transform and models

.gitignore

@@ -26,3 +26,6 @@ __pycache__/
 # data
 spatialdata-sandbox
 *.zarr/
+
+# temp files
+temp/

.pre-commit-config.yaml

@@ -11,7 +11,7 @@ repos:
       hooks:
           - id: black
     - repo: https://github.com/pre-commit/mirrors-prettier
-      rev: v2.7.1
+      rev: v3.0.0-alpha.4
       hooks:
           - id: prettier
     - repo: https://github.com/asottile/blacken-docs
@@ -23,7 +23,7 @@ repos:
       hooks:
           - id: isort
     - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v0.982
+      rev: v0.991
       hooks:
           - id: mypy
             additional_dependencies: [numpy==1.22.0, types-requests]
@@ -40,7 +40,7 @@ repos:
                 - flake8-bugbear
                 - flake8-blind-except
     - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.3.0
+      rev: v4.4.0
       hooks:
           - id: detect-private-key
           - id: check-ast
@@ -50,7 +50,7 @@ repos:
           - id: trailing-whitespace
           - id: check-case-conflict
     - repo: https://github.com/PyCQA/autoflake
-      rev: v1.7.1
+      rev: v2.0.0
       hooks:
           - id: autoflake
             args:
@@ -59,7 +59,7 @@ repos:
                 - --remove-unused-variable
                 - --ignore-init-module-imports
     - repo: https://github.com/PyCQA/flake8
-      rev: 5.0.4
+      rev: 6.0.0
       hooks:
           - id: flake8
             additional_dependencies:
@@ -70,7 +70,7 @@ repos:
                 - flake8-bugbear
                 - flake8-blind-except
     - repo: https://github.com/asottile/pyupgrade
-      rev: v3.0.0
+      rev: v3.2.2
       hooks:
           - id: pyupgrade
             args: [--py3-plus, --py38-plus, --keep-runtime-typing]

docs/design_doc.md

@@ -280,6 +280,20 @@ Transforms map Elements between coordinate systems. Each `Transform` object must
 
 Here is a short list of examples of the elements used to represent some spatial omics datasets. Real world will be available as notebooks [in this repository](https://github.com/scverse/spatialdata-notebooks), furthermore, some draft [implementations are available here](https://github.com/giovp/spatialdata-sandbox).
 
+API
+
+```python
+import spatialdata as sd
+from spatialdata import SpatialData
+
+sdata = SpatialData(...)
+points = sd.transform(sdata.points["image1"], tgt="tgt_space")
+sdata = sd.transform(sdata, tgt="tgt_space")
+```
+
+The transfromation object should not have a method to apply itself to an element.
+`SpatialData` can have a `transform` method, that can be applied to either a `SpatialData` object or an element.
+
 #### Layout of a SpatialData object
 
 The layout of some common datasets.

pyproject.toml

@@ -22,7 +22,20 @@ version = "0.0.1.dev0"
 requires-python = ">=3.8"
 license = {file = "LICENSE"}
 readme = "README.md"
-dependencies = ["anndata","numpy","xarray","zarr","ome_zarr"]
+dependencies = [
+    "anndata",
+    "numpy",
+    "xarray",
+    "zarr",
+    "ome_zarr",
+    "spatial_image",
+    "multiscale_spatial_image",
+    "xarray-schema",
+    "geopandas",
+    "pandera",
+    "shapely==2.0rc1",
+    "rich",
+]
 
 [project.optional-dependencies]
 dev = [

spatialdata/__init__.py

@@ -2,5 +2,49 @@
 
 __version__ = version("spatialdata")
 
-from spatialdata._core.spatialdata import SpatialData
-from spatialdata._core.transform import Transform
+__all__ = [
+    "SpatialData",
+    "Identity",
+    # "MapIndex",
+    "MapAxis",
+    "Translation",
+    "Scale",
+    "Affine",
+    "Rotation",
+    "Sequence",
+    # "Displacements",
+    # "Coordinates",
+    # "VectorField",
+    # "InverseOf",
+    # "Bijection",
+    # "ByDimension",
+    "Image3DModel",
+    "Image2DModel",
+    "Labels2DModel",
+    "Labels3DModel",
+    "PointsModel",
+    "PolygonsModel",
+    "ShapesModel",
+    "TableModel",
+]
+
+from spatialdata._core._spatialdata import SpatialData
+from spatialdata._core.models import (
+    Image2DModel,
+    Image3DModel,
+    Labels2DModel,
+    Labels3DModel,
+    PointsModel,
+    PolygonsModel,
+    ShapesModel,
+    TableModel,
+)
+from spatialdata._core.transformations import (  # Bijection,; ByDimension,; Coordinates,; Displacements,; InverseOf,; MapIndex,; VectorField,
+    Affine,
+    Identity,
+    MapAxis,
+    Rotation,
+    Scale,
+    Sequence,
+    Translation,
+)

spatialdata/_constants/_constants.py

@@ -0,0 +1,15 @@
+from enum import unique
+
+from spatialdata._constants._enum import ModeEnum
+
+
+@unique
+class RasterType(ModeEnum):
+    IMAGE = "Image"
+    LABEL = "Label"
+
+
+@unique
+class ShapeType(ModeEnum):
+    CIRCLE = "Circle"
+    SQUARE = "Square"

spatialdata/_core/__init__.py

@@ -1 +1 @@
-from spatialdata._core.spatialdata import SpatialData
+from spatialdata._core._spatialdata import SpatialData