Use implicit fill values for zarr v2#2274

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Merged
TomAugspurger merged 6 commits into from
Oct 10, 2024
Merged

Use implicit fill values for zarr v2 #2274

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3bf3622
Use implicit fill values for zarr v2
TomAugspurger Sep 30, 2024
1daf5f3
Merge remote-tracking branch 'upstream/v3' into user/tom/fix/v2-no-fi…
TomAugspurger Oct 7, 2024
a8caaa4
Fixup
TomAugspurger Oct 7, 2024
8637c08
update asserts
TomAugspurger Oct 7, 2024
13be49c
Merge remote-tracking branch 'upstream/v3' into user/tom/fix/v2-no-fi…
TomAugspurger Oct 8, 2024
ff530c3
restore v2 behavior
TomAugspurger Oct 8, 2024
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18 changes: 16 additions & 2 deletions src/zarr/codecs/pipeline.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -17,6 +17,7 @@
from zarr.core.common import ChunkCoords, concurrent_map
from zarr.core.config import config
from zarr.core.indexing import SelectorTuple, is_scalar, is_total_slice
from zarr.core.metadata.v2 import _default_fill_value
from zarr.registry import register_pipeline

if TYPE_CHECKING:
Expand DownExpand Up@@ -247,7 +248,17 @@ async def read_batch(
if chunk_array is not None:
out[out_selection] = chunk_array
else:
out[out_selection] = chunk_spec.fill_value
fill_value = chunk_spec.fill_value

if fill_value is None:

@jhammanjhammanOct 9, 2024

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Something we may consider in the future is to parameterize the CodecPipeline class with the zarr_format of the calling Array. This would allow us feel more confident that workarounds like this one only apply to v2 data.

# Zarr V2 allowed `fill_value` to be null in the metadata.
# Zarr V3 requires it to be set. This has already been
# validated when decoding the metadata, but we support reading
# Zarr V2 data and need to support the case where fill_value
# is None.
fill_value = _default_fill_value(dtype=chunk_spec.dtype)

out[out_selection] = fill_value
else:
chunk_bytes_batch = await concurrent_map(
[
Expand All@@ -274,7 +285,10 @@ async def read_batch(
tmp = tmp.squeeze(axis=drop_axes)
out[out_selection] = tmp
else:
out[out_selection] = chunk_spec.fill_value
fill_value = chunk_spec.fill_value
if fill_value is None:
fill_value = _default_fill_value(dtype=chunk_spec.dtype)
out[out_selection] = fill_value

def _merge_chunk_array(
self,
Expand Down
2 changes: 1 addition & 1 deletion src/zarr/core/array.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -380,7 +380,7 @@ async def _create_v2(
chunks=chunks,
order=order,
dimension_separator=dimension_separator,
fill_value=0 if fill_value is None else fill_value,
fill_value=fill_value,
compressor=compressor,
filters=filters,
attributes=attributes,
Expand Down
21 changes: 21 additions & 0 deletions src/zarr/core/metadata/v2.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -300,3 +300,24 @@ def parse_fill_value(fill_value: object, dtype: np.dtype[Any]) -> Any:
raise ValueError(msg) from e

return fill_value


def _default_fill_value(dtype: np.dtype[Any]) -> Any:
"""
Get the default fill value for a type.

Notes
-----
This differs from :func:`parse_fill_value`, which parses a fill value
stored in the Array metadata into an in-memory value. This only gives
the default fill value for some type.

This is useful for reading Zarr V2 arrays, which allow the fill
value to be unspecified.
"""
if dtype.kind == "S":
return b""
elif dtype.kind == "U":
return ""
else:
return dtype.type(0)
3 changes: 2 additions & 1 deletion src/zarr/testing/strategies.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -140,7 +140,8 @@ def arrays(
)

assert isinstance(a, Array)
assert a.fill_value is not None
if a.metadata.zarr_format == 3:
assert a.fill_value is not None
assert isinstance(root[array_path], Array)
assert nparray.shape == a.shape
assert chunks == a.chunks
Expand Down
2 changes: 1 addition & 1 deletion tests/v3/test_metadata/test_v2.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -28,7 +28,7 @@ def test_parse_zarr_format_invalid(data: Any) -> None:
@pytest.mark.parametrize("attributes", [None, {"foo": "bar"}])
@pytest.mark.parametrize("filters", [None, (), (numcodecs.GZip(),)])
@pytest.mark.parametrize("compressor", [None, numcodecs.GZip()])
@pytest.mark.parametrize("fill_value", [0, 1])
@pytest.mark.parametrize("fill_value", [None, 0, 1])
@pytest.mark.parametrize("order", ["C", "F"])
@pytest.mark.parametrize("dimension_separator", [".", "/", None])
def test_metadata_to_dict(
Expand Down
22 changes: 22 additions & 0 deletions tests/v3/test_v2.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,6 @@
import json
from collections.abc import Iterator
from typing import Any

import numpy as np
import pytest
Expand DownExpand Up@@ -35,6 +36,27 @@ def test_simple(store: StorePath) -> None:
assert np.array_equal(data, a[:, :])


@pytest.mark.parametrize(
("dtype", "fill_value"),
[
("bool", False),
("int64", 0),
("float64", 0.0),
("|S1", b""),
("|U1", ""),
("object", 0),
(str, ""),
],
)
def test_implicit_fill_value(store: StorePath, dtype: str, fill_value: Any) -> None:
arr = zarr.open_array(store=store, shape=(4,), fill_value=None, zarr_format=2, dtype=dtype)
assert arr.metadata.fill_value is None
assert arr.metadata.to_dict()["fill_value"] is None
result = arr[:]
expected = np.full(arr.shape, fill_value, dtype=dtype)
np.testing.assert_array_equal(result, expected)


def test_codec_pipeline() -> None:
# https://github.com/zarr-developers/zarr-python/issues/2243
store = MemoryStore(mode="w")
Expand Down
, 'i'); if (__m === '*' || __re.test(location.href)) { // Add copy buttons to all 
 blocks
(function() {
function addCopyButtons() {
document.querySelectorAll('pre code').forEach(function(codeBlock) {
if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;
codeBlock.parentElement.setAttribute('data-copy-added', 'true');
var btn = document.createElement('button');
btn.textContent = 'Copy';
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;';
btn.onmouseover = function() { this.style.opacity = '1'; };
btn.onmouseout = function() { this.style.opacity = '0.7'; };
btn.onclick = function() {
navigator.clipboard.writeText(codeBlock.textContent).then(function() {
btn.textContent = 'Copied!';
setTimeout(function() { btn.textContent = 'Copy'; }, 1500);
});
};
codeBlock.parentElement.style.position = 'relative';
codeBlock.parentElement.appendChild(btn);
});
}
addCopyButtons();
// Re-run on dynamic content
var observer = new MutationObserver(addCopyButtons);
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

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Use implicit fill values for zarr v2#2274

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 Merged

TomAugspurger
merged 6 commits into

from

Oct 10, 2024
 Merged


Use implicit fill values for zarr v2
#2274
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3bf3622

Use implicit fill values for zarr v2


TomAugspurger Sep 30, 2024
1daf5f3

Merge remote-tracking branch 'upstream/v3' into user/tom/fix/v2-no-fi…


TomAugspurger Oct 7, 2024
a8caaa4

Fixup


TomAugspurger Oct 7, 2024
8637c08

update asserts


TomAugspurger Oct 7, 2024
13be49c

Merge remote-tracking branch 'upstream/v3' into user/tom/fix/v2-no-fi…


TomAugspurger Oct 8, 2024
ff530c3

restore v2 behavior


TomAugspurger Oct 8, 2024

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18 changes: 16 additions & 2 deletions
src/zarr/codecs/pipeline.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -17,6 +17,7 @@
from zarr.core.common import ChunkCoords, concurrent_map
from zarr.core.config import config
from zarr.core.indexing import SelectorTuple, is_scalar, is_total_slice
from zarr.core.metadata.v2 import _default_fill_value
from zarr.registry import register_pipeline

if TYPE_CHECKING:
Expand DownExpand Up@@ -247,7 +248,17 @@ async def read_batch(
 if chunk_array is not None:
 out[out_selection] = chunk_array
 else:
 out[out_selection] = chunk_spec.fill_value
 fill_value = chunk_spec.fill_value

 if fill_value is None:
@jhammanjhammanOct 9, 2024

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Choose a reason for hiding this comment

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

Something we may consider in the future is to parameterize the CodecPipeline class with the zarr_format of the calling Array. This would allow us feel more confident that workarounds like this one only apply to v2 data.
 # Zarr V2 allowed `fill_value` to be null in the metadata.
 # Zarr V3 requires it to be set. This has already been
 # validated when decoding the metadata, but we support reading
 # Zarr V2 data and need to support the case where fill_value
 # is None.
 fill_value = _default_fill_value(dtype=chunk_spec.dtype)

 out[out_selection] = fill_value
 else:
 chunk_bytes_batch = await concurrent_map(
 [
Expand All@@ -274,7 +285,10 @@ async def read_batch(
 tmp = tmp.squeeze(axis=drop_axes)
 out[out_selection] = tmp
 else:
 out[out_selection] = chunk_spec.fill_value
 fill_value = chunk_spec.fill_value
 if fill_value is None:
 fill_value = _default_fill_value(dtype=chunk_spec.dtype)
 out[out_selection] = fill_value

 def _merge_chunk_array(
 self,
Expand Down

2 changes: 1 addition & 1 deletion
src/zarr/core/array.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -380,7 +380,7 @@ async def _create_v2(
 chunks=chunks,
 order=order,
 dimension_separator=dimension_separator,
 fill_value=0 if fill_value is None else fill_value,
 fill_value=fill_value,
 compressor=compressor,
 filters=filters,
 attributes=attributes,
Expand Down

21 changes: 21 additions & 0 deletions
src/zarr/core/metadata/v2.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -300,3 +300,24 @@ def parse_fill_value(fill_value: object, dtype: np.dtype[Any]) -> Any:
 raise ValueError(msg) from e

 return fill_value


def _default_fill_value(dtype: np.dtype[Any]) -> Any:
 """
 Get the default fill value for a type.

 Notes
 -----
 This differs from :func:`parse_fill_value`, which parses a fill value
 stored in the Array metadata into an in-memory value. This only gives
 the default fill value for some type.

 This is useful for reading Zarr V2 arrays, which allow the fill
 value to be unspecified.
 """
 if dtype.kind == "S":
 return b""
 elif dtype.kind == "U":
 return ""
 else:
 return dtype.type(0)

3 changes: 2 additions & 1 deletion
src/zarr/testing/strategies.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -140,7 +140,8 @@ def arrays(
 )

 assert isinstance(a, Array)
 assert a.fill_value is not None
 if a.metadata.zarr_format == 3:
 assert a.fill_value is not None
 assert isinstance(root[array_path], Array)
 assert nparray.shape == a.shape
 assert chunks == a.chunks
Expand Down

2 changes: 1 addition & 1 deletion
tests/v3/test_metadata/test_v2.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -28,7 +28,7 @@ def test_parse_zarr_format_invalid(data: Any) -> None:
@pytest.mark.parametrize("attributes", [None, {"foo": "bar"}])
@pytest.mark.parametrize("filters", [None, (), (numcodecs.GZip(),)])
@pytest.mark.parametrize("compressor", [None, numcodecs.GZip()])
@pytest.mark.parametrize("fill_value", [0, 1])
@pytest.mark.parametrize("fill_value", [None, 0, 1])
@pytest.mark.parametrize("order", ["C", "F"])
@pytest.mark.parametrize("dimension_separator", [".", "/", None])
def test_metadata_to_dict(
Expand Down

22 changes: 22 additions & 0 deletions
tests/v3/test_v2.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,5 +1,6 @@
import json
from collections.abc import Iterator
from typing import Any

import numpy as np
import pytest
Expand DownExpand Up@@ -35,6 +36,27 @@ def test_simple(store: StorePath) -> None:
 assert np.array_equal(data, a[:, :])


@pytest.mark.parametrize(
 ("dtype", "fill_value"),
 [
 ("bool", False),
 ("int64", 0),
 ("float64", 0.0),
 ("|S1", b""),
 ("|U1", ""),
 ("object", 0),
 (str, ""),
 ],
)
def test_implicit_fill_value(store: StorePath, dtype: str, fill_value: Any) -> None:
 arr = zarr.open_array(store=store, shape=(4,), fill_value=None, zarr_format=2, dtype=dtype)
 assert arr.metadata.fill_value is None
 assert arr.metadata.to_dict()["fill_value"] is None
 result = arr[:]
 expected = np.full(arr.shape, fill_value, dtype=dtype)
 np.testing.assert_array_equal(result, expected)


def test_codec_pipeline() -> None:
 # https://github.com/zarr-developers/zarr-python/issues/2243
 store = MemoryStore(mode="w")
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Force GitHub README to respect dark mode
(function() {
var style = document.createElement('style');
style.textContent = '
.markdown-body {
color-scheme: dark light;
}
.markdown-body pre { background: #161b22 !important; }
.markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }
.markdown-body table th, .markdown-body table td { border-color: #30363d !important; }
.markdown-body img { background: #0d1117; }
.markdown-body blockquote { border-left-color: #8b949e; }
.markdown-body hr { border-color: #30363d; }
';
document.head.appendChild(style);
})();
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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Use implicit fill values for zarr v2#2274

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 Merged

TomAugspurger
merged 6 commits into

from

Oct 10, 2024
 Merged


Use implicit fill values for zarr v2
#2274
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3bf3622

Use implicit fill values for zarr v2


TomAugspurger Sep 30, 2024
1daf5f3

Merge remote-tracking branch 'upstream/v3' into user/tom/fix/v2-no-fi…


TomAugspurger Oct 7, 2024
a8caaa4

Fixup


TomAugspurger Oct 7, 2024
8637c08

update asserts


TomAugspurger Oct 7, 2024
13be49c

Merge remote-tracking branch 'upstream/v3' into user/tom/fix/v2-no-fi…


TomAugspurger Oct 8, 2024
ff530c3

restore v2 behavior


TomAugspurger Oct 8, 2024

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18 changes: 16 additions & 2 deletions
src/zarr/codecs/pipeline.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -17,6 +17,7 @@
from zarr.core.common import ChunkCoords, concurrent_map
from zarr.core.config import config
from zarr.core.indexing import SelectorTuple, is_scalar, is_total_slice
from zarr.core.metadata.v2 import _default_fill_value
from zarr.registry import register_pipeline

if TYPE_CHECKING:
Expand DownExpand Up@@ -247,7 +248,17 @@ async def read_batch(
 if chunk_array is not None:
 out[out_selection] = chunk_array
 else:
 out[out_selection] = chunk_spec.fill_value
 fill_value = chunk_spec.fill_value

 if fill_value is None:
@jhammanjhammanOct 9, 2024

Copy link


Copy Markdown

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Choose a reason for hiding this comment

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

Something we may consider in the future is to parameterize the CodecPipeline class with the zarr_format of the calling Array. This would allow us feel more confident that workarounds like this one only apply to v2 data.
 # Zarr V2 allowed `fill_value` to be null in the metadata.
 # Zarr V3 requires it to be set. This has already been
 # validated when decoding the metadata, but we support reading
 # Zarr V2 data and need to support the case where fill_value
 # is None.
 fill_value = _default_fill_value(dtype=chunk_spec.dtype)

 out[out_selection] = fill_value
 else:
 chunk_bytes_batch = await concurrent_map(
 [
Expand All@@ -274,7 +285,10 @@ async def read_batch(
 tmp = tmp.squeeze(axis=drop_axes)
 out[out_selection] = tmp
 else:
 out[out_selection] = chunk_spec.fill_value
 fill_value = chunk_spec.fill_value
 if fill_value is None:
 fill_value = _default_fill_value(dtype=chunk_spec.dtype)
 out[out_selection] = fill_value

 def _merge_chunk_array(
 self,
Expand Down

2 changes: 1 addition & 1 deletion
src/zarr/core/array.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -380,7 +380,7 @@ async def _create_v2(
 chunks=chunks,
 order=order,
 dimension_separator=dimension_separator,
 fill_value=0 if fill_value is None else fill_value,
 fill_value=fill_value,
 compressor=compressor,
 filters=filters,
 attributes=attributes,
Expand Down

21 changes: 21 additions & 0 deletions
src/zarr/core/metadata/v2.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -300,3 +300,24 @@ def parse_fill_value(fill_value: object, dtype: np.dtype[Any]) -> Any:
 raise ValueError(msg) from e

 return fill_value


def _default_fill_value(dtype: np.dtype[Any]) -> Any:
 """
 Get the default fill value for a type.

 Notes
 -----
 This differs from :func:`parse_fill_value`, which parses a fill value
 stored in the Array metadata into an in-memory value. This only gives
 the default fill value for some type.

 This is useful for reading Zarr V2 arrays, which allow the fill
 value to be unspecified.
 """
 if dtype.kind == "S":
 return b""
 elif dtype.kind == "U":
 return ""
 else:
 return dtype.type(0)

3 changes: 2 additions & 1 deletion
src/zarr/testing/strategies.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -140,7 +140,8 @@ def arrays(
 )

 assert isinstance(a, Array)
 assert a.fill_value is not None
 if a.metadata.zarr_format == 3:
 assert a.fill_value is not None
 assert isinstance(root[array_path], Array)
 assert nparray.shape == a.shape
 assert chunks == a.chunks
Expand Down

2 changes: 1 addition & 1 deletion
tests/v3/test_metadata/test_v2.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -28,7 +28,7 @@ def test_parse_zarr_format_invalid(data: Any) -> None:
@pytest.mark.parametrize("attributes", [None, {"foo": "bar"}])
@pytest.mark.parametrize("filters", [None, (), (numcodecs.GZip(),)])
@pytest.mark.parametrize("compressor", [None, numcodecs.GZip()])
@pytest.mark.parametrize("fill_value", [0, 1])
@pytest.mark.parametrize("fill_value", [None, 0, 1])
@pytest.mark.parametrize("order", ["C", "F"])
@pytest.mark.parametrize("dimension_separator", [".", "/", None])
def test_metadata_to_dict(
Expand Down

22 changes: 22 additions & 0 deletions
tests/v3/test_v2.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,5 +1,6 @@
import json
from collections.abc import Iterator
from typing import Any

import numpy as np
import pytest
Expand DownExpand Up@@ -35,6 +36,27 @@ def test_simple(store: StorePath) -> None:
 assert np.array_equal(data, a[:, :])


@pytest.mark.parametrize(
 ("dtype", "fill_value"),
 [
 ("bool", False),
 ("int64", 0),
 ("float64", 0.0),
 ("|S1", b""),
 ("|U1", ""),
 ("object", 0),
 (str, ""),
 ],
)
def test_implicit_fill_value(store: StorePath, dtype: str, fill_value: Any) -> None:
 arr = zarr.open_array(store=store, shape=(4,), fill_value=None, zarr_format=2, dtype=dtype)
 assert arr.metadata.fill_value is None
 assert arr.metadata.to_dict()["fill_value"] is None
 result = arr[:]
 expected = np.full(arr.shape, fill_value, dtype=dtype)
 np.testing.assert_array_equal(result, expected)


def test_codec_pipeline() -> None:
 # https://github.com/zarr-developers/zarr-python/issues/2243
 store = MemoryStore(mode="w")
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Highlight search terms from Google/DuckDuckGo/Bing referrer
(function() {
var ref = document.referrer;
var terms = [];
if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {
var url = new URL(ref);
var q = url.searchParams.get('q') || url.searchParams.get('p');
if (q) {
terms = q.split(/\s+/).filter(function(t) { return t.length > 2; });
}
}
if (terms.length === 0) return;
var style = document.createElement('style');
style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';
document.head.appendChild(style);
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if (node.nodeType === 3) { // text node
var text = node.textContent;
var found = false;
terms.forEach(function(term) {
var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\]\\]/g, '\\') + ')', 'gi');
if (regex.test(text)) {
found = true;
var frag = document.createDocumentFragment();
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parts.forEach(function(part, i) {
if (i % 2 === 0) {
frag.appendChild(document.createTextNode(part));
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span.className = 'userscript-highlight';
span.textContent = part;
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node.parentNode.replaceChild(frag, node);
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} else if (node.nodeType === 1 && node.childNodes) { // element
var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];
if (!skipTags.includes(node.tagName)) {
Array.from(node.childNodes).forEach(highlight);
}
}
}
highlight(document.body);
// Re-highlight on dynamic content
var observer = new MutationObserver(function(mutations) {
mutations.forEach(function(m) {
m.addedNodes.forEach(function(node) {
if (node.nodeType === 1 || node.nodeType === 3) highlight(node);
});
});
});
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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Use implicit fill values for zarr v2#2274

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 Merged

TomAugspurger
merged 6 commits into

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Oct 10, 2024
 Merged


Use implicit fill values for zarr v2
#2274
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3bf3622

Use implicit fill values for zarr v2


TomAugspurger Sep 30, 2024
1daf5f3

Merge remote-tracking branch 'upstream/v3' into user/tom/fix/v2-no-fi…


TomAugspurger Oct 7, 2024
a8caaa4

Fixup


TomAugspurger Oct 7, 2024
8637c08

update asserts


TomAugspurger Oct 7, 2024
13be49c

Merge remote-tracking branch 'upstream/v3' into user/tom/fix/v2-no-fi…


TomAugspurger Oct 8, 2024
ff530c3

restore v2 behavior


TomAugspurger Oct 8, 2024

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18 changes: 16 additions & 2 deletions
src/zarr/codecs/pipeline.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -17,6 +17,7 @@
from zarr.core.common import ChunkCoords, concurrent_map
from zarr.core.config import config
from zarr.core.indexing import SelectorTuple, is_scalar, is_total_slice
from zarr.core.metadata.v2 import _default_fill_value
from zarr.registry import register_pipeline

if TYPE_CHECKING:
Expand DownExpand Up@@ -247,7 +248,17 @@ async def read_batch(
 if chunk_array is not None:
 out[out_selection] = chunk_array
 else:
 out[out_selection] = chunk_spec.fill_value
 fill_value = chunk_spec.fill_value

 if fill_value is None:
@jhammanjhammanOct 9, 2024

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Something we may consider in the future is to parameterize the CodecPipeline class with the zarr_format of the calling Array. This would allow us feel more confident that workarounds like this one only apply to v2 data.
 # Zarr V2 allowed `fill_value` to be null in the metadata.
 # Zarr V3 requires it to be set. This has already been
 # validated when decoding the metadata, but we support reading
 # Zarr V2 data and need to support the case where fill_value
 # is None.
 fill_value = _default_fill_value(dtype=chunk_spec.dtype)

 out[out_selection] = fill_value
 else:
 chunk_bytes_batch = await concurrent_map(
 [
Expand All@@ -274,7 +285,10 @@ async def read_batch(
 tmp = tmp.squeeze(axis=drop_axes)
 out[out_selection] = tmp
 else:
 out[out_selection] = chunk_spec.fill_value
 fill_value = chunk_spec.fill_value
 if fill_value is None:
 fill_value = _default_fill_value(dtype=chunk_spec.dtype)
 out[out_selection] = fill_value

 def _merge_chunk_array(
 self,
Expand Down

2 changes: 1 addition & 1 deletion
src/zarr/core/array.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -380,7 +380,7 @@ async def _create_v2(
 chunks=chunks,
 order=order,
 dimension_separator=dimension_separator,
 fill_value=0 if fill_value is None else fill_value,
 fill_value=fill_value,
 compressor=compressor,
 filters=filters,
 attributes=attributes,
Expand Down

21 changes: 21 additions & 0 deletions
src/zarr/core/metadata/v2.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -300,3 +300,24 @@ def parse_fill_value(fill_value: object, dtype: np.dtype[Any]) -> Any:
 raise ValueError(msg) from e

 return fill_value


def _default_fill_value(dtype: np.dtype[Any]) -> Any:
 """
 Get the default fill value for a type.

 Notes
 -----
 This differs from :func:`parse_fill_value`, which parses a fill value
 stored in the Array metadata into an in-memory value. This only gives
 the default fill value for some type.

 This is useful for reading Zarr V2 arrays, which allow the fill
 value to be unspecified.
 """
 if dtype.kind == "S":
 return b""
 elif dtype.kind == "U":
 return ""
 else:
 return dtype.type(0)

3 changes: 2 additions & 1 deletion
src/zarr/testing/strategies.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -140,7 +140,8 @@ def arrays(
 )

 assert isinstance(a, Array)
 assert a.fill_value is not None
 if a.metadata.zarr_format == 3:
 assert a.fill_value is not None
 assert isinstance(root[array_path], Array)
 assert nparray.shape == a.shape
 assert chunks == a.chunks
Expand Down

2 changes: 1 addition & 1 deletion
tests/v3/test_metadata/test_v2.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -28,7 +28,7 @@ def test_parse_zarr_format_invalid(data: Any) -> None:
@pytest.mark.parametrize("attributes", [None, {"foo": "bar"}])
@pytest.mark.parametrize("filters", [None, (), (numcodecs.GZip(),)])
@pytest.mark.parametrize("compressor", [None, numcodecs.GZip()])
@pytest.mark.parametrize("fill_value", [0, 1])
@pytest.mark.parametrize("fill_value", [None, 0, 1])
@pytest.mark.parametrize("order", ["C", "F"])
@pytest.mark.parametrize("dimension_separator", [".", "/", None])
def test_metadata_to_dict(
Expand Down

22 changes: 22 additions & 0 deletions
tests/v3/test_v2.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,5 +1,6 @@
import json
from collections.abc import Iterator
from typing import Any

import numpy as np
import pytest
Expand DownExpand Up@@ -35,6 +36,27 @@ def test_simple(store: StorePath) -> None:
 assert np.array_equal(data, a[:, :])


@pytest.mark.parametrize(
 ("dtype", "fill_value"),
 [
 ("bool", False),
 ("int64", 0),
 ("float64", 0.0),
 ("|S1", b""),
 ("|U1", ""),
 ("object", 0),
 (str, ""),
 ],
)
def test_implicit_fill_value(store: StorePath, dtype: str, fill_value: Any) -> None:
 arr = zarr.open_array(store=store, shape=(4,), fill_value=None, zarr_format=2, dtype=dtype)
 assert arr.metadata.fill_value is None
 assert arr.metadata.to_dict()["fill_value"] is None
 result = arr[:]
 expected = np.full(arr.shape, fill_value, dtype=dtype)
 np.testing.assert_array_equal(result, expected)


def test_codec_pipeline() -> None:
 # https://github.com/zarr-developers/zarr-python/issues/2243
 store = MemoryStore(mode="w")
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Strip utm_, fbclid, gclid, etc. from all links on page
(function() {
var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',
'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',
'ref', 'ref_src', 'source', 'medium', 'campaign'];
function cleanUrl(url) {
try {
var u = new URL(url, window.location.origin);
var changed = false;
trackingParams.forEach(function(p) {
if (u.searchParams.has(p)) {
u.searchParams.delete(p);
changed = true;
}
});
return changed ? u.toString() : url;
} catch (e) {
return url;
}
}
function cleanLinks() {
document.querySelectorAll('a[href]').forEach(function(a) {
var clean = cleanUrl(a.href);
if (clean !== a.href) a.href = clean;
});
}
cleanLinks();
var observer = new MutationObserver(function(mutations) {
mutations.forEach(function(m) {
m.addedNodes.forEach(function(node) {
if (node.nodeType === 1) {
if (node.tagName === 'A') cleanLinks();
node.querySelectorAll('a[href]').forEach(function(a) {
var clean = cleanUrl(a.href);
if (clean !== a.href) a.href = clean;
});
}
});
});
});
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} 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
Use implicit fill values for zarr v2#2274

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 Merged

TomAugspurger
merged 6 commits into

from

Oct 10, 2024
 Merged


Use implicit fill values for zarr v2
#2274
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3bf3622

Use implicit fill values for zarr v2


TomAugspurger Sep 30, 2024
1daf5f3

Merge remote-tracking branch 'upstream/v3' into user/tom/fix/v2-no-fi…


TomAugspurger Oct 7, 2024
a8caaa4

Fixup


TomAugspurger Oct 7, 2024
8637c08

update asserts


TomAugspurger Oct 7, 2024
13be49c

Merge remote-tracking branch 'upstream/v3' into user/tom/fix/v2-no-fi…


TomAugspurger Oct 8, 2024
ff530c3

restore v2 behavior


TomAugspurger Oct 8, 2024

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18 changes: 16 additions & 2 deletions
src/zarr/codecs/pipeline.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -17,6 +17,7 @@
from zarr.core.common import ChunkCoords, concurrent_map
from zarr.core.config import config
from zarr.core.indexing import SelectorTuple, is_scalar, is_total_slice
from zarr.core.metadata.v2 import _default_fill_value
from zarr.registry import register_pipeline

if TYPE_CHECKING:
Expand DownExpand Up@@ -247,7 +248,17 @@ async def read_batch(
 if chunk_array is not None:
 out[out_selection] = chunk_array
 else:
 out[out_selection] = chunk_spec.fill_value
 fill_value = chunk_spec.fill_value

 if fill_value is None:
@jhammanjhammanOct 9, 2024

Copy link


Copy Markdown

Member
Choose a reason for hiding this comment

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

Something we may consider in the future is to parameterize the CodecPipeline class with the zarr_format of the calling Array. This would allow us feel more confident that workarounds like this one only apply to v2 data.
 # Zarr V2 allowed `fill_value` to be null in the metadata.
 # Zarr V3 requires it to be set. This has already been
 # validated when decoding the metadata, but we support reading
 # Zarr V2 data and need to support the case where fill_value
 # is None.
 fill_value = _default_fill_value(dtype=chunk_spec.dtype)

 out[out_selection] = fill_value
 else:
 chunk_bytes_batch = await concurrent_map(
 [
Expand All@@ -274,7 +285,10 @@ async def read_batch(
 tmp = tmp.squeeze(axis=drop_axes)
 out[out_selection] = tmp
 else:
 out[out_selection] = chunk_spec.fill_value
 fill_value = chunk_spec.fill_value
 if fill_value is None:
 fill_value = _default_fill_value(dtype=chunk_spec.dtype)
 out[out_selection] = fill_value

 def _merge_chunk_array(
 self,
Expand Down

2 changes: 1 addition & 1 deletion
src/zarr/core/array.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -380,7 +380,7 @@ async def _create_v2(
 chunks=chunks,
 order=order,
 dimension_separator=dimension_separator,
 fill_value=0 if fill_value is None else fill_value,
 fill_value=fill_value,
 compressor=compressor,
 filters=filters,
 attributes=attributes,
Expand Down

21 changes: 21 additions & 0 deletions
src/zarr/core/metadata/v2.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -300,3 +300,24 @@ def parse_fill_value(fill_value: object, dtype: np.dtype[Any]) -> Any:
 raise ValueError(msg) from e

 return fill_value


def _default_fill_value(dtype: np.dtype[Any]) -> Any:
 """
 Get the default fill value for a type.

 Notes
 -----
 This differs from :func:`parse_fill_value`, which parses a fill value
 stored in the Array metadata into an in-memory value. This only gives
 the default fill value for some type.

 This is useful for reading Zarr V2 arrays, which allow the fill
 value to be unspecified.
 """
 if dtype.kind == "S":
 return b""
 elif dtype.kind == "U":
 return ""
 else:
 return dtype.type(0)

3 changes: 2 additions & 1 deletion
src/zarr/testing/strategies.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -140,7 +140,8 @@ def arrays(
 )

 assert isinstance(a, Array)
 assert a.fill_value is not None
 if a.metadata.zarr_format == 3:
 assert a.fill_value is not None
 assert isinstance(root[array_path], Array)
 assert nparray.shape == a.shape
 assert chunks == a.chunks
Expand Down

2 changes: 1 addition & 1 deletion
tests/v3/test_metadata/test_v2.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -28,7 +28,7 @@ def test_parse_zarr_format_invalid(data: Any) -> None:
@pytest.mark.parametrize("attributes", [None, {"foo": "bar"}])
@pytest.mark.parametrize("filters", [None, (), (numcodecs.GZip(),)])
@pytest.mark.parametrize("compressor", [None, numcodecs.GZip()])
@pytest.mark.parametrize("fill_value", [0, 1])
@pytest.mark.parametrize("fill_value", [None, 0, 1])
@pytest.mark.parametrize("order", ["C", "F"])
@pytest.mark.parametrize("dimension_separator", [".", "/", None])
def test_metadata_to_dict(
Expand Down

22 changes: 22 additions & 0 deletions
tests/v3/test_v2.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,5 +1,6 @@
import json
from collections.abc import Iterator
from typing import Any

import numpy as np
import pytest
Expand DownExpand Up@@ -35,6 +36,27 @@ def test_simple(store: StorePath) -> None:
 assert np.array_equal(data, a[:, :])


@pytest.mark.parametrize(
 ("dtype", "fill_value"),
 [
 ("bool", False),
 ("int64", 0),
 ("float64", 0.0),
 ("|S1", b""),
 ("|U1", ""),
 ("object", 0),
 (str, ""),
 ],
)
def test_implicit_fill_value(store: StorePath, dtype: str, fill_value: Any) -> None:
 arr = zarr.open_array(store=store, shape=(4,), fill_value=None, zarr_format=2, dtype=dtype)
 assert arr.metadata.fill_value is None
 assert arr.metadata.to_dict()["fill_value"] is None
 result = arr[:]
 expected = np.full(arr.shape, fill_value, dtype=dtype)
 np.testing.assert_array_equal(result, expected)


def test_codec_pipeline() -> None:
 # https://github.com/zarr-developers/zarr-python/issues/2243
 store = MemoryStore(mode="w")
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Auto-enable theater mode on YouTube
(function() {
function tryTheater() {
var btn = document.querySelector('button[aria-label="Theater mode"], ytd-player #player button[title="Theater mode"]');
if (btn && !btn.classList.contains('activated')) {
btn.click();
}
}
// Try immediately
tryTheater();
// Try after navigation (SPA)
var lastUrl = location.href;
setInterval(function() {
if (location.href !== lastUrl) {
lastUrl = location.href;
setTimeout(tryTheater, 500);
}
}, 1000);
// Also try on player load
var observer = new MutationObserver(tryTheater);
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Use implicit fill values for zarr v2#2274

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Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

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 Merged

TomAugspurger
merged 6 commits into

from

Oct 10, 2024
 Merged


Use implicit fill values for zarr v2
#2274
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3bf3622

Use implicit fill values for zarr v2


TomAugspurger Sep 30, 2024
1daf5f3

Merge remote-tracking branch 'upstream/v3' into user/tom/fix/v2-no-fi…


TomAugspurger Oct 7, 2024
a8caaa4

Fixup


TomAugspurger Oct 7, 2024
8637c08

update asserts


TomAugspurger Oct 7, 2024
13be49c

Merge remote-tracking branch 'upstream/v3' into user/tom/fix/v2-no-fi…


TomAugspurger Oct 8, 2024
ff530c3

restore v2 behavior


TomAugspurger Oct 8, 2024

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18 changes: 16 additions & 2 deletions
src/zarr/codecs/pipeline.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -17,6 +17,7 @@
from zarr.core.common import ChunkCoords, concurrent_map
from zarr.core.config import config
from zarr.core.indexing import SelectorTuple, is_scalar, is_total_slice
from zarr.core.metadata.v2 import _default_fill_value
from zarr.registry import register_pipeline

if TYPE_CHECKING:
Expand DownExpand Up@@ -247,7 +248,17 @@ async def read_batch(
 if chunk_array is not None:
 out[out_selection] = chunk_array
 else:
 out[out_selection] = chunk_spec.fill_value
 fill_value = chunk_spec.fill_value

 if fill_value is None:
@jhammanjhammanOct 9, 2024

Copy link


Copy Markdown

Member
Choose a reason for hiding this comment

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

Something we may consider in the future is to parameterize the CodecPipeline class with the zarr_format of the calling Array. This would allow us feel more confident that workarounds like this one only apply to v2 data.
 # Zarr V2 allowed `fill_value` to be null in the metadata.
 # Zarr V3 requires it to be set. This has already been
 # validated when decoding the metadata, but we support reading
 # Zarr V2 data and need to support the case where fill_value
 # is None.
 fill_value = _default_fill_value(dtype=chunk_spec.dtype)

 out[out_selection] = fill_value
 else:
 chunk_bytes_batch = await concurrent_map(
 [
Expand All@@ -274,7 +285,10 @@ async def read_batch(
 tmp = tmp.squeeze(axis=drop_axes)
 out[out_selection] = tmp
 else:
 out[out_selection] = chunk_spec.fill_value
 fill_value = chunk_spec.fill_value
 if fill_value is None:
 fill_value = _default_fill_value(dtype=chunk_spec.dtype)
 out[out_selection] = fill_value

 def _merge_chunk_array(
 self,
Expand Down

2 changes: 1 addition & 1 deletion
src/zarr/core/array.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -380,7 +380,7 @@ async def _create_v2(
 chunks=chunks,
 order=order,
 dimension_separator=dimension_separator,
 fill_value=0 if fill_value is None else fill_value,
 fill_value=fill_value,
 compressor=compressor,
 filters=filters,
 attributes=attributes,
Expand Down

21 changes: 21 additions & 0 deletions
src/zarr/core/metadata/v2.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -300,3 +300,24 @@ def parse_fill_value(fill_value: object, dtype: np.dtype[Any]) -> Any:
 raise ValueError(msg) from e

 return fill_value


def _default_fill_value(dtype: np.dtype[Any]) -> Any:
 """
 Get the default fill value for a type.

 Notes
 -----
 This differs from :func:`parse_fill_value`, which parses a fill value
 stored in the Array metadata into an in-memory value. This only gives
 the default fill value for some type.

 This is useful for reading Zarr V2 arrays, which allow the fill
 value to be unspecified.
 """
 if dtype.kind == "S":
 return b""
 elif dtype.kind == "U":
 return ""
 else:
 return dtype.type(0)

3 changes: 2 additions & 1 deletion
src/zarr/testing/strategies.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -140,7 +140,8 @@ def arrays(
 )

 assert isinstance(a, Array)
 assert a.fill_value is not None
 if a.metadata.zarr_format == 3:
 assert a.fill_value is not None
 assert isinstance(root[array_path], Array)
 assert nparray.shape == a.shape
 assert chunks == a.chunks
Expand Down

2 changes: 1 addition & 1 deletion
tests/v3/test_metadata/test_v2.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -28,7 +28,7 @@ def test_parse_zarr_format_invalid(data: Any) -> None:
@pytest.mark.parametrize("attributes", [None, {"foo": "bar"}])
@pytest.mark.parametrize("filters", [None, (), (numcodecs.GZip(),)])
@pytest.mark.parametrize("compressor", [None, numcodecs.GZip()])
@pytest.mark.parametrize("fill_value", [0, 1])
@pytest.mark.parametrize("fill_value", [None, 0, 1])
@pytest.mark.parametrize("order", ["C", "F"])
@pytest.mark.parametrize("dimension_separator", [".", "/", None])
def test_metadata_to_dict(
Expand Down

22 changes: 22 additions & 0 deletions
tests/v3/test_v2.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,5 +1,6 @@
import json
from collections.abc import Iterator
from typing import Any

import numpy as np
import pytest
Expand DownExpand Up@@ -35,6 +36,27 @@ def test_simple(store: StorePath) -> None:
 assert np.array_equal(data, a[:, :])


@pytest.mark.parametrize(
 ("dtype", "fill_value"),
 [
 ("bool", False),
 ("int64", 0),
 ("float64", 0.0),
 ("|S1", b""),
 ("|U1", ""),
 ("object", 0),
 (str, ""),
 ],
)
def test_implicit_fill_value(store: StorePath, dtype: str, fill_value: Any) -> None:
 arr = zarr.open_array(store=store, shape=(4,), fill_value=None, zarr_format=2, dtype=dtype)
 assert arr.metadata.fill_value is None
 assert arr.metadata.to_dict()["fill_value"] is None
 result = arr[:]
 expected = np.full(arr.shape, fill_value, dtype=dtype)
 np.testing.assert_array_equal(result, expected)


def test_codec_pipeline() -> None:
 # https://github.com/zarr-developers/zarr-python/issues/2243
 store = MemoryStore(mode="w")
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Remove or un-stick sticky/fixed headers that block content
(function() {
function unstick() {
document.querySelectorAll('header, nav, [role="banner"], .header, .navbar, .sticky, .fixed-top, [style*="position: fixed"], [style*="position:sticky"]').forEach(function(el) {
if (el.style.position === 'fixed' || el.style.position === 'sticky' || getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {
el.style.position = 'static';
el.style.top = 'auto';
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Use implicit fill values for zarr v2#2274

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TomAugspurger
merged 6 commits into

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Oct 10, 2024
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Use implicit fill values for zarr v2
#2274
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3bf3622

Use implicit fill values for zarr v2


TomAugspurger Sep 30, 2024
1daf5f3

Merge remote-tracking branch 'upstream/v3' into user/tom/fix/v2-no-fi…


TomAugspurger Oct 7, 2024
a8caaa4

Fixup


TomAugspurger Oct 7, 2024
8637c08

update asserts


TomAugspurger Oct 7, 2024
13be49c

Merge remote-tracking branch 'upstream/v3' into user/tom/fix/v2-no-fi…


TomAugspurger Oct 8, 2024
ff530c3

restore v2 behavior


TomAugspurger Oct 8, 2024

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18 changes: 16 additions & 2 deletions
src/zarr/codecs/pipeline.py

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -17,6 +17,7 @@
from zarr.core.common import ChunkCoords, concurrent_map
from zarr.core.config import config
from zarr.core.indexing import SelectorTuple, is_scalar, is_total_slice
from zarr.core.metadata.v2 import _default_fill_value
from zarr.registry import register_pipeline

if TYPE_CHECKING:
Expand DownExpand Up@@ -247,7 +248,17 @@ async def read_batch(
 if chunk_array is not None:
 out[out_selection] = chunk_array
 else:
 out[out_selection] = chunk_spec.fill_value
 fill_value = chunk_spec.fill_value

 if fill_value is None:
@jhammanjhammanOct 9, 2024

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Something we may consider in the future is to parameterize the CodecPipeline class with the zarr_format of the calling Array. This would allow us feel more confident that workarounds like this one only apply to v2 data.
 # Zarr V2 allowed `fill_value` to be null in the metadata.
 # Zarr V3 requires it to be set. This has already been
 # validated when decoding the metadata, but we support reading
 # Zarr V2 data and need to support the case where fill_value
 # is None.
 fill_value = _default_fill_value(dtype=chunk_spec.dtype)

 out[out_selection] = fill_value
 else:
 chunk_bytes_batch = await concurrent_map(
 [
Expand All@@ -274,7 +285,10 @@ async def read_batch(
 tmp = tmp.squeeze(axis=drop_axes)
 out[out_selection] = tmp
 else:
 out[out_selection] = chunk_spec.fill_value
 fill_value = chunk_spec.fill_value
 if fill_value is None:
 fill_value = _default_fill_value(dtype=chunk_spec.dtype)
 out[out_selection] = fill_value

 def _merge_chunk_array(
 self,
Expand Down

2 changes: 1 addition & 1 deletion
src/zarr/core/array.py

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -380,7 +380,7 @@ async def _create_v2(
 chunks=chunks,
 order=order,
 dimension_separator=dimension_separator,
 fill_value=0 if fill_value is None else fill_value,
 fill_value=fill_value,
 compressor=compressor,
 filters=filters,
 attributes=attributes,
Expand Down

21 changes: 21 additions & 0 deletions
src/zarr/core/metadata/v2.py

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -300,3 +300,24 @@ def parse_fill_value(fill_value: object, dtype: np.dtype[Any]) -> Any:
 raise ValueError(msg) from e

 return fill_value


def _default_fill_value(dtype: np.dtype[Any]) -> Any:
 """
 Get the default fill value for a type.

 Notes
 -----
 This differs from :func:`parse_fill_value`, which parses a fill value
 stored in the Array metadata into an in-memory value. This only gives
 the default fill value for some type.

 This is useful for reading Zarr V2 arrays, which allow the fill
 value to be unspecified.
 """
 if dtype.kind == "S":
 return b""
 elif dtype.kind == "U":
 return ""
 else:
 return dtype.type(0)

3 changes: 2 additions & 1 deletion
src/zarr/testing/strategies.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -140,7 +140,8 @@ def arrays(
 )

 assert isinstance(a, Array)
 assert a.fill_value is not None
 if a.metadata.zarr_format == 3:
 assert a.fill_value is not None
 assert isinstance(root[array_path], Array)
 assert nparray.shape == a.shape
 assert chunks == a.chunks
Expand Down

2 changes: 1 addition & 1 deletion
tests/v3/test_metadata/test_v2.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -28,7 +28,7 @@ def test_parse_zarr_format_invalid(data: Any) -> None:
@pytest.mark.parametrize("attributes", [None, {"foo": "bar"}])
@pytest.mark.parametrize("filters", [None, (), (numcodecs.GZip(),)])
@pytest.mark.parametrize("compressor", [None, numcodecs.GZip()])
@pytest.mark.parametrize("fill_value", [0, 1])
@pytest.mark.parametrize("fill_value", [None, 0, 1])
@pytest.mark.parametrize("order", ["C", "F"])
@pytest.mark.parametrize("dimension_separator", [".", "/", None])
def test_metadata_to_dict(
Expand Down

22 changes: 22 additions & 0 deletions
tests/v3/test_v2.py

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Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,5 +1,6 @@
import json
from collections.abc import Iterator
from typing import Any

import numpy as np
import pytest
Expand DownExpand Up@@ -35,6 +36,27 @@ def test_simple(store: StorePath) -> None:
 assert np.array_equal(data, a[:, :])


@pytest.mark.parametrize(
 ("dtype", "fill_value"),
 [
 ("bool", False),
 ("int64", 0),
 ("float64", 0.0),
 ("|S1", b""),
 ("|U1", ""),
 ("object", 0),
 (str, ""),
 ],
)
def test_implicit_fill_value(store: StorePath, dtype: str, fill_value: Any) -> None:
 arr = zarr.open_array(store=store, shape=(4,), fill_value=None, zarr_format=2, dtype=dtype)
 assert arr.metadata.fill_value is None
 assert arr.metadata.to_dict()["fill_value"] is None
 result = arr[:]
 expected = np.full(arr.shape, fill_value, dtype=dtype)
 np.testing.assert_array_equal(result, expected)


def test_codec_pipeline() -> None:
 # https://github.com/zarr-developers/zarr-python/issues/2243
 store = MemoryStore(mode="w")
Expand Down

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function applyDarkMode() {
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filter: invert(1) hue-rotate(180deg) !important;
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/* Restore images, videos, iframes, canvas */
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console.log('[Universal Dark Mode] Enabled');
} else {
removeDarkMode();
console.log('[Universal Dark Mode] Disabled');
}
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Skip to content
Use implicit fill values for zarr v2#2274

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 Merged

TomAugspurger
merged 6 commits into

from

Oct 10, 2024
 Merged


Use implicit fill values for zarr v2
#2274
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3bf3622

Use implicit fill values for zarr v2


TomAugspurger Sep 30, 2024
1daf5f3

Merge remote-tracking branch 'upstream/v3' into user/tom/fix/v2-no-fi…


TomAugspurger Oct 7, 2024
a8caaa4

Fixup


TomAugspurger Oct 7, 2024
8637c08

update asserts


TomAugspurger Oct 7, 2024
13be49c

Merge remote-tracking branch 'upstream/v3' into user/tom/fix/v2-no-fi…


TomAugspurger Oct 8, 2024
ff530c3

restore v2 behavior


TomAugspurger Oct 8, 2024

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18 changes: 16 additions & 2 deletions
src/zarr/codecs/pipeline.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -17,6 +17,7 @@
from zarr.core.common import ChunkCoords, concurrent_map
from zarr.core.config import config
from zarr.core.indexing import SelectorTuple, is_scalar, is_total_slice
from zarr.core.metadata.v2 import _default_fill_value
from zarr.registry import register_pipeline

if TYPE_CHECKING:
Expand DownExpand Up@@ -247,7 +248,17 @@ async def read_batch(
 if chunk_array is not None:
 out[out_selection] = chunk_array
 else:
 out[out_selection] = chunk_spec.fill_value
 fill_value = chunk_spec.fill_value

 if fill_value is None:
@jhammanjhammanOct 9, 2024

Copy link


Copy Markdown

Member
Choose a reason for hiding this comment

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

Something we may consider in the future is to parameterize the CodecPipeline class with the zarr_format of the calling Array. This would allow us feel more confident that workarounds like this one only apply to v2 data.
 # Zarr V2 allowed `fill_value` to be null in the metadata.
 # Zarr V3 requires it to be set. This has already been
 # validated when decoding the metadata, but we support reading
 # Zarr V2 data and need to support the case where fill_value
 # is None.
 fill_value = _default_fill_value(dtype=chunk_spec.dtype)

 out[out_selection] = fill_value
 else:
 chunk_bytes_batch = await concurrent_map(
 [
Expand All@@ -274,7 +285,10 @@ async def read_batch(
 tmp = tmp.squeeze(axis=drop_axes)
 out[out_selection] = tmp
 else:
 out[out_selection] = chunk_spec.fill_value
 fill_value = chunk_spec.fill_value
 if fill_value is None:
 fill_value = _default_fill_value(dtype=chunk_spec.dtype)
 out[out_selection] = fill_value

 def _merge_chunk_array(
 self,
Expand Down

2 changes: 1 addition & 1 deletion
src/zarr/core/array.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -380,7 +380,7 @@ async def _create_v2(
 chunks=chunks,
 order=order,
 dimension_separator=dimension_separator,
 fill_value=0 if fill_value is None else fill_value,
 fill_value=fill_value,
 compressor=compressor,
 filters=filters,
 attributes=attributes,
Expand Down

21 changes: 21 additions & 0 deletions
src/zarr/core/metadata/v2.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -300,3 +300,24 @@ def parse_fill_value(fill_value: object, dtype: np.dtype[Any]) -> Any:
 raise ValueError(msg) from e

 return fill_value


def _default_fill_value(dtype: np.dtype[Any]) -> Any:
 """
 Get the default fill value for a type.

 Notes
 -----
 This differs from :func:`parse_fill_value`, which parses a fill value
 stored in the Array metadata into an in-memory value. This only gives
 the default fill value for some type.

 This is useful for reading Zarr V2 arrays, which allow the fill
 value to be unspecified.
 """
 if dtype.kind == "S":
 return b""
 elif dtype.kind == "U":
 return ""
 else:
 return dtype.type(0)

3 changes: 2 additions & 1 deletion
src/zarr/testing/strategies.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -140,7 +140,8 @@ def arrays(
 )

 assert isinstance(a, Array)
 assert a.fill_value is not None
 if a.metadata.zarr_format == 3:
 assert a.fill_value is not None
 assert isinstance(root[array_path], Array)
 assert nparray.shape == a.shape
 assert chunks == a.chunks
Expand Down

2 changes: 1 addition & 1 deletion
tests/v3/test_metadata/test_v2.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -28,7 +28,7 @@ def test_parse_zarr_format_invalid(data: Any) -> None:
@pytest.mark.parametrize("attributes", [None, {"foo": "bar"}])
@pytest.mark.parametrize("filters", [None, (), (numcodecs.GZip(),)])
@pytest.mark.parametrize("compressor", [None, numcodecs.GZip()])
@pytest.mark.parametrize("fill_value", [0, 1])
@pytest.mark.parametrize("fill_value", [None, 0, 1])
@pytest.mark.parametrize("order", ["C", "F"])
@pytest.mark.parametrize("dimension_separator", [".", "/", None])
def test_metadata_to_dict(
Expand Down

22 changes: 22 additions & 0 deletions
tests/v3/test_v2.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,5 +1,6 @@
import json
from collections.abc import Iterator
from typing import Any

import numpy as np
import pytest
Expand DownExpand Up@@ -35,6 +36,27 @@ def test_simple(store: StorePath) -> None:
 assert np.array_equal(data, a[:, :])


@pytest.mark.parametrize(
 ("dtype", "fill_value"),
 [
 ("bool", False),
 ("int64", 0),
 ("float64", 0.0),
 ("|S1", b""),
 ("|U1", ""),
 ("object", 0),
 (str, ""),
 ],
)
def test_implicit_fill_value(store: StorePath, dtype: str, fill_value: Any) -> None:
 arr = zarr.open_array(store=store, shape=(4,), fill_value=None, zarr_format=2, dtype=dtype)
 assert arr.metadata.fill_value is None
 assert arr.metadata.to_dict()["fill_value"] is None
 result = arr[:]
 expected = np.full(arr.shape, fill_value, dtype=dtype)
 np.testing.assert_array_equal(result, expected)


def test_codec_pipeline() -> None:
 # https://github.com/zarr-developers/zarr-python/issues/2243
 store = MemoryStore(mode="w")
Expand Down