def Export(self,
data,
outFile,
xslice,
yslice,
zslice,
metadata=None,
events=None,
origName=None,
progressCallback=None):
from PYME.contrib.gohlke import tifffile
from PYME.IO import dataWrap
def _bool_to_uint8(data):
if data.dtype == 'bool':
return data.astype('uint8')
else:
return data
if data.nbytes > 2e9:
warnings.warn(
'Data is larger than 2GB, generated TIFF may not read in all software'
)
if data.nbytes > 4e9:
raise RuntimeError(
'TIFF has a maximum file size of 4GB, crop data or save as HDF'
)
dw = dataWrap.ListWrap([
numpy.atleast_3d(
_bool_to_uint8(data[xslice, yslice, zslice, i].squeeze()))
for i in range(data.shape[3])
])
#xmd = None
if not metadata is None:
xmd = MetaDataHandler.OMEXMLMDHandler(mdToCopy=metadata)
if not origName is 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]))
description = xmd.getXML(dw)
else:
description = None
tifffile.imsave_f(outFile, dw, description=description)
if progressCallback:
try:
progressCallback(100, 100)
except:
pass
def Export(self,
data,
outFile,
xslice,
yslice,
zslice,
metadata=None,
events=None,
origName=None,
progressCallback=None):
from PYME.contrib.gohlke import tifffile
from PYME.IO import dataWrap
def _bool_to_uint8(data):
if data.dtype == 'bool':
return data.astype('uint8')
else:
return data
dw = dataWrap.ListWrap([
numpy.atleast_3d(
_bool_to_uint8(data[xslice, yslice, zslice, i].squeeze()))
for i in range(data.shape[3])
])
#xmd = None
if not metadata is None:
xmd = MetaDataHandler.OMEXMLMDHandler(mdToCopy=metadata)
if not origName is 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]))
description = xmd.getXML(dw)
else:
description = None
tifffile.imsave_f(outFile, dw, description=description)
if progressCallback:
try:
progressCallback(100, 100)
except:
pass
def OnMakeComposites(self, event):
import numpy as np
dlg = CompositeDialog(self.dsviewer, self.dsviewer.image)
imageNames = dlg.imageNames
#dispNames = dlg.dispNames
if dlg.ShowModal() == wx.ID_OK:
#others = [dispNames[n] for n in dlg.GetSelections()]
others = dlg.GetSelections()
#master, mchan = _getImage(dlg.GetMaster())
ignoreZ = dlg.GetIgnoreZ()
interp = dlg.GetInterp()
if interp:
order = 3
else:
order = 0
shape, origin, voxelsize = dlg.shape, dlg.origin, dlg.voxelsize
print((shape, origin, voxelsize))
if len(others) > 0:
newNames = []
newData = []
for otherN in others:
other, chan = _getImage(otherN)
try:
cn = other.mdh.getEntry('ChannelNames')[chan]
otherName = '%s - %s' % (os.path.split(other.filename)[1], cn)
except:
if other.data.shape[3] == 1:
otherName = os.path.split(other.filename)[1]
else:
otherName = '%s - %d' % (os.path.split(other.filename)[1], chan)
newNames.append(otherName)
if isinstance(other.data, dataWrap.ListWrap):
od = other.data.dataList[chan]
else:
od = other.data
if ignoreZ:
originsEqual = np.allclose(other.origin[:2], origin[:2], atol=1)
else:
originsEqual = np.allclose(other.origin, origin, atol=1)
shiftField = dlg.GetShiftmap(otherN)
print(shape[:3], other.data.shape[:3])
if (not np.allclose(other.pixelSize, voxelsize[0], rtol=.001)) or (not (other.data.shape[:3] == shape[:3])) or (not originsEqual) or shiftField:
#need to rescale ...
print(('Remapping ', otherN, originsEqual, other.origin, np.allclose(other.pixelSize, voxelsize[0], rtol=.001),(not (other.data.shape[:3] == shape[:3])), shiftField, other.pixelSize, ignoreZ))
#print origin, voxelsize
od = self.RemapData(other, chan, shape, voxelsize, origin, shiftField = shiftField, ignoreZ=ignoreZ, order=order)
newData += [od]
pre = common_prefix(newNames)
print(pre)
lPre = len(pre)
newNames = [n[lPre:] for n in newNames]
mdh = MetaDataHandler.NestedClassMDHandler(self.image.mdh)
mdh.setEntry('ChannelNames', newNames)
mdh['voxelsize.x'] = voxelsize[0]/1e3
mdh['voxelsize.y'] = voxelsize[1]/1e3
mdh['voxelsize.z'] = voxelsize[2]/1e3
mdh['Origin.x'] = origin[0]
mdh['Origin.y'] = origin[1]
mdh['Origin.z'] = origin[2]
View3D(dataWrap.ListWrap(newData, 3), 'Composite', mdh=mdh, mode = self.dsviewer.mode, parent=wx.GetTopLevelParent(self.dsviewer), glCanvas=self.dsviewer.glCanvas)
dlg.Destroy()