fix tests from modified get_element_instances#287

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Merged
LucaMarconato merged 8 commits into from
Dec 26, 2024
Merged

fix tests from modified get_element_instances#287

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a067448
fix tests
giovp Jul 9, 2024
9cbaa92
cleanup
giovp Jul 9, 2024
ca9f0f6
upload correct images
giovp Jul 10, 2024
42a4ee6
one more fix
giovp Jul 10, 2024
dd9e106
Merge branch 'main' into giovp/get_element_instances
LucaMarconato Dec 26, 2024
0d7ced9
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Dec 26, 2024
75ed8a0
uploaded ground-truth image from docker env
LucaMarconato Dec 26, 2024
7935a44
Merge branch 'giovp/get_element_instances' of https://github.com/scve…
LucaMarconato Dec 26, 2024
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27 changes: 26 additions & 1 deletion tests/pl/test_render_labels.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -5,8 +5,9 @@
import pandas as pd
import pytest
import scanpy as sc
from anndata import AnnData
from spatial_image import to_spatial_image
from spatialdata import SpatialData, deepcopy
from spatialdata import SpatialData, deepcopy, get_element_instances
from spatialdata.models import TableModel

import spatialdata_plot # noqa: F401
Expand DownExpand Up@@ -208,3 +209,27 @@ def test_plot_subset_categorical_label_maintains_order_when_palette_overwrite(se
sdata_blobs.pl.render_labels(
"blobs_labels", color="which_max", groups=["channel_0_sum"], palette="red"
).pl.show(ax=axs[1])

def test_plot_label_categorical_color(self, sdata_blobs: SpatialData):
self._make_tablemodel_with_categorical_labels(sdata_blobs, labels_name="blobs_labels")
sdata_blobs.pl.render_labels("blobs_labels", color="category").pl.show()

def _make_tablemodel_with_categorical_labels(self, sdata_blobs, labels_name: str):
instances = get_element_instances(sdata_blobs[labels_name])
n_obs = len(instances)
adata = AnnData(
RNG.normal(size=(n_obs, 10)),
obs=pd.DataFrame(RNG.normal(size=(n_obs, 3)), columns=["a", "b", "c"]),
)
adata.obs["instance_id"] = instances.values
adata.obs["category"] = RNG.choice(["a", "b", "c"], size=adata.n_obs)
adata.obs["category"][:3] = ["a", "b", "c"]
adata.obs["region"] = labels_name
table = TableModel.parse(
adata=adata,
region_key="region",
instance_key="instance_id",
region=labels_name,
)
sdata_blobs["other_table"] = table
sdata_blobs["other_table"].obs["category"] = sdata_blobs["other_table"].obs["category"].astype("category")
, '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 tests from modified get_element_instances#287

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 Merged

LucaMarconato
merged 8 commits into

from

Dec 26, 2024
 Merged


fix tests from modified get_element_instances#287
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a067448

fix tests


giovp Jul 9, 2024
9cbaa92

cleanup


giovp Jul 9, 2024
ca9f0f6

upload correct images


giovp Jul 10, 2024
42a4ee6

one more fix


giovp Jul 10, 2024
dd9e106

Merge branch 'main' into giovp/get_element_instances


LucaMarconato Dec 26, 2024
0d7ced9

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Dec 26, 2024
75ed8a0

uploaded ground-truth image from docker env


LucaMarconato Dec 26, 2024
7935a44

Merge branch 'giovp/get_element_instances' of https://github.com/scve…


LucaMarconato Dec 26, 2024

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27 changes: 26 additions & 1 deletion
tests/pl/test_render_labels.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -5,8 +5,9 @@
import pandas as pd
import pytest
import scanpy as sc
from anndata import AnnData
from spatial_image import to_spatial_image
from spatialdata import SpatialData, deepcopy
from spatialdata import SpatialData, deepcopy, get_element_instances
from spatialdata.models import TableModel

import spatialdata_plot # noqa: F401
Expand DownExpand Up@@ -208,3 +209,27 @@ def test_plot_subset_categorical_label_maintains_order_when_palette_overwrite(se
 sdata_blobs.pl.render_labels(
 "blobs_labels", color="which_max", groups=["channel_0_sum"], palette="red"
 ).pl.show(ax=axs[1])

 def test_plot_label_categorical_color(self, sdata_blobs: SpatialData):
 self._make_tablemodel_with_categorical_labels(sdata_blobs, labels_name="blobs_labels")
 sdata_blobs.pl.render_labels("blobs_labels", color="category").pl.show()

 def _make_tablemodel_with_categorical_labels(self, sdata_blobs, labels_name: str):
 instances = get_element_instances(sdata_blobs[labels_name])
 n_obs = len(instances)
 adata = AnnData(
 RNG.normal(size=(n_obs, 10)),
 obs=pd.DataFrame(RNG.normal(size=(n_obs, 3)), columns=["a", "b", "c"]),
 )
 adata.obs["instance_id"] = instances.values
 adata.obs["category"] = RNG.choice(["a", "b", "c"], size=adata.n_obs)
 adata.obs["category"][:3] = ["a", "b", "c"]
 adata.obs["region"] = labels_name
 table = TableModel.parse(
 adata=adata,
 region_key="region",
 instance_key="instance_id",
 region=labels_name,
 )
 sdata_blobs["other_table"] = table
 sdata_blobs["other_table"].obs["category"] = sdata_blobs["other_table"].obs["category"].astype("category")

, '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('^' + ".*" + '

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fix tests from modified get_element_instances#287

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 Merged

LucaMarconato
merged 8 commits into

from

Dec 26, 2024
 Merged


fix tests from modified get_element_instances#287
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a067448

fix tests


giovp Jul 9, 2024
9cbaa92

cleanup


giovp Jul 9, 2024
ca9f0f6

upload correct images


giovp Jul 10, 2024
42a4ee6

one more fix


giovp Jul 10, 2024
dd9e106

Merge branch 'main' into giovp/get_element_instances


LucaMarconato Dec 26, 2024
0d7ced9

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Dec 26, 2024
75ed8a0

uploaded ground-truth image from docker env


LucaMarconato Dec 26, 2024
7935a44

Merge branch 'giovp/get_element_instances' of https://github.com/scve…


LucaMarconato Dec 26, 2024

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27 changes: 26 additions & 1 deletion
tests/pl/test_render_labels.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -5,8 +5,9 @@
import pandas as pd
import pytest
import scanpy as sc
from anndata import AnnData
from spatial_image import to_spatial_image
from spatialdata import SpatialData, deepcopy
from spatialdata import SpatialData, deepcopy, get_element_instances
from spatialdata.models import TableModel

import spatialdata_plot # noqa: F401
Expand DownExpand Up@@ -208,3 +209,27 @@ def test_plot_subset_categorical_label_maintains_order_when_palette_overwrite(se
 sdata_blobs.pl.render_labels(
 "blobs_labels", color="which_max", groups=["channel_0_sum"], palette="red"
 ).pl.show(ax=axs[1])

 def test_plot_label_categorical_color(self, sdata_blobs: SpatialData):
 self._make_tablemodel_with_categorical_labels(sdata_blobs, labels_name="blobs_labels")
 sdata_blobs.pl.render_labels("blobs_labels", color="category").pl.show()

 def _make_tablemodel_with_categorical_labels(self, sdata_blobs, labels_name: str):
 instances = get_element_instances(sdata_blobs[labels_name])
 n_obs = len(instances)
 adata = AnnData(
 RNG.normal(size=(n_obs, 10)),
 obs=pd.DataFrame(RNG.normal(size=(n_obs, 3)), columns=["a", "b", "c"]),
 )
 adata.obs["instance_id"] = instances.values
 adata.obs["category"] = RNG.choice(["a", "b", "c"], size=adata.n_obs)
 adata.obs["category"][:3] = ["a", "b", "c"]
 adata.obs["region"] = labels_name
 table = TableModel.parse(
 adata=adata,
 region_key="region",
 instance_key="instance_id",
 region=labels_name,
 )
 sdata_blobs["other_table"] = table
 sdata_blobs["other_table"].obs["category"] = sdata_blobs["other_table"].obs["category"].astype("category")

, '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('^' + ".*" + '

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fix tests from modified get_element_instances#287

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 Merged

LucaMarconato
merged 8 commits into

from

Dec 26, 2024
 Merged


fix tests from modified get_element_instances#287
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a067448

fix tests


giovp Jul 9, 2024
9cbaa92

cleanup


giovp Jul 9, 2024
ca9f0f6

upload correct images


giovp Jul 10, 2024
42a4ee6

one more fix


giovp Jul 10, 2024
dd9e106

Merge branch 'main' into giovp/get_element_instances


LucaMarconato Dec 26, 2024
0d7ced9

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Dec 26, 2024
75ed8a0

uploaded ground-truth image from docker env


LucaMarconato Dec 26, 2024
7935a44

Merge branch 'giovp/get_element_instances' of https://github.com/scve…


LucaMarconato Dec 26, 2024

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27 changes: 26 additions & 1 deletion
tests/pl/test_render_labels.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -5,8 +5,9 @@
import pandas as pd
import pytest
import scanpy as sc
from anndata import AnnData
from spatial_image import to_spatial_image
from spatialdata import SpatialData, deepcopy
from spatialdata import SpatialData, deepcopy, get_element_instances
from spatialdata.models import TableModel

import spatialdata_plot # noqa: F401
Expand DownExpand Up@@ -208,3 +209,27 @@ def test_plot_subset_categorical_label_maintains_order_when_palette_overwrite(se
 sdata_blobs.pl.render_labels(
 "blobs_labels", color="which_max", groups=["channel_0_sum"], palette="red"
 ).pl.show(ax=axs[1])

 def test_plot_label_categorical_color(self, sdata_blobs: SpatialData):
 self._make_tablemodel_with_categorical_labels(sdata_blobs, labels_name="blobs_labels")
 sdata_blobs.pl.render_labels("blobs_labels", color="category").pl.show()

 def _make_tablemodel_with_categorical_labels(self, sdata_blobs, labels_name: str):
 instances = get_element_instances(sdata_blobs[labels_name])
 n_obs = len(instances)
 adata = AnnData(
 RNG.normal(size=(n_obs, 10)),
 obs=pd.DataFrame(RNG.normal(size=(n_obs, 3)), columns=["a", "b", "c"]),
 )
 adata.obs["instance_id"] = instances.values
 adata.obs["category"] = RNG.choice(["a", "b", "c"], size=adata.n_obs)
 adata.obs["category"][:3] = ["a", "b", "c"]
 adata.obs["region"] = labels_name
 table = TableModel.parse(
 adata=adata,
 region_key="region",
 instance_key="instance_id",
 region=labels_name,
 )
 sdata_blobs["other_table"] = table
 sdata_blobs["other_table"].obs["category"] = sdata_blobs["other_table"].obs["category"].astype("category")

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

Skip to content
fix tests from modified get_element_instances#287

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 Merged

LucaMarconato
merged 8 commits into

from

Dec 26, 2024
 Merged


fix tests from modified get_element_instances#287
Show file tree
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8 commits


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a067448

fix tests


giovp Jul 9, 2024
9cbaa92

cleanup


giovp Jul 9, 2024
ca9f0f6

upload correct images


giovp Jul 10, 2024
42a4ee6

one more fix


giovp Jul 10, 2024
dd9e106

Merge branch 'main' into giovp/get_element_instances


LucaMarconato Dec 26, 2024
0d7ced9

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Dec 26, 2024
75ed8a0

uploaded ground-truth image from docker env


LucaMarconato Dec 26, 2024
7935a44

Merge branch 'giovp/get_element_instances' of https://github.com/scve…


LucaMarconato Dec 26, 2024

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27 changes: 26 additions & 1 deletion
tests/pl/test_render_labels.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -5,8 +5,9 @@
import pandas as pd
import pytest
import scanpy as sc
from anndata import AnnData
from spatial_image import to_spatial_image
from spatialdata import SpatialData, deepcopy
from spatialdata import SpatialData, deepcopy, get_element_instances
from spatialdata.models import TableModel

import spatialdata_plot # noqa: F401
Expand DownExpand Up@@ -208,3 +209,27 @@ def test_plot_subset_categorical_label_maintains_order_when_palette_overwrite(se
 sdata_blobs.pl.render_labels(
 "blobs_labels", color="which_max", groups=["channel_0_sum"], palette="red"
 ).pl.show(ax=axs[1])

 def test_plot_label_categorical_color(self, sdata_blobs: SpatialData):
 self._make_tablemodel_with_categorical_labels(sdata_blobs, labels_name="blobs_labels")
 sdata_blobs.pl.render_labels("blobs_labels", color="category").pl.show()

 def _make_tablemodel_with_categorical_labels(self, sdata_blobs, labels_name: str):
 instances = get_element_instances(sdata_blobs[labels_name])
 n_obs = len(instances)
 adata = AnnData(
 RNG.normal(size=(n_obs, 10)),
 obs=pd.DataFrame(RNG.normal(size=(n_obs, 3)), columns=["a", "b", "c"]),
 )
 adata.obs["instance_id"] = instances.values
 adata.obs["category"] = RNG.choice(["a", "b", "c"], size=adata.n_obs)
 adata.obs["category"][:3] = ["a", "b", "c"]
 adata.obs["region"] = labels_name
 table = TableModel.parse(
 adata=adata,
 region_key="region",
 instance_key="instance_id",
 region=labels_name,
 )
 sdata_blobs["other_table"] = table
 sdata_blobs["other_table"].obs["category"] = sdata_blobs["other_table"].obs["category"].astype("category")

, '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('^' + ".*" + '

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fix tests from modified get_element_instances#287

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 Merged

LucaMarconato
merged 8 commits into

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Dec 26, 2024
 Merged


fix tests from modified get_element_instances#287
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a067448

fix tests


giovp Jul 9, 2024
9cbaa92

cleanup


giovp Jul 9, 2024
ca9f0f6

upload correct images


giovp Jul 10, 2024
42a4ee6

one more fix


giovp Jul 10, 2024
dd9e106

Merge branch 'main' into giovp/get_element_instances


LucaMarconato Dec 26, 2024
0d7ced9

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Dec 26, 2024
75ed8a0

uploaded ground-truth image from docker env


LucaMarconato Dec 26, 2024
7935a44

Merge branch 'giovp/get_element_instances' of https://github.com/scve…


LucaMarconato Dec 26, 2024

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27 changes: 26 additions & 1 deletion
tests/pl/test_render_labels.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -5,8 +5,9 @@
import pandas as pd
import pytest
import scanpy as sc
from anndata import AnnData
from spatial_image import to_spatial_image
from spatialdata import SpatialData, deepcopy
from spatialdata import SpatialData, deepcopy, get_element_instances
from spatialdata.models import TableModel

import spatialdata_plot # noqa: F401
Expand DownExpand Up@@ -208,3 +209,27 @@ def test_plot_subset_categorical_label_maintains_order_when_palette_overwrite(se
 sdata_blobs.pl.render_labels(
 "blobs_labels", color="which_max", groups=["channel_0_sum"], palette="red"
 ).pl.show(ax=axs[1])

 def test_plot_label_categorical_color(self, sdata_blobs: SpatialData):
 self._make_tablemodel_with_categorical_labels(sdata_blobs, labels_name="blobs_labels")
 sdata_blobs.pl.render_labels("blobs_labels", color="category").pl.show()

 def _make_tablemodel_with_categorical_labels(self, sdata_blobs, labels_name: str):
 instances = get_element_instances(sdata_blobs[labels_name])
 n_obs = len(instances)
 adata = AnnData(
 RNG.normal(size=(n_obs, 10)),
 obs=pd.DataFrame(RNG.normal(size=(n_obs, 3)), columns=["a", "b", "c"]),
 )
 adata.obs["instance_id"] = instances.values
 adata.obs["category"] = RNG.choice(["a", "b", "c"], size=adata.n_obs)
 adata.obs["category"][:3] = ["a", "b", "c"]
 adata.obs["region"] = labels_name
 table = TableModel.parse(
 adata=adata,
 region_key="region",
 instance_key="instance_id",
 region=labels_name,
 )
 sdata_blobs["other_table"] = table
 sdata_blobs["other_table"].obs["category"] = sdata_blobs["other_table"].obs["category"].astype("category")

, '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('^' + ".*" + '

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fix tests from modified get_element_instances#287

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 Merged

LucaMarconato
merged 8 commits into

from

Dec 26, 2024
 Merged


fix tests from modified get_element_instances#287
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a067448

fix tests


giovp Jul 9, 2024
9cbaa92

cleanup


giovp Jul 9, 2024
ca9f0f6

upload correct images


giovp Jul 10, 2024
42a4ee6

one more fix


giovp Jul 10, 2024
dd9e106

Merge branch 'main' into giovp/get_element_instances


LucaMarconato Dec 26, 2024
0d7ced9

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Dec 26, 2024
75ed8a0

uploaded ground-truth image from docker env


LucaMarconato Dec 26, 2024
7935a44

Merge branch 'giovp/get_element_instances' of https://github.com/scve…


LucaMarconato Dec 26, 2024

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27 changes: 26 additions & 1 deletion
tests/pl/test_render_labels.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -5,8 +5,9 @@
import pandas as pd
import pytest
import scanpy as sc
from anndata import AnnData
from spatial_image import to_spatial_image
from spatialdata import SpatialData, deepcopy
from spatialdata import SpatialData, deepcopy, get_element_instances
from spatialdata.models import TableModel

import spatialdata_plot # noqa: F401
Expand DownExpand Up@@ -208,3 +209,27 @@ def test_plot_subset_categorical_label_maintains_order_when_palette_overwrite(se
 sdata_blobs.pl.render_labels(
 "blobs_labels", color="which_max", groups=["channel_0_sum"], palette="red"
 ).pl.show(ax=axs[1])

 def test_plot_label_categorical_color(self, sdata_blobs: SpatialData):
 self._make_tablemodel_with_categorical_labels(sdata_blobs, labels_name="blobs_labels")
 sdata_blobs.pl.render_labels("blobs_labels", color="category").pl.show()

 def _make_tablemodel_with_categorical_labels(self, sdata_blobs, labels_name: str):
 instances = get_element_instances(sdata_blobs[labels_name])
 n_obs = len(instances)
 adata = AnnData(
 RNG.normal(size=(n_obs, 10)),
 obs=pd.DataFrame(RNG.normal(size=(n_obs, 3)), columns=["a", "b", "c"]),
 )
 adata.obs["instance_id"] = instances.values
 adata.obs["category"] = RNG.choice(["a", "b", "c"], size=adata.n_obs)
 adata.obs["category"][:3] = ["a", "b", "c"]
 adata.obs["region"] = labels_name
 table = TableModel.parse(
 adata=adata,
 region_key="region",
 instance_key="instance_id",
 region=labels_name,
 )
 sdata_blobs["other_table"] = table
 sdata_blobs["other_table"].obs["category"] = sdata_blobs["other_table"].obs["category"].astype("category")

, '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); }
})();
})();

Skip to content
fix tests from modified get_element_instances#287

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 Merged

LucaMarconato
merged 8 commits into

from

Dec 26, 2024
 Merged


fix tests from modified get_element_instances#287
Show file tree
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8 commits


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a067448

fix tests


giovp Jul 9, 2024
9cbaa92

cleanup


giovp Jul 9, 2024
ca9f0f6

upload correct images


giovp Jul 10, 2024
42a4ee6

one more fix


giovp Jul 10, 2024
dd9e106

Merge branch 'main' into giovp/get_element_instances


LucaMarconato Dec 26, 2024
0d7ced9

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Dec 26, 2024
75ed8a0

uploaded ground-truth image from docker env


LucaMarconato Dec 26, 2024
7935a44

Merge branch 'giovp/get_element_instances' of https://github.com/scve…


LucaMarconato Dec 26, 2024

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Binary file addedtests/_images/Labels_label_categorical_color.png

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27 changes: 26 additions & 1 deletion
tests/pl/test_render_labels.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -5,8 +5,9 @@
import pandas as pd
import pytest
import scanpy as sc
from anndata import AnnData
from spatial_image import to_spatial_image
from spatialdata import SpatialData, deepcopy
from spatialdata import SpatialData, deepcopy, get_element_instances
from spatialdata.models import TableModel

import spatialdata_plot # noqa: F401
Expand DownExpand Up@@ -208,3 +209,27 @@ def test_plot_subset_categorical_label_maintains_order_when_palette_overwrite(se
 sdata_blobs.pl.render_labels(
 "blobs_labels", color="which_max", groups=["channel_0_sum"], palette="red"
 ).pl.show(ax=axs[1])

 def test_plot_label_categorical_color(self, sdata_blobs: SpatialData):
 self._make_tablemodel_with_categorical_labels(sdata_blobs, labels_name="blobs_labels")
 sdata_blobs.pl.render_labels("blobs_labels", color="category").pl.show()

 def _make_tablemodel_with_categorical_labels(self, sdata_blobs, labels_name: str):
 instances = get_element_instances(sdata_blobs[labels_name])
 n_obs = len(instances)
 adata = AnnData(
 RNG.normal(size=(n_obs, 10)),
 obs=pd.DataFrame(RNG.normal(size=(n_obs, 3)), columns=["a", "b", "c"]),
 )
 adata.obs["instance_id"] = instances.values
 adata.obs["category"] = RNG.choice(["a", "b", "c"], size=adata.n_obs)
 adata.obs["category"][:3] = ["a", "b", "c"]
 adata.obs["region"] = labels_name
 table = TableModel.parse(
 adata=adata,
 region_key="region",
 instance_key="instance_id",
 region=labels_name,
 )
 sdata_blobs["other_table"] = table
 sdata_blobs["other_table"].obs["category"] = sdata_blobs["other_table"].obs["category"].astype("category")