MAINT: Housekeeping and more verbose debugging outputs #302
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
oesteban
force-pushed
the
enh/more-verbose-debug-mode
branch
from
632f6e0 to
dacfb63
Compare
effigies
reviewed
Nov 17, 2022
| debug_ref = (~xfm).apply(fmap_ref, reference=nii_target) | ||
| debug_ref.header.set_qform(nii_target.affine, code=1) | ||
| debug_ref.header.set_sform(nii_target.affine, code=1) | ||
| debug_ref.to_filename(Path() / "debug_fmapref.nii.gz") |
There was a problem hiding this comment.
Odd idiom.
>>> Path() / "debug_fmapref.nii.gz"
PosixPath('debug_fmapref.nii.gz')So this is the same as:
debug_ref.to_filename("debug_fmapref.nii.gz")| debug_ref.to_filename(Path() / "debug_fmapref.nii.gz") | ||
|
|
||
| # Generate a new transform | ||
| newaff = np.linalg.inv(np.linalg.inv(coeff.affine) @ (~xfm).matrix) |
There was a problem hiding this comment.
I don't understand why you're replacing A @ B with ~(~B @ ~A).
| @@ -103,7 +103,9 @@ def init_unwarp_wf(omp_nthreads=1, debug=False, name="unwarp_wf"): | |||
|
|
|||
| rotime = pe.Node(GetReadoutTime(), name="rotime") | |||
| rotime.interface._always_run = debug | |||
| resample = pe.Node(ApplyCoeffsField(num_threads=omp_nthreads), name="resample") | |||
| resample = pe.Node(ApplyCoeffsField( | |||
| num_threads=omp_nthreads if not debug else 1 | |||
There was a problem hiding this comment.
Just as a thought, I wonder if this would be more or less clear:
resample = pe.Node(ApplyCoeffsField(num_threads=debug or omp_nthreads), name="resample")Since bools are a subclass of int, it will be 1 if debug is True or omp_nthreads if debug is False.
>>> ApplyCoeffsField(num_threads=True).inputs
in_coeff = <undefined>
in_data = <undefined>
in_xfms = <undefined>
num_threads = 1
pe_dir = <undefined>
ro_time = <undefined>
|
Can be backported to 2.1.0 if needed. |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
No description provided.