Merge pull request #10 from 8bitsam/cookie-src

Cookiecutting - src directory

Author: sbillinge

src/diffpy/__init__.py

@@ -1,27 +1,23 @@
 #!/usr/bin/env python
 ##############################################################################
 #
-# diffpy            by DANSE Diffraction group
-#                   Simon J. L. Billinge
-#                   (c) 2008 Trustees of the Columbia University
-#                   in the City of New York.  All rights reserved.
+# (c) 2024 The Trustees of Columbia University in the City of New York.
+# All rights reserved.
 #
-# File coded by:    Pavol Juhas
+# File coded by: Billinge Group members and community contributors.
 #
-# See AUTHORS.txt for a list of people who contributed.
-# See LICENSENOTICE.txt for license information.
+# See GitHub contributions for a more detailed list of contributors.
+# https://github.com/diffpy/fourigui/graphs/contributors
+#
+# See LICENSE.rst for license information.
 #
 ##############################################################################
 
-"""diffpy - tools for structure analysis by diffraction.
-
-Blank namespace package.
-"""
+"""Blank namespace package for module diffpy."""
 
 
 from pkgutil import extend_path
 
 __path__ = extend_path(__path__, __name__)
 
-
 # End of file

src/diffpy/fourigui/__init__.py

@@ -1,18 +1,9 @@
-#!/usr/bin/env python
-##############################################################################
-#
-# diffpy.fourigui   by DANSE Diffraction group
-#                   Simon J. L. Billinge
-#                   (c) 2008 Trustees of the Columbia University
-#                   in the City of New York.  All rights reserved.
-#
-# File coded by:    Sani Harouna-Mayer
-#
-# See AUTHORS.txt for a list of people who contributed.
-# See LICENSENOTICE.txt for license information.
-#
-##############################################################################
-# TODO add description
-"""\
-'{{cookiecutter.short_description}}'
-"""
+"""Tool for visualizing 3D diffraction and PDF Images"""
+
+# from . import fourigui
+from .version import __version__
+
+# silence the pyflakes syntax checker
+assert __version__ or True
+
+# End of file

src/diffpy/fourigui/tests/__init__.py

@@ -0,0 +1,19 @@
+import json
+from pathlib import Path
+
+import pytest
+
+
+@pytest.fixture
+def user_filesystem(tmp_path):
+    base_dir = Path(tmp_path)
+    home_dir = base_dir / "home_dir"
+    home_dir.mkdir(parents=True, exist_ok=True)
+    cwd_dir = base_dir / "cwd_dir"
+    cwd_dir.mkdir(parents=True, exist_ok=True)
+
+    home_config_data = {"username": "home_username", "email": "[email protected]"}
+    with open(home_dir / "diffpyconfig.json", "w") as f:
+        json.dump(home_config_data, f)
+
+    yield tmp_path

src/diffpy/fourigui/tests/conftest.py

@@ -0,0 +1,35 @@
+#!/usr/bin/env python
+##############################################################################
+#
+# (c) 2024 The Trustees of Columbia University in the City of New York.
+# All rights reserved.
+#
+# File coded by: Billinge Group members and community contributors.
+#
+# See GitHub contributions for a more detailed list of contributors.
+# https://github.com/diffpy/fourigui/graphs/contributors
+#
+# See LICENSE.rst for license information.
+#
+##############################################################################
+
+"""
+Convenience module for debugging the unit tests using
+
+python -m diffpy.fourigui.tests.debug
+
+Exceptions raised by failed tests or other errors are not caught.
+"""
+
+
+if __name__ == "__main__":
+    import sys
+
+    from diffpy.fourigui.tests import testsuite
+
+    pattern = sys.argv[1] if len(sys.argv) > 1 else ""
+    suite = testsuite(pattern)
+    suite.debug()
+
+
+# End of file

src/diffpy/fourigui/tests/debug.py

@@ -0,0 +1,158 @@
+import unittest
+
+import h5py
+import numpy as np
+
+from src.diffpy.fourigui.fourigui import Gui
+
+
+class TestGui(unittest.TestCase):
+    def setUp(self):
+        # set up gui
+        self.test_gui = Gui()
+
+        # set up test data
+        self.test_sofq = h5py.File("diffpy/tests/testdata/sofq.h5")["data"]
+        self.test_sofq_cut_10to40px = h5py.File(
+            "diffpy/tests/testdata/sofq_cut_10to40px.h5"
+        )["data"]
+        self.test_sofq_cut_15to35px = h5py.File(
+            "diffpy/tests/testdata/sofq_cut_15to35px.h5"
+        )["data"]
+        self.test_gofr = h5py.File("diffpy/tests/testdata/gofr.h5")["data"]
+        self.test_gofr_cut_10to40px = h5py.File(
+            "diffpy/tests/testdata/gofr_from_sofq_cut_10to40px.h5"
+        )["data"]
+        self.test_gofr_cut_15to35px = h5py.File(
+            "diffpy/tests/testdata/gofr_from_sofq_cut_15to35px.h5"
+        )["data"]
+
+    def test_load_cube_testdataset1(self):
+        # given
+        self.test_gui.filename_entry.delete(0, "end")
+        self.test_gui.filename_entry.insert(0, "diffpy/tests/testdata/sofq.h5")
+
+        # when
+        self.test_gui.load_cube()
+        result = self.test_gui.cube
+
+        # then
+        self.assertTrue(np.allclose(result, self.test_sofq))
+
+    def test_load_cube_testdataset2(self):
+        # given
+        self.test_gui.filename_entry.delete(0, "end")
+        self.test_gui.filename_entry.insert(
+            0, "diffpy/tests/testdata/sofq_cut_10to40px.h5"
+        )
+
+        # when
+        self.test_gui.load_cube()
+        result = self.test_gui.cube
+
+        # then
+        self.assertTrue(
+            np.allclose(
+                np.nan_to_num(result), np.nan_to_num(self.test_sofq_cut_10to40px)
+            )
+        )
+
+    def test_load_cube_testdataset3(self):
+        # given
+        self.test_gui.filename_entry.delete(0, "end")
+        self.test_gui.filename_entry.insert(
+            0, "diffpy/tests/testdata/sofq_cut_15to35px.h5"
+        )
+
+        # when
+        self.test_gui.load_cube()
+        result = self.test_gui.cube
+
+        # then
+        self.assertTrue(
+            np.allclose(
+                np.nan_to_num(result), np.nan_to_num(self.test_sofq_cut_15to35px)
+            )
+        )
+
+    def test_fft_testdataset1(self):
+        # given
+        self.test_gui.plot_plane = (
+            lambda *a, **b: ()
+        )  # overwrite plot_plane which requires not initialized attribute im
+        self.test_gui.cube = self.test_sofq
+
+        # when
+        self.test_gui.fft()
+        result = self.test_gui.cube
+
+        # then
+        self.assertTrue(np.allclose(result, self.test_gofr))
+
+    def test_fft_testdataset2(self):
+        # given
+        self.test_gui.plot_plane = (
+            lambda *a, **b: ()
+        )  # overwrite plot_plane which requires not initialized attribute im
+        self.test_gui.cube = self.test_sofq_cut_10to40px
+
+        # when
+        self.test_gui.fft()
+        result = self.test_gui.cube
+
+        # then
+        self.assertTrue(np.allclose(result, self.test_gofr_cut_10to40px))
+
+    def test_fft_testdataset3(self):
+        # given
+        self.test_gui.plot_plane = (
+            lambda *a, **b: ()
+        )  # overwrite plot_plane which requires not initialized attribute im
+        self.test_gui.cube = self.test_sofq_cut_15to35px
+
+        # when
+        self.test_gui.fft()
+        result = self.test_gui.cube
+
+        # then
+        self.assertTrue(np.allclose(result, self.test_gofr_cut_15to35px))
+
+    def test_applycutoff_range1(self):
+        # given
+        self.test_gui.plot_plane = lambda *a, **b: ()
+        self.test_gui.cube = self.test_sofq
+        self.test_gui.qminentry.insert(0, "10")
+        self.test_gui.qmaxentry.insert(0, "40")
+
+        # when
+        self.test_gui.applycutoff()
+        result = self.test_gui.cube
+
+        # then
+        self.assertTrue(
+            np.allclose(
+                np.nan_to_num(result), np.nan_to_num(self.test_sofq_cut_10to40px)
+            )
+        )
+
+    def test_applycutoff_range2(self):
+        # given
+        self.test_gui.plot_plane = lambda *a, **b: ()
+        self.test_gui.cube = self.test_sofq
+        self.test_gui.qminentry.insert(0, "15")
+        self.test_gui.qmaxentry.insert(0, "35")
+
+        # when
+        self.test_gui.applycutoff()
+        result = self.test_gui.cube
+
+        # then
+        self.assertTrue(
+            np.allclose(
+                np.nan_to_num(result), np.nan_to_num(self.test_sofq_cut_15to35px)
+            )
+        )
+
+
+if __name__ == "__main__":
+    unittest.main()

src/diffpy/fourigui/tests/integration_test.py

@@ -0,0 +1,56 @@
+#!/usr/bin/env python
+##############################################################################
+#
+# (c) 2024 The Trustees of Columbia University in the City of New York.
+# All rights reserved.
+#
+# File coded by: Billinge Group members and community contributors.
+#
+# See GitHub contributions for a more detailed list of contributors.
+# https://github.com/diffpy/fourigui/graphs/contributors
+#
+# See LICENSE.rst for license information.
+#
+##############################################################################
+"""Convenience module for executing all unit tests with
+python -m diffpy.fourigui.tests.run
+"""
+
+if __name__ == "__main__":
+    import sys
+
+    # show warnings by default
+    if not sys.warnoptions:
+        import os
+        import warnings
+
+        warnings.simplefilter("default")
+        # also affect subprocesses
+        os.environ["PYTHONWARNINGS"] = "default"
+    import diffpy.fourigui.tests.integration_test as integration_test
+    import diffpy.fourigui.tests.unit_test as unit_test
+
+    # produce zero exit code for a successful test
+    sys.exit(
+        (not integration_test.main().wasSuccessful())
+        or (not unit_test.main().wasSuccessful())
+    )
+
+
+# Consider upgrading to pytest
+# import sys
+#
+# import pytest
+#
+# if __name__ == "__main__":
+#     # show output results from every test function
+#     args = ["-v"]
+#     # show the message output for skipped and expected failure tests
+#     if len(sys.argv) > 1:
+#         args.extend(sys.argv[1:])
+#     print("pytest arguments: {}".format(args))
+#     # call pytest and exit with the return code from pytest
+#     exit_res = pytest.main(args)
+#     sys.exit(exit_res)
+
+# End of file

src/diffpy/fourigui/tests/run.py

@@ -0,0 +1,52 @@
+import h5py
+import numpy as np
+
+
+def cutcube(fname_uncut_cube, fname_cut_cube, qmin, qmax):
+
+    cube = h5py.File(fname_uncut_cube, "r")["data"]
+
+    X, Y, Z = cube.shape
+    sphere = np.ones((X, Y, Z))
+    r2_inner = qmin**2
+    r2_outer = qmax**2
+    XS, YS, ZS = np.meshgrid(np.arange(X), np.arange(Y), np.arange(Z))
+    R2 = (XS - X // 2) ** 2 + (YS - Y // 2) ** 2 + (ZS - Z // 2) ** 2
+    mask = (R2 <= r2_inner) | (R2 >= r2_outer)
+    sphere[mask] = np.nan
+
+    f = h5py.File(fname_cut_cube, "w")
+    f.create_dataset("data", data=cube * sphere)
+    f.close()
+
+
+def fftcube(fname_reci, fname_real):
+
+    fftholder = h5py.File(fname_reci, "r")["data"]
+
+    fftholder = np.nan_to_num(fftholder)
+    size = list(fftholder.shape)
+    fftholder = np.fft.ifftshift(fftholder)
+    fftholder = np.fft.fftn(fftholder, s=size, norm="ortho")
+    fftholder = np.fft.fftshift(fftholder)
+    fftholder = fftholder.real
+
+    f = h5py.File(fname_real, "w")
+    f.create_dataset("data", data=fftholder)
+    f.close()
+
+
+def dummydata(fname="dummydata.h5"):
+    dummydata = np.ones((3, 3, 3))
+
+    f = h5py.File(fname, "w")
+    f.create_dataset("data", data=dummydata)
+    f.close()
+
+
+# cutcube("sofq.h5", "sofq_cut_10to40px.h5", 10, 40)
+# cutcube("sofq.h5", "sofq_cut_15to35px.h5", 15, 35)
+# fftcube("sofq.h5", "gofr.h5")
+# fftcube("sofq_cut_10to40px.h5", "gofr_from_sofq_cut_10to40px.h5")
+# fftcube("sofq_cut_15to35px.h5", "gofr_from_sofq_cut_15to35px.h5")
+dummydata()