reflectorch 1.2.1__py3-none-any.whl → 1.4.0__py3-none-any.whl

reflectorch/models/networks/residual_net.py

@@ -18,15 +18,21 @@ class ResidualMLP(nn.Module):
             repeats_per_block: int = 2,
             activation: str = 'relu',
             use_batch_norm: bool = True,
+            use_layer_norm: bool = False,
             dropout_rate: float = 0.0,
             residual: bool = True,
             adaptive_activation: bool = False,
             conditioning: str = 'glu',
+            concat_condition_first_layer: bool = True,
+            film_with_tanh: bool = False,
     ):
         super().__init__()
 
-        dim_first_layer = dim_in + dim_condition
+        self.concat_condition_first_layer = concat_condition_first_layer
+
+        dim_first_layer = dim_in + dim_condition if concat_condition_first_layer else dim_in
         self.first_layer = nn.Linear(dim_first_layer, layer_width)
+
         self.blocks = nn.ModuleList(
             [
                 ResidualBlock(
@@ -35,24 +41,28 @@ class ResidualMLP(nn.Module):
                     repeats_per_block=repeats_per_block,
                     activation=activation,
                     use_batch_norm=use_batch_norm,
+                    use_layer_norm=use_layer_norm,
                     dropout_rate=dropout_rate,
                     residual=residual,
                     adaptive_activation=adaptive_activation,
                     conditioning = conditioning,
+                    film_with_tanh = film_with_tanh,
                 )
                 for _ in range(num_blocks)
             ]
         )
+
         self.last_layer = nn.Linear(layer_width, dim_out)
 
     def forward(self, x, condition=None):
-        if condition is None:
-            x = self.first_layer(x)
-        else:
+        if self.concat_condition_first_layer and condition is not None:
             x = self.first_layer(torch.cat([x, condition], dim=-1))
+        else:
+            x = self.first_layer(x)
 
         for block in self.blocks:
             x = block(x, condition=condition)
+
         x = self.last_layer(x)
 
         return x
@@ -68,19 +78,23 @@ class ResidualBlock(nn.Module):
             repeats_per_block: int = 2,
             activation: str = 'relu',
             use_batch_norm: bool = False,
+            use_layer_norm: bool = False,
             dropout_rate: float = 0.0,
             residual: bool = True,
             adaptive_activation: bool = False,
             conditioning: str = 'glu',
+            film_with_tanh: bool = False,
     ):
         super().__init__()
          
         self.residual = residual
         self.repeats_per_block = repeats_per_block
         self.use_batch_norm = use_batch_norm
+        self.use_layer_norm = use_layer_norm
         self.dropout_rate = dropout_rate
         self.adaptive_activation = adaptive_activation
         self.conditioning = conditioning
+        self.film_with_tanh = film_with_tanh
 
         if not adaptive_activation:
             self.activation = activation_by_name(activation)()
@@ -92,7 +106,11 @@ class ResidualBlock(nn.Module):
         if use_batch_norm:
             self.batch_norm_layers = nn.ModuleList(
                 [nn.BatchNorm1d(layer_width, eps=1e-3) for _ in range(repeats_per_block)]
-            )
+             )
+        elif use_layer_norm:
+            self.layer_norm_layers = nn.ModuleList(
+                [nn.LayerNorm(layer_width) for _ in range(repeats_per_block)]
+             )
 
         if dim_condition:
             if conditioning == 'glu':
@@ -113,12 +131,17 @@ class ResidualBlock(nn.Module):
         for i in range(self.repeats_per_block):
             if self.use_batch_norm:
                 x = self.batch_norm_layers[i](x)
+            elif self.use_layer_norm:
+                x = self.layer_norm_layers[i](x)
+
             if not self.adaptive_activation:
                 x = self.activation(x)
             else:
                 x = self.activation_layers[i](x)
+
             if self.dropout_rate > 0 and i == self.repeats_per_block - 1:
                 x = self.dropout(x)
+
             x = self.linear_layers[i](x)
         
         if condition is not None:
@@ -126,6 +149,9 @@ class ResidualBlock(nn.Module):
                 x = F.glu(torch.cat((x, self.condition_layer(condition)), dim=-1), dim=-1)
             elif self.conditioning == 'film':
                 gamma, beta = torch.chunk(self.condition_layer(condition), chunks=2, dim=-1)
+                if self.film_with_tanh:
+                    tanh = nn.Tanh()
+                    gamma, beta = tanh(gamma), tanh(beta)
                 x = x * gamma + beta
 
         return x0 + x if self.residual else x

reflectorch/runs/train.py

@@ -72,7 +72,6 @@ def run_train_on_cluster(config_name: str):
 
 def _change_to_test_config(config, batch_size: int, num_iterations: int):
     config = dict(config)
-    config['training']['logger']['use_neptune'] = False
     config['training']['num_iterations'] = num_iterations
     config['training']['batch_size'] = batch_size
     config['training']['update_tqdm_freq'] = 1

reflectorch/runs/utils.py

@@ -136,7 +136,7 @@ def get_callbacks_from_config(config: dict, folder_paths: dict = None) -> Tuple[
         if callback:
             callbacks.append(callback)
 
-    if train_conf['logger']['use_neptune']:
+    if 'logger' in train_conf.keys():
         callbacks.append(LogLosses())
 
     return tuple(callbacks)
@@ -162,9 +162,9 @@ def get_trainer_from_config(config: dict, folder_paths: dict = None):
 
     optim_cls = getattr(torch.optim, train_conf['optimizer'])
 
-    logger = None
+    logger_conf = train_conf.get('logger', None)
+    logger = init_from_conf(logger_conf) if logger_conf and logger_conf.get('cls') else None 
 
-    train_with_q_input = train_conf.get('train_with_q_input', False)
     clip_grad_norm_max = train_conf.get('clip_grad_norm_max', None)
 
     trainer_cls = globals().get(train_conf['trainer_cls']) if 'trainer_cls' in train_conf else PointEstimatorTrainer
@@ -173,10 +173,13 @@ def get_trainer_from_config(config: dict, folder_paths: dict = None):
 
     trainer = trainer_cls(
         model, dset, train_conf['lr'], train_conf['batch_size'], clip_grad_norm_max=clip_grad_norm_max,
-        logger=logger, optim_cls=optim_cls, train_with_q_input=train_with_q_input, 
+        logger=logger, optim_cls=optim_cls, 
         **trainer_kwargs
     )
 
+    if train_conf.get('train_with_q_input', False) and getattr(trainer, 'train_with_q_input', None) is not None: #only for back-compatibility with configs in older versions
+        trainer.train_with_q_input = True
+
     return trainer
 
 
@@ -187,7 +190,7 @@ def get_trainer_by_name(config_name, config_dir=None, model_path=None, load_weig
     Args:
         config_name (str): name of the configuration file
         config_dir (str): path of the configuration directory
-        model_path (str, optional): path to the network weights.
+        model_path (str, optional): path to the network weights. The default path is 'saved_models' located in the package directory
         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'.
 
@@ -195,8 +198,7 @@ def get_trainer_by_name(config_name, config_dir=None, model_path=None, load_weig
         Trainer: the trainer object
     """
     config = load_config(config_name, config_dir)
-    config['model']['network']['pretrained_name'] = None
-    config['training']['logger']['use_neptune'] = False
+    #config['model']['network']['pretrained_name'] = None
 
     config['model']['network']['device'] = inference_device
     config['dset']['prior_sampler']['kwargs']['device'] = inference_device
@@ -219,7 +221,7 @@ def get_trainer_by_name(config_name, config_dir=None, model_path=None, load_weig
 
     if str(model_path).endswith('.pt'):
         try:
-            state_dict = torch.load(model_path, map_location=inference_device)
+            state_dict = torch.load(model_path, map_location=inference_device, weights_only=False)
         except Exception as err:
             raise RuntimeError(f'Could not load model from {model_path}') from err
 
@@ -238,7 +240,7 @@ def get_trainer_by_name(config_name, config_dir=None, model_path=None, load_weig
         raise RuntimeError('Weigths file with unknown extension')
 
     return trainer
-
+ 
 def get_callbacks_by_name(config_name, config_dir=None):
     """Initializes the trainer callbacks based on a configuration file
 
@@ -276,7 +278,7 @@ def load_pretrained(model, model_name: str, saved_models_dir: Path):
         raise FileNotFoundError(f'File {str(model_path)} does not exist.')
     
     try:
-        pretrained = torch.load(model_path)
+        pretrained = torch.load(model_path, weights_only=False)
     except Exception as err:
         raise RuntimeError(f'Could not load model from {str(model_path)}') from err
     
@@ -293,6 +295,8 @@ def load_pretrained(model, model_name: str, saved_models_dir: Path):
 def init_dset(config: dict):
     """Initializes the dataset / dataloader object"""
     dset_cls = globals().get(config['cls']) if 'cls' in config else ReflectivityDataLoader
+    dset_kwargs = config.get('kwargs', {})
+
     prior_sampler = init_from_conf(config['prior_sampler'])
     intensity_noise = init_from_conf(config['intensity_noise'])
     q_generator = init_from_conf(config['q_generator'])
@@ -307,6 +311,7 @@ def init_dset(config: dict):
         curves_scaler=curves_scaler,
         smearing=smearing,
         q_noise=q_noise,
+        **dset_kwargs,
     )
 
     return dset
@@ -356,12 +361,44 @@ def convert_pt_to_safetensors(input_dir):
                 continue
 
             print(f"Converting {pt_file_path} to .safetensors format.")
-            data_pt = torch.load(pt_file_path)
+            data_pt = torch.load(pt_file_path, weights_only=False)
             model_state_dict = data_pt["model"]
             model_state_dict = split_complex_tensors(model_state_dict) #handle tensors with complex dtype which are not natively supported by safetensors
 
             safetensors.torch.save_file(tensors=model_state_dict, filename=safetensors_file_path)
 
+def convert_files_to_safetensors(files):
+    """
+    Converts specified .pt files to .safetensors format.
+
+    Args:
+        files (str or list of str): Path(s) to .pt files containing model state dictionaries.
+    """
+    if isinstance(files, str):
+        files = [files]
+
+    for pt_file_path in files:
+        if not pt_file_path.endswith('.pt'):
+            print(f"Skipping {pt_file_path}: not a .pt file.")
+            continue
+
+        if not os.path.exists(pt_file_path):
+            print(f"File {pt_file_path} does not exist.")
+            continue
+
+        safetensors_file_path = pt_file_path[:-3] + '.safetensors'
+
+        if os.path.exists(safetensors_file_path):
+            print(f"Skipping {pt_file_path}: .safetensors version already exists.")
+            continue
+
+        print(f"Converting {pt_file_path} to .safetensors format.")
+        data_pt = torch.load(pt_file_path, weights_only=False)
+        model_state_dict = data_pt["model"]
+        model_state_dict = split_complex_tensors(model_state_dict)
+
+        safetensors.torch.save_file(tensors=model_state_dict, filename=safetensors_file_path)
+
 def load_state_dict_safetensors(model, filename, device):
     state_dict = safetensors.torch.load_file(filename=filename, device=device)
     state_dict = recombine_complex_tensors(state_dict)

reflectorch/utils.py

@@ -66,3 +66,33 @@ def energy_to_wavelength(energy: float):
 def wavelength_to_energy(wavelength: float):
     """Conversion from photon wavelength (angstroms) to photon energy (eV)"""
     return 1.2398 / wavelength * 1e4
+
+def get_filtering_mask(Q, R, dR, threshold=0.3, consecutive=3,
+                        remove_singles=True, remove_consecutives=True,
+                        q_start_trunc=0.1):
+    Q, R, dR = Q.copy(), R.copy(), dR.copy()
+    rel_error = np.abs(dR / R)
+
+    # Mask for singles
+    mask_singles = (rel_error >= threshold) if remove_singles else np.zeros_like(Q, dtype=bool)
+
+    # Mask for truncation
+    mask_consecutive = np.zeros_like(Q, dtype=bool)
+    if remove_consecutives:
+        count = 0
+        cutoff_idx = None
+        for i in range(len(Q)):
+            if Q[i] < q_start_trunc:
+                continue
+            if rel_error[i] >= threshold:
+                count += 1
+                if count >= consecutive:
+                    cutoff_idx = i - consecutive + 1
+                    break
+            else:
+                count = 0
+        if cutoff_idx is not None:
+            mask_consecutive[cutoff_idx:] = True
+
+    final_mask = mask_singles | mask_consecutive
+    return ~final_mask

{reflectorch-1.2.1.dist-info → reflectorch-1.4.0.dist-info}/METADATA

@@ -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>
@@ -11,32 +11,33 @@ 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: torch >=1.8.1
+Requires-Dist: numpy
+Requires-Dist: torch>=1.8.1
 Requires-Dist: scipy
 Requires-Dist: tqdm
 Requires-Dist: PyYAML
 Requires-Dist: click
 Requires-Dist: matplotlib
 Requires-Dist: ipywidgets
-Requires-Dist: huggingface-hub
+Requires-Dist: huggingface_hub
 Requires-Dist: safetensors
-Provides-Extra: build
-Requires-Dist: build ; extra == 'build'
-Requires-Dist: twine ; extra == 'build'
-Provides-Extra: docs
-Requires-Dist: jupyter-book ; extra == 'docs'
-Requires-Dist: sphinx ; extra == 'docs'
+Requires-Dist: tensorboard
 Provides-Extra: tests
-Requires-Dist: pytest ; extra == 'tests'
-Requires-Dist: pytest-cov ; extra == 'tests'
+Requires-Dist: pytest; extra == "tests"
+Requires-Dist: pytest-cov; extra == "tests"
+Provides-Extra: docs
+Requires-Dist: jupyter-book; extra == "docs"
+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: pytest-cov ; extra == 'tests'
 [![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.dist-info → reflectorch-1.4.0.dist-info}/RECORD

@@ -3,16 +3,16 @@ reflectorch/paths.py,sha256=Z_VRVknkqRn03ULShc8YCp0czqqMJ9w2CRuUi8e2OV0,814
 reflectorch/test_config.py,sha256=1T7pMJ-WYLEu-4WtYMQxcJrqXvgdpvJ1yi2qINd0kNA,99
 reflectorch/train.py,sha256=-c8ac1fpjrCiEwnAaXg_rcBNl1stO1V5p5afx_78xHs,87
 reflectorch/train_on_cluster.py,sha256=aG3_g5_rzL8iL1tvtdY9ueJTo1f2Pn8lGJgudrrRknU,109
-reflectorch/utils.py,sha256=ehG5dU02_WIFPIVGPsSjHl3Ji10MQ8-jsCwRkwUO7D4,1993
-reflectorch/data_generation/__init__.py,sha256=TcF7kf16GCsQpp6cIXj-s4vb_gjrtv7tgXwLSeI8Xy8,3353
-reflectorch/data_generation/dataset.py,sha256=wEHMIzA1XQGQkzkN8WQRNqG53lyzxIVc80nMJKs0mgI,7273
+reflectorch/utils.py,sha256=LotpOM0Goh7OCvWdXqNuLz-HBW1lfQ_PoTknI17ZkIA,3031
+reflectorch/data_generation/__init__.py,sha256=UTa2sO5XWoD3wlpl5pAwfRTy0dLkILxyxRpnx1r6zN4,3465
+reflectorch/data_generation/dataset.py,sha256=f2uYb8j8H88owZJhg9aMP7qen00_o2cXmDvA69yJwr8,8316
 reflectorch/data_generation/likelihoods.py,sha256=gnqmsEfsZnCC6WuPcIe9rFl4SeiLv_LyNlTVM-5YTE8,2862
-reflectorch/data_generation/noise.py,sha256=c4ytClId3t3T5FO8r0NqAVz-x_zYWAJ2VkpxcvssrVY,16159
+reflectorch/data_generation/noise.py,sha256=Ps9lDKUjtjcpUfJ_L9zTmlj88GyicjNs962lLVEg2aI,22090
 reflectorch/data_generation/process_data.py,sha256=iBvWB4_X5TTIZTacsq9baBZPyGCRyI1G-J3l1BVMuD4,1180
-reflectorch/data_generation/q_generator.py,sha256=Etlp_6Tj2it2nK8PQSWgQZBLh8_459P985GrZs9U1lE,8529
+reflectorch/data_generation/q_generator.py,sha256=PX0RbdUC0EAeWYpaxzAddOMvS4fTfAehAEcI_l-GEns,11515
 reflectorch/data_generation/scale_curves.py,sha256=hNZoGkA9FMdLUarp0fwj5nCDYvpy9NbSiO85_rCaNr8,4084
-reflectorch/data_generation/smearing.py,sha256=MfHQ2sa-wPu5stO835m8i1-3NnJYvxS3qpzNs1jXWAE,3109
-reflectorch/data_generation/utils.py,sha256=3Di6I5Ihy2rm8NMeCEvIVqH0IXFEX2bcxkHSc6y9WgU,5607
+reflectorch/data_generation/smearing.py,sha256=ZQ4bzHegUOVhNWOTHAi3KfNau85bchp1FX1NV0Kp7s8,4538
+reflectorch/data_generation/utils.py,sha256=x5y6mRSeh57ZqvENkI6kS7NTpRspotSR6a0K0SrvlLg,8549
 reflectorch/data_generation/priors/__init__.py,sha256=ZUaQUgNR44MQGYcPVJaSzzoE270710RqdKAPcaBNHWo,1941
 reflectorch/data_generation/priors/base.py,sha256=JNa2A3F4IWaEwV7gyTQjVdCRevUI43UUpTOm1U3XA8k,1705
 reflectorch/data_generation/priors/exp_subprior_sampler.py,sha256=hjHey_32HGgZ4ojOAhmmx8jcQPCyvcPRgxMlfthSdOo,11551
@@ -20,64 +20,69 @@ reflectorch/data_generation/priors/independent_priors.py,sha256=ZdFCW4Ea6cK9f0Pn
 reflectorch/data_generation/priors/multilayer_models.py,sha256=lAf-HJPbIDnbD1ecDTvx03TfA4jLN5tTLbwaBCiYgWM,7763
 reflectorch/data_generation/priors/multilayer_structures.py,sha256=b1LTkzMK_R2hgbAmif96zRRzZRV2V-dD7eSTaNalMU8,3693
 reflectorch/data_generation/priors/no_constraints.py,sha256=qioTThJ17NixCaMIIf4dusPtvcK_uI2jOoysyXKnkZ4,7292
-reflectorch/data_generation/priors/parametric_models.py,sha256=vaAGcm9Ky-coidNliE4R1YvoqCcbNwEwJVCwwmkKI4E,25139
-reflectorch/data_generation/priors/parametric_subpriors.py,sha256=mN4MELBOQurNponknB_1n46fiNncXkI5PnnPL3hJee4,14352
+reflectorch/data_generation/priors/parametric_models.py,sha256=TwXRol5zfVVo05FKWMTlVIwIw5P2l7hgCzISG1kVTHw,29330
+reflectorch/data_generation/priors/parametric_subpriors.py,sha256=KPW3Y12A5ba405ofGdGny_FIzoFMd90IkQcvVcYhpxE,15164
 reflectorch/data_generation/priors/params.py,sha256=JpH-LRxTztc0QP-3QwjLdu0MsVc1rSixtcscYGs_2Ew,8238
-reflectorch/data_generation/priors/sampler_strategies.py,sha256=U-v5dXpFLJq939aQKvNl7n1Lih-y97K8WJCXBFRQiA0,13059
+reflectorch/data_generation/priors/sampler_strategies.py,sha256=ls9NRwjIsQJlgqv_m9l9MVm3tu4Ivafq5OzG2Q0sI3w,15791
 reflectorch/data_generation/priors/scaler_mixin.py,sha256=gI64v2KOZugSJWaLKASR34fn6qVFl-aoeVA1BR5yXNg,2648
 reflectorch/data_generation/priors/subprior_sampler.py,sha256=TE8DOQhxVr69VmWSjwHyElpgVjOhZKBIPChFWNVYzRc,14769
 reflectorch/data_generation/priors/utils.py,sha256=bmIZYHq95gG68kETfNH6ygR39oitUEJ0eCO_Fb8maH0,3836
-reflectorch/data_generation/reflectivity/__init__.py,sha256=MxVtNqO52iORdual2TtmSRN41TC9VmVSFH5ov-wuAJc,3202
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{reflectorch-1.2.1.dist-info → reflectorch-1.4.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (72.1.0)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: true
 Tag: py3-none-any