From 1ed3a3932ca87690202b5cdb3896da9c68e845a2 Mon Sep 17 00:00:00 2001
From: Zack Singer <jordan.singer@udri.udayton.edu>
Date: Fri, 17 Nov 2023 13:28:56 -0500
Subject: [PATCH 01/20] Add inverse_distortion speedups

---
 .github/workflows/package.yml                 |   2 +-
 .github/workflows/test.yml                    |  33 ++--
 hexrd/distortion/ge_41rt.py                   | 178 ++++--------------
 hexrd/transforms/cpp_sublibrary/Makefile      |  18 ++
 .../cpp_sublibrary/src/inverse_distortion.cpp |  31 +++
 install_build_dependencies.py                 |  72 +++++++
 setup.py                                      |  58 ++++++
 tests/test_inverse_distortion.py              |  86 +++++++++
 8 files changed, 316 insertions(+), 162 deletions(-)
 create mode 100644 hexrd/transforms/cpp_sublibrary/Makefile
 create mode 100644 hexrd/transforms/cpp_sublibrary/src/inverse_distortion.cpp
 create mode 100644 install_build_dependencies.py
 create mode 100644 tests/test_inverse_distortion.py

diff --git a/.github/workflows/package.yml b/.github/workflows/package.yml
index a728867b6..735dae606 100644
--- a/.github/workflows/package.yml
+++ b/.github/workflows/package.yml
@@ -2,7 +2,7 @@ name: conda-package
 
 on:
   push:
-    branches: [ master ]
+    branches: [ master, inverse-distortion ]
     tags: ["*"]
   pull_request:
     branches: [ master ]
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index ea3cd94ca..4a8c24d02 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -2,10 +2,13 @@ name: test
 
 on:
   push:
-    branches: [ master ]
+    branches: [ master, inverse-distortion ]
   pull_request:
     branches: [ master ]
 
+env:
+  CONDA_PREFIX: ${{ github.workspace }}/miniconda3/envs/hexrd
+
 jobs:
   pytest:
     name: ${{ matrix.config.name }}
@@ -15,21 +18,14 @@ jobs:
       matrix:
         python-version: [3.11]
         config:
-        - {
-            name: "Linux",
-            os: ubuntu-latest
-          }
-        - {
-            name: "MacOSX",
-            os: macos-latest
-          }
-        - {
-            name: "Windows",
-            os: windows-latest
-          }
+          - {name: "Linux", os: ubuntu-latest}
+          - {name: "MacOSX", os: macos-latest}
+          - {name: "Windows", os: windows-latest}
+
     defaults:
       run:
         shell: bash
+
     steps:
 
     - name: Set up Python ${{ matrix.python-version }}
@@ -60,9 +56,9 @@ jobs:
           pip install fabio==0.12
       if: ${{ matrix.config.os == 'macos-latest'}}
 
-    - name: Install HEXRD
+    - name: Install Build Dependencies
       run: |
-          pip install .
+        python install_build_dependencies.py
       working-directory: hexrd
 
     - name: Install requirements-dev.txt
@@ -70,9 +66,14 @@ jobs:
           pip install -r tests/requirements-dev.txt
       working-directory: hexrd
 
+    - name: Install HEXRD
+      run: |
+          pip install .
+      working-directory: hexrd
+
     - name: Run tests
       env:
         HEXRD_EXAMPLE_REPO_PATH: ${{ github.workspace }}/examples
       run: |
           pytest -s tests/
-      working-directory: hexrd
+      working-directory: hexrd
\ No newline at end of file
diff --git a/hexrd/distortion/ge_41rt.py b/hexrd/distortion/ge_41rt.py
index 0cad7646e..9b1ee67f9 100644
--- a/hexrd/distortion/ge_41rt.py
+++ b/hexrd/distortion/ge_41rt.py
@@ -2,151 +2,39 @@
 import numpy as np
 
 from hexrd import constants as cnst
-from hexrd.constants import USE_NUMBA
-if USE_NUMBA:
-    import numba
+import numba
 
 from .distortionabc import DistortionABC
 from .registry import _RegisterDistortionClass
 from .utils import newton
+from hexrd.extensions import inverse_distortion
 
 RHO_MAX = 204.8  # max radius in mm for ge detector
 
-if USE_NUMBA:
-    @numba.njit(nogil=True, cache=True)
-    def _ge_41rt_inverse_distortion(out, in_, rhoMax, params):
-        maxiter = 100
-        prec = cnst.epsf
-
-        p0, p1, p2, p3, p4, p5 = params[0:6]
-        rxi = 1.0/rhoMax
-        for el in range(len(in_)):
-            xi, yi = in_[el, 0:2]
-            ri = np.sqrt(xi*xi + yi*yi)
-            if ri < cnst.sqrt_epsf:
-                ri_inv = 0.0
-            else:
-                ri_inv = 1.0/ri
-            sinni = yi*ri_inv
-            cosni = xi*ri_inv
-            ro = ri
-            cos2ni = cosni*cosni - sinni*sinni
-            sin2ni = 2*sinni*cosni
-            cos4ni = cos2ni*cos2ni - sin2ni*sin2ni
-            # newton solver iteration
-            for i in range(maxiter):
-                ratio = ri*rxi
-                fx = (p0*ratio**p3*cos2ni +
-                      p1*ratio**p4*cos4ni +
-                      p2*ratio**p5 + 1)*ri - ro  # f(x)
-                fxp = (p0*ratio**p3*cos2ni*(p3+1) +
-                       p1*ratio**p4*cos4ni*(p4+1) +
-                       p2*ratio**p5*(p5+1) + 1)  # f'(x)
-
-                delta = fx/fxp
-                ri = ri - delta
-                # convergence check for newton
-                if np.abs(delta) <= prec*np.abs(ri):
-                    break
-
-            xi = ri*cosni
-            yi = ri*sinni
-            out[el, 0] = xi
-            out[el, 1] = yi
-
-        return out
-
-    @numba.njit(nogil=True, cache=True)
-    def _ge_41rt_distortion(out, in_, rhoMax, params):
-        p0, p1, p2, p3, p4, p5 = params[0:6]
-        rxi = 1.0/rhoMax
-
-        for el in range(len(in_)):
-            xi, yi = in_[el, 0:2]
-            ri = np.sqrt(xi*xi + yi*yi)
-            if ri < cnst.sqrt_epsf:
-                ri_inv = 0.0
-            else:
-                ri_inv = 1.0/ri
-            sinni = yi*ri_inv
-            cosni = xi*ri_inv
-            cos2ni = cosni*cosni - sinni*sinni
-            sin2ni = 2*sinni*cosni
-            cos4ni = cos2ni*cos2ni - sin2ni*sin2ni
-            ratio = ri*rxi
-
-            ri = (p0*ratio**p3*cos2ni
-                  + p1*ratio**p4*cos4ni
-                  + p2*ratio**p5
-                  + 1)*ri
-            xi = ri*cosni
-            yi = ri*sinni
-            out[el, 0] = xi
-            out[el, 1] = yi
-
-        return out
-else:
-    # non-numba versions for the direct and inverse distortion
-    def _ge_41rt_inverse_distortion(out, in_, rhoMax, params):
-        maxiter = 100
-        prec = cnst.epsf
-
-        p0, p1, p2, p3, p4, p5 = params[0:6]
-        rxi = 1.0/rhoMax
-
-        xi, yi = in_[:, 0], in_[:, 1]
+@numba.njit(nogil=True, cache=True, fastmath=True)
+def _ge_41rt_inverse_distortion(inputs, rhoMax, params):
+    radii = np.hypot(inputs[:, 0], inputs[:, 1])
+    inverted_radii = np.reciprocal(radii)
+    cosines = inputs[:, 0]*inverted_radii
+    cosine_double_angles = 2*np.square(cosines)-1
+    cosine_quadruple_angles = 2*np.square(cosine_double_angles)-1
+    sqrt_p_is = rhoMax / np.sqrt(-(params[0]*cosine_double_angles+params[1]*cosine_quadruple_angles+params[2]))
+    solutions = (2/np.sqrt(3))*sqrt_p_is*np.cos(np.arccos(((-3*np.sqrt(3)/2)*radii/sqrt_p_is))/3+4*np.pi/3)
+
+    return solutions[:, None] * inputs * inverted_radii[:, None]
+
+@numba.njit(nogil=True, cache=True)
+def _ge_41rt_distortion(out, in_, rhoMax, params):
+    p0, p1, p2, p3, p4, p5 = params[0:6]
+    rxi = 1.0/rhoMax
+
+    for el in range(len(in_)):
+        xi, yi = in_[el, 0:2]
         ri = np.sqrt(xi*xi + yi*yi)
-        # !!! adding fix TypeError when processings list of coords
-        zfix = []
-        if np.any(ri) < cnst.sqrt_epsf:
-            zfix = ri < cnst.sqrt_epsf
-            ri[zfix] = 1.0
-        ri_inv = 1.0/ri
-        ri_inv[zfix] = 0.
-
-        sinni = yi*ri_inv
-        cosni = xi*ri_inv
-        ro = ri
-        cos2ni = cosni*cosni - sinni*sinni
-        sin2ni = 2*sinni*cosni
-        cos4ni = cos2ni*cos2ni - sin2ni*sin2ni
-
-        # newton solver iteration
-        #
-        # FIXME: looks like we hae a problem here,
-        #        should iterate over single coord pairs?
-        for i in range(maxiter):
-            ratio = ri*rxi
-            fx = (p0*ratio**p3*cos2ni +
-                  p1*ratio**p4*cos4ni +
-                  p2*ratio**p5 + 1)*ri - ro  # f(x)
-            fxp = (p0*ratio**p3*cos2ni*(p3+1) +
-                   p1*ratio**p4*cos4ni*(p4+1) +
-                   p2*ratio**p5*(p5+1) + 1)  # f'(x)
-
-            delta = fx/fxp
-            ri = ri - delta
-
-            # convergence check for newton
-            if np.max(np.abs(delta/ri)) <= prec:
-                break
-
-        out[:, 0] = ri*cosni
-        out[:, 1] = ri*sinni
-
-        return out
-
-    def _ge_41rt_distortion(out, in_, rhoMax, params):
-        p0, p1, p2, p3, p4, p5 = params[0:6]
-        rxi = 1.0/rhoMax
-
-        xi, yi = in_[:, 0], in_[:, 1]
-
-        # !!! included fix on ValueError for array--like in_
-        ri = np.sqrt(xi*xi + yi*yi)
-        ri[ri < cnst.sqrt_epsf] = np.inf
-        ri_inv = 1.0/ri
-
+        if ri < cnst.sqrt_epsf:
+            ri_inv = 0.0
+        else:
+            ri_inv = 1.0/ri
         sinni = yi*ri_inv
         cosni = xi*ri_inv
         cos2ni = cosni*cosni - sinni*sinni
@@ -158,11 +46,12 @@ def _ge_41rt_distortion(out, in_, rhoMax, params):
               + p1*ratio**p4*cos4ni
               + p2*ratio**p5
               + 1)*ri
-        out[:, 0] = ri*cosni
-        out[:, 1] = ri*sinni
-
-        return out
+        xi = ri*cosni
+        yi = ri*sinni
+        out[el, 0] = xi
+        out[el, 1] = yi
 
+    return out
 
 def _rho_scl_func_inv(ri, ni, ro, rx, p):
     retval = (p[0]*(ri/rx)**p[3] * np.cos(2.0 * ni) +
@@ -222,8 +111,7 @@ def apply_inverse(self, xy_in):
             return xy_in
         else:
             xy_in = np.asarray(xy_in, dtype=float)
-            xy_out = np.empty_like(xy_in)
-            _ge_41rt_inverse_distortion(
-                xy_out, xy_in, float(RHO_MAX), np.asarray(self.params)
+            xy_out = inverse_distortion.ge_41rt_inverse_distortion(
+                xy_in, float(RHO_MAX), np.asarray(self.params[:3])
             )
-            return xy_out
+            return xy_out
\ No newline at end of file
diff --git a/hexrd/transforms/cpp_sublibrary/Makefile b/hexrd/transforms/cpp_sublibrary/Makefile
new file mode 100644
index 000000000..7ce236b58
--- /dev/null
+++ b/hexrd/transforms/cpp_sublibrary/Makefile
@@ -0,0 +1,18 @@
+CXX = c++
+CXXFLAGS = -O3 -Wall -shared -fPIC -funroll-loops -Wno-maybe-uninitialized -fopenmp
+INCLUDES = -I/${CONDA_PREFIX}/include/eigen3/ -I/${CONDA_PREFIX}/include/xsimd -I/${CONDA_PREFIX}/include -I/${CONDA_PREFIX}/include/python3.11/
+SRCS_INVERSE_DISTORTION = src/inverse_distortion.cpp
+TARGET_DIR = ../../extensions/
+TARGET_NAME_INVERSE_DISTORTION = inverse_distortion
+EXTENSION_SUFFIX = $(shell python3-config --extension-suffix)
+
+all: inverse_distortion
+
+inverse_distortion: $(TARGET_DIR)$(TARGET_NAME_INVERSE_DISTORTION)$(EXTENSION_SUFFIX)
+
+$(TARGET_DIR)$(TARGET_NAME_INVERSE_DISTORTION)$(EXTENSION_SUFFIX): $(SRCS_INVERSE_DISTORTION)
+	$(CXX) $(CXXFLAGS) $(PYBIND_INCLUDES) $< -o $@ $(INCLUDES)
+
+.PHONY: clean inverse_distortion
+clean:
+	rm -f $(TARGET_DIR)$(TARGET_NAME_INVERSE_DISTORTION)$(EXTENSION_SUFFIX)
\ No newline at end of file
diff --git a/hexrd/transforms/cpp_sublibrary/src/inverse_distortion.cpp b/hexrd/transforms/cpp_sublibrary/src/inverse_distortion.cpp
new file mode 100644
index 000000000..21a0001b5
--- /dev/null
+++ b/hexrd/transforms/cpp_sublibrary/src/inverse_distortion.cpp
@@ -0,0 +1,31 @@
+#include <pybind11/pybind11.h>
+#include <pybind11/eigen.h>
+#include <Eigen/Core>
+
+namespace py = pybind11;
+constexpr double FOUR_THIRDS_PI = 4.1887902;
+constexpr double N_THREE_HALVES_SQRT_3 = -2.59807621;
+constexpr double TWO_OVER_SQRT_THREE = 1.154700538;
+
+Eigen::ArrayXXd ge_41rt_inverse_distortion(const Eigen::ArrayXXd& inputs, const double rhoMax, const Eigen::ArrayXd& params) {
+  Eigen::ArrayXd radii = inputs.matrix().rowwise().norm();
+  if (radii.maxCoeff() < 1e-10) {
+    return Eigen::ArrayXXd::Zero(inputs.rows(), inputs.cols());
+  }
+  Eigen::ArrayXd inverted_radii = radii.cwiseInverse();
+  Eigen::ArrayXd cosines = inputs.col(0) * inverted_radii;
+  Eigen::ArrayXd cosine_double_angles = 2*cosines.square() - 1;
+  Eigen::ArrayXd cosine_quadruple_angles = 2*cosine_double_angles.square() - 1;
+  Eigen::ArrayXd sqrt_p_is = rhoMax / (-params[0]*cosine_double_angles - params[1]*cosine_quadruple_angles - params[2]).sqrt();
+  Eigen::ArrayXd solutions = TWO_OVER_SQRT_THREE*sqrt_p_is*(acos(N_THREE_HALVES_SQRT_3*radii/sqrt_p_is)/3 + FOUR_THIRDS_PI).cos();
+  Eigen::ArrayXXd results = solutions.rowwise().replicate(inputs.cols()).array() * inputs * inverted_radii.rowwise().replicate(inputs.cols()).array();
+
+  return results;
+}
+
+PYBIND11_MODULE(inverse_distortion, m)
+{
+  m.doc() = "HEXRD inverse distribution plugin";
+
+  m.def("ge_41rt_inverse_distortion", &ge_41rt_inverse_distortion, "Inverse distortion for ge_41rt");
+}
diff --git a/install_build_dependencies.py b/install_build_dependencies.py
new file mode 100644
index 000000000..38c8a9f73
--- /dev/null
+++ b/install_build_dependencies.py
@@ -0,0 +1,72 @@
+import hashlib
+import os
+from pathlib import Path
+import shutil
+import tarfile
+import tempfile
+import urllib.request
+
+# Define where to place the libraries
+CONDA_INCLUDE_PATH = os.path.join(os.getenv('CONDA_PREFIX'), 'include')
+
+def get_file_md5(filepath):
+  with open(filepath, 'rb') as rf:
+    return hashlib.md5(rf.read()).hexdigest()
+
+def download_and_extract_tgz(url, md5sum, path):
+  temp_dir = tempfile.gettempdir()
+  temp_file = Path(temp_dir) / '_hexrd_temp_file'
+  if temp_file.exists():
+    temp_file.unlink()
+
+  urllib.request.urlretrieve(url, temp_file)
+
+  file_md5sum = get_file_md5(temp_file)
+  if file_md5sum != md5sum:
+    raise Exception(
+      f'md5sum "{file_md5sum}" of file from "{url}" '
+      f'does not match expected md5sum "{md5sum}"'
+    )
+
+  os.makedirs(path, exist_ok=True)
+  with tarfile.open(temp_file, 'r:gz') as tarball:
+    tarball.extractall(path)
+
+  temp_file.unlink()
+
+def download_xsimd(path):
+  url = 'https://github.com/xtensor-stack/xsimd/archive/refs/tags/7.6.0.tar.gz'
+  md5sum = '6e52c2af8b3cb4688993a0e70825f4e8'
+  out_dir_name = 'xsimd-7.6.0'
+
+  with tempfile.TemporaryDirectory() as temp_dir:
+    download_and_extract_tgz(url, md5sum, temp_dir)
+
+    target_path = Path(path) / 'xsimd'
+    if target_path.exists():
+      shutil.rmtree(target_path)
+
+    os.makedirs(path, exist_ok=True)
+    shutil.move(str(Path(temp_dir) / out_dir_name / 'include/xsimd'), str(Path(path) / 'xsimd/xsimd'))
+
+  return str(target_path)
+
+
+def download_eigen(path):
+  url = 'https://gitlab.com/libeigen/eigen/-/archive/3.4.0/eigen-3.4.0.tar.gz'
+  md5sum = '4c527a9171d71a72a9d4186e65bea559'
+  out_dir_name = 'eigen-3.4.0'
+
+  download_and_extract_tgz(url, md5sum, path)
+
+  target_path = Path(path) / 'eigen3'
+  if target_path.exists():
+      shutil.rmtree(target_path)
+
+  shutil.move(str(Path(path) / out_dir_name), str(Path(path) / 'eigen3'))
+
+  return str(target_path)
+
+# Call the functions to download and place the libraries
+download_eigen(CONDA_INCLUDE_PATH)
+download_xsimd(CONDA_INCLUDE_PATH)
diff --git a/setup.py b/setup.py
index 317ce8869..6543e961e 100644
--- a/setup.py
+++ b/setup.py
@@ -3,9 +3,11 @@
 import os
 from pathlib import Path
 from setuptools import setup, find_packages, Extension
+import sysconfig
 import sys
 
 import numpy
+import pybind11
 np_include_dir = numpy.get_include()
 
 install_reqs = [
@@ -36,6 +38,15 @@
 else:
     compiler_optimize_flags = []
 
+# This a hack to get around the fact that scikit-image on conda-forge doesn't install
+# dist info so setuptools can't find it, even though its there, which results in
+# pkg_resources.DistributionNotFound, even though the package is available. So we
+# only added it if we aren't building with conda.
+# appdirs has the same issue.
+if os.environ.get('CONDA_BUILD') != '1':
+    install_reqs.append('scikit-image')
+    install_reqs.append('appdirs')
+
 
 # extension for convolution from astropy
 def get_convolution_extensions():
@@ -56,6 +67,52 @@ def get_convolution_extensions():
 
     return [_convolve_ext]
 
+def get_include_path(library_name):
+    env_var_hint = os.getenv(f"{library_name.upper()}_INCLUDE_DIR")
+    if env_var_hint is not None and os.path.exists(env_var_hint):
+        return env_var_hint
+    conda_include_dir = os.getenv('CONDA_PREFIX')
+    if conda_include_dir:
+        conda_include_dir = os.path.join(conda_include_dir, 'include')
+        full_path = os.path.join(conda_include_dir, library_name)
+        if os.path.exists(full_path):
+            return full_path
+    possible_directories = [
+        sysconfig.get_path('include'),
+        "/usr/include",
+        "/usr/local/include",
+    ]
+    for directory in possible_directories:
+        full_path = os.path.join(directory, library_name)
+        if os.path.exists(full_path):
+            return full_path
+    raise Exception(f"The {library_name} library was not found in any known directory.")
+
+def get_cpp_extensions():
+    cpp_transform_pkgdir = Path('hexrd') / 'transforms/cpp_sublibrary'
+    src_files = [str(cpp_transform_pkgdir / 'src/inverse_distortion.cpp')]
+
+    extra_compile_args = ['-O3', '-Wall', '-shared', '-std=c++11', '-funroll-loops']
+    if not sys.platform.startswith('win'):
+        extra_compile_args.append('-fPIC')
+
+    # Define include directories
+    include_dirs = [
+        sysconfig.get_path('include'),
+        get_include_path('eigen3'),
+        get_include_path('xsimd'),
+        pybind11.get_include(),
+        numpy.get_include(),
+    ]
+
+    inverse_distortion_ext = Extension(name='hexrd.extensions.inverse_distortion',
+                                       sources=[src_files[1]],
+                                       extra_compile_args=extra_compile_args,
+                                       include_dirs=include_dirs,
+                                       language='c++')
+
+    return [inverse_distortion_ext]
+
 
 def get_old_xfcapi_extension_modules():
     # for transforms
@@ -88,6 +145,7 @@ def get_extension_modules():
         get_old_xfcapi_extension_modules(),
         get_new_xfcapi_extension_modules(),
         get_convolution_extensions(),
+        get_cpp_extensions(),
     ) for item in sublist]
 
 
diff --git a/tests/test_inverse_distortion.py b/tests/test_inverse_distortion.py
new file mode 100644
index 000000000..147f4fc6c
--- /dev/null
+++ b/tests/test_inverse_distortion.py
@@ -0,0 +1,86 @@
+import numpy as np
+import sys
+sys.path.append('..')
+from hexrd.distortion.ge_41rt import _ge_41rt_inverse_distortion
+
+RHO_MAX = 204.8
+params = [-2.277777438488093e-05, -8.763805995117837e-05, -0.00047451698761967085]
+
+big_test_in = np.array([[ 47.031483 ,  -5.2170362],
+                        [ 60.0171   ,  27.218563 ],
+                        [ 60.697784 ,  25.48354  ],
+                        [ 56.90082  , -35.88738  ],
+                        [ 55.631718 , -37.62758  ],
+                        [ 41.258152 , -63.237328 ],
+                        [ 78.00906  ,  -8.576369 ],
+                        [ 77.7207   , -10.315189 ],
+                        [ 73.20562  ,  32.426453 ],
+                        [ 92.81449  , -13.717096 ],
+                        [101.26153  ,  18.790167 ],
+                        [ 33.428936 ,  99.08392  ],
+                        [101.51741  ,  17.049505 ],
+                        [ 85.12195  ,  59.84272  ],
+                        [-44.172375 ,  11.69572  ],
+                        [-57.850574 , -19.013659 ],
+                        [-57.169926 , -20.749386 ],
+                        [-52.772987 ,  44.117252 ],
+                        [-54.043003 ,  42.37685  ],
+                        [-74.88209  ,  16.800816 ],
+                        [-70.36986  , -25.959877 ],
+                        [-38.385185 ,  69.727234 ],
+                        [-75.17097  ,  15.061297 ],
+                        [-89.98957  ,  20.207851 ],
+                        [-98.708176 , -10.574363 ],
+                        [-82.30401  , -53.390797 ],
+                        [-98.45244  , -12.316093 ]], dtype=np.float32)
+
+big_test_out = np.array([[ 47.03288205,  -5.21719147],
+                         [ 60.02002476,  27.21988891],
+                         [ 60.70080301,  25.48480692],
+                         [ 56.90341105, -35.88901181],
+                         [ 55.63418288, -37.62924612],
+                         [ 41.26039938, -63.24077218],
+                         [ 78.01561783,  -8.57708985],
+                         [ 77.72717551, -10.31604838],
+                         [ 73.21095917,  32.42881771],
+                         [ 92.82553762, -13.71872887],
+                         [101.27584945,  18.79282435],
+                         [ 33.43310185,  99.09627097],
+                         [101.5318596 ,  17.05193195],
+                         [ 85.13101706,  59.84909563],
+                         [-44.17351296,  11.69602109],
+                         [-57.85318107, -19.01451522],
+                         [-57.17243759, -20.75029751],
+                         [-52.77530392,  44.11918895],
+                         [-54.04540365,  42.37873249],
+                         [-74.88783308,  16.80210463],
+                         [-70.37458323, -25.96162026],
+                         [-38.38762237,  69.73166096],
+                         [-75.17679039,  15.06246417],
+                         [-89.99957766,  20.21009857],
+                         [-98.72150605, -10.57579081],
+                         [-82.31199676, -53.39597868],
+                         [-98.46565139, -12.31774635]])
+
+def test_known_values():
+  xy_in = np.array([[140.40087891, 117.74253845]])
+  expected_output = np.array([[140.44540352, 117.77987754]])
+  xy_out = _ge_41rt_inverse_distortion(xy_in, RHO_MAX, params)
+  assert np.allclose(xy_out, expected_output)
+
+def test_big_input():
+  xy_out = _ge_41rt_inverse_distortion(big_test_in, RHO_MAX, params)
+  assert np.allclose(xy_out, big_test_out)
+
+def test_large_input():
+  xy_in = np.array([[1e5, 1e5]])
+  xy_out = _ge_41rt_inverse_distortion(xy_in, RHO_MAX, params)
+  # No specific expected output here, just ensure it doesn't fail
+  assert xy_out.shape == xy_in.shape
+
+def test_random_values():
+  np.random.seed(42)  # Set seed for reproducibility
+  xy_in = np.random.rand(10, 2) * 200
+  xy_out = _ge_41rt_inverse_distortion(xy_in, RHO_MAX, params)
+  # Verify function does not raise any exception
+  assert xy_out.shape == xy_in.shape

From 6c2128c73ff19f8032637c84e306773b5c39a320 Mon Sep 17 00:00:00 2001
From: Zack Singer <jordan.singer@udri.udayton.edu>
Date: Fri, 17 Nov 2023 13:39:35 -0500
Subject: [PATCH 02/20] Include pybind11 in the build pipeline

---
 install_build_dependencies.py | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/install_build_dependencies.py b/install_build_dependencies.py
index 38c8a9f73..d9fc0eba7 100644
--- a/install_build_dependencies.py
+++ b/install_build_dependencies.py
@@ -67,6 +67,22 @@ def download_eigen(path):
 
   return str(target_path)
 
+def download_pybind11(path):
+  url = 'https://github.com/pybind/pybind11/archive/refs/tags/v2.11.0.tar.gz'
+  md5sum = '90c4946e87c64d8d8fc0ae4edf35d780'
+  out_dir_name = 'pybind11-2.11.0'
+
+  download_and_extract_tgz(url, md5sum, path)
+
+  target_path = Path(path) / 'pybind11'
+  if target_path.exists():
+      shutil.rmtree(target_path)
+
+  shutil.move(str(Path(path) / out_dir_name), str(Path(path) / 'pybind11'))
+
+  return str(target_path)
+
 # Call the functions to download and place the libraries
 download_eigen(CONDA_INCLUDE_PATH)
 download_xsimd(CONDA_INCLUDE_PATH)
+download_pybind11(CONDA_INCLUDE_PATH)

From 188657cce4e22d49a0092dd6433a541363daf235 Mon Sep 17 00:00:00 2001
From: Zack Singer <jordan.singer@udri.udayton.edu>
Date: Fri, 17 Nov 2023 13:45:51 -0500
Subject: [PATCH 03/20] Add pybind11 to meta.yaml

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index dc9d6a44b..f08833fec 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,2 +1,2 @@
 [build-system]
-requires = ["setuptools", "wheel", "numpy<1.27", "setuptools_scm[toml]"]
+requires = ["setuptools", "wheel", "numpy<1.27", "setuptools_scm[toml]", "pybind11>=2.11.0"]

From 74c5cf7be872b67ea3062d731dfe347bbf443697 Mon Sep 17 00:00:00 2001
From: Zack Singer <jordan.singer@udri.udayton.edu>
Date: Fri, 17 Nov 2023 13:48:49 -0500
Subject: [PATCH 04/20] Fix off-by-1 error in setup file

---
 pyproject.toml | 2 +-
 setup.py       | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index f08833fec..dc9d6a44b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,2 +1,2 @@
 [build-system]
-requires = ["setuptools", "wheel", "numpy<1.27", "setuptools_scm[toml]", "pybind11>=2.11.0"]
+requires = ["setuptools", "wheel", "numpy<1.27", "setuptools_scm[toml]"]
diff --git a/setup.py b/setup.py
index 6543e961e..17c92fccd 100644
--- a/setup.py
+++ b/setup.py
@@ -106,7 +106,7 @@ def get_cpp_extensions():
     ]
 
     inverse_distortion_ext = Extension(name='hexrd.extensions.inverse_distortion',
-                                       sources=[src_files[1]],
+                                       sources=[src_files[0]],
                                        extra_compile_args=extra_compile_args,
                                        include_dirs=include_dirs,
                                        language='c++')

From 5e53d43e12e3e88422c97341bc426195a09bec79 Mon Sep 17 00:00:00 2001
From: Zack Singer <jordan.singer@udri.udayton.edu>
Date: Fri, 17 Nov 2023 13:50:13 -0500
Subject: [PATCH 05/20] Re-add pybind11 to toml

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index dc9d6a44b..f08833fec 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,2 +1,2 @@
 [build-system]
-requires = ["setuptools", "wheel", "numpy<1.27", "setuptools_scm[toml]"]
+requires = ["setuptools", "wheel", "numpy<1.27", "setuptools_scm[toml]", "pybind11>=2.11.0"]

From e6bf94380592dcd686788c4d709bd25312bb91c0 Mon Sep 17 00:00:00 2001
From: Zack Singer <jordan.singer@udri.udayton.edu>
Date: Fri, 17 Nov 2023 14:58:07 -0500
Subject: [PATCH 06/20] Include unit tests for inverse distortion

---
 conda.recipe/meta.yaml           |  1 +
 hexrd/distortion/ge_41rt.py      | 11 ++++++++---
 tests/test_inverse_distortion.py | 27 +++++++++++++++++++++------
 3 files changed, 30 insertions(+), 9 deletions(-)

diff --git a/conda.recipe/meta.yaml b/conda.recipe/meta.yaml
index ae2011a40..606a0ca57 100644
--- a/conda.recipe/meta.yaml
+++ b/conda.recipe/meta.yaml
@@ -20,6 +20,7 @@ requirements:
     - numpy >=1.20                           # [build_platform != target_platform]
     # Numba is only here to make sure we use a version of numpy that is compatible
     - numba                                  # [build_platform != target_platform]
+    - pybind11                               # [build_platform != target_platform]
   host:
     - python {{ python }}
     - numpy >=1.20
diff --git a/hexrd/distortion/ge_41rt.py b/hexrd/distortion/ge_41rt.py
index 9b1ee67f9..cc9c3e585 100644
--- a/hexrd/distortion/ge_41rt.py
+++ b/hexrd/distortion/ge_41rt.py
@@ -1,18 +1,23 @@
 """GE41RT Detector Distortion"""
-import numpy as np
+from typing import List
 
-from hexrd import constants as cnst
+import numpy as np
 import numba
 
 from .distortionabc import DistortionABC
 from .registry import _RegisterDistortionClass
 from .utils import newton
+
+from hexrd import constants as cnst
 from hexrd.extensions import inverse_distortion
 
 RHO_MAX = 204.8  # max radius in mm for ge detector
 
+# NOTE: Deprecated in favor of inverse_distortion.ge_41rt_inverse_distortion
 @numba.njit(nogil=True, cache=True, fastmath=True)
-def _ge_41rt_inverse_distortion(inputs, rhoMax, params):
+def _ge_41rt_inverse_distortion(inputs: np.ndarray[np.float64, np.float64],
+                                rhoMax: float,
+                                params: List[float]):
     radii = np.hypot(inputs[:, 0], inputs[:, 1])
     inverted_radii = np.reciprocal(radii)
     cosines = inputs[:, 0]*inverted_radii
diff --git a/tests/test_inverse_distortion.py b/tests/test_inverse_distortion.py
index 147f4fc6c..11f4dc53e 100644
--- a/tests/test_inverse_distortion.py
+++ b/tests/test_inverse_distortion.py
@@ -1,7 +1,9 @@
+import pickle
+
 import numpy as np
 import sys
 sys.path.append('..')
-from hexrd.distortion.ge_41rt import _ge_41rt_inverse_distortion
+from hexrd.extensions import inverse_distortion
 
 RHO_MAX = 204.8
 params = [-2.277777438488093e-05, -8.763805995117837e-05, -0.00047451698761967085]
@@ -65,22 +67,35 @@
 def test_known_values():
   xy_in = np.array([[140.40087891, 117.74253845]])
   expected_output = np.array([[140.44540352, 117.77987754]])
-  xy_out = _ge_41rt_inverse_distortion(xy_in, RHO_MAX, params)
+  xy_out = inverse_distortion.ge_41rt_inverse_distortion(xy_in, RHO_MAX, params)
   assert np.allclose(xy_out, expected_output)
 
 def test_big_input():
-  xy_out = _ge_41rt_inverse_distortion(big_test_in, RHO_MAX, params)
+  xy_out = inverse_distortion.ge_41rt_inverse_distortion(big_test_in, RHO_MAX, params)
   assert np.allclose(xy_out, big_test_out)
 
 def test_large_input():
   xy_in = np.array([[1e5, 1e5]])
-  xy_out = _ge_41rt_inverse_distortion(xy_in, RHO_MAX, params)
+  xy_out = inverse_distortion.ge_41rt_inverse_distortion(xy_in, RHO_MAX, params)
   # No specific expected output here, just ensure it doesn't fail
   assert xy_out.shape == xy_in.shape
 
+def test_logged_data():
+    # Load logged data
+    with open('data/inverse_distortion_in_out.pkl', 'rb') as f:
+        logged_data = pickle.load(f)
+
+    logged_inputs = logged_data['inputs']
+    logged_outputs = logged_data['outputs']
+    logged_params = logged_data['params']
+
+    for xy_in, xy_out_expected, params in zip(logged_inputs, logged_outputs, logged_params):
+        xy_out = inverse_distortion.ge_41rt_inverse_distortion(xy_in, RHO_MAX, params)
+        assert np.allclose(xy_out, xy_out_expected, atol=1e-6)
+
 def test_random_values():
-  np.random.seed(42)  # Set seed for reproducibility
+  np.random.seed(42)
   xy_in = np.random.rand(10, 2) * 200
-  xy_out = _ge_41rt_inverse_distortion(xy_in, RHO_MAX, params)
+  xy_out = inverse_distortion.ge_41rt_inverse_distortion(xy_in, RHO_MAX, params)
   # Verify function does not raise any exception
   assert xy_out.shape == xy_in.shape

From f92af5b9cb4342ad369a23c81ea51e88b1821b94 Mon Sep 17 00:00:00 2001
From: Zack Singer <jordan.singer@udri.udayton.edu>
Date: Fri, 17 Nov 2023 15:08:52 -0500
Subject: [PATCH 07/20] Fix pickle pathing

---
 tests/data/inverse_distortion_in_out.pkl | Bin 0 -> 11303 bytes
 tests/test_inverse_distortion.py         |   9 +++++----
 2 files changed, 5 insertions(+), 4 deletions(-)
 create mode 100644 tests/data/inverse_distortion_in_out.pkl

diff --git a/tests/data/inverse_distortion_in_out.pkl b/tests/data/inverse_distortion_in_out.pkl
new file mode 100644
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literal 0
HcmV?d00001

diff --git a/tests/test_inverse_distortion.py b/tests/test_inverse_distortion.py
index 11f4dc53e..5d7d94b9e 100644
--- a/tests/test_inverse_distortion.py
+++ b/tests/test_inverse_distortion.py
@@ -1,10 +1,11 @@
+import os
 import pickle
 
 import numpy as np
-import sys
-sys.path.append('..')
 from hexrd.extensions import inverse_distortion
 
+test_dir = os.path.dirname(os.path.abspath(__file__))
+
 RHO_MAX = 204.8
 params = [-2.277777438488093e-05, -8.763805995117837e-05, -0.00047451698761967085]
 
@@ -82,7 +83,7 @@ def test_large_input():
 
 def test_logged_data():
     # Load logged data
-    with open('data/inverse_distortion_in_out.pkl', 'rb') as f:
+    with open(os.path.join(test_dir, "data", "inverse_distortion_in_out.pkl"), 'rb') as f:
         logged_data = pickle.load(f)
 
     logged_inputs = logged_data['inputs']
@@ -91,7 +92,7 @@ def test_logged_data():
 
     for xy_in, xy_out_expected, params in zip(logged_inputs, logged_outputs, logged_params):
         xy_out = inverse_distortion.ge_41rt_inverse_distortion(xy_in, RHO_MAX, params)
-        assert np.allclose(xy_out, xy_out_expected, atol=1e-6)
+        assert np.allclose(xy_out, xy_out_expected, atol=1e-7)
 
 def test_random_values():
   np.random.seed(42)

From 30bf00ccfee32f944754ea97bfdff4eb66e734f6 Mon Sep 17 00:00:00 2001
From: Zack Singer <jordan.singer@udri.udayton.edu>
Date: Fri, 17 Nov 2023 15:15:01 -0500
Subject: [PATCH 08/20] Add installation procedures to package.yml instructions

---
 .github/workflows/package.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/package.yml b/.github/workflows/package.yml
index 735dae606..bc28e7daa 100644
--- a/.github/workflows/package.yml
+++ b/.github/workflows/package.yml
@@ -52,6 +52,7 @@ jobs:
           conda activate hexrd
           conda install --override-channels -c conda-forge anaconda-client conda-build conda
 
+          python install_build_dependencies.py
       # This is need to ensure ~/.profile or ~/.bashrc are used so the activate
       # command works.
       shell: bash -l {0}

From 309bbc3404f1663d1083a3388c48e2c335451f87 Mon Sep 17 00:00:00 2001
From: Zack Singer <jordan.singer@udri.udayton.edu>
Date: Fri, 17 Nov 2023 15:52:27 -0500
Subject: [PATCH 09/20] Add pybind11 to package.yml installs

---
 .github/workflows/package.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/package.yml b/.github/workflows/package.yml
index bc28e7daa..4c81d5d7c 100644
--- a/.github/workflows/package.yml
+++ b/.github/workflows/package.yml
@@ -50,7 +50,7 @@ jobs:
           conda config --set solver libmamba
 
           conda activate hexrd
-          conda install --override-channels -c conda-forge anaconda-client conda-build conda
+          conda install --override-channels -c conda-forge anaconda-client conda-build conda pybind11
 
           python install_build_dependencies.py
       # This is need to ensure ~/.profile or ~/.bashrc are used so the activate

From 8ad311417ae86e39b6d8f06595a73077464fd223 Mon Sep 17 00:00:00 2001
From: Zack Singer <jordan.singer@udri.udayton.edu>
Date: Fri, 17 Nov 2023 15:54:23 -0500
Subject: [PATCH 10/20] Remove push trigger for github action

---
 .github/workflows/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 4a8c24d02..c5fd898ff 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -2,7 +2,7 @@ name: test
 
 on:
   push:
-    branches: [ master, inverse-distortion ]
+    branches: [ master ]
   pull_request:
     branches: [ master ]
 

From d70f84272f7e2e5fcd2b2656dfc833ab0920c644 Mon Sep 17 00:00:00 2001
From: Zack Singer <jordan.singer@udri.udayton.edu>
Date: Fri, 17 Nov 2023 15:55:08 -0500
Subject: [PATCH 11/20] Remove action trigger for this branch in package

---
 .github/workflows/package.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/package.yml b/.github/workflows/package.yml
index 4c81d5d7c..bdfebab8c 100644
--- a/.github/workflows/package.yml
+++ b/.github/workflows/package.yml
@@ -2,7 +2,7 @@ name: conda-package
 
 on:
   push:
-    branches: [ master, inverse-distortion ]
+    branches: [ master ]
     tags: ["*"]
   pull_request:
     branches: [ master ]

From f7632feefacdf10da30c44874c9d1465e80ca5e3 Mon Sep 17 00:00:00 2001
From: Patrick Avery <patrick.avery@kitware.com>
Date: Mon, 20 Nov 2023 18:57:44 -0600
Subject: [PATCH 12/20] A few minor updates

Signed-off-by: Patrick Avery <patrick.avery@kitware.com>
---
 .github/workflows/package.yml                 |   3 +-
 .github/workflows/test.yml                    |  31 +++---
 install_build_dependencies.py                 |  88 ---------------
 scripts/install/install_build_dependencies.py | 100 ++++++++++++++++++
 setup.py                                      |  48 ++++-----
 5 files changed, 139 insertions(+), 131 deletions(-)
 delete mode 100644 install_build_dependencies.py
 create mode 100755 scripts/install/install_build_dependencies.py

diff --git a/.github/workflows/package.yml b/.github/workflows/package.yml
index bdfebab8c..a728867b6 100644
--- a/.github/workflows/package.yml
+++ b/.github/workflows/package.yml
@@ -50,9 +50,8 @@ jobs:
           conda config --set solver libmamba
 
           conda activate hexrd
-          conda install --override-channels -c conda-forge anaconda-client conda-build conda pybind11
+          conda install --override-channels -c conda-forge anaconda-client conda-build conda
 
-          python install_build_dependencies.py
       # This is need to ensure ~/.profile or ~/.bashrc are used so the activate
       # command works.
       shell: bash -l {0}
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index c5fd898ff..ea3cd94ca 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -6,9 +6,6 @@ on:
   pull_request:
     branches: [ master ]
 
-env:
-  CONDA_PREFIX: ${{ github.workspace }}/miniconda3/envs/hexrd
-
 jobs:
   pytest:
     name: ${{ matrix.config.name }}
@@ -18,14 +15,21 @@ jobs:
       matrix:
         python-version: [3.11]
         config:
-          - {name: "Linux", os: ubuntu-latest}
-          - {name: "MacOSX", os: macos-latest}
-          - {name: "Windows", os: windows-latest}
-
+        - {
+            name: "Linux",
+            os: ubuntu-latest
+          }
+        - {
+            name: "MacOSX",
+            os: macos-latest
+          }
+        - {
+            name: "Windows",
+            os: windows-latest
+          }
     defaults:
       run:
         shell: bash
-
     steps:
 
     - name: Set up Python ${{ matrix.python-version }}
@@ -56,9 +60,9 @@ jobs:
           pip install fabio==0.12
       if: ${{ matrix.config.os == 'macos-latest'}}
 
-    - name: Install Build Dependencies
+    - name: Install HEXRD
       run: |
-        python install_build_dependencies.py
+          pip install .
       working-directory: hexrd
 
     - name: Install requirements-dev.txt
@@ -66,14 +70,9 @@ jobs:
           pip install -r tests/requirements-dev.txt
       working-directory: hexrd
 
-    - name: Install HEXRD
-      run: |
-          pip install .
-      working-directory: hexrd
-
     - name: Run tests
       env:
         HEXRD_EXAMPLE_REPO_PATH: ${{ github.workspace }}/examples
       run: |
           pytest -s tests/
-      working-directory: hexrd
\ No newline at end of file
+      working-directory: hexrd
diff --git a/install_build_dependencies.py b/install_build_dependencies.py
deleted file mode 100644
index d9fc0eba7..000000000
--- a/install_build_dependencies.py
+++ /dev/null
@@ -1,88 +0,0 @@
-import hashlib
-import os
-from pathlib import Path
-import shutil
-import tarfile
-import tempfile
-import urllib.request
-
-# Define where to place the libraries
-CONDA_INCLUDE_PATH = os.path.join(os.getenv('CONDA_PREFIX'), 'include')
-
-def get_file_md5(filepath):
-  with open(filepath, 'rb') as rf:
-    return hashlib.md5(rf.read()).hexdigest()
-
-def download_and_extract_tgz(url, md5sum, path):
-  temp_dir = tempfile.gettempdir()
-  temp_file = Path(temp_dir) / '_hexrd_temp_file'
-  if temp_file.exists():
-    temp_file.unlink()
-
-  urllib.request.urlretrieve(url, temp_file)
-
-  file_md5sum = get_file_md5(temp_file)
-  if file_md5sum != md5sum:
-    raise Exception(
-      f'md5sum "{file_md5sum}" of file from "{url}" '
-      f'does not match expected md5sum "{md5sum}"'
-    )
-
-  os.makedirs(path, exist_ok=True)
-  with tarfile.open(temp_file, 'r:gz') as tarball:
-    tarball.extractall(path)
-
-  temp_file.unlink()
-
-def download_xsimd(path):
-  url = 'https://github.com/xtensor-stack/xsimd/archive/refs/tags/7.6.0.tar.gz'
-  md5sum = '6e52c2af8b3cb4688993a0e70825f4e8'
-  out_dir_name = 'xsimd-7.6.0'
-
-  with tempfile.TemporaryDirectory() as temp_dir:
-    download_and_extract_tgz(url, md5sum, temp_dir)
-
-    target_path = Path(path) / 'xsimd'
-    if target_path.exists():
-      shutil.rmtree(target_path)
-
-    os.makedirs(path, exist_ok=True)
-    shutil.move(str(Path(temp_dir) / out_dir_name / 'include/xsimd'), str(Path(path) / 'xsimd/xsimd'))
-
-  return str(target_path)
-
-
-def download_eigen(path):
-  url = 'https://gitlab.com/libeigen/eigen/-/archive/3.4.0/eigen-3.4.0.tar.gz'
-  md5sum = '4c527a9171d71a72a9d4186e65bea559'
-  out_dir_name = 'eigen-3.4.0'
-
-  download_and_extract_tgz(url, md5sum, path)
-
-  target_path = Path(path) / 'eigen3'
-  if target_path.exists():
-      shutil.rmtree(target_path)
-
-  shutil.move(str(Path(path) / out_dir_name), str(Path(path) / 'eigen3'))
-
-  return str(target_path)
-
-def download_pybind11(path):
-  url = 'https://github.com/pybind/pybind11/archive/refs/tags/v2.11.0.tar.gz'
-  md5sum = '90c4946e87c64d8d8fc0ae4edf35d780'
-  out_dir_name = 'pybind11-2.11.0'
-
-  download_and_extract_tgz(url, md5sum, path)
-
-  target_path = Path(path) / 'pybind11'
-  if target_path.exists():
-      shutil.rmtree(target_path)
-
-  shutil.move(str(Path(path) / out_dir_name), str(Path(path) / 'pybind11'))
-
-  return str(target_path)
-
-# Call the functions to download and place the libraries
-download_eigen(CONDA_INCLUDE_PATH)
-download_xsimd(CONDA_INCLUDE_PATH)
-download_pybind11(CONDA_INCLUDE_PATH)
diff --git a/scripts/install/install_build_dependencies.py b/scripts/install/install_build_dependencies.py
new file mode 100755
index 000000000..983013deb
--- /dev/null
+++ b/scripts/install/install_build_dependencies.py
@@ -0,0 +1,100 @@
+#!/usr/bin/env python3
+
+import hashlib
+import os
+from pathlib import Path
+import shutil
+import tarfile
+import tempfile
+import urllib.request
+
+
+def get_file_md5(filepath):
+    with open(filepath, 'rb') as rf:
+        return hashlib.md5(rf.read()).hexdigest()
+
+
+def download_and_extract_tgz(url, md5sum, path):
+    temp_dir = tempfile.gettempdir()
+    temp_file = Path(temp_dir) / '_hexrd_temp_file'
+    if temp_file.exists():
+        temp_file.unlink()
+
+    urllib.request.urlretrieve(url, temp_file)
+
+    file_md5sum = get_file_md5(temp_file)
+    if file_md5sum != md5sum:
+        raise Exception(
+            f'md5sum "{file_md5sum}" of file from "{url}" '
+            f'does not match expected md5sum "{md5sum}"'
+        )
+
+    os.makedirs(path, exist_ok=True)
+    with tarfile.open(temp_file, 'r:gz') as tarball:
+        tarball.extractall(path)
+
+    temp_file.unlink()
+
+
+def download_xsimd(path):
+    url = 'https://github.com/xtensor-stack/xsimd/archive/refs/tags/7.6.0.tar.gz'  # noqa
+    md5sum = '6e52c2af8b3cb4688993a0e70825f4e8'
+    out_dir_name = 'xsimd-7.6.0'
+
+    with tempfile.TemporaryDirectory() as temp_dir:
+        download_and_extract_tgz(url, md5sum, temp_dir)
+
+        target_path = Path(path) / 'xsimd'
+        if target_path.exists():
+            shutil.rmtree(target_path)
+
+        os.makedirs(path, exist_ok=True)
+        shutil.move(str(Path(temp_dir) / out_dir_name / 'include/xsimd'),
+                    str(Path(path) / 'xsimd/xsimd'))
+
+    return str(target_path)
+
+
+def download_eigen(path):
+    url = 'https://gitlab.com/libeigen/eigen/-/archive/3.4.0/eigen-3.4.0.tar.gz'  # noqa
+    md5sum = '4c527a9171d71a72a9d4186e65bea559'
+    out_dir_name = 'eigen-3.4.0'
+
+    download_and_extract_tgz(url, md5sum, path)
+
+    target_path = Path(path) / 'eigen3'
+    if target_path.exists():
+        shutil.rmtree(target_path)
+
+    shutil.move(str(Path(path) / out_dir_name), str(Path(path) / 'eigen3'))
+
+    return str(target_path)
+
+
+def download_pybind11(path):
+    url = 'https://github.com/pybind/pybind11/archive/refs/tags/v2.11.0.tar.gz'
+    md5sum = '90c4946e87c64d8d8fc0ae4edf35d780'
+    out_dir_name = 'pybind11-2.11.0'
+
+    download_and_extract_tgz(url, md5sum, path)
+
+    target_path = Path(path) / 'pybind11'
+    if target_path.exists():
+        shutil.rmtree(target_path)
+
+    shutil.move(str(Path(path) / out_dir_name), str(Path(path) / 'pybind11'))
+
+    return str(target_path)
+
+
+if __name__ == '__main__':
+    import sys
+
+    if len(sys.argv) < 2:
+        sys.exit('<script> <destination')
+
+    destination = sys.argv[1]
+
+    # Call the functions to download and place the libraries
+    download_eigen(destination)
+    download_xsimd(destination)
diff --git a/setup.py b/setup.py
index 17c92fccd..04e56c259 100644
--- a/setup.py
+++ b/setup.py
@@ -3,6 +3,7 @@
 import os
 from pathlib import Path
 from setuptools import setup, find_packages, Extension
+import subprocess
 import sysconfig
 import sys
 
@@ -38,15 +39,6 @@
 else:
     compiler_optimize_flags = []
 
-# This a hack to get around the fact that scikit-image on conda-forge doesn't install
-# dist info so setuptools can't find it, even though its there, which results in
-# pkg_resources.DistributionNotFound, even though the package is available. So we
-# only added it if we aren't building with conda.
-# appdirs has the same issue.
-if os.environ.get('CONDA_BUILD') != '1':
-    install_reqs.append('scikit-image')
-    install_reqs.append('appdirs')
-
 
 # extension for convolution from astropy
 def get_convolution_extensions():
@@ -54,7 +46,7 @@ def get_convolution_extensions():
 
     src_files = [str(c_convolve_pkgdir / 'src/convolve.c')]
 
-    extra_compile_args=['-UNDEBUG']
+    extra_compile_args = ['-UNDEBUG']
     if not sys.platform.startswith('win'):
         extra_compile_args.append('-fPIC')
     extra_compile_args += compiler_optimize_flags
@@ -67,26 +59,32 @@ def get_convolution_extensions():
 
     return [_convolve_ext]
 
+
 def get_include_path(library_name):
     env_var_hint = os.getenv(f"{library_name.upper()}_INCLUDE_DIR")
     if env_var_hint is not None and os.path.exists(env_var_hint):
         return env_var_hint
+
     conda_include_dir = os.getenv('CONDA_PREFIX')
     if conda_include_dir:
-        conda_include_dir = os.path.join(conda_include_dir, 'include')
-        full_path = os.path.join(conda_include_dir, library_name)
-        if os.path.exists(full_path):
-            return full_path
-    possible_directories = [
-        sysconfig.get_path('include'),
-        "/usr/include",
-        "/usr/local/include",
-    ]
-    for directory in possible_directories:
-        full_path = os.path.join(directory, library_name)
-        if os.path.exists(full_path):
-            return full_path
-    raise Exception(f"The {library_name} library was not found in any known directory.")
+        full_path = Path(conda_include_dir) / 'include' / library_name
+        if full_path.exists():
+            return str(full_path)
+
+    build_include_dir = Path(__file__).parent / 'build/include'
+    full_path = build_include_dir / library_name
+    if full_path.exists():
+        return full_path
+
+    # If the path doesn't exist, then install it there
+    scripts_path = Path(__file__).parent / 'scripts'
+    install_script = scripts_path / 'install/install_build_dependencies.py'
+
+    subprocess.run([sys.executable, install_script, str(build_include_dir)])
+
+    # It should exist now
+    return full_path
+
 
 def get_cpp_extensions():
     cpp_transform_pkgdir = Path('hexrd') / 'transforms/cpp_sublibrary'
@@ -181,7 +179,7 @@ def get_extension_modules():
     ext_modules=ext_modules,
     packages=find_packages(),
     include_package_data=True,
-    package_data={'':['Anomalous.h5']},
+    package_data={'': ['Anomalous.h5']},
     python_requires='>=3.9',
     install_requires=install_reqs
 )

From daafa05d95c3352951ebc3ff802c975e6f9b8cfa Mon Sep 17 00:00:00 2001
From: Patrick Avery <patrick.avery@kitware.com>
Date: Mon, 20 Nov 2023 19:00:20 -0600
Subject: [PATCH 13/20] Use xsimd and eigen from conda-forge for packages

Also update the conda build compiler to be C++

Signed-off-by: Patrick Avery <patrick.avery@kitware.com>
---
 conda.recipe/meta.yaml                        |  5 +++-
 scripts/install/install_build_dependencies.py | 28 ++++++++++++++-----
 setup.py                                      | 15 ++++++----
 3 files changed, 35 insertions(+), 13 deletions(-)

diff --git a/conda.recipe/meta.yaml b/conda.recipe/meta.yaml
index 606a0ca57..19482d5c6 100644
--- a/conda.recipe/meta.yaml
+++ b/conda.recipe/meta.yaml
@@ -14,7 +14,7 @@ build:
 requirements:
   build:
     # This is so that we can build cross-platform for osx-arm64
-    - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
     - python {{ python }}                    # [build_platform != target_platform]
     - cross-python_{{ target_platform }}     # [build_platform != target_platform]
     - numpy >=1.20                           # [build_platform != target_platform]
@@ -28,6 +28,9 @@ requirements:
     - setuptools_scm
     # Numba is only here to make sure we use a version of numpy that is compatible
     - numba
+    - pybind11
+    - xsimd
+    - eigen
 
   run:
     - appdirs
diff --git a/scripts/install/install_build_dependencies.py b/scripts/install/install_build_dependencies.py
index 983013deb..ca1688faa 100755
--- a/scripts/install/install_build_dependencies.py
+++ b/scripts/install/install_build_dependencies.py
@@ -55,7 +55,7 @@ def download_xsimd(path):
     return str(target_path)
 
 
-def download_eigen(path):
+def download_eigen3(path):
     url = 'https://gitlab.com/libeigen/eigen/-/archive/3.4.0/eigen-3.4.0.tar.gz'  # noqa
     md5sum = '4c527a9171d71a72a9d4186e65bea559'
     out_dir_name = 'eigen-3.4.0'
@@ -87,14 +87,28 @@ def download_pybind11(path):
     return str(target_path)
 
 
+INSTALL_FUNCTIONS = {
+    'eigen3': download_eigen3,
+    'xsimd': download_xsimd,
+    'pybind11': download_pybind11,
+}
+
+
+def install(library, destination):
+    if library not in INSTALL_FUNCTIONS:
+        raise NotImplementedError(library)
+
+    return INSTALL_FUNCTIONS[library](destination)
+
+
 if __name__ == '__main__':
     import sys
 
-    if len(sys.argv) < 2:
-        sys.exit('<script> <destination')
+    if len(sys.argv) < 3:
+        sys.exit('<script> <library> <destination>')
 
-    destination = sys.argv[1]
+    library = sys.argv[1]
+    destination = sys.argv[2]
 
-    # Call the functions to download and place the libraries
-    download_eigen(destination)
-    download_xsimd(destination)
+    print(f'Installing "{library}" to "{destination}"')
+    install(library, destination)
diff --git a/setup.py b/setup.py
index 04e56c259..a6f0b8ae3 100644
--- a/setup.py
+++ b/setup.py
@@ -4,7 +4,6 @@
 from pathlib import Path
 from setuptools import setup, find_packages, Extension
 import subprocess
-import sysconfig
 import sys
 
 import numpy
@@ -69,7 +68,7 @@ def get_include_path(library_name):
     if conda_include_dir:
         full_path = Path(conda_include_dir) / 'include' / library_name
         if full_path.exists():
-            return str(full_path)
+            return full_path
 
     build_include_dir = Path(__file__).parent / 'build/include'
     full_path = build_include_dir / library_name
@@ -80,7 +79,14 @@ def get_include_path(library_name):
     scripts_path = Path(__file__).parent / 'scripts'
     install_script = scripts_path / 'install/install_build_dependencies.py'
 
-    subprocess.run([sys.executable, install_script, str(build_include_dir)])
+    args = [
+        sys.executable,
+        install_script,
+        library_name,
+        build_include_dir,
+    ]
+
+    result = subprocess.run(args, check=True)
 
     # It should exist now
     return full_path
@@ -96,7 +102,6 @@ def get_cpp_extensions():
 
     # Define include directories
     include_dirs = [
-        sysconfig.get_path('include'),
         get_include_path('eigen3'),
         get_include_path('xsimd'),
         pybind11.get_include(),
@@ -104,7 +109,7 @@ def get_cpp_extensions():
     ]
 
     inverse_distortion_ext = Extension(name='hexrd.extensions.inverse_distortion',
-                                       sources=[src_files[0]],
+                                       sources=src_files,
                                        extra_compile_args=extra_compile_args,
                                        include_dirs=include_dirs,
                                        language='c++')

From a7d696e753b328df958ae0fb6026e2f8f132c039 Mon Sep 17 00:00:00 2001
From: Patrick Avery <patrick.avery@kitware.com>
Date: Tue, 21 Nov 2023 08:07:11 -0600
Subject: [PATCH 14/20] Fix flake8 issues in setup.py

Signed-off-by: Patrick Avery <patrick.avery@kitware.com>
---
 setup.py | 32 ++++++++++++++++++--------------
 1 file changed, 18 insertions(+), 14 deletions(-)

diff --git a/setup.py b/setup.py
index a6f0b8ae3..d0372da90 100644
--- a/setup.py
+++ b/setup.py
@@ -17,7 +17,7 @@
     'h5py',
     'lmfit',
     'numba',
-    'numpy<1.27',  # NOTE: bump this to support the latest version numba supports
+    'numpy<1.27',  # noqa NOTE: bump this to support the latest version numba supports
     'psutil',
     'pycifrw',
     'pyyaml',
@@ -49,9 +49,10 @@ def get_convolution_extensions():
     if not sys.platform.startswith('win'):
         extra_compile_args.append('-fPIC')
     extra_compile_args += compiler_optimize_flags
-    # Add '-Rpass-missed=.*' to ``extra_compile_args`` when compiling with clang
-    # to report missed optimizations
-    _convolve_ext = Extension(name='hexrd.convolution._convolve', sources=src_files,
+    # Add '-Rpass-missed=.*' to ``extra_compile_args`` when compiling with
+    # clang to report missed optimizations
+    _convolve_ext = Extension(name='hexrd.convolution._convolve',
+                              sources=src_files,
                               extra_compile_args=extra_compile_args,
                               include_dirs=[numpy.get_include()],
                               language='c')
@@ -86,7 +87,7 @@ def get_include_path(library_name):
         build_include_dir,
     ]
 
-    result = subprocess.run(args, check=True)
+    subprocess.run(args, check=True)
 
     # It should exist now
     return full_path
@@ -96,7 +97,8 @@ def get_cpp_extensions():
     cpp_transform_pkgdir = Path('hexrd') / 'transforms/cpp_sublibrary'
     src_files = [str(cpp_transform_pkgdir / 'src/inverse_distortion.cpp')]
 
-    extra_compile_args = ['-O3', '-Wall', '-shared', '-std=c++11', '-funroll-loops']
+    extra_compile_args = ['-O3', '-Wall', '-shared', '-std=c++11',
+                          '-funroll-loops']
     if not sys.platform.startswith('win'):
         extra_compile_args.append('-fPIC')
 
@@ -108,11 +110,13 @@ def get_cpp_extensions():
         numpy.get_include(),
     ]
 
-    inverse_distortion_ext = Extension(name='hexrd.extensions.inverse_distortion',
-                                       sources=src_files,
-                                       extra_compile_args=extra_compile_args,
-                                       include_dirs=include_dirs,
-                                       language='c++')
+    inverse_distortion_ext = Extension(
+        name='hexrd.extensions.inverse_distortion',
+        sources=src_files,
+        extra_compile_args=extra_compile_args,
+        include_dirs=include_dirs,
+        language='c++',
+    )
 
     return [inverse_distortion_ext]
 
@@ -163,8 +167,8 @@ def get_extension_modules():
     name='hexrd',
     use_scm_version=True,
     setup_requires=['setuptools-scm'],
-    description = 'hexrd X-ray diffraction data analysis tool',
-    long_description = open('README.md').read(),
+    description='hexrd X-ray diffraction data analysis tool',
+    long_description=open('README.md').read(),
     author='The hexrd Development Team',
     author_email='joelvbernier@me.com',
     url='https://github.com/HEXRD/hexrd',
@@ -180,7 +184,7 @@ def get_extension_modules():
         'Programming Language :: Python :: 3.10',
         'Programming Language :: Python :: 3.11',
     ],
-    entry_points = entry_points,
+    entry_points=entry_points,
     ext_modules=ext_modules,
     packages=find_packages(),
     include_package_data=True,

From 1ade6aacad718b9afa49917d585e8ac1e4714713 Mon Sep 17 00:00:00 2001
From: Patrick Avery <patrick.avery@kitware.com>
Date: Wed, 22 Nov 2023 19:09:01 -0600
Subject: [PATCH 15/20] Add json numpy encoder/decoder

This also adds a quick test to verify that it works properly.

Signed-off-by: Patrick Avery <patrick.avery@kitware.com>
---
 hexrd/utils/json.py      | 40 ++++++++++++++++++++++++++++++++
 tests/test_utils_json.py | 50 ++++++++++++++++++++++++++++++++++++++++
 2 files changed, 90 insertions(+)
 create mode 100644 hexrd/utils/json.py
 create mode 100644 tests/test_utils_json.py

diff --git a/hexrd/utils/json.py b/hexrd/utils/json.py
new file mode 100644
index 000000000..0d42d9374
--- /dev/null
+++ b/hexrd/utils/json.py
@@ -0,0 +1,40 @@
+import base64
+import io
+import json
+
+import numpy as np
+
+ndarray_key = '!__hexrd_ndarray__'
+
+class NumpyEncoder(json.JSONEncoder):
+    def default(self, obj):
+        if isinstance(obj, np.ndarray):
+            # Write it as an npy file
+            with io.BytesIO() as bytes_io:
+                np.save(bytes_io, obj, allow_pickle=False)
+                data = bytes_io.getvalue()
+
+            return {
+                # Need to base64 encode it so it is json-valid
+                ndarray_key: base64.b64encode(data).decode('ascii')
+            }
+
+        # Let the base class default method raise the TypeError
+        return super().default(obj)
+
+
+class NumpyDecoder(json.JSONDecoder):
+    def __init__(self, *args, **kwargs):
+        kwargs = {
+            'object_hook': self.object_hook,
+            **kwargs,
+        }
+        super().__init__(*args, **kwargs)
+
+    def object_hook(self, obj):
+        if ndarray_key in obj:
+            data = base64.b64decode(obj[ndarray_key])
+            with io.BytesIO(data) as bytes_io:
+                return np.load(bytes_io)
+
+        return obj
diff --git a/tests/test_utils_json.py b/tests/test_utils_json.py
new file mode 100644
index 000000000..1bd557565
--- /dev/null
+++ b/tests/test_utils_json.py
@@ -0,0 +1,50 @@
+import json
+
+import numpy as np
+
+from hexrd.utils.json import NumpyDecoder, NumpyEncoder
+
+
+def test_decode_encode():
+    to_test = [
+        {
+            'floating': np.arange(50, dtype=np.float16),
+            'complex': np.arange(20, dtype=np.complex128),
+        },
+        {
+            'nested': {
+                'int8': np.arange(27, dtype=np.int8).reshape((3, 3, 3)),
+                'uint8': np.arange(8, dtype=np.uint8).reshape((2, 4)),
+                'not_numpy': 3,
+            }
+        },
+        np.array([0, 5, 4]),
+        5,
+        'string',
+    ]
+
+    output = json.dumps(to_test, cls=NumpyEncoder)
+    converted_back = json.loads(output, cls=NumpyDecoder)
+
+    assert _json_equal(to_test, converted_back)
+
+
+def _json_equal(a, b):
+    if isinstance(a, np.ndarray):
+        return np.array_equal(a, b) and a.dtype == b.dtype
+
+    if isinstance(a, dict):
+        if list(a) != list(b):
+            return False
+
+        for k in a:
+            return _json_equal(a[k], b[k])
+
+    if isinstance(a, list):
+        if len(a) != len(b):
+            return False
+
+        for i in range(len(a)):
+            return _json_equal(a[i], b[i])
+
+    return a == b

From f235676289ea55fc13aa95636f82f0901d27f5cf Mon Sep 17 00:00:00 2001
From: Patrick Avery <patrick.avery@kitware.com>
Date: Wed, 22 Nov 2023 19:18:22 -0600
Subject: [PATCH 16/20] Fix flake8 issues

I ran `black -l 80 -S ./test_inverse_distortion.py`

Signed-off-by: Patrick Avery <patrick.avery@kitware.com>
---
 tests/test_inverse_distortion.py | 182 ++++++++++++++++++-------------
 1 file changed, 107 insertions(+), 75 deletions(-)

diff --git a/tests/test_inverse_distortion.py b/tests/test_inverse_distortion.py
index 5d7d94b9e..a22d422ed 100644
--- a/tests/test_inverse_distortion.py
+++ b/tests/test_inverse_distortion.py
@@ -7,96 +7,128 @@
 test_dir = os.path.dirname(os.path.abspath(__file__))
 
 RHO_MAX = 204.8
-params = [-2.277777438488093e-05, -8.763805995117837e-05, -0.00047451698761967085]
-
-big_test_in = np.array([[ 47.031483 ,  -5.2170362],
-                        [ 60.0171   ,  27.218563 ],
-                        [ 60.697784 ,  25.48354  ],
-                        [ 56.90082  , -35.88738  ],
-                        [ 55.631718 , -37.62758  ],
-                        [ 41.258152 , -63.237328 ],
-                        [ 78.00906  ,  -8.576369 ],
-                        [ 77.7207   , -10.315189 ],
-                        [ 73.20562  ,  32.426453 ],
-                        [ 92.81449  , -13.717096 ],
-                        [101.26153  ,  18.790167 ],
-                        [ 33.428936 ,  99.08392  ],
-                        [101.51741  ,  17.049505 ],
-                        [ 85.12195  ,  59.84272  ],
-                        [-44.172375 ,  11.69572  ],
-                        [-57.850574 , -19.013659 ],
-                        [-57.169926 , -20.749386 ],
-                        [-52.772987 ,  44.117252 ],
-                        [-54.043003 ,  42.37685  ],
-                        [-74.88209  ,  16.800816 ],
-                        [-70.36986  , -25.959877 ],
-                        [-38.385185 ,  69.727234 ],
-                        [-75.17097  ,  15.061297 ],
-                        [-89.98957  ,  20.207851 ],
-                        [-98.708176 , -10.574363 ],
-                        [-82.30401  , -53.390797 ],
-                        [-98.45244  , -12.316093 ]], dtype=np.float32)
-
-big_test_out = np.array([[ 47.03288205,  -5.21719147],
-                         [ 60.02002476,  27.21988891],
-                         [ 60.70080301,  25.48480692],
-                         [ 56.90341105, -35.88901181],
-                         [ 55.63418288, -37.62924612],
-                         [ 41.26039938, -63.24077218],
-                         [ 78.01561783,  -8.57708985],
-                         [ 77.72717551, -10.31604838],
-                         [ 73.21095917,  32.42881771],
-                         [ 92.82553762, -13.71872887],
-                         [101.27584945,  18.79282435],
-                         [ 33.43310185,  99.09627097],
-                         [101.5318596 ,  17.05193195],
-                         [ 85.13101706,  59.84909563],
-                         [-44.17351296,  11.69602109],
-                         [-57.85318107, -19.01451522],
-                         [-57.17243759, -20.75029751],
-                         [-52.77530392,  44.11918895],
-                         [-54.04540365,  42.37873249],
-                         [-74.88783308,  16.80210463],
-                         [-70.37458323, -25.96162026],
-                         [-38.38762237,  69.73166096],
-                         [-75.17679039,  15.06246417],
-                         [-89.99957766,  20.21009857],
-                         [-98.72150605, -10.57579081],
-                         [-82.31199676, -53.39597868],
-                         [-98.46565139, -12.31774635]])
+params = [
+    -2.277777438488093e-05,
+    -8.763805995117837e-05,
+    -0.00047451698761967085,
+]
+
+big_test_in = np.array(
+    [
+        [47.031483, -5.2170362],
+        [60.0171, 27.218563],
+        [60.697784, 25.48354],
+        [56.90082, -35.88738],
+        [55.631718, -37.62758],
+        [41.258152, -63.237328],
+        [78.00906, -8.576369],
+        [77.7207, -10.315189],
+        [73.20562, 32.426453],
+        [92.81449, -13.717096],
+        [101.26153, 18.790167],
+        [33.428936, 99.08392],
+        [101.51741, 17.049505],
+        [85.12195, 59.84272],
+        [-44.172375, 11.69572],
+        [-57.850574, -19.013659],
+        [-57.169926, -20.749386],
+        [-52.772987, 44.117252],
+        [-54.043003, 42.37685],
+        [-74.88209, 16.800816],
+        [-70.36986, -25.959877],
+        [-38.385185, 69.727234],
+        [-75.17097, 15.061297],
+        [-89.98957, 20.207851],
+        [-98.708176, -10.574363],
+        [-82.30401, -53.390797],
+        [-98.45244, -12.316093],
+    ],
+    dtype=np.float32,
+)
+
+big_test_out = np.array(
+    [
+        [47.03288205, -5.21719147],
+        [60.02002476, 27.21988891],
+        [60.70080301, 25.48480692],
+        [56.90341105, -35.88901181],
+        [55.63418288, -37.62924612],
+        [41.26039938, -63.24077218],
+        [78.01561783, -8.57708985],
+        [77.72717551, -10.31604838],
+        [73.21095917, 32.42881771],
+        [92.82553762, -13.71872887],
+        [101.27584945, 18.79282435],
+        [33.43310185, 99.09627097],
+        [101.5318596, 17.05193195],
+        [85.13101706, 59.84909563],
+        [-44.17351296, 11.69602109],
+        [-57.85318107, -19.01451522],
+        [-57.17243759, -20.75029751],
+        [-52.77530392, 44.11918895],
+        [-54.04540365, 42.37873249],
+        [-74.88783308, 16.80210463],
+        [-70.37458323, -25.96162026],
+        [-38.38762237, 69.73166096],
+        [-75.17679039, 15.06246417],
+        [-89.99957766, 20.21009857],
+        [-98.72150605, -10.57579081],
+        [-82.31199676, -53.39597868],
+        [-98.46565139, -12.31774635],
+    ]
+)
+
 
 def test_known_values():
-  xy_in = np.array([[140.40087891, 117.74253845]])
-  expected_output = np.array([[140.44540352, 117.77987754]])
-  xy_out = inverse_distortion.ge_41rt_inverse_distortion(xy_in, RHO_MAX, params)
-  assert np.allclose(xy_out, expected_output)
+    xy_in = np.array([[140.40087891, 117.74253845]])
+    expected_output = np.array([[140.44540352, 117.77987754]])
+    xy_out = inverse_distortion.ge_41rt_inverse_distortion(
+        xy_in, RHO_MAX, params
+    )
+    assert np.allclose(xy_out, expected_output)
+
 
 def test_big_input():
-  xy_out = inverse_distortion.ge_41rt_inverse_distortion(big_test_in, RHO_MAX, params)
-  assert np.allclose(xy_out, big_test_out)
+    xy_out = inverse_distortion.ge_41rt_inverse_distortion(
+        big_test_in, RHO_MAX, params
+    )
+    assert np.allclose(xy_out, big_test_out)
+
 
 def test_large_input():
-  xy_in = np.array([[1e5, 1e5]])
-  xy_out = inverse_distortion.ge_41rt_inverse_distortion(xy_in, RHO_MAX, params)
-  # No specific expected output here, just ensure it doesn't fail
-  assert xy_out.shape == xy_in.shape
+    xy_in = np.array([[1e5, 1e5]])
+    xy_out = inverse_distortion.ge_41rt_inverse_distortion(
+        xy_in, RHO_MAX, params
+    )
+    # No specific expected output here, just ensure it doesn't fail
+    assert xy_out.shape == xy_in.shape
+
 
 def test_logged_data():
     # Load logged data
-    with open(os.path.join(test_dir, "data", "inverse_distortion_in_out.pkl"), 'rb') as f:
+    with open(
+        os.path.join(test_dir, "data", "inverse_distortion_in_out.pkl"), 'rb'
+    ) as f:
         logged_data = pickle.load(f)
 
     logged_inputs = logged_data['inputs']
     logged_outputs = logged_data['outputs']
     logged_params = logged_data['params']
 
-    for xy_in, xy_out_expected, params in zip(logged_inputs, logged_outputs, logged_params):
-        xy_out = inverse_distortion.ge_41rt_inverse_distortion(xy_in, RHO_MAX, params)
+    for xy_in, xy_out_expected, params in zip(
+        logged_inputs, logged_outputs, logged_params
+    ):
+        xy_out = inverse_distortion.ge_41rt_inverse_distortion(
+            xy_in, RHO_MAX, params
+        )
         assert np.allclose(xy_out, xy_out_expected, atol=1e-7)
 
+
 def test_random_values():
-  np.random.seed(42)
-  xy_in = np.random.rand(10, 2) * 200
-  xy_out = inverse_distortion.ge_41rt_inverse_distortion(xy_in, RHO_MAX, params)
-  # Verify function does not raise any exception
-  assert xy_out.shape == xy_in.shape
+    np.random.seed(42)
+    xy_in = np.random.rand(10, 2) * 200
+    xy_out = inverse_distortion.ge_41rt_inverse_distortion(
+        xy_in, RHO_MAX, params
+    )
+    # Verify function does not raise any exception
+    assert xy_out.shape == xy_in.shape

From 44593cb9f6aa39fbafdff2ec3b200eacaa1e0429 Mon Sep 17 00:00:00 2001
From: Patrick Avery <patrick.avery@kitware.com>
Date: Wed, 22 Nov 2023 19:25:08 -0600
Subject: [PATCH 17/20] Fix remaining pep8 issues

Signed-off-by: Patrick Avery <patrick.avery@kitware.com>
---
 hexrd/distortion/ge_41rt.py | 104 +++++++++++++++++++++++-------------
 hexrd/utils/json.py         |   1 +
 2 files changed, 67 insertions(+), 38 deletions(-)

diff --git a/hexrd/distortion/ge_41rt.py b/hexrd/distortion/ge_41rt.py
index cc9c3e585..8c52aee95 100644
--- a/hexrd/distortion/ge_41rt.py
+++ b/hexrd/distortion/ge_41rt.py
@@ -13,72 +13,101 @@
 
 RHO_MAX = 204.8  # max radius in mm for ge detector
 
+
 # NOTE: Deprecated in favor of inverse_distortion.ge_41rt_inverse_distortion
 @numba.njit(nogil=True, cache=True, fastmath=True)
-def _ge_41rt_inverse_distortion(inputs: np.ndarray[np.float64, np.float64],
-                                rhoMax: float,
-                                params: List[float]):
+def _ge_41rt_inverse_distortion(
+    inputs: np.ndarray[np.float64, np.float64],
+    rhoMax: float,
+    params: List[float],
+):
     radii = np.hypot(inputs[:, 0], inputs[:, 1])
     inverted_radii = np.reciprocal(radii)
-    cosines = inputs[:, 0]*inverted_radii
-    cosine_double_angles = 2*np.square(cosines)-1
-    cosine_quadruple_angles = 2*np.square(cosine_double_angles)-1
-    sqrt_p_is = rhoMax / np.sqrt(-(params[0]*cosine_double_angles+params[1]*cosine_quadruple_angles+params[2]))
-    solutions = (2/np.sqrt(3))*sqrt_p_is*np.cos(np.arccos(((-3*np.sqrt(3)/2)*radii/sqrt_p_is))/3+4*np.pi/3)
+    cosines = inputs[:, 0] * inverted_radii
+    cosine_double_angles = 2 * np.square(cosines) - 1
+    cosine_quadruple_angles = 2 * np.square(cosine_double_angles) - 1
+    sqrt_p_is = rhoMax / np.sqrt(
+        -(
+            params[0] * cosine_double_angles
+            + params[1] * cosine_quadruple_angles
+            + params[2]
+        )
+    )
+    solutions = (
+        (2 / np.sqrt(3))
+        * sqrt_p_is
+        * np.cos(
+            np.arccos(((-3 * np.sqrt(3) / 2) * radii / sqrt_p_is)) / 3
+            + 4 * np.pi / 3
+        )
+    )
 
     return solutions[:, None] * inputs * inverted_radii[:, None]
 
+
 @numba.njit(nogil=True, cache=True)
 def _ge_41rt_distortion(out, in_, rhoMax, params):
     p0, p1, p2, p3, p4, p5 = params[0:6]
-    rxi = 1.0/rhoMax
+    rxi = 1.0 / rhoMax
 
     for el in range(len(in_)):
         xi, yi = in_[el, 0:2]
-        ri = np.sqrt(xi*xi + yi*yi)
+        ri = np.sqrt(xi * xi + yi * yi)
         if ri < cnst.sqrt_epsf:
             ri_inv = 0.0
         else:
-            ri_inv = 1.0/ri
-        sinni = yi*ri_inv
-        cosni = xi*ri_inv
-        cos2ni = cosni*cosni - sinni*sinni
-        sin2ni = 2*sinni*cosni
-        cos4ni = cos2ni*cos2ni - sin2ni*sin2ni
-        ratio = ri*rxi
-
-        ri = (p0*ratio**p3*cos2ni
-              + p1*ratio**p4*cos4ni
-              + p2*ratio**p5
-              + 1)*ri
-        xi = ri*cosni
-        yi = ri*sinni
+            ri_inv = 1.0 / ri
+        sinni = yi * ri_inv
+        cosni = xi * ri_inv
+        cos2ni = cosni * cosni - sinni * sinni
+        sin2ni = 2 * sinni * cosni
+        cos4ni = cos2ni * cos2ni - sin2ni * sin2ni
+        ratio = ri * rxi
+
+        ri = (
+            p0 * ratio**p3 * cos2ni
+            + p1 * ratio**p4 * cos4ni
+            + p2 * ratio**p5
+            + 1
+        ) * ri
+        xi = ri * cosni
+        yi = ri * sinni
         out[el, 0] = xi
         out[el, 1] = yi
 
     return out
 
+
 def _rho_scl_func_inv(ri, ni, ro, rx, p):
-    retval = (p[0]*(ri/rx)**p[3] * np.cos(2.0 * ni) +
-              p[1]*(ri/rx)**p[4] * np.cos(4.0 * ni) +
-              p[2]*(ri/rx)**p[5] + 1)*ri - ro
+    retval = (
+        p[0] * (ri / rx) ** p[3] * np.cos(2.0 * ni)
+        + p[1] * (ri / rx) ** p[4] * np.cos(4.0 * ni)
+        + p[2] * (ri / rx) ** p[5]
+        + 1
+    ) * ri - ro
     return retval
 
 
 def _rho_scl_dfunc_inv(ri, ni, ro, rx, p):
-    retval = p[0]*(ri/rx)**p[3] * np.cos(2.0 * ni) * (p[3] + 1) + \
-        p[1]*(ri/rx)**p[4] * np.cos(4.0 * ni) * (p[4] + 1) + \
-        p[2]*(ri/rx)**p[5] * (p[5] + 1) + 1
+    retval = (
+        p[0] * (ri / rx) ** p[3] * np.cos(2.0 * ni) * (p[3] + 1)
+        + p[1] * (ri / rx) ** p[4] * np.cos(4.0 * ni) * (p[4] + 1)
+        + p[2] * (ri / rx) ** p[5] * (p[5] + 1)
+        + 1
+    )
     return retval
 
 
 def inverse_distortion_numpy(rho0, eta0, rhoMax, params):
-    return newton(rho0, _rho_scl_func_inv, _rho_scl_dfunc_inv,
-                  (eta0, rho0, rhoMax, params))
+    return newton(
+        rho0,
+        _rho_scl_func_inv,
+        _rho_scl_dfunc_inv,
+        (eta0, rho0, rhoMax, params),
+    )
 
 
 class GE_41RT(DistortionABC, metaclass=_RegisterDistortionClass):
-
     maptype = "GE_41RT"
 
     def __init__(self, params, **kwargs):
@@ -95,10 +124,9 @@ def params(self, x):
 
     @property
     def is_trivial(self):
-        return \
-            self.params[0] == 0 and \
-            self.params[1] == 0 and \
-            self.params[2] == 0
+        return (
+            self.params[0] == 0 and self.params[1] == 0 and self.params[2] == 0
+        )
 
     def apply(self, xy_in):
         if self.is_trivial:
@@ -119,4 +147,4 @@ def apply_inverse(self, xy_in):
             xy_out = inverse_distortion.ge_41rt_inverse_distortion(
                 xy_in, float(RHO_MAX), np.asarray(self.params[:3])
             )
-            return xy_out
\ No newline at end of file
+            return xy_out
diff --git a/hexrd/utils/json.py b/hexrd/utils/json.py
index 0d42d9374..88941a472 100644
--- a/hexrd/utils/json.py
+++ b/hexrd/utils/json.py
@@ -6,6 +6,7 @@
 
 ndarray_key = '!__hexrd_ndarray__'
 
+
 class NumpyEncoder(json.JSONEncoder):
     def default(self, obj):
         if isinstance(obj, np.ndarray):

From 988e5ccac75883424c4500083f2a3fb2af0b7fb8 Mon Sep 17 00:00:00 2001
From: Patrick Avery <patrick.avery@kitware.com>
Date: Fri, 24 Nov 2023 13:39:08 -0600
Subject: [PATCH 18/20] Add NumpyToNativeEncoder with a test

NumpyToNativeEncoder is a custom JSON encoder that encodes numpy types
into native types so it can be saved in JSON.

There is no corresponding decoder, since the JSON just contains native
types and does not need special decoding.

Signed-off-by: Patrick Avery <patrick.avery@kitware.com>
---
 hexrd/utils/json.py      | 12 +++++++++++-
 tests/test_utils_json.py | 32 +++++++++++++++++++++++++++++++-
 2 files changed, 42 insertions(+), 2 deletions(-)

diff --git a/hexrd/utils/json.py b/hexrd/utils/json.py
index 88941a472..46a3e9ff9 100644
--- a/hexrd/utils/json.py
+++ b/hexrd/utils/json.py
@@ -7,6 +7,17 @@
 ndarray_key = '!__hexrd_ndarray__'
 
 
+class NumpyToNativeEncoder(json.JSONEncoder):
+    # Change all Numpy arrays to native types during JSON encoding
+    def default(self, obj):
+        if isinstance(obj, np.ndarray):
+            return obj.tolist()
+        elif isinstance(obj, (np.generic, np.number)):
+            return obj.item()
+
+        return super().default(obj)
+
+
 class NumpyEncoder(json.JSONEncoder):
     def default(self, obj):
         if isinstance(obj, np.ndarray):
@@ -20,7 +31,6 @@ def default(self, obj):
                 ndarray_key: base64.b64encode(data).decode('ascii')
             }
 
-        # Let the base class default method raise the TypeError
         return super().default(obj)
 
 
diff --git a/tests/test_utils_json.py b/tests/test_utils_json.py
index 1bd557565..3824c9640 100644
--- a/tests/test_utils_json.py
+++ b/tests/test_utils_json.py
@@ -2,7 +2,7 @@
 
 import numpy as np
 
-from hexrd.utils.json import NumpyDecoder, NumpyEncoder
+from hexrd.utils.json import NumpyDecoder, NumpyEncoder, NumpyToNativeEncoder
 
 
 def test_decode_encode():
@@ -29,6 +29,36 @@ def test_decode_encode():
     assert _json_equal(to_test, converted_back)
 
 
+def test_numpy_to_native():
+    to_test = {
+        'inside': np.arange(27, dtype=np.int8).reshape((3, 3, 3)),
+        'nested': {
+            'float': np.arange(4, dtype=np.float32).reshape((2, 2)),
+        },
+        'float': np.float64(8.3),
+    }
+
+    inside_to_list = to_test['inside'].tolist()
+    nested_float_to_value = to_test['nested']['float'].tolist()
+    float_to_value = to_test['float'].item()
+
+    encoded = json.dumps(to_test, cls=NumpyToNativeEncoder)
+    output = json.loads(encoded)
+
+    assert (
+        isinstance(output['inside'], list) and
+        output['inside'] == to_test['inside'].tolist()
+    )
+    assert (
+        isinstance(output['float'], float) and
+        output['float'] == to_test['float'].item()
+    )
+    assert (
+        isinstance(output['nested']['float'], list) and
+        output['nested']['float'] == to_test['nested']['float'].tolist()
+    )
+
+
 def _json_equal(a, b):
     if isinstance(a, np.ndarray):
         return np.array_equal(a, b) and a.dtype == b.dtype

From 8a9cee702fd7a9f37a9c17ca1a244e698023dbf0 Mon Sep 17 00:00:00 2001
From: Patrick Avery <patrick.avery@kitware.com>
Date: Fri, 24 Nov 2023 14:33:13 -0600
Subject: [PATCH 19/20] Use raw_unicode_escape instead of base64 encoding

We can consider other encodings as well. Just need to get the bytes to
a string and back. The raw_unicode_escale appears to work.

Signed-off-by: Patrick Avery <patrick.avery@kitware.com>
---
 hexrd/utils/json.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/hexrd/utils/json.py b/hexrd/utils/json.py
index 46a3e9ff9..f56e707f1 100644
--- a/hexrd/utils/json.py
+++ b/hexrd/utils/json.py
@@ -1,4 +1,3 @@
-import base64
 import io
 import json
 
@@ -27,8 +26,7 @@ def default(self, obj):
                 data = bytes_io.getvalue()
 
             return {
-                # Need to base64 encode it so it is json-valid
-                ndarray_key: base64.b64encode(data).decode('ascii')
+                ndarray_key: data.decode('raw_unicode_escape')
             }
 
         return super().default(obj)
@@ -44,7 +42,7 @@ def __init__(self, *args, **kwargs):
 
     def object_hook(self, obj):
         if ndarray_key in obj:
-            data = base64.b64decode(obj[ndarray_key])
+            data = obj[ndarray_key].encode('raw_unicode_escape')
             with io.BytesIO(data) as bytes_io:
                 return np.load(bytes_io)
 

From e3d1ebf3c8033dd099da3afe576cdbb07bb9264a Mon Sep 17 00:00:00 2001
From: Zack Singer <jordan.singer@udri.udayton.edu>
Date: Fri, 24 Nov 2023 15:51:28 -0500
Subject: [PATCH 20/20] Change inverse-dist unit tests to use np ser-deser

---
 tests/data/inverse_distortion_in_out.json | 689 ++++++++++++++++++++++
 tests/data/inverse_distortion_in_out.pkl  | Bin 11303 -> 0 bytes
 tests/test_inverse_distortion.py          |  95 +--
 3 files changed, 700 insertions(+), 84 deletions(-)
 create mode 100644 tests/data/inverse_distortion_in_out.json
 delete mode 100644 tests/data/inverse_distortion_in_out.pkl

diff --git a/tests/data/inverse_distortion_in_out.json b/tests/data/inverse_distortion_in_out.json
new file mode 100644
index 000000000..64aea1c14
--- /dev/null
+++ b/tests/data/inverse_distortion_in_out.json
@@ -0,0 +1,689 @@
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diff --git a/tests/test_inverse_distortion.py b/tests/test_inverse_distortion.py
index a22d422ed..dd1fb8427 100644
--- a/tests/test_inverse_distortion.py
+++ b/tests/test_inverse_distortion.py
@@ -1,9 +1,10 @@
 import os
-import pickle
+import json
 
 import numpy as np
 from hexrd.extensions import inverse_distortion
 
+
 test_dir = os.path.dirname(os.path.abspath(__file__))
 
 RHO_MAX = 204.8
@@ -13,71 +14,6 @@
     -0.00047451698761967085,
 ]
 
-big_test_in = np.array(
-    [
-        [47.031483, -5.2170362],
-        [60.0171, 27.218563],
-        [60.697784, 25.48354],
-        [56.90082, -35.88738],
-        [55.631718, -37.62758],
-        [41.258152, -63.237328],
-        [78.00906, -8.576369],
-        [77.7207, -10.315189],
-        [73.20562, 32.426453],
-        [92.81449, -13.717096],
-        [101.26153, 18.790167],
-        [33.428936, 99.08392],
-        [101.51741, 17.049505],
-        [85.12195, 59.84272],
-        [-44.172375, 11.69572],
-        [-57.850574, -19.013659],
-        [-57.169926, -20.749386],
-        [-52.772987, 44.117252],
-        [-54.043003, 42.37685],
-        [-74.88209, 16.800816],
-        [-70.36986, -25.959877],
-        [-38.385185, 69.727234],
-        [-75.17097, 15.061297],
-        [-89.98957, 20.207851],
-        [-98.708176, -10.574363],
-        [-82.30401, -53.390797],
-        [-98.45244, -12.316093],
-    ],
-    dtype=np.float32,
-)
-
-big_test_out = np.array(
-    [
-        [47.03288205, -5.21719147],
-        [60.02002476, 27.21988891],
-        [60.70080301, 25.48480692],
-        [56.90341105, -35.88901181],
-        [55.63418288, -37.62924612],
-        [41.26039938, -63.24077218],
-        [78.01561783, -8.57708985],
-        [77.72717551, -10.31604838],
-        [73.21095917, 32.42881771],
-        [92.82553762, -13.71872887],
-        [101.27584945, 18.79282435],
-        [33.43310185, 99.09627097],
-        [101.5318596, 17.05193195],
-        [85.13101706, 59.84909563],
-        [-44.17351296, 11.69602109],
-        [-57.85318107, -19.01451522],
-        [-57.17243759, -20.75029751],
-        [-52.77530392, 44.11918895],
-        [-54.04540365, 42.37873249],
-        [-74.88783308, 16.80210463],
-        [-70.37458323, -25.96162026],
-        [-38.38762237, 69.73166096],
-        [-75.17679039, 15.06246417],
-        [-89.99957766, 20.21009857],
-        [-98.72150605, -10.57579081],
-        [-82.31199676, -53.39597868],
-        [-98.46565139, -12.31774635],
-    ]
-)
-
 
 def test_known_values():
     xy_in = np.array([[140.40087891, 117.74253845]])
@@ -88,13 +24,6 @@ def test_known_values():
     assert np.allclose(xy_out, expected_output)
 
 
-def test_big_input():
-    xy_out = inverse_distortion.ge_41rt_inverse_distortion(
-        big_test_in, RHO_MAX, params
-    )
-    assert np.allclose(xy_out, big_test_out)
-
-
 def test_large_input():
     xy_in = np.array([[1e5, 1e5]])
     xy_out = inverse_distortion.ge_41rt_inverse_distortion(
@@ -105,21 +34,19 @@ def test_large_input():
 
 
 def test_logged_data():
-    # Load logged data
     with open(
-        os.path.join(test_dir, "data", "inverse_distortion_in_out.pkl"), 'rb'
+        os.path.join(test_dir, 'data', 'inverse_distortion_in_out.json'),
+        encoding='utf-8'
     ) as f:
-        logged_data = pickle.load(f)
+        example_data = json.load(f)
 
-    logged_inputs = logged_data['inputs']
-    logged_outputs = logged_data['outputs']
-    logged_params = logged_data['params']
+    for example in example_data:
+        xy_in = np.asarray(example['logged_inputs'])
+        xy_out_expected = np.asarray(example['logged_outputs'])
+        example_params = np.asarray(example['logged_params'])
 
-    for xy_in, xy_out_expected, params in zip(
-        logged_inputs, logged_outputs, logged_params
-    ):
         xy_out = inverse_distortion.ge_41rt_inverse_distortion(
-            xy_in, RHO_MAX, params
+            xy_in, RHO_MAX, example_params
         )
         assert np.allclose(xy_out, xy_out_expected, atol=1e-7)
 
@@ -130,5 +57,5 @@ def test_random_values():
     xy_out = inverse_distortion.ge_41rt_inverse_distortion(
         xy_in, RHO_MAX, params
     )
-    # Verify function does not raise any exception
+    # Verify function doesn't raise any exceptions
     assert xy_out.shape == xy_in.shape