Thorben's drtile is necessary for the graph and need to be included into the installer.
It might be convenient to put it on a open project repository.

Encompasses #40

Encompasses #40, #42

I disabled the checkbox for one of the images I loaded, but can still draw labels on it.

Should we simply omit this feature? To make it functional, we would also need a comment / warning that appears if the user tries, without success, to label an image for which labeling has been disabled.

WinXP

When I load three 2D color pictures, I get a blue vertical and a green horizontal line in the middle of the picture. Presumably this is a vestige of a 3D rendering (slice indicator).

I can switch these off by clicking on "slice intersection", but I think for 2D pictures they shouldn't be there in the first place.

Encompasses #40, #42

The mac version of ilastik, gives a segfault when closed.
The last message on the console is cleaning up ....
Problem still to be better investigated.

WinXP: The thumbnails for the console and the GUI that are used in the task bar, or that become visible upon alt-tab, are not identical: they have different subsampling artefacts, with the symbol for the GUI looking better.

It uses calls python2.7. A casual user of the git checkout might run this script. Better move it to scripts/

for example: overlay chooser

WinXP

If I click on "Data -> Add", and select a directory, I get the following warning (no crash):

fatal: Not a git repository (or any of the parent directories): .git

Currently, the feature dialog implements its own preview dialog.

• Either we re-use the ImageView2D or we show the context size directly in the main window somehow.
• If we use an embedded preview, it wood be good to be able to switch between X,Y and Z slice view.

for example: saving the segmentation

Depends on #21 (new layout of main window)

Encompasses #40, #42

The support fro image fomats like tiff of Qt have some problemes of compatbility with py2app which cannot detects plugins, look the discussion http://stackoverflow.com/questions/885906/enabling-jpeg-support-for-qimage-in-py2exe-compiled-python-scripts.
I have spent quite same time trying the suggested fixies but they all don't work.
An easy workoround would be to replace the support for tiff which it is now menaged by Qt with vigra.
This should be a faily easy change in the code of the export view.

To reproduce:
Download file from here:
http://ilastik.org/download.php?cat=12_Documentation&file=cell.ilp

and open it with ilastik's rc-05-06 branch

Deserializing Module Classification
ClassificationModuleMgr::deserialize
-> looking for classifiers in /Project/classifiers
Traceback (most recent call last):
File "/home/thorben/phd/src/ilastik/ilastik/modules/project_gui/gui/projectRibbon.py", line 116, in on_btnOpen_clicked
self.openProject(fileName)
File "/home/thorben/phd/src/ilastik/ilastik/modules/project_gui/gui/projectRibbon.py", line 96, in openProject
self.parent.project = projectClass.Project.loadFromDisk(str(fileName), self.parent.featureCache)
File "/home/thorben/phd/src/ilastik/ilastik/core/projectClass.py", line 124, in loadFromDisk
dataMgr = dataMgrModule.DataMgr.deserialize(projectG, dataG)
File "/home/thorben/phd/src/ilastik/ilastik/core/dataMgr.py", line 531, in deserialize
dataMgr.module[k].deserialize(projectG)
File "/home/thorben/phd/src/ilastik/ilastik/modules/classification/core/classificationMgr.py", line 294, in deserialize
self.classifier.deserialize(f[h5G.name + '/classifiers/' + cid])
File "/home/thorben/phd/src/ilastik/ilastik/modules/classification/core/classifiers/classifierRandomForest.py", line 100, in deserialize
treeCount += h5G.file[allForestsPath+"/"+t+"/options/tree_count"][0]
File "/usr/lib64/python2.7/site-packages/h5py/highlevel.py", line 390, in getitem
return self._get18(name)
File "/usr/lib64/python2.7/site-packages/h5py/highlevel.py", line 351, in _get18
objinfo = h5o.get_info(self.id, name, lapl=self._lapl)
File "h5o_body.pyx", line 165, in h5py.h5o.get_info (h5py/h5o.c:2228)
h5py._stub.KeyError: 'Message type not found (Object header: Object not found)'

Depends on #39 (designer widgets)

This functionality should either be implemented in a sane way in the volumeeditor or removed.
The previous implementation was removed in volumeeditor 'refactor-to-mvc branch'.

The lazyflow module depends on the greenlet python module, which is a (simple to install) C extension for Python.
We need to package this on all three platforms.

This is not too hard (it uses easy_install), but it needs we need to repackage Ilastik and cannot just drop in the new code into the old binaries.

Currently we have at least the following widgets:

• ImageView2D + its HUD widget
• QuadSplitter
• OverlayWidget
• LabelListWidget
• Ribbons (are they completely deprecated?)
• Statusbar
• Several widgets that are inside ilastik dialogs right now

Convert these to be used in Qt designer, so that we can easily rearrange these GUI elements.
For reference see:

• http://www.qtcentre.org/wiki/index.php?title=Designing_Custom_Controls_with_PyQt&oldid=2944
• http://diotavelli.net/PyQtWiki/Using_Python_Custom_Widgets_in_Qt_Designer

Depends on: finished volumeeditor refactoring, finished ilastik GUI refactoring

Time estimate: 1-2 days

E.g. change the title line on gitorious, or make a commit which has that in its description

Depends on #8

Win XP 32: worked on a project, pressed "save as", then cancelled, resulted in:

C:\Programme\ilastik-0.5.06\ilastik\core\projectClass.py:104: DeprecationWarning
: BaseException.message has been deprecated as of Python 2.6
print e.message
Invalid file name (Invalid arguments to routine: Bad value)
Traceback (most recent call last):
File "C:\Programme\ilastik-0.5.06\ilastik\core\projectClass.py", line 84, in s
aveToDisk
fileHandle = h5py.File(fileName,'w')
File "C:\Programme\ilastik-0.5.06\lib\site-packages\h5py\highlevel.py", line 7
93, in init
self.fid = self._generate_fid(name, mode, plist)
File "C:\Programme\ilastik-0.5.06\lib\site-packages\h5py\highlevel.py", line 8
33, in _generate_fid
fid = h5f.create(name, h5f.ACC_TRUNC, fapl=plist)
File "h5f.pyx", line 87, in h5py.h5f.create (h5py\h5f.c:1414)
ValueError: Invalid file name (Invalid arguments to routine: Bad value)
saved Project to

Encompasses #40