From e1ecfe82004f779db4abf81545a0872c902ac17e Mon Sep 17 00:00:00 2001
From: Matthew Webster <mwebster@jalapeno.fmrib.ox.ac.uk>
Date: Thu, 16 Jul 2020 14:42:11 +0100
Subject: [PATCH] ENH: allow dtifit to crash for invalid tests
---
unit_tests/fdt/dtifit/feedsRun | 33 ++++++++++++++++++++++-----------
1 file changed, 22 insertions(+), 11 deletions(-)
diff --git a/unit_tests/fdt/dtifit/feedsRun b/unit_tests/fdt/dtifit/feedsRun
index d6ddd43..144e51f 100755
--- a/unit_tests/fdt/dtifit/feedsRun
+++ b/unit_tests/fdt/dtifit/feedsRun
@@ -6,7 +6,7 @@ No noise is added, so we expect (near-)perfect fits
"""
import sys
import os
-from subprocess import run
+from subprocess import run, CalledProcessError
import numpy as np
from numpy import testing
import nibabel as nib
@@ -141,16 +141,13 @@ def fit_data(directory):
:yield: tuple with
- - base name of the output files
+ - base name of the output files (CalledProcessError if dtifit crashed)
- boolean indicating whether the --kurt flag was set
- boolean indicating whether the --kudtdir flag was set
"""
for kurtdir in (False, True):
for main_kurt in (False, True):
for wls in (False, True): # in this noise-free data the --wls flag should not matter
- if wls and kurtdir:
- # weighted least square not implemented for kurtdir
- continue
cmd = [
'dtifit',
'-k', f'{directory}/ref_data.nii.gz',
@@ -160,6 +157,7 @@ def fit_data(directory):
'--sse',
'--save_tensor',
]
+
base_output = f'{directory}/dti'
if wls:
cmd += ['--wls']
@@ -171,19 +169,29 @@ def fit_data(directory):
cmd += ['--kurtdir']
base_output += '_kurtdir'
cmd.extend(['-o', base_output])
- run(cmd, check=True)
- yield base_output, main_kurt, kurtdir
+ try:
+ run(cmd, check=True)
+ except CalledProcessError as e:
+ yield e, main_kurt, kurtdir, wls
+ else:
+ yield base_output, main_kurt, kurtdir, wls
# Loops through multiple ways to generate and fit the data and check the output
for directory, multi_shell, kurt in gen_data():
- for base_output, fkurt, fkurtdir in fit_data(directory):
+ for base_output, fkurt, fkurtdir, fwls in fit_data(directory):
print('testing', base_output)
if (
- (kurt == 0 and (multi_shell or not (fkurt or fkurtdir))) or
- (kurt == 1 and fkurt and not fkurtdir) or
- (kurt == 2 and fkurtdir)
+ (
+ (kurt == 0 and (multi_shell or not (fkurt or fkurtdir))) or
+ (kurt == 1 and fkurt and not fkurtdir) or
+ (kurt == 2 and fkurtdir)
+ ) and (not (fwls and fkurtdir))
):
+ if isinstance(base_output, CalledProcessError): # dtifit crashed
+ print("dtifit crashed on what should be a valid run. Error message printed above.")
+ raise base_output
+
def compare(name):
ref = nib.load(f'{directory}/ref_{name}.nii.gz').get_fdata()
fit = nib.load(f'{base_output}_{name}.nii.gz').get_fdata()
@@ -243,6 +251,9 @@ for directory, multi_shell, kurt in gen_data():
assert not os.path.isfile(f'{base_output}_kurt3.nii.gz')
assert not os.path.isfile(f'{base_output}_MK.nii.gz')
else:
+ if isinstance(base_output, CalledProcessError): # dtifit crashed
+ print("dtifit crashed on an invalid run, which is fine")
+ continue
if fkurtdir and (not multi_shell or kurt == 1):
continue # unpredictable whether this works or not
print('This fit should be invalid')
--
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