WIP, RFC: Optimize setitem with chunk equal to fill_value - #367

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WIP, RFC: Optimize setitem with chunk equal to fill_value#367
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jakirkham:opt_setitem_fill_value

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Fixes#366

If a chunk only contains the fill_value, delete the key-value pair for that chunk instead of storing the array. Should cutdown on storage space require for the Array. Also should improve the performance of copying one Array to another.

TODO:

  • Add unit tests and/or doctests in docstrings
  • Add docstrings and API docs for any new/modified user-facing classes and functions
  • New/modified features documented in docs/tutorial.rst
  • Changes documented in docs/release.rst
  • Docs build locally (e.g., run tox -e docs)
  • AppVeyor and Travis CI passes
  • Test coverage is 100% (Coveralls passes)

Matches how these lines are written in `_set_basic_selection_zd`.
Add a simple check to see if the key-value pair is just being set with a
chunk equal to the fill value. If so, simply delete the key-value pair
instead of storing a chunk that only contains the fill value. The Array
will behave the same externally. However this will cutdown on the space
require to store the Array. Also will make sure that copying one Array
to another Array won't dramatically effect the storage size.
@rabernat

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I have a very large, relatively sparse (lots of empty chunks) array. I would really like to avoid writing all those empty chunks to disk.

So 👍 to this!

Comment threadzarr/core.py
chunk[selection] = value

# clear chunk if it only contains the fill value
if np.all(np.equal(chunk, self._fill_value)):

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This seems like it could sometimes be an expensive operation. So it should be optional.

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How large are typical chunk sizes for you?

@d-v-bd-v-bApr 27, 2021

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regardless of chunk size, in many cases the user knows in advance whether this check will ever be useful. For dense imaging data, this conditional will almost never evaluate to true; for sparse data, this conditional will often evaluate to true. So the user should have some discretion over whether this check occurs.

@jakirkham

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Thanks! Yeah that was the idea behind it.

There was funkiness with ZipStore as deletion is not supported there.

Can give this another look 🙂

@joshmoore

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I actually assumed recently that this was the default.

@jakirkham

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Nope, but I think we discussed recently how we might get this to work for ZipStore and other non-deletable stores by just making the value b''. So I think we may be able to generalize this a bit

@d-v-b

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I was also bitten by thinking that was the default! Would love to see this merged.

@d-v-b

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@jakirkham I would be happy to move this PR forward, but I don't think I have push access to your fork. I made some changes (added a kwarg to the Array constructor, and added tests) here: https://github.com/d-v-b/zarr-python/tree/opt_setitem_fill_value

@jakirkham

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Sounds good. In that case feel free to send a PR to zarr-developers. Am going to close this out.

@jakirkham
jakirkham deleted the opt_setitem_fill_value branch May 11, 2021 02:07
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Optimize storing fill_value to Array

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})();
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try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '
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WIP, RFC: Optimize setitem with chunk equal to fill_value - #367

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jakirkham wants to merge 2 commits into
zarr-developers:masterfrom
jakirkham:opt_setitem_fill_value
Closed

WIP, RFC: Optimize setitem with chunk equal to fill_value#367
jakirkham wants to merge 2 commits into
zarr-developers:masterfrom
jakirkham:opt_setitem_fill_value

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Fixes#366

If a chunk only contains the fill_value, delete the key-value pair for that chunk instead of storing the array. Should cutdown on storage space require for the Array. Also should improve the performance of copying one Array to another.

TODO:

  • Add unit tests and/or doctests in docstrings
  • Add docstrings and API docs for any new/modified user-facing classes and functions
  • New/modified features documented in docs/tutorial.rst
  • Changes documented in docs/release.rst
  • Docs build locally (e.g., run tox -e docs)
  • AppVeyor and Travis CI passes
  • Test coverage is 100% (Coveralls passes)

Matches how these lines are written in `_set_basic_selection_zd`.
Add a simple check to see if the key-value pair is just being set with a
chunk equal to the fill value. If so, simply delete the key-value pair
instead of storing a chunk that only contains the fill value. The Array
will behave the same externally. However this will cutdown on the space
require to store the Array. Also will make sure that copying one Array
to another Array won't dramatically effect the storage size.
@rabernat

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Contributor

I have a very large, relatively sparse (lots of empty chunks) array. I would really like to avoid writing all those empty chunks to disk.

So 👍 to this!

Comment threadzarr/core.py
chunk[selection] = value

# clear chunk if it only contains the fill value
if np.all(np.equal(chunk, self._fill_value)):

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

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This seems like it could sometimes be an expensive operation. So it should be optional.

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How large are typical chunk sizes for you?

@d-v-bd-v-bApr 27, 2021

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regardless of chunk size, in many cases the user knows in advance whether this check will ever be useful. For dense imaging data, this conditional will almost never evaluate to true; for sparse data, this conditional will often evaluate to true. So the user should have some discretion over whether this check occurs.

@jakirkham

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MemberAuthor

Thanks! Yeah that was the idea behind it.

There was funkiness with ZipStore as deletion is not supported there.

Can give this another look 🙂

@joshmoore

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I actually assumed recently that this was the default.

@jakirkham

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Nope, but I think we discussed recently how we might get this to work for ZipStore and other non-deletable stores by just making the value b''. So I think we may be able to generalize this a bit

@d-v-b

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I was also bitten by thinking that was the default! Would love to see this merged.

@d-v-b

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@jakirkham I would be happy to move this PR forward, but I don't think I have push access to your fork. I made some changes (added a kwarg to the Array constructor, and added tests) here: https://github.com/d-v-b/zarr-python/tree/opt_setitem_fill_value

@jakirkham

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Sounds good. In that case feel free to send a PR to zarr-developers. Am going to close this out.

@jakirkham
jakirkham deleted the opt_setitem_fill_value branch May 11, 2021 02:07
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Optimize storing fill_value to Array

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@jakirkham@rabernat@joshmoore@d-v-b
, '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('^' + ".*" + '
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WIP, RFC: Optimize setitem with chunk equal to fill_value - #367

Closed
jakirkham wants to merge 2 commits into
zarr-developers:masterfrom
jakirkham:opt_setitem_fill_value
Closed

WIP, RFC: Optimize setitem with chunk equal to fill_value#367
jakirkham wants to merge 2 commits into
zarr-developers:masterfrom
jakirkham:opt_setitem_fill_value

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Fixes#366

If a chunk only contains the fill_value, delete the key-value pair for that chunk instead of storing the array. Should cutdown on storage space require for the Array. Also should improve the performance of copying one Array to another.

TODO:

  • Add unit tests and/or doctests in docstrings
  • Add docstrings and API docs for any new/modified user-facing classes and functions
  • New/modified features documented in docs/tutorial.rst
  • Changes documented in docs/release.rst
  • Docs build locally (e.g., run tox -e docs)
  • AppVeyor and Travis CI passes
  • Test coverage is 100% (Coveralls passes)

Matches how these lines are written in `_set_basic_selection_zd`.
Add a simple check to see if the key-value pair is just being set with a
chunk equal to the fill value. If so, simply delete the key-value pair
instead of storing a chunk that only contains the fill value. The Array
will behave the same externally. However this will cutdown on the space
require to store the Array. Also will make sure that copying one Array
to another Array won't dramatically effect the storage size.
@rabernat

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Contributor

I have a very large, relatively sparse (lots of empty chunks) array. I would really like to avoid writing all those empty chunks to disk.

So 👍 to this!

Comment threadzarr/core.py
chunk[selection] = value

# clear chunk if it only contains the fill value
if np.all(np.equal(chunk, self._fill_value)):

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This seems like it could sometimes be an expensive operation. So it should be optional.

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MemberAuthor

Choose a reason for hiding this comment

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How large are typical chunk sizes for you?

@d-v-bd-v-bApr 27, 2021

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regardless of chunk size, in many cases the user knows in advance whether this check will ever be useful. For dense imaging data, this conditional will almost never evaluate to true; for sparse data, this conditional will often evaluate to true. So the user should have some discretion over whether this check occurs.

@jakirkham

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MemberAuthor

Thanks! Yeah that was the idea behind it.

There was funkiness with ZipStore as deletion is not supported there.

Can give this another look 🙂

@joshmoore

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I actually assumed recently that this was the default.

@jakirkham

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Nope, but I think we discussed recently how we might get this to work for ZipStore and other non-deletable stores by just making the value b''. So I think we may be able to generalize this a bit

@d-v-b

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I was also bitten by thinking that was the default! Would love to see this merged.

@d-v-b

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@jakirkham I would be happy to move this PR forward, but I don't think I have push access to your fork. I made some changes (added a kwarg to the Array constructor, and added tests) here: https://github.com/d-v-b/zarr-python/tree/opt_setitem_fill_value

@jakirkham

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Sounds good. In that case feel free to send a PR to zarr-developers. Am going to close this out.

@jakirkham
jakirkham deleted the opt_setitem_fill_value branch May 11, 2021 02:07
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Optimize storing fill_value to Array

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@jakirkham@rabernat@joshmoore@d-v-b
, '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('^' + ".*" + '
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WIP, RFC: Optimize setitem with chunk equal to fill_value - #367

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jakirkham wants to merge 2 commits into
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jakirkham:opt_setitem_fill_value
Closed

WIP, RFC: Optimize setitem with chunk equal to fill_value#367
jakirkham wants to merge 2 commits into
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Fixes#366

If a chunk only contains the fill_value, delete the key-value pair for that chunk instead of storing the array. Should cutdown on storage space require for the Array. Also should improve the performance of copying one Array to another.

TODO:

  • Add unit tests and/or doctests in docstrings
  • Add docstrings and API docs for any new/modified user-facing classes and functions
  • New/modified features documented in docs/tutorial.rst
  • Changes documented in docs/release.rst
  • Docs build locally (e.g., run tox -e docs)
  • AppVeyor and Travis CI passes
  • Test coverage is 100% (Coveralls passes)

Matches how these lines are written in `_set_basic_selection_zd`.
Add a simple check to see if the key-value pair is just being set with a
chunk equal to the fill value. If so, simply delete the key-value pair
instead of storing a chunk that only contains the fill value. The Array
will behave the same externally. However this will cutdown on the space
require to store the Array. Also will make sure that copying one Array
to another Array won't dramatically effect the storage size.
@rabernat

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Contributor

I have a very large, relatively sparse (lots of empty chunks) array. I would really like to avoid writing all those empty chunks to disk.

So 👍 to this!

Comment threadzarr/core.py
chunk[selection] = value

# clear chunk if it only contains the fill value
if np.all(np.equal(chunk, self._fill_value)):

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This seems like it could sometimes be an expensive operation. So it should be optional.

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MemberAuthor

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How large are typical chunk sizes for you?

@d-v-bd-v-bApr 27, 2021

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regardless of chunk size, in many cases the user knows in advance whether this check will ever be useful. For dense imaging data, this conditional will almost never evaluate to true; for sparse data, this conditional will often evaluate to true. So the user should have some discretion over whether this check occurs.

@jakirkham

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Copy Markdown
MemberAuthor

Thanks! Yeah that was the idea behind it.

There was funkiness with ZipStore as deletion is not supported there.

Can give this another look 🙂

@joshmoore

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I actually assumed recently that this was the default.

@jakirkham

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Nope, but I think we discussed recently how we might get this to work for ZipStore and other non-deletable stores by just making the value b''. So I think we may be able to generalize this a bit

@d-v-b

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I was also bitten by thinking that was the default! Would love to see this merged.

@d-v-b

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@jakirkham I would be happy to move this PR forward, but I don't think I have push access to your fork. I made some changes (added a kwarg to the Array constructor, and added tests) here: https://github.com/d-v-b/zarr-python/tree/opt_setitem_fill_value

@jakirkham

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Sounds good. In that case feel free to send a PR to zarr-developers. Am going to close this out.

@jakirkham
jakirkham deleted the opt_setitem_fill_value branch May 11, 2021 02:07
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Optimize storing fill_value to Array

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@jakirkham@rabernat@joshmoore@d-v-b
, '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" + '
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WIP, RFC: Optimize setitem with chunk equal to fill_value - #367

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Closed

WIP, RFC: Optimize setitem with chunk equal to fill_value#367
jakirkham wants to merge 2 commits into
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jakirkham:opt_setitem_fill_value

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Fixes#366

If a chunk only contains the fill_value, delete the key-value pair for that chunk instead of storing the array. Should cutdown on storage space require for the Array. Also should improve the performance of copying one Array to another.

TODO:

  • Add unit tests and/or doctests in docstrings
  • Add docstrings and API docs for any new/modified user-facing classes and functions
  • New/modified features documented in docs/tutorial.rst
  • Changes documented in docs/release.rst
  • Docs build locally (e.g., run tox -e docs)
  • AppVeyor and Travis CI passes
  • Test coverage is 100% (Coveralls passes)

Matches how these lines are written in `_set_basic_selection_zd`.
Add a simple check to see if the key-value pair is just being set with a
chunk equal to the fill value. If so, simply delete the key-value pair
instead of storing a chunk that only contains the fill value. The Array
will behave the same externally. However this will cutdown on the space
require to store the Array. Also will make sure that copying one Array
to another Array won't dramatically effect the storage size.
@rabernat

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Contributor

I have a very large, relatively sparse (lots of empty chunks) array. I would really like to avoid writing all those empty chunks to disk.

So 👍 to this!

Comment threadzarr/core.py
chunk[selection] = value

# clear chunk if it only contains the fill value
if np.all(np.equal(chunk, self._fill_value)):

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This seems like it could sometimes be an expensive operation. So it should be optional.

Copy link
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MemberAuthor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

How large are typical chunk sizes for you?

@d-v-bd-v-bApr 27, 2021

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regardless of chunk size, in many cases the user knows in advance whether this check will ever be useful. For dense imaging data, this conditional will almost never evaluate to true; for sparse data, this conditional will often evaluate to true. So the user should have some discretion over whether this check occurs.

@jakirkham

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Copy Markdown
MemberAuthor

Thanks! Yeah that was the idea behind it.

There was funkiness with ZipStore as deletion is not supported there.

Can give this another look 🙂

@joshmoore

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I actually assumed recently that this was the default.

@jakirkham

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MemberAuthor

Nope, but I think we discussed recently how we might get this to work for ZipStore and other non-deletable stores by just making the value b''. So I think we may be able to generalize this a bit

@d-v-b

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I was also bitten by thinking that was the default! Would love to see this merged.

@d-v-b

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@jakirkham I would be happy to move this PR forward, but I don't think I have push access to your fork. I made some changes (added a kwarg to the Array constructor, and added tests) here: https://github.com/d-v-b/zarr-python/tree/opt_setitem_fill_value

@jakirkham

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Sounds good. In that case feel free to send a PR to zarr-developers. Am going to close this out.

@jakirkham
jakirkham deleted the opt_setitem_fill_value branch May 11, 2021 02:07
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Optimize storing fill_value to Array

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@jakirkham@rabernat@joshmoore@d-v-b
, '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('^' + ".*" + '
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WIP, RFC: Optimize setitem with chunk equal to fill_value - #367

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jakirkham:opt_setitem_fill_value
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WIP, RFC: Optimize setitem with chunk equal to fill_value#367
jakirkham wants to merge 2 commits into
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jakirkham:opt_setitem_fill_value

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Fixes#366

If a chunk only contains the fill_value, delete the key-value pair for that chunk instead of storing the array. Should cutdown on storage space require for the Array. Also should improve the performance of copying one Array to another.

TODO:

  • Add unit tests and/or doctests in docstrings
  • Add docstrings and API docs for any new/modified user-facing classes and functions
  • New/modified features documented in docs/tutorial.rst
  • Changes documented in docs/release.rst
  • Docs build locally (e.g., run tox -e docs)
  • AppVeyor and Travis CI passes
  • Test coverage is 100% (Coveralls passes)

Matches how these lines are written in `_set_basic_selection_zd`.
Add a simple check to see if the key-value pair is just being set with a
chunk equal to the fill value. If so, simply delete the key-value pair
instead of storing a chunk that only contains the fill value. The Array
will behave the same externally. However this will cutdown on the space
require to store the Array. Also will make sure that copying one Array
to another Array won't dramatically effect the storage size.
@rabernat

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I have a very large, relatively sparse (lots of empty chunks) array. I would really like to avoid writing all those empty chunks to disk.

So 👍 to this!

Comment threadzarr/core.py
chunk[selection] = value

# clear chunk if it only contains the fill value
if np.all(np.equal(chunk, self._fill_value)):

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This seems like it could sometimes be an expensive operation. So it should be optional.

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How large are typical chunk sizes for you?

@d-v-bd-v-bApr 27, 2021

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regardless of chunk size, in many cases the user knows in advance whether this check will ever be useful. For dense imaging data, this conditional will almost never evaluate to true; for sparse data, this conditional will often evaluate to true. So the user should have some discretion over whether this check occurs.

@jakirkham

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Thanks! Yeah that was the idea behind it.

There was funkiness with ZipStore as deletion is not supported there.

Can give this another look 🙂

@joshmoore

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I actually assumed recently that this was the default.

@jakirkham

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Nope, but I think we discussed recently how we might get this to work for ZipStore and other non-deletable stores by just making the value b''. So I think we may be able to generalize this a bit

@d-v-b

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I was also bitten by thinking that was the default! Would love to see this merged.

@d-v-b

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@jakirkham I would be happy to move this PR forward, but I don't think I have push access to your fork. I made some changes (added a kwarg to the Array constructor, and added tests) here: https://github.com/d-v-b/zarr-python/tree/opt_setitem_fill_value

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Sounds good. In that case feel free to send a PR to zarr-developers. Am going to close this out.

@jakirkham
jakirkham deleted the opt_setitem_fill_value branch May 11, 2021 02:07
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Optimize storing fill_value to Array

4 participants

@jakirkham@rabernat@joshmoore@d-v-b
, '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('^' + ".*" + '
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WIP, RFC: Optimize setitem with chunk equal to fill_value - #367

Closed
jakirkham wants to merge 2 commits into
zarr-developers:masterfrom
jakirkham:opt_setitem_fill_value
Closed

WIP, RFC: Optimize setitem with chunk equal to fill_value#367
jakirkham wants to merge 2 commits into
zarr-developers:masterfrom
jakirkham:opt_setitem_fill_value

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Fixes#366

If a chunk only contains the fill_value, delete the key-value pair for that chunk instead of storing the array. Should cutdown on storage space require for the Array. Also should improve the performance of copying one Array to another.

TODO:

  • Add unit tests and/or doctests in docstrings
  • Add docstrings and API docs for any new/modified user-facing classes and functions
  • New/modified features documented in docs/tutorial.rst
  • Changes documented in docs/release.rst
  • Docs build locally (e.g., run tox -e docs)
  • AppVeyor and Travis CI passes
  • Test coverage is 100% (Coveralls passes)

Matches how these lines are written in `_set_basic_selection_zd`.
Add a simple check to see if the key-value pair is just being set with a
chunk equal to the fill value. If so, simply delete the key-value pair
instead of storing a chunk that only contains the fill value. The Array
will behave the same externally. However this will cutdown on the space
require to store the Array. Also will make sure that copying one Array
to another Array won't dramatically effect the storage size.
@rabernat

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Contributor

I have a very large, relatively sparse (lots of empty chunks) array. I would really like to avoid writing all those empty chunks to disk.

So 👍 to this!

Comment threadzarr/core.py
chunk[selection] = value

# clear chunk if it only contains the fill value
if np.all(np.equal(chunk, self._fill_value)):

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This seems like it could sometimes be an expensive operation. So it should be optional.

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How large are typical chunk sizes for you?

@d-v-bd-v-bApr 27, 2021

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regardless of chunk size, in many cases the user knows in advance whether this check will ever be useful. For dense imaging data, this conditional will almost never evaluate to true; for sparse data, this conditional will often evaluate to true. So the user should have some discretion over whether this check occurs.

@jakirkham

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MemberAuthor

Thanks! Yeah that was the idea behind it.

There was funkiness with ZipStore as deletion is not supported there.

Can give this another look 🙂

@joshmoore

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I actually assumed recently that this was the default.

@jakirkham

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Nope, but I think we discussed recently how we might get this to work for ZipStore and other non-deletable stores by just making the value b''. So I think we may be able to generalize this a bit

@d-v-b

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I was also bitten by thinking that was the default! Would love to see this merged.

@d-v-b

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@jakirkham I would be happy to move this PR forward, but I don't think I have push access to your fork. I made some changes (added a kwarg to the Array constructor, and added tests) here: https://github.com/d-v-b/zarr-python/tree/opt_setitem_fill_value

@jakirkham

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Sounds good. In that case feel free to send a PR to zarr-developers. Am going to close this out.

@jakirkham
jakirkham deleted the opt_setitem_fill_value branch May 11, 2021 02:07
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Optimize storing fill_value to Array

4 participants

@jakirkham@rabernat@joshmoore@d-v-b
, '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

WIP, RFC: Optimize setitem with chunk equal to fill_value - #367

Closed
jakirkham wants to merge 2 commits into
zarr-developers:masterfrom
jakirkham:opt_setitem_fill_value
Closed

WIP, RFC: Optimize setitem with chunk equal to fill_value#367
jakirkham wants to merge 2 commits into
zarr-developers:masterfrom
jakirkham:opt_setitem_fill_value

Conversation

@jakirkham

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Fixes#366

If a chunk only contains the fill_value, delete the key-value pair for that chunk instead of storing the array. Should cutdown on storage space require for the Array. Also should improve the performance of copying one Array to another.

TODO:

  • Add unit tests and/or doctests in docstrings
  • Add docstrings and API docs for any new/modified user-facing classes and functions
  • New/modified features documented in docs/tutorial.rst
  • Changes documented in docs/release.rst
  • Docs build locally (e.g., run tox -e docs)
  • AppVeyor and Travis CI passes
  • Test coverage is 100% (Coveralls passes)

Matches how these lines are written in `_set_basic_selection_zd`.
Add a simple check to see if the key-value pair is just being set with a
chunk equal to the fill value. If so, simply delete the key-value pair
instead of storing a chunk that only contains the fill value. The Array
will behave the same externally. However this will cutdown on the space
require to store the Array. Also will make sure that copying one Array
to another Array won't dramatically effect the storage size.
@rabernat

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Copy Markdown
Contributor

I have a very large, relatively sparse (lots of empty chunks) array. I would really like to avoid writing all those empty chunks to disk.

So 👍 to this!

Comment threadzarr/core.py
chunk[selection] = value

# clear chunk if it only contains the fill value
if np.all(np.equal(chunk, self._fill_value)):

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This seems like it could sometimes be an expensive operation. So it should be optional.

Copy link
Copy Markdown
MemberAuthor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

How large are typical chunk sizes for you?

@d-v-bd-v-bApr 27, 2021

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regardless of chunk size, in many cases the user knows in advance whether this check will ever be useful. For dense imaging data, this conditional will almost never evaluate to true; for sparse data, this conditional will often evaluate to true. So the user should have some discretion over whether this check occurs.

@jakirkham

Copy link
Copy Markdown
MemberAuthor

Thanks! Yeah that was the idea behind it.

There was funkiness with ZipStore as deletion is not supported there.

Can give this another look 🙂

@joshmoore

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I actually assumed recently that this was the default.

@jakirkham

Copy link
Copy Markdown
MemberAuthor

Nope, but I think we discussed recently how we might get this to work for ZipStore and other non-deletable stores by just making the value b''. So I think we may be able to generalize this a bit

@d-v-b

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I was also bitten by thinking that was the default! Would love to see this merged.

@d-v-b

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@jakirkham I would be happy to move this PR forward, but I don't think I have push access to your fork. I made some changes (added a kwarg to the Array constructor, and added tests) here: https://github.com/d-v-b/zarr-python/tree/opt_setitem_fill_value

@jakirkham

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Sounds good. In that case feel free to send a PR to zarr-developers. Am going to close this out.

@jakirkham
jakirkham deleted the opt_setitem_fill_value branch May 11, 2021 02:07
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Optimize storing fill_value to Array

4 participants

@jakirkham@rabernat@joshmoore@d-v-b