Custom title when multiple coordinate system present and no coordinate system specified #269

Open
Open
Custom title when multiple coordinate system present and no coordinate system specified#269
Labels
🗣️ discussionNeeds further discussionenhancementNew feature or requestpriority: medium

Description

@LucaMarconato
LucaMarconato
opened on May 30, 2024

When there is a object with 2 coordinate systems and pl.show() is called without specifying coordinate_systems, by default two subplots are created. If the user adjust the title=, both titles are changed, leading to a plot that is confusing, especially if it was not clear that the object (or an element of the object) was aligned to multiple coordinate systems.

This is exactly what happened in the following plots (that appeared from a bug reported by a user).

before setting the title

Screenshot 2024-05-30 at 11 55 06

after setting the title

not sure why the order changes but no big deal, not the point of this issue
Screenshot 2024-05-30 at 11 55 11

solution for this case

Solution for the user: here the fix is to specify coordinate_systems='global', which will lead to a single plot.

proposed solution

Discussed also with @melorona. I proposed to change the default behavior as follows:

  • coordinate_systems will have a new default of None.
  • if the object has a single coordinate system and coordinate_system is None, this will be plotted
  • elif the object has multiple coordinate system and coordinate_system is None and one of them is called 'global' (defined in from spatialdata.models._utils import DEFAULT_COORDINATE_SYSTEM), this will be plotted
  • if coordinate_system is not None and coordinate_system is available, this will be plotted
  • else (i.e. if coordinate_system is None, multiple coordinate systems are present and none of them is called 'global', or if coordinate_system is not None and it's not available in the data, then an error will be raised, printing the list of available coordinate systems.

What will change for the user:

  • with this change, by default we won't plot multiple coordinate systems; if this is still the desired behavior, the user can still pass a list of coordinate systems.

Extra comments:

  • with the incoming "transformations refactoring" it will be required to specify which coordinate system to plot because elements will not contain an explicit list of coordinate systems they are aligned to but there will only be a big graph of transformations where a lot of coordinate systems can be aligned to a lot of other coordinate systems. So it will be important to plot only what the user asks for
  • in general, the current default behavior is useful when there are multiple FOVs for a dataset (like in the MIBITOF example dataset); but in other cases where there is the same data in multiple coordinate systems, like in Xenium, or where the number of FOVs is very large, like in CosMx, the currently implemented default behavior is suboptimal, and requiring the proposed new default would be handier.

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      Skip to content
      Custom title when multiple coordinate system present and no coordinate system specified #269
      Open
      Open
      Custom title when multiple coordinate system present and no coordinate system specified#269
      Labels
      🗣️ discussionNeeds further discussionenhancementNew feature or requestpriority: medium
      Description
      @LucaMarconato
      LucaMarconato
      opened on May 30, 2024
      When there is a object with 2 coordinate systems and pl.show() is called without specifying coordinate_systems, by default two subplots are created. If the user adjust the title=, both titles are changed, leading to a plot that is confusing, especially if it was not clear that the object (or an element of the object) was aligned to multiple coordinate systems.
      This is exactly what happened in the following plots (that appeared from a bug reported by a user).
      before setting the title
      Screenshot 2024-05-30 at 11 55 06
      after setting the title
      not sure why the order changes but no big deal, not the point of this issue
      Screenshot 2024-05-30 at 11 55 11
      solution for this case
      Solution for the user: here the fix is to specify coordinate_systems='global', which will lead to a single plot.
      proposed solution
      Discussed also with @melorona. I proposed to change the default behavior as follows:
      • coordinate_systems will have a new default of None.
      • if the object has a single coordinate system and coordinate_system is None, this will be plotted
      • elif the object has multiple coordinate system and coordinate_system is None and one of them is called 'global' (defined in  from spatialdata.models._utils import DEFAULT_COORDINATE_SYSTEM), this will be plotted
      • if coordinate_system is not None and coordinate_system is available, this will be plotted
      • else (i.e. if coordinate_system is None, multiple coordinate systems are present and none of them is called 'global', or if coordinate_system is not None and it's not available in the data, then an error will be raised, printing the list of available coordinate systems.
      What will change for the user:
      • with this change, by default we won't plot multiple coordinate systems; if this is still the desired behavior, the user can still pass a list of coordinate systems.
      Extra comments:
      • with the incoming "transformations refactoring" it will be required to specify which coordinate system to plot because elements will not contain an explicit list of coordinate systems they are aligned to but there will only be a big graph of transformations where a lot of coordinate systems can be aligned to a lot of other coordinate systems. So it will be important to plot only what the user asks for
      • in general, the current default behavior is useful when there are multiple FOVs for a dataset (like in the MIBITOF example dataset); but in other cases where there is the same data in multiple coordinate systems, like in Xenium, or where the number of FOVs is very large, like in CosMx, the currently implemented default behavior is suboptimal, and requiring the proposed new default would be handier.
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var __re = new RegExp('^' + ".*" + '

          Skip to content
          Custom title when multiple coordinate system present and no coordinate system specified #269
          Open
          Open
          Custom title when multiple coordinate system present and no coordinate system specified#269
          Labels
          🗣️ discussionNeeds further discussionenhancementNew feature or requestpriority: medium
          Description
          @LucaMarconato
          LucaMarconato
          opened on May 30, 2024
          When there is a object with 2 coordinate systems and pl.show() is called without specifying coordinate_systems, by default two subplots are created. If the user adjust the title=, both titles are changed, leading to a plot that is confusing, especially if it was not clear that the object (or an element of the object) was aligned to multiple coordinate systems.
          This is exactly what happened in the following plots (that appeared from a bug reported by a user).
          before setting the title
          Screenshot 2024-05-30 at 11 55 06
          after setting the title
          not sure why the order changes but no big deal, not the point of this issue
          Screenshot 2024-05-30 at 11 55 11
          solution for this case
          Solution for the user: here the fix is to specify coordinate_systems='global', which will lead to a single plot.
          proposed solution
          Discussed also with @melorona. I proposed to change the default behavior as follows:
          • coordinate_systems will have a new default of None.
          • if the object has a single coordinate system and coordinate_system is None, this will be plotted
          • elif the object has multiple coordinate system and coordinate_system is None and one of them is called 'global' (defined in  from spatialdata.models._utils import DEFAULT_COORDINATE_SYSTEM), this will be plotted
          • if coordinate_system is not None and coordinate_system is available, this will be plotted
          • else (i.e. if coordinate_system is None, multiple coordinate systems are present and none of them is called 'global', or if coordinate_system is not None and it's not available in the data, then an error will be raised, printing the list of available coordinate systems.
          What will change for the user:
          • with this change, by default we won't plot multiple coordinate systems; if this is still the desired behavior, the user can still pass a list of coordinate systems.
          Extra comments:
          • with the incoming "transformations refactoring" it will be required to specify which coordinate system to plot because elements will not contain an explicit list of coordinate systems they are aligned to but there will only be a big graph of transformations where a lot of coordinate systems can be aligned to a lot of other coordinate systems. So it will be important to plot only what the user asks for
          • in general, the current default behavior is useful when there are multiple FOVs for a dataset (like in the MIBITOF example dataset); but in other cases where there is the same data in multiple coordinate systems, like in Xenium, or where the number of FOVs is very large, like in CosMx, the currently implemented default behavior is suboptimal, and requiring the proposed new default would be handier.
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(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

              Skip to content
              Custom title when multiple coordinate system present and no coordinate system specified #269
              Open
              Open
              Custom title when multiple coordinate system present and no coordinate system specified#269
              Labels
              🗣️ discussionNeeds further discussionenhancementNew feature or requestpriority: medium
              Description
              @LucaMarconato
              LucaMarconato
              opened on May 30, 2024
              When there is a object with 2 coordinate systems and pl.show() is called without specifying coordinate_systems, by default two subplots are created. If the user adjust the title=, both titles are changed, leading to a plot that is confusing, especially if it was not clear that the object (or an element of the object) was aligned to multiple coordinate systems.
              This is exactly what happened in the following plots (that appeared from a bug reported by a user).
              before setting the title
              Screenshot 2024-05-30 at 11 55 06
              after setting the title
              not sure why the order changes but no big deal, not the point of this issue
              Screenshot 2024-05-30 at 11 55 11
              solution for this case
              Solution for the user: here the fix is to specify coordinate_systems='global', which will lead to a single plot.
              proposed solution
              Discussed also with @melorona. I proposed to change the default behavior as follows:
              • coordinate_systems will have a new default of None.
              • if the object has a single coordinate system and coordinate_system is None, this will be plotted
              • elif the object has multiple coordinate system and coordinate_system is None and one of them is called 'global' (defined in  from spatialdata.models._utils import DEFAULT_COORDINATE_SYSTEM), this will be plotted
              • if coordinate_system is not None and coordinate_system is available, this will be plotted
              • else (i.e. if coordinate_system is None, multiple coordinate systems are present and none of them is called 'global', or if coordinate_system is not None and it's not available in the data, then an error will be raised, printing the list of available coordinate systems.
              What will change for the user:
              • with this change, by default we won't plot multiple coordinate systems; if this is still the desired behavior, the user can still pass a list of coordinate systems.
              Extra comments:
              • with the incoming "transformations refactoring" it will be required to specify which coordinate system to plot because elements will not contain an explicit list of coordinate systems they are aligned to but there will only be a big graph of transformations where a lot of coordinate systems can be aligned to a lot of other coordinate systems. So it will be important to plot only what the user asks for
              • in general, the current default behavior is useful when there are multiple FOVs for a dataset (like in the MIBITOF example dataset); but in other cases where there is the same data in multiple coordinate systems, like in Xenium, or where the number of FOVs is very large, like in CosMx, the currently implemented default behavior is suboptimal, and requiring the proposed new default would be handier.
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, 'i');
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(function(){
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var __m = "youtube.com";
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                  Skip to content
                  Custom title when multiple coordinate system present and no coordinate system specified #269
                  Open
                  Open
                  Custom title when multiple coordinate system present and no coordinate system specified#269
                  Labels
                  🗣️ discussionNeeds further discussionenhancementNew feature or requestpriority: medium
                  Description
                  @LucaMarconato
                  LucaMarconato
                  opened on May 30, 2024
                  When there is a object with 2 coordinate systems and pl.show() is called without specifying coordinate_systems, by default two subplots are created. If the user adjust the title=, both titles are changed, leading to a plot that is confusing, especially if it was not clear that the object (or an element of the object) was aligned to multiple coordinate systems.
                  This is exactly what happened in the following plots (that appeared from a bug reported by a user).
                  before setting the title
                  Screenshot 2024-05-30 at 11 55 06
                  after setting the title
                  not sure why the order changes but no big deal, not the point of this issue
                  Screenshot 2024-05-30 at 11 55 11
                  solution for this case
                  Solution for the user: here the fix is to specify coordinate_systems='global', which will lead to a single plot.
                  proposed solution
                  Discussed also with @melorona. I proposed to change the default behavior as follows:
                  • coordinate_systems will have a new default of None.
                  • if the object has a single coordinate system and coordinate_system is None, this will be plotted
                  • elif the object has multiple coordinate system and coordinate_system is None and one of them is called 'global' (defined in  from spatialdata.models._utils import DEFAULT_COORDINATE_SYSTEM), this will be plotted
                  • if coordinate_system is not None and coordinate_system is available, this will be plotted
                  • else (i.e. if coordinate_system is None, multiple coordinate systems are present and none of them is called 'global', or if coordinate_system is not None and it's not available in the data, then an error will be raised, printing the list of available coordinate systems.
                  What will change for the user:
                  • with this change, by default we won't plot multiple coordinate systems; if this is still the desired behavior, the user can still pass a list of coordinate systems.
                  Extra comments:
                  • with the incoming "transformations refactoring" it will be required to specify which coordinate system to plot because elements will not contain an explicit list of coordinate systems they are aligned to but there will only be a big graph of transformations where a lot of coordinate systems can be aligned to a lot of other coordinate systems. So it will be important to plot only what the user asks for
                  • in general, the current default behavior is useful when there are multiple FOVs for a dataset (like in the MIBITOF example dataset); but in other cases where there is the same data in multiple coordinate systems, like in Xenium, or where the number of FOVs is very large, like in CosMx, the currently implemented default behavior is suboptimal, and requiring the proposed new default would be handier.
                  Metadata
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(function(){
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var __m = "*";
var __re = new RegExp('^' + ".*" + '

                      Skip to content
                      Custom title when multiple coordinate system present and no coordinate system specified #269
                      Open
                      Open
                      Custom title when multiple coordinate system present and no coordinate system specified#269
                      Labels
                      🗣️ discussionNeeds further discussionenhancementNew feature or requestpriority: medium
                      Description
                      @LucaMarconato
                      LucaMarconato
                      opened on May 30, 2024
                      When there is a object with 2 coordinate systems and pl.show() is called without specifying coordinate_systems, by default two subplots are created. If the user adjust the title=, both titles are changed, leading to a plot that is confusing, especially if it was not clear that the object (or an element of the object) was aligned to multiple coordinate systems.
                      This is exactly what happened in the following plots (that appeared from a bug reported by a user).
                      before setting the title
                      Screenshot 2024-05-30 at 11 55 06
                      after setting the title
                      not sure why the order changes but no big deal, not the point of this issue
                      Screenshot 2024-05-30 at 11 55 11
                      solution for this case
                      Solution for the user: here the fix is to specify coordinate_systems='global', which will lead to a single plot.
                      proposed solution
                      Discussed also with @melorona. I proposed to change the default behavior as follows:
                      • coordinate_systems will have a new default of None.
                      • if the object has a single coordinate system and coordinate_system is None, this will be plotted
                      • elif the object has multiple coordinate system and coordinate_system is None and one of them is called 'global' (defined in  from spatialdata.models._utils import DEFAULT_COORDINATE_SYSTEM), this will be plotted
                      • if coordinate_system is not None and coordinate_system is available, this will be plotted
                      • else (i.e. if coordinate_system is None, multiple coordinate systems are present and none of them is called 'global', or if coordinate_system is not None and it's not available in the data, then an error will be raised, printing the list of available coordinate systems.
                      What will change for the user:
                      • with this change, by default we won't plot multiple coordinate systems; if this is still the desired behavior, the user can still pass a list of coordinate systems.
                      Extra comments:
                      • with the incoming "transformations refactoring" it will be required to specify which coordinate system to plot because elements will not contain an explicit list of coordinate systems they are aligned to but there will only be a big graph of transformations where a lot of coordinate systems can be aligned to a lot of other coordinate systems. So it will be important to plot only what the user asks for
                      • in general, the current default behavior is useful when there are multiple FOVs for a dataset (like in the MIBITOF example dataset); but in other cases where there is the same data in multiple coordinate systems, like in Xenium, or where the number of FOVs is very large, like in CosMx, the currently implemented default behavior is suboptimal, and requiring the proposed new default would be handier.
                      Metadata
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, 'i');
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(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

                          Skip to content
                          Custom title when multiple coordinate system present and no coordinate system specified #269
                          Open
                          Open
                          Custom title when multiple coordinate system present and no coordinate system specified#269
                          Labels
                          🗣️ discussionNeeds further discussionenhancementNew feature or requestpriority: medium
                          Description
                          @LucaMarconato
                          LucaMarconato
                          opened on May 30, 2024
                          When there is a object with 2 coordinate systems and pl.show() is called without specifying coordinate_systems, by default two subplots are created. If the user adjust the title=, both titles are changed, leading to a plot that is confusing, especially if it was not clear that the object (or an element of the object) was aligned to multiple coordinate systems.
                          This is exactly what happened in the following plots (that appeared from a bug reported by a user).
                          before setting the title
                          Screenshot 2024-05-30 at 11 55 06
                          after setting the title
                          not sure why the order changes but no big deal, not the point of this issue
                          Screenshot 2024-05-30 at 11 55 11
                          solution for this case
                          Solution for the user: here the fix is to specify coordinate_systems='global', which will lead to a single plot.
                          proposed solution
                          Discussed also with @melorona. I proposed to change the default behavior as follows:
                          • coordinate_systems will have a new default of None.
                          • if the object has a single coordinate system and coordinate_system is None, this will be plotted
                          • elif the object has multiple coordinate system and coordinate_system is None and one of them is called 'global' (defined in  from spatialdata.models._utils import DEFAULT_COORDINATE_SYSTEM), this will be plotted
                          • if coordinate_system is not None and coordinate_system is available, this will be plotted
                          • else (i.e. if coordinate_system is None, multiple coordinate systems are present and none of them is called 'global', or if coordinate_system is not None and it's not available in the data, then an error will be raised, printing the list of available coordinate systems.
                          What will change for the user:
                          • with this change, by default we won't plot multiple coordinate systems; if this is still the desired behavior, the user can still pass a list of coordinate systems.
                          Extra comments:
                          • with the incoming "transformations refactoring" it will be required to specify which coordinate system to plot because elements will not contain an explicit list of coordinate systems they are aligned to but there will only be a big graph of transformations where a lot of coordinate systems can be aligned to a lot of other coordinate systems. So it will be important to plot only what the user asks for
                          • in general, the current default behavior is useful when there are multiple FOVs for a dataset (like in the MIBITOF example dataset); but in other cases where there is the same data in multiple coordinate systems, like in Xenium, or where the number of FOVs is very large, like in CosMx, the currently implemented default behavior is suboptimal, and requiring the proposed new default would be handier.
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
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                              Custom title when multiple coordinate system present and no coordinate system specified #269
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                              Custom title when multiple coordinate system present and no coordinate system specified#269
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                              🗣️ discussionNeeds further discussionenhancementNew feature or requestpriority: medium
                              Description
                              @LucaMarconato
                              LucaMarconato
                              opened on May 30, 2024
                              When there is a object with 2 coordinate systems and pl.show() is called without specifying coordinate_systems, by default two subplots are created. If the user adjust the title=, both titles are changed, leading to a plot that is confusing, especially if it was not clear that the object (or an element of the object) was aligned to multiple coordinate systems.
                              This is exactly what happened in the following plots (that appeared from a bug reported by a user).
                              before setting the title
                              Screenshot 2024-05-30 at 11 55 06
                              after setting the title
                              not sure why the order changes but no big deal, not the point of this issue
                              Screenshot 2024-05-30 at 11 55 11
                              solution for this case
                              Solution for the user: here the fix is to specify coordinate_systems='global', which will lead to a single plot.
                              proposed solution
                              Discussed also with @melorona. I proposed to change the default behavior as follows:
                              • coordinate_systems will have a new default of None.
                              • if the object has a single coordinate system and coordinate_system is None, this will be plotted
                              • elif the object has multiple coordinate system and coordinate_system is None and one of them is called 'global' (defined in  from spatialdata.models._utils import DEFAULT_COORDINATE_SYSTEM), this will be plotted
                              • if coordinate_system is not None and coordinate_system is available, this will be plotted
                              • else (i.e. if coordinate_system is None, multiple coordinate systems are present and none of them is called 'global', or if coordinate_system is not None and it's not available in the data, then an error will be raised, printing the list of available coordinate systems.
                              What will change for the user:
                              • with this change, by default we won't plot multiple coordinate systems; if this is still the desired behavior, the user can still pass a list of coordinate systems.
                              Extra comments:
                              • with the incoming "transformations refactoring" it will be required to specify which coordinate system to plot because elements will not contain an explicit list of coordinate systems they are aligned to but there will only be a big graph of transformations where a lot of coordinate systems can be aligned to a lot of other coordinate systems. So it will be important to plot only what the user asks for
                              • in general, the current default behavior is useful when there are multiple FOVs for a dataset (like in the MIBITOF example dataset); but in other cases where there is the same data in multiple coordinate systems, like in Xenium, or where the number of FOVs is very large, like in CosMx, the currently implemented default behavior is suboptimal, and requiring the proposed new default would be handier.
                              Metadata
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                              Assignees
                              No one assigned
                                Labels
                                🗣️ discussionNeeds further discussionenhancementNew feature or requestpriority: medium
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                                  No milestone
                                  Relationships
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