careamics 0.0.6__py3-none-any.whl → 0.0.7__py3-none-any.whl

careamics/models/lvae/stochastic.py

@@ -193,6 +193,7 @@ class NormalStochasticBlock(nn.Module):
         z: torch.Tensor
             The sampled latent tensor.
         """
+        kl_samplewise_restricted = None
         if mode_pred is False:  # if not predicting
             if analytical_kl:
                 kl_elementwise = kl_divergence(q, p)

careamics/utils/metrics.py

@@ -14,6 +14,31 @@ from torchmetrics.image import MultiScaleStructuralSimilarityIndexMeasure
 # TODO: does this add additional dependency?
 
 
+# TODO revisit metric for notebook
+def avg_range_invariant_psnr(
+    pred: np.ndarray,
+    target: np.ndarray,
+) -> float:
+    """Compute the average range-invariant PSNR.
+
+    Parameters
+    ----------
+    pred : np.ndarray
+        Predicted images.
+    target : np.ndarray
+        Target images.
+
+    Returns
+    -------
+    float
+        Average range-invariant PSNR value.
+    """
+    psnr_arr = []
+    for i in range(pred.shape[0]):
+        psnr_arr.append(scale_invariant_psnr(pred[i], target[i]))
+    return np.mean(psnr_arr)
+
+
 def psnr(gt: np.ndarray, pred: np.ndarray, data_range: float) -> float:
     """
     Peak Signal to Noise Ratio.

careamics/utils/plotting.py

@@ -0,0 +1,78 @@
+"""Plotting utilities."""
+
+from typing import Optional
+
+import matplotlib.pyplot as plt
+import numpy as np
+import torch
+from numpy.typing import NDArray
+
+from careamics.models.lvae.noise_models import GaussianMixtureNoiseModel
+
+
+def plot_noise_model_probability_distribution(
+    noise_model: GaussianMixtureNoiseModel,
+    signalBinIndex: int,
+    histogram: NDArray,
+    channel: Optional[str] = None,
+    number_of_bins: int = 100,
+) -> None:
+    """Plot probability distribution P(x|s) for a certain ground truth signal.
+
+    Predictions from both Histogram and GMM-based
+    Noise models are displayed for comparison.
+
+    Parameters
+    ----------
+    noise_model : GaussianMixtureNoiseModel
+        Trained GaussianMixtureNoiseModel.
+    signalBinIndex : int
+        Index of signal bin. Values go from 0 to number of bins (`n_bin`).
+    histogram : NDArray
+        Histogram based noise model.
+    channel : Optional[str], optional
+        Channel name used for plotting. Default is None.
+    number_of_bins : int, optional
+        Number of bins in the resulting histogram. Default is 100.
+    """
+    min_signal = noise_model.min_signal.item()
+    max_signal = noise_model.max_signal.item()
+    bin_size = (max_signal - min_signal) / number_of_bins
+
+    query_signal_normalized = signalBinIndex / number_of_bins
+    query_signal = query_signal_normalized * (max_signal - min_signal) + min_signal
+    query_signal += bin_size / 2
+    query_signal = torch.tensor(query_signal)
+
+    query_observations = torch.arange(min_signal, max_signal, bin_size)
+    query_observations += bin_size / 2
+
+    likelihoods = noise_model.likelihood(
+        observations=query_observations, signals=query_signal
+    ).numpy()
+
+    plt.figure(figsize=(12, 5))
+    if channel:
+        plt.suptitle(f"Noise model for channel {channel}")
+    else:
+        plt.suptitle("Noise model")
+
+    plt.subplot(1, 2, 1)
+    plt.xlabel("Observation Bin")
+    plt.ylabel("Signal Bin")
+    plt.imshow(histogram**0.25, cmap="gray")
+    plt.axhline(y=signalBinIndex + 0.5, linewidth=5, color="blue", alpha=0.5)
+
+    plt.subplot(1, 2, 2)
+    plt.plot(
+        query_observations,
+        likelihoods,
+        label="GMM : " + " signal = " + str(np.round(query_signal, 2)),
+        marker=".",
+        color="red",
+        linewidth=2,
+    )
+    plt.xlabel("Observations (x) for signal s = " + str(query_signal))
+    plt.ylabel("Probability Density")
+    plt.title("Probability Distribution P(x|s) at signal =" + str(query_signal))
+    plt.legend()

{careamics-0.0.6.dist-info → careamics-0.0.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: careamics
-Version: 0.0.6
+Version: 0.0.7
 Summary: Toolbox for running N2V and friends.
 Project-URL: homepage, https://careamics.github.io/
 Project-URL: repository, https://github.com/CAREamics/careamics
@@ -17,16 +17,18 @@ Classifier: Programming Language :: Python :: 3.12
 Classifier: Typing :: Typed
 Requires-Python: >=3.9
 Requires-Dist: bioimageio-core==0.7
+Requires-Dist: matplotlib<=3.10.0
 Requires-Dist: numpy<2.0.0
 Requires-Dist: pillow<=11.1.0
 Requires-Dist: psutil<=6.1.1
 Requires-Dist: pydantic<2.11,>=2.5
 Requires-Dist: pytorch-lightning<=2.5.0.post0,>=2.2
 Requires-Dist: pyyaml!=6.0.0,<=6.0.2
-Requires-Dist: scikit-image<=0.25.0
+Requires-Dist: scikit-image<=0.25.1
 Requires-Dist: tifffile<=2025.1.10
-Requires-Dist: torch<=2.5.1,>=2.0
+Requires-Dist: torch<=2.6.0,>=2.0
 Requires-Dist: torchvision<=0.20.1
+Requires-Dist: torchvision<=0.21.0
 Requires-Dist: typer<=0.15.1,>=0.12.3
 Requires-Dist: zarr<3.0.0
 Provides-Extra: dev

{careamics-0.0.6.dist-info → careamics-0.0.7.dist-info}/RECORD

@@ -10,7 +10,7 @@ careamics/config/__init__.py,sha256=c5FXtcQrtROHdLRl4cHpKo6V4_E4yr6HxYgNwqH9CHg,
 careamics/config/callback_model.py,sha256=EeYHqpMIPQwyNxLRzzX32Uncl5mZuB1bJO76RHpNymg,4555
 careamics/config/care_configuration.py,sha256=hSfNJ-dooHm4ujG6Q3Hawr8zDeYy1HNiebtM7gxsh7s,2714
 careamics/config/configuration.py,sha256=KmLeXHkFhQTrcru1erhfVf3tHvQdoi12ls_u254rtDw,11114
-careamics/config/configuration_factories.py,sha256=-kdoLQ0dkV4xlcUx_odrtMsvL4NqGYg5-4HVl3PqY4c,32423
+careamics/config/configuration_factories.py,sha256=9civH9r1yfXcYeXJS61ft3Wsn8PoODNeqzGU45CTFCs,35460
 careamics/config/configuration_io.py,sha256=ks9R8lRCBY_m0sdy1k4ZWFPKEFSp7K9X47jCG4d0FY4,2353
 careamics/config/inference_model.py,sha256=UE_-ZmCX6LFCbDBOwyGnvuAboF_JNX2m2LcF0WiwgCI,6961
 careamics/config/likelihood_model.py,sha256=VorUtc0_-xIWNxwVrd1kBba-003ICdVMtxpcDCxH4Io,2259
@@ -22,9 +22,9 @@ careamics/config/optimizer_models.py,sha256=OWpTydRBBR8wt_af1mZHNNwvL_RtnRFopAOd
 careamics/config/tile_information.py,sha256=c-_xrVPOgcnjiEzQ-9A_GhNPamObkMANbeHaRP29R-4,2059
 careamics/config/training_model.py,sha256=67_ipo_-LxhT4-WqAs40Sg8PjU--my43Qn3BhjvlXxM,3212
 careamics/config/algorithms/__init__.py,sha256=on5D6zBO9Lu-Tf5To8xpF6owIFqdN7RSmZdpyXDOaNw,404
-careamics/config/algorithms/care_algorithm_model.py,sha256=mdMDc0Vr0V7LZmksdjNDlRx3ofwy57IMXygY_vg6hPY,1175
-careamics/config/algorithms/n2n_algorithm_model.py,sha256=FO04TRecvMPikz_s2WupwODzi4g3x84g1HXRPgMAZWo,1015
-careamics/config/algorithms/n2v_algorithm_model.py,sha256=TBAUKeFxdRtomYhFrVqfq31hpOiNQO2YOogYzVVFknM,919
+careamics/config/algorithms/care_algorithm_model.py,sha256=-AEfzrA4HugYwMdDHqcc_i1H9kycXKS0YyRwT_MCCPo,951
+careamics/config/algorithms/n2n_algorithm_model.py,sha256=aWG6-YYB9T2e-QirxC-YijosO3QNA0rJRPIQZrorSi0,799
+careamics/config/algorithms/n2v_algorithm_model.py,sha256=b1M1ab9D8rhCG7RmhmaDi5rjHJjaQXebTdUEewJBnNg,709
 careamics/config/algorithms/unet_algorithm_model.py,sha256=OaBFVlhsb9YhF3f2x1ImazvfnZ4_DPWvYWihRwurkeg,2587
 careamics/config/algorithms/vae_algorithm_model.py,sha256=1ZrShUGHA7zbjSiCQwhUSv7l7Hr7MbpcLOw8ucM27p8,4680
 careamics/config/architectures/__init__.py,sha256=lYUz56R7LDqVQWQDLkLgJL8VtOyxc_ege1r4bXGEBqA,220
@@ -32,11 +32,11 @@ careamics/config/architectures/architecture_model.py,sha256=gXn4gdLrQP3bmTQxIhzk
 careamics/config/architectures/lvae_model.py,sha256=lwOiJYNUqPrZFl9SpPLYon77EiRbe2eI7pmpx45rO78,7606
 careamics/config/architectures/unet_model.py,sha256=HJJWf-wuYTv8KXMwikdjeB8htg1QOt0IyQbMuBt1LUI,3556
 careamics/config/data/__init__.py,sha256=ijFNSRKkKVF8fw6ym8kXq_wNhdwkWXxuNj2XKtD3KjE,218
-careamics/config/data/data_model.py,sha256=lSAIjpxuLaw1GMJ0rOHOZghYBwqWwlZf5sCphwAKMUc,11111
+careamics/config/data/data_model.py,sha256=Z-sy6bJ_JYT5fzbVwLOH1PnjRkVY0YAmNG5OnQAd-SQ,12635
 careamics/config/data/n2v_data_model.py,sha256=-n5cncmcrd4-KUSmEk8rXAONMC7sfbYfGmshVNuySCU,5915
 careamics/config/support/__init__.py,sha256=ktWvxbTkRXnQPS_N84l9E2B5kTZVdd64SIjsJIQKB-k,1041
 careamics/config/support/supported_activations.py,sha256=CqOWoziIK5jZZXJO7G7cGg3TTid1POqv8FXqxjXxyME,535
-careamics/config/support/supported_algorithms.py,sha256=ivLECrplTLjSUsa7AyT1n2aOo_WM3sMJJlW3OOT1fPk,846
+careamics/config/support/supported_algorithms.py,sha256=w6YzcIqGZ_bS85Tw1s7TEltBDXLt4SzgN3Tc6s19dGU,946
 careamics/config/support/supported_architectures.py,sha256=pOxvHOAIUkc7HCO0IIg4K22h-Ti5ErtcIkGOjN-zh1s,340
 careamics/config/support/supported_data.py,sha256=T_mDiWLFMVji_EpjBABUObAJcnv-XBnqp9XUZP37Tdk,2902
 careamics/config/support/supported_loggers.py,sha256=ubSOkGoYabGbm_jmyc1R3eFcvcP-sHmuyiBi_d3_wLg,197
@@ -52,7 +52,8 @@ careamics/config/transformations/transform_model.py,sha256=6UVbXnxm-LLZOQQ-ZBwWw
 careamics/config/transformations/transform_unions.py,sha256=uqlI8Nm827bKfMbDQLVhKFtT9e7TJ_zIYDBdHlOuQ1I,1137
 careamics/config/transformations/xy_flip_model.py,sha256=zU-uZ1b1zNZWckbho3onN-B7BHKhN7jbgbNZyRQhv2s,1025
 careamics/config/transformations/xy_random_rotate90_model.py,sha256=6sYKmtCLvz0SV1qZgBSHUTH-CUjwvHnohq1HyPntbyE,894
-careamics/config/validators/__init__.py,sha256=iv0nVI0W7j9DxFPwh0DjRCzM9P8oLQn4Gwi5rfuFrrI,180
+careamics/config/validators/__init__.py,sha256=zRrIse0O3ImwG97NphEupFVm3Ib9nEJhpNNrKGyDTps,423
+careamics/config/validators/model_validators.py,sha256=9OCdlf7rmndtTpmQ8COLaEjURYYmszic_RjY9mzS-k4,1941
 careamics/config/validators/validator_utils.py,sha256=NVkEOr5AQK4JXWNtmgeQgAaJOyieJNb5PHCjlcqNeew,2611
 careamics/dataset/__init__.py,sha256=31vop67zbtGesENEIig-LLw1q2lCydMFc_YWgfK2Yt4,547
 careamics/dataset/in_memory_dataset.py,sha256=MV_Vf4siIP-g7VKhxN4rU7MZXpaHKvfwr8ZXqk44Qhs,9958
@@ -87,10 +88,10 @@ careamics/file_io/write/tiff.py,sha256=tBGIgl-I1sMyBivgx-dOTBykXBODkgwPH8MT3_4KA
 careamics/lightning/__init__.py,sha256=ATCVAGnX08Ik4TxbIv0-cXb52UinR42JgvZh_GIMSpc,588
 careamics/lightning/lightning_module.py,sha256=3nzRcjv7dlWmWjoWmGaBV7D6d698xMp3XO7fpIrZhwA,22630
 careamics/lightning/predict_data_module.py,sha256=JNwujK6QwObSx6P25ghpGl2f2gGT3KVgYMTlonZzH20,12745
-careamics/lightning/train_data_module.py,sha256=7fti07y2TTV_Airl-D9FRTJf7AmsFmErSKnWUGLQE58,28699
+careamics/lightning/train_data_module.py,sha256=LeTyjNtAJw8nNiw2k6Ifuw0fAgppyZyRxyEGbDq30Fo,28309
 careamics/lightning/callbacks/__init__.py,sha256=eA5ltzYNzuO0uMEr1jG4wP01b0s29s5I03WGJ290qkw,312
 careamics/lightning/callbacks/hyperparameters_callback.py,sha256=u45knOZHwoVHz6yYfrnERQuozT_SfZ1OrKP0QjeU4EM,1495
-careamics/lightning/callbacks/progress_bar_callback.py,sha256=RilGAVUa90AlCLdooIGJF2cAcHAjGn24zKZiBmRRkwg,2438
+careamics/lightning/callbacks/progress_bar_callback.py,sha256=w-j_nk2ysyc4THKfwWbpkiKGeqNUpLGtm-8dYBgla2c,2443
 careamics/lightning/callbacks/prediction_writer_callback/__init__.py,sha256=ZVf3vaSU_NjSjrKbI24H0kK9WAiP9oKXfhP670EaWMo,548
 careamics/lightning/callbacks/prediction_writer_callback/file_path_utils.py,sha256=i4vGGiVLslafi-5iuvkAKzBgZ0BpwTTxSTo31oViFz4,1480
 careamics/lightning/callbacks/prediction_writer_callback/prediction_writer_callback.py,sha256=8HHUSKcG7G0FSCVPnpGQHLfpara5mnKAwsiiyWp2wzo,8210
@@ -104,8 +105,8 @@ careamics/losses/lvae/__init__.py,sha256=0FNtMLHrOMfagtWkaBdz1NTjyf2y0QLgysxJv5j
 careamics/losses/lvae/loss_utils.py,sha256=QxzA2N1TglR4H0X0uyTWWytDagE1lA9IB_TK1lms3ao,2720
 careamics/losses/lvae/losses.py,sha256=wHT1dx04BZ_OI-_S7cFQ5hFmMetm6FSnuZfwZBBtIpY,17977
 careamics/lvae_training/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-careamics/lvae_training/calibration.py,sha256=CvtmRC1s-2XHDjt1XG3RdHlPgCOaoCweJMKZYmDmgnU,6508
-careamics/lvae_training/eval_utils.py,sha256=RU1FYK9z1Hno6b6n7XyTTOu6An0MX0_6C8Og9FFqpyM,30949
+careamics/lvae_training/calibration.py,sha256=xHbiLcY2csYos3s7rRSqp7P7G-9wzULcSo1JfVzfIjE,7239
+careamics/lvae_training/eval_utils.py,sha256=7N1thslU4IU1lM1tGg3-wa8AFf5_R2lOSQ7ZZ91AUII,30030
 careamics/lvae_training/get_config.py,sha256=dwVfaQS7nzjQss0E1gGLUpQpjPcOWwLgIhbu3Z0I1rg,3068
 careamics/lvae_training/lightning_module.py,sha256=ryr7iHqCMzCl5esi6_gEcnKFDQkMrw0EXK9Zfgv1Nek,27186
 careamics/lvae_training/metrics.py,sha256=KTDAKhe3vh-YxzGibjtkIG2nnUyujbnwqX4xGwaRXwE,6718
@@ -113,10 +114,10 @@ careamics/lvae_training/train_lvae.py,sha256=lJEBlBGdISVkZBcEnPNRYgJ7VbapYzZHRaF
 careamics/lvae_training/train_utils.py,sha256=e-d4QsF-li8MmAPkAmB1daHpkuU16nBTnQFZYqpTjn4,3567
 careamics/lvae_training/dataset/__init__.py,sha256=dvdHHaRA9ZfOt_uOnXkYyra2_b0Wsxs8qmrze6zxJAE,377
 careamics/lvae_training/dataset/config.py,sha256=hGIggj5uOZrFBK54o9vii0sG5WGhF_E32URKIIzQMec,4342
-careamics/lvae_training/dataset/lc_dataset.py,sha256=xErygllUu6Q-PfPZ24sHf5_NP7YGHD2NVyzmDZgDd2U,10697
-careamics/lvae_training/dataset/multich_dataset.py,sha256=J1QWXlTSLZ40D3MFKw2StarZpq82sFeaHSXk7j48RAc,41608
+careamics/lvae_training/dataset/lc_dataset.py,sha256=r4PffRXzuTJ0tLWei4B3wq6f1Q34raaZQzZ0IQXi8OI,10762
+careamics/lvae_training/dataset/multich_dataset.py,sha256=5yMC6bgEIYHBsjFj5gXlc68xJQz8A05TYbYfOo-TdUQ,41672
 careamics/lvae_training/dataset/multifile_dataset.py,sha256=hJBs6iBrf_FcyUYzg8rDjvKEICHxDYyXVOj-5L0F6FE,10273
-careamics/lvae_training/dataset/types.py,sha256=zfi-zMmMe7GTaX-MYrYfVbAM4D2LPHrJkmqSFl9ulxA,632
+careamics/lvae_training/dataset/types.py,sha256=SQ99hV9R3iwrRLJs-aRkL3OlmrWWkCrca2JqkntoWZs,633
 careamics/lvae_training/dataset/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 careamics/lvae_training/dataset/utils/data_utils.py,sha256=8PvRPqSbYHPCl87cycZHxXIFOT_EoBV-8XCt3ZLh36s,3125
 careamics/lvae_training/dataset/utils/empty_patch_fetcher.py,sha256=OFjeqhZ6vFULJsF5tnoByhEhE8aLHujFToU_yyqMCP4,2266
@@ -137,10 +138,10 @@ careamics/models/model_factory.py,sha256=GWbouERvEfHj_BrpKHYgrPAj8dpdoh1R-X--Jt0
 careamics/models/unet.py,sha256=9m8GxsTXX9c0mC-eVe2ZXQn2afose1CG6Z8vIhELb7I,14308
 careamics/models/lvae/__init__.py,sha256=6dT6uqgT__V08EjoTGxXguTbTkySZmByS9J2Bj6WWLM,53
 careamics/models/lvae/layers.py,sha256=UPxZiZjgnBnPs_wdSzcP-_s17MEw4P1CoIZzn4OdUA0,57944
-careamics/models/lvae/likelihoods.py,sha256=SHsaZZTjGg8TO6JkvjdQOZtu8CCOvlSxtqRBZhrGXKk,12098
-careamics/models/lvae/lvae.py,sha256=AWll857rAnlvjTom5CX0CpbEcf-ci_Icoz5wFKVLu5E,34220
-careamics/models/lvae/noise_models.py,sha256=dFWM9DDJ7qzsyiT8sDWR8THbEiZmu3XnW5UzGJl7Mck,21834
-careamics/models/lvae/stochastic.py,sha256=019M6BBR6GtYjUVF6pcOTOsfEAYeg0vclz55V6Fl4yY,16588
+careamics/models/lvae/likelihoods.py,sha256=qRYRewQv6PqzJO-7nDnFkK86-R8dI4HSp1_ilRSc2I4,12233
+careamics/models/lvae/lvae.py,sha256=Jlw3mxVCxMDtjMvBWI9C9javHHyrngm8RfTYPsYhbI4,34767
+careamics/models/lvae/noise_models.py,sha256=lpSygXsJmD_erP0V72u9i5CX51wpopLNCH_YjmEL29s,24095
+careamics/models/lvae/stochastic.py,sha256=wiTrLBSYwOvsF1araKxUHy1CHp1mdH9bazctVo0NchA,16628
 careamics/models/lvae/utils.py,sha256=EE3paHu3vhCaqfOrGypzUsImZJO94uBhx8q6kZ-R36o,11516
 careamics/prediction_utils/__init__.py,sha256=k5hsPGY8FOkwIT0fQgrUz7fVCH2NlwuOdZiISdXjEWg,270
 careamics/prediction_utils/lvae_prediction.py,sha256=ZwPFCSeUGsULIMoMQWRYKHfLFaDm7UKyGaUMVfSUqfs,6210
@@ -163,14 +164,15 @@ careamics/utils/base_enum.py,sha256=bz1D8mDx5V5hdnJ3WAzJXWHJTbgwAky5FprUt9F5cMA,
 careamics/utils/context.py,sha256=SoTZfzG6fO4SDOGHOTL2Xlm1n1CSgb9B57GVhrEkFls,1436
 careamics/utils/lightning_utils.py,sha256=DMMmqx-AlNtddBCqm8b_W3h09qUetz32OMPhdDieFwg,1769
 careamics/utils/logging.py,sha256=5U4VsQ4m4OajtirLH6qUjrM1CAc-oXeCsd6JyROjkWE,10337
-careamics/utils/metrics.py,sha256=yAoCvrZ1kQx-kT9xdTBYz-oh0I52ef6uBnw8qgzpwn8,10318
+careamics/utils/metrics.py,sha256=i9TQNzVF6lUL9c6OwRZFFDhelZfinkEDpWSCKeduscc,10853
 careamics/utils/path_utils.py,sha256=8AugiG5DOmzgSnTCJI8vypXaPE0XhnR-9pzeiFUZ-0I,554
+careamics/utils/plotting.py,sha256=cea1GQB932j2UA3IQZnh-0EenQdnjzPOFoGoFKJ4how,2518
 careamics/utils/ram.py,sha256=tksyn8dVX_iJXmrDZDGub32hFZWIaNxnMheO5G1p43I,244
 careamics/utils/receptive_field.py,sha256=Y2h4c8S6glX3qcx5KHDmO17Kkuyey9voxfoXyqcAfiM,3296
 careamics/utils/serializers.py,sha256=mILUhz75IMpGKnEzcYu9hlOPG8YIiIW09fk6eZM7Y8k,1427
 careamics/utils/torch_utils.py,sha256=_Cf3HdlIRl5hxfpUg9aofCSlcW7GSsIJxsbSORXko0U,3010
-careamics-0.0.6.dist-info/METADATA,sha256=Hz6RQlh5szAGllr7baFnc86U_sSC2fCjvU4FhjmhYMk,3898
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