diff --git a/py4DSTEM/__init__.py b/py4DSTEM/__init__.py
index adf757d1b..d5df63f5e 100644
--- a/py4DSTEM/__init__.py
+++ b/py4DSTEM/__init__.py
@@ -52,17 +52,25 @@
     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
 
-# TODO - crystal
-# TODO - ptycho
-# TODO - others
-
-# TODO - where
-from py4DSTEM.process import (
-    PolarDatacube,
-)
+from py4DSTEM.process import wholepatternfit
 
 
 ### more submodules
diff --git a/py4DSTEM/braggvectors/diskdetection_aiml.py b/py4DSTEM/braggvectors/diskdetection_aiml.py
index abcb70291..4d23ebf6c 100644
--- a/py4DSTEM/braggvectors/diskdetection_aiml.py
+++ b/py4DSTEM/braggvectors/diskdetection_aiml.py
@@ -559,7 +559,7 @@ def find_Bragg_disks_aiml(
     model_path=None,
     distributed=None,
     CUDA=True,
-    **kwargs
+    **kwargs,
 ):
     """
     Finds the Bragg disks in all diffraction patterns of datacube by AI/ML method. This method
diff --git a/py4DSTEM/braggvectors/diskdetection_aiml_cuda.py b/py4DSTEM/braggvectors/diskdetection_aiml_cuda.py
index 64a43156a..d23770586 100644
--- a/py4DSTEM/braggvectors/diskdetection_aiml_cuda.py
+++ b/py4DSTEM/braggvectors/diskdetection_aiml_cuda.py
@@ -265,7 +265,7 @@ def _find_Bragg_disks_aiml_single_DP_CUDA(
     blocks=None,
     threads=None,
     model_path=None,
-    **kwargs
+    **kwargs,
 ):
     """
     Finds the Bragg disks in single DP by AI/ML method. This method utilizes FCU-Net
diff --git a/py4DSTEM/braggvectors/diskdetection_parallel_new.py b/py4DSTEM/braggvectors/diskdetection_parallel_new.py
index ddfc93049..dccc0dd4b 100644
--- a/py4DSTEM/braggvectors/diskdetection_parallel_new.py
+++ b/py4DSTEM/braggvectors/diskdetection_parallel_new.py
@@ -100,7 +100,7 @@ def beta_parallel_disk_detection(
     close_dask_client=False,
     return_dask_client=True,
     *args,
-    **kwargs
+    **kwargs,
 ):
     """
     This is not fully validated currently so may not work, please report bugs on the py4DSTEM github page.
@@ -225,7 +225,7 @@ def beta_parallel_disk_detection(
             probe_kernel_FT=dask_probe_delayed[0, 0],
             # probe_kernel_FT=delayed_probe_kernel_FT,
             *args,
-            **kwargs
+            **kwargs,
         )  # passing through args from earlier or should I use
         # corrPower=corrPower,
         # sigma=sigma_gaussianFilter,
diff --git a/py4DSTEM/io/filereaders/read_mib.py b/py4DSTEM/io/filereaders/read_mib.py
index 079c9d1bd..7456bd594 100644
--- a/py4DSTEM/io/filereaders/read_mib.py
+++ b/py4DSTEM/io/filereaders/read_mib.py
@@ -14,7 +14,7 @@ def load_mib(
     reshape=True,
     flip=True,
     scan=(256, 256),
-    **kwargs
+    **kwargs,
 ):
     """
     Read a MIB file and return as py4DSTEM DataCube.
diff --git a/py4DSTEM/process/diffraction/crystal_viz.py b/py4DSTEM/process/diffraction/crystal_viz.py
index f7837695a..94cf75b8c 100644
--- a/py4DSTEM/process/diffraction/crystal_viz.py
+++ b/py4DSTEM/process/diffraction/crystal_viz.py
@@ -2093,7 +2093,7 @@ def plot_ring_pattern(
     figsize=(10, 10),
     returnfig=False,
     input_fig_handle=None,
-    **kwargs
+    **kwargs,
 ):
     """
     2D plot of diffraction rings
diff --git a/py4DSTEM/visualize/show.py b/py4DSTEM/visualize/show.py
index fcc05777e..8462eec7d 100644
--- a/py4DSTEM/visualize/show.py
+++ b/py4DSTEM/visualize/show.py
@@ -77,7 +77,7 @@ def show(
     title=None,
     show_fft=False,
     show_cbar=False,
-    **kwargs
+    **kwargs,
 ):
     """
     General visualization function for 2D arrays.
@@ -904,7 +904,7 @@ def show_Q(
     gridlabelsize=12,
     gridlabelcolor="k",
     alpha=0.35,
-    **kwargs
+    **kwargs,
 ):
     """
     Shows a diffraction space image with options for several overlays to define the scale,
@@ -1144,7 +1144,7 @@ def show_rectangles(
     alpha=0.25,
     linewidth=2,
     returnfig=False,
-    **kwargs
+    **kwargs,
 ):
     """
     Visualization function which plots a 2D array with one or more overlayed rectangles.
@@ -1197,7 +1197,7 @@ def show_circles(
     alpha=0.3,
     linewidth=2,
     returnfig=False,
-    **kwargs
+    **kwargs,
 ):
     """
     Visualization function which plots a 2D array with one or more overlayed circles.
@@ -1252,7 +1252,7 @@ def show_ellipses(
     alpha=0.3,
     linewidth=2,
     returnfig=False,
-    **kwargs
+    **kwargs,
 ):
     """
     Visualization function which plots a 2D array with one or more overlayed ellipses.
@@ -1308,7 +1308,7 @@ def show_annuli(
     alpha=0.3,
     linewidth=2,
     returnfig=False,
-    **kwargs
+    **kwargs,
 ):
     """
     Visualization function which plots a 2D array with one or more overlayed annuli.
@@ -1360,7 +1360,7 @@ def show_points(
     open_circles=False,
     title=None,
     returnfig=False,
-    **kwargs
+    **kwargs,
 ):
     """
     Plots a 2D array with one or more points.
diff --git a/py4DSTEM/visualize/vis_RQ.py b/py4DSTEM/visualize/vis_RQ.py
index 6c2fbff3c..85c0eb042 100644
--- a/py4DSTEM/visualize/vis_RQ.py
+++ b/py4DSTEM/visualize/vis_RQ.py
@@ -15,7 +15,7 @@ def show_selected_dp(
     pointsize=50,
     pointcolor="r",
     scaling="log",
-    **kwargs
+    **kwargs,
 ):
     """ """
     dp = datacube.data[rx, ry, :, :]
diff --git a/py4DSTEM/visualize/vis_special.py b/py4DSTEM/visualize/vis_special.py
index acacb6184..c1e9d6b19 100644
--- a/py4DSTEM/visualize/vis_special.py
+++ b/py4DSTEM/visualize/vis_special.py
@@ -31,7 +31,7 @@ def show_elliptical_fit(
     linewidth_ann=2,
     linewidth_ell=2,
     returnfig=False,
-    **kwargs
+    **kwargs,
 ):
     """
     Plots an elliptical curve over its annular fit region.
@@ -97,7 +97,7 @@ def show_amorphous_ring_fit(
     ellipse_alpha=0.7,
     ellipse_lw=2,
     returnfig=False,
-    **kwargs
+    **kwargs,
 ):
     """
     Display a diffraction pattern with a fit to its amorphous ring, interleaving
@@ -225,7 +225,7 @@ def show_qprofile(
     ticklabelsize=14,
     grid=True,
     label=None,
-    **kwargs
+    **kwargs,
 ):
     """
     Plots a diffraction space radial profile.
@@ -302,7 +302,7 @@ def show_voronoi(
     color_lines="w",
     max_dist=None,
     returnfig=False,
-    **kwargs
+    **kwargs,
 ):
     """
     words
@@ -375,7 +375,7 @@ def show_class_BPs_grid(
     axsize=(6, 6),
     titlesize=0,
     get_bordercolor=None,
-    **kwargs
+    **kwargs,
 ):
     """
     words
@@ -430,7 +430,7 @@ def select_point(
     color_selected="r",
     size=20,
     returnfig=False,
-    **kwargs
+    **kwargs,
 ):
     """
     Show enumerated index labels for a set of points, with one selected point highlighted
@@ -555,7 +555,7 @@ def show_selected_dps(
     HW=None,
     figsize_im=(6, 6),
     figsize_dp=(4, 4),
-    **kwargs
+    **kwargs,
 ):
     """
     Shows two plots: first, a real space image overlaid with colored dots
@@ -718,7 +718,7 @@ def show_complex(
     pixelunits="pixels",
     pixelsize=1,
     returnfig=False,
-    **kwargs
+    **kwargs,
 ):
     """
     Function to plot complex arrays