using MITTENS about mittens

[mattcieslak]

Excellent! MITTENS is a favorite project of mine that hasn't seen much interest, let me know if you have questions about its outputs or use

[mattcieslak]

hi @vnbcs, could you try building the singularity image directly from dockerhub like

singularity build mittens.sif docker://pennbbl/mittens:latest

This should produce a working image, but please let me know if otherwise

[vnbcs]

That worked! I am now running Python3.7 in the Singularity shell. I am trying write_files("odf-8", 35, 1). According to tqdm, it will be processing for the next hour. I will update you on the results. Thanks!

[vnbcs]

Hello again! write_files("odf-8", 35, 1) ran, and I moved the fortran files into src. I tried to install the package with pip install -e ., but received an error saying the package was already installed. I once again ran the following code, this time in the Singularity shell.

from mittens import MITTENS
fn ='/path_goes_here/subj-id_dwi.odf.gqi.1.25.fib.gz'
mitns = MITTENS(reconstruction=fn)

And again I got back a module not found error. There is still no folder mittens/fortran. Here's the full traceback:

>>> mitns = MITTENS(reconstruction=fn)
INFO:mittens._mittens:
Using
------
  Step Size:            0.8660 Voxels 
  ODF Resolution:       odf8
  Max Angle:            35.00 Degrees
  Angle Weights:        flat
  Angle weight power:   1.0
INFO:mittens.external.dsi_studio:Loading DSI Studio ODF data
WARNING:mittens.external.dsi_studio:Unable to load real affine image 
INFO:mittens._mittens:Loaded ODF data: (209526, 321)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/path_goes_here/MITTENS/mittens/_mittens.py", line 177, in __init__
    self._initialize_nulls()
  File "/path_goes_here/MITTENS/mittens/_mittens.py", line 187, in _initialize_nulls
    self.singleODF_funcs = self.get_prob_funcs("singleODF")
  File "/path_goes_here/MITTENS/mittens/_mittens.py", line 290, in get_prob_funcs
    module = importlib.import_module("mittens.fortran." + requested_module)
  File "/usr/local/miniconda/lib/python3.7/importlib/__init__.py", line 127, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 1006, in _gcd_import
  File "<frozen importlib._bootstrap>", line 983, in _find_and_load
  File "<frozen importlib._bootstrap>", line 953, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
  File "<frozen importlib._bootstrap>", line 1006, in _gcd_import
  File "<frozen importlib._bootstrap>", line 983, in _find_and_load
  File "<frozen importlib._bootstrap>", line 965, in _find_and_load_unlocked
ModuleNotFoundError: No module named 'mittens.fortran'

What do you recommend? Thanks again!

[jlhanson5]

I'm less familiar with MITTENS, but I'm helping @vnbcs out (and I am semi-familiar with DWI). Any thoughts on the issues that we were running into? Anyone else run into these errors?

[mattcieslak]

I wonder if this is a docker/singularity issue. Would you be interested in screen-sharing to debug some time later this week?

[vnbcs]

that would be great! you can email me at [email protected]