From a9c3e1767bf44417788a753c50f5d9c86b2ae863 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Thu, 30 Jul 2020 11:55:12 +0100
Subject: [PATCH] ENH: Rewrote fslcreatehd test in python, expanded tests to
handle 4th dim of (0, 1), and to handle modification of existing image
---
unit_tests/fslcreatehd/feedsRun | 265 +++++++++++++++++++++-----------
1 file changed, 176 insertions(+), 89 deletions(-)
diff --git a/unit_tests/fslcreatehd/feedsRun b/unit_tests/fslcreatehd/feedsRun
index 8563ff9..136e138 100755
--- a/unit_tests/fslcreatehd/feedsRun
+++ b/unit_tests/fslcreatehd/feedsRun
@@ -1,96 +1,183 @@
-#!/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
- echo "$n1 != $n2"
- return 0;
- fi
-
- return 1;
-}
-
-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 $args; return 1; fi
-
- return 0
+# 2=char, 4=short, 8=int, 16=float, 64=double
+DTYPE_MAPPING = {
+ 2 : np.uint8,
+ 4 : np.int16,
+ 8 : np.int32,
+ 16 : np.float32,
+ 64 : np.float64
}
-tests="
-5 5 5 1 2 2 2 1 0 0 0 2
-5 5 5 1 2 2 2 1 0 0 0 4
-5 5 5 1 2 2 2 1 0 0 0 8
-5 5 5 1 2 2 2 1 0 0 0 16
-5 5 5 1 2 2 2 1 1 2 3 64
-5 5 5 1 0.5 1.5 1.25 1 0 0 0 2
-5 5 5 1 0.5 1.5 1.25 1.5 0 0 0 2
-5 5 5 1 0.5 1.5 1.25 0.5 0 0 0 2
-
-30 30 30 5 5 10 3 5 10 20 10 2
-"
-
-echo "$tests" | while IFS= read -r test; do
- if [[ $test =~ ^\ *$ ]]; then
- continue
- fi
-
- rm `imglob -extension fslcreatehd_test_img` &> /dev/null || true
- fslcreatehd $test fslcreatehd_test_img
- fslcreatehd_test 4 $test fslcreatehd_test_img
-
-done
+def validate_result(imgfile, expshape, exppixdim, exporigin, expdtype):
+
+ img = nib.load(imgfile)
+ hdr = img.header
+ expshape = list(expshape)
+ exppixdim = list(exppixdim)
+ exporigin = list(exporigin)
+
+ if (len(expshape) == 3) or \
+ expshape[3] in (0, 1):
+ expndims = 3
+ else:
+ expndims = 4
+
+ expaffine = np.diag(exppixdim[:3] + [1])
+ expaffine[0, 0] *= -1
+ expaffine[:3, 3] = exporigin
+ expaffine[0, 3] *= exppixdim[0]
+ expaffine[1, 3] *= -exppixdim[1]
+ expaffine[2, 3] *= -exppixdim[2]
+
+ assert len(img.shape) == expndims
+ 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())
--
GitLab