careamics 0.0.1__py3-none-any.whl → 0.1.0rc2__py3-none-any.whl

careamics/utils/validators.py

@@ -0,0 +1,170 @@
+"""
+Validator functions.
+
+These functions are used to validate dimensions and axes of inputs.
+"""
+from typing import List
+
+import numpy as np
+
+AXES = "STCZYX"
+
+
+def check_axes_validity(axes: str) -> None:
+    """
+    Sanity check on axes.
+
+    The constraints on the axes are the following:
+    - must be a combination of 'STCZYX'
+    - must not contain duplicates
+    - must contain at least 2 contiguous axes: X and Y
+    - must contain at most 4 axes
+    - cannot contain both S and T axes
+    - C is currently not allowed
+
+    Parameters
+    ----------
+    axes : str
+        Axes to validate.
+    """
+    _axes = axes.upper()
+
+    # Minimum is 2 (XY) and maximum is 4 (TZYX)
+    if len(_axes) < 2 or len(_axes) > 4:
+        raise ValueError(
+            f"Invalid axes {axes}. Must contain at least 2 and at most 4 axes."
+        )
+
+    # all characters must be in REF_AXES = 'STCZYX'
+    if not all(s in AXES for s in _axes):
+        raise ValueError(f"Invalid axes {axes}. Must be a combination of {AXES}.")
+
+    # check for repeating characters
+    for i, s in enumerate(_axes):
+        if i != _axes.rfind(s):
+            raise ValueError(
+                f"Invalid axes {axes}. Cannot contain duplicate axes"
+                f" (got multiple {axes[i]})."
+            )
+
+    # currently no implementation for C
+    if "C" in _axes:
+        raise NotImplementedError("Currently, C axis is not supported.")
+
+    # prevent S and T axes at the same time
+    if "T" in _axes and "S" in _axes:
+        raise NotImplementedError(
+            f"Invalid axes {axes}. Cannot contain both S and T axes."
+        )
+
+    # prior: X and Y contiguous (#FancyComments)
+    # right now the next check is invalidating this, but in the future, we might
+    # allow random order of axes (or at least XY and YX)
+    if "XY" not in _axes and "YX" not in _axes:
+        raise ValueError(f"Invalid axes {axes}. X and Y must be contiguous.")
+
+    # check that the axes are in the right order
+    for i, s in enumerate(_axes):
+        if i < len(_axes) - 1:
+            index_s = AXES.find(s)
+            index_next = AXES.find(_axes[i + 1])
+
+            if index_s > index_next:
+                raise ValueError(
+                    f"Invalid axes {axes}. Axes must be in the order {AXES}."
+                )
+
+
+def add_axes(input_array: np.ndarray, axes: str) -> np.ndarray:
+    """
+    Add missing axes to the input, typically batch and channel.
+
+    This method validates the axes first. Then it inspects the input array and add
+    missing dimensions if necessary.
+
+    Parameters
+    ----------
+    input_array : np.ndarray
+        Input array.
+    axes : str
+        Axes to add.
+
+    Returns
+    -------
+    np.ndarray
+        Array with new singleton axes.
+    """
+    # validate axes
+    check_axes_validity(axes)
+
+    # is 3D
+    is_3D = "Z" in axes
+
+    # number of dims
+    n_dims = 5 if is_3D else 4
+
+    # array of dim 2, 3 or 4
+    if len(input_array.shape) < n_dims:
+        if "S" not in axes and "T" not in axes:
+            input_array = input_array[np.newaxis, ...]
+
+        # still missing C dimension
+        if len(input_array.shape) < n_dims:
+            input_array = input_array[:, np.newaxis, ...]
+
+    return input_array
+
+
+def check_tiling_validity(tile_shape: List[int], overlaps: List[int]) -> None:
+    """
+    Check that the tiling parameters are valid.
+
+    Parameters
+    ----------
+    tile_shape : List[int]
+        Shape of the tiles.
+    overlaps : List[int]
+        Overlap between tiles.
+
+    Raises
+    ------
+    ValueError
+        If one of the parameters is None.
+    ValueError
+        If one of the element is zero.
+    ValueError
+        If one of the element is non-divisible by 2.
+    ValueError
+        If the number of elements in `overlaps` and `tile_shape` is different.
+    ValueError
+        If one of the overlaps is larger than the corresponding tile shape.
+    """
+    # cannot be None
+    if tile_shape is None or overlaps is None:
+        raise ValueError(
+            "Cannot use tiling without specifying `tile_shape` and "
+            "`overlaps`, make sure they have been correctly specified."
+        )
+
+    # non-zero and divisible by two
+    for dims_list in [tile_shape, overlaps]:
+        for dim in dims_list:
+            if dim < 1:
+                raise ValueError(f"Entry must be non-null positive (got {dim}).")
+
+            if dim % 2 != 0:
+                raise ValueError(f"Entry must be divisible by 2 (got {dim}).")
+
+    # same length
+    if len(overlaps) != len(tile_shape):
+        raise ValueError(
+            f"Overlaps ({len(overlaps)}) and tile shape ({len(tile_shape)}) must "
+            f"have the same number of dimensions."
+        )
+
+    # overlaps smaller than tile shape
+    for overlap, tile_dim in zip(overlaps, tile_shape):
+        if overlap >= tile_dim:
+            raise ValueError(
+                f"Overlap ({overlap}) must be smaller than tile shape ({tile_dim})."
+            )

careamics/utils/wandb.py

@@ -0,0 +1,121 @@
+"""
+A WandB logger for CAREamics.
+
+Implements a WandB class for use within the Engine.
+"""
+import sys
+from pathlib import Path
+from typing import Dict, Union
+
+import torch
+import wandb
+
+from careamics.config import Configuration
+
+
+def is_notebook() -> bool:
+    """
+    Check if the code is executed from a notebook or a qtconsole.
+
+    Returns
+    -------
+    bool
+        True if the code is executed from a notebooks, False otherwise.
+    """
+    try:
+        from IPython import get_ipython
+
+        shell = get_ipython().__class__.__name__
+        if shell == "ZMQInteractiveShell":
+            return True  # Jupyter notebook or qtconsole
+        else:
+            return False
+    except (NameError, ModuleNotFoundError):
+        return False
+
+
+class WandBLogging:
+    """
+    WandB logging class.
+
+    Parameters
+    ----------
+    experiment_name : str
+        Name of the experiment.
+    log_path : Path
+        Path in which to save the WandB log.
+    config : Configuration
+        Configuration of the model.
+    model_to_watch : torch.nn.Module
+        Model.
+    save_code : bool, optional
+        Whether to save the code, by default True.
+    """
+
+    def __init__(
+        self,
+        experiment_name: str,
+        log_path: Path,
+        config: Configuration,
+        model_to_watch: torch.nn.Module,
+        save_code: bool = True,
+    ):
+        """
+        Constructor.
+
+        Parameters
+        ----------
+        experiment_name : str
+            Name of the experiment.
+        log_path : Path
+            Path in which to save the WandB log.
+        config : Configuration
+            Configuration of the model.
+        model_to_watch : torch.nn.Module
+            Model.
+        save_code : bool, optional
+            Whether to save the code, by default True.
+        """
+        self.run = wandb.init(
+            project="careamics-restoration",
+            dir=log_path,
+            name=experiment_name,
+            config=config.model_dump() if config else None,
+            # save_code=save_code,
+        )
+        if model_to_watch:
+            wandb.watch(model_to_watch, log="all", log_freq=1)
+        if save_code:
+            if is_notebook():
+                # Get all sys path and select the root
+                code_path = Path([p for p in sys.path if "caremics" in p][-1]).parent
+            else:
+                code_path = Path("../")
+            self.log_code(code_path)
+
+    def log_metrics(self, metric_dict: Dict) -> None:
+        """
+        Log metrics to wandb.
+
+        Parameters
+        ----------
+        metric_dict : Dict
+            New metrics entry.
+        """
+        self.run.log(metric_dict, commit=True)
+
+    def log_code(self, code_path: Union[str, Path]) -> None:
+        """
+        Log code to wandb.
+
+        Parameters
+        ----------
+        code_path : Union[str, Path]
+            Path to the code.
+        """
+        self.run.log_code(
+            root=code_path,
+            include_fn=lambda path: path.endswith(".py")
+            or path.endswith(".yml")
+            or path.endswith(".yaml"),
+        )

careamics-0.1.0rc2.dist-info/METADATA

@@ -0,0 +1,81 @@
+Metadata-Version: 2.1
+Name: careamics
+Version: 0.1.0rc2
+Summary: Toolbox for running N2V and friends.
+Project-URL: homepage, https://careamics.github.io/
+Project-URL: repository, https://github.com/CAREamics/careamics
+Author-email: Igor Zubarev <igor.zubarev@fht.org>, Joran Deschamps <joran.deschamps@fht.org>, Vera Galinova <vera.galinova@fht.org>, Mehdi Seifi <mehdi.seifi@fht.org>
+License: BSD-3-Clause
+License-File: LICENSE
+Classifier: Development Status :: 3 - Alpha
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Typing :: Typed
+Requires-Python: >=3.8
+Requires-Dist: bioimageio-core
+Requires-Dist: pydantic>=2.0
+Requires-Dist: pyyaml
+Requires-Dist: scikit-image
+Requires-Dist: tifffile
+Requires-Dist: torch
+Requires-Dist: torchvision
+Requires-Dist: zarr
+Provides-Extra: all
+Requires-Dist: careamics-portfolio; extra == 'all'
+Requires-Dist: ipython; extra == 'all'
+Requires-Dist: itkwidgets; extra == 'all'
+Requires-Dist: jupyter; extra == 'all'
+Requires-Dist: pre-commit; extra == 'all'
+Requires-Dist: pytest; extra == 'all'
+Requires-Dist: pytest-cov; extra == 'all'
+Requires-Dist: torchsummary; extra == 'all'
+Requires-Dist: wandb; extra == 'all'
+Provides-Extra: dev
+Requires-Dist: pre-commit; extra == 'dev'
+Requires-Dist: pytest; extra == 'dev'
+Requires-Dist: pytest-cov; extra == 'dev'
+Provides-Extra: notebooks
+Requires-Dist: careamics-portfolio; extra == 'notebooks'
+Requires-Dist: ipython; extra == 'notebooks'
+Requires-Dist: itkwidgets; extra == 'notebooks'
+Requires-Dist: jupyter; extra == 'notebooks'
+Requires-Dist: torchsummary; extra == 'notebooks'
+Requires-Dist: wandb; extra == 'notebooks'
+Provides-Extra: test
+Requires-Dist: pytest; extra == 'test'
+Requires-Dist: pytest-cov; extra == 'test'
+Requires-Dist: wandb; extra == 'test'
+Description-Content-Type: text/markdown
+
+<p align="center">
+  <a href="https://careamics.github.io/">
+    <img src="https://raw.githubusercontent.com/CAREamics/.github/main/profile/images/banner_careamics.png">
+  </a>
+</p>
+
+# CAREamics
+
+[![License](https://img.shields.io/pypi/l/careamics.svg?color=green)](https://github.com/CAREamics/careamics/blob/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/careamics.svg?color=green)](https://pypi.org/project/careamics)
+[![Python Version](https://img.shields.io/pypi/pyversions/careamics.svg?color=green)](https://python.org)
+[![CI](https://github.com/CAREamics/careamics/actions/workflows/ci.yml/badge.svg)](https://github.com/CAREamics/careamics/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/CAREamics/careamics/branch/main/graph/badge.svg)](https://codecov.io/gh/CAREamics/careamics)
+
+## Installation
+
+``` bash
+pip install careamics
+```
+For more details on the options please follow the installation [guide](https://careamics.github.io/installation/).
+
+<!-- 
+## Contributing
+
+## Citing us 
+
+-->

careamics-0.1.0rc2.dist-info/RECORD

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{careamics-0.0.1.dist-info → careamics-0.1.0rc2.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: hatchling 1.17.0
+Generator: hatchling 1.21.0
 Root-Is-Purelib: true
 Tag: py3-none-any

{careamics-0.0.1.dist-info → careamics-0.1.0rc2.dist-info}/licenses/LICENSE

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2023, Jug lab
+Copyright (c) 2023, CAREamics contributors
 
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are met:

careamics-0.0.1.dist-info/METADATA

@@ -1,46 +0,0 @@
-Metadata-Version: 2.1
-Name: careamics
-Version: 0.0.1
-Summary: CAREamics
-Project-URL: homepage, https://careamics.github.io/
-Project-URL: repository, https://github.com/CAREamics/careamics
-Author-email: Igor Zubarev <igor.zubarev@fht.org>, Joran Deschamps <joran.deschamps@fht.org>
-License: BSD-3-Clause
-License-File: LICENSE
-Classifier: Development Status :: 3 - Alpha
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Requires-Python: >=3.8
-Provides-Extra: dev
-Requires-Dist: black; extra == 'dev'
-Requires-Dist: ipython; extra == 'dev'
-Requires-Dist: mypy; extra == 'dev'
-Requires-Dist: pdbpp; extra == 'dev'
-Requires-Dist: rich; extra == 'dev'
-Requires-Dist: ruff; extra == 'dev'
-Provides-Extra: test
-Requires-Dist: pytest; extra == 'test'
-Requires-Dist: pytest-cov; extra == 'test'
-Description-Content-Type: text/markdown
-
-<p align="center">
-  <a href="https://careamics.github.io/">
-    <img src="https://github.com/CAREamics/.github/blob/main/profile/images/banner_careamics.png">
-  </a>
-</p>
-
-
-[![License](https://img.shields.io/pypi/l/careamics.svg?color=green)](https://github.com/CAREamics/careamics/raw/main/LICENSE)
-[![PyPI](https://img.shields.io/pypi/v/careamics.svg?color=green)](https://pypi.org/project/careamics)
-[![Python Version](https://img.shields.io/pypi/pyversions/careamics.svg?color=green)](https://python.org)
-[![CI](https://github.com/CAREamics/careamics/actions/workflows/ci.yml/badge.svg)](https://github.com/CAREamics/careamics/actions/workflows/ci.yml)
-[![codecov](https://codecov.io/gh/CAREamics/careamics/branch/main/graph/badge.svg)](https://codecov.io/gh/CAREamics/careamics)
-
-
-Stay tuned for DL goodies with CAREamics!
-
-Currently, this version is a place-holder, next version will contain the 
-first usable algorithms, as well as examples.

careamics-0.0.1.dist-info/RECORD

@@ -1,6 +0,0 @@
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