schema and dataclasses (wip)

[giovp]

No description provided.

[codecov-commenter]

Codecov Report

Merging #40 (8293dfb) into feature/transform (cf3eeb3) will not change coverage.
The diff coverage is 0.00%.

Additional details and impacted files

@@ Coverage Diff @@## feature/transform #40 +/- ##
=================================================
Coverage 0.00% 0.00% =================================================
Files 14 15 +1 Lines 1119 1158 +39 =================================================
- Misses 1119 1158 +39 

Flag	Coverage Δ
unittests	0.00% <0.00%> (ø)

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
spatialdata/_core/models.py	0.00% <0.00%> (ø)

[giovp]

polygons IO only works with pip install git+https://github.com/shapely/shapely.git@refs/pull/1559/head --no-binary shapely (branch where to/from_ragged_array is added).

[giovp]

open questions:

• can we have a SpatialData with only one table (no labels, regions etc.) ?
  Yes -> Region is not mandatory.
  We can store only images and labels without tables
• empty SpatialData should be possible.
  No
• if region: str what is the table annotating?
• can we/shall we check for consistency of instance_key ?

[giovp]

@ivirshup this AnnData(obsm={"spatial": data}) doesn't work. Quite important if we want to save shapes/points in anndata with coordinates in obsm (and X potentially None ). What should we do?

[giovp]

basically if adata.uns["transform"] = spatialdata.Transform(...) it can't ofc be serialized so it needs to be popped. However, that would change the in-memory representation. Can only copy or someone has better idea?

[giovp]

zarr group hierarchy of elements:

Image

.
├── image0
│ └── 0
│ └── 0
│ └── 0
├── image01
│ └── 0
│ └── 0
│ └── 0
└── image012
└── 0
└── 0
└── 0

Labels

.
├── label0
│ └── labels
│ └── label0
│ └── 0
│ └── 0
├── label01
│ └── labels
│ └── label01
│ └── 0
│ └── 0
└── label012
└── labels
└── label012
└── 0
└── 0

Shapes

.
├── shapes0
│ └── shapes
│ └── shapes0
│ ├── X
│ │ └── 0
...
└── shapes01
└── shapes
└── shapes01
├── X
│ └── 0
...

Polygons

.
├── polygons0
│ └── polygons
│ └── polygons0
│ ├── coords
│ │ └── 0
│ └── offsets
│ └── 0
├── polygons01
│ └── polygons
│ └── polygons01
│ ├── coords
│ │ └── 0
│ └── offsets
│ └── 0
└── polygons012
└── polygons
└── polygons012
├── coords
│ └── 0
└── offsets
└── 0

Table

.
└── table
└── table
├── X
│ ├── data
│ ├── indices
│ └── indptr
├── layers
├── obs

and the SpatialData specific attributes are in path in .zattr, e.g. for polygons

"path": {
"geos": {
"geometry_name": "POLYGON",
"geometry_type": 3
}
}

let's use this for discussion, think we can improve a bit.

[giovp]

No description provided.

[codecov-commenter]

Codecov Report

Merging #40 (8293dfb) into feature/transform (cf3eeb3) will not change coverage.
The diff coverage is 0.00%.

Additional details and impacted files

@@ Coverage Diff @@## feature/transform #40 +/- ##
=================================================
Coverage 0.00% 0.00% =================================================
Files 14 15 +1 Lines 1119 1158 +39 =================================================
- Misses 1119 1158 +39 

Flag	Coverage Δ
unittests	0.00% <0.00%> (ø)

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
spatialdata/_core/models.py	0.00% <0.00%> (ø)

[giovp]

polygons IO only works with pip install git+https://github.com/shapely/shapely.git@refs/pull/1559/head --no-binary shapely (branch where to/from_ragged_array is added).

[giovp]

open questions:

• can we have a SpatialData with only one table (no labels, regions etc.) ?
  Yes -> Region is not mandatory.
  We can store only images and labels without tables
• empty SpatialData should be possible.
  No
• if region: str what is the table annotating?
• can we/shall we check for consistency of instance_key ?

[giovp]

@ivirshup this AnnData(obsm={"spatial": data}) doesn't work. Quite important if we want to save shapes/points in anndata with coordinates in obsm (and X potentially None ). What should we do?

[giovp]

basically if adata.uns["transform"] = spatialdata.Transform(...) it can't ofc be serialized so it needs to be popped. However, that would change the in-memory representation. Can only copy or someone has better idea?

[giovp]

zarr group hierarchy of elements:

Image

.
├── image0
│ └── 0
│ └── 0
│ └── 0
├── image01
│ └── 0
│ └── 0
│ └── 0
└── image012
└── 0
└── 0
└── 0

Labels

.
├── label0
│ └── labels
│ └── label0
│ └── 0
│ └── 0
├── label01
│ └── labels
│ └── label01
│ └── 0
│ └── 0
└── label012
└── labels
└── label012
└── 0
└── 0

Shapes

.
├── shapes0
│ └── shapes
│ └── shapes0
│ ├── X
│ │ └── 0
...
└── shapes01
└── shapes
└── shapes01
├── X
│ └── 0
...

Polygons

.
├── polygons0
│ └── polygons
│ └── polygons0
│ ├── coords
│ │ └── 0
│ └── offsets
│ └── 0
├── polygons01
│ └── polygons
│ └── polygons01
│ ├── coords
│ │ └── 0
│ └── offsets
│ └── 0
└── polygons012
└── polygons
└── polygons012
├── coords
│ └── 0
└── offsets
└── 0

Table

.
└── table
└── table
├── X
│ ├── data
│ ├── indices
│ └── indptr
├── layers
├── obs

and the SpatialData specific attributes are in path in .zattr, e.g. for polygons

"path": {
"geos": {
"geometry_name": "POLYGON",
"geometry_type": 3
}
}

let's use this for discussion, think we can improve a bit.

[giovp]

No description provided.

[codecov-commenter]

Codecov Report

Merging #40 (8293dfb) into feature/transform (cf3eeb3) will not change coverage.
The diff coverage is 0.00%.

Additional details and impacted files

@@ Coverage Diff @@## feature/transform #40 +/- ##
=================================================
Coverage 0.00% 0.00% =================================================
Files 14 15 +1 Lines 1119 1158 +39 =================================================
- Misses 1119 1158 +39 

Flag	Coverage Δ
unittests	0.00% <0.00%> (ø)

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
spatialdata/_core/models.py	0.00% <0.00%> (ø)

[giovp]

polygons IO only works with pip install git+https://github.com/shapely/shapely.git@refs/pull/1559/head --no-binary shapely (branch where to/from_ragged_array is added).

[giovp]

open questions:

• can we have a SpatialData with only one table (no labels, regions etc.) ?
  Yes -> Region is not mandatory.
  We can store only images and labels without tables
• empty SpatialData should be possible.
  No
• if region: str what is the table annotating?
• can we/shall we check for consistency of instance_key ?

[giovp]

@ivirshup this AnnData(obsm={"spatial": data}) doesn't work. Quite important if we want to save shapes/points in anndata with coordinates in obsm (and X potentially None ). What should we do?

[giovp]

basically if adata.uns["transform"] = spatialdata.Transform(...) it can't ofc be serialized so it needs to be popped. However, that would change the in-memory representation. Can only copy or someone has better idea?

[giovp]

zarr group hierarchy of elements:

Image

.
├── image0
│ └── 0
│ └── 0
│ └── 0
├── image01
│ └── 0
│ └── 0
│ └── 0
└── image012
└── 0
└── 0
└── 0

Labels

.
├── label0
│ └── labels
│ └── label0
│ └── 0
│ └── 0
├── label01
│ └── labels
│ └── label01
│ └── 0
│ └── 0
└── label012
└── labels
└── label012
└── 0
└── 0

Shapes

.
├── shapes0
│ └── shapes
│ └── shapes0
│ ├── X
│ │ └── 0
...
└── shapes01
└── shapes
└── shapes01
├── X
│ └── 0
...

Polygons

.
├── polygons0
│ └── polygons
│ └── polygons0
│ ├── coords
│ │ └── 0
│ └── offsets
│ └── 0
├── polygons01
│ └── polygons
│ └── polygons01
│ ├── coords
│ │ └── 0
│ └── offsets
│ └── 0
└── polygons012
└── polygons
└── polygons012
├── coords
│ └── 0
└── offsets
└── 0

Table

.
└── table
└── table
├── X
│ ├── data
│ ├── indices
│ └── indptr
├── layers
├── obs

and the SpatialData specific attributes are in path in .zattr, e.g. for polygons

"path": {
"geos": {
"geometry_name": "POLYGON",
"geometry_type": 3
}
}

let's use this for discussion, think we can improve a bit.

[giovp]

No description provided.

[codecov-commenter]

Codecov Report

Merging #40 (8293dfb) into feature/transform (cf3eeb3) will not change coverage.
The diff coverage is 0.00%.

Additional details and impacted files

@@ Coverage Diff @@## feature/transform #40 +/- ##
=================================================
Coverage 0.00% 0.00% =================================================
Files 14 15 +1 Lines 1119 1158 +39 =================================================
- Misses 1119 1158 +39 

Flag	Coverage Δ
unittests	0.00% <0.00%> (ø)

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
spatialdata/_core/models.py	0.00% <0.00%> (ø)

[giovp]

polygons IO only works with pip install git+https://github.com/shapely/shapely.git@refs/pull/1559/head --no-binary shapely (branch where to/from_ragged_array is added).

[giovp]

open questions:

• can we have a SpatialData with only one table (no labels, regions etc.) ?
  Yes -> Region is not mandatory.
  We can store only images and labels without tables
• empty SpatialData should be possible.
  No
• if region: str what is the table annotating?
• can we/shall we check for consistency of instance_key ?

[giovp]

@ivirshup this AnnData(obsm={"spatial": data}) doesn't work. Quite important if we want to save shapes/points in anndata with coordinates in obsm (and X potentially None ). What should we do?

[giovp]

basically if adata.uns["transform"] = spatialdata.Transform(...) it can't ofc be serialized so it needs to be popped. However, that would change the in-memory representation. Can only copy or someone has better idea?

[giovp]

zarr group hierarchy of elements:

Image

.
├── image0
│ └── 0
│ └── 0
│ └── 0
├── image01
│ └── 0
│ └── 0
│ └── 0
└── image012
└── 0
└── 0
└── 0

Labels

.
├── label0
│ └── labels
│ └── label0
│ └── 0
│ └── 0
├── label01
│ └── labels
│ └── label01
│ └── 0
│ └── 0
└── label012
└── labels
└── label012
└── 0
└── 0

Shapes

.
├── shapes0
│ └── shapes
│ └── shapes0
│ ├── X
│ │ └── 0
...
└── shapes01
└── shapes
└── shapes01
├── X
│ └── 0
...

Polygons

.
├── polygons0
│ └── polygons
│ └── polygons0
│ ├── coords
│ │ └── 0
│ └── offsets
│ └── 0
├── polygons01
│ └── polygons
│ └── polygons01
│ ├── coords
│ │ └── 0
│ └── offsets
│ └── 0
└── polygons012
└── polygons
└── polygons012
├── coords
│ └── 0
└── offsets
└── 0

Table

.
└── table
└── table
├── X
│ ├── data
│ ├── indices
│ └── indptr
├── layers
├── obs

and the SpatialData specific attributes are in path in .zattr, e.g. for polygons

"path": {
"geos": {
"geometry_name": "POLYGON",
"geometry_type": 3
}
}

let's use this for discussion, think we can improve a bit.

[giovp]

No description provided.

[codecov-commenter]

Codecov Report

Merging #40 (8293dfb) into feature/transform (cf3eeb3) will not change coverage.
The diff coverage is 0.00%.

Additional details and impacted files

@@ Coverage Diff @@## feature/transform #40 +/- ##
=================================================
Coverage 0.00% 0.00% =================================================
Files 14 15 +1 Lines 1119 1158 +39 =================================================
- Misses 1119 1158 +39 

Flag	Coverage Δ
unittests	0.00% <0.00%> (ø)

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
spatialdata/_core/models.py	0.00% <0.00%> (ø)

[giovp]

polygons IO only works with pip install git+https://github.com/shapely/shapely.git@refs/pull/1559/head --no-binary shapely (branch where to/from_ragged_array is added).

[giovp]

open questions:

• can we have a SpatialData with only one table (no labels, regions etc.) ?
  Yes -> Region is not mandatory.
  We can store only images and labels without tables
• empty SpatialData should be possible.
  No
• if region: str what is the table annotating?
• can we/shall we check for consistency of instance_key ?

[giovp]

@ivirshup this AnnData(obsm={"spatial": data}) doesn't work. Quite important if we want to save shapes/points in anndata with coordinates in obsm (and X potentially None ). What should we do?

[giovp]

basically if adata.uns["transform"] = spatialdata.Transform(...) it can't ofc be serialized so it needs to be popped. However, that would change the in-memory representation. Can only copy or someone has better idea?

[giovp]

zarr group hierarchy of elements:

Image

.
├── image0
│ └── 0
│ └── 0
│ └── 0
├── image01
│ └── 0
│ └── 0
│ └── 0
└── image012
└── 0
└── 0
└── 0

Labels

.
├── label0
│ └── labels
│ └── label0
│ └── 0
│ └── 0
├── label01
│ └── labels
│ └── label01
│ └── 0
│ └── 0
└── label012
└── labels
└── label012
└── 0
└── 0

Shapes

.
├── shapes0
│ └── shapes
│ └── shapes0
│ ├── X
│ │ └── 0
...
└── shapes01
└── shapes
└── shapes01
├── X
│ └── 0
...

Polygons

.
├── polygons0
│ └── polygons
│ └── polygons0
│ ├── coords
│ │ └── 0
│ └── offsets
│ └── 0
├── polygons01
│ └── polygons
│ └── polygons01
│ ├── coords
│ │ └── 0
│ └── offsets
│ └── 0
└── polygons012
└── polygons
└── polygons012
├── coords
│ └── 0
└── offsets
└── 0

Table

.
└── table
└── table
├── X
│ ├── data
│ ├── indices
│ └── indptr
├── layers
├── obs

and the SpatialData specific attributes are in path in .zattr, e.g. for polygons

"path": {
"geos": {
"geometry_name": "POLYGON",
"geometry_type": 3
}
}

let's use this for discussion, think we can improve a bit.

[giovp]

No description provided.

[codecov-commenter]

Codecov Report

Merging #40 (8293dfb) into feature/transform (cf3eeb3) will not change coverage.
The diff coverage is 0.00%.

Additional details and impacted files

@@ Coverage Diff @@## feature/transform #40 +/- ##
=================================================
Coverage 0.00% 0.00% =================================================
Files 14 15 +1 Lines 1119 1158 +39 =================================================
- Misses 1119 1158 +39 

Flag	Coverage Δ
unittests	0.00% <0.00%> (ø)

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
spatialdata/_core/models.py	0.00% <0.00%> (ø)

[giovp]

polygons IO only works with pip install git+https://github.com/shapely/shapely.git@refs/pull/1559/head --no-binary shapely (branch where to/from_ragged_array is added).

[giovp]

open questions:

• can we have a SpatialData with only one table (no labels, regions etc.) ?
  Yes -> Region is not mandatory.
  We can store only images and labels without tables
• empty SpatialData should be possible.
  No
• if region: str what is the table annotating?
• can we/shall we check for consistency of instance_key ?

[giovp]

@ivirshup this AnnData(obsm={"spatial": data}) doesn't work. Quite important if we want to save shapes/points in anndata with coordinates in obsm (and X potentially None ). What should we do?

[giovp]

basically if adata.uns["transform"] = spatialdata.Transform(...) it can't ofc be serialized so it needs to be popped. However, that would change the in-memory representation. Can only copy or someone has better idea?

[giovp]

zarr group hierarchy of elements:

Image

.
├── image0
│ └── 0
│ └── 0
│ └── 0
├── image01
│ └── 0
│ └── 0
│ └── 0
└── image012
└── 0
└── 0
└── 0

Labels

.
├── label0
│ └── labels
│ └── label0
│ └── 0
│ └── 0
├── label01
│ └── labels
│ └── label01
│ └── 0
│ └── 0
└── label012
└── labels
└── label012
└── 0
└── 0

Shapes

.
├── shapes0
│ └── shapes
│ └── shapes0
│ ├── X
│ │ └── 0
...
└── shapes01
└── shapes
└── shapes01
├── X
│ └── 0
...

Polygons

.
├── polygons0
│ └── polygons
│ └── polygons0
│ ├── coords
│ │ └── 0
│ └── offsets
│ └── 0
├── polygons01
│ └── polygons
│ └── polygons01
│ ├── coords
│ │ └── 0
│ └── offsets
│ └── 0
└── polygons012
└── polygons
└── polygons012
├── coords
│ └── 0
└── offsets
└── 0

Table

.
└── table
└── table
├── X
│ ├── data
│ ├── indices
│ └── indptr
├── layers
├── obs

and the SpatialData specific attributes are in path in .zattr, e.g. for polygons

"path": {
"geos": {
"geometry_name": "POLYGON",
"geometry_type": 3
}
}

let's use this for discussion, think we can improve a bit.

[giovp]

No description provided.

[codecov-commenter]

Codecov Report

Merging #40 (8293dfb) into feature/transform (cf3eeb3) will not change coverage.
The diff coverage is 0.00%.

Additional details and impacted files

@@ Coverage Diff @@## feature/transform #40 +/- ##
=================================================
Coverage 0.00% 0.00% =================================================
Files 14 15 +1 Lines 1119 1158 +39 =================================================
- Misses 1119 1158 +39 

Flag	Coverage Δ
unittests	0.00% <0.00%> (ø)

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
spatialdata/_core/models.py	0.00% <0.00%> (ø)

[giovp]

polygons IO only works with pip install git+https://github.com/shapely/shapely.git@refs/pull/1559/head --no-binary shapely (branch where to/from_ragged_array is added).

[giovp]

open questions:

• can we have a SpatialData with only one table (no labels, regions etc.) ?
  Yes -> Region is not mandatory.
  We can store only images and labels without tables
• empty SpatialData should be possible.
  No
• if region: str what is the table annotating?
• can we/shall we check for consistency of instance_key ?

[giovp]

@ivirshup this AnnData(obsm={"spatial": data}) doesn't work. Quite important if we want to save shapes/points in anndata with coordinates in obsm (and X potentially None ). What should we do?

[giovp]

basically if adata.uns["transform"] = spatialdata.Transform(...) it can't ofc be serialized so it needs to be popped. However, that would change the in-memory representation. Can only copy or someone has better idea?

[giovp]

zarr group hierarchy of elements:

Image

.
├── image0
│ └── 0
│ └── 0
│ └── 0
├── image01
│ └── 0
│ └── 0
│ └── 0
└── image012
└── 0
└── 0
└── 0

Labels

.
├── label0
│ └── labels
│ └── label0
│ └── 0
│ └── 0
├── label01
│ └── labels
│ └── label01
│ └── 0
│ └── 0
└── label012
└── labels
└── label012
└── 0
└── 0

Shapes

.
├── shapes0
│ └── shapes
│ └── shapes0
│ ├── X
│ │ └── 0
...
└── shapes01
└── shapes
└── shapes01
├── X
│ └── 0
...

Polygons

.
├── polygons0
│ └── polygons
│ └── polygons0
│ ├── coords
│ │ └── 0
│ └── offsets
│ └── 0
├── polygons01
│ └── polygons
│ └── polygons01
│ ├── coords
│ │ └── 0
│ └── offsets
│ └── 0
└── polygons012
└── polygons
└── polygons012
├── coords
│ └── 0
└── offsets
└── 0

Table

.
└── table
└── table
├── X
│ ├── data
│ ├── indices
│ └── indptr
├── layers
├── obs

and the SpatialData specific attributes are in path in .zattr, e.g. for polygons

"path": {
"geos": {
"geometry_name": "POLYGON",
"geometry_type": 3
}
}

let's use this for discussion, think we can improve a bit.

[giovp]

No description provided.

[codecov-commenter]

Codecov Report

Merging #40 (8293dfb) into feature/transform (cf3eeb3) will not change coverage.
The diff coverage is 0.00%.

Additional details and impacted files

@@ Coverage Diff @@## feature/transform #40 +/- ##
=================================================
Coverage 0.00% 0.00% =================================================
Files 14 15 +1 Lines 1119 1158 +39 =================================================
- Misses 1119 1158 +39 

Flag	Coverage Δ
unittests	0.00% <0.00%> (ø)

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
spatialdata/_core/models.py	0.00% <0.00%> (ø)

[giovp]

polygons IO only works with pip install git+https://github.com/shapely/shapely.git@refs/pull/1559/head --no-binary shapely (branch where to/from_ragged_array is added).

[giovp]

open questions:

• can we have a SpatialData with only one table (no labels, regions etc.) ?
  Yes -> Region is not mandatory.
  We can store only images and labels without tables
• empty SpatialData should be possible.
  No
• if region: str what is the table annotating?
• can we/shall we check for consistency of instance_key ?

[giovp]

@ivirshup this AnnData(obsm={"spatial": data}) doesn't work. Quite important if we want to save shapes/points in anndata with coordinates in obsm (and X potentially None ). What should we do?

[giovp]

basically if adata.uns["transform"] = spatialdata.Transform(...) it can't ofc be serialized so it needs to be popped. However, that would change the in-memory representation. Can only copy or someone has better idea?

[giovp]

zarr group hierarchy of elements:

Image

.
├── image0
│ └── 0
│ └── 0
│ └── 0
├── image01
│ └── 0
│ └── 0
│ └── 0
└── image012
└── 0
└── 0
└── 0

Labels

.
├── label0
│ └── labels
│ └── label0
│ └── 0
│ └── 0
├── label01
│ └── labels
│ └── label01
│ └── 0
│ └── 0
└── label012
└── labels
└── label012
└── 0
└── 0

Shapes

.
├── shapes0
│ └── shapes
│ └── shapes0
│ ├── X
│ │ └── 0
...
└── shapes01
└── shapes
└── shapes01
├── X
│ └── 0
...

Polygons

.
├── polygons0
│ └── polygons
│ └── polygons0
│ ├── coords
│ │ └── 0
│ └── offsets
│ └── 0
├── polygons01
│ └── polygons
│ └── polygons01
│ ├── coords
│ │ └── 0
│ └── offsets
│ └── 0
└── polygons012
└── polygons
└── polygons012
├── coords
│ └── 0
└── offsets
└── 0

Table

.
└── table
└── table
├── X
│ ├── data
│ ├── indices
│ └── indptr
├── layers
├── obs

and the SpatialData specific attributes are in path in .zattr, e.g. for polygons

"path": {
"geos": {
"geometry_name": "POLYGON",
"geometry_type": 3
}
}

let's use this for discussion, think we can improve a bit.