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brain-view-cmnd_install_compile.txt
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brain-view-cmnd_install_compile.txt
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#to get the source code into the current folder in terminal:
bzr branch lp:brain-view/0.1 /brain_view_new {this folder should not already exists}
#changes to brain-view2.pro:
comment MINCDIR
comment QAURTERDIR
#in terminal in the directory of the brain-view2.pro: (on topolino and not other machines!)
export LD_LIBRARY_PATH=/projects/mice/share/arch/linux64/lib/:/projects/mice/share/arch/linux64/include:/projects/mice/share/arch/linux/lib/:/usr/:/usr/lib/:/usr/include/:/micehome/sghanavati/lib:$LD_LIBRARY_PATH
echo $LD_LIBRARY_PATH
/projects/mice/share/arch/linux64/lib:/projects/mice/share/arch/linux64/bin/VTKbin/bin:/projects/mice/share/arch/linux/lib:/micehome/sghanavati/lib/:/micehome/sghanavati/lib/:/projects/mice/share/arch/linux64/include/:/usr/:/usr/lib/:/projects/mice/share/arch/linux64/
make clean
qmake-qt4 MINCDIR=/projects/mice/share/arch/linux-3_2_0-36-generic-x86_64-eglibc-2_15/ QUARTERDIR=/projects/mice/share/arch/linux-3_2_0-36-generic-x86_64-eglibc-2_15/ brain-view2.pro
#qmake-qt4 MINCDIR=/projects/mice/share/arch/linux-x86_64-eglibc2_11_1/ QUARTERDIR=/projects/mice/share/arch/linux-x86_64-eglibc2_11_1/ brain-view2.pro
#qmake-qt4 MINCDIR=/projects/mice/share/arch/linux64/ QUARTERDIR=/micehome/sghanavati/ brain-view2.pro
(this will give -I/projects/mice/share/arch/linux64/include and -L/projects/mice/share/arch/linux64//lib/ in Makefile)
#qmake-qt4 MINCDIR=/projects/mice/share/arch/linux64 QUARTERDIR=/micehome/sghanavati/ brain-view2.pro
(this will give -I/projects/mice/share/arch/linux-x86_64-glibc2_3/include and -L/projects/mice/share/arch/linux64/lib/ in Makefile)
make or {make -lqt}?
or make -j4 (to use 4 processors)
./brain-view2 /tmp/test.obj
./brain-view2 ../test_brainview_line.obj
./brain-view2 ../test_brainview_line.obj ../file_tree_mask_blur_5branch.db
./brain-view2 ../file_tree_mask_blur_5branch.obj ../file_tree_mask_blur_5branch_graph2graph.h5
./brain-view2 ../file_tree_5branch_segmentID_graph2graph.h5
test:
dir: /projects/souris/jason/human/darren/201105/processed-3T
brain-view2 avg-left.obj avg-left-threesubjects.vertstats avg-right.obj avg-right-threesubjects.vertstats
##############################################################################################################################################
To make the test data:
ssh -X bianca
Run vessel tracking: get file_tree_5branch.obj and file_tree_5branch.h5
h5ls -r file_tree_5branch.h5
ssh -X bianca:
export PYTHONPATH=/home/jgsled/lib64_ubuntu_hardy/python:$PYTHONPATH
python /projects/souris/sghanavati/Brain_view/Prepare_codes/Prepare4Brainview.py:
python /micehome/jgsled/bin/tree2graph.py file_tree_5branch.h5 file_tree_5branch.db
python /micehome/jgsled/bin/delete_internal_leaves.py input.db output.db
*correct location of vertices : # optimize location of branch points
graph_analysis.adjust_junctions(g, vertex_offsets)
*correct radius by 1.6*old_radius : # diameters need to corrected for estimation bias due to blurring
diameters = [h.edge_property(edge, 'diameter') for edge in h.edge_list()]
diameters = array(diameters)*1.06
python /projects/souris/sghanavati/Brain_view/Prepare_codes/graph2graphsegmentID.py input.db output_basename
python /projects/souris/sghanavati/Brain_view/Prepare_codes/graph2cylinder.py input.db output_basename
python /micehome/jgsled/bin/graph2graph.py file_tree_5branch.db file_tree_5branch_graph2graph.h5
python /micehome/jgsled/bin/graph2obj.py graph.db graph.obj
h5ls -r file_tree_5branch_graph2graph.h5
h5ls -rv file_tree_5branch_graph2graph.h5
###########################################################################################################################################
To make a polygon.obj:
marching-cubes input.mnc output.obj intensity_threshold
or
python /home/jsgled/bin/graph2isosurf.py graph.db template.mnc output.obj
or
python /home/jsgled/bin/path2isosurf.py path.db/h5 template.mnc output.obj
################################################################################################################################
Brainview module streams:
sghanavati@topolino:/projects/souris/sghanavati/Brain_view/brainview0_1_lineobj_h5_v5_cylinder$ ./brain-view2 /projects/souris/sghanavati/code_results/follow_tree/MCid_456/MCid_456_tree3.obj
Debug. >>MainWindow::MainWindow()
Debug. [ MainWindow() ] Settings path 1: "/home/sghanavati/.config/MINC/brain-view.conf"
Debug. [ MainWindow() ] Settings path 2: "/home/sghanavati/.config/MINC/brain-view.ini"
Debug. [ MainWindow() ] Application Pid: 20988
Debug. >>MainWindow::createActions()
Debug. <<MainWindow::createActions()
Debug. >>MainWindow::createMenus()
Debug. <<MainWindow::createMenus()
Debug. >>MainWindow::initColourbars()
Debug. [ initColourbars() ] TextureDir: "/home/sghanavati/.config/MINC/textures/"
Debug. [ initColourbars() ] Texture file full path: ":/resources/colourbars/sunrise.png"
Debug. [ initColourbars() ] Texture file basename: "sunrise"
Debug. [ initColourbars() ] Texture file full path: ":/resources/colourbars/hotblue.png"
Debug. [ initColourbars() ] Texture file basename: "hotblue"
Debug. [ initColourbars() ] Texture file full path: ":/resources/colourbars/spectral.png"
Debug. [ initColourbars() ] Texture file basename: "spectral"
Debug. [ initColourbars() ] Texture file full path: ":/resources/colourbars/hotred.png"
Debug. [ initColourbars() ] Texture file basename: "hotred"
Debug. [ initColourbars() ] Texture file full path: ":/resources/colourbars/full_saturation.png"
Debug. [ initColourbars() ] Texture file basename: "full_saturation"
Debug. <<MainWindow::initColourbars()
Debug. >>BrainQuarter::BrainQuarter()
Debug. <<BrainQuarter::BrainQuarter()
Debug. <<ResourceForm::ResourceForm()
Debug. >>ResourceForm::ResourceForm()
Debug. <<MainWindow::MainWindow()
Debug: Loading ... /projects/souris/sghanavati/code_results/follow_tree/MCid_456/MCid_456_tree3.obj
Debug. >>MainWindow::openFile()
Debug. >>ResourceForm::insertGeometry()
Debug. >>GeometryScene::GeometryScene()
Debug. <<GeometryScene::GeometryScene()
Debug. >>GeometryScene::loadGeometry()
Debug. >>BrainQuarter::getRootSeparator()
Before MessageBox
After MessageBox
in loadGeometry flag_label = 0 => user doesn't want to label the loaded geometry!
Debug. >>GeometryNode::loadObj()
object_is_line =1
Loading Line object number: 0
Debug. >>GeometryNode::loadLines
ID: 537037
Debug. <<GeometryNode::loadLines()
Debug. <<GeometryNode::loadObj()
Debug: << geometry->loadObj # 0 status = true
Debug. <<GeometryScene::loadGeometry()
Debug. >>ResourceForm::insertGeometry():lastGeometry
Debug. <<ResourceForm::insertGeometry():lastGeometry
Debug. <<ResourceForm::insertGeometry():connect pointPicked viewer
Debug. >>ResourceForm::viewAll()
Debug. <<ResourceForm::viewAll()
Debug. >>ResourceForm::somethingChanged()
Debug. >>TreeModel::somethingChanged()
Debug. [ somethingChanged() ] GRUNKLE
Debug. <<TreeModel::somethingChanged()
Debug. >>ResourceForm::somethingChanged()
Debug. <<ResourceForm::insertGeometry()
Debug. <<MainWindow::openFile()
Debug: Showing the window ...
Debug. >>BrainQuarter::minimumSizeHint()
Debug: Going to event loop ...
Debug. <<ResourceForm::setPropertyForm()
Debug. >>GeometryNode::createForm()
Debug. <<GeometryNode::createForm()
Debug. >>ResourceForm::setPropertyForm()
Debug. <<ResourceForm::selectedItem()
Eeeek 0
Debug. >>ResourceForm::selectedItem()
Debug. >>GeometryNode::colourDialog()
Debug. >>GeometryNode::updateColour()
Debug. <<GeometryNode::updateColour()
Debug. <<GeometryNode::colourDialog()
Debug. >>MainWindow::openFileFromDialog()
Debug. >>MainWindow::openFile()
Debug. >>ResourceForm::insertGeometry()
Debug. >>GeometryScene::GeometryScene()
Debug. <<GeometryScene::GeometryScene()
Debug. >>GeometryScene::loadGeometry()
Debug. >>BrainQuarter::getRootSeparator()
Before MessageBox
After MessageBox
in loadGeometry flag_label = 0 => user doesn't want to label the loaded geometry!
Debug. >>GeometryNode::loadObj()
object_is_line =0
Loading Polygon object number: 0
Debug. >>GeometryNode::loadPolygons()
ID: 28644761
Debug. <<GeometryNode::loadPolygons()
Debug. <<GeometryNode::loadObj()
Debug: << geometry->loadObj # 0 status = true
Debug. <<GeometryScene::loadGeometry()
Debug. >>ResourceForm::insertGeometry():lastGeometry
Debug. <<ResourceForm::insertGeometry():lastGeometry
Debug. <<ResourceForm::insertGeometry():connect pointPicked viewer
Debug. >>ResourceForm::viewAll()
Debug. <<ResourceForm::viewAll()
Debug. >>ResourceForm::somethingChanged()
Debug. >>TreeModel::somethingChanged()
Debug. [ somethingChanged() ] GRUNKLE
Debug. <<TreeModel::somethingChanged()
Debug. >>ResourceForm::somethingChanged()
Debug. <<ResourceForm::insertGeometry()
Debug. <<MainWindow::openFile()
Debug. <<MainWindow::openFileFromDialog()
Debug. <<ResourceForm::setPropertyForm()
Debug. >>GeometryNode::destroyForm()
Debug. <<GeometryNode::destroyForm()
Debug. >>GeometryNode::destroyForm()
Debug. <<GeometryNode::destroyForm()
Debug. >>GeometryNode::createForm()
Debug. <<GeometryNode::createForm()
Debug. >>ResourceForm::setPropertyForm()
Debug. <<ResourceForm::selectedItem()
Eeeek 1
Debug. >>ResourceForm::selectedItem()
Debug. >>GeometryNode::updateTransparency()
Debug. <<GeometryNode::updateTransparency()
Debug. <<BrainQuarter::getPickedPoint()
Woooohooo!
Woooohooo!
Debug. <<BrainQuarter::getPickedPoint()
Woooohooo!
Woooohooo!
On geometry ...
Found: -0.325689 -8.57235 -1.76005
Texture: 0 0 0 1
Material Index 0
ID: 28644761
Picked point on Polygon obejct!
Picker - num points: 5
Index: 1110490
Found point1: -0.325689 -8.57235 -1.76005
Found point2: -0.339997 -8.5145 -1.86302
Found center tag: -0.332843 -8.54342 -1.81153
Debug. >>GeometryScene::pickReceived()
Debug. <<GeometryScene::pickReceived()
Debug. >>GeometryScene::pickReceived()
picked point does belong to this scene
Debug. >>ResourceForm::somethingChanged()
Debug. >>TreeModel::somethingChanged()
Debug. [ somethingChanged() ] GRUNKLE
Debug. <<TreeModel::somethingChanged()
Debug. >>ResourceForm::somethingChanged()
Debug. <<GeometryScene::pickReceived()
Debug. <<BrainQuarter::getPickedPoint()
Debug. <<BrainQuarter::getPickedPoint()
Woooohooo!
Woooohooo!
Woooohooo!
Woooohooo!
On geometry ...
Found: -1.6792 -7.67394 -1.71271
Texture: 0 0 0 1
Material Index 82459
ID: 537037
Picked point on Line obejct!
Index p0: 82459
Debug. >>GeometryScene::pickReceived()
Debug. <<GeometryScene::pickReceived()
Debug. >>GeometryScene::pickReceived()
Debug. <<GeometryScene::pickReceived()
Debug. <<BrainQuarter::getPickedPoint()
Woooohooo!