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Commit a9c3e176 authored by Paul McCarthy's avatar Paul McCarthy :mountain_bicyclist:
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ENH: Rewrote fslcreatehd test in python, expanded tests to handle 4th dim of (0, 

1), and to handle modification of existing image
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#!/bin/bash #!/usr/bin/env python
set -e import os
import sys
import subprocess as sp
import numpy as np
import nibabel as nib
function neq() {
n1=$1
n2=$2
result=`echo "$n1 == $n2" | bc`
if [[ "$result" == "0" ]]; then # 2=char, 4=short, 8=int, 16=float, 64=double
echo "$n1 != $n2" DTYPE_MAPPING = {
return 0; 2 : np.uint8,
fi 4 : np.int16,
8 : np.int32,
return 1; 16 : np.float32,
} 64 : np.float64
function fslcreatehd_test() {
dim0=$1; shift
dim1=$1; shift
dim2=$1; shift
dim3=$1; shift
dim4=$1; shift
pixdim1=$1; shift
pixdim2=$1; shift
pixdim3=$1; shift
pixdim4=$1; shift
originx=$1; shift
originy=$1; shift
originz=$1; shift
dtype=$1; shift
fname=$1; shift
args="$dim0 $dim1 $dim2 $dim3 $pixdim1 $pixdim2 $pixdim3 $pixdim4 $originx $originy $originz $dtype $fname"
originx=`echo " $originx * $pixdim1" | bc`
originy=`echo "-$originy * $pixdim2" | bc`
originz=`echo "-$originz * $pixdim3" | bc`
got_dim0=` fslhd $fname | egrep "^dim0" | tr -s '\t' | cut -f 2`
got_dim1=` fslhd $fname | egrep "^dim1" | tr -s '\t' | cut -f 2`
got_dim2=` fslhd $fname | egrep "^dim2" | tr -s '\t' | cut -f 2`
got_dim3=` fslhd $fname | egrep "^dim3" | tr -s '\t' | cut -f 2`
got_dim4=` fslhd $fname | egrep "^dim4" | tr -s '\t' | cut -f 2`
got_pixdim1=`fslhd $fname | egrep "^pixdim1" | tr -s '\t' | cut -f 2`
got_pixdim2=`fslhd $fname | egrep "^pixdim2" | tr -s '\t' | cut -f 2`
got_pixdim3=`fslhd $fname | egrep "^pixdim3" | tr -s '\t' | cut -f 2`
got_pixdim4=`fslhd $fname | egrep "^pixdim4" | tr -s '\t' | cut -f 2`
got_dtype=` fslhd $fname | egrep "^datatype" | tr -s '\t' | cut -f 2`
got_originx=`fslhd $fname | egrep "^sto_xyz:1" | cut -d ' ' -f 4`
got_originy=`fslhd $fname | egrep "^sto_xyz:2" | cut -d ' ' -f 4`
got_originz=`fslhd $fname | egrep "^sto_xyz:3" | cut -d ' ' -f 4`
if neq $dim0 $got_dim0; then echo $args; return 1; fi
if neq $dim1 $got_dim1; then echo $args; return 1; fi
if neq $dim2 $got_dim2; then echo $args; return 1; fi
if neq $dim3 $got_dim3; then echo $args; return 1; fi
if neq $dim4 $got_dim4; then echo $args; return 1; fi
if neq $pixdim1 $got_pixdim1; then echo $args; return 1; fi
if neq $pixdim2 $got_pixdim2; then echo $args; return 1; fi
if neq $pixdim3 $got_pixdim3; then echo $args; return 1; fi
if neq $pixdim4 $got_pixdim4; then echo $args; return 1; fi
if neq $dtype $got_dtype; then echo $args; return 1; fi
if neq $originx $got_originx; then echo $args; return 1; fi
if neq $originy $got_originy; then echo $args; return 1; fi
if neq $originz $got_originz; then echo $args; return 1; fi
return 0
} }
tests=" def validate_result(imgfile, expshape, exppixdim, exporigin, expdtype):
5 5 5 1 2 2 2 1 0 0 0 2
5 5 5 1 2 2 2 1 0 0 0 4 img = nib.load(imgfile)
5 5 5 1 2 2 2 1 0 0 0 8 hdr = img.header
5 5 5 1 2 2 2 1 0 0 0 16 expshape = list(expshape)
5 5 5 1 2 2 2 1 1 2 3 64 exppixdim = list(exppixdim)
5 5 5 1 0.5 1.5 1.25 1 0 0 0 2 exporigin = list(exporigin)
5 5 5 1 0.5 1.5 1.25 1.5 0 0 0 2
5 5 5 1 0.5 1.5 1.25 0.5 0 0 0 2 if (len(expshape) == 3) or \
expshape[3] in (0, 1):
30 30 30 5 5 10 3 5 10 20 10 2 expndims = 3
" else:
expndims = 4
echo "$tests" | while IFS= read -r test; do
if [[ $test =~ ^\ *$ ]]; then expaffine = np.diag(exppixdim[:3] + [1])
continue expaffine[0, 0] *= -1
fi expaffine[:3, 3] = exporigin
expaffine[0, 3] *= exppixdim[0]
rm `imglob -extension fslcreatehd_test_img` &> /dev/null || true expaffine[1, 3] *= -exppixdim[1]
fslcreatehd $test fslcreatehd_test_img expaffine[2, 3] *= -exppixdim[2]
fslcreatehd_test 4 $test fslcreatehd_test_img
assert len(img.shape) == expndims
done assert list(img.shape) == expshape[ :expndims]
assert list(hdr.get_zooms()) == exppixdim[:expndims]
assert img.get_data_dtype() == expdtype
assert np.all(np.isclose(img.affine, expaffine))
def create_image(shape, pixdim, origin, dtype):
pixdim = list(pixdim)
affine = np.diag(pixdim[:3] + [1])
affine[:3, 3] = origin
data = np.random.randint(1, 100, shape).astype(dtype)
hdr = nib.Nifti1Header()
hdr.set_data_dtype(dtype)
hdr.set_data_shape(shape)
hdr.set_zooms(pixdim[:len(shape)])
return nib.Nifti1Image(data, affine, hdr)
def test_new_file():
tests = [
# 4th dim of size 0 or 1 should
# result in a 3D image (this
# is coded in validate_result)
' 5 5 5 0 2 2 2 0 0 0 0 2',
' 5 5 5 0 2 2 2 1 0 0 0 2',
' 5 5 5 1 2 2 2 1 0 0 0 2',
' 5 5 5 1 2 2 2 1 0 0 0 4',
' 5 5 5 1 2 2 2 1 0 0 0 8',
' 5 5 5 1 2 2 2 1 0 0 0 16',
' 5 5 5 1 2 2 2 1 1 2 3 64',
' 5 5 5 1 0.5 1.5 1.25 1 0 0 0 2',
' 5 5 5 1 0.5 1.5 1.25 1.5 0 0 0 2',
' 5 5 5 1 0.5 1.5 1.25 0.5 0 0 0 2',
'30 30 30 5 5 10 3 5 10 20 10 2',
]
for test in tests:
args = list(test.split())
imgfile = 'image.nii.gz'
sp.run(['fslcreatehd'] + args + [imgfile])
args = [float(a) for a in args]
expshape = args[:4]
exppixdim = args[4:8]
exporigin = args[8:11]
expdtype = DTYPE_MAPPING[args[11]]
try:
validate_result(
imgfile, expshape, exppixdim, exporigin, expdtype)
finally:
os.remove(imgfile)
def test_existing_file():
# each test is a tuple containing:
# - dtype_of_existing_image
# - shape_of_existing_image
# - exp_shape (set to None if image should not be overwritten)
# - fslcreatehd_args
tests = [
# 4th dim of 0 or 1 should result in a 3D image
(2, (5, 5, 5), None, '5 5 5 0 2 2 2 1 0 0 0 2'),
(2, (5, 5, 5), None, '5 5 5 0 2 2 2 1 1 2 3 2'),
(2, (5, 5, 5), None, '5 5 5 1 2 2 2 2 0 0 0 2'),
# dtype arg should be ignored for existing images
(2, (5, 5, 5), None, '5 5 5 0 2 2 2 1 0 0 0 4'),
(4, (5, 5, 5), None, '5 5 5 0 2 2 2 1 0 0 0 2'),
# data should be overwritten if any
# of the first 3 dims are different,
# or if a 4th dim is specified
(2, (5, 5, 5), (5, 3, 5), '5 3 5 0 2 2 2 2 0 0 0 2'),
(2, (5, 5, 5), (5, 3, 5), '5 3 5 0 2 2 2 2 0 0 0 4'),
(2, (5, 5, 5), (5, 3, 5), '5 3 5 1 2 2 2 2 0 0 0 2'),
(2, (5, 5, 5), (5, 3, 5), '5 3 5 1 2 2 2 2 1 2 3 2'),
(2, (5, 5, 5), (5, 3, 5, 5), '5 3 5 5 2 2 2 2 0 0 0 2'),
(2, (5, 5, 5), (5, 3, 5, 5), '5 3 5 5 2 2 2 2 1 2 3 2'),
# 4D - same rules apply
(2, (5, 5, 5, 5), None, '5 5 5 5 2 2 2 2 0 0 0 2'),
(2, (5, 5, 5, 5), None, '5 5 5 5 2 2 2 2 0 0 0 2'),
(2, (5, 5, 5, 5), None, '5 5 5 5 2 2 2 2 0 0 0 4'),
(4, (5, 5, 5, 5), None, '5 5 5 5 2 2 2 2 0 0 0 2'),
(2, (5, 5, 5, 5), None, '5 5 5 5 2 2 2 2 1 2 3 2'),
# data overwritten if nelements
# change
(2, (5, 5, 5, 5), (5, 5, 5), '5 5 5 0 2 2 2 2 0 0 0 2'),
(2, (5, 5, 5, 5), (5, 5, 5), '5 5 5 1 2 2 2 2 0 0 0 2'),
(2, (5, 5, 5, 5), (5, 3, 5), '5 3 5 0 2 2 2 2 0 0 0 2'),
(2, (5, 5, 5, 5), (5, 3, 5), '5 3 5 1 2 2 2 2 0 0 0 2'),
(2, (5, 5, 5, 5), (5, 3, 5), '5 3 5 1 2 2 2 2 1 2 3 2'),
(2, (5, 5, 5, 5), (5, 5, 5, 2), '5 5 5 2 2 2 2 2 0 0 0 2'),
(2, (5, 5, 5, 5), (5, 3, 5, 5), '5 3 5 5 2 2 2 2 0 0 0 2'),
(2, (5, 5, 5, 5), (5, 3, 5, 5), '5 3 5 5 2 2 2 2 1 2 3 2'),
]
for (dtype, shape, expshape, args) in tests:
imgfile = 'image.nii.gz'
dtype = DTYPE_MAPPING[dtype]
args = list(args.split())
img = create_image(shape, (1, 1, 1, 1), (0, 0, 0), dtype)
img.to_filename(imgfile)
sp.run(['fslcreatehd'] + args + [imgfile])
checkdata = expshape is None
if expshape is None:
expshape = shape
args = [float(a) for a in args]
exppixdim = args[4:8]
exporigin = args[8:11]
try:
validate_result(imgfile, expshape, exppixdim, exporigin, dtype)
if checkdata:
data = np.asanyarray(img.dataobj)
datacopy = np.asanyarray(nib.load(imgfile).dataobj)
assert np.all(data == datacopy)
finally:
os.remove(imgfile)
def main():
test_new_file()
test_existing_file()
if __name__ == '__main__':
sys.exit(main())
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