fix: write OME channel labels as strings#5

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fix: write OME channel labels as strings #5

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15 changes: 10 additions & 5 deletions src/spatialdata/_io/_utils.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -153,15 +153,20 @@ def overwrite_channel_names(group: zarr.Group, element: DataArray | DataTree) ->
else:
channel_names = element["scale0"]["image"].coords["c"].data.tolist()

channel_metadata = [{"label": name} for name in channel_names]
attrs = group.attrs.asdict()
channel_metadata = [{"label": str(name)} for name in channel_names]
spatialdata_attrs = attrs.get("spatialdata_attrs", {})
spatialdata_attrs["channel_names"] = channel_names
attrs["spatialdata_attrs"] = spatialdata_attrs
# We don't use the ome-zarr load node API, and ome-zarr-py >= 0.18 emits no `omero` block, so default to empty.
omero_meta = group.attrs.get("omero") or group.attrs.get("ome", {}).get("omero") or {}
omero_meta = attrs.get("omero") or attrs.get("ome", {}).get("omero") or {}
omero_meta["channels"] = channel_metadata
if ome_meta := group.attrs.get("ome", None):
if ome_meta := attrs.get("ome", None):
ome_meta["omero"] = omero_meta
group.attrs["ome"] = ome_meta
attrs["ome"] = ome_meta
else:
group.attrs["omero"] = omero_meta
attrs["omero"] = omero_meta
group.attrs.put(attrs)


def _write_metadata(
Expand Down
5 changes: 5 additions & 0 deletions src/spatialdata/_io/io_raster.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -168,6 +168,9 @@ def _read_multiscale(
nodes: list[Node] = []
image_loc = ZarrLocation(store, fmt=reader_format)
if exists := image_loc.exists():
spatialdata_channels = (
zarr.open_group(store=image_loc.store, mode="r").attrs.get(ATTRS_KEY, {}).get("channel_names")
)
image_reader = Reader(image_loc)()
image_nodes = list(image_reader)
nodes = _get_multiscale_nodes(image_nodes, nodes)
Expand DownExpand Up@@ -213,6 +216,8 @@ def _read_multiscale(
channels = [d["label"] for d in legacy_channels_metadata["channels"]]
if omero_metadata is not None:
channels = [d["label"] for d in omero_metadata["channels"]]
if spatialdata_channels is not None:
channels = spatialdata_channels
axes = [i["name"] for i in node.metadata["axes"]]
if len(datasets) > 1:
arrays = [node.load(Multiscales).array(resolution=d) for d in datasets]
Expand Down
19 changes: 19 additions & 0 deletions tests/io/test_metadata.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -5,6 +5,7 @@
import tempfile

import pytest
import zarr

from spatialdata import SpatialData, read_zarr
from spatialdata._io._utils import _is_element_self_contained
Expand DownExpand Up@@ -117,6 +118,24 @@ def test_save_transformations_incremental(element_name, full_sdata, caplog):


# test io for channel names
@pytest.mark.parametrize("expected", [[0, 1, 2], ["0", "1", "2"]], ids=["integers", "numeric-strings"])
def test_channel_names_store_string_labels_without_changing_coordinates(
images: SpatialData, tmp_path, expected: list[int] | list[str]
) -> None:
path = tmp_path / "sdata.zarr"
image = images["image2d_xarray"].assign_coords(c=expected)
SpatialData(images={"image": image}).write(path)
root = zarr.open_group(path, mode="r")
attrs = root["images"]["image"].attrs
omero = attrs.get("omero") or attrs["ome"]["omero"]
labels = [channel["label"] for channel in omero["channels"]]
channel_names = attrs["spatialdata_attrs"]["channel_names"]
root.store.close()
assert labels == [str(value) for value in expected]
assert channel_names == expected
assert get_channel_names(SpatialData.read(path)["image"]) == expected


@pytest.mark.parametrize("write", ["overwrite", "write", "no"])
def test_save_channel_names_incremental(images: SpatialData, write: str) -> None:
old_channels2d = get_channel_names(images["image2d"])
Expand Down
Loading
, '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" + '

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fix: write OME channel labels as strings#5

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fix: write OME channel labels as strings
#5
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15 changes: 10 additions & 5 deletions
src/spatialdata/_io/_utils.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -153,15 +153,20 @@ def overwrite_channel_names(group: zarr.Group, element: DataArray | DataTree) ->
 else:
 channel_names = element["scale0"]["image"].coords["c"].data.tolist()

 channel_metadata = [{"label": name} for name in channel_names]
 attrs = group.attrs.asdict()
 channel_metadata = [{"label": str(name)} for name in channel_names]
 spatialdata_attrs = attrs.get("spatialdata_attrs", {})
 spatialdata_attrs["channel_names"] = channel_names
 attrs["spatialdata_attrs"] = spatialdata_attrs
 # We don't use the ome-zarr load node API, and ome-zarr-py >= 0.18 emits no `omero` block, so default to empty.
 omero_meta = group.attrs.get("omero") or group.attrs.get("ome", {}).get("omero") or {}
 omero_meta = attrs.get("omero") or attrs.get("ome", {}).get("omero") or {}
 omero_meta["channels"] = channel_metadata
 if ome_meta := group.attrs.get("ome", None):
 if ome_meta := attrs.get("ome", None):
 ome_meta["omero"] = omero_meta
group.attrs["ome"] = ome_meta
 attrs["ome"] = ome_meta
 else:
 group.attrs["omero"] = omero_meta
 attrs["omero"] = omero_meta
 group.attrs.put(attrs)


def _write_metadata(
Expand Down

5 changes: 5 additions & 0 deletions
src/spatialdata/_io/io_raster.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -168,6 +168,9 @@ def _read_multiscale(
 nodes: list[Node] = []
 image_loc = ZarrLocation(store, fmt=reader_format)
 if exists := image_loc.exists():
 spatialdata_channels = (
 zarr.open_group(store=image_loc.store, mode="r").attrs.get(ATTRS_KEY, {}).get("channel_names")
 )
 image_reader = Reader(image_loc)()
 image_nodes = list(image_reader)
 nodes = _get_multiscale_nodes(image_nodes, nodes)
Expand DownExpand Up@@ -213,6 +216,8 @@ def _read_multiscale(
 channels = [d["label"] for d in legacy_channels_metadata["channels"]]
 if omero_metadata is not None:
 channels = [d["label"] for d in omero_metadata["channels"]]
 if spatialdata_channels is not None:
 channels = spatialdata_channels
 axes = [i["name"] for i in node.metadata["axes"]]
 if len(datasets) > 1:
 arrays = [node.load(Multiscales).array(resolution=d) for d in datasets]
Expand Down

19 changes: 19 additions & 0 deletions
tests/io/test_metadata.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -5,6 +5,7 @@
import tempfile

import pytest
import zarr

from spatialdata import SpatialData, read_zarr
from spatialdata._io._utils import _is_element_self_contained
Expand DownExpand Up@@ -117,6 +118,24 @@ def test_save_transformations_incremental(element_name, full_sdata, caplog):


# test io for channel names
@pytest.mark.parametrize("expected", [[0, 1, 2], ["0", "1", "2"]], ids=["integers", "numeric-strings"])
def test_channel_names_store_string_labels_without_changing_coordinates(
 images: SpatialData, tmp_path, expected: list[int] | list[str]
) -> None:
 path = tmp_path / "sdata.zarr"
 image = images["image2d_xarray"].assign_coords(c=expected)
 SpatialData(images={"image": image}).write(path)
 root = zarr.open_group(path, mode="r")
 attrs = root["images"]["image"].attrs
 omero = attrs.get("omero") or attrs["ome"]["omero"]
 labels = [channel["label"] for channel in omero["channels"]]
 channel_names = attrs["spatialdata_attrs"]["channel_names"]
 root.store.close()
 assert labels == [str(value) for value in expected]
 assert channel_names == expected
 assert get_channel_names(SpatialData.read(path)["image"]) == expected


@pytest.mark.parametrize("write", ["overwrite", "write", "no"])
def test_save_channel_names_incremental(images: SpatialData, write: str) -> None:
 old_channels2d = get_channel_names(images["image2d"])
Expand Down
Loading

, '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
fix: write OME channel labels as strings#5

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

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 Draft

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commit into

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Choose a base branch

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+34

−5

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fix: write OME channel labels as strings
#5
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15 changes: 10 additions & 5 deletions
src/spatialdata/_io/_utils.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -153,15 +153,20 @@ def overwrite_channel_names(group: zarr.Group, element: DataArray | DataTree) ->
 else:
 channel_names = element["scale0"]["image"].coords["c"].data.tolist()

 channel_metadata = [{"label": name} for name in channel_names]
 attrs = group.attrs.asdict()
 channel_metadata = [{"label": str(name)} for name in channel_names]
 spatialdata_attrs = attrs.get("spatialdata_attrs", {})
 spatialdata_attrs["channel_names"] = channel_names
 attrs["spatialdata_attrs"] = spatialdata_attrs
 # We don't use the ome-zarr load node API, and ome-zarr-py >= 0.18 emits no `omero` block, so default to empty.
 omero_meta = group.attrs.get("omero") or group.attrs.get("ome", {}).get("omero") or {}
 omero_meta = attrs.get("omero") or attrs.get("ome", {}).get("omero") or {}
 omero_meta["channels"] = channel_metadata
 if ome_meta := group.attrs.get("ome", None):
 if ome_meta := attrs.get("ome", None):
 ome_meta["omero"] = omero_meta
group.attrs["ome"] = ome_meta
 attrs["ome"] = ome_meta
 else:
 group.attrs["omero"] = omero_meta
 attrs["omero"] = omero_meta
 group.attrs.put(attrs)


def _write_metadata(
Expand Down

5 changes: 5 additions & 0 deletions
src/spatialdata/_io/io_raster.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -168,6 +168,9 @@ def _read_multiscale(
 nodes: list[Node] = []
 image_loc = ZarrLocation(store, fmt=reader_format)
 if exists := image_loc.exists():
 spatialdata_channels = (
 zarr.open_group(store=image_loc.store, mode="r").attrs.get(ATTRS_KEY, {}).get("channel_names")
 )
 image_reader = Reader(image_loc)()
 image_nodes = list(image_reader)
 nodes = _get_multiscale_nodes(image_nodes, nodes)
Expand DownExpand Up@@ -213,6 +216,8 @@ def _read_multiscale(
 channels = [d["label"] for d in legacy_channels_metadata["channels"]]
 if omero_metadata is not None:
 channels = [d["label"] for d in omero_metadata["channels"]]
 if spatialdata_channels is not None:
 channels = spatialdata_channels
 axes = [i["name"] for i in node.metadata["axes"]]
 if len(datasets) > 1:
 arrays = [node.load(Multiscales).array(resolution=d) for d in datasets]
Expand Down

19 changes: 19 additions & 0 deletions
tests/io/test_metadata.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -5,6 +5,7 @@
import tempfile

import pytest
import zarr

from spatialdata import SpatialData, read_zarr
from spatialdata._io._utils import _is_element_self_contained
Expand DownExpand Up@@ -117,6 +118,24 @@ def test_save_transformations_incremental(element_name, full_sdata, caplog):


# test io for channel names
@pytest.mark.parametrize("expected", [[0, 1, 2], ["0", "1", "2"]], ids=["integers", "numeric-strings"])
def test_channel_names_store_string_labels_without_changing_coordinates(
 images: SpatialData, tmp_path, expected: list[int] | list[str]
) -> None:
 path = tmp_path / "sdata.zarr"
 image = images["image2d_xarray"].assign_coords(c=expected)
 SpatialData(images={"image": image}).write(path)
 root = zarr.open_group(path, mode="r")
 attrs = root["images"]["image"].attrs
 omero = attrs.get("omero") or attrs["ome"]["omero"]
 labels = [channel["label"] for channel in omero["channels"]]
 channel_names = attrs["spatialdata_attrs"]["channel_names"]
 root.store.close()
 assert labels == [str(value) for value in expected]
 assert channel_names == expected
 assert get_channel_names(SpatialData.read(path)["image"]) == expected


@pytest.mark.parametrize("write", ["overwrite", "write", "no"])
def test_save_channel_names_incremental(images: SpatialData, write: str) -> None:
 old_channels2d = get_channel_names(images["image2d"])
Expand Down
Loading

, '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
fix: write OME channel labels as strings#5

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 Draft

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commit into

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Choose a base branch

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+34

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fix: write OME channel labels as strings
#5
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15 changes: 10 additions & 5 deletions
src/spatialdata/_io/_utils.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -153,15 +153,20 @@ def overwrite_channel_names(group: zarr.Group, element: DataArray | DataTree) ->
 else:
 channel_names = element["scale0"]["image"].coords["c"].data.tolist()

 channel_metadata = [{"label": name} for name in channel_names]
 attrs = group.attrs.asdict()
 channel_metadata = [{"label": str(name)} for name in channel_names]
 spatialdata_attrs = attrs.get("spatialdata_attrs", {})
 spatialdata_attrs["channel_names"] = channel_names
 attrs["spatialdata_attrs"] = spatialdata_attrs
 # We don't use the ome-zarr load node API, and ome-zarr-py >= 0.18 emits no `omero` block, so default to empty.
 omero_meta = group.attrs.get("omero") or group.attrs.get("ome", {}).get("omero") or {}
 omero_meta = attrs.get("omero") or attrs.get("ome", {}).get("omero") or {}
 omero_meta["channels"] = channel_metadata
 if ome_meta := group.attrs.get("ome", None):
 if ome_meta := attrs.get("ome", None):
 ome_meta["omero"] = omero_meta
group.attrs["ome"] = ome_meta
 attrs["ome"] = ome_meta
 else:
 group.attrs["omero"] = omero_meta
 attrs["omero"] = omero_meta
 group.attrs.put(attrs)


def _write_metadata(
Expand Down

5 changes: 5 additions & 0 deletions
src/spatialdata/_io/io_raster.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -168,6 +168,9 @@ def _read_multiscale(
 nodes: list[Node] = []
 image_loc = ZarrLocation(store, fmt=reader_format)
 if exists := image_loc.exists():
 spatialdata_channels = (
 zarr.open_group(store=image_loc.store, mode="r").attrs.get(ATTRS_KEY, {}).get("channel_names")
 )
 image_reader = Reader(image_loc)()
 image_nodes = list(image_reader)
 nodes = _get_multiscale_nodes(image_nodes, nodes)
Expand DownExpand Up@@ -213,6 +216,8 @@ def _read_multiscale(
 channels = [d["label"] for d in legacy_channels_metadata["channels"]]
 if omero_metadata is not None:
 channels = [d["label"] for d in omero_metadata["channels"]]
 if spatialdata_channels is not None:
 channels = spatialdata_channels
 axes = [i["name"] for i in node.metadata["axes"]]
 if len(datasets) > 1:
 arrays = [node.load(Multiscales).array(resolution=d) for d in datasets]
Expand Down

19 changes: 19 additions & 0 deletions
tests/io/test_metadata.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -5,6 +5,7 @@
import tempfile

import pytest
import zarr

from spatialdata import SpatialData, read_zarr
from spatialdata._io._utils import _is_element_self_contained
Expand DownExpand Up@@ -117,6 +118,24 @@ def test_save_transformations_incremental(element_name, full_sdata, caplog):


# test io for channel names
@pytest.mark.parametrize("expected", [[0, 1, 2], ["0", "1", "2"]], ids=["integers", "numeric-strings"])
def test_channel_names_store_string_labels_without_changing_coordinates(
 images: SpatialData, tmp_path, expected: list[int] | list[str]
) -> None:
 path = tmp_path / "sdata.zarr"
 image = images["image2d_xarray"].assign_coords(c=expected)
 SpatialData(images={"image": image}).write(path)
 root = zarr.open_group(path, mode="r")
 attrs = root["images"]["image"].attrs
 omero = attrs.get("omero") or attrs["ome"]["omero"]
 labels = [channel["label"] for channel in omero["channels"]]
 channel_names = attrs["spatialdata_attrs"]["channel_names"]
 root.store.close()
 assert labels == [str(value) for value in expected]
 assert channel_names == expected
 assert get_channel_names(SpatialData.read(path)["image"]) == expected


@pytest.mark.parametrize("write", ["overwrite", "write", "no"])
def test_save_channel_names_incremental(images: SpatialData, write: str) -> None:
 old_channels2d = get_channel_names(images["image2d"])
Expand Down
Loading

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

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fix: write OME channel labels as strings#5

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fix: write OME channel labels as strings
#5
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15 changes: 10 additions & 5 deletions
src/spatialdata/_io/_utils.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -153,15 +153,20 @@ def overwrite_channel_names(group: zarr.Group, element: DataArray | DataTree) ->
 else:
 channel_names = element["scale0"]["image"].coords["c"].data.tolist()

 channel_metadata = [{"label": name} for name in channel_names]
 attrs = group.attrs.asdict()
 channel_metadata = [{"label": str(name)} for name in channel_names]
 spatialdata_attrs = attrs.get("spatialdata_attrs", {})
 spatialdata_attrs["channel_names"] = channel_names
 attrs["spatialdata_attrs"] = spatialdata_attrs
 # We don't use the ome-zarr load node API, and ome-zarr-py >= 0.18 emits no `omero` block, so default to empty.
 omero_meta = group.attrs.get("omero") or group.attrs.get("ome", {}).get("omero") or {}
 omero_meta = attrs.get("omero") or attrs.get("ome", {}).get("omero") or {}
 omero_meta["channels"] = channel_metadata
 if ome_meta := group.attrs.get("ome", None):
 if ome_meta := attrs.get("ome", None):
 ome_meta["omero"] = omero_meta
group.attrs["ome"] = ome_meta
 attrs["ome"] = ome_meta
 else:
 group.attrs["omero"] = omero_meta
 attrs["omero"] = omero_meta
 group.attrs.put(attrs)


def _write_metadata(
Expand Down

5 changes: 5 additions & 0 deletions
src/spatialdata/_io/io_raster.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -168,6 +168,9 @@ def _read_multiscale(
 nodes: list[Node] = []
 image_loc = ZarrLocation(store, fmt=reader_format)
 if exists := image_loc.exists():
 spatialdata_channels = (
 zarr.open_group(store=image_loc.store, mode="r").attrs.get(ATTRS_KEY, {}).get("channel_names")
 )
 image_reader = Reader(image_loc)()
 image_nodes = list(image_reader)
 nodes = _get_multiscale_nodes(image_nodes, nodes)
Expand DownExpand Up@@ -213,6 +216,8 @@ def _read_multiscale(
 channels = [d["label"] for d in legacy_channels_metadata["channels"]]
 if omero_metadata is not None:
 channels = [d["label"] for d in omero_metadata["channels"]]
 if spatialdata_channels is not None:
 channels = spatialdata_channels
 axes = [i["name"] for i in node.metadata["axes"]]
 if len(datasets) > 1:
 arrays = [node.load(Multiscales).array(resolution=d) for d in datasets]
Expand Down

19 changes: 19 additions & 0 deletions
tests/io/test_metadata.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -5,6 +5,7 @@
import tempfile

import pytest
import zarr

from spatialdata import SpatialData, read_zarr
from spatialdata._io._utils import _is_element_self_contained
Expand DownExpand Up@@ -117,6 +118,24 @@ def test_save_transformations_incremental(element_name, full_sdata, caplog):


# test io for channel names
@pytest.mark.parametrize("expected", [[0, 1, 2], ["0", "1", "2"]], ids=["integers", "numeric-strings"])
def test_channel_names_store_string_labels_without_changing_coordinates(
 images: SpatialData, tmp_path, expected: list[int] | list[str]
) -> None:
 path = tmp_path / "sdata.zarr"
 image = images["image2d_xarray"].assign_coords(c=expected)
 SpatialData(images={"image": image}).write(path)
 root = zarr.open_group(path, mode="r")
 attrs = root["images"]["image"].attrs
 omero = attrs.get("omero") or attrs["ome"]["omero"]
 labels = [channel["label"] for channel in omero["channels"]]
 channel_names = attrs["spatialdata_attrs"]["channel_names"]
 root.store.close()
 assert labels == [str(value) for value in expected]
 assert channel_names == expected
 assert get_channel_names(SpatialData.read(path)["image"]) == expected


@pytest.mark.parametrize("write", ["overwrite", "write", "no"])
def test_save_channel_names_incremental(images: SpatialData, write: str) -> None:
 old_channels2d = get_channel_names(images["image2d"])
Expand Down
Loading

, '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
fix: write OME channel labels as strings#5

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fix: write OME channel labels as strings
#5
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15 changes: 10 additions & 5 deletions
src/spatialdata/_io/_utils.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -153,15 +153,20 @@ def overwrite_channel_names(group: zarr.Group, element: DataArray | DataTree) ->
 else:
 channel_names = element["scale0"]["image"].coords["c"].data.tolist()

 channel_metadata = [{"label": name} for name in channel_names]
 attrs = group.attrs.asdict()
 channel_metadata = [{"label": str(name)} for name in channel_names]
 spatialdata_attrs = attrs.get("spatialdata_attrs", {})
 spatialdata_attrs["channel_names"] = channel_names
 attrs["spatialdata_attrs"] = spatialdata_attrs
 # We don't use the ome-zarr load node API, and ome-zarr-py >= 0.18 emits no `omero` block, so default to empty.
 omero_meta = group.attrs.get("omero") or group.attrs.get("ome", {}).get("omero") or {}
 omero_meta = attrs.get("omero") or attrs.get("ome", {}).get("omero") or {}
 omero_meta["channels"] = channel_metadata
 if ome_meta := group.attrs.get("ome", None):
 if ome_meta := attrs.get("ome", None):
 ome_meta["omero"] = omero_meta
group.attrs["ome"] = ome_meta
 attrs["ome"] = ome_meta
 else:
 group.attrs["omero"] = omero_meta
 attrs["omero"] = omero_meta
 group.attrs.put(attrs)


def _write_metadata(
Expand Down

5 changes: 5 additions & 0 deletions
src/spatialdata/_io/io_raster.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -168,6 +168,9 @@ def _read_multiscale(
 nodes: list[Node] = []
 image_loc = ZarrLocation(store, fmt=reader_format)
 if exists := image_loc.exists():
 spatialdata_channels = (
 zarr.open_group(store=image_loc.store, mode="r").attrs.get(ATTRS_KEY, {}).get("channel_names")
 )
 image_reader = Reader(image_loc)()
 image_nodes = list(image_reader)
 nodes = _get_multiscale_nodes(image_nodes, nodes)
Expand DownExpand Up@@ -213,6 +216,8 @@ def _read_multiscale(
 channels = [d["label"] for d in legacy_channels_metadata["channels"]]
 if omero_metadata is not None:
 channels = [d["label"] for d in omero_metadata["channels"]]
 if spatialdata_channels is not None:
 channels = spatialdata_channels
 axes = [i["name"] for i in node.metadata["axes"]]
 if len(datasets) > 1:
 arrays = [node.load(Multiscales).array(resolution=d) for d in datasets]
Expand Down

19 changes: 19 additions & 0 deletions
tests/io/test_metadata.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -5,6 +5,7 @@
import tempfile

import pytest
import zarr

from spatialdata import SpatialData, read_zarr
from spatialdata._io._utils import _is_element_self_contained
Expand DownExpand Up@@ -117,6 +118,24 @@ def test_save_transformations_incremental(element_name, full_sdata, caplog):


# test io for channel names
@pytest.mark.parametrize("expected", [[0, 1, 2], ["0", "1", "2"]], ids=["integers", "numeric-strings"])
def test_channel_names_store_string_labels_without_changing_coordinates(
 images: SpatialData, tmp_path, expected: list[int] | list[str]
) -> None:
 path = tmp_path / "sdata.zarr"
 image = images["image2d_xarray"].assign_coords(c=expected)
 SpatialData(images={"image": image}).write(path)
 root = zarr.open_group(path, mode="r")
 attrs = root["images"]["image"].attrs
 omero = attrs.get("omero") or attrs["ome"]["omero"]
 labels = [channel["label"] for channel in omero["channels"]]
 channel_names = attrs["spatialdata_attrs"]["channel_names"]
 root.store.close()
 assert labels == [str(value) for value in expected]
 assert channel_names == expected
 assert get_channel_names(SpatialData.read(path)["image"]) == expected


@pytest.mark.parametrize("write", ["overwrite", "write", "no"])
def test_save_channel_names_incremental(images: SpatialData, write: str) -> None:
 old_channels2d = get_channel_names(images["image2d"])
Expand Down
Loading

, '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
fix: write OME channel labels as strings#5

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fix: write OME channel labels as strings
#5
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15 changes: 10 additions & 5 deletions
src/spatialdata/_io/_utils.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -153,15 +153,20 @@ def overwrite_channel_names(group: zarr.Group, element: DataArray | DataTree) ->
 else:
 channel_names = element["scale0"]["image"].coords["c"].data.tolist()

 channel_metadata = [{"label": name} for name in channel_names]
 attrs = group.attrs.asdict()
 channel_metadata = [{"label": str(name)} for name in channel_names]
 spatialdata_attrs = attrs.get("spatialdata_attrs", {})
 spatialdata_attrs["channel_names"] = channel_names
 attrs["spatialdata_attrs"] = spatialdata_attrs
 # We don't use the ome-zarr load node API, and ome-zarr-py >= 0.18 emits no `omero` block, so default to empty.
 omero_meta = group.attrs.get("omero") or group.attrs.get("ome", {}).get("omero") or {}
 omero_meta = attrs.get("omero") or attrs.get("ome", {}).get("omero") or {}
 omero_meta["channels"] = channel_metadata
 if ome_meta := group.attrs.get("ome", None):
 if ome_meta := attrs.get("ome", None):
 ome_meta["omero"] = omero_meta
group.attrs["ome"] = ome_meta
 attrs["ome"] = ome_meta
 else:
 group.attrs["omero"] = omero_meta
 attrs["omero"] = omero_meta
 group.attrs.put(attrs)


def _write_metadata(
Expand Down

5 changes: 5 additions & 0 deletions
src/spatialdata/_io/io_raster.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -168,6 +168,9 @@ def _read_multiscale(
 nodes: list[Node] = []
 image_loc = ZarrLocation(store, fmt=reader_format)
 if exists := image_loc.exists():
 spatialdata_channels = (
 zarr.open_group(store=image_loc.store, mode="r").attrs.get(ATTRS_KEY, {}).get("channel_names")
 )
 image_reader = Reader(image_loc)()
 image_nodes = list(image_reader)
 nodes = _get_multiscale_nodes(image_nodes, nodes)
Expand DownExpand Up@@ -213,6 +216,8 @@ def _read_multiscale(
 channels = [d["label"] for d in legacy_channels_metadata["channels"]]
 if omero_metadata is not None:
 channels = [d["label"] for d in omero_metadata["channels"]]
 if spatialdata_channels is not None:
 channels = spatialdata_channels
 axes = [i["name"] for i in node.metadata["axes"]]
 if len(datasets) > 1:
 arrays = [node.load(Multiscales).array(resolution=d) for d in datasets]
Expand Down

19 changes: 19 additions & 0 deletions
tests/io/test_metadata.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -5,6 +5,7 @@
import tempfile

import pytest
import zarr

from spatialdata import SpatialData, read_zarr
from spatialdata._io._utils import _is_element_self_contained
Expand DownExpand Up@@ -117,6 +118,24 @@ def test_save_transformations_incremental(element_name, full_sdata, caplog):


# test io for channel names
@pytest.mark.parametrize("expected", [[0, 1, 2], ["0", "1", "2"]], ids=["integers", "numeric-strings"])
def test_channel_names_store_string_labels_without_changing_coordinates(
 images: SpatialData, tmp_path, expected: list[int] | list[str]
) -> None:
 path = tmp_path / "sdata.zarr"
 image = images["image2d_xarray"].assign_coords(c=expected)
 SpatialData(images={"image": image}).write(path)
 root = zarr.open_group(path, mode="r")
 attrs = root["images"]["image"].attrs
 omero = attrs.get("omero") or attrs["ome"]["omero"]
 labels = [channel["label"] for channel in omero["channels"]]
 channel_names = attrs["spatialdata_attrs"]["channel_names"]
 root.store.close()
 assert labels == [str(value) for value in expected]
 assert channel_names == expected
 assert get_channel_names(SpatialData.read(path)["image"]) == expected


@pytest.mark.parametrize("write", ["overwrite", "write", "no"])
def test_save_channel_names_incremental(images: SpatialData, write: str) -> None:
 old_channels2d = get_channel_names(images["image2d"])
Expand Down
Loading

, '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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fix: write OME channel labels as strings#5

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fix: write OME channel labels as strings
#5
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15 changes: 10 additions & 5 deletions
src/spatialdata/_io/_utils.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -153,15 +153,20 @@ def overwrite_channel_names(group: zarr.Group, element: DataArray | DataTree) ->
 else:
 channel_names = element["scale0"]["image"].coords["c"].data.tolist()

 channel_metadata = [{"label": name} for name in channel_names]
 attrs = group.attrs.asdict()
 channel_metadata = [{"label": str(name)} for name in channel_names]
 spatialdata_attrs = attrs.get("spatialdata_attrs", {})
 spatialdata_attrs["channel_names"] = channel_names
 attrs["spatialdata_attrs"] = spatialdata_attrs
 # We don't use the ome-zarr load node API, and ome-zarr-py >= 0.18 emits no `omero` block, so default to empty.
 omero_meta = group.attrs.get("omero") or group.attrs.get("ome", {}).get("omero") or {}
 omero_meta = attrs.get("omero") or attrs.get("ome", {}).get("omero") or {}
 omero_meta["channels"] = channel_metadata
 if ome_meta := group.attrs.get("ome", None):
 if ome_meta := attrs.get("ome", None):
 ome_meta["omero"] = omero_meta
group.attrs["ome"] = ome_meta
 attrs["ome"] = ome_meta
 else:
 group.attrs["omero"] = omero_meta
 attrs["omero"] = omero_meta
 group.attrs.put(attrs)


def _write_metadata(
Expand Down

5 changes: 5 additions & 0 deletions
src/spatialdata/_io/io_raster.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -168,6 +168,9 @@ def _read_multiscale(
 nodes: list[Node] = []
 image_loc = ZarrLocation(store, fmt=reader_format)
 if exists := image_loc.exists():
 spatialdata_channels = (
 zarr.open_group(store=image_loc.store, mode="r").attrs.get(ATTRS_KEY, {}).get("channel_names")
 )
 image_reader = Reader(image_loc)()
 image_nodes = list(image_reader)
 nodes = _get_multiscale_nodes(image_nodes, nodes)
Expand DownExpand Up@@ -213,6 +216,8 @@ def _read_multiscale(
 channels = [d["label"] for d in legacy_channels_metadata["channels"]]
 if omero_metadata is not None:
 channels = [d["label"] for d in omero_metadata["channels"]]
 if spatialdata_channels is not None:
 channels = spatialdata_channels
 axes = [i["name"] for i in node.metadata["axes"]]
 if len(datasets) > 1:
 arrays = [node.load(Multiscales).array(resolution=d) for d in datasets]
Expand Down

19 changes: 19 additions & 0 deletions
tests/io/test_metadata.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -5,6 +5,7 @@
import tempfile

import pytest
import zarr

from spatialdata import SpatialData, read_zarr
from spatialdata._io._utils import _is_element_self_contained
Expand DownExpand Up@@ -117,6 +118,24 @@ def test_save_transformations_incremental(element_name, full_sdata, caplog):


# test io for channel names
@pytest.mark.parametrize("expected", [[0, 1, 2], ["0", "1", "2"]], ids=["integers", "numeric-strings"])
def test_channel_names_store_string_labels_without_changing_coordinates(
 images: SpatialData, tmp_path, expected: list[int] | list[str]
) -> None:
 path = tmp_path / "sdata.zarr"
 image = images["image2d_xarray"].assign_coords(c=expected)
 SpatialData(images={"image": image}).write(path)
 root = zarr.open_group(path, mode="r")
 attrs = root["images"]["image"].attrs
 omero = attrs.get("omero") or attrs["ome"]["omero"]
 labels = [channel["label"] for channel in omero["channels"]]
 channel_names = attrs["spatialdata_attrs"]["channel_names"]
 root.store.close()
 assert labels == [str(value) for value in expected]
 assert channel_names == expected
 assert get_channel_names(SpatialData.read(path)["image"]) == expected


@pytest.mark.parametrize("write", ["overwrite", "write", "no"])
def test_save_channel_names_incremental(images: SpatialData, write: str) -> None:
 old_channels2d = get_channel_names(images["image2d"])
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