ivoflipse / devide Goto Github PK

On Windows, sqlite3 is part of the python binaries.  On Linux, the sqlite3
module only works if sqlite3-dev was installed during the johannes python
build.

1. Add the sqlite3-dev check during johannes build.
2. Make sure the binary-building step has a pyinstaller hook for pysqlite3

It should be possible to do rudimentary volume editing, for example to
modify a mask or fix a leaking segmentation.

Startup a wxVTKRWI: interact with the left mouse button, now press and
release the middle mouse button, now release the left button.  Mouse is
still captured.  Click somewhere in the scene, you can now not focus any
other DeVIDE windows, until you click on the console, and back on DeVIDE.

The DICOMBrowser module is coming along nicely.  For this to be shipped
with future releases, we'll need a standard GDCM2 installation.  Create a
johannes install_package (also think about swig!) so that it gets built.

For evaluating mask-based segmentation approaches, a volume overlap module
would be useful.  Base this on the CodeRunner-based approach you made for
Damir and Peter, and also on the new multi-line text output mixin (Issue 33).

There should be a scheduler option to switch schedulers, at the moment
between hybrid and event(-driven).  Hybrid scheduler is the default.

Select graph editor, now try to activate for example file menu with Alt-F.
 No go.

Based on the planned GDCM2 support (see issue 3), create a graphical DICOM
browser.  It should be possible to use this to browse local DICOM
repositories and also to select subsets of DICOM files to be imported as
datasets into DeVIDE networks.

At the moment, johannes is not making use of the vtktudoss install target,
but is simply setting it up to be used from its build directory.

It should also be possible to edit the window/level in a slice3dVWR (option
somewhere in the module main menu, does not have to be in the interface). 
This is useful for example when the data has outliers and the automatic
window/level determination is borked.

With version 8.2, mixing tabs and spaces in a python file, then loading and
executing that in the CodeRunner silently doesn't work.  Also lines
consisting of just whitespace are problematic.

This is an interpreter problem, but the CodeRunner should probably check
for these types of errors before submitting.

1. Create some test cases (and tests!)
2. Make logic for sanitising code (more than already happens).

Would work as follows:
python johannes.py -w wd --no-build-check vtkdevide,vtktudoss

would do the whole thing, but would skip vtkdevide's and vtktudoss's simple
build check, so that these builds would be performed regardless of whether
johannes thinks that they've already been done.

This is useful when you've made small modifications to one of the source
directories, and wish the build and install for that package to be redone.

The installer building system needs to be updated.  makeRelease.sh and
makePackage.sh both need to be streamlined (remove things made redundant by
johannes) and possibly converted to Python.  In the process, make the
windows building more windowsy (i.e. not requiring bash anymore).

This issue is fixed when I can build binaries for posix and nt
automatically after a johannes-driven build.

It is not more better enough

'3' goes stereo (harmless), but 'f' does fly to, and this sometimes warps
the camera.  Disable all these keys to prevent problems.

At the moment trying to get fully functioning DICOMBrowser out the door
ASAP.  When released, refactor DICOM slice viewer code out into re-usable
class for use in other DeVIDE modules.

Do Help | About, now drag the about box in steps over the graph editor.  It
will leave trails (in the form of about box images) all over the editor. 
This is related to some of the exception changes I introduced in the
wxVTKRWI (probably the event.Skip() somewhere). Diagnose and fix in the
wxVTKRWI.

The BinaryBallStructuringElement (and also the Cross element) is not
available in the ITK 3.4 wrapping build.  This could be due to a build
config error.  Find and fix, we need Gaetan's morphology code!

Create a new transfer function editor module.  Look at the colormap editor
in ParaView or the KWWidgets transfer function editor for inspiration.

Re-run script to generate + configure all VTK basic modules.

The new 3-D graph editor doesn't support rubber banding yet (the old one
did).  Before releasing again, this has to be fixed.

wxAUI has been wrapped and is now part of wxPython.  Convert to using that
(instead of PyAUI).

To reproduce:
1. plonk down a glyph (any glyph) on the graph editor canvas
2. zoom in and out with the mouse wheel
3. notice how the text adapts incorrectly to the zoom level

The glyph text labels are currently defined by specifying a rectangle. 
However, the font sizing code is doing something weird, as at certain zoom
levels the text looks like crap.

Debug and fix this problem, might be at VTK level.

This is just a reminder to port relevant 8.2 branch fixes back onto trunk.

First is r2804.

Current DeVIDE DICOM support, based on DCMTK, is quite mature.  However,
GDCM2 reads many more types of DICOM and the write support seems to be
better.  Consider integrating GDCM2 for DICOM support, and perhaps even
dropping DCMTK (although DCMTK will be necessary if we ever want to
function as a DICOM node on the network)

On windows, johannes should start by checking that all the prerequisites
are available (or runnable), for example svn, cvs, devenv, patch.  If these
are not available, it should refuse to run, unless the user has instructed
it to override the checking.

DeVIDE about box has incorrect details, especially related to the fact that
we now have a build system that generates consistently versioned libraries
on all platforms.  Fix these details.

At the moment, ITK filters mostly do 3-D floating point.  Create some
generic utilities so that ITK modules can dynamically specialise based on
input type.

Would be best to instantiate at first set_input(), then keep that class
hanging around until the next type change.  This way, we could get
streaming / hybrid scheduling to work with ITK Modules as well.

After 8.5 release with DICOMBrowser, create sqlite-based caching for dicom
directory searches.  After first search, all dicom metadata and thumbnails
will be put in user-configurable sqlite database.  Database can be
re-created with "scan" and refreshed with "rescan" (only new files are
added, deleted files are discarded from the db).

location of db is written away with module config.  When user loads config,
DICOMBrowser is ready for action without any scanning.

Currently moving a module block just leaves its connections hanging there,
they are updated when the block is dropped.  These should somehow move with
the block (or you should use a preview move).

Make black border around everything.  Generally prettify the module blocks,
they are darned ugly at the moment.

A number of dependency checks are done by johannes.py on Windows.  Some of
these should also be done on posix: svn, cvs and patch.

Place two modules horizontally really far apart, but at the same height. 
Now connect them.  Move them closer to each other, and notice how the
vertical overshoot is drastically affected.

Analyze the problem and try to fix.

The mentioned test is counting segmented voxels with
vtkImageAccumulate.GetVoxelCount(), which gives the TOTAL voxel count.

This test should count SEGMENTED voxels with something like:
GetOutput().GetPointData().GetScalars().GetTuple1(1) 

I.e. the second bin in the histogram, which should contain all 1-valued
voxels.  To be sure, threshold everything to 0 and 1 unsigned chars, then
use the second bin.

Bring the changelog summary up to date for the 8.2 release.  People like
that sort of thing.

Create new module that can be used to give information about _any_ input it
gets.  It should have specific clauses for checking common types of objects
(vtk, itk, numpy, etc) and output relevant information.

Bonus points if you can make an InstantVis window for the incoming data.

1. Remove proprietary code.
2. Cleanup and add some more documentation.
3. Import DeVIDE SVN repo from the TU Delft to code.google.com

johannes needs to build python 2.5.2 (just released).

Suggestion by Bart: implement a slice-by-slice segmentation module that's
based on a parametric active contour that can also be manipulated manually.
 When going to the next slice, transfer the contour and let it relax once,
before allowing the user to start playing again.

After all contours have been set, allow the creation of a polygonal surface
defined by the contours.

Pan the graph editor, then load the network.  It often appears out of the
scene.  Make logic so that after network loading, the canvas zooms and pans
so that it nicely frames the loaded network.

Fire up the help editor, update things for the 8.2 release:
* copyright message
* pointers to website, project site and blog
* pointers to more documentation.

Start DeVIDE up, instantiate a slice3dVWR.  Instead of seeing the full
interface, you only see a single button in the top left corner.  Resizing
the window makes the rest appear.

This appeared with the upgrade to wxPython 2.8.7.1, but could very possibly
be related to issue 7, so let's solve that first.

Create new module that can take anything as output, analyse the data
stream, and then give detailed reporting (perhaps even a small
visualisation) concerning the nature of the data.

Adapt scriptedConfigModuleMixin or make new mixin for modules that have
simple multi-line text (report-like) output, for example statistics modules.

Pressing F1 on the posix version brings up the help, but without any
contents.  The htb file is in the correct location (as far as I can see).

At the moment (200802) pyinstaller does everything we need, albeit after
years of evolution and customisation to facilitate the pyinstaller packaging.

bbfreeze (http://pypi.python.org/pypi/bbfreeze/) is looking very promising.
 It supports more types of resources (at least judging by the
documentation), and what I like especially is that it automatically
packages also a py.exe along with your own executable, where py.exe is a
stand-alone python interpreter with access to everything that your program has.

Do a feasability study concerning the use of bbfreeze for DeVIDE.  If it
would really improve things (what's there to improve at the moment),
consider switching.

I made a nice numpy-based N-D pca routine in FitEllipsoidToMask that takes
a list of points and spits out principal components and what not.

This should be moved out and into either the misc_kit or the numpy_kit.

Besides the normal dataflow ports and connections, observer connections
should also be available.  These operate completely outside of the data
flow scheduling, instead employing real-time subject-observer constructions.

This type of connection should be used for monitoring light-weight data
entities, such as algorithm parameters, metadata, etc.

Johannes can build a subset of packages.  When using this functionality, it
should do some dependency checking.  For example, gdcm can only be built if
the swig and vtk install packages are also executed in the same subset.

install packages should specify a list of dependecies (module-level list of
strings, bound to "dependencies"), and johannes should check that these
have been specified in the subset together with the given install package.

It would be useful having different network segments on different tabs of
the graph editor.  All modules would still be maintained by the
ModuleManager, but the scheduler would only schedule the current tab.