Changelog

Contents

Changelog#

Pyxel version numbers are in the of form x.y.z.

  • The major release number (x) is incremented if a feature release includes a significant backward incompatible change that affects a significant fraction of users.

  • The minor release number (y) is incremented on each feature release. Minor releases include updated stdlib stubs from typeshed.

  • The point release number (z) is incremented when there are fixes only.

Pyxel doesn’t use SemVer anymore, since most minor releases have at least minor backward incompatible changes.

2.8.2 / 2025-01-27#

This release fixes two models from Data Processing.

Models#

2.8.1 / 2025-01-16#

This is a quick release to fix a bug in model load_star_map in Scene Generation with astroquery version 0.4.8+

Models#

Others#

  • Add new CI/CD pipelines to check functional tests. (See !1021).

  • Remove references to Python 3.9 and ‘xarray-datatree’. (See !1022).

2.8 / 2025-01-15#

This release introduces significant updates and new features.

🆕 New model exponential_qe in Charge Generation#

Model exponential_qe from Charge Generation has been added.

This model computes the Quantum Efficiency (QE) of a detector based on key characteristics such as:

  • Front/Back Illumination

  • Charge Collection Efficiency

  • Absorption coefficient

  • Reflectivity

  • Epilayer thickness

  • Poly gate thickness

🆕 FITS Header Propagation#

It is now possible to propagate the FITS header, read using model the load_image from Photon Collection with a FITS Image data file into the FITS output file(s).

For example, if the FITS file my_image.fits contains a FITS header into its HDU (Header Data Unit) ‘RAW’, you can extract and store it into an output FITS file by using the following YAML configuration:

observation:   # or 'exposure'
  outputs:
    output_folder: 'output'             # <== output FITS file(s) will be save in this folder
    save_data_to_file:
      - detector.image.array: ['fits']  # <== generate at least one FITS file

cmos_detector:
  ...

pipeline:
  photon_collection:
    func: pyxel.models.photon_collection.load_image
    enabled: true
    arguments:
      image_file: my_image.fits         # <== input FITS filename
      convert_to_photons: false
      include_header: true
      header_section_index: 'RAW'       # <== HDU where to retrieve the FITS header (optional)

   ...

⌨️ Add more instructions for setting a development environment with uv#

Add additional instructions in the contribution guide on how to set up a development environment using uv (Unified Python Packaging).

Breaking changes#

Support for Python 3.9 has been dropped.

The minimum versions of some dependencies were also changed:

Package

Old

New

astropy

4.3

5.2+

typing-extensions

4.5

4.9+

xarray

2023.12.0

2024.10.0+

Core#

  • Add compatibility withASDF version 4. (See !999).

  • Support DataTree from xarray >= 2024.10.0. (See !1008).

  • Use fsspec capability with Astropy 5.2+. (See !1013).

  • Refactor and simplify code for Observation mode with Dask enabled. (See !1016).

Documentation#

Models#

Others#

  • Minor refactoring using ruff check --preview. (See !998).

  • Fix issue with ruff 0.8 and 0.9. (See !1000 and !1001).

  • Remove support of Python 3.9. (See !1007).

  • Add support for Python 3.12. (See !1003).

  • Use decorator @typing_extensions.deprecated to deprecated ‘old’ code (See !1018).

2.7 / 2024-11-11#

This release brings a number of bug fixes and improvements.

Fix memory leak issue with function pyxel.run and command python -m pyxel in Observation mode#

A critical memory leak that occur when running the command pyxel -m pyxel configuration.yaml or the python function pyxel.run('configuration.yaml') in Observation mode with parameter with_dask enabled is fixed.

This fix prevents the computer from running out of memory in Observation mode.

New feature: return list of output filenames with function pyxel.run#

The pyxel.run command now returns a list of generated output filenames.

Example:

>>> import pyxel
>>> filenames = pyxel.run('observation.yaml')
>>> filenames
   id data_format bucket_name                     filename
0   0        fits       image  detector_image_array_1.fits
1   1        fits       image  detector_image_array_2.fits
2   2        fits       image  detector_image_array_3.fits
3   3        fits       image  detector_image_array_4.fits
4   4        fits       image  detector_image_array_5.fits
5   5        fits       image  detector_image_array_6.fits

Core#

Documentation#

  • Fix documentation for model AC/DC crosstalks from Charge Measurement model group by Antoine Kaszczyc from CRAL (Centre de Recherche Astrophysique de Lyon). (See !983).

  • When running uvx force to use a python version. (See !987).

Models#

Others#

  • Pin to xarray < 2024.10.0. (See !978).

  • Simplify usage of ruff check and ruff format. (See !991).

2.6.1 / 2024-10-14#

This release brings a number of bug fixes since version 2.6

Core#

  • Cannot set readout time as a single value. (See !973).

  • Fix bug when trying to set observation.readout.times in Observation mode. (See !972).

  • Cannot set readout time as a single value. (See !973).

  • Fix bug in function pyxel.plotting.plot_ptc. (See !974).

Models#

  • Fix bug in model mean_variance when only a single readout time is provided. (See !975).

2.6 / 2024-10-11#

This release brings a number of bug fixes and improvements.

📈Plotting utilities#

A new plotting utilities library has been added in pyxel.plotting.

The first plot is the function pyxel.plotting.plot_ptc to plot a Photon Transfer Curve (PTC) on log-log scale using Matplotlib.

💪Observation mode with dask enabled#

When using Observation mode with with_dask enabled in pyxel.run_mode, the output is a DataTree containing Dask Arrays instead of Numpy Arrays. With the Dask Arrays, the resulting DataTree can handle data larger than the available memory. This allows for efficient processing and computation on large-scale data without memory constraints.

More information on how to work with Xarray and Dask, check out the Xarray tutorial with Dask.

Example of YAML file with with_dask enabled:

observation:
  with_dask: true
  ...

and how to use it:

>>> import pyxel
>>> config = pyxel.load('observation.yaml')
>>> data_tree = pyxel.run_mode(
...     mode=config.running_mode,
...     detector=config.detector,
...     pipeline=config.pipeline,
... )

>>> data_tree['/bucket']
<xarray.DataArray 'bucket'>
Group: /bucket
    ...
    Data variables:
        photon         (temperature, ..., time, y, x)  dask.array<chunksize=(1, ..., 100, 256, 256)>
        ...
        image          (temperature, ..., time, y, x)  dask.array<chunksize=(1, ..., 100, 256, 256)>

>>> data_tree['/bucket'].compute()
...

Core#

  • Improved Observation mode with dask enabled. (See !951).

  • Add compatibility with xarray 2024.09.0. (See !953).

  • Use method xarray.drop_vars instead of xarray.drop. (See !955).

  • Fix bug when using function load_table with data containing only a single column. (See !954).

  • Fix bug when using parameter debug with pyxel.run_mode. (See !957).

  • Remove progress bar when running Observation mode with Dask enabled. (See !958).

  • Force parameter with_inherited_coords in pyxel.run_mode to True if ‘Scene’ is not empty. (See !962).

  • Fix bug in Observation mode. (See !967).

  • Add new module pyxel.plotting. (See !966).

  • Better error message when a parameter for Observation mode is wrong. (See !968).

Documentation#

Models#

Others#

  • Apply ruff format on the source code. (See !950).

  • Add more tests for command line tool pyxel-sim. (See !964).

2.5.1 / 2024-09-12#

This release is to fix a bug with xarray version 2024.9.0

Others#

  • Pin xarray version to <2024.9.0. (See !946).

2.5 / 2024-09-11#

This release brings a number of bugfixes and improvements.

🚀 New way to quickly install and use Pyxel 🚀#

We’ve introduced a new quickstart setup guide for faster and easier installation and use of Pyxel with uv.

How to get Started:#

  1. First, install uv by following the installation guide here.

  2. Then, run the following commands to download the Pyxel tutorial notebooks (~200 MB) and open them in Jupyter Lab:

$ uvx pyxel-sim download-examples
Downloading examples: 388MB [00:08, 47.9MB/s]
Done in folder /.../pyxel-examples.

$ cd pyxel-examples
$ uvx --with pyxel-sim[model] jupyter lab
[Server App] Jupyter Server is running at:
[Server App] http://localhost:8888/lab?token=...

This streamlined process makes it simpler to get Pyxel up and running quickly !

New parameter with_inherited_coords for pyxel.run_mode function#

A new optional with_inherited_coords parameter has been added to the pyxel.run_mode function. This ensures that coordinates are inherited within the DataTree, simplifying the hierarchical structure and reducing data redundancy. For more detail, see Xarray issue #9077.

⚠️ This parameter is provisional. ⚠️

Example:

>>> import pyxel
>>> cfg = pyxel.load('configuration.yaml')

>>> result = pyxel.run_mode(
...     mode=cfg.running_mode,
...     detector=cfg.detector,
...     pipeline=cfg.pipeline,
...     with_inherited_coords=True,    # <== Use parameter 'with_inherited_coords'
... )        
>>> result
<xarray.DataTree>
Group: /
│   Dimensions:  ()
│   Data variables:
│       *empty*
│   Attributes:
│       pyxel version:  2.4.1+37.gff6da221.dirty
│       running mode:   Exposure
├── Group: /bucket
│   │   Dimensions:  (time: 100, y: 64, x: 64)
│   │   Coordinates:
│   │     * y        (y) int64 512B 0 1 2 3 4 5 6 7 8 9 ... 55 56 57 58 59 60 61 62 63
│   │     * x        (x) int64 512B 0 1 2 3 4 5 6 7 8 9 ... 55 56 57 58 59 60 61 62 63
│   │     * time     (time) float64 800B 0.0001 0.0001103 0.0001216 ... 1.437 1.585
│   │   Data variables:
│   │       photon   (time, y, x) float64 3MB 98.0 101.0 97.0 ... 1.465e+05 1.478e+05
|   |       ...
│   │       image    (time, y, x) uint16 819kB 79 76 73 74 ... 63018 62978 62896 63024
│   └── Group: /bucket/scene
└── Group: /data
    └── Group: /data/mean_variance
        └── Group: /data/mean_variance/image
                Dimensions:       (pipeline_idx: 100)
                Coordinates:
                  * pipeline_idx  (pipeline_idx) int64 800B 1 2 3 4 5 6 7 ... 94 95 96 97 98 99
                Data variables:
                    mean          (pipeline_idx) float64 800B 7.316 8.086 ... 6.299e+04
                    variance      (pipeline_idx) float64 800B 12.17 13.45 ... 1.348e+03

Breaking changes#

The minimum versions of some dependencies were changed:

Package

Old

New

matplotlib

3.1

3.6+

numba

0.56.4

1.24+

numpy

1.23

1.24+

pandas

1.5+

scikit-image

0.20.0+

scipy

1.10+

xarray

2022.6

2023.12.0+

Core#

  • Add error message when a YAML file uses Observation mode without parameters. (See !933).

  • Add possibility to use strings in the parameters fields in a YAML observation file. (See !936).

  • Add better error message when a pipeline failed during Observation mode. (See !937).

  • Add new parameter with_inherited_coords into function pyxel.run_mode. (See !939).

Documentation#

  • Update documentation about the new dependencies. (See !934).

Models#

Others#

  • Add compatibility to xarray 2024.07.0. (See !929).

  • Improved printable representation of classes Configuration, DetectionPipeline and Observation. (See !935).

  • Speed import time for pyxel. (See !943).

  • Add Python script pyxel-sim. (See !944).

2.4.1 / 2024-07-10#

The documentation was not updated for version 2.4.1 (missing environment file, …).

Others#

  • Add missing files for version 2.4.1. (See !922).

2.4 / 2024-07-10#

This release brings a number of bugfixes and improvements.

New parameter working_directory for the YAML file

A new optional parameter working_directory has been added in the YAML configuration files. This parameter defines the current working directory, which will be used ad the base directory for all relative paths used in the YAML configuration file.

See the following example:

working_directory: ~/my_folder     # <== define working directory to `~/my_folder` (optional)
simulation:
  mode: calibration
  calibration:
    target_data_path: ['CTI/input/data.fits']  # <==      will be converted as
#                       +-----------------+         `~/my_folder/CTI/input/data.fits`
#                               |                    +---------+
#                           relative path                 |
#                                               from 'working_directory'

New parameter --override for the command line tool

A new optional parameter --override in the pyxel run command line tool allows users to override specific configuration parameters from a YAML configuration file.

This can be particularly useful for making quick adjustments to the configuration without modifying the original YAML file

Example of running the configuration configuration.yaml and overriding its parameters exposure.outputs.output_folder and pipeline.photon_collection.load_image.arguments.image_file

$ python -m pyxel run configuration.yaml --override exposure.outputs.output_folder=new_folder \
                                         --override pipeline.photon_collection.load_image.arguments.image_file=new_image.fits

from this YAML configuration file:

exposure:
  outputs:
     output_folder: old_folder

pipeline:
  photon_collection:
    - name: load_image
      func: pyxel.models.photon_collection.load_image
      enabled: true
      arguments:
        image_file: data/Pleiades_HST.fits

New parameter stepsize for model CosmiX

A new optional parameter stepsize has been added for model Cosmix in group Charge Generation.

This parameter allows adding defined step size files when running_mode: stepsize is enabled.

Example of a YAML configuration file to use this parameter:

- name: cosmix
  func: pyxel.models.charge_generation.cosmix
  enabled: true
  arguments:
    simulation_mode: cosmic_ray
    running_mode: "stepsize"
    particle_type: proton
    initial_energy: 100.          # MeV
    particles_per_second: 100
    incident_angles:
    starting_position:
    spectrum_file: 'data/proton_L2_solarMax_11mm_Shielding.txt'
    seed: 4321
    stepsize:
      - type: proton
        energy:    100.0  # MeV
        thickness: 40.0   # um
        filename:  pyxel/models/charge_generation/cosmix/data/stepsize_proton_100MeV_40um_Si_10k.ascii
      - type: proton
        energy:    100.0  # MeV
        thickness: 50.0   # um
        filename:  pyxel/models/charge_generation/cosmix/data/stepsize_proton_100MeV_50um_Si_10k.ascii
      - type: proton
        energy:    100.0  # MeV
        thickness: 60.0   # um
        filename:  pyxel/models/charge_generation/cosmix/data/stepsize_proton_100MeV_60um_Si_10k.ascii
      - type: proton
        energy:    100.0  # MeV
        thickness: 70.0   # um
        filename:  pyxel/models/charge_generation/cosmix/data/stepsize_proton_100MeV_70um_Si_10k.ascii
      - type: proton
        energy:    100.0  # MeV
        thickness: 100.0   # um
        filename:  pyxel/models/charge_generation/cosmix/data/stepsize_proton_100MeV_100um_Si_10k.ascii

Updated dependencies#

The minimum versions of some dependencies were changed:

Package

Old

New

hvplot

0.9+

Core#

  • Add new parameter working_directory in YAML configuration files. (See !838).

  • Use DataTree from module xarray.core.datatree when possible. (See !897).

  • Add an option to override parameter(s) from pyxel -m run. (See !903).

  • Function pyxel.run_mode does not generate DataTree internally. (See !906).

  • Add more info in the header of generated FITS files. (See !904).

  • Reinject FITS header of inputs file(s) into output file(s). (See !905).

  • Cannot access attribute observation from processor. (See !907).

  • Improve error message when loading an non-existing model. (See !912).

Documentation#

Models#

Others#

  • Remove dependency to netcdf4. (See !914).

  • Fix issues found by ruff 0.5. (See !902 and !915).

  • Add unit tests for class APDCharacteristics. (See !910).

  • Add compatibility with Numpy 2. (See !913).

  • Fix some issues in some tests. (See !916).

  • Bump hvplot to version 0.9. (See !917).

2.3 / 2024-06-19#

This release brings a number of bugfixes and improvements.

Core#

  • Add option to generate a new model directly in the console with pyxel -m create-model. (See !894).

Documentation#

  • Fix issue with netcdf4 version 1.7.1. (See !896).

  • Add more documentation about ‘developer install’. (See !895).

Others#

2.2 / 2024-05-29#

This release brings a number of bugfixes and improvements.

Documentation#

Models#

Others#

2.1.1 / 2024-03-19#

Add missing documentation on version 2.1 (and 2.1.1).

2.1 / 2024-03-19#

This release brings a number of bugfixes and improvements.

The Pyxel Wheel package size has been reduced from 22 MB to less than 1 MB.

Several serious bugs where solved in models:

Parameter outputs in the YAML configuration is now optional. See the following examples:

Before:

exposure:

  readout:
    times: [1., 5., 7.]
    non_destructive:  false

  outputs:
    output_folder: my_folder    # An output folder is generated but nothing is stored there.
                                # It is still compulsory to add 'outputs'

After:

exposure:

  readout:
    times: [1., 5., 7.]
    non_destructive:  false

  # No need to add 'outputs'

Core#

  • Parameter outputs is optional in YAML files. (See !872).

  • Add more units in outputs generated by pyxel.run_mode(). (See !873).

Documentation#

  • Add more documentation. (See !876).

Models#

Others#

  • Improved tests when an optional dependency is not installed. (See !866).

  • Reduce size of wheel file. (See !868).

  • Bump ‘versioneer’ from 0.28 to 0.29. (See !869).

  • Fix issue with Mypy 1.9. (See !871).

  • Add more rules in ‘ruff’. (See !870).

  • Move pyxel_schema.json into folder pyxel/static. (See !874).

2.0 / 2024-02-22#

This is a major release of Pyxel that brings number of new features such as support for multi-wavelength.

Version 2.0 brings a number of bugfixes, improvements and deprecations.

Breaking Changes#

Removed models#

The deprecated models in optics and photon_generation model groups are removed.

The deprecated model simple_aperture in photon_collection is removed.

New unit for wavelength#

Parameter wavelength in model optical_psf in photon_collection is defined in nanometer instead of meter.

Before

- name: optical_psf
  func: pyxel.models.photon_collection.optical_psf
  enabled: true
  arguments:
    wavelength: 0.6e-6          # wavelength in meters

Now

- name: optical_psf
  func: pyxel.models.photon_collection.optical_psf
  enabled: true
  arguments:
    wavelength: 600          # wavelength in nm
#               ^^^                          ^^
#               new

Updated dependencies#

The minimum versions of some dependencies were changed:

Package

Old

New

Bokeh

3.3+

Core#

Documentation#

  • Update documentation about quick start installation. (See !830).

  • Use sphinx-design instead of sphinx-panels in the documentation. (See !831).

  • Restructure documentation api. (See !840).

  • Add more documentations. (See !829, !841 and !846).

  • Output files generated by detector_import_export notebook guide are saved into a temporary file. (See !842).

  • Add links from Pyxel Data directly into the documentation. (See !861).

  • Remove references to ‘gitlab.esa.int’ with Docker. (See !834).

  • Update documentation for 2.0. (See !856).

Models#

Others#

1.15 / 2024-01-29#

This release brings a number of bugfixes and improvements.

The bucket Photon can now be 2D or 3D (with additional dimension wavelength).

A new function pyxel.display_scene() was added to display the scene, which is generated by models inside the Scene Generation.

New models were added to Photon Collection and Charge Generation that can manage multi-wavelength photons.

The following new models were added:

Breaking Changes#

The model argument pixel_scale was moved to the Detector.geometry.

The model aperture in photon_collection is deprecated and will be removed in Pyxel 2.0. Please use simple_collection instead.

Core#

  • Create 3D photon container, add it as an output of function pyxel.run_mode and merge it with Photon. (See !673 , !766 , !813 and !815).

  • Moving pixel scale parameter to detector geometry. (See !816).

  • Add new function pyxel.display_scene to display a scene container in a Detector object. (See !819).

Models#

  • Add model that converts 3D scene to 3D photon. (See !760).

  • Implement a wavelength-dependency for the QE map. (See !765).

  • Add model “load_PSF_wavelength”. (See !686).

  • Refactor aperture and simple collection. (See !818).

  • Add model ‘optical_psf_multi_wavelength’ from group ‘Photon Collection’. (See !820).

  • Pointing jitter model. (See !814 and !822).

Others#

  • Convert DeprecationWarning to FutureWarning. (See !821).

1.14 / 2024-01-19#

This release brings a number of bugfixes and improvements.

The functions pyxel.exposure_mode(...), pyxel.observation_mode(...) and pyxel.calibration_mode(...) are deprecated and will be removed in Pyxel 2.0. These functions are replaced by pyxel.run_mode(...)

Core#

  • Move “intermediate_steps” from data to parent data_tree. (See !788).

  • Improved method Detector.to_xarray(). (See !787).

  • Improved method Scene.to_xarray(). (See !799).

  • Added deprecated warnings to pyxel.calibration_mode(), pyxel.exposure_mode(), pyxel.observation_mode(). (See !802 and !804).

Documentation#

  • Add documentation for Detector.scene. (See !800).

Models#

  • Add a caching mechanism with model load_star_map from Scene Generation. (See !798).

  • Use Charge array instead of Photon array in model physical_non_linearity_with_saturation from Charge Measurement. (See !807).

Others#

  • Catch exception ModuleNotFoundError instead of ImportError. (See !789).

  • Refactor functions in state.py. (See !790).

  • Add missing packages in environment.yml. (See !792).

  • Fix for Xarray 2023.12.0. (See !793 and !809).

  • Prepare for Numpy 2. (See !795).

  • Parameter with_intermediate_steps is not optional in function run_pipeline. (See !794).

  • Package sep must be an optional package. (See !805).

  • Speedup function run_mode. (See !806).

  • Improved some error messages. (See !810).

  • Year correction in ESA copyright. (See !796 and !811).

1.13.1 / 2023-11-28#

This release brings a number of bugfixes and improvements.

With the new breaking changes in version 1.13 the pixel array was reset also when using non-destructive readout mode. This new release fixes the bug. The error message is improved when an array is not initialized and the documentation for the model groups is updated, such that the user is better informed.

Core#

  • Add better error message when a ‘Photon’, ‘Pixel’, ‘Signal’ and ‘Image’ data containers are not initialized. (See !780).

  • Small refactoring of methods ‘Detector.from_dict’ and ‘Detector.to_dict’. (See !781).

  • Non destructive readout, signal is not increasing. (See !783).

Documentation#

  • Review model descriptions in reference documentation. (See !784).

1.13 / 2023-11-22#

This release brings a number of bugfixes and improvements.

Breaking changes#

The containers such as Photon, Pixel, Signal and Image are not initialized before running a pipeline. The models must initialize the containers.

Core#

  • Removed deprecated Detector.set_output_dir method and Detector.output_dir property. (See !759).

  • Image data bucket only allows integer data. (See !764).

  • Fix issue in Observation mode with a 2D parameter. (See !770).

  • Changed Array class initializer. The internal array is initialized to None not np.zeroes. (See !767).

  • Remove attribute input_image from Detector. (See !772).

  • Fix bug in Array.__repr__. (See !773).

  • Fix bugs in Calibration mode. (See !774).

  • Add two new load_table_v2 and load_image_v2 functions. These functions are more flexible than load_table and load_image and are provisional. (See !775).

Models#

  • Improvements in model ‘pulse_processing’ in Model group ‘phasing’. (See !665).

  • Model ‘amplifier_crosstalk’ is moved from ‘readout_electronics’ to ‘charge_measurement’. (See !763).

  • Remove warnings from model ‘Cosmix’ from ‘Charge Generation. (See !768).

  • Remove all warnings in dark current model. (See !769).

  • Fix issue with model ‘wavelength_dependence_airs’ in ‘Photon Collection’. (See !776 and !777).

Others#

  • Minor refactoring. (See !756).

  • Check more packages with function pyxel.show_versions(). (See !757).

  • Fix issues when running Mypy 1.7. (See !762).

  • Remove conda package ‘memray’ from ‘environment.yml’. (See !782).

1.12 / 2023-10-27#

This release brings a number of bugfixes, documentation and improvements.

The function pyxel.display_detector used in the jupyter notebooks to visualise the detector at each stage of the pipeline, has now the option to display in logarithmic scale besides the linear scale and to change the color of the image. The bin size and the x-axis range can now be changed in the related histogram plot.

Core#

  • In ‘Custom Observation’ mode, add a sanity test to verify input custom data. (See !749).

  • Nan output and missing output in observation mode. (See !750).

  • Improved function pyxel.display_detector. (See !739).

  • Add filter to ignore warnings in scene_generation. (See !751).

  • Reduce warning in dark current model. (See !643).

Documentation#

1.11.1 / 2023-10-19#

This release brings one bugfix.

Others#

  • Remove Scopesim as a dependency of Pyxel. (See !745).

1.11 / 2023-10-18#

This release brings a number of bugfixes, documentation and improvements.

The following new models were added:

Parameter data_type is now optional in model simple_adc in Readout Electronics. If this parameter is not provided then it is inferred from adc_bit_resolution in Detector.

Core#

  • Bug when using with a configuration file with extension ‘.yml’ instead of ‘.yaml’. (See !737).

  • Speedup function pyxel.load. (See !738).

  • Add Scene to pyxel.run_mode. (See !740).

  • Fix bug with the output of pyxel.run_mode. The ‘image’ container has type float64 instead of int. (See !742).

Documentation#

  • Add info about Jupyter book being not interactive. (See !726).

  • Add new icon/badge ‘I want to contribute !’ (See !727).

  • Update EMCCD cic model multiplication_register_cic in Charge Transfer. (See !728).

  • Fix documentation for model load_charge in charge_generation. (See !743).

Models#

Others#

  • Fix issues with mypy and Matplotlib 3.8. (See !734).

  • Add poppy as a dependency in Conda. (See !741).

1.10.2 / 2023-08-29#

This release brings a bugfix with the conda package.

1.10.1 / 2023-08-28#

This release brings a bugfix.

Others#

  • Update lacosmic dependency to optional. (See !721).

1.10 / 2023-08-28#

This release brings a number of bugfixes, documentation and improvements.

The Pixel Coordinate conventions is now clarified.

The following new models were added:

A new parameter with_intermediate_steps in function pyxel.run_mode has been added. With this parameter, it is now possible to display all intermediate steps executed in the pipeline. This parameter is provisional and may change in the future.

Breaking changes#

Bucket Detector.processed_data is removed. This bucket was used in the Data Processing group and is now replaced by the Detector.data bucket.

Core#

Documentation#

  • Add questions to FAQ. (See !688 and !692).

  • Data link missing. Add link to DataTree. (See !676).

  • Add documentation for methods .plot() and .to_xarray() for Pixel, Photon, Signal, Image and Phase. (See !533).

  • Add more info in documentation about Data Processing models. (See !640).

Models#

Others#

  • Refactoring. (See !682).

  • Reduce code complexity by enabling McCabe plugin ruff. (See !257).

  • Add rule ‘pep8-naming’ to ‘ruff’. (See !699).

  • Fix coverage and generate an HTML report. (See !704 and !706).

  • Fix issue E721 found by flake8 version 6.1.0. (See !708).

  • Apply ‘ruff’ to folder ‘tests’. (See !718).

1.9.1 / 2023-07-07#

This release brings a number of bugfixes.

Models#

  • Fix an error in a formula for model ‘dead_time’ in ‘readout_electronics’. (See !681).

  • New model ‘Wavelength dependence AIRS’ for ‘Photon Collection’. (See !677).

Others#

  • Cannot load a FITS file from an HTTP URL. (See !672).

  • Refactoring. (See !679).

1.9 / 2023-06-01#

This release brings a number of bugfixes and documentation improvements.

Detector contains a new bucket data which contains a xarray.DataTree (see !631)

Breaking changes#

Function pyxel.run_mode is not (yet) stable and may change.

Support for Python 3.8 has been dropped and support for Python 3.11 has been added.

The minimum versions of some dependencies were changed:

Package

Old

New

Python

3.8+

3.9+

Poppy

1.0.3

1.1.0+

Core#

Documentation#

Models#

Others#

  • Remove support to Python 3.8. (See !633).

  • Add units to data buckets in display detector. (See !641).

  • Adding more linter rules to ‘ruff’. (See !644).

  • Fix CI/CD pipelines. (See !650).

  • Add compatibility to Python 3.11. (See !651).

  • Move and update ‘requirements-dev.txt’. (See !654).

  • Fixed Windows compatibility issue with several tests. (See !655).

  • Add missing packages in pyxel.show_versions(). (See !657).

  • Poppy version 1.0.3 is not compatible with numpy 1.24. (See !659).

  • Remove noisy error messages when using ‘tox’. (See !662).

1.8 / 2023-03-30#

This release brings a number of bugfixes and documentation improvements.

A new function pyxel.run_mode has been added and will replace pyxel.exposure_mode, pyxel.observation_mode and pyxel.calibration_mode functions. This function pyxel.run_mode always returns an Xarray Dataset

A new parameter custom_dir_name has been added to customize the name of the output folder.

Example of a configuration file:

exposure:   # This is also valid for 'observation:' and 'calibration:'
  outputs:
    output_folder: output
    custom_dir_name: custom    # <= NEW
    save_data_to_file:

In this example, a new output folder output/custom_... will be created.

In the calibration configuration files, it is now possible to add different boundaries for values defined as a list.

Example of configuration file before:

parameters:   
  - key:              pipeline.charge_transfer.cdm.arguments.beta
    values:           _
    logarithmic:      false
    boundaries:       [0.1, 0.9]
  - key:              pipeline.charge_transfer.cdm.arguments.trap_release_times
    values:           [_, _, _, _]
    logarithmic:      true
    boundaries:       [1.e-5, 1.e-1]   # Same boundaries for the four values
  - key:              pipeline.charge_transfer.cdm.arguments.trap_densities
    values:           [_, _, _, _]
    logarithmic:      true
    boundaries:       [1.e-2, 1.e+2]   # Same boundaries for the four values

and after:

parameters:   
  - key:              pipeline.charge_transfer.cdm.arguments.beta
    values:           _
    logarithmic:      false
    boundaries:       [0.1, 0.9]
  - key:              pipeline.charge_transfer.cdm.arguments.trap_release_times
    values:           [_, _, _, _]
    logarithmic:      true
    boundaries:       [1.e-5, 1.e-1]   # Same boundaries for the four values
  - key:              pipeline.charge_transfer.cdm.arguments.trap_densities
    values:           [_, _, _, _]
    logarithmic:      true
    boundaries:                       # NEW different boundaries for the four values
      - [1.e-2, 1.e+2]
      - [1.e-3, 1.e+3]
      - [1.e-4, 1.e+4]
      - [1.e-5, 1.e+5]

Breaking changes#

The minimum versions of some dependencies were changed:

Package

Old

New

numpy

1.20

1.21

xarray

0.19

2022.06

Core#

  • Multiple boundary conditions for calibration mode. It’s now possible to add different boundaries condition (See !612).

  • Add a option to force data type in function ‘load_table’. (See !615).

  • Observation mode, build table with string not only float. (See !613).

  • Check that in exposure readout time is strictly increasing. (See !516).

  • Improve Calibration Dataset output. (See !624).

  • Add new function ‘pyxel.run_mode’. (See !623 and !630).

  • Fix warning message in Calibration. (See !625).

  • Add charge detector bucket to xarray output when charge is not a dataframe. (See !629).

  • Add photon and charge buckets also to calibration mode. (See !632).

  • Ability to name the outputs instread of timestamp directory creation. (See !211).

Documentation#

  • Use ‘Sphinx 5’ and ‘Sphinx Book Theme 1’. (See !621).

  • Update links in Documentation Tutorials & Examples. (See !628).

Models#

  • Add new ‘Source Extractor’ for ‘Data Processing’ model group. (See !634).

Others#

  • Set minimum version of numpy to 1.21. (See !614).

  • Use ‘ruff’ in CI/CD. (See !616).

  • Add compatibility to Pandas 2.0. (See !627).

1.7 / 2023-02-09#

This release brings a number of bugfixes and documentation improvements.

The first peer-reviewed paper of Pyxel was published in the Journal of Astronomical Telescops, Instruments, and Systems and Pyxel has now an entry in the Astrophysics Source Code Library.

A new model group ‘Photon Collection’ was added to replace the groups ‘Photon Generation’ and ‘Optics’. All models from ‘Photon Generation’ and ‘Optics’ are copied into ‘Photon Collection’. The current models from ‘Photon Generation’ and ‘Optics’ are obsolete/deprecated and will be removed in version 2.0.

Example of migration from a model from ‘Photon Generation’ to ‘Optics’:

Before:

pipeline:
  photon_generation:
    - name: shot_noise
      func: pyxel.models.photon_generation.shot_noise
      enabled: true

  optics:
    - name: optical_psf
      func: pyxel.models.optics.optical_psf
      enabled: true
      arguments:
        fov_arcsec: 5 # FOV in arcseconds
        pixelscale: 0.01 #arcsec/pixel

After:

pipeline:
  photon_collection:
# ^^^^^^^^^^^^^^^^^
#     modified
    - name: shot_noise
      func: pyxel.models.photon_collection.shot_noise
#           ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^~~~~~~~~~~~
#                             modified
      enabled: true

    - name: optical_psf
      func: pyxel.models.photon_collection.optical_psf
#           ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^~~~~~~~~~~~~
#                             modified
      enabled: true
      arguments:
        fov_arcsec: 5 # FOV in arcseconds
        pixelscale: 0.01 #arcsec/pixel

Core#

  • Remove python37. (See !594).

Documentation#

  • Add Pyxel paper in documentation + Gitlab page. (See !589).

  • Added citation segment in README.md. (See !591).

  • Update FAQ. (See !592 and !593).

  • Add documentation about ModelGroup ‘Photon Collection’. (See !598 and !602).

  • Add Pyxel to ASCL.net. (See !603).

  • Update contribution guide with steps for a merge request. (See !607).

  • Add more information in the contribution guide. (See !606).

Models#

  • Cannot reload a ‘detector’ from model ‘pyxel.load_detector’. (See !588).

  • Move all models in ModelGroup ‘Photon Generation and ‘Optics’ into a new ModelGroup ‘Photon Collection’. All models in ‘Photon Generation’ and ‘Optics’ are obsolete/deprecated and will be removed in version 2.0. (See !597).

  • Add new ModelGroup ‘Scene Generation’. (See !600).

  • Add new decorator ‘deprecated’ to deprecate old models. (See !604).

Others#

  • Remove CCDCharacteristics, CMOSCharacteristics and MKIDCharacteristics. (See !590).

  • Simplification when using ‘group models’ when generating a JSON Schema file. (See !596).

  • Create a ‘tox’ environment to check if the JSON schema is unchanged. (See !601).

  • Fix issues when running tests without having ‘asdf’ installed. (See !605).

1.6.1 / 2023-01-09#

This release brings a number of bugfixes and documentation improvements.

Core#

  • Bug in data processing model group. (See !585).

Documentation#

  • Update documentation example. (See !584).

1.6 / 2023-01-05#

This release brings a number of bugfixes and documentation improvements. A single release candidate (1.6rc0) was made to fix some issues.

The JSON Schema files for the ‘stable’ and ‘latest’ are respectively located in https://esa.gitlab.io/pyxel/pyxel_schema.json and https://esa.gitlab.io/pyxel/pyxel_schema_latest.json. And detailed How-to guide about JSON Schema is available.

Add new models load_detector and save_detector for each Model Groups to load/inject or to save/extract a Detector object to/from a running pipeline. Add new model group data_processing with a new model statistics.

Core#

  • Add ‘Detector.load’ and ‘Detector.save’. (See !559).

  • Add method Detector.to_xarray(). (See !563).

  • Add parameter ‘header’ in function ‘load_table’. (See !565).

  • Add new model group ‘Data Processing’. (See !566).

  • Improve error message when validation an ‘Observation’ configuration. (See !571).

Documentation#

  • Add JSON Schema in the documentation. (See !543).

  • Fix issues sphinx. (See !574).

  • Add more documentation when installing from ‘continuous_integration/environment.yml’. (See !581).

  • Correct image in Documentation. (See !576).

Models#

  • Add models load_detector and save_detector to load/save a detector from/to a file. (See !545 and !562).

  • Add option to current PRNU model. (See !568)

Others#

  • Add unit tests to charge deposition in MCT model. (See !553).

  • Move JSON Schema files to https://esa.gitlab.io/pyxel (See !555 and !556).

  • Remove old Python 2.x type annotations. (See !557).

  • Fix issue when generating the JSON Schema file. (See !558).

  • Add a CI/CD pipeline to generate/check the JSON Schema file. (See !535).

  • Refactoring with ‘refurb’. (See !560).

  • Use ‘pyproject.toml’. (See !530).

  • Fix issue with unit test ‘json schema’. (See !569).

  • Move ‘environment.yml’ in folder ‘continuous_integration’. (See !570).

  • Enable ‘License Compliance’. (See !567).

  • Add attrs as dependency. (See !573).

  • Create Wheel files in CI/CD. (See !575).

  • Pygmo error in calibration. (See !580).

1.5 / 2022-11-21#

This is a minor release that brings documentation improvements.

Documentation#

  • Add more information about installation of ‘poppy’. (See !541).

  • Add more information about ‘wheel’ file in the contribution guide. (See !542).

  • Add more installation documentation. (See !547).

Others#

  • The minimum version of ‘holoview’ (See !540) was changed:

    Package

    Old

    New

    holoviews

    undef

    1.15

  • Create a new Conda Environment file to install ‘pyxel’ version 1.4. (See !546 and !548).

1.4 / 2022-11-15#

This release brings a number of bugfixes and documentation improvements. A new ‘charge_deposition_in_mct’ model is added in the ‘Charge Generation’ group and it’s now possible to import/export a Detector object to/from an ASDF file.

Core#

  • Implement multi-wavelength photon descriptions in Detector.scene. (See !505).

  • Implement a function that converts from scopesim.Source object to Scene object. (See !506).

  • Refactor and simplify Calibration and Observation classes. (See !507 and !508.

  • Import/Export a Detector from/to an ASDF file. (See !513).

  • Identical argument names for different models crashes observation mode. (See !524).

  • Add methods ‘.plot()’ and ‘.to_xarray’ for ‘Pixel’, ‘Photon’, ‘Signal’, ‘Image’ and ‘Phase’. (See !528).

Documentation#

  • Add a ‘copy’ button in documentation to copy code blocks. (See !506).

  • Fix typos in the documentation. (See !517).

  • Update doc for reading in files in exposure mode (See !534).

Models#

  • Create a simple cosmic ray model based on stopping power curves. (See !339).

  • Check correct range for dark_current. (See !522).

  • Add option for dark current non uniformity. (See !425).

Others#

  • Improved JSON Schema. (See !509).

  • Add more information in the output xarray. (See !515).

  • Remove decorator ‘temporary_random_state’. (See !519).

  • Fix issue that runs two CI/CD pipeline. (See !520).

  • Enable creating a ‘Calibration’ configuration without installing pygmo. (See !521).

  • Add unit tests for ‘Observation’ mode. (See !523).

  • Fix bug in observation mode when using bad value. (See !525).

  • Remove used unit tests ‘test_pyxel_loader’. (See !531).

  • ‘JupyterLab’ as an optional dependency of Pyxel. (See !532).

1.3.2 / 2022-09-08#

This is a minor release to add a new reference about the latest SPIE paper.

Documentation#

  • Add a reference to new paper from SPIE presented at SPIE Astronomical Telescopes & Instrumentation conference. (See !502).

1.3.1 / 2022-09-07#

This release is a bugfix to resolve issues with command pyxel create-model.

Documentation#

  • Clarify full installation in the documentation. (See !500).

Others#

  • Command pyxel create-model is not working with Pyxel 1.3. (See !499).

1.3 / 2022-08-30#

Documentation#

  • Update documentation. (See !412 and !496).

Models#

Others#

  • Exposed configuration.build_configuration to the developer API as a private function.
    First contribution by Kieran Leschinski. (See !494).

  • Function create model not working properly. (See !495).

1.2.1 / 2022-08-05#

Documentation.#

  • Fix issues with latest version of ‘fsspec’ (2022.7.1) and ‘doc8’ (1.0.0). (See !491).

1.2.0 / 2022-07-12#

Core#

  • Fix bug in ‘ModelFitting.convert_to_parameters’. (See !484).

  • Implement new fitness function ‘reduced_chi_squared’. (See !485).

  • In ‘Archipelago’, fix warnings with deprecated pandas function. Replace deprecated function DataFrame.append by pandas.concat. (See !487).

Documentation#

  • Add benchmarks in the documentation at this link https://esa.gitlab.io/pyxel/benchmarks. (See !486).

  • Add more information about installation from ‘conda’ and ‘pip’. (See !488).

Models#

Others#

  • The minimum versions of dependencies ‘astropy’, ‘holoviews’ and ‘xarray’ (See !481) were changed:

    Package

    Old

    New

    astropy

    undef

    4.3

    holoviews

    undef

    1.14.2

    numpy

    1.17

    1.20

    xarray

    undef

    0.19

  • Speedup start-up time of Pyxel. (See !482).

1.1.2 / 2022-06-06#

Models#

  • Fix for: Charge generation model suppressing shot noise. Solution from Gitter by Lawrence Jones. (See !475).

  • Fix for: Redundant normalization in SAR ADC model. (See !478).

Others#

  • Provide multi-line string to ‘pyxel.load. (See !476).

  • Fix issue with Mypy when using Numpy 1.22. (See !477).

1.1.1 / 2022-05-13#

Core#

  • Add fsspec >= 2021 compatibility. (See !469).

  • Implement parameters ‘adc_voltage’ and ‘adc_bit_resolution’ in ‘Characteristics.to_dict’. (See !470).

Documentation#

  • Add new icon/badge ‘I want to contribute !’ (See !727).

  • Add how-to guide about saving/loading a Detector object. (See !468).

Models#

  • Add a temperature dependent dark current model. (See !460).

  • Add new model to simulate noise with SAR ADC. (See !461).

Others#

  • Fix issues found by ‘mypy’ version 0.950 and ‘myst-nb’ version 0.14.0. (See !471).

1.1.0 / 2022-04-22#

Core#

  • Remove maximum limit for attributes ‘col’ and ‘row’ in class Geometry. The previous limit was set at a maximum of 10000 columns and 10000 rows. (See !434).

  • Replace deprecated appeding to dataframes with concatenating. (See !444).

  • Add an APD detector. Based on code from James Gilbert. (See !449).

  • Implement a property setter for the attribute times in class Readout. (See !455).

  • Convert a Detector (CCD, CMOS…) to a dictionary and vice versa. (See !267).

  • Implement methods Detector.from_hdf5 and Detector.to_hdf5. (See !448).

  • Fix issues when saving/loading CMOS, APD and MKID Detector objects. (See !463).

Documentation#

  • Convert Changelog from Restructured Text to Markdown format. (See !456).

  • Write in documentation a list of available models for each detector type. (See !457).

Models#

  • Add a DC offset model. Based on code from James Gilbert. (See !452).

  • Add kTC reset noise model. (See !451).

  • Add an APD dark current model. Based on code from James Gilbert. (See !453).

  • Add an APD gain model. (See !450).

  • Add an APD readout noise model. Based on code from James Gilbert. (See !454).

  • Add a simple model that loads and applies PSF from a file. (See !459).

  • Fix models for usage in non-destructive mode. (See !465).

Others#

  • Updated poppy dependency to version 1.0.2. The previous version of poppy are not compatible with astropy version 5.0.1. (See !431).

  • Fix an issue when building the documentation with Python 3.8. (See !436).

  • Create a static JSON Schema file. (See !445 and !446).

  • Bump pre-commit hook versions. (See !447).

1.0.0 / 2022-02-10#

We are happy to announce that Pyxel has reached a stable version 1.0.0! Pyxel releases will use semantic versioning notation. Version 1.0 brings a simplified user experience, new models, parallel computing in observation mode, updated documentation, new examples, various bug fixes and much more. Excited for what comes next, stay tuned!

Changes since last version:

Documentation#

  • Add pyxel brief history to documentation. (See !429).

1.0.0-rc.6 / 2022-02-09#

Others#

  • Update function display_persist. (See !426).

1.0.0-rc.5 / 2022-02-09#

Others#

  • Implement option to save outputs in common picture formats. (See !416).

  • Update MANIFEST.in. (See !423).

1.0.0-rc.4 / 2022-01-27#

Models#

  • Fix a bug when converting to photons in load_image. (See !419).

Others#

  • Pin astropy version due to a bug. (See !420).

1.0.0-rc.3 / 2022-01-26#

Core#

  • Improve digitization models and detector digitization characteristics. (See !413).

  • Remove default values from detector properties. (See !415).

Documentation#

  • Put labels to model API to know which data structures are models changing. (See !405).

  • Improved acronyms. (See !414).

Models#

  • Nghxrg model replacing pixel array instead of adding. (See !404).

  • Optimize persistence model. (See !285).

  • Fix for persistence model when using long time steps. (See !407).

  • Rename TARS to Cosmix. (See !409).

  • Add a simple ADC model. (See !410).

Others#

  • Fix mypy issues with new version of numpy 1.22.0. (See !408).

1.0.0-rc.2 / 2022-01-18#

Core#

  • Fix Characteristics validation checks. (See !402).

1.0.0-rc.1 / 2022-01-18#

Core#

  • Rename detector properties using whole words. (See !292).

  • Review classes Material and Environment. (See !393).

Documentation#

  • Add more documentation for CCDCharacteristics, CMOSCharacteristics, …. (See !399).

Others#

  • Small simplification. From Albern S.. (See !395).

  • Updated ESA Copyright to 2022. (See !396).

  • Fix issue with licenses. (See !397).

  • Remove dead code. (See !398).

0.11.7 / 2022-01-07#

Documentation#

  • Fix broken links in the documentation. (See !388).

  • Fix links for ‘suggest_edit’ button in the documentation. (See !389).

  • Add better documentation for running modes.. (See !390).

Models#

  • Refactoring of CDM model. (See !375).

Others#

  • Add netcdf4 to function show_versions. (See !383).

  • Fix issue with script ‘download_last_environment_artifact.py’. (See !386).

0.11.6 / 2021-12-13#

Core#

  • Add new attribute ‘Config.detector’. (See !378).

Documentation#

  • Split documentation into ‘stable’ and ‘latest’’. (See !380).

Others#

  • Include netcdf4 in dependencies. (See !374).

0.11.5 / 2021-12-07#

Core#

  • Fix an issue with calibration. (See !353).

  • Use an array in ‘Charge’ besides a dataframe. (See !351).

  • Move some general processing function into a common folder. (See !359).

  • Use detector.time_step in charge_generation models and allow floats in Charge arrays. (See !365).

Models#

  • Model ‘nghxrg’ is not working on Windows. (See !361).

  • Remove alignment model. (See !364).

  • Implement a non-linear FWC. (See !338).

  • Create a dark current model. (See !310).

0.11.4 / 2021-11-23#

Core#

  • Implement array-like data structures as numpy custom array containers. (See !325).

Documentation#

  • Add more internal links in the documentation. (See !333).

  • Move ‘optical_psf’ documentation to RST file. (See !343).

Models#

  • Move some models from ‘readout_electronics’ into separated files. (See !323).

  • Display model’s name when running a pipeline. (See !335).

  • Add option to enable or disable progress bar in TARS model. (See !337).

Others#

  • Use ‘deployment’ in CI/CD. (See !336).

  • Fix an issue in CI/CD. (See !340).

  • Swap the environments name ‘production’ and ‘development’. (See !342).

0.11.3 / 2021-11-15#

Core#

  • Multiply photon flux with detector time step in photon generation models. (See !305).

  • Initialize Photon class in detector reset function instead in models. (See !309).

  • Resolve “Use a ‘with’ statement to set a seed with ‘numpy.random’. (See !175).

Others#

  • Remove some TODOs. (See !288).

0.11.2 / 2021-11-09#

Core#

  • Remove unnecessary warnings when Pygmo is not installed. (See !286).

  • Remove parallel computing with Numba. (See !290).

  • Use library ‘click’ to generate a Command Line Interface for script ‘pyxel/run.py’. (See !287).

  • Simplify imports of sub packages. (See !296).

  • Fix an issue in imports. (See !297).

  • Re-enable dask for observation mode. (See !172).

Documentation#

  • Make pyxel compatible with Python 3.9. (See !289).

  • Update adding new models documentation with best practices. (See !293).

  • Add a ‘Asking for help’ chapter in the documentation. (See !299).

Others#

  • Fix issue with xarray 0.20. (See !291).

  • Updated black, isort and blackdoc in ‘.pre-commit.yaml’. (See !294).

  • Partially reduce Pyxel start-up time. (See !302).

0.11.1 / 2021-10-29#

Models#

  • Add a readout noise model for CMOS detectors. (See !283).

0.11 / 2021-10-27#

Core#

  • Output folder already existing when running ‘load’ two times. (See !232).

  • Implement normalisation for calibration mode. (See !266).

  • Refactor class Charge. (See !271).

  • Add new detector MKID. Enrico Biancalani (See !206).

  • Refactor single and dynamic mode into one named observation. (See !263).

  • Include observation mode functions in parametric mode. (See !264).

  • Include observation mode functions in calibration mode. (See !265).

  • Rename observation to exposure and parametric to observation. (See !274).

  • Improve the speed of function detector.reset. (See !273).

  • Optimize the speed of calibration in time-domain. (See !276).

Documentation#

  • Add more information about how-to release to Conda Forge. (See !252).

  • Update documentation on the refactored running modes. (See !277).

  • Update installation instructions for using pip and conda. (See !279).

  • Fix typos in installation instructions in documentation. (See !280).

Models#

  • Fix for consecutive photon generation models. (See !193).

  • Add model Arctic. (See !229).

  • Improve the speed of model ‘charge_profile’. (See !268).

  • Simple conversion model not working with dark frames. (See !281).

Others#

  • Use tryceratops for try and except styling. (See !255).

  • Add a pipeline time profiling function. (See !259).

  • Add unit tests for model ‘charge_profile’. (See !269).

  • Add unit tests for class ‘Charge’. (See !270).

  • Add unit tests for function ‘calibration.util.check_range. (See !278).

0.10.2 / 2021-09-02#

Core#

  • Enable logarithmic timing in dynamic mode. (See !249).

Others#

  • Fix issue with latest version of Mypy. (See !253).

0.10.1 / 2021-08-18#

Core#

  • Add more debugging information when Calibration mode fails. (See !228).

  • Add more debugging information in function ‘get_obj_att’. (See !243).

  • Separate configuration loader from scripts in ‘inputs_outputs’. (See !250).

Documentation#

  • Install a specific conda package version. (See !235).

Others#

  • Resolved calibration not allowing one column text files (See !233).

  • Update dependency to ‘pygmo’ from 2.11 to 2.16.1. (See !234).

  • Use mypy version 0.812. (See !247).

0.10 / 2021-06-13#

Core#

  • Add capability to save outputs of parametric mode as a xarray dataset. (See !212).

  • Add capability to save calibration result dataset to disk from YAML. (See !214).

  • Hide built-in Pyxel plotting capabilities (matplotlib figures from YAML). (See !213).

  • dynamic mode progress bar. (See !219).

  • Add capability to create models through command line using a template. (See !217).

  • Improved dynamic mode. (See !229).

  • Fix issue in creating parametric datasets. (See !230).

Documentation#

  • Update installation section. (See !220).

  • Update documentation on parametric and dynamic mode. (See !228).

Models#

  • Fix TARS model. (See !227).

  • Persistence model updated in charge_collection/persistence.py (See !224).

Others#

  • Fix circular import in parametric.py. (See !216).

  • Add compatibility to Mypy 0.900. (See !223).

0.9.1 / 2021-05-17#

Core#

  • Add missing packages when running ‘pyxel.show_versions(). (See !193).

  • Fix issues with ‘fsspec’ version 0.9. (See !198).

  • Refactoring class `Arguments. (See !203).

  • Add new detector MKID. Enrico Biancalani (See !206).

Others#

  • Fix issue when displaying current version. (See !196).

  • Cannot import sub-packages ‘calibration’ and ‘models.optics’. (See !189).

  • Drop support for Python 3.6. (See !199).

  • Solve typing issues with numpy. (See !200).

  • Add functions to display calibration inputs and outputs in notebooks. (See !194).

  • Fix issue with the latest click version and pipeline ‘license’. (See !208).

  • Resolve “Add ‘LICENSE.txt’ in MANIFEST.in”. (See !207).

0.9 / 2021-03-25#

Core#

  • Fix a circular import in ‘pyxel.data_structure’. (See !171).

  • Add ability to download Pyxel examples from command line. (See !176).

  • Add capability to read files from remote filesystems (e.g. http, ftp, …). (See !169).

  • Add a mechanism to set option in Pyxel. (See !170).

  • Add capability to cache files in functions ‘load_image’ and ‘load_data’. (See !177).

  • Add a stripe pattern illumination model. (See !174).

  • Add methods to display a Detector or an array of the Detector. (See !173).

  • Initiate Processor object inside running mode functions. (See !184).

  • Add HTML display methods for objects. (See !185).

  • Add ability to display input image in the display_detector function. (See !186).

  • Issue when creating islands in a Grid. (See !188).

Documentation#

  • Use the ‘Documentation System’. (See !178).

  • Use the ‘Documentation System’. (See !181).

  • Add an ‘overview’ page for each section in the documentation. (See !183).

Others#

  • Add a new badge for Binder. (See !163).

  • Fix issue when generating documentation in CI/CD. (See !179).

  • Always execute stage ‘doc’ in CI/CD. (See !183).

  • Pyxel version cannot be retrieved. (See !189).

  • Remove pyviz from dependencies. (See !191).

Pipelines#

  • Calibration - Export champions for every evolution and every island. (See !164).

  • Calibration - Extract best individuals. (See !165).

  • Calibration - Fix an issue when extracting parameters. (See !166).

0.8.1 / 2021-01-26#

Documentation#

  • Enabled sphinxcontrib-bibtex version 2. (See #155).

Others#

  • Add a new badge for Google Group. (See !157).

  • Prepare Pyxel to be uploadable on PyPI. (See !161).

0.8 / 2020-12-11#

Core#

  • Improved user friendliness. (See #144).

  • Simplified the look of YAML configuration files. (See #118).

  • Extracted functions to run modes separately from pyxel.run.run() (See #61).

  • Refactored YAML loader, returns a class Configuration instead of a dictionary. (See #60).

  • Created new classes Single and Dynamic to store running mode parameters. (See #121).

  • Split class Outputs for different modes and moved to inputs_ouputs. (See #149).

  • Added a simple Inter Pixel Capacitance model for CMOS detectors. (See #65).

  • Added a model for the amplifier crosstalk. (See #116).

  • Added ability to load custom QE maps. (See #117).

  • Use ‘Dask’ for Calibration mode. (See !145).

Others#

  • Change licence to MIT. (See !142).

  • Change Pyxel’s package name to ‘pyxel-sim’. (See !144).

  • Added a ‘How to release’ guide. (See #109).

  • Remove_folder_examples_data. (See !148).

  • Fix typo in documentation. (See !149).

  • Updated documentation according to v0.8. (See !153).

0.7 / 2020-10-22#

Core#

  • Update .gitignore file. (See !123).

  • Added capability to load more image formats and tests. (See !113).

  • Create a function ‘pyxel.show_versions(). (See !114).

  • Shorter path to import/reference the models. (See !126).

  • Remove deprecated methods from Photon class. (See !119).

  • Instances of ‘DetectionPipeline’ are not serializable. (See !120).

  • Cannot run ‘calibration’ pipeline with multiprocessing or ipyparallel islands. (See !121).

  • Make package and script ‘pyxel’ executable. (See !112).

  • Created a function inputs_outputs.load_table(). (See !132).

  • Reimplement convolution in POPPY optical_psf model. (See #52).

  • Add property ‘Detector.numbytes’ and/or method ‘Detector.memory_usage()’ (See !116).

  • Created jupyxel.py for jupyter notebook visualization. (See !122).

Documentation#

  • Remove comments for magic methods. (See !127).

0.6 / 2020-09-16#

  • Improved contributing guide (See #68).

  • Remove file ‘.gitlab-ci-doc.yml’ (See #73).

  • Change license and add copyrights to all source files. (See #69).

  • Fix issues with example file ‘examples/calibration_CDM_beta.yaml’. (See #75).

  • Fix issues with example file ‘examples/calibration_CDM_irrad.yaml’. (See #76).

  • Updated Jupyter notebooks examples. (See #87).

  • Apply command ‘isort’ to the code base.

  • Refactor class ParametricPlotArgs. (See #77).

  • Create class SinglePlot. (See #78).

  • Create class CalibrationPlot. (See #79).

  • Create class ParametricPlot. (See #80).

  • Add templates for bug report, feature request and merge request. (See #105).

  • Parallel computing for ‘parametric’ mode. (See #111).

  • Improved docker image. (See #96).

  • Fix calibration pipeline. (See #113).

  • CI/CD pipeline ‘licenses-latests’ fails. (See #125).

0.5 / 2019-12-20#

  • Clean-up code.

  • Remove any dependencies to esapy_config (See #54).

  • Refactor charge generation models to avoid code duplication (See #49).

  • Implement multi-threaded/multi-processing mode (See #44).

0.4 / 2019-07-09#

  • Running modes implemented:

    • Calibration mode for model fitting and detector optimization

    • Dynamic mode for time-dependent (destructive and non-destructive) detector readout

    • Parallel option for Parametric mode

  • Models added:

    • CDM Charge Transfer Inefficiency model

    • POPPY physical optical propagation model

    • SAR ADC signal digitization model

  • Outputs class for post-processing and saving results

  • Logging, setup and versioneer

  • Examples

  • Documentation

0.3 / 2018-03-26#

  • Single and Parametric mode have been implemented

  • Infrastructure code has been placed in 2 new projects: esapy_config and esapy_web

  • Web interface (GUI) is dynamically generated based on attrs definitions

  • NGHxRG noise generator model has been added

0.2 / 2018-01-18#

  • TARS cosmic ray model has been reimplemented and added

0.1 / 2018-01-10#

  • Prototype: first pipeline for a CCD detector

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