spatialproteomics 0.4.0__tar.gz

spatialproteomics-0.4.0/LICENSE

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+MIT License
+
+Copyright (c) 2022 Harald Vöhringer, Matthias Meyer-Bender
+
+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.

spatialproteomics-0.4.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: spatialproteomics
+Version: 0.4.0
+Summary: 
+Author: Harald Vohringer
+Requires-Python: >=3.8,<4.0
+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
+Provides-Extra: docs
+Requires-Dist: Sphinx (==4.2.0) ; extra == "docs"
+Requires-Dist: matplotlib (>=3.5.3,<4.0.0)
+Requires-Dist: nbsphinx (==0.8.9) ; extra == "docs"
+Requires-Dist: scikit-image (>=0.19.3,<0.20.0)
+Requires-Dist: scikit-learn (>=1.2.2,<2.0.0)
+Requires-Dist: sphinx-rtd-theme (==1.0.0) ; extra == "docs"
+Requires-Dist: sphinxcontrib-napoleon (==0.7) ; extra == "docs"
+Requires-Dist: tqdm (>=4.64.0,<5.0.0)
+Requires-Dist: xarray (>=2022.6.0,<2023.0.0)
+Requires-Dist: zarr (>=2.14.2,<3.0.0)

spatialproteomics-0.4.0/pyproject.toml

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+[tool.poetry]
+name = "spatialproteomics"
+packages = [
+    { include = "spatialproteomics" },
+]
+version = "0.4.0"
+description = ""
+authors = ["Harald Vohringer", "Matthias Meyer-Bender"]
+
+[tool.poetry.dependencies]
+python = ">=3.8,<4.0"
+xarray = "^2022.6.0"
+scikit-image = "^0.19.3"
+matplotlib = "^3.5.3"
+Sphinx = { version = "4.2.0", optional = true }
+sphinx-rtd-theme = { version = "1.0.0", optional = true }
+sphinxcontrib-napoleon = { version = "0.7", optional = true }
+nbsphinx = { version = "0.8.9", optional = true }
+tqdm = "^4.64.0"
+scikit-learn = "^1.2.2"
+zarr = "^2.14.2"
+
+[tool.poetry.dev-dependencies]
+pytest = "^7.1.2"
+pytest-cov = "^3.0.0"
+black = "^22.6.0"
+isort = "^5.10.1"
+flake8 = "^5.0.4"
+bandit = "^1.7.4"
+safety = "^2.1.1"
+
+[tool.poetry.extras]
+docs = ["Sphinx", "sphinx-rtd-theme", "sphinxcontrib-napoleon", "nbsphinx"]
+
+[build-system]
+requires = ["poetry-core>=1.0.0"]
+build-backend = "poetry.core.masonry.api"
+
+[tool.black]
+line-length = 120

spatialproteomics-0.4.0/setup.py

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+# -*- coding: utf-8 -*-
+from setuptools import setup
+
+packages = \
+['spatialproteomics',
+ 'spatialproteomics.ext',
+ 'spatialproteomics.la',
+ 'spatialproteomics.pl',
+ 'spatialproteomics.pp',
+ 'spatialproteomics.tl']
+
+package_data = \
+{'': ['*']}
+
+install_requires = \
+['matplotlib>=3.5.3,<4.0.0',
+ 'scikit-image>=0.19.3,<0.20.0',
+ 'scikit-learn>=1.2.2,<2.0.0',
+ 'tqdm>=4.64.0,<5.0.0',
+ 'xarray>=2022.6.0,<2023.0.0',
+ 'zarr>=2.14.2,<3.0.0']
+
+extras_require = \
+{'docs': ['Sphinx==4.2.0',
+          'sphinx-rtd-theme==1.0.0',
+          'sphinxcontrib-napoleon==0.7',
+          'nbsphinx==0.8.9']}
+
+setup_kwargs = {
+    'name': 'spatialproteomics',
+    'version': '0.4.0',
+    'description': '',
+    'long_description': 'None',
+    'author': 'Harald Vohringer',
+    'author_email': 'None',
+    'maintainer': 'None',
+    'maintainer_email': 'None',
+    'url': 'None',
+    'packages': packages,
+    'package_data': package_data,
+    'install_requires': install_requires,
+    'extras_require': extras_require,
+    'python_requires': '>=3.8,<4.0',
+}
+
+
+setup(**setup_kwargs)

spatialproteomics-0.4.0/spatialproteomics/__init__.py

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+from .constants import (
+    Apricot,
+    Beige,
+    Black,
+    Blue,
+    Brown,
+    Cyan,
+    Dims,
+    Features,
+    Green,
+    Grey,
+    Lavender,
+    Layers,
+    Lime,
+    Magenta,
+    Maroon,
+    Mint,
+    Navy,
+    Olive,
+    Orange,
+    Pink,
+    Props,
+    Purple,
+    Red,
+    Teal,
+    White,
+    Yellow,
+)
+from .container import load_image_data
+from .ext import ExternalAccessor
+from .la import LabelAccessor
+from .pl import PlotAccessor
+from .pp import (
+    PreprocessingAccessor,
+    arcsinh_mean_intensity,
+    arcsinh_median_intensity,
+    arcsinh_sum_intensity,
+    arcsinh_var_intensity,
+    detect_peaks_num,
+    is_positive,
+    mean_intensity,
+    percentage_positive,
+    sum_intensity,
+)
+from .tl import TwoComponentGaussianMixture
+
+__all__ = [
+    "load_image_data",
+    "PreprocessingAccessor",
+    "LabelAccessor",
+    "PlotAccessor",
+    "SegmentationAccessor",
+    "ExternalAccessor",
+    "Layers",
+    "Dims",
+    "Features",
+    "Props",
+    "sum_intensity",
+    "mean_intensity",
+    "arcsinh_sum_intensity",
+    "arcsinh_mean_intensity",
+    "arcsinh_var_intensity",
+    "arcsinh_median_intensity",
+    "merge_segmentation",
+    "detect_peaks_num",
+    "percentage_positive",
+    "is_positive",
+    "TwoComponentGaussianMixture",
+    "Apricot",
+    "Beige",
+    "Black",
+    "Blue",
+    "Brown",
+    "Cyan",
+    "Dims",
+    "Features",
+    "Green",
+    "Grey",
+    "Lavender",
+    "Layers",
+    "Lime",
+    "Magenta",
+    "Maroon",
+    "Mint",
+    "Navy",
+    "Olive",
+    "Orange",
+    "Pink",
+    "Props",
+    "Purple",
+    "Red",
+    "Teal",
+    "White",
+    "Yellow",
+]

spatialproteomics-0.4.0/spatialproteomics/base_logger.py

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+import logging
+
+logger = logging
+logger.basicConfig(format="%(message)s", level=logging.INFO)

spatialproteomics-0.4.0/spatialproteomics/constants.py

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+Red = "#e6194B"
+Green = "#3cb44b"
+Yellow = "#ffe119"
+Blue = "#4363d8"
+Orange = "#f58231"
+Purple = "#911eb4"
+Cyan = "#42d4f4"
+Magenta = "#f032e6"
+Lime = "#bfef45"
+Pink = "#fabed4"
+Teal = "#469990"
+Lavender = "#dcbeff"
+Brown = "#9A6324"
+Beige = "#fffac8"
+Maroon = "#800000"
+Mint = "#aaffc3"
+Olive = "#808000"
+Apricot = "#ffd8b1"
+Navy = "#000075"
+Grey = "#a9a9a9"
+White = "#ffffff"
+Black = "#000000"
+
+
+class Layers(object):
+    IMAGE = "_image"
+    SEGMENTATION = "_segmentation"
+    COORDINATES = "_coordinates"
+    LABELS = "_labels"
+    DATA = "_data"
+    PLOT = "_plot"
+    OBS = "_obs"
+    NEIGHBORS = "_neighbors"
+    INTENSITY = "_intensity"
+
+
+class Dims(object):
+    CHANNELS = "channels"
+    X = "x"
+    Y = "y"
+    RGBA = "rgba"
+    CELLS = "cells"
+    COORDINATES = "coordinates"
+    LABELS = "labels"
+    FEATURES = "features"
+    PROPS = "props"
+    NEIGHBORS = "neighbors"
+    IMAGE = ["channels", "x", "y"]
+    COLORED_IMAGE = ["channels", "x", "y", "rgba"]
+    SEGMENTATION = ["x", "y"]
+    DATA = ["cell_idx", "channels"]
+
+
+class Attrs(object):
+    IMAGE_COLORS = "image_colors"
+    LABEL_COLORS = "label_colors"
+    LABEL_NAMES = "label_names"
+
+
+class Props(object):
+    COLOR = "_color"
+    NAME = "_name"
+
+
+class Features(object):
+    LABELS = "_labels"
+    X = "centroid-1"
+    Y = "centroid-0"
+
+
+class Labels(object):
+    UNLABELED = "Unlabeled"
+
+
+COLORS = [
+    "#FFFF00",
+    "#1CE6FF",
+    "#FF34FF",
+    "#FF4A46",
+    "#008941",
+    "#006FA6",
+    "#A30059",
+    "#FFDBE5",
+    "#7A4900",
+    "#0000A6",
+    "#63FFAC",
+    "#B79762",
+    "#004D43",
+    "#8FB0FF",
+    "#997D87",
+    "#5A0007",
+    "#809693",
+    "#6A3A4C",
+    "#1B4400",
+    "#4FC601",
+    "#3B5DFF",
+    "#4A3B53",
+    "#FF2F80",
+    "#61615A",
+    "#BA0900",
+    "#6B7900",
+    "#00C2A0",
+    "#FFAA92",
+    "#FF90C9",
+    "#B903AA",
+    "#D16100",
+    "#DDEFFF",
+    "#000035",
+    "#7B4F4B",
+    "#A1C299",
+    "#0AA6D8",
+    "#013349",
+    "#00846F",
+    "#372101",
+    "#FFB500",
+    "#C2FFED",
+    "#A079BF",
+    "#CC0744",
+    "#C0B9B2",
+    "#C2FF99",
+    "#00489C",
+    "#6F0062",
+    "#0CBD66",
+    "#EEC3FF",
+    "#456D75",
+    "#B77B68",
+    "#7A87A1",
+    "#788D66",
+    "#885578",
+    "#FAD09F",
+    "#FF8A9A",
+    "#D157A0",
+    "#BEC459",
+    "#456648",
+    "#0086ED",
+    "#886F4C",
+    "#34362D",
+    "#B4A8BD",
+    "#00A6AA",
+    "#452C2C",
+    "#636375",
+    "#A3C8C9",
+    "#FF913F",
+    "#938A81",
+    "#575329",
+    "#00FECF",
+    "#B05B6F",
+    "#8CD0FF",
+    "#3B9700",
+    "#04F757",
+    "#C8A1A1",
+    "#1E6E00",
+    "#7900D7",
+    "#A77500",
+    "#6367A9",
+    "#A05837",
+    "#6B002C",
+    "#772600",
+    "#D790FF",
+    "#9B9700",
+    "#549E79",
+    "#FFF69F",
+    "#72418F",
+    "#BC23FF",
+    "#99ADC0",
+    "#3A2465",
+    "#922329",
+    "#5B4534",
+    "#FDE8DC",
+    "#404E55",
+    "#0089A3",
+    "#CB7E98",
+    "#A4E804",
+    "#324E72",
+]
+
+
+PROPS_DICT = {"centroid-1": Features.X, "centroid-0": Features.Y}

spatialproteomics-0.4.0/spatialproteomics/container.py

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+from typing import List, Union
+
+import numpy as np
+import pandas as pd
+import xarray as xr
+
+from .constants import Dims, Layers
+
+
+def load_image_data(
+    image: np.ndarray,
+    channel_coords: Union[str, List[str]],
+    segmentation: Union[None, np.ndarray] = None,
+    labels: Union[None, pd.DataFrame] = None,
+    cell_col: str = "cell",
+    label_col: str = "label",
+    copy_segmentation: bool = False,
+    copy_image: bool = False,
+):
+    """Creates a image container.
+
+    Creates an Xarray dataset with images, segmentation, and
+    coordinate fields.
+
+    Parameters
+    ----------
+    image : np.ndarray
+        np.ndarray with image.shape = (n, x, y)
+    channel_coords: str | List[str]
+        list with the names for each channel
+
+    Returns
+    -------
+    xr.Dataset
+        An X-array dataset with all fields.
+    """
+    if copy_image:
+        image = image.copy()
+
+    if type(channel_coords) is str:
+        channel_coords = [channel_coords]
+
+    if image.ndim == 2:
+        image = np.expand_dims(image, 0)
+
+    channel_dim, y_dim, x_dim = image.shape
+
+    assert len(channel_coords) == channel_dim, "Length of channel_coords must match image.shape[0]."
+
+    if labels is not None:
+        assert segmentation is not None, "Labels may only be provided in conjunction with a segmentation."
+
+    im = xr.DataArray(
+        image,
+        coords=[channel_coords, range(y_dim), range(x_dim)],
+        dims=[Dims.CHANNELS, Dims.Y, Dims.X],
+        name=Layers.IMAGE,
+    )
+
+    dataset = xr.Dataset(data_vars={Layers.IMAGE: im})
+
+    if segmentation is not None:
+        dataset = dataset.pp.add_segmentation(segmentation, copy=copy_segmentation)
+
+        if labels is not None:
+            dataset = dataset.pp.add_labels(labels, cell_col=cell_col, label_col=label_col)
+
+    else:
+        dataset = xr.Dataset(data_vars={Layers.IMAGE: im})
+
+    return dataset

spatialproteomics-0.4.0/spatialproteomics/ext/__init__.py

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+from .external import ExternalAccessor
+
+__all__ = [
+    "ExternalAccessor",
+]