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jp-dark committed Oct 16, 2024
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Expand Up @@ -656,8 +656,6 @@ Summary of opertions:
| register_geometry_dataframe | Adds a `CoordinateTransform` to an existing `GeometryDataFrame` in this `SOMAScene`. |
| register_multiscale_image | Adds a `CoordinateTransform` to an existing `MultiscaleImage` in this `SOMAScene`. |

### Operations

### Operation: register\_<var>object_type</var>

Each <code>add_new\_<var>object_type</var></code> method takes an existing SOMA object in the scene, adds a transformation from the scene to the object, and returns the object. The returned object has the same `context` value as the existing scene and is [owned by the current scene](#operation-close-collection-types).
Expand All @@ -680,42 +678,6 @@ A `SOMADataFrame` is indexed by one or more dataframe columns (also known as "di

`SOMADataFrame` rows require unique coordinates. In other words, the read and write operations will assume that any given coordinate tuple for indexed columns uniquely identifies a single dataframe row.

## SOMAPointCloud

Summary of operations:

| Operation | Description |
| ----------------------------------------- | ----------------------------------------------------- |
| static create(uri, ...) -> SOMAPointCloud | Create a `SOMAPointCloud`. |
| get soma_type | Returns the constant "SOMADataFrame". |
| get schema -> Arrow.Schema | Return data schema, in the form of an Arrow `Schema`. |
| get index_column_names -> [string, ...] | Return index (dimension) column names. |
| get count -> int | Return the number of rows in the `SOMAPointCloud`. |
| read | Read a subset of data from the `SOMAPointCloud`. |
| write | Write a subset of data to the `SOMAPointCloud`. |

A `SOMADataFrame` is indexed by one or more dataframe columns (also known as "dimensions"). The name and order of dimensions is specified at the time of creation. [Slices](#indexing-and-slicing) are addressable by the user-specified dimensions. The `soma_joinid` column may be specified as an index column.

`SOMADataFrame` rows require unique coordinates. In other words, the read and write operations will assume that any given coordinate tuple for indexed columns uniquely identifies a single dataframe row.

## SOMAGeometryDataFrame

Summary of operations:

| Operation | Description |
| ------------------------------------------------ | --------------------------------------------------------- |
| static create(uri, ...) -> SOMAGemetoryDataFrame | Create a `SOMAGeometryDataFrame`. |
| get soma_type | Returns the constant "SOMAGeometryDataFrame". |
| get schema -> Arrow.Schema | Return data schema, in the form of an Arrow `Schema`. |
| get index_column_names -> [string, ...] | Return index (dimension) column names. |
| get count -> int | Return the number of rows in the `SOMAGeometryDataFrame`. |
| read | Read a subset of data from the `SOMAGeometryDataFrame`. |
| write | Write a subset of data to the `SOMADataFrame`. |

A `SOMADataFrame` is indexed by one or more dataframe columns (also known as "dimensions"). The name and order of dimensions is specified at the time of creation. [Slices](#indexing-and-slicing) are addressable by the user-specified dimensions. The `soma_joinid` column may be specified as an index column.

`SOMADataFrame` rows require unique coordinates. In other words, the read and write operations will assume that any given coordinate tuple for indexed columns uniquely identifies a single dataframe row.

### Operation: create()

Create a new `SOMADataFrame` with user-specified URI and schema.
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