February 2006 Commit Log

Number of Commits:
208
Number of Active Developers:
23
callahan 2006-02-28 17:44 Rev.: 33370

Add a function for computing the closest points between two lines.

57 lines of code changed in 3 files:

dav 2006-02-28 17:37 Rev.: 33369

Added the PNG .h include path to the compile line.

1 lines of code changed in 1 file:

dav 2006-02-28 16:47 Rev.: 33368

First try at fixing png checks. Needed to include image_defs.h to get
the HAVE_PNG flags... then put #if's around all the png references...
Darby will be verifying that I did this correclty.

Removed the png_testdefs.h.in file as it duplicated what is already in
image_testdefs.h. -Dav

30 lines of code changed in 2 files:

harman 2006-02-28 14:43 Rev.: 33366

shift the cellPosition by -dx/2 if variable is (X,Y,Z)FC variable

28 lines of code changed in 1 file:

darbyb 2006-02-28 12:59 Rev.: 33364

Remove dependency on ImageMagick. Now use PNG library to read/write files and use ImageMagick's convert program (if available) to convert to appropriate file.

691 lines of code changed in 8 files:

sachse 2006-02-28 11:20 Rev.: 33361

bug fixes: get_cell=>get_node, indexing

19 lines of code changed in 1 file:

mdavis 2006-02-27 19:16 Rev.: 33360

Remove dead code: Core/Geom/OpenGLContext.[cc,h] and Dataflow/Modules/Render/ViewImage.cc

10 lines of code changed in 10 files:

mdavis 2006-02-27 16:02 Rev.: 33359

Allow spaces in Subnet names

1 lines of code changed in 1 file:

jfsheph 2006-02-27 15:37 Rev.: 33358

Adding mesh smoothing via a smart Laplacian scheme that guarantees L-infinity improvement for element shape for tet and hex meshes using the MESQUITE libraries. Also, fixed an initialization bug in MeshQuality to ensure that the low metrics are reported correctly and changed an error to a warning in the IsoClip for hexes module.

635 lines of code changed in 6 files:

kuzimmer 2006-02-27 15:35 Rev.: 33357

add a 'show boundary values' button to GridVisualizer

35 lines of code changed in 2 files:

worthen 2006-02-27 13:18 Rev.: 33356

Fix deadlock in experimental tcl thread mode

4 lines of code changed in 1 file:

harman 2006-02-27 11:12 Rev.: 33355

added the debugging variables
grad_P_(X,Y,Z)FC & grad_dp_(X,Y,Z)FC
These pressure gradients come directly from the face centered velocity
calculations.

guni2dRT fails on this, for no good reason.

104 lines of code changed in 6 files:

mdavis 2006-02-24 19:16 Rev.: 33354

Look for Freetype2 in Thirdparty

36 lines of code changed in 2 files:

mdavis 2006-02-24 16:30 Rev.: 33352

Fix GDCM

2 lines of code changed in 2 files:

mdavis 2006-02-24 16:19 Rev.: 33351

Change --with-insight flag to not use /lib/InsightToolkit extension. Change -litkniftiio and -litkznz to -lITKniftiio and -lITKznz

162 lines of code changed in 2 files:

mdavis 2006-02-24 15:27 Rev.: 33350

Fix mouse actions

1 lines of code changed in 1 file:

callahan 2006-02-24 14:39 Rev.: 33349

Fix debugging code

3 lines of code changed in 1 file:

mdavis 2006-02-24 13:55 Rev.: 33348

Add string_to_unsigned_long

8 lines of code changed in 2 files:

callahan 2006-02-24 13:49 Rev.: 33347

Add all elements to the output list in TetVolMesh::insert_node_in_cell_2. Shrink duplicate code.

54 lines of code changed in 2 files:

callahan 2006-02-24 13:20 Rev.: 33346

Fix bug in setting neighbors correctly on triangle splits (in TriSurfMesh::insert_node_into_face). Also fix bug in not sending changed neighbor elements along. Send all of them from the mesh function.

29 lines of code changed in 2 files:

harman 2006-02-24 10:20 Rev.: 33344

printData:
-d_dbgLevel is now a vector<int>
-d_dbgBeginIndx d_dbg_EndIndx are now vector<IntVector>
Can now print out multiple levels of data during a sus run. I'll change
all the input files later.

55 lines of code changed in 4 files:

callahan 2006-02-23 19:14 Rev.: 33343

Fix bug in compute_edges, a resync would not clear the array resulting in a bad edge table and memory leak.

1 lines of code changed in 1 file:

callahan 2006-02-23 16:14 Rev.: 33342

Clean up synchronize_lock usage in TriSurfMesh. Lock all of synchronize() rather than individual functions. Rewrite of orient_faces, needs testing.

36 lines of code changed in 1 file:

mdavis 2006-02-23 15:51 Rev.: 33341

Header for last checkin

3 lines of code changed in 1 file:

mdavis 2006-02-23 15:47 Rev.: 33340

Fix tcl error on windoze

107 lines of code changed in 1 file:

worthen 2006-02-23 15:22 Rev.: 33339

Port Insight to windows, fix recent commits and Containers to work with Windows, and use an $(OBJEXT) in make variables instead of assuming .o for compiling

884 lines of code changed in 66 files:

dav 2006-02-23 15:03 Rev.: 33338

The useFake* scripts now take an 'on' or 'off' parameter. This
prevents them from automatically toggling the on/off setting which
might not be what the user would expect. The make target in
StandAlone/sub.mk defaults to 'on'... you can use it multiple times
and it will just ignore subsequent invocations. If you want to undo
the useFake*, you will have to call the script by hand.

87 lines of code changed in 7 files:

jfsheph 2006-02-23 14:47 Rev.: 33337

removing an unneeded file

0 lines of code changed in 1 file:

jfsheph 2006-02-23 14:46 Rev.: 33336

ongoing updates in an attempt to add a MESQUITE interface. Thanks to Marty for his continual efforts in helping me get something that will work...

899 lines of code changed in 5 files:

callahan 2006-02-22 18:44 Rev.: 33335

Patch up edge_neighbors in insert_node_in_face

61 lines of code changed in 1 file:

mjc 2006-02-22 18:06 Rev.: 33334

initial commit supporting subnets again

313 lines of code changed in 6 files:

callahan 2006-02-22 16:12 Rev.: 33332

Fix TriSurfMesh::insert_node_in_face to handle degeneracies and boundaries.

179 lines of code changed in 2 files:

callahan 2006-02-22 14:58 Rev.: 33331

Preliminary framework for inserting fields into a trisurfmesh in the InsertField module.

259 lines of code changed in 5 files:

callahan 2006-02-22 14:46 Rev.: 33330

Fix closest_point_on_tri implementation.

26 lines of code changed in 1 file:

mdavis 2006-02-22 12:21 Rev.: 33328

Fix display of 2D transfer function in slice views. Was incorrectly using value volume instead of gradient magnitude volume

1 lines of code changed in 1 file:

mdavis 2006-02-22 11:11 Rev.: 33327

Save point positions to disk

9 lines of code changed in 1 file:

mjc 2006-02-22 09:32 Rev.: 33326

clarify gui dependent methods through gui_ naming scheme

54 lines of code changed in 2 files:

mjc 2006-02-22 09:31 Rev.: 33325

addition of subnets to the dtd

10 lines of code changed in 1 file:

mjc 2006-02-22 09:31 Rev.: 33324

formatting changes

61 lines of code changed in 1 file:

dav 2006-02-21 18:41 Rev.: 33323

Fixed typo in variable name

2 lines of code changed in 1 file:

dav 2006-02-21 18:32 Rev.: 33322

A nets/compare_mms.srn

Added an example net that shows the use of the CompareMMS module.

M Dataflow/GUI/CompareMMS.tcl

- Added the field name and time (which come across from the C++ side).
- Added radio buttons to select which field to output (original, exact, or diff).
- set_to_exact() is not used yet.

M Dataflow/Modules/Selectors/FieldExtractor.cc

Added the timestep 'time' to the field through the properties so that
the CompareMMS module can use that time for generating the exact
solution.

M Dataflow/Modules/Operators/CompareMMS.cc

Updated so it does its job now. Probably can be cleaned up some, but
it is in fairly good shape now.

274 lines of code changed in 4 files:

dav 2006-02-21 18:23 Rev.: 33321

Fixed the check for 32/64 bit version that the user specifies when it
is different from what the machine natively creates.

Added warning output message for AIX for when configure yanks the
carpet out from beneath you and puts in the compiler that it thinks
you should use.

27 lines of code changed in 2 files:

dav 2006-02-21 18:18 Rev.: 33320

Updated documentation on label_pair

4 lines of code changed in 1 file:

kuzimmer 2006-02-21 14:10 Rev.: 33318

Changed MAX* constants to *_MAX definitions found in float.h and limits.h. Changed sci_values.h to reflect this change. Users should still include sci_values.h, so modifications for platform specific issues can be handled there.

129 lines of code changed in 69 files:

mdavis 2006-02-21 13:45 Rev.: 33317

Fixes loading .srn nets when an existing net is already loaded. Because TCL sucks and does not unset variables right away, we have to insert an artifical wait to load the net after clearCanvas. This is only a temporary fix, but it works.

2 lines of code changed in 1 file:

worthen 2006-02-21 12:47 Rev.: 33316

Remove newalgo and NEWALGO (confusing names). Have inputs and GS refer to the same subdir name, except with tests which require the inputs from a different dir. Fix dumping of *-short.log for short errors on Models, UCF, etc., the ones that use different args to sus than their input folders

38 lines of code changed in 1 file:

harman 2006-02-20 15:06 Rev.: 33314

added operating system conditional for MPMICE tests.

- eliminated the need for the variable uda_dir. We now search the goldStandards
component directory for the uda that you want to compare against. This means that
every regression test must have a uniquely named uda.

29 lines of code changed in 1 file:

harman 2006-02-20 11:16 Rev.: 33313

removed dead blazer weeds. Is this from the day's of Bob Kesler?

0 lines of code changed in 2 files:

sachse 2006-02-18 18:37 Rev.: 33312

Dynamic compilation added, generalization of dipole

431 lines of code changed in 2 files:

sachse 2006-02-17 20:01 Rev.: 33311

get_weights and get_derivate_weights defined as static

44 lines of code changed in 22 files:

sachse 2006-02-17 19:00 Rev.: 33310

get_derivate_weights added

9 lines of code changed in 1 file:

guilkey 2006-02-17 17:02 Rev.: 33309

Attempting to clarify the explicit heat conducton code by more correctly
naming variables and adding a little documentation.

98 lines of code changed in 7 files:

dav 2006-02-17 16:54 Rev.: 33308

Untabified the file.

The only real update I made was to add keyboard bindings for the left
and right arrow keys... I couldn't stand having to use the mouse to
move forward and backward in time... These are the lines that do
this:

bind $w <KeyPress-Right> "$this incTime"
bind $w <KeyPress-Left> "$this decTime"

(Also added the (simple) decTime and incTime functions to do the
actual work.)

160 lines of code changed in 1 file:

mdavis 2006-02-17 16:17 Rev.: 33307

Add checkbutton to enable/disable filtering of 3D textures

9 lines of code changed in 1 file:

harman 2006-02-17 16:09 Rev.: 33306

changed some of the debugging printouts

16 lines of code changed in 2 files:

worthen 2006-02-17 15:36 Rev.: 33305

Put time before delt (to look nicer) in the index.xml file

2 lines of code changed in 1 file:

dgroulx 2006-02-17 15:23 Rev.: 33304

Added setprecision(17) to the double to string converters when we store the current time in
the master index.xml file, since it was being truncated and irking the regression tester.

2 lines of code changed in 1 file:

yguo 2006-02-17 15:01 Rev.: 33302

Modify the subroutine of comparing if two doubles are equal.

9 lines of code changed in 1 file:

yguo 2006-02-17 15:00 Rev.: 33301

Modify the subroutine of comparing if two doubles are equal by adding in a parameter "tolerance".

1 lines of code changed in 1 file:

yguo 2006-02-17 14:59 Rev.: 33300

Add the effect of crack surface traction due to frictional sliding on J-integral.

111 lines of code changed in 1 file:

yguo 2006-02-17 14:57 Rev.: 33299

Comment out "if(KI<0.) KI=0.; " in crack propagation simulation.

0 lines of code changed in 2 files:

callahan 2006-02-17 14:17 Rev.: 33298

Consolidate the synchronization locking in TriSurfMesh

46 lines of code changed in 1 file:

guilkey 2006-02-17 13:54 Rev.: 33297

Cleaned up some of the conditionals related to whether or not fracture
is involved.

9 lines of code changed in 1 file:

dgroulx 2006-02-17 13:48 Rev.: 33296

Modifed how timesteps were being lazily loaded so that they will actually be loaded now when needed.

28 lines of code changed in 2 files:

guilkey 2006-02-17 11:53 Rev.: 33295

80 column format, it's not just a good idea, it's the law. (Well, it oughta
be.) scheduleTimeAdvance formatting.

79 lines of code changed in 1 file:

guilkey 2006-02-17 10:30 Rev.: 33294

Implemented a means to end_on_max_time_exactly if so specified in the
Time section of the input file. The final delT will be adjust to hit
the desired time.

Also, removed some unused code from MPM-IdealGas.cc

8 lines of code changed in 4 files:

dav 2006-02-16 19:25 Rev.: 33293

Fixed typo so that compilation would pass... Thanks for helping me pad
my commit stats. ;-)

1 lines of code changed in 1 file:

callahan 2006-02-16 19:06 Rev.: 33292

Fix debug assert, wrong number of nodes.

1 lines of code changed in 1 file:

dav 2006-02-16 18:50 Rev.: 33291

Major update:
------------
Simplified the (XML) calls appendElement() and appendChild() by
removing the embedded newline and tab parameters. The XML outputer
(libxml2) will indent things properly without them. Also cleaned up
the ProblemSpec.cc file to remove the appendText() call which was
commented out and thus not doing anything.

Minor updates:
-------------
In some files placed the function return type on a separate line.

In StandAlone, sus requires Core/Datatypes (because of a circular
dependency that will be removed soon... however, this allows sus to
run on the SGI's for now).

Removed extra ";" from the end of MMS class constructors.

Added field name to ScalarMinMax (which I only partially checked in before).

Some restructuring of CompareMMS.cc, but it is not functional yet.

967 lines of code changed in 138 files:

dav 2006-02-16 18:30 Rev.: 33290


First round of clean up of these files... in the next round they will
have to be moved somewhere else to remove the circular dependency they
create on Core/Datatypes. These changes where made to clean up the
files as I was trying to determine why the SGI build was breaking.

M FieldInformation.h

Removed #include <TypeDescription> as it is not used.

M FieldInformation.cc

Removed the "namespace SCIRun {" construct from the .cc file. Use
"using namespace SCIRun;" instead. Also use std::string to clean up
the file some. Put the function return type on its own line.

1 lines of code changed in 2 files:

dav 2006-02-16 18:26 Rev.: 33288

M Core/GUI/Util.tcl

Added the label_pair utility function. Creates a label/text_var pair.

M Packages/Uintah/Dataflow/GUI/ScalarMinMax.tcl

Added in the field_name to the GUI. Added separators between the min
and max sections. Now use the label_pair utility from Core/Util.

M Packages/Uintah/Dataflow/XML/CompareMMS.xml

Take in a Scalar Field (instead of an UDA) (at least for now).

M Packages/Uintah/Dataflow/GUI/CompareMMS.tcl

Basic GUI updates, still needs lots of work.

68 lines of code changed in 5 files:

mdavis 2006-02-16 18:00 Rev.: 33287

Cleanup ProgressReporter class. Remvoed un-needed ProgressReporter::update_progress(int, int) method, and replaced w/ call to ProgressReporter(double) method. Removed double Module::progress; and use base class protected double ProgressReporter::progress_percent_; instead

45 lines of code changed in 9 files:

bigler 2006-02-16 17:32 Rev.: 33286


Added float version of SmoothStep and Interpolate.

0 lines of code changed in 2 files:

dgroulx 2006-02-16 16:18 Rev.: 33285

DataArchive should now only load timestep files as needed.

81 lines of code changed in 4 files:

callahan 2006-02-16 13:37 Rev.: 33284

Fix clockwise/counterclockwise case

2 lines of code changed in 1 file:

darbyb 2006-02-15 22:24 Rev.: 33283

Fix configuring --with-teem

2 lines of code changed in 2 files:

mdavis 2006-02-15 18:18 Rev.: 33282

Remove dynamic input ports from Painter - as Bundles effectively allow dynamic # of input upstream anyways.

This allows incoming data on the first port and the filter port to move from the first port to the last port - thus eliminating confusion when a user executs the Painter module and it does nothing when data is connected to the first port.

The second port is now reserved for filter input and will only be used when the Painter module is expecting incoming data from a tool.


81 lines of code changed in 4 files:

mdavis 2006-02-15 18:04 Rev.: 33281

Finish Painter Tools conversion from mouse callbacks to more general Event based mechanism to allow for event fallthrough.

Added Crop Tool (key 'a'). Unlike BioImage/Viewslices it uses internal call to nrrdCrop instead of having external UnuCrop module perform op. Rewrote crop frame drawing code to be much more succinct.

Moved FloodfillTool and StatisticsTool to newer Event mechanism.

Assume nrrd data w/ center of nrrdCenterUnknown is nrrdCenterNode to match default range.

Fix Painter::NrrdVolume::vector_to_index.

Factor Painter::execute into:
-Painter::receive_filter_bundles()
-Painter::receive_normal_bundles()
-Painter::extract_data_from_bundles()
-Painter::recompute_volume_list()
-Painter::send_data()

Move Painter::update_event_state() -> Painter::Event::update_state()

Remove Event::dx_, and Event::dy_, Event::pick_x_, and Event::pick_y_ and require the tool to store that data if it needs it (Those tools are: Zoom, Pan, and CLUT)

Remove Painter::handle_gui_mouse_motion, as tools just handle the event now
Remove Painter::handle_gui_mouse_button_release, as tools just handle the event now





460 lines of code changed in 4 files:

callahan 2006-02-15 16:13 Rev.: 33280

Allow default constructor for StackVector.

0 lines of code changed in 2 files:

callahan 2006-02-15 16:12 Rev.: 33279

Correct extraction of the inserted field and changes made to it for the InsertField module.

37 lines of code changed in 1 file:

jfsheph 2006-02-15 15:39 Rev.: 33278

removing absolute paths for included header files

40 lines of code changed in 8 files:

zgao 2006-02-15 15:26 Rev.: 33277

add initail condition for mms

133 lines of code changed in 3 files:

jfsheph 2006-02-15 15:21 Rev.: 33276

update on-the-fly to compile and link against conditionally compiled packages

20 lines of code changed in 1 file:

jfsheph 2006-02-15 14:23 Rev.: 33275

adding the outline of the MESQUITE interface. Just updates, no functionality, yet.

1500 lines of code changed in 7 files:

kuzimmer 2006-02-15 13:57 Rev.: 33274

got rid of an unnecessary dynamic cast

3 lines of code changed in 1 file:

kuzimmer 2006-02-15 13:55 Rev.: 33273

got rid of some unneccessary dynamic casts and ressurected the ability to render a single textured polygon if, the input mesh is an ImageMesh

10 lines of code changed in 2 files:

amorris 2006-02-15 12:16 Rev.: 33272

Updated selective instrumentation file.

0 lines of code changed in 2 files:

harman 2006-02-15 10:23 Rev.: 33271

Coarsen()
changed switchDebug_AMR_refine to switchDebug_AMR_coarsen

2 lines of code changed in 1 file:

callahan 2006-02-14 18:38 Rev.: 33270

Preliminary surface extraction for the inserted field in the InsertField module.

174 lines of code changed in 2 files:

callahan 2006-02-14 17:54 Rev.: 33269

Add ASSERTMSG checking for element size to add_elem functions.

11 lines of code changed in 7 files:

harman 2006-02-14 17:53 Rev.: 33268

set default value for
cout.precision(8)

if(do_varsummary){ // for finding fuzz
cout.precision(16)

4 lines of code changed in 1 file:

callahan 2006-02-14 17:47 Rev.: 33267

Insert fields with non-triangle faces

150 lines of code changed in 2 files:

harman 2006-02-14 17:46 Rev.: 33266

cout.precision(16) -- needed for catching fuzz

1 lines of code changed in 1 file:

amorris 2006-02-14 13:34 Rev.: 33265

Added instructions for using TAU with Uintah.

92 lines of code changed in 1 file:

amorris 2006-02-14 13:27 Rev.: 33264

Disabled use of PMPI routines when USE_TAU_PROFILING is defined.

0 lines of code changed in 2 files:

amorris 2006-02-14 13:26 Rev.: 33263

Commented out TAU_PROFILE_INIT, it's causing problems with LAM MPI.

2 lines of code changed in 1 file:

harman 2006-02-14 09:39 Rev.: 33259

Need to use mpi for hypre

1 lines of code changed in 1 file:

dav 2006-02-13 18:32 Rev.: 33258

Fix extra > on include... Keeping one checkin in front of James... :-)

1 lines of code changed in 1 file:

jeroen 2006-02-13 18:12 Rev.: 33257

A few tools to simplify the process of writing dynamically compiled libraries and functions. These classes can be used to find a correctly templated version of GenericField.

1028 lines of code changed in 5 files:

jeroen 2006-02-13 16:47 Rev.: 33256

Bug fixes

266 lines of code changed in 9 files:

mjc 2006-02-13 15:12 Rev.: 33254

fix bug with loading old .net files from the load or insert menus

10 lines of code changed in 1 file:

jfsheph 2006-02-13 14:05 Rev.: 33253

some code cleanup and updates to use newly provided functionality.

299 lines of code changed in 4 files:

harman 2006-02-12 19:57 Rev.: 33251

hypre1.9.0

4 lines of code changed in 1 file:

jeroen 2006-02-12 13:54 Rev.: 33250

Rewrote BuidFEMatrix, so other modules can call it as a library function. Added a converter from matrix to field (as the route using nrrds is still broken). Improved functions to build membrane models in a volume conductor

1056 lines of code changed in 17 files:

harman 2006-02-11 18:22 Rev.: 33249

It should now run.

1 lines of code changed in 1 file:

harman 2006-02-11 18:21 Rev.: 33248

backed out the previous changes.

1 lines of code changed in 1 file:

harman 2006-02-11 17:48 Rev.: 33247

comma

2 lines of code changed in 2 files:

mdavis 2006-02-11 17:39 Rev.: 33246

Fix compiler warning

2 lines of code changed in 1 file:

mdavis 2006-02-11 17:36 Rev.: 33245

Intermediate commit of rewrite of Painter tools to use new general event driven mechanism. Allows for fallthrough of events to create composite tools.

Tools converted: ColorLookupTable, Zoom, Autoview, Probe, & Pan
Tools left to convert: Crop & loodfill

Rename Painter::MouseState to Painter::Event to better reflect actual use.

357 lines of code changed in 4 files:

mdavis 2006-02-11 00:15 Rev.: 33244

Remove outdated network. Use Segmenter.srn now

0 lines of code changed in 1 file:

mdavis 2006-02-11 00:13 Rev.: 33243

Painter crash fixes. Eliminates two crashes:
1. Crash while moving the mouse cursor in the window while a filter finishes.
2. Crash when painting exactly 12 strokes.

Paint Brush cursor now displays correctly in all windows

Paint Brush is faster updating between strokes, also uses less memory

Filters now display text telling user to 'Please wait...' while filter executes

Window open to correct view if UI was pressed after execution of module

Port caching of filters was turned off, as some filters were re-exeucting when not wanted

Fix bug deleting layers that were originally created by copying active layer

Smarter logic about which layer to make active next after deleting acitve layer


287 lines of code changed in 5 files:

jas 2006-02-10 23:08 Rev.: 33242

Add outputProblemSpec calls needed for restart.

96 lines of code changed in 6 files:

borodai 2006-02-10 21:02 Rev.: 33241

Trying to fix a problem I can not even reproduce.

0 lines of code changed in 2 files:

ayla 2006-02-10 18:23 Rev.: 33239

Undoing accidental commit (rev 33237).

37 lines of code changed in 10 files:

ayla 2006-02-10 18:02 Rev.: 33237

GUI updates.

1375 lines of code changed in 10 files:

harman 2006-02-10 17:55 Rev.: 33236

Linux configure line: now using hypre1.9.0
(I'll change the IRIX configure line as soon as ls works on the sci filesystem. On
second thought ....)

2 lines of code changed in 1 file:

harman 2006-02-10 17:31 Rev.: 33235

Small fix so it works on multiple levels and multiple patches.

10 lines of code changed in 1 file:

harman 2006-02-10 17:30 Rev.: 33234

added implicit advect amr test. This need hypre 1.9.0

2 lines of code changed in 1 file:

sachse 2006-02-10 15:03

Generalization

221 lines of code changed in 2 files:

mdavis 2006-02-10 14:23 Rev.: 33230

Fix module positioning when loading .srn files by adding default parameter to specify absolute positioning to addModouleAtPosition

4 lines of code changed in 2 files:

mdavis 2006-02-10 14:15 Rev.: 33229

Update positions of windows

15 lines of code changed in 1 file:

mdavis 2006-02-10 14:10 Rev.: 33228

Change TCL window id of Painter GUI so .srn nets open GUI properly. Commit Segmenter.srn, an XML version of Segmenter.net

374 lines of code changed in 2 files:

mjc 2006-02-10 12:57 Rev.: 33227

Show validation and parsing errors in a dialog box instead of in the shell

20 lines of code changed in 1 file:

callahan 2006-02-10 12:47 Rev.: 33226

Need to include tcl defines before we include tcl files, rearrange includes.

4 lines of code changed in 3 files:

jas 2006-02-10 04:26 Rev.: 33224

Add missing ifdefs.

4 lines of code changed in 1 file:

mdavis 2006-02-10 02:42 Rev.: 33223

Dataflow/GUI/Painter.tcl
Dataflow/Modules/Render/Painter.cc
Dataflow/Modules/Render/Painter.h
Dataflow/Modules/Render/PainterBrushTool.cc
Dataflow/Modules/Render/sub.mk
Dataflow/Modules/Render/PainterTools.cc
----------------------------------------------
Summary:
Major upgrade to Painter Module tools/layers/and events.

Added ITK Filter Tools to Painter Module.
-Curvature Anisotropic Diffusion Filter - 'd' key
-Gradient Magnitude Filter - 'g' key
-Connected Component Filter - 'k' key
-Fill Holes Filter (Dilate/Erode) - 'j' key
-Threshold Segmentation Filter - 'h' key
-'1' key sets source layer
-'2' key sets seed layer

Other tools:
-Delete layer - 'x' key
-Copy layer - 'c' key
-New layer - 'v' key

All tools now quit instantly by hitting the 'q' key

ITK (and soon all) tools will complete their action by pressing spacebar

Most tools will fallthrough to default tools when not handling the event. This allows the user to perform default actions like: pan, zoom, change slices, change layers, etc... while in the tool.

Slightly increased font size for demo.

Moved Painter::BrushTool to its own file PainterBrushTool.cc, for future expansion of this complex tool.


Core/Geom/TextRenderer.cc
----------------------------
Added ability to layout multiple lines of text w/ carriage returns


Core/GuiInterface/GuiContext.h
Core/GuiInterface/GuiContext.cc
-----------------------------------
Added GuiContext::find_child(string) for setting variables that were passed down the dataflow via nrrd keyvalue pairs and itk meta data dictionaries.


Core/GuiInterface/TCLKeysyms.h
----------------------------------
keysym map for Painter Module handling of keypress events


Packages/Insight/Dataflow/Modules/Filters/ThresholdSegmentationLevelSetImageFilter.cc
Packages/Insight/Dataflow/Modules/Filters/ConfidenceConnectedImageFilter.cc
Packages/Insight/Dataflow/Modules/Converters/NrrdToImage.cc
------------------------------------------------
Cleaner support of passing down key/value pairs and setting them w/out using TCL explicitly.




2075 lines of code changed in 16 files:

mjc 2006-02-09 21:31 Rev.: 33222

introduce xml filetype with validating dtd for scirun network file saving, SCIRun now saves only in this format, while loading old '.net' files as well as new '.srn' files (which are xml)

1493 lines of code changed in 11 files:

dmw 2006-02-09 20:13 Rev.: 33221

- Add missing library dependency to link line (fixes build on OSX)

26 lines of code changed in 2 files:

harman 2006-02-09 18:08 Rev.: 33220

lineExtract:
- Added more bulletproofing on defining the starting and ending pts

ICE:
problemSetup()
- moved analysisModule problemSetup after Models problemSetup
AnalysisModules need to know about the models variables.

16 lines of code changed in 2 files:

borodai 2006-02-09 16:13 Rev.: 33219

Cleanup

3 lines of code changed in 2 files:

callahan 2006-02-09 16:00 Rev.: 33218

Output the new mesh and mapping matrix for PointCloudMesh insertions.

162 lines of code changed in 2 files:

jas 2006-02-09 15:56 Rev.: 33217

Fixes for running and restarting of IMPM.
Add a MPMCommon for routines common to both IMPM and SerialMPM.

162 lines of code changed in 8 files:

zgao 2006-02-09 15:40 Rev.: 33216

change the way of obtaining the parameters for MMS

75 lines of code changed in 18 files:

callahan 2006-02-09 13:16 Rev.: 33215

Fix MESH_NO_NEIGHBOR for 64bitness

6 lines of code changed in 1 file:

sbabaeiz 2006-02-09 12:53 Rev.: 33214

Instead of adding the module I had developed for Eric Voth to solve the BEM-ESI problem to SCIRun, I modified the existing SetupBEMatrix.cc, so now it works for both BEM-ECG and BEM-ESI problems.

454 lines of code changed in 2 files:

sbabaeiz 2006-02-09 12:51 Rev.: 33213

I added the general BEM matrices to a new class BuildBEMatrix (cc and h) in /src/Packages/BioPSE/Core/Algorithms/NumApproximation/ and added BuildBEMatrix.cc file in the corresponding sub.mk file. Then changed SetupBEMatrix.h and SetupBEMatrix.cc accordingly

802 lines of code changed in 2 files:

sbabaeiz 2006-02-09 12:41 Rev.: 33212

I added the general BEM matrices to a new class BuildBEMatrix (cc and h) in /src/Packages/BioPSE/Core/Algorithms/NumApproximation/ and added BuildBEMatrix.cc file in the corresponding sub.mk file. Then changed SetupBEMatrix.h and SetupBEMatrix.cc accordingly

0 lines of code changed in 2 files:

sbabaeiz 2006-02-09 12:24 Rev.: 33211

I added two functions Concat_row() and Concat_cols() to DenseMatrix class as Friend functions: (lines 160 and 161 in DenseMatrix.h , lines 1120-1155 in DenseMatrix.cc)

42 lines of code changed in 2 files:

callahan 2006-02-09 11:29 Rev.: 33210

Add more ports to InsertField

10 lines of code changed in 2 files:

callahan 2006-02-09 11:23 Rev.: 33209

Test networks for TetVolMesh splitting using the InsertField module.

0 lines of code changed in 3 files:

mdavis 2006-02-09 11:10 Rev.: 33208

Bump up SCIRUN_RCFILE_VERISON to match SCIRUN_VERSION

1 lines of code changed in 1 file:

callahan 2006-02-09 10:59 Rev.: 33207

Don't add points outside of the field.

6 lines of code changed in 1 file:

jeroen 2006-02-09 10:46 Rev.: 33206

Added new modules and FieldAlgorithms for computation of geometry of cellular models

2752 lines of code changed in 22 files:

worthen 2006-02-08 20:30 Rev.: 33203

remove xmlblah files

0 lines of code changed in 1 file:

callahan 2006-02-08 16:15 Rev.: 33202

Move InsertField into the FieldsCreate category.

2 lines of code changed in 2 files:

callahan 2006-02-08 16:12 Rev.: 33201

Fix get_elems compilation for ScanlineMesh.

2 lines of code changed in 1 file:

callahan 2006-02-08 16:10 Rev.: 33200

Fix CurveMesh compilation error in the Unstructure module.

1 lines of code changed in 1 file:

callahan 2006-02-08 15:51 Rev.: 33199

Minor code cleanup.

4 lines of code changed in 1 file:

jas 2006-02-08 14:16 Rev.: 33198

Remove the dependency on the MPM library.

0 lines of code changed in 1 file:

jas 2006-02-08 14:15 Rev.: 33197

Remove the MPMLabel* in the various function declarations so they
match the base class declarations.

44 lines of code changed in 17 files:

dav 2006-02-08 13:21 Rev.: 33196

Fixing compile for SGI... (and gcc 4.1, and mac)

M OnTheFlyAnalysis/AnalysisModule.h

Rearranged #includes. // This didn't make a difference in fixing the
// compile error, but did make it easier for me to read.

M OnTheFlyAnalysis/sub.mk

This lib requires libCore_Geometry... (I think my Mac build picked this up.)

M OnTheFlyAnalysis/AnalysisModuleFactory.cc

Needs to include SimulationState.h (even though it really isn't used
here) for some reason so that the SGI CC can resolve the type when it
creates the corresponding Handle.

M ICE/Advection/FluxDatatypes.h

Needs #include TypeUtils and Endian.h to be able to resolve all of the
swapbytes() functions.

9 lines of code changed in 5 files:

dav 2006-02-08 13:17 Rev.: 33195


M sub.mk

More 'quiet' work... Fspec creation is now quiet.

5 lines of code changed in 1 file:

dav 2006-02-08 13:15 Rev.: 33194

M FreeType.h

Indented # statements so I could parse them. Moved 'using' statements
into the namespace block to help minimize global namespace polution.

0 lines of code changed in 2 files:

dav 2006-02-08 13:14 Rev.: 33193

M configVars.mk.in
M scripts/so_epilogue.mk

More work on 'quiet' build... Fortran is now quiet. Fixed spacing on
one of the print outs.

10 lines of code changed in 2 files:

kuzimmer 2006-02-08 12:56 Rev.: 33192

make the axis buttons and position slider update properly when update is set to 'release' or 'auto'

14 lines of code changed in 1 file:

callahan 2006-02-07 16:27 Rev.: 33187

Remove and clean up debugging prints.

4 lines of code changed in 2 files:

harman 2006-02-07 16:20 Rev.: 33186

ICE.cc
__________________________________
-only call data analysis functions/tasks if the object exists.

lineExtract.c
__________________________________
- added ability to dump out CCVariable<Vector> variables.

65 lines of code changed in 2 files:

worthen 2006-02-07 15:53 Rev.: 33184

Fix compile, and hopefully left Todd's logic intact

3 lines of code changed in 1 file:

callahan 2006-02-07 15:46 Rev.: 33183

Remove and clean up debugging prints.

3 lines of code changed in 2 files:

callahan 2006-02-07 15:16 Rev.: 33182

Remove and clean up debugging prints.

3 lines of code changed in 5 files:

callahan 2006-02-07 15:15 Rev.: 33181

Move synchronize_lock_ locking around, lock all of synchronize().

13 lines of code changed in 1 file:

borodai 2006-02-07 14:09 Rev.: 33180

Allow any shape wall at the bottom of the domain and pressure BC around wall.

21 lines of code changed in 1 file:

callahan 2006-02-07 13:55 Rev.: 33179

Fix compiler warning

3 lines of code changed in 1 file:

callahan 2006-02-07 13:44 Rev.: 33178

Minor cleanups to the Mesh files. Fix whitespacing, remove commented out code, fix some comments. Also fixed a normalize bug in TriSurfMesh associated with Normal generation.

4344 lines of code changed in 14 files:

harman 2006-02-07 13:39 Rev.: 33177

-new on-the-fly analysis component.
-new Analysis module, lineExtract
user specifies data extraction lines, variables to dump, starting and stoping times
For each point along the line a file is generated and data is dumped to it
at a user specified frequency. These files can then be pasted into one huge Excel/Matlab data file
for statistical analysis.
(initial commit, only CCVariable<double> variables. Restarts and multiple processors don't work)

734 lines of code changed in 11 files:

luitjens 2006-02-07 09:37 Rev.: 33175

52 lines of code changed in 1 file:

worthen 2006-02-06 20:29 Rev.: 33174

If using gfortran on linux, use tthe 'end' style of fortran underscore

2 lines of code changed in 2 files:

dav 2006-02-06 19:33 Rev.: 33173

Gcc 4.1 fixes.

M Core/Geometry/Point.h
M Core/Persistent/Persistent.h

AffineCombination (Point.h) and auto_istream (Persistent.h) were never
actually 'declared'. There were made 'friends' which on many
compilers is a good enough declaration... however, apparently on gcc
4.1, it isn't... so I've added declarations for them just outside the
classes they are friends to. [Note, we've run into this problem
before for other classes, and this seems to be the correct fix. Let
me know if you have other ideas.]

M Packages/BioPSE/Dataflow/Modules/Inverse/Tikhonov.cc

Can't use ClassName::function() (Tikhonov::mat_mult()) inside the
class... at least not on gcc 4.1.

20 lines of code changed in 3 files:

kuzimmer 2006-02-06 17:32 Rev.: 33172

update so that uda2nrrd will build by typing 'make uda2nrrd' from the build root

2 lines of code changed in 1 file:

jas 2006-02-06 16:05 Rev.: 33171

Remove the circular dependency. Get rid of unneeded library dependencies.

3 lines of code changed in 8 files:

dav 2006-02-06 15:40 Rev.: 33170

Make ImageMagick optional... it is going away very soon anyway.

11 lines of code changed in 2 files:

jas 2006-02-06 14:21 Rev.: 33169

Fix misspellings of shear in outputProblemSpec.

10 lines of code changed in 7 files:

harman 2006-02-06 13:48 Rev.: 33168

added task compute_maxRHS()

removed tasks compute_matrix_CFI_weights() & matrixBC_CFI_finePatch() not used.

zeroMatrix_RHS_UnderFinePatches()
-no longer zeroing out rhs. This is taken care of in setupRHS

MultiLevelPressureSolve()
- added missing computes and requires and transferFrom calls.

setupRHS()
- moved calculation of max_rhs to compute_maxRHS() to simplify the impAMRICE code.

AMRICE.h
__________________________________
refluxingOperator()
- removed coeff calculation from y & z faces. It was previously deleted
from the x face.

ICE/MPMICE.cc
__________________________________
added compute_maxRHS to schedule timeAdvanced

185 lines of code changed in 6 files:

mdavis 2006-02-06 13:16 Rev.: 33167

Take down stack size

0 lines of code changed in 2 files:

jas 2006-02-06 13:14 Rev.: 33166

Add function registerParticleState which is only used by MPMMaterial.

7 lines of code changed in 2 files:

jas 2006-02-06 13:10 Rev.: 33165

Add a dummy NoneCheck which will dump out the problem spec when
none is declared in the StabilityCheck. Add a doIt() which returns true
for all "real" StabilityChecks, but is false for NoneCheck. Instead of
checking (!d_stability) use (d_stability->doIt()).

114 lines of code changed in 9 files:

mdavis 2006-02-06 13:02 Rev.: 33164

Fix compatibility w/ older versions of Freetype 2. Fix return values on TextRenderer when freetype is not configured

18 lines of code changed in 6 files:

worthen 2006-02-06 10:21 Rev.: 33163

Fix windows compile

0 lines of code changed in 4 files:

harman 2006-02-06 09:40 Rev.: 33162

set the default value for d_doRefluxing.

2 lines of code changed in 1 file:

worthen 2006-02-04 01:50 Rev.: 33161

Fix for windows, and for without freetype

24 lines of code changed in 3 files:

worthen 2006-02-04 00:09 Rev.: 33160

fix win32

0 lines of code changed in 2 files:

mdavis 2006-02-03 17:24 Rev.: 33158

Rewrite FreeType text rendering into Core/Util/TextRenderer class. Renders to texture, than renders texture to screen. Replaced FreeTypeTextTexture calls in Dataflow/Modules/Painter.cc with calls to new TextRenderer class. Much faster overall performance, and more specifically painting is faster. Added profiling to painter w/ SCIRUN_PROFILE environment var

1024 lines of code changed in 8 files:

mdavis 2006-02-03 17:16 Rev.: 33157

Simple profiling class that allows for nesting and reporting total time and percentage spent between profiler calls. Only tested/working on linux machines for now.

268 lines of code changed in 3 files:

worthen 2006-02-03 14:13 Rev.: 33156

Search 3P for xml2 if xml2-config not found (which it will probably only not be found on windows)

353 lines of code changed in 2 files:

jas 2006-02-03 13:55 Rev.: 33155

Add additional library for gcc-4.0 compile.

1 lines of code changed in 1 file:

harman 2006-02-03 13:27 Rev.: 33154

so it compiles without petsc.

0 lines of code changed in 2 files:

callahan 2006-02-03 13:22 Rev.: 33153

Add a RayTriangleIntersection test to CompGeom.h

166 lines of code changed in 4 files:

jas 2006-02-03 12:05 Rev.: 33152

Object to hold exchange coefficients and output the problemSpec.

146 lines of code changed in 2 files:

jas 2006-02-03 12:02 Rev.: 33151

Add.

78 lines of code changed in 2 files:

jas 2006-02-03 11:53 Rev.: 33150

Write out the problemSpecification for various pieces of a material that are
needed for restarting.

3128 lines of code changed in 388 files:

harman 2006-02-03 10:35 Rev.: 33149

fix the Linux compile

2 lines of code changed in 2 files:

jfsheph 2006-02-02 20:19 Rev.: 33148

Adding Euler checks to the list of mesh quality metrics to alert the user of any probable mesh topology problems.

51 lines of code changed in 1 file:

callahan 2006-02-02 19:02 Rev.: 33147

Consolidate the functions that resync the mesh on edit operations into create_syncinfo and delete_syncinfo functions. Other minor cleanups.

83 lines of code changed in 1 file:

dav 2006-02-02 17:36 Rev.: 33146

M scripts/so_epilogue.mk
M scripts/program.mk
M configVars.mk.in

Allowed for 'quiet' build. If you set the environment variable
SCI_MAKE_BE_QUIET to 'true', then instead of the entire compile line
being printed, only the name of the file will be shown. By default,
this behavior is off and you won't see it, but I suggest you give it a
try. If you run into compilation errors where you need to see the
compile line, you can just unset that environment variable.

M Packages/Uintah/CCA/Components/ICE/AMRICE.h
M Packages/Uintah/CCA/Components/ICE/impAMRICE.cc
M Packages/Uintah/CCA/Components/ICE/AMRICE.cc

Moved template files from AMRICE.cc to AMRICE.h... this fixed a
problem (on the SGI) where impAMRICE.cc needed certain template
functions and thus the compiler (CC) pulled in ICE.cc (don't know why
it was ICE.cc, but it was). This caused compilation errors. By
moving the template files to that .h file, this problem goes away, yet
the organization of the functions still remains good.

M Packages/Uintah/StandAlone/sub.mk

Uda2nrrd depends on Core/Basis...


742 lines of code changed in 7 files:

dav 2006-02-02 17:28 Rev.: 33145

Commented out unused var.

1 lines of code changed in 1 file:

kuzimmer 2006-02-02 02:03 Rev.: 33144

Made uda2nrrd work with new field types.

246 lines of code changed in 2 files:

callahan 2006-02-01 18:12 Rev.: 33143

Add contour insertion capability into the InsertField class

102 lines of code changed in 2 files:

callahan 2006-02-01 18:12 Rev.: 33142

Fix constructor type

1 lines of code changed in 1 file:

callahan 2006-02-01 18:10 Rev.: 33141

Add dynamic search grid functionality to the SearchGridConstructor class.

187 lines of code changed in 3 files:

harman 2006-02-01 17:33 Rev.: 33139

Added ability to add reflux correction to the rhs at all the coarse/fine interfaces.
Something is still not right

355 lines of code changed in 17 files:

worthen 2006-02-01 15:18 Rev.: 33137

This should (in theory) pass the AMRICE memory leak RT

9 lines of code changed in 1 file:

worthen 2006-02-01 14:24 Rev.: 33135

Remove some (hopefully all) memory leaks from the amr RT tests

4 lines of code changed in 2 files:

worthen 2006-02-01 13:51 Rev.: 33134

Fix Load Balancer restart

2 lines of code changed in 1 file:

jeroen 2006-02-01 13:26 Rev.: 33133

Updates to modules

225 lines of code changed in 16 files:

worthen 2006-02-01 13:21 Rev.: 33132

reenable hotblob 3l problem

3 lines of code changed in 1 file:

worthen 2006-02-01 13:20 Rev.: 33131

fix compare_uda to choose interior cell/node when there are overlapping patches

12 lines of code changed in 1 file:

callahan 2006-02-01 13:19 Rev.: 33130

Fix tabbing, add comment.

26 lines of code changed in 1 file:

worthen 2006-02-01 12:37 Rev.: 33129

Fix xml inclusion

1 lines of code changed in 1 file:

January 2006 »

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