pykrait 0.1.0__tar.gz

pykrait-0.1.0/.gitignore

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pykrait-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2025 Pentabyteman
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

pykrait-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: pykrait
+Version: 0.1.0
+Summary: Python Calcium Recording Analysis and Inference Toolbox
+Author-email: Pentabyteman <22663502+Pentabyteman@users.noreply.github.com>
+License: MIT
+License-File: LICENSE
+Requires-Python: >=3.10
+Requires-Dist: aicspylibczi>=3.1.1
+Requires-Dist: cellpose>=4.0.5
+Requires-Dist: dask>=2025.5.1
+Requires-Dist: fsspec>=2022.8.0
+Requires-Dist: imagecodecs>=2025.3.30
+Requires-Dist: lxml>=5.4.0
+Requires-Dist: matplotlib>=3.10.3
+Requires-Dist: numpy<2
+Requires-Dist: ome-types>=0.5.3
+Requires-Dist: ome-zarr>=0.10.2
+Requires-Dist: pip>=25.1.1
+Requires-Dist: pydantic<2
+Requires-Dist: pyyaml>=6.0.2
+Requires-Dist: resource-backed-dask-array>=0.1.0
+Requires-Dist: scikit-image>=0.25.2
+Requires-Dist: scipy>=1.15.3
+Requires-Dist: tifffile<2023.3.15,>=2021.8.30
+Requires-Dist: wrapt>=1.17.2
+Requires-Dist: xarray>2025
+Requires-Dist: xmlschema>=4.0.1
+Requires-Dist: zarr<2.16.0,>=2.6
+Description-Content-Type: text/markdown
+
+# pyKrait - Python Calcium Recording Analysis and Inference Toolbox
+
+![Logo](docs/logo.png)
+
+## Overview
+
+**pyKrait** is a Python package designed to facilitate automated analysis of calcium imaging data. 
+
+## Installation
+
+```bash
+pip install pykrait
+```
+
+## Documentation
+
+See the [docs](docs/) folder for detailed guides and API reference.
+
+## License
+
+This project is licensed under the GNU Lesser General Public License (GLP). See the [LICENSE](LICENSE) file for details.
+
+## Contributing
+
+Contributions are welcome! Please open issues or submit pull requests.

pykrait-0.1.0/README.md

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+# pyKrait - Python Calcium Recording Analysis and Inference Toolbox
+
+![Logo](docs/logo.png)
+
+## Overview
+
+**pyKrait** is a Python package designed to facilitate automated analysis of calcium imaging data. 
+
+## Installation
+
+```bash
+pip install pykrait
+```
+
+## Documentation
+
+See the [docs](docs/) folder for detailed guides and API reference.
+
+## License
+
+This project is licensed under the GNU Lesser General Public License (GLP). See the [LICENSE](LICENSE) file for details.
+
+## Contributing
+
+Contributions are welcome! Please open issues or submit pull requests.

pykrait-0.1.0/pyproject.toml

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+[project]
+name = "pykrait"
+version = "0.1.0"
+description = "Python Calcium Recording Analysis and Inference Toolbox"
+readme = { file = "README.md", content-type = "text/markdown" }
+license = { text = "MIT" }
+authors = [
+    { name = "Pentabyteman", email = "22663502+Pentabyteman@users.noreply.github.com" }
+]
+requires-python = ">=3.10"
+dependencies = [
+    "aicspylibczi>=3.1.1",
+    "cellpose>=4.0.5",
+    "dask>=2025.5.1",
+    "fsspec>=2022.8.0",
+    "imagecodecs>=2025.3.30",
+    "lxml>=5.4.0",
+    "matplotlib>=3.10.3",
+    "numpy<2",
+    "ome-types>=0.5.3",
+    "ome-zarr>=0.10.2",
+    "pip>=25.1.1",
+    "pydantic<2",
+    "pyyaml>=6.0.2",
+    "resource-backed-dask-array>=0.1.0",
+    "scikit-image>=0.25.2",
+    "scipy>=1.15.3",
+    "tifffile>=2021.8.30,<2023.3.15",
+    "wrapt>=1.17.2",
+    "xarray>2025",
+    "xmlschema>=4.0.1",
+    "zarr>=2.6,<2.16.0",
+]
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[tool.hatch.build.targets.sdist]
+include = ["src/**", "pyproject.toml", "README.md"]
+
+[tool.hatch.build.targets.wheel]
+only-include = ["src"]
+
+[tool.hatch.metadata]
+allow-direct-references = true
+
+[tool.pytest.ini_options]
+pythonpath = ["src"]
+testpaths = ["tests"]
+
+[tool.coverage.run]
+source = ["stavromueller_beta"]
+
+[tool.coverage.report]
+show_missing = true
+skip_covered = true
+
+[dependency-groups]
+dev = [
+    "build>=1.2.2.post1",
+    "hatch>=1.14.1",
+    "ipywidgets>=8.1.7",
+    "pydata-sphinx-theme>=0.16.1",
+    "ruff>=0.11.13",
+    "sphinx>=8.1.3",
+    "sphinx-autoapi>=3.6.0",
+    "sphinx-favicon>=1.0.1",
+    "tomli>=2.2.1",
+    "twine>=6.1.0",
+]

pykrait-0.1.0/src/pykrait/__init__.py

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+

pykrait-0.1.0/src/pykrait/io/io.py

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+import os
+import xml.etree.ElementTree as ET
+import dask.array as da
+import warnings
+import re
+from aicsimageio import AICSImage
+
+ALLOWED_IMAGE_EXTENSIONS =[".czi", ".tif", ".tiff"]
+
+def load_timelapse_lazy(
+    file_path: str,
+) -> list[da.Array, float, float, float]:
+    """Load a timelapse image file lazily using AICSImageIO, returning a Dask array of the image data along with the frame interval and pixel sizes.
+
+    Currently supports CZI and TIF/TIFF files. The image data is returned as a Dask array with shape (T, C, Y, X) where T is time, C is channels, Y is height, and X is width. The Z dimension is dropped if it has only one slice.
+
+    :param file_path: input file path to the timelapse image file
+    :type file_path: str
+    :raises TypeError: if filepath is not a string
+    :raises FileNotFoundError: if the file does not exist
+    :raises ValueError: if the extension is not supported
+    :raises ValueError: if the image does not have the expected 5D shape (TCZYX)
+    :raises ValueError: if the image has more than one Z slice and Z cannot be automatically dropped
+    :return: returns a list of a Dask array containing the image data, the frame interval in seconds, and pixel sizes in micrometers (Y, X)
+    :rtype: list[da.Array, float, float, float]
+    """
+    if not isinstance(file_path, str):
+        raise TypeError("file_path must be a string")
+    
+    if not os.path.exists(file_path):
+        raise FileNotFoundError(f"File not found: {file_path}")
+    
+    ext = os.path.splitext(file_path)[-1].lower()
+    if ext not in ALLOWED_IMAGE_EXTENSIONS:
+        raise ValueError(f"Image to load has the unsupported file format '{ext}'. Supported file formats are: {ALLOWED_IMAGE_EXTENSIONS}")
+
+    # Load with AICSImage using Dask
+    img = AICSImage(file_path, reconstruct_mosaic=False)
+
+    # extract the relevant metadata
+    pixel_sizes = img.physical_pixel_sizes  # Units are in micrometers (µm)
+    y_um = round(pixel_sizes.Y, 2) if pixel_sizes else None
+    x_um = round(pixel_sizes.X, 2) if pixel_sizes else None
+
+    frame_interval = None
+
+    # accessing frame interval from tif/tiff meadata
+    if ext == ".tiff" or ext == ".tif":
+        try:
+            match = re.search(r"finterval=([0-9.]+)", img.metadata)
+            raw_finterval = float(match.group(1))
+            frame_interval = round(raw_finterval, 2) # Output: 1.26
+        except Exception as e:
+            warnings.warn(
+                f"Failed to extract frame interval from TIFF/TIF metadata: {type(e).__name__}: {e}", 
+                UserWarning
+            )
+
+    # accessing frame interval from czi metadata
+    elif ext == ".czi":
+        try:
+            frame_time_elem = img.metadata.findall(".//FrameTime")
+            # select the last FrameTime element if there are multiple and round to 2 decimal places
+            frame_interval = round(float(frame_time_elem[-1].text), 2)
+        except Exception as e:
+            warnings.warn(
+                f"Failed to extract frame interval from CZI metadata: {type(e).__name__}: {e}", 
+                UserWarning
+            )
+
+    # trying to extract frame interval from OME-XML metadata
+    else:
+        try:
+            root = ET.fromstring(img.ome_metadata)
+            namespace = {'ome': 'http://www.openmicroscopy.org/Schemas/OME/2016-06'}
+            pixels_elem = root.find('.//ome:Pixels', namespaces=namespace)
+            if pixels_elem is not None and 'TimeIncrement' in pixels_elem.attrib:
+                frame_interval = float(pixels_elem.attrib['TimeIncrement'])
+        except Exception as e:
+            warnings.warn(
+            f"Failed to extract frame interval from OME-XML: {type(e).__name__}: {e}", 
+            UserWarning
+            )
+    
+    dask_img = img.dask_data  # TCZYX
+
+    if dask_img.ndim != 5:
+        raise ValueError(f"Expected 5D image (TCZYX), but got shape {dask_img.shape}")
+
+    T, C, Z, Y, X = dask_img.shape
+
+    if Z == 1:
+        dask_img = dask_img[:, :, 0, :, :]  # shape: (T, C, Z, Y, X)
+    else:
+        raise ValueError(f"Cannot drop Z dimension automatically: Z={Z}. Consider handling it explicitly.")
+
+    print(f"Returning lazy array of shape {dask_img.shape} (T, C, Y, X)")
+    return dask_img, frame_interval, y_um, x_um
+
+def get_files_from_folder(
+    folder: str,
+    extension: str = ".czi",
+) -> list[str]:
+    """returns all files from a folder with specified extensions.
+
+    :param folder: path to the folder
+    :type folder: str
+    :param extensions: str of file extension (default is ".czi")
+    :type extensions: str
+    :return: list of file paths with the specified extensions
+    :rtype: list[str]
+    """
+    if not os.path.isdir(folder):
+        raise NotADirectoryError(f"Provided path is not a directory: {folder}")
+
+    files = [os.path.join(folder, f) for f in os.listdir(folder) if os.path.isfile(os.path.join(folder, f)) and os.path.splitext(f)[-1].lower() == extension]
+    return files

pykrait-0.1.0/src/pykrait/pipeline/__init__.py

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+