diff --git a/package.json b/package.json index 22d7376..9766fc9 100644 --- a/package.json +++ b/package.json @@ -4,8 +4,8 @@ "version": "1.2.8rc1", "description": "Quickly extract ROIs from cloud-hosted medical scans.", "main": "./out/main/index.js", - "author": "Weaver Goldman ", - "homepage": "https://github.com/We-Gold/ouroboros", + "author": "Weaver Goldman and David Northover ", + "homepage": "https://github.com/ChengLabResearch/ouroboros", "scripts": { "format": "prettier --write .", "lint": "eslint . --ext .js,.jsx,.cjs,.mjs,.ts,.tsx,.cts,.mts --fix", diff --git a/python/ouroboros/cli.py b/python/ouroboros/cli.py index 0cc1dfe..8543bb2 100644 --- a/python/ouroboros/cli.py +++ b/python/ouroboros/cli.py @@ -1,8 +1,13 @@ import argparse +import json from multiprocessing import freeze_support +from pathlib import Path import sys -from ouroboros.common.pipelines import backproject_pipeline, slice_pipeline +import numpy as np +from scipy.spatial.transform import Rotation as R + +from ouroboros.common.pipelines import backproject_pipeline, slice_pipeline, geometry_pipeline from ouroboros.helpers.models import pretty_json_output from ouroboros.helpers.options import ( DEFAULT_BACKPROJECT_OPTIONS, @@ -57,6 +62,21 @@ def main(): help="Export sample options files into the current folder.", ) + # Create the parser for the geometry command + parser_geometry = subparsers.add_parser( + "geometry", help="Output the geometry of the spline." + ) + parser_geometry.add_argument( + "options", + type=str, + help="The path to the options json file.", + ) + parser_geometry.add_argument( + "--include-ng", + action="store_true", + help="Include Neuroglancer points and angles." + ) + # Parse the arguments args = parser.parse_args() @@ -68,10 +88,50 @@ def main(): handle_backproject(args) case "sample-options": handle_sample_options() + case "geometry": + handle_geometry(args) case _: parser.print_help() +def handle_geometry(args): + print(f"Loading slice options from: {args.options}") + slice_options = SliceOptions.load_from_json(args.options) + + if isinstance(slice_options, str): + print("Exiting due to errors loading slice options.", file=sys.stderr) + sys.exit(1) + + print("Slice options loaded successfully.") + pipeline, input_data = geometry_pipeline(slice_options) + + _, error = pipeline.process(input_data) + + if error: + print(f"Pipeline Error: {error}", file=sys.stderr) + + rects_output = Path(slice_options.output_file_folder, f"{slice_options.output_file_name}_rects").with_suffix(".npy") + np.save(rects_output, input_data.slice_rects) + + if args.include_ng: + ng_output = Path(slice_options.output_file_folder, f"{slice_options.output_file_name}_ng").with_suffix(".json") + rot_matrix = np.empty((3, len(input_data.slice_rects), 3)) + + rot_matrix[0] = (input_data.slice_rects[:, 1, :] - input_data.slice_rects[:, 0, :]) / slice_options.slice_width + rot_matrix[1] = (input_data.slice_rects[:, 3, :] - input_data.slice_rects[:, 0, :]) / slice_options.slice_height + rot_matrix[2] = np.divide(np.cross(rot_matrix[0], rot_matrix[1], axis=1), + (slice_options.slice_width * slice_options.slice_height)) + centers = (input_data.slice_rects[:, 0, :] + input_data.slice_rects[:, 2, :]) / 2 + quats = R.from_matrix(rot_matrix.transpose(1, 0, 2)).as_quat() + + ng_points = [] + for point in range(len(input_data.slice_rects)): + ng_points.append({"position": centers[point].tolist(), "crossSectionOrientation": quats[point].tolist()}) + + with open(ng_output, "w") as handle: + json.dump(ng_points, handle) + + def handle_slice(args): print(f"Loading slice options from: {args.options}") slice_options = SliceOptions.load_from_json(args.options) diff --git a/python/ouroboros/common/pipelines.py b/python/ouroboros/common/pipelines.py index f9a4e3f..6e773e2 100644 --- a/python/ouroboros/common/pipelines.py +++ b/python/ouroboros/common/pipelines.py @@ -10,6 +10,37 @@ ) +def geometry_pipeline(slice_options: SliceOptions) -> tuple[Pipeline, PipelineInput]: + """ + Creates a pipeline for slicing a volume, as well as the default input data for the pipeline. + + Parameters + ---------- + slice_options : SliceOptions + The options for slicing the volume. + include-ng : bool, optional + Whether to include neuroglancer output data, default false. + + Returns + ------- + tuple[Pipeline, PipelineInput] + The pipeline for slicing the volume and the default input data for the pipeline + """ + + pipeline = Pipeline( + [ + ParseJSONPipelineStep(), + SlicesGeometryPipelineStep() + ] + ) + + default_input_data = PipelineInput( + slice_options=slice_options, json_path=slice_options.neuroglancer_json + ) + + return pipeline, default_input_data + + def slice_pipeline(slice_options: SliceOptions, verbose: bool = False) -> tuple[Pipeline, PipelineInput]: """ Creates a pipeline for slicing a volume, as well as the default input data for the pipeline. diff --git a/python/ouroboros/helpers/files.py b/python/ouroboros/helpers/files.py index 896a082..03ff151 100644 --- a/python/ouroboros/helpers/files.py +++ b/python/ouroboros/helpers/files.py @@ -218,6 +218,7 @@ def volume_from_intermediates(path: Path, shape: DataShape, discrete: bool = Fal nz = np.flatnonzero(vol[0]) vol[0, nz] /= vol[1, nz] if discrete: + vol[0] = np.round(vol[0], 2) vol[0, vol[0] % 1 != 0] = 0 return vol[0] diff --git a/python/poetry.lock b/python/poetry.lock index d0c64dc..72717f6 100644 --- a/python/poetry.lock +++ b/python/poetry.lock @@ -2,14 +2,14 @@ [[package]] name = "altgraph" -version = "0.17.4" +version = "0.17.5" description = "Python graph (network) package" optional = false python-versions = "*" groups = ["dev"] files = [ - {file = "altgraph-0.17.4-py2.py3-none-any.whl", hash = "sha256:642743b4750de17e655e6711601b077bc6598dbfa3ba5fa2b2a35ce12b508dff"}, - {file = "altgraph-0.17.4.tar.gz", hash = "sha256:1b5afbb98f6c4dcadb2e2ae6ab9fa994bbb8c1d75f4fa96d340f9437ae454406"}, + {file = "altgraph-0.17.5-py2.py3-none-any.whl", hash = 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