Merge pull request #367 from jadball/master

Minor notebook bugfixes, tiny changes to refinement manager logic

ImageD11/nbGui/S3DXRD/4_visualise.ipynb

@@ -290,10 +290,10 @@
    },
    "outputs": [],
    "source": [
-    "# look at unit cells\n",
+    "# look at unit cells - mean of a, b, c for cubic for now\n",
     "\n",
     "fig, ax = plt.subplots()\n",
-    "ax.hist(tmap.unitcell[0, :, :, :3].ravel(), bins=1000)\n",
+    "ax.hist(tmap.unitcell[0, :, :, :3].mean(axis=-1).ravel(), bins=1000)\n",
     "ax.set_xlabel('unitcell of pixel')\n",
     "plt.show()"
    ]

ImageD11/nbGui/S3DXRD/tomo_3_refinement_minor_phase.ipynb

@@ -564,6 +564,11 @@
     "\n",
     "        refine = PBPRefine(dset=ds, y0=y0, fpks=fpks, 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=forref)\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",
+    "        refine.pbpmap_filename = os.path.splitext(refine.pbpmap_filename)[0] + f'_{phase_str}.h5'\n",
+    "        refine.refinedmap_filename = os.path.splitext(refine.refinedmap_filename)[0] + f'_{phase_str}.h5'\n",
+    "        \n",
     "        refine.setmap(pmap)\n",
     "        refine.setpeaks(cf_2d)\n",
     "        refine.mask = pmap.best_npks > 0\n",

ImageD11/nbGui/calibration/silicon_calib.ipynb

@@ -39,7 +39,8 @@
     "import ImageD11.columnfile\n",
     "import ImageD11.indexing\n",
     "import ImageD11.grain\n",
-    "import ImageD11.nbGui.fit_geometry"
+    "import ImageD11.nbGui.fit_geometry\n",
+    "import silx.io"
    ]
   },
   {
@@ -154,7 +155,7 @@
    "source": [
     "# guess the detector distance in um\n",
     "# you can also manually specify\n",
-    "distance_guess = auto_guess_distance(ds.masterfile, ds.scans[-1])  # detector distance in um\n",
+    "distance_guess = auto_guess_distance(dset.masterfile, dset.scans[-1])  # detector distance in um\n",
     "# distance_guess = 140000  # 140 mm"
    ]
   },
@@ -220,22 +221,6 @@
     "ui.fitGui()"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "tags": []
-   },
-   "outputs": [],
-   "source": [
-    "ui.valuewidgets['fit_tolerance'].value = 0.5\n",
-    "ui.fit(2,9)\n",
-    "ui.valuewidgets['fit_tolerance'].value = 0.05\n",
-    "ui.fit(3,21)\n",
-    "ui.fit(0,180)\n",
-    "ui.updateGui()"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,

ImageD11/sinograms/point_by_point.py

@@ -628,6 +628,7 @@ def __init__(self,
                  ifrac=None,
                  forref=None,
                  y0=0.0,
+                 min_grain_npks=6
                  ):
         self.dset = dset
         self.phase_name = phase_name
@@ -647,6 +648,7 @@ def __init__(self,
         # refinement parameters
         self.hkl_tol_refine = hkl_tol_refine
         self.hkl_tol_refine_merged = hkl_tol_refine_merged
+        self.min_grain_npks = min_grain_npks
         # geometry stuff
         self.ystep = self.dset.ystep
         self.y0 = y0
@@ -961,7 +963,7 @@ def to_h5(self, filename=None, h5group='PBPRefine'):
 
             # other pars we need for refinement
             pars = ['phase_name', 'hkl_tol_origins', 'hkl_tol_refine', 'hkl_tol_refine_merged', 'fpks', 'ds_tol',
-                    'etacut', 'ifrac', 'forref', 'y0']
+                    'etacut', 'ifrac', 'forref', 'y0', 'min_grain_npks']
 
             for par in pars:
                 try:
@@ -974,6 +976,7 @@ def to_h5(self, filename=None, h5group='PBPRefine'):
     def from_h5(cls, filename, h5group='PBPRefine'):
         # load the stuff in
         # then make an object
+        manager_filename = filename
 
         with h5py.File(filename, "r") as hin:
             parent_group = hin[h5group]
@@ -997,7 +1000,7 @@ def from_h5(cls, filename, h5group='PBPRefine'):
                     continue
 
             pars = ['phase_name', 'hkl_tol_origins', 'hkl_tol_refine', 'hkl_tol_refine_merged', 'fpks', 'ds_tol',
-                    'etacut', 'ifrac', 'forref', 'y0']
+                    'etacut', 'ifrac', 'forref', 'y0', 'min_grain_npks']
             pars_dict = {}
             for par in pars:
                 try:
@@ -1007,6 +1010,7 @@ def from_h5(cls, filename, h5group='PBPRefine'):
         # load the dataset
         dset = ImageD11.sinograms.dataset.load(dsfile)
         refine_obj = cls(dset=dset, **pars_dict)
+        refine_obj.own_filename = manager_filename
         for filename_attr, filename in filenames.items():
             setattr(refine_obj, filename_attr, filename)
         for array_attr, array in arrays.items():
@@ -1030,7 +1034,6 @@ def from_h5(cls, filename, h5group='PBPRefine'):
             refine_obj.loadmap(refine_obj.refinedmap_filename, refined=True)
         except (AttributeError, OSError):
             pass
-
         return refine_obj
 
     def get_origins(self, guess_speed=True, guess_npks=10000, save_peaks_after=True):
@@ -1168,7 +1171,8 @@ def run_refine(self, points_step_space=None, npoints=None, output_filename=None,
                                                                         pars['chi'],
                                                                         pars['wavelength'],
                                                                         tol=self.hkl_tol_refine,
-                                                                        merge_tol=self.hkl_tol_refine_merged
+                                                                        merge_tol=self.hkl_tol_refine_merged,
+                                                                        min_grain_npks=int(self.min_grain_npks)
                                                                         )
             # now we match how the indexer returns dodgy values
             # mask nan 3x3 entires to identity matrix