Skip to content

fix: write OME channel labels as strings#1168

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.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
stanbot8 wants to merge 1 commit into
base:main
Choose a base branch
from
Open

fix: write OME channel labels as strings #1168

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
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
, 'i'); if (__m === '*' || __re.test(location.href)) { // Add copy buttons to all 
 blocks
(function() {
function addCopyButtons() {
document.querySelectorAll('pre code').forEach(function(codeBlock) {
if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;
codeBlock.parentElement.setAttribute('data-copy-added', 'true');
var btn = document.createElement('button');
btn.textContent = 'Copy';
btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';
btn.onmouseover = function() { this.style.opacity = '1'; };
btn.onmouseout = function() { this.style.opacity = '0.7'; };
btn.onclick = function() {
navigator.clipboard.writeText(codeBlock.textContent).then(function() {
btn.textContent = 'Copied!';
setTimeout(function() { btn.textContent = 'Copy'; }, 1500);
});
};
codeBlock.parentElement.style.position = 'relative';
codeBlock.parentElement.appendChild(btn);
});
}
addCopyButtons();
// Re-run on dynamic content
var observer = new MutationObserver(addCopyButtons);
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '
fix: write OME channel labels as strings by stanbot8 · Pull Request #1168 · scverse/spatialdata · GitHub
Skip to content
fix: write OME channel labels as strings#1168

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.

 Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and
privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
Sign in
to your account

 Open

stanbot8
wants to merge
1
commit into

base:main
Choose a base branch

from

 Open


fix: write OME channel labels as strings
#1168
Show file tree
Hide file tree
 Changes from all commits
Commits

Show all changes


1 commit


Select commit


File filter

Filter by extension
Filter by extension
Conversations

Failed to load comments. 
Loading
Jump to

Jump to file


Failed to load files. 
Loading
 Diff view

 Diff view


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

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Force GitHub README to respect dark mode
(function() {
var style = document.createElement('style');
style.textContent = '
.markdown-body {
color-scheme: dark light;
}
.markdown-body pre { background: #161b22 !important; }
.markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }
.markdown-body table th, .markdown-body table td { border-color: #30363d !important; }
.markdown-body img { background: #0d1117; }
.markdown-body blockquote { border-left-color: #8b949e; }
.markdown-body hr { border-color: #30363d; }
';
document.head.appendChild(style);
})();
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
fix: write OME channel labels as strings by stanbot8 · Pull Request #1168 · scverse/spatialdata · GitHub
Skip to content
fix: write OME channel labels as strings#1168

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.

 Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and
privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
Sign in
to your account

 Open

stanbot8
wants to merge
1
commit into

base:main
Choose a base branch

from

 Open


fix: write OME channel labels as strings
#1168
Show file tree
Hide file tree
 Changes from all commits
Commits

Show all changes


1 commit


Select commit


File filter

Filter by extension
Filter by extension
Conversations

Failed to load comments. 
Loading
Jump to

Jump to file


Failed to load files. 
Loading
 Diff view

 Diff view


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

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Highlight search terms from Google/DuckDuckGo/Bing referrer
(function() {
var ref = document.referrer;
var terms = [];
if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {
var url = new URL(ref);
var q = url.searchParams.get('q') || url.searchParams.get('p');
if (q) {
terms = q.split(/\s+/).filter(function(t) { return t.length > 2; });
}
}
if (terms.length === 0) return;
var style = document.createElement('style');
style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';
document.head.appendChild(style);
function highlight(node) {
if (node.nodeType === 3) { // text node
var text = node.textContent;
var found = false;
terms.forEach(function(term) {
var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\]\\]/g, '\\') + ')', 'gi');
if (regex.test(text)) {
found = true;
var frag = document.createDocumentFragment();
var parts = text.split(regex);
parts.forEach(function(part, i) {
if (i % 2 === 0) {
frag.appendChild(document.createTextNode(part));
} else {
var span = document.createElement('span');
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('^' + ".*" + '
fix: write OME channel labels as strings by stanbot8 · Pull Request #1168 · scverse/spatialdata · GitHub
Skip to content
fix: write OME channel labels as strings#1168

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.

 Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and
privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
Sign in
to your account

 Open

stanbot8
wants to merge
1
commit into

base:main
Choose a base branch

from

 Open


fix: write OME channel labels as strings
#1168
Show file tree
Hide file tree
 Changes from all commits
Commits

Show all changes


1 commit


Select commit


File filter

Filter by extension
Filter by extension
Conversations

Failed to load comments. 
Loading
Jump to

Jump to file


Failed to load files. 
Loading
 Diff view

 Diff view


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

, '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" + '
fix: write OME channel labels as strings by stanbot8 · Pull Request #1168 · scverse/spatialdata · GitHub
Skip to content
fix: write OME channel labels as strings#1168

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.

 Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and
privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
Sign in
to your account

 Open

stanbot8
wants to merge
1
commit into

base:main
Choose a base branch

from

 Open


fix: write OME channel labels as strings
#1168
Show file tree
Hide file tree
 Changes from all commits
Commits

Show all changes


1 commit


Select commit


File filter

Filter by extension
Filter by extension
Conversations

Failed to load comments. 
Loading
Jump to

Jump to file


Failed to load files. 
Loading
 Diff view

 Diff view


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

, '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('^' + ".*" + '
fix: write OME channel labels as strings by stanbot8 · Pull Request #1168 · scverse/spatialdata · GitHub
Skip to content
fix: write OME channel labels as strings#1168

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.

 Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and
privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
Sign in
to your account

 Open

stanbot8
wants to merge
1
commit into

base:main
Choose a base branch

from

 Open


fix: write OME channel labels as strings
#1168
Show file tree
Hide file tree
 Changes from all commits
Commits

Show all changes


1 commit


Select commit


File filter

Filter by extension
Filter by extension
Conversations

Failed to load comments. 
Loading
Jump to

Jump to file


Failed to load files. 
Loading
 Diff view

 Diff view


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

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Remove or un-stick sticky/fixed headers that block content
(function() {
function unstick() {
document.querySelectorAll('header, nav, [role="banner"], .header, .navbar, .sticky, .fixed-top, [style*="position: fixed"], [style*="position:sticky"]').forEach(function(el) {
if (el.style.position === 'fixed' || el.style.position === 'sticky' || getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {
el.style.position = 'static';
el.style.top = 'auto';
el.style.zIndex = 'auto';
}
});
}
unstick();
var observer = new MutationObserver(unstick);
observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });
})();
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
})();
fix: write OME channel labels as strings by stanbot8 · Pull Request #1168 · scverse/spatialdata · GitHub
Skip to content
fix: write OME channel labels as strings#1168

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.

 Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and
privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
Sign in
to your account

 Open

stanbot8
wants to merge
1
commit into

base:main
Choose a base branch

from

 Open


fix: write OME channel labels as strings
#1168
Show file tree
Hide file tree
 Changes from all commits
Commits

Show all changes


1 commit


Select commit


File filter

Filter by extension
Filter by extension
Conversations

Failed to load comments. 
Loading
Jump to

Jump to file


Failed to load files. 
Loading
 Diff view

 Diff view


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