resolve ben/v15->py4dstem/dev conflicts

py4DSTEM/__init__.py

@@ -2,9 +2,10 @@
 from emdfile import tqdmnd
 
 
-### io
+### Utility functions
+from py4DSTEM.utils import *
 
-# substructure
+### IO substructure
 from emdfile import (
     Node,
     Root,
@@ -15,17 +16,13 @@
     Custom,
     print_h5_tree,
 )
-
 _emd_hook = True
 
-# structure
+# IO structure
 from py4DSTEM import io
 from py4DSTEM.io import import_file, read, save
 
-
-### basic data classes
-
-# data
+### Basic data classes
 from py4DSTEM.data import (
     Data,
     Calibration,
@@ -34,60 +31,29 @@
     QPoints,
 )
 
-# datacube
-from py4DSTEM.datacube import DataCube, VirtualImage, VirtualDiffraction
-
-
-### visualization
-
+### Visualization
 from py4DSTEM import visualize
 from py4DSTEM.visualize import show, show_complex
 
-### analysis classes
-
-# braggvectors
-from py4DSTEM.braggvectors import (
-    Probe,
-    BraggVectors,
-    BraggVectorMap,
-)
-
+# Analysis classes
+from py4DSTEM.datacube import DataCube
+from py4DSTEM.datacube import VirtualImage, VirtualDiffraction
+from py4DSTEM.datacube.diskdetection import Probe
+from py4DSTEM.braggvectors import BraggVectors, BraggVectorMap
 from py4DSTEM.process import classification
-
-
-# diffraction
 from py4DSTEM.process.diffraction import Crystal, Orientation
-
-
-# ptycho
 from py4DSTEM.process import phase
-
-
-# polar
 from py4DSTEM.process.polar import PolarDatacube
-
-
-# strain
 from py4DSTEM.process.strain.strain import StrainMap
-
 from py4DSTEM.process import wholepatternfit
 
 
-### more submodules
-# TODO
-
-from py4DSTEM import preprocess
-from py4DSTEM import process
-
-
-### utilities
-
-# config
+### 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/braggvectors/__init__.py

@@ -1,8 +1,5 @@
-from py4DSTEM.braggvectors.probe import Probe
 from py4DSTEM.braggvectors.braggvectors import BraggVectors
 from py4DSTEM.braggvectors.braggvector_methods import BraggVectorMap
-from py4DSTEM.braggvectors.diskdetection import *
-from py4DSTEM.braggvectors.probe import *
 
 # from .diskdetection_aiml import *
 # from .diskdetection_parallel_new import *

py4DSTEM/braggvectors/braggvector_methods.py

@@ -2,13 +2,15 @@
 from __future__ import annotations
 import inspect
 from warnings import warn
-
+from scipy.ndimage import gaussian_filter
 import matplotlib.pyplot as plt
 import numpy as np
+
 from emdfile import Array, Metadata, _read_metadata, tqdmnd
 from py4DSTEM import show
+from py4DSTEM.utils import get_CoM
 from py4DSTEM.datacube import VirtualImage
-from scipy.ndimage import gaussian_filter
+
 
 
 class BraggVectorMethods:
@@ -384,8 +386,6 @@ def measure_origin(
                     np.argmax(gaussian_filter(bvm, 10)), (Q_Nx, Q_Ny)
                 )
             else:
-                from py4DSTEM.process.utils import get_CoM
-
                 x0, y0 = get_CoM(bvm)
         else:
             x0, y0 = center_guess

py4DSTEM/datacube/__init__.py

@@ -3,3 +3,5 @@
 from py4DSTEM.datacube.datacube import DataCube
 from py4DSTEM.datacube.virtualimage import VirtualImage
 from py4DSTEM.datacube.virtualdiffraction import VirtualDiffraction
+from py4DSTEM.datacube.diskdetection.probe import Probe
+

py4DSTEM/datacube/datacube.py

@@ -8,21 +8,27 @@
     distance_transform_edt,
     binary_fill_holes,
     gaussian_filter1d,
-    gaussian_filter,
-)
+    gaussian_filter,)
 from typing import Optional, Union
 
 from emdfile import Array, Metadata, Node, Root, tqdmnd
 from py4DSTEM.data import Data, Calibration
-from py4DSTEM.datacube.virtualimage import DataCubeVirtualImager
-from py4DSTEM.datacube.virtualdiffraction import DataCubeVirtualDiffraction
+from py4DSTEM.datacube.preprocess import Preprocessor
+from py4DSTEM.datacube.virtualimage import VirtualImager
+from py4DSTEM.datacube.virtualdiffraction import VirtualDiffractioner
+from py4DSTEM.datacube.diskdetection import BraggFinder
+from py4DSTEM.datacube.diskdetection import ProbeMaker
+
 
 
 class DataCube(
     Array,
     Data,
-    DataCubeVirtualImager,
-    DataCubeVirtualDiffraction,
+    Preprocessor,
+    VirtualImager,
+    VirtualDiffractioner,
+    BraggFinder,
+    ProbeMaker,
 ):
     """
     Storage and processing methods for 4D-STEM datasets.
@@ -304,16 +310,6 @@ def add(self, data, name=""):
         if isinstance(data, np.ndarray):
             data = Array(data=data, name=name)
         self.attach(data)
-
-    def set_scan_shape(self, Rshape):
-        """
-        Reshape the data given the real space scan shape.
-
-        Accepts:
-            Rshape (2-tuple)
-        """
-        from py4DSTEM.preprocess import set_scan_shape
-
         assert len(Rshape) == 2, "Rshape must have a length of 2"
         d = set_scan_shape(self, Rshape[0], Rshape[1])
         return d
@@ -1342,3 +1338,4 @@ def get_braggmask(self, braggvectors, rx, ry, radius):
             qr = np.hypot(self.qxx_raw - vects.qx[idx], self.qyy_raw - vects.qy[idx])
             mask = np.logical_and(mask, qr > radius)
         return mask
+

py4DSTEM/datacube/diskdetection/__init__.py

@@ -0,0 +1,5 @@
+
+from py4DSTEM.datacube.diskdetection.probe import Probe,ProbeMaker
+from py4DSTEM.datacube.diskdetection.braggfinder import BraggFinder
+
+