Unable to save object arrays #691

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Closed
Unable to save object arrays#691
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bugPotential issues with the zarr-python library

Description

@imilas
imilas
opened on Jan 18, 2021

Issue

I am unable to save variable length arrays to disk. I also cannot save JSON or Pickle object arrays to disk. Simple examples are given below.

Sorry if I missed something obvious in the documents. I cannot find an example of object arrays being saved to disk, so this could be entirely a syntax issue. Thanks for your time.

Example 1:

z = zarr.empty(4, dtype=object, object_codec=numcodecs.VLenArray(int))
print(z)
print(z.filters)
z[0] = np.array([1, 3, 5])
z[1] = np.array([4])
z[2] = np.array([7, 9, 14])
zarr.save("test1.zarr",z)

Example 2:

z = zarr.empty(5, dtype=object, object_codec=numcodecs.JSON())
print(z)
print(z.filters)
z[0] = 42
z[1] = 'foo'
z[2] = ['bar', 'baz', 'qux']
z[3] = {'a': 1, 'b': 2.2}
zarr.save("test2.zarr",z)

Problem description

Saving object arrays (as defined in the tutorial) results in the "ValueError: missing object_codec for object array" error.

The error occurs in the following line:

~/miniconda3/lib/python3.8/site-packages/zarr/storage.py in _init_array_metadata(store, shape, chunks, dtype, compressor, fill_value, order, overwrite, path, chunk_store, filters, object_codec)
386 if not filters:
387 # there are no filters so we can be sure there is no object codec
--> 388 raise ValueError('missing object_codec for object array')
389 else:
390 # one of the filters may be an object codec, issue a warning rather

As far as I can tell, the filters and codecs are defined in both cases.
Is it possible to save the arrays defined above to disk?

Version and installation information

zarr.version: 2.4.0
numcodecs.version:0.7.2
python version : Python 3.8.5
OS: linux
both pip and conda installations were tested

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      , 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
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}
} 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
      Unable to save object arrays #691
      Closed
      Closed
      Unable to save object arrays#691
      Labels
      bugPotential issues with the zarr-python library
      Description
      @imilas
      imilas
      opened on Jan 18, 2021
      Issue
      I am unable to save variable length arrays to disk. I also cannot save JSON or Pickle object arrays to disk. Simple examples are given below.
      Sorry if I missed something obvious in the documents. I cannot find an example of object arrays being saved to disk, so this could be entirely a syntax issue. Thanks for your time.
      Example 1:
      z = zarr.empty(4, dtype=object, object_codec=numcodecs.VLenArray(int))
print(z)
print(z.filters)
z[0] = np.array([1, 3, 5])
z[1] = np.array([4])
z[2] = np.array([7, 9, 14])
zarr.save("test1.zarr",z)

      Example 2:
      z = zarr.empty(5, dtype=object, object_codec=numcodecs.JSON())
print(z)
print(z.filters)
z[0] = 42
z[1] = 'foo'
z[2] = ['bar', 'baz', 'qux']
z[3] = {'a': 1, 'b': 2.2}
zarr.save("test2.zarr",z)

      Problem description
      Saving object arrays (as defined in the tutorial) results in the "ValueError: missing object_codec for object array" error.
      The error occurs in the following line:
      ~/miniconda3/lib/python3.8/site-packages/zarr/storage.py in _init_array_metadata(store, shape, chunks, dtype, compressor, fill_value, order, overwrite, path, chunk_store, filters, object_codec)
386 if not filters:
387 # there are no filters so we can be sure there is no object codec
--> 388 raise ValueError('missing object_codec for object array')
389 else:
390 # one of the filters may be an object codec, issue a warning rather

      As far as I can tell, the filters and codecs are defined in both cases.
      
Is it possible to save the arrays defined above to disk?
      Version and installation information
      zarr.version: 2.4.0
      
numcodecs.version:0.7.2
      
python version : Python 3.8.5
      
OS: linux
      
both pip and conda installations were tested
      Activity
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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
          Unable to save object arrays #691
          Closed
          Closed
          Unable to save object arrays#691
          Labels
          bugPotential issues with the zarr-python library
          Description
          @imilas
          imilas
          opened on Jan 18, 2021
          Issue
          I am unable to save variable length arrays to disk. I also cannot save JSON or Pickle object arrays to disk. Simple examples are given below.
          Sorry if I missed something obvious in the documents. I cannot find an example of object arrays being saved to disk, so this could be entirely a syntax issue. Thanks for your time.
          Example 1:
          z = zarr.empty(4, dtype=object, object_codec=numcodecs.VLenArray(int))
print(z)
print(z.filters)
z[0] = np.array([1, 3, 5])
z[1] = np.array([4])
z[2] = np.array([7, 9, 14])
zarr.save("test1.zarr",z)

          Example 2:
          z = zarr.empty(5, dtype=object, object_codec=numcodecs.JSON())
print(z)
print(z.filters)
z[0] = 42
z[1] = 'foo'
z[2] = ['bar', 'baz', 'qux']
z[3] = {'a': 1, 'b': 2.2}
zarr.save("test2.zarr",z)

          Problem description
          Saving object arrays (as defined in the tutorial) results in the "ValueError: missing object_codec for object array" error.
          The error occurs in the following line:
          ~/miniconda3/lib/python3.8/site-packages/zarr/storage.py in _init_array_metadata(store, shape, chunks, dtype, compressor, fill_value, order, overwrite, path, chunk_store, filters, object_codec)
386 if not filters:
387 # there are no filters so we can be sure there is no object codec
--> 388 raise ValueError('missing object_codec for object array')
389 else:
390 # one of the filters may be an object codec, issue a warning rather

          As far as I can tell, the filters and codecs are defined in both cases.
          
Is it possible to save the arrays defined above to disk?
          Version and installation information
          zarr.version: 2.4.0
          
numcodecs.version:0.7.2
          
python version : Python 3.8.5
          
OS: linux
          
both pip and conda installations were tested
          Activity
          Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
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          No one assigned
            Labels
            bugPotential issues with the zarr-python library
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, '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
              Unable to save object arrays #691
              Closed
              Closed
              Unable to save object arrays#691
              Labels
              bugPotential issues with the zarr-python library
              Description
              @imilas
              imilas
              opened on Jan 18, 2021
              Issue
              I am unable to save variable length arrays to disk. I also cannot save JSON or Pickle object arrays to disk. Simple examples are given below.
              Sorry if I missed something obvious in the documents. I cannot find an example of object arrays being saved to disk, so this could be entirely a syntax issue. Thanks for your time.
              Example 1:
              z = zarr.empty(4, dtype=object, object_codec=numcodecs.VLenArray(int))
print(z)
print(z.filters)
z[0] = np.array([1, 3, 5])
z[1] = np.array([4])
z[2] = np.array([7, 9, 14])
zarr.save("test1.zarr",z)

              Example 2:
              z = zarr.empty(5, dtype=object, object_codec=numcodecs.JSON())
print(z)
print(z.filters)
z[0] = 42
z[1] = 'foo'
z[2] = ['bar', 'baz', 'qux']
z[3] = {'a': 1, 'b': 2.2}
zarr.save("test2.zarr",z)

              Problem description
              Saving object arrays (as defined in the tutorial) results in the "ValueError: missing object_codec for object array" error.
              The error occurs in the following line:
              ~/miniconda3/lib/python3.8/site-packages/zarr/storage.py in _init_array_metadata(store, shape, chunks, dtype, compressor, fill_value, order, overwrite, path, chunk_store, filters, object_codec)
386 if not filters:
387 # there are no filters so we can be sure there is no object codec
--> 388 raise ValueError('missing object_codec for object array')
389 else:
390 # one of the filters may be an object codec, issue a warning rather

              As far as I can tell, the filters and codecs are defined in both cases.
              
Is it possible to save the arrays defined above to disk?
              Version and installation information
              zarr.version: 2.4.0
              
numcodecs.version:0.7.2
              
python version : Python 3.8.5
              
OS: linux
              
both pip and conda installations were tested
              Activity
              Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
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                Labels
                bugPotential issues with the zarr-python library
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, '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
                  Unable to save object arrays #691
                  Closed
                  Closed
                  Unable to save object arrays#691
                  Labels
                  bugPotential issues with the zarr-python library
                  Description
                  @imilas
                  imilas
                  opened on Jan 18, 2021
                  Issue
                  I am unable to save variable length arrays to disk. I also cannot save JSON or Pickle object arrays to disk. Simple examples are given below.
                  Sorry if I missed something obvious in the documents. I cannot find an example of object arrays being saved to disk, so this could be entirely a syntax issue. Thanks for your time.
                  Example 1:
                  z = zarr.empty(4, dtype=object, object_codec=numcodecs.VLenArray(int))
print(z)
print(z.filters)
z[0] = np.array([1, 3, 5])
z[1] = np.array([4])
z[2] = np.array([7, 9, 14])
zarr.save("test1.zarr",z)

                  Example 2:
                  z = zarr.empty(5, dtype=object, object_codec=numcodecs.JSON())
print(z)
print(z.filters)
z[0] = 42
z[1] = 'foo'
z[2] = ['bar', 'baz', 'qux']
z[3] = {'a': 1, 'b': 2.2}
zarr.save("test2.zarr",z)

                  Problem description
                  Saving object arrays (as defined in the tutorial) results in the "ValueError: missing object_codec for object array" error.
                  The error occurs in the following line:
                  ~/miniconda3/lib/python3.8/site-packages/zarr/storage.py in _init_array_metadata(store, shape, chunks, dtype, compressor, fill_value, order, overwrite, path, chunk_store, filters, object_codec)
386 if not filters:
387 # there are no filters so we can be sure there is no object codec
--> 388 raise ValueError('missing object_codec for object array')
389 else:
390 # one of the filters may be an object codec, issue a warning rather

                  As far as I can tell, the filters and codecs are defined in both cases.
                  
Is it possible to save the arrays defined above to disk?
                  Version and installation information
                  zarr.version: 2.4.0
                  
numcodecs.version:0.7.2
                  
python version : Python 3.8.5
                  
OS: linux
                  
both pip and conda installations were tested
                  Activity
                  Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
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                  No one assigned
                    Labels
                    bugPotential issues with the zarr-python library
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, '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
                      Unable to save object arrays #691
                      Closed
                      Closed
                      Unable to save object arrays#691
                      Labels
                      bugPotential issues with the zarr-python library
                      Description
                      @imilas
                      imilas
                      opened on Jan 18, 2021
                      Issue
                      I am unable to save variable length arrays to disk. I also cannot save JSON or Pickle object arrays to disk. Simple examples are given below.
                      Sorry if I missed something obvious in the documents. I cannot find an example of object arrays being saved to disk, so this could be entirely a syntax issue. Thanks for your time.
                      Example 1:
                      z = zarr.empty(4, dtype=object, object_codec=numcodecs.VLenArray(int))
print(z)
print(z.filters)
z[0] = np.array([1, 3, 5])
z[1] = np.array([4])
z[2] = np.array([7, 9, 14])
zarr.save("test1.zarr",z)

                      Example 2:
                      z = zarr.empty(5, dtype=object, object_codec=numcodecs.JSON())
print(z)
print(z.filters)
z[0] = 42
z[1] = 'foo'
z[2] = ['bar', 'baz', 'qux']
z[3] = {'a': 1, 'b': 2.2}
zarr.save("test2.zarr",z)

                      Problem description
                      Saving object arrays (as defined in the tutorial) results in the "ValueError: missing object_codec for object array" error.
                      The error occurs in the following line:
                      ~/miniconda3/lib/python3.8/site-packages/zarr/storage.py in _init_array_metadata(store, shape, chunks, dtype, compressor, fill_value, order, overwrite, path, chunk_store, filters, object_codec)
386 if not filters:
387 # there are no filters so we can be sure there is no object codec
--> 388 raise ValueError('missing object_codec for object array')
389 else:
390 # one of the filters may be an object codec, issue a warning rather

                      As far as I can tell, the filters and codecs are defined in both cases.
                      
Is it possible to save the arrays defined above to disk?
                      Version and installation information
                      zarr.version: 2.4.0
                      
numcodecs.version:0.7.2
                      
python version : Python 3.8.5
                      
OS: linux
                      
both pip and conda installations were tested
                      Activity
                      Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
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                      No one assigned
                        Labels
                        bugPotential issues with the zarr-python library
                        Type
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, '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
                          Unable to save object arrays #691
                          Closed
                          Closed
                          Unable to save object arrays#691
                          Labels
                          bugPotential issues with the zarr-python library
                          Description
                          @imilas
                          imilas
                          opened on Jan 18, 2021
                          Issue
                          I am unable to save variable length arrays to disk. I also cannot save JSON or Pickle object arrays to disk. Simple examples are given below.
                          Sorry if I missed something obvious in the documents. I cannot find an example of object arrays being saved to disk, so this could be entirely a syntax issue. Thanks for your time.
                          Example 1:
                          z = zarr.empty(4, dtype=object, object_codec=numcodecs.VLenArray(int))
print(z)
print(z.filters)
z[0] = np.array([1, 3, 5])
z[1] = np.array([4])
z[2] = np.array([7, 9, 14])
zarr.save("test1.zarr",z)

                          Example 2:
                          z = zarr.empty(5, dtype=object, object_codec=numcodecs.JSON())
print(z)
print(z.filters)
z[0] = 42
z[1] = 'foo'
z[2] = ['bar', 'baz', 'qux']
z[3] = {'a': 1, 'b': 2.2}
zarr.save("test2.zarr",z)

                          Problem description
                          Saving object arrays (as defined in the tutorial) results in the "ValueError: missing object_codec for object array" error.
                          The error occurs in the following line:
                          ~/miniconda3/lib/python3.8/site-packages/zarr/storage.py in _init_array_metadata(store, shape, chunks, dtype, compressor, fill_value, order, overwrite, path, chunk_store, filters, object_codec)
386 if not filters:
387 # there are no filters so we can be sure there is no object codec
--> 388 raise ValueError('missing object_codec for object array')
389 else:
390 # one of the filters may be an object codec, issue a warning rather

                          As far as I can tell, the filters and codecs are defined in both cases.
                          
Is it possible to save the arrays defined above to disk?
                          Version and installation information
                          zarr.version: 2.4.0
                          
numcodecs.version:0.7.2
                          
python version : Python 3.8.5
                          
OS: linux
                          
both pip and conda installations were tested
                          Activity
                          Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
                          Metadata
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                          Assignees
                          No one assigned
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                            bugPotential issues with the zarr-python library
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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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                              Unable to save object arrays #691
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                              Unable to save object arrays#691
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                              bugPotential issues with the zarr-python library
                              Description
                              @imilas
                              imilas
                              opened on Jan 18, 2021
                              Issue
                              I am unable to save variable length arrays to disk. I also cannot save JSON or Pickle object arrays to disk. Simple examples are given below.
                              Sorry if I missed something obvious in the documents. I cannot find an example of object arrays being saved to disk, so this could be entirely a syntax issue. Thanks for your time.
                              Example 1:
                              z = zarr.empty(4, dtype=object, object_codec=numcodecs.VLenArray(int))
print(z)
print(z.filters)
z[0] = np.array([1, 3, 5])
z[1] = np.array([4])
z[2] = np.array([7, 9, 14])
zarr.save("test1.zarr",z)

                              Example 2:
                              z = zarr.empty(5, dtype=object, object_codec=numcodecs.JSON())
print(z)
print(z.filters)
z[0] = 42
z[1] = 'foo'
z[2] = ['bar', 'baz', 'qux']
z[3] = {'a': 1, 'b': 2.2}
zarr.save("test2.zarr",z)

                              Problem description
                              Saving object arrays (as defined in the tutorial) results in the "ValueError: missing object_codec for object array" error.
                              The error occurs in the following line:
                              ~/miniconda3/lib/python3.8/site-packages/zarr/storage.py in _init_array_metadata(store, shape, chunks, dtype, compressor, fill_value, order, overwrite, path, chunk_store, filters, object_codec)
386 if not filters:
387 # there are no filters so we can be sure there is no object codec
--> 388 raise ValueError('missing object_codec for object array')
389 else:
390 # one of the filters may be an object codec, issue a warning rather

                              As far as I can tell, the filters and codecs are defined in both cases.
                              
Is it possible to save the arrays defined above to disk?
                              Version and installation information
                              zarr.version: 2.4.0
                              
numcodecs.version:0.7.2
                              
python version : Python 3.8.5
                              
OS: linux
                              
both pip and conda installations were tested
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