From c1c447d3defffb64964042c7c159c7ddb1aa1c39 Mon Sep 17 00:00:00 2001 From: "Christopher L. Crutchfield" Date: Sat, 9 Nov 2024 12:58:32 -0800 Subject: [PATCH] feat: label studio generator --- .vscode/launch.json | 22 +- fishsense_lite/commands/calibrate_laser.py | 10 +- fishsense_lite/commands/calibrate_lens.py | 8 +- .../commands/field_calibrate_laser.py | 10 +- fishsense_lite/commands/label_studio.py | 251 +++++++++ fishsense_lite/commands/preprocess.py | 24 +- fishsense_lite/commands/process.py | 9 +- fishsense_lite/run.py | 2 + fishsense_lite/utils.py | 37 ++ poetry.lock | 488 +++++++++--------- 10 files changed, 561 insertions(+), 300 deletions(-) create mode 100644 fishsense_lite/commands/label_studio.py create mode 100644 fishsense_lite/utils.py diff --git a/.vscode/launch.json b/.vscode/launch.json index 57074ed..79f5c3f 100644 --- a/.vscode/launch.json +++ b/.vscode/launch.json @@ -11,7 +11,7 @@ "module": "fishsense_lite", "justMyCode": false, "args": [ - "process", + "label-studio", "--help" ] }, @@ -118,5 +118,25 @@ // "--overwrite", ] }, + { + "name": "Label Studio", + "type": "debugpy", + "request": "launch", + "module": "fishsense_lite", + "justMyCode": false, + "args": [ + "label-studio", + "~/Data/082923_Pool Calibration/082929_Slate_FSL01/*.ORF", + "--lens-calibration", + "~/Data/calibration-parameters/FSL-01D/fsl-01d-lens-raw.pkg", + "--laser-position", + "-4", "-11", "0", + "--laser-axis", + "0", "0", "1", + "--output", + "./output", + "--overwrite", + ] + }, ] } \ No newline at end of file diff --git a/fishsense_lite/commands/calibrate_laser.py b/fishsense_lite/commands/calibrate_laser.py index 8f71719..275e206 100644 --- a/fishsense_lite/commands/calibrate_laser.py +++ b/fishsense_lite/commands/calibrate_laser.py @@ -13,13 +13,7 @@ from pyfishsensedev.laser.nn_laser_detector import NNLaserDetector from pyfishsensedev.plane_detector.checkerboard_detector import CheckerboardDetector - -def uint16_2_double(img: np.ndarray) -> np.ndarray: - return img.astype(np.float64) / 65535 - - -def uint16_2_uint8(img: np.ndarray) -> np.ndarray: - return (uint16_2_double(img) * 255).astype(np.uint8) +from fishsense_lite.utils import uint16_2_uint8 @ray.remote(num_gpus=0.25) @@ -125,6 +119,7 @@ def lens_calibration(self, value: str): "--laser-position", short_name="-p", nargs=3, + required=True, help="The laser position in centimeter inputed as x y z for the FishSense Lite product line.", ) def laser_position(self) -> List[int]: @@ -139,6 +134,7 @@ def laser_position(self, value: List[int]): "--laser-axis", short_name="-a", nargs=3, + required=True, help="The laser axis unit vector inputed as x y z for the FishSense Lite product line.", ) def laser_axis(self) -> List[float]: diff --git a/fishsense_lite/commands/calibrate_lens.py b/fishsense_lite/commands/calibrate_lens.py index 25f8a3b..eb0c8e2 100644 --- a/fishsense_lite/commands/calibrate_lens.py +++ b/fishsense_lite/commands/calibrate_lens.py @@ -9,13 +9,7 @@ from pyfishsensedev.image.image_processors import RawProcessor from pyfishsensedev.plane_detector.checkerboard_detector import CheckerboardDetector - -def uint16_2_double(img: np.ndarray) -> np.ndarray: - return img.astype(np.float64) / 65535 - - -def uint16_2_uint8(img: np.ndarray) -> np.ndarray: - return (uint16_2_double(img) * 255).astype(np.uint8) +from fishsense_lite.utils import uint16_2_uint8 @ray.remote(num_gpus=0.1) diff --git a/fishsense_lite/commands/field_calibrate_laser.py b/fishsense_lite/commands/field_calibrate_laser.py index 026d9e5..39c729a 100644 --- a/fishsense_lite/commands/field_calibrate_laser.py +++ b/fishsense_lite/commands/field_calibrate_laser.py @@ -16,13 +16,7 @@ from pyfishsensedev.library.homography import viz2d from pyfishsensedev.plane_detector.slate_detector import SlateDetector - -def uint16_2_double(img: np.ndarray) -> np.ndarray: - return img.astype(np.float64) / 65535 - - -def uint16_2_uint8(img: np.ndarray) -> np.ndarray: - return (uint16_2_double(img) * 255).astype(np.uint8) +from fishsense_lite.utils import uint16_2_uint8 @ray.remote(num_gpus=0.25) @@ -135,6 +129,7 @@ def lens_calibration(self, value: str): "--laser-position", short_name="-p", nargs=3, + required=True, help="The laser position in centimeter inputed as x y z for the FishSense Lite product line.", ) def laser_position(self) -> List[int]: @@ -149,6 +144,7 @@ def laser_position(self, value: List[int]): "--laser-axis", short_name="-a", nargs=3, + required=True, help="The laser axis unit vector inputed as x y z for the FishSense Lite product line.", ) def laser_axis(self) -> List[float]: diff --git a/fishsense_lite/commands/label_studio.py b/fishsense_lite/commands/label_studio.py new file mode 100644 index 0000000..d859068 --- /dev/null +++ b/fishsense_lite/commands/label_studio.py @@ -0,0 +1,251 @@ +"""Module which represents the FishSense Lite Label Studio CLI.""" + +import json +import random +import string +from glob import glob +from pathlib import Path +from typing import List, Tuple + +import cv2 +import numpy as np +import ray +import torch +from fishsense_common.pluggable_cli import Command, argument +from pyfishsensedev.calibration import LaserCalibration, LensCalibration +from pyfishsensedev.image.image_processors import RawProcessor +from pyfishsensedev.image.image_rectifier import ImageRectifier +from pyfishsensedev.laser.nn_laser_detector import NNLaserDetector + +from fishsense_lite import __version__ +from fishsense_lite.utils import get_output_file, get_root, uint16_2_uint8 + + +@ray.remote(num_gpus=0.25) +def execute_laser( + input_file: Path, + lens_calibration: LensCalibration, + estimated_laser_calibration: LaserCalibration, + root: Path, + output: Path, + overwrite: bool, +) -> Tuple[np.ndarray, int, int]: + device = "cuda" if torch.cuda.is_available() else "cpu" + output_file = get_output_file(input_file, root, output, "jpg") + + if output_file.exists() and not overwrite: + return None, None, None + + dark_raw_processor = RawProcessor(enable_histogram_equalization=False) + image_dark = uint16_2_uint8(dark_raw_processor.load_and_process(input_file)) + + height, width, _ = image_dark.shape + + image_rectifier = ImageRectifier(lens_calibration) + image_dark = image_rectifier.rectify(image_dark) + + laser_detector = NNLaserDetector( + lens_calibration, estimated_laser_calibration, device + ) + laser_image_coord = laser_detector.find_laser(image_dark) + + output_file.parent.mkdir(parents=True, exist_ok=True) + cv2.imwrite(output_file.absolute().as_posix(), image_dark) + + return output_file, laser_image_coord, width, height + + +class Data: + def __init__(self, img: str): + self.img = img + + +class LaserValue: + def __init__(self, x: float, y: float, width: int, height: int): + self.x = x / float(width) * 100 + self.y = y / float(height) * 100 + self.width = 0.25 + self.keypointlabels = ["Red Laser"] + + +class LaserResult: + def __init__(self, laser_image_coord: np.ndarray, width: int, height: int): + self.original_width = width + self.original_height = height + self.image_rotation = 0 + self.value = LaserValue( + laser_image_coord[0], laser_image_coord[1], width, height + ) + + letters_and_numbers = string.ascii_letters + string.digits + + self.id = "".join(random.choice(letters_and_numbers) for i in range(10)) + self.from_name = "kp-1" + self.to_name = "img-1" + self.type = "keypointlabels" + + +class LaserPrediction: + def __init__(self, laser_image_coord: np.ndarray, width: int, height: int): + self.model_version = __version__ + self.results = [LaserResult(laser_image_coord, width, height)] + + +class LaserLabelStudioJSON: + def __init__( + self, img: str, laser_image_coord: np.ndarray, width: int, height: int + ): + self.data = Data(img) + self.predictions = [LaserPrediction(laser_image_coord, width, height)] + + +class LabelStudioCommand(Command): + """Command which represents the FishSense Lite Label Studio CLI.""" + + @property + def name(self) -> str: + return "label-studio" + + @property + def description(self) -> str: + return "Outputs data in a format for comsuption with Label Studio." + + @property + @argument("data", required=True, help="A glob that represents the data to process.") + def data(self) -> List[str]: + return self.__data + + @data.setter + def data(self, value: List[str]): + self.__data = value + + @property + @argument( + "--laser-position", + short_name="-p", + nargs=3, + required=True, + help="The laser position in centimeter inputed as x y z for the FishSense Lite product line.", + ) + def laser_position(self) -> List[int]: + return self.__laser_position + + @laser_position.setter + def laser_position(self, value: List[int]): + self.__laser_position = value + + @property + @argument( + "--laser-axis", + short_name="-a", + nargs=3, + required=True, + help="The laser axis unit vector inputed as x y z for the FishSense Lite product line.", + ) + def laser_axis(self) -> List[float]: + return self.__laser_axis + + @laser_axis.setter + def laser_axis(self, value: List[float]): + self.__laser_axis = value + + @property + @argument( + "--lens-calibration", + short_name="-l", + required=True, + help="Lens calibration package for the FishSense Lite.", + ) + def lens_calibration(self) -> str: + return self.__lens_calibration + + @lens_calibration.setter + def lens_calibration(self, value: str): + self.__lens_calibration = value + + @property + @argument( + "--output", + short_name="-o", + required=True, + help="The path to store the resulting database.", + ) + def output_path(self) -> str: + return self.__output_path + + @output_path.setter + def output_path(self, value: str): + self.__output_path = value + + @property + @argument("--overwrite", flag=True, help="Overwrite the calibration if it exists.") + def overwrite(self) -> bool: + return self.__overwrite + + @overwrite.setter + def overwrite(self, value: bool): + self.__overwrite = value + + def __init__(self): + super().__init__() + + self.__data: List[str] = None + self.__lens_calibration: str = None + self.__laser_position: List[int] = None + self.__laser_axis: List[float] = None + self.__output_path: str = None + self.__overwrite: bool = None + + def __call__(self): + self.init_ray() + + files = {Path(f).absolute() for g in self.data for f in glob(g, recursive=True)} + root = get_root(files) + + lens_calibration = LensCalibration() + lens_calibration.load(Path(self.lens_calibration)) + + estimated_laser_calibration = LaserCalibration( + np.array(self.laser_axis), np.array(self.laser_position) + ) + + output = Path(self.output_path) + + self.__build_laser_json( + files, lens_calibration, estimated_laser_calibration, root, output + ) + + def __build_laser_json( + self, + files: List[Path], + lens_calibration: LensCalibration, + estimated_laser_calibration: LaserCalibration, + root: Path, + output: Path, + ): + output = output / "laser" + output.mkdir(parents=True, exist_ok=True) + + laser_json_path = output / "label_studio.json" + if laser_json_path.exists() and not self.overwrite: + return + + futures = [ + execute_laser.remote( + f, + lens_calibration, + estimated_laser_calibration, + root, + output, + self.overwrite, + ) + for f in files + ] + + laser_json_objects = [ + LaserLabelStudioJSON(f.relative_to(output.absolute()).as_posix(), l, w, h) + for f, l, w, h in self.tqdm(futures, total=len(files)) + ] + + with open(laser_json_path, "w") as f: + f.write(json.dumps(laser_json_objects, default=vars)) diff --git a/fishsense_lite/commands/preprocess.py b/fishsense_lite/commands/preprocess.py index a7470b6..b9c7296 100644 --- a/fishsense_lite/commands/preprocess.py +++ b/fishsense_lite/commands/preprocess.py @@ -9,13 +9,7 @@ from pyfishsensedev.calibration import LensCalibration from pyfishsensedev.image import ImageRectifier, RawProcessor - -def uint16_2_double(img: np.ndarray) -> np.ndarray: - return img.astype(np.float64) / 65535 - - -def uint16_2_uint8(img: np.ndarray) -> np.ndarray: - return (uint16_2_double(img) * 255).astype(np.uint8) +from fishsense_lite.utils import get_output_file, get_root, uint16_2_uint8 @ray.remote(num_gpus=0.1) @@ -28,15 +22,7 @@ def execute( format: str, overwrite: bool, ): - output_file = Path( - input_file.absolute() - .as_posix() - .replace(root.as_posix(), output.absolute().as_posix()) - .replace( - input_file.suffix, - f".{format}", - ) - ) + output_file = get_output_file(input_file, root, output, format) if not overwrite and output_file.exists(): return @@ -158,11 +144,7 @@ def __call__(self): files = {Path(f).absolute() for g in self.data for f in glob(g, recursive=True)} # Find the singular path that defines the root of all of our data. - root = files - while len(root) > 1: - max_count = max(len(f.parts) for f in root) - root = {f.parent if len(f.parts) == max_count else f for f in root} - root = root.pop() + root = get_root(files) lens_calibration = LensCalibration() lens_calibration.load(Path(self.lens_calibration)) diff --git a/fishsense_lite/commands/process.py b/fishsense_lite/commands/process.py index 2ffbba3..3693480 100644 --- a/fishsense_lite/commands/process.py +++ b/fishsense_lite/commands/process.py @@ -18,14 +18,7 @@ from fishsense_lite.database import Database from fishsense_lite.result_status import ResultStatus - - -def uint16_2_double(img: np.ndarray) -> np.ndarray: - return img.astype(np.float64) / 65535 - - -def uint16_2_uint8(img: np.ndarray) -> np.ndarray: - return (uint16_2_double(img) * 255).astype(np.uint8) +from fishsense_lite.utils import uint16_2_uint8 @ray.remote(num_gpus=0.25) diff --git a/fishsense_lite/run.py b/fishsense_lite/run.py index e6e12aa..3494f9c 100644 --- a/fishsense_lite/run.py +++ b/fishsense_lite/run.py @@ -5,6 +5,7 @@ from fishsense_lite.commands.calibrate_laser import CalibrateLaser from fishsense_lite.commands.calibrate_lens import CalibrateLens from fishsense_lite.commands.field_calibrate_laser import FieldCalibrateLaser +from fishsense_lite.commands.label_studio import LabelStudioCommand from fishsense_lite.commands.preprocess import Preprocess from fishsense_lite.commands.process import Process @@ -21,6 +22,7 @@ def main(): cli.add(FieldCalibrateLaser()) cli.add(Preprocess()) cli.add(Process()) + cli.add(LabelStudioCommand()) cli() diff --git a/fishsense_lite/utils.py b/fishsense_lite/utils.py new file mode 100644 index 0000000..dfeafeb --- /dev/null +++ b/fishsense_lite/utils.py @@ -0,0 +1,37 @@ +from pathlib import Path +from typing import List + +import numpy as np + + +def get_output_file(input_file: Path, root: Path, output: Path, extension: str) -> Path: + return Path( + input_file.absolute() + .as_posix() + .replace(root.as_posix(), output.absolute().as_posix()) + .replace( + input_file.suffix, + f".{extension}", + ) + ) + + +def get_root(files: List[Path]) -> Path | None: + if not files: + return None + + root = files + while len(root) > 1: + max_count = max(len(f.parts) for f in root) + root = {f.parent if len(f.parts) == max_count else f for f in root} + root = root.pop() + + return root + + +def uint16_2_double(img: np.ndarray) -> np.ndarray: + return img.astype(np.float64) / 65535 + + +def uint16_2_uint8(img: np.ndarray) -> np.ndarray: + return (uint16_2_double(img) * 255).astype(np.uint8) diff --git a/poetry.lock b/poetry.lock index dc180e9..a57d349 100644 --- a/poetry.lock +++ b/poetry.lock @@ -503,37 +503,37 @@ tests = ["pytest", "pytest-cov", "pytest-xdist"] [[package]] name = "debugpy" -version = "1.8.7" +version = "1.8.8" description = "An implementation of the Debug Adapter Protocol for Python" optional = false python-versions = ">=3.8" files = [ - {file = "debugpy-1.8.7-cp310-cp310-macosx_14_0_x86_64.whl", hash = "sha256:95fe04a573b8b22896c404365e03f4eda0ce0ba135b7667a1e57bd079793b96b"}, - {file = "debugpy-1.8.7-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:628a11f4b295ffb4141d8242a9bb52b77ad4a63a2ad19217a93be0f77f2c28c9"}, - {file = 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