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transform() fails on large partitioned points with duplicate index #1095

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transform() fails on large partitioned points with duplicate index#1095

Description

@enric-bazz
enric-bazz
opened on Mar 17, 2026

With the recent unreleased spatialdata version, transform() fails when a points element comes from a large parquet file that gets partitioned.

Reproduce

importnumpyasnpimportpandasaspdimportdask.dataframeasddimportspatialdataassdn=40_000_000# number of pointsdf=pd.DataFrame({
"x": 100*np.random.rand(n),
"y": 100*np.random.rand(n),
})
df.to_parquet("/tmp/points_file.parquet")
ddf=dd.read_parquet("/tmp/points_file.parquet")
points=sd.models.PointsModel.parse(ddf)
sdata=sd.SpatialData.init_from_elements({"transcripts": points})
sd.transform(sdata, to_coordinate_system='global')

Error

ValueError: cannot reindex on an axis with duplicate labels
Traceback (most recent call last):
File "<ipython-input-1>", line 1
sd.transform(sdata, to_coordinate_system='global')
File ".../spatialdata/_core/operations/transform.py", line 288, in _
return data.transform_to_coordinate_system(target_coordinate_system=to_coordinate_system)
File ".../spatialdata/_core/spatialdata.py", line 880, in transform_to_coordinate_system
transformed = sdata.transform_element_to_coordinate_system(...)
File ".../spatialdata/_core/spatialdata.py", line 819, in transform_element_to_coordinate_system
transformed = transform(element, to_coordinate_system=target_coordinate_system, maintain_positioning=maintain_positioning)
File ".../spatialdata/_core/operations/transform.py", line 466, in _
new_col = pd.Series(new_ax.data.flatten().compute(), index=transformed.index)
File ".../pandas/core/indexes/base.py", line 4436, in reindex
raise ValueError("cannot reindex on an axis with duplicate labels")

Note: This is the root cause of this issue I encountered previously.

Environment

  • spatialdata version: 0.7.3a1.dev9+g094b86905
  • dask: 2026.1.1
  • pandas: 2.3.3

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try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '
`transform()` fails on large partitioned points with duplicate index · Issue #1095 · scverse/spatialdata · GitHub
      Skip to content
      transform() fails on large partitioned points with duplicate index #1095
      Closed
      Closed
      transform() fails on large partitioned points with duplicate index#1095
      Description
      @enric-bazz
      enric-bazz
      opened on Mar 17, 2026
      With the recent unreleased spatialdata version, transform() fails when a points element comes from a large parquet file that gets partitioned.
      Reproduce
      importnumpyasnpimportpandasaspdimportdask.dataframeasddimportspatialdataassdn=40_000_000# number of pointsdf=pd.DataFrame({
"x": 100*np.random.rand(n),
"y": 100*np.random.rand(n),
})
df.to_parquet("/tmp/points_file.parquet")
ddf=dd.read_parquet("/tmp/points_file.parquet")
points=sd.models.PointsModel.parse(ddf)
sdata=sd.SpatialData.init_from_elements({"transcripts": points})
sd.transform(sdata, to_coordinate_system='global')
      Error
      ValueError: cannot reindex on an axis with duplicate labels
Traceback (most recent call last):
File "<ipython-input-1>", line 1
sd.transform(sdata, to_coordinate_system='global')
File ".../spatialdata/_core/operations/transform.py", line 288, in _
return data.transform_to_coordinate_system(target_coordinate_system=to_coordinate_system)
File ".../spatialdata/_core/spatialdata.py", line 880, in transform_to_coordinate_system
transformed = sdata.transform_element_to_coordinate_system(...)
File ".../spatialdata/_core/spatialdata.py", line 819, in transform_element_to_coordinate_system
transformed = transform(element, to_coordinate_system=target_coordinate_system, maintain_positioning=maintain_positioning)
File ".../spatialdata/_core/operations/transform.py", line 466, in _
new_col = pd.Series(new_ax.data.flatten().compute(), index=transformed.index)
File ".../pandas/core/indexes/base.py", line 4436, in reindex
raise ValueError("cannot reindex on an axis with duplicate labels")

      Note: This is the root cause of this issue I encountered previously.
      Environment
      • spatialdata version: 0.7.3a1.dev9+g094b86905
      • dask: 2026.1.1
      • pandas: 2.3.3
      Metadata
      Metadata
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      No one assigned
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        No labels
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        No type
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        No projects
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          No milestone
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          None yet
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          No branches or pull requests
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try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
`transform()` fails on large partitioned points with duplicate index · Issue #1095 · scverse/spatialdata · GitHub
          Skip to content
          transform() fails on large partitioned points with duplicate index #1095
          Closed
          Closed
          transform() fails on large partitioned points with duplicate index#1095
          Description
          @enric-bazz
          enric-bazz
          opened on Mar 17, 2026
          With the recent unreleased spatialdata version, transform() fails when a points element comes from a large parquet file that gets partitioned.
          Reproduce
          importnumpyasnpimportpandasaspdimportdask.dataframeasddimportspatialdataassdn=40_000_000# number of pointsdf=pd.DataFrame({
"x": 100*np.random.rand(n),
"y": 100*np.random.rand(n),
})
df.to_parquet("/tmp/points_file.parquet")
ddf=dd.read_parquet("/tmp/points_file.parquet")
points=sd.models.PointsModel.parse(ddf)
sdata=sd.SpatialData.init_from_elements({"transcripts": points})
sd.transform(sdata, to_coordinate_system='global')
          Error
          ValueError: cannot reindex on an axis with duplicate labels
Traceback (most recent call last):
File "<ipython-input-1>", line 1
sd.transform(sdata, to_coordinate_system='global')
File ".../spatialdata/_core/operations/transform.py", line 288, in _
return data.transform_to_coordinate_system(target_coordinate_system=to_coordinate_system)
File ".../spatialdata/_core/spatialdata.py", line 880, in transform_to_coordinate_system
transformed = sdata.transform_element_to_coordinate_system(...)
File ".../spatialdata/_core/spatialdata.py", line 819, in transform_element_to_coordinate_system
transformed = transform(element, to_coordinate_system=target_coordinate_system, maintain_positioning=maintain_positioning)
File ".../spatialdata/_core/operations/transform.py", line 466, in _
new_col = pd.Series(new_ax.data.flatten().compute(), index=transformed.index)
File ".../pandas/core/indexes/base.py", line 4436, in reindex
raise ValueError("cannot reindex on an axis with duplicate labels")

          Note: This is the root cause of this issue I encountered previously.
          Environment
          • spatialdata version: 0.7.3a1.dev9+g094b86905
          • dask: 2026.1.1
          • pandas: 2.3.3
          Metadata
          Metadata
          Assignees
          No one assigned
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            No labels
            No labels
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            No type
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            No projects
              Milestone
              No milestone
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              None yet
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              No branches or pull requests
              Issue actions
              
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(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
`transform()` fails on large partitioned points with duplicate index · Issue #1095 · scverse/spatialdata · GitHub
              Skip to content
              transform() fails on large partitioned points with duplicate index #1095
              Closed
              Closed
              transform() fails on large partitioned points with duplicate index#1095
              Description
              @enric-bazz
              enric-bazz
              opened on Mar 17, 2026
              With the recent unreleased spatialdata version, transform() fails when a points element comes from a large parquet file that gets partitioned.
              Reproduce
              importnumpyasnpimportpandasaspdimportdask.dataframeasddimportspatialdataassdn=40_000_000# number of pointsdf=pd.DataFrame({
"x": 100*np.random.rand(n),
"y": 100*np.random.rand(n),
})
df.to_parquet("/tmp/points_file.parquet")
ddf=dd.read_parquet("/tmp/points_file.parquet")
points=sd.models.PointsModel.parse(ddf)
sdata=sd.SpatialData.init_from_elements({"transcripts": points})
sd.transform(sdata, to_coordinate_system='global')
              Error
              ValueError: cannot reindex on an axis with duplicate labels
Traceback (most recent call last):
File "<ipython-input-1>", line 1
sd.transform(sdata, to_coordinate_system='global')
File ".../spatialdata/_core/operations/transform.py", line 288, in _
return data.transform_to_coordinate_system(target_coordinate_system=to_coordinate_system)
File ".../spatialdata/_core/spatialdata.py", line 880, in transform_to_coordinate_system
transformed = sdata.transform_element_to_coordinate_system(...)
File ".../spatialdata/_core/spatialdata.py", line 819, in transform_element_to_coordinate_system
transformed = transform(element, to_coordinate_system=target_coordinate_system, maintain_positioning=maintain_positioning)
File ".../spatialdata/_core/operations/transform.py", line 466, in _
new_col = pd.Series(new_ax.data.flatten().compute(), index=transformed.index)
File ".../pandas/core/indexes/base.py", line 4436, in reindex
raise ValueError("cannot reindex on an axis with duplicate labels")

              Note: This is the root cause of this issue I encountered previously.
              Environment
              • spatialdata version: 0.7.3a1.dev9+g094b86905
              • dask: 2026.1.1
              • pandas: 2.3.3
              Metadata
              Metadata
              Assignees
              No one assigned
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                No labels
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                No type
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                No projects
                  Milestone
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                  No branches or pull requests
                  Issue actions
                  
, 'i');
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try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '
`transform()` fails on large partitioned points with duplicate index · Issue #1095 · scverse/spatialdata · GitHub
                  Skip to content
                  transform() fails on large partitioned points with duplicate index #1095
                  Closed
                  Closed
                  transform() fails on large partitioned points with duplicate index#1095
                  Description
                  @enric-bazz
                  enric-bazz
                  opened on Mar 17, 2026
                  With the recent unreleased spatialdata version, transform() fails when a points element comes from a large parquet file that gets partitioned.
                  Reproduce
                  importnumpyasnpimportpandasaspdimportdask.dataframeasddimportspatialdataassdn=40_000_000# number of pointsdf=pd.DataFrame({
"x": 100*np.random.rand(n),
"y": 100*np.random.rand(n),
})
df.to_parquet("/tmp/points_file.parquet")
ddf=dd.read_parquet("/tmp/points_file.parquet")
points=sd.models.PointsModel.parse(ddf)
sdata=sd.SpatialData.init_from_elements({"transcripts": points})
sd.transform(sdata, to_coordinate_system='global')
                  Error
                  ValueError: cannot reindex on an axis with duplicate labels
Traceback (most recent call last):
File "<ipython-input-1>", line 1
sd.transform(sdata, to_coordinate_system='global')
File ".../spatialdata/_core/operations/transform.py", line 288, in _
return data.transform_to_coordinate_system(target_coordinate_system=to_coordinate_system)
File ".../spatialdata/_core/spatialdata.py", line 880, in transform_to_coordinate_system
transformed = sdata.transform_element_to_coordinate_system(...)
File ".../spatialdata/_core/spatialdata.py", line 819, in transform_element_to_coordinate_system
transformed = transform(element, to_coordinate_system=target_coordinate_system, maintain_positioning=maintain_positioning)
File ".../spatialdata/_core/operations/transform.py", line 466, in _
new_col = pd.Series(new_ax.data.flatten().compute(), index=transformed.index)
File ".../pandas/core/indexes/base.py", line 4436, in reindex
raise ValueError("cannot reindex on an axis with duplicate labels")

                  Note: This is the root cause of this issue I encountered previously.
                  Environment
                  • spatialdata version: 0.7.3a1.dev9+g094b86905
                  • dask: 2026.1.1
                  • pandas: 2.3.3
                  Metadata
                  Metadata
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                  No one assigned
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                    No labels
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                    No type
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                    No projects
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                      No branches or pull requests
                      Issue actions
                      
, 'i');
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(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
`transform()` fails on large partitioned points with duplicate index · Issue #1095 · scverse/spatialdata · GitHub
                      Skip to content
                      transform() fails on large partitioned points with duplicate index #1095
                      Closed
                      Closed
                      transform() fails on large partitioned points with duplicate index#1095
                      Description
                      @enric-bazz
                      enric-bazz
                      opened on Mar 17, 2026
                      With the recent unreleased spatialdata version, transform() fails when a points element comes from a large parquet file that gets partitioned.
                      Reproduce
                      importnumpyasnpimportpandasaspdimportdask.dataframeasddimportspatialdataassdn=40_000_000# number of pointsdf=pd.DataFrame({
"x": 100*np.random.rand(n),
"y": 100*np.random.rand(n),
})
df.to_parquet("/tmp/points_file.parquet")
ddf=dd.read_parquet("/tmp/points_file.parquet")
points=sd.models.PointsModel.parse(ddf)
sdata=sd.SpatialData.init_from_elements({"transcripts": points})
sd.transform(sdata, to_coordinate_system='global')
                      Error
                      ValueError: cannot reindex on an axis with duplicate labels
Traceback (most recent call last):
File "<ipython-input-1>", line 1
sd.transform(sdata, to_coordinate_system='global')
File ".../spatialdata/_core/operations/transform.py", line 288, in _
return data.transform_to_coordinate_system(target_coordinate_system=to_coordinate_system)
File ".../spatialdata/_core/spatialdata.py", line 880, in transform_to_coordinate_system
transformed = sdata.transform_element_to_coordinate_system(...)
File ".../spatialdata/_core/spatialdata.py", line 819, in transform_element_to_coordinate_system
transformed = transform(element, to_coordinate_system=target_coordinate_system, maintain_positioning=maintain_positioning)
File ".../spatialdata/_core/operations/transform.py", line 466, in _
new_col = pd.Series(new_ax.data.flatten().compute(), index=transformed.index)
File ".../pandas/core/indexes/base.py", line 4436, in reindex
raise ValueError("cannot reindex on an axis with duplicate labels")

                      Note: This is the root cause of this issue I encountered previously.
                      Environment
                      • spatialdata version: 0.7.3a1.dev9+g094b86905
                      • dask: 2026.1.1
                      • pandas: 2.3.3
                      Metadata
                      Metadata
                      Assignees
                      No one assigned
                        Labels
                        No labels
                        No labels
                        Type
                        No type
                        Projects
                        No projects
                          Milestone
                          No milestone
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                          None yet
                          Development
                          No branches or pull requests
                          Issue actions
                          
, 'i');
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(function(){
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var __m = "*";
var __re = new RegExp('^' + ".*" + '
`transform()` fails on large partitioned points with duplicate index · Issue #1095 · scverse/spatialdata · GitHub
                          Skip to content
                          transform() fails on large partitioned points with duplicate index #1095
                          Closed
                          Closed
                          transform() fails on large partitioned points with duplicate index#1095
                          Description
                          @enric-bazz
                          enric-bazz
                          opened on Mar 17, 2026
                          With the recent unreleased spatialdata version, transform() fails when a points element comes from a large parquet file that gets partitioned.
                          Reproduce
                          importnumpyasnpimportpandasaspdimportdask.dataframeasddimportspatialdataassdn=40_000_000# number of pointsdf=pd.DataFrame({
"x": 100*np.random.rand(n),
"y": 100*np.random.rand(n),
})
df.to_parquet("/tmp/points_file.parquet")
ddf=dd.read_parquet("/tmp/points_file.parquet")
points=sd.models.PointsModel.parse(ddf)
sdata=sd.SpatialData.init_from_elements({"transcripts": points})
sd.transform(sdata, to_coordinate_system='global')
                          Error
                          ValueError: cannot reindex on an axis with duplicate labels
Traceback (most recent call last):
File "<ipython-input-1>", line 1
sd.transform(sdata, to_coordinate_system='global')
File ".../spatialdata/_core/operations/transform.py", line 288, in _
return data.transform_to_coordinate_system(target_coordinate_system=to_coordinate_system)
File ".../spatialdata/_core/spatialdata.py", line 880, in transform_to_coordinate_system
transformed = sdata.transform_element_to_coordinate_system(...)
File ".../spatialdata/_core/spatialdata.py", line 819, in transform_element_to_coordinate_system
transformed = transform(element, to_coordinate_system=target_coordinate_system, maintain_positioning=maintain_positioning)
File ".../spatialdata/_core/operations/transform.py", line 466, in _
new_col = pd.Series(new_ax.data.flatten().compute(), index=transformed.index)
File ".../pandas/core/indexes/base.py", line 4436, in reindex
raise ValueError("cannot reindex on an axis with duplicate labels")

                          Note: This is the root cause of this issue I encountered previously.
                          Environment
                          • spatialdata version: 0.7.3a1.dev9+g094b86905
                          • dask: 2026.1.1
                          • pandas: 2.3.3
                          Metadata
                          Metadata
                          Assignees
                          No one assigned
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                            No labels
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`transform()` fails on large partitioned points with duplicate index · Issue #1095 · scverse/spatialdata · GitHub
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                              transform() fails on large partitioned points with duplicate index #1095
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                              transform() fails on large partitioned points with duplicate index#1095
                              Description
                              @enric-bazz
                              enric-bazz
                              opened on Mar 17, 2026
                              With the recent unreleased spatialdata version, transform() fails when a points element comes from a large parquet file that gets partitioned.
                              Reproduce
                              importnumpyasnpimportpandasaspdimportdask.dataframeasddimportspatialdataassdn=40_000_000# number of pointsdf=pd.DataFrame({
"x": 100*np.random.rand(n),
"y": 100*np.random.rand(n),
})
df.to_parquet("/tmp/points_file.parquet")
ddf=dd.read_parquet("/tmp/points_file.parquet")
points=sd.models.PointsModel.parse(ddf)
sdata=sd.SpatialData.init_from_elements({"transcripts": points})
sd.transform(sdata, to_coordinate_system='global')
                              Error
                              ValueError: cannot reindex on an axis with duplicate labels
Traceback (most recent call last):
File "<ipython-input-1>", line 1
sd.transform(sdata, to_coordinate_system='global')
File ".../spatialdata/_core/operations/transform.py", line 288, in _
return data.transform_to_coordinate_system(target_coordinate_system=to_coordinate_system)
File ".../spatialdata/_core/spatialdata.py", line 880, in transform_to_coordinate_system
transformed = sdata.transform_element_to_coordinate_system(...)
File ".../spatialdata/_core/spatialdata.py", line 819, in transform_element_to_coordinate_system
transformed = transform(element, to_coordinate_system=target_coordinate_system, maintain_positioning=maintain_positioning)
File ".../spatialdata/_core/operations/transform.py", line 466, in _
new_col = pd.Series(new_ax.data.flatten().compute(), index=transformed.index)
File ".../pandas/core/indexes/base.py", line 4436, in reindex
raise ValueError("cannot reindex on an axis with duplicate labels")

                              Note: This is the root cause of this issue I encountered previously.
                              Environment
                              • spatialdata version: 0.7.3a1.dev9+g094b86905
                              • dask: 2026.1.1
                              • pandas: 2.3.3
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