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[x] Exports: Pixi can export several ways. You can choose to export the currently selected sprite alone, the currently selected animation, all the layers, and a full image of the current document. The hotkey for exporting is (cmd/ctrl + p). Contextually you can also choose an export scale, if you prefer to scale up your sprite for posting online etc.
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[x] Palettes: Pixi comes with several palettes from LoSpec (.hex). If you just select the dropdown for palettes in the Tools window, Pixi will load and display the palette. Pixi comes with an "assets" folder, which you can drop additional .hex files into the palettes subfolder to have them available for selection as well.
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[x] Sprites: There is a sprite origin editor built into Pixi. If you select the Sprites sidebar item or press the hotkey (s), you can see a list of all sprites in the file. (ctrl/cmd) or (shift) selection will work in this mode, and you can select multiple sprites to edit. The origin sliders will show you where your origin is placed. This is helpful for selecting the point at which you wish to draw your sprites in your final framework, for instance, setting the origin to a characters feet so they sort correctly when drawing later.
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[x] Animations: Pixi comes with an animation editor. There is a sidebar selection for Animations or you can press the hotkey (a) to switch to the animation window and animation tool. Holding down (cmd/ctrl) and click-dragging will create a new animation, while just clicking and dragging without holding down (cmd/ctrl) will select a new set of sprites for the currently selected animation.
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[x] Layers: There is a Layers sidebar option allowing you to create and reorder layers by clicking the + icon and dragging the new layer above or below existing layers.
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[x] Packer: There is a sprite packer built into Pixi to help ease the workflow of getting your projects artwork into a framework for drawing efficiently. You have the choice in the Packer sidebar option to pack the entire project, the currently open file, or all open files. When you press Pack, the relevant files will be loaded and all sprites will be packed individually (layers will not be flattened, each layer will be packed individually). When you select Export which will appear after successfully packing, you can choose a location and name to export your sprite sheet and data. Do not include a file extension for this, just a name, as multiple files will be output. The .atlas file that is exported as well is just a JSON output of the sprite's origins and location on the sprite sheet.
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[x] History: Each action that modifies a file's state will trigger a history item. Drawing, changing animation FPS, changing sprite origins, renaming, etc will all be undoable and redoable. Currently the hotkeys for undo and redo are (ctrl/cmd + z) and (ctrl/cmd + shift + z).
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[x] Colors: Above the palettes, which you can select to change the primary and secondary colors, are the primary and secondary color buttons. Pressing either of them with the left mouse button will swap the two colors, while right clicking will show a color picker for the given color.
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[x] Themes: In the Settings pane, at the very bottom you can find a Style dropdown, which offers two themes by default, dark and light. With either selected, you can right click the colors shown to change them with a color picker. If you wish, you can also click Save As... when done editing and a window should open at the themes folder allowing you to save your new theme for use or sharing. Currently the user's settings are not saved... but this is something I'm looking to do soon.