Bug fixes

jadball · Jan 25, 2025 · 69d5e52 · 69d5e52
1 parent 2725757
commit 69d5e52
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Showing 3 changed files with 13 additions and 8 deletions.
diff --git a/ImageD11/nbGui/S3DXRD/tomo_3_refinement.ipynb b/ImageD11/nbGui/S3DXRD/tomo_3_refinement.ipynb
@@ -488,7 +488,7 @@
     "        pmap = tensor_map.to_pbpmap(z_layer=0, default_npks=default_npks, default_nuniq=default_nuniq)\n",
     "        pmap.choose_best(1)\n",
     "\n",
-    "        refine = PBPRefine(dset=ds, y0=y0, hkl_tol_origins=hkl_tol_origins, hkl_tol_refine=hkl_tol_refine, hkl_tol_refine_merged=hkl_tol_refine_merged, ds_tol=ds_tol, ifrac=ifrac, phase_name=minor_phase_str, forref=rings_to_refine)\n",
+    "        refine = PBPRefine(dset=ds, y0=y0, hkl_tol_origins=hkl_tol_origins, hkl_tol_refine=hkl_tol_refine, hkl_tol_refine_merged=hkl_tol_refine_merged, ds_tol=ds_tol, ifrac=ifrac, phase_name=phase_str, forref=rings_to_refine)\n",
     "        \n",
     "        refine.own_filename = os.path.splitext(refine.own_filename)[0] + f'_{phase_str}.h5'\n",
     "        refine.icolf_filename = os.path.splitext(refine.icolf_filename)[0] + f'_{phase_str}.h5'\n",

diff --git a/ImageD11/sinograms/point_by_point.py b/ImageD11/sinograms/point_by_point.py
@@ -1592,10 +1592,18 @@ def refine_map(refine_points, all_pbpmap_ubis, ri_col, rj_col, sx_grid, sy_grid,
 
                 if grain_npks > min_grain_npks:
                     w, ubifit, residuals, rank, sing_vals = weighted_lstsq_ubi_fit(grain_ydist, gve_grain, hkl)
+
+                    problem_fitting = False
+                    try:
+                        # get U from UBI without using ImageD11 grain class
+                        ucell = ubi_to_unitcell(ubifit)
+                        U = ubi_and_ucell_to_u(ubifit, ucell)
+                    except:
+                        problem_fitting = True
 
                     # check the quality of the fit
                     worth_fitting = (ubifit is not None) and (rank == 3) and (np.linalg.cond(ubifit) < 1e14) and (
-                            np.linalg.det(ubifit) > 0) and (np.linalg.matrix_rank(ubifit) == 3)
+                            np.linalg.det(ubifit) > 0) and (np.linalg.matrix_rank(ubifit) == 3) and (not np.any(np.isnan(U))) and (not problem_fitting)
 
                     # do we like the quality?
                     if worth_fitting:
@@ -1631,9 +1639,6 @@ def refine_map(refine_points, all_pbpmap_ubis, ri_col, rj_col, sx_grid, sy_grid,
                         hkl = hkli[:, grain_peak_mask]
                         ydist = ydist_grain[grain_peak_mask]
 
-                        # get U from UBI without using ImageD11 grain class
-                        ucell = ubi_to_unitcell(ubifit)
-                        U = ubi_and_ucell_to_u(ubi_out, ucell)
                         gve0 = U.dot(B0).dot(hkl.astype(np.float64))
                         gTg0 = np.sum(gve_grain_strainfit * gve0, axis=0)
                         gTg = np.sum(gve_grain_strainfit * gve_grain_strainfit, axis=0)

diff --git a/test/papermill_test_notebooks.py b/test/papermill_test_notebooks.py
@@ -35,7 +35,7 @@ def noteboook_exec_pmill(nb_input_path, nb_output_path, params_dict):
     print('Executing notebook', nb_input_path)
     # change output path if it already exists, in case we run the same notebook twice
     if os.path.exists(nb_output_path):
-        nb_output_path.replace('.ipynb', '_2.ipynb')
+        nb_output_path = nb_output_path.replace('.ipynb', '_2.ipynb')
     papermill.execute_notebook(
        nb_input_path,
        nb_output_path,
@@ -430,7 +430,7 @@ def test_FeAu_JADB_pbp():
         {'PYTHONPATH': sys.path[0],  # pbp_2_visualise.ipynb - minor phase
          'dset_file': dset_file,
          'phase_str': 'Au',
-         'min_unique': 5,
+         'min_unique': 10,
          'dset_prefix': "top_",
         },
         {'PYTHONPATH': sys.path[0],  # pbp_3_refinement.ipynb - major phase
@@ -452,7 +452,7 @@ def test_FeAu_JADB_pbp():
         {'PYTHONPATH': sys.path[0],  # pbp_3_refinement.ipynb - minor phase
          'dset_file': dset_file,
          'phase_str': 'Au',
-         'min_unique': 5,
+         'min_unique': 10,
          'manual_threshold': None,
          'y0': -16.0,
          'hkl_tol_origins': 0.05,