Nested storage detection in Zarr V2 #707

Closed
Closed
Nested storage detection in Zarr V2#707

Description

@joshmoore
joshmoore
opened on Mar 5, 2021

see: ome/ngff#29 and bcdev/jzarr#17

In order to better handle Zarr arrays created with NestedDirectoryStorage or FSStore(key_separator="/"), SabineEmbacher and I have been working on a "protocol heuristic" that can be used by V2 implementations to detect nested chunking rather than requiring the user to specify it correctly.

tl;dr: This proposes a new key for .zarray which it would be good to have feedback on.

Proposal

When creating a zarr array:

  • add to .zarray json: {"dimension_separator": "/"}
  • always write a 0-position chunk

When opening an array:

  • try to read the separator character from the .zarray json
  • if not available, try to find a 0-position chunk
  • if not available, at every read action try to find chunks with both standard variants until the situation is clarified. (Standard separator list ["/", "."])

Points for discussion:

  • The name dimension_separator differs from the code implementation key_separator to reduce confusion about whether every separator in the key name is effected.
  • There has been some discussion (community call, gitter) about whether or not "/" could become the default.
  • Is an addition to the .zarray metadata sufficiently low impact to be rolled into v2?

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      , 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
       blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

      Skip to content
      Nested storage detection in Zarr V2 #707
      Closed
      Closed
      Nested storage detection in Zarr V2#707
      Description
      @joshmoore
      joshmoore
      opened on Mar 5, 2021
      see: ome/ngff#29 and bcdev/jzarr#17
      In order to better handle Zarr arrays created with NestedDirectoryStorage or FSStore(key_separator="/"), SabineEmbacher and I have been working on a "protocol heuristic" that can be used by V2 implementations to detect nested chunking rather than requiring the user to specify it correctly.
      tl;dr: This proposes a new key for .zarray which it would be good to have feedback on.
      Proposal
      When creating a zarr array:
      • add to .zarray json: {"dimension_separator": "/"}
      • always write a 0-position chunk
      When opening an array:
      • try to read the separator character from the .zarray json
      • if not available, try to find a 0-position chunk
      • if not available, at every read action try to find chunks with both standard variants until the situation is clarified. (Standard separator list ["/", "."])
      Points for discussion:
      • The name dimension_separator differs from the code implementation key_separator to reduce confusion about whether every separator in the key name is effected.
      • There has been some discussion (community call, gitter) about whether or not "/" could become the default.
      • Is an addition to the .zarray metadata sufficiently low impact to be rolled into v2?
      Metadata
      Metadata
      Assignees
      No one assigned
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        No labels
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        No type
        Projects
        No projects
          Milestone
          No milestone
          Relationships
          None yet
          Development
          No branches or pull requests
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

          Skip to content
          Nested storage detection in Zarr V2 #707
          Closed
          Closed
          Nested storage detection in Zarr V2#707
          Description
          @joshmoore
          joshmoore
          opened on Mar 5, 2021
          see: ome/ngff#29 and bcdev/jzarr#17
          In order to better handle Zarr arrays created with NestedDirectoryStorage or FSStore(key_separator="/"), SabineEmbacher and I have been working on a "protocol heuristic" that can be used by V2 implementations to detect nested chunking rather than requiring the user to specify it correctly.
          tl;dr: This proposes a new key for .zarray which it would be good to have feedback on.
          Proposal
          When creating a zarr array:
          • add to .zarray json: {"dimension_separator": "/"}
          • always write a 0-position chunk
          When opening an array:
          • try to read the separator character from the .zarray json
          • if not available, try to find a 0-position chunk
          • if not available, at every read action try to find chunks with both standard variants until the situation is clarified. (Standard separator list ["/", "."])
          Points for discussion:
          • The name dimension_separator differs from the code implementation key_separator to reduce confusion about whether every separator in the key name is effected.
          • There has been some discussion (community call, gitter) about whether or not "/" could become the default.
          • Is an addition to the .zarray metadata sufficiently low impact to be rolled into v2?
          Metadata
          Metadata
          Assignees
          No one assigned
            Labels
            No labels
            No labels
            Type
            No type
            Projects
            No projects
              Milestone
              No milestone
              Relationships
              None yet
              Development
              No branches or pull requests
              Issue actions
              
, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

              Skip to content
              Nested storage detection in Zarr V2 #707
              Closed
              Closed
              Nested storage detection in Zarr V2#707
              Description
              @joshmoore
              joshmoore
              opened on Mar 5, 2021
              see: ome/ngff#29 and bcdev/jzarr#17
              In order to better handle Zarr arrays created with NestedDirectoryStorage or FSStore(key_separator="/"), SabineEmbacher and I have been working on a "protocol heuristic" that can be used by V2 implementations to detect nested chunking rather than requiring the user to specify it correctly.
              tl;dr: This proposes a new key for .zarray which it would be good to have feedback on.
              Proposal
              When creating a zarr array:
              • add to .zarray json: {"dimension_separator": "/"}
              • always write a 0-position chunk
              When opening an array:
              • try to read the separator character from the .zarray json
              • if not available, try to find a 0-position chunk
              • if not available, at every read action try to find chunks with both standard variants until the situation is clarified. (Standard separator list ["/", "."])
              Points for discussion:
              • The name dimension_separator differs from the code implementation key_separator to reduce confusion about whether every separator in the key name is effected.
              • There has been some discussion (community call, gitter) about whether or not "/" could become the default.
              • Is an addition to the .zarray metadata sufficiently low impact to be rolled into v2?
              Metadata
              Metadata
              Assignees
              No one assigned
                Labels
                No labels
                No labels
                Type
                No type
                Projects
                No projects
                  Milestone
                  No milestone
                  Relationships
                  None yet
                  Development
                  No branches or pull requests
                  Issue actions
                  
, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

                  Skip to content
                  Nested storage detection in Zarr V2 #707
                  Closed
                  Closed
                  Nested storage detection in Zarr V2#707
                  Description
                  @joshmoore
                  joshmoore
                  opened on Mar 5, 2021
                  see: ome/ngff#29 and bcdev/jzarr#17
                  In order to better handle Zarr arrays created with NestedDirectoryStorage or FSStore(key_separator="/"), SabineEmbacher and I have been working on a "protocol heuristic" that can be used by V2 implementations to detect nested chunking rather than requiring the user to specify it correctly.
                  tl;dr: This proposes a new key for .zarray which it would be good to have feedback on.
                  Proposal
                  When creating a zarr array:
                  • add to .zarray json: {"dimension_separator": "/"}
                  • always write a 0-position chunk
                  When opening an array:
                  • try to read the separator character from the .zarray json
                  • if not available, try to find a 0-position chunk
                  • if not available, at every read action try to find chunks with both standard variants until the situation is clarified. (Standard separator list ["/", "."])
                  Points for discussion:
                  • The name dimension_separator differs from the code implementation key_separator to reduce confusion about whether every separator in the key name is effected.
                  • There has been some discussion (community call, gitter) about whether or not "/" could become the default.
                  • Is an addition to the .zarray metadata sufficiently low impact to be rolled into v2?
                  Metadata
                  Metadata
                  Assignees
                  No one assigned
                    Labels
                    No labels
                    No labels
                    Type
                    No type
                    Projects
                    No projects
                      Milestone
                      No milestone
                      Relationships
                      None yet
                      Development
                      No branches or pull requests
                      Issue actions
                      
, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

                      Skip to content
                      Nested storage detection in Zarr V2 #707
                      Closed
                      Closed
                      Nested storage detection in Zarr V2#707
                      Description
                      @joshmoore
                      joshmoore
                      opened on Mar 5, 2021
                      see: ome/ngff#29 and bcdev/jzarr#17
                      In order to better handle Zarr arrays created with NestedDirectoryStorage or FSStore(key_separator="/"), SabineEmbacher and I have been working on a "protocol heuristic" that can be used by V2 implementations to detect nested chunking rather than requiring the user to specify it correctly.
                      tl;dr: This proposes a new key for .zarray which it would be good to have feedback on.
                      Proposal
                      When creating a zarr array:
                      • add to .zarray json: {"dimension_separator": "/"}
                      • always write a 0-position chunk
                      When opening an array:
                      • try to read the separator character from the .zarray json
                      • if not available, try to find a 0-position chunk
                      • if not available, at every read action try to find chunks with both standard variants until the situation is clarified. (Standard separator list ["/", "."])
                      Points for discussion:
                      • The name dimension_separator differs from the code implementation key_separator to reduce confusion about whether every separator in the key name is effected.
                      • There has been some discussion (community call, gitter) about whether or not "/" could become the default.
                      • Is an addition to the .zarray metadata sufficiently low impact to be rolled into v2?
                      Metadata
                      Metadata
                      Assignees
                      No one assigned
                        Labels
                        No labels
                        No labels
                        Type
                        No type
                        Projects
                        No projects
                          Milestone
                          No milestone
                          Relationships
                          None yet
                          Development
                          No branches or pull requests
                          Issue actions
                          
, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

                          Skip to content
                          Nested storage detection in Zarr V2 #707
                          Closed
                          Closed
                          Nested storage detection in Zarr V2#707
                          Description
                          @joshmoore
                          joshmoore
                          opened on Mar 5, 2021
                          see: ome/ngff#29 and bcdev/jzarr#17
                          In order to better handle Zarr arrays created with NestedDirectoryStorage or FSStore(key_separator="/"), SabineEmbacher and I have been working on a "protocol heuristic" that can be used by V2 implementations to detect nested chunking rather than requiring the user to specify it correctly.
                          tl;dr: This proposes a new key for .zarray which it would be good to have feedback on.
                          Proposal
                          When creating a zarr array:
                          • add to .zarray json: {"dimension_separator": "/"}
                          • always write a 0-position chunk
                          When opening an array:
                          • try to read the separator character from the .zarray json
                          • if not available, try to find a 0-position chunk
                          • if not available, at every read action try to find chunks with both standard variants until the situation is clarified. (Standard separator list ["/", "."])
                          Points for discussion:
                          • The name dimension_separator differs from the code implementation key_separator to reduce confusion about whether every separator in the key name is effected.
                          • There has been some discussion (community call, gitter) about whether or not "/" could become the default.
                          • Is an addition to the .zarray metadata sufficiently low impact to be rolled into v2?
                          Metadata
                          Metadata
                          Assignees
                          No one assigned
                            Labels
                            No labels
                            No labels
                            Type
                            No type
                            Projects
                            No projects
                              Milestone
                              No milestone
                              Relationships
                              None yet
                              Development
                              No branches or pull requests
                              Issue actions
                              
, '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); }
})();
})();

                              Skip to content
                              Nested storage detection in Zarr V2 #707
                              Closed
                              Closed
                              Nested storage detection in Zarr V2#707
                              Description
                              @joshmoore
                              joshmoore
                              opened on Mar 5, 2021
                              see: ome/ngff#29 and bcdev/jzarr#17
                              In order to better handle Zarr arrays created with NestedDirectoryStorage or FSStore(key_separator="/"), SabineEmbacher and I have been working on a "protocol heuristic" that can be used by V2 implementations to detect nested chunking rather than requiring the user to specify it correctly.
                              tl;dr: This proposes a new key for .zarray which it would be good to have feedback on.
                              Proposal
                              When creating a zarr array:
                              • add to .zarray json: {"dimension_separator": "/"}
                              • always write a 0-position chunk
                              When opening an array:
                              • try to read the separator character from the .zarray json
                              • if not available, try to find a 0-position chunk
                              • if not available, at every read action try to find chunks with both standard variants until the situation is clarified. (Standard separator list ["/", "."])
                              Points for discussion:
                              • The name dimension_separator differs from the code implementation key_separator to reduce confusion about whether every separator in the key name is effected.
                              • There has been some discussion (community call, gitter) about whether or not "/" could become the default.
                              • Is an addition to the .zarray metadata sufficiently low impact to be rolled into v2?
                              Metadata
                              Metadata
                              Assignees
                              No one assigned
                                Labels
                                No labels
                                No labels
                                Type
                                No type
                                Projects
                                No projects
                                  Milestone
                                  No milestone
                                  Relationships
                                  None yet
                                  Development
                                  No branches or pull requests
                                  Issue actions