anisa 0.0.1b1__tar.gz

anisa-0.0.1b1/LICENSE

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+MIT License
+
+Copyright (c) 2026 Jan Ilavsky
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

anisa-0.0.1b1/PKG-INFO

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+Metadata-Version: 2.4
+Name: anisa
+Version: 0.0.1b1
+Summary: Small-angle scattering modelling of anisotropic particle populations (successor of Igor AnisoSAS).
+Author-email: Jan Ilavsky <ilavsky@anl.gov>
+Maintainer-email: Jan Ilavsky <ilavsky@anl.gov>
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/jilavsky/anisa
+Project-URL: Repository, https://github.com/jilavsky/anisa
+Project-URL: Changelog, https://github.com/jilavsky/anisa/blob/main/CHANGELOG.md
+Project-URL: Bug Tracker, https://github.com/jilavsky/anisa/issues
+Keywords: SAXS,SANS,USAXS,small-angle scattering,anisotropy,spheroids,orientation distribution,X-ray scattering,neutron scattering,SAS
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+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: Topic :: Scientific/Engineering :: Physics
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=2.0
+Requires-Dist: scipy>=1.8.0
+Requires-Dist: h5py>=3.0.0
+Requires-Dist: pyirena<2,>=1.2.1
+Provides-Extra: gui
+Requires-Dist: PySide6!=6.10.*,!=6.9.1,>=6.8; extra == "gui"
+Requires-Dist: pyqtgraph>=0.13.7; extra == "gui"
+Requires-Dist: pyirena[qtplot]<2,>=1.2.1; extra == "gui"
+Provides-Extra: mcp
+Requires-Dist: mcp<2.0,>=1.0.0; extra == "mcp"
+Requires-Dist: matplotlib>=3.5.0; extra == "mcp"
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: pytest-timeout; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
+Requires-Dist: build; extra == "dev"
+Requires-Dist: twine; extra == "dev"
+Provides-Extra: all
+Requires-Dist: anisa[gui]; extra == "all"
+Requires-Dist: anisa[mcp]; extra == "all"
+Requires-Dist: anisa[dev]; extra == "all"
+Dynamic: license-file
+
+# Anisa
+
+Small-angle scattering (SAXS / USAXS / SANS) modelling of **anisotropic particle populations**.
+
+Anisa fits populations of spheroids with orientation distributions to several 1D cuts I(Q),
+each measured along a different direction of Q in the sample frame. It is the Python successor
+of the Igor Pro AnisoSAS macros (theory: A. J. Allen, NIST 2001). Compared with the Igor
+version it is faster, uses multiple cores, and has no fixed limit on the number of directions
+or populations.
+
+> **Status: beta (0.0.1b1).** The engine, data input, fitting, GUI, results files, command line,
+> MCP server and Bernardyn export are done and tested on synthetic data; it has not yet been
+> validated on real measurements, so expect changes. See
+> [PLAN.md](https://github.com/jilavsky/anisa/blob/main/PLAN.md) for the plan and progress.
+
+Anisa is part of the pyIrena family:
+- **[pyIrena](https://github.com/jilavsky/pyirena)** — data input (NXcanSAS HDF5 and ASCII) and
+  shared GUI pieces.
+- **[Bernardyn](https://github.com/jilavsky/Bernardyn)** — publication plots.
+- **Aida** — agent workbench, which will use the Anisa MCP server.
+
+All of them install into the same Python environment.
+
+## Installation
+
+Not on PyPI yet. From a source checkout:
+
+```bash
+conda env create -f environment.yml     # creates the "anisa" environment
+conda activate anisa
+```
+
+To add Anisa to an existing pyIrena or Bernardyn environment instead:
+
+```bash
+pip install -e ".[gui]"
+```
+
+Python 3.10–3.13. The GUI uses PySide6 (never PyQt6).
+
+## Using the GUI
+
+```bash
+anisa-gui                      # or: python -m anisa.gui
+```
+
+1. *File → Create test system* writes a synthetic data set with known parameters (prolate,
+   oblate, both with different alignment, interference, spheres, 12 directions; `TRUTH.txt`
+   lists the answer) and opens it with perturbed starting values; press **Fit** to see it
+   recover them. *Create demo data…* does the same for the three-population coating example. (Or *Add data…* /
+   drag files onto the directions table to load your own: NXcanSAS HDF5 or text.)
+2. Give each direction its angles α_Q (from the sample normal) and ω_Q (azimuth) in the table.
+3. Set the particle parameters of each population, tick **Fit?** for those to vary, and press
+   **Fit**. The errors appear next to the fitted values; *Uncertainty…* refits re-drawn data for a
+   Monte-Carlo estimate; *Revert fit* returns to the values before the fit.
+4. The **Anisotropy** tab shows the model as a function of the direction of Q (polar plots, or
+   I(angle)) with your measured cuts on top, which is the quickest check that the orientation
+   distributions make sense.
+
+After a fit, *File → Save results (HDF5)…* writes one `NAME.anisa.h5` with the data, model
+curves, parameters and errors of all directions (an NXcanSAS entry per direction, so pyIrena
+opens each); *File → Open* reads it back.
+
+## Command line
+
+```bash
+anisa testdata folder --system prolate_oblate        # synthetic data with known truth
+anisa info    folder/prolate_oblate/prolate_oblate_start.anisa.json
+anisa fit     folder/prolate_oblate/prolate_oblate_start.anisa.json --mc 20 --text
+anisa calc    project.anisa.json --results out.anisa.h5
+anisa export-bernardyn project.anisa.json plot     # needs Bernardyn installed
+anisa anisotropy project.anisa.json --sweep alpha --fixed 0 --q 0.01 0.05 --csv scan.csv
+```
+
+The project file is the one the GUI saves; every command prints JSON (`anisa.api` has the same
+functions for Python).
+
+## MCP server (agents)
+
+```bash
+pip install "anisa[mcp]"
+ANISA_DATA_ROOT=/path/to/data anisa-mcp          # stdio server
+aida mcp server add anisa --command anisa-mcp    # register with Aida
+```
+
+Tools (`anisa_` prefix): `list_files`, `describe`, `calculate`, `fit`, `anisotropy`,
+`read_results`, `list_test_systems`, `write_test_system`. They are the `anisa.api` functions;
+file access is confined to `ANISA_DATA_ROOT` (default: the working directory).
+
+## Example
+
+```python
+import numpy as np
+from anisa.core import AnisaModel, Direction, Population, Engine
+from anisa.core.orientation import AngularDistribution
+
+# oblate disks (beta = 0.2) with their axes along the sample z axis
+pop = Population(radius=800.0, beta=0.2, volume_fraction=0.03, delta_rho=2e11,
+                 alpha_dist=AngularDistribution(par1=0.0, par2=12.0))
+model = AnisaModel([Direction(alpha_q=0.0), Direction(alpha_q=90.0)], [pop])
+
+q = np.geomspace(1e-4, 0.1, 200)
+result = Engine().evaluate(model, [q, q])
+along_z, across_z = (d.intensity for d in result.directions)   # I(Q) in 1/cm
+```
+
+Any number of directions and populations is allowed. Parameters and their Igor names:
+[docs/parameters.md](https://github.com/jilavsky/anisa/blob/main/docs/parameters.md).
+
+Synthetic multi-direction data with known parameters, for trying things out:
+
+```bash
+python -m anisa.demo demo_data            # NXcanSAS files + demo.anisa.json (the truth)
+```
+
+```python
+from anisa.core import fit
+from anisa.io.project import load_project
+
+model = load_project("demo_data/demo_start.anisa.json")   # perturbed start, fit flags set
+result = fit(model)                                        # model now holds the best parameters
+for p in result.parameters:
+    print(p.parameter.label, p.value, "+-", p.std)
+```
+
+## Units
+
+- Q in Å⁻¹.
+- Intensity in cm⁻¹ (absolute).
+- Radii in Å.
+- Scattering contrast Δρ in cm⁻² (Δρ, not Δρ²).
+- Angles in degrees.
+
+## License
+
+MIT — see [LICENSE](LICENSE).

anisa-0.0.1b1/README.md

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+# Anisa
+
+Small-angle scattering (SAXS / USAXS / SANS) modelling of **anisotropic particle populations**.
+
+Anisa fits populations of spheroids with orientation distributions to several 1D cuts I(Q),
+each measured along a different direction of Q in the sample frame. It is the Python successor
+of the Igor Pro AnisoSAS macros (theory: A. J. Allen, NIST 2001). Compared with the Igor
+version it is faster, uses multiple cores, and has no fixed limit on the number of directions
+or populations.
+
+> **Status: beta (0.0.1b1).** The engine, data input, fitting, GUI, results files, command line,
+> MCP server and Bernardyn export are done and tested on synthetic data; it has not yet been
+> validated on real measurements, so expect changes. See
+> [PLAN.md](https://github.com/jilavsky/anisa/blob/main/PLAN.md) for the plan and progress.
+
+Anisa is part of the pyIrena family:
+- **[pyIrena](https://github.com/jilavsky/pyirena)** — data input (NXcanSAS HDF5 and ASCII) and
+  shared GUI pieces.
+- **[Bernardyn](https://github.com/jilavsky/Bernardyn)** — publication plots.
+- **Aida** — agent workbench, which will use the Anisa MCP server.
+
+All of them install into the same Python environment.
+
+## Installation
+
+Not on PyPI yet. From a source checkout:
+
+```bash
+conda env create -f environment.yml     # creates the "anisa" environment
+conda activate anisa
+```
+
+To add Anisa to an existing pyIrena or Bernardyn environment instead:
+
+```bash
+pip install -e ".[gui]"
+```
+
+Python 3.10–3.13. The GUI uses PySide6 (never PyQt6).
+
+## Using the GUI
+
+```bash
+anisa-gui                      # or: python -m anisa.gui
+```
+
+1. *File → Create test system* writes a synthetic data set with known parameters (prolate,
+   oblate, both with different alignment, interference, spheres, 12 directions; `TRUTH.txt`
+   lists the answer) and opens it with perturbed starting values; press **Fit** to see it
+   recover them. *Create demo data…* does the same for the three-population coating example. (Or *Add data…* /
+   drag files onto the directions table to load your own: NXcanSAS HDF5 or text.)
+2. Give each direction its angles α_Q (from the sample normal) and ω_Q (azimuth) in the table.
+3. Set the particle parameters of each population, tick **Fit?** for those to vary, and press
+   **Fit**. The errors appear next to the fitted values; *Uncertainty…* refits re-drawn data for a
+   Monte-Carlo estimate; *Revert fit* returns to the values before the fit.
+4. The **Anisotropy** tab shows the model as a function of the direction of Q (polar plots, or
+   I(angle)) with your measured cuts on top, which is the quickest check that the orientation
+   distributions make sense.
+
+After a fit, *File → Save results (HDF5)…* writes one `NAME.anisa.h5` with the data, model
+curves, parameters and errors of all directions (an NXcanSAS entry per direction, so pyIrena
+opens each); *File → Open* reads it back.
+
+## Command line
+
+```bash
+anisa testdata folder --system prolate_oblate        # synthetic data with known truth
+anisa info    folder/prolate_oblate/prolate_oblate_start.anisa.json
+anisa fit     folder/prolate_oblate/prolate_oblate_start.anisa.json --mc 20 --text
+anisa calc    project.anisa.json --results out.anisa.h5
+anisa export-bernardyn project.anisa.json plot     # needs Bernardyn installed
+anisa anisotropy project.anisa.json --sweep alpha --fixed 0 --q 0.01 0.05 --csv scan.csv
+```
+
+The project file is the one the GUI saves; every command prints JSON (`anisa.api` has the same
+functions for Python).
+
+## MCP server (agents)
+
+```bash
+pip install "anisa[mcp]"
+ANISA_DATA_ROOT=/path/to/data anisa-mcp          # stdio server
+aida mcp server add anisa --command anisa-mcp    # register with Aida
+```
+
+Tools (`anisa_` prefix): `list_files`, `describe`, `calculate`, `fit`, `anisotropy`,
+`read_results`, `list_test_systems`, `write_test_system`. They are the `anisa.api` functions;
+file access is confined to `ANISA_DATA_ROOT` (default: the working directory).
+
+## Example
+
+```python
+import numpy as np
+from anisa.core import AnisaModel, Direction, Population, Engine
+from anisa.core.orientation import AngularDistribution
+
+# oblate disks (beta = 0.2) with their axes along the sample z axis
+pop = Population(radius=800.0, beta=0.2, volume_fraction=0.03, delta_rho=2e11,
+                 alpha_dist=AngularDistribution(par1=0.0, par2=12.0))
+model = AnisaModel([Direction(alpha_q=0.0), Direction(alpha_q=90.0)], [pop])
+
+q = np.geomspace(1e-4, 0.1, 200)
+result = Engine().evaluate(model, [q, q])
+along_z, across_z = (d.intensity for d in result.directions)   # I(Q) in 1/cm
+```
+
+Any number of directions and populations is allowed. Parameters and their Igor names:
+[docs/parameters.md](https://github.com/jilavsky/anisa/blob/main/docs/parameters.md).
+
+Synthetic multi-direction data with known parameters, for trying things out:
+
+```bash
+python -m anisa.demo demo_data            # NXcanSAS files + demo.anisa.json (the truth)
+```
+
+```python
+from anisa.core import fit
+from anisa.io.project import load_project
+
+model = load_project("demo_data/demo_start.anisa.json")   # perturbed start, fit flags set
+result = fit(model)                                        # model now holds the best parameters
+for p in result.parameters:
+    print(p.parameter.label, p.value, "+-", p.std)
+```
+
+## Units
+
+- Q in Å⁻¹.
+- Intensity in cm⁻¹ (absolute).
+- Radii in Å.
+- Scattering contrast Δρ in cm⁻² (Δρ, not Δρ²).
+- Angles in degrees.
+
+## License
+
+MIT — see [LICENSE](LICENSE).

anisa-0.0.1b1/anisa/__init__.py

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+"""
+Anisa: small-angle scattering modelling of anisotropic particle populations.
+
+Python successor of the Igor Pro AnisoSAS macros (J. Ilavsky, theory by A. J. Allen,
+NIST 2001). Populations of axially symmetric spheroids with orientation distributions
+p(alpha) * b(omega) are modelled against 1D cuts measured along several directions of Q
+in the sample frame.
+
+Layers:
+    core: numerical model (numpy/scipy only)
+    io:   data input through pyirena.io, project JSON, HDF5 results
+    gui:  PySide6 GUI (optional extra ``anisa[gui]``)
+
+See PLAN.md for the development plan.
+"""
+
+# Single-source the version from the installed package metadata
+# (pyproject.toml is the source of truth).
+from importlib.metadata import PackageNotFoundError
+from importlib.metadata import version as _pkg_version
+
+try:
+    __version__ = _pkg_version("anisa")
+except PackageNotFoundError:  # pragma: no cover - only in uninstalled source trees
+    __version__ = "0.0.0+unknown"
+
+__author__ = "Jan Ilavsky"

anisa-0.0.1b1/anisa/__main__.py

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+"""``python -m anisa`` is the command line (see :mod:`anisa.cli`)."""
+
+from anisa.cli import main
+
+raise SystemExit(main())