Give user option to save on original grid (#304)

* Allow original grid saving

* Add uncertainties for main parameters. (#299)

* Add uncertainties for main parameters.

* Works for all parameters now

* Fix other tests

* loosen tolerance to 1e-4 from 1e-5

* Lower tolerance more

* Remove comment

* [pre-commit.ci] auto fixes from pre-commit hooks

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Rebasing

* Remove duplicated test

* Indent

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: Sparks29032

docs/source/morphpy.rst

@@ -83,6 +83,12 @@ get_diff: bool
     Return the difference function (morphed function minus target function) instead of
     the morphed function (default). When save is enabled, the difference function
     is saved instead of the morphed function.
+original_grid: bool
+    Save/return the morphed function on the original grid.
+    Automatically disabled when --get-diff enabled.
+    Default: save/return the morphed function on the
+    grid defined by the intersection of the original
+    and target grids.
 verbose: bool
     Print additional header details to saved files. These include details about the morph
     inputs and outputs.

news/choose-grid.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* User now has option to select which grid they want the morphed function returned on. The default grid is still the intersection of the original and target grid. The option --original-grid changes the returned grid to be the original grid instead.
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

src/diffpy/morph/morphapp.py

@@ -103,6 +103,19 @@ def morph_error(self, msg, error):
             "grid of the objective and target function."
         ),
     )
+    parser.add_option(
+        "-o",
+        "--original-grid",
+        action="store_true",
+        dest="original_grid",
+        help=(
+            "Save/return the morphed function on the original grid. "
+            "Automatically disabled when --get-diff enabled. "
+            "Default: save/return the morphed function on the "
+            "grid defined by the intersection of the original "
+            "and target grids. "
+        ),
+    )
     parser.add_option(
         "-v",
         "--verbose",
@@ -797,7 +810,8 @@ def single_morph(
     pcc = tools.get_pearson(chain)
     # Replace the MorphRGrid with Morph identity
     # This removes the r-range morph as mentioned above
-    mrg = morphs.Morph()
+    if opts.original_grid is not None:
+        chain[chain.index(mrg)] = morphs.Morph()
     chain(x_morph, y_morph, x_target, y_target)
 
     # FOR FUTURE MAINTAINERS

tests/test_morphio.py

@@ -7,6 +7,7 @@
 
 from diffpy.morph.morphapp import (
     create_option_parser,
+    multiple_morphs,
     multiple_targets,
     single_morph,
 )
@@ -28,6 +29,11 @@
 test_saving_succinct = testsaving_dir.joinpath("succinct")
 test_saving_verbose = testsaving_dir.joinpath("verbose")
 test_saving_verbose_unc = testsaving_dir.joinpath("verbose_unc")
+
+test_saving_grid = testsaving_dir.joinpath("grids")
+test_saving_grid_default = test_saving_grid.joinpath("default")
+test_saving_grid_original = test_saving_grid.joinpath("original")
+
 tssf = testdata_dir.joinpath("testsequence_serialfile.json")
 
 
@@ -220,7 +226,7 @@ def test_morph_outputs(self, setup, tmp_path):
         pargs = [morph_file, testsequence_dir]
         multiple_targets(self.parser, opts, pargs, stdout_flag=False)
 
-        # Save a single verbose morph
+        # Save a single verbose morph with un certainties
         svum = tmp_verbose_unc.joinpath("single_verbose_unc_morph.cgr")
         svum_name = svum.resolve().as_posix()
         opts, pargs = self.parser.parse_args(
@@ -239,7 +245,6 @@ def test_morph_outputs(self, setup, tmp_path):
         pargs = [morph_file, target_file]
         single_morph(self.parser, opts, pargs, stdout_flag=False)
 
-        # Check the saved files are the same for verbose
         common = []
         for item in tmp_verbose_unc.glob("**/*.*"):
             if item.is_file():
@@ -251,6 +256,78 @@ def test_morph_outputs(self, setup, tmp_path):
                     expected = filter(ignore_path, tf)
                     are_files_same(actual, expected)
 
+    def test_grid_selection(self, setup, tmp_path):
+        morph_file = self.testfiles[0]
+
+        # Save on default grid
+        tmp_default = tmp_path.joinpath("default")
+        tmp_default_name = tmp_default.resolve().as_posix()
+
+        opts, pargs = self.parser.parse_args(
+            [
+                "--multiple-morphs",
+                "-s",
+                tmp_default_name,
+                "-n",
+                "--save-names-file",
+                tssf,
+                "--xmax",
+                "35",
+            ]
+        )
+
+        pargs = [testsequence_dir, morph_file]
+        multiple_morphs(self.parser, opts, pargs, stdout_flag=False)
+
+        tmp_default_morphs = tmp_default.joinpath("Morphs")
+
+        # Check the saved files are the same for default grid
+        common = []
+        for item in tmp_default_morphs.glob("**/*.*"):
+            if item.is_file():
+                common.append(item.relative_to(tmp_default_morphs).as_posix())
+        for file in common:
+            with open(tmp_default_morphs.joinpath(file)) as gf:
+                with open(test_saving_grid_default.joinpath(file)) as tf:
+                    actual = filter(ignore_path, gf)
+                    expected = filter(ignore_path, tf)
+                    are_files_same(actual, expected)
+
+        # Save on original grid
+        tmp_original = tmp_path.joinpath("original")
+        tmp_original_name = tmp_original.resolve().as_posix()
+
+        opts, pargs = self.parser.parse_args(
+            [
+                "--multiple-morphs",
+                "-s",
+                tmp_original_name,
+                "-n",
+                "--save-names-file",
+                tssf,
+                "--xmax",
+                "35",
+                "-o",
+            ]
+        )
+
+        pargs = [testsequence_dir, morph_file]
+        multiple_morphs(self.parser, opts, pargs, stdout_flag=False)
+
+        tmp_original_morphs = tmp_default.joinpath("Morphs")
+
+        # Check the saved files are the same for original grid
+        common = []
+        for item in tmp_original_morphs.glob("**/*.*"):
+            if item.is_file():
+                common.append(item.relative_to(tmp_original_morphs).as_posix())
+        for file in common:
+            with open(tmp_original_morphs.joinpath(file)) as gf:
+                with open(test_saving_grid_original.joinpath(file)) as tf:
+                    actual = filter(ignore_path, gf)
+                    expected = filter(ignore_path, tf)
+                    are_files_same(actual, expected)
+
     # Similar format as test_morph_outputs
     def test_morph_diff_outputs(self, setup, tmp_path):
         morph_file = self.testfiles[0]

tests/test_morphpy.py

@@ -148,6 +148,23 @@ def test_morph_opts(self, setup_morph):
             except AttributeError:
                 pass
 
+    def test_morphpy_grid_selection(self, setup_morph):
+        morph_file = self.testfiles[0]
+        _, grm = morph(morph_file, morph_file)
+        # Notice that this is a strict less than, not a less than or equal to.
+        # This is because xmax is an exclusive function (see MorphRGrid).
+        grm_truncated_grid = grm[:, 0][grm[:, 0] < 35]
+        grm_truncated_func = grm[:, 1][grm[:, 0] < 35]
+        grm_truncated = np.array([grm_truncated_grid, grm_truncated_func]).T
+
+        _, grt_default = morph(morph_file, morph_file, xmax=35)
+        assert np.allclose(grt_default, grm_truncated)
+
+        _, grt_original = morph(
+            morph_file, morph_file, xmax=35, original_grid=True
+        )
+        assert np.allclose(grt_original, grm)
+
     def test_morph(self, setup_morph):
         morph_results = {}
         morph_file = self.testfiles[0]