reflectorch 1.0.1__tar.gz → 1.1.0__tar.gz

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-1.0.1 → reflectorch-1.1.0}/PKG-INFO

@@ -1,9 +1,9 @@
 Metadata-Version: 2.1
 Name: reflectorch
-Version: 1.0.1
+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"
@@ -47,12 +46,12 @@ 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)
 [![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://schreiber-lab.github.io/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) -->
 
 
@@ -92,16 +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/).
 
-![](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>
+[![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/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).
+[![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.
 
-![](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-1.0.1 → reflectorch-1.1.0}/README.md

@@ -7,12 +7,12 @@
 [![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)
 [![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://schreiber-lab.github.io/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) -->
 
 
@@ -52,16 +52,21 @@ 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/).
 
-![](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>
+[![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/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).
+[![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.
 
-![](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/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-1.0.1 → reflectorch-1.1.0}/pyproject.toml

@@ -4,13 +4,14 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "reflectorch"
-version = "1.0.1"
+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-1.0.1 → 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-1.0.1 → 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-1.0.1 → reflectorch-1.1.0}/reflectorch.egg-info/PKG-INFO

@@ -1,9 +1,9 @@
 Metadata-Version: 2.1
 Name: reflectorch
-Version: 1.0.1
+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"
@@ -47,12 +46,12 @@ 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)
 [![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://schreiber-lab.github.io/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) -->
 
 
@@ -92,16 +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/).
 
-![](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>
+[![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/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).
+[![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.
 
-![](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},