diff --git a/docs/cli.md b/docs/cli.md deleted file mode 100644 index d9e7067..0000000 --- a/docs/cli.md +++ /dev/null @@ -1 +0,0 @@ -::: geococo.cli diff --git a/docs/fiftyone.md b/docs/fiftyone.md deleted file mode 100644 index 10899ec..0000000 --- a/docs/fiftyone.md +++ /dev/null @@ -1 +0,0 @@ -## To be continued \ No newline at end of file diff --git a/docs/img/android-chrome-192x192.png b/docs/img/android-chrome-192x192.png deleted file mode 100644 index 8567ac5..0000000 Binary files a/docs/img/android-chrome-192x192.png and /dev/null differ diff --git a/docs/img/android-chrome-512x512.png b/docs/img/android-chrome-512x512.png deleted file mode 100644 index 6f0d2bb..0000000 Binary files a/docs/img/android-chrome-512x512.png and /dev/null differ diff --git a/docs/img/apple-touch-icon.png b/docs/img/apple-touch-icon.png deleted file mode 100644 index d4b9862..0000000 Binary files a/docs/img/apple-touch-icon.png and /dev/null differ diff --git a/docs/img/favicon-16x16.png b/docs/img/favicon-16x16.png deleted file mode 100644 index 5811fc6..0000000 Binary files a/docs/img/favicon-16x16.png and /dev/null differ diff --git a/docs/img/favicon-32x32.png b/docs/img/favicon-32x32.png deleted file mode 100644 index 56853c9..0000000 Binary files a/docs/img/favicon-32x32.png and /dev/null differ diff --git a/docs/img/favicon.ico b/docs/img/favicon.ico deleted file mode 100644 index 83e8d71..0000000 Binary files a/docs/img/favicon.ico and /dev/null differ diff --git a/docs/img/site.webmanifest b/docs/img/site.webmanifest deleted file mode 100644 index 45dc8a2..0000000 --- a/docs/img/site.webmanifest +++ /dev/null @@ -1 +0,0 @@ -{"name":"","short_name":"","icons":[{"src":"/android-chrome-192x192.png","sizes":"192x192","type":"image/png"},{"src":"/android-chrome-512x512.png","sizes":"512x512","type":"image/png"}],"theme_color":"#ffffff","background_color":"#ffffff","display":"standalone"} \ No newline at end of file diff --git a/docs/img/splash.png b/docs/img/splash.png deleted file mode 100644 index b3c161c..0000000 Binary files a/docs/img/splash.png and /dev/null differ diff --git a/docs/index.md b/docs/index.md deleted file mode 100644 index 1e593f4..0000000 --- a/docs/index.md +++ /dev/null @@ -1,175 +0,0 @@ -# Welcome to geococo's documentation! -![geococo logo](https://github.com/jaspersiebring/GeoCOCO/assets/25051531/b2a2db16-1400-4c43-b044-a924a378ef84) - -Easily transform your GIS annotations into [Microsoft's Common Objects In Context (COCO)](https://cocodataset.org/#format-data) datasets with GeoCOCO. This tool allows users to leverage the advanced digitizing solutions of modern GIS software for the annotations of image objects in geographic imagery. - -Built with `Pydantic` and `pycocotools`, it features a complete implementation of the COCO standard for object detection with out-of-the-box support for JSON-encoding and RLE compression. The resulting datasets are versioned, easily extendable with new annotations and fully compatible with other data applications that accept the COCO format. - -## Key features -- User-friendly: GeoCOCO is designed for ease of use, requiring minimal configuration and domain knowledge -- Version Control: Datasets created with GeoCOCO are versioned and designed for expansion with future annotations -- Command-line Tool: Use GeoCOCO from your terminal to create, append and copy COCO datasets -- Python Module: Integrate GeoCOCO in your own data applications with the `geococo` package -- Representation: GeoCOCO maximizes label representation through an adaptive moving window approach -- COCO Standard: Output datasets are fully compatible with other COCO-accepting applications -- Compact File Size: JSON-encoding and RLE compression are employed to ensure compact file sizes - -## Installation -Installing from the Python Package Index (PyPI): -```` -# Install from PYPI with Python's package installer (pip) -pip install geococo -```` - -## Example of usage - -After installing `geococo`, there are a number of ways you can interact with its API. - -#### Command line interface - The easiest way to use `geococo` is to simply call it from your preferred terminal with one of three commands: `new`, `add` and `copy`. - -```` -$ geococo --help -Usage: geococo [OPTIONS] COMMAND [ARGS]... - - Transform your GIS annotations into COCO datasets. - -Options: - --help Show this message and exit. - -Commands: - add Transform and add GIS annotations to an existing CocoDataset - copy Copy and (optionally) update the metadata of an existing CocoDataset - new Initialize a new CocoDataset with user-prompted metadata -```` - -Starting a new CocoDataset (will prompt user for metadata like Description and Contributor) - -```` -$ geococo new dataset.json -```` - -Adding new annotations to existing CocoDataset (will increment version based on input data and update any new categories/images) -```` -$ geococo add image.tif labels.shp dataset.json images/ 512 512 --id-attribute ids -```` - -For more information on the different commands, call `geococo COMMAND` with `--help`. -```` -$ geococo add --help -Usage: geococo add [OPTIONS] IMAGE_PATH LABELS_PATH JSON_PATH OUTPUT_DIR WIDTH - HEIGHT - - Transform and add GIS annotations to an existing COCO dataset. - - This method generates a COCO dataset by moving across the given image - (image_path) with a moving window (width, height), constantly checking for - intersecting annotations (labels_path) that represent image objects in said - image (e.g. buildings in satellite imagery; denoted by (super)category name - and/or id). Each valid intersection will add n Annotations entries to the - dataset (json_path) and save a subset of the input image that contained - these entries (output_dir). - - The output data size depends on your input labels, as the moving window - adjusts its step size to accommodate the average annotation size, optimizing - dataset representation and minimizing tool configuration. Each addition will - also increment the dataset version: patch if using the same image_path, - minor if using a new image_path, and major if using a new output_dir. - -Arguments: - IMAGE_PATH Path to geospatial image containing image objects [required] - LABELS_PATH Path to vector file containing annotated image objects - [required] - JSON_PATH Path to json file containing the COCO dataset [required] - OUTPUT_DIR Path to output directory for image subsets [required] - WIDTH Width of image subsets [required] - HEIGHT Height of image subsets [required] - -Options: - --id-attribute TEXT Name of column containing category_id values - (optional if --name_attribute is given) - --name-attribute TEXT Name of column containing category_name values - (optional if --id_attribute is given) - --super-attribute TEXT Name of column containing supercategory values - --help Show this message and exit. -```` - - -#### Python module -This is recommended for most developers as it gives you more granular control over the various steps. It does assume a basic familiarity with the `geopandas` and `rasterio` packages (i.e. GIS modules that help you manage vector and raster data respectively). - -```` -import pathlib -import geopandas as gpd -import rasterio -from geococo import create_dataset, load_dataset, save_dataset, append_dataset - -# Replace this with your preferred output paths -data_path = pathlib.Path("path/to/your/coco/output/images") -json_path = pathlib.Path("path/to/your/coco/json/file") - -# Dimensions of the moving window and output images -width, height = 512, 512 - -# Starting a new CocoDataset -description = "My First Dataset" -contributor = "User" - -# version and date_created are automatically set -dataset = create_dataset(description=description, contributor=contributor) -# You can also load existing COCO datasets -# dataset = load_dataset(json_path=json_path) - -# Loading GIS data with rasterio and geopandas -labels = gpd.read_file(some_labels_path) -raster_source = rasterio.open(some_image_path) - -# (Optional) Apply any spatial or attribute queries here -# labels = labels.loc[labels["ids"].isin([1, 2, 3])] -# labels = labels.loc[labels.within(some_polygon)] - -# Find and save all Annotation instances -dataset = append_dataset( - dataset=dataset, - images_dir=data_path, - src=raster_source, - labels=labels, - window_bounds=[(width, height)], - id_attribute=None, # column with category_id values - name_attribute="ids", # column with category_name values - super_attribute=None, # optional column with super_category values -) - -# Encode CocoDataset instance as JSON and save to json_path -save_dataset(dataset=dataset, json_path=json_path) -```` - -## Visualization with FiftyOne -Like the official COCO project, the open source tool [FiftyOne](https://docs.voxel51.com/) can be used to visualize and evaluate your datasets. To do this, you'll need the `fiftyone` and `pycocotools` packages. Note that `geococo` does not install `fiftyone` by default, so you'll need to install it separately (instructions for installation can be found [here](https://docs.voxel51.com/getting_started/install.html)). Once you have `fiftyone` installed, you can use the following command to inspect your COCO dataset in your web browser. - -```` -# requires pycocotools and fiftyone -import fiftyone as fo -import fiftyone.zoo as foz -import pathlib - -data_path = pathlib.Path("path/to/your/coco/output/images") -json_path = pathlib.Path("path/to/your/coco/json/file") - -# Load COCO formatted dataset -coco_dataset = fo.Dataset.from_dir( - dataset_type=fo.types.COCODetectionDataset, - data_path=data_path, - labels_path=json_path, - include_id=True, -) - -# Launch the app -session = fo.launch_app(coco_dataset, port=5151) -```` - -

- - -

- diff --git a/docs/leafmap.md b/docs/leafmap.md deleted file mode 100644 index 10899ec..0000000 --- a/docs/leafmap.md +++ /dev/null @@ -1 +0,0 @@ -## To be continued \ No newline at end of file diff --git a/docs/models.md b/docs/models.md deleted file mode 100644 index ba0ca82..0000000 --- a/docs/models.md +++ /dev/null @@ -1,13 +0,0 @@ -::: geococo.coco_models - options: - members: - - Info - - Image - - Annotation - - Category - - RleDict - - Source - - CocoDataset - show_root_heading: false - merge_init_into_class: false - show_if_no_docstring: false \ No newline at end of file diff --git a/docs/processing.md b/docs/processing.md deleted file mode 100644 index 17a40c4..0000000 --- a/docs/processing.md +++ /dev/null @@ -1,16 +0,0 @@ -::: geococo.coco_manager - options: - members: - - create_dataset - - load_dataset - - save_dataset - show_root_heading: false - - -::: geococo.coco_processing - options: - members: - - append_dataset - show_root_heading: false - - diff --git a/docs/utils.md b/docs/utils.md deleted file mode 100644 index 3454d2d..0000000 --- a/docs/utils.md +++ /dev/null @@ -1 +0,0 @@ -::: geococo.utils diff --git a/mkdocs.yml b/mkdocs.yml deleted file mode 100644 index 96f9eca..0000000 --- a/mkdocs.yml +++ /dev/null @@ -1,61 +0,0 @@ -site_name: "GeoCOCO: Transform your GIS annotations into COCO datasets" -site_description: Transform your GIS annotations into COCO datasets -site_url: https://jaspersiebring.github.io/geococo/ -repo_url: https://github.com/jaspersiebring/geococo -repo_name: jaspersiebring/geococo - -nav: -- Quickstart: index.md -- API Documentation: - - COCO Models: models.md - - COCO Processing: processing.md - - Typer CLI: cli.md - - Utilities: utils.md -- References: - - License: https://github.com/jaspersiebring/GeoCOCO/blob/main/LICENSE - -theme: - name: material - favicon: img/favicon.ico - logo: img/favicon.ico - palette: - - media: "(prefers-color-scheme: light)" - scheme: default - primary: light green - accent: light green - toggle: - icon: material/lightbulb-outline - name: "Switch to dark mode" - - media: "(prefers-color-scheme: dark)" - scheme: slate - primary: light green - accent: light green - toggle: - icon: material/lightbulb - name: "Switch to light mode" - highlightjs: true - locale: en - features: - - content.code.annotate - - content.code.copy - - navigation.instant - - navigation.tracking - - navigation.sections - - navigation.top - - navigation.indexes - - toc.follow - -plugins: - - search - - mkdocstrings: - default_handler: python - handlers: - python: - import: - - url: https://docs.python-requests.org/en/master/objects.inv - domains: [std, py] - options: - docstring_style: sphinx - docstring_section_style: table - summary: true - separate_signature: true diff --git a/poetry.lock b/poetry.lock index 0d94561..c3ff826 100644 --- a/poetry.lock +++ b/poetry.lock @@ -33,20 +33,6 @@ docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib- tests = ["attrs[tests-no-zope]", "zope-interface"] tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"] -[[package]] -name = "babel" -version = "2.12.1" -description = "Internationalization utilities" -optional = false -python-versions = ">=3.7" -files = [ - {file = "Babel-2.12.1-py3-none-any.whl", hash = "sha256:b4246fb7677d3b98f501a39d43396d3cafdc8eadb045f4a31be01863f655c610"}, - {file = "Babel-2.12.1.tar.gz", hash = "sha256:cc2d99999cd01d44420ae725a21c9e3711b3aadc7976d6147f622d8581963455"}, -] - -[package.dependencies] -pytz = {version = ">=2015.7", markers = "python_version < \"3.9\""} - [[package]] name = "black" version = "23.9.1" @@ -606,48 +592,6 @@ pandas = ">=1.1.0" pyproj = ">=3.0.1" shapely = ">=1.7.1" -[[package]] -name = "ghp-import" -version = "2.1.0" -description = "Copy your docs directly to the gh-pages branch." -optional = false -python-versions = "*" -files = [ - {file = "ghp-import-2.1.0.tar.gz", hash = "sha256:9c535c4c61193c2df8871222567d7fd7e5014d835f97dc7b7439069e2413d343"}, - {file = "ghp_import-2.1.0-py3-none-any.whl", hash = "sha256:8337dd7b50877f163d4c0289bc1f1c7f127550241988d568c1db512c4324a619"}, -] - -[package.dependencies] -python-dateutil = ">=2.8.1" - -[package.extras] -dev = ["flake8", "markdown", "twine", "wheel"] - -[[package]] -name = "griffe" -version = "0.36.2" -description = "Signatures for entire Python programs. 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