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Readme docs update, re-order usage table info #454

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Readme docs update, re-order usage table info #454

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a68bbc6
Update README useage table
GenevieveBuckley Jun 10, 2022
9fca1b1
Reorder usage table subsections & remove colons
GenevieveBuckley Jun 10, 2022
42ac229
Fix formatting of table sub-heading
GenevieveBuckley Jun 14, 2022
abbd0fa
Merge branch 'saalfeldlab:master' into readme-docs-update
GenevieveBuckley Jun 17, 2022
a0042be
Update README to fix terminology for side panel
GenevieveBuckley Jun 17, 2022
5f39c00
Update README, links to Paintera tutorial videos
GenevieveBuckley Jul 5, 2022
dccd1b2
Update README link to BigDataViewer navigation docs
GenevieveBuckley Jul 15, 2022
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91 changes: 57 additions & 34 deletions README.md
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Expand Up @@ -271,52 +271,75 @@ Usage: Paintera [--add-n5-container=<container>...

## Usage

Tutorial videos:
* [10 minute overview of Paintera](https://www.youtube.com/watch?v=rNJotgwUYqc)
* [1 hour in-depth Paintera tutorial](https://www.youtube.com/watch?v=ZDcK0aCLoRc)

| Action | Description |
| --------------- | ----------- |
| `P` | Show Status bar on right side |
| (`Shift` +) `Ctrl` + `Tab` | Cycle current source forward (backward) |
| `Ctrl` + `O` | Show open dataset dialog |
| -------------- | ----------- |
| **Opening data** |
| `Ctrl` + `O` | Show open dataset dialog |
| `Ctrl` + `Shift` + `N` | Create new label dataset |
| `P` | Toggle visibility of side panel menu on right hand side |
| `V` | Toggle visibility of current source dataset |
| `Ctrl` + `Tab` | Cycle current source dataset forward |
| `Shift` + `Ctrl` + `Tab` | Cycle current source dataset backward |
| **Navigation controls** |
| Paintera shares the same navigation controls as BigDataViewer. More information is [available here](https://imagej.net/plugins/bdv/#basic-navigation) |
| Mouse scroll wheel, or left/right arrow keys | Scroll through image z planes |
| `Ctrl` + `Shift` + mouse scroll wheel, or up/down arrow keys | Zoom in/out |
| Right mouse click and drag | Pan across image |
| Left/right arrow keys | Rotate view in the same plane |
| Left mouse click and drag | Rotate view to a non-orthoslice image plane |
| `Shift` + `Z` | Reset view: un-rotate but keep scale and translation |
| `M` | Maximize current view |
| `Shift` + `M` | Maximize split view of one slicing viewer and 3D scene |
| `Shift` + `Z` | Un-rotate but keep scale and translation |
| left click | toggle id under cursor if current source is label source (de-select all others) |
| right click / `Ctrl` left click | toggle id under cursor if current source is label source (append to current selection) |
| `Ctrl`+`A` | Select all ids |
| `Ctrl`+`Shift`+`A` | Select all ids in current view |
| `Shift` left click | Merge id under cursor with id that was last toggled active (if any) |
| `Shift` right click | Split id under cursor from id that was last toggled active (if any) |
| `Space` left click/drag | Paint with id that was last toggled active (if any) |
| `Space` right click/drag | Erase within canvas only |
| `Shift` + `Space` right click/drag | Paint background label |
| `Space` wheel | change brush size |
| `F` + left click | 2D Flood-fill in current viewer plane with id that was last toggled active (if any) |
| `Shift` + `F` + left click | Flood-fill with id that was last toggled active (if any) |
| `N` | Select new, previously unused id |
| `S` | Enter shape interpolation mode ( [Shape Interpolation Mode](#shape-interpolation-mode) ) |
| `Ctrl` + `C` | Show dialog to commit canvas and/or assignments |
| `C` | Increment ARGB stream seed by one |
| `Shift` + `C` | Decrement ARGB stream seed by one |
| **Labelling** |
| ***Selecting labels*** |
| Left click | toggle label id under cursor if current source is label source (de-select all others) |
| Right click / `Ctrl` + left click | toggle label id under cursor if current source is label source (append to current selection) |
| `Ctrl` + `A` | Select all label ids |
| `Ctrl` + `Shift` + `A` | Select all label ids in current view |
| `Shift` + `V` | Toggle visibility of not-selected label ids in current source dataset (if dataset is a label source) |
| ***Drawing labels*** |
| `N` | Select new, previously unused label id (you must have a label id selected to paint labels) |
| `Space` + left click/drag | Paint with id that was last toggled active (if any) |
| `Space` + right click/drag | Erase within canvas only |
| `Shift` + `Space` right click/drag | Erase commited/saved label. Paints with the background label id
| `Space` + mouse scroll wheel | Change brush size |
| Left click | Select/deselect the label under the mouse cursor |
| ***Label id color mapping*** |
| `C` | Change label id color mapping (increments ARGB stream seed by one) |
| `Shift` + `C` | Change label id color mapping (decrements ARGB stream seed by one) |
| `Ctrl` + `Shift` + `C` | Show ARGB stream seed spinner |
| `Ctrl` + `Enter` | Merge all selected ids |
| `V` | Toggle visibility of current source |
| `Shift` + `V` | Toggle visibility of not-selected ids in current source (if label source) |
| `R` | Clear mesh caches and refresh meshes (if current source is label source) |
| `L` | Lock last selected segment (if label source) |
| ***Merge/split labels*** |
| `Shift` + right click | Split label id under cursor from id that was last toggled active (if any) |
| `Shift` + left click | Merge label id under cursor with id that was last toggled active (if any) |
| `Ctrl` + `Enter` | Merge all selected label ids |
| ***Flood fill labels*** |
| `F` + left click | 2D Flood-fill in current viewer plane with label id that was last toggled active (if any) |
| `Shift` + `F` + left click | Flood-fill in all image planes with label id that was last toggled active (if any) |
| ***Label shape interpolation mode*** |
| `S` | Enter shape interpolation mode (See [Shape Interpolation Mode](#shape-interpolation-mode) table below) |
| **Bookmarks** |
| `B` | Bookmark current location with the current view settings |
| `Shift` + `B` | Open dialog to add a location bookmark and include a text note |
| `Ctrl` + `B` | Open dialog to select a bookmarked location |
| **Saving** |
| `Ctrl` + `C` | Show dialog to commit canvas and/or assignments |
| `Ctrl` + `S` | Save current project state. Note: This does not commit/persist canvas. Use the `commit canvas` dialog to persist any painted labels across sessions. |
| `Ctrl` + `Shift` + `N` | Create new label dataset |
| `B` | Add bookmark with current global and 3D viewer transforms |
| `Shift` + `B` | Open dialog to add bookmark with text note |
| `Ctrl`+`B` | Open dialog to select bookmark |
| **Scripting** |
| `Shortcut` + `Alt` + `T` | Open scripting REPL |

### Shape interpolation mode

| Action | Description |
| --------------- | ----------- |
| `1` / `2` | Edit first/last section when previewing interpolated shape |
| `Left Arrow` | `Right Arrow` | Edit the previous/next section when previewing interpolated shape
| `S` | Enter shape interpolation mode |
| `Esc` | Exit shape interpolation mode |
| `1` / `2` / ... / `0`| Edit first/middle/last section when previewing interpolated shape |
| `Left Arrow` / `Right Arrow` | Edit the previous/next section when previewing interpolated shape
| `Enter` | Commit interpolated shape into canvas |
| `Esc` | Abort shape interpolation mode |

The mode is activated by pressing the `S` key when the current source is a label source. Then, you can select the objects in the sections by left/right clicking (scrolling automatically fixes the selection in the current section).

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