Merge pull request py4dstem#597 from py4dstem/phase_contrast_refactor

You get a Mixin, you get a Mixin, every ptycho class gets a Mixin Former-commit-id: 8096597
bsavitzky · Jan 22, 2024 · a1be36d · a1be36d
2 parents cc4f407 + 399300e
commit a1be36d
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Showing 32 changed files with 15,744 additions and 24,174 deletions.
diff --git a/.github/workflows/check_install_dev.yml b/.github/workflows/check_install_dev.yml
@@ -16,7 +16,7 @@ jobs:
                 allow_failure: [false]
                 runs-on: [ubuntu-latest]
                 architecture: [x86_64]
-                python-version: ["3.9", "3.10", "3.11", "3.12"]
+                python-version: ["3.10", "3.11", "3.12"]
                 # include:
                 #     - python-version: "3.12.0-beta.4"
                 #       runs-on: ubuntu-latest

diff --git a/.github/workflows/check_install_main.yml b/.github/workflows/check_install_main.yml
@@ -16,7 +16,7 @@ jobs:
                 allow_failure: [false]
                 runs-on: [ubuntu-latest, windows-latest, macos-latest]
                 architecture: [x86_64]
-                python-version: ["3.9", "3.10", "3.11", "3.12"]
+                python-version: ["3.10", "3.11", "3.12"]
                 #include:
                 #    - python-version: "3.12.0-beta.4"
                 #      runs-on: ubuntu-latest

diff --git a/.github/workflows/check_install_quick.yml b/.github/workflows/check_install_quick.yml
@@ -20,7 +20,7 @@ jobs:
                 allow_failure: [false]
                 runs-on: [ubuntu-latest] 
                 architecture: [x86_64]
-                python-version: ["3.9", "3.12"]
+                python-version: ["3.10", "3.12"]
                 # Currently no public runners available for this but this or arm64 should work next time
                 # include:
                 #     - python-version: "3.10"
@@ -42,4 +42,4 @@ jobs:
                 python -c "import py4DSTEM; print(py4DSTEM.__version__)"
             # - name: Check machine arch
             #   run: |
-            #     python -c "import platform; print(platform.machine())"
+            #     python -c "import platform; print(platform.machine())"
diff --git a/py4DSTEM/preprocess/preprocess.py b/py4DSTEM/preprocess/preprocess.py
@@ -576,7 +576,9 @@ def resample_data_diffraction(
             resampling_factor = np.array(output_size) / np.array(datacube.shape[-2:])
 
         resampling_factor = np.concatenate(((1, 1), resampling_factor))
-        datacube.data = zoom(datacube.data, resampling_factor, order=1)
+        datacube.data = zoom(
+            datacube.data, resampling_factor, order=1, mode="grid-wrap", grid_mode=True
+        )
         datacube.calibration.set_Q_pixel_size(
             datacube.calibration.get_Q_pixel_size() / resampling_factor[2]
         )

diff --git a/py4DSTEM/process/phase/__init__.py b/py4DSTEM/process/phase/__init__.py
@@ -2,15 +2,15 @@
 
 _emd_hook = True
 
-from py4DSTEM.process.phase.iterative_dpc import DPCReconstruction
-from py4DSTEM.process.phase.iterative_mixedstate_multislice_ptychography import MixedstateMultislicePtychographicReconstruction
-from py4DSTEM.process.phase.iterative_mixedstate_ptychography import MixedstatePtychographicReconstruction
-from py4DSTEM.process.phase.iterative_multislice_ptychography import MultislicePtychographicReconstruction
-from py4DSTEM.process.phase.iterative_overlap_magnetic_tomography import OverlapMagneticTomographicReconstruction
-from py4DSTEM.process.phase.iterative_overlap_tomography import OverlapTomographicReconstruction
-from py4DSTEM.process.phase.iterative_parallax import ParallaxReconstruction
-from py4DSTEM.process.phase.iterative_simultaneous_ptychography import SimultaneousPtychographicReconstruction
-from py4DSTEM.process.phase.iterative_singleslice_ptychography import SingleslicePtychographicReconstruction
+from py4DSTEM.process.phase.dpc import DPC
+from py4DSTEM.process.phase.magnetic_ptychographic_tomography import MagneticPtychographicTomography
+from py4DSTEM.process.phase.magnetic_ptychography import MagneticPtychography
+from py4DSTEM.process.phase.mixedstate_multislice_ptychography import MixedstateMultislicePtychography
+from py4DSTEM.process.phase.mixedstate_ptychography import MixedstatePtychography
+from py4DSTEM.process.phase.multislice_ptychography import MultislicePtychography
+from py4DSTEM.process.phase.parallax import Parallax
+from py4DSTEM.process.phase.ptychographic_tomography import PtychographicTomography
+from py4DSTEM.process.phase.singleslice_ptychography import SingleslicePtychography
 from py4DSTEM.process.phase.parameter_optimize import OptimizationParameter, PtychographyOptimizer
 
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