HRTEM normalization issue and 4D-STEM hdf5 issue rectified

HamishGBrown · Oct 30, 2020 · 96c98e2 · 96c98e2
1 parent 0ee2a89
commit 96c98e2
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Showing 3 changed files with 6 additions and 5 deletions.
diff --git a/pyms/Premixed_routines.py b/pyms/Premixed_routines.py
@@ -752,9 +752,11 @@ def STEM_multislice(
         DPshape, _, Ksize = workout_4DSTEM_datacube_DP_size(
             FourD_STEM, real_dim, gridshape
         )
-        scanshape = generate_STEM_raster(
-            real_dim, eV, app, tiling=tiling, ROI=ROI
-        ).shape[:-1]
+        if scan_posn is None:
+            scan_posn = generate_STEM_raster(
+                real_dim, eV, app, tiling=tiling, ROI=ROI
+            )
+        scanshape = scan_posn.shape[:-1]
         Rpix = nyquist_sampling(eV=eV, alpha=app)
 
         # Make a datacube for each thickness of interest

diff --git a/pyms/py_multislice.py b/pyms/py_multislice.py
@@ -982,7 +982,6 @@ def STEM(
         probes = complex_mul(probe_.view(1, *probe_.size()), probes)
 
         # Thickness series
-        #  - need to take the difference between sequential thickness variations
         for it, t in enumerate(nslices_):
 
             # Evaluate exit surface wave function from input probes

diff --git a/pyms/utils/torch_utils.py b/pyms/utils/torch_utils.py
@@ -432,7 +432,7 @@ def crop_to_bandwidth_limit_torch(
     limit=2 / 3,
     qspace_in=True,
     qspace_out=True,
-    norm="conserve_L2",
+    norm="conserve_norm",
 ):
     """Crop an array to its bandwidth limit (remove superfluous array entries)."""
     # Check if array is complex or not