diff --git a/Makefile b/Makefile index 8d6dd91..05bff5d 100644 --- a/Makefile +++ b/Makefile @@ -19,4 +19,4 @@ lint: $(POETRY) run mypy --ignore-missing-imports --install-types --non-interactive plotdigitizer tests fmt: - black plotdigitizer/* tests/* + $(POETRY) run ruff format . diff --git a/issues/9-transparent-image/151915768-7d6fca3b-8967-4a0b-a1b9-a1815ad5aa3a.jpg b/issues/9-transparent-image/151915768-7d6fca3b-8967-4a0b-a1b9-a1815ad5aa3a.jpg new file mode 100644 index 0000000..a197ae9 Binary files /dev/null and b/issues/9-transparent-image/151915768-7d6fca3b-8967-4a0b-a1b9-a1815ad5aa3a.jpg differ diff --git a/issues/Makefile b/issues/Makefile new file mode 100644 index 0000000..cd579ad --- /dev/null +++ b/issues/Makefile @@ -0,0 +1,5 @@ +issue_9: ./9-transparent-image/151915768-7d6fca3b-8967-4a0b-a1b9-a1815ad5aa3a.jpg + cd .. && poetry install + poetry run plotdigitizer \ + -p 0,0 -p 80,0 -p 0,800 \ + $< diff --git a/plotdigitizer/__main__.py b/plotdigitizer/__main__.py new file mode 100644 index 0000000..5d6a810 --- /dev/null +++ b/plotdigitizer/__main__.py @@ -0,0 +1,3 @@ +from .main import main + +main() diff --git a/plotdigitizer/plotdigitizer.py b/plotdigitizer/plotdigitizer.py index d35d0d1..1310e42 100644 --- a/plotdigitizer/plotdigitizer.py +++ b/plotdigitizer/plotdigitizer.py @@ -12,6 +12,8 @@ import numpy as np import numpy.typing as npt import numpy.polynomial.polynomial as poly +import typer +from typing_extensions import Annotated import plotdigitizer.grid as grid from plotdigitizer.trajectory import find_trajectory, normalize @@ -35,6 +37,8 @@ img_: npt.NDArray[np.float64] = np.zeros((1, 1)) +app = typer.Typer() + def cache() -> Path: c = Path(tempfile.gettempdir()) / "plotdigitizer" @@ -224,12 +228,51 @@ def process_image(img): return traj -def run(args): +@app.command() +def digitize_plot( + infile: Path, + data_point: Annotated[ + T.List[str], + typer.Option( + "--data-point", + "-p", + help="Datapoints (min 3 required). You have to click on them later " + "e.g. `-p 0,0 -p 10,0 -p 0,1`. Make sure that point are comma " + "separated without any space.", + ), + ], + location: Annotated[ + T.List[str], + typer.Option( + "--location", + "-l", + help="Location of a points on figure in pixels (integer)[." + " These values should appear in the same order as -p option." + " If not given, you will be asked to click on the figure.", + ), + ] = [], + plot_file: Annotated[ + T.Optional[Path], + typer.Option("--plot-file", help="Plot the final result. Requires matplotlib"), + ] = None, + output: Annotated[ + T.Optional[Path], + typer.Option( + "--output", "-o", help="Name of the output file (default .traj.csv)" + ), + ] = None, + preprocess: Annotated[ + bool, + typer.Option( + "--preprocess", + "-P", + help="Preprocess the image. Useful with bad resolution images", + ), + ] = False, +): global locations_, points_ - global img_, args_ - args_ = args + global img_ - infile = Path(args.INPUT) assert infile.exists(), f"{infile} does not exists." logging.info(f"Extracting trajectories from {infile}") @@ -238,25 +281,25 @@ def run(args): img_ = normalize(img_) # erosion after dilation (closes gaps) - if args_.preprocess: + if preprocess: kernel = np.ones((1, 1), np.uint8) img_ = cv.morphologyEx(img_, cv.MORPH_CLOSE, kernel) - save_img_in_cache(img_, Path(f"{args_.INPUT.name}.close.png")) + save_img_in_cache(img_, Path(f"{infile.name}.close.png")) # remove grids. img_ = grid.remove_grid(img_) - save_img_in_cache(img_, Path(f"{args_.INPUT.name}.without_grid.png")) + save_img_in_cache(img_, Path(f"{infile.name}.without_grid.png")) # rescale it again. img_ = normalize(img_) logging.debug(" {img_.min()=} {img_.max()=}") assert img_.max() <= 255 assert img_.min() < img_.mean() < img_.max(), "Could not read meaningful data" - save_img_in_cache(img_, args_.INPUT.name) + save_img_in_cache(img_, infile.name) - points_ = list_to_points(args.data_point) - locations_ = list_to_points(args.location) - logging.debug(f"data points {args.data_point} → location on image {args.location}") + points_ = list_to_points(data_point) + locations_ = list_to_points(location) + logging.debug(f"data points {data_point} → location on image {location}") if len(locations_) != len(points_): logging.warning( @@ -267,65 +310,15 @@ def run(args): traj = process_image(img_) - if args_.plot is not None: - plot_traj(traj, args_.plot) + if plot_file is not None: + plot_traj(traj, plot_file) - outfile = args.output or f"{args.INPUT}.traj.csv" + outfile = output or f"{infile}.traj.csv" with open(outfile, "w") as f: for r in traj: f.write("%g %g\n" % (r)) logging.info("Wrote trajectory to %s" % outfile) -def main(): - # Argument parser. - import argparse - - description = """Digitize image.""" - parser = argparse.ArgumentParser(description=description) - parser.add_argument("INPUT", type=Path, help="Input image file.") - parser.add_argument( - "--data-point", - "-p", - required=True, - action="append", - help="Datapoints (min 3 required). You have to click on them later." - " At least 3 points are recommended. e.g -p 0,0 -p 10,0 -p 0,1 " - "Make sure that point are comma separated without any space.", - ) - parser.add_argument( - "--location", - "-l", - required=False, - default=[], - action="append", - help="Location of a points on figure in pixels (integer)." - " These values should appear in the same order as -p option." - " If not given, you will be asked to click on the figure.", - ) - parser.add_argument( - "--plot", - default=None, - required=False, - help="Plot the final result. Requires matplotlib.", - ) - parser.add_argument( - "--output", - "-o", - required=False, - type=str, - help="Name of the output file else trajectory will be written to " - " .traj.csv", - ) - parser.add_argument( - "--preprocess", - required=False, - action="store_true", - help="Preprocess the image. Useful with bad resolution images.", - ) - args = parser.parse_args() - run(args) - - -if __name__ == "__main__": - main() +def main() -> T.Any: + return app() diff --git a/poetry.lock b/poetry.lock index 72ded61..4968c8c 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,19 +1,33 @@ -# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. 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