from __future__ import annotations
import os
from pathlib import Path
from typing import Literal, Union
import pandas as pd
__current_file_dir = Path(os.path.dirname(os.path.abspath(__file__)))
from skimage.io import imread
from typing import TYPE_CHECKING
import numpy as np
from ._remote_registry import fetch_snp
if TYPE_CHECKING:
from phenotypic._core._image import Image
from phenotypic._core._grid_image import GridImage
def _image_loader(
filepath,
mode: Literal["array", "Image", "GridImage", "filepath"],
**kwargs
) -> Union[np.ndarray, Image, GridImage]:
from phenotypic import Image, GridImage
match mode:
case "array":
return imread(filepath)
case "Image":
return Image.imread(filepath, **kwargs)
case "GridImage":
return GridImage.imread(filepath, **kwargs)
case "filepath":
return filepath
case _:
raise ValueError(f"Unknown mode: {mode}")
[docs]
def load_plate_12hr(
mode: Literal["array", "Image", "GridImage"] = "array",
) -> Union[np.ndarray, Image, GridImage]:
"""Returns a plate image of a K. Marxianus colony 96 array plate at 12 hrs"""
return _image_loader(__current_file_dir / "StandardDay1.jpg", mode)
[docs]
def load_plate_72hr(
mode: Literal["array", "Image", "GridImage"] = "array",
) -> Union[np.ndarray, Image, GridImage]:
"""Return a image of a k. marxianus colony 96 array plate at 72 hrs"""
return _image_loader(__current_file_dir / "StandardDay6.jpg", mode)
[docs]
def load_early_colony(
mode: Literal["array", "Image", "GridImage"] = "array",
) -> Union[np.ndarray, Image, GridImage]:
"""Returns a colony image array of K. Marxianus at 12 hrs"""
return _image_loader(__current_file_dir / "early_colony.png", mode)
[docs]
def load_faint_early_colony(
mode: Literal["array", "Image", "GridImage"] = "array",
) -> Union[np.ndarray, Image, GridImage]:
"""Returns a faint colony image array of K. Marxianus at 12 hrs"""
return _image_loader(__current_file_dir / "early_colony_faint.png", mode)
[docs]
def load_colony(
mode: Literal["array", "Image", "GridImage"] = "array",
) -> Union[np.ndarray, Image, GridImage]:
"""Returns a colony image array of K. Marxianus at 72 hrs"""
return _image_loader(__current_file_dir / "later_colony.png", mode)
def load_meas() -> pd.DataFrame:
"""
Loads sample measurements for 3 strains using each of the measurement modules
Returns:
pd.DataFrame: A DataFrame containing the loaded measurement data.
"""
return pd.read_csv(__current_file_dir / "meas/all_meas.csv", index_col=0)
def load_area_meas() -> pd.DataFrame:
"""
Loads sample measurements for 3 strains using area measurements
Returns:
pd.DataFrame: A DataFrame containing the sample area measurement data.
"""
return pd.read_csv(__current_file_dir / "meas/area_meas.csv", index_col=0)
[docs]
def load_yeast_plate(
mode: Literal["array", "Image", "GridImage"] = "GridImage",
) -> Union[np.ndarray, Image, GridImage]:
"""Load an image Neurospora filamentous fungi 96-well plate image cropped to the center.
Returns a pre-cropped plate image of Neurospora filamentous fungi arranged
in a 96-well grid. Irregular hyphal morphology with spreading growth --
suitable for filamentous fungi tutorials and how-to guides.
Args:
mode: Return format. Default: ``'GridImage'``.
Returns:
The plate image in the requested format.
"""
return _image_loader(
__current_file_dir / "snp-imager-samples/"
"RhodotorulaYeastCenterCrop.png",
mode=mode,
nrows=2,
ncols=4
)
def load_yeast_plate_large(
mode: Literal["array", "Image", "GridImage"] = "GridImage",
) -> Union[np.ndarray, Image, GridImage]:
"""Load a cropped Rhodotorula yeast 96-well plate image.
Returns a pre-cropped plate image of Rhodotorula yeast colonies arranged
in a standard 96-well grid (8 rows x 12 columns). Round colony morphology
with clean background -- suitable as the default sample for most tutorials
and how-to guides.
Args:
mode: Return format. Default: ``'GridImage'``.
Returns:
The plate image in the requested format.
"""
return _image_loader(
fetch_snp("RhodotorulaYeastCropped.png"), mode
)
[docs]
def load_fungi_plate(
mode: Literal["array", "Image", "GridImage"] = "GridImage",
) -> Union[np.ndarray, Image, GridImage]:
"""Load an image Neurospora filamentous fungi 96-well plate image cropped to the center.
Returns a pre-cropped plate image of Neurospora filamentous fungi arranged
in a 96-well grid. Irregular hyphal morphology with spreading growth --
suitable for filamentous fungi tutorials and how-to guides.
Args:
mode: Return format. Default: ``'GridImage'``.
Returns:
The plate image in the requested format.
"""
return _image_loader(
__current_file_dir / "snp-imager-samples/"
"NeurosporaFilamentousFungiCenterCrop.png",
mode=mode,
nrows=2,
ncols=4
)
def load_fungi_plate_large(
mode: Literal["array", "Image", "GridImage"] = "GridImage",
) -> Union[np.ndarray, Image, GridImage]:
"""Load a cropped Neurospora filamentous fungi 96-well plate image.
Returns a pre-cropped plate image of Neurospora filamentous fungi arranged
in a 96-well grid. Irregular hyphal morphology with spreading growth --
suitable for filamentous fungi tutorials and how-to guides.
Args:
mode: Return format. Default: ``'GridImage'``.
Returns:
The plate image in the requested format.
"""
return _image_loader(
fetch_snp("NeurosporaFilamentousFungiCropped.png"),
mode,
nrows=6,
ncols=10
)
[docs]
def load_yeast_plate_full(
mode: Literal["array", "Image", "GridImage"] = "Image",
) -> Union[np.ndarray, Image, GridImage]:
"""Load a full (uncropped) Rhodotorula yeast plate image with color checker.
Returns the full plate image including scanner margins and a color checker
target. Use for tutorials and how-to guides that demonstrate cropping
(``ImageCropper``), padding (``ImagePadder``), vignetting correction
(``VignetteCorrector``), or color correction (``ColorCorrector``).
Args:
mode: Return format. Default: ``'Image'``.
Returns:
The full plate image in the requested format.
"""
return _image_loader(
fetch_snp("RhodotorulaYeastFullPlate.png"), mode
)
[docs]
def load_fungi_plate_full(
mode: Literal["array", "Image", "GridImage"] = "GridImage",
) -> Union[np.ndarray, Image, GridImage]:
"""Load a full (uncropped) Neurospora filamentous fungi plate image with color checker.
Returns the full plate image including scanner margins and a color checker
target. Use for fungi-specific correction workflow tutorials.
Args:
mode: Return format. Default: ``'Image'``.
Returns:
The full plate image in the requested format.
"""
return _image_loader(
fetch_snp("NeurosporaFilamentousFungiFullPlate.png"),
mode,
nrows=6, ncols=10
)
