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Merged
merged 12 commits into from
Mar 17, 2025
Merged

Unit testing tolerances + more consistent definition of SNR #79

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25b29d9
Oliver's approach
oliverchampion Aug 14, 2024
eea774c
removed expected fail as it passes
oliverchampion Aug 20, 2024
8d1a418
changes made as requested
oliverchampion Jan 3, 2025
1bcb389
Boundary testing and timing
oliverchampion Jan 4, 2025
1d26bad
Test whether initial guesses and fit bounds are reasonable
oliverchampion Jan 4, 2025
9beef6d
Merge branch 'main' into Unit_Testing_Tolerances
oliverchampion Jan 4, 2025
889a2c1
fixed errors after merge with main
oliverchampion Jan 4, 2025
66cb0db
bounds test automatically check whether bounds are relevant
oliverchampion Jan 6, 2025
ba9fa91
update
oliverchampion Mar 7, 2025
59767b5
Merge branch 'main' into Unit_Testing_Tolerances
oliverchampion Mar 12, 2025
d785c4d
Automated testing compatible with Wrapper
oliverchampion Mar 12, 2025
01d51aa
error python 3.11 fixed(?)
oliverchampion Mar 17, 2025
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6 changes: 3 additions & 3 deletions phantoms/MR_XCAT_qMRI/sim_ivim_sig.py
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Original file line number Diff line number Diff line change
Expand Up @@ -459,9 +459,9 @@ def parse_bvalues_file(file_path):
signals = np.squeeze(voxels[int(voxels.shape[0] * voxel_selector_fraction)]).tolist()
generic_data[name] = {
'noise': noise,
'D': np.mean(Dim[selector], axis=0),
'f': np.mean(fim[selector], axis=0),
'Dp': np.mean(Dpim[selector], axis=0),
'D': np.median(Dim[selector], axis=0),
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Median now?

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Yes, somehow there was a weird rounding happening in the np.mean that made values become 0.0000000000000001 off or so. So all round values become D= 0.0029999999999 instead of 0.003 etc.

'f': np.median(fim[selector], axis=0),
'Dp': np.median(Dpim[selector], axis=0),
'data': signals
}
generic_data['config'] = {
Expand Down
109 changes: 16 additions & 93 deletions tests/IVIMmodels/unit_tests/algorithms.json
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Expand Up @@ -16,92 +16,35 @@
],
"IAR_LU_biexp": {
"tolerances": {
"rtol": {
"f": 5,
"D": 5,
"Dp": 25
},
"atol": {
"f": 1e-2,
"D": 1e-2,
"Dp": 1e-1
}

}
},
"IAR_LU_modified_mix": {
"tolerances": {
"rtol": {
"f": 5,
"D": 5,
"Dp": 25
},
"atol": {
"f": 1e-2,
"D": 1e-2,
"Dp": 1e-1
}

}
},
"IAR_LU_modified_topopro": {
"tolerances": {
"rtol": {
"f": 5,
"D": 5,
"Dp": 25
},
"atol": {
"f": 1e-2,
"D": 1e-2,
"Dp": 1e-1
}

}
},
"IAR_LU_segmented_2step": {
"tolerances": {
"rtol": {
"f": 5,
"D": 5,
"Dp": 25
},
"atol": {
"f": 1e-2,
"D": 1e-2,
"Dp": 1e-1
}

}
},
"IAR_LU_segmented_3step": {
"tolerances": {
"rtol": {
"f": 5,
"D": 5,
"Dp": 25
},
"atol": {
"f": 1e-2,
"D": 1e-2,
"Dp": 1e-1
}

}
},
"IAR_LU_subtracted": {
"tolerances": {
"rtol": {
"f": 5,
"D": 5,
"Dp": 25
},
"atol": {
"f": 1e-2,
"D": 1e-2,
"Dp": 1e-1
}

}
},
"ETP_SRI_LinearFitting": {
"xfail_names": {
"Vein": true
},
"options": {
"thresholds": [500]
},
Expand All @@ -117,51 +60,31 @@
"Dp": 0
},
"dynamic_rtol": {
"offset": 0,
"noise": 0,
"ratio": 0,
"noiseCrossRatio": 10,
"f": 1,
"offset": 0.001,
"noise": 200,
"scale_f": false,
"f": 2,
"D": 1,
"Dp": 2
"Dp": 3
},
"dynamic_atol": {
"offset": 5e-2,
"noise": 0,
"ratio": 0,
"noiseCrossRatio": 10,
"noise": 10,
"scale_f": false,
"f": 1,
"D": 1,
"D": 0.001,
"Dp": 2
}
}
},
"OGC_AmsterdamUMC_biexp_segmented": {
"tolerances": {
"rtol": {
"f": 5,
"D": 5,
"Dp": 25
},
"atol": {
"f": 1e-2,
"D": 1e-2,
"Dp": 1e-1
}

}
},
"OJ_GU_seg": {
"tolerances": {
"rtol": {
"f": 5,
"D": 5,
"Dp": 25
},
"atol": {
"f": 1e-2,
"D": 1e-2,
"Dp": 1e-1
}

}
}
}
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