At present, image_array
has shape
[0,0,0]
. complex_image_data
seems alright though (its shape after as_array
is [2,256,256]
).
I haven't checked the corresponding SIRF demo.
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@evgueni-ovtchinnikov I've moved this issue here. I have checked that on my VM both the notebook and actual demo work fine. However, on an archlinux install both fail. This could be a gadgetron server issue but Gadgetron's unit-tests and integration tests work. I have no clue what to do about it. would it help if I see if I can give you access to the archlinux system?
@KrisThielemans: access to archlinux would certainly help - how else can i investigate what goes wrong there :)
what is archlinux anyway?
we've seen problems with the other Gadgetron demos returning only 1 image as opposed to both repetitions. Seems to be related to reading the ISMRMRD file.
@evgueni-ovtchinnikov I've tried rebuilding with our version of HDF5 as opposed to the system one. Same problem unfortunately.
we have this same problem now on the new VM. Everything is fine until here https://github.com/CCPPETMR/SIRF/blob/ea4a56f9f07ae5a17d74887fbca002dc69313b5c/examples/Python/MR/Gadgetron/fully_sampled_recon_three_chains.py#L109
c=complex_image_data.as_array()
c.shape
returns (2, 256, 256)
, and a display of the numpy.abs(c)
looks fine.
However, the extracted array is not https://github.com/CCPPETMR/SIRF/blob/ea4a56f9f07ae5a17d74887fbca002dc69313b5c/examples/Python/MR/Gadgetron/fully_sampled_recon_three_chains.py#L114-L118
In [44]: real_image_data.number()
Out[44]: 0
In [45]: real_image_data.as_array().shape
Out[45]: (0, 0, 0)
This could be a Gadgetron change/bug I guess.
caused by bugs in new ExtractGadget, Gadgetron issue #743 created