stacklp 0.1.0__tar.gz

stacklp-0.1.0/PKG-INFO

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+Metadata-Version: 2.3
+Name: stacklp
+Version: 0.1.0
+Summary: This library contains various functions to manage stack of images.
+Requires-Dist: arrlp
+Requires-Dist: corelp
+Requires-Dist: numpy
+Requires-Dist: tifffile
+Requires-Python: >=3.12
+Description-Content-Type: text/markdown
+
+# stackLP
+
+```text
+Author        : Lancelot PINCET
+GitHub        : https://github.com/LancelotPincet/stackLP
+HTTPS         : https://github.com/LancelotPincet/stackLP.git
+SSH           : git@github.com:LancelotPincet/stackLP.git
+PyPI          : https://pypi.org/project/stackLP
+Docs          : https://stackLP.readthedocs.io
+```
+
+**This library contains various functions to manage stack of images.**
+
+stackLP is available on [PyPI](https://pypi.org/project/stackLP) for pip installs.
+For more information, do not hesitate to consult the [Documentation](https://stackLP.readthedocs.io).
+
+---
+
+## MIT License
+
+<details>
+<summary>details</summary>
+
+Intellectual property behind this Library is protected via an [MIT license](LICENSE). This means everyone can *freely* use it in a personnal, academic or commercial manner, if they **keep the copyright name** at the top of the codes.
+
+The library can be redistributed, *with or without modifications*, in open or closed projects. However the **MIT license must be conserved**. For example in a commercial closed project, this means the **copyright and license must be visible somewhere**, like in the documentation or credits.
+
+The license also explains that the **code performances are not warrantied**, and you are responsible for how you are using it. For more information on your rights and obligations please refer to [descriptive websites](https://en.wikipedia.org/wiki/MIT_License), or contact author for approvales.
+
+</details>

stacklp-0.1.0/README.md

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+# stackLP
+
+```text
+Author        : Lancelot PINCET
+GitHub        : https://github.com/LancelotPincet/stackLP
+HTTPS         : https://github.com/LancelotPincet/stackLP.git
+SSH           : git@github.com:LancelotPincet/stackLP.git
+PyPI          : https://pypi.org/project/stackLP
+Docs          : https://stackLP.readthedocs.io
+```
+
+**This library contains various functions to manage stack of images.**
+
+stackLP is available on [PyPI](https://pypi.org/project/stackLP) for pip installs.
+For more information, do not hesitate to consult the [Documentation](https://stackLP.readthedocs.io).
+
+---
+
+## MIT License
+
+<details>
+<summary>details</summary>
+
+Intellectual property behind this Library is protected via an [MIT license](LICENSE). This means everyone can *freely* use it in a personnal, academic or commercial manner, if they **keep the copyright name** at the top of the codes.
+
+The library can be redistributed, *with or without modifications*, in open or closed projects. However the **MIT license must be conserved**. For example in a commercial closed project, this means the **copyright and license must be visible somewhere**, like in the documentation or credits.
+
+The license also explains that the **code performances are not warrantied**, and you are responsible for how you are using it. For more information on your rights and obligations please refer to [descriptive websites](https://en.wikipedia.org/wiki/MIT_License), or contact author for approvales.
+
+</details>

stacklp-0.1.0/pyproject.toml

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+[project]
+name = "stacklp"
+version = "0.1.0"
+description = "This library contains various functions to manage stack of images."
+readme = "README.md"
+requires-python = ">=3.12"
+dependencies = [ "arrlp", "corelp", "numpy", "tifffile",]
+
+[build-system]
+requires = [ "uv_build",]
+build-backend = "uv_build"
+
+[dependency-groups]
+tests = [ "pytest",]
+docs = [ "sphinx", "sphinx-design", "sphinx-rtd-theme", "toml",]
+anaconda = [ "ipykernel", "spyder-kernels",]
+
+[tool.uv]
+required-environments = [ "sys_platform == 'linux' and platform_machine == 'x86_64'", "sys_platform == 'win32' and (platform_machine == 'AMD64' or platform_machine == 'x86_64')",]
+
+[tool.uv.sources.arrlp]
+workspace = true
+
+[tool.uv.sources.corelp]
+workspace = true

stacklp-0.1.0/src/stacklp/__init__.py

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+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+# Date          : 2026-02-10
+# Author        : Lancelot PINCET
+# GitHub        : https://github.com/LancelotPincet
+# Library       : stackLP
+
+"""
+This library contains various functions to manage stack of images.
+"""
+
+
+
+# %% Source import
+sources = {
+'appendtif': 'stacklp.modules.appendtif_LP.appendtif',
+'remove_bleach': 'stacklp.modules.remove_bleach_LP.remove_bleach'
+}
+
+
+
+# %% Lazy imports
+from corelp import getmodule
+__getattr__, __all__ = getmodule(sources)

stacklp-0.1.0/src/stacklp/modules/appendtif_LP/_functions/__template__.py

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+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+# Author        : Lancelot PINCET
+# GitHub        : https://github.com/LancelotPincet
+
+
+
+# %% Libraries
+
+
+
+
+# %% Function
+def temp(**kwargs) :
+    '''
+    TODO
+    '''
+
+    print('Hello world!')

stacklp-0.1.0/src/stacklp/modules/appendtif_LP/appendtif.py

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+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+# Date          : 2026-02-10
+# Author        : Lancelot PINCET
+# GitHub        : https://github.com/LancelotPincet
+# Library       : stackLP
+# Module        : appendtif
+
+"""
+This function appends a stack to a tif file.
+"""
+
+
+
+# %% Libraries
+import tifffile as tiff
+import os
+from pathlib import Path
+
+
+
+# %% Function
+def appendtif(tif:str, stack, *, photometric='minisblack', flush=False) :
+    '''
+    This function appends a stack to a tif file.
+    
+    Parameters
+    ----------
+    tif : str or tiff.TiffWriter
+        path to file or TiffWritter of preopened file.
+    stack : array
+        image stack to add to tiff file
+    photometric : str
+        image mode ['minisblack', 'miniswhite', 'rgb']
+    flush : str
+        True to flush buffered data to disk when using TiffWritter
+
+    Examples
+    --------
+    >>> from stacklp import appendtif
+    ...
+    >>> appendtif() # TODO
+    '''
+
+    if isinstance(tif, str) or isinstance(tif, type(Path(''))) :
+        with tiff.TiffWriter(Path(tif), bigtiff=True, append=True) as tif :
+            return appendtif(tif, stack, photometric=photometric, flush=flush)
+    else :
+        tif.write(stack, photometric=photometric, metadata=None, contiguous=False)
+        if flush :
+            fd = tif._fh.fileno()
+            os.fsync(fd)  # Force OS to write buffered data to disk
+
+
+
+# %% Test function run
+if __name__ == "__main__":
+    from corelp import test
+    test(__file__)

stacklp-0.1.0/src/stacklp/modules/appendtif_LP/test_appendtif.py

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+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+# Date          : 2026-02-10
+# Author        : Lancelot PINCET
+# GitHub        : https://github.com/LancelotPincet
+# Library       : template_[library]
+# Module        : appendtif
+
+"""
+This file allows to test appendtif
+
+appendtif : This function appends a stack to a tif file.
+"""
+
+
+
+# %% Libraries
+from corelp import print, debug
+import pytest
+from template_[lowerlib] import appendtif
+debug_folder = debug(__file__)
+
+
+
+# %% Function test
+def test_function() :
+    '''
+    Test appendtif function
+    '''
+    print('Hello world!')
+
+
+
+# %% Instance fixture
+@pytest.fixture()
+def instance() :
+    '''
+    Create a new instance at each test function
+    '''
+    return appendtif()
+
+def test_instance(instance) :
+    '''
+    Test on fixture
+    '''
+    pass
+
+
+# %% Returns test
+@pytest.mark.parametrize("args, kwargs, expected, message", [
+    #([], {}, None, ""),
+    ([], {}, None, ""),
+])
+def test_returns(args, kwargs, expected, message) :
+    '''
+    Test appendtif return values
+    '''
+    assert appendtif(*args, **kwargs) == expected, message
+
+
+
+# %% Error test
+@pytest.mark.parametrize("args, kwargs, error, error_message", [
+    #([], {}, None, ""),
+    ([], {}, None, ""),
+])
+def test_errors(args, kwargs, error, error_message) :
+    '''
+    Test appendtif error values
+    '''
+    with pytest.raises(error, match=error_message) :
+        appendtif(*args, **kwargs)
+
+
+
+# %% Test function run
+if __name__ == "__main__":
+    from corelp import test
+    test(__file__)

stacklp-0.1.0/src/stacklp/modules/remove_bleach_LP/_functions/__template__.py

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+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+# Author        : Lancelot PINCET
+# GitHub        : https://github.com/LancelotPincet
+
+
+
+# %% Libraries
+
+
+
+
+# %% Function
+def temp(**kwargs) :
+    '''
+    TODO
+    '''
+
+    print('Hello world!')

stacklp-0.1.0/src/stacklp/modules/remove_bleach_LP/remove_bleach.py

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+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+# Date          : 2026-02-10
+# Author        : Lancelot PINCET
+# GitHub        : https://github.com/LancelotPincet
+# Library       : stackLP
+# Module        : remove_bleach
+
+"""
+This function normalizes frames to avoid bleaching effects in time.
+"""
+
+
+
+# %% Libraries
+from arrlp import img_correlate, xp
+
+
+
+# %% Function
+def remove_bleach(stack, *, out=None, window=10, cuda=False, parallel=False, print=None) :
+    '''
+    This function normalizes frames to avoid bleaching effects in time.
+    
+    Parameters
+    ----------
+    stack : array
+        stack to correct.
+    out : array
+        stack to return.
+    window : int
+        percent of image to define kernel.
+    cuda : bool
+        True to apply cuda.
+    parallel : bool
+        True to apply parallel.
+    print : object
+        print object to print status.
+
+    Returns
+    -------
+    nobleach : array
+        stack copy without bleach.
+
+    Examples
+    --------
+    >>> from stacklp import remove_bleach
+    ...
+    >>> remove_bleach(stack, window=10)
+    '''
+
+    y, x = stack.shape[1], stack.shape[2]
+    channels = stack.ndim == 4
+    _xp = xp(cuda)
+    stack = _xp.asarray(stack)
+
+    # Correlation
+    if print is not None : print('Applying correlations to remove bleach:')
+    window = min(int(y * window / 100), int(x * window / 100))
+    out = img_correlate(stack, window=window, cuda=cuda, parallel=parallel, stacks=True, channels=channels, out=out, print=print)
+    if print is not None : print('Done correlations.')
+
+    # Normalizing
+    if print is not None : print('Normalizing...')
+    slice_mean = out.mean(axis=0)
+    for pos in range(len(stack)) :
+        out[pos] = stack[pos] / out[pos] * slice_mean
+    if print is not None : print('Done normalizing.')
+
+    return out
+
+
+
+# %% Test function run
+if __name__ == "__main__":
+    from corelp import test
+    test(__file__)

stacklp-0.1.0/src/stacklp/modules/remove_bleach_LP/test_remove_bleach.py

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+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+# Date          : 2026-02-10
+# Author        : Lancelot PINCET
+# GitHub        : https://github.com/LancelotPincet
+# Library       : template_[library]
+# Module        : remove_bleach
+
+"""
+This file allows to test remove_bleach
+
+remove_bleach : This function normalizes frames to avoid bleaching effects in time.
+"""
+
+
+
+# %% Libraries
+from corelp import print, debug
+import pytest
+from template_[lowerlib] import remove_bleach
+debug_folder = debug(__file__)
+
+
+
+# %% Function test
+def test_function() :
+    '''
+    Test remove_bleach function
+    '''
+    print('Hello world!')
+
+
+
+# %% Instance fixture
+@pytest.fixture()
+def instance() :
+    '''
+    Create a new instance at each test function
+    '''
+    return remove_bleach()
+
+def test_instance(instance) :
+    '''
+    Test on fixture
+    '''
+    pass
+
+
+# %% Returns test
+@pytest.mark.parametrize("args, kwargs, expected, message", [
+    #([], {}, None, ""),
+    ([], {}, None, ""),
+])
+def test_returns(args, kwargs, expected, message) :
+    '''
+    Test remove_bleach return values
+    '''
+    assert remove_bleach(*args, **kwargs) == expected, message
+
+
+
+# %% Error test
+@pytest.mark.parametrize("args, kwargs, error, error_message", [
+    #([], {}, None, ""),
+    ([], {}, None, ""),
+])
+def test_errors(args, kwargs, error, error_message) :
+    '''
+    Test remove_bleach error values
+    '''
+    with pytest.raises(error, match=error_message) :
+        remove_bleach(*args, **kwargs)
+
+
+
+# %% Test function run
+if __name__ == "__main__":
+    from corelp import test
+    test(__file__)