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Adding image to same slot for backed sdata #374

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Adding image to same slot for backed sdata#374

Description

@ArneDefauw
ArneDefauw
opened on Oct 10, 2023

When writing an image to zarr with overwrite=True, I found some unexpected behaviour.
Below I give a mimimal example to reproduce the issue.

This works, as expected. I can overwrite image layer 'image'.

import spatialdata
import numpy as np
sdata = spatialdata.SpatialData()
sdata.write( 'sdata.zarr' )
arr=np.random.rand( 1,100,100 )
spatialelement=spatialdata.models.Image2DModel.parse(
arr, dims=[ 'c' ,'y', 'x' ],
)
sdata.add_image( name="image", image=spatialelement , overwrite=True )
sdata.add_image( name="image", image=spatialelement , overwrite=True )

However, when I add some processing (e.g. multiplying by two) before replacing sdata["image" ]:

spatialelement=spatialdata.models.Image2DModel.parse(
sdata[ "image" ].data*2, dims=[ 'c' ,'y', 'x' ],
)
sdata.add_image( name="image", image=spatialelement , overwrite=True )

I get the error:

ValueError Traceback (most recent call last)
in SpatialData.add_image(self, name, image, storage_options, overwrite)
659 target_path = os.path.realpath(os.path.join(self.path, "images", name))
660 if target_path in files:
--> 661 raise ValueError(
662 "Cannot add the image to the SpatialData object because it would overwrite an element that it is"
663 "using for backing. See more here: #138"
664 )
665 self._add_image_in_memory(name=name, image=image, overwrite=overwrite)
666 # old code to support overwriting the backing file
667 # with tempfile.TemporaryDirectory() as tmpdir:
668 # store = parse_url(Path(tmpdir) / "data.zarr", mode="w").store
(...)
692 # image = _read_multiscale(str(tgt_element_path), raster_type="image")
693 # self._add_image_in_memory(name=name, image=image, overwrite=True)

ValueError: Cannot add the image to the SpatialData object because it would overwrite an element that it isusing for backing. See more here: #138

However, if I do a persist(), I am allowed to overwrite:

spatialelement=spatialdata.models.Image2DModel.parse(
(sdata[ "image" ].data*2).persist(), dims=[ 'c' ,'y', 'x' ],
)
sdata.add_image( name="image", image=spatialelement , overwrite=True )

And I am also allowed to do this (typical scenario where you want to do some processing twice with e.g. different parameters etc.):

spatialelement=spatialdata.models.Image2DModel.parse(
sdata[ "image" ].data*2, dims=[ 'c' ,'y', 'x' ],
)
sdata.add_image( name="image2", image=spatialelement , overwrite=True )
spatialelement=spatialdata.models.Image2DModel.parse(
sdata[ "image" ].data*2, dims=[ 'c' ,'y', 'x' ],
)
sdata.add_image( name="image2", image=spatialelement , overwrite=True )

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Adding image to same slot for backed sdata · Issue #374 · scverse/spatialdata · GitHub
      Skip to content
      Adding image to same slot for backed sdata #374
      Open
      Open
      Adding image to same slot for backed sdata#374
      Description
      @ArneDefauw
      ArneDefauw
      opened on Oct 10, 2023
      When writing an image to zarr with overwrite=True, I found some unexpected behaviour.
      
Below I give a mimimal example to reproduce the issue.
      This works, as expected. I can overwrite image layer 'image'.
      import spatialdata
import numpy as np
sdata = spatialdata.SpatialData()
sdata.write( 'sdata.zarr' )
arr=np.random.rand( 1,100,100 )
spatialelement=spatialdata.models.Image2DModel.parse(
arr, dims=[ 'c' ,'y', 'x' ],
)
sdata.add_image( name="image", image=spatialelement , overwrite=True )
sdata.add_image( name="image", image=spatialelement , overwrite=True )

      However, when I add some processing (e.g. multiplying by two) before replacing sdata["image" ]:
      spatialelement=spatialdata.models.Image2DModel.parse(
sdata[ "image" ].data*2, dims=[ 'c' ,'y', 'x' ],
)
sdata.add_image( name="image", image=spatialelement , overwrite=True )

      I get the error:
      ValueError Traceback (most recent call last)
      
in SpatialData.add_image(self, name, image, storage_options, overwrite)
      
659 target_path = os.path.realpath(os.path.join(self.path, "images", name))
      
660 if target_path in files:
      
--> 661 raise ValueError(
      
662 "Cannot add the image to the SpatialData object because it would overwrite an element that it is"
      
663 "using for backing. See more here: #138"
      
664 )
      
665 self._add_image_in_memory(name=name, image=image, overwrite=overwrite)
      
666 # old code to support overwriting the backing file
      
667 # with tempfile.TemporaryDirectory() as tmpdir:
      
668 # store = parse_url(Path(tmpdir) / "data.zarr", mode="w").store
      
(...)
      
692 # image = _read_multiscale(str(tgt_element_path), raster_type="image")
      
693 # self._add_image_in_memory(name=name, image=image, overwrite=True)
      ValueError: Cannot add the image to the SpatialData object because it would overwrite an element that it isusing for backing. See more here: #138
      However, if I do a persist(), I am allowed to overwrite:
      spatialelement=spatialdata.models.Image2DModel.parse(
(sdata[ "image" ].data*2).persist(), dims=[ 'c' ,'y', 'x' ],
)
sdata.add_image( name="image", image=spatialelement , overwrite=True )

      And I am also allowed to do this (typical scenario where you want to do some processing twice with e.g. different parameters etc.):
      spatialelement=spatialdata.models.Image2DModel.parse(
sdata[ "image" ].data*2, dims=[ 'c' ,'y', 'x' ],
)
sdata.add_image( name="image2", image=spatialelement , overwrite=True )
spatialelement=spatialdata.models.Image2DModel.parse(
sdata[ "image" ].data*2, dims=[ 'c' ,'y', 'x' ],
)
sdata.add_image( name="image2", image=spatialelement , overwrite=True )

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try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
Adding image to same slot for backed sdata · Issue #374 · scverse/spatialdata · GitHub
          Skip to content
          Adding image to same slot for backed sdata #374
          Open
          Open
          Adding image to same slot for backed sdata#374
          Description
          @ArneDefauw
          ArneDefauw
          opened on Oct 10, 2023
          When writing an image to zarr with overwrite=True, I found some unexpected behaviour.
          
Below I give a mimimal example to reproduce the issue.
          This works, as expected. I can overwrite image layer 'image'.
          import spatialdata
import numpy as np
sdata = spatialdata.SpatialData()
sdata.write( 'sdata.zarr' )
arr=np.random.rand( 1,100,100 )
spatialelement=spatialdata.models.Image2DModel.parse(
arr, dims=[ 'c' ,'y', 'x' ],
)
sdata.add_image( name="image", image=spatialelement , overwrite=True )
sdata.add_image( name="image", image=spatialelement , overwrite=True )

          However, when I add some processing (e.g. multiplying by two) before replacing sdata["image" ]:
          spatialelement=spatialdata.models.Image2DModel.parse(
sdata[ "image" ].data*2, dims=[ 'c' ,'y', 'x' ],
)
sdata.add_image( name="image", image=spatialelement , overwrite=True )

          I get the error:
          ValueError Traceback (most recent call last)
          
in SpatialData.add_image(self, name, image, storage_options, overwrite)
          
659 target_path = os.path.realpath(os.path.join(self.path, "images", name))
          
660 if target_path in files:
          
--> 661 raise ValueError(
          
662 "Cannot add the image to the SpatialData object because it would overwrite an element that it is"
          
663 "using for backing. See more here: #138"
          
664 )
          
665 self._add_image_in_memory(name=name, image=image, overwrite=overwrite)
          
666 # old code to support overwriting the backing file
          
667 # with tempfile.TemporaryDirectory() as tmpdir:
          
668 # store = parse_url(Path(tmpdir) / "data.zarr", mode="w").store
          
(...)
          
692 # image = _read_multiscale(str(tgt_element_path), raster_type="image")
          
693 # self._add_image_in_memory(name=name, image=image, overwrite=True)
          ValueError: Cannot add the image to the SpatialData object because it would overwrite an element that it isusing for backing. See more here: #138
          However, if I do a persist(), I am allowed to overwrite:
          spatialelement=spatialdata.models.Image2DModel.parse(
(sdata[ "image" ].data*2).persist(), dims=[ 'c' ,'y', 'x' ],
)
sdata.add_image( name="image", image=spatialelement , overwrite=True )

          And I am also allowed to do this (typical scenario where you want to do some processing twice with e.g. different parameters etc.):
          spatialelement=spatialdata.models.Image2DModel.parse(
sdata[ "image" ].data*2, dims=[ 'c' ,'y', 'x' ],
)
sdata.add_image( name="image2", image=spatialelement , overwrite=True )
spatialelement=spatialdata.models.Image2DModel.parse(
sdata[ "image" ].data*2, dims=[ 'c' ,'y', 'x' ],
)
sdata.add_image( name="image2", image=spatialelement , overwrite=True )

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(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
Adding image to same slot for backed sdata · Issue #374 · scverse/spatialdata · GitHub
              Skip to content
              Adding image to same slot for backed sdata #374
              Open
              Open
              Adding image to same slot for backed sdata#374
              Description
              @ArneDefauw
              ArneDefauw
              opened on Oct 10, 2023
              When writing an image to zarr with overwrite=True, I found some unexpected behaviour.
              
Below I give a mimimal example to reproduce the issue.
              This works, as expected. I can overwrite image layer 'image'.
              import spatialdata
import numpy as np
sdata = spatialdata.SpatialData()
sdata.write( 'sdata.zarr' )
arr=np.random.rand( 1,100,100 )
spatialelement=spatialdata.models.Image2DModel.parse(
arr, dims=[ 'c' ,'y', 'x' ],
)
sdata.add_image( name="image", image=spatialelement , overwrite=True )
sdata.add_image( name="image", image=spatialelement , overwrite=True )

              However, when I add some processing (e.g. multiplying by two) before replacing sdata["image" ]:
              spatialelement=spatialdata.models.Image2DModel.parse(
sdata[ "image" ].data*2, dims=[ 'c' ,'y', 'x' ],
)
sdata.add_image( name="image", image=spatialelement , overwrite=True )

              I get the error:
              ValueError Traceback (most recent call last)
              
in SpatialData.add_image(self, name, image, storage_options, overwrite)
              
659 target_path = os.path.realpath(os.path.join(self.path, "images", name))
              
660 if target_path in files:
              
--> 661 raise ValueError(
              
662 "Cannot add the image to the SpatialData object because it would overwrite an element that it is"
              
663 "using for backing. See more here: #138"
              
664 )
              
665 self._add_image_in_memory(name=name, image=image, overwrite=overwrite)
              
666 # old code to support overwriting the backing file
              
667 # with tempfile.TemporaryDirectory() as tmpdir:
              
668 # store = parse_url(Path(tmpdir) / "data.zarr", mode="w").store
              
(...)
              
692 # image = _read_multiscale(str(tgt_element_path), raster_type="image")
              
693 # self._add_image_in_memory(name=name, image=image, overwrite=True)
              ValueError: Cannot add the image to the SpatialData object because it would overwrite an element that it isusing for backing. See more here: #138
              However, if I do a persist(), I am allowed to overwrite:
              spatialelement=spatialdata.models.Image2DModel.parse(
(sdata[ "image" ].data*2).persist(), dims=[ 'c' ,'y', 'x' ],
)
sdata.add_image( name="image", image=spatialelement , overwrite=True )

              And I am also allowed to do this (typical scenario where you want to do some processing twice with e.g. different parameters etc.):
              spatialelement=spatialdata.models.Image2DModel.parse(
sdata[ "image" ].data*2, dims=[ 'c' ,'y', 'x' ],
)
sdata.add_image( name="image2", image=spatialelement , overwrite=True )
spatialelement=spatialdata.models.Image2DModel.parse(
sdata[ "image" ].data*2, dims=[ 'c' ,'y', 'x' ],
)
sdata.add_image( name="image2", image=spatialelement , overwrite=True )

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, 'i');
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(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '
Adding image to same slot for backed sdata · Issue #374 · scverse/spatialdata · GitHub
                  Skip to content
                  Adding image to same slot for backed sdata #374
                  Open
                  Open
                  Adding image to same slot for backed sdata#374
                  Description
                  @ArneDefauw
                  ArneDefauw
                  opened on Oct 10, 2023
                  When writing an image to zarr with overwrite=True, I found some unexpected behaviour.
                  
Below I give a mimimal example to reproduce the issue.
                  This works, as expected. I can overwrite image layer 'image'.
                  import spatialdata
import numpy as np
sdata = spatialdata.SpatialData()
sdata.write( 'sdata.zarr' )
arr=np.random.rand( 1,100,100 )
spatialelement=spatialdata.models.Image2DModel.parse(
arr, dims=[ 'c' ,'y', 'x' ],
)
sdata.add_image( name="image", image=spatialelement , overwrite=True )
sdata.add_image( name="image", image=spatialelement , overwrite=True )

                  However, when I add some processing (e.g. multiplying by two) before replacing sdata["image" ]:
                  spatialelement=spatialdata.models.Image2DModel.parse(
sdata[ "image" ].data*2, dims=[ 'c' ,'y', 'x' ],
)
sdata.add_image( name="image", image=spatialelement , overwrite=True )

                  I get the error:
                  ValueError Traceback (most recent call last)
                  
in SpatialData.add_image(self, name, image, storage_options, overwrite)
                  
659 target_path = os.path.realpath(os.path.join(self.path, "images", name))
                  
660 if target_path in files:
                  
--> 661 raise ValueError(
                  
662 "Cannot add the image to the SpatialData object because it would overwrite an element that it is"
                  
663 "using for backing. See more here: #138"
                  
664 )
                  
665 self._add_image_in_memory(name=name, image=image, overwrite=overwrite)
                  
666 # old code to support overwriting the backing file
                  
667 # with tempfile.TemporaryDirectory() as tmpdir:
                  
668 # store = parse_url(Path(tmpdir) / "data.zarr", mode="w").store
                  
(...)
                  
692 # image = _read_multiscale(str(tgt_element_path), raster_type="image")
                  
693 # self._add_image_in_memory(name=name, image=image, overwrite=True)
                  ValueError: Cannot add the image to the SpatialData object because it would overwrite an element that it isusing for backing. See more here: #138
                  However, if I do a persist(), I am allowed to overwrite:
                  spatialelement=spatialdata.models.Image2DModel.parse(
(sdata[ "image" ].data*2).persist(), dims=[ 'c' ,'y', 'x' ],
)
sdata.add_image( name="image", image=spatialelement , overwrite=True )

                  And I am also allowed to do this (typical scenario where you want to do some processing twice with e.g. different parameters etc.):
                  spatialelement=spatialdata.models.Image2DModel.parse(
sdata[ "image" ].data*2, dims=[ 'c' ,'y', 'x' ],
)
sdata.add_image( name="image2", image=spatialelement , overwrite=True )
spatialelement=spatialdata.models.Image2DModel.parse(
sdata[ "image" ].data*2, dims=[ 'c' ,'y', 'x' ],
)
sdata.add_image( name="image2", image=spatialelement , overwrite=True )

                  Metadata
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                    No type
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})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
Adding image to same slot for backed sdata · Issue #374 · scverse/spatialdata · GitHub
                      Skip to content
                      Adding image to same slot for backed sdata #374
                      Open
                      Open
                      Adding image to same slot for backed sdata#374
                      Description
                      @ArneDefauw
                      ArneDefauw
                      opened on Oct 10, 2023
                      When writing an image to zarr with overwrite=True, I found some unexpected behaviour.
                      
Below I give a mimimal example to reproduce the issue.
                      This works, as expected. I can overwrite image layer 'image'.
                      import spatialdata
import numpy as np
sdata = spatialdata.SpatialData()
sdata.write( 'sdata.zarr' )
arr=np.random.rand( 1,100,100 )
spatialelement=spatialdata.models.Image2DModel.parse(
arr, dims=[ 'c' ,'y', 'x' ],
)
sdata.add_image( name="image", image=spatialelement , overwrite=True )
sdata.add_image( name="image", image=spatialelement , overwrite=True )

                      However, when I add some processing (e.g. multiplying by two) before replacing sdata["image" ]:
                      spatialelement=spatialdata.models.Image2DModel.parse(
sdata[ "image" ].data*2, dims=[ 'c' ,'y', 'x' ],
)
sdata.add_image( name="image", image=spatialelement , overwrite=True )

                      I get the error:
                      ValueError Traceback (most recent call last)
                      
in SpatialData.add_image(self, name, image, storage_options, overwrite)
                      
659 target_path = os.path.realpath(os.path.join(self.path, "images", name))
                      
660 if target_path in files:
                      
--> 661 raise ValueError(
                      
662 "Cannot add the image to the SpatialData object because it would overwrite an element that it is"
                      
663 "using for backing. See more here: #138"
                      
664 )
                      
665 self._add_image_in_memory(name=name, image=image, overwrite=overwrite)
                      
666 # old code to support overwriting the backing file
                      
667 # with tempfile.TemporaryDirectory() as tmpdir:
                      
668 # store = parse_url(Path(tmpdir) / "data.zarr", mode="w").store
                      
(...)
                      
692 # image = _read_multiscale(str(tgt_element_path), raster_type="image")
                      
693 # self._add_image_in_memory(name=name, image=image, overwrite=True)
                      ValueError: Cannot add the image to the SpatialData object because it would overwrite an element that it isusing for backing. See more here: #138
                      However, if I do a persist(), I am allowed to overwrite:
                      spatialelement=spatialdata.models.Image2DModel.parse(
(sdata[ "image" ].data*2).persist(), dims=[ 'c' ,'y', 'x' ],
)
sdata.add_image( name="image", image=spatialelement , overwrite=True )

                      And I am also allowed to do this (typical scenario where you want to do some processing twice with e.g. different parameters etc.):
                      spatialelement=spatialdata.models.Image2DModel.parse(
sdata[ "image" ].data*2, dims=[ 'c' ,'y', 'x' ],
)
sdata.add_image( name="image2", image=spatialelement , overwrite=True )
spatialelement=spatialdata.models.Image2DModel.parse(
sdata[ "image" ].data*2, dims=[ 'c' ,'y', 'x' ],
)
sdata.add_image( name="image2", image=spatialelement , overwrite=True )

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Adding image to same slot for backed sdata · Issue #374 · scverse/spatialdata · GitHub
                          Skip to content
                          Adding image to same slot for backed sdata #374
                          Open
                          Open
                          Adding image to same slot for backed sdata#374
                          Description
                          @ArneDefauw
                          ArneDefauw
                          opened on Oct 10, 2023
                          When writing an image to zarr with overwrite=True, I found some unexpected behaviour.
                          
Below I give a mimimal example to reproduce the issue.
                          This works, as expected. I can overwrite image layer 'image'.
                          import spatialdata
import numpy as np
sdata = spatialdata.SpatialData()
sdata.write( 'sdata.zarr' )
arr=np.random.rand( 1,100,100 )
spatialelement=spatialdata.models.Image2DModel.parse(
arr, dims=[ 'c' ,'y', 'x' ],
)
sdata.add_image( name="image", image=spatialelement , overwrite=True )
sdata.add_image( name="image", image=spatialelement , overwrite=True )

                          However, when I add some processing (e.g. multiplying by two) before replacing sdata["image" ]:
                          spatialelement=spatialdata.models.Image2DModel.parse(
sdata[ "image" ].data*2, dims=[ 'c' ,'y', 'x' ],
)
sdata.add_image( name="image", image=spatialelement , overwrite=True )

                          I get the error:
                          ValueError Traceback (most recent call last)
                          
in SpatialData.add_image(self, name, image, storage_options, overwrite)
                          
659 target_path = os.path.realpath(os.path.join(self.path, "images", name))
                          
660 if target_path in files:
                          
--> 661 raise ValueError(
                          
662 "Cannot add the image to the SpatialData object because it would overwrite an element that it is"
                          
663 "using for backing. See more here: #138"
                          
664 )
                          
665 self._add_image_in_memory(name=name, image=image, overwrite=overwrite)
                          
666 # old code to support overwriting the backing file
                          
667 # with tempfile.TemporaryDirectory() as tmpdir:
                          
668 # store = parse_url(Path(tmpdir) / "data.zarr", mode="w").store
                          
(...)
                          
692 # image = _read_multiscale(str(tgt_element_path), raster_type="image")
                          
693 # self._add_image_in_memory(name=name, image=image, overwrite=True)
                          ValueError: Cannot add the image to the SpatialData object because it would overwrite an element that it isusing for backing. See more here: #138
                          However, if I do a persist(), I am allowed to overwrite:
                          spatialelement=spatialdata.models.Image2DModel.parse(
(sdata[ "image" ].data*2).persist(), dims=[ 'c' ,'y', 'x' ],
)
sdata.add_image( name="image", image=spatialelement , overwrite=True )

                          And I am also allowed to do this (typical scenario where you want to do some processing twice with e.g. different parameters etc.):
                          spatialelement=spatialdata.models.Image2DModel.parse(
sdata[ "image" ].data*2, dims=[ 'c' ,'y', 'x' ],
)
sdata.add_image( name="image2", image=spatialelement , overwrite=True )
spatialelement=spatialdata.models.Image2DModel.parse(
sdata[ "image" ].data*2, dims=[ 'c' ,'y', 'x' ],
)
sdata.add_image( name="image2", image=spatialelement , overwrite=True )

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if (!enabled) return;
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if (!style) {
style = document.createElement('style');
style.id = 'universal-dark-mode-style';
document.head.appendChild(style);
}
// Dark mode CSS - inverts colors but preserves images/video
style.textContent = '
/* Invert everything except media */
html {
filter: invert(1) hue-rotate(180deg) !important;
background: #1a1a2e !important;
}
/* Restore images, videos, iframes, canvas */
img, video, iframe, canvas, svg, picture, [style*="background-image"] {
filter: invert(1) hue-rotate(180deg) !important;
}
/* Preserve specific elements that should not be inverted */
.no-dark-mode, .no-dark-mode *,
[data-theme="light"], [data-theme="light"],
.ace_editor, .ace_editor *,
.CodeMirror, .CodeMirror *,
.monaco-editor, .monaco-editor *,
.markdown-body pre, .markdown-body pre *,
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pre code, pre code * {
filter: none !important;
}
/* Fix common UI elements */
.modal, .popup, .dropdown-menu, .tooltip, .popover {
filter: invert(1) hue-rotate(180deg) !important;
background: #2d2d44 !important;
border-color: #444 !important;
}
/* Scrollbars */
::-webkit-scrollbar { background: #1a1a2e !important; }
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';
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applyDarkMode();
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})();
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();
Adding image to same slot for backed sdata · Issue #374 · scverse/spatialdata · GitHub
                              Skip to content
                              Adding image to same slot for backed sdata #374
                              Open
                              Open
                              Adding image to same slot for backed sdata#374
                              Description
                              @ArneDefauw
                              ArneDefauw
                              opened on Oct 10, 2023
                              When writing an image to zarr with overwrite=True, I found some unexpected behaviour.
                              
Below I give a mimimal example to reproduce the issue.
                              This works, as expected. I can overwrite image layer 'image'.
                              import spatialdata
import numpy as np
sdata = spatialdata.SpatialData()
sdata.write( 'sdata.zarr' )
arr=np.random.rand( 1,100,100 )
spatialelement=spatialdata.models.Image2DModel.parse(
arr, dims=[ 'c' ,'y', 'x' ],
)
sdata.add_image( name="image", image=spatialelement , overwrite=True )
sdata.add_image( name="image", image=spatialelement , overwrite=True )

                              However, when I add some processing (e.g. multiplying by two) before replacing sdata["image" ]:
                              spatialelement=spatialdata.models.Image2DModel.parse(
sdata[ "image" ].data*2, dims=[ 'c' ,'y', 'x' ],
)
sdata.add_image( name="image", image=spatialelement , overwrite=True )

                              I get the error:
                              ValueError Traceback (most recent call last)
                              
in SpatialData.add_image(self, name, image, storage_options, overwrite)
                              
659 target_path = os.path.realpath(os.path.join(self.path, "images", name))
                              
660 if target_path in files:
                              
--> 661 raise ValueError(
                              
662 "Cannot add the image to the SpatialData object because it would overwrite an element that it is"
                              
663 "using for backing. See more here: #138"
                              
664 )
                              
665 self._add_image_in_memory(name=name, image=image, overwrite=overwrite)
                              
666 # old code to support overwriting the backing file
                              
667 # with tempfile.TemporaryDirectory() as tmpdir:
                              
668 # store = parse_url(Path(tmpdir) / "data.zarr", mode="w").store
                              
(...)
                              
692 # image = _read_multiscale(str(tgt_element_path), raster_type="image")
                              
693 # self._add_image_in_memory(name=name, image=image, overwrite=True)
                              ValueError: Cannot add the image to the SpatialData object because it would overwrite an element that it isusing for backing. See more here: #138
                              However, if I do a persist(), I am allowed to overwrite:
                              spatialelement=spatialdata.models.Image2DModel.parse(
(sdata[ "image" ].data*2).persist(), dims=[ 'c' ,'y', 'x' ],
)
sdata.add_image( name="image", image=spatialelement , overwrite=True )

                              And I am also allowed to do this (typical scenario where you want to do some processing twice with e.g. different parameters etc.):
                              spatialelement=spatialdata.models.Image2DModel.parse(
sdata[ "image" ].data*2, dims=[ 'c' ,'y', 'x' ],
)
sdata.add_image( name="image2", image=spatialelement , overwrite=True )
spatialelement=spatialdata.models.Image2DModel.parse(
sdata[ "image" ].data*2, dims=[ 'c' ,'y', 'x' ],
)
sdata.add_image( name="image2", image=spatialelement , overwrite=True )

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