torch-ctf-estimation 0.6.0__tar.gz

torch_ctf_estimation-0.6.0/.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
+*.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/
+
+# Files downloaded for unit tests
+**/tests/tmp/
+
+# 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
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+# ruff
+.ruff_cache/
+
+# IDEs
+.idea/
+.vscode/
+
+# Mojo extension compile cache (experimental torch-fourier-slice kernels)
+__mojocache__/
+*.mojopkg
+# experimental demo outputs
+packages/primitives/torch-fourier-slice/examples/*.npz
+packages/primitives/torch-fourier-slice/examples/*.png
+packages/primitives/torch-fourier-slice/examples/*.gif
+# Personal local notes (not for commit)
+notes/*.local.md
+
+lightning_logs/

torch_ctf_estimation-0.6.0/LICENSE

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+BSD 3-Clause License
+
+Copyright (c) 2020-2026, TeamTomo
+All rights reserved.
+
+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_estimation-0.6.0/PKG-INFO

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+Metadata-Version: 2.5
+Name: torch-ctf-estimation
+Version: 0.6.0
+Summary: Contrast transfer function estimation for cryo-EM images in PyTorch
+Project-URL: homepage, https://github.com/teamtomo/teamtomo
+Project-URL: repository, https://github.com/teamtomo/teamtomo
+Author-email: Alister Burt <alisterburt@gmail.com>, 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 :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Typing :: Typed
+Requires-Python: >=3.11
+Requires-Dist: einops
+Requires-Dist: numpy
+Requires-Dist: pydantic<3,>=2.0
+Requires-Dist: scipy
+Requires-Dist: teamtomo-basemodel
+Requires-Dist: torch
+Requires-Dist: torch-ctf
+Requires-Dist: torch-cubic-spline-grids
+Requires-Dist: torch-fourier-filter
+Requires-Dist: torch-fourier-rescale
+Requires-Dist: torch-grid-utils
+Requires-Dist: torch-image-interpolation
+Requires-Dist: torchvision
+Provides-Extra: plot
+Requires-Dist: matplotlib; extra == 'plot'
+Description-Content-Type: text/markdown
+
+# torch-ctf-estimation
+
+Contrast transfer function estimation for cryo-EM images in PyTorch.
+
+## Overview
+
+`torch-ctf-estimation` fits defocus, astigmatism, and (optionally) sample
+thickness from a micrograph power spectrum.
+
+- 1D defocus on the mean spectrum, then 2D defocus / astigmatism on patches
+- Spatial defocus as a spline grid or a linear tilt model
+- 1D thickness grid search against a thickness-modulated CTF, with optional
+  joint defocus+thickness refinement (1D scalar or 2D field)
+- Laser phase plate (LPP) CTF support via `torch-ctf`
+
+This package is the algorithm: `estimate_ctf` (defocus only) and
+`estimate_ctf_and_thickness` (defocus + thickness) are self-contained
+compositions of the lower-level primitives, usable directly from notebooks,
+tests, or another program. Downstream tools can chain these primitives
+differently and add optics / metrics file I/O.
+
+## Installation
+
+This package is part of the [TeamTomo monorepo](https://github.com/teamtomo/teamtomo).
+See the main repository README for development setup instructions.
+
+## Usage
+
+```python
+import torch
+from torch_ctf_estimation import estimate_ctf
+from torch_ctf_estimation.models import CTFFittingParams, OpticalParams
+
+image = torch.randn(1024, 1024)
+optical = OpticalParams(
+    pixel_spacing_angstroms=1.0,
+    voltage_kev=300.0,
+    spherical_aberration_mm=2.7,
+    amplitude_contrast_fraction=0.07,
+)
+fitting = CTFFittingParams(
+    defocus_grid_resolution=(1, 3, 3),
+    frequency_fit_range_angstroms=(30.0, 5.0),
+    defocus_range_microns=(0.5, 5.0),
+    patch_sidelength=128,
+)
+mean_ps, result1d, result2d = estimate_ctf(image, optical, fitting)
+```
+
+To also estimate sample thickness, use `estimate_ctf_and_thickness` with a
+`ThicknessParams`:
+
+```python
+from torch_ctf_estimation import estimate_ctf_and_thickness
+from torch_ctf_estimation.models import ThicknessParams
+
+thickness = ThicknessParams(refine_dim="2d")
+result = estimate_ctf_and_thickness(image, optical, fitting, thickness)
+result.result2d, result.thickness1d, result.thickness_joint
+```

torch_ctf_estimation-0.6.0/README.md

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+# torch-ctf-estimation
+
+Contrast transfer function estimation for cryo-EM images in PyTorch.
+
+## Overview
+
+`torch-ctf-estimation` fits defocus, astigmatism, and (optionally) sample
+thickness from a micrograph power spectrum.
+
+- 1D defocus on the mean spectrum, then 2D defocus / astigmatism on patches
+- Spatial defocus as a spline grid or a linear tilt model
+- 1D thickness grid search against a thickness-modulated CTF, with optional
+  joint defocus+thickness refinement (1D scalar or 2D field)
+- Laser phase plate (LPP) CTF support via `torch-ctf`
+
+This package is the algorithm: `estimate_ctf` (defocus only) and
+`estimate_ctf_and_thickness` (defocus + thickness) are self-contained
+compositions of the lower-level primitives, usable directly from notebooks,
+tests, or another program. Downstream tools can chain these primitives
+differently and add optics / metrics file I/O.
+
+## Installation
+
+This package is part of the [TeamTomo monorepo](https://github.com/teamtomo/teamtomo).
+See the main repository README for development setup instructions.
+
+## Usage
+
+```python
+import torch
+from torch_ctf_estimation import estimate_ctf
+from torch_ctf_estimation.models import CTFFittingParams, OpticalParams
+
+image = torch.randn(1024, 1024)
+optical = OpticalParams(
+    pixel_spacing_angstroms=1.0,
+    voltage_kev=300.0,
+    spherical_aberration_mm=2.7,
+    amplitude_contrast_fraction=0.07,
+)
+fitting = CTFFittingParams(
+    defocus_grid_resolution=(1, 3, 3),
+    frequency_fit_range_angstroms=(30.0, 5.0),
+    defocus_range_microns=(0.5, 5.0),
+    patch_sidelength=128,
+)
+mean_ps, result1d, result2d = estimate_ctf(image, optical, fitting)
+```
+
+To also estimate sample thickness, use `estimate_ctf_and_thickness` with a
+`ThicknessParams`:
+
+```python
+from torch_ctf_estimation import estimate_ctf_and_thickness
+from torch_ctf_estimation.models import ThicknessParams
+
+thickness = ThicknessParams(refine_dim="2d")
+result = estimate_ctf_and_thickness(image, optical, fitting, thickness)
+result.result2d, result.thickness1d, result.thickness_joint
+```

torch_ctf_estimation-0.6.0/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"
+tag-pattern = "^torch-ctf-estimation@v(?P<version>.+)$"
+fallback-version = "0.5.0"
+
+[tool.hatch.version.raw-options]
+search_parent_directories = true
+tag_regex = "^torch-ctf-estimation@v(?P<version>\\d+\\.\\d+\\.\\d+.*)$"
+git_describe_command = "git describe --dirty --tags --long --match 'torch-ctf-estimation@v[0-9]*.[0-9]*.[0-9]*'"
+
+# 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-estimation"
+dynamic = ["version"]
+description = "Contrast transfer function estimation for cryo-EM images in PyTorch"
+readme = "README.md"
+requires-python = ">=3.11"
+license = { text = "BSD-3-Clause" }
+authors = [
+    { name = "Alister Burt", email = "alisterburt@gmail.com" },
+    { name = "Josh Dickerson", email = "jdickerson@berkeley.edu" },
+]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "License :: OSI Approved :: BSD License",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
+    "Typing :: Typed",
+]
+dependencies = [
+    "einops",
+    "numpy",
+    "pydantic>=2.0,<3",
+    "scipy",
+    "teamtomo-basemodel",
+    "torch",
+    "torch-ctf",
+    "torch-cubic-spline-grids",
+    "torch-fourier-filter",
+    "torch-fourier-rescale",
+    "torch-grid-utils",
+    "torch-image-interpolation",
+    "torchvision",
+]
+
+[project.optional-dependencies]
+plot = ["matplotlib"]
+
+[project.urls]
+homepage = "https://github.com/teamtomo/teamtomo"
+repository = "https://github.com/teamtomo/teamtomo"
+
+[dependency-groups]
+test = ["pytest", "pytest-cov"]
+dev = [
+    { include-group = "test" },
+    "ipython",
+    "mypy",
+    "pdbpp",
+    "pre-commit",
+    "rich",
+    "ruff",
+]
+
+[tool.ruff]
+line-length = 88
+target-version = "py311"
+src = ["src"]
+
+[tool.ruff.lint]
+pydocstyle = { convention = "numpy" }
+select = [
+    "E",
+    "W",
+    "F",
+    "D",
+    "D417",
+    "I",
+    "UP",
+    "C4",
+    "B",
+    "A001",
+    "RUF",
+    "TCH",
+    "TID",
+]
+ignore = [
+    "D401",
+]
+
+[tool.ruff.lint.per-file-ignores]
+"tests/*.py" = ["D", "S"]
+
+[tool.ruff.format]
+docstring-code-format = true
+skip-magic-trailing-comma = false
+
+[tool.mypy]
+files = "src/**/"
+strict = true
+disallow_any_generics = false
+disallow_subclassing_any = false
+show_error_codes = true
+pretty = true
+
+[tool.pytest.ini_options]
+minversion = "7.0"
+testpaths = ["tests"]
+filterwarnings = [
+    "error",
+    "ignore:CUDA initialization:UserWarning",
+    "ignore:Linear defocus gradient from 1D fits:UserWarning",
+    "ignore:Linear defocus gradient angle was NaN:UserWarning",
+]
+
+[tool.coverage.report]
+show_missing = true
+exclude_lines = [
+    "pragma: no cover",
+    "if TYPE_CHECKING:",
+    "@overload",
+    "except ImportError",
+    "\\.\\.\\.",
+    "raise NotImplementedError()",
+    "pass",
+]
+
+[tool.coverage.run]
+source = ["torch_ctf_estimation"]
+
+[tool.check-manifest]
+ignore = [".pre-commit-config.yaml", ".ruff_cache/**/*", "tests/**/*"]

torch_ctf_estimation-0.6.0/src/torch_ctf_estimation/__init__.py

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+"""Contrast transfer function estimation for cryo-EM images in PyTorch."""
+
+from importlib.metadata import PackageNotFoundError, version
+
+try:
+    __version__ = version("torch-ctf-estimation")
+except PackageNotFoundError:
+    __version__ = "uninstalled"
+__author__ = "Alister Burt"
+__email__ = "alisterburt@gmail.com"
+
+from torch_ctf_estimation.estimate_ctf import (
+    CTFEstimationResult,
+    estimate_ctf,
+    estimate_ctf_and_thickness,
+)
+from torch_ctf_estimation.estimate_ctf_1d import (
+    estimate_ctf_1d,
+    estimate_thickness_1d,
+    fit_background_spline_1d,
+    refine_defocus_and_thickness_1d,
+)
+from torch_ctf_estimation.estimate_ctf_2d import (
+    estimate_ctf_2d,
+    estimate_defocus_2d_at_1x1,
+    estimate_thickness_2d,
+    refine_defocus_and_thickness_2d,
+)
+from torch_ctf_estimation.models import (
+    CTFFittingParams,
+    Defocus1DResults,
+    Defocus2DResults,
+    LaserParams,
+    OpticalParams,
+    Thickness1DResults,
+    Thickness2DResults,
+    ThicknessParams,
+)
+from torch_ctf_estimation.utils.defocus_field_from_1d import defocus_field_from_1d_fits
+from torch_ctf_estimation.utils.laser_axis_mask import (
+    apply_laser_axis_mask,
+    build_laser_axis_mask,
+)
+from torch_ctf_estimation.utils.patches import (
+    compute_patch_power_spectra,
+    extract_ctf_patches,
+    normalised_patch_positions,
+)
+from torch_ctf_estimation.utils.prepare_image import prepare_image_for_ctf
+
+__all__ = [
+    "CTFEstimationResult",
+    "CTFFittingParams",
+    "Defocus1DResults",
+    "Defocus2DResults",
+    "LaserParams",
+    "OpticalParams",
+    "Thickness1DResults",
+    "Thickness2DResults",
+    "ThicknessParams",
+    "apply_laser_axis_mask",
+    "build_laser_axis_mask",
+    "compute_patch_power_spectra",
+    "defocus_field_from_1d_fits",
+    "estimate_ctf",
+    "estimate_ctf_1d",
+    "estimate_ctf_2d",
+    "estimate_ctf_and_thickness",
+    "estimate_defocus_2d_at_1x1",
+    "estimate_thickness_1d",
+    "estimate_thickness_2d",
+    "extract_ctf_patches",
+    "fit_background_spline_1d",
+    "normalised_patch_positions",
+    "prepare_image_for_ctf",
+    "refine_defocus_and_thickness_1d",
+    "refine_defocus_and_thickness_2d",
+]