Add options for var cluster_finder_X:
1. number of neighbors (for better segmentation of clusters)
2. option to empty the surrounding pixels
---------
Co-authored-by: xiangyu.xie <xiangyu.xie@psi.ch>
- Allowing the users more flexibility to play around with custom eta
functions without touching the c++ code
- passing vector of eta values to ``transform_eta_values``
```
from aare import Interpolator, ClusterVector, Etai, Cluster
import numpy as np
def custom_eta(cluster_pixel_coordinate_x, cluster_pixel_coordinate_y, cluster_data):
# dummy custom eta function that just returns the sum of the cluster data
eta = Etai()
eta.x = 0.1 # dummy x value
eta.y = 0.1 # dummy y value
eta.sum = np.sum(cluster_data) # sum of the cluster data as the "energy
return eta
# Create a dummy eta distribution and bins
eta_distribution = np.zeros((10, 10, 1)) # dummy eta distribution
etax_bins = np.linspace(0, 1.0, 11)
etay_bins = np.linspace(0, 1.0, 11)
e_bins = np.array([0., 10.]) # dummy energy bins
# Create the interpolator
interpolator = Interpolator(eta_distribution, etax_bins, etay_bins, e_bins)
# Create a dummy cluster vector
cluster_vector = ClusterVector()
cluster_vector.push_back(Cluster(10, 5, np.ones(shape=9, dtype = np.int32)))
cluster_vector.push_back(Cluster(20, 10, np.ones(shape=9, dtype = np.int32)))
# Create dummy etas for the clusters
cluster_array = np.array(cluster_vector)
etas = np.array([custom_eta(cluster["x"], cluster["y"], cluster["data"]) for cluster in cluster_array])
# transform eta values to uniform coordinates
uniform_coordinates = interpolator.transform_eta_values(etas)
# Interpolate to get the photon coordinates e.g. apply interpolation logic
photon_coordinates_x = cluster_array["x"] + uniform_coordinates["x"] # add to pixel coordinate
photon_coordinates_y = cluster_array["y"] + uniform_coordinates["y"] # add to pixel coordinate
```
advantage: full control over interpolation logic,
downside: inefficient quite some loops in python
- passing pre computed eta values to interpolate function
```
Interpolator.interpolate(cluster_vector, etas)
```
downside: less flexibility in interpolation logic.
downside: People might misuse it instead of using interpolate directly
with a pre compiled eta function implemented in c++
To improve codebase quality and reduce human error, this PR introduces
the pre-commit framework. This ensures that all code adheres to project
standards before it is even committed, maintaining a consistent style
and catching common mistakes early.
Key Changes:
- Code Formatting: Automated C++ formatting using clang-format (based on
the project's .clang-format file).
- Syntax Validation: Basic checks for file integrity and syntax.
- Spell Check: Automated scanning for typos in source code and comments.
- CMake Formatting: Standardization of CMakeLists.txt and .cmake
configuration files.
- GitHub Workflow: Added a CI action that validates every Pull Request
against the pre-commit configuration to ensure compliance.
The configuration includes a [ci] block to handle automated fixes within
the PR. Currently, this is disabled. If we want the CI to automatically
commit formatting fixes back to the PR branch, this can be toggled to
true in .pre-commit-config.yaml.
```yaml
ci:
autofix_commit_msg: [pre-commit] auto fixes from pre-commit hooks
autofix_prs: false
autoupdate_schedule: monthly
```
The last large commit with the fit functions, for example, was not
formatted according to the clang-format rules. This PR would allow to
avoid similar mistakes in the future.
Python fomat with `ruff` for tests and sanitiser for `.ipynb` notebooks
can be added as well.
- Set parameter starting values, limits or fix through name as well as
index
- Updated parameter names for the scurve
- Fast approximation to erf function (~10% speedup of fitting)
---------
Co-authored-by: Khalil Ferjaoui <khalilferjaoui@yahoo.fr>
## Unified Minuit2 fitting framework with FitModel API
### Models (`Models.hpp`)
Consolidate all model structs (Gaussian, RisingScurve, FallingScurve)
into a
single header. Each model provides: `eval`, `eval_and_grad`, `is_valid`,
`estimate_par`, `compute_steps`, and `param_info` metadata. No Minuit2
dependency.
### Chi2 functors (`Chi2.hpp`)
Generic `Chi2Model1DGrad` (analytic gradient) templated on the model
struct.
Replaces the separate Chi2Gaussian, Chi2GaussianGradient,
Chi2Scurves, and Chi2ScurvesGradient headers.
### FitModel (`FitModel.hpp`)
Configuration object wrapping `MnUserParameters`, strategy, tolerance,
and
user-override tracking. User constraints (fixed parameters, start
values, limits)
always take precedence over automatic data-driven estimates.
### Fit functions (`Fit.hpp`)
- `fit_pixel<Model, FCN>(model, x, y, y_err)` -> single-pixel,
self-contained
- `fit_pixel<Model, FCN>(model, upar_local, x, y, y_err)` -> pre-cloned
upar for hot loops
- `fit_3d<Model, FCN>(model, x, y, y_err, ..., n_threads)` ->
row-parallel over pixel grid
### Python bindings
- `Pol1`, `Pol2`, `Gaussian`, `RisingScurve`, `FallingScurve` model
classes with
`FixParameter`, `SetParLimits`, `SetParameter`, and properties for
`max_calls`, `tolerance`, `compute_errors`
- Single `fit(model, x, y, y_err, n_threads)` dispatch replacing the old
`fit_gaus_minuit`, `fit_gaus_minuit_grad`, `fit_scurve_minuit_grad`,
etc.
### Benchmarks
- Updated `fit_benchmark.cpp` (Google Benchmark) to use the new FitModel
API
- Jupyter notebooks for 1D and 3D S-curve fitting (lmfit vs Minuit2
analytic)
- ~1.8x speedup over lmfit, near-linear thread scaling up to physical
core count
---------
Co-authored-by: Erik Fröjdh <erik.frojdh@psi.ch>
- Fixed failing conda builds (numpy >=2.1 and added pytest-check)
- added cibuildwheel settings for osx
- Bumped cibuildwheel to 3.4.0 in pipeline
- build also for macos-latest
- fixed conda workflow which was only on developer branch (now main and
pr to main)
Matterhorn10 Transform
some other Transformations from pyctbGUI
added method get_reading_mode for easier error handling in decoders
## TODO:
- proper error handling for all other decoders
- proper documentation for all other decoders
- refactoring all other decoders to store hard coded values in a Struct
ChipSpecification
Erik Fröjdh
maliakal_d
lunin_l
mazzol_a
hinger_v