utilities (query, mask, etc.)

[HelenaLC]

No description provided.

[Copilot]

Pull request overview

Updates SpatialData’s query() utilities and their tests/docs, focusing on bounding-box subsetting across element types.

Changes:

• Simplifies query() for ImageArray/LabelArray to direct array slicing and clamps xmax/ymax to object dimensions.
• Reworks query() for ShapeFrame to use sf::st_crop() and updates tests accordingly.
• Updates documentation/examples and adds sf::st_crop to imports.

Reviewed changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 5 comments.

File	Description
R/query.R	Refactors query() methods (notably Image/Label/Shape) and adds bbox validation.
tests/testthat/test-query.R	Updates expectations for new query behavior (esp. ShapeFrame, ImageArray transform assertions).
man/query.Rd	Syncs generated docs/examples with updated method signatures.
NAMESPACE	Adds sf::st_crop import to support ShapeFrame cropping.

Comments suppressed due to low confidence (1)

man/query.Rd:27

• The Rd still documents j as a general argument (“index or name of coordinate space”), but query,ImageArray/LabelArray/ShapeFrame no longer accept j while query,PointFrame still requires it. Please update the argument documentation to reflect which methods accept/ignore j (or restore consistent method signatures) to avoid confusing users.

\S4method{query}{ImageArray}(x, ...)

\S4method{query}{LabelArray}(x, ...)

\S4method{query}{ShapeFrame}(x, ...)

\S4method{query}{PointFrame}(x, j, ...)
}
\arguments{
\item{x}{\code{SpatialData} element.}

\item{j}{scalar character or integer; index or name of coordinate space.}

\item{...}{optional arguments passed to and from other methods.}

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

[Copilot]

Pull request overview

Copilot reviewed 4 out of 4 changed files in this pull request and generated 4 comments.

Comments suppressed due to low confidence (1)

man/query.Rd:27

• The Rd still documents argument j in the shared \arguments section, but the ImageArray and PointFrame method signatures in \usage no longer include j. This makes ?query misleading for those methods. Consider documenting j as SpatialData-only (or restoring j consistently across methods).

\arguments{
\item{x}{\code{SpatialData} element.}

\item{j}{scalar character or integer; index or name of coordinate space.}

\item{...}{optional arguments passed to and from other methods.}

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

[Copilot]

Pull request overview

Copilot reviewed 4 out of 4 changed files in this pull request and generated 8 comments.

Comments suppressed due to low confidence (1)

man/query.Rd:28

• The documentation still lists j as an argument for query() globally, but the ImageArray/PointFrame methods no longer accept j (per the updated \usage). This can confuse users about which methods support coordinate-space selection. Consider clarifying in the Rd (and/or roxygen) that j only applies to the SpatialData method (or reintroducing j consistently).

\arguments{
\item{x}{\code{SpatialData} element.}

\item{j}{scalar character or integer; index or name of coordinate space.}

\item{...}{optional arguments passed to and from other methods.}
}

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

[Copilot]

Pull request overview

Copilot reviewed 4 out of 4 changed files in this pull request and generated 9 comments.

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

[Copilot]

Pull request overview

Copilot reviewed 11 out of 11 changed files in this pull request and generated 7 comments.

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

[Copilot]

Pull request overview

Copilot reviewed 16 out of 16 changed files in this pull request and generated 5 comments.

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.