torch-ctf 0.0.1__tar.gz

torch_ctf-0.0.1/.copier-answers.yml

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+# Do not edit - changes here will be overwritten by Copier
+_commit: v1
+_src_path: gh:pydev-guide/pyrepo-copier
+author_email: jdickerson@berkeley.edu
+author_name: Josh Dickerson
+github_username: jdickerson95
+mode: tooling
+module_name: torch_ctf
+project_name: torch-ctf
+project_short_description: CTF calculation for cryoEM in torch
+

torch_ctf-0.0.1/.github/ISSUE_TEMPLATE.md

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+* torch-ctf version:
+* Python version:
+* Operating System:
+
+### Description
+
+Describe what you were trying to get done.
+Tell us what happened, what went wrong, and what you expected to happen.
+
+### What I Did
+
+```
+Paste the command(s) you ran and the output.
+If there was a crash, please include the traceback here.
+```

torch_ctf-0.0.1/.github/TEST_FAIL_TEMPLATE.md

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+---
+title: "{{ env.TITLE }}"
+labels: [bug]
+---
+The {{ workflow }} workflow failed on {{ date | date("YYYY-MM-DD HH:mm") }} UTC
+
+The most recent failing test was on {{ env.PLATFORM }} py{{ env.PYTHON }}
+with commit: {{ sha }}
+
+Full run: https://github.com/{{ repo }}/actions/runs/{{ env.RUN_ID }}
+
+(This post will be updated if another test fails, as long as this issue remains open.)

torch_ctf-0.0.1/.github/dependabot.yml

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+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    commit-message:
+      prefix: "ci(dependabot):"

torch_ctf-0.0.1/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: [main]
+    tags: [v*]
+  pull_request:
+  workflow_dispatch:
+  schedule:
+    # run every week (for --pre release tests)
+    - cron: "0 0 * * 0"
+
+# cancel in-progress runs that use the same workflow and branch
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  check-manifest:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+      - run: pipx run check-manifest
+
+  test:
+    name: ${{ matrix.platform }} (${{ matrix.python-version }})
+    runs-on: ${{ matrix.platform }}
+    env:
+      UV_PRERELEASE: ${{ github.event_name == 'schedule' && 'allow' || 'if-necessary-or-explicit' }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"]
+        platform: [ubuntu-latest, macos-latest, windows-latest]
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - name: 🐍 Set up Python ${{ matrix.python-version }}
+        uses: astral-sh/setup-uv@v7
+        with:
+          python-version: ${{ matrix.python-version }}
+          enable-cache: true
+
+      - name: Install Dependencies
+        run: uv sync --no-dev --group test
+
+      - name: 🧪 Run Tests
+        run: uv run pytest --cov --cov-report=xml --cov-report=term-missing
+
+      # If something goes wrong with --pre tests, we can open an issue in the repo
+      - name: 📝 Report --pre Failures
+        if: failure() && github.event_name == 'schedule'
+        uses: JasonEtco/create-an-issue@v2
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          PLATFORM: ${{ matrix.platform }}
+          PYTHON: ${{ matrix.python-version }}
+          RUN_ID: ${{ github.run_id }}
+          TITLE: "[test-bot] pip install --pre is failing"
+        with:
+          filename: .github/TEST_FAIL_TEMPLATE.md
+          update_existing: true
+
+      - name: Coverage
+        uses: codecov/codecov-action@v5
+        # with:
+        #   token: ${{ secrets.CODECOV_TOKEN }}
+
+  build-and-inspect-package:
+    name: Build & inspect package.
+    needs: test
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+      - uses: hynek/build-and-inspect-python-package@v2
+
+  upload-to-pypi:
+    name: Upload package to PyPI
+    needs: build-and-inspect-package
+    if: success() && startsWith(github.ref, 'refs/tags/') && github.event_name != 'schedule'
+    runs-on: ubuntu-latest
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing on PyPi
+      # see https://docs.pypi.org/trusted-publishers/
+      id-token: write
+      # This permission allows writing releases
+      contents: write
+
+    steps:
+      - name: Download built artifact to dist/
+        uses: actions/download-artifact@v7
+        with:
+          name: Packages
+          path: dist
+      - name: 🚢 Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+      - uses: softprops/action-gh-release@v2
+        with:
+          generate_release_notes: true
+          files: './dist/*'

torch_ctf-0.0.1/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+.DS_Store
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+# ruff
+.ruff_cache/
+
+# IDE settings
+.vscode/
+.idea/

torch_ctf-0.0.1/.pre-commit-config.yaml

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+# enable pre-commit.ci at https://pre-commit.ci/
+# it adds:
+# 1. auto fixing pull requests
+# 2. auto updating the pre-commit configuration
+ci:
+  autoupdate_schedule: monthly
+  autofix_commit_msg: "style(pre-commit.ci): auto fixes [...]"
+  autoupdate_commit_msg: "ci(pre-commit.ci): autoupdate"
+
+repos:
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: v0.24.1
+    hooks:
+      - id: validate-pyproject
+
+  - repo: https://github.com/rhysd/actionlint
+    rev: v1.7.7
+    hooks:
+      - id: actionlint
+
+  - repo: https://github.com/adhtruong/mirrors-typos
+    rev: v1.36.2
+    hooks:
+      - id: typos
+        args: [--force-exclude]  # omitting --write-changes
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.13.0
+    hooks:
+      - id: ruff-check
+        args: [--fix]  # may also add '--unsafe-fixes'
+      - id: ruff-format
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.18.1
+    hooks:
+      - id: mypy
+        files: "^src/"
+        # # you have to add the things you want to type check against here
+        # additional_dependencies:
+        #   - numpy
+

torch_ctf-0.0.1/LICENSE

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+BSD 3-Clause License
+
+Copyright (c) 2023, Josh Dickerson
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

torch_ctf-0.0.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: torch-ctf
+Version: 0.0.1
+Summary: CTF calculation for cryoEM in torch
+Project-URL: homepage, https://github.com/jdickerson95/torch-ctf
+Project-URL: repository, https://github.com/jdickerson95/torch-ctf
+Author-email: Josh Dickerson <jdickerson@berkeley.edu>
+License: BSD-3-Clause
+License-File: LICENSE
+Classifier: Development Status :: 3 - Alpha
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Typing :: Typed
+Requires-Python: >=3.10
+Requires-Dist: einops
+Requires-Dist: scipy
+Requires-Dist: torch
+Requires-Dist: torch-grid-utils>=v0.1.0
+Description-Content-Type: text/markdown
+
+# torch-ctf
+
+[![License](https://img.shields.io/pypi/l/torch-ctf.svg?color=green)](https://github.com/jdickerson95/torch-ctf/raw/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/torch-ctf.svg?color=green)](https://pypi.org/project/torch-ctf)
+[![Python Version](https://img.shields.io/pypi/pyversions/torch-ctf.svg?color=green)](https://python.org)
+[![CI](https://github.com/jdickerson95/torch-ctf/actions/workflows/ci.yml/badge.svg)](https://github.com/jdickerson95/torch-ctf/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/jdickerson95/torch-ctf/branch/main/graph/badge.svg)](https://codecov.io/gh/jdickerson95/torch-ctf)
+
+CTF calculation for cryoEM in torch
+
+## Development
+
+The easiest way to get started is to use the [github cli](https://cli.github.com)
+and [uv](https://docs.astral.sh/uv/getting-started/installation/):
+
+```sh
+gh repo fork jdickerson95/torch-ctf --clone
+# or just
+# gh repo clone jdickerson95/torch-ctf
+cd torch-ctf
+uv sync
+```
+
+Run tests:
+
+```sh
+uv run pytest
+```
+
+Lint files:
+
+```sh
+uv run pre-commit run --all-files
+```

torch_ctf-0.0.1/README.md

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+# torch-ctf
+
+[![License](https://img.shields.io/pypi/l/torch-ctf.svg?color=green)](https://github.com/jdickerson95/torch-ctf/raw/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/torch-ctf.svg?color=green)](https://pypi.org/project/torch-ctf)
+[![Python Version](https://img.shields.io/pypi/pyversions/torch-ctf.svg?color=green)](https://python.org)
+[![CI](https://github.com/jdickerson95/torch-ctf/actions/workflows/ci.yml/badge.svg)](https://github.com/jdickerson95/torch-ctf/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/jdickerson95/torch-ctf/branch/main/graph/badge.svg)](https://codecov.io/gh/jdickerson95/torch-ctf)
+
+CTF calculation for cryoEM in torch
+
+## Development
+
+The easiest way to get started is to use the [github cli](https://cli.github.com)
+and [uv](https://docs.astral.sh/uv/getting-started/installation/):
+
+```sh
+gh repo fork jdickerson95/torch-ctf --clone
+# or just
+# gh repo clone jdickerson95/torch-ctf
+cd torch-ctf
+uv sync
+```
+
+Run tests:
+
+```sh
+uv run pytest
+```
+
+Lint files:
+
+```sh
+uv run pre-commit run --all-files
+```

torch_ctf-0.0.1/pyproject.toml

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+# https://peps.python.org/pep-0517/
+[build-system]
+requires = ["hatchling", "hatch-vcs"]
+build-backend = "hatchling.build"
+
+# https://hatch.pypa.io/latest/config/metadata/
+[tool.hatch.version]
+source = "vcs"
+
+# read more about configuring hatch at:
+# https://hatch.pypa.io/latest/config/build/
+[tool.hatch.build.targets.wheel]
+only-include = ["src"]
+sources = ["src"]
+
+# https://peps.python.org/pep-0621/
+[project]
+name = "torch-ctf"
+dynamic = ["version"]
+description = "CTF calculation for cryoEM in torch"
+readme = "README.md"
+requires-python = ">=3.10"
+license = { text = "BSD-3-Clause" }
+authors = [{ name = "Josh Dickerson", email = "jdickerson@berkeley.edu" }]
+# https://pypi.org/classifiers/
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "License :: OSI Approved :: BSD License",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
+    "Typing :: Typed",
+]
+# add your package dependencies here
+dependencies = [
+    "torch",
+    "scipy",
+    "einops",
+    "torch-grid-utils>=v0.1.0",
+]
+
+# https://peps.python.org/pep-0621/#dependencies-optional-dependencies
+# add dependencies for "extra" features here.  Not dev dependencies.
+# [project.optional-dependencies]
+# name = ["dependency"]
+
+[project.urls]
+homepage = "https://github.com/jdickerson95/torch-ctf"
+repository = "https://github.com/jdickerson95/torch-ctf"
+
+# Entry points
+# https://peps.python.org/pep-0621/#entry-points
+# same as console_scripts entry point
+# [project.scripts]
+# torch-ctf-cli = "torch_ctf:main_cli"
+
+# [project.entry-points."some.group"]
+# tomatoes = "torch_ctf:main_tomatoes"
+
+# https://peps.python.org/pep-0735/
+# setup with `uv sync` or `pip install -e . --group dev`
+[dependency-groups]
+test = ["pytest", "pytest-cov"]
+dev = [
+    { include-group = "test" },
+    "ipython",
+    "mypy",
+    "pdbpp",  # https://github.com/pdbpp/pdbpp
+    "pre-commit-uv",
+    "rich",  # https://github.com/Textualize/rich
+    "ruff",
+]
+
+[tool.uv.sources]
+torch-ctf = { workspace = true }
+
+# https://docs.astral.sh/ruff
+[tool.ruff]
+line-length = 88
+target-version = "py310"
+src = ["src"]
+fix = true
+# unsafe-fixes = true
+
+[tool.ruff.lint]
+pydocstyle = { convention = "numpy" }
+select = [
+    "E",    # style errors
+    "W",    # style warnings
+    "F",    # flakes
+    "D",    # pydocstyle
+    "D417", # Missing argument descriptions in Docstrings
+    "I",    # isort
+    "UP",   # pyupgrade
+    "C4",   # flake8-comprehensions
+    "B",    # flake8-bugbear
+    "A001", # flake8-builtins
+    "RUF",  # ruff-specific rules
+    "TC",   # flake8-type-checking
+    "TID",  # flake8-tidy-imports
+]
+ignore = [
+    "D401", # First line should be in imperative mood (remove to opt in)
+]
+
+[tool.ruff.lint.per-file-ignores]
+"tests/*.py" = ["D", "S"]
+"docs/*.py" = ["D", "A"]
+"src/torch_ctf/ctf_lpp.py" = ["RUF002", "RUF003"]
+
+# https://docs.astral.sh/ruff/formatter/
+[tool.ruff.format]
+docstring-code-format = true
+skip-magic-trailing-comma = false  # default is false
+
+# https://docs.pytest.org/
+[tool.pytest.ini_options]
+minversion = "7.0"
+addopts = ["--color=yes"]
+testpaths = ["tests"]
+filterwarnings = ["error"]
+
+# https://mypy.readthedocs.io/en/stable/config_file.html
+[tool.mypy]
+files = "src/**/"
+strict = true
+disallow_any_generics = false
+disallow_subclassing_any = false
+show_error_codes = true
+pretty = true
+# plugins = ["pydantic.mypy"]
+
+# # module specific overrides
+# [[tool.mypy.overrides]]
+# module = ["numpy.*",]
+# ignore_errors = true
+
+# https://coverage.readthedocs.io/
+[tool.coverage.report]
+show_missing = true
+exclude_lines = [
+    "pragma: no cover",
+    "if TYPE_CHECKING:",
+    "@overload",
+    "except ImportError",
+    "raise AssertionError",
+    "\\.\\.\\.",
+    "raise NotImplementedError()",
+    "pass",
+]
+
+[tool.coverage.run]
+source = ["torch_ctf"]
+
+# https://github.com/mgedmin/check-manifest#configuration
+# add files that you want check-manifest to explicitly ignore here
+# (files that are in the repo but shouldn't go in the package)
+[tool.check-manifest]
+ignore = [
+    ".pre-commit-config.yaml",
+    ".ruff_cache/**/*",
+    "tests/**/*",
+    "uv.lock",
+]
+
+# https://github.com/crate-ci/typos/blob/master/docs/reference.md
+[tool.typos.default]
+extend-ignore-identifiers-re = []

torch_ctf-0.0.1/src/torch_ctf/__init__.py

@@ -0,0 +1,61 @@
+"""CTF calculation for cryoEM in torch."""
+
+from importlib.metadata import PackageNotFoundError, version
+
+from torch_ctf.ctf_1d import calculate_ctf_1d
+from torch_ctf.ctf_2d import calculate_ctf_2d
+from torch_ctf.ctf_aberrations import (
+    apply_even_zernikes,
+    apply_odd_zernikes,
+    beam_tilt_to_zernike_coeffs,
+    calculate_defocus_phase_aberration,
+    calculate_relativistic_electron_wavelength,
+    resolve_odd_zernikes,
+)
+from torch_ctf.ctf_ewald import calculate_ctfp_and_ctfq_2d, get_ctf_weighting
+from torch_ctf.ctf_lpp import (
+    calc_LPP_ctf_2D,
+    calc_LPP_phase,
+    calculate_relativistic_beta,
+    calculate_relativistic_gamma,
+    get_eta,
+    get_eta0_from_peak_phase_deg,
+    initialize_laser_params,
+    make_laser_coords,
+)
+from torch_ctf.ctf_utils import (
+    calculate_additional_phase_shift,
+    calculate_amplitude_contrast_equivalent_phase_shift,
+    calculate_total_phase_shift,
+)
+
+try:
+    __version__ = version("torch-ctf")
+except PackageNotFoundError:
+    __version__ = "uninstalled"
+__author__ = "Josh Dickerson"
+__email__ = "jdickerson@berkeley.edu"
+
+__all__ = [
+    "apply_even_zernikes",
+    "apply_odd_zernikes",
+    "beam_tilt_to_zernike_coeffs",
+    "calc_LPP_ctf_2D",
+    "calc_LPP_phase",
+    "calculate_additional_phase_shift",
+    "calculate_amplitude_contrast_equivalent_phase_shift",
+    "calculate_ctf_1d",
+    "calculate_ctf_2d",
+    "calculate_ctfp_and_ctfq_2d",
+    "calculate_defocus_phase_aberration",
+    "calculate_relativistic_beta",
+    "calculate_relativistic_electron_wavelength",
+    "calculate_relativistic_gamma",
+    "calculate_total_phase_shift",
+    "get_ctf_weighting",
+    "get_eta",
+    "get_eta0_from_peak_phase_deg",
+    "initialize_laser_params",
+    "make_laser_coords",
+    "resolve_odd_zernikes",
+]