def setup_infile(): global tmp_infile, tmp_dir ext = Info.output_type_to_ext(Info.output_type()) tmp_dir = tempfile.mkdtemp() tmp_infile = os.path.join(tmp_dir, 'foo' + ext) open(tmp_infile, 'w') return tmp_infile, tmp_dir
def setup_infile(tmpdir): ext = Info.output_type_to_ext(Info.output_type()) tmp_dir = str(tmpdir) tmp_infile = os.path.join(tmp_dir, 'foo' + ext) open(tmp_infile, 'w') return (tmp_infile, tmp_dir)
def setup_infile(): global tmp_infile, tmp_dir ext = Info.output_type_to_ext(Info.output_type()) tmp_dir = tempfile.mkdtemp() tmp_infile = os.path.join(tmp_dir, 'foo' + ext) file(tmp_infile, 'w') return tmp_infile, tmp_dir
def setup_flirt(tmpdir): ext = Info.output_type_to_ext(Info.output_type()) infile = tmpdir.join("infile" + ext) infile.open("w") reffile = tmpdir.join("reffile" + ext) reffile.open("w") return (tmpdir, infile.strpath, reffile.strpath)
def setup_flirt(tmpdir): ext = Info.output_type_to_ext(Info.output_type()) tmp_dir = str(tmpdir) _, infile = tempfile.mkstemp(suffix=ext, dir=tmp_dir) _, reffile = tempfile.mkstemp(suffix=ext, dir=tmp_dir) return (tmp_dir, infile, reffile)
def setup_infile(): global tmp_infile, tmp_dir ext = Info.output_type_to_ext(Info.output_type()) tmp_dir = tempfile.mkdtemp() tmp_infile = os.path.join(tmp_dir, "foo" + ext) open(tmp_infile, "w") return tmp_infile, tmp_dir
def setup_flirt(tmpdir): ext = Info.output_type_to_ext(Info.output_type()) infile = tmpdir.join("infile"+ext) infile.open("w") reffile = tmpdir.join("reffile"+ext) reffile.open("w") return (tmpdir, infile.strpath, reffile.strpath)
def create_files_in_directory(request): func_prev_type = set_output_type(request.param) testdir = os.path.realpath(mkdtemp()) origdir = os.getcwd() os.chdir(testdir) filelist = ['a.nii', 'b.nii'] for f in filelist: hdr = nb.Nifti1Header() shape = (3, 3, 3, 4) hdr.set_data_shape(shape) img = np.random.random(shape) nb.save(nb.Nifti1Image(img, np.eye(4), hdr), os.path.join(testdir, f)) out_ext = Info.output_type_to_ext(Info.output_type()) def fin(): if os.path.exists(testdir): rmtree(testdir) set_output_type(func_prev_type) os.chdir(origdir) request.addfinalizer(fin) return (filelist, testdir, out_ext)
def setup_infile(): global tmp_infile, tmp_dir, cwd cwd = os.getcwd() ext = Info.output_type_to_ext(Info.output_type()) tmp_dir = tempfile.mkdtemp() tmp_infile = os.path.join(tmp_dir, 'foo' + ext) open(tmp_infile, 'w') os.chdir(tmp_dir) return tmp_infile, tmp_dir
def setup_infile(): global tmp_infile, tmp_dir, cwd cwd = os.getcwd() ext = Info.output_type_to_ext(Info.output_type()) tmp_dir = tempfile.mkdtemp() tmp_infile = os.path.join(tmp_dir, 'foo' + ext) file(tmp_infile, 'w') os.chdir(tmp_dir) return tmp_infile, tmp_dir
def setup_infile(request): ext = Info.output_type_to_ext(Info.output_type()) tmp_dir = tempfile.mkdtemp() tmp_infile = os.path.join(tmp_dir, 'foo' + ext) open(tmp_infile, 'w') def fin(): shutil.rmtree(tmp_dir) request.addfinalizer(fin) return (tmp_infile, tmp_dir)
def setup_flirt(request): ext = Info.output_type_to_ext(Info.output_type()) tmpdir = tempfile.mkdtemp() _, infile = tempfile.mkstemp(suffix=ext, dir=tmpdir) _, reffile = tempfile.mkstemp(suffix=ext, dir=tmpdir) def teardown_flirt(): shutil.rmtree(tmpdir) request.addfinalizer(teardown_flirt) return (tmpdir, infile, reffile)
def create_files_in_directory_plus_output_type(request, tmpdir): func_prev_type = set_output_type(request.param) origdir = tmpdir.chdir() filelist = ['a.nii', 'b.nii'] nifti_image_files(tmpdir.strpath, filelist, shape=(3,3,3,4)) out_ext = Info.output_type_to_ext(Info.output_type()) def fin(): set_output_type(func_prev_type) origdir.chdir() request.addfinalizer(fin) return (filelist, tmpdir.strpath, out_ext)
def create_files_in_directory_plus_output_type(request, tmpdir): func_prev_type = set_output_type(request.param) origdir = tmpdir.chdir() filelist = ['a.nii', 'b.nii'] nifti_image_files(tmpdir.strpath, filelist, shape=(3, 3, 3, 4)) out_ext = Info.output_type_to_ext(Info.output_type()) def fin(): set_output_type(func_prev_type) origdir.chdir() request.addfinalizer(fin) return (filelist, tmpdir.strpath, out_ext)
def create_files_in_directory(): testdir = os.path.realpath(mkdtemp()) origdir = os.getcwd() os.chdir(testdir) filelist = ['a.nii', 'b.nii'] for f in filelist: hdr = nb.Nifti1Header() shape = (3, 3, 3, 4) hdr.set_data_shape(shape) img = np.random.random(shape) nb.save(nb.Nifti1Image(img, np.eye(4), hdr), os.path.join(testdir, f)) out_ext = Info.output_type_to_ext(Info.output_type()) return filelist, testdir, origdir, out_ext
def setup_infile(tmpdir): ext = Info.output_type_to_ext(Info.output_type()) tmp_infile = tmpdir.join('foo' + ext) tmp_infile.open("w") return (tmp_infile.strpath, tmpdir.strpath)
def fsl_name(obj, fname): """Create valid fsl name, including file extension for output type. """ ext = Info.output_type_to_ext(obj.inputs.output_type) return fname + ext