[CCPPETMR/SIRF] fully_sampled_recon_three_chains.ipynb fails (with SIRF master) (#293)

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Kris Thielemans

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Jan 12, 2019, 4:41:44 AM1/12/19
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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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Kris Thielemans

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Jan 12, 2019, 4:45:05 AM1/12/19
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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?

evgueni-ovtchinnikov

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Jan 14, 2019, 5:20:19 AM1/14/19
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@KrisThielemans: access to archlinux would certainly help - how else can i investigate what goes wrong there :)
what is archlinux anyway?

Kris Thielemans

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Jan 29, 2019, 3:31:33 PM1/29/19
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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.

Kris Thielemans

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Jan 29, 2019, 3:32:00 PM1/29/19
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@evgueni-ovtchinnikov I've tried rebuilding with our version of HDF5 as opposed to the system one. Same problem unfortunately.

Kris Thielemans

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May 23, 2019, 3:16:10 AM5/23/19
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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)

Kris Thielemans

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May 23, 2019, 3:16:50 AM5/23/19
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This could be a Gadgetron change/bug I guess.

Evgueni Ovtchinnikov

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Sep 6, 2019, 9:44:32 AM9/6/19
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caused by bugs in new ExtractGadget, Gadgetron issue #743 created

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