WIP: Provide a meta array to change array type returned#501

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jakirkham wants to merge 10 commits into from
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WIP: Provide a meta array to change array type returned #501

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3fed74c
Ensure contiguous data using `astype`
jakirkham Nov 15, 2019
9fe4add
Add changelog entry about ensure contiguous data
jakirkham Nov 15, 2019
4f72ce0
Accept a meta array in the Array constructor
jakirkham Nov 15, 2019
028b4b2
Use NumPy's `*_like` function to allocate arrays
jakirkham Nov 15, 2019
313c81b
Include `_meta_array` when pickling `Array`
jakirkham Nov 15, 2019
08f55b2
Workaround the absence of `flags` and `writeable`
jakirkham Nov 15, 2019
a82018f
Configure Groups to support `meta_array`
jakirkham Nov 15, 2019
fda8d19
Passthrough Group's `_meta_array`
jakirkham Nov 15, 2019
c43ec94
Include `_meta_array` when pickling `Group`
jakirkham Nov 15, 2019
ab2a732
Merge branch 'master' into use_array_like
joshmoore Feb 18, 2021
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3 changes: 3 additions & 0 deletions docs/release.rst
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -124,6 +124,9 @@ Enhancements
* Ensure contiguous data using ``astype``.
By :user:`John Kirkham <jakirkham>`; :issue:`513`.

* Ensure contiguous data using ``astype``.
By :user:`John Kirkham <jakirkham>`; :issue:`513`.

* Refactor out ``_tofile``/``_fromfile`` from ``DirectoryStore``.
By :user:`John Kirkham <jakirkham>`; :issue:`503`.

Expand Down
46 changes: 38 additions & 8 deletions zarr/core.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -76,6 +76,9 @@ class Array:
read and decompressed when possible.

.. versionadded:: 2.7
meta_array : array, optional
An array instance to use for determining arrays to create and return
to users.

Attributes
----------
Expand DownExpand Up@@ -137,6 +140,7 @@ def __init__(
cache_metadata=True,
cache_attrs=True,
partial_decompress=False,
meta_array=None
):
# N.B., expect at this point store is fully initialized with all
# configuration metadata fully specified and normalized
Expand All@@ -148,6 +152,10 @@ def __init__(
self._key_prefix = self._path + '/'
else:
self._key_prefix = ''
if meta_array is not None:
self._meta_array = np.empty_like(meta_array)
else:
self._meta_array = np.empty(())
self._read_only = bool(read_only)
self._synchronizer = synchronizer
self._cache_metadata = cache_metadata
Expand DownExpand Up@@ -746,7 +754,7 @@ def _get_basic_selection_zd(self, selection, out=None, fields=None):

except KeyError:
# chunk not initialized
chunk = np.zeros((), dtype=self._dtype)
chunk = np.zeros_like(self._meta_array, shape=(), dtype=self._dtype)
if self._fill_value is not None:
chunk.fill(self._fill_value)

Expand DownExpand Up@@ -1050,7 +1058,8 @@ def _get_selection(self, indexer, out=None, fields=None):

# setup output array
if out is None:
out = np.empty(out_shape, dtype=out_dtype, order=self._order)
out = np.empty_like(self._meta_array, shape=out_shape,
dtype=out_dtype, order=self._order)
else:
check_array_shape('out', out, out_shape)

Expand DownExpand Up@@ -1516,7 +1525,7 @@ def _set_basic_selection_zd(self, selection, value, fields=None):

except KeyError:
# chunk not initialized
chunk = np.zeros((), dtype=self._dtype)
chunk = np.zeros_like(self._meta_array, shape=(), dtype=self._dtype)
if self._fill_value is not None:
chunk.fill(self._fill_value)

Expand DownExpand Up@@ -1746,6 +1755,23 @@ def _chunk_getitem(self, chunk_coords, chunk_selection, out, out_selection,
self._process_chunk(out, cdata, chunk_selection, drop_axes,
out_is_ndarray, fields, out_selection)

if (out_is_ndarray and
not fields and
is_contiguous_selection(out_selection) and
is_total_slice(chunk_selection, self._chunks) and
not self._filters and
self._dtype != object):

dest = out[out_selection]
write_direct = (
getattr(getattr(dest, "flags", None), "writeable", True) and (
(self._order == 'C' and dest.flags.c_contiguous) or
(self._order == 'F' and dest.flags.f_contiguous)
)
)

if write_direct:

def _chunk_getitems(self, lchunk_coords, lchunk_selection, out, lout_selection,
drop_axes=None, fields=None):
"""As _chunk_getitem, but for lists of chunks
Expand DownExpand Up@@ -1848,7 +1874,8 @@ def _process_for_setitem(self, ckey, chunk_selection, value, fields=None):
if is_scalar(value, self._dtype):

# setup array filled with value
chunk = np.empty(self._chunks, dtype=self._dtype, order=self._order)
chunk = np.empty_like(self._meta_array, shape=self._chunks,
dtype=self._dtype, order=self._order)
chunk.fill(value)

else:
Expand All@@ -1868,20 +1895,22 @@ def _process_for_setitem(self, ckey, chunk_selection, value, fields=None):

# chunk not initialized
if self._fill_value is not None:
chunk = np.empty(self._chunks, dtype=self._dtype, order=self._order)
chunk = np.empty_like(self._meta_array, shape=self._chunks,
dtype=self._dtype, order=self._order)
chunk.fill(self._fill_value)
elif self._dtype == object:
chunk = np.empty(self._chunks, dtype=self._dtype, order=self._order)
else:
# N.B., use zeros here so any region beyond the array has consistent
# and compressible data
chunk = np.zeros(self._chunks, dtype=self._dtype, order=self._order)
chunk = np.zeros_like(self._meta_array, shape=self._chunks,
dtype=self._dtype, order=self._order)

else:

# decode chunk
chunk = self._decode_chunk(cdata)
if not chunk.flags.writeable:
if not getattr(getattr(chunk, "flags", None), "writeable", True):
chunk = chunk.copy(order='K')

# modify
Expand DownExpand Up@@ -2113,7 +2142,8 @@ def hexdigest(self, hashname="sha1"):

def __getstate__(self):
return (self._store, self._path, self._read_only, self._chunk_store,
self._synchronizer, self._cache_metadata, self._attrs.cache)
self._synchronizer, self._cache_metadata, self._attrs.cache,
self._meta_array)

def __setstate__(self, state):
self.__init__(*state)
Expand Down
19 changes: 14 additions & 5 deletions zarr/hierarchy.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -44,6 +44,8 @@ class Group(MutableMapping):
to all attribute read operations.
synchronizer : object, optional
Array synchronizer.
meta_array : array, optional
An array to base allocations off of.

Attributes
----------
Expand DownExpand Up@@ -95,7 +97,7 @@ class Group(MutableMapping):
"""

def __init__(self, store, path=None, read_only=False, chunk_store=None,
cache_attrs=True, synchronizer=None):
cache_attrs=True, synchronizer=None, meta_array=None):
self._store = store
self._chunk_store = chunk_store
self._path = normalize_storage_path(path)
Expand All@@ -105,6 +107,10 @@ def __init__(self, store, path=None, read_only=False, chunk_store=None,
self._key_prefix = ''
self._read_only = read_only
self._synchronizer = synchronizer
if meta_array is not None:
self._meta_array = np.empty_like(meta_array)
else:
self._meta_array = np.empty(())

# guard conditions
if contains_array(store, path=self._path):
Expand DownExpand Up@@ -282,7 +288,7 @@ def typestr(o):

def __getstate__(self):
return (self._store, self._path, self._read_only, self._chunk_store,
self.attrs.cache, self._synchronizer)
self.attrs.cache, self._synchronizer, self._meta_array)

def __setstate__(self, state):
self.__init__(*state)
Expand DownExpand Up@@ -340,11 +346,13 @@ def __getitem__(self, item):
if contains_array(self._store, path):
return Array(self._store, read_only=self._read_only, path=path,
chunk_store=self._chunk_store,
synchronizer=self._synchronizer, cache_attrs=self.attrs.cache)
synchronizer=self._synchronizer, cache_attrs=self.attrs.cache,
meta_array=self._meta_array)
elif contains_group(self._store, path):
return Group(self._store, read_only=self._read_only, path=path,
chunk_store=self._chunk_store, cache_attrs=self.attrs.cache,
synchronizer=self._synchronizer)
synchronizer=self._synchronizer,
meta_array=self._meta_array)
else:
raise KeyError(item)

Expand DownExpand Up@@ -863,7 +871,8 @@ def _require_dataset_nosync(self, name, shape, dtype=None, exact=False,
cache_attrs = kwargs.get('cache_attrs', self.attrs.cache)
a = Array(self._store, path=path, read_only=self._read_only,
chunk_store=self._chunk_store, synchronizer=synchronizer,
cache_metadata=cache_metadata, cache_attrs=cache_attrs)
cache_metadata=cache_metadata, cache_attrs=cache_attrs,
meta_array=self._meta_array)
shape = normalize_shape(shape)
if shape != a.shape:
raise TypeError('shape do not match existing array; expected {}, got {}'
Expand Down
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

Skip to content
WIP: Provide a meta array to change array type returned#501

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to your account

 Closed

jakirkham
wants to merge
10
commits into

from

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WIP: Provide a meta array to change array type returned
#501
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3fed74c

Ensure contiguous data using `astype`


jakirkham Nov 15, 2019
9fe4add

Add changelog entry about ensure contiguous data


jakirkham Nov 15, 2019
4f72ce0

Accept a meta array in the Array constructor


jakirkham Nov 15, 2019
028b4b2

Use NumPy's `*_like` function to allocate arrays


jakirkham Nov 15, 2019
313c81b

Include `_meta_array` when pickling `Array`


jakirkham Nov 15, 2019
08f55b2

Workaround the absence of `flags` and `writeable`


jakirkham Nov 15, 2019
a82018f

Configure Groups to support `meta_array`


jakirkham Nov 15, 2019
fda8d19

Passthrough Group's `_meta_array`


jakirkham Nov 15, 2019
c43ec94

Include `_meta_array` when pickling `Group`


jakirkham Nov 15, 2019
ab2a732

Merge branch 'master' into use_array_like


joshmoore Feb 18, 2021

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3 changes: 3 additions & 0 deletions
docs/release.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -124,6 +124,9 @@ Enhancements
* Ensure contiguous data using ``astype``.
 By :user:`John Kirkham <jakirkham>`; :issue:`513`.

* Ensure contiguous data using ``astype``.
 By :user:`John Kirkham <jakirkham>`; :issue:`513`.

* Refactor out ``_tofile``/``_fromfile`` from ``DirectoryStore``.
 By :user:`John Kirkham <jakirkham>`; :issue:`503`.

Expand Down

46 changes: 38 additions & 8 deletions
zarr/core.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -76,6 +76,9 @@ class Array:
 read and decompressed when possible.

 .. versionadded:: 2.7
 meta_array : array, optional
 An array instance to use for determining arrays to create and return
 to users.

 Attributes
 ----------
Expand DownExpand Up@@ -137,6 +140,7 @@ def __init__(
 cache_metadata=True,
 cache_attrs=True,
 partial_decompress=False,
 meta_array=None
 ):
 # N.B., expect at this point store is fully initialized with all
 # configuration metadata fully specified and normalized
Expand All@@ -148,6 +152,10 @@ def __init__(
 self._key_prefix = self._path + '/'
 else:
 self._key_prefix = ''
 if meta_array is not None:
 self._meta_array = np.empty_like(meta_array)
 else:
 self._meta_array = np.empty(())
 self._read_only = bool(read_only)
 self._synchronizer = synchronizer
 self._cache_metadata = cache_metadata
Expand DownExpand Up@@ -746,7 +754,7 @@ def _get_basic_selection_zd(self, selection, out=None, fields=None):

 except KeyError:
 # chunk not initialized
 chunk = np.zeros((), dtype=self._dtype)
 chunk = np.zeros_like(self._meta_array, shape=(), dtype=self._dtype)
 if self._fill_value is not None:
 chunk.fill(self._fill_value)

Expand DownExpand Up@@ -1050,7 +1058,8 @@ def _get_selection(self, indexer, out=None, fields=None):

 # setup output array
 if out is None:
 out = np.empty(out_shape, dtype=out_dtype, order=self._order)
 out = np.empty_like(self._meta_array, shape=out_shape,
 dtype=out_dtype, order=self._order)
 else:
 check_array_shape('out', out, out_shape)

Expand DownExpand Up@@ -1516,7 +1525,7 @@ def _set_basic_selection_zd(self, selection, value, fields=None):

 except KeyError:
 # chunk not initialized
 chunk = np.zeros((), dtype=self._dtype)
 chunk = np.zeros_like(self._meta_array, shape=(), dtype=self._dtype)
 if self._fill_value is not None:
 chunk.fill(self._fill_value)

Expand DownExpand Up@@ -1746,6 +1755,23 @@ def _chunk_getitem(self, chunk_coords, chunk_selection, out, out_selection,
 self._process_chunk(out, cdata, chunk_selection, drop_axes,
 out_is_ndarray, fields, out_selection)

 if (out_is_ndarray and
 not fields and
 is_contiguous_selection(out_selection) and
 is_total_slice(chunk_selection, self._chunks) and
 not self._filters and
 self._dtype != object):

 dest = out[out_selection]
 write_direct = (
 getattr(getattr(dest, "flags", None), "writeable", True) and (
 (self._order == 'C' and dest.flags.c_contiguous) or
 (self._order == 'F' and dest.flags.f_contiguous)
 )
 )

 if write_direct:

 def _chunk_getitems(self, lchunk_coords, lchunk_selection, out, lout_selection,
 drop_axes=None, fields=None):
 """As _chunk_getitem, but for lists of chunks
Expand DownExpand Up@@ -1848,7 +1874,8 @@ def _process_for_setitem(self, ckey, chunk_selection, value, fields=None):
 if is_scalar(value, self._dtype):

 # setup array filled with value
 chunk = np.empty(self._chunks, dtype=self._dtype, order=self._order)
 chunk = np.empty_like(self._meta_array, shape=self._chunks,
 dtype=self._dtype, order=self._order)
 chunk.fill(value)

 else:
Expand All@@ -1868,20 +1895,22 @@ def _process_for_setitem(self, ckey, chunk_selection, value, fields=None):

 # chunk not initialized
 if self._fill_value is not None:
 chunk = np.empty(self._chunks, dtype=self._dtype, order=self._order)
 chunk = np.empty_like(self._meta_array, shape=self._chunks,
 dtype=self._dtype, order=self._order)
 chunk.fill(self._fill_value)
 elif self._dtype == object:
 chunk = np.empty(self._chunks, dtype=self._dtype, order=self._order)
 else:
 # N.B., use zeros here so any region beyond the array has consistent
 # and compressible data
 chunk = np.zeros(self._chunks, dtype=self._dtype, order=self._order)
 chunk = np.zeros_like(self._meta_array, shape=self._chunks,
 dtype=self._dtype, order=self._order)

 else:

 # decode chunk
 chunk = self._decode_chunk(cdata)
 if not chunk.flags.writeable:
 if not getattr(getattr(chunk, "flags", None), "writeable", True):
 chunk = chunk.copy(order='K')

 # modify
Expand DownExpand Up@@ -2113,7 +2142,8 @@ def hexdigest(self, hashname="sha1"):

 def __getstate__(self):
 return (self._store, self._path, self._read_only, self._chunk_store,
 self._synchronizer, self._cache_metadata, self._attrs.cache)
 self._synchronizer, self._cache_metadata, self._attrs.cache,
 self._meta_array)

 def __setstate__(self, state):
 self.__init__(*state)
Expand Down

19 changes: 14 additions & 5 deletions
zarr/hierarchy.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -44,6 +44,8 @@ class Group(MutableMapping):
 to all attribute read operations.
 synchronizer : object, optional
 Array synchronizer.
 meta_array : array, optional
 An array to base allocations off of.

 Attributes
 ----------
Expand DownExpand Up@@ -95,7 +97,7 @@ class Group(MutableMapping):
 """

 def __init__(self, store, path=None, read_only=False, chunk_store=None,
 cache_attrs=True, synchronizer=None):
 cache_attrs=True, synchronizer=None, meta_array=None):
 self._store = store
 self._chunk_store = chunk_store
 self._path = normalize_storage_path(path)
Expand All@@ -105,6 +107,10 @@ def __init__(self, store, path=None, read_only=False, chunk_store=None,
 self._key_prefix = ''
 self._read_only = read_only
 self._synchronizer = synchronizer
 if meta_array is not None:
 self._meta_array = np.empty_like(meta_array)
 else:
 self._meta_array = np.empty(())

 # guard conditions
 if contains_array(store, path=self._path):
Expand DownExpand Up@@ -282,7 +288,7 @@ def typestr(o):

 def __getstate__(self):
 return (self._store, self._path, self._read_only, self._chunk_store,
 self.attrs.cache, self._synchronizer)
 self.attrs.cache, self._synchronizer, self._meta_array)

 def __setstate__(self, state):
 self.__init__(*state)
Expand DownExpand Up@@ -340,11 +346,13 @@ def __getitem__(self, item):
 if contains_array(self._store, path):
 return Array(self._store, read_only=self._read_only, path=path,
 chunk_store=self._chunk_store,
 synchronizer=self._synchronizer, cache_attrs=self.attrs.cache)
 synchronizer=self._synchronizer, cache_attrs=self.attrs.cache,
 meta_array=self._meta_array)
 elif contains_group(self._store, path):
 return Group(self._store, read_only=self._read_only, path=path,
 chunk_store=self._chunk_store, cache_attrs=self.attrs.cache,
 synchronizer=self._synchronizer)
 synchronizer=self._synchronizer,
 meta_array=self._meta_array)
 else:
 raise KeyError(item)

Expand DownExpand Up@@ -863,7 +871,8 @@ def _require_dataset_nosync(self, name, shape, dtype=None, exact=False,
 cache_attrs = kwargs.get('cache_attrs', self.attrs.cache)
 a = Array(self._store, path=path, read_only=self._read_only,
 chunk_store=self._chunk_store, synchronizer=synchronizer,
 cache_metadata=cache_metadata, cache_attrs=cache_attrs)
 cache_metadata=cache_metadata, cache_attrs=cache_attrs,
 meta_array=self._meta_array)
 shape = normalize_shape(shape)
 if shape != a.shape:
 raise TypeError('shape do not match existing array; expected {}, got {}'
Expand Down

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

Skip to content
WIP: Provide a meta array to change array type returned#501

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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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 Closed

jakirkham
wants to merge
10
commits into

from

 Closed


WIP: Provide a meta array to change array type returned
#501
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Commits

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Hold shift + click to select a range
3fed74c

Ensure contiguous data using `astype`


jakirkham Nov 15, 2019
9fe4add

Add changelog entry about ensure contiguous data


jakirkham Nov 15, 2019
4f72ce0

Accept a meta array in the Array constructor


jakirkham Nov 15, 2019
028b4b2

Use NumPy's `*_like` function to allocate arrays


jakirkham Nov 15, 2019
313c81b

Include `_meta_array` when pickling `Array`


jakirkham Nov 15, 2019
08f55b2

Workaround the absence of `flags` and `writeable`


jakirkham Nov 15, 2019
a82018f

Configure Groups to support `meta_array`


jakirkham Nov 15, 2019
fda8d19

Passthrough Group's `_meta_array`


jakirkham Nov 15, 2019
c43ec94

Include `_meta_array` when pickling `Group`


jakirkham Nov 15, 2019
ab2a732

Merge branch 'master' into use_array_like


joshmoore Feb 18, 2021

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3 changes: 3 additions & 0 deletions
docs/release.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -124,6 +124,9 @@ Enhancements
* Ensure contiguous data using ``astype``.
 By :user:`John Kirkham <jakirkham>`; :issue:`513`.

* Ensure contiguous data using ``astype``.
 By :user:`John Kirkham <jakirkham>`; :issue:`513`.

* Refactor out ``_tofile``/``_fromfile`` from ``DirectoryStore``.
 By :user:`John Kirkham <jakirkham>`; :issue:`503`.

Expand Down

46 changes: 38 additions & 8 deletions
zarr/core.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -76,6 +76,9 @@ class Array:
 read and decompressed when possible.

 .. versionadded:: 2.7
 meta_array : array, optional
 An array instance to use for determining arrays to create and return
 to users.

 Attributes
 ----------
Expand DownExpand Up@@ -137,6 +140,7 @@ def __init__(
 cache_metadata=True,
 cache_attrs=True,
 partial_decompress=False,
 meta_array=None
 ):
 # N.B., expect at this point store is fully initialized with all
 # configuration metadata fully specified and normalized
Expand All@@ -148,6 +152,10 @@ def __init__(
 self._key_prefix = self._path + '/'
 else:
 self._key_prefix = ''
 if meta_array is not None:
 self._meta_array = np.empty_like(meta_array)
 else:
 self._meta_array = np.empty(())
 self._read_only = bool(read_only)
 self._synchronizer = synchronizer
 self._cache_metadata = cache_metadata
Expand DownExpand Up@@ -746,7 +754,7 @@ def _get_basic_selection_zd(self, selection, out=None, fields=None):

 except KeyError:
 # chunk not initialized
 chunk = np.zeros((), dtype=self._dtype)
 chunk = np.zeros_like(self._meta_array, shape=(), dtype=self._dtype)
 if self._fill_value is not None:
 chunk.fill(self._fill_value)

Expand DownExpand Up@@ -1050,7 +1058,8 @@ def _get_selection(self, indexer, out=None, fields=None):

 # setup output array
 if out is None:
 out = np.empty(out_shape, dtype=out_dtype, order=self._order)
 out = np.empty_like(self._meta_array, shape=out_shape,
 dtype=out_dtype, order=self._order)
 else:
 check_array_shape('out', out, out_shape)

Expand DownExpand Up@@ -1516,7 +1525,7 @@ def _set_basic_selection_zd(self, selection, value, fields=None):

 except KeyError:
 # chunk not initialized
 chunk = np.zeros((), dtype=self._dtype)
 chunk = np.zeros_like(self._meta_array, shape=(), dtype=self._dtype)
 if self._fill_value is not None:
 chunk.fill(self._fill_value)

Expand DownExpand Up@@ -1746,6 +1755,23 @@ def _chunk_getitem(self, chunk_coords, chunk_selection, out, out_selection,
 self._process_chunk(out, cdata, chunk_selection, drop_axes,
 out_is_ndarray, fields, out_selection)

 if (out_is_ndarray and
 not fields and
 is_contiguous_selection(out_selection) and
 is_total_slice(chunk_selection, self._chunks) and
 not self._filters and
 self._dtype != object):

 dest = out[out_selection]
 write_direct = (
 getattr(getattr(dest, "flags", None), "writeable", True) and (
 (self._order == 'C' and dest.flags.c_contiguous) or
 (self._order == 'F' and dest.flags.f_contiguous)
 )
 )

 if write_direct:

 def _chunk_getitems(self, lchunk_coords, lchunk_selection, out, lout_selection,
 drop_axes=None, fields=None):
 """As _chunk_getitem, but for lists of chunks
Expand DownExpand Up@@ -1848,7 +1874,8 @@ def _process_for_setitem(self, ckey, chunk_selection, value, fields=None):
 if is_scalar(value, self._dtype):

 # setup array filled with value
 chunk = np.empty(self._chunks, dtype=self._dtype, order=self._order)
 chunk = np.empty_like(self._meta_array, shape=self._chunks,
 dtype=self._dtype, order=self._order)
 chunk.fill(value)

 else:
Expand All@@ -1868,20 +1895,22 @@ def _process_for_setitem(self, ckey, chunk_selection, value, fields=None):

 # chunk not initialized
 if self._fill_value is not None:
 chunk = np.empty(self._chunks, dtype=self._dtype, order=self._order)
 chunk = np.empty_like(self._meta_array, shape=self._chunks,
 dtype=self._dtype, order=self._order)
 chunk.fill(self._fill_value)
 elif self._dtype == object:
 chunk = np.empty(self._chunks, dtype=self._dtype, order=self._order)
 else:
 # N.B., use zeros here so any region beyond the array has consistent
 # and compressible data
 chunk = np.zeros(self._chunks, dtype=self._dtype, order=self._order)
 chunk = np.zeros_like(self._meta_array, shape=self._chunks,
 dtype=self._dtype, order=self._order)

 else:

 # decode chunk
 chunk = self._decode_chunk(cdata)
 if not chunk.flags.writeable:
 if not getattr(getattr(chunk, "flags", None), "writeable", True):
 chunk = chunk.copy(order='K')

 # modify
Expand DownExpand Up@@ -2113,7 +2142,8 @@ def hexdigest(self, hashname="sha1"):

 def __getstate__(self):
 return (self._store, self._path, self._read_only, self._chunk_store,
 self._synchronizer, self._cache_metadata, self._attrs.cache)
 self._synchronizer, self._cache_metadata, self._attrs.cache,
 self._meta_array)

 def __setstate__(self, state):
 self.__init__(*state)
Expand Down

19 changes: 14 additions & 5 deletions
zarr/hierarchy.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -44,6 +44,8 @@ class Group(MutableMapping):
 to all attribute read operations.
 synchronizer : object, optional
 Array synchronizer.
 meta_array : array, optional
 An array to base allocations off of.

 Attributes
 ----------
Expand DownExpand Up@@ -95,7 +97,7 @@ class Group(MutableMapping):
 """

 def __init__(self, store, path=None, read_only=False, chunk_store=None,
 cache_attrs=True, synchronizer=None):
 cache_attrs=True, synchronizer=None, meta_array=None):
 self._store = store
 self._chunk_store = chunk_store
 self._path = normalize_storage_path(path)
Expand All@@ -105,6 +107,10 @@ def __init__(self, store, path=None, read_only=False, chunk_store=None,
 self._key_prefix = ''
 self._read_only = read_only
 self._synchronizer = synchronizer
 if meta_array is not None:
 self._meta_array = np.empty_like(meta_array)
 else:
 self._meta_array = np.empty(())

 # guard conditions
 if contains_array(store, path=self._path):
Expand DownExpand Up@@ -282,7 +288,7 @@ def typestr(o):

 def __getstate__(self):
 return (self._store, self._path, self._read_only, self._chunk_store,
 self.attrs.cache, self._synchronizer)
 self.attrs.cache, self._synchronizer, self._meta_array)

 def __setstate__(self, state):
 self.__init__(*state)
Expand DownExpand Up@@ -340,11 +346,13 @@ def __getitem__(self, item):
 if contains_array(self._store, path):
 return Array(self._store, read_only=self._read_only, path=path,
 chunk_store=self._chunk_store,
 synchronizer=self._synchronizer, cache_attrs=self.attrs.cache)
 synchronizer=self._synchronizer, cache_attrs=self.attrs.cache,
 meta_array=self._meta_array)
 elif contains_group(self._store, path):
 return Group(self._store, read_only=self._read_only, path=path,
 chunk_store=self._chunk_store, cache_attrs=self.attrs.cache,
 synchronizer=self._synchronizer)
 synchronizer=self._synchronizer,
 meta_array=self._meta_array)
 else:
 raise KeyError(item)

Expand DownExpand Up@@ -863,7 +871,8 @@ def _require_dataset_nosync(self, name, shape, dtype=None, exact=False,
 cache_attrs = kwargs.get('cache_attrs', self.attrs.cache)
 a = Array(self._store, path=path, read_only=self._read_only,
 chunk_store=self._chunk_store, synchronizer=synchronizer,
 cache_metadata=cache_metadata, cache_attrs=cache_attrs)
 cache_metadata=cache_metadata, cache_attrs=cache_attrs,
 meta_array=self._meta_array)
 shape = normalize_shape(shape)
 if shape != a.shape:
 raise TypeError('shape do not match existing array; expected {}, got {}'
Expand Down

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

Skip to content
WIP: Provide a meta array to change array type returned#501

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 Closed

jakirkham
wants to merge
10
commits into

from

 Closed


WIP: Provide a meta array to change array type returned
#501
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3fed74c

Ensure contiguous data using `astype`


jakirkham Nov 15, 2019
9fe4add

Add changelog entry about ensure contiguous data


jakirkham Nov 15, 2019
4f72ce0

Accept a meta array in the Array constructor


jakirkham Nov 15, 2019
028b4b2

Use NumPy's `*_like` function to allocate arrays


jakirkham Nov 15, 2019
313c81b

Include `_meta_array` when pickling `Array`


jakirkham Nov 15, 2019
08f55b2

Workaround the absence of `flags` and `writeable`


jakirkham Nov 15, 2019
a82018f

Configure Groups to support `meta_array`


jakirkham Nov 15, 2019
fda8d19

Passthrough Group's `_meta_array`


jakirkham Nov 15, 2019
c43ec94

Include `_meta_array` when pickling `Group`


jakirkham Nov 15, 2019
ab2a732

Merge branch 'master' into use_array_like


joshmoore Feb 18, 2021

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3 changes: 3 additions & 0 deletions
docs/release.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -124,6 +124,9 @@ Enhancements
* Ensure contiguous data using ``astype``.
 By :user:`John Kirkham <jakirkham>`; :issue:`513`.

* Ensure contiguous data using ``astype``.
 By :user:`John Kirkham <jakirkham>`; :issue:`513`.

* Refactor out ``_tofile``/``_fromfile`` from ``DirectoryStore``.
 By :user:`John Kirkham <jakirkham>`; :issue:`503`.

Expand Down

46 changes: 38 additions & 8 deletions
zarr/core.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -76,6 +76,9 @@ class Array:
 read and decompressed when possible.

 .. versionadded:: 2.7
 meta_array : array, optional
 An array instance to use for determining arrays to create and return
 to users.

 Attributes
 ----------
Expand DownExpand Up@@ -137,6 +140,7 @@ def __init__(
 cache_metadata=True,
 cache_attrs=True,
 partial_decompress=False,
 meta_array=None
 ):
 # N.B., expect at this point store is fully initialized with all
 # configuration metadata fully specified and normalized
Expand All@@ -148,6 +152,10 @@ def __init__(
 self._key_prefix = self._path + '/'
 else:
 self._key_prefix = ''
 if meta_array is not None:
 self._meta_array = np.empty_like(meta_array)
 else:
 self._meta_array = np.empty(())
 self._read_only = bool(read_only)
 self._synchronizer = synchronizer
 self._cache_metadata = cache_metadata
Expand DownExpand Up@@ -746,7 +754,7 @@ def _get_basic_selection_zd(self, selection, out=None, fields=None):

 except KeyError:
 # chunk not initialized
 chunk = np.zeros((), dtype=self._dtype)
 chunk = np.zeros_like(self._meta_array, shape=(), dtype=self._dtype)
 if self._fill_value is not None:
 chunk.fill(self._fill_value)

Expand DownExpand Up@@ -1050,7 +1058,8 @@ def _get_selection(self, indexer, out=None, fields=None):

 # setup output array
 if out is None:
 out = np.empty(out_shape, dtype=out_dtype, order=self._order)
 out = np.empty_like(self._meta_array, shape=out_shape,
 dtype=out_dtype, order=self._order)
 else:
 check_array_shape('out', out, out_shape)

Expand DownExpand Up@@ -1516,7 +1525,7 @@ def _set_basic_selection_zd(self, selection, value, fields=None):

 except KeyError:
 # chunk not initialized
 chunk = np.zeros((), dtype=self._dtype)
 chunk = np.zeros_like(self._meta_array, shape=(), dtype=self._dtype)
 if self._fill_value is not None:
 chunk.fill(self._fill_value)

Expand DownExpand Up@@ -1746,6 +1755,23 @@ def _chunk_getitem(self, chunk_coords, chunk_selection, out, out_selection,
 self._process_chunk(out, cdata, chunk_selection, drop_axes,
 out_is_ndarray, fields, out_selection)

 if (out_is_ndarray and
 not fields and
 is_contiguous_selection(out_selection) and
 is_total_slice(chunk_selection, self._chunks) and
 not self._filters and
 self._dtype != object):

 dest = out[out_selection]
 write_direct = (
 getattr(getattr(dest, "flags", None), "writeable", True) and (
 (self._order == 'C' and dest.flags.c_contiguous) or
 (self._order == 'F' and dest.flags.f_contiguous)
 )
 )

 if write_direct:

 def _chunk_getitems(self, lchunk_coords, lchunk_selection, out, lout_selection,
 drop_axes=None, fields=None):
 """As _chunk_getitem, but for lists of chunks
Expand DownExpand Up@@ -1848,7 +1874,8 @@ def _process_for_setitem(self, ckey, chunk_selection, value, fields=None):
 if is_scalar(value, self._dtype):

 # setup array filled with value
 chunk = np.empty(self._chunks, dtype=self._dtype, order=self._order)
 chunk = np.empty_like(self._meta_array, shape=self._chunks,
 dtype=self._dtype, order=self._order)
 chunk.fill(value)

 else:
Expand All@@ -1868,20 +1895,22 @@ def _process_for_setitem(self, ckey, chunk_selection, value, fields=None):

 # chunk not initialized
 if self._fill_value is not None:
 chunk = np.empty(self._chunks, dtype=self._dtype, order=self._order)
 chunk = np.empty_like(self._meta_array, shape=self._chunks,
 dtype=self._dtype, order=self._order)
 chunk.fill(self._fill_value)
 elif self._dtype == object:
 chunk = np.empty(self._chunks, dtype=self._dtype, order=self._order)
 else:
 # N.B., use zeros here so any region beyond the array has consistent
 # and compressible data
 chunk = np.zeros(self._chunks, dtype=self._dtype, order=self._order)
 chunk = np.zeros_like(self._meta_array, shape=self._chunks,
 dtype=self._dtype, order=self._order)

 else:

 # decode chunk
 chunk = self._decode_chunk(cdata)
 if not chunk.flags.writeable:
 if not getattr(getattr(chunk, "flags", None), "writeable", True):
 chunk = chunk.copy(order='K')

 # modify
Expand DownExpand Up@@ -2113,7 +2142,8 @@ def hexdigest(self, hashname="sha1"):

 def __getstate__(self):
 return (self._store, self._path, self._read_only, self._chunk_store,
 self._synchronizer, self._cache_metadata, self._attrs.cache)
 self._synchronizer, self._cache_metadata, self._attrs.cache,
 self._meta_array)

 def __setstate__(self, state):
 self.__init__(*state)
Expand Down

19 changes: 14 additions & 5 deletions
zarr/hierarchy.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -44,6 +44,8 @@ class Group(MutableMapping):
 to all attribute read operations.
 synchronizer : object, optional
 Array synchronizer.
 meta_array : array, optional
 An array to base allocations off of.

 Attributes
 ----------
Expand DownExpand Up@@ -95,7 +97,7 @@ class Group(MutableMapping):
 """

 def __init__(self, store, path=None, read_only=False, chunk_store=None,
 cache_attrs=True, synchronizer=None):
 cache_attrs=True, synchronizer=None, meta_array=None):
 self._store = store
 self._chunk_store = chunk_store
 self._path = normalize_storage_path(path)
Expand All@@ -105,6 +107,10 @@ def __init__(self, store, path=None, read_only=False, chunk_store=None,
 self._key_prefix = ''
 self._read_only = read_only
 self._synchronizer = synchronizer
 if meta_array is not None:
 self._meta_array = np.empty_like(meta_array)
 else:
 self._meta_array = np.empty(())

 # guard conditions
 if contains_array(store, path=self._path):
Expand DownExpand Up@@ -282,7 +288,7 @@ def typestr(o):

 def __getstate__(self):
 return (self._store, self._path, self._read_only, self._chunk_store,
 self.attrs.cache, self._synchronizer)
 self.attrs.cache, self._synchronizer, self._meta_array)

 def __setstate__(self, state):
 self.__init__(*state)
Expand DownExpand Up@@ -340,11 +346,13 @@ def __getitem__(self, item):
 if contains_array(self._store, path):
 return Array(self._store, read_only=self._read_only, path=path,
 chunk_store=self._chunk_store,
 synchronizer=self._synchronizer, cache_attrs=self.attrs.cache)
 synchronizer=self._synchronizer, cache_attrs=self.attrs.cache,
 meta_array=self._meta_array)
 elif contains_group(self._store, path):
 return Group(self._store, read_only=self._read_only, path=path,
 chunk_store=self._chunk_store, cache_attrs=self.attrs.cache,
 synchronizer=self._synchronizer)
 synchronizer=self._synchronizer,
 meta_array=self._meta_array)
 else:
 raise KeyError(item)

Expand DownExpand Up@@ -863,7 +871,8 @@ def _require_dataset_nosync(self, name, shape, dtype=None, exact=False,
 cache_attrs = kwargs.get('cache_attrs', self.attrs.cache)
 a = Array(self._store, path=path, read_only=self._read_only,
 chunk_store=self._chunk_store, synchronizer=synchronizer,
 cache_metadata=cache_metadata, cache_attrs=cache_attrs)
 cache_metadata=cache_metadata, cache_attrs=cache_attrs,
 meta_array=self._meta_array)
 shape = normalize_shape(shape)
 if shape != a.shape:
 raise TypeError('shape do not match existing array; expected {}, got {}'
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

Skip to content
WIP: Provide a meta array to change array type returned#501

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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.

 Sign up for GitHub

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privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
Sign in
to your account

 Closed

jakirkham
wants to merge
10
commits into

from

 Closed


WIP: Provide a meta array to change array type returned
#501
Show file tree
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Commits

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Select commit
Hold shift + click to select a range
3fed74c

Ensure contiguous data using `astype`


jakirkham Nov 15, 2019
9fe4add

Add changelog entry about ensure contiguous data


jakirkham Nov 15, 2019
4f72ce0

Accept a meta array in the Array constructor


jakirkham Nov 15, 2019
028b4b2

Use NumPy's `*_like` function to allocate arrays


jakirkham Nov 15, 2019
313c81b

Include `_meta_array` when pickling `Array`


jakirkham Nov 15, 2019
08f55b2

Workaround the absence of `flags` and `writeable`


jakirkham Nov 15, 2019
a82018f

Configure Groups to support `meta_array`


jakirkham Nov 15, 2019
fda8d19

Passthrough Group's `_meta_array`


jakirkham Nov 15, 2019
c43ec94

Include `_meta_array` when pickling `Group`


jakirkham Nov 15, 2019
ab2a732

Merge branch 'master' into use_array_like


joshmoore Feb 18, 2021

File filter

Filter by extension
Filter by extension
Conversations

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Jump to

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3 changes: 3 additions & 0 deletions
docs/release.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -124,6 +124,9 @@ Enhancements
* Ensure contiguous data using ``astype``.
 By :user:`John Kirkham <jakirkham>`; :issue:`513`.

* Ensure contiguous data using ``astype``.
 By :user:`John Kirkham <jakirkham>`; :issue:`513`.

* Refactor out ``_tofile``/``_fromfile`` from ``DirectoryStore``.
 By :user:`John Kirkham <jakirkham>`; :issue:`503`.

Expand Down

46 changes: 38 additions & 8 deletions
zarr/core.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -76,6 +76,9 @@ class Array:
 read and decompressed when possible.

 .. versionadded:: 2.7
 meta_array : array, optional
 An array instance to use for determining arrays to create and return
 to users.

 Attributes
 ----------
Expand DownExpand Up@@ -137,6 +140,7 @@ def __init__(
 cache_metadata=True,
 cache_attrs=True,
 partial_decompress=False,
 meta_array=None
 ):
 # N.B., expect at this point store is fully initialized with all
 # configuration metadata fully specified and normalized
Expand All@@ -148,6 +152,10 @@ def __init__(
 self._key_prefix = self._path + '/'
 else:
 self._key_prefix = ''
 if meta_array is not None:
 self._meta_array = np.empty_like(meta_array)
 else:
 self._meta_array = np.empty(())
 self._read_only = bool(read_only)
 self._synchronizer = synchronizer
 self._cache_metadata = cache_metadata
Expand DownExpand Up@@ -746,7 +754,7 @@ def _get_basic_selection_zd(self, selection, out=None, fields=None):

 except KeyError:
 # chunk not initialized
 chunk = np.zeros((), dtype=self._dtype)
 chunk = np.zeros_like(self._meta_array, shape=(), dtype=self._dtype)
 if self._fill_value is not None:
 chunk.fill(self._fill_value)

Expand DownExpand Up@@ -1050,7 +1058,8 @@ def _get_selection(self, indexer, out=None, fields=None):

 # setup output array
 if out is None:
 out = np.empty(out_shape, dtype=out_dtype, order=self._order)
 out = np.empty_like(self._meta_array, shape=out_shape,
 dtype=out_dtype, order=self._order)
 else:
 check_array_shape('out', out, out_shape)

Expand DownExpand Up@@ -1516,7 +1525,7 @@ def _set_basic_selection_zd(self, selection, value, fields=None):

 except KeyError:
 # chunk not initialized
 chunk = np.zeros((), dtype=self._dtype)
 chunk = np.zeros_like(self._meta_array, shape=(), dtype=self._dtype)
 if self._fill_value is not None:
 chunk.fill(self._fill_value)

Expand DownExpand Up@@ -1746,6 +1755,23 @@ def _chunk_getitem(self, chunk_coords, chunk_selection, out, out_selection,
 self._process_chunk(out, cdata, chunk_selection, drop_axes,
 out_is_ndarray, fields, out_selection)

 if (out_is_ndarray and
 not fields and
 is_contiguous_selection(out_selection) and
 is_total_slice(chunk_selection, self._chunks) and
 not self._filters and
 self._dtype != object):

 dest = out[out_selection]
 write_direct = (
 getattr(getattr(dest, "flags", None), "writeable", True) and (
 (self._order == 'C' and dest.flags.c_contiguous) or
 (self._order == 'F' and dest.flags.f_contiguous)
 )
 )

 if write_direct:

 def _chunk_getitems(self, lchunk_coords, lchunk_selection, out, lout_selection,
 drop_axes=None, fields=None):
 """As _chunk_getitem, but for lists of chunks
Expand DownExpand Up@@ -1848,7 +1874,8 @@ def _process_for_setitem(self, ckey, chunk_selection, value, fields=None):
 if is_scalar(value, self._dtype):

 # setup array filled with value
 chunk = np.empty(self._chunks, dtype=self._dtype, order=self._order)
 chunk = np.empty_like(self._meta_array, shape=self._chunks,
 dtype=self._dtype, order=self._order)
 chunk.fill(value)

 else:
Expand All@@ -1868,20 +1895,22 @@ def _process_for_setitem(self, ckey, chunk_selection, value, fields=None):

 # chunk not initialized
 if self._fill_value is not None:
 chunk = np.empty(self._chunks, dtype=self._dtype, order=self._order)
 chunk = np.empty_like(self._meta_array, shape=self._chunks,
 dtype=self._dtype, order=self._order)
 chunk.fill(self._fill_value)
 elif self._dtype == object:
 chunk = np.empty(self._chunks, dtype=self._dtype, order=self._order)
 else:
 # N.B., use zeros here so any region beyond the array has consistent
 # and compressible data
 chunk = np.zeros(self._chunks, dtype=self._dtype, order=self._order)
 chunk = np.zeros_like(self._meta_array, shape=self._chunks,
 dtype=self._dtype, order=self._order)

 else:

 # decode chunk
 chunk = self._decode_chunk(cdata)
 if not chunk.flags.writeable:
 if not getattr(getattr(chunk, "flags", None), "writeable", True):
 chunk = chunk.copy(order='K')

 # modify
Expand DownExpand Up@@ -2113,7 +2142,8 @@ def hexdigest(self, hashname="sha1"):

 def __getstate__(self):
 return (self._store, self._path, self._read_only, self._chunk_store,
 self._synchronizer, self._cache_metadata, self._attrs.cache)
 self._synchronizer, self._cache_metadata, self._attrs.cache,
 self._meta_array)

 def __setstate__(self, state):
 self.__init__(*state)
Expand Down

19 changes: 14 additions & 5 deletions
zarr/hierarchy.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -44,6 +44,8 @@ class Group(MutableMapping):
 to all attribute read operations.
 synchronizer : object, optional
 Array synchronizer.
 meta_array : array, optional
 An array to base allocations off of.

 Attributes
 ----------
Expand DownExpand Up@@ -95,7 +97,7 @@ class Group(MutableMapping):
 """

 def __init__(self, store, path=None, read_only=False, chunk_store=None,
 cache_attrs=True, synchronizer=None):
 cache_attrs=True, synchronizer=None, meta_array=None):
 self._store = store
 self._chunk_store = chunk_store
 self._path = normalize_storage_path(path)
Expand All@@ -105,6 +107,10 @@ def __init__(self, store, path=None, read_only=False, chunk_store=None,
 self._key_prefix = ''
 self._read_only = read_only
 self._synchronizer = synchronizer
 if meta_array is not None:
 self._meta_array = np.empty_like(meta_array)
 else:
 self._meta_array = np.empty(())

 # guard conditions
 if contains_array(store, path=self._path):
Expand DownExpand Up@@ -282,7 +288,7 @@ def typestr(o):

 def __getstate__(self):
 return (self._store, self._path, self._read_only, self._chunk_store,
 self.attrs.cache, self._synchronizer)
 self.attrs.cache, self._synchronizer, self._meta_array)

 def __setstate__(self, state):
 self.__init__(*state)
Expand DownExpand Up@@ -340,11 +346,13 @@ def __getitem__(self, item):
 if contains_array(self._store, path):
 return Array(self._store, read_only=self._read_only, path=path,
 chunk_store=self._chunk_store,
 synchronizer=self._synchronizer, cache_attrs=self.attrs.cache)
 synchronizer=self._synchronizer, cache_attrs=self.attrs.cache,
 meta_array=self._meta_array)
 elif contains_group(self._store, path):
 return Group(self._store, read_only=self._read_only, path=path,
 chunk_store=self._chunk_store, cache_attrs=self.attrs.cache,
 synchronizer=self._synchronizer)
 synchronizer=self._synchronizer,
 meta_array=self._meta_array)
 else:
 raise KeyError(item)

Expand DownExpand Up@@ -863,7 +871,8 @@ def _require_dataset_nosync(self, name, shape, dtype=None, exact=False,
 cache_attrs = kwargs.get('cache_attrs', self.attrs.cache)
 a = Array(self._store, path=path, read_only=self._read_only,
 chunk_store=self._chunk_store, synchronizer=synchronizer,
 cache_metadata=cache_metadata, cache_attrs=cache_attrs)
 cache_metadata=cache_metadata, cache_attrs=cache_attrs,
 meta_array=self._meta_array)
 shape = normalize_shape(shape)
 if shape != a.shape:
 raise TypeError('shape do not match existing array; expected {}, got {}'
Expand Down

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

Skip to content
WIP: Provide a meta array to change array type returned#501

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jakirkham
wants to merge
10
commits into

from

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WIP: Provide a meta array to change array type returned
#501
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3fed74c

Ensure contiguous data using `astype`


jakirkham Nov 15, 2019
9fe4add

Add changelog entry about ensure contiguous data


jakirkham Nov 15, 2019
4f72ce0

Accept a meta array in the Array constructor


jakirkham Nov 15, 2019
028b4b2

Use NumPy's `*_like` function to allocate arrays


jakirkham Nov 15, 2019
313c81b

Include `_meta_array` when pickling `Array`


jakirkham Nov 15, 2019
08f55b2

Workaround the absence of `flags` and `writeable`


jakirkham Nov 15, 2019
a82018f

Configure Groups to support `meta_array`


jakirkham Nov 15, 2019
fda8d19

Passthrough Group's `_meta_array`


jakirkham Nov 15, 2019
c43ec94

Include `_meta_array` when pickling `Group`


jakirkham Nov 15, 2019
ab2a732

Merge branch 'master' into use_array_like


joshmoore Feb 18, 2021

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3 changes: 3 additions & 0 deletions
docs/release.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -124,6 +124,9 @@ Enhancements
* Ensure contiguous data using ``astype``.
 By :user:`John Kirkham <jakirkham>`; :issue:`513`.

* Ensure contiguous data using ``astype``.
 By :user:`John Kirkham <jakirkham>`; :issue:`513`.

* Refactor out ``_tofile``/``_fromfile`` from ``DirectoryStore``.
 By :user:`John Kirkham <jakirkham>`; :issue:`503`.

Expand Down

46 changes: 38 additions & 8 deletions
zarr/core.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -76,6 +76,9 @@ class Array:
 read and decompressed when possible.

 .. versionadded:: 2.7
 meta_array : array, optional
 An array instance to use for determining arrays to create and return
 to users.

 Attributes
 ----------
Expand DownExpand Up@@ -137,6 +140,7 @@ def __init__(
 cache_metadata=True,
 cache_attrs=True,
 partial_decompress=False,
 meta_array=None
 ):
 # N.B., expect at this point store is fully initialized with all
 # configuration metadata fully specified and normalized
Expand All@@ -148,6 +152,10 @@ def __init__(
 self._key_prefix = self._path + '/'
 else:
 self._key_prefix = ''
 if meta_array is not None:
 self._meta_array = np.empty_like(meta_array)
 else:
 self._meta_array = np.empty(())
 self._read_only = bool(read_only)
 self._synchronizer = synchronizer
 self._cache_metadata = cache_metadata
Expand DownExpand Up@@ -746,7 +754,7 @@ def _get_basic_selection_zd(self, selection, out=None, fields=None):

 except KeyError:
 # chunk not initialized
 chunk = np.zeros((), dtype=self._dtype)
 chunk = np.zeros_like(self._meta_array, shape=(), dtype=self._dtype)
 if self._fill_value is not None:
 chunk.fill(self._fill_value)

Expand DownExpand Up@@ -1050,7 +1058,8 @@ def _get_selection(self, indexer, out=None, fields=None):

 # setup output array
 if out is None:
 out = np.empty(out_shape, dtype=out_dtype, order=self._order)
 out = np.empty_like(self._meta_array, shape=out_shape,
 dtype=out_dtype, order=self._order)
 else:
 check_array_shape('out', out, out_shape)

Expand DownExpand Up@@ -1516,7 +1525,7 @@ def _set_basic_selection_zd(self, selection, value, fields=None):

 except KeyError:
 # chunk not initialized
 chunk = np.zeros((), dtype=self._dtype)
 chunk = np.zeros_like(self._meta_array, shape=(), dtype=self._dtype)
 if self._fill_value is not None:
 chunk.fill(self._fill_value)

Expand DownExpand Up@@ -1746,6 +1755,23 @@ def _chunk_getitem(self, chunk_coords, chunk_selection, out, out_selection,
 self._process_chunk(out, cdata, chunk_selection, drop_axes,
 out_is_ndarray, fields, out_selection)

 if (out_is_ndarray and
 not fields and
 is_contiguous_selection(out_selection) and
 is_total_slice(chunk_selection, self._chunks) and
 not self._filters and
 self._dtype != object):

 dest = out[out_selection]
 write_direct = (
 getattr(getattr(dest, "flags", None), "writeable", True) and (
 (self._order == 'C' and dest.flags.c_contiguous) or
 (self._order == 'F' and dest.flags.f_contiguous)
 )
 )

 if write_direct:

 def _chunk_getitems(self, lchunk_coords, lchunk_selection, out, lout_selection,
 drop_axes=None, fields=None):
 """As _chunk_getitem, but for lists of chunks
Expand DownExpand Up@@ -1848,7 +1874,8 @@ def _process_for_setitem(self, ckey, chunk_selection, value, fields=None):
 if is_scalar(value, self._dtype):

 # setup array filled with value
 chunk = np.empty(self._chunks, dtype=self._dtype, order=self._order)
 chunk = np.empty_like(self._meta_array, shape=self._chunks,
 dtype=self._dtype, order=self._order)
 chunk.fill(value)

 else:
Expand All@@ -1868,20 +1895,22 @@ def _process_for_setitem(self, ckey, chunk_selection, value, fields=None):

 # chunk not initialized
 if self._fill_value is not None:
 chunk = np.empty(self._chunks, dtype=self._dtype, order=self._order)
 chunk = np.empty_like(self._meta_array, shape=self._chunks,
 dtype=self._dtype, order=self._order)
 chunk.fill(self._fill_value)
 elif self._dtype == object:
 chunk = np.empty(self._chunks, dtype=self._dtype, order=self._order)
 else:
 # N.B., use zeros here so any region beyond the array has consistent
 # and compressible data
 chunk = np.zeros(self._chunks, dtype=self._dtype, order=self._order)
 chunk = np.zeros_like(self._meta_array, shape=self._chunks,
 dtype=self._dtype, order=self._order)

 else:

 # decode chunk
 chunk = self._decode_chunk(cdata)
 if not chunk.flags.writeable:
 if not getattr(getattr(chunk, "flags", None), "writeable", True):
 chunk = chunk.copy(order='K')

 # modify
Expand DownExpand Up@@ -2113,7 +2142,8 @@ def hexdigest(self, hashname="sha1"):

 def __getstate__(self):
 return (self._store, self._path, self._read_only, self._chunk_store,
 self._synchronizer, self._cache_metadata, self._attrs.cache)
 self._synchronizer, self._cache_metadata, self._attrs.cache,
 self._meta_array)

 def __setstate__(self, state):
 self.__init__(*state)
Expand Down

19 changes: 14 additions & 5 deletions
zarr/hierarchy.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -44,6 +44,8 @@ class Group(MutableMapping):
 to all attribute read operations.
 synchronizer : object, optional
 Array synchronizer.
 meta_array : array, optional
 An array to base allocations off of.

 Attributes
 ----------
Expand DownExpand Up@@ -95,7 +97,7 @@ class Group(MutableMapping):
 """

 def __init__(self, store, path=None, read_only=False, chunk_store=None,
 cache_attrs=True, synchronizer=None):
 cache_attrs=True, synchronizer=None, meta_array=None):
 self._store = store
 self._chunk_store = chunk_store
 self._path = normalize_storage_path(path)
Expand All@@ -105,6 +107,10 @@ def __init__(self, store, path=None, read_only=False, chunk_store=None,
 self._key_prefix = ''
 self._read_only = read_only
 self._synchronizer = synchronizer
 if meta_array is not None:
 self._meta_array = np.empty_like(meta_array)
 else:
 self._meta_array = np.empty(())

 # guard conditions
 if contains_array(store, path=self._path):
Expand DownExpand Up@@ -282,7 +288,7 @@ def typestr(o):

 def __getstate__(self):
 return (self._store, self._path, self._read_only, self._chunk_store,
 self.attrs.cache, self._synchronizer)
 self.attrs.cache, self._synchronizer, self._meta_array)

 def __setstate__(self, state):
 self.__init__(*state)
Expand DownExpand Up@@ -340,11 +346,13 @@ def __getitem__(self, item):
 if contains_array(self._store, path):
 return Array(self._store, read_only=self._read_only, path=path,
 chunk_store=self._chunk_store,
 synchronizer=self._synchronizer, cache_attrs=self.attrs.cache)
 synchronizer=self._synchronizer, cache_attrs=self.attrs.cache,
 meta_array=self._meta_array)
 elif contains_group(self._store, path):
 return Group(self._store, read_only=self._read_only, path=path,
 chunk_store=self._chunk_store, cache_attrs=self.attrs.cache,
 synchronizer=self._synchronizer)
 synchronizer=self._synchronizer,
 meta_array=self._meta_array)
 else:
 raise KeyError(item)

Expand DownExpand Up@@ -863,7 +871,8 @@ def _require_dataset_nosync(self, name, shape, dtype=None, exact=False,
 cache_attrs = kwargs.get('cache_attrs', self.attrs.cache)
 a = Array(self._store, path=path, read_only=self._read_only,
 chunk_store=self._chunk_store, synchronizer=synchronizer,
 cache_metadata=cache_metadata, cache_attrs=cache_attrs)
 cache_metadata=cache_metadata, cache_attrs=cache_attrs,
 meta_array=self._meta_array)
 shape = normalize_shape(shape)
 if shape != a.shape:
 raise TypeError('shape do not match existing array; expected {}, got {}'
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
WIP: Provide a meta array to change array type returned#501

New issue

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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privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
Sign in
to your account

 Closed

jakirkham
wants to merge
10
commits into

from

 Closed


WIP: Provide a meta array to change array type returned
#501
Show file tree
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 Changes from all commits
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3fed74c

Ensure contiguous data using `astype`


jakirkham Nov 15, 2019
9fe4add

Add changelog entry about ensure contiguous data


jakirkham Nov 15, 2019
4f72ce0

Accept a meta array in the Array constructor


jakirkham Nov 15, 2019
028b4b2

Use NumPy's `*_like` function to allocate arrays


jakirkham Nov 15, 2019
313c81b

Include `_meta_array` when pickling `Array`


jakirkham Nov 15, 2019
08f55b2

Workaround the absence of `flags` and `writeable`


jakirkham Nov 15, 2019
a82018f

Configure Groups to support `meta_array`


jakirkham Nov 15, 2019
fda8d19

Passthrough Group's `_meta_array`


jakirkham Nov 15, 2019
c43ec94

Include `_meta_array` when pickling `Group`


jakirkham Nov 15, 2019
ab2a732

Merge branch 'master' into use_array_like


joshmoore Feb 18, 2021

File filter

Filter by extension
Filter by extension
Conversations

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3 changes: 3 additions & 0 deletions
docs/release.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -124,6 +124,9 @@ Enhancements
* Ensure contiguous data using ``astype``.
 By :user:`John Kirkham <jakirkham>`; :issue:`513`.

* Ensure contiguous data using ``astype``.
 By :user:`John Kirkham <jakirkham>`; :issue:`513`.

* Refactor out ``_tofile``/``_fromfile`` from ``DirectoryStore``.
 By :user:`John Kirkham <jakirkham>`; :issue:`503`.

Expand Down

46 changes: 38 additions & 8 deletions
zarr/core.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -76,6 +76,9 @@ class Array:
 read and decompressed when possible.

 .. versionadded:: 2.7
 meta_array : array, optional
 An array instance to use for determining arrays to create and return
 to users.

 Attributes
 ----------
Expand DownExpand Up@@ -137,6 +140,7 @@ def __init__(
 cache_metadata=True,
 cache_attrs=True,
 partial_decompress=False,
 meta_array=None
 ):
 # N.B., expect at this point store is fully initialized with all
 # configuration metadata fully specified and normalized
Expand All@@ -148,6 +152,10 @@ def __init__(
 self._key_prefix = self._path + '/'
 else:
 self._key_prefix = ''
 if meta_array is not None:
 self._meta_array = np.empty_like(meta_array)
 else:
 self._meta_array = np.empty(())
 self._read_only = bool(read_only)
 self._synchronizer = synchronizer
 self._cache_metadata = cache_metadata
Expand DownExpand Up@@ -746,7 +754,7 @@ def _get_basic_selection_zd(self, selection, out=None, fields=None):

 except KeyError:
 # chunk not initialized
 chunk = np.zeros((), dtype=self._dtype)
 chunk = np.zeros_like(self._meta_array, shape=(), dtype=self._dtype)
 if self._fill_value is not None:
 chunk.fill(self._fill_value)

Expand DownExpand Up@@ -1050,7 +1058,8 @@ def _get_selection(self, indexer, out=None, fields=None):

 # setup output array
 if out is None:
 out = np.empty(out_shape, dtype=out_dtype, order=self._order)
 out = np.empty_like(self._meta_array, shape=out_shape,
 dtype=out_dtype, order=self._order)
 else:
 check_array_shape('out', out, out_shape)

Expand DownExpand Up@@ -1516,7 +1525,7 @@ def _set_basic_selection_zd(self, selection, value, fields=None):

 except KeyError:
 # chunk not initialized
 chunk = np.zeros((), dtype=self._dtype)
 chunk = np.zeros_like(self._meta_array, shape=(), dtype=self._dtype)
 if self._fill_value is not None:
 chunk.fill(self._fill_value)

Expand DownExpand Up@@ -1746,6 +1755,23 @@ def _chunk_getitem(self, chunk_coords, chunk_selection, out, out_selection,
 self._process_chunk(out, cdata, chunk_selection, drop_axes,
 out_is_ndarray, fields, out_selection)

 if (out_is_ndarray and
 not fields and
 is_contiguous_selection(out_selection) and
 is_total_slice(chunk_selection, self._chunks) and
 not self._filters and
 self._dtype != object):

 dest = out[out_selection]
 write_direct = (
 getattr(getattr(dest, "flags", None), "writeable", True) and (
 (self._order == 'C' and dest.flags.c_contiguous) or
 (self._order == 'F' and dest.flags.f_contiguous)
 )
 )

 if write_direct:

 def _chunk_getitems(self, lchunk_coords, lchunk_selection, out, lout_selection,
 drop_axes=None, fields=None):
 """As _chunk_getitem, but for lists of chunks
Expand DownExpand Up@@ -1848,7 +1874,8 @@ def _process_for_setitem(self, ckey, chunk_selection, value, fields=None):
 if is_scalar(value, self._dtype):

 # setup array filled with value
 chunk = np.empty(self._chunks, dtype=self._dtype, order=self._order)
 chunk = np.empty_like(self._meta_array, shape=self._chunks,
 dtype=self._dtype, order=self._order)
 chunk.fill(value)

 else:
Expand All@@ -1868,20 +1895,22 @@ def _process_for_setitem(self, ckey, chunk_selection, value, fields=None):

 # chunk not initialized
 if self._fill_value is not None:
 chunk = np.empty(self._chunks, dtype=self._dtype, order=self._order)
 chunk = np.empty_like(self._meta_array, shape=self._chunks,
 dtype=self._dtype, order=self._order)
 chunk.fill(self._fill_value)
 elif self._dtype == object:
 chunk = np.empty(self._chunks, dtype=self._dtype, order=self._order)
 else:
 # N.B., use zeros here so any region beyond the array has consistent
 # and compressible data
 chunk = np.zeros(self._chunks, dtype=self._dtype, order=self._order)
 chunk = np.zeros_like(self._meta_array, shape=self._chunks,
 dtype=self._dtype, order=self._order)

 else:

 # decode chunk
 chunk = self._decode_chunk(cdata)
 if not chunk.flags.writeable:
 if not getattr(getattr(chunk, "flags", None), "writeable", True):
 chunk = chunk.copy(order='K')

 # modify
Expand DownExpand Up@@ -2113,7 +2142,8 @@ def hexdigest(self, hashname="sha1"):

 def __getstate__(self):
 return (self._store, self._path, self._read_only, self._chunk_store,
 self._synchronizer, self._cache_metadata, self._attrs.cache)
 self._synchronizer, self._cache_metadata, self._attrs.cache,
 self._meta_array)

 def __setstate__(self, state):
 self.__init__(*state)
Expand Down

19 changes: 14 additions & 5 deletions
zarr/hierarchy.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -44,6 +44,8 @@ class Group(MutableMapping):
 to all attribute read operations.
 synchronizer : object, optional
 Array synchronizer.
 meta_array : array, optional
 An array to base allocations off of.

 Attributes
 ----------
Expand DownExpand Up@@ -95,7 +97,7 @@ class Group(MutableMapping):
 """

 def __init__(self, store, path=None, read_only=False, chunk_store=None,
 cache_attrs=True, synchronizer=None):
 cache_attrs=True, synchronizer=None, meta_array=None):
 self._store = store
 self._chunk_store = chunk_store
 self._path = normalize_storage_path(path)
Expand All@@ -105,6 +107,10 @@ def __init__(self, store, path=None, read_only=False, chunk_store=None,
 self._key_prefix = ''
 self._read_only = read_only
 self._synchronizer = synchronizer
 if meta_array is not None:
 self._meta_array = np.empty_like(meta_array)
 else:
 self._meta_array = np.empty(())

 # guard conditions
 if contains_array(store, path=self._path):
Expand DownExpand Up@@ -282,7 +288,7 @@ def typestr(o):

 def __getstate__(self):
 return (self._store, self._path, self._read_only, self._chunk_store,
 self.attrs.cache, self._synchronizer)
 self.attrs.cache, self._synchronizer, self._meta_array)

 def __setstate__(self, state):
 self.__init__(*state)
Expand DownExpand Up@@ -340,11 +346,13 @@ def __getitem__(self, item):
 if contains_array(self._store, path):
 return Array(self._store, read_only=self._read_only, path=path,
 chunk_store=self._chunk_store,
 synchronizer=self._synchronizer, cache_attrs=self.attrs.cache)
 synchronizer=self._synchronizer, cache_attrs=self.attrs.cache,
 meta_array=self._meta_array)
 elif contains_group(self._store, path):
 return Group(self._store, read_only=self._read_only, path=path,
 chunk_store=self._chunk_store, cache_attrs=self.attrs.cache,
 synchronizer=self._synchronizer)
 synchronizer=self._synchronizer,
 meta_array=self._meta_array)
 else:
 raise KeyError(item)

Expand DownExpand Up@@ -863,7 +871,8 @@ def _require_dataset_nosync(self, name, shape, dtype=None, exact=False,
 cache_attrs = kwargs.get('cache_attrs', self.attrs.cache)
 a = Array(self._store, path=path, read_only=self._read_only,
 chunk_store=self._chunk_store, synchronizer=synchronizer,
 cache_metadata=cache_metadata, cache_attrs=cache_attrs)
 cache_metadata=cache_metadata, cache_attrs=cache_attrs,
 meta_array=self._meta_array)
 shape = normalize_shape(shape)
 if shape != a.shape:
 raise TypeError('shape do not match existing array; expected {}, got {}'
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

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WIP: Provide a meta array to change array type returned
#501
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3fed74c

Ensure contiguous data using `astype`


jakirkham Nov 15, 2019
9fe4add

Add changelog entry about ensure contiguous data


jakirkham Nov 15, 2019
4f72ce0

Accept a meta array in the Array constructor


jakirkham Nov 15, 2019
028b4b2

Use NumPy's `*_like` function to allocate arrays


jakirkham Nov 15, 2019
313c81b

Include `_meta_array` when pickling `Array`


jakirkham Nov 15, 2019
08f55b2

Workaround the absence of `flags` and `writeable`


jakirkham Nov 15, 2019
a82018f

Configure Groups to support `meta_array`


jakirkham Nov 15, 2019
fda8d19

Passthrough Group's `_meta_array`


jakirkham Nov 15, 2019
c43ec94

Include `_meta_array` when pickling `Group`


jakirkham Nov 15, 2019
ab2a732

Merge branch 'master' into use_array_like


joshmoore Feb 18, 2021

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3 changes: 3 additions & 0 deletions
docs/release.rst

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -124,6 +124,9 @@ Enhancements
* Ensure contiguous data using ``astype``.
 By :user:`John Kirkham <jakirkham>`; :issue:`513`.

* Ensure contiguous data using ``astype``.
 By :user:`John Kirkham <jakirkham>`; :issue:`513`.

* Refactor out ``_tofile``/``_fromfile`` from ``DirectoryStore``.
 By :user:`John Kirkham <jakirkham>`; :issue:`503`.

Expand Down

46 changes: 38 additions & 8 deletions
zarr/core.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -76,6 +76,9 @@ class Array:
 read and decompressed when possible.

 .. versionadded:: 2.7
 meta_array : array, optional
 An array instance to use for determining arrays to create and return
 to users.

 Attributes
 ----------
Expand DownExpand Up@@ -137,6 +140,7 @@ def __init__(
 cache_metadata=True,
 cache_attrs=True,
 partial_decompress=False,
 meta_array=None
 ):
 # N.B., expect at this point store is fully initialized with all
 # configuration metadata fully specified and normalized
Expand All@@ -148,6 +152,10 @@ def __init__(
 self._key_prefix = self._path + '/'
 else:
 self._key_prefix = ''
 if meta_array is not None:
 self._meta_array = np.empty_like(meta_array)
 else:
 self._meta_array = np.empty(())
 self._read_only = bool(read_only)
 self._synchronizer = synchronizer
 self._cache_metadata = cache_metadata
Expand DownExpand Up@@ -746,7 +754,7 @@ def _get_basic_selection_zd(self, selection, out=None, fields=None):

 except KeyError:
 # chunk not initialized
 chunk = np.zeros((), dtype=self._dtype)
 chunk = np.zeros_like(self._meta_array, shape=(), dtype=self._dtype)
 if self._fill_value is not None:
 chunk.fill(self._fill_value)

Expand DownExpand Up@@ -1050,7 +1058,8 @@ def _get_selection(self, indexer, out=None, fields=None):

 # setup output array
 if out is None:
 out = np.empty(out_shape, dtype=out_dtype, order=self._order)
 out = np.empty_like(self._meta_array, shape=out_shape,
 dtype=out_dtype, order=self._order)
 else:
 check_array_shape('out', out, out_shape)

Expand DownExpand Up@@ -1516,7 +1525,7 @@ def _set_basic_selection_zd(self, selection, value, fields=None):

 except KeyError:
 # chunk not initialized
 chunk = np.zeros((), dtype=self._dtype)
 chunk = np.zeros_like(self._meta_array, shape=(), dtype=self._dtype)
 if self._fill_value is not None:
 chunk.fill(self._fill_value)

Expand DownExpand Up@@ -1746,6 +1755,23 @@ def _chunk_getitem(self, chunk_coords, chunk_selection, out, out_selection,
 self._process_chunk(out, cdata, chunk_selection, drop_axes,
 out_is_ndarray, fields, out_selection)

 if (out_is_ndarray and
 not fields and
 is_contiguous_selection(out_selection) and
 is_total_slice(chunk_selection, self._chunks) and
 not self._filters and
 self._dtype != object):

 dest = out[out_selection]
 write_direct = (
 getattr(getattr(dest, "flags", None), "writeable", True) and (
 (self._order == 'C' and dest.flags.c_contiguous) or
 (self._order == 'F' and dest.flags.f_contiguous)
 )
 )

 if write_direct:

 def _chunk_getitems(self, lchunk_coords, lchunk_selection, out, lout_selection,
 drop_axes=None, fields=None):
 """As _chunk_getitem, but for lists of chunks
Expand DownExpand Up@@ -1848,7 +1874,8 @@ def _process_for_setitem(self, ckey, chunk_selection, value, fields=None):
 if is_scalar(value, self._dtype):

 # setup array filled with value
 chunk = np.empty(self._chunks, dtype=self._dtype, order=self._order)
 chunk = np.empty_like(self._meta_array, shape=self._chunks,
 dtype=self._dtype, order=self._order)
 chunk.fill(value)

 else:
Expand All@@ -1868,20 +1895,22 @@ def _process_for_setitem(self, ckey, chunk_selection, value, fields=None):

 # chunk not initialized
 if self._fill_value is not None:
 chunk = np.empty(self._chunks, dtype=self._dtype, order=self._order)
 chunk = np.empty_like(self._meta_array, shape=self._chunks,
 dtype=self._dtype, order=self._order)
 chunk.fill(self._fill_value)
 elif self._dtype == object:
 chunk = np.empty(self._chunks, dtype=self._dtype, order=self._order)
 else:
 # N.B., use zeros here so any region beyond the array has consistent
 # and compressible data
 chunk = np.zeros(self._chunks, dtype=self._dtype, order=self._order)
 chunk = np.zeros_like(self._meta_array, shape=self._chunks,
 dtype=self._dtype, order=self._order)

 else:

 # decode chunk
 chunk = self._decode_chunk(cdata)
 if not chunk.flags.writeable:
 if not getattr(getattr(chunk, "flags", None), "writeable", True):
 chunk = chunk.copy(order='K')

 # modify
Expand DownExpand Up@@ -2113,7 +2142,8 @@ def hexdigest(self, hashname="sha1"):

 def __getstate__(self):
 return (self._store, self._path, self._read_only, self._chunk_store,
 self._synchronizer, self._cache_metadata, self._attrs.cache)
 self._synchronizer, self._cache_metadata, self._attrs.cache,
 self._meta_array)

 def __setstate__(self, state):
 self.__init__(*state)
Expand Down

19 changes: 14 additions & 5 deletions
zarr/hierarchy.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -44,6 +44,8 @@ class Group(MutableMapping):
 to all attribute read operations.
 synchronizer : object, optional
 Array synchronizer.
 meta_array : array, optional
 An array to base allocations off of.

 Attributes
 ----------
Expand DownExpand Up@@ -95,7 +97,7 @@ class Group(MutableMapping):
 """

 def __init__(self, store, path=None, read_only=False, chunk_store=None,
 cache_attrs=True, synchronizer=None):
 cache_attrs=True, synchronizer=None, meta_array=None):
 self._store = store
 self._chunk_store = chunk_store
 self._path = normalize_storage_path(path)
Expand All@@ -105,6 +107,10 @@ def __init__(self, store, path=None, read_only=False, chunk_store=None,
 self._key_prefix = ''
 self._read_only = read_only
 self._synchronizer = synchronizer
 if meta_array is not None:
 self._meta_array = np.empty_like(meta_array)
 else:
 self._meta_array = np.empty(())

 # guard conditions
 if contains_array(store, path=self._path):
Expand DownExpand Up@@ -282,7 +288,7 @@ def typestr(o):

 def __getstate__(self):
 return (self._store, self._path, self._read_only, self._chunk_store,
 self.attrs.cache, self._synchronizer)
 self.attrs.cache, self._synchronizer, self._meta_array)

 def __setstate__(self, state):
 self.__init__(*state)
Expand DownExpand Up@@ -340,11 +346,13 @@ def __getitem__(self, item):
 if contains_array(self._store, path):
 return Array(self._store, read_only=self._read_only, path=path,
 chunk_store=self._chunk_store,
 synchronizer=self._synchronizer, cache_attrs=self.attrs.cache)
 synchronizer=self._synchronizer, cache_attrs=self.attrs.cache,
 meta_array=self._meta_array)
 elif contains_group(self._store, path):
 return Group(self._store, read_only=self._read_only, path=path,
 chunk_store=self._chunk_store, cache_attrs=self.attrs.cache,
 synchronizer=self._synchronizer)
 synchronizer=self._synchronizer,
 meta_array=self._meta_array)
 else:
 raise KeyError(item)

Expand DownExpand Up@@ -863,7 +871,8 @@ def _require_dataset_nosync(self, name, shape, dtype=None, exact=False,
 cache_attrs = kwargs.get('cache_attrs', self.attrs.cache)
 a = Array(self._store, path=path, read_only=self._read_only,
 chunk_store=self._chunk_store, synchronizer=synchronizer,
 cache_metadata=cache_metadata, cache_attrs=cache_attrs)
 cache_metadata=cache_metadata, cache_attrs=cache_attrs,
 meta_array=self._meta_array)
 shape = normalize_shape(shape)
 if shape != a.shape:
 raise TypeError('shape do not match existing array; expected {}, got {}'
Expand Down