From 460386017ce38eb1a187d55d398fcb93068e650b Mon Sep 17 00:00:00 2001
From: bsavitzky <ben.savitzky@gmail.com>
Date: Tue, 14 Nov 2023 12:23:18 -0800
Subject: [PATCH 01/16] fixes polar transform docstring

---
 py4DSTEM/process/polar/polar_datacube.py | 36 ++++++++++++++++++------
 1 file changed, 28 insertions(+), 8 deletions(-)

diff --git a/py4DSTEM/process/polar/polar_datacube.py b/py4DSTEM/process/polar/polar_datacube.py
index 56071c534..4c06d4c09 100644
--- a/py4DSTEM/process/polar/polar_datacube.py
+++ b/py4DSTEM/process/polar/polar_datacube.py
@@ -292,16 +292,36 @@ def transform(self):
             these values directly. Length 2 list of ints uses the calibrated
             origin value at this scan position. None uses the calibrated mean
             origin.
+        ellipse : tuple or None
+            Variable behavior depending on the arg type. Length 3 tuples uses
+            these values directly (a,b,theta). None uses the calibrated value.
         mask : boolean array or None
             A mask applied to the data before transformation.  The value of
-            masked pixels (0's) in the output is determined by `returnval`. Note
-            that this mask is applied in combination with any mask at
-            PolarData.mask.
-        returnval : 'masked' or 'nan' or None
-            Controls the returned data. 'masked' returns a numpy masked array.
-            'nan' returns a normal numpy array with masked pixels set to np.nan.
-            None returns a 2-tuple of numpy arrays - the transformed data with
-            masked pixels set to 0, and the transformed mask.
+            masked pixels in the output is determined by `returnval`. Note that
+            this mask is applied in combination with any mask at PolarData.mask.
+        mask_thresh : number
+            Pixels in the transformed mask with values below this number are
+            considered masked, and will be populated by the values specified
+            by `returnval`.
+        returnval : 'masked' or 'nan' or 'all' or 'zeros' or 'all_zeros'
+            Controls the returned data, including how un-sampled points
+            are handled.
+              - 'masked' returns a numpy masked array.
+              - 'nan' returns a normal numpy array with unsampled pixels set to
+                np.nan.
+              - 'all' returns a 4-tuple of numpy arrays - the transformed data
+                with unsampled pixels set to 'nan', the normalization array, the
+                normalization array scaled to account for the q-dependent
+                sampling density, and the polar boolean mask
+              - 'zeros' returns a normal numpy with unsampled pixels set to 0
+              - 'all_zeros' returns the same 4-tuple as 'all', but with unsampled
+                pixels in the transformed data array set to zeros.
+
+         Returns
+        --------
+        variable
+            see `returnval`, above. Default is a masked array representing
+            the polar transformed data.
         """
         return self._polar_data_getter._transform
 

From 079d4b989bb73799d69cd747c920022a5b2953c3 Mon Sep 17 00:00:00 2001
From: Stephanie Ribet <stephanie.ribet@gmail.com>
Date: Tue, 14 Nov 2023 18:02:03 -0800
Subject: [PATCH 02/16] filter_2D_maxima

---
 py4DSTEM/preprocess/utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/py4DSTEM/preprocess/utils.py b/py4DSTEM/preprocess/utils.py
index 829f66608..752e2f81c 100644
--- a/py4DSTEM/preprocess/utils.py
+++ b/py4DSTEM/preprocess/utils.py
@@ -293,7 +293,7 @@ def filter_2D_maxima(
     if minSpacing > 0:
         deletemask = np.zeros(len(maxima), dtype=bool)
         for i in range(len(maxima)):
-            if deletemask[i] is False:
+            if deletemask[i] == False:
                 tooClose = (
                     (maxima["x"] - maxima["x"][i]) ** 2
                     + (maxima["y"] - maxima["y"][i]) ** 2

From d0c8a2a8b35d91218045b275e6fbefe9b873bf7b Mon Sep 17 00:00:00 2001
From: alex-rakowski <alexrakowski90@gmail.com>
Date: Tue, 14 Nov 2023 18:38:47 -0800
Subject: [PATCH 03/16] deletemask[i] == False

---
 py4DSTEM/braggvectors/diskdetection_aiml_cuda.py | 2 +-
 py4DSTEM/braggvectors/diskdetection_cuda.py      | 2 +-
 py4DSTEM/braggvectors/threshold.py               | 4 ++--
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/py4DSTEM/braggvectors/diskdetection_aiml_cuda.py b/py4DSTEM/braggvectors/diskdetection_aiml_cuda.py
index d23770586..95e1ef0cb 100644
--- a/py4DSTEM/braggvectors/diskdetection_aiml_cuda.py
+++ b/py4DSTEM/braggvectors/diskdetection_aiml_cuda.py
@@ -496,7 +496,7 @@ def get_maxima_2D_cp(
         if minSpacing > 0:
             deletemask = np.zeros(len(maxima), dtype=bool)
             for i in range(len(maxima)):
-                if deletemask[i] is False:
+                if deletemask[i] == False:  # noqa: E712
                     tooClose = (
                         (maxima["x"] - maxima["x"][i]) ** 2
                         + (maxima["y"] - maxima["y"][i]) ** 2
diff --git a/py4DSTEM/braggvectors/diskdetection_cuda.py b/py4DSTEM/braggvectors/diskdetection_cuda.py
index 670361b3b..19e1d0c10 100644
--- a/py4DSTEM/braggvectors/diskdetection_cuda.py
+++ b/py4DSTEM/braggvectors/diskdetection_cuda.py
@@ -482,7 +482,7 @@ def get_maxima_2D(
         if minSpacing > 0:
             deletemask = np.zeros(len(maxima), dtype=bool)
             for i in range(len(maxima)):
-                if deletemask[i] is False:
+                if deletemask[i] == False:  # noqa: E712
                     tooClose = (
                         (maxima["x"] - maxima["x"][i]) ** 2
                         + (maxima["y"] - maxima["y"][i]) ** 2
diff --git a/py4DSTEM/braggvectors/threshold.py b/py4DSTEM/braggvectors/threshold.py
index c6c1c4afc..4cc4c98ec 100644
--- a/py4DSTEM/braggvectors/threshold.py
+++ b/py4DSTEM/braggvectors/threshold.py
@@ -52,7 +52,7 @@ def threshold_Braggpeaks(
             r2 = minPeakSpacing**2
             deletemask = np.zeros(pointlist.length, dtype=bool)
             for i in range(pointlist.length):
-                if deletemask[i] is False:
+                if deletemask[i] == False:  # noqa: E712
                     tooClose = (
                         (pointlist.data["qx"] - pointlist.data["qx"][i]) ** 2
                         + (pointlist.data["qy"] - pointlist.data["qy"][i]) ** 2
@@ -160,7 +160,7 @@ def universal_threshold(
             r2 = minPeakSpacing**2
             deletemask = np.zeros(pointlist.length, dtype=bool)
             for i in range(pointlist.length):
-                if deletemask[i] is False:
+                if deletemask[i] == False:  # noqa: E712
                     tooClose = (
                         (pointlist.data["qx"] - pointlist.data["qx"][i]) ** 2
                         + (pointlist.data["qy"] - pointlist.data["qy"][i]) ** 2

From 2481818f487a0a0710d510c53756ffd644946707 Mon Sep 17 00:00:00 2001
From: alex-rakowski <alexrakowski90@gmail.com>
Date: Tue, 14 Nov 2023 21:45:40 -0800
Subject: [PATCH 04/16] more is to == errors

---
 py4DSTEM/braggvectors/threshold.py                           | 4 ++--
 py4DSTEM/process/calibration/ellipse.py                      | 4 ++--
 py4DSTEM/process/calibration/qpixelsize.py                   | 2 +-
 py4DSTEM/process/classification/braggvectorclassification.py | 4 ++--
 py4DSTEM/process/classification/featurization.py             | 2 +-
 py4DSTEM/process/diffraction/crystal_phase.py                | 2 +-
 6 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/py4DSTEM/braggvectors/threshold.py b/py4DSTEM/braggvectors/threshold.py
index 4cc4c98ec..472d57d19 100644
--- a/py4DSTEM/braggvectors/threshold.py
+++ b/py4DSTEM/braggvectors/threshold.py
@@ -1,7 +1,7 @@
 # Bragg peaks thresholding fns
 
 import numpy as np
-
+import numpy.typing as npt
 from emdfile import tqdmnd, PointListArray
 
 
@@ -158,7 +158,7 @@ def universal_threshold(
         # Remove peaks that are too close together
         if maxNumPeaks is not False:
             r2 = minPeakSpacing**2
-            deletemask = np.zeros(pointlist.length, dtype=bool)
+            deletemask: npt.NDArray = np.zeros(pointlist.length, dtype=bool)
             for i in range(pointlist.length):
                 if deletemask[i] == False:  # noqa: E712
                     tooClose = (
diff --git a/py4DSTEM/process/calibration/ellipse.py b/py4DSTEM/process/calibration/ellipse.py
index e6a216cf1..0cf4c1ed1 100644
--- a/py4DSTEM/process/calibration/ellipse.py
+++ b/py4DSTEM/process/calibration/ellipse.py
@@ -63,8 +63,8 @@ def fit_ellipse_1D(ar, center=None, fitradii=None, mask=None):
     rr = np.sqrt((xx - x0) ** 2 + (yy - y0) ** 2)
     _mask = (rr > ri) * (rr <= ro)
     if mask is not None:
-        _mask *= mask is False
-    xs, ys = np.nonzero(_mask)
+        _mask *= mask == False # noqa: E712
+    xs, ys = np.nonzero(_mask)  
     vals = ar[_mask]
 
     # Get initial parameters guess
diff --git a/py4DSTEM/process/calibration/qpixelsize.py b/py4DSTEM/process/calibration/qpixelsize.py
index 0510fad06..d59d5a45c 100644
--- a/py4DSTEM/process/calibration/qpixelsize.py
+++ b/py4DSTEM/process/calibration/qpixelsize.py
@@ -60,6 +60,6 @@ def get_dq_from_indexed_peaks(qs, hkl, a):
     # Get pixel size
     dq = 1 / (c * a)
     qs_fit = d_inv[mask] / a
-    hkl_fit = [hkl[i] for i in range(len(hkl)) if mask[i] is True]
+    hkl_fit = [hkl[i] for i in range(len(hkl)) if mask[i] == True]  # noqa: E712
 
     return dq, qs_fit, hkl_fit
diff --git a/py4DSTEM/process/classification/braggvectorclassification.py b/py4DSTEM/process/classification/braggvectorclassification.py
index 4956f7630..c3e36273f 100644
--- a/py4DSTEM/process/classification/braggvectorclassification.py
+++ b/py4DSTEM/process/classification/braggvectorclassification.py
@@ -594,8 +594,8 @@ def merge_iterative(self, threshBPs=0.1, threshScanPosition=0.1):
             W_merge = W_merge[:, 1:]
             H_merge = H_merge[1:, :]
 
-            W_ = np.hstack((W_[:, merged is False], W_merge))
-            H_ = np.vstack((H_[merged is False, :], H_merge))
+            W_ = np.hstack((W_[:, merged == False], W_merge))  # noqa: E712
+            H_ = np.vstack((H_[merged == False, :], H_merge))  # noqa: E712
             Nc_ = W_.shape[1]
 
             if len(merge_candidates) == 0:
diff --git a/py4DSTEM/process/classification/featurization.py b/py4DSTEM/process/classification/featurization.py
index b462ea1eb..126583413 100644
--- a/py4DSTEM/process/classification/featurization.py
+++ b/py4DSTEM/process/classification/featurization.py
@@ -182,7 +182,7 @@ def from_braggvectors(
                                     (pointlist.data["qy"] / q_pixel_size) + Q_Ny / 2
                                 ).astype(int),
                             ]
-                            is False
+                            == False  # noqa: E712
                         ),
                         True,
                         False,
diff --git a/py4DSTEM/process/diffraction/crystal_phase.py b/py4DSTEM/process/diffraction/crystal_phase.py
index bac1cf8c7..d28616aa9 100644
--- a/py4DSTEM/process/diffraction/crystal_phase.py
+++ b/py4DSTEM/process/diffraction/crystal_phase.py
@@ -276,7 +276,7 @@ def quantify_phase_pointlist(
         if len(pointlist["qx"]) > 0:
             if mask_peaks is not None:
                 for i in range(len(mask_peaks)):
-                    if mask_peaks[i] is None:
+                    if mask_peaks[i] == None:  # noqa: E711
                         continue
                     inds_mask = np.where(
                         pointlist_peak_intensity_matches[:, mask_peaks[i]] != 0

From de42ddc96fb4a2eb689eaef240f3935540e7f140 Mon Sep 17 00:00:00 2001
From: alex-rakowski <alexrakowski90@gmail.com>
Date: Tue, 14 Nov 2023 21:47:08 -0800
Subject: [PATCH 05/16] black

---
 py4DSTEM/process/calibration/ellipse.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/py4DSTEM/process/calibration/ellipse.py b/py4DSTEM/process/calibration/ellipse.py
index 0cf4c1ed1..2954de377 100644
--- a/py4DSTEM/process/calibration/ellipse.py
+++ b/py4DSTEM/process/calibration/ellipse.py
@@ -63,8 +63,8 @@ def fit_ellipse_1D(ar, center=None, fitradii=None, mask=None):
     rr = np.sqrt((xx - x0) ** 2 + (yy - y0) ** 2)
     _mask = (rr > ri) * (rr <= ro)
     if mask is not None:
-        _mask *= mask == False # noqa: E712
-    xs, ys = np.nonzero(_mask)  
+        _mask *= mask == False  # noqa: E712
+    xs, ys = np.nonzero(_mask)
     vals = ar[_mask]
 
     # Get initial parameters guess

From 497438ffb7b0c9907a3033e8008d7a156c0e9656 Mon Sep 17 00:00:00 2001
From: alex-rakowski <alexrakowski90@gmail.com>
Date: Tue, 14 Nov 2023 22:04:43 -0800
Subject: [PATCH 06/16] this commit looks like it went wrong

---
 py4DSTEM/preprocess/utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/py4DSTEM/preprocess/utils.py b/py4DSTEM/preprocess/utils.py
index 829f66608..dcd890ef8 100644
--- a/py4DSTEM/preprocess/utils.py
+++ b/py4DSTEM/preprocess/utils.py
@@ -293,7 +293,7 @@ def filter_2D_maxima(
     if minSpacing > 0:
         deletemask = np.zeros(len(maxima), dtype=bool)
         for i in range(len(maxima)):
-            if deletemask[i] is False:
+            if deletemask[i] == False:  # noqa: E712
                 tooClose = (
                     (maxima["x"] - maxima["x"][i]) ** 2
                     + (maxima["y"] - maxima["y"][i]) ** 2

From 497b7d278b05f28754e5821e14b0fe11d05593f6 Mon Sep 17 00:00:00 2001
From: bsavitzky <ben.savitzky@gmail.com>
Date: Wed, 15 Nov 2023 12:03:14 -0800
Subject: [PATCH 07/16] fixes flake options syntax

---
 .github/linters/.flake8 | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/.github/linters/.flake8 b/.github/linters/.flake8
index e30e76b99..97dbb6614 100644
--- a/.github/linters/.flake8
+++ b/.github/linters/.flake8
@@ -1,2 +1,14 @@
 [flake8]
-select: "F402,F404,F812,F823,F831,F821,F822,E112,E113,E901,E902,E999"
+select:
+    F402
+    F404
+    F812
+    F823
+    F831
+    F821
+    F822
+    E112
+    E113
+    E901
+    E902
+    E999

From 06f3a4369fc4790283757ecf12f665591303c804 Mon Sep 17 00:00:00 2001
From: bsavitzky <ben.savitzky@gmail.com>
Date: Wed, 15 Nov 2023 12:04:57 -0800
Subject: [PATCH 08/16] fixes flake options syntax

---
 .github/linters/.flake8 | 25 +++++++++++++------------
 1 file changed, 13 insertions(+), 12 deletions(-)

diff --git a/.github/linters/.flake8 b/.github/linters/.flake8
index 97dbb6614..736dd1bd9 100644
--- a/.github/linters/.flake8
+++ b/.github/linters/.flake8
@@ -1,14 +1,15 @@
 [flake8]
 select:
-    F402
-    F404
-    F812
-    F823
-    F831
-    F821
-    F822
-    E112
-    E113
-    E901
-    E902
-    E999
+    F402,
+    F404,
+    F812,
+    F823,
+    F831,
+    F821,
+    F822,
+    E112,
+    E113,
+    E901,
+    E902,
+    E999,
+

From ac9c0d144f712fbc592bdc6085a6c3687d6c7dfe Mon Sep 17 00:00:00 2001
From: bsavitzky <ben.savitzky@gmail.com>
Date: Wed, 15 Nov 2023 12:10:35 -0800
Subject: [PATCH 09/16] moves .flake9 config

---
 .github/linters/.flake8 => .flake8 | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename .github/linters/.flake8 => .flake8 (100%)

diff --git a/.github/linters/.flake8 b/.flake8
similarity index 100%
rename from .github/linters/.flake8
rename to .flake8

From afcc531c4a1f18236b8fe2f605a26a1bdac71b74 Mon Sep 17 00:00:00 2001
From: bsavitzky <ben.savitzky@gmail.com>
Date: Thu, 16 Nov 2023 08:48:22 -0800
Subject: [PATCH 10/16] reverts accidental merge

---
 .flake8                 | 15 ---------------
 .github/linters/.flake8 |  2 ++
 2 files changed, 2 insertions(+), 15 deletions(-)
 delete mode 100644 .flake8
 create mode 100644 .github/linters/.flake8

diff --git a/.flake8 b/.flake8
deleted file mode 100644
index 736dd1bd9..000000000
--- a/.flake8
+++ /dev/null
@@ -1,15 +0,0 @@
-[flake8]
-select:
-    F402,
-    F404,
-    F812,
-    F823,
-    F831,
-    F821,
-    F822,
-    E112,
-    E113,
-    E901,
-    E902,
-    E999,
-
diff --git a/.github/linters/.flake8 b/.github/linters/.flake8
new file mode 100644
index 000000000..e30e76b99
--- /dev/null
+++ b/.github/linters/.flake8
@@ -0,0 +1,2 @@
+[flake8]
+select: "F402,F404,F812,F823,F831,F821,F822,E112,E113,E901,E902,E999"

From 564742ddb4c86846a27b88490aeff12fd83da4df Mon Sep 17 00:00:00 2001
From: alex-rakowski <alexrakowski90@gmail.com>
Date: Thu, 16 Nov 2023 22:50:11 -0800
Subject: [PATCH 11/16] is to ==

---
 py4DSTEM/io/filereaders/read_K2.py | 14 +++++++-------
 py4DSTEM/preprocess/radialbkgrd.py |  2 +-
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/py4DSTEM/io/filereaders/read_K2.py b/py4DSTEM/io/filereaders/read_K2.py
index e0a5dae1f..5df91f2dc 100644
--- a/py4DSTEM/io/filereaders/read_K2.py
+++ b/py4DSTEM/io/filereaders/read_K2.py
@@ -336,9 +336,9 @@ def _find_offsets(self):
             for i in range(8):
                 sync = False
                 frame = 0
-                while sync is False:
+                while sync == False:  # noqa: E712
                     sync = self._bin_files[i][frame]["block"] == block_id
-                    if sync is False:
+                    if sync == False:  # noqa: E712
                         frame += 1
                 self._shutter_offsets[i] += frame
             print("Offsets are currently ", self._shutter_offsets)
@@ -358,7 +358,7 @@ def _find_offsets(self):
                     sync = False
                     next_frame = stripe[j]["frame"]
 
-        if sync is False:
+        if sync == False:  # noqa: E712
             # the first frame is incomplete, so we need to seek the next one
             print(
                 f"First frame ({first_frame}) incomplete, seeking frame {next_frame}..."
@@ -366,12 +366,12 @@ def _find_offsets(self):
             for i in range(8):
                 sync = False
                 frame = 0
-                while sync is False:
+                while sync == False:  # noqa: E712
                     sync = (
                         self._bin_files[i][self._shutter_offsets[i] + frame]["frame"]
                         == next_frame
                     )
-                    if sync is False:
+                    if sync == False:  # noqa: E712
                         frame += 1
                 self._shutter_offsets[i] += frame
             print("Offsets are now ", self._shutter_offsets)
@@ -387,7 +387,7 @@ def _find_offsets(self):
                 ]
                 if np.any(stripe[:]["frame"] != first_frame):
                     sync = False
-            if sync is True:
+            if sync == True:  # noqa: E712
                 print("New frame is complete!")
             else:
                 print("Next frame also incomplete!!!! Data may be corrupt?")
@@ -397,7 +397,7 @@ def _find_offsets(self):
         for i in range(8):
             shutter = False
             frame = 0
-            while shutter is False:
+            while shutter == False:  # noqa: E712
                 offset = self._shutter_offsets[i] + (frame * 32)
                 stripe = self._bin_files[i][offset : offset + 32]
                 shutter = stripe[0]["shutter"]
diff --git a/py4DSTEM/preprocess/radialbkgrd.py b/py4DSTEM/preprocess/radialbkgrd.py
index da225ed74..1fcb859cd 100644
--- a/py4DSTEM/preprocess/radialbkgrd.py
+++ b/py4DSTEM/preprocess/radialbkgrd.py
@@ -80,7 +80,7 @@ def get_1D_polar_background(
     # Crop polar data to maximum distance which contains information from original image
     if (polarData.mask.sum(axis=(0)) == polarData.shape[0]).any():
         ii = polarData.data.shape[1] - 1
-        while polarData.mask[:, ii].all() is True:
+        while polarData.mask[:, ii].all() == True:  # noqa: E712
             ii = ii - 1
         maximalDistance = ii
         polarData = polarData[:, 0:maximalDistance]

From 683d7c39947a7809ecbcb6ba1ab1d34758bb87d0 Mon Sep 17 00:00:00 2001
From: alex-rakowski <alexrakowski90@gmail.com>
Date: Thu, 16 Nov 2023 22:50:23 -0800
Subject: [PATCH 12/16] removing type hint

---
 py4DSTEM/braggvectors/threshold.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/py4DSTEM/braggvectors/threshold.py b/py4DSTEM/braggvectors/threshold.py
index 472d57d19..7e19404b1 100644
--- a/py4DSTEM/braggvectors/threshold.py
+++ b/py4DSTEM/braggvectors/threshold.py
@@ -1,7 +1,6 @@
 # Bragg peaks thresholding fns
 
 import numpy as np
-import numpy.typing as npt
 from emdfile import tqdmnd, PointListArray
 
 
@@ -158,7 +157,7 @@ def universal_threshold(
         # Remove peaks that are too close together
         if maxNumPeaks is not False:
             r2 = minPeakSpacing**2
-            deletemask: npt.NDArray = np.zeros(pointlist.length, dtype=bool)
+            deletemask = np.zeros(pointlist.length, dtype=bool)
             for i in range(pointlist.length):
                 if deletemask[i] == False:  # noqa: E712
                     tooClose = (

From b573c1c1349d7e845ca0199b1737a95496c0679a Mon Sep 17 00:00:00 2001
From: alex-rakowski <alexrakowski90@gmail.com>
Date: Mon, 20 Nov 2023 13:52:52 -0800
Subject: [PATCH 13/16] bug fix to __init__ func

---
 py4DSTEM/process/wholepatternfit/wp_models.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/py4DSTEM/process/wholepatternfit/wp_models.py b/py4DSTEM/process/wholepatternfit/wp_models.py
index 3d53c1743..c0907a11e 100644
--- a/py4DSTEM/process/wholepatternfit/wp_models.py
+++ b/py4DSTEM/process/wholepatternfit/wp_models.py
@@ -1117,7 +1117,7 @@ def __init__(
         name="Complex Overlapped Disk Lattice",
         verbose=False,
     ):
-        return NotImplementedError(
+        raise NotImplementedError(
             "This model type has not been updated for use with the new architecture."
         )
 

From d823606db7d0f1b832e08896e0efceeebc12ba6f Mon Sep 17 00:00:00 2001
From: Colin <cophus@gmail.com>
Date: Mon, 20 Nov 2023 14:16:09 -0800
Subject: [PATCH 14/16] Removing the extra factor of 2/pi

---
 py4DSTEM/process/polar/polar_analysis.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/py4DSTEM/process/polar/polar_analysis.py b/py4DSTEM/process/polar/polar_analysis.py
index 4f053dcfa..5050a7d46 100644
--- a/py4DSTEM/process/polar/polar_analysis.py
+++ b/py4DSTEM/process/polar/polar_analysis.py
@@ -411,7 +411,6 @@ def calculate_pair_dist_function(
     if density is not None:
         pdf = pdf_reduced.copy()
         pdf[1:] /= 4 * np.pi * density * r[1:] * (r[1] - r[0])
-        pdf *= 2 / np.pi
         pdf += 1
 
         # damp and clip values below zero

From 9a037082a2a188a3f923740b14ea4bed8169c267 Mon Sep 17 00:00:00 2001
From: Colin <cophus@gmail.com>
Date: Mon, 20 Nov 2023 14:17:48 -0800
Subject: [PATCH 15/16] Making positivity optional

---
 py4DSTEM/process/polar/polar_analysis.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/py4DSTEM/process/polar/polar_analysis.py b/py4DSTEM/process/polar/polar_analysis.py
index 5050a7d46..67c623ce5 100644
--- a/py4DSTEM/process/polar/polar_analysis.py
+++ b/py4DSTEM/process/polar/polar_analysis.py
@@ -218,6 +218,7 @@ def calculate_pair_dist_function(
     r_max=20.0,
     r_step=0.02,
     damp_origin_fluctuations=True,
+    enforce_positivity=True,
     density=None,
     plot_background_fits=False,
     plot_sf_estimate=False,
@@ -281,6 +282,8 @@ def calculate_pair_dist_function(
         The value of the PDF approaching the origin should be zero, however numerical
         instability may result in non-physical finite values there. This flag toggles
         damping the value of the PDF to zero near the origin.
+    enforce_positivity: 
+        Force all pdf values to be >0.
     density : number or None
         The density of the sample, if known.  If this is not provided, only the
         reduced PDF is calculated.  If this value is provided, the PDF is also
@@ -416,7 +419,8 @@ def calculate_pair_dist_function(
         # damp and clip values below zero
         if damp_origin_fluctuations:
             pdf *= r_mask
-        pdf = np.maximum(pdf, 0.0)
+        if enforce_positivity:
+            pdf = np.maximum(pdf, 0.0)
 
         # store results
         self.pdf = pdf

From 00fb124e2f5388c24407b6d854c99fe6735cc4c3 Mon Sep 17 00:00:00 2001
From: SE Zeltmann <steven.zeltmann@lbl.gov>
Date: Mon, 20 Nov 2023 18:29:01 -0500
Subject: [PATCH 16/16] format with black

---
 py4DSTEM/process/polar/polar_analysis.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/py4DSTEM/process/polar/polar_analysis.py b/py4DSTEM/process/polar/polar_analysis.py
index 67c623ce5..7df00a235 100644
--- a/py4DSTEM/process/polar/polar_analysis.py
+++ b/py4DSTEM/process/polar/polar_analysis.py
@@ -282,7 +282,7 @@ def calculate_pair_dist_function(
         The value of the PDF approaching the origin should be zero, however numerical
         instability may result in non-physical finite values there. This flag toggles
         damping the value of the PDF to zero near the origin.
-    enforce_positivity: 
+    enforce_positivity:
         Force all pdf values to be >0.
     density : number or None
         The density of the sample, if known.  If this is not provided, only the