From 9e88e793a6fd6da0e4cdbe181609c06a96b2d0fd Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Tue, 23 Jul 2024 15:19:23 +0100
Subject: [PATCH] TEST: Test ensuring that imcp does not modify data
---
fsl/tests/__init__.py | 8 ++++
fsl/tests/test_dicom.py | 2 +-
fsl/tests/test_immv_imcp.py | 83 ++++++++++++++++++++++++++++++++-----
3 files changed, 81 insertions(+), 12 deletions(-)
diff --git a/fsl/tests/__init__.py b/fsl/tests/__init__.py
index a758db12..2846ee5c 100644
--- a/fsl/tests/__init__.py
+++ b/fsl/tests/__init__.py
@@ -10,6 +10,7 @@
import os
import sys
import glob
+import hashlib
import shutil
import fnmatch
import logging
@@ -439,3 +440,10 @@ def make_random_mask(filename, shape, xform, premask=None, minones=1):
img.save(filename)
return img
+
+
+def sha256(filename):
+ hashobj = hashlib.sha256()
+ with open(filename, 'rb') as f:
+ hashobj.update(f.read())
+ return hashobj.hexdigest()
diff --git a/fsl/tests/test_dicom.py b/fsl/tests/test_dicom.py
index dfda97f2..ca68ebd8 100644
--- a/fsl/tests/test_dicom.py
+++ b/fsl/tests/test_dicom.py
@@ -151,7 +151,7 @@ def test_scanDir():
datafile = op.join(datadir, 'example_dicom.tbz2')
with tarfile.open(datafile) as f:
- f.extractall()
+ f.extractall(filter='data')
series = fsldcm.scanDir('.')
assert len(series) == 2
diff --git a/fsl/tests/test_immv_imcp.py b/fsl/tests/test_immv_imcp.py
index 7b3e3fcb..b4b80ffc 100644
--- a/fsl/tests/test_immv_imcp.py
+++ b/fsl/tests/test_immv_imcp.py
@@ -7,22 +7,26 @@
from __future__ import print_function
+import gzip
+import itertools as it
+import os.path as op
+import os
+import shutil
+import tempfile
+from unittest import mock
-import os.path as op
-import os
-import shutil
-import tempfile
-
-import numpy as np
+import numpy as np
import nibabel as nib
-import fsl.utils.imcp as imcp
-import fsl.data.image as fslimage
+import fsl.utils.imcp as imcp
+import fsl.utils.tempdir as tempdir
+import fsl.data.image as fslimage
-from fsl.tests import make_random_image
-from fsl.tests import make_dummy_file
-from fsl.tests import looks_like_image
+from fsl.tests import (make_random_image,
+ make_dummy_file,
+ looks_like_image,
+ sha256)
real_print = print
@@ -315,3 +319,60 @@ def test_imcp_shouldPass(move=False):
def test_immv_shouldPass():
test_imcp_shouldPass(move=True)
+
+
+def test_imcp_data_unmodified():
+ """Test that the data in an imcp'd image file is not modified. """
+
+ dtypes = [
+ np.int16,
+ np.int32,
+ np.float32,
+ np.float64]
+
+ slints = [(None, None), (1, 0), (3, 1.5)]
+
+ for dtype, (slope, inter) in it.product(dtypes, slints):
+ with tempdir.tempdir():
+ data = np.random.randint(1, 100, (10, 10, 10)).astype(dtype)
+ hdr = nib.Nifti1Header()
+ hdr.set_data_dtype(dtype)
+ hdr.set_data_shape((10, 10, 10))
+ hdr.set_slope_inter(slope, inter)
+ hdr.set_sform(np.eye(4))
+
+ # write header/data separately, as otherwise
+ # nibabel will automatically rescale the data
+ with open('image.nii', 'wb') as f:
+ hdr.write_to(f)
+ f.write(data.tobytes())
+
+ # Input/output formats the same,
+ # should induce a straight file copy
+ imcp.imcp('image.nii', 'copied.nii', useDefaultExt=False)
+
+ # uncompresed->compressed will cause imcp
+ # to load in the image, rather than doing a
+ # file copy
+ with mock.patch.dict(os.environ, FSLOUTPUTTYPE='NIFTI_GZ'):
+ imcp.imcp('image.nii', 'converted.nii.gz', useDefaultExt=True)
+
+ # copied files should be identical
+ assert sha256('image.nii') == sha256('copied.nii')
+
+ # Converted files should have the same
+ # data, slope, and intercept. Read result
+ # header/data separately to avoid nibabel
+ # auto-rescaling.
+ with gzip.open('converted.nii.gz', 'rb') as f:
+ gothdr = nib.Nifti1Header.from_fileobj(f)
+ databytes = f.read()
+
+ gotdata = np.frombuffer(databytes, dtype=dtype).reshape((10, 10, 10))
+
+ # Data should be binary identical
+ assert np.all(gotdata == data)
+
+ if slope is None: slope = 1
+ if inter is None: inter = 0
+ assert np.all(np.isclose(gothdr.get_slope_inter(), (slope, inter)))
--
GitLab