lts5 / connectomeviewer Goto Github PK

using linking cameras for 3d views

This displays a slice of brain tissue from brainmaps.org.

Idea

This could make a nice plugin for the ConnectomeViewer. An idea
would be to extend the Connectome File Format to contain slices
which are spatially located. At this location, a clickable box
might be displayed that pop-us up according slices using
PIL, matplotlib (os done here) or the web.

create a tutorial based on example script

using fos, make a chaco histrogram that allows to select the range and from-to brain region, selecting the fibers that have the corresponding fa.

with cfflib

Show edges of nodes with high degree (a kind of thresholding). Other: select the percentual mass of edges and slide over the Range (e.g. show me 10% of the edges in the medium range)

Try to copy libexpat.dll to sytem folder...
...succeeded!
Try to copy libgiftiio.so to sytem folder
...succeeded!
Try to copy zlib1.dll to sytem folder
...succeeded!
Adding Startmenu link ...
Traceback (most recent call last):
File "", line 94, in
File "", line 53, in install
UnicodeEncodeError: 'ascii' codec can't encode characters in position 36-41: ordinal not in range(128)

e.g add a tutorial and an example script (with example data). last part of the pipeline.

can be done easily using networkx and better edge setter for the 3d view. probably other graph viz have already better ways to do this?

Alex's EMBAL package to be release

how to deal with templates? where to store these (e.g. nipy way?) or .enthought app folder.
download on demand?

Kind of analysis Output
∘ Matrix for all values
∘ 3D View
∘ 3D View with metrics
∘ network statistics
• GUI:
∘ select
‣ group-based analysis
‣ single subject comparison
∘ select the subjects / groups
∘ select the procedure
‣ plos biology paper procedure
‣ nbs
‣ bss
∘ select the parameters
∘ generate the script
∘ execute the script
∘ visualize the data

e.g. surface loading in separate thread

tutorial explaining the steps to extract a network for a given species from the semantic connectome wiki and visualize and analyse it with connectomeviewer

simulataneously.

I found another bug when trying to implement the code provided in your matlab matrix tutorial.
cfile.py, the add_network_from_matrix_with_pos method creates
a network object that has no specified graph object, but the constructor for network automatically fails when no graph object is specified. To fix this I added a short circuit operator that checks if self.graph is None before checking if self.graph.number_of_edges() > 0, though I am sure there is a more elegant way of resolving this error.

Quite recently, I got error messages when I want to start my Envisage
app under Ubuntu 10.04 32 bit, not using EPD:

/usr/lib/python2.6/dist-packages/enthought/traits/ui/toolkit.py:128:
UserWarning: Unable to import the 'wx' backend for traits UI; using the
'null' toolkit instead.
"using the 'null' toolkit instead." % toolkit_name )

add eeg / meg forward / inverse solutions

using openmeeg http://www-sop.inria.fr/odyssee/software/OpenMEEG/
also EMBAL for inverse solutions http://embal.gforge.inria.fr/

• visualization interface for amplitude distributions on surfaces
• wrapping openmeeg nicely to include it into connectomeviewer. precompile for linux 32/64bit.
• inputs stored in cff: dipoles + head meshes + sensors
• automatically generate the cond and geom files

When you select in the Preferences to show all node labels, they are created.
When you now toggle a node label with g, yet another label appears instead of removing the displayed one.

the converter converts to cff1.0, needs update if requested

show how to move your camera on a path. for now, you can see on the mayavi documentation on how to do it.

i.e. template atlases for different species/coordinate spaces etc.

think about using/shipping a web-based graph viewer:

• GraphMLViewer http://www.yworks.com/en/products_graphmlviewer_about.html
• gexfwalker?

Hello, I had a trouble installing through pip, and noticed a solution.

Problem: install stops when installing by pip

C:\Users\hoge\Temp\pip-q2cnxn-build>pip install -e .
Obtaining file:///C:/Users/cosac/hoge/Temp/pip-q2cnxn-build
    Complete output from command python setup.py egg_info:
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "C:\Users\cosac\AppData\Local\Temp\pip-q2cnxn-build\setup.py", line 48, in <module>
        package_check('traits', INFO_VARS['traits_min_version'],version_getter=_traits_version)
      File "build_helpers.py", line 176, in package_check
        have_version = version_getter(pkg_name)
      File "C:\Users\cosac\AppData\Local\Temp\pip-q2cnxn-build\setup.py", line 33, in _traits_version
        from traits import version
    ImportError: cannot import name version

Command "python setup.py egg_info" failed with error code 1 in C:\Users\hoge\Temp\pip-q2cnxn-build\

Problem was traits does not have "version", at leaset in my environment (through anaconda, traits ver. 4.6, python 2.7)

# line 32-34
def _traits_version(pkg_name):
    from traits import version
    return version.__version__

I modified the function to return traits.__version__, which worked.

I hope that it helps for other users.

in setup.py, test for

install_requires = ["EnvisageCore >= 3.1.1",
"EnvisagePlugins >= 3.1.1",
"TraitsBackendWX >= 3.2.0",
"EnthoughtBase >= 3.0.3",
"TraitsGUI >= 3.1.0",
"Chaco >= 3.2.0",
"lxml >= 2.2.2"

CodeOracle
http://nipy.sourceforge.net/dipy/examples_built/nii_2_tracks.html

INFO - root.cviewer.plugins.cff.network - Initialize with empty directed
Graph
ERROR - root.cviewer.plugins.cff.network - Cannot set weight key for
network : Random Network

Ansonsten wäre es nützlich zu wissen wie man Eigenschafter der
Visualisierung direkt von der Konsole aus oder mit python scripts
anpassen kann

example nipype tutorial (with example multi-modal datasets) that outputs processed
data into a connectome file that is loaded in connectomeviewer.

ability to cluster, i.e. reoder nodes to see community structure

start discussion related to inclusion of
http://nipy.sourceforge.net/nipy/stable/neurospin/viz.html
visualization utilities in the connectomeviewer

The layout is wrong (CFF View hidden) on first startup.

write it myself using the examples or wait for dipy people to complete/release

On a fresh NeuroDebian VM (6.0.2), installation of LTS5-connectomeviewer-release-2.0.0-RC2-0-g2317482.tar.gz goes without problem. On startup:

brain@neurodebian:~$ connectomeviewer -v
INFO - root - *****
INFO - root - logfile: /home/brain/.enthought/ch.connectome.viewer/cviewer.log
INFO - root - cviewer version: 2.0.0-RC2
INFO - root - python executable: /usr/bin/python
INFO - root - python version: 2.6.6 (r266:84292, Dec 27 2010, 00:02:40) [GCC 4.4.5]
INFO - root - uname: Linux neurodebian 2.6.32-5-686 #1 SMP Tue Mar 8 21:36:00 UTC 2011 i686
INFO - root - distribution: debian 6.0.1
INFO - root - execution date and time: Friday, 13. May 2011 10:29AM
INFO - root - *****
INFO - root - Plugins
INFO - root - *******
INFO - root - Added ConnectomeFile2Plugin
INFO - root - Added CViewerUIPlugin
INFO - root - Added BindingsPlugin
INFO - root - Added Oracle Plugin
INFO - root - Added Network Based Statistics (NBS) Plugin
INFO - root - Added Diffusion in Python (DiPy) Plugin
INFO - root - Added Connectome Mapper Plugin
Exception occurred in traits notification handler.
Please check the log file for details.
Exception occurred in traits notification handler for object: <enthought.envisage.ui.workbench.workbench_window.WorkbenchWindow object at 0xb0c8adc>, trait: active_perspective, old value: None, new value: Perspective(cviewer.perspective.viewer_perspective)
Traceback (most recent call last):
File "/usr/lib/python2.6/dist-packages/enthought/traits/trait_notifiers.py", line 358, in call_3
self.handler( object, old, new )
File "/usr/lib/python2.6/dist-packages/enthought/pyface/workbench/workbench_window.py", line 812, in _active_perspective_changed
self._show_perspective(old, new)
File "/usr/lib/python2.6/dist-packages/enthought/pyface/workbench/workbench_window.py", line 767, in _show_perspective
new.create(self)
File "/usr/lib/python2.6/dist-packages/enthought/pyface/workbench/perspective.py", line 90, in create
self._add_contents(window, self.contents)
File "/usr/lib/python2.6/dist-packages/enthought/pyface/workbench/perspective.py", line 115, in _add_contents
view.visible = False
AttributeError: 'NoneType' object has no attribute 'visible'
Traceback (most recent call last):
File "/usr/local/bin/connectomeviewer", line 4, in
main()
File "/usr/local/lib/python2.6/dist-packages/cviewer/run.py", line 88, in main
cviewer.main(sys.argv[1:])
File "/usr/local/lib/python2.6/dist-packages/cviewer/app.py", line 314, in main
self.application.run()
File "/usr/local/lib/python2.6/dist-packages/cviewer/cviewer_workbench_application.py", line 74, in run
window.open()
File "/usr/lib/python2.6/dist-packages/enthought/pyface/workbench/workbench_window.py", line 144, in open
self._create()
File "/usr/lib/python2.6/dist-packages/enthought/pyface/ui/wx/application_window.py", line 157, in _create
self._create_trim_widgets(self.control)
File "/usr/lib/python2.6/dist-packages/enthought/pyface/i_application_window.py", line 104, in _create_trim_widgets
self._create_menu_bar(parent)
File "/usr/lib/python2.6/dist-packages/enthought/pyface/ui/wx/application_window.py", line 92, in _create_menu_bar
menu_bar = self.menu_bar_manager.create_menu_bar(parent)
File "/usr/lib/python2.6/dist-packages/enthought/pyface/workbench/action/menu_bar_manager.py", line 31, in create_menu_bar
parent, controller=controller
File "/usr/lib/python2.6/dist-packages/enthought/pyface/ui/wx/action/menu_bar_manager.py", line 49, in create_menu_bar
menu = item.create_menu(parent, controller)
File "/usr/lib/python2.6/dist-packages/enthought/pyface/ui/wx/action/menu_manager.py", line 58, in create_menu
return _Menu(self, parent, controller)
File "/usr/lib/python2.6/dist-packages/enthought/pyface/ui/wx/action/menu_manager.py", line 110, in init
self.refresh()
File "/usr/lib/python2.6/dist-packages/enthought/pyface/ui/wx/action/menu_manager.py", line 151, in refresh
for group in manager.groups:
File "/usr/lib/python2.6/dist-packages/enthought/pyface/workbench/action/view_menu_manager.py", line 70, in _groups_default
self._view_group = self._create_view_group(self.window)
File "/usr/lib/python2.6/dist-packages/enthought/pyface/workbench/action/view_menu_manager.py", line 124, in _create_view_group
self._initialize_view_group(window, group)
File "/usr/lib/python2.6/dist-packages/enthought/pyface/workbench/action/view_menu_manager.py", line 132, in _initialize_view_group
views.sort(None, lambda view: view.name)
File "/usr/lib/python2.6/dist-packages/enthought/pyface/workbench/action/view_menu_manager.py", line 132, in
views.sort(None, lambda view: view.name)
AttributeError: 'NoneType' object has no attribute 'name'

http://www.connectomeviewer.org/documentation/users/tutorials/tut_addnet.html

In [14]: cfile.add_network_from_matrix_with_pos(name='Random Network', \
    matrix = np.random.random( (20,20) ), pos = np.random.random( (20, 3) ) * 10, \
    directed = True)
.......:        
ERROR - root.cviewer.plugins.cff.network - Cannot initialize network. No graph information available
ERROR:root.cviewer.plugins.cff.network:Cannot initialize network. No graph information available
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)

/usr/local/lib/python2.6/dist-packages/ConnectomeViewer-0.1.6-py2.6-linux-x86_64.egg/cviewer/plugins/cff/network.pyc in __init__(self, name, src, directed, pickled_graph, hierarchical, hypergraph, graph)
    162         else:
    163             # try grabbing first edge from the graph

--> 164             if self.graph.number_of_edges() > 0:
    165                 it = self.graph.edges_iter(data=True)
    166                 edg = it.next()

AttributeError: 'NoneType' object has no attribute 'number_of_edges'

    # initializes the weight key of the graph
    # with the first edgekey
    if len(self.edgekeys) > 0:
        edgk = self.edgekeys.keys()
        if not 'weight' in edgk:
            self.set_weight_key(edgk[0])
    else:
        # try grabbing first edge from the graph
        if self.graph.number_of_edges() > 0:
            it = self.graph.edges_iter(data=True)
            edg = it.next()
            if len(edg[2]) > 0:
                # if it has a weigth key, just leave it
                edgk = edg[2].keys()
                if not 'weight' in edgk:
                    self.set_weight_key(edgk[0])
        else:
            logger.error('Cannot set weight key for network : ' + self.networkname)

generate an overview of the currently loaded dataset with
statistics as pdf

create cfflib, add a documentation for cfflib etc.

For CodeOracle
http://nipy.sourceforge.net/dipy/examples_built/tractography_clustering.html

The current installation instructions on a fresh NeuroDebian machine lead to the following:

brain@neurodebian:~/nibabel$ connectomeviewer -v
INFO - root - *****
INFO - root - logfile: /home/brain/.enthought/ch.connectome.viewer/cviewer.log
INFO - root - cviewer version: 2.0.0-RC1 
INFO - root - python executable: /usr/bin/python
INFO - root - python version: 2.6.6 (r266:84292, Dec 26 2010, 22:31:48) [GCC 4.4.5]
INFO - root - uname: Linux neurodebian 2.6.32-5-amd64 #1 SMP Wed Jan 12 03:40:32 UTC 2011 x86_64 
INFO - root - distribution: debian 6.0.1 
INFO - root - execution date and time: Sunday, 17. April 2011 06:44PM
INFO - root - *****
INFO - root - Plugins
INFO - root - *******
INFO - root - Added ConnectomeFile2Plugin
INFO - root - Added CViewerUIPlugin
INFO - root - Added BindingsPlugin
INFO - root - Added Oracle Plugin
INFO - root - Added sLORETA Converter Plugin
INFO - root - Added Network Based Statistics (NBS) Plugin
INFO - root - Added Diffusion in Python (DiPy) Plugin
Exception occurred in traits notification handler.
Please check the log file for details.
Exception occurred in traits notification handler for object: , trait: active_perspective, old value: None, new value: Perspective(cviewer.perspective.viewer_perspective)
Traceback (most recent call last):
  File "/usr/lib/python2.6/dist-packages/enthought/traits/trait_notifiers.py", line 358, in call_3
    self.handler( object, old, new )
  File "/usr/lib/python2.6/dist-packages/enthought/pyface/workbench/workbench_window.py", line 812, in _active_perspective_changed
    self._show_perspective(old, new)
  File "/usr/lib/python2.6/dist-packages/enthought/pyface/workbench/workbench_window.py", line 748, in _show_perspective
    self.layout.set_view_memento(view_memento)
  File "/usr/lib/python2.6/dist-packages/enthought/pyface/ui/wx/workbench/workbench_window_layout.py", line 268, in set_view_memento
    self._wx_view_dock_window.set_structure(memento, handler)
  File "/usr/lib/python2.6/dist-packages/enthought/pyface/ui/wx/workbench/workbench_dock_window.py", line 151, in set_structure
    sizer.SetStructure(self.control.GetParent(), structure, handler)
  File "/usr/lib/python2.6/dist-packages/enthought/pyface/dock/dock_sizer.py", line 3972, in SetStructure
    control = handler.resolve_id( id )
  File "/usr/lib/python2.6/dist-packages/enthought/pyface/ui/wx/workbench/view_set_structure_handler.py", line 59, in resolve_id
    view = window.get_view_by_id(id)
  File "/usr/lib/python2.6/dist-packages/enthought/pyface/workbench/workbench_window.py", line 466, in get_view_by_id
    for view in self.views:
  File "/usr/lib/python2.6/dist-packages/enthought/envisage/ui/workbench/workbench_window.py", line 155, in _views_default
    return [factory(window=self) for factory in self._views]
  File "/usr/local/lib/python2.6/dist-packages/cviewer/plugins/cff2/cff_plugin.py", line 100, in _cfile_view_factory
    from cviewer.plugins.cff2.ui.cff_view import CFFView
  File "/usr/local/lib/python2.6/dist-packages/cviewer/plugins/cff2/ui/cff_view.py", line 20, in 
    from cviewer.plugins.cff2.cfile import CFile
  File "/usr/local/lib/python2.6/dist-packages/cviewer/plugins/cff2/cfile.py", line 20, in 
    from csurface import CSurface
  File "/usr/local/lib/python2.6/dist-packages/cviewer/plugins/cff2/csurface.py", line 19, in 
    from cviewer.plugins.cff2.csurface_darray import CSurfaceDarray
  File "/usr/local/lib/python2.6/dist-packages/cviewer/plugins/cff2/csurface_darray.py", line 18, in 
    from nibabel.gifti.util import intent_codes
ImportError: cannot import name intent_codes
Traceback (most recent call last):
  File "/usr/local/bin/connectomeviewer", line 4, in 
    main()
  File "/usr/local/lib/python2.6/dist-packages/cviewer/run.py", line 88, in main
    cviewer.main(sys.argv[1:])
  File "/usr/local/lib/python2.6/dist-packages/cviewer/app.py", line 304, in main
    self.application.run()
  File "/usr/local/lib/python2.6/dist-packages/cviewer/cviewer_workbench_application.py", line 74, in run
    window.open()
  File "/usr/lib/python2.6/dist-packages/enthought/pyface/workbench/workbench_window.py", line 144, in open
    self._create()
  File "/usr/lib/python2.6/dist-packages/enthought/pyface/ui/wx/application_window.py", line 157, in _create
    self._create_trim_widgets(self.control)
  File "/usr/lib/python2.6/dist-packages/enthought/pyface/i_application_window.py", line 104, in _create_trim_widgets
    self._create_menu_bar(parent)
  File "/usr/lib/python2.6/dist-packages/enthought/pyface/ui/wx/application_window.py", line 92, in _create_menu_bar
    menu_bar = self.menu_bar_manager.create_menu_bar(parent)
  File "/usr/lib/python2.6/dist-packages/enthought/pyface/workbench/action/menu_bar_manager.py", line 31, in create_menu_bar
    parent, controller=controller
  File "/usr/lib/python2.6/dist-packages/enthought/pyface/ui/wx/action/menu_bar_manager.py", line 49, in create_menu_bar
    menu = item.create_menu(parent, controller)
  File "/usr/lib/python2.6/dist-packages/enthought/pyface/ui/wx/action/menu_manager.py", line 58, in create_menu
    return _Menu(self, parent, controller)
  File "/usr/lib/python2.6/dist-packages/enthought/pyface/ui/wx/action/menu_manager.py", line 110, in __init__
    self.refresh()
  File "/usr/lib/python2.6/dist-packages/enthought/pyface/ui/wx/action/menu_manager.py", line 151, in refresh
    for group in manager.groups:
  File "/usr/lib/python2.6/dist-packages/enthought/pyface/workbench/action/view_menu_manager.py", line 70, in _groups_default
    self._view_group = self._create_view_group(self.window)
  File "/usr/lib/python2.6/dist-packages/enthought/pyface/workbench/action/view_menu_manager.py", line 124, in _create_view_group
    self._initialize_view_group(window, group)
  File "/usr/lib/python2.6/dist-packages/enthought/pyface/workbench/action/view_menu_manager.py", line 131, in _initialize_view_group
    views = window.views[:]
  File "/usr/lib/python2.6/dist-packages/enthought/envisage/ui/workbench/workbench_window.py", line 155, in _views_default
    return [factory(window=self) for factory in self._views]
  File "/usr/local/lib/python2.6/dist-packages/cviewer/plugins/cff2/cff_plugin.py", line 100, in _cfile_view_factory
    from cviewer.plugins.cff2.ui.cff_view import CFFView
  File "/usr/local/lib/python2.6/dist-packages/cviewer/plugins/cff2/ui/cff_view.py", line 20, in 
    from cviewer.plugins.cff2.cfile import CFile
  File "/usr/local/lib/python2.6/dist-packages/cviewer/plugins/cff2/cfile.py", line 20, in 
    from csurface import CSurface
  File "/usr/local/lib/python2.6/dist-packages/cviewer/plugins/cff2/csurface.py", line 19, in 
    from cviewer.plugins.cff2.csurface_darray import CSurfaceDarray
  File "/usr/local/lib/python2.6/dist-packages/cviewer/plugins/cff2/csurface_darray.py", line 18, in 
    from nibabel.gifti.util import intent_codes
ImportError: cannot import name intent_codes

It looks like a very specific version of nibabel is required. The official 1.0.2 release does not have intent_codes in nibabel.gifti.util, and it was recently moved in the dev branch ( nipy/nibabel@02310a5 ). Using the dev version from one commit before this seems to work:

git clone https://github.com/nipy/nibabel.git
cd nibabel
git checkout 2d3eae006
sudo python setup.py install
connectomeviewer -v

to make connectomeviewer xnat ready for upcoming decades of happy data sharing.

The From / To / Value fields are empty for an example datasets.

initiate discussion to package bct-cpp for debian
CC neurodebian-devel http://lists.alioth.debian.org/mailman/listinfo/neurodebian-devel

include in the correct perspective.

Hi,
Just FYI, for me installation of required ubuntu packages (line 36 or installation script) didn't run unless I removed "python-dicom" from the list. One consequence of not removing it was that cviewer doesn't install with IPython (it has normal Python window instead),
thanks,
spiro

Ubuntu 10.04 LTS on amd64

The tabbed panels showing the thresholding options for the "Edge Parameter" dialog does now show up correctly in Windows XP, but it does in Linux.

right click on surface to render and layout graph (as double-click)

not only on surface as it is now

include it as external lib and write tutorial
http://packages.python.org/pyxnat/

including example with
http://central.xnat.org