Merge pull request #5 from niaid/FixPackageNamingIn2ngpc

Fix package naming in2ngpc

pytools/ng/mrc2ngpc.py

@@ -59,7 +59,7 @@ def main(input_image, output_precompute, flat, gzip):
         check_process = True
 
         # Task 1: Convert mrc to NIFTI with SimpleITK script
-        py_code_main = "import sys; from ngtool.mrc2nifti import main; sys.exit(main())"
+        py_code_main = "import sys; from pytools.ng.mrc2nifti import main; sys.exit(main())"
         cmd = [sys.executable, "-c", py_code_main, input_image, nifti_filename]
 
         logger.info("Executing conversion of MRC to NIFTI..")

test/fixtures.py

@@ -0,0 +1,29 @@
+#
+#  Licensed under the Apache License, Version 2.0 (the "License");
+#  you may not use this file except in compliance with the License.
+#  You may obtain a copy of the License at
+#
+#         http://www.apache.org/licenses/LICENSE-2.0.txt
+#
+#  Unless required by applicable law or agreed to in writing, software
+#  distributed under the License is distributed on an "AS IS" BASIS,
+#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#  See the License for the specific language governing permissions and
+#  limitations under the License.
+#
+import pytest
+import SimpleITK as sitk
+
+
+@pytest.fixture(
+    scope="session",
+    params=[sitk.sitkUInt8, sitk.sitkInt16, sitk.sitkUInt16, sitk.sitkFloat32],
+)
+def image_mrc(request, tmp_path_factory):
+    pixel_type = request.param
+    print(f"Calling image_mrc with {sitk.GetPixelIDValueAsString(pixel_type)}")
+    fn = f"image_mrc_{sitk.GetPixelIDValueAsString(pixel_type).replace(' ', '_')}.mrc"
+    img = sitk.Image([10, 9, 8], pixel_type)
+    fn = tmp_path_factory.mktemp("data").joinpath(fn)
+    sitk.WriteImage(img, str(fn))
+    return str(fn)

test/test_mrc2ngpc.py

@@ -1,4 +1,3 @@
-#
 #  Licensed under the Apache License, Version 2.0 (the "License");
 #  you may not use this file except in compliance with the License.
 #  You may obtain a copy of the License at
@@ -13,34 +12,19 @@
 #
 
 from click.testing import CliRunner
-from pytools.ng.mrc2nifti import main
+import pytools.ng.mrc2ngpc
 import pytest
 import SimpleITK as sitk
 import numpy as np
-
-
-@pytest.fixture(
-    scope="session",
-    params=[sitk.sitkUInt8, sitk.sitkInt16, sitk.sitkUInt16, sitk.sitkFloat32],
-)
-def image_mrc(request, tmp_path_factory):
-
-    pixel_type = request.param
-    print(f"Calling image_mrc with {sitk.GetPixelIDValueAsString(pixel_type)}")
-    fn = f"image_mrc_{sitk.GetPixelIDValueAsString(pixel_type).replace(' ', '_')}.mrc"
-    img = sitk.Image([10, 9, 8], pixel_type)
-    fn = tmp_path_factory.mktemp("data").joinpath(fn)
-    sitk.WriteImage(img, str(fn))
-    return str(fn)
-
+from fixtures import image_mrc
 
 args = ["--help", "--version"]
 
 
 @pytest.mark.parametrize("cli_args", args)
-def test_mrc2nifti_main_help(cli_args):
+def test_mrc2ngpc_main_help(cli_args):
     runner = CliRunner()
-    result = runner.invoke(main, cli_args.split())
+    result = runner.invoke(pytools.ng.mrc2ngpc.main, cli_args.split())
     assert not result.exception
 
 
@@ -54,13 +38,8 @@ def test_mrc2nifti_main_help(cli_args):
     ],
     indirect=["image_mrc"],
 )
-def test_mrc2nifti(image_mrc, expected_pixel_type):
+def test_mrc2ngpc(image_mrc, expected_pixel_type):
     runner = CliRunner()
     with runner.isolated_filesystem():
-        result = runner.invoke(main, [image_mrc, "out.nii"])
+        result = runner.invoke(pytools.ng.mrc2ngpc.main, [image_mrc, "out_ngpc"])
         assert not result.exception
-        img = sitk.ReadImage("out.nii")
-
-    assert img.GetPixelID() == expected_pixel_type
-    assert img.GetSize() == (10, 9, 8)
-    np.testing.assert_allclose(img.GetSpacing(), (1e-7, 1e-7, 1e-7))

test/test_mrc2nii.py

@@ -0,0 +1,51 @@
+#
+#  Licensed under the Apache License, Version 2.0 (the "License");
+#  you may not use this file except in compliance with the License.
+#  You may obtain a copy of the License at
+#
+#         http://www.apache.org/licenses/LICENSE-2.0.txt
+#
+#  Unless required by applicable law or agreed to in writing, software
+#  distributed under the License is distributed on an "AS IS" BASIS,
+#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#  See the License for the specific language governing permissions and
+#  limitations under the License.
+#
+
+from click.testing import CliRunner
+import pytools.ng.mrc2nifti
+import pytest
+import SimpleITK as sitk
+import numpy as np
+from fixtures import image_mrc
+
+args = ["--help", "--version"]
+
+
+@pytest.mark.parametrize("cli_args", args)
+def test_mrc2nifti_main_help(cli_args):
+    runner = CliRunner()
+    result = runner.invoke(pytools.ng.mrc2nifti.main, cli_args.split())
+    assert not result.exception
+
+
+@pytest.mark.parametrize(
+    "image_mrc,expected_pixel_type",
+    [
+        (sitk.sitkUInt8, sitk.sitkUInt8),
+        (sitk.sitkInt16, sitk.sitkUInt16),
+        (sitk.sitkUInt16, sitk.sitkUInt16),
+        (sitk.sitkFloat32, sitk.sitkFloat32),
+    ],
+    indirect=["image_mrc"],
+)
+def test_mrc2nifti(image_mrc, expected_pixel_type):
+    runner = CliRunner()
+    with runner.isolated_filesystem():
+        result = runner.invoke(pytools.ng.mrc2nifti.main, [image_mrc, "out.nii"])
+        assert not result.exception
+        img = sitk.ReadImage("out.nii")
+
+    assert img.GetPixelID() == expected_pixel_type
+    assert img.GetSize() == (10, 9, 8)
+    np.testing.assert_allclose(img.GetSpacing(), (1e-7, 1e-7, 1e-7))