Add `dataset_id` prefix to tables in Visium HD
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评估
调研方向
首先定位创建 Tables 条目的 Visium HD reader 代码,并将其命名方式与 issue 中显示的 Images 和 Shapes 进行比较。完成的标准是:Visium HD 的 Tables 名称包含 dataset_id 前缀,与其他元素保持一致,并在拼接 SpatialData 对象时避免重复的 Table 名称。
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描述
Thanks for the clarification. That makes sense.
One small detail. Should not the elements in
Tablesbe renamed as well? Right now they are not (see above). If I try to concatenate two visium_hdSpatialDataobjects I get a warning about identical names and they are given unique names which are not ideal because do not follow the original patterns, making it harder to know which ones came from where.>> sdata1 SpatialData object ├── Images │ ├── 'HM_hires_image': DataArray[cyx] (3, 5057, 6000) │ └── 'HM_lowres_image': DataArray[cyx] (3, 506, 600) ├── Shapes │ ├── 'HM_square_002um': GeoDataFrame shape: (2942291, 1) (2D shapes) │ ├── 'HM_square_008um': GeoDataFrame shape: (187571, 1) (2D shapes) │ └── 'HM_square_016um': GeoDataFrame shape: (48206, 1) (2D shapes) └── Tables ├── 'square_002um': AnnData (2942291, 18085) ├── 'square_008um': AnnData (187571, 18085) └── 'square_016um': AnnData (48206, 18085) with coordinate systems: ▸ 'downscaled_hires', with elements: HM_hires_image (Images), HM_square_002um (Shapes), HM_square_008um (Shapes), HM_square_016um (Shapes) ▸ 'downscaled_lowres', with elements: HM_lowres_image (Images), HM_square_002um (Shapes), HM_square_008um (Shapes), HM_square_016um (Shapes) ▸ 'global', with elements: HM_hires_image (Images), HM_lowres_image (Images), HM_square_002um (Shapes), HM_square_008um (Shapes), HM_square_016um (Shapes) >> sdata2 SpatialData object ├── Images │ ├── 'RS_hires_image': DataArray[cyx] (3, 6000, 5163) │ └── 'RS_lowres_image': DataArray[cyx] (3, 600, 517) ├── Shapes │ ├── 'RS_square_002um': GeoDataFrame shape: (2493008, 1) (2D shapes) │ ├── 'RS_square_008um': GeoDataFrame shape: (160049, 1) (2D shapes) │ └── 'RS_square_016um': GeoDataFrame shape: (41439, 1) (2D shapes) └── Tables ├── 'square_002um': AnnData (2493008, 18085) ├── 'square_008um': AnnData (160049, 18085) └── 'square_016um': AnnData (41439, 18085) with coordinate systems: ▸ 'downscaled_hires', with elements: RS_hires_image (Images), RS_square_002um (Shapes), RS_square_008um (Shapes), RS_square_016um (Shapes) ▸ 'downscaled_lowres', with elements: RS_lowres_image (Images), RS_square_002um (Shapes), RS_square_008um (Shapes), RS_square_016um (Shapes) ▸ 'global', with elements: RS_hires_image (Images), RS_lowres_image (Images), RS_square_002um (Shapes), RS_square_008um (Shapes), RS_square_016um (Shapes) >> sd.concatenate([sdata1, sdata2]) <stdin>:1: UserWarning: Duplicate table names found. Tables will be added with integer suffix. Set `concatenate_tables` to `True` if concatenation is wished for instead. SpatialData object ├── Images │ ├── 'HM_hires_image': DataArray[cyx] (3, 5057, 6000) │ ├── 'HM_lowres_image': DataArray[cyx] (3, 506, 600) │ ├── 'RS_hires_image': DataArray[cyx] (3, 6000, 5163) │ └── 'RS_lowres_image': DataArray[cyx] (3, 600, 517) ├── Shapes │ ├── 'HM_square_002um': GeoDataFrame shape: (2942291, 1) (2D shapes) │ ├── 'HM_square_008um': GeoDataFrame shape: (187571, 1) (2D shapes) │ ├── 'HM_square_016um': GeoDataFrame shape: (48206, 1) (2D shapes) │ ├── 'RS_square_002um': GeoDataFrame shape: (2493008, 1) (2D shapes) │ ├── 'RS_square_008um': GeoDataFrame shape: (160049, 1) (2D shapes) │ └── 'RS_square_016um': GeoDataFrame shape: (41439, 1) (2D shapes) └── Tables ├── 'square_002um_0': AnnData (2942291, 18085) ├── 'square_002um_1': AnnData (2493008, 18085) ├── 'square_008um_0': AnnData (187571, 18085) ├── 'square_008um_1': AnnData (160049, 18085) ├── 'square_016um_0': AnnData (48206, 18085) └── 'square_016um_1': AnnData (41439, 18085) with coordinate systems: ▸ 'downscaled_hires', with elements: HM_hires_image (Images), RS_hires_image (Images), HM_square_002um (Shapes), HM_square_008um (Shapes), HM_square_016um (Shapes), RS_square_002um (Shapes), RS_square_008um (Shapes), RS_square_016um (Shapes) ▸ 'downscaled_lowres', with elements: HM_lowres_image (Images), RS_lowres_image (Images), HM_square_002um (Shapes), HM_square_008um (Shapes), HM_square_016um (Shapes), RS_square_002um (Shapes), RS_square_008um (Shapes), RS_square_016um (Shapes) ▸ 'global', with elements: HM_hires_image (Images), HM_lowres_image (Images), RS_hires_image (Images), RS_lowres_image (Images), HM_square_002um (Shapes), HM_square_008um (Shapes), HM_square_016um (Shapes), RS_square_002um (Shapes), RS_square_008um (Shapes), RS_square_016um (Shapes)
Originally posted by @ddiez in #212
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