Lensless

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Added
~~~~~

- Trainable reconstruction can return intermediate outputs (between pre- and post-processing).
- Auto-download for DRUNet model.
- ``utils.dataset.DiffuserCamMirflickr`` helper class for Mirflickr dataset.
- Option to crop section of image for computing loss when training unrolled.
- Option to learn color filter of RGB mask.
- Trainable mask for Adafruit LCD.
- Utility for capture image.
- Option to freeze/unfreeze/add pre- and post-processor components during training.
- Option to skip unrolled training and just use U-Net.
- Dataset objects for Adafruit LCD: measured CelebA and hardware-in-the-loop.
- Option to add auxiliary loss from output of camera inversion.
- Option to specify denoiser to iterative methods for plug-and-play.
- Model repository of trained models in ``lensless.recon.model_dict``.
- TrainableInversion component as in FlatNet.
- ``lensless.recon.utils.get_drunet_function_v2`` which doesn't normalize each color channel.
- Option to add noise to DiffuserCamMirflickr dataset.
- Option to initialize pre- and post-processor with components from another model.

Changed
~~~~~~~

- Better logic for saving best model. Based on desired metric rather than last epoch, and intermediate models can be saved.
- Optional normalization in ``utils.io.load_image``.

Bugfix
~~~~~~

- Support for unrolled reconstruction with grayscale, needed to copy to three channels for LPIPS.
- Fix bad train/test split for DiffuserCamMirflickr in unrolled training.
- Resize utility.
- Aperture, index to dimension conversion.
- Submodule imports.

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Added
~~~~~

- Sensor module.
- Single-script and Telegram demo.
- Link and citation for JOSS.
- Authors at top of source code files.
- Add paramiko as dependency for remote capture and display.
- Mask module, for CodedAperture (FlatCam), PhaseContour (PhlatCam), and FresnelZoneAperture.
- Script for measuring arbitrary dataset (from Raspberry Pi).
- Support for preprocessing and postprocessing, such as denoising, in ``TrainableReconstructionAlgorithm``. Both trainable and fix postprocessing can be used.
- Utilities to load a trained DruNet model for use as postprocessing in ``TrainableReconstructionAlgorithm``.
- Unified interface for dataset. See ``utils.dataset.DualDataset``.
- New simulated dataset compatible with new data format ([(batch_size), depth, width, height, color]). See ``utils.dataset.SimulatedFarFieldDataset``.
- New dataset for pair of original image and their measurement from a screen. See ``utils.dataset.MeasuredDataset`` and ``utils.dataset.MeasuredDatasetSimulatedOriginal``.
- Support for unrolled loading and inference in the script ``admm.py``.
- Tikhonov reconstruction for coded aperture measurements (MLS / MURA): numpy and Pytorch support.
- New ``Trainer`` class to train ``TrainableReconstructionAlgorithm`` with PyTorch.
- New ``TrainableMask`` and ``TrainablePSF`` class to train/fine-tune a mask from a dataset.
- New ``SimulatedDatasetTrainableMask`` class to train/fine-tune a mask for measurement.
- PyTorch support for ``lensless.utils.io.rgb2gray``.


Changed
~~~~~~~

- Simpler remote capture and display scripts with Hydra.
- Group source code into four modules: ``hardware``, ``recon``, ``utils``, ``eval``.
- Split scripts into subfolders.
- Displaying 3D reconstructions now shows projections on all three axis.


Bugfix
~~~~~~

- Fix overwriting of sensor parameters when downsampling.
- Displaying 3D reconstructions by summing values along axis would produce un-normalized values.

--------------------

Bugfix
~~~~~~

- Fix rendering of README on PyPI.

--------------------

Added
~~~~~

- Documentation files and configuration, using Sphinx.
- Implementations for ``autocorr2d`` and ``RealFFTConvolve2D``.
- Benchmarking tool for ReconstructionAlgorithm
- ``n_iter`` parameter for ReconstructionAlgorithm constructor, so don't need to pass to ``apply``.
- Support of 3D reconstruction for Gradient Descent and APGD, with and without Pytorch.
- Option to warm-start reconstruction algorithm with ``initial_est``.
- TrainableReconstructionAlgorithm class inherited from ReconstructionAlgorithm and torch.module for use with pytorch autograd and optimizers.
- Unrolled version of FISTA and ADMM as TrainableReconstructionAlgorithm with learnable parameters.
- ``train_unrolled.py`` script for training unrolled algorithms.
- ``benchmark_recon.py`` script for benchmarking and comparing reconstruction algorithms.
- Added ``reconstruction_error`` to ``ReconstructionAlgorithm`` .
- Added support for npy/npz image in load_image.

Changed
~~~~~~~

- README.md to READ.rst for documentation.
- CONTRIBUTING and CHANGELOG, to .rst for documentation.
- Shorten README to separate contents in different pages of docs.
- Fix typo in GradientDescent class name.
- Updated to Pycsou V2, as ``pip install pycsou`` (Pycsou V1) may not work on some machines.
- PSF are now always stored as 4D Data [depth, width, height, color], Data are stored as [(batch_size), depth, width, height, color] batch_size being optional. Grayscale data has a color axis of length 1 and 2D data has a depth axis of length 1.
- Added batch support to RealFFTConvolve2D.
- ``ReconstructionAlgorithm.update`` now take the number of the current iteration to allow for unrolled algorithms.
- ``ReconstructionAlgorithm.apply`` now takes a reset parameter (default true) to automaticaly call reset.
- Call to reset in ``ReconstructionAlgorithm.__init__`` is now optional (see reset parameter).
- Make sure image estimate is reset when reset() is called, either to zeros/mean data or to self._initial_est if set.

Bugfix
~~~~~~

- Loading grayscale PSFs would cause an dimension error when removing the background pixels.

--------------------

Added
~~~~~

- Example of RGB reconstruction with complex-valued FFT: ``scripts/recon/apgd_pycsou.py``


Bugfix
~~~~~~

- Possible shape mismatch when using the real-valued FFT: forward and
backward.

--------------------


Added
~~~~~

- Scripts for collecting MNIST.
- Option to collect grayscale data.


Changed
~~~~~~~

- Restructure example scripts, i.e. subfolder ``recon`` for reconstructions.
- Remove heavy installs from setup (e.g. pycsou, lpips, skikit-image).