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TheChymera opened this issue Feb 20, 2024 · 4 comments
Open

How to get nipy testdata for network-sandboxed testing #561

TheChymera opened this issue Feb 20, 2024 · 4 comments

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@TheChymera
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Currently sandboxed tests fail because of missing data: https://ppb.chymera.eu/d39f86.html

I found a guide for getting nipy data, but I don't seem to get the required files.
E.g. /var/tmp/portage/sci-libs/nipy-0.6.0/homedir/.nipy/tests/data/group_t_images.tar.gz is not in:

[deco]/tmp ❱ tree nipy-templates-0.2/templates/
nipy-templates-0.2/templates/
├── colin27
│   └── 2mm
│       └── T1.nii.gz
├── config.ini
└── ICBM152
    ├── 1mm
    │   └── T1_brain.nii.gz
    └── 2mm
        └── T1.nii.gz

6 directories, 4 files
[deco]/tmp ❱ tree nipy-data-0.3/data/
nipy-data-0.3/data/
├── config.ini
├── fiac
│   └── fiac0
│       ├── mask.nii.gz
│       ├── run1_design.npz
│       ├── run1.nii.gz
│       ├── run2_design.npz
│       └── run2.nii.gz
└── neurospin
    ├── language_babies
    │   └── offset_002.npz
    └── sulcal2000
        ├── nobias_ammon.nii.gz
        └── nobias_anubis.nii.gz

6 directories, 9 files
@matthew-brett
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We need to update those instructions, but a) the package versions have been updated to 0.3, and b) you need the nipy-data package for that particular file. As in:

curl -OL http://nipy.org/data-packages/nipy-data-0.3.tar.gz
curl -OL http://nipy.org/data-packages/nipy-templates-0.3.tar.gz

@TheChymera
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TheChymera commented Feb 20, 2024 •
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@matthew-brett the nipy-data I have is already 0.3, as seen in the code above. Do I have the wrong 0.3 archive, or is there a different archive I need for e.g. group_t_images.tar.gz?

@TheChymera TheChymera reopened this Feb 20, 2024
@matthew-brett
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Oops - so sorry - I should have read more carefully. Some of the examples are broken, because the FTP site with the relevant data went down : ftp://ftp.cea.fr/pub/dsv/madic/download/nipy - see examples/labs/need_data/get_data_light.py. I'm afraid I have no way of getting those images now. So we're going to have to orphan those tests.

@TheChymera
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TheChymera commented Feb 27, 2024 •
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Is the data permanently lost, or is this something you might come across again at an indeterminate moment in the future?

I'm sure somebody must have it locally from some old tests they ran if it's been the same data for a long time.ä
If not, do you remember how it was generated?

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@matthew-brett @TheChymera