small bug fixes

Author: joelvbernier

hexrd/cli/findorientations.py

@@ -81,7 +81,7 @@ def execute(args, parser):
 
     # prepare the analysis directory
     quats_f = os.path.join(cfg.working_dir, 'accepted_orientations.dat')
-    if os.path.exists(quats_f) and not args.force:
+    if os.path.exists(quats_f) and not (args.force or args.clean):
         logger.error(
             '%s already exists. Change yml file or specify "force"', quats_f
             )
@@ -111,7 +111,7 @@ def execute(args, parser):
         pr.enable()
 
     # process the data
-    find_orientations(cfg, hkls=args.hkls, profile=args.profile)
+    find_orientations(cfg, hkls=args.hkls, clean=args.clean, profile=args.profile)
 
     if args.profile:
         pr.disable()

hexrd/findorientations.py

@@ -203,9 +203,10 @@ def quat_distance(x, y):
                 min_samples=min_samples,
                 metric='precomputed'
                 )
+            cl = np.array(labels, dtype=int) # convert to array
             noise_points = cl == -1 # index for marking noise
-            cl = np.array(labels, dtype=int) + 1 # move index to 1
-            cl[noise_points] = -1 # re-mark noise
+            cl += 1 # move index to 1-based instead of 0
+            cl[noise_points] = -1 # re-mark noise as -1
             logger.info("dbscan found %d noise points", sum(noise_points))
         elif algorithm == 'fclusterdata':
             cl = cluster.hierarchy.fclusterdata(
@@ -242,24 +243,28 @@ def quat_distance(x, y):
     return np.atleast_2d(qbar), cl
 
 
-def load_eta_ome_maps(cfg, pd, reader, detector, hkls=None):
+def load_eta_ome_maps(cfg, pd, reader, detector, hkls=None, clean=False):
     fn = os.path.join(
         cfg.working_dir,
         cfg.find_orientations.orientation_maps.file
         )
-    try:
-        res = cPickle.load(open(fn, 'r'))
-        pd = res.planeData
-        available_hkls = pd.hkls.T
-        logger.info('loaded eta/ome orientation maps from %s', fn)
-        hkls = [str(i) for i in available_hkls[res.iHKLList]]
-        logger.info(
-            'hkls used to generate orientation maps: %s', hkls)
-        return res
-    except (AttributeError, IOError):
+    
+    if not clean:
+        try:
+            res = cPickle.load(open(fn, 'r'))
+            pd = res.planeData
+            available_hkls = pd.hkls.T
+            logger.info('loaded eta/ome orientation maps from %s', fn)
+            hkls = [str(i) for i in available_hkls[res.iHKLList]]
+            logger.info(
+                'hkls used to generate orientation maps: %s', hkls)
+            return res
+        except (AttributeError, IOError):
+            return generate_eta_ome_maps(cfg, pd, reader, detector, hkls)
+    else:
+        logger.info('clean option specified; recomputing eta/ome orientation maps')
         return generate_eta_ome_maps(cfg, pd, reader, detector, hkls)
 
-
 def generate_eta_ome_maps(cfg, pd, reader, detector, hkls=None):
 
     available_hkls = pd.hkls.T
@@ -303,7 +308,7 @@ def generate_eta_ome_maps(cfg, pd, reader, detector, hkls=None):
     return eta_ome
 
 
-def find_orientations(cfg, hkls=None, profile=False):
+def find_orientations(cfg, hkls=None, clean=False, profile=False):
     """
     Takes a config dict as input, generally a yml document
 
@@ -338,7 +343,7 @@ def find_orientations(cfg, hkls=None, profile=False):
     logger.info("beginning analysis '%s'", cfg.analysis_name)
 
     # load the eta_ome orientation maps
-    eta_ome = load_eta_ome_maps(cfg, pd, reader, detector, hkls)
+    eta_ome = load_eta_ome_maps(cfg, pd, reader, detector, hkls=hkls, clean=clean)
 
     ome_range = (np.min(eta_ome.omeEdges),
                  np.max(eta_ome.omeEdges)