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2.0.3 #6

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merged 5 commits into from
May 3, 2023
Merged

2.0.3 #6

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ed8e3e5
bump version
jopo666 Apr 20, 2023
12e72f1
remove logo it takes too much space
jopo666 Apr 20, 2023
fd30183
simplify cli interface
jopo666 May 3, 2023
017aa3f
fix concurrency bug with CziBackend
jopo666 May 3, 2023
8da4c24
new build
jopo666 May 3, 2023
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242 changes: 122 additions & 120 deletions histoprep/_cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,21 +13,21 @@

from histoprep import SlideReader

LOGO = """
██╗ ██╗██╗███████╗████████╗ ██████╗ ██████╗ ██████╗ ███████╗██████╗
██║ ██║██║██╔════╝╚══██╔══╝██╔═══██╗██╔══██╗██╔══██╗██╔════╝██╔══██╗
███████║██║███████╗ ██║ ██║ ██║██████╔╝██████╔╝█████╗ ██████╔╝
██╔══██║██║╚════██║ ██║ ██║ ██║██╔═══╝ ██╔══██╗██╔══╝ ██╔═══╝
██║ ██║██║███████║ ██║ ╚██████╔╝██║ ██║ ██║███████╗██║
╚═╝ ╚═╝╚═╝╚══════╝ ╚═╝ ╚═════╝ ╚═╝ ╚═╝ ╚═╝╚══════╝╚═╝
by jopo666 (2023)
"""
# LOGO = """
# ██╗ ██╗██╗███████╗████████╗ ██████╗ ██████╗ ██████╗ ███████╗██████╗
# ██║ ██║██║██╔════╝╚══██╔══╝██╔═══██╗██╔══██╗██╔══██╗██╔════╝██╔══██╗
# ███████║██║███████╗ ██║ ██║ ██║██████╔╝██████╔╝█████╗ ██████╔╝
# ██╔══██║██║╚════██║ ██║ ██║ ██║██╔═══╝ ██╔══██╗██╔══╝ ██╔═══╝
# ██║ ██║██║███████║ ██║ ╚██████╔╝██║ ██║ ██║███████╗██║
# ╚═╝ ╚═╝╚═╝╚══════╝ ╚═╝ ╚═════╝ ╚═╝ ╚═╝ ╚═╝╚══════╝╚═╝
# by jopo666 (2023)
# """
# Rich-click options.
click.rich_click.USE_RICH_MARKUP = True
click.rich_click.RANGE_STRING = ""
click.rich_click.HEADER_TEXT = LOGO
# click.rich_click.HEADER_TEXT = LOGO
click.rich_click.STYLE_HEADER_TEXT = "dim"
click.rich_click.MAX_WIDTH = 120
click.rich_click.MAX_WIDTH = 100
click.rich_click.SHOW_METAVARS_COLUMN = False
click.rich_click.APPEND_METAVARS_HELP = True
click.rich_click.GROUP_ARGUMENTS_OPTIONS = True
Expand All @@ -39,17 +39,15 @@
"--height",
"--overlap",
"--max-background",
"--out-of-bounds",
"--in-bounds",
]
SAVE_OPTIONS = [
"--save-metrics",
"--save-masks",
"--save-thumbnails",
"--metrics",
"--masks",
"--overwrite",
"--unfinished",
"--format",
"--image-format",
"--quality",
"--use-csv",
"--num-workers",
]
TISSUE_OPTIONS = [
Expand All @@ -63,11 +61,36 @@
"HistoPrep": [
{"name": "Input/output", "options": IO_OPTIONS},
{"name": "Tile extraction", "options": TILE_OPTIONS},
{"name": "Tile saving", "options": SAVE_OPTIONS},
{"name": "Tissue detection", "options": TISSUE_OPTIONS},
{"name": "Tile saving", "options": SAVE_OPTIONS},
]
}

DEFAULT_OPTIONS = {
# Input/output
"backend": None,
# Tile extraction.
"level": 0,
"width": 640,
"height": None,
"overlap": 0.0,
"max_background": 0.75,
"in_bounds": False,
# Tissue detection.
"threshold": None,
"multiplier": 1.05,
"tissue_level": None,
"max_dimension": 8192,
"sigma": 1.0,
"save_metrics": False,
"save_masks": False,
"overwrite": False,
"overwrite_unfinished": False,
"image_format": "jpeg",
"quality": 80,
"num_workers": None,
}


def glob_pattern(*args) -> list[Path]:
pattern = args[-1]
Expand Down Expand Up @@ -103,10 +126,9 @@ def glob_pattern(*args) -> list[Path]:
help="Parent directory for all outputs.",
)
@click.option( # backend
"-b",
"--backend",
type=click.Choice(choices=["PIL", "OPENSLIDE", "CZI"], case_sensitive=False),
default=None,
default=DEFAULT_OPTIONS["backend"],
show_default="automatic",
help="Backend for reading slides.",
)
Expand All @@ -116,24 +138,25 @@ def glob_pattern(*args) -> list[Path]:
"--level",
metavar="INT",
type=click.IntRange(min=0),
default=0,
default=DEFAULT_OPTIONS["level"],
show_default=True,
help="Slide pyramid level for tile extraction.",
help="Pyramid level for tile extraction.",
)
@click.option( # width
"-w",
"--width",
metavar="INT",
type=click.IntRange(min=0, min_open=False),
default=640,
default=DEFAULT_OPTIONS["width"],
show_default=True,
help="Tile width.",
)
@click.option( # height
"-h",
"--height",
metavar="INT",
type=click.IntRange(min=0, min_open=False),
default=None,
default=DEFAULT_OPTIONS["height"],
show_default="width",
help="Tile height.",
)
Expand All @@ -142,141 +165,122 @@ def glob_pattern(*args) -> list[Path]:
"--overlap",
metavar="FLOAT",
type=click.FloatRange(min=0, max=1, min_open=False, max_open=False),
default=0.0,
default=DEFAULT_OPTIONS["overlap"],
show_default=True,
help="Overlap between neighbouring tiles.",
)
@click.option( # background
"-m",
"-b",
"--max-background",
metavar="FLOAT",
type=click.FloatRange(min=0, max=1, min_open=True, max_open=True),
default=0.75,
default=DEFAULT_OPTIONS["max_background"],
show_default=True,
help="Maximum background in tile.",
help="Maximum background for tiles.",
)
@click.option( # out-of-bounds
"--out-of-bounds",
type=click.BOOL,
default=True,
show_default=True,
help="Allow tiles to go out-of-bounds. ",
"--in-bounds",
show_default="False",
is_flag=True,
help="Do not allow tiles to go out-of-bounds. ",
)
# Saving.
@click.option( # save_metrics
"--save-metrics",
type=click.BOOL,
default=True,
# Tissue.
@click.option( # threshold
"-t",
"--threshold",
metavar="INT",
type=click.IntRange(min=0, max=255, min_open=False),
default=DEFAULT_OPTIONS["threshold"],
show_default="Otsu",
help="Global thresholding value.",
)
@click.option( # multiplier
"-x",
"--multiplier",
metavar="FLOAT",
type=click.FloatRange(min=0, min_open=False),
default=DEFAULT_OPTIONS["multiplier"],
show_default=True,
help="Save image metrics to metadata.",
help="Multiplier for Otsu's threshold.",
)
@click.option( # save_masks
"--save-masks",
type=click.BOOL,
default=False,
@click.option( # tissue_level
"--tissue-level",
metavar="INT",
type=click.IntRange(min=0),
default=DEFAULT_OPTIONS["tissue_level"],
show_default="max_dimension",
help="Pyramid level for tissue detection.",
)
@click.option( # max_dimension
"--max-dimension",
metavar="INT",
type=click.IntRange(min=0),
default=DEFAULT_OPTIONS["max_dimension"],
show_default=True,
help="Save tissue masks for each tile.",
help="Maximum dimension for tissue detection.",
)
@click.option( # save_thumbnails
"--save-thumbnails",
type=click.BOOL,
default=True,
@click.option( # sigma
"--sigma",
metavar="FLOAT",
type=click.FloatRange(min=0),
default=DEFAULT_OPTIONS["sigma"],
show_default=True,
help="Save thumbnail images.",
help="Sigma for gaussian blurring.",
)
# Saving.
@click.option( # save_metrics
"--metrics",
"save_metrics",
show_default="False",
is_flag=True,
help="Save image metrics.",
)
@click.option( # save_masks
"--masks",
"save_masks",
show_default="False",
is_flag=True,
help="Save tissue masks.",
)
@click.option( # overwrite
"-z",
"--overwrite",
type=click.BOOL,
default=False,
show_default=True,
show_default="False",
is_flag=True,
help="Overwrite any existing slide outputs.",
)
@click.option( # overwrite_unfinished
"-u",
"--unfinished",
"overwrite_unfinished",
type=click.BOOL,
default=False,
show_default=True,
show_default="False",
is_flag=True,
help="Overwrite only if metadata is missing.",
)
@click.option( # format
"--format",
"image_format",
"--image-format",
type=click.STRING,
default="jpeg",
default=DEFAULT_OPTIONS["image_format"],
show_default=True,
help="File format for tiles.",
help="File format for tile images.",
)
@click.option( # quality
"--quality",
metavar="INT",
type=click.IntRange(min=0, max=100),
default=80,
default=DEFAULT_OPTIONS["quality"],
show_default=True,
help="Quality for jpeg-compression.",
)
@click.option( # overwrite_unfinished
"-c",
"--use-csv",
type=click.BOOL,
default=False,
show_default=True,
help="Write metadata to csv-files instead of parquet files.",
)
@click.option( # num_workers
"-j",
"--num-workers",
metavar="INT",
type=click.IntRange(min=0, min_open=False),
default=None,
default=DEFAULT_OPTIONS["num_workers"],
show_default="CPU-count",
help="Number of data saving workers.",
)
# Tissue.
@click.option( # threshold
"-t",
"--threshold",
metavar="INT",
type=click.IntRange(min=0, max=255, min_open=False),
default=None,
show_default="Otsu's threshold",
help="Global threshold value for tissue detection.",
)
@click.option( # multiplier
"-x",
"--multiplier",
metavar="FLOAT",
type=click.FloatRange(min=0, min_open=False),
default=1.05,
show_default=True,
help="Multiplier for Otsu's threshold. Ignored if threshold is set.",
)
@click.option( # tissue_level
"--tissue-level",
metavar="INT",
type=click.IntRange(min=0),
default=None,
show_default="max_dimension",
help="Slide pyramid level for tissue detection.",
)
@click.option( # max_dimension
"--max-dimension",
metavar="INT",
type=click.IntRange(min=0),
default=8192,
show_default=True,
help="Select first pyramid level with both dimensions smaller than this value.",
)
@click.option( # sigma
"--sigma",
metavar="FLOAT",
type=click.FloatRange(min=0),
default=1.0,
show_default=True,
help="Sigma for gaussian blurring during tissue detection.",
)
def cut_slides(
paths: list[Union[str, Path]],
parent_dir: Union[str, Path],
Expand All @@ -294,20 +298,18 @@ def cut_slides(
height: Optional[int] = None,
overlap: float = 0.0,
max_background: float = 0.75,
out_of_bounds: bool = True,
in_bounds: bool = False,
# Tile saving.
save_metrics: bool = True,
save_masks: bool = True,
save_thumbnails: bool = True,
save_metrics: bool = False,
save_masks: bool = False,
overwrite: bool = False,
overwrite_unfinished: bool = False,
image_format: str = "jpeg",
quality: int = 80,
use_csv: bool = False,
num_workers: Optional[int] = None,
) -> None:
"""CLI interface to extract tile images from slides."""
# Filter slide paths.
"""Extract tile images from histological slides."""
paths = filter_slide_paths(
all_paths=[x if isinstance(x, Path) else Path(x) for x in paths],
parent_dir=parent_dir,
Expand All @@ -328,15 +330,15 @@ def cut_slides(
"width": width,
"height": height,
"overlap": overlap,
"out_of_bounds": out_of_bounds,
"out_of_bounds": not in_bounds,
"max_background": max_background,
},
"save_kwargs": {
"parent_dir": parent_dir,
"level": level,
"save_metrics": save_metrics,
"save_masks": save_masks,
"save_thumbnails": save_thumbnails,
"save_thumbnails": True,
"image_format": image_format,
"quality": quality,
"use_csv": use_csv,
Expand Down
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