def SetData(self, data):
"""
Set / replace the data associated with the image. This is primarily used in the acquisition program when we want
a live view of constantly updating data. It is also used for the same purpose during deconvolution.
Parameters
----------
data : numpy array or PYME.IO.DataSources datasource
Returns
-------
"""
#the data does not need to be a numpy array - it could also be, eg., queue data
#on a remote server - wrap so that is is indexable like an array
self.data = dataWrap.Wrap(data)
def SetDataStack(self, datasource):
self.ds = dataWrap.Wrap(datasource) #make sure data is wrapped
nchans = self.ds.shape[self.ds.ndim - 1]
self.nz = self.ds.shape[2]
if (self.ds.ndim >= 5):
self.nt = self.ds.shape[3]
else:
self.nt = 1
if not nchans == len(self.Chans):
if nchans == 1:
self.Chans = [0]
self.Gains = [1]
self.Offs = [0]
self.cmaps = [cm.gray]
try:
if np.iscomplexobj(self.ds[0, 0, 0, 0, 0]):
self.cmaps = [cm.jet]
self.cmax_offset = -np.pi
self.cmax_scale = 1. / (2 * np.pi)
except IndexError:
pass
self.show = [True]
else:
self.Chans = []
self.Gains = []
self.Offs = []
self.cmaps = []
self.show = []
cms = [cm.r, cm.g, cm.b]
for i in range(nchans):
self.Chans.append(i)
self.Gains.append(1.)
self.Offs.append(0.)
self.cmaps.append(cms[i % len(cms)])
self.show.append(True)
self.names = ['Chan %d' % i for i in range(nchans)]
self.OnChange()
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()