Release into main version 0.14.10

.github/workflows/black.yml

@@ -10,5 +10,5 @@ jobs:
  lint:
  runs-on: ubuntu-latest
  steps:
- - uses: actions/checkout@v3
+ - uses: actions/checkout@v4
  - uses: psf/black@stable

.github/workflows/build-flake.yml

@@ -18,9 +18,9 @@ jobs:
  runs-on: ubuntu-latest
 
  steps:
- - uses: actions/checkout@v3
+ - uses: actions/checkout@v4
  - name: Set up Python 3.10
- uses: actions/setup-python@v3
+ uses: actions/setup-python@v5
  with:
  python-version: "3.10"
  - name: Install dependencies

.github/workflows/check_install_dev.yml

@@ -28,10 +28,10 @@ jobs:
  # runs-on: macos-latest
  # allow_failure: true
  steps:
- - uses: actions/checkout@v3
+ - uses: actions/checkout@v4
 
  - name: Setup Python ${{ matrix.python-version }}
- uses: actions/setup-python@v4
+ uses: actions/setup-python@v5
  with:
  python-version: ${{ matrix.python-version }}
  - name: Install repo

.github/workflows/check_install_main.yml

@@ -28,10 +28,10 @@ jobs:
  # runs-on: macos-latest
  # allow_failure: true
  steps:
- - uses: actions/checkout@v3
+ - uses: actions/checkout@v4
 
  - name: Setup Python ${{ matrix.python-version }}
- uses: actions/setup-python@v4
+ uses: actions/setup-python@v5
  with:
  python-version: ${{ matrix.python-version }}
  - name: Install repo

.github/workflows/check_install_quick.yml

@@ -28,10 +28,10 @@ jobs:
  # runs-on: macos-latest
  # allow_failure: true
  steps:
- - uses: actions/checkout@v3
+ - uses: actions/checkout@v4
 
  - name: Setup Python ${{ matrix.python-version }}
- uses: actions/setup-python@v4
+ uses: actions/setup-python@v5
  with:
  python-version: ${{ matrix.python-version }}
  - name: Install repo

.github/workflows/linter.yml

@@ -11,13 +11,13 @@ jobs:
  runs-on: ubuntu-latest
  steps:
  - name: Checkout code
- uses: actions/checkout@v3
+ uses: actions/checkout@v4
  with:
  # Full git history is needed to get a proper list of changed files within `super-linter`
  fetch-depth: 0
 
  - name: Lint Code Base
- uses: github/super-linter@v4
+ uses: github/super-linter@v5
  env:
  VALIDATE_ALL_CODEBASE: false
  VALIDATE_PYTHON_FLAKE8: true

.github/workflows/pypi_upload.yml

@@ -6,22 +6,22 @@ on:
  push:
  branches:
  - main
- pull_request:
- branches:
- - main
+ # pull_request:
+ #  branches:
+ #  - main
 
 jobs:
  update_version:
  runs-on: ubuntu-latest
  name: Check if version.py is changed and update if the version.py is not changed
  steps:
- - uses: actions/checkout@v3
+ - uses: actions/checkout@v4
  with:
  fetch-depth: 0 
  token: ${{ secrets.GH_ACTION_VERSION_UPDATE }} 
  - name: Get changed files
  id: changed-files-specific
- uses: tj-actions/changed-files@v41
+ uses: tj-actions/changed-files@v43
  with:
  files: |
  py4DSTEM/version.py
@@ -39,47 +39,47 @@ jobs:
  git config --global user.email "[email protected]"
  git config --global user.name "bsavitzky"
  git commit -a -m "Auto-update version number (GH Action)"
- git push origin main
- sync_with_dev:
- needs: update_version
- runs-on: ubuntu-latest
- name: Sync main with dev
- steps:
- - name: Sync main with dev
- uses: actions/checkout@v3
- with:
- ref: dev
- fetch-depth: 0
- token: ${{ secrets.GH_ACTION_VERSION_UPDATE }}
- - run: |
- # set strategy to default merge
- git config pull.rebase false
- git config --global user.email "[email protected]"
- git config --global user.name "bsavitzky"
- git pull origin main --commit --no-edit
- git push origin dev
- deploy:
- needs: sync_with_dev
- runs-on: ubuntu-latest
- name: Deploy to PyPI
- steps:
- - uses: actions/checkout@v3
- with:
- ref: dev
- - name: Set up Python
- uses: actions/setup-python@v2
- with:
- python-version: 3.8
- - name: Install dependencies
- run: |
- python -m pip install --upgrade pip
- pip install build
- - name: Build package
- run: python -m build
- - name: Publish package
- uses: pypa/gh-action-pypi-publish@release/v1
- with:
- user: __token__
- password: ${{ secrets.PYPI_API_TOKEN }}
+ git push origin
+ # sync_with_dev:
+ #  needs: update_version
+ #  runs-on: ubuntu-latest
+ #  name: Sync main with dev
+ #  steps:
+ #  - name: Sync main with dev
+ #  uses: actions/checkout@v4
+ #  with:
+ #  ref: dev
+ #  fetch-depth: 0
+ #  token: ${{ secrets.GH_ACTION_VERSION_UPDATE }}
+ #  - run: |
+ #  # set strategy to default merge
+ #  git config pull.rebase false
+ #  git config --global user.email "[email protected]"
+ #  git config --global user.name "bsavitzky"
+ #  git pull origin main --commit --no-edit
+ #  git push origin dev
+ # deploy:
+ #  needs: sync_with_dev
+ #  runs-on: ubuntu-latest
+ #  name: Deploy to PyPI
+ #  steps:
+ #  - uses: actions/checkout@v4
+ #  with:
+ #  ref: dev
+ #  - name: Set up Python
+ #  uses: actions/setup-python@v5
+ #  with:
+ #  python-version: 3.8
+ #  - name: Install dependencies
+ #  run: |
+ #  python -m pip install --upgrade pip
+ #  pip install build
+ #  - name: Build package
+ #  run: python -m build
+ #  - name: Publish package
+ #  uses: pypa/gh-action-pypi-publish@release/v1
+ #  with:
+ #  user: __token__
+ #  password: ${{ secrets.PYPI_API_TOKEN }}
 
 

README.md

@@ -1,7 +1,7 @@
 
 > :warning: **py4DSTEM version 0.14 update** :warning: Warning: this is a major update and we expect some workflows to break. You can still install previous versions of py4DSTEM [as discussed here](#legacyinstall)
 
-
+> :warning: **Phase retrieval refactor version 0.14.9** :warning: Warning: The phase-retrieval modules in py4DSTEM (DPC, parallax, and ptychography) underwent a major refactor in version 0.14.9 and as such older tutorial notebooks will not work as expected. Notably, class names have been pruned to remove the trailing "Reconstruction" (`DPCReconstruction` -> `DPC` etc.), and regularization functions have dropped the `_iter` suffix (and are instead specified as boolean flags). We are working on updating the tutorial notebooks to reflect these changes. In the meantime, there's some more information in the relevant pull request [here](https://github.com/py4dstem/py4DSTEM/pull/597#issuecomment-1890325568).
 
 ![py4DSTEM logo](/images/py4DSTEM_logo.png)
 

docs/papers.md

@@ -5,57 +5,76 @@
 
 Please email [email protected] if you have used py4DSTEM for analysis and your paper is not listed below!
 
-### 2022 (9)
+### 2023 (0)
 
-[Correlative image learning of chemo-mechanics in phase-transforming solids](https://www.nature.com/articles/s41563-021-01191-0), Nature Materials (2022)
 
-[Correlative analysis of structure and chemistry of LixFePO4 platelets using 4D-STEM and X-ray ptychography](https://doi.org/10.1016/j.mattod.2021.10.031), Materials Today 52, 102 (2022).
 
-[Visualizing Grain Statistics in MOCVD WSe2 through Four-Dimensional Scanning Transmission Electron Microscopy](https://doi.org/10.1021/acs.nanolett.1c04315), Nano Letters 22, 2578 (2022).
+### 2022 (16)
 
-[Electric field control of chirality](https://doi.org/10.1126/sciadv.abj8030), Science Advances 8 (2022).
 
-[Real-Time Interactive 4D-STEM Phase-Contrast Imaging From Electron Event Representation Data: Less computation with the right representation](https://doi.org/10.1109/MSP.2021.3120981),  IEEE Signal Processing Magazine 39, 25 (2022).
+[Disentangling multiple scattering with deep learning: application to strain mapping from electron diffraction patterns](https://doi.org/10.1038/s41524-022-00939-9), J Munshi*, A Rakowski*, et al., npj Computational Materials 8, 254 (2022)
 
-[Microstructural dependence of defect formation in iron-oxide thin films](https://doi.org/10.1016/j.apsusc.2022.152844), Applied Surface Science 589, 152844 (2022).
+[Flexible CO2 Sensor Architecture with Selective Nitrogen Functionalities by One-Step Laser-Induced Conversion of Versatile Organic Ink](https://doi.org/10.1002/adfm.202207406), H Wang et al., Advanced Functional Materials 32, 2207406 (2022)
 
-[Chemical and Structural Alterations in the Amorphous Structure of Obsidian due to Nanolites](https://doi.org/10.1017/S1431927621013957), Microscopy and Microanalysis 28, 289 (2022).
+[Defect Contrast with 4D-STEM: Understanding Crystalline Order with Virtual Detectors and Beam Modification](https://doi.org/10.1093/micmic/ozad045) SM Ribet et al., Microscopy and Microanalysis 29, 1087 (2023).
 
-[Nanoscale characterization of crystalline and amorphous phases in silicon oxycarbide ceramics using 4D-STEM](https://doi.org/10.1016/j.matchar.2021.111512), Materials Characterization 181, 111512 (2021).
+[Structural heterogeneity in non-crystalline TexSe1−x thin films](https://doi.org/10.1063/5.0094600), B Sari et al., Applied Physics Letters 121, 012101 (2022)
 
-[Disentangling multiple scattering with deep learning: application to strain mapping from electron diffraction patterns](https://arxiv.org/abs/2202.00204), arXiv:2202.00204 (2022).
+[Cryogenic 4D-STEM analysis of an amorphouscrystalline polymer blend: Combined nanocrystalline and amorphous phase mapping](https://doi.org/10.1016/j.isci.2022.103882), J Donohue et al., iScience 25, 103882 (2022)
+
+[Hydrogen-assisted decohesion associated with nanosized grain boundary κ-carbides in a high-Mn lightweight steel](https://doi.org/10.1016/j.actamat.2022.118392), MN Elkot et al., Acta Materialia
+ 241, 118392 (2022)
+
+[4D-STEM Ptychography for Electron-Beam-Sensitive Materials](https://doi.org/10.1021/acscentsci.2c01137), G Li et al., ACS Central Science 8, 1579 (2022)
+
+[Developing a Chemical and Structural Understanding of the Surface Oxide in a Niobium Superconducting Qubit](https://doi.org/10.1021/acsnano.2c07913), AA Murthy et al., ACS Nano 16, 17257 (2022)
+
+[Correlative image learning of chemo-mechanics in phase-transforming solids](https://www.nature.com/articles/s41563-021-01191-0), HD Deng et al., Nature Materials (2022)
+
+[Correlative analysis of structure and chemistry of LixFePO4 platelets using 4D-STEM and X-ray ptychography](https://doi.org/10.1016/j.mattod.2021.10.031), LA Hughes*, BH Savitzky, et al., Materials Today 52, 102 (2022)
+
+[Visualizing Grain Statistics in MOCVD WSe2 through Four-Dimensional Scanning Transmission Electron Microscopy](https://doi.org/10.1021/acs.nanolett.1c04315), A Londoño-Calderon et al., Nano Letters 22, 2578 (2022)
+
+[Electric field control of chirality](https://doi.org/10.1126/sciadv.abj8030), P Behera et al., Science Advances 8 (2022)
+
+[Real-Time Interactive 4D-STEM Phase-Contrast Imaging From Electron Event Representation Data: Less computation with the right representation](https://doi.org/10.1109/MSP.2021.3120981), P Pelz et al., IEEE Signal Processing Magazine 39, 25 (2022)
+
+[Microstructural dependence of defect formation in iron-oxide thin films](https://doi.org/10.1016/j.apsusc.2022.152844), BK Derby et al., Applied Surface Science 589, 152844 (2022)
+
+[Chemical and Structural Alterations in the Amorphous Structure of Obsidian due to Nanolites](https://doi.org/10.1017/S1431927621013957), E Kennedy et al., Microscopy and Microanalysis 28, 289 (2022)
+
+[Nanoscale characterization of crystalline and amorphous phases in silicon oxycarbide ceramics using 4D-STEM](https://doi.org/10.1016/j.matchar.2021.111512), Ni Yang et al., Materials Characterization 181, 111512 (2021)
 
 
 
 ### 2021 (10)
 
-[Cryoforged nanotwinned titanium with ultrahigh strength and ductility](https://doi.org/10.1126/science.abe7252), Science 16, 373, 1363 (2021).
+[Cryoforged nanotwinned titanium with ultrahigh strength and ductility](https://doi.org/10.1126/science.abe7252), Science 16, 373, 1363 (2021)
 
-[Strain fields in twisted bilayer graphene](https://doi.org/10.1038/s41563-021-00973-w), Nature Materials 20, 956 (2021).
+[Strain fields in twisted bilayer graphene](https://doi.org/10.1038/s41563-021-00973-w), Nature Materials 20, 956 (2021)
 
-[Determination of Grain-Boundary Structure and Electrostatic Characteristics in a SrTiO3 Bicrystal by Four-Dimensional Electron Microscopy](https://doi.org/10.1021/acs.nanolett.1c02960), Nanoletters 21, 9138 (2021).
+[Determination of Grain-Boundary Structure and Electrostatic Characteristics in a SrTiO3 Bicrystal by Four-Dimensional Electron Microscopy](https://doi.org/10.1021/acs.nanolett.1c02960), Nanoletters 21, 9138 (2021)
 
 [Local Lattice Deformation of Tellurene Grain Boundaries by Four-Dimensional Electron Microscopy](https://pubs.acs.org/doi/10.1021/acs.jpcc.1c00308), Journal of Physical Chemistry C 125, 3396 (2021).
 
-[Extreme mixing in nanoscale transition metal alloys](https://doi.org/10.1016/j.matt.2021.04.014), Matter 4, 2340 (2021).
+[Extreme mixing in nanoscale transition metal alloys](https://doi.org/10.1016/j.matt.2021.04.014), Matter 4, 2340 (2021)
 
-[Multibeam Electron Diffraction](https://doi.org/10.1017/S1431927620024770), Microscopy and Microanalysis 27, 129 (2021).
+[Multibeam Electron Diffraction](https://doi.org/10.1017/S1431927620024770), Microscopy and Microanalysis 27, 129 (2021)
 
-[A Fast Algorithm for Scanning Transmission Electron Microscopy Imaging and 4D-STEM Diffraction Simulations](https://doi.org/10.1017/S1431927621012083), Microscopy and Microanalysis 27, 835 (2021).
+[A Fast Algorithm for Scanning Transmission Electron Microscopy Imaging and 4D-STEM Diffraction Simulations](https://doi.org/10.1017/S1431927621012083), Microscopy and Microanalysis 27, 835 (2021)
 
-[Fast Grain Mapping with Sub-Nanometer Resolution Using 4D-STEM with Grain Classification by Principal Component Analysis and Non-Negative Matrix Factorization](https://doi.org/10.1017/S1431927621011946), Microscopy and Microanalysis 27, 794
+[Fast Grain Mapping with Sub-Nanometer Resolution Using 4D-STEM with Grain Classification by Principal Component Analysis and Non-Negative Matrix Factorization](https://doi.org/10.1017/S1431927621011946), Microscopy and Microanalysis 27, 794 (2021)
 
-[Prismatic 2.0 – Simulation software for scanning and high resolution transmission electron microscopy (STEM and HRTEM)](https://doi.org/10.1016/j.micron.2021.103141), Micron 151, 103141 (2021).
+[Prismatic 2.0 – Simulation software for scanning and high resolution transmission electron microscopy (STEM and HRTEM)](https://doi.org/10.1016/j.micron.2021.103141), Micron 151, 103141 (2021)
 
-[4D-STEM of Beam-Sensitive Materials](https://doi.org/10.1021/acs.accounts.1c00073), Accounts of Chemical Research 54, 2543 (2021).
+[4D-STEM of Beam-Sensitive Materials](https://doi.org/10.1021/acs.accounts.1c00073), Accounts of Chemical Research 54, 2543 (2021)
 
 
 ### 2020 (3)
 
-[Patterned probes for high precision 4D-STEM bragg measurements](https://doi.org/10.1063/5.0015532), Ultramicroscopy 209, 112890 (2020).
-
+[Patterned probes for high precision 4D-STEM bragg measurements](https://doi.org/10.1063/5.0015532), Ultramicroscopy 209, 112890 (2020)
 
-[Tilted fluctuation electron microscopy](https://doi.org/10.1063/5.0015532), Applied Physics Letters 117, 091903 (2020).
+[Tilted fluctuation electron microscopy](https://doi.org/10.1063/5.0015532), Applied Physics Letters 117, 091903 (2020)
 
 [4D-STEM elastic stress state characterisation of a TWIP steel nanotwin](https://arxiv.org/abs/2004.03982), arXiv:2004.03982
 

py4DSTEM/braggvectors/diskdetection_cuda.py

@@ -156,9 +156,11 @@ def find_Bragg_disks_CUDA(
  patt_idx = batch_idx * batch_size + subbatch_idx
  rx, ry = np.unravel_index(patt_idx, (datacube.R_Nx, datacube.R_Ny))
  batched_subcube[subbatch_idx, :, :] = cp.array(
- datacube.data[rx, ry, :, :]
- if filter_function is None
- else filter_function(datacube.data[rx, ry, :, :]),
+ (
+ datacube.data[rx, ry, :, :]
+ if filter_function is None
+ else filter_function(datacube.data[rx, ry, :, :])
+ ),
  dtype=cp.float32,
  )
 

py4DSTEM/datacube/datacube.py

@@ -405,7 +405,9 @@ def pad_Q(self, N=None, output_size=None):
  d = pad_data_diffraction(self, pad_factor=N, output_size=output_size)
  return d
 
- def resample_Q(self, N=None, output_size=None, method="bilinear"):
+ def resample_Q(
+ self, N=None, output_size=None, method="bilinear", conserve_array_sums=False
+ ):
  """
  Resamples the data in diffraction space by resampling factor N, or to match output_size,
  using either 'fourier' or 'bilinear' interpolation.
@@ -418,7 +420,11 @@ def resample_Q(self, N=None, output_size=None, method="bilinear"):
  from py4DSTEM.preprocess import resample_data_diffraction
 
  d = resample_data_diffraction(
- self, resampling_factor=N, output_size=output_size, method=method
+ self,
+ resampling_factor=N,
+ output_size=output_size,
+ method=method,
+ conserve_array_sums=conserve_array_sums,
  )
  return d
 
@@ -479,13 +485,29 @@ def filter_hot_pixels(self, thresh, ind_compare=1, return_mask=False):
  """
  from py4DSTEM.preprocess import filter_hot_pixels
 
- d = filter_hot_pixels(
+ datacube = filter_hot_pixels(
  self,
  thresh,
  ind_compare,
  return_mask,
  )
- return d
+ return datacube
+
+ def median_filter_masked_pixels(self, mask, kernel_width: int = 3):
+ """
+ This function fixes a datacube where the same pixels are consistently
+ bad. It requires a mask that identifies all the bad pixels in the dataset.
+ Then for each diffraction pattern, a median kernel is applied around each
+ bad pixel with the specified width.
+ """
+ from py4DSTEM.preprocess import median_filter_masked_pixels
+
+ datacube = median_filter_masked_pixels(
+ self,
+ mask,
+ kernel_width,
+ )
+ return datacube
 
  # Probe
 
@@ -494,7 +516,7 @@ def get_vacuum_probe(
  ROI=None,
  align=True,
  mask=None,
- threshold=0.2,
+ threshold=0.0,
  expansion=12,
  opening=3,
  verbose=False,

py4DSTEM/io/importfile.py

@@ -75,7 +75,7 @@ def import_file(
  "gatan_K2_bin",
  "mib",
  "arina",
- "abTEM"
+ "abTEM",
  # "kitware_counted",
  ], "Error: filetype not recognized"
 

py4DSTEM/io/legacy/legacy13/v13_emd_classes/io.py

@@ -361,7 +361,7 @@ def Array_to_h5(array, group):
  data = grp.create_dataset(
  "data",
  shape=array.data.shape,
- data=array.data
+ data=array.data,
  # dtype = type(array.data)
  )
  data.attrs.create(