- handles file reading of disabled udp ports
- adds members disabled_udp_ports in master file as an optional
- adds member diasbled_udp_port_types in master file as an optional
- Treats enabled udp ports as ROIs
- merges/combines consecutive ROis into one
### To discuss:
- right now can only handle either ROI or disabled udp ports (disabled
udp ports has higher precedence)
- Should Frames in File be removed from Master File as value is nonsense
for disabled udp ports
---------
Co-authored-by: Erik Fröjdh <erik.frojdh@psi.ch>
Optimized pedestal tracking with FastPedestal and performance improvements to the cluster finder.
- ~2x faster hitting 14k FPS on benchmark dataset on 16 core threadripper pro
**Changes**
- No bounds check on interior of frame. (only within half of a cluster)
(~15% improvement)
- Cache threshold (std*n_rms) Biggest improvement comes from not
computing std for each access
- Cache pedestal subtracted frame
- Switched to FastPedestal which assumes we reached steady state
**Things tried but rejected:**
- Always store cluster values, commit on val==max (~15% drop in frame
rate)
**Options**
- using 16 bit clusters and 16 bit pedestal. (slows down the single
threaded case but allow us to reach 12k with multi threading)
**Other notes on performance**
- Passing in memory frames from python and doing nothing: 0.8us/frame
- Passing + pedestal subtraction: 28us/frame
- Passing + pedestal + cluster finding (no store): 652us/frame
- Passing + pedestal + cluster finding: 886 us/frame
- Reading files from nfs shares tops out at ~1GB/s for single threaded
reads.
- MultiThreadedFileReader uses our File wrapper to read a generic file
in parallel
- Placed in aare::experimental to show that it's not production ready
- Move Chi2.hpp from include/aare/ to src/ (private)
- Pimpl on FitModel<Model>: MnUserParameters/MnStrategy behind opaque
src/FitModelImpl.hpp, no Minuit2 includes in public headers
- Move fit_pixel/fit_3d bodies to Fit.cpp with explicit instantiations
for all 8 models; drop FCN template param from public API
- CMake: aare::Minuit2 wrapped in $<BUILD_INTERFACE:...> (hidden from
exported targets, same pattern as lmfit), MINUIT2_INSTALL OFF, Chi2.hpp
removed from PUBLICHEADERS
- Update python bindings and benchmark callsites accordingly
---------
Co-authored-by: Erik Fröjdh <erik.frojdh@psi.ch>
Co-authored-by: Alice <alice.mazzoleni@psi.ch>
With C++20 `fmt::print(s)` expects a compile time format string and
otherwise fails complaining about consteval. To get runtime formatting
use `fmt::print(fmt::runtime(s))`
If AARE_FETCH_MINUIT is set to OFF we first look for a standalone
Minuit2 and if that is not found we try to find Minuit2 as a part of
ROOT.
In both cases we make an alias to allow for simpler use of the target
later.
It still doesn't solve the issue that we install Minuit to when we fetch
it but that can be addressed in a separate PR.
closes #316
Multi threaded filling of per pixel histograms for example for detector calibration
1. PixelHistogram - Generic variant expects already pedestal subtracted
data
2. PedestalTrackingHistogram - Terrible name, useful class. Keeps it's
own pedestal and does conversion and pedestal tracking in the worker
threads.
---------
Co-authored-by: Lars Erik Fröjd <froejdh_e@pc-jungfrau-02.psi.ch>
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.
## 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>
Reading multiple ROI's for aare
- read_frame, read_n etc throws for multiple ROIs
- new functions read_ROIs, read_n_ROIs
- read_roi_into (used for python bindings - to not copy)
all these functions use get_frame or get_frame_into where one passes the
roi_index
## Refactoring:
- each roi keeps track of its subfiles that one has to open e.g.
subfiles can be opened several times
- refactored class DetectorGeometry - keep track of the updated module
geometries in new class ROIGeometry.
- ModuleGeometry updates based on ROI
## ROIGeometry:
- stores number of modules overlapping with ROI and its indices
- size of ROI
Note: only tested size of the resulting frames not the actual values
---------
Co-authored-by: Erik Fröjdh <erik.frojdh@psi.ch>
Co-authored-by: Erik Fröjdh <erik.frojdh@gmail.com>
- New aare:to_string/string_to similar to what we have in
slsDetectorPackage
- Added members period and exptime to RawMasterFile
- Parsing exposure time and period for json and raw master file formats
- Parsing of RawMasterFile from string stream to enable test without
files
Comments:
- to_string is at the moment not a public header. Can make it later if
needed. This gives us full freedom with the API
- FileConfig should probably be deprecated need to look into it.
Meanwhile removed python bindings and string conv
- added rosenblatttransform
- added 3x3 eta methods
- interpolation can be used with various eta functions
- added documentation for interpolation, eta calculation
- exposed full eta struct in python
- disable ClusterFinder for 2x2 clusters
- factory function for ClusterVector
---------
Co-authored-by: Dhanya Thattil <dhanya.thattil@psi.ch>
Co-authored-by: Erik Fröjdh <erik.frojdh@psi.ch>
- Removed unused ClusterFile.cpp (code from before it was templated)
- Updated the list of .cpp files in CMakeLists.txt to match alphabetic
listing in the browser
This PR is a fix/improvement to a problem that Jonathan had. (#156) The
original implementation opened all subfiles at once witch works for
normal sized datasets but fails at a certain point (thousands of files).
- This solution uses RawSubFile to manage the different file indicies
and only opens the file we need
- Added logger.h from slsDetectorPackage for debug printing (in
production no messages should be visible)
hinger_v
mazzol_aandErik Fröjdh
lunin_l
