updates'

py4DSTEM/__init__.py

@@ -1,60 +1,34 @@
 from py4DSTEM.version import __version__
-from emdfile import tqdmnd
-
 
-### Utility functions
+# Utilities
+from emdfile import tqdmnd
 from py4DSTEM.utils import *
-
-### IO substructure
-from emdfile import (
-    Node,
-    Root,
-    Metadata,
-    Array,
-    PointList,
-    PointListArray,
-    Custom,
-    print_h5_tree,
-)
+# IO
+from emdfile import (Node,Root,Metadata,Array,PointList,PointListArray,Custom,
+    print_h5_tree,)
 _emd_hook = True
-
-# IO structure
 from py4DSTEM import io
 from py4DSTEM.io import import_file, read, save
-
-### Basic data classes
-from py4DSTEM.data import (
-    Data,
-    Calibration,
-    DiffractionSlice,
-    RealSlice,
-    QPoints,
-)
-
-### Visualization
+### CLASSES
+# Data
+from py4DSTEM.data import (Data,Calibration,DiffractionSlice,RealSlice,QPoints,)
+# Visualization
 from py4DSTEM import visualize
 from py4DSTEM.visualize import show, show_complex
-
 # Analysis classes
-from py4DSTEM.datacube import DataCube
-from py4DSTEM.datacube import VirtualImage, VirtualDiffraction
+from py4DSTEM.datacube import DataCube,VirtualImage,VirtualDiffraction
 from py4DSTEM.datacube.diskdetection import Probe
 from py4DSTEM.braggvectors import BraggVectors, BraggVectorMap
-from py4DSTEM.process import classification
+from py4DSTEM.clustering import ACCHOO, VoronoiClustering
 from py4DSTEM.process.diffraction import Crystal, Orientation
 from py4DSTEM.process import phase
 from py4DSTEM.process.polar import PolarDatacube
 from py4DSTEM.process.strain.strain import StrainMap
 from py4DSTEM.process import wholepatternfit
-from py4DSTEM.acchoo import ACCHOO
-
-
 ### Config
 from py4DSTEM.utils.configuration_checker import check_config
 # TODO - config .toml
-
 # testing
 from os.path import dirname, join
-
 _TESTPATH = join(dirname(__file__), "../test/unit_test_data")
 

py4DSTEM/clustering/__init__.py

@@ -0,0 +1,5 @@
+from py4DSTEM.clustering.acchoo import ACCHOO
+from py4DSTEM.clustering.voronoiclustering import *
+from py4DSTEM.clustering.classutils import *
+from py4DSTEM.clustering.featurization import *
+

py4DSTEM/acchoo/acchoo.py → py4DSTEM/clustering/acchoo.py

@@ -106,16 +106,6 @@ def __init__(
             threshold intensity for data points to be counted as 'empty' or not
         min_inten : bool
             data inclusion intensity threshold
-        #dist_frac_tol : number
-        #    data points which are just over a voronoi ridge from a masked to an
-        #    unmasked channel may be ignored if the distance fraction
-        #    (dist_to_masked_vor_point / dis_to_unmasked_vor_point) is under this
-        #    threshold tolerance. 1 (default) is no tolerance; 1.05 means if the
-        #    distance to the closest masked seed is within 5% of the closest
-        #    unmasked seed distance, the point is disregarded
-        #numb_frac_tol : number
-        #    unmasked data points will be ignored unless their fraction of the total
-        #    number of points is greater than numb_frac_tol
         seed_picker : str in 'max' or 'most' or 'random' or 'front' or 'back'
             strategy for choosing crystal seed points
         num_lowq : int
@@ -225,7 +215,7 @@ def get_kpoints(self, p, vp={}, show=True):
         self._voronoi_vertices = get_voronoi_vertices(
             self._voronoi, self.d.Qshape[0], self.d.Qshape[1])
         # show
-        print(f"Identified {len(ans)} points")
+        print(f"Identified {len(ans)} diffraction maxima; setting up voronoi channel data basis.")
         if show:
             show_points(
                 self.bvm,
@@ -280,6 +270,17 @@ def _seedloop(self):
                 print(f'Setting out at seed {seed}!')
             self._new_path(seed)
             return True
+        # pick a seed from a seeded pixel
+        elif np.sum(self.labels==3)>0:
+            loop = np.sum(self.labels==3)>0
+            while loop:
+                seed = self._pick_seeded_seed(seed_picker=self.seed_picker)
+                if self._verbose:
+                    print(f'setting out at a merged seed path at seed {seed}')
+                self._reset_path_vars()
+                loop = self._seeded_path(seed)
+                loop = np.sum(self.labels==3)>0
+                pass
         # are we done?
         else:
             if self._verbose:
@@ -329,29 +330,31 @@ def _new_path(self,seed):
             loop = self._xtal_search_loop(seed)
             if self._verbose:
                 print(f"Found {len(self._crystals_curr)} crystals: {self._crystals_curr}")
+                if loop:
+                    print("Score still above threshold, continuing search...")
+                else:
+                    print("Score satisfies threshold, exiting crystal search loop.")
         # loop - walk
         self._put_on_shoes_and_coat(seed)
         # finalize current path
         self._finalize_path_and_update_crystals(seed)
-        # enter seeded path loops
-        loop = np.sum(self.labels==3)>0
-        while loop:
-            seed = self._pick_seeded_seed(seed_picker=self.seed_picker)
-            if self._verbose:
-                print(f'setting out at a merged seed path at seed {seed}')
-            self._reset_path_vars()
-            loop = self._seeded_path(seed)
-            loop = np.sum(self.labels==3)>0
-            pass
+#        # enter seeded path loops
+#        loop = np.sum(self.labels==3)>0
+#        while loop:
+#            seed = self._pick_seeded_seed(seed_picker=self.seed_picker)
+#            if self._verbose:
+#                print(f'setting out at a merged seed path at seed {seed}')
+#            self._reset_path_vars()
+#            loop = self._seeded_path(seed)
+#            loop = np.sum(self.labels==3)>0
+#            pass
         if self._verbose:
             print("Exiting _new_path...")
         pass
 
     def _xtal_search_loop(self,seed):
         """ Find a crystal set and mask, then _put_on_shoes_and_coat
         """
-        if self._vv:
-            print('Commencing crystal search...')
         x,y,inten = self._data_curr
         channels = self._data_channels_curr
         # prepare boolean mask
@@ -372,7 +375,8 @@ def _xtal_search_loop(self,seed):
         for idx,channel in enumerate(channels):
             if channels[idx] in self._b_opts_curr:
                 m[idx] = 0 # don't pick current opts
-        self._get_b_next_opts(m)
+        if len(x[m])>0:
+            self._get_b_next_opts(m)
         crystal_opts, mask_opts = self._get_crystal_opts_curr()
         self._score_crystal_options_and_update(crystal_opts,mask_opts)
         # are we done?
@@ -512,7 +516,8 @@ def _xtal_search_seeded_internalloop(self,seed):
         # first get basis vector options & new crystal options
         # then compute permutation scores and update vars
         self._crystals_n_opts += 1
-        self._get_b_next_opts(m)
+        if len(x[m])>0:
+            self._get_b_next_opts(m)
         crystal_opts, mask_opts = self._get_crystal_opts_curr()
         # merge new and existing xtal masks
         self._score_crystal_options_and_update_addxtal(crystal_opts,mask_opts)
@@ -891,8 +896,6 @@ def _get_crystal_opts_curr(self):
         # return
         return crystals_opts, masks_opts
 
-    ### Misc. Utilities ###
-
     # data
     def _get_data(self,seed):
         data = self.d.cal[seed[0],seed[1]]