Skip to content
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

Jump to bottom

Fix broken cross links in docs #392

Closed
wants to merge 1 commit into from
Closed

Fix broken cross links in docs #392

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
2 changes: 1 addition & 1 deletion docs/developers/architecture/app_model.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,7 @@ Currently, the primary purpose of the `app` is to compose the following
[commands](app-model-commands) (the actual callable objects) that have been
registered with the application. Accessible via `app.commands`.
* {class}`~app_model.registries.MenusRegistry`: maintains all of the
[menus and submenus](appp-model-menus) that have been registered with the application.
[menus and submenus](app-model-menus) that have been registered with the application.
Accessible via `app.menus`.
* {class}`~app_model.registries.KeyBindingsRegistry`: maintains the association
between a [KeyBinding](app-model-keybindings) and a command ID in the
Expand Down
10 changes: 7 additions & 3 deletions docs/naps/9-multiple-canvases.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -75,7 +75,7 @@ Providing native support in napari would allow developers to more easily create
* There will be no possibility of a viewer with no canvases.
* Users shall be able to add, remove, and (maybe[^maybe-rearrange]) rearrange canvases.

[^maybe-rearrange]: Exact UI/UX may is yet to be decided, see [UI Architecture](#UI-Design-and-Architecture) for some discussion.
[^maybe-rearrange]: Exact UI/UX may is yet to be decided, see [UI Architecture](nap_9_design_and_architecture) for some discussion.

### Design Considerations & Decisions
Part of this design document is intended to capture the desired behavior and prevent scope creep. At the extreme “multiple canvases” can be achieved with “multiple viewers”. Therefore we need to draw a line somewhere to differentiate a “canvas” from a “viewer”. [^napari-lite]
Expand Down Expand Up @@ -164,8 +164,10 @@ Slice state for each layer is currently stored on the Layer model. Again, see [N
> Also - the various `_<Layer>SliceResponse` classes introduced by async slicing may already fill much of this role. Another option to consider here is to codify a protocol ([`typing.Protocol`](https://docs.python.org/3/library/typing.html#typing.Protocol)) for these classes. Even this protocol may not be necessary - early prototypes use these classes as-is with minimal modifications.
> [name=Ashley A]

(nap_9_design_and_architecture)

Comment on lines +167 to +168
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Suggested change
(nap_9_design_and_architecture)
(nap_9_design_and_architecture)=

Right now the link in the footer doesn't work, because this renders like this:
image

I think this should fix it.

Copy link
Collaborator Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

🤦 I must have done this half asleep, will fix!

Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

no worries 😄
and no rush!

Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Actually we can just use the old label, what doesn't work is the capitalization. So we can just change the reference to read (#ui-design-and-architecture)

### UI Design and Architecture
Specific UI design and architecture remains to be determined. This will be explored as part of step 4 in the [Implementation Plan](#Implementation). UI design needs additional refinement and exploration, and this is expected to continue after basic/core implementation propsed in this NAP is complete. UI changes may also be described in a separate NAP along with a discussion of convenience functions and affordances for common operations. Some placeholder or experimental code will be used in the meantime as a prototype implementation.
Specific UI design and architecture remains to be determined. This will be explored as part of step 4 in the [Implementation Plan](nap_9_implementation). UI design needs additional refinement and exploration, and this is expected to continue after basic/core implementation propsed in this NAP is complete. UI changes may also be described in a separate NAP along with a discussion of convenience functions and affordances for common operations. Some placeholder or experimental code will be used in the meantime as a prototype implementation.
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Same here, using just (#implementation) works


Some open questions here are (for example):
* Should each canvas also have visible dims sliders, or can we keep one set of dims sliders that changes based on the active (selected) canvas?
Expand Down Expand Up @@ -194,6 +196,8 @@ See other image viewers for examples for multiple canvases (mostly demonstrating
* [OHIF/Cornerstone.js](https://www.cornerstonejs.org/live-examples/crosshairs)
* [neuroglancer](https://neuroglancer-demo.appspot.com/#!%7B%22dimensions%22:%7B%22x%22:%5B8e-9%2C%22m%22%5D%2C%22y%22:%5B8e-9%2C%22m%22%5D%2C%22z%22:%5B8e-9%2C%22m%22%5D%7D%2C%22position%22:%5B2914.500732421875%2C3088.243408203125%2C4045%5D%2C%22crossSectionScale%22:3.762185354999915%2C%22projectionOrientation%22:%5B0.31435418128967285%2C0.8142172694206238%2C0.4843378961086273%2C-0.06040274351835251%5D%2C%22projectionScale%22:4593.980956070107%2C%22layers%22:%5B%7B%22type%22:%22image%22%2C%22source%22:%22precomputed://gs://neuroglancer-public-data/flyem_fib-25/image%22%2C%22tab%22:%22source%22%2C%22name%22:%22image%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%22precomputed://gs://neuroglancer-public-data/flyem_fib-25/ground_truth%22%2C%22tab%22:%22source%22%2C%22segments%22:%5B%2221894%22%2C%2222060%22%2C%22158571%22%2C%2224436%22%2C%222515%22%5D%2C%22name%22:%22ground-truth%22%7D%5D%2C%22showSlices%22:false%2C%22layout%22:%224panel%22%7D)

(nap_9_implementation)

Comment on lines +199 to +200
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Suggested change
(nap_9_implementation)
(nap_9_implementation)=

Same as above, the link doesn't work.

## Implementation

1. Introduce minimally disruptive `_canvases` attribute on the ViewerModel
Expand Down Expand Up @@ -221,7 +225,7 @@ See other image viewers for examples for multiple canvases (mostly demonstrating
* Update main widget as `ViewerModel` “active” canvas changes, storing additional canvases and swapping them out as necessary

4. Update `QtViewer` to show multiple canvases simultaneously
* This is exploratory work at the moment, see [UI Architecture](#UI-Design-and-Architecture) section below
* This is exploratory work at the moment, see [UI Architecture](nap_9_design_and_architectures) section below

[^async-only]: Depending on the timeline and prototype implementation, it may be acceptable/preferable for multi-canvas feature to rely on (currently experimental) async slicing ([see NAP-4](https://napari.org/stable/naps/4-async-slicing.html)).

Expand Down
5 changes: 3 additions & 2 deletions docs/tutorials/processing/dask.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -111,6 +111,8 @@ napari.view_image(stack, contrast_limits=[0,2000], multiscale=False)
*Note: providing the* `contrast_limits` *and* `multiscale` *arguments prevents* `napari` *from trying to calculate the data min/max, which can take an extremely long time with big data.
See [napari issue #736](https://github.com/napari/napari/issues/736) for further discussion.*

(dask_image)=

Comment on lines +114 to +115
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Suggested change
(dask_image)=
(dask_image)=

Right now the link below doesn't work. I think this is the fix.

## Make your life easier with `dask-image`

This pattern for creating a `dask.array` from image data
Expand Down Expand Up @@ -205,7 +207,7 @@ directory. The dataset is 3.69 GB unzipped.
```

While we could use plain `dask` through `delayed`, as we have shown above, we
will [make our lives easier](make-your-life-easier-with-dask-image) here and use
will [make our lives easier](dask_images) here and use
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Perfectly fine to create a new target, but FYI if we do [make our lives easier](#make-your-life-easier-with-dask-image) the automatic label works.

`dask-image`.

Using [dask_image.imread](https://image.dask.org/en/latest/dask_image.imread.html#module-dask_image.imread),
Expand Down Expand Up @@ -326,4 +328,3 @@ ready to show you the result on demand!
- [Documentation on dask.delayed](https://docs.dask.org/en/latest/delayed.html)
- [Dask working notes on dask-image](https://blog.dask.org/2019/06/20/load-image-data)
- [Dask working notes on image processing with `dask.array.map_blocks`](https://blog.dask.org/2019/08/09/image-itk)
- [](brain_dataset_tutorial.md)
Loading