### Install development dependencies

Source: https://github.com/scverse/spatialdata/blob/main/docs/contributing.md

Install the package in editable mode with development, testing, and documentation dependencies.

```bash
cd spatialdata-io
pip install -e ".[dev,test,doc]"
```

--------------------------------

### Install test dependencies

Source: https://github.com/scverse/spatialdata/blob/main/docs/contributing.md

Install the package with development and testing dependencies required for running tests.

```bash
pip install '-e[dev,test]'
```

--------------------------------

### Install SpatialData with Extra Dependencies

Source: https://github.com/scverse/spatialdata/blob/main/README.md

Use this command to install the 'spatialdata' package with all optional dependencies included. This is recommended for a full-featured installation.

```bash
pip install "spatialdata[extra]"
```

--------------------------------

### Install Airspeed Velocity and Dependencies

Source: https://github.com/scverse/spatialdata/blob/main/benchmarks/README.md

Installs the airspeed velocity framework and necessary dependencies for benchmarking. Ensure your working directory is the root of the SpatialData repository.

```bash
pip install -e '.[docs,test,benchmark]'
```

--------------------------------

### Install SpatialData via PyPI

Source: https://github.com/scverse/spatialdata/blob/main/docs/installation.md

Use this command to install the base SpatialData package from the Python Package Index.

```bash
pip install spatialdata
```

--------------------------------

### Install SpatialData Development Version from GitHub

Source: https://github.com/scverse/spatialdata/blob/main/docs/installation.md

Install the latest development version of SpatialData directly from its GitHub repository.

```bash
pip install git+https://github.com/scverse/spatialdata
```

--------------------------------

### Check Editable Install Path

Source: https://github.com/scverse/spatialdata/blob/main/docs/installation.md

Verify if an editable installation of SpatialData has been overridden by a PyPI installation. If the path contains 'site-packages', re-run the editable install command.

```python
import spatialdata; print(spatialdata.__path__)
```

--------------------------------

### Editable Install SpatialData from Cloned Repository

Source: https://github.com/scverse/spatialdata/blob/main/docs/installation.md

Perform an editable installation of SpatialData after cloning the repository. This is recommended for developers contributing to the project.

```bash
pip install -e .
```

--------------------------------

### Install SpatialData and Related Packages via Mamba

Source: https://github.com/scverse/spatialdata/blob/main/README.md

This command installs SpatialData and related visualization and I/O packages using Mamba. Note that conda installation is currently not recommended due to dependency issues, but this command is provided for reference.

```bash
mamba install -c conda-forge spatialdata napari-spatialdata spatialdata-io spatialdata-plot
```

--------------------------------

### Run all benchmarks

Source: https://github.com/scverse/spatialdata/blob/main/benchmarks/README.md

Executes all benchmarks defined in the project. This command can take a significant amount of time and may require specific environment setup (e.g., conda). It demonstrates the output format of `asv run` when encountering environment issues.

```bash
$ asv run
```

--------------------------------

### Install SpatialData with PyTorch DataLoader

Source: https://github.com/scverse/spatialdata/blob/main/docs/installation.md

Install SpatialData with the PyTorch dataloader dependency. This is required if you plan to use PyTorch-based data loading functionalities.

```bash
pip install "spatialdata[torch]"
```

--------------------------------

### Install SpatialData Ecosystem via Conda

Source: https://github.com/scverse/spatialdata/blob/main/docs/installation.md

Install SpatialData and related packages (spatialdata-io, spatialdata-plot, napari-spatialdata) using the conda-forge channel. Note: Latest versions might not be available on conda-forge.

```bash
mamba install -c conda-forge spatialdata spatialdata-io spatialdata-plot napari-spatialdata
```

--------------------------------

### Raccoon Dataset

Source: https://github.com/scverse/spatialdata/blob/main/docs/api/datasets.md

Loads the raccoon dataset, a small dataset for testing and examples.

```APIDOC
## GET /datasets/raccoon

### Description
Loads the raccoon dataset, a small dataset for testing and examples.

### Method
GET

### Endpoint
/datasets/raccoon

### Parameters
None

### Request Example
None

### Response
#### Success Response (200)
- **data** (SpatialData) - The raccoon dataset.

#### Response Example
```json
{
  "data": "SpatialData object representing the raccoon dataset"
}
```
```

--------------------------------

### Example of Scale Transformation in SpatialData

Source: https://github.com/scverse/spatialdata/blob/main/docs/design_doc.md

Demonstrates applying a Scale transformation to an image. Axes present in the element but not in the transformation are passed through, while axes in the transformation but not the element are ignored.

```python
Scale([2, 3, 4], axes=('x', 'y', 'z'))
```

--------------------------------

### Blobs Dataset

Source: https://github.com/scverse/spatialdata/blob/main/docs/api/datasets.md

Loads the blobs dataset, a small dataset for testing and examples.

```APIDOC
## GET /datasets/blobs

### Description
Loads the blobs dataset, a small dataset for testing and examples.

### Method
GET

### Endpoint
/datasets/blobs

### Parameters
None

### Request Example
None

### Response
#### Success Response (200)
- **data** (SpatialData) - The blobs dataset.

#### Response Example
```json
{
  "data": "SpatialData object representing the blobs dataset"
}
```
```

--------------------------------

### Blobs Annotating Element Dataset

Source: https://github.com/scverse/spatialdata/blob/main/docs/api/datasets.md

Loads the blobs_annotating_element dataset, a small dataset for testing and examples.

```APIDOC
## GET /datasets/blobs_annotating_element

### Description
Loads the blobs_annotating_element dataset, a small dataset for testing and examples.

### Method
GET

### Endpoint
/datasets/blobs_annotating_element

### Parameters
None

### Request Example
None

### Response
#### Success Response (200)
- **data** (SpatialData) - The blobs_annotating_element dataset.

#### Response Example
```json
{
  "data": "SpatialData object representing the blobs_annotating_element dataset"
}
```
```

--------------------------------

### Build documentation locally

Source: https://github.com/scverse/spatialdata/blob/main/docs/contributing.md

Commands to navigate to the documentation directory, build the HTML output, and open the index file in a browser.

```bash
cd docs
make html
open _build/html/index.html
```

--------------------------------

### Run a single dataloader benchmark method

Source: https://github.com/scverse/spatialdata/blob/main/benchmarks/README.md

Executes a specific dataloader benchmark method, such as `time_init` or `time_fetch`, in the current environment.

```bash
asv run --python=same --show-stderr -b TimeDataloader.time_init
asv run --python=same --show-stderr -b TimeDataloader.time_fetch
```

--------------------------------

### Build and Run SpatialData Docker Image

Source: https://github.com/scverse/spatialdata/blob/main/docs/installation.md

Build a Docker image containing SpatialData with PyTorch, spatialdata-io, and spatialdata-plot. This command is for Apple Silicon machines; omit --build-arg for others.

```bash
# this is for Apple Silicon machines, if you are not using such machine you can omit the --build-arg
docker build --build-arg TARGETPLATFORM=linux/arm64 --tag spatialdata .
docker run -it spatialdata
```

--------------------------------

### Run all import benchmarks

Source: https://github.com/scverse/spatialdata/blob/main/benchmarks/README.md

Executes all import-related benchmarks in the current environment. Use `-b timeraw` to target raw import timing functions.

```bash
asv run --python=same --show-stderr -b timeraw
```

--------------------------------

### Run Spatialdata Benchmark Module

Source: https://github.com/scverse/spatialdata/blob/main/benchmarks/README.md

Use this command to execute the spatialdata benchmark module. Ensure your environment is set up correctly.

```bash
python -m benchmarks.spatialdata_benchmark
```

--------------------------------

### Enable pre-commit hooks

Source: https://github.com/scverse/spatialdata/blob/main/docs/contributing.md

Initialize pre-commit hooks in the local repository to enforce consistent code styling.

```bash
pre-commit install
```

--------------------------------

### Continuous comparison of dataloader benchmarks

Source: https://github.com/scverse/spatialdata/blob/main/benchmarks/README.md

Compares the current branch's dataloader benchmarks against a specified branch (e.g., `main`) in a single command. Uses `HEAD` to refer to the current branch tip.

```bash
asv continuous --show-stderr -v -b TimeDataloader main HEAD
```

--------------------------------

### Collect and compare import benchmark results

Source: https://github.com/scverse/spatialdata/blob/main/benchmarks/README.md

Collects import benchmark results for two specified commits (e.g., `main` and `HEAD`) separately and then compares them. This allows for more detailed analysis.

```bash
# 1. Collect results for the tip of main and the tip of your branch
asv run --show-stderr -b timeraw main
asv run --show-stderr -b timeraw HEAD

# 2. Print a side-by-side comparison
asv compare main HEAD
```

--------------------------------

### Run import benchmarks reusing current environment

Source: https://github.com/scverse/spatialdata/blob/main/benchmarks/README.md

Runs import benchmarks using the current Python environment to speed up the process, at the cost of accuracy. Requires stashing and restoring git state.

```bash
asv run --python=same --show-stderr -b timeraw HEAD

git stash && git checkout main
asv run --python=same --show-stderr -b timeraw HEAD
git checkout - && git stash pop

asv compare main HEAD
```

--------------------------------

### Continuous comparison of import benchmarks

Source: https://github.com/scverse/spatialdata/blob/main/benchmarks/README.md

Compares the current branch's import benchmarks against a specified branch (e.g., `main`) in a single command. The `-v` flag provides per-sample timings.

```bash
asv continuous --show-stderr -v -b timeraw main faster-import
```

--------------------------------

### Run all dataloader benchmarks

Source: https://github.com/scverse/spatialdata/blob/main/benchmarks/README.md

Executes all dataloader benchmarks in the current environment. Targets benchmarks related to `TimeDataloader`.

```bash
asv run --python=same --show-stderr -b TimeDataloader
```

--------------------------------

### Run a single import benchmark

Source: https://github.com/scverse/spatialdata/blob/main/benchmarks/README.md

Executes a specific import benchmark, `timeraw_import_spatialdata`, in the current environment. This is useful for isolating performance issues.

```bash
asv run --python=same --show-stderr -b timeraw_import_spatialdata
```

--------------------------------

### Push tags to GitHub

Source: https://github.com/scverse/spatialdata/blob/main/docs/contributing.md

Command to publish local version tags to the remote repository.

```bash
git push --tags
```

--------------------------------

### Run tests with pytest

Source: https://github.com/scverse/spatialdata/blob/main/docs/contributing.md

Execute the full test suite from the root of the repository using pytest.

```bash
pytest
```

--------------------------------

### Run time_query_bounding_box benchmark

Source: https://github.com/scverse/spatialdata/blob/main/benchmarks/README.md

Executes the `time_query_bounding_box` benchmark, which measures the performance of spatial querying without a spatial index. The output table shows timings for different numbers of transcripts per cell and whether filtering is enabled.

```bash
asv run --python=same --show-stderr -b time_query_bounding_box
```

--------------------------------

### Pull and Run Published Docker Image

Source: https://github.com/scverse/spatialdata/blob/main/docs/installation.md

Pull a specific version of the SpatialData Docker image from GitHub Container Registry and run it. Replace the tag with the desired image version.

```bash
docker pull ghcr.io/scverse/spatialdata:spatialdata0.3.0_spatialdata-io0.1.7_spatialdata-plot0.2.9
docker run -it ghcr.io/scverse/spatialdata:spatialdata0.3.0_spatialdata-io0.1.7_spatialdata-plot0.2.9
```

--------------------------------

### Integrate pre-commit changes

Source: https://github.com/scverse/spatialdata/blob/main/docs/contributing.md

Pull changes from the remote repository using rebase to incorporate automatic fixes applied by pre-commit.ci.

```bash
git pull --rebase
```

--------------------------------

### Update version with bump2version

Source: https://github.com/scverse/spatialdata/blob/main/docs/contributing.md

Commands to increment the project version number according to semantic versioning rules.

```bash
bump2version patch
bump2version minor
bump2version major
```

--------------------------------

### Testing Utilities API

Source: https://github.com/scverse/spatialdata/blob/main/docs/api/testing.md

Functions for asserting the identity and equality of spatial data objects and their elements.

```APIDOC
## Testing Utilities

### Description
Provides functions to assert the identity and equality of spatial data objects and their constituent elements.

### Functions

#### `assert_spatial_data_objects_are_identical`

##### Description
Asserts that two `SpatialData` objects are identical.

##### Parameters
- `adata1` (SpatialData) - The first `SpatialData` object.
- `adata2` (SpatialData) - The second `SpatialData` object.

#### `assert_elements_are_identical`

##### Description
Asserts that two elements (e.g., DataFrames, Arrays) are identical.

##### Parameters
- `element1` (Any) - The first element to compare.
- `element2` (Any) - The second element to compare.

#### `assert_elements_dict_are_identical`

##### Description
Asserts that two dictionaries of elements are identical.

##### Parameters
- `elements1` (Dict[str, Any]) - The first dictionary of elements.
- `elements2` (Dict[str, Any]) - The second dictionary of elements.
```

--------------------------------

### Create SpatialData Object from MERSCOPE Data

Source: https://github.com/scverse/spatialdata/blob/main/docs/user_guide.md

Initializes a SpatialData object using the spatialdata-io reader for MERSCOPE data.

```python
sdata = spatialdata_io.merscope(
    'merscope_ex/' # path to the folder with MERSCOPE files
    )
```

--------------------------------

### get_dask_backing_files

Source: https://github.com/scverse/spatialdata/blob/main/docs/api/io.md

Retrieves the list of files backing the Dask arrays in a SpatialData object.

```APIDOC
## get_dask_backing_files

### Description
Returns a list of file paths that are currently backing the Dask arrays within the provided SpatialData object.

### Method
FUNCTION

### Endpoint
spatialdata.get_dask_backing_files
```

--------------------------------

### SpatialData Transformation Classes

Source: https://github.com/scverse/spatialdata/blob/main/docs/api/transformations.md

Overview of the available transformation classes for coordinate system mapping.

```APIDOC
## Transformation Classes

### Description
The following classes are used to define transformations between elements and coordinate systems in `SpatialData`.

### Classes
- **BaseTransformation**: The base class for all transformations.
- **Identity**: Represents an identity transformation.
- **MapAxis**: Maps axes between coordinate systems.
- **Translation**: Represents a translation transformation.
- **Scale**: Represents a scaling transformation.
- **Affine**: Represents an affine transformation.
- **Sequence**: Represents a sequence of transformations.
```

--------------------------------

### Transformation Management API

Source: https://github.com/scverse/spatialdata/blob/main/docs/api/transformations_utils.md

Functions for retrieving, setting, and removing transformation information.

```APIDOC
## GET / Transformations

### Description
Retrieves the transformation associated with a given coordinate system.

### Method
GET

### Endpoint
`/transformations` (conceptual, refers to function usage)

### Parameters
#### Query Parameters
- **coordinate_system** (str) - Required - The target coordinate system.

### Response
#### Success Response (200)
- **transformation** (dict) - The transformation matrix or object.

## POST / Transformations

### Description
Sets a transformation for a given coordinate system.

### Method
POST

### Endpoint
`/transformations` (conceptual, refers to function usage)

### Parameters
#### Query Parameters
- **coordinate_system** (str) - Required - The coordinate system to set the transformation for.
- **transformation** (dict) - Required - The transformation matrix or object to set.

### Response
#### Success Response (200)
- **status** (str) - Confirmation message.

## DELETE / Transformations

### Description
Removes the transformation associated with a given coordinate system.

### Method
DELETE

### Endpoint
`/transformations` (conceptual, refers to function usage)

### Parameters
#### Query Parameters
- **coordinate_system** (str) - Required - The coordinate system whose transformation should be removed.

### Response
#### Success Response (200)
- **status** (str) - Confirmation message.
```

--------------------------------

### Landmark Transformation API

Source: https://github.com/scverse/spatialdata/blob/main/docs/api/transformations_utils.md

Functions specifically for transforming or aligning based on landmarks.

```APIDOC
## GET /transformations/between_landmarks

### Description
Gets the transformation between two sets of landmarks.

### Method
GET

### Endpoint
`/transformations/between_landmarks` (conceptual, refers to function usage)

### Parameters
#### Query Parameters
- **source_landmarks** (dict) - Required - The source landmarks.
- **target_landmarks** (dict) - Required - The target landmarks.

### Response
#### Success Response (200)
- **transformation** (dict) - The transformation matrix or object.

## DELETE /transformations/to_coordinate_system

### Description
Removes all transformations leading to a specific coordinate system.

### Method
DELETE

### Endpoint
`/transformations/to_coordinate_system` (conceptual, refers to function usage)

### Parameters
#### Query Parameters
- **coordinate_system** (str) - Required - The coordinate system to remove transformations to.

### Response
#### Success Response (200)
- **status** (str) - Confirmation message.
```

--------------------------------

### ImageTilesDataset Class

Source: https://github.com/scverse/spatialdata/blob/main/docs/api/dataloader.md

Documentation for the ImageTilesDataset class located in the spatialdata.dataloader module.

```APIDOC
## Class: ImageTilesDataset

### Description
A dataset class designed for handling image tiles within the spatialdata framework.

### Module
spatialdata.dataloader
```

--------------------------------

### Read SpatialData Zarr Dataset

Source: https://github.com/scverse/spatialdata/blob/main/docs/user_guide.md

Loads a SpatialData object from a Zarr file.

```python
sdata = sd.read_zarr(“your-dataset.zarr")
```

--------------------------------

### SpatialData Format Classes

Source: https://github.com/scverse/spatialdata/blob/main/docs/api/data_formats.md

Overview of the available format classes for Raster, Shapes, Points, and Tables data types.

```APIDOC
## SpatialData Format Classes

### Description
The SpatialData format is defined as a set of versioned subclasses of `ome_zarr.format.Format`. These classes ensure backward compatibility for different data elements.

### Format Classes
- **CurrentRasterFormat** - The latest format implementation for raster data.
- **RasterFormatV01** - Version 0.1 of the raster format.
- **CurrentShapesFormat** - The latest format implementation for shapes data.
- **ShapesFormatV01** - Version 0.1 of the shapes format.
- **ShapesFormatV02** - Version 0.2 of the shapes format.
- **CurrentPointsFormat** - The latest format implementation for points data.
- **PointsFormatV01** - Version 0.1 of the points format.
- **CurrentTablesFormat** - The latest format implementation for tables data.
- **TablesFormatV01** - Version 0.1 of the tables format.
```

--------------------------------

### Visualize SpatialData Layers

Source: https://github.com/scverse/spatialdata/blob/main/docs/user_guide.md

Use the spatialdata-plot syntax to render specific elements or chain multiple layers for visualization.

```python
sdata.pl.render_<element_type>("<element_name>").pl.show()
```

```python
(
    sdata
    .pl.render_image(
        "image_layer_name"
    )
    .pl.render_shapes(
        "shape_layer_name"
    )
    .pl.show()
)
```

--------------------------------

### Spatial Data Table and Element Matching Operations

Source: https://github.com/scverse/spatialdata/blob/main/docs/api/operations.md

Functions for joining spatial element tables, matching elements to tables, and vice versa, as well as filtering data based on table queries.

```APIDOC
## Spatial Data Table and Element Matching

### Description
Operations related to integrating and matching spatial elements with tabular data.

### Methods
- `join_spatialelement_table`
- `match_element_to_table`
- `match_table_to_element`
- `match_sdata_to_table`
- `filter_by_table_query`

### Usage
These functions facilitate the linkage and filtering of spatial data based on associated metadata.
```

--------------------------------

### SpatialData Models Overview

Source: https://github.com/scverse/spatialdata/blob/main/docs/api/models.md

Definitions of the core data models used to represent spatial elements in the SpatialData framework.

```APIDOC
## SpatialData Models

### Description
The following models represent the core building-blocks for spatial data structures within the library.

### Models
- **Image2DModel**: Represents 2D image data.
- **Image3DModel**: Represents 3D image data.
- **Labels2DModel**: Represents 2D label/segmentation data.
- **Labels3DModel**: Represents 3D label/segmentation data.
- **ShapesModel**: Represents spatial shapes (e.g., polygons, circles).
- **PointsModel**: Represents point-based spatial data.
- **TableModel**: Represents tabular data associated with spatial elements.
```

--------------------------------

### read_zarr

Source: https://github.com/scverse/spatialdata/blob/main/docs/api/io.md

Reads spatial data from a Zarr store.

```APIDOC
## read_zarr

### Description
Reads spatial data from a Zarr store into a SpatialData object.

### Method
FUNCTION

### Endpoint
spatialdata.read_zarr
```

--------------------------------

### SpatialElement

Source: https://github.com/scverse/spatialdata/blob/main/docs/api/models_utils.md

Represents a generic spatial element.

```APIDOC
## SpatialElement

### Description
A base class or type alias representing a generic spatial element in spatialdata.

### Type
`SpatialElement`
```

--------------------------------

### Coordinate System Transformation API

Source: https://github.com/scverse/spatialdata/blob/main/docs/api/transformations_utils.md

Functions for transforming data between different coordinate systems.

```APIDOC
## GET /transformations/between_coordinate_systems

### Description
Gets the transformation between two specified coordinate systems.

### Method
GET

### Endpoint
`/transformations/between_coordinate_systems` (conceptual, refers to function usage)

### Parameters
#### Query Parameters
- **source_coordinate_system** (str) - Required - The source coordinate system.
- **target_coordinate_system** (str) - Required - The target coordinate system.

### Response
#### Success Response (200)
- **transformation** (dict) - The transformation matrix or object.

## POST /transformations/align_elements

### Description
Aligns elements using landmarks between two coordinate systems.

### Method
POST

### Endpoint
`/transformations/align_elements` (conceptual, refers to function usage)

### Parameters
#### Request Body
- **source_coordinate_system** (str) - Required - The source coordinate system.
- **target_coordinate_system** (str) - Required - The target coordinate system.
- **source_landmarks** (dict) - Required - Landmarks in the source coordinate system.
- **target_landmarks** (dict) - Required - Landmarks in the target coordinate system.

### Response
#### Success Response (200)
- **transformation** (dict) - The computed transformation matrix or object.
```

--------------------------------

### Spatial Data Transformation and Rasterization Operations

Source: https://github.com/scverse/spatialdata/blob/main/docs/api/operations.md

Operations for concatenating, transforming, rasterizing, and converting spatial data into different formats like circles and polygons.

```APIDOC
## Spatial Data Transformation and Rasterization

### Description
Functions for manipulating and converting `SpatialData` objects, including concatenation, transformations, and rasterization.

### Methods
- `concatenate`
- `transform`
- `rasterize`
- `rasterize_bins`
- `rasterize_bins_link_table_to_labels`
- `to_circles`
- `to_polygons`

### Usage
These operations are useful for data preprocessing, format conversion, and preparing data for analysis.
```

--------------------------------

### get_model

Source: https://github.com/scverse/spatialdata/blob/main/docs/api/models_utils.md

Retrieves the model class for a given spatial element type.

```APIDOC
## get_model

### Description
Retrieves the model class for a given spatial element type.

### Signature
`get_model(element: SpatialElement)`

### Parameters
* **element** (`SpatialElement`) - The spatial element to get the model for.
```

--------------------------------

### Spatial Data Relabeling and Utility Operations

Source: https://github.com/scverse/spatialdata/blob/main/docs/api/operations.md

Operations for relabeling sequential data, checking extent equality, deep copying, and retrieving pyramid levels.

```APIDOC
## Spatial Data Relabeling and Utility Functions

### Description
Utility functions for managing and inspecting `SpatialData` objects.

### Methods
- `relabel_sequential`
- `are_extents_equal`
- `deepcopy`
- `get_pyramid_levels`
- `sanitize_name`
- `sanitize_table`

### Usage
These functions provide essential utilities for data cleaning, validation, and management.
```

--------------------------------

### set_channel_names

Source: https://github.com/scverse/spatialdata/blob/main/docs/api/models_utils.md

Sets the channel names for a spatial element.

```APIDOC
## set_channel_names

### Description
Sets the channel names for a spatial element.

### Signature
`set_channel_names(element: SpatialElement, channel_names: list[str])`

### Parameters
* **element** (`SpatialElement`) - The spatial element to set channel names for.
* **channel_names** (`list[str]`) - A list of channel names.
```

--------------------------------

### Spatial Data Aggregation and Mapping Operations

Source: https://github.com/scverse/spatialdata/blob/main/docs/api/operations.md

Operations for aggregating spatial data, mapping rasters, and unpadding raster data.

```APIDOC
## Spatial Data Aggregation and Mapping

### Description
Functions for aggregating spatial data and performing operations on raster data.

### Methods
- `aggregate`
- `map_raster`
- `unpad_raster`

### Usage
These functions enable summarization of spatial data and manipulation of raster representations.
```

--------------------------------

### force_2d

Source: https://github.com/scverse/spatialdata/blob/main/docs/api/models_utils.md

Forces a spatial element to be 2D by dropping the z-axis if present.

```APIDOC
## force_2d

### Description
Forces a spatial element to be 2D by dropping the z-axis if present.

### Signature
`force_2d(element: SpatialElement)`

### Parameters
* **element** (`SpatialElement`) - The spatial element to convert to 2D.
```

--------------------------------

### Spatial Data Query Operations

Source: https://github.com/scverse/spatialdata/blob/main/docs/api/operations.md

Operations for querying spatial data based on bounding boxes and polygons, and retrieving specific data values or element instances.

```APIDOC
## Operations on SpatialData Objects

### Description
This section covers operations for querying and retrieving data from `SpatialData` objects.

### Methods
- `bounding_box_query`
- `polygon_query`
- `get_values`
- `get_element_instances`
- `get_extent`
- `get_centroids`

### Usage
These functions allow for efficient spatial subsetting and data extraction.
```

--------------------------------

### points_dask_dataframe_to_geopandas

Source: https://github.com/scverse/spatialdata/blob/main/docs/api/models_utils.md

Converts a Dask DataFrame of points to a GeoPandas DataFrame.

```APIDOC
## points_dask_dataframe_to_geopandas

### Description
Converts a Dask DataFrame of points to a GeoPandas DataFrame.

### Signature
`points_dask_dataframe_to_geopandas(points: dd.DataFrame)`

### Parameters
* **points** (`dd.DataFrame`) - The Dask DataFrame containing points.
```

--------------------------------

### Add GeoJSON Annotations to SpatialData

Source: https://github.com/scverse/spatialdata/blob/main/docs/user_guide.md

Use ShapesModel to parse and add external geojson files as shapes to the SpatialData object.

```python
from spatialdata.models import ShapesModel
sdata['very_interesting_regions']=ShapesModel.parse('path_to_geojson')
```

--------------------------------

### get_channel_names

Source: https://github.com/scverse/spatialdata/blob/main/docs/api/models_utils.md

Retrieves the channel names from a spatial element.

```APIDOC
## get_channel_names

### Description
Retrieves the channel names from a spatial element.

### Signature
`get_channel_names(element: SpatialElement)`

### Parameters
* **element** (`SpatialElement`) - The spatial element to get channel names from.
```

--------------------------------

### points_geopandas_to_dask_dataframe

Source: https://github.com/scverse/spatialdata/blob/main/docs/api/models_utils.md

Converts a GeoPandas DataFrame of points to a Dask DataFrame.

```APIDOC
## points_geopandas_to_dask_dataframe

### Description
Converts a GeoPandas DataFrame of points to a Dask DataFrame.

### Signature
`points_geopandas_to_dask_dataframe(points: gpd.GeoDataFrame)`

### Parameters
* **points** (`gpd.GeoDataFrame`) - The GeoPandas DataFrame containing points.
```

--------------------------------

### Disable Dask Tune Optimization for Points Data

Source: https://github.com/scverse/spatialdata/blob/main/docs/index.md

Use this context manager to disable dask graph optimization for Points dataframes with more than one partition, preventing potential errors. This is useful when performing operations directly on the dask dataframe.

```python
from spatialdata import disable_dask_tune_optimization
import contextlib
...

with disable_dask_tune_optimization() if data.npartitions > 1 else contextlib.nullcontext():
    <your operation on points dask dataframe>
```

--------------------------------

### validate_element

Source: https://github.com/scverse/spatialdata/blob/main/docs/api/models_utils.md

Validates a spatial element against its model.

```APIDOC
## validate_element

### Description
Validates a spatial element against its model.

### Signature
`validate_element(element: SpatialElement)`

### Parameters
* **element** (`SpatialElement`) - The spatial element to validate.
```

--------------------------------

### get_spatial_axes

Source: https://github.com/scverse/spatialdata/blob/main/docs/api/models_utils.md

Retrieves the spatial axes of a spatial element.

```APIDOC
## get_spatial_axes

### Description
Retrieves the spatial axes of a spatial element.

### Signature
`get_spatial_axes(element: SpatialElement)`

### Parameters
* **element** (`SpatialElement`) - The spatial element to get the spatial axes from.
```

--------------------------------

### get_axes_names

Source: https://github.com/scverse/spatialdata/blob/main/docs/api/models_utils.md

Retrieves the names of the axes for a spatial element.

```APIDOC
## get_axes_names

### Description
Retrieves the names of the axes for a spatial element.

### Signature
`get_axes_names(element: SpatialElement)`

### Parameters
* **element** (`SpatialElement`) - The spatial element to get the axes names from.
```

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