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Changing the default b0_threshold in gtab #1667

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merged 21 commits into from Dec 6, 2018
Merged

Changing the default b0_threshold in gtab #1667

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791a611
changing b0 default values in gtab
ShreyasFadnavis Nov 22, 2018
a5fe036
del
ShreyasFadnavis Nov 22, 2018
44bfd35
changing b0_throshold in workflow functions
ShreyasFadnavis Nov 22, 2018
6c21c68
changed tests for gradients.py b0_threshold
ShreyasFadnavis Nov 22, 2018
01c64bc
added warnings
ShreyasFadnavis Nov 25, 2018
af9f442
changed to warn
ShreyasFadnavis Nov 25, 2018
693bc01
changes in tests for warnings
ShreyasFadnavis Nov 25, 2018
48b7399
fixed -ve b0
ShreyasFadnavis Nov 25, 2018
e747cbe
fixed b0_threhold
ShreyasFadnavis Nov 26, 2018
98ea627
warning in test_shm
ShreyasFadnavis Nov 27, 2018
8434ff2
added tests for warning
ShreyasFadnavis Nov 27, 2018
d48817c
fixed WF_DKI
ShreyasFadnavis Nov 27, 2018
33301cc
del
ShreyasFadnavis Nov 27, 2018
4334d7c
minor fix
ShreyasFadnavis Nov 30, 2018
675d1b6
IVIM warning
ShreyasFadnavis Dec 5, 2018
9ce0ad9
IVIM Warning Added
ShreyasFadnavis Dec 5, 2018
8f04ff9
Merge branch 'master' into csd-b0
ShreyasFadnavis Dec 5, 2018
76f3730
Removed Conflicts
ShreyasFadnavis Dec 5, 2018
617484a
Removed more Conflicts
ShreyasFadnavis Dec 5, 2018
497847f
minor fix
ShreyasFadnavis Dec 5, 2018
c67427b
fixed WF
ShreyasFadnavis Dec 5, 2018
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3 changes: 3 additions & 0 deletions dipy/reconst/ivim.py
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Expand Up @@ -215,6 +215,9 @@ def __init__(self, gtab, split_b_D=400.0, split_b_S0=200., bounds=None,
e_s += "The IVIM model requires signal measured at 0 bvalue"
raise ValueError(e_s)

if gtab.b0_threshold > 0:
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Any chance to get a test for this behavior in the IVIM tests?

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@arokem I will create a new issue and create a new PR with the tests for the same!

warnings.warn('The default b0_threshold > 0 and is now set to 50')
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I don't understand this warning.

As I user, I would infer that this means that you have changed my b0_threshold to 50.

I would propose to raise an Error (instead of the warning) with the following string:

"The IVIM model requires a measurement at b==0. As of version 0.15, the default b0_threshold for the GradientTable object is set to 50, so if you used the default settings to initialize the gtab input to the IVIM model, you may have provided a gtab with b0_threshold larger than 0. Please initialize the gtab input with b0_threshold=0"

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@arokem Thank you so much for this! I shall refactor accordingly!


ReconstModel.__init__(self, gtab)
self.split_b_D = split_b_D
self.split_b_S0 = split_b_S0
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