if you are using .h5's, Modules>Load Images only has an option for .tiff's, you can work around this by doing the following:
import h5py as h5py
#see h5py documentation, 'r' is for read
aa=h5py.File(datapath,'r')
# find the name of the dataset object
list(aa.keys())
#call the dataset object
dset=aa['data']
#convert from h5 dataset to numpy array
a=dset[()]
a.shape #in t,x,y
type(a) # make sure it's a numpyarray
meta = \
{
"origin": "Tutorial example",
"fps": 10.0,
"date": "20220602_cd036_000",
"scanner_pos": [0,1,2,3,4,5,6]
}
# Create ImgData instance
imgdata = ImgData(a.T, meta) # use a.T to get [x, y, t] (time last)
# Create a work environment instance
work_env = ViewerWorkEnv(imgdata)
# Set the current Viewer Work Environment from this new instance
vi.viewer.workEnv = work_env
# Update the viewer with the new work environment
# this MUST be run whenever you replace the viewer work environment (the previous line)
update_workEnv()
Hello folks,
if you are using .h5's, Modules>Load Images only has an option for .tiff's, you can work around this by doing the following: