ilastik/volumina

Volume Slicing and Editing

Volumina - Volume Slicing and Editing Library

Installing

conda install -c ilastik-forge -c conda-forge volumina

Using Volumina as an Image Viewer

Currently, only format supported is .npy.

Open an .npy image and display it:

# Usage: volumina image axisorder
volumina <myimage.npy> yx

axisorder should correspond to the data. Only t (time), c (channel), and the spacial axes x, y, z are valid.

Volumina Development

Create a development environment

To set up a development environment, we currently recommend to follow Contributing Guidelines of our main repository ilastik: CONTRIBUTING

volumina's Issues

ImageView2D: test doesn't show all tiles, some tiles are distorted

possibly linked to: #42

estimated time: 1 day

Test for RGB data

Implement PositionModel

Currently, the NavigationControl holds the position (model) internally.
To provide a public interface, we have should have a separate position model, to which the controler can listen.

Estimated time: 2h

HUD should be independant of image scene, is controlled by ViewManager

The ImageView2D should not know what axis it displays with regard to it being part of a 3D viewer.

time estimate: 1h
time spent: free time, ca. 1h

Test on Mac

Setup testing on a Mac machine.

Unify usage of the words 'patches' and 'tiles'

Patches are sometimes not painted due to unavailable paint engine

Seldomly patches are not painted and the according tile is white or contains some garbage.
The following error is printed:

QPainter::begin: Paint device returned engine == 0, type: 3
QPainter::setOpacity: Painter not active
QPainter::end: Painter not active, aborted

To reproduce this bug, set use very small patches (like 10x10) on big data and try a few times.

Est. time: 3 days

Links:
http://www.developer.nokia.com/Community/Wiki/QPainter::begin:Paint_device_returned_engine_%3D%3D_0

Draw component diagram of current architecture

Find out about ownership relations and signalling pathway of the current code. This is necessary to refactor towards the desired architecture (cf. Wiki).

Est. 4 hours

Maximize area of image views: move dock out/in buttons into HUD

the absolute zoom level can be set via NavigationControler attribute

Test code not running on MacOS

Make the test code run on MacOS.

time estimate: 0.5days (thorbenk)

cyclic dependencies between volumeeditor.view3d and volumeeditor.resources

Workaround in view3d.py needs a proper fix:

_icondir = path.dirname(__file__+'/../resources/icons')

Also see:

• http://effbot.org/zone/import-confusion.htm
• http://stackoverflow.com/questions/894864/circular-dependency-in-python

spent time: 20min

Test slice image export functionality

Test functionality concerned with exporting images to harddrive.

Design an architecture for the volumeeditor

Roughly sketch the components and their interactions.

Test on Windows

Setup testing on Windows machine.

Axis colors are wrong

the NavigationControler should handle zooming

sane signaling for slice view repaints: displayNewSlice, repaint, update unification, go over viewManager

time estimate (thorbenk): 2.5h
actual time: 1h (but see follow up ticket)

Eliminate ImageView2D.porting_image, porting_overlay, porting_overlaywidget

This is part of the refactoring of the data model.

Qt Quarterly article on how to implement an OpenGL canvas

http://doc.qt.nokia.com/qq/qq26-openglcanvas.html

Separate volumeeditor into VolumeEditor and VolumeEditorWidget

Part of cleaning up the public inteface of the library.

Est. time: 2 hours

Test for labeling

Replicate labeling as in the old ilastik:

• brushes
• colors

Related to #18, #30

Remove FakeOverlayWidget legacy code

Remove the dependency on a fake OverlayWidget.

re-enable VolumeEditor.updateInfoLabels

after #50 was fixed, this should take
estimated time: 20min

   def updateInfoLabels(self, axis, x, y, valid):
        if not valid:
            return       
#FIXME: resurrect
#        pos = (posX, posY, posZ) = self._imageViews[axis].coordinateUnderCursor()
#        colorValues = self.overlayWidget.getOverlayRef("Raw Data").getOverlaySlice(pos[axis], axis, time=0, channel=0)._data[x,y]
#        
#        self.posLabel.setText("<b>x:</b> %03i  <b>y:</b> %03i  <b>z:</b> %03i" % (posX, posY, posZ))
#        
#        #FIXME RGB is a special case only
#        if isinstance(colorValues, numpy.ndarray):
#            self.pixelValuesLabel.setText("<b>R:</b> %03i  <b>G:</b> %03i  <b>B:</b> %03i" % (colorValues[0], colorValues[1], colorValues[2]))
#        else:
#            self.pixelValuesLabel.setText("<b>Gray:</b> %03i" %int(colorValues))

Test for multichannel/multitime data

Write a test for multichannel data:

• is old behaviour stil replicable?
• what about rgb vs. multichannel?
• how is time dealt with?

Step 1:
create 5d raw data as numpy array
est. time: 2 hours
done

Refactor towards a LabelPaintingControler MV pattern

Examine the old labeling code and refactor it into its own controler connecting with the imageViews.

Estimated time: 2 days

Related to #18, #7

Repair labeling: converting from QGraphicsLineItem to actual pixels in the real data

Question:

• Can we render the path directly to ForegroundLayer without doing the roundtrip over the QGraphiccsLineItem?

Estimated time: 2 days

Related to #7, #30

Remove all dependencies on ilastikdeps

slice intersection marker: use QAction to synchronize initial state with toggle button

See FIXME in volumeeditor.py

Specify volume data interface

OverlayItem takes a data object in its init. Specify the interface of this object for proper ducktyping and decoupling from ilastik. It should be a subset of the DataAccesor interface from ilastik. Document it in the docstring.

est. time: 2 days

Crosshair cursor should snap to pixel center

NavigationControler shouldn't connect itself to the view events

To further decouple, connect the signals originating from the imageViews to the NavigationCrontroler slots from the outside. A controler shouldn't know, where the incoming signals are coming from.

3d+channels data: switching between channels does not work

Refactor ViewManager according to MVC pattern

time estimate: 0.5 day

Development takes place in 'refactor-to-mvc' branch.

time spent: Bernhard+Thorben: Friday afternoon + Saturday

Document exact architecture of refactored code

Draw a component diagram of the architecture using the real Classes and their connections (instead of the rough sketch, what we want to do currently in the wiki). Document design principles.

Implement PositionModel

Currently, the NavigationControler holds the position (model) internally.
To provide a public interface, we have should have a separate position model, to which the controler can listen.

Estimated time: 2h

Crosshair and brush are not properly aligned

During labling, the crosshair and the brush are shifted by a few pixel relative to each other. This is confusing for the user, because he needs to know where exactly the lables will be placed.

imageView2D test segfaults

crosshair cursor updating is broken

time estimate:

• refactor CrossHair cursor (belongs into scene): 1h
• enable updating: 30min

time spent:

• 1.5h start of refactoring in 'refactor-to-mvc' branch
• another 1.5h into refactoring the cursor works again

Artefacts in ImageView2d when resizeing the volumeeditor

When the volumeeditor window ist resizesed the old lines and crosshair are drawn at the old position outside the image until.
When zooming is used, the image is redrawn and the artefacts disapear. Possible solution could be to reimplement the resize event, that after the resize the imageViews are redrawn correctly.

"clean" target to remove *.pyc files

Add "clean" target to build system to remove *.pyc files. pyc files of deleted/renamed py files remain in the filesystem and are causing mayhem from time to time.

Improve performance of cross hair cursor?

Here is an interesting post about how to do a fast cross hair cursor in QGraphicsView:

http://stackoverflow.com/questions/4698029/best-way-to-create-a-long-line-or-cross-line-cursor-in-qt-graphicsview

Image export icon on slice views

Add an icon to the slice views to expert the currently visible slice to an image file. Maybe remove the cumbersome ExportDialog stuff (I don't think it is really needed after this improvement).

Object picking

After pixel-level labeling is done, add object-level labeling (what we used to call picking in ilastik 0.5) and all the corresponding overlay highlighting, etc, issues. Including how to store and pass those objects.

Data normalization belongs into the data model

The OverlayItem already is a 5D datastructure with additional annotations like colortable. However the actual conversion takes place in the ImageSceneRender with a large number of if-else-switches. Move the conversion functions into OverlayItem.

Tiled based drawing leads to artifacts in software mode

At certain zoom levels, one can see the edges between tiles. Possible solution: make the tiles overlap by one pixel.

updated estimated time: 0.25 hours

Undo/Redo

• http://doc.qt.nokia.com/latest/tools-undoframework.html
• http://doc.qt.nokia.com/latest/qundo.html
• http://doc.qt.nokia.com/latest/qundocommand.html

Slicesectionlines are not shown correctly in all 3 Views when moveing the cursor

imageView2D test (OpenGL) misrenders

possibly linked to #21

the viewport of x,y,z slices is changeable from the NavigationControler