code unit test coverage

src/mrsimulator/simulator/sampling_scheme.py

@@ -23,23 +23,34 @@ def generate_custom_sampling(alpha, beta, weight, triangle_mesh=False):
     return sampling
 
 
-def step_averaging(N_alpha: int, N_beta: int, triangle_mesh=True):
+def check_triangulation(triangle_mesh: bool, integration_volume: str):
+    """Check if triangulation can be applied"""
+    if triangle_mesh and integration_volume != "sphere":
+        raise NotImplementedError(
+            "Triangulation of non sphere geometry is not implemented."
+        )
+
+
+def step_averaging(
+    N_alpha: int, N_beta: int, triangle_mesh=True, integration_volume="sphere"
+):
     """Generate STEP averaging samples.
 
     Args:
         N_alpha: number of points along the alpha dimension.
         beta: number of points along the beta dimension.
         triangle_mesh: generate ConvexHull triangulation of points.
     """
-    sphereType = "sphere"
+    check_triangulation(triangle_mesh, integration_volume)
+
     norm_step = 0.0
-    if sphereType == "sphere":
+    if integration_volume == "sphere":
         a = [1.0, 0.0, 1.0]
         b = 1.0
-    if sphereType == "hemisphere":
+    if integration_volume == "hemisphere":
         a = [1.0, 0.0, 1.0]
         b = 2.0
-    if sphereType == "octant":
+    if integration_volume == "octant":
         a = [2.0, 1.0, 8.0]
         b = 2.0
 
@@ -64,29 +75,30 @@ def step_averaging(N_alpha: int, N_beta: int, triangle_mesh=True):
 def get_zcw_number(M):
     """ZCW number"""
     # returns the number of ZCW angles for the given integer M=2,3,4,...
-    gM = 5
-    gMminus1 = 3
-    sum = 5
+    g_m = 5
+    g_minus1 = 3
+    local_sum = 5
     for _ in range(M + 1):
-        sum = gM + gMminus1
-        gMminus1 = gM
-        gM = sum
-    return sum
+        local_sum = g_m + g_minus1
+        g_minus1 = g_m
+        g_m = local_sum
+    return local_sum
 
 
-def zcw_averaging(M: int, triangle_mesh=True):
+def zcw_averaging(M: int, triangle_mesh=True, integration_volume="sphere"):
     """Generate ZCW averaging samples.
 
     Args:
         M: ZCW point generation factor.
         triangle_mesh: generate ConvexHull triangulation of points.
     """
-    sphereType = "sphere"
-    if sphereType == "sphere":
+    check_triangulation(triangle_mesh, integration_volume)
+
+    if integration_volume == "sphere":
         c = [1.0, 2.0, 1.0]
-    if sphereType == "hemisphere":
+    if integration_volume == "hemisphere":
         c = [-1.0, 1.0, 1.0]
-    if sphereType == "octant":
+    if integration_volume == "octant":
         c = [-1.0, 1.0, 4.0]
 
     N = get_zcw_number(M)
@@ -99,11 +111,11 @@ def zcw_averaging(M: int, triangle_mesh=True):
     return generate_custom_sampling(alpha, beta, weight, triangle_mesh)
 
 
-if __name__ == "__main__":
-    sampling = zcw_averaging(M=21)
-    rad2deg = 180.0 / np.pi
-    nd_array = np.array(
-        [sampling.alpha * rad2deg, sampling.beta * rad2deg, sampling.weight]
-    ).T
-    size = sampling.alpha.size
-    np.savetxt(f"zcw{size}.cry", nd_array, header=str(size), fmt="%.6e")
+# if __name__ == "__main__":
+#     sampling = zcw_averaging(M=21)
+#     rad2deg = 180.0 / np.pi
+#     nd_array = np.array(
+#         [sampling.alpha * rad2deg, sampling.beta * rad2deg, sampling.weight]
+#     ).T
+#     size = sampling.alpha.size
+#     np.savetxt(f"zcw{size}.cry", nd_array, header=str(size), fmt="%.6e")

tests/spectral_integration_tests/test_custom_sampling_lineshape.py

@@ -1,4 +1,5 @@
 import numpy as np
+import pytest
 from mrsimulator import Simulator
 from mrsimulator import Site
 from mrsimulator import SpinSystem
@@ -40,10 +41,12 @@ def test_one_d():
     spec_asg = sim.methods[0].simulation.y[0].components[0].real
 
     sim.config.custom_sampling = zcw_averaging(M=12)
+    assert sim.config.get_orientations_count() == 2584
     sim.run()
     spec_zcw = sim.methods[0].simulation.y[0].components[0].real
 
     sim.config.custom_sampling = step_averaging(N_alpha=51, N_beta=51)
+    assert sim.config.get_orientations_count() == 2601
     sim.run()
     spec_step = sim.methods[0].simulation.y[0].components[0].real
 
@@ -115,3 +118,25 @@ def test_internal_external_averaging_spectrum():
     np.testing.assert_almost_equal(spec_step_interp, spec_step_bin, decimal=2)
     np.testing.assert_almost_equal(spec_asg_interp, spec_step_interp, decimal=3)
     np.testing.assert_almost_equal(spec_asg_interp, spec_zcw_interp, decimal=3)
+
+
+def test_sampling_triangulation():
+    error = "Triangulation of non sphere geometry is not implemented."
+    for vol in ["octant", "hemisphere"]:
+        with pytest.raises(NotImplementedError, match=error):
+            _ = step_averaging(
+                N_alpha=50, N_beta=50, triangle_mesh=True, integration_volume=vol
+            )
+
+        with pytest.raises(NotImplementedError, match=error):
+            _ = zcw_averaging(M=5, triangle_mesh=True, integration_volume=vol)
+
+
+def test_sampling_non_sphere():
+    for vol in ["octant", "hemisphere"]:
+        step_s = step_averaging(
+            N_alpha=50, N_beta=50, triangle_mesh=False, integration_volume=vol
+        )
+        assert step_s.alpha.size == 2500
+        zcw_s = zcw_averaging(M=5, triangle_mesh=False, integration_volume=vol)
+        assert zcw_s.alpha.size == 89

tests/spectral_integration_tests/test_lineshapes.py

@@ -1,4 +1,6 @@
 """Lineshape Test."""
+from copy import deepcopy
+from os import mkdir
 from os import path
 from pprint import pformat
 
@@ -43,6 +45,9 @@ def report_pdf(report):
 
 def compile_plots(dim, rep, info, title=None, report=None, label="simpson"):
     """Test report plot"""
+    if not __GENERATE_REPORT__:
+        return
+
     _, ax = plt.subplots(1, 2, figsize=(9, 4), gridspec_kw={"width_ratios": [1, 1]})
 
     for i, res in enumerate(rep[:1]):
@@ -79,6 +84,27 @@ def compile_plots(dim, rep, info, title=None, report=None, label="simpson"):
     plt.close()
 
 
+def test_pdf():
+    global __GENERATE_REPORT__
+    temp_status = deepcopy(__GENERATE_REPORT__)
+    __GENERATE_REPORT__ = True
+
+    is_present = path.isdir("_temp")
+    if not is_present:
+        mkdir("_temp")
+    filename = "_temp/lineshapes_report_scrap.pdf"
+    report_file = PdfPages(filename)
+    dim = np.arange(10)
+    res = [np.arange(10), np.arange(10)]
+    info = {"config": 1, "spin_systems": 2, "methods": 3}
+    compile_plots(dim, [res], info, title="Shielding Sidebands", report=report_file)
+    report_file.close()
+    is_file = path.isfile(filename)
+    assert is_file
+
+    __GENERATE_REPORT__ = temp_status
+
+
 def check_all_close(res, message, rel_limit):
     """Check if the vectos in res are all close within relative limits"""
     for item in res:
@@ -110,8 +136,7 @@ def test_pure_shielding_sideband_simpson(report):
         )
         res.append([data_mrsimulator, data_source])
 
-        if __GENERATE_REPORT__:
-            compile_plots(dim, res, info, title="Shielding Sidebands", report=report)
+        compile_plots(dim, res, info, title="Shielding Sidebands", report=report)
 
         message = f"{error_message} test0{i}.json"
         check_all_close(res, message, rel_limit=2.5)
@@ -137,8 +162,7 @@ def test_pure_quadrupolar_sidebands_simpson(report):
             )
             res.append([data_mrsimulator, data_source])
 
-        if __GENERATE_REPORT__:
-            compile_plots(dim, res, info, title="Quad Sidebands", report=report)
+        compile_plots(dim, res, info, title="Quad Sidebands", report=report)
 
         message = f"{error_message} test0{i:02d}.json"
         check_all_close(res, message, rel_limit=1.5)
@@ -150,7 +174,6 @@ def test_csa_plus_quadrupolar_lineshape_simpson(report):
     )
     path_ = path.join(SIMPSON_TEST_PATH, "csa_quad")
     for i in range(10):
-        print(i)
         filename = path.join(path_, f"test{i:02d}", f"test{i:02d}.json")
         res = []
         for volume in VOLUMES:
@@ -159,14 +182,13 @@ def test_csa_plus_quadrupolar_lineshape_simpson(report):
             )
             res.append([data_mrsimulator, data_source])
 
-        if __GENERATE_REPORT__:
-            compile_plots(
-                dim,
-                res,
-                info,
-                title="Quad + Shielding Sidebands",
-                report=report,
-            )
+        compile_plots(
+            dim,
+            res,
+            info,
+            title="Quad + Shielding Sidebands",
+            report=report,
+        )
 
         message = f"{error_message} test0{i:02d}.json"
         check_all_close(res, message, rel_limit=0.9)
@@ -186,14 +208,13 @@ def test_1st_order_quadrupolar_lineshape_simpson(report):
             )
             res.append([data_mrsimulator, data_source])
 
-        if __GENERATE_REPORT__:
-            compile_plots(
-                dim,
-                res,
-                info,
-                title="1st Order Quadrupolar Lineshape",
-                report=report,
-            )
+        compile_plots(
+            dim,
+            res,
+            info,
+            title="1st Order Quadrupolar Lineshape",
+            report=report,
+        )
 
         message = f"{error_message} test0{i:02d}.json"
         check_all_close(res, message, rel_limit=1.0)
@@ -211,8 +232,7 @@ def test_j_coupling_lineshape_simpson(report):
             )
             res.append([data_mrsimulator, data_source])
 
-        if __GENERATE_REPORT__:
-            compile_plots(dim, res, info, title="J-coupling Spectra", report=report)
+        compile_plots(dim, res, info, title="J-coupling Spectra", report=report)
 
         message = f"{error_message} test0{i:02d}.json"
         check_all_close(res, message, rel_limit=1.1)
@@ -232,10 +252,7 @@ def test_dipolar_coupling_lineshape_simpson(report):
             )
             res.append([data_mrsimulator, data_source])
 
-        if __GENERATE_REPORT__:
-            compile_plots(
-                dim, res, info, title="Dipolar-coupling Spectra", report=report
-            )
+        compile_plots(dim, res, info, title="Dipolar-coupling Spectra", report=report)
 
         message = f"{error_message} test0{i:02d}.json"
         check_all_close(res, message, rel_limit=1.5)
@@ -262,15 +279,14 @@ def test_quad_csa_cross_rmnsim(report):
             )
             res.append([data_mrsimulator, data_source])
 
-            if __GENERATE_REPORT__:
-                compile_plots(
-                    dim,
-                    res,
-                    info,
-                    title="Quad-CSA 2nd Order Cross-Term",
-                    report=report,
-                    label="rmnsim",
-                )
+            compile_plots(
+                dim,
+                res,
+                info,
+                title="Quad-CSA 2nd Order Cross-Term",
+                report=report,
+                label="rmnsim",
+            )
 
             message = f"{error_message} test0{i}.json"
             check_all_close(res, message, rel_limit=0.3)
@@ -301,15 +317,14 @@ def test_pure_shielding_static_lineshape_python_brute(report):
         )
         res.append([data_mrsimulator, data_source])
 
-        if __GENERATE_REPORT__:
-            compile_plots(
-                dim,
-                res,
-                info,
-                title="Shielding Static Lineshape (Brute Force)",
-                report=report,
-                label="Brute",
-            )
+        compile_plots(
+            dim,
+            res,
+            info,
+            title="Shielding Static Lineshape (Brute Force)",
+            report=report,
+            label="Brute",
+        )
 
         message = f"{error_message} test0{i}.json"
         check_all_close(res, message, rel_limit=2)
@@ -338,15 +353,14 @@ def test_pure_quadrupolar_lineshape_python_brute(report):
         )
         res.append([data_mrsimulator, data_source])
 
-        if __GENERATE_REPORT__:
-            compile_plots(
-                dim,
-                res,
-                info,
-                title="Quad Lineshape Self-Test",
-                report=report,
-                label="self",
-            )
+        compile_plots(
+            dim,
+            res,
+            info,
+            title="Quad Lineshape Self-Test",
+            report=report,
+            label="self",
+        )
 
         message = f"{error_message} test0{i:02d}.json"
         check_all_close(res, message, rel_limit=1.5)

tests/spectral_integration_tests/utils.py

@@ -67,8 +67,6 @@ def get_data(filename):
 def get_csdm_data(source_file, quantity):
     """Get data from csdm object"""
     csdm = cp.load(source_file)
-    if quantity == "time":
-        csdm = csdm.fft()
     data_source = csdm.y[0].components[0]
     return data_source