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1d197a4 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 | """CLI entrypoints for DeepIVUS."""
import datetime
import os
from typing import Optional
import click
from deepivus.config import resolve_bifurcation_threshold
@click.group()
def cli() -> None:
"""DeepIVUS CLI."""
@cli.command("segment")
@click.argument("dicom_path", type=click.Path(exists=True, dir_okay=False))
@click.option(
"--output-prefix",
"-o",
default=None,
type=str,
help="Output path prefix (without extension). Defaults to output/<timestamp>/<input filename>.",
)
@click.option(
"--fps",
default=None,
type=float,
help="Overlay video FPS. Defaults to DICOM CineRate or 30.",
)
@click.option(
"--bifurcation-threshold",
default=None,
show_default=False,
type=click.FloatRange(min=0.0, max=1.0),
help="Threshold for bifurcation classifier labels. Defaults to threshold.json beside the selected bifurcation model.",
)
@click.option(
"--framewise/--no-framewise",
default=False,
show_default=True,
help="Run inference frame-by-frame (batch_size=1) to simulate realtime processing.",
)
def segment_cmd(
dicom_path: str,
output_prefix: Optional[str],
fps: Optional[float],
bifurcation_threshold: Optional[float],
framewise: bool,
) -> None:
"""Segment lumen and classify bifurcation for all frames."""
from .pipeline import segment_and_export
if output_prefix is None:
stem = os.path.splitext(os.path.basename(dicom_path))[0]
output_root = os.path.join(os.getcwd(), "output")
os.makedirs(output_root, exist_ok=True)
run_folder = datetime.datetime.now().strftime("%Y%m%d_%H%M%S")
output_dir = os.path.join(output_root, run_folder)
suffix = 1
while os.path.exists(output_dir):
output_dir = os.path.join(output_root, f"{run_folder}_{suffix}")
suffix += 1
os.makedirs(output_dir, exist_ok=True)
output_prefix = os.path.join(output_dir, stem)
else:
output_dir = os.path.dirname(os.path.abspath(output_prefix))
os.makedirs(output_dir, exist_ok=True)
if bifurcation_threshold is None:
bifurcation_threshold = resolve_bifurcation_threshold(default=0.5)
(
xml_path,
json_path,
top_conf_json_path,
video_path,
bif_overlay_video_path,
bif_json_path,
bif_summary_path,
) = segment_and_export(
dicom_path,
output_prefix,
fps,
bifurcation_threshold,
framewise=framewise,
)
click.echo(f"Contours XML: {xml_path}")
click.echo(f"Contours JSONL: {json_path}")
click.echo(f"Top confidence JSONL: {top_conf_json_path}")
click.echo(f"Overlay video: {video_path}")
click.echo(f"Overlay video (with bifurcation flags): {bif_overlay_video_path}")
click.echo(f"Bifurcation predictions JSONL: {bif_json_path}")
click.echo(f"Bifurcation summary JSON: {bif_summary_path}")
@cli.command("edit-annotations")
@click.argument("dicom_path", type=click.Path(exists=True, dir_okay=False))
@click.option(
"--annotations-path",
default=None,
type=click.Path(exists=True, dir_okay=False),
help=(
"Base contour JSONL to edit. "
"Defaults to latest output/<timestamp>/<dicom_stem>_contours.jsonl."
),
)
@click.option(
"--edits-path",
default=None,
type=click.Path(dir_okay=False),
help="Path for edited annotations JSONL. Defaults beside base file as *_edited_annotations.jsonl.",
)
@click.option(
"--output-root",
default="output",
show_default=True,
type=click.Path(file_okay=False),
help="Root folder containing pipeline outputs used for default annotation discovery.",
)
def edit_annotations_cmd(
dicom_path: str,
annotations_path: Optional[str],
edits_path: Optional[str],
output_root: str,
) -> None:
"""Open GUI editor to review and adjust contour coordinates frame-by-frame."""
from .gui import launch_annotation_editor
launch_annotation_editor(
dicom_path=dicom_path,
annotations_path=annotations_path,
edits_path=edits_path,
output_root=output_root,
)
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