added overlap testing to fitgrains

Author: Joel Bernier

hexrd/findorientations.py

@@ -478,7 +478,9 @@ def find_orientations(cfg, hkls=None, clean=False, profile=False):
                 fmt="%.18e",
                 delimiter="\t"
                 )
-
+            pass
+        pass # close conditional on grid search
+    
     # generate the completion maps
     logger.info("Running paintgrid on %d trial orientations", quats.shape[1])
     if profile:

hexrd/fitgrains.py

@@ -126,6 +126,7 @@ def get_data(cfg, show_progress=False, force=False, clean=False):
         'omega_step': cfg.image_series.omega.step,
         'omega_stop': cfg.image_series.omega.stop,
         'omega_tol': cfg.fit_grains.tolerance.omega,
+        'overlap_table': os.path.join(cfg.analysis_dir, 'overlap_table.npz'),
         'panel_buffer': cfg.fit_grains.panel_buffer,
         'pixel_pitch': instrument_cfg['detector']['pixels']['size'],
         'plane_data': pd,
@@ -327,6 +328,22 @@ def fit_grains(self, grain_id, grain_params, refit_tol=None):
             idx = np.logical_and(valid_refl_ids, unsat_spots)
             pass # end if edge case
 
+        # if an overlap table has been written, load it and use it
+        overlaps = np.zeros(len(refl_table), dtype=bool)
+        try:
+            ot = np.load(self._p['overlap_table'])
+            for key in ot.keys():
+                for this_table in ot[key]:
+                    these_overlaps = np.where(
+                        this_table[:, 0] == grain_id)[0]
+                    if len(these_overlaps) > 0:
+                        mark_these = np.array(this_table[these_overlaps, 1], dtype=int)
+                        overlaps[mark_these] = True
+            idx = np.logical_and(idx, ~overlaps)
+        except IOError, IndexError:
+            #print "no overlap table found"
+            pass
+        
         # completeness from pullspots only; incl saturated
         completeness = sum(valid_refl_ids)/float(len(valid_refl_ids))
 

hexrd/xrd/crystallography.py

@@ -870,7 +870,6 @@ def getMergedRanges(self, cullDupl=False):
         tThLoIdx = 0
         tThHiCur = 0.
         for iHKL, nonoverlapNext in enumerate(nonoverlapNexts):
-            print tThLoIdx
             tThHi = tThRanges[iHKL, -1]
             if not nonoverlapNext:
                 if cullDupl and abs(tThs[iHKL] - tThs[iHKL+1]) < sqrt_epsf:

hexrd/xrd/indexer.py

@@ -753,7 +753,7 @@ def paintGrid(quats, etaOmeMaps,
     # omeIndices = mapIndices[1].T.flatten()
     # etaIndices = num.tile(range(numEtas), (numOmes))
     # omeIndices = num.tile(range(numOmes), (numEtas))
-    # j_eta, i_ome = np.meshgrid(range(numEtas), range(numOmes))
+    # j_eta, i_ome = num.meshgrid(range(numEtas), range(numOmes))
     # etaIndices = j_eta.flatten()
     # omeIndices = i_ome.flatten()
     etaIndices = num.r_[range(numEtas)]
@@ -851,7 +851,7 @@ def paintGrid(quats, etaOmeMaps,
 
 def _meshgrid2d(x, y):
     """
-    A special-cased implementation of np.meshgrid, for just
+    A special-cased implementation of num.meshgrid, for just
     two arguments. Found to be about 3x faster on some simple
     test arguments.
     """
@@ -877,7 +877,7 @@ def _normalize_ranges(starts, stops, offset, ccw=False):
     if ccw:
         starts, stops = stops, starts
 
-    # results are in the range of [0, 2*np.pi]
+    # results are in the range of [0, 2*num.pi]
     if not num.all(starts < stops):
         raise ValueError('Invalid angle ranges')
 

hexrd/xrd/xrdutil.py

@@ -4143,7 +4143,7 @@ def pullSpots(pd, detector_params, grain_params, reader,
                 f1 = rdr.read(nframes=len(oidx1), nskip=oidx1[0])
                 r2 = rdr.makeNew()
                 f2 = r2.read(nframes=len(oidx2), nskip=oidx2[0])
-                frames = num.zeros(sdims, dtype=f1.dtype)
+                frames = num.zeros((sdims[0], reader.get_nrows(), reader.get_ncols()), dtype=f1.dtype)
                 frames[:len(oidx1), :, :] = f1
                 frames[len(oidx1):, :, :] = f2
             else:
@@ -4281,7 +4281,7 @@ def pullSpots(pd, detector_params, grain_params, reader,
         # output dictionary
         if save_spot_list:
             w_dict = {}
-            w_dict['peakID']        = peakID
+            w_dict['peakId']        = peakId
             w_dict['hkl']           = hkl
             w_dict['dims']          = sdims
             w_dict['points']        = ( angs[2] + d2r*ome_del,
@@ -4291,7 +4291,7 @@ def pullSpots(pd, detector_params, grain_params, reader,
             w_dict['crd']           = xy_eval
             w_dict['con']           = conn
             w_dict['refl_ang_com']  = com_angs
-            if peakID >= 0:
+            if peakId >= 0:
                 w_dict['refl_xyo']  = (new_xy[0], new_xy[1], com_angs[2])
             else:
                 w_dict['refl_xyo']  = tuple(num.nan*num.ones(3))
@@ -4321,7 +4321,7 @@ def pullSpots(pd, detector_params, grain_params, reader,
             pass
         iRefl += 1
         pass
-    fid.close()
+    if filename is not None: fid.close()
 
     return spot_list