reflectorch 1.0.0__tar.gz → 1.1.0__tar.gz

reflectorch-1.1.0/.github/workflows/draft-pdf.yml

@@ -0,0 +1,24 @@
+name: Draft PDF
+on: [push]
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: paper/paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v3
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
+          path: paper/paper.pdf

reflectorch-1.1.0/LICENSE.txt

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 Reflectorch Developers
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

reflectorch-1.1.0/MANIFEST.in

@@ -0,0 +1,13 @@
+include configs/*
+exclude saved_models/*.pt
+exclude notebooks/*
+exclude paper/*
+exclude documentation/*
+exclude docs/*
+prune docs/*
+exclude .github/*
+
+include exp_data/data_C60.pt
+include exp_data/data_PTCDI-C3.pt
+include exp_data/33a.dat
+include exp_data/DIP-nSi_34a.dat

{reflectorch-1.0.0 → reflectorch-1.1.0}/PKG-INFO

@@ -1,9 +1,9 @@
 Metadata-Version: 2.1
 Name: reflectorch
-Version: 1.0.0
+Version: 1.1.0
 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>, Alexander Hinderhofer <alexander.hinderhofer@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>
 Project-URL: Source, https://github.com/schreiber-lab/reflectorch/
 Project-URL: Issues, https://github.com/schreiber-lab/reflectorch/issues
 Project-URL: Documentation, https://schreiber-lab.github.io/reflectorch/
@@ -26,7 +26,6 @@ Requires-Dist: PyYAML
 Requires-Dist: click
 Requires-Dist: matplotlib
 Requires-Dist: ipywidgets
-Requires-Dist: torchinfo
 Requires-Dist: huggingface_hub
 Provides-Extra: tests
 Requires-Dist: pytest; extra == "tests"
@@ -47,31 +46,34 @@ Requires-Dist: twine; extra == "build"
 [![YAML](https://img.shields.io/badge/yaml-%23ffffff.svg?style=for-the-badge&logo=yaml&logoColor=151515)](https://yaml.org/)
 [![Hugging Face](https://img.shields.io/badge/Hugging%20Face-%23FFD700.svg?style=for-the-badge&logo=huggingface&logoColor=black)](https://huggingface.co/valentinsingularity/reflectivity)
 
-[![License: GPLv3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 [![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)
-[![Jupyter Book Documentation](https://jupyterbook.org/badge.svg)](https://schreiber-lab.github.io/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) -->
 
 
-**Reflectorch** is a machine learning Python package for the analysis of X-ray and neutron reflectometry data based on Pytorch (written by [Vladimir Starostin](https://github.com/StarostinV/) & [Valentin Munteanu](https://github.com/valentinsingularity)). It provides functionality for the fast simulation of reflectometry curves on the GPU, customizable setup of the physical parameterization model and neural network architecture via YAML configuration files, and prior-aware training of neural networks as described in our paper [Neural network analysis of neutron and X-ray reflectivity data incorporating prior knowledge](https://doi.org/10.1107/S1600576724002115).
+**Reflectorch** is a machine learning Python package for the analysis of X-ray and neutron reflectometry data, written by [Vladimir Starostin](https://github.com/StarostinV/) & [Valentin Munteanu](https://github.com/valentinsingularity) at the University of Tübingen. It provides functionality for the fast simulation of reflectometry curves on the GPU, customizable setup of the physical parameterization model and neural network architecture via YAML configuration files, and prior-aware training of neural networks as described in our paper [Neural network analysis of neutron and X-ray reflectivity data incorporating prior knowledge](https://doi.org/10.1107/S1600576724002115).
 
 ## Installation
 
-**Reflectorch** can be installed either from [![PyPi](https://img.shields.io/badge/PyPi-3776AB.svg?style=flat&logo=pypi&logoColor=white)](https://pypi.org/project/reflectorch/) via ``pip`` or from [![conda-forge](https://img.shields.io/badge/conda--forge-44A833.svg?style=flat&logo=conda-forge&logoColor=white)](https://anaconda.org/conda-forge/reflectorch/) via ``conda``:
+**Reflectorch** can be installed from [![PyPi](https://img.shields.io/badge/PyPi-3776AB.svg?style=flat&logo=pypi&logoColor=white)](https://pypi.org/project/reflectorch/) via ``pip``:
+
+<!-- or from [![conda-forge](https://img.shields.io/badge/conda--forge-44A833.svg?style=flat&logo=conda-forge&logoColor=white)](https://anaconda.org/conda-forge/reflectorch/) via ``conda``: -->
 
 ```bash
 pip install reflectorch
 ```
 
-or
+<!-- or
 
 ```bash
 conda install -c conda-forge reflectorch
-```
+``` -->
 
-Additionally, one can clone the entire Github repository and install the package in editable mode:
+Alternatively, one can clone the entire Github repository and install the package in editable mode:
 
 ```bash
 git clone https://github.com/schreiber-lab/reflectorch.git
@@ -89,16 +91,21 @@ Users with Nvidia **GPU**s need to additionally install **Pytorch with CUDA supp
 
 ## Get started
 
-![](https://img.shields.io/badge/Documentation%20Page-%23FFDD33.svg?style=flat&logo=read-the-docs&logoColor=black) The full documentation of the package, containing tutorials and the API reference, was built with [Jupyter Book](https://jupyterbook.org/) and [Sphinx](https://www.sphinx-doc.org) and it is hosted at the address: [https://schreiber-lab.github.io/reflectorch/](https://schreiber-lab.github.io/reflectorch/).
+[![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/)
+ The full documentation of the package, containing tutorials and the API reference, was built with [Jupyter Book](https://jupyterbook.org/) and [Sphinx](https://www.sphinx-doc.org) and it is hosted at the address: [https://schreiber-lab.github.io/reflectorch/](https://schreiber-lab.github.io/reflectorch/).
+
+[![Interactive Notebook](https://img.shields.io/badge/Interactive%20Notebook-%23F9AB00.svg?style=flat&logo=google-colab&logoColor=black)](https://colab.research.google.com/drive/1rf_M8S_5kYvUoK0-9-AYal_fO3oFl7ck?usp=sharing)
+We provide an interactive Google Colab notebook for exploring the basic functionality of the package: [![Explore reflectorch in Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1rf_M8S_5kYvUoK0-9-AYal_fO3oFl7ck?usp=sharing)<br>
 
-![](https://img.shields.io/badge/Interactive%20Notebook-%23F9AB00.svg?style=flat&logo=google-colab&logoColor=black) We provide an interactive Google Colab notebook for exploring the basic functionality of the package: [![Explore reflectorch in Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1rf_M8S_5kYvUoK0-9-AYal_fO3oFl7ck?usp=sharing)<br>
+[![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).
 
-![](https://img.shields.io/badge/Hugging%20Face-%23FFD700.svg?style=flat&logo=huggingface&logoColor=black) 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.
 
-![](https://img.shields.io/badge/Docker-2496ED.svg?style=flat&logo=docker&logoColor=white) Docker images for reflectorch *will* be hosted on Dockerhub.
 
 ## Citation
-If you find our work useful in your research, please cite:
+If you find our work useful in your research, please cite as follows:
 ```
 @Article{Munteanu2024,
   author    = {Munteanu, Valentin and Starostin, Vladimir and Greco, Alessandro and Pithan, Linus and Gerlach, Alexander and Hinderhofer, Alexander and Kowarik, Stefan and Schreiber, Frank},

reflectorch-1.1.0/README.md

@@ -0,0 +1,83 @@
+# Reflectorch
+
+[![PyTorch](https://img.shields.io/badge/PyTorch-%23EE4C2C.svg?style=for-the-badge&logo=PyTorch&logoColor=white)](https://pytorch.org/)
+[![NumPy](https://img.shields.io/badge/numpy-%23013243.svg?style=for-the-badge&logo=numpy&logoColor=white)](https://numpy.org/)
+[![SciPy](https://img.shields.io/badge/SciPy-%230C55A5.svg?style=for-the-badge&logo=scipy&logoColor=%white)](https://scipy.org/)
+[![Matplotlib](https://img.shields.io/badge/Matplotlib-%23ffffff.svg?style=for-the-badge&logo=Matplotlib&logoColor=black)](https://matplotlib.org/)
+[![YAML](https://img.shields.io/badge/yaml-%23ffffff.svg?style=for-the-badge&logo=yaml&logoColor=151515)](https://yaml.org/)
+[![Hugging Face](https://img.shields.io/badge/Hugging%20Face-%23FFD700.svg?style=for-the-badge&logo=huggingface&logoColor=black)](https://huggingface.co/valentinsingularity/reflectivity)
+
+[![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)
+[![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) -->
+
+
+**Reflectorch** is a machine learning Python package for the analysis of X-ray and neutron reflectometry data, written by [Vladimir Starostin](https://github.com/StarostinV/) & [Valentin Munteanu](https://github.com/valentinsingularity) at the University of Tübingen. It provides functionality for the fast simulation of reflectometry curves on the GPU, customizable setup of the physical parameterization model and neural network architecture via YAML configuration files, and prior-aware training of neural networks as described in our paper [Neural network analysis of neutron and X-ray reflectivity data incorporating prior knowledge](https://doi.org/10.1107/S1600576724002115).
+
+## Installation
+
+**Reflectorch** can be installed from [![PyPi](https://img.shields.io/badge/PyPi-3776AB.svg?style=flat&logo=pypi&logoColor=white)](https://pypi.org/project/reflectorch/) via ``pip``:
+
+<!-- or from [![conda-forge](https://img.shields.io/badge/conda--forge-44A833.svg?style=flat&logo=conda-forge&logoColor=white)](https://anaconda.org/conda-forge/reflectorch/) via ``conda``: -->
+
+```bash
+pip install reflectorch
+```
+
+<!-- or
+
+```bash
+conda install -c conda-forge reflectorch
+``` -->
+
+Alternatively, one can clone the entire Github repository and install the package in editable mode:
+
+```bash
+git clone https://github.com/schreiber-lab/reflectorch.git
+pip install -e .
+```
+
+For development purposes, the package can be installed together with the optional dependencies for building the distribution, testing and documentation:
+
+```bash
+git clone https://github.com/schreiber-lab/reflectorch.git
+pip install -e .[tests,docs,build]
+```
+
+Users with Nvidia **GPU**s need to additionally install **Pytorch with CUDA support** corresponding to their hardware and operating system according to the instructions from the [Pytorch website](https://pytorch.org/get-started/locally/)
+
+## Get started
+
+[![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/)
+ The full documentation of the package, containing tutorials and the API reference, was built with [Jupyter Book](https://jupyterbook.org/) and [Sphinx](https://www.sphinx-doc.org) and it is hosted at the address: [https://schreiber-lab.github.io/reflectorch/](https://schreiber-lab.github.io/reflectorch/).
+
+[![Interactive Notebook](https://img.shields.io/badge/Interactive%20Notebook-%23F9AB00.svg?style=flat&logo=google-colab&logoColor=black)](https://colab.research.google.com/drive/1rf_M8S_5kYvUoK0-9-AYal_fO3oFl7ck?usp=sharing)
+We provide an interactive Google Colab notebook for exploring the basic functionality of the package: [![Explore reflectorch in Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1rf_M8S_5kYvUoK0-9-AYal_fO3oFl7ck?usp=sharing)<br>
+
+[![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.
+
+
+## Citation
+If you find our work useful in your research, please cite as follows:
+```
+@Article{Munteanu2024,
+  author    = {Munteanu, Valentin and Starostin, Vladimir and Greco, Alessandro and Pithan, Linus and Gerlach, Alexander and Hinderhofer, Alexander and Kowarik, Stefan and Schreiber, Frank},
+  journal   = {Journal of Applied Crystallography},
+  title     = {Neural network analysis of neutron and X-ray reflectivity data incorporating prior knowledge},
+  year      = {2024},
+  issn      = {1600-5767},
+  month     = mar,
+  number    = {2},
+  volume    = {57},
+  doi       = {10.1107/s1600576724002115},
+  publisher = {International Union of Crystallography (IUCr)},
+}
+```

reflectorch-1.1.0/configs/c_test_safetensors.yaml

@@ -0,0 +1,103 @@
+general:
+  name: c_test_safetensors
+  root_dir: null
+  
+dset:
+  cls: ReflectivityDataLoader
+  prior_sampler:
+    cls: SubpriorParametricSampler
+    kwargs:
+      param_ranges:
+        thicknesses: [1., 500.]
+        roughnesses: [0., 60.]
+        slds: [0., 25.]
+      bound_width_ranges:
+        thicknesses: [1.0e-2, 500.]
+        roughnesses: [1.0e-2, 60.]
+        slds: [ 1.0e-2, 4.]
+      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'
+      
+  intensity_noise:
+    cls: BasicExpIntensityNoise
+    kwargs:
+      relative_errors: [0.0, 0.2]
+      abs_errors: 0.0
+      consistent_rel_err: true
+      logdist: false
+      apply_shift: true
+      shift_range: [-0.3, 0.3]
+      apply_scaling: true
+      scale_range: [-0.02, 0.02]
+      apply_background: false
+      background_range: [1.0e-10, 1.0e-8]
+
+  q_noise:
+    cls: BasicQNoiseGenerator
+    kwargs:
+      shift_std: 1.0e-3
+      noise_std: [0., 1.0e-3]
+      
+  curves_scaler:
+    cls: LogAffineCurvesScaler
+    kwargs:
+      weight: 0.2
+      bias: 1.0
+      eps: 1.0e-10
+
+model:
+  network:
+    cls: NetworkWithPriorsConvEmb
+    pretrained_name: null
+    device: 'cuda'
+    kwargs:
+      in_channels: 1
+      hidden_channels: [32, 64, 128, 256, 512]
+      dim_embedding: 128
+      dim_avpool: 1
+      embedding_net_activation: 'gelu'
+      use_batch_norm: true
+      dim_out: 8
+      layer_width: 512
+      num_blocks: 6
+      repeats_per_block: 2
+      mlp_activation: 'gelu'
+      dropout_rate: 0.0 
+      pretrained_embedding_net: null
+       
+training:
+  num_iterations: 10000
+  batch_size: 4096
+  lr: 1.0e-4
+  grad_accumulation_steps: 1
+  clip_grad_norm_max: null
+  train_with_q_input: False
+  update_tqdm_freq: 1
+  optimizer: AdamW
+  trainer_kwargs:
+    optim_kwargs:
+      betas: [0.9, 0.999]
+      weight_decay: 0.0005
+  callbacks:
+    save_best_model:
+      enable: true
+      freq: 500
+    lr_scheduler:
+      cls: StepLR
+      kwargs:
+        step_size: 500
+        gamma: 0.5
+  logger:
+    use_neptune: false

{reflectorch-1.0.0 → reflectorch-1.1.0}/pyproject.toml

@@ -4,13 +4,14 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "reflectorch"
-version = "1.0.0"
+version = "1.1.0"
 authors = [
     {name = "Vladimir Starostin", email="vladimir.starostin@uni-tuebingen.de"},
     {name = "Valentin Munteanu", email="valentin.munteanu@uni-tuebingen.de"}
 ]
 maintainers = [
     {name = "Valentin Munteanu", email="valentin.munteanu@uni-tuebingen.de"},
+    {name = "Vladimir Starostin", email="vladimir.starostin@uni-tuebingen.de"},
     {name = "Alexander Hinderhofer", email="alexander.hinderhofer@uni-tuebingen.de"}
 ]
 description = "A Pytorch-based package for the analysis of reflectometry data"
@@ -36,7 +37,6 @@ dependencies = [
     "click",
     "matplotlib",
     "ipywidgets",
-    "torchinfo",
     "huggingface_hub",
 ]
 

{reflectorch-1.0.0 → reflectorch-1.1.0}/reflectorch/data_generation/priors/sampler_strategies.py

@@ -283,7 +283,7 @@ def constrained_roughness_and_isld_sampler(
     params[..., roughness_mask] = roughnesses
 
     max_isld = torch.minimum(
-        params[..., sld_mask] * coef_isld,
+        torch.abs(params[..., sld_mask]) * coef_isld,
         total_max_bounds[..., isld_mask]
     )
     min_isld = total_min_bounds[..., isld_mask]

{reflectorch-1.0.0 → reflectorch-1.1.0}/reflectorch/inference/__init__.py

@@ -1,4 +1,5 @@
 from reflectorch.inference.inference_model import InferenceModel, EasyInferenceModel
+from reflectorch.inference.query_matcher import HuggingfaceQueryMatcher
 from reflectorch.inference.multilayer_inference_model import MultilayerInferenceModel
 from reflectorch.inference.preprocess_exp import (
     StandardPreprocessing,
@@ -13,6 +14,7 @@ __all__ = [
     "InferenceModel",
     "EasyInferenceModel",
     "MultilayerInferenceModel",
+    "HuggingfaceQueryMatcher",
     "StandardPreprocessing",
     "standard_preprocessing",
     "ReflGradientFit",

reflectorch-1.1.0/reflectorch/inference/query_matcher.py

@@ -0,0 +1,82 @@
+import os
+import tempfile
+import yaml
+from huggingface_hub import hf_hub_download, list_repo_files
+
+class HuggingfaceQueryMatcher:
+    """Downloads the available configurations files to a temporary directory and provides functionality for filtering those configuration files matching user specified queries.
+    
+    Args:
+        repo_id (str): The Hugging Face repository ID.
+        config_dir (str): Directory within the repo where YAML files are stored.
+    """
+    def __init__(self, repo_id='valentinsingularity/reflectivity', config_dir='configs'):
+        self.repo_id = repo_id
+        self.config_dir = config_dir
+        self.cache = {
+            'parsed_configs': None,
+            'temp_dir': None
+        }
+        self._renew_cache()
+
+    def _renew_cache(self):
+        temp_dir = tempfile.mkdtemp()
+        print(f"Temporary directory created at: {temp_dir}")
+
+        repo_files = list_repo_files(self.repo_id, repo_type='model')
+        config_files = [file for file in repo_files if file.startswith(self.config_dir) and file.endswith('.yaml')]
+
+        downloaded_files = []
+        for file in config_files:
+            file_path = hf_hub_download(repo_id=self.repo_id, filename=file, local_dir=temp_dir, repo_type='model')
+            downloaded_files.append(file_path)
+        
+        parsed_configs = {}
+        for file_path in downloaded_files:
+            with open(file_path, 'r') as file:
+                config_data = yaml.safe_load(file)
+                file_name = os.path.basename(file_path)
+                parsed_configs[file_name] = config_data
+        
+        self.cache['parsed_configs'] = parsed_configs
+        self.cache['temp_dir'] = temp_dir
+
+    def get_matching_configs(self, query):
+        """retrieves configuration files that match the user specified query.
+        
+        Args:
+            query (dict): Dictionary of key-value pairs to filter configurations, e.g. ``query = {'dset.prior_sampler.kwargs.max_num_layers': 3, 'dset.prior_sampler.kwargs.param_ranges.slds': [0., 100.]}``.
+                          For keys containing the ``param_ranges`` subkey a configuration is selected if the value of the query (i.e. desired parameter range) 
+                          is a subrange of the parameter range in the configuration, in all other cases the values must match exactly.
+        
+        Returns:
+            list: List of file names that match the query.
+        """
+        
+        filtered_configs = []
+        
+        for file_name, config_data in self.cache['parsed_configs'].items():
+            if self.matches_query(config_data, query):
+                filtered_configs.append(file_name)
+        
+        return filtered_configs
+    
+    def matches_query(self, config_data, query):
+        for q_key, q_value in query.items():
+            keys = q_key.split('.')
+            value = self.deep_get(config_data, keys)
+            if 'param_ranges' in keys:
+                if q_value[0] < value[0] or q_value[1] > value[1]:
+                    return False
+            else: 
+                if value != q_value:
+                    return False
+                
+        return True
+
+    def deep_get(self, d, keys):
+        for key in keys:
+            if isinstance(d, dict):
+                d = d.get(key, None)
+
+        return d

{reflectorch-1.0.0 → reflectorch-1.1.0}/reflectorch/runs/utils.py

@@ -177,7 +177,7 @@ def get_trainer_from_config(config: dict, folder_paths: dict = None):
     return trainer
 
 
-def get_trainer_by_name(config_name, config_dir=None, model_path=None, load_weights: bool = True, inference_device = None):
+def get_trainer_by_name(config_name, config_dir=None, model_path=None, load_weights: bool = True, inference_device: str = 'cuda'):
     """Initializes a trainer object based on a configuration file (i.e. the model name) and optionally loads \
         saved weights into the network
 
@@ -186,7 +186,7 @@ def get_trainer_by_name(config_name, config_dir=None, model_path=None, load_weig
         config_dir (str): path of the configuration directory
         model_path (str, optional): path to the network weights.
         load_weights (bool, optional): if True the saved network weights are loaded into the network. Defaults to True.
-
+        inference_device (str, optional): overwrites the device in the configuration file for the purpose of inference on a different device then the training was performed on. Defaults to 'cuda'.
 
     Returns:
         Trainer: the trainer object
@@ -195,10 +195,9 @@ def get_trainer_by_name(config_name, config_dir=None, model_path=None, load_weig
     config['model']['network']['pretrained_name'] = None
     config['training']['logger']['use_neptune'] = False
 
-    if inference_device:
-        config['model']['network']['device'] = inference_device
-        config['dset']['prior_sampler']['kwargs']['device'] = inference_device
-        config['dset']['q_generator']['kwargs']['device'] = inference_device
+    config['model']['network']['device'] = inference_device
+    config['dset']['prior_sampler']['kwargs']['device'] = inference_device
+    config['dset']['q_generator']['kwargs']['device'] = inference_device
 
     trainer = get_trainer_from_config(config)
 
@@ -216,7 +215,7 @@ def get_trainer_by_name(config_name, config_dir=None, model_path=None, load_weig
         model_path = SAVED_MODELS_DIR / model_name
 
     try:
-        state_dict = torch.load(model_path)
+        state_dict = torch.load(model_path, map_location=inference_device)
     except Exception as err:
         raise RuntimeError(f'Could not load model from {model_path}') from err
 

{reflectorch-1.0.0 → reflectorch-1.1.0}/reflectorch.egg-info/PKG-INFO

@@ -1,9 +1,9 @@
 Metadata-Version: 2.1
 Name: reflectorch
-Version: 1.0.0
+Version: 1.1.0
 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>, Alexander Hinderhofer <alexander.hinderhofer@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>
 Project-URL: Source, https://github.com/schreiber-lab/reflectorch/
 Project-URL: Issues, https://github.com/schreiber-lab/reflectorch/issues
 Project-URL: Documentation, https://schreiber-lab.github.io/reflectorch/
@@ -26,7 +26,6 @@ Requires-Dist: PyYAML
 Requires-Dist: click
 Requires-Dist: matplotlib
 Requires-Dist: ipywidgets
-Requires-Dist: torchinfo
 Requires-Dist: huggingface_hub
 Provides-Extra: tests
 Requires-Dist: pytest; extra == "tests"
@@ -47,31 +46,34 @@ Requires-Dist: twine; extra == "build"
 [![YAML](https://img.shields.io/badge/yaml-%23ffffff.svg?style=for-the-badge&logo=yaml&logoColor=151515)](https://yaml.org/)
 [![Hugging Face](https://img.shields.io/badge/Hugging%20Face-%23FFD700.svg?style=for-the-badge&logo=huggingface&logoColor=black)](https://huggingface.co/valentinsingularity/reflectivity)
 
-[![License: GPLv3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 [![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)
-[![Jupyter Book Documentation](https://jupyterbook.org/badge.svg)](https://schreiber-lab.github.io/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) -->
 
 
-**Reflectorch** is a machine learning Python package for the analysis of X-ray and neutron reflectometry data based on Pytorch (written by [Vladimir Starostin](https://github.com/StarostinV/) & [Valentin Munteanu](https://github.com/valentinsingularity)). It provides functionality for the fast simulation of reflectometry curves on the GPU, customizable setup of the physical parameterization model and neural network architecture via YAML configuration files, and prior-aware training of neural networks as described in our paper [Neural network analysis of neutron and X-ray reflectivity data incorporating prior knowledge](https://doi.org/10.1107/S1600576724002115).
+**Reflectorch** is a machine learning Python package for the analysis of X-ray and neutron reflectometry data, written by [Vladimir Starostin](https://github.com/StarostinV/) & [Valentin Munteanu](https://github.com/valentinsingularity) at the University of Tübingen. It provides functionality for the fast simulation of reflectometry curves on the GPU, customizable setup of the physical parameterization model and neural network architecture via YAML configuration files, and prior-aware training of neural networks as described in our paper [Neural network analysis of neutron and X-ray reflectivity data incorporating prior knowledge](https://doi.org/10.1107/S1600576724002115).
 
 ## Installation
 
-**Reflectorch** can be installed either from [![PyPi](https://img.shields.io/badge/PyPi-3776AB.svg?style=flat&logo=pypi&logoColor=white)](https://pypi.org/project/reflectorch/) via ``pip`` or from [![conda-forge](https://img.shields.io/badge/conda--forge-44A833.svg?style=flat&logo=conda-forge&logoColor=white)](https://anaconda.org/conda-forge/reflectorch/) via ``conda``:
+**Reflectorch** can be installed from [![PyPi](https://img.shields.io/badge/PyPi-3776AB.svg?style=flat&logo=pypi&logoColor=white)](https://pypi.org/project/reflectorch/) via ``pip``:
+
+<!-- or from [![conda-forge](https://img.shields.io/badge/conda--forge-44A833.svg?style=flat&logo=conda-forge&logoColor=white)](https://anaconda.org/conda-forge/reflectorch/) via ``conda``: -->
 
 ```bash
 pip install reflectorch
 ```
 
-or
+<!-- or
 
 ```bash
 conda install -c conda-forge reflectorch
-```
+``` -->
 
-Additionally, one can clone the entire Github repository and install the package in editable mode:
+Alternatively, one can clone the entire Github repository and install the package in editable mode:
 
 ```bash
 git clone https://github.com/schreiber-lab/reflectorch.git
@@ -89,16 +91,21 @@ Users with Nvidia **GPU**s need to additionally install **Pytorch with CUDA supp
 
 ## Get started
 
-![](https://img.shields.io/badge/Documentation%20Page-%23FFDD33.svg?style=flat&logo=read-the-docs&logoColor=black) The full documentation of the package, containing tutorials and the API reference, was built with [Jupyter Book](https://jupyterbook.org/) and [Sphinx](https://www.sphinx-doc.org) and it is hosted at the address: [https://schreiber-lab.github.io/reflectorch/](https://schreiber-lab.github.io/reflectorch/).
+[![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/)
+ The full documentation of the package, containing tutorials and the API reference, was built with [Jupyter Book](https://jupyterbook.org/) and [Sphinx](https://www.sphinx-doc.org) and it is hosted at the address: [https://schreiber-lab.github.io/reflectorch/](https://schreiber-lab.github.io/reflectorch/).
+
+[![Interactive Notebook](https://img.shields.io/badge/Interactive%20Notebook-%23F9AB00.svg?style=flat&logo=google-colab&logoColor=black)](https://colab.research.google.com/drive/1rf_M8S_5kYvUoK0-9-AYal_fO3oFl7ck?usp=sharing)
+We provide an interactive Google Colab notebook for exploring the basic functionality of the package: [![Explore reflectorch in Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1rf_M8S_5kYvUoK0-9-AYal_fO3oFl7ck?usp=sharing)<br>
 
-![](https://img.shields.io/badge/Interactive%20Notebook-%23F9AB00.svg?style=flat&logo=google-colab&logoColor=black) We provide an interactive Google Colab notebook for exploring the basic functionality of the package: [![Explore reflectorch in Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1rf_M8S_5kYvUoK0-9-AYal_fO3oFl7ck?usp=sharing)<br>
+[![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).
 
-![](https://img.shields.io/badge/Hugging%20Face-%23FFD700.svg?style=flat&logo=huggingface&logoColor=black) 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.
 
-![](https://img.shields.io/badge/Docker-2496ED.svg?style=flat&logo=docker&logoColor=white) Docker images for reflectorch *will* be hosted on Dockerhub.
 
 ## Citation
-If you find our work useful in your research, please cite:
+If you find our work useful in your research, please cite as follows:
 ```
 @Article{Munteanu2024,
   author    = {Munteanu, Valentin and Starostin, Vladimir and Greco, Alessandro and Pithan, Linus and Gerlach, Alexander and Hinderhofer, Alexander and Kowarik, Stefan and Schreiber, Frank},