Adding moire lattices

py4DSTEM/__init__.py

@@ -1,6 +1,11 @@
 from py4DSTEM.version import __version__
 from emdfile import tqdmnd
 
+# test paths
+from os.path import dirname,join
+_TESTPATH = join(dirname(__file__), "test/unit_test_data")
+
+
 
 ### io
 
@@ -79,7 +84,16 @@
 
 # TODO - config .toml
 
+# <<<<<<< HEAD
+
+
+# classes
+
+# from py4DSTEM.process.diffraction import Crystal
+
+# =======
 # testing
 from os.path import dirname, join
 
 _TESTPATH = join(dirname(__file__), "../test/unit_test_data")
+# >>>>>>> dev

py4DSTEM/braggvectors/diskdetection.py

@@ -553,8 +553,12 @@ def _find_Bragg_disks_CUDA_unbatched(
  )
 
  # Populate a BraggVectors instance and return
- braggvectors = BraggVectors(datacube.Rshape, datacube.Qshape)
- braggvectors._v_uncal = peaks
+ braggvectors = BraggVectors(
+ datacube.Rshape,
+ datacube.Qshape,
+ name = peaks.name)
+ braggvectors.set_raw_vectors(peaks)
+
  return braggvectors
 
 
@@ -598,8 +602,12 @@ def _find_Bragg_disks_CUDA_batched(
  )
 
  # Populate a BraggVectors instance and return
- braggvectors = BraggVectors(datacube.Rshape, datacube.Qshape)
- braggvectors._v_uncal = peaks
+ braggvectors = BraggVectors(
+ datacube.Rshape,
+ datacube.Qshape,
+ name = peaks.name)
+ braggvectors.set_raw_vectors(peaks)
+
  return braggvectors
 
 

py4DSTEM/datacube/virtualimage.py

@@ -314,15 +314,15 @@ def position_detector(
  self,
  mode,
  geometry,
- data=None,
- centered=None,
- calibrated=None,
- shift_center=False,
- scan_position=None,
- invert=False,
- color="r",
- alpha=0.7,
- **kwargs,
+ data = None,
+ centered = None,
+ calibrated = None,
+ shift_center = False,
+ scan_position = None,
+ invert = False,
+ color = 'c',
+ alpha = 0.7,
+ **kwargs
  ):
  """
  Position a virtual detector by displaying a mask over a diffraction

py4DSTEM/preprocess/preprocess.py

@@ -209,6 +209,20 @@ def bin_data_diffraction(datacube, bin_factor, dtype=None):
  Qpixsize = datacube.calibration.get_Q_pixel_size() * bin_factor
  Qpixunits = datacube.calibration.get_Q_pixel_units()
 
+ # set dims
+ datacube.set_dim(
+ 2,
+ [0,Qpixsize],
+ units = Qpixunits,
+ name = 'Qx'
+ )
+ datacube.set_dim(
+ 3,
+ [0,Qpixsize],
+ units = Qpixunits,
+ name = 'Qy'
+ )
+
  datacube.set_dim(2, [0, Qpixsize], units=Qpixunits, name="Qx")
  datacube.set_dim(3, [0, Qpixsize], units=Qpixunits, name="Qy")