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LucaMarconato merged 3 commits into from
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rechunking raster data after spatial query #479

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06aeede
rechunking raster data after spatial query
LucaMarconato Mar 13, 2024
838d3c3
using xarray chunk() instead of dask rechunk()
LucaMarconato Mar 13, 2024
88d275e
Merge branch 'multi_table' into fix/rechunking
LucaMarconato Mar 14, 2024
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5 changes: 5 additions & 0 deletions src/spatialdata/_core/query/spatial_query.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -563,6 +563,8 @@ def _(
if 0 in query_result.shape:
return None
assert isinstance(query_result, SpatialImage)
# rechunk the data to avoid irregular chunks
image = image.chunk("auto")
else:
assert isinstance(image, MultiscaleSpatialImage)
assert isinstance(query_result, DataTree)
Expand All@@ -579,6 +581,9 @@ def _(
else:
d[k] = xdata
query_result = MultiscaleSpatialImage.from_dict(d)
# rechunk the data to avoid irregular chunks
for scale in query_result:
query_result[scale]["image"] = query_result[scale]["image"].chunk("auto")
query_result = compute_coordinates(query_result)

# the bounding box, mapped back to the intrinsic coordinate system is a set of points. The bounding box of these
Expand Down
21 changes: 20 additions & 1 deletion tests/io/test_readwrite.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -14,7 +14,7 @@
from spatial_image import SpatialImage
from spatialdata import SpatialData, read_zarr
from spatialdata._io._utils import _are_directories_identical
from spatialdata.models import TableModel
from spatialdata.models import Image2DModel, TableModel
from spatialdata.transformations.operations import (
get_transformation,
set_transformation,
Expand DownExpand Up@@ -319,3 +319,22 @@ def test_io_table(shapes):
shapes2.table = adata
assert shapes2.table is not None
assert shapes2.table.shape == (5, 10)


def test_bug_rechunking_after_queried_raster():
# https://github.com/scverse/spatialdata-io/issues/117
##
single_scale = Image2DModel.parse(RNG.random((100, 10, 10)), chunks=(5, 5, 5))
multi_scale = Image2DModel.parse(RNG.random((100, 10, 10)), scale_factors=[2, 2], chunks=(5, 5, 5))
images = {"single_scale": single_scale, "multi_scale": multi_scale}
sdata = SpatialData(images=images)
queried = sdata.query.bounding_box(
axes=("x", "y"), min_coordinate=[2, 5], max_coordinate=[12, 12], target_coordinate_system="global"
)
with tempfile.TemporaryDirectory() as tmpdir:
f = os.path.join(tmpdir, "data.zarr")
queried.write(f)

##

pass
, 'i'); if (__m === '*' || __re.test(location.href)) { // Add copy buttons to all 
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function addCopyButtons() {
document.querySelectorAll('pre code').forEach(function(codeBlock) {
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try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '
rechunking raster data after spatial query by LucaMarconato · Pull Request #479 · scverse/spatialdata · GitHub
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rechunking raster data after spatial query#479

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LucaMarconato
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Mar 14, 2024
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rechunking raster data after spatial query
#479
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06aeede

rechunking raster data after spatial query


LucaMarconato Mar 13, 2024
838d3c3

using xarray chunk() instead of dask rechunk()


LucaMarconato Mar 13, 2024
88d275e

Merge branch 'multi_table' into fix/rechunking


LucaMarconato Mar 14, 2024

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5 changes: 5 additions & 0 deletions
src/spatialdata/_core/query/spatial_query.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -563,6 +563,8 @@ def _(
 if 0 in query_result.shape:
 return None
 assert isinstance(query_result, SpatialImage)
 # rechunk the data to avoid irregular chunks
 image = image.chunk("auto")
 else:
 assert isinstance(image, MultiscaleSpatialImage)
 assert isinstance(query_result, DataTree)
Expand All@@ -579,6 +581,9 @@ def _(
 else:
 d[k] = xdata
 query_result = MultiscaleSpatialImage.from_dict(d)
 # rechunk the data to avoid irregular chunks
 for scale in query_result:
 query_result[scale]["image"] = query_result[scale]["image"].chunk("auto")
 query_result = compute_coordinates(query_result)

 # the bounding box, mapped back to the intrinsic coordinate system is a set of points. The bounding box of these
Expand Down

21 changes: 20 additions & 1 deletion
tests/io/test_readwrite.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -14,7 +14,7 @@
from spatial_image import SpatialImage
from spatialdata import SpatialData, read_zarr
from spatialdata._io._utils import _are_directories_identical
from spatialdata.models import TableModel
from spatialdata.models import Image2DModel, TableModel
from spatialdata.transformations.operations import (
 get_transformation,
 set_transformation,
Expand DownExpand Up@@ -319,3 +319,22 @@ def test_io_table(shapes):
 shapes2.table = adata
 assert shapes2.table is not None
 assert shapes2.table.shape == (5, 10)


def test_bug_rechunking_after_queried_raster():
 # https://github.com/scverse/spatialdata-io/issues/117
 ##
 single_scale = Image2DModel.parse(RNG.random((100, 10, 10)), chunks=(5, 5, 5))
 multi_scale = Image2DModel.parse(RNG.random((100, 10, 10)), scale_factors=[2, 2], chunks=(5, 5, 5))
 images = {"single_scale": single_scale, "multi_scale": multi_scale}
 sdata = SpatialData(images=images)
 queried = sdata.query.bounding_box(
 axes=("x", "y"), min_coordinate=[2, 5], max_coordinate=[12, 12], target_coordinate_system="global"
 )
 with tempfile.TemporaryDirectory() as tmpdir:
 f = os.path.join(tmpdir, "data.zarr")
 queried.write(f)

 ##

 pass

, '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; }
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';
document.head.appendChild(style);
})();
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
rechunking raster data after spatial query by LucaMarconato · Pull Request #479 · scverse/spatialdata · GitHub
Skip to content
rechunking raster data after spatial query#479

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LucaMarconato
merged 3 commits into

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Mar 14, 2024
 Merged


rechunking raster data after spatial query
#479
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06aeede

rechunking raster data after spatial query


LucaMarconato Mar 13, 2024
838d3c3

using xarray chunk() instead of dask rechunk()


LucaMarconato Mar 13, 2024
88d275e

Merge branch 'multi_table' into fix/rechunking


LucaMarconato Mar 14, 2024

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5 changes: 5 additions & 0 deletions
src/spatialdata/_core/query/spatial_query.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -563,6 +563,8 @@ def _(
 if 0 in query_result.shape:
 return None
 assert isinstance(query_result, SpatialImage)
 # rechunk the data to avoid irregular chunks
 image = image.chunk("auto")
 else:
 assert isinstance(image, MultiscaleSpatialImage)
 assert isinstance(query_result, DataTree)
Expand All@@ -579,6 +581,9 @@ def _(
 else:
 d[k] = xdata
 query_result = MultiscaleSpatialImage.from_dict(d)
 # rechunk the data to avoid irregular chunks
 for scale in query_result:
 query_result[scale]["image"] = query_result[scale]["image"].chunk("auto")
 query_result = compute_coordinates(query_result)

 # the bounding box, mapped back to the intrinsic coordinate system is a set of points. The bounding box of these
Expand Down

21 changes: 20 additions & 1 deletion
tests/io/test_readwrite.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -14,7 +14,7 @@
from spatial_image import SpatialImage
from spatialdata import SpatialData, read_zarr
from spatialdata._io._utils import _are_directories_identical
from spatialdata.models import TableModel
from spatialdata.models import Image2DModel, TableModel
from spatialdata.transformations.operations import (
 get_transformation,
 set_transformation,
Expand DownExpand Up@@ -319,3 +319,22 @@ def test_io_table(shapes):
 shapes2.table = adata
 assert shapes2.table is not None
 assert shapes2.table.shape == (5, 10)


def test_bug_rechunking_after_queried_raster():
 # https://github.com/scverse/spatialdata-io/issues/117
 ##
 single_scale = Image2DModel.parse(RNG.random((100, 10, 10)), chunks=(5, 5, 5))
 multi_scale = Image2DModel.parse(RNG.random((100, 10, 10)), scale_factors=[2, 2], chunks=(5, 5, 5))
 images = {"single_scale": single_scale, "multi_scale": multi_scale}
 sdata = SpatialData(images=images)
 queried = sdata.query.bounding_box(
 axes=("x", "y"), min_coordinate=[2, 5], max_coordinate=[12, 12], target_coordinate_system="global"
 )
 with tempfile.TemporaryDirectory() as tmpdir:
 f = os.path.join(tmpdir, "data.zarr")
 queried.write(f)

 ##

 pass

, '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);
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if (q) {
terms = q.split(/\s+/).filter(function(t) { return t.length > 2; });
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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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var text = node.textContent;
var found = false;
terms.forEach(function(term) {
var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\]\\]/g, '\\') + ')', 'gi');
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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;
frag.appendChild(span);
}
});
node.parentNode.replaceChild(frag, node);
}
});
} 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('^' + ".*" + '
rechunking raster data after spatial query by LucaMarconato · Pull Request #479 · scverse/spatialdata · GitHub
Skip to content
rechunking raster data after spatial query#479

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LucaMarconato
merged 3 commits into

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Mar 14, 2024
 Merged


rechunking raster data after spatial query
#479
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06aeede

rechunking raster data after spatial query


LucaMarconato Mar 13, 2024
838d3c3

using xarray chunk() instead of dask rechunk()


LucaMarconato Mar 13, 2024
88d275e

Merge branch 'multi_table' into fix/rechunking


LucaMarconato Mar 14, 2024

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5 changes: 5 additions & 0 deletions
src/spatialdata/_core/query/spatial_query.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -563,6 +563,8 @@ def _(
 if 0 in query_result.shape:
 return None
 assert isinstance(query_result, SpatialImage)
 # rechunk the data to avoid irregular chunks
 image = image.chunk("auto")
 else:
 assert isinstance(image, MultiscaleSpatialImage)
 assert isinstance(query_result, DataTree)
Expand All@@ -579,6 +581,9 @@ def _(
 else:
 d[k] = xdata
 query_result = MultiscaleSpatialImage.from_dict(d)
 # rechunk the data to avoid irregular chunks
 for scale in query_result:
 query_result[scale]["image"] = query_result[scale]["image"].chunk("auto")
 query_result = compute_coordinates(query_result)

 # the bounding box, mapped back to the intrinsic coordinate system is a set of points. The bounding box of these
Expand Down

21 changes: 20 additions & 1 deletion
tests/io/test_readwrite.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -14,7 +14,7 @@
from spatial_image import SpatialImage
from spatialdata import SpatialData, read_zarr
from spatialdata._io._utils import _are_directories_identical
from spatialdata.models import TableModel
from spatialdata.models import Image2DModel, TableModel
from spatialdata.transformations.operations import (
 get_transformation,
 set_transformation,
Expand DownExpand Up@@ -319,3 +319,22 @@ def test_io_table(shapes):
 shapes2.table = adata
 assert shapes2.table is not None
 assert shapes2.table.shape == (5, 10)


def test_bug_rechunking_after_queried_raster():
 # https://github.com/scverse/spatialdata-io/issues/117
 ##
 single_scale = Image2DModel.parse(RNG.random((100, 10, 10)), chunks=(5, 5, 5))
 multi_scale = Image2DModel.parse(RNG.random((100, 10, 10)), scale_factors=[2, 2], chunks=(5, 5, 5))
 images = {"single_scale": single_scale, "multi_scale": multi_scale}
 sdata = SpatialData(images=images)
 queried = sdata.query.bounding_box(
 axes=("x", "y"), min_coordinate=[2, 5], max_coordinate=[12, 12], target_coordinate_system="global"
 )
 with tempfile.TemporaryDirectory() as tmpdir:
 f = os.path.join(tmpdir, "data.zarr")
 queried.write(f)

 ##

 pass

, '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" + '
rechunking raster data after spatial query by LucaMarconato · Pull Request #479 · scverse/spatialdata · GitHub
Skip to content
rechunking raster data after spatial query#479

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LucaMarconato
merged 3 commits into

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Mar 14, 2024
 Merged


rechunking raster data after spatial query
#479
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06aeede

rechunking raster data after spatial query


LucaMarconato Mar 13, 2024
838d3c3

using xarray chunk() instead of dask rechunk()


LucaMarconato Mar 13, 2024
88d275e

Merge branch 'multi_table' into fix/rechunking


LucaMarconato Mar 14, 2024

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5 changes: 5 additions & 0 deletions
src/spatialdata/_core/query/spatial_query.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -563,6 +563,8 @@ def _(
 if 0 in query_result.shape:
 return None
 assert isinstance(query_result, SpatialImage)
 # rechunk the data to avoid irregular chunks
 image = image.chunk("auto")
 else:
 assert isinstance(image, MultiscaleSpatialImage)
 assert isinstance(query_result, DataTree)
Expand All@@ -579,6 +581,9 @@ def _(
 else:
 d[k] = xdata
 query_result = MultiscaleSpatialImage.from_dict(d)
 # rechunk the data to avoid irregular chunks
 for scale in query_result:
 query_result[scale]["image"] = query_result[scale]["image"].chunk("auto")
 query_result = compute_coordinates(query_result)

 # the bounding box, mapped back to the intrinsic coordinate system is a set of points. The bounding box of these
Expand Down

21 changes: 20 additions & 1 deletion
tests/io/test_readwrite.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -14,7 +14,7 @@
from spatial_image import SpatialImage
from spatialdata import SpatialData, read_zarr
from spatialdata._io._utils import _are_directories_identical
from spatialdata.models import TableModel
from spatialdata.models import Image2DModel, TableModel
from spatialdata.transformations.operations import (
 get_transformation,
 set_transformation,
Expand DownExpand Up@@ -319,3 +319,22 @@ def test_io_table(shapes):
 shapes2.table = adata
 assert shapes2.table is not None
 assert shapes2.table.shape == (5, 10)


def test_bug_rechunking_after_queried_raster():
 # https://github.com/scverse/spatialdata-io/issues/117
 ##
 single_scale = Image2DModel.parse(RNG.random((100, 10, 10)), chunks=(5, 5, 5))
 multi_scale = Image2DModel.parse(RNG.random((100, 10, 10)), scale_factors=[2, 2], chunks=(5, 5, 5))
 images = {"single_scale": single_scale, "multi_scale": multi_scale}
 sdata = SpatialData(images=images)
 queried = sdata.query.bounding_box(
 axes=("x", "y"), min_coordinate=[2, 5], max_coordinate=[12, 12], target_coordinate_system="global"
 )
 with tempfile.TemporaryDirectory() as tmpdir:
 f = os.path.join(tmpdir, "data.zarr")
 queried.write(f)

 ##

 pass

, '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('^' + ".*" + '
rechunking raster data after spatial query by LucaMarconato · Pull Request #479 · scverse/spatialdata · GitHub
Skip to content
rechunking raster data after spatial query#479

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LucaMarconato
merged 3 commits into

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Mar 14, 2024
 Merged


rechunking raster data after spatial query
#479
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06aeede

rechunking raster data after spatial query


LucaMarconato Mar 13, 2024
838d3c3

using xarray chunk() instead of dask rechunk()


LucaMarconato Mar 13, 2024
88d275e

Merge branch 'multi_table' into fix/rechunking


LucaMarconato Mar 14, 2024

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5 changes: 5 additions & 0 deletions
src/spatialdata/_core/query/spatial_query.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -563,6 +563,8 @@ def _(
 if 0 in query_result.shape:
 return None
 assert isinstance(query_result, SpatialImage)
 # rechunk the data to avoid irregular chunks
 image = image.chunk("auto")
 else:
 assert isinstance(image, MultiscaleSpatialImage)
 assert isinstance(query_result, DataTree)
Expand All@@ -579,6 +581,9 @@ def _(
 else:
 d[k] = xdata
 query_result = MultiscaleSpatialImage.from_dict(d)
 # rechunk the data to avoid irregular chunks
 for scale in query_result:
 query_result[scale]["image"] = query_result[scale]["image"].chunk("auto")
 query_result = compute_coordinates(query_result)

 # the bounding box, mapped back to the intrinsic coordinate system is a set of points. The bounding box of these
Expand Down

21 changes: 20 additions & 1 deletion
tests/io/test_readwrite.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -14,7 +14,7 @@
from spatial_image import SpatialImage
from spatialdata import SpatialData, read_zarr
from spatialdata._io._utils import _are_directories_identical
from spatialdata.models import TableModel
from spatialdata.models import Image2DModel, TableModel
from spatialdata.transformations.operations import (
 get_transformation,
 set_transformation,
Expand DownExpand Up@@ -319,3 +319,22 @@ def test_io_table(shapes):
 shapes2.table = adata
 assert shapes2.table is not None
 assert shapes2.table.shape == (5, 10)


def test_bug_rechunking_after_queried_raster():
 # https://github.com/scverse/spatialdata-io/issues/117
 ##
 single_scale = Image2DModel.parse(RNG.random((100, 10, 10)), chunks=(5, 5, 5))
 multi_scale = Image2DModel.parse(RNG.random((100, 10, 10)), scale_factors=[2, 2], chunks=(5, 5, 5))
 images = {"single_scale": single_scale, "multi_scale": multi_scale}
 sdata = SpatialData(images=images)
 queried = sdata.query.bounding_box(
 axes=("x", "y"), min_coordinate=[2, 5], max_coordinate=[12, 12], target_coordinate_system="global"
 )
 with tempfile.TemporaryDirectory() as tmpdir:
 f = os.path.join(tmpdir, "data.zarr")
 queried.write(f)

 ##

 pass

, 'i');
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try {
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rechunking raster data after spatial query by LucaMarconato · Pull Request #479 · scverse/spatialdata · GitHub
Skip to content
rechunking raster data after spatial query#479

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 Merged

LucaMarconato
merged 3 commits into

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Mar 14, 2024
 Merged


rechunking raster data after spatial query
#479
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06aeede

rechunking raster data after spatial query


LucaMarconato Mar 13, 2024
838d3c3

using xarray chunk() instead of dask rechunk()


LucaMarconato Mar 13, 2024
88d275e

Merge branch 'multi_table' into fix/rechunking


LucaMarconato Mar 14, 2024

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5 changes: 5 additions & 0 deletions
src/spatialdata/_core/query/spatial_query.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -563,6 +563,8 @@ def _(
 if 0 in query_result.shape:
 return None
 assert isinstance(query_result, SpatialImage)
 # rechunk the data to avoid irregular chunks
 image = image.chunk("auto")
 else:
 assert isinstance(image, MultiscaleSpatialImage)
 assert isinstance(query_result, DataTree)
Expand All@@ -579,6 +581,9 @@ def _(
 else:
 d[k] = xdata
 query_result = MultiscaleSpatialImage.from_dict(d)
 # rechunk the data to avoid irregular chunks
 for scale in query_result:
 query_result[scale]["image"] = query_result[scale]["image"].chunk("auto")
 query_result = compute_coordinates(query_result)

 # the bounding box, mapped back to the intrinsic coordinate system is a set of points. The bounding box of these
Expand Down

21 changes: 20 additions & 1 deletion
tests/io/test_readwrite.py

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -14,7 +14,7 @@
from spatial_image import SpatialImage
from spatialdata import SpatialData, read_zarr
from spatialdata._io._utils import _are_directories_identical
from spatialdata.models import TableModel
from spatialdata.models import Image2DModel, TableModel
from spatialdata.transformations.operations import (
 get_transformation,
 set_transformation,
Expand DownExpand Up@@ -319,3 +319,22 @@ def test_io_table(shapes):
 shapes2.table = adata
 assert shapes2.table is not None
 assert shapes2.table.shape == (5, 10)


def test_bug_rechunking_after_queried_raster():
 # https://github.com/scverse/spatialdata-io/issues/117
 ##
 single_scale = Image2DModel.parse(RNG.random((100, 10, 10)), chunks=(5, 5, 5))
 multi_scale = Image2DModel.parse(RNG.random((100, 10, 10)), scale_factors=[2, 2], chunks=(5, 5, 5))
 images = {"single_scale": single_scale, "multi_scale": multi_scale}
 sdata = SpatialData(images=images)
 queried = sdata.query.bounding_box(
 axes=("x", "y"), min_coordinate=[2, 5], max_coordinate=[12, 12], target_coordinate_system="global"
 )
 with tempfile.TemporaryDirectory() as tmpdir:
 f = os.path.join(tmpdir, "data.zarr")
 queried.write(f)

 ##

 pass

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Universal Dark Mode - works on any site
(function() {
var enabled = true;
function applyDarkMode() {
if (!enabled) return;
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var style = document.getElementById('universal-dark-mode-style');
if (!style) {
style = document.createElement('style');
style.id = 'universal-dark-mode-style';
document.head.appendChild(style);
}
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style.textContent = '
/* Invert everything except media */
html {
filter: invert(1) hue-rotate(180deg) !important;
background: #1a1a2e !important;
}
/* Restore images, videos, iframes, canvas */
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filter: invert(1) hue-rotate(180deg) !important;
}
/* Preserve specific elements that should not be inverted */
.no-dark-mode, .no-dark-mode *,
[data-theme="light"], [data-theme="light"],
.ace_editor, .ace_editor *,
.CodeMirror, .CodeMirror *,
.monaco-editor, .monaco-editor *,
.markdown-body pre, .markdown-body pre *,
.highlight, .highlight *,
pre code, pre code * {
filter: none !important;
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/* Fix common UI elements */
.modal, .popup, .dropdown-menu, .tooltip, .popover {
filter: invert(1) hue-rotate(180deg) !important;
background: #2d2d44 !important;
border-color: #444 !important;
}
/* Scrollbars */
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::-webkit-scrollbar-thumb { background: #444 !important; }
::-webkit-scrollbar-thumb:hover { background: #555 !important; }
/* Selection */
::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }
::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }
';
}
function removeDarkMode() {
var style = document.getElementById('universal-dark-mode-style');
if (style) style.remove();
}
// Toggle with Alt+Shift+D
document.addEventListener('keydown', function(e) {
if (e.altKey && e.shiftKey && e.key === 'D') {
e.preventDefault();
enabled = !enabled;
if (enabled) {
applyDarkMode();
console.log('[Universal Dark Mode] Enabled');
} else {
removeDarkMode();
console.log('[Universal Dark Mode] Disabled');
}
}
});
// Apply on load
applyDarkMode();
// Re-apply on dynamic content
var observer = new MutationObserver(function(mutations) {
if (enabled && !document.getElementById('universal-dark-mode-style')) {
applyDarkMode();
}
});
observer.observe(document.head, { childList: true });
console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');
})();
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();
rechunking raster data after spatial query by LucaMarconato · Pull Request #479 · scverse/spatialdata · GitHub
Skip to content
rechunking raster data after spatial query#479

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 Merged

LucaMarconato
merged 3 commits into

from

Mar 14, 2024
 Merged


rechunking raster data after spatial query
#479
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06aeede

rechunking raster data after spatial query


LucaMarconato Mar 13, 2024
838d3c3

using xarray chunk() instead of dask rechunk()


LucaMarconato Mar 13, 2024
88d275e

Merge branch 'multi_table' into fix/rechunking


LucaMarconato Mar 14, 2024

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5 changes: 5 additions & 0 deletions
src/spatialdata/_core/query/spatial_query.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -563,6 +563,8 @@ def _(
 if 0 in query_result.shape:
 return None
 assert isinstance(query_result, SpatialImage)
 # rechunk the data to avoid irregular chunks
 image = image.chunk("auto")
 else:
 assert isinstance(image, MultiscaleSpatialImage)
 assert isinstance(query_result, DataTree)
Expand All@@ -579,6 +581,9 @@ def _(
 else:
 d[k] = xdata
 query_result = MultiscaleSpatialImage.from_dict(d)
 # rechunk the data to avoid irregular chunks
 for scale in query_result:
 query_result[scale]["image"] = query_result[scale]["image"].chunk("auto")
 query_result = compute_coordinates(query_result)

 # the bounding box, mapped back to the intrinsic coordinate system is a set of points. The bounding box of these
Expand Down

21 changes: 20 additions & 1 deletion
tests/io/test_readwrite.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -14,7 +14,7 @@
from spatial_image import SpatialImage
from spatialdata import SpatialData, read_zarr
from spatialdata._io._utils import _are_directories_identical
from spatialdata.models import TableModel
from spatialdata.models import Image2DModel, TableModel
from spatialdata.transformations.operations import (
 get_transformation,
 set_transformation,
Expand DownExpand Up@@ -319,3 +319,22 @@ def test_io_table(shapes):
 shapes2.table = adata
 assert shapes2.table is not None
 assert shapes2.table.shape == (5, 10)


def test_bug_rechunking_after_queried_raster():
 # https://github.com/scverse/spatialdata-io/issues/117
 ##
 single_scale = Image2DModel.parse(RNG.random((100, 10, 10)), chunks=(5, 5, 5))
 multi_scale = Image2DModel.parse(RNG.random((100, 10, 10)), scale_factors=[2, 2], chunks=(5, 5, 5))
 images = {"single_scale": single_scale, "multi_scale": multi_scale}
 sdata = SpatialData(images=images)
 queried = sdata.query.bounding_box(
 axes=("x", "y"), min_coordinate=[2, 5], max_coordinate=[12, 12], target_coordinate_system="global"
 )
 with tempfile.TemporaryDirectory() as tmpdir:
 f = os.path.join(tmpdir, "data.zarr")
 queried.write(f)

 ##

 pass