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get_extent switches x and y #335

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get_extent switches x and y#335
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@Sonja-Stockhaus
Sonja-Stockhaus
opened on Aug 9, 2023

Hey @timtreis , @LucaMarconato ,

So in the branch feature/get_extent there is the new get_extent function which should be outsourced from spatialdata-plot.
I just compared it to the _get_extent function from spatialdata-plot and it looks like both compute the same numbers but the spatialdata output has the x and y coordinates switched which seems to be a bug. I added code to hopefully reproduce the issue.

Would be cool if you could have a look at it :)

importspatialdataassdimportspatialdata_plot# This example doesn't really work with blobs (bc it has identical x and y extents), so I used the example data from https://s3.embl.de/spatialdata/spatialdata-sandbox/visium_associated_xenium_io.zipvisium_sdata=sd.read_zarr("visium_associated_xenium_io.zarr")
print("Old function (from spatialdata-plot):")
print(spatialdata_plot.pl.utils._get_extent(visium_sdata))
# output format is [xmin, xmax, ymin, ymax], so for "global" I get xmax = 19505

image

print("New function (from spatialdata):")
print(sd._core.data_extent.get_extent(visium_sdata, coordinate_system="global"))
# This would imply ymax = 19505

image

print("Ground truth:")
print(visium_sdata.images)
# (c: 3, y: 21571, x: 19505) would mean the spatialdata output is incorrect because x and y are swapped

image

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get_extent switches x and y · Issue #335 · scverse/spatialdata · GitHub
    Skip to content
    get_extent switches x and y #335
    Closed
    #318
    Closed
    get_extent switches x and y#335
    #318
    Labels
    bug 🚨Something isn't working
    Description
    @Sonja-Stockhaus
    Sonja-Stockhaus
    opened on Aug 9, 2023
    Hey @timtreis , @LucaMarconato ,
    So in the branch feature/get_extent there is the new get_extent function which should be outsourced from spatialdata-plot.
    
I just compared it to the _get_extent function from spatialdata-plot and it looks like both compute the same numbers but the spatialdata output has the x and y coordinates switched which seems to be a bug. I added code to hopefully reproduce the issue.
    Would be cool if you could have a look at it :)
    importspatialdataassdimportspatialdata_plot# This example doesn't really work with blobs (bc it has identical x and y extents), so I used the example data from https://s3.embl.de/spatialdata/spatialdata-sandbox/visium_associated_xenium_io.zipvisium_sdata=sd.read_zarr("visium_associated_xenium_io.zarr")
print("Old function (from spatialdata-plot):")
print(spatialdata_plot.pl.utils._get_extent(visium_sdata))
# output format is [xmin, xmax, ymin, ymax], so for "global" I get xmax = 19505
    image
    print("New function (from spatialdata):")
print(sd._core.data_extent.get_extent(visium_sdata, coordinate_system="global"))
# This would imply ymax = 19505

    image
    print("Ground truth:")
print(visium_sdata.images)
# (c: 3, y: 21571, x: 19505) would mean the spatialdata output is incorrect because x and y are swapped

    image
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get_extent switches x and y · Issue #335 · scverse/spatialdata · GitHub
      Skip to content
      get_extent switches x and y #335
      Closed
      #318
      Closed
      get_extent switches x and y#335
      #318
      Labels
      bug 🚨Something isn't working
      Description
      @Sonja-Stockhaus
      Sonja-Stockhaus
      opened on Aug 9, 2023
      Hey @timtreis , @LucaMarconato ,
      So in the branch feature/get_extent there is the new get_extent function which should be outsourced from spatialdata-plot.
      
I just compared it to the _get_extent function from spatialdata-plot and it looks like both compute the same numbers but the spatialdata output has the x and y coordinates switched which seems to be a bug. I added code to hopefully reproduce the issue.
      Would be cool if you could have a look at it :)
      importspatialdataassdimportspatialdata_plot# This example doesn't really work with blobs (bc it has identical x and y extents), so I used the example data from https://s3.embl.de/spatialdata/spatialdata-sandbox/visium_associated_xenium_io.zipvisium_sdata=sd.read_zarr("visium_associated_xenium_io.zarr")
print("Old function (from spatialdata-plot):")
print(spatialdata_plot.pl.utils._get_extent(visium_sdata))
# output format is [xmin, xmax, ymin, ymax], so for "global" I get xmax = 19505
      image
      print("New function (from spatialdata):")
print(sd._core.data_extent.get_extent(visium_sdata, coordinate_system="global"))
# This would imply ymax = 19505

      image
      print("Ground truth:")
print(visium_sdata.images)
# (c: 3, y: 21571, x: 19505) would mean the spatialdata output is incorrect because x and y are swapped

      image
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var __m = "*";
var __re = new RegExp('^' + ".*" + '
get_extent switches x and y · Issue #335 · scverse/spatialdata · GitHub
        Skip to content
        get_extent switches x and y #335
        Closed
        #318
        Closed
        get_extent switches x and y#335
        #318
        Labels
        bug 🚨Something isn't working
        Description
        @Sonja-Stockhaus
        Sonja-Stockhaus
        opened on Aug 9, 2023
        Hey @timtreis , @LucaMarconato ,
        So in the branch feature/get_extent there is the new get_extent function which should be outsourced from spatialdata-plot.
        
I just compared it to the _get_extent function from spatialdata-plot and it looks like both compute the same numbers but the spatialdata output has the x and y coordinates switched which seems to be a bug. I added code to hopefully reproduce the issue.
        Would be cool if you could have a look at it :)
        importspatialdataassdimportspatialdata_plot# This example doesn't really work with blobs (bc it has identical x and y extents), so I used the example data from https://s3.embl.de/spatialdata/spatialdata-sandbox/visium_associated_xenium_io.zipvisium_sdata=sd.read_zarr("visium_associated_xenium_io.zarr")
print("Old function (from spatialdata-plot):")
print(spatialdata_plot.pl.utils._get_extent(visium_sdata))
# output format is [xmin, xmax, ymin, ymax], so for "global" I get xmax = 19505
        image
        print("New function (from spatialdata):")
print(sd._core.data_extent.get_extent(visium_sdata, coordinate_system="global"))
# This would imply ymax = 19505

        image
        print("Ground truth:")
print(visium_sdata.images)
# (c: 3, y: 21571, x: 19505) would mean the spatialdata output is incorrect because x and y are swapped

        image
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get_extent switches x and y · Issue #335 · scverse/spatialdata · GitHub
          Skip to content
          get_extent switches x and y #335
          Closed
          #318
          Closed
          get_extent switches x and y#335
          #318
          Labels
          bug 🚨Something isn't working
          Description
          @Sonja-Stockhaus
          Sonja-Stockhaus
          opened on Aug 9, 2023
          Hey @timtreis , @LucaMarconato ,
          So in the branch feature/get_extent there is the new get_extent function which should be outsourced from spatialdata-plot.
          
I just compared it to the _get_extent function from spatialdata-plot and it looks like both compute the same numbers but the spatialdata output has the x and y coordinates switched which seems to be a bug. I added code to hopefully reproduce the issue.
          Would be cool if you could have a look at it :)
          importspatialdataassdimportspatialdata_plot# This example doesn't really work with blobs (bc it has identical x and y extents), so I used the example data from https://s3.embl.de/spatialdata/spatialdata-sandbox/visium_associated_xenium_io.zipvisium_sdata=sd.read_zarr("visium_associated_xenium_io.zarr")
print("Old function (from spatialdata-plot):")
print(spatialdata_plot.pl.utils._get_extent(visium_sdata))
# output format is [xmin, xmax, ymin, ymax], so for "global" I get xmax = 19505
          image
          print("New function (from spatialdata):")
print(sd._core.data_extent.get_extent(visium_sdata, coordinate_system="global"))
# This would imply ymax = 19505

          image
          print("Ground truth:")
print(visium_sdata.images)
# (c: 3, y: 21571, x: 19505) would mean the spatialdata output is incorrect because x and y are swapped

          image
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get_extent switches x and y · Issue #335 · scverse/spatialdata · GitHub
            Skip to content
            get_extent switches x and y #335
            Closed
            #318
            Closed
            get_extent switches x and y#335
            #318
            Labels
            bug 🚨Something isn't working
            Description
            @Sonja-Stockhaus
            Sonja-Stockhaus
            opened on Aug 9, 2023
            Hey @timtreis , @LucaMarconato ,
            So in the branch feature/get_extent there is the new get_extent function which should be outsourced from spatialdata-plot.
            
I just compared it to the _get_extent function from spatialdata-plot and it looks like both compute the same numbers but the spatialdata output has the x and y coordinates switched which seems to be a bug. I added code to hopefully reproduce the issue.
            Would be cool if you could have a look at it :)
            importspatialdataassdimportspatialdata_plot# This example doesn't really work with blobs (bc it has identical x and y extents), so I used the example data from https://s3.embl.de/spatialdata/spatialdata-sandbox/visium_associated_xenium_io.zipvisium_sdata=sd.read_zarr("visium_associated_xenium_io.zarr")
print("Old function (from spatialdata-plot):")
print(spatialdata_plot.pl.utils._get_extent(visium_sdata))
# output format is [xmin, xmax, ymin, ymax], so for "global" I get xmax = 19505
            image
            print("New function (from spatialdata):")
print(sd._core.data_extent.get_extent(visium_sdata, coordinate_system="global"))
# This would imply ymax = 19505

            image
            print("Ground truth:")
print(visium_sdata.images)
# (c: 3, y: 21571, x: 19505) would mean the spatialdata output is incorrect because x and y are swapped

            image
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get_extent switches x and y · Issue #335 · scverse/spatialdata · GitHub
              Skip to content
              get_extent switches x and y #335
              Closed
              #318
              Closed
              get_extent switches x and y#335
              #318
              Labels
              bug 🚨Something isn't working
              Description
              @Sonja-Stockhaus
              Sonja-Stockhaus
              opened on Aug 9, 2023
              Hey @timtreis , @LucaMarconato ,
              So in the branch feature/get_extent there is the new get_extent function which should be outsourced from spatialdata-plot.
              
I just compared it to the _get_extent function from spatialdata-plot and it looks like both compute the same numbers but the spatialdata output has the x and y coordinates switched which seems to be a bug. I added code to hopefully reproduce the issue.
              Would be cool if you could have a look at it :)
              importspatialdataassdimportspatialdata_plot# This example doesn't really work with blobs (bc it has identical x and y extents), so I used the example data from https://s3.embl.de/spatialdata/spatialdata-sandbox/visium_associated_xenium_io.zipvisium_sdata=sd.read_zarr("visium_associated_xenium_io.zarr")
print("Old function (from spatialdata-plot):")
print(spatialdata_plot.pl.utils._get_extent(visium_sdata))
# output format is [xmin, xmax, ymin, ymax], so for "global" I get xmax = 19505
              image
              print("New function (from spatialdata):")
print(sd._core.data_extent.get_extent(visium_sdata, coordinate_system="global"))
# This would imply ymax = 19505

              image
              print("Ground truth:")
print(visium_sdata.images)
# (c: 3, y: 21571, x: 19505) would mean the spatialdata output is incorrect because x and y are swapped

              image
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