coordinate-transformer 0.2.3__tar.gz

coordinate_transformer-0.2.3/.circleci/config.yml

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+version: 2.1
+
+jobs:
+  test:
+    docker:
+      - image: cimg/python:3.12
+    steps:
+      - checkout
+      - run:
+          name: Install dependencies
+          command: |
+            python -m pip install --upgrade pip
+            python -m pip install -e ".[test]"
+      - run:
+          name: Run linter
+          command: ruff check .
+      - run:
+          name: Run tests
+          command: pytest --junitxml=test-results/results.xml --cov=coordinate_transformer --cov-report=term-missing
+      - store_test_results:
+          path: test-results
+
+  test-min-python:
+    docker:
+      - image: cimg/python:3.10
+    steps:
+      - checkout
+      - run:
+          name: Install dependencies
+          command: |
+            python -m pip install --upgrade pip
+            python -m pip install -e ".[test]"
+      - run:
+          name: Run tests
+          command: pytest
+
+workflows:
+  ci:
+    jobs:
+      - test
+      - test-min-python

coordinate_transformer-0.2.3/.github/workflows/publish_pypi.yml

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+name: Publish to PyPI
+
+on:
+  push:
+    tags:
+      - "v*"
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.12"]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -e ".[test]"
+      - name: Lint
+        if: matrix.python-version == '3.12'
+        run: ruff check .
+      - name: Run tests
+        run: pytest --tb=short
+
+  build:
+    needs: test
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0  # full history needed for setuptools-scm
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - name: Install build tools
+        run: python -m pip install --upgrade pip build setuptools-scm
+      - name: Verify version from tag
+        run: python -m setuptools_scm
+      - name: Build sdist and wheel
+        run: python -m build
+      - name: Check dist contents
+        run: ls -la dist/
+      - uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+  publish:
+    needs: build
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write  # required for trusted publishing via OIDC
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+
+  github-release:
+    needs: publish
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+      - name: Create GitHub Release
+        env:
+          GH_TOKEN: ${{ github.token }}
+        run: gh release create "${{ github.ref_name }}" --generate-notes

coordinate_transformer-0.2.3/.gitignore

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+.pixi
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+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
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+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
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+# Abstra is an AI-powered process automation framework.
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+# Learn more at https://abstra.io/docs
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+# Visual Studio Code
+#  Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore 
+#  that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#  and can be added to the global gitignore or merged into this file. However, if you prefer, 
+#  you could uncomment the following to ignore the entire vscode folder
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+.cursorignore
+.cursorindexingignore
+
+# Marimo
+marimo/_static/
+marimo/_lsp/
+__marimo__/
+
+*.NMD

coordinate_transformer-0.2.3/LICENSE

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+MIT License
+
+Copyright (c) 2026 High-Throughput Materials Discovery for Extreme Conditions (HTMDEC)
+
+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.

coordinate_transformer-0.2.3/PKG-INFO

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+Metadata-Version: 2.4
+Name: coordinate-transformer
+Version: 0.2.3
+Summary: Config-driven affine coordinate transforms for lab instruments
+License: MIT
+Requires-Python: >=3.9
+License-File: LICENSE
+Requires-Dist: numpy>=1.26
+Requires-Dist: PyYAML>=6.0
+Provides-Extra: notebook
+Requires-Dist: jupyter>=1.0; extra == "notebook"
+Requires-Dist: ipykernel>=6.29; extra == "notebook"
+Provides-Extra: test
+Requires-Dist: pytest>=8.0; extra == "test"
+Requires-Dist: pytest-cov>=5.0; extra == "test"
+Requires-Dist: ruff>=0.4; extra == "test"
+Dynamic: license-file

coordinate_transformer-0.2.3/README.md

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+# Coordinate Transformer
+
+Config-driven affine coordinate transforms for lab instruments. (updated to v0.2.1 for PyPI)
+
+This repository provides a small Python module that reads instrument calibration data from `instrument_coordinate_transforms.yaml`, fits a 2D affine transform for each instrument, and converts `(x, y)` points between an instrument coordinate system and a canonical sample coordinate system.
+
+The current configuration includes these instruments:
+
+- `MAXIMA`
+- `HELIX`
+- `SPHINX`
+
+## Repository contents
+
+- `src/coordinate_transformer/` is the package with the `CoordinateTransformer` class and a small CLI
+- `instrument_coordinate_transforms.yaml` is the calibration data config based on the canonical sample coordinate system
+- `coordinate_transform_example.ipynb` is a simple example notebook showing the transformer in action
+- `tests/` is the test suite (40 tests covering transforms, validation, batch operations, and the CLI)
+- `pyproject.toml` has project metadata, build configuration, and dependency groups
+- `.circleci/` contains the CircleCI pipeline configuration for continuous integration
+- `.github/workflows/` contains the GitHub Actions workflow for publishing to PyPI on tagged releases
+- `LICENSE` is the MIT license
+
+## How it works
+
+For each instrument, the YAML file contains three calibration point pairs:
+
+- `instrument: [x_inst, y_inst]`
+- `sample: [x_sample, y_sample]`
+
+The module fits a 2D affine transform from instrument coordinates to sample coordinates. With three non-collinear calibration pairs, the transform is determined exactly. If you later provide more than three calibration pairs, the code will fit the transform by least squares.
+
+## Requirements
+
+- Python 3.9+
+
+Core dependencies (installed automatically):
+
+- `numpy`
+- `PyYAML`
+
+Optional extras:
+
+- `pip install coordinate-transformer[notebook]` adds `jupyter` and `ipykernel` for running the example notebook
+- `pip install coordinate-transformer[test]` adds `pytest`, `pytest-cov`, and `ruff` for testing and linting
+
+## Installation
+
+### From PyPI
+
+```bash
+pip install coordinate-transformer
+```
+
+### Development installation
+
+Clone the repository, create a virtual environment, and install in editable mode with test dependencies:
+
+#### macOS / Linux
+
+```bash
+python -m venv .venv
+source .venv/bin/activate
+python -m pip install --upgrade pip
+pip install -e ".[test]"
+```
+
+#### Windows PowerShell
+
+```powershell
+python -m venv .venv
+.venv\Scripts\Activate.ps1
+python -m pip install --upgrade pip
+pip install -e ".[test]"
+```
+
+## Running tests
+
+```bash
+pip install -e ".[test]"
+pytest
+```
+
+Linting is available via:
+
+```bash
+ruff check .
+```
+
+CI runs automatically on CircleCI (for every push) and GitHub Actions (for tagged releases).
+
+## YAML configuration
+
+The transformer is driven by `instrument_coordinate_transforms.yaml`.
+
+The top-level structure is:
+
+```yaml
+canonical_system:
+  origin: bottom-left
+  x_positive: right
+  y_positive: up
+  units: mm
+  sample_width: 40.0
+  sample_height: 40.0
+
+instruments:
+  - name: MAXIMA
+    units: mm
+    calibration_points:
+      - instrument: [x1, y1]
+        sample: [x1s, y1s]
+      - instrument: [x2, y2]
+        sample: [x2s, y2s]
+      - instrument: [x3, y3]
+        sample: [x3s, y3s]
+```
+
+To update an instrument, edit its calibration points in the YAML. To add another instrument, add another entry under `instruments` with at least three non-collinear calibration pairs.
+
+## Using the class
+
+Import the class and load the YAML file:
+
+```python
+from coordinate_transformer import CoordinateTransformer
+
+transformer = CoordinateTransformer.from_yaml("instrument_coordinate_transforms.yaml")
+```
+
+### List available instruments
+
+```python
+transformer.instruments()
+```
+
+### Transform one point into sample coordinates
+
+```python
+x_sample, y_sample = transformer.transform("MAXIMA", -14.0, -20.0)
+print(x_sample, y_sample)
+```
+
+### Inverse transform from sample coordinates back to an instrument frame
+
+```python
+x_inst, y_inst = transformer.inverse_transform("SPHINX", 40.0, 40.0)
+print(x_inst, y_inst)
+```
+
+### Transform a batch of points
+
+```python
+import numpy as np
+
+points = np.array([
+    [125.319, 148.213],
+    [124.924, 107.753],
+    [165.189, 107.350],
+])
+
+sample_points = transformer.transform_points("SPHINX", points)
+print(sample_points)
+```
+
+### Inspect the affine matrix for one instrument
+
+```python
+matrix = transformer.get_transform("HELIX").matrix
+print(matrix)
+```
+
+### Validate calibration fit
+
+```python
+errors = transformer.validate()
+print(errors)
+```
+
+This returns the maximum calibration-point residual for each instrument.
+
+## API summary
+
+### `CoordinateTransformer`
+
+Main methods:
+
+- `CoordinateTransformer.from_yaml(path)`
+- `instruments()`
+- `get_transform(instrument_name)`
+- `transform(instrument_name, x, y)`
+- `inverse_transform(instrument_name, x, y)`
+- `transform_points(instrument_name, points)`
+- `inverse_transform_points(instrument_name, points)`
+- `validate()`
+- `summary()`
+
+### `InstrumentTransform`
+
+Returned by `get_transform(...)`. Useful attributes and methods:
+
+- `name`
+- `units`
+- `matrix`
+- `inverse_matrix`
+- `transform_point(x, y)`
+- `inverse_transform_point(x, y)`
+- `transform_points(points)`
+- `inverse_transform_points(points)`
+- `calibration_residuals()`
+- `max_calibration_error()`
+
+## Command-line usage
+
+The module also includes a small CLI.
+
+### Transform an instrument point into sample coordinates
+
+```bash
+python -m coordinate_transformer instrument_coordinate_transforms.yaml MAXIMA -14 -20
+```
+
+### Inverse transform from sample coordinates into instrument coordinates
+
+```bash
+python -m coordinate_transformer instrument_coordinate_transforms.yaml SPHINX 40 40 --inverse
+```
+
+### Show the fitted affine matrix
+
+```bash
+python -m coordinate_transformer instrument_coordinate_transforms.yaml HELIX 8 8 --show-matrix
+```
+
+### Using the console script
+
+After installation, `coordinate-transformer` is also available as a standalone command:
+
+```bash
+coordinate-transformer instrument_coordinate_transforms.yaml MAXIMA -14 -20
+```
+
+## Running the example notebook
+
+After installing the environment:
+
+```bash
+jupyter notebook coordinate_transform_example.ipynb
+```
+
+The notebook demonstrates how to:
+
+- load the YAML configuration
+- inspect the canonical coordinate system
+- list instruments
+- validate calibration errors
+- transform a single point
+- transform a batch of points
+- perform an inverse transform
+- inspect a fitted affine matrix
+
+If you want to use the notebook with a dedicated kernel, you can register the environment explicitly:
+
+```bash
+python -m ipykernel install --user --name coordinate-transformer --display-name "Python (coordinate-transformer)"
+```
+
+Then choose that kernel in Jupyter.
+
+## Versioning and releases
+
+The version is derived automatically from git tags using [setuptools-scm](https://github.com/pypa/setuptools-scm). To release a new version:
+
+1. Tag the commit with a `v` prefix (e.g., `git tag v0.2.0`)
+2. Push the tag: `git push origin --tags`
+3. The GitHub Actions workflow will publish to PyPI automatically
+
+## Notes
+
+- At least three non-collinear calibration points are required per instrument.
+- If the calibration points are degenerate, the code raises an error.
+- Units are recorded per instrument, but the transform assumes your calibration pairs already define the correct mapping into the canonical sample units.
+- The current implementation uses a full affine model, so it can represent translation, rotation, reflection, scaling, shear, or combinations of those.
+
+## Typical update workflow
+
+1. Edit `instrument_coordinate_transforms.yaml`
+2. Replace or add calibration points for the relevant instrument
+3. Reload the transformer:
+
+```python
+transformer = CoordinateTransformer.from_yaml("instrument_coordinate_transforms.yaml")
+```
+
+4. Re-run `transformer.validate()`
+5. Re-run the example notebook if needed