFile = os.path.splitext(outFile)[0] + '.xml'
xmd.writeXML(xmlFile)
