reflectorch 1.2.1__tar.gz → 1.4.0__tar.gz

{reflectorch-1.2.1 → reflectorch-1.4.0}/.github/workflows/draft-pdf.yml

@@ -15,7 +15,7 @@ jobs:
           # This should be the path to the paper within your repo.
           paper-path: paper/paper.md
       - name: Upload
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: paper
           # This is the output path where Pandoc will write the compiled

{reflectorch-1.2.1 → reflectorch-1.4.0}/.gitignore

@@ -38,4 +38,7 @@ var/
 documentation/_build/*
 
 # Don't ignore .pt files in the exp_data directory
-!exp_data/*.pt
+!exp_data/*.pt
+
+#Other
+tensorboard_runs

reflectorch-1.4.0/CONTRIBUTING.md

@@ -0,0 +1,28 @@
+# Contributing to Reflectorch
+
+## 1. Reporting Issues
+
+If you encounter bugs, want to suggest features, or have questions, please open an issue using the [GitHub issue tracker](https://github.com/schreiber-lab/reflectorch/issues).
+
+When reporting a bug, please include:
+- A clear description of the issue
+- Steps to reproduce the bug (if applicable)
+- Any relevant error messages or screenshots
+
+## 2. Contributing Code
+
+To contribute code:
+
+1. **Fork** the repository.
+2. Make your changes in a new branch.
+3. Ensure your code is clear and well-documented.
+4. If applicable, add or update tests.
+5. Submit a [pull request](https://github.com/schreiber-lab/reflectorch/pulls) with a description of your changes.
+
+### Documentation
+
+If your changes affect user-facing features, please update the documentation accordingly. Documentation is built using [Jupyter Book](https://jupyterbook.org/). You can build it locally using:
+
+```bash
+jupyter-book build documentation
+```

{reflectorch-1.2.1 → reflectorch-1.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: reflectorch
-Version: 1.2.1
+Version: 1.4.0
 Summary: A Pytorch-based package for the analysis of reflectometry data
 Author-email: Vladimir Starostin <vladimir.starostin@uni-tuebingen.de>, Valentin Munteanu <valentin.munteanu@uni-tuebingen.de>
 Maintainer-email: Valentin Munteanu <valentin.munteanu@uni-tuebingen.de>, Vladimir Starostin <vladimir.starostin@uni-tuebingen.de>, Alexander Hinderhofer <alexander.hinderhofer@uni-tuebingen.de>
@@ -11,14 +11,13 @@ Keywords: reflectometry,machine learning
 Classifier: Programming Language :: Python :: 3
 Classifier: Operating System :: OS Independent
 Classifier: Environment :: GPU :: NVIDIA CUDA
-Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
 Classifier: Development Status :: 4 - Beta
 Classifier: Topic :: Scientific/Engineering :: Physics
 Classifier: Intended Audience :: Science/Research
 Requires-Python: >=3.7
 Description-Content-Type: text/markdown
 License-File: LICENSE.txt
-Requires-Dist: numpy<2.0,>=1.18.1
+Requires-Dist: numpy
 Requires-Dist: torch>=1.8.1
 Requires-Dist: scipy
 Requires-Dist: tqdm
@@ -28,6 +27,7 @@ Requires-Dist: matplotlib
 Requires-Dist: ipywidgets
 Requires-Dist: huggingface_hub
 Requires-Dist: safetensors
+Requires-Dist: tensorboard
 Provides-Extra: tests
 Requires-Dist: pytest; extra == "tests"
 Requires-Dist: pytest-cov; extra == "tests"
@@ -37,6 +37,7 @@ Requires-Dist: sphinx; extra == "docs"
 Provides-Extra: build
 Requires-Dist: build; extra == "build"
 Requires-Dist: twine; extra == "build"
+Dynamic: license-file
 
 # Reflectorch
 
@@ -50,7 +51,7 @@ Requires-Dist: twine; extra == "build"
 [![Python version](https://img.shields.io/badge/python-3.7%7C3.8%7C3.9%7C3.10%7C3.11%7C3.12-blue.svg)](https://www.python.org/)
 ![CI workflow status](https://github.com/schreiber-lab/reflectorch/actions/workflows/ci.yml/badge.svg)
 ![Repos size](https://img.shields.io/github/repo-size/schreiber-lab/reflectorch)
-[![CodeFactor](https://www.codefactor.io/repository/github/schreiber-lab/reflectorch/badge)](https://www.codefactor.io/repository/github/schreiber-lab/reflectorch)
+<!-- [![CodeFactor](https://www.codefactor.io/repository/github/schreiber-lab/reflectorch/badge)](https://www.codefactor.io/repository/github/schreiber-lab/reflectorch) -->
 [![Jupyter Book Documentation](https://jupyterbook.org/badge.svg)](https://jupyterbook.org/)
 [![Documentation Page](https://img.shields.io/badge/Documentation%20Page-%23FFDD33.svg?style=flat&logo=read-the-docs&logoColor=black)](https://schreiber-lab.github.io/reflectorch/)
 <!-- [![Code style: Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff) -->
@@ -101,9 +102,11 @@ We provide an interactive Google Colab notebook for exploring the basic function
 [![Hugging Face](https://img.shields.io/badge/Hugging%20Face-%23FFD700.svg?style=flat&logo=huggingface&logoColor=black)](https://huggingface.co/valentinsingularity/reflectivity)
 Configuration files and the corresponding pretrained model weights are hosted on Huggingface: [https://huggingface.co/valentinsingularity/reflectivity](https://huggingface.co/valentinsingularity/reflectivity).
 
-[![Docker](https://img.shields.io/badge/Docker-2496ED.svg?style=flat&logo=docker&logoColor=white)](https://hub.docker.com/)
-Docker images for reflectorch *will* be hosted on Dockerhub.
+<!-- [![Docker](https://img.shields.io/badge/Docker-2496ED.svg?style=flat&logo=docker&logoColor=white)](https://hub.docker.com/)
+Docker images for reflectorch *will* be hosted on Dockerhub. -->
 
+## Contributing
+If you'd like to contribute to the package, please see our [Contributing Guidelines](CONTRIBUTING.md) for details.
 
 ## Citation
 If you find our work useful in your research, please cite as follows:

{reflectorch-1.2.1 → reflectorch-1.4.0}/README.md

@@ -10,7 +10,7 @@
 [![Python version](https://img.shields.io/badge/python-3.7%7C3.8%7C3.9%7C3.10%7C3.11%7C3.12-blue.svg)](https://www.python.org/)
 ![CI workflow status](https://github.com/schreiber-lab/reflectorch/actions/workflows/ci.yml/badge.svg)
 ![Repos size](https://img.shields.io/github/repo-size/schreiber-lab/reflectorch)
-[![CodeFactor](https://www.codefactor.io/repository/github/schreiber-lab/reflectorch/badge)](https://www.codefactor.io/repository/github/schreiber-lab/reflectorch)
+<!-- [![CodeFactor](https://www.codefactor.io/repository/github/schreiber-lab/reflectorch/badge)](https://www.codefactor.io/repository/github/schreiber-lab/reflectorch) -->
 [![Jupyter Book Documentation](https://jupyterbook.org/badge.svg)](https://jupyterbook.org/)
 [![Documentation Page](https://img.shields.io/badge/Documentation%20Page-%23FFDD33.svg?style=flat&logo=read-the-docs&logoColor=black)](https://schreiber-lab.github.io/reflectorch/)
 <!-- [![Code style: Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff) -->
@@ -61,9 +61,11 @@ We provide an interactive Google Colab notebook for exploring the basic function
 [![Hugging Face](https://img.shields.io/badge/Hugging%20Face-%23FFD700.svg?style=flat&logo=huggingface&logoColor=black)](https://huggingface.co/valentinsingularity/reflectivity)
 Configuration files and the corresponding pretrained model weights are hosted on Huggingface: [https://huggingface.co/valentinsingularity/reflectivity](https://huggingface.co/valentinsingularity/reflectivity).
 
-[![Docker](https://img.shields.io/badge/Docker-2496ED.svg?style=flat&logo=docker&logoColor=white)](https://hub.docker.com/)
-Docker images for reflectorch *will* be hosted on Dockerhub.
+<!-- [![Docker](https://img.shields.io/badge/Docker-2496ED.svg?style=flat&logo=docker&logoColor=white)](https://hub.docker.com/)
+Docker images for reflectorch *will* be hosted on Dockerhub. -->
 
+## Contributing
+If you'd like to contribute to the package, please see our [Contributing Guidelines](CONTRIBUTING.md) for details.
 
 ## Citation
 If you find our work useful in your research, please cite as follows:

reflectorch-1.4.0/configs/a_base_point_neutron_conv_standard.yaml

@@ -0,0 +1,129 @@
+general:
+  name: a_base_point_neutron_conv_standard
+  root_dir: null
+  
+dset:
+  cls: ReflectivityDataLoader
+  prior_sampler:
+    cls: SubpriorParametricSampler
+    kwargs:
+      param_ranges:
+        thicknesses: [1., 500.]
+        roughnesses: [0., 60.]
+        slds: [-8., 16.]
+      bound_width_ranges:
+        thicknesses: [1.0e-2, 500.]
+        roughnesses: [1.0e-2, 60.]
+        slds: [1.0e-2, 5.]
+      model_name: standard_model
+      max_num_layers: 2
+      constrained_roughness: true
+      max_thickness_share: 0.5
+      logdist: false
+      scale_params_by_ranges: false
+      scaled_range: [-1., 1.]
+      device: 'cuda'
+      
+  q_generator:
+    cls: ConstantQ
+    kwargs:
+      q: [0.02, 0.15, 128]
+      device: 'cuda'
+
+  # q_generator:
+  #   cls: VariableQ
+  #   kwargs:
+  #     q_min_range: [0.005, 0.03]
+  #     q_max_range: [0.15, 0.3]
+  #     n_q_range: [128, 128]
+  #     device: 'cuda'
+      
+  intensity_noise:
+    cls: GaussianExpIntensityNoise
+    kwargs:
+      relative_errors: [0.01, 0.3]
+      consistent_rel_err: false
+      apply_shift: false
+      shift_range: [-0.3, 0.3]
+      apply_background: true
+      background_range: [1.0e-10, 1.0e-4]
+      add_to_context: true
+
+  smearing:
+    cls: Smearing
+    kwargs:
+      sigma_range: [0.01, 0.10]
+      constant_dq: False
+      gauss_num: 17
+      share_smeared: 1.0
+      
+  curves_scaler:
+    cls: LogAffineCurvesScaler
+    kwargs:
+      weight: 0.2
+      bias: 1.0
+      eps: 1.0e-10
+
+model:
+  network:
+    cls: NetworkWithPriors
+    pretrained_name: null
+    device: 'cuda'
+    kwargs:
+      embedding_net_type: 'conv'
+      embedding_net_kwargs:
+        in_channels: 1
+        hidden_channels: [32, 64, 128, 256, 512]
+        kernel_size: 3
+        dim_embedding: 128
+        dim_avpool: 1
+        use_batch_norm: true
+        use_se: false
+        activation: 'gelu'
+      pretrained_embedding_net: null
+      dim_out: 8
+      dim_conditioning_params: 0
+      layer_width: 512
+      num_blocks: 6
+      repeats_per_block: 2
+      residual: true
+      use_batch_norm: true
+      use_layer_norm: false
+      mlp_activation: 'gelu'
+      dropout_rate: 0.0 
+      tanh_output: false
+      conditioning: 'concat' # 'concat', 'glu', 'film'
+      concat_condition_first_layer: false
+       
+training:
+  trainer_cls: PointEstimatorTrainer
+  num_iterations: 100000
+  batch_size: 4096
+  lr: 1.0e-3
+  grad_accumulation_steps: 1
+  clip_grad_norm_max: null
+  update_tqdm_freq: 1
+  optimizer: AdamW
+  trainer_kwargs:
+    train_with_q_input: false
+    condition_on_q_resolutions: false
+    rescale_loss_interval_width: true
+    use_l1_loss: true
+    optim_kwargs:
+      betas: [0.9, 0.999]
+      weight_decay: 0.0005
+  callbacks:
+    save_best_model:
+      enable: true
+      freq: 500
+    lr_scheduler:
+      cls: CosineAnnealingWithWarmup
+      kwargs:
+        min_lr: 1.0e-6
+        warmup_iters: 500
+        total_iters: 100000
+
+  # logger:
+  #   cls: TensorBoardLogger
+  #   kwargs:
+  #     log_dir: "tensorboard_runs/test_1"

reflectorch-1.4.0/configs/a_base_point_xray_conv_absorption.yaml

@@ -0,0 +1,117 @@
+general:
+  name: a_base_point_xray_conv_absorption
+  root_dir: null
+  
+dset:
+  cls: ReflectivityDataLoader
+  prior_sampler:
+    cls: SubpriorParametricSampler
+    kwargs:
+      param_ranges:
+        thicknesses: [1., 500.]
+        roughnesses: [0., 60.]
+        slds: [0., 150.]
+        islds: [0., 30.]
+      bound_width_ranges:
+        thicknesses: [1.0e-2, 500.]
+        roughnesses: [1.0e-2, 60.]
+        slds: [ 1.0e-2, 5.]
+        islds: [1.0e-2, 5.]
+      model_name: model_with_absorption
+      max_num_layers: 2
+      constrained_roughness: true
+      constrained_isld: true
+      max_thickness_share: 0.5
+      max_sld_share: 0.2
+      logdist: false
+      scale_params_by_ranges: false
+      scaled_range: [-1., 1.]
+      device: 'cuda'
+      
+  q_generator:
+    cls: ConstantQ
+    kwargs:
+      q: [0.02, 0.15, 128]
+      device: 'cuda'
+
+  intensity_noise:
+    cls: GaussianExpIntensityNoise
+    kwargs:
+      relative_errors: [0.01, 0.3]
+      consistent_rel_err: false
+      apply_shift: false #true
+      shift_range: [-0.3, 0.3]
+      add_to_context: true
+      
+  curves_scaler:
+    cls: LogAffineCurvesScaler
+    kwargs:
+      weight: 0.2
+      bias: 1.0
+      eps: 1.0e-10
+
+model:
+  network:
+    cls: NetworkWithPriors
+    pretrained_name: null
+    device: 'cuda'
+    kwargs:
+      embedding_net_type: 'conv'
+      embedding_net_kwargs:
+        in_channels: 1
+        hidden_channels: [32, 64, 128, 256, 512]
+        kernel_size: 3
+        dim_embedding: 128
+        dim_avpool: 1
+        use_batch_norm: true
+        use_se: false
+        activation: 'gelu'
+      pretrained_embedding_net: null
+      dim_out: 11
+      dim_conditioning_params: 0
+      layer_width: 512
+      num_blocks: 6
+      repeats_per_block: 2
+      residual: true
+      use_batch_norm: true
+      use_layer_norm: false
+      mlp_activation: 'gelu'
+      dropout_rate: 0.0 
+      tanh_output: false
+      conditioning: 'concat' # 'concat', 'glu', 'film'
+      concat_condition_first_layer: false
+       
+training:
+  trainer_cls: PointEstimatorTrainer
+  num_iterations: 10000
+  batch_size: 4096
+  lr: 1.0e-3
+  grad_accumulation_steps: 1
+  clip_grad_norm_max: null
+  update_tqdm_freq: 1
+  optimizer: AdamW
+  trainer_kwargs:
+    train_with_q_input: false
+    train_with_sigmas: false
+    condition_on_q_resolutions: false
+    use_curve_reconstruction_loss: false
+    rescale_loss_interval_width: true #false
+    use_l1_loss: true #false
+    optim_kwargs:
+      betas: [0.9, 0.999]
+      weight_decay: 0.0005
+  callbacks:
+    save_best_model:
+      enable: true
+      freq: 500
+    lr_scheduler:
+      cls: CosineAnnealingWithWarmup
+      kwargs:
+        min_lr: 1.0e-6
+        warmup_iters: 100
+        total_iters: 10000
+
+  # logger:
+  #   cls: TensorBoardLogger
+  #   kwargs:
+  #     log_dir: "tensorboard_runs/test_1"

reflectorch-1.4.0/configs/a_base_point_xray_conv_standard.yaml

@@ -0,0 +1,119 @@
+general:
+  name: a_base_point_xray_conv_standard
+  root_dir: null
+  
+dset:
+  cls: ReflectivityDataLoader
+  prior_sampler:
+    cls: SubpriorParametricSampler
+    kwargs:
+      param_ranges:
+        thicknesses: [1., 500.]
+        roughnesses: [0., 60.]
+        slds: [0., 50.]
+      bound_width_ranges:
+        thicknesses: [1.0e-2, 500.]
+        roughnesses: [1.0e-2, 60.]
+        slds: [1.0e-2, 5.]
+      model_name: standard_model
+      max_num_layers: 2
+      constrained_roughness: true
+      max_thickness_share: 0.5
+      logdist: false
+      scale_params_by_ranges: false
+      scaled_range: [-1., 1.]
+      device: 'cuda'
+      
+  q_generator:
+    cls: ConstantQ
+    kwargs:
+      q: [0.02, 0.15, 128]
+      device: 'cuda'
+
+  # q_generator:
+  #   cls: VariableQ
+  #   kwargs:
+  #     q_min_range: [0.005, 0.03]
+  #     q_max_range: [0.15, 0.3]
+  #     n_q_range: [128, 128]
+  #     device: 'cuda'
+      
+  intensity_noise:
+    cls: GaussianExpIntensityNoise
+    kwargs:
+      relative_errors: [0.01, 0.3]
+      consistent_rel_err: false
+      apply_shift: true
+      shift_range: [-0.3, 0.3]
+      add_to_context: true
+ 
+  curves_scaler:
+    cls: LogAffineCurvesScaler
+    kwargs:
+      weight: 0.2
+      bias: 1.0
+      eps: 1.0e-10
+
+model:
+  network:
+    cls: NetworkWithPriors
+    pretrained_name: null
+    device: 'cuda'
+    kwargs:
+      embedding_net_type: 'conv'
+      embedding_net_kwargs:
+        in_channels: 1
+        hidden_channels: [32, 64, 128, 256, 512]
+        kernel_size: 3
+        dim_embedding: 128
+        dim_avpool: 1
+        use_batch_norm: true
+        use_se: false
+        activation: 'gelu'
+      pretrained_embedding_net: null
+      dim_out: 8
+      dim_conditioning_params: 0
+      layer_width: 512
+      num_blocks: 8
+      repeats_per_block: 2
+      residual: true
+      use_batch_norm: true
+      use_layer_norm: false
+      mlp_activation: 'gelu'
+      dropout_rate: 0.0 
+      tanh_output: false
+      conditioning: 'film' # 'concat', 'glu', 'film'
+      concat_condition_first_layer: false
+       
+training:
+  trainer_cls: PointEstimatorTrainer
+  num_iterations: 100000
+  batch_size: 4096
+  lr: 1.0e-3
+  grad_accumulation_steps: 1
+  clip_grad_norm_max: null
+  update_tqdm_freq: 1
+  optimizer: AdamW
+  trainer_kwargs:
+    train_with_q_input: false
+    condition_on_q_resolutions: false
+    rescale_loss_interval_width: true
+    use_l1_loss: true
+    optim_kwargs:
+      betas: [0.9, 0.999]
+      weight_decay: 0.0005
+  callbacks:
+    save_best_model:
+      enable: true
+      freq: 500
+    lr_scheduler:
+      cls: CosineAnnealingWithWarmup
+      kwargs:
+        min_lr: 1.0e-6
+        warmup_iters: 500
+        total_iters: 100000
+
+  # logger:
+  #   cls: TensorBoardLogger
+  #   kwargs:
+  #     log_dir: "tensorboard_runs/test_1"

reflectorch-1.4.0/configs/b_mc_point_neutron_conv_standard_L1_InputDq.yaml

@@ -0,0 +1,118 @@
+general:
+  name: b_mc_point_neutron_conv_standard_L1_InputDq
+  root_dir: null
+  
+dset:
+  cls: ReflectivityDataLoader
+  prior_sampler:
+    cls: SubpriorParametricSampler
+    kwargs:
+      param_ranges:
+        thicknesses: [1., 1000.]
+        roughnesses: [0., 60.]
+        slds: [-8., 16.]
+      bound_width_ranges:
+        thicknesses: [1.0e-2, 1000.]
+        roughnesses: [1.0e-2, 60.]
+        slds: [1.0e-2, 5.]
+      model_name: standard_model
+      max_num_layers: 1
+      constrained_roughness: true
+      max_thickness_share: 0.5
+      logdist: false
+      scale_params_by_ranges: false
+      scaled_range: [-1., 1.]
+      device: 'cuda'
+      
+  q_generator:
+    cls: ConstantQ
+    kwargs:
+      q: [0.005, 0.2, 128]
+      device: 'cuda'
+
+  intensity_noise:
+    cls: GaussianExpIntensityNoise
+    kwargs:
+      relative_errors: [0.01, 0.3]
+      consistent_rel_err: false
+      apply_shift: true
+      shift_range: [-0.3, 0.3]
+      apply_background: true
+      background_range: [1.0e-10, 1.0e-4]
+      add_to_context: true
+
+  smearing:
+    cls: Smearing
+    kwargs:
+      sigma_range: [0.01, 0.10]
+      constant_dq: False
+      gauss_num: 17
+      share_smeared: 0.8
+      
+  curves_scaler:
+    cls: LogAffineCurvesScaler
+    kwargs:
+      weight: 0.2
+      bias: 1.0
+      eps: 1.0e-10
+
+model:
+  network:
+    cls: NetworkWithPriors
+    pretrained_name: null
+    device: 'cuda'
+    kwargs:
+      embedding_net_type: 'conv'
+      embedding_net_kwargs:
+        in_channels: 1
+        hidden_channels: [32, 64, 128, 256, 512]
+        kernel_size: 3
+        dim_embedding: 128
+        dim_avpool: 1
+        use_batch_norm: true
+        use_se: false
+        activation: 'gelu'
+      pretrained_embedding_net: null
+      dim_out: 5
+      dim_conditioning_params: 1
+      layer_width: 512
+      num_blocks: 8
+      repeats_per_block: 2
+      residual: true
+      use_batch_norm: true
+      use_layer_norm: false
+      mlp_activation: 'gelu'
+      dropout_rate: 0.0 
+      tanh_output: false
+      conditioning: 'film'
+      concat_condition_first_layer: true ### back. comp.
+       
+training:
+  trainer_cls: PointEstimatorTrainer
+  num_iterations: 100000
+  batch_size: 4096
+  lr: 1.0e-3
+  grad_accumulation_steps: 1
+  clip_grad_norm_max: null
+  update_tqdm_freq: 1
+  optimizer: AdamW
+  trainer_kwargs:
+    train_with_q_input: false
+    train_with_sigmas: false
+    condition_on_q_resolutions: true
+    use_curve_reconstruction_loss: false
+    rescale_loss_interval_width: true
+    use_l1_loss: true
+    optim_kwargs:
+      betas: [0.9, 0.999]
+      weight_decay: 0.0005
+  callbacks:
+    save_best_model:
+      enable: true
+      freq: 500
+    lr_scheduler:
+      cls: CosineAnnealingWithWarmup
+      kwargs:
+        min_lr: 1.0e-6
+        warmup_iters: 500
+        total_iters: 100000