Merge pull request #252 from carnisj/test_runner

Implement large unit tests for runners

bcdi/__init__.py

@@ -6,4 +6,4 @@
 #       authors:
 #         Jerome Carnis, carnis_jerome@yahoo.fr
 """The main bcdi package, which contains the whole framework."""
-__version__ = "0.2.5"
+__version__ = "0.2.6"

bcdi/graph/graph_utils.py

@@ -1413,7 +1413,7 @@ def linecut(
     num_points = int(
         np.sqrt(sum((val[1] - val[0] + 1) ** 2 for _, val in enumerate(indices)))
     )
-    print("num_points", num_points)
+
     cut = map_coordinates(
         input=array,
         coordinates=np.vstack(

bcdi/utils/parameters.py

@@ -48,7 +48,17 @@ def __init__(self, key, value, allowed):
 
 
 class ConfigChecker(ABC):
-    """Validate and configure parameters."""
+    """
+    Validate and configure parameters.
+
+    :param initial_params: the dictionary of parameters to validate and configure
+    :param default_values: an optional dictionary of default values for keys in
+     initial_params
+    :param logger: an optional Logger
+    :param match_length_params: a tuple of keys from initial_params which should match
+     a certain length (e.g. the number of scans)
+    :param required_params: a tuple of keys that have to be present in initial_params
+    """
 
     def __init__(
         self,
@@ -286,9 +296,13 @@ def _configure_params(self) -> None:
         if self.initial_params["align_q"]:
             if self.initial_params["ref_axis_q"] not in {"x", "y", "z"}:
                 raise ValueError("ref_axis_q should be either 'x', 'y' or 'z'")
-            self._checked_params[
-                "comment"
-            ] += f"_align-q-{self.initial_params['ref_axis_q']}"
+            if (
+                not self._checked_params["use_rawdata"]
+                and self._checked_params["interpolation_method"] == "linearization"
+            ):
+                self._checked_params[
+                    "comment"
+                ] += f"_align-q-{self.initial_params['ref_axis_q']}"
 
         if (
             self.initial_params["backend"].lower() == "agg"
@@ -506,7 +520,7 @@ def valid_param(key: str, value: Any) -> Tuple[Any, bool]:
     elif key == "config_file":
         valid.valid_container(value, container_types=str, min_length=1, name=key)
         if not os.path.isfile(value):
-            raise ValueError(f"The file {value} does not exist")
+            raise ValueError(f"The file '{value}' does not exist")
     elif key == "correlation_threshold":
         valid.valid_item(
             value, allowed_types=Real, min_included=0, max_included=1, name=key
@@ -736,7 +750,7 @@ def valid_param(key: str, value: Any) -> Tuple[Any, bool]:
             value = (value,)
         valid.valid_container(
             value,
-            container_types=list,
+            container_types=(tuple, list),
             item_types=str,
             min_length=1,
             allow_none=True,
@@ -745,7 +759,7 @@ def valid_param(key: str, value: Any) -> Tuple[Any, bool]:
         if value is not None:
             for val in value:
                 if not os.path.isfile(val):
-                    raise ValueError(f"The file {val} does not exist")
+                    raise ValueError(f"The file '{val}' does not exist")
     elif key in {"ref_axis_q", "ref_axis"}:
         allowed = {"x", "y", "z"}
         if value not in allowed:

bcdi/utils/parser.py

@@ -219,7 +219,7 @@ def file_path(self, value):
         if pathlib.Path(value).suffix != ".yml":
             raise ValueError("Expecting a YAML config file")
         if not os.path.isfile(value):
-            raise ValueError(f"The file {value} does not exist")
+            raise ValueError(f"The config file '{value}' does not exist")
         self._file_path = value
 
     @staticmethod

doc/HISTORY.rst

@@ -1,5 +1,5 @@
-Future:
--------
+Version 0.2.6:
+--------------
 
 * Fix deprecation warning with the method `pandas.DataFrame.append`
 

doc/modules/utils/index.rst

@@ -44,7 +44,7 @@ API Reference
 parameters
 ^^^^^^^^^^
 
-Function related to the validation of configuration parameters.
+Classes and functions related to the validation of configuration parameters.
 
 API Reference
 -------------

tests/postprocessing/test_postprocessing_runner.py

@@ -0,0 +1,72 @@
+# -*- coding: utf-8 -*-
+
+# BCDI: tools for pre(post)-processing Bragg coherent X-ray diffraction imaging data
+#   (c) 07/2017-06/2019 : CNRS UMR 7344 IM2NP
+#   (c) 07/2019-05/2021 : DESY PHOTON SCIENCE
+#       authors:
+#         Jerome Carnis, carnis_jerome@yahoo.fr
+
+from functools import reduce
+import h5py
+import numpy as np
+from pathlib import Path
+import tempfile
+from typing import Dict, Optional
+import unittest
+import yaml
+
+from bcdi.postprocessing.postprocessing_runner import run
+from bcdi.utils.parser import ConfigParser
+from tests.config import run_tests
+
+here = Path(__file__).parent
+THIS_DIR = str(here)
+CONFIG = str(here.parents[1] / "bcdi/examples/S11_config_postprocessing.yml")
+
+
+class TestRun(unittest.TestCase):
+    """Large test for the postprocessing script bcdi_strain.py."""
+
+    def setUp(self) -> None:
+        self.args: Optional[Dict] = None
+        self.command_line_args = {
+            "backend": "Agg",
+            "reconstruction_files": str(
+                here.parents[1]
+                / "bcdi/examples/S11_modes_252_420_392_prebinning_1_1_1.h5"
+            ),
+        }
+        self.parser = ConfigParser(CONFIG, self.command_line_args)
+        if not Path(
+            yaml.load(self.parser.raw_config, Loader=yaml.SafeLoader)["root_folder"]
+        ).is_dir():
+            self.skipTest(
+                reason="This test can only run locally with the example dataset"
+            )
+
+    def test_run(self):
+        expected_q_com = [0, 2.77555, 0]
+        expected_volume = 23217408
+        with tempfile.TemporaryDirectory() as tmpdir:
+            self.args = self.parser.load_arguments()
+            self.args["save_dir"] = (tmpdir,)
+            run(self.args)
+
+            with h5py.File(
+                f"{tmpdir}/S11_ampdispstrain_mode_crystalframe.h5",
+                "r",
+            ) as h5file:
+                amp = h5file["output/amp"][()]
+                voxel_sizes = h5file["output/voxel_sizes"][()]
+                q_com = h5file["output/q_com"][()]
+        amp = amp / amp.max()
+        amp[amp < self.args["isosurface_strain"]] = 0
+        amp[np.nonzero(amp)] = 1
+        volume = amp.sum() * reduce(lambda x, y: x * y, voxel_sizes)
+
+        self.assertEqual(volume, expected_volume)
+        self.assertTrue(np.allclose(q_com, expected_q_com))
+
+
+if __name__ == "__main__":
+    run_tests(TestRun)

tests/preprocessing/test_preprocessing_runner.py

@@ -0,0 +1,72 @@
+# -*- coding: utf-8 -*-
+
+# BCDI: tools for pre(post)-processing Bragg coherent X-ray diffraction imaging data
+#   (c) 07/2017-06/2019 : CNRS UMR 7344 IM2NP
+#   (c) 07/2019-05/2021 : DESY PHOTON SCIENCE
+#       authors:
+#         Jerome Carnis, carnis_jerome@yahoo.fr
+
+from functools import reduce
+import h5py
+import numpy as np
+from pathlib import Path
+import tempfile
+from typing import Dict, Optional
+import unittest
+import yaml
+
+from bcdi.preprocessing.preprocessing_runner import run
+from bcdi.utils.parser import ConfigParser
+from tests.config import run_tests
+
+here = Path(__file__).parent
+THIS_DIR = str(here)
+CONFIG = str(here.parents[1] / "bcdi/examples/S11_config_preprocessing.yml")
+
+
+class TestRun(unittest.TestCase):
+    """Large test for the preprocessing script bcdi_preprocessing_BCDI.py."""
+
+    def setUp(self) -> None:
+        self.args: Optional[Dict] = None
+        self.command_line_args = {
+            "backend": "Agg",
+            "flag_interact": False,
+        }
+        self.parser = ConfigParser(CONFIG, self.command_line_args)
+        if not Path(
+            yaml.load(self.parser.raw_config, Loader=yaml.SafeLoader)["root_folder"]
+        ).is_dir():
+            self.skipTest(
+                reason="This test can only run locally with the example dataset"
+            )
+
+    def test_run(self):
+        expected_bragg_inplane = 0.4926488901267543
+        expected_bragg_outofplane = 35.36269069963432
+        expected_bragg_peak = [127, 214, 316]
+        expected_q = [-0.84164063, 2.63974482, -0.03198209]
+        with tempfile.TemporaryDirectory() as tmpdir:
+            self.args = self.parser.load_arguments()
+            self.args["save_dir"] = (tmpdir,)
+            run(self.args)
+
+            with h5py.File(
+                f"{tmpdir}/S11_preprocessing_norm_256_256_256_1_2_2.h5",
+                "r",
+            ) as h5file:
+                bragg_inplane = h5file["output/bragg_inplane"][()]
+                bragg_outofplane = h5file["output/bragg_outofplane"][()]
+                bragg_peak = h5file["output/bragg_peak"][()]
+                q = h5file["output/q"][()]
+
+        self.assertAlmostEqual(bragg_inplane, expected_bragg_inplane)
+        self.assertAlmostEqual(bragg_outofplane, expected_bragg_outofplane)
+        self.assertTrue(
+            val1 == val2 for val1, val2 in zip(bragg_peak, expected_bragg_peak)
+        )
+        self.assertTrue(np.allclose(q, expected_q))
+
+
+if __name__ == "__main__":
+    run_tests(TestRun)

tests/utils/test_parameters.py

@@ -294,6 +294,8 @@ def test_check_config_interpolate_reload_orthogonal(self):
 
     def test_check_config_align_q(self):
         self.checker.initial_params["align_q"] = True
+        self.checker._checked_params["use_rawdata"] = False
+        self.checker._checked_params["interpolation_method"] = "linearization"
         out = self.checker.check_config()
         self.assertEqual(
             out["comment"],

tests/utils/test_parser.py

@@ -16,7 +16,7 @@
 CONFIG = str(here.parents[1] / "bcdi/examples/S11_config_postprocessing.yml")
 
 
-class Test_str_to_list(unittest.TestCase):
+class TestStrToList(unittest.TestCase):
     """
     Tests on the function str_to_list.
 
@@ -146,4 +146,4 @@ def test_repr(self):
 
 if __name__ == "__main__":
     run_tests(TestConfigParser)
-    run_tests(Test_str_to_list)
+    run_tests(TestStrToList)