Fixed aberrant mtr values #2503
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jcohenadad
added
bug
Otherwise new function in qmri/mt is failing
charleygros
reviewed
Oct 23, 2019
| @@ -13,16 +13,41 @@ | |||
| logger = logging.getLogger(__name__) | |||
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| def compute_mtr(nii_mt1, nii_mt0): | |||
| def divide_after_removing_zero(dividend, divisor, threshold, replacement=np.nan): | |||
charleygros
approved these changes
Oct 23, 2019
| type=float, | ||
| help="Threshold to clip MTR output values in case of division by small number. This threshold is applied on the" | ||
| "absolute value. Default: 100.", | ||
| default=100 |
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So values will be between -100 and 100, is it right? or am I misunderstanding?
If so, could it be helpful to mention this in the help?
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agreed-- clarified in 509c99b
jcohenadad
added a commit
that referenced
this pull request
Dec 18, 2019
* sct_compute_mtr: Force saving as float64 * sct_compute_mtr: Changed dtype output to float32 (enough) * image: Fixed bug where dtype was not set in the nibabel hdr * qmri/mt: Created function divide_after_removing_zero() * qmri/mt: Fixed dtype bug * test_qmri: Now testing with input array Otherwise new function in qmri/mt is failing * image: Fixed bug when using SCT-specific dtype 'minimize' * sct_compute_mtr: Added param -thr * sct_compute_mtr: now showing logger and SCT version info on run * qmri/mt: Adding verbose about clipping, nan replacement * Clarified threshold range in help Former-commit-id: 7b2e5a195cb355a5080d8eff4327a5c22846c770 [formerly 6c4643d [formerly ccfd787]] Former-commit-id: b4636e6ad64fd615afc09c4fe796bb84ad1f0593 Former-commit-id: 0b5efe5
jcohenadad
added a commit
that referenced
this pull request
Dec 18, 2019
* sct_compute_mtr: Force saving as float64 * sct_compute_mtr: Changed dtype output to float32 (enough) * image: Fixed bug where dtype was not set in the nibabel hdr * qmri/mt: Created function divide_after_removing_zero() * qmri/mt: Fixed dtype bug * test_qmri: Now testing with input array Otherwise new function in qmri/mt is failing * image: Fixed bug when using SCT-specific dtype 'minimize' * sct_compute_mtr: Added param -thr * sct_compute_mtr: now showing logger and SCT version info on run * qmri/mt: Adding verbose about clipping, nan replacement * Clarified threshold range in help Former-commit-id: ccfd787
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A combination of issues yielded aberrant MTR values as the output of
sct_compute_mtr:This PR fixes it by:
-thrFixes #2501