fsleyes.plugins.tools.edittransform

This module provides the EditTransformPanel (a.k.a. “Nudge”) class, a FSLeyes control panel which allows the user to adjust the voxToWorldMat of an Image overlay.

class fsleyes.plugins.tools.edittransform.EditTransformAction(overlayList, displayCtx, ortho)

Bases: fsleyes.actions.togglecontrolpanel.ToggleControlPanelAction

The EditTransformAction just toggles an EditTransformPanel. It is added under the FSLeyes Tools menu.

static supportedViews()

The EditTransformAction is restricted for use with OrthoPanel views.

__init__(overlayList, displayCtx, ortho)

Create an EditTransformAction.

destroy()

Called when the OrthoPanel that owns this action is closed. Clears references, removes listeners, and calls the base class destroy method.

__selectedOverlayChanged(*a)

Called when the selected overlay changes. Enables/disables this action (and hence the bound Tools menu item) depending on whether the overlay is an image.

__module__ = 'fsleyes.plugins.tools.edittransform'

class fsleyes.plugins.tools.edittransform.EditTransformPanel(parent, overlayList, displayCtx, ortho)

Bases: fsleyes.controls.controlpanel.ControlPanel

The EditTransformPanel class is a FSLeyes control panel which allows the user to adjust the voxToWorldMat of an Image overlay.

Controls are provided allowing the user to construct a transformation matrix from scales, offsets, and rotations. While the user is adjusting the transformation, the NiftiOpts.displayXform is used to update the overlay display in real time. When the user clicks the Apply button, the transformation is applied to the image’s voxToWorldMat attribute.

This panel also has buttons which allow the user to load/save the transformation matrix - they use functions in the applyflirtxfm and saveflirtxfm modules to load, save, and calculate transformation matrices. When the user loads a matrix, it is used in place of the Image.voxToWorldMat transformation.

Note

The effect of editing the transformation will only be visible if the DisplayContext.displaySpace is set to 'world', or to some image which is not being edited. A warning is shown at the top of the panel if the displaySpace is not set appropriately.

static ignoreControl()

Tells the FSLeyes plugin system not to add the EditTransformPanel as an option to the FSLeyes settings menu. Instead, the EditTransformAction action is added to the tools menu.

static supportedViews()

Overrides ControlMixin.supportedViews(). The EditTransformPanel is only intended to be added to OrthoPanel views.

static defaultLayout()

Returns a dictionary of arguments to be passed to the ViewPanel.togglePanel() method when an EditTransformPanel is created.

__init__(parent, overlayList, displayCtx, ortho)

Create an EditTransformPanel.

Parameters

• parent – The wx parent object.

• overlayList – The OverlayList instance.

• displayCtx – The DisplayContext instance.

• ortho – The OrthoPanel instance.

destroy()

Must be called when this EditTransformPanel is no longer needed. Removes listeners and cleans up references.

__registerOverlay(overlay)

Called by __selectedOverlayChanged(). Stores a reference to the given overlay.

__deregisterOverlay()

Called by __selectedOverlayChanged(). Clears references to the most recently registered overlay.

__overlayNameChanged(*a)

Called when the Display.name of the currently selected overlay changes. Updates the name label.

__selectedOverlayChanged(*a)

Called when the DisplayContext.selectedOverlay or OverlayList.overlays properties change. If the newly selected overlay is an Image, it is registered, and the transform widgets reset.

__formatXform(xform, ctrl)

Format the given xform on the given wx.StaticText ctrl.

__getCurrentXformComponents()

Returns the components of the transformation matrix defined by the scale, offset and rotation widgets.

__getCurrentXform()

Returns the current transformation matrix defined by the scale, offset, and rotation widgets.

__xformChanged(ev=None)

Called when any of the scale, offset, or rotate widgets are modified. Updates the NiftiOpts.displayXform for the overlay currently being edited.

__onApply(ev)

Called when the Apply button is pushed. Sets the voxToWorldMat attribute of the Image instance being transformed.

__resetAllOverlays()

Resets the NiftiOpts.displayXform matrix for all overlays that have been modified, and clears the internal transformation matrix cache.

This method is called by __onReset() and __onCancel().

__onReset(ev=None)

Called when the Reset button is pushed. Resets the transformation.

__onLoadFlirt(ev)

Called when the user clicks the Load FLIRT transform button. Prompts the user to choose a FLIRT transformation matrix and reference image, and then applies the transformation.

__onSaveFlirt(ev)

Called when the user clicks the Save FLIRT button. Saves the current transformation to a FLIRT matrix file.

__onCancel(ev=None)

Called when the Cancel button is pushed. Resets the NiftiOpts.displayXform attribute of the overlay being transformed, and then calls OrthoPanel.toggleEditTransformPanel() to close this panel.

__module__ = 'fsleyes.plugins.tools.edittransform'