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taydentayden
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Refactor CLI with better type hinting (#127)
* Refactor CLI with better type hinting * Add gpu test flag * Remove shell completion (Slow and buggy - removing for now)
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-59
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‎docs/cli.md

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Original file line numberDiff line numberDiff line change
@@ -11,8 +11,6 @@ $ kom --help
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Options
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--version -v
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--install-completion [bash|zsh|fish|powershell|pwsh] Install completion for the specified shell. [default: None]
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--show-completion [bash|zsh|fish|powershell|pwsh] Show completion for the specified shell, to copy it or customize the installation. [default: None]
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--help -h Show this message and exit.
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Commands

‎kelp_o_matic/cli.py

Lines changed: 134 additions & 57 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,7 @@
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from pathlib import Path
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from typing import Optional
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from typing import Annotated, Optional
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4+
import torch
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import typer
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67
from kelp_o_matic import (
@@ -9,42 +10,71 @@
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find_mussels as find_mussels_,
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)
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12-
cli = typer.Typer(context_settings={"help_option_names": ["-h", "--help"]})
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cli = typer.Typer(context_settings={"help_option_names": ["-h", "--help"]}, add_completion=False)
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@cli.command()
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def find_kelp(
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source: Path = typer.Argument(..., help="Input image with Byte data type."),
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dest: Path = typer.Argument(..., help="File path location to save output to."),
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species: bool = typer.Option(
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False,
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"--species/--presence",
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help="Segment to species or presence/absence level.",
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),
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crop_size: int = typer.Option(
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1024,
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help="The data window size to run through the segmentation model.",
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),
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use_nir: bool = typer.Option(
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False,
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"--rgbi/--rgb",
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help="Use RGB and NIR bands for classification. Assumes RGBI ordering.",
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),
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band_order: Optional[list[int]] = typer.Option(
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None,
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"-b",
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help="GDAL-style band re-ordering flag. Defaults to RGB or RGBI order. "
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"To e.g., reorder a BGRI image at runtime, pass flags `-b 3 -b 2 -b 1 -b 4`.",
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),
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use_gpu: bool = typer.Option(
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True, "--gpu/--no-gpu", help="Enable or disable GPU, if available."
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),
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use_tta: bool = typer.Option(
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False,
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"--tta/--no-tta",
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help="Use test time augmentation to improve accuracy at the cost of "
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"processing time.",
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),
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source: Annotated[
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Path,
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typer.Argument(
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exists=True,
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dir_okay=False,
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file_okay=True,
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readable=True,
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help="Input image with Byte data type.",
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),
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],
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dest: Annotated[
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Path,
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typer.Argument(
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exists=True,
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dir_okay=False,
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file_okay=True,
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writable=True,
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help="File path location to save output to.",
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),
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],
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species: Annotated[
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bool,
40+
typer.Option(
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"--species/--presence",
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help="Segment to species or presence/absence level.",
43+
),
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] = False,
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crop_size: Annotated[
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int,
47+
typer.Option(
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help="The data window size to run through the segmentation model.",
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),
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] = 1024,
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use_nir: Annotated[
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bool,
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typer.Option(
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"--rgbi/--rgb",
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help="Use RGB and NIR bands for classification. Assumes RGBI ordering.",
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),
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] = False,
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band_order: Annotated[
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Optional[list[int]],
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typer.Option(
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"-b",
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help="GDAL-style band re-ordering flag. Defaults to RGB or RGBI order. "
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"To e.g., reorder a BGRI image at runtime, pass flags `-b 3 -b 2 -b 1 -b 4`.",
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),
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] = None,
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use_gpu: Annotated[
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bool,
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typer.Option("--gpu/--no-gpu", help="Enable or disable GPU, if available."),
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] = True,
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use_tta: Annotated[
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bool,
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typer.Option(
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"--tta/--no-tta",
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help="Use test time augmentation to improve accuracy at the cost of "
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"processing time.",
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),
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] = False,
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):
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"""
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Detect kelp in image at path SOURCE and output the resulting classification raster
@@ -55,27 +85,52 @@ def find_kelp(
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@cli.command()
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def find_mussels(
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source: Path = typer.Argument(..., help="Input image with Byte data type."),
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dest: Path = typer.Argument(..., help="File path location to save output to."),
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crop_size: int = typer.Option(
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1024,
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help="The data window size to run through the segmentation model.",
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),
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band_order: Optional[list[int]] = typer.Option(
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None,
66-
"-b",
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help="GDAL-style band re-ordering flag. Defaults to RGB order. "
68-
"To e.g., reorder a BGR image at runtime, pass flags `-b 3 -b 2 -b 1`.",
69-
),
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use_gpu: bool = typer.Option(
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True, "--gpu/--no-gpu", help="Enable or disable GPU, if available."
72-
),
73-
use_tta: bool = typer.Option(
74-
False,
75-
"--tta/--no-tta",
76-
help="Use test time augmentation to improve accuracy at the cost of "
77-
"processing time.",
78-
),
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source: Annotated[
89+
Path,
90+
typer.Argument(
91+
exists=True,
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dir_okay=False,
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file_okay=True,
94+
readable=True,
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help="Input image with Byte data type.",
96+
),
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],
98+
dest: Annotated[
99+
Path,
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typer.Argument(
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exists=True,
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dir_okay=False,
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file_okay=True,
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writable=True,
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help="File path location to save output to.",
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),
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],
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crop_size: Annotated[
109+
int,
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typer.Option(
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help="The data window size to run through the segmentation model.",
112+
),
113+
] = 1024,
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band_order: Annotated[
115+
Optional[list[int]],
116+
typer.Option(
117+
"-b",
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help="GDAL-style band re-ordering flag. Defaults to RGB or RGBI order. "
119+
"To e.g., reorder a BGRI image at runtime, pass flags `-b 3 -b 2 -b 1 -b 4`.",
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),
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] = None,
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use_gpu: Annotated[
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bool,
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typer.Option("--gpu/--no-gpu", help="Enable or disable GPU, if available."),
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] = True,
126+
use_tta: Annotated[
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bool,
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typer.Option(
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"--tta/--no-tta",
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help="Use test time augmentation to improve accuracy at the cost of "
131+
"processing time.",
132+
),
133+
] = False,
79134
):
80135
"""
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Detect mussels in image at path SOURCE and output the resulting classification
@@ -90,11 +145,33 @@ def version_callback(value: bool) -> None:
90145
raise typer.Exit()
91146

92147

148+
def gpu_callback(value: bool) -> None:
149+
if value:
150+
typer.echo(f"GPU detected: {torch.cuda.is_available()}")
151+
raise typer.Exit()
152+
153+
93154
@cli.callback()
94155
def main(
95-
version: bool = typer.Option(
96-
None, "--version", "-v", callback=version_callback, is_eager=True
97-
),
156+
version: Annotated[
157+
bool,
158+
typer.Option(
159+
"--version",
160+
"-v",
161+
callback=version_callback,
162+
is_eager=True,
163+
help="Show version and exit.",
164+
),
165+
] = False,
166+
gpu_test: Annotated[
167+
bool,
168+
typer.Option(
169+
"--gpu-test",
170+
callback=gpu_callback,
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is_eager=True,
172+
help="Test if GPU is detected and exit.",
173+
),
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] = False,
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):
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return
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