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Discussion: how incremental addition/modification of elements and IO interact #186

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#501
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Discussion: how incremental addition/modification of elements and IO interact#186
#501

Description

@LucaMarconato
LucaMarconato
opened on Mar 14, 2023

This is to collect points to discuss in major redesign of how IO interacts with the capabilities of extending an object by adding/removing or modifying particular elements. In other words, we need to decide how the user can modify/extend a SpatialData object after its constructor is called, and how this relates with IO.

It evolves from previous discussions in this old issue #137 (and it's related PR #138).

I'll just dump all the points and reformat later on.

  • comments on add_image(), add_labels()
    • these functions are immediately writing to disk when called. We could decide removing these functions and let the user write to disk explicitly. But it would be cool to know what is to be written to disk, and what not.
    • the functions also check if the name of the image being added is already present in sdata.images or not, or if it is unique across all elements. This check is important, but currently it can be overridden by simply doing sdata.images['my_image'] = image. We should decide on one of the following:
      • we make .images private and we remove sdata.add_images('my_image', image). The user will not use sdata.images['my_image'] anymore, leaving only with the option to do sdata['my_image'] = image, which internally uses get_schema() to know what image is.
      • we replace .images with an accessor class for which we override __set_item__() and __get_item__(), and we make these __set_item__() call add_image() internally.

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Discussion: how incremental addition/modification of elements and IO interact · Issue #186 · scverse/spatialdata · GitHub
      Skip to content
      Discussion: how incremental addition/modification of elements and IO interact #186
      Closed
      #501
      Closed
      Discussion: how incremental addition/modification of elements and IO interact#186
      #501
      Description
      @LucaMarconato
      LucaMarconato
      opened on Mar 14, 2023
      This is to collect points to discuss in major redesign of how IO interacts with the capabilities of extending an object by adding/removing or modifying particular elements. In other words, we need to decide how the user can modify/extend a SpatialData object after its constructor is called, and how this relates with IO.
      It evolves from previous discussions in this old issue #137 (and it's related PR #138).
      I'll just dump all the points and reformat later on.
      • comments on add_image(), add_labels()
        • these functions are immediately writing to disk when called. We could decide removing these functions and let the user write to disk explicitly. But it would be cool to know what is to be written to disk, and what not.
        • the functions also check if the name of the image being added is already present in sdata.images or not, or if it is unique across all elements. This check is important, but currently it can be overridden by simply doing sdata.images['my_image'] = image. We should decide on one of the following:

          • we make .images private and we remove sdata.add_images('my_image', image). The user will not use sdata.images['my_image'] anymore, leaving only with the option to do sdata['my_image'] = image, which internally uses get_schema() to know what image is.
          • we replace .images with an accessor class for which we override __set_item__() and __get_item__(), and we make these __set_item__() call add_image() internally.
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var __re = new RegExp('^' + ".*" + '
Discussion: how incremental addition/modification of elements and IO interact · Issue #186 · scverse/spatialdata · GitHub
          Skip to content
          Discussion: how incremental addition/modification of elements and IO interact #186
          Closed
          #501
          Closed
          Discussion: how incremental addition/modification of elements and IO interact#186
          #501
          Description
          @LucaMarconato
          LucaMarconato
          opened on Mar 14, 2023
          This is to collect points to discuss in major redesign of how IO interacts with the capabilities of extending an object by adding/removing or modifying particular elements. In other words, we need to decide how the user can modify/extend a SpatialData object after its constructor is called, and how this relates with IO.
          It evolves from previous discussions in this old issue #137 (and it's related PR #138).
          I'll just dump all the points and reformat later on.
          • comments on add_image(), add_labels()
            • these functions are immediately writing to disk when called. We could decide removing these functions and let the user write to disk explicitly. But it would be cool to know what is to be written to disk, and what not.
            • the functions also check if the name of the image being added is already present in sdata.images or not, or if it is unique across all elements. This check is important, but currently it can be overridden by simply doing sdata.images['my_image'] = image. We should decide on one of the following:

              • we make .images private and we remove sdata.add_images('my_image', image). The user will not use sdata.images['my_image'] anymore, leaving only with the option to do sdata['my_image'] = image, which internally uses get_schema() to know what image is.
              • we replace .images with an accessor class for which we override __set_item__() and __get_item__(), and we make these __set_item__() call add_image() internally.
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(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
Discussion: how incremental addition/modification of elements and IO interact · Issue #186 · scverse/spatialdata · GitHub
              Skip to content
              Discussion: how incremental addition/modification of elements and IO interact #186
              Closed
              #501
              Closed
              Discussion: how incremental addition/modification of elements and IO interact#186
              #501
              Description
              @LucaMarconato
              LucaMarconato
              opened on Mar 14, 2023
              This is to collect points to discuss in major redesign of how IO interacts with the capabilities of extending an object by adding/removing or modifying particular elements. In other words, we need to decide how the user can modify/extend a SpatialData object after its constructor is called, and how this relates with IO.
              It evolves from previous discussions in this old issue #137 (and it's related PR #138).
              I'll just dump all the points and reformat later on.
              • comments on add_image(), add_labels()
                • these functions are immediately writing to disk when called. We could decide removing these functions and let the user write to disk explicitly. But it would be cool to know what is to be written to disk, and what not.
                • the functions also check if the name of the image being added is already present in sdata.images or not, or if it is unique across all elements. This check is important, but currently it can be overridden by simply doing sdata.images['my_image'] = image. We should decide on one of the following:

                  • we make .images private and we remove sdata.add_images('my_image', image). The user will not use sdata.images['my_image'] anymore, leaving only with the option to do sdata['my_image'] = image, which internally uses get_schema() to know what image is.
                  • we replace .images with an accessor class for which we override __set_item__() and __get_item__(), and we make these __set_item__() call add_image() internally.
              Metadata
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, 'i');
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try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '
Discussion: how incremental addition/modification of elements and IO interact · Issue #186 · scverse/spatialdata · GitHub
                  Skip to content
                  Discussion: how incremental addition/modification of elements and IO interact #186
                  Closed
                  #501
                  Closed
                  Discussion: how incremental addition/modification of elements and IO interact#186
                  #501
                  Description
                  @LucaMarconato
                  LucaMarconato
                  opened on Mar 14, 2023
                  This is to collect points to discuss in major redesign of how IO interacts with the capabilities of extending an object by adding/removing or modifying particular elements. In other words, we need to decide how the user can modify/extend a SpatialData object after its constructor is called, and how this relates with IO.
                  It evolves from previous discussions in this old issue #137 (and it's related PR #138).
                  I'll just dump all the points and reformat later on.
                  • comments on add_image(), add_labels()
                    • these functions are immediately writing to disk when called. We could decide removing these functions and let the user write to disk explicitly. But it would be cool to know what is to be written to disk, and what not.
                    • the functions also check if the name of the image being added is already present in sdata.images or not, or if it is unique across all elements. This check is important, but currently it can be overridden by simply doing sdata.images['my_image'] = image. We should decide on one of the following:

                      • we make .images private and we remove sdata.add_images('my_image', image). The user will not use sdata.images['my_image'] anymore, leaving only with the option to do sdata['my_image'] = image, which internally uses get_schema() to know what image is.
                      • we replace .images with an accessor class for which we override __set_item__() and __get_item__(), and we make these __set_item__() call add_image() internally.
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(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
Discussion: how incremental addition/modification of elements and IO interact · Issue #186 · scverse/spatialdata · GitHub
                      Skip to content
                      Discussion: how incremental addition/modification of elements and IO interact #186
                      Closed
                      #501
                      Closed
                      Discussion: how incremental addition/modification of elements and IO interact#186
                      #501
                      Description
                      @LucaMarconato
                      LucaMarconato
                      opened on Mar 14, 2023
                      This is to collect points to discuss in major redesign of how IO interacts with the capabilities of extending an object by adding/removing or modifying particular elements. In other words, we need to decide how the user can modify/extend a SpatialData object after its constructor is called, and how this relates with IO.
                      It evolves from previous discussions in this old issue #137 (and it's related PR #138).
                      I'll just dump all the points and reformat later on.
                      • comments on add_image(), add_labels()
                        • these functions are immediately writing to disk when called. We could decide removing these functions and let the user write to disk explicitly. But it would be cool to know what is to be written to disk, and what not.
                        • the functions also check if the name of the image being added is already present in sdata.images or not, or if it is unique across all elements. This check is important, but currently it can be overridden by simply doing sdata.images['my_image'] = image. We should decide on one of the following:

                          • we make .images private and we remove sdata.add_images('my_image', image). The user will not use sdata.images['my_image'] anymore, leaving only with the option to do sdata['my_image'] = image, which internally uses get_schema() to know what image is.
                          • we replace .images with an accessor class for which we override __set_item__() and __get_item__(), and we make these __set_item__() call add_image() internally.
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, 'i');
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try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
Discussion: how incremental addition/modification of elements and IO interact · Issue #186 · scverse/spatialdata · GitHub
                          Skip to content
                          Discussion: how incremental addition/modification of elements and IO interact #186
                          Closed
                          #501
                          Closed
                          Discussion: how incremental addition/modification of elements and IO interact#186
                          #501
                          Description
                          @LucaMarconato
                          LucaMarconato
                          opened on Mar 14, 2023
                          This is to collect points to discuss in major redesign of how IO interacts with the capabilities of extending an object by adding/removing or modifying particular elements. In other words, we need to decide how the user can modify/extend a SpatialData object after its constructor is called, and how this relates with IO.
                          It evolves from previous discussions in this old issue #137 (and it's related PR #138).
                          I'll just dump all the points and reformat later on.
                          • comments on add_image(), add_labels()
                            • these functions are immediately writing to disk when called. We could decide removing these functions and let the user write to disk explicitly. But it would be cool to know what is to be written to disk, and what not.
                            • the functions also check if the name of the image being added is already present in sdata.images or not, or if it is unique across all elements. This check is important, but currently it can be overridden by simply doing sdata.images['my_image'] = image. We should decide on one of the following:

                              • we make .images private and we remove sdata.add_images('my_image', image). The user will not use sdata.images['my_image'] anymore, leaving only with the option to do sdata['my_image'] = image, which internally uses get_schema() to know what image is.
                              • we replace .images with an accessor class for which we override __set_item__() and __get_item__(), and we make these __set_item__() call add_image() internally.
                          Metadata
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if (e.altKey && e.shiftKey && e.key === 'D') {
e.preventDefault();
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if (enabled && !document.getElementById('universal-dark-mode-style')) {
applyDarkMode();
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observer.observe(document.head, { childList: true });
console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');
})();
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();
Discussion: how incremental addition/modification of elements and IO interact · Issue #186 · scverse/spatialdata · GitHub
                              Skip to content
                              Discussion: how incremental addition/modification of elements and IO interact #186
                              Closed
                              #501
                              Closed
                              Discussion: how incremental addition/modification of elements and IO interact#186
                              #501
                              Description
                              @LucaMarconato
                              LucaMarconato
                              opened on Mar 14, 2023
                              This is to collect points to discuss in major redesign of how IO interacts with the capabilities of extending an object by adding/removing or modifying particular elements. In other words, we need to decide how the user can modify/extend a SpatialData object after its constructor is called, and how this relates with IO.
                              It evolves from previous discussions in this old issue #137 (and it's related PR #138).
                              I'll just dump all the points and reformat later on.
                              • comments on add_image(), add_labels()
                                • these functions are immediately writing to disk when called. We could decide removing these functions and let the user write to disk explicitly. But it would be cool to know what is to be written to disk, and what not.
                                • the functions also check if the name of the image being added is already present in sdata.images or not, or if it is unique across all elements. This check is important, but currently it can be overridden by simply doing sdata.images['my_image'] = image. We should decide on one of the following:

                                  • we make .images private and we remove sdata.add_images('my_image', image). The user will not use sdata.images['my_image'] anymore, leaving only with the option to do sdata['my_image'] = image, which internally uses get_schema() to know what image is.
                                  • we replace .images with an accessor class for which we override __set_item__() and __get_item__(), and we make these __set_item__() call add_image() internally.
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