cosmx - ValueError: Affine matrix must be homogeneous.

Hi,

I'm trying to read in some CosMx data - I have a dataset formatted into a folder with the CellLabels and CellComposite directories and then the relevant CSV files. When I execute the code below:

adata3 = sp.cosmx(sample_dir,
                  dataset_id = 'GCIN10692_TMA2')

I get the following error:

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In[21], line 1
----> 1 adata3 = sp.cosmx(sample_dir,
      2                   dataset_id = 'GCIN10692_TMA2')

File [/path/to/in839/analysis/init-rocker-renv/venv/lib/python3.12/site-packages/spatialdata_io/readers/cosmx.py:148](http://localhost:8888/lab/tree/venv/lib/python3.12/site-packages/spatialdata_io/readers/cosmx.py#line=147), in cosmx(path, dataset_id, transcripts, imread_kwargs, image_models_kwargs)
    146     glob = table[idx, :].obs[[CosmxKeys.X_GLOBAL_CELL, CosmxKeys.Y_GLOBAL_CELL]].values
    147     out = estimate_transform(ttype="affine", src=loc, dst=glob)
--> 148     affine_transforms_to_global[fov] = Affine(
    149         # out.params, input_coordinate_system=input_cs, output_coordinate_system=output_cs
    150         out.params,
    151         input_axes=("x", "y"),
    152         output_axes=("x", "y"),
    153     )
    155 table.obsm["global"] = table.obs[[CosmxKeys.X_GLOBAL_CELL, CosmxKeys.Y_GLOBAL_CELL]].to_numpy()
    156 table.obsm["spatial"] = table.obs[[CosmxKeys.X_LOCAL_CELL, CosmxKeys.Y_LOCAL_CELL]].to_numpy()

File [/path/to/in839/analysis/init-rocker-renv/venv/lib/python3.12/site-packages/spatialdata/transformations/transformations.py:523](http://localhost:8888/lab/tree/venv/lib/python3.12/site-packages/spatialdata/transformations/transformations.py#line=522), in Affine.__init__(self, matrix, input_axes, output_axes)
    521     raise ValueError("Invalid shape for affine matrix.")
    522 if not np.array_equal(self.matrix[-1, :-1], np.zeros(len(input_axes))):
--> 523     raise ValueError("Affine matrix must be homogeneous.")
    524 assert self.matrix[-1, -1] == 1.0

ValueError: Affine matrix must be homogeneous.

Any recommendations on how to address this?

Cheers

Reproduce the failure with sp.cosmx(sample_dir, dataset_id='GCIN10692_TMA2') and inspect spatialdata_io/readers/cosmx.py around line 148. Then read spatialdata/transformations/transformations.py around line 523 to understand the matrix validation; done means the reported CosMx dataset loads without the homogeneous-affine error.