NAMIC Wiki - User contributions [en]

Project Week 25/Interactive Manipulation of Plots and Graphs

2018-02-14T16:15:39Z

Davide:

__NOTOC__

Back to [[Project_Week_25#Projects|Projects List]]

==Key Investigators==

*[http://www.rug.nl/staff/davide.punzo/ Davide Punzo] (Kapteyn Astronomical Institute, University of Groningen, The Netherlands)
*[http://www.spl.harvard.edu/pages/People/pieper Steve Pieper] (Isomics Inc., USA)
*[https://www.kitware.com/jean-christophe-fillion-robin/ Jean-Christophe Fillion-Robin] (Kitware Inc., USA)
*[http://perk.cs.queensu.ca/users/lasso Andras Lasso] (Queen's University, Canada)

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|
Implementing the following plotting and graphs infrastructure enhancement:
* Panning a zoomed section of the graphs;
* Click and Drag a point;
* Data selection (select many points at once).
|
* Review if jqPlot can satisfy our requirements
* Implement them
|
* Once updated to jqplot version 1.0.9 (necessary for click and drag) the plotting does not work anymore. The infrastructure needs to be updated. Data selection will be hard to achieve.
* We decided to switch to [http://www.vtk.org/features-2d-plots-and-charts/ vtkPlots] (jqplot will be preserved for producing plots at publication quality level). The new infrastructure will allow a direct C++ integration of the vtkTable into the plotting (e.g., all the observations and data handling are automatically set), better performance (i.e., interactive performance up to hundreds of thousands of points) and easier customization.
* VTK PLOTS already have the following interactive desired functionality: zooming (middle click), panning (left click) and data selection (right click).
* The following widget, MRML and View classes have been designed and implemented: vtkMRMLPlotViewNode, vtkMRMLPlotNode, qMRMLPlotWidget, qMRMLPlotViewControllerWidget and qMRMLPlotView.
* A New Plot Layout has been created (index 36) and exposed to the qSlicerAppMainWindow widget.
* TO DO: connecting the new infrastructure with the Table Module.
* TO DO: implementing click and drag style interactor (e.g., https://echnotstechno.wordpress.com/2014/08/13/interactive-2d-plots-with-vtk-the-visualization-toolkit/ ).
* '''Implemented''' : https://www.slicer.org/wiki/Documentation/Nightly/Developers/Plots
https://www.youtube.com/watch?v=5Ag0PzYw0Hk&index=4&list=PLctSHxZgiJy6TZCu56v4qqb_uIdUL_KEz
|}

==Illustrations==
The idea is to be able to modify the parameters (in the table) of a model (blue object in the 3D View) directly from the plotting window.

[[image:SlicerAstroWiki13.png|1200px]]

VTKPLOTS sin and cos plus data selection (red crosses) example:

[[image:vtkPlots.png|1200px]]

==Background and References==
*https://www.slicer.org/wiki/Developer_Meetings/20170425
*http://www.jqplot.com/examples/customHighlighterCursorTrendline.php
*http://www.jqplot.com/examples/zooming.php
*[https://github.com/Punzo/SlicerAstro/wiki/ SlicerAstro]

[[image:SlicerAstroLogo.png|400px]]

*(Just for fun: how the gas in a galaxy looks like in 3D https://www.youtube.com/watch?v=yLjW9nbdO8g )

Project Week 25/Interactive Manipulation of Plots and Graphs

2018-02-14T16:15:27Z

Davide:

__NOTOC__

Back to [[Project_Week_25#Projects|Projects List]]

==Key Investigators==

*[http://www.rug.nl/staff/davide.punzo/ Davide Punzo] (Kapteyn Astronomical Institute, University of Groningen, The Netherlands)
*[http://www.spl.harvard.edu/pages/People/pieper Steve Pieper] (Isomics Inc., USA)
*[https://www.kitware.com/jean-christophe-fillion-robin/ Jean-Christophe Fillion-Robin] (Kitware Inc., USA)
*[http://perk.cs.queensu.ca/users/lasso Andras Lasso] (Queen's University, Canada)

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|
Implementing the following plotting and graphs infrastructure enhancement:
* Panning a zoomed section of the graphs;
* Click and Drag a point;
* Data selection (select many points at once).
|
* Review if jqPlot can satisfy our requirements
* Implement them
|
* Once updated to jqplot version 1.0.9 (necessary for click and drag) the plotting does not work anymore. The infrastructure needs to be updated. Data selection will be hard to achieve.
* We decided to switch to [http://www.vtk.org/features-2d-plots-and-charts/ vtkPlots] (jqplot will be preserved for producing plots at publication quality level). The new infrastructure will allow a direct C++ integration of the vtkTable into the plotting (e.g., all the observations and data handling are automatically set), better performance (i.e., interactive performance up to hundreds of thousands of points) and easier customization.
* VTK PLOTS already have the following interactive desired functionality: zooming (middle click), panning (left click) and data selection (right click).
* The following widget, MRML and View classes have been designed and implemented: vtkMRMLPlotViewNode, vtkMRMLPlotNode, qMRMLPlotWidget, qMRMLPlotViewControllerWidget and qMRMLPlotView.
* A New Plot Layout has been created (index 36) and exposed to the qSlicerAppMainWindow widget.
* TO DO: connecting the new infrastructure with the Table Module.
* TO DO: implementing click and drag style interactor (e.g., https://echnotstechno.wordpress.com/2014/08/13/interactive-2d-plots-with-vtk-the-visualization-toolkit/ ).
* '''Implemented'''
https://www.slicer.org/wiki/Documentation/Nightly/Developers/Plots
https://www.youtube.com/watch?v=5Ag0PzYw0Hk&index=4&list=PLctSHxZgiJy6TZCu56v4qqb_uIdUL_KEz
|}

==Illustrations==
The idea is to be able to modify the parameters (in the table) of a model (blue object in the 3D View) directly from the plotting window.

[[image:SlicerAstroWiki13.png|1200px]]

VTKPLOTS sin and cos plus data selection (red crosses) example:

[[image:vtkPlots.png|1200px]]

==Background and References==
*https://www.slicer.org/wiki/Developer_Meetings/20170425
*http://www.jqplot.com/examples/customHighlighterCursorTrendline.php
*http://www.jqplot.com/examples/zooming.php
*[https://github.com/Punzo/SlicerAstro/wiki/ SlicerAstro]

[[image:SlicerAstroLogo.png|400px]]

*(Just for fun: how the gas in a galaxy looks like in 3D https://www.youtube.com/watch?v=yLjW9nbdO8g )

2016 Summer Project Week/3D Lasso Selection

2018-02-14T16:15:12Z

Davide:

__NOTOC__
<gallery>
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]
Image:SlicerAstro3DSelection1.pdf|3-D selection
</gallery>

==Key Investigators==
* Davide Punzo
* Csaba Pinter
* Andras Lasso
* Steve Pieper

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Adding a CloudLasso selection tool in the Segmentation editor for grid data. The Segmetation editor already works on 3D View. Therefore, it should streightforward to implement a draw effect on the 3D and apply a grid CloudLasso selection.
* Example of CloudLasso selection on particles https://www.youtube.com/watch?v=xqUkXol6oX8&hd=1
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Discuss with Csaba, Andras and Steve the implementation.
* Do it!
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Design and Implementation discussed with Andras, Steve and Csaba.
* Collected feedback from some users on the desired feature (e.g. an "eraser" 3D Lasso is also requested).
* The project it is not finished, however in this week we created a solid base (many useful implementation feedback and coding sharing by Andras, Steve and Csaba). The project will continued/finished in the next weeks.
* '''Implemented'''
https://www.youtube.com/watch?v=eDqfabv5xUY&list=PLctSHxZgiJy6TZCu56v4qqb_uIdUL_KEz&index=2
</div>
</div>

Project Week 25/Interactive Manipulation of Plots and Graphs

2018-02-14T16:14:48Z

Davide: /* Project Description */

__NOTOC__

Back to [[Project_Week_25#Projects|Projects List]]

==Key Investigators==

*[http://www.rug.nl/staff/davide.punzo/ Davide Punzo] (Kapteyn Astronomical Institute, University of Groningen, The Netherlands)
*[http://www.spl.harvard.edu/pages/People/pieper Steve Pieper] (Isomics Inc., USA)
*[https://www.kitware.com/jean-christophe-fillion-robin/ Jean-Christophe Fillion-Robin] (Kitware Inc., USA)
*[http://perk.cs.queensu.ca/users/lasso Andras Lasso] (Queen's University, Canada)

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|
Implementing the following plotting and graphs infrastructure enhancement:
* Panning a zoomed section of the graphs;
* Click and Drag a point;
* Data selection (select many points at once).
|
* Review if jqPlot can satisfy our requirements
* Implement them
|
* Once updated to jqplot version 1.0.9 (necessary for click and drag) the plotting does not work anymore. The infrastructure needs to be updated. Data selection will be hard to achieve.
* We decided to switch to [http://www.vtk.org/features-2d-plots-and-charts/ vtkPlots] (jqplot will be preserved for producing plots at publication quality level). The new infrastructure will allow a direct C++ integration of the vtkTable into the plotting (e.g., all the observations and data handling are automatically set), better performance (i.e., interactive performance up to hundreds of thousands of points) and easier customization.
* VTK PLOTS already have the following interactive desired functionality: zooming (middle click), panning (left click) and data selection (right click).
* The following widget, MRML and View classes have been designed and implemented: vtkMRMLPlotViewNode, vtkMRMLPlotNode, qMRMLPlotWidget, qMRMLPlotViewControllerWidget and qMRMLPlotView.
* A New Plot Layout has been created (index 36) and exposed to the qSlicerAppMainWindow widget.
* TO DO: connecting the new infrastructure with the Table Module.
* TO DO: implementing click and drag style interactor (e.g., https://echnotstechno.wordpress.com/2014/08/13/interactive-2d-plots-with-vtk-the-visualization-toolkit/ ).
* Implemented: https://www.slicer.org/wiki/Documentation/Nightly/Developers/Plots
https://www.youtube.com/watch?v=5Ag0PzYw0Hk&index=4&list=PLctSHxZgiJy6TZCu56v4qqb_uIdUL_KEz
|}

==Illustrations==
The idea is to be able to modify the parameters (in the table) of a model (blue object in the 3D View) directly from the plotting window.

[[image:SlicerAstroWiki13.png|1200px]]

VTKPLOTS sin and cos plus data selection (red crosses) example:

[[image:vtkPlots.png|1200px]]

==Background and References==
*https://www.slicer.org/wiki/Developer_Meetings/20170425
*http://www.jqplot.com/examples/customHighlighterCursorTrendline.php
*http://www.jqplot.com/examples/zooming.php
*[https://github.com/Punzo/SlicerAstro/wiki/ SlicerAstro]

[[image:SlicerAstroLogo.png|400px]]

*(Just for fun: how the gas in a galaxy looks like in 3D https://www.youtube.com/watch?v=yLjW9nbdO8g )

2016 Summer Project Week/3D Lasso Selection

2018-02-14T16:13:03Z

Davide:

__NOTOC__
<gallery>
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]
Image:SlicerAstro3DSelection1.pdf|3-D selection
</gallery>

==Key Investigators==
* Davide Punzo
* Csaba Pinter
* Andras Lasso
* Steve Pieper

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Adding a CloudLasso selection tool in the Segmentation editor for grid data. The Segmetation editor already works on 3D View. Therefore, it should streightforward to implement a draw effect on the 3D and apply a grid CloudLasso selection.
* Example of CloudLasso selection on particles https://www.youtube.com/watch?v=xqUkXol6oX8&hd=1
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Discuss with Csaba, Andras and Steve the implementation.
* Do it!
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Design and Implementation discussed with Andras, Steve and Csaba.
* Collected feedback from some users on the desired feature (e.g. an "eraser" 3D Lasso is also requested).
* The project it is not finished, however in this week we created a solid base (many useful implementation feedback and coding sharing by Andras, Steve and Csaba). The project will continued/finished in the next weeks.
* Implemented: https://www.youtube.com/watch?v=eDqfabv5xUY&list=PLctSHxZgiJy6TZCu56v4qqb_uIdUL_KEz&index=2
</div>
</div>

2016 Summer Project Week/3D Lasso Selection

2018-02-14T16:11:31Z

Davide:

__NOTOC__
<gallery>
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]
Image:SlicerAstro3DSelection1.pdf|3-D selection
</gallery>

==Key Investigators==
* Davide Punzo
* Csaba Pinter
* Andras Lasso
* Steve Pieper

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Adding a CloudLasso selection tool in the Segmentation editor for grid data. The Segmetation editor already works on 3-D View. Therefore, it should streightforward to implement a draw effect on the 3-D and apply a grid CloudLasso selection.
* Example of CloudLasso selection on particles https://www.youtube.com/watch?v=xqUkXol6oX8&hd=1
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Discuss with Csaba, Andras and Steve the implementation.
* Do it!
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Design and Implementation discussed with Andras, Steve and Csaba.
* Collected feedback from some users on the desired feature (e.g. an "eraser" 3-D Lasso is also requested).
* Generalized qSlicerSegmentEditorAbstractLabelEffect::appendPolyMask to work also in 3-DView (i.e. It will be easier for developer to implement editor effect working in 3-D).
* The project it is not finished, however in this week we created a solid base (many useful implementation feedback and coding sharing by Andras, Steve and Csaba). The project will continued/finished next week.
* Implementing Rectangular effect in the 3-D View, STATUS: still not working, but in good progress.
* Implementing Lasso effect in 3-D View, STATUS: I'll start to implement it on next week and it will be built on the basis of the rectangular effect.
* Implemented: https://www.youtube.com/watch?v=eDqfabv5xUY&list=PLctSHxZgiJy6TZCu56v4qqb_uIdUL_KEz&index=2
</div>
</div>

2015 Summer Project Week:Astronomy

2018-02-14T16:10:02Z

Davide: /* Key Investigators */

__NOTOC__
<gallery>
Image:WEIN069a.png |[[2015_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
*Davide Punzo, Kapteyn Astronomical Institute, University of Groningen, Netherlands
*Steve Pieper, Isomics

==Project Description==

Upcoming HI (neutral Hydrogen) surveys will deliver large datasets, and automated processing using
the full 3-D information (two positional dimensions and one spectral dimension) to find and
characterize HI objects is imperative. In this context, visualization is an essential
tool for enabling qualitative and quantitative human control on an automated source finding and
analysis pipeline. Visual Analytics, the combination of automated data processing
and human reasoning, creativity and intuition, supported by interactive visualization, enables
flexible and fast interaction with the 3-D data, helping the astronomer to deal with the analysis
of complex sources. 3-D visualization, coupled to modeling, provides additional capabilities
helping the discovery and analysis of subtle structures in the 3-D domain.

[https://www.youtube.com/watch?v=yLjW9nbdO8g gas component of WEIN069]
[https://www.youtube.com/watch?v=sS_5LrOS5bo APERTIF future daily observation]

[http://arxiv.org/abs/1505.06976 arXiv publication link]

[https://github.com/Punzo/SlicerAstro SlicerAstro git repository]

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* proper visualization of astronomical data cubes: using data astronomical data formats, such as FITS (http://en.wikipedia.org/wiki/FITS), and astronomical world coordinates system (WCS);
* generation of flux density profiles, moment maps and position-velocity diagrams linked with the 3-D view;
* enabling interactive smoothing in all three dimensions and multiscale analysis, such as wavelet lifting;
* interactive 3-D selection of HI sources;
* interactive HI data modeling coupled to visualization;
* introduction of the SAMP protocol (Simple Application Messaging Protocol) to enable interoperability with Topcat, and other VO (virtual observatory) tools and catalogs.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* discuss the best approaches;
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress: </h3>

<h3>outcome from 1st day: coordinates, labels and units. </h3>
*VTK_FITS reader (and writer) and the Slicer AstroVolume module done;
*data probe coordinates: factorize getPixelString in the logic of the volumes and use the WCSlib in the logic of AstroVolume;
*ruler widget: takes units properly -> OK;
*text on slices view: takes units properly -> OK;
*"spacing annotation" (horizontal widget showing the physical spacing): problem, makeScalingRuler method is hardcoded with mm and cm. Moreover we'd like a different design -> is factoring the class vtkPVScalarBarActor in the logic of the volumes a solution?;
*units: we have different unit for the third axes and we have also units for flux (pixel intensity), how to handle these?;

*question on AstroVolume and wcs: AstroVolume module allocates a vtkMRMLScalarVolumeNode, therefore I am adding the *wcs (it is a struct) in the vtkMRMLAstroVolumeStorageNode. Is this adequate? or it is better to do a vtkMRMLAstroVolumeNode child of vtkMRMLScalarVolumeNode and store the *wcs there (in this case it is not possible to use anymore CLI modules, but allows a better infrastructure)?

<h3>outcome from 2nd day: deeper investigation on units module. </h3>
*unitsLogic->AddUnitNode add a MRMLUnitsNode to the Scene, but from an interface point of view in Settings only two quantities are allocated qSlicerUnitsSettingsPanelPrivate::setMRMLScene -> quantities << "length" << "time"; (in principle adding "length1" << "length2" << "length3", should update automatically the interface).
*AstroVolume and wcs: let's do an vtkMRMLAstroVolumeNode and for the moment lose the skill to use CLI modules. In future we can see some tricks in the COMBOBOX to allow the use of them if they will be required from the users.

<h3>outcome from 3rd day: </h3>
*vtkMRMLAstroVolumeNode with *wcs struct integrated in SlicerAstro extension.
*working on modifications to the Units module for adding velocity and intensity quantities.
*Engineering solutions for data probe and slice view annotations hardcoded features will be addressed after the Units module.

2015 Summer Project Week:Astronomy

2018-02-14T16:09:20Z

Davide:

__NOTOC__
<gallery>
Image:WEIN069a.png |[[2015_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
*Davide Punzo, Kapteyn Astronomical Institute, University of Groningen, Netherlands
*anyone interested is very welcome

==Project Description==

Upcoming HI (neutral Hydrogen) surveys will deliver large datasets, and automated processing using
the full 3-D information (two positional dimensions and one spectral dimension) to find and
characterize HI objects is imperative. In this context, visualization is an essential
tool for enabling qualitative and quantitative human control on an automated source finding and
analysis pipeline. Visual Analytics, the combination of automated data processing
and human reasoning, creativity and intuition, supported by interactive visualization, enables
flexible and fast interaction with the 3-D data, helping the astronomer to deal with the analysis
of complex sources. 3-D visualization, coupled to modeling, provides additional capabilities
helping the discovery and analysis of subtle structures in the 3-D domain.

[https://www.youtube.com/watch?v=yLjW9nbdO8g gas component of WEIN069]
[https://www.youtube.com/watch?v=sS_5LrOS5bo APERTIF future daily observation]

[http://arxiv.org/abs/1505.06976 arXiv publication link]

[https://github.com/Punzo/SlicerAstro SlicerAstro git repository]

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* proper visualization of astronomical data cubes: using data astronomical data formats, such as FITS (http://en.wikipedia.org/wiki/FITS), and astronomical world coordinates system (WCS);
* generation of flux density profiles, moment maps and position-velocity diagrams linked with the 3-D view;
* enabling interactive smoothing in all three dimensions and multiscale analysis, such as wavelet lifting;
* interactive 3-D selection of HI sources;
* interactive HI data modeling coupled to visualization;
* introduction of the SAMP protocol (Simple Application Messaging Protocol) to enable interoperability with Topcat, and other VO (virtual observatory) tools and catalogs.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* discuss the best approaches;
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress: </h3>

<h3>outcome from 1st day: coordinates, labels and units. </h3>
*VTK_FITS reader (and writer) and the Slicer AstroVolume module done;
*data probe coordinates: factorize getPixelString in the logic of the volumes and use the WCSlib in the logic of AstroVolume;
*ruler widget: takes units properly -> OK;
*text on slices view: takes units properly -> OK;
*"spacing annotation" (horizontal widget showing the physical spacing): problem, makeScalingRuler method is hardcoded with mm and cm. Moreover we'd like a different design -> is factoring the class vtkPVScalarBarActor in the logic of the volumes a solution?;
*units: we have different unit for the third axes and we have also units for flux (pixel intensity), how to handle these?;

*question on AstroVolume and wcs: AstroVolume module allocates a vtkMRMLScalarVolumeNode, therefore I am adding the *wcs (it is a struct) in the vtkMRMLAstroVolumeStorageNode. Is this adequate? or it is better to do a vtkMRMLAstroVolumeNode child of vtkMRMLScalarVolumeNode and store the *wcs there (in this case it is not possible to use anymore CLI modules, but allows a better infrastructure)?

<h3>outcome from 2nd day: deeper investigation on units module. </h3>
*unitsLogic->AddUnitNode add a MRMLUnitsNode to the Scene, but from an interface point of view in Settings only two quantities are allocated qSlicerUnitsSettingsPanelPrivate::setMRMLScene -> quantities << "length" << "time"; (in principle adding "length1" << "length2" << "length3", should update automatically the interface).
*AstroVolume and wcs: let's do an vtkMRMLAstroVolumeNode and for the moment lose the skill to use CLI modules. In future we can see some tricks in the COMBOBOX to allow the use of them if they will be required from the users.

<h3>outcome from 3rd day: </h3>
*vtkMRMLAstroVolumeNode with *wcs struct integrated in SlicerAstro extension.
*working on modifications to the Units module for adding velocity and intensity quantities.
*Engineering solutions for data probe and slice view annotations hardcoded features will be addressed after the Units module.

2015 Summer Project Week:Astronomy

2018-02-14T16:08:34Z

Davide:

__NOTOC__
<gallery>
Image:WEIN069a.png |[[2015_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
*Davide Punzo, Kapteyn Astronomical Institute, University of Groningen, Netherlands
*anyone interested is very welcome

==Project Description==

Upcoming HI (neutral Hydrogen) surveys will deliver large datasets, and automated processing using
the full 3-D information (two positional dimensions and one spectral dimension) to find and
characterize HI objects is imperative. In this context, visualization is an essential
tool for enabling qualitative and quantitative human control on an automated source finding and
analysis pipeline. Visual Analytics, the combination of automated data processing
and human reasoning, creativity and intuition, supported by interactive visualization, enables
flexible and fast interaction with the 3-D data, helping the astronomer to deal with the analysis
of complex sources. 3-D visualization, coupled to modeling, provides additional capabilities
helping the discovery and analysis of subtle structures in the 3-D domain.

[https://www.youtube.com/watch?v=yLjW9nbdO8g gas component of WEIN069]
[https://www.youtube.com/watch?v=sS_5LrOS5bo APERTIF future daily observation]

[http://arxiv.org/abs/1505.06976 arXiv publication link]

[https://github.com/Punzo/SlicerAstro SlicerAstro git repository]

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* proper visualization of astronomical data cubes: using data astronomical data formats, such as FITS (http://en.wikipedia.org/wiki/FITS), and astronomical world coordinates system (WCS);
* generation of flux density profiles, moment maps and position-velocity diagrams linked with the 3-D view;
* enabling interactive smoothing in all three dimensions and multiscale analysis, such as wavelet lifting;
* interactive 3-D selection of HI sources;
* interactive HI data modeling coupled to visualization;
* introduction of the SAMP protocol (Simple Application Messaging Protocol) to enable interoperability with Topcat, and other VO (virtual observatory) tools and catalogs.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* discuss the best approaches;
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress: </h3>
*VTK_FITS reader (and writer) and the Slicer AstroVolume module done; working on VTK_WCS_transformation.

<h3>outcome from 1st day: coordinates, labels and units. </h3>
*data probe coordinates: factorize getPixelString in the logic of the volumes and use the WCSlib in the logic of AstroVolume;
*ruler widget: takes units properly -> OK;
*text on slices view: takes units properly -> OK;
*"spacing annotation" (horizontal widget showing the physical spacing): problem, makeScalingRuler method is hardcoded with mm and cm. Moreover we'd like a different design -> is factoring the class vtkPVScalarBarActor in the logic of the volumes a solution?;
*units: we have different unit for the third axes and we have also units for flux (pixel intensity), how to handle these?;

*question on AstroVolume and wcs: AstroVolume module allocates a vtkMRMLScalarVolumeNode, therefore I am adding the *wcs (it is a struct) in the vtkMRMLAstroVolumeStorageNode. Is this adequate? or it is better to do a vtkMRMLAstroVolumeNode child of vtkMRMLScalarVolumeNode and store the *wcs there (in this case it is not possible to use anymore CLI modules, but allows a better infrastructure)?

<h3>outcome from 2nd day: deeper investigation on units module. </h3>
*unitsLogic->AddUnitNode add a MRMLUnitsNode to the Scene, but from an interface point of view in Settings only two quantities are allocated qSlicerUnitsSettingsPanelPrivate::setMRMLScene -> quantities << "length" << "time"; (in principle adding "length1" << "length2" << "length3", should update automatically the interface).
*AstroVolume and wcs: let's do an vtkMRMLAstroVolumeNode and for the moment lose the skill to use CLI modules. In future we can see some tricks in the COMBOBOX to allow the use of them if they will be required from the users.

<h3>outcome from 3rd day: </h3>
*vtkMRMLAstroVolumeNode with *wcs struct integrated in SlicerAstro extension.
*working on modifications to the Units module for adding velocity and intensity quantities.
*Engineering solutions for data probe and slice view annotations hardcoded features will be addressed after the Units module.

2015 Summer Project Week:Astronomy

2018-02-14T16:07:26Z

Davide:

__NOTOC__
<gallery>
Image:WEIN069a.png |[[2015_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
*Davide Punzo, Kapteyn Astronomical Institute, University of Groningen, Netherlands
*anyone interested is very welcome

==Project Description==

Upcoming HI (neutral Hydrogen) surveys will deliver large datasets, and automated processing using
the full 3-D information (two positional dimensions and one spectral dimension) to find and
characterize HI objects is imperative. In this context, visualization is an essential
tool for enabling qualitative and quantitative human control on an automated source finding and
analysis pipeline. Visual Analytics, the combination of automated data processing
and human reasoning, creativity and intuition, supported by interactive visualization, enables
flexible and fast interaction with the 3-D data, helping the astronomer to deal with the analysis
of complex sources. 3-D visualization, coupled to modeling, provides additional capabilities
helping the discovery and analysis of subtle structures in the 3-D domain.

[https://www.youtube.com/watch?v=yLjW9nbdO8g gas component of WEIN069]
[https://www.youtube.com/watch?v=sS_5LrOS5bo APERTIF future daily observation]

[http://arxiv.org/abs/1505.06976 arXiv publication link]

[https://github.com/Punzo/SlicerAstro SlicerAstro git repository]

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* proper visualization of astronomical data cubes: using data astronomical data formats, such as FITS (http://en.wikipedia.org/wiki/FITS), and astronomical world coordinates system (WCS);
* generation of flux density profiles, moment maps and position-velocity diagrams linked with the 3-D view;
* enabling interactive smoothing in all three dimensions and multiscale analysis, such as wavelet lifting;
* interactive 3-D selection of HI sources;
* interactive HI data modeling coupled to visualization;
* introduction of the SAMP protocol (Simple Application Messaging Protocol) to enable interoperability with Topcat, and other VO (virtual observatory) tools and catalogs.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* finish the first objective;
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress: </h3>
*VTK_FITS reader (and writer) and the Slicer AstroVolume module done; working on VTK_WCS_transformation.

<h3>outcome from 1st day: coordinates, labels and units. </h3>
*data probe coordinates: factorize getPixelString in the logic of the volumes and use the WCSlib in the logic of AstroVolume;
*ruler widget: takes units properly -> OK;
*text on slices view: takes units properly -> OK;
*"spacing annotation" (horizontal widget showing the physical spacing): problem, makeScalingRuler method is hardcoded with mm and cm. Moreover we'd like a different design -> is factoring the class vtkPVScalarBarActor in the logic of the volumes a solution?;
*units: we have different unit for the third axes and we have also units for flux (pixel intensity), how to handle these?;

*question on AstroVolume and wcs: AstroVolume module allocates a vtkMRMLScalarVolumeNode, therefore I am adding the *wcs (it is a struct) in the vtkMRMLAstroVolumeStorageNode. Is this adequate? or it is better to do a vtkMRMLAstroVolumeNode child of vtkMRMLScalarVolumeNode and store the *wcs there (in this case it is not possible to use anymore CLI modules, but allows a better infrastructure)?

<h3>outcome from 2nd day: deeper investigation on units module. </h3>
*unitsLogic->AddUnitNode add a MRMLUnitsNode to the Scene, but from an interface point of view in Settings only two quantities are allocated qSlicerUnitsSettingsPanelPrivate::setMRMLScene -> quantities << "length" << "time"; (in principle adding "length1" << "length2" << "length3", should update automatically the interface).
*AstroVolume and wcs: let's do an vtkMRMLAstroVolumeNode and for the moment lose the skill to use CLI modules. In future we can see some tricks in the COMBOBOX to allow the use of them if they will be required from the users.

<h3>outcome from 3rd day: </h3>
*vtkMRMLAstroVolumeNode with *wcs struct integrated in SlicerAstro extension.
*working on modifications to the Units module for adding velocity and intensity quantities.
*Engineering solutions for data probe and slice view annotations hardcoded features will be addressed after the Units module.

2015 Summer Project Week:Astronomy

2018-02-14T16:06:48Z

Davide:

__NOTOC__
<gallery>
Image:WEIN069a.png |[[2015_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
*Davide Punzo, Kapteyn Astronomical Institute, University of Groningen, Netherlands
*anyone interested is very welcome

==Project Description==

Upcoming HI (neutral Hydrogen) surveys will deliver large datasets, and automated processing using
the full 3-D information (two positional dimensions and one spectral dimension) to find and
characterize HI objects is imperative. In this context, visualization is an essential
tool for enabling qualitative and quantitative human control on an automated source finding and
analysis pipeline. Visual Analytics, the combination of automated data processing
and human reasoning, creativity and intuition, supported by interactive visualization, enables
flexible and fast interaction with the 3-D data, helping the astronomer to deal with the analysis
of complex sources. 3-D visualization, coupled to modeling, provides additional capabilities
helping the discovery and analysis of subtle structures in the 3-D domain.

[https://www.youtube.com/watch?v=yLjW9nbdO8g gas component of WEIN069]
[https://www.youtube.com/watch?v=sS_5LrOS5bo APERTIF future daily observation]

[http://arxiv.org/abs/1505.06976 arXiv publication link]

[https://github.com/Punzo/SlicerAstro SlicerAstro git repository]

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* proper visualization of astronomical data cubes: using data astronomical data formats, such as FITS (http://en.wikipedia.org/wiki/FITS), and astronomical world coordinates system (WCS);
* generation of flux density profiles, moment maps and position-velocity diagrams linked with the 3-D view;
* enabling interactive smoothing in all three dimensions and multiscale analysis, such as wavelet lifting;
* interactive 3-D selection of HI sources;
* interactive HI data modeling coupled to visualization;
* introduction of the SAMP protocol (Simple Application Messaging Protocol) to enable interoperability with Topcat, and other VO (virtual observatory) tools and catalogs.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* finish the first objective;
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress: </h3>
*VTK_FITS reader (and writer) and the Slicer AstroVolume module done; working on VTK_WCS_transformation.
</div>
</div>

<h3> CIAO</h3>
<h3> CIAO</h3>
<h3> CIAO</h3>

<h3>outcome from 1st day: coordinates, labels and units. </h3>
*data probe coordinates: factorize getPixelString in the logic of the volumes and use the WCSlib in the logic of AstroVolume;
*ruler widget: takes units properly -> OK;
*text on slices view: takes units properly -> OK;
*"spacing annotation" (horizontal widget showing the physical spacing): problem, makeScalingRuler method is hardcoded with mm and cm. Moreover we'd like a different design -> is factoring the class vtkPVScalarBarActor in the logic of the volumes a solution?;
*units: we have different unit for the third axes and we have also units for flux (pixel intensity), how to handle these?;

*question on AstroVolume and wcs: AstroVolume module allocates a vtkMRMLScalarVolumeNode, therefore I am adding the *wcs (it is a struct) in the vtkMRMLAstroVolumeStorageNode. Is this adequate? or it is better to do a vtkMRMLAstroVolumeNode child of vtkMRMLScalarVolumeNode and store the *wcs there (in this case it is not possible to use anymore CLI modules, but allows a better infrastructure)?

<h3>outcome from 2nd day: deeper investigation on units module. </h3>
*unitsLogic->AddUnitNode add a MRMLUnitsNode to the Scene, but from an interface point of view in Settings only two quantities are allocated qSlicerUnitsSettingsPanelPrivate::setMRMLScene -> quantities << "length" << "time"; (in principle adding "length1" << "length2" << "length3", should update automatically the interface).
*AstroVolume and wcs: let's do an vtkMRMLAstroVolumeNode and for the moment lose the skill to use CLI modules. In future we can see some tricks in the COMBOBOX to allow the use of them if they will be required from the users.

<h3>outcome from 3rd day: </h3>
*vtkMRMLAstroVolumeNode with *wcs struct integrated in SlicerAstro extension.
*working on modifications to the Units module for adding velocity and intensity quantities.
*Engineering solutions for data probe and slice view annotations hardcoded features will be addressed after the Units module.

2015 Summer Project Week:Astronomy

2018-02-14T16:06:29Z

Davide:

__NOTOC__
<gallery>
Image:WEIN069a.png |[[2015_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
*Davide Punzo, Kapteyn Astronomical Institute, University of Groningen, Netherlands
*anyone interested is very welcome

==Project Description==

Upcoming HI (neutral Hydrogen) surveys will deliver large datasets, and automated processing using
the full 3-D information (two positional dimensions and one spectral dimension) to find and
characterize HI objects is imperative. In this context, visualization is an essential
tool for enabling qualitative and quantitative human control on an automated source finding and
analysis pipeline. Visual Analytics, the combination of automated data processing
and human reasoning, creativity and intuition, supported by interactive visualization, enables
flexible and fast interaction with the 3-D data, helping the astronomer to deal with the analysis
of complex sources. 3-D visualization, coupled to modeling, provides additional capabilities
helping the discovery and analysis of subtle structures in the 3-D domain.

[https://www.youtube.com/watch?v=yLjW9nbdO8g gas component of WEIN069]
[https://www.youtube.com/watch?v=sS_5LrOS5bo APERTIF future daily observation]

[http://arxiv.org/abs/1505.06976 arXiv publication link]

[https://github.com/Punzo/SlicerAstro SlicerAstro git repository]

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* proper visualization of astronomical data cubes: using data astronomical data formats, such as FITS (http://en.wikipedia.org/wiki/FITS), and astronomical world coordinates system (WCS);
* generation of flux density profiles, moment maps and position-velocity diagrams linked with the 3-D view;
* enabling interactive smoothing in all three dimensions and multiscale analysis, such as wavelet lifting;
* interactive 3-D selection of HI sources;
* interactive HI data modeling coupled to visualization;
* introduction of the SAMP protocol (Simple Application Messaging Protocol) to enable interoperability with Topcat, and other VO (virtual observatory) tools and catalogs.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* finish the first objective;
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress: </h3>
*VTK_FITS reader (and writer) and the Slicer AstroVolume module done; working on VTK_WCS_transformation.
</div>
</div>

<h3> CIAO</h3>
<h3> CIAO</h3>

<h3>outcome from 1st day: coordinates, labels and units. </h3>
*data probe coordinates: factorize getPixelString in the logic of the volumes and use the WCSlib in the logic of AstroVolume;
*ruler widget: takes units properly -> OK;
*text on slices view: takes units properly -> OK;
*"spacing annotation" (horizontal widget showing the physical spacing): problem, makeScalingRuler method is hardcoded with mm and cm. Moreover we'd like a different design -> is factoring the class vtkPVScalarBarActor in the logic of the volumes a solution?;
*units: we have different unit for the third axes and we have also units for flux (pixel intensity), how to handle these?;

*question on AstroVolume and wcs: AstroVolume module allocates a vtkMRMLScalarVolumeNode, therefore I am adding the *wcs (it is a struct) in the vtkMRMLAstroVolumeStorageNode. Is this adequate? or it is better to do a vtkMRMLAstroVolumeNode child of vtkMRMLScalarVolumeNode and store the *wcs there (in this case it is not possible to use anymore CLI modules, but allows a better infrastructure)?

<h3>outcome from 2nd day: deeper investigation on units module. </h3>
*unitsLogic->AddUnitNode add a MRMLUnitsNode to the Scene, but from an interface point of view in Settings only two quantities are allocated qSlicerUnitsSettingsPanelPrivate::setMRMLScene -> quantities << "length" << "time"; (in principle adding "length1" << "length2" << "length3", should update automatically the interface).
*AstroVolume and wcs: let's do an vtkMRMLAstroVolumeNode and for the moment lose the skill to use CLI modules. In future we can see some tricks in the COMBOBOX to allow the use of them if they will be required from the users.

<h3>outcome from 3rd day: </h3>
*vtkMRMLAstroVolumeNode with *wcs struct integrated in SlicerAstro extension.
*working on modifications to the Units module for adding velocity and intensity quantities.
*Engineering solutions for data probe and slice view annotations hardcoded features will be addressed after the Units module.

2015 Summer Project Week:Astronomy

2018-02-14T16:06:07Z

Davide:

__NOTOC__
<gallery>
Image:WEIN069a.png |[[2015_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
*Davide Punzo, Kapteyn Astronomical Institute, University of Groningen, Netherlands
*anyone interested is very welcome

==Project Description==

Upcoming HI (neutral Hydrogen) surveys will deliver large datasets, and automated processing using
the full 3-D information (two positional dimensions and one spectral dimension) to find and
characterize HI objects is imperative. In this context, visualization is an essential
tool for enabling qualitative and quantitative human control on an automated source finding and
analysis pipeline. Visual Analytics, the combination of automated data processing
and human reasoning, creativity and intuition, supported by interactive visualization, enables
flexible and fast interaction with the 3-D data, helping the astronomer to deal with the analysis
of complex sources. 3-D visualization, coupled to modeling, provides additional capabilities
helping the discovery and analysis of subtle structures in the 3-D domain.

[https://www.youtube.com/watch?v=yLjW9nbdO8g gas component of WEIN069]
[https://www.youtube.com/watch?v=sS_5LrOS5bo APERTIF future daily observation]

[http://arxiv.org/abs/1505.06976 arXiv publication link]

[https://github.com/Punzo/SlicerAstro SlicerAstro git repository]

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* proper visualization of astronomical data cubes: using data astronomical data formats, such as FITS (http://en.wikipedia.org/wiki/FITS), and astronomical world coordinates system (WCS);
* generation of flux density profiles, moment maps and position-velocity diagrams linked with the 3-D view;
* enabling interactive smoothing in all three dimensions and multiscale analysis, such as wavelet lifting;
* interactive 3-D selection of HI sources;
* interactive HI data modeling coupled to visualization;
* introduction of the SAMP protocol (Simple Application Messaging Protocol) to enable interoperability with Topcat, and other VO (virtual observatory) tools and catalogs.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* finish the first objective;
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress: </h3>
*VTK_FITS reader (and writer) and the Slicer AstroVolume module done; working on VTK_WCS_transformation.
</div>
</div>

<h3> CIAO</h3>

<h3>outcome from 1st day: coordinates, labels and units. </h3>
*data probe coordinates: factorize getPixelString in the logic of the volumes and use the WCSlib in the logic of AstroVolume;
*ruler widget: takes units properly -> OK;
*text on slices view: takes units properly -> OK;
*"spacing annotation" (horizontal widget showing the physical spacing): problem, makeScalingRuler method is hardcoded with mm and cm. Moreover we'd like a different design -> is factoring the class vtkPVScalarBarActor in the logic of the volumes a solution?;
*units: we have different unit for the third axes and we have also units for flux (pixel intensity), how to handle these?;

*question on AstroVolume and wcs: AstroVolume module allocates a vtkMRMLScalarVolumeNode, therefore I am adding the *wcs (it is a struct) in the vtkMRMLAstroVolumeStorageNode. Is this adequate? or it is better to do a vtkMRMLAstroVolumeNode child of vtkMRMLScalarVolumeNode and store the *wcs there (in this case it is not possible to use anymore CLI modules, but allows a better infrastructure)?

<h3>outcome from 2nd day: deeper investigation on units module. </h3>
*unitsLogic->AddUnitNode add a MRMLUnitsNode to the Scene, but from an interface point of view in Settings only two quantities are allocated qSlicerUnitsSettingsPanelPrivate::setMRMLScene -> quantities << "length" << "time"; (in principle adding "length1" << "length2" << "length3", should update automatically the interface).
*AstroVolume and wcs: let's do an vtkMRMLAstroVolumeNode and for the moment lose the skill to use CLI modules. In future we can see some tricks in the COMBOBOX to allow the use of them if they will be required from the users.

<h3>outcome from 3rd day: </h3>
*vtkMRMLAstroVolumeNode with *wcs struct integrated in SlicerAstro extension.
*working on modifications to the Units module for adding velocity and intensity quantities.
*Engineering solutions for data probe and slice view annotations hardcoded features will be addressed after the Units module.

2015 Summer Project Week:Astronomy

2018-02-14T16:05:51Z

Davide:

__NOTOC__
<gallery>
Image:WEIN069a.png |[[2015_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
*Davide Punzo, Kapteyn Astronomical Institute, University of Groningen, Netherlands
*anyone interested is very welcome

==Project Description==

Upcoming HI (neutral Hydrogen) surveys will deliver large datasets, and automated processing using
the full 3-D information (two positional dimensions and one spectral dimension) to find and
characterize HI objects is imperative. In this context, visualization is an essential
tool for enabling qualitative and quantitative human control on an automated source finding and
analysis pipeline. Visual Analytics, the combination of automated data processing
and human reasoning, creativity and intuition, supported by interactive visualization, enables
flexible and fast interaction with the 3-D data, helping the astronomer to deal with the analysis
of complex sources. 3-D visualization, coupled to modeling, provides additional capabilities
helping the discovery and analysis of subtle structures in the 3-D domain.

[https://www.youtube.com/watch?v=yLjW9nbdO8g gas component of WEIN069]
[https://www.youtube.com/watch?v=sS_5LrOS5bo APERTIF future daily observation]

[http://arxiv.org/abs/1505.06976 arXiv publication link]

[https://github.com/Punzo/SlicerAstro SlicerAstro git repository]

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* proper visualization of astronomical data cubes: using data astronomical data formats, such as FITS (http://en.wikipedia.org/wiki/FITS), and astronomical world coordinates system (WCS);
* generation of flux density profiles, moment maps and position-velocity diagrams linked with the 3-D view;
* enabling interactive smoothing in all three dimensions and multiscale analysis, such as wavelet lifting;
* interactive 3-D selection of HI sources;
* interactive HI data modeling coupled to visualization;
* introduction of the SAMP protocol (Simple Application Messaging Protocol) to enable interoperability with Topcat, and other VO (virtual observatory) tools and catalogs.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* finish the first objective;
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress: </h3>
*VTK_FITS reader (and writer) and the Slicer AstroVolume module done; working on VTK_WCS_transformation.
</div>
</div>

<h3> </h3>

<h3>outcome from 1st day: coordinates, labels and units. </h3>
*data probe coordinates: factorize getPixelString in the logic of the volumes and use the WCSlib in the logic of AstroVolume;
*ruler widget: takes units properly -> OK;
*text on slices view: takes units properly -> OK;
*"spacing annotation" (horizontal widget showing the physical spacing): problem, makeScalingRuler method is hardcoded with mm and cm. Moreover we'd like a different design -> is factoring the class vtkPVScalarBarActor in the logic of the volumes a solution?;
*units: we have different unit for the third axes and we have also units for flux (pixel intensity), how to handle these?;

*question on AstroVolume and wcs: AstroVolume module allocates a vtkMRMLScalarVolumeNode, therefore I am adding the *wcs (it is a struct) in the vtkMRMLAstroVolumeStorageNode. Is this adequate? or it is better to do a vtkMRMLAstroVolumeNode child of vtkMRMLScalarVolumeNode and store the *wcs there (in this case it is not possible to use anymore CLI modules, but allows a better infrastructure)?

<h3>outcome from 2nd day: deeper investigation on units module. </h3>
*unitsLogic->AddUnitNode add a MRMLUnitsNode to the Scene, but from an interface point of view in Settings only two quantities are allocated qSlicerUnitsSettingsPanelPrivate::setMRMLScene -> quantities << "length" << "time"; (in principle adding "length1" << "length2" << "length3", should update automatically the interface).
*AstroVolume and wcs: let's do an vtkMRMLAstroVolumeNode and for the moment lose the skill to use CLI modules. In future we can see some tricks in the COMBOBOX to allow the use of them if they will be required from the users.

<h3>outcome from 3rd day: </h3>
*vtkMRMLAstroVolumeNode with *wcs struct integrated in SlicerAstro extension.
*working on modifications to the Units module for adding velocity and intensity quantities.
*Engineering solutions for data probe and slice view annotations hardcoded features will be addressed after the Units module.

2015 Summer Project Week:Astronomy

2018-02-14T16:05:15Z

Davide:

__NOTOC__
<gallery>
Image:WEIN069a.png |[[2015_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
*Davide Punzo, Kapteyn Astronomical Institute, University of Groningen, Netherlands
*anyone interested is very welcome

==Project Description==

Upcoming HI (neutral Hydrogen) surveys will deliver large datasets, and automated processing using
the full 3-D information (two positional dimensions and one spectral dimension) to find and
characterize HI objects is imperative. In this context, visualization is an essential
tool for enabling qualitative and quantitative human control on an automated source finding and
analysis pipeline. Visual Analytics, the combination of automated data processing
and human reasoning, creativity and intuition, supported by interactive visualization, enables
flexible and fast interaction with the 3-D data, helping the astronomer to deal with the analysis
of complex sources. 3-D visualization, coupled to modeling, provides additional capabilities
helping the discovery and analysis of subtle structures in the 3-D domain.

[https://www.youtube.com/watch?v=yLjW9nbdO8g gas component of WEIN069]
[https://www.youtube.com/watch?v=sS_5LrOS5bo APERTIF future daily observation]

[http://arxiv.org/abs/1505.06976 arXiv publication link]

[https://github.com/Punzo/SlicerAstro SlicerAstro git repository]

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* proper visualization of astronomical data cubes: using data astronomical data formats, such as FITS (http://en.wikipedia.org/wiki/FITS), and astronomical world coordinates system (WCS);
* generation of flux density profiles, moment maps and position-velocity diagrams linked with the 3-D view;
* enabling interactive smoothing in all three dimensions and multiscale analysis, such as wavelet lifting;
* interactive 3-D selection of HI sources;
* interactive HI data modeling coupled to visualization;
* introduction of the SAMP protocol (Simple Application Messaging Protocol) to enable interoperability with Topcat, and other VO (virtual observatory) tools and catalogs.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* finish the first objective;
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress: </h3>
*VTK_FITS reader (and writer) and the Slicer AstroVolume module done; working on VTK_WCS_transformation.
</div>
</div>

<h3>outcome from 1st day: coordinates, labels and units. </h3>
*data probe coordinates: factorize getPixelString in the logic of the volumes and use the WCSlib in the logic of AstroVolume;
*ruler widget: takes units properly -> OK;
*text on slices view: takes units properly -> OK;
*"spacing annotation" (horizontal widget showing the physical spacing): problem, makeScalingRuler method is hardcoded with mm and cm. Moreover we'd like a different design -> is factoring the class vtkPVScalarBarActor in the logic of the volumes a solution?;
*units: we have different unit for the third axes and we have also units for flux (pixel intensity), how to handle these?;

*question on AstroVolume and wcs: AstroVolume module allocates a vtkMRMLScalarVolumeNode, therefore I am adding the *wcs (it is a struct) in the vtkMRMLAstroVolumeStorageNode. Is this adequate? or it is better to do a vtkMRMLAstroVolumeNode child of vtkMRMLScalarVolumeNode and store the *wcs there (in this case it is not possible to use anymore CLI modules, but allows a better infrastructure)?

<h3>outcome from 2nd day: deeper investigation on units module. </h3>
*unitsLogic->AddUnitNode add a MRMLUnitsNode to the Scene, but from an interface point of view in Settings only two quantities are allocated qSlicerUnitsSettingsPanelPrivate::setMRMLScene -> quantities << "length" << "time"; (in principle adding "length1" << "length2" << "length3", should update automatically the interface).
*AstroVolume and wcs: let's do an vtkMRMLAstroVolumeNode and for the moment lose the skill to use CLI modules. In future we can see some tricks in the COMBOBOX to allow the use of them if they will be required from the users.

<h3>outcome from 3rd day: </h3>
*vtkMRMLAstroVolumeNode with *wcs struct integrated in SlicerAstro extension.
*working on modifications to the Units module for adding velocity and intensity quantities.
*Engineering solutions for data probe and slice view annotations hardcoded features will be addressed after the Units module.

Project Week 25/Interactive Manipulation of Plots and Graphs

2017-06-30T10:20:09Z

Davide:

__NOTOC__

Back to [[Project_Week_25#Projects|Projects List]]

==Key Investigators==

*[http://www.rug.nl/staff/davide.punzo/ Davide Punzo] (Kapteyn Astronomical Institute, University of Groningen, The Netherlands)
*[http://www.spl.harvard.edu/pages/People/pieper Steve Pieper] (Isomics Inc., USA)
*[https://www.kitware.com/jean-christophe-fillion-robin/ Jean-Christophe Fillion-Robin] (Kitware Inc., USA)
*[http://perk.cs.queensu.ca/users/lasso Andras Lasso] (Queen's University, Canada)

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|
Implementing the following plotting and graphs infrastructure enhancement:
* Panning a zoomed section of the graphs;
* Click and Drag a point;
* Data selection (select many points at once).
|
* Review if jqPlot can satisfy our requirements
* Implement them
|
* Once updated to jqplot version 1.0.9 (necessary for click and drag) the plotting does not work anymore. The infrastructure needs to be updated. Data selection will be hard to achieve.
* We decided to switch to [http://www.vtk.org/features-2d-plots-and-charts/ vtkPlots] (jqplot will be preserved for producing plots at publication quality level). The new infrastructure will allow a direct C++ integration of the vtkTable into the plotting (e.g., all the observations and data handling are automatically set), better performance (i.e., interactive performance up to hundreds of thousands of points) and easier customization.
* VTK PLOTS already have the following interactive desired functionality: zooming (middle click), panning (left click) and data selection (right click).
* The following widget, MRML and View classes have been designed and implemented: vtkMRMLPlotViewNode, vtkMRMLPlotNode, qMRMLPlotWidget, qMRMLPlotViewControllerWidget and qMRMLPlotView.
* A New Plot Layout has been created (index 36) and exposed to the qSlicerAppMainWindow widget.
* TO DO: connecting the new infrastructure with the Table Module.
* TO DO: implementing click and drag style interactor (e.g., https://echnotstechno.wordpress.com/2014/08/13/interactive-2d-plots-with-vtk-the-visualization-toolkit/ ).
|}

==Illustrations==
The idea is to be able to modify the parameters (in the table) of a model (blue object in the 3D View) directly from the plotting window.

[[image:SlicerAstroWiki13.png|1200px]]

VTKPLOTS sin and cos plus data selection (red crosses) example:

[[image:vtkPlots.png|1200px]]

==Background and References==
*https://www.slicer.org/wiki/Developer_Meetings/20170425
*http://www.jqplot.com/examples/customHighlighterCursorTrendline.php
*http://www.jqplot.com/examples/zooming.php
*[https://github.com/Punzo/SlicerAstro/wiki/ SlicerAstro]

[[image:SlicerAstroLogo.png|400px]]

*(Just for fun: how the gas in a galaxy looks like in 3D https://www.youtube.com/watch?v=yLjW9nbdO8g )

Project Week 25/Interactive Manipulation of Plots and Graphs

2017-06-30T10:19:33Z

Davide:

__NOTOC__

Back to [[Project_Week_25#Projects|Projects List]]

==Key Investigators==

*[http://www.rug.nl/staff/davide.punzo/ Davide Punzo] (Kapteyn Astronomical Institute, University of Groningen, The Netherlands)
*[http://www.spl.harvard.edu/pages/People/pieper Steve Pieper] (Isomics Inc., USA)
*[https://www.kitware.com/jean-christophe-fillion-robin/ Jean-Christophe Fillion-Robin] (Kitware Inc., USA)
*[http://perk.cs.queensu.ca/users/lasso Andras Lasso] (Queen's University, Canada)

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|
Implementing the following plotting and graphs infrastructure enhancement:
* Panning a zoomed section of the graphs;
* Click and Drag a point;
* Data selection (select many points at once).
|
* Review if jqPlot can satisfy our requirements
* Implement them
|
* Once updated to jqplot version 1.0.9 (necessary for click and drag) the plotting does not work anymore. The infrastructure needs to be update. Data selection will be hard to achieve.
* We decided to switch to [http://www.vtk.org/features-2d-plots-and-charts/ vtkPlots] (jqplot will be preserved for producing plots at publication quality level). The new infrastructure will allow a direct C++ integration of the vtkTable into the plotting (e.g., all the observations and data handling are automatically set), better performance (i.e., interactive performance up to hundreds of thousands of points) and easier customization.
* VTK PLOTS already have the following interactive desired functionality: zooming (middle click), panning (left click) and data selection (right click).
* The following widget, MRML and View classes have been designed and implemented: vtkMRMLPlotViewNode, vtkMRMLPlotNode, qMRMLPlotWidget, qMRMLPlotViewControllerWidget and qMRMLPlotView.
* A New Plot Layout has been created (index 36) and exposed to the qSlicerAppMainWindow widget.
* TO DO: connecting the new infrastructure with the Table Module.
* TO DO: implementing click and drag style interactor (e.g., https://echnotstechno.wordpress.com/2014/08/13/interactive-2d-plots-with-vtk-the-visualization-toolkit/ ).
|}

==Illustrations==
The idea is to be able to modify the parameters (in the table) of a model (blue object in the 3D View) directly from the plotting window.

[[image:SlicerAstroWiki13.png|1200px]]

VTKPLOTS sin and cos plus data selection (red crosses) example:

[[image:vtkPlots.png|1200px]]

==Background and References==
*https://www.slicer.org/wiki/Developer_Meetings/20170425
*http://www.jqplot.com/examples/customHighlighterCursorTrendline.php
*http://www.jqplot.com/examples/zooming.php
*[https://github.com/Punzo/SlicerAstro/wiki/ SlicerAstro]

[[image:SlicerAstroLogo.png|400px]]

*(Just for fun: how the gas in a galaxy looks like in 3D https://www.youtube.com/watch?v=yLjW9nbdO8g )

Project Week 25/Interactive Manipulation of Plots and Graphs

2017-06-30T10:17:10Z

Davide: /* Project Description */

__NOTOC__

Back to [[Project_Week_25#Projects|Projects List]]

==Key Investigators==

*[http://www.rug.nl/staff/davide.punzo/ Davide Punzo] (Kapteyn Astronomical Institute, University of Groningen, The Netherlands)
*[http://www.spl.harvard.edu/pages/People/pieper Steve Pieper] (Isomics Inc., USA)
*[https://www.kitware.com/jean-christophe-fillion-robin/ Jean-Christophe Fillion-Robin] (Kitware Inc., USA)
*[http://perk.cs.queensu.ca/users/lasso Andras Lasso] (Queen's University, Canada)

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|
Implementing the following plotting and graphs infrastructure enhancement:
* Panning a zoomed section of the graphs;
* Click and Drag a point;
* Data selection (select many points at once).
|
* Review if jqPlot can satisfy our requirements
* Implement them
|
* Once updated to jqplot version 1.0.9 (necessary for click and drag) the plotting does not work anymore. The infrastructure needs to be update. Plus data selection will hard to achieve.
* We decided to switch to [http://www.vtk.org/features-2d-plots-and-charts/ vtkPlots] (jqplot will be preserved for producing plots at publication quality level). The new infrastructure will allow a direct C++ integration of the vtkTable into the plotting (e.g., all the observations and data handling are automatically set), better performance (i.e., interactive performance up to hundreds of thousands of points) and easier customization.
* VTK PLOTS already have the following interactive desired functionality: zooming (middle click), panning (left click) and data selection (right click).
* The following widget, MRML and View classes have been designed and implemented: vtkMRMLPlotViewNode, vtkMRMLPlotNode, qMRMLPlotWidget, qMRMLPlotViewControllerWidget and qMRMLPlotView.
* A New Plot Layout has been created (index 36) and exposed to the qSlicerAppMainWindow widget.
* TO DO: connecting the new infrastructure with the Table Module.
* TO DO: implementing click and drag style interactor (e.g., https://echnotstechno.wordpress.com/2014/08/13/interactive-2d-plots-with-vtk-the-visualization-toolkit/ ).
|}

==Illustrations==
The idea is to be able to modify the parameters (in the table) of a model (blue object in the 3D View) directly from the plotting window.

[[image:SlicerAstroWiki13.png|1200px]]

VTKPLOTS sin and cos plus data selection (red crosses) example:

[[image:vtkPlots.png|1200px]]

==Background and References==
*https://www.slicer.org/wiki/Developer_Meetings/20170425
*http://www.jqplot.com/examples/customHighlighterCursorTrendline.php
*http://www.jqplot.com/examples/zooming.php
*[https://github.com/Punzo/SlicerAstro/wiki/ SlicerAstro]

[[image:SlicerAstroLogo.png|400px]]

*(Just for fun: how the gas in a galaxy looks like in 3D https://www.youtube.com/watch?v=yLjW9nbdO8g )

Project Week 25/Interactive Manipulation of Plots and Graphs

2017-06-30T10:16:11Z

Davide: /* Illustrations */

__NOTOC__

Back to [[Project_Week_25#Projects|Projects List]]

==Key Investigators==

*[http://www.rug.nl/staff/davide.punzo/ Davide Punzo] (Kapteyn Astronomical Institute, University of Groningen, The Netherlands)
*[http://www.spl.harvard.edu/pages/People/pieper Steve Pieper] (Isomics Inc., USA)
*[https://www.kitware.com/jean-christophe-fillion-robin/ Jean-Christophe Fillion-Robin] (Kitware Inc., USA)
*[http://perk.cs.queensu.ca/users/lasso Andras Lasso] (Queen's University, Canada)

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|
Implementing the following plotting and graphs infrastructure enhancement:
* Panning a zoomed section of the graphs;
* Click and Drag a point;
* Data selection (select many points at once).
|
* Review if jqPlot can satisfy our requirements
* Implement them
|
* Once updated to jqplot version 1.0.9 (necessary for click and drag) the plotting does not work anymore. The infrastructure needs update.
* We decided to switch to [http://www.vtk.org/features-2d-plots-and-charts/ vtkPlots] (jqplot will be preserved for producing plots at publication quality level). The new infrastructure will allow a direct C++ integration of the vtkTable into the plotting (e.g., all the observations and data handling are automatically set), better performance (i.e., interactive performance up to hundreds of thousands of points) and easier customization.
* VTK PLOTS already have the following interactive desired functionality: zooming (middle click), panning (left click) and data selection (right click).
* The following widget, MRML and View classes have been designed and implemented: vtkMRMLPlotViewNode, vtkMRMLPlotNode, qMRMLPlotWidget, qMRMLPlotViewControllerWidget and qMRMLPlotView.
* A New Plot Layout has been created (index 36) and exposed to the qSlicerAppMainWindow widget.
* TO DO: connecting the new infrastructure with the Table Module.
* TO DO: implementing click and drag style interactor (e.g., https://echnotstechno.wordpress.com/2014/08/13/interactive-2d-plots-with-vtk-the-visualization-toolkit/ ).
|}

==Illustrations==
The idea is to be able to modify the parameters (in the table) of a model (blue object in the 3D View) directly from the plotting window.

[[image:SlicerAstroWiki13.png|1200px]]

VTKPLOTS sin and cos plus data selection (red crosses) example:

[[image:vtkPlots.png|1200px]]

==Background and References==
*https://www.slicer.org/wiki/Developer_Meetings/20170425
*http://www.jqplot.com/examples/customHighlighterCursorTrendline.php
*http://www.jqplot.com/examples/zooming.php
*[https://github.com/Punzo/SlicerAstro/wiki/ SlicerAstro]

[[image:SlicerAstroLogo.png|400px]]

*(Just for fun: how the gas in a galaxy looks like in 3D https://www.youtube.com/watch?v=yLjW9nbdO8g )

File:VtkPlots.png

2017-06-30T10:15:09Z

Davide:

Project Week 25/Interactive Manipulation of Plots and Graphs

2017-06-30T10:13:15Z

Davide:

__NOTOC__

Back to [[Project_Week_25#Projects|Projects List]]

==Key Investigators==

*[http://www.rug.nl/staff/davide.punzo/ Davide Punzo] (Kapteyn Astronomical Institute, University of Groningen, The Netherlands)
*[http://www.spl.harvard.edu/pages/People/pieper Steve Pieper] (Isomics Inc., USA)
*[https://www.kitware.com/jean-christophe-fillion-robin/ Jean-Christophe Fillion-Robin] (Kitware Inc., USA)
*[http://perk.cs.queensu.ca/users/lasso Andras Lasso] (Queen's University, Canada)

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|
Implementing the following plotting and graphs infrastructure enhancement:
* Panning a zoomed section of the graphs;
* Click and Drag a point;
* Data selection (select many points at once).
|
* Review if jqPlot can satisfy our requirements
* Implement them
|
* Once updated to jqplot version 1.0.9 (necessary for click and drag) the plotting does not work anymore. The infrastructure needs update.
* We decided to switch to [http://www.vtk.org/features-2d-plots-and-charts/ vtkPlots] (jqplot will be preserved for producing plots at publication quality level). The new infrastructure will allow a direct C++ integration of the vtkTable into the plotting (e.g., all the observations and data handling are automatically set), better performance (i.e., interactive performance up to hundreds of thousands of points) and easier customization.
* VTK PLOTS already have the following interactive desired functionality: zooming (middle click), panning (left click) and data selection (right click).
* The following widget, MRML and View classes have been designed and implemented: vtkMRMLPlotViewNode, vtkMRMLPlotNode, qMRMLPlotWidget, qMRMLPlotViewControllerWidget and qMRMLPlotView.
* A New Plot Layout has been created (index 36) and exposed to the qSlicerAppMainWindow widget.
* TO DO: connecting the new infrastructure with the Table Module.
* TO DO: implementing click and drag style interactor (e.g., https://echnotstechno.wordpress.com/2014/08/13/interactive-2d-plots-with-vtk-the-visualization-toolkit/ ).
|}

==Illustrations==
The idea is to be able to modify the parameters (in the table) of a model (blue object in the 3D View) directly from the plotting window.

[[image:SlicerAstroWiki13.png|1200px]]

==Background and References==
*https://www.slicer.org/wiki/Developer_Meetings/20170425
*http://www.jqplot.com/examples/customHighlighterCursorTrendline.php
*http://www.jqplot.com/examples/zooming.php
*[https://github.com/Punzo/SlicerAstro/wiki/ SlicerAstro]

[[image:SlicerAstroLogo.png|400px]]

*(Just for fun: how the gas in a galaxy looks like in 3D https://www.youtube.com/watch?v=yLjW9nbdO8g )

Project Week 25/Interactive Manipulation of Plots and Graphs

2017-06-26T09:25:14Z

Davide: /* Illustrations */

Project Week 25/Interactive Manipulation of Plots and Graphs

2017-06-26T09:24:58Z

Davide: /* Illustrations */

Project Week 25/Interactive Manipulation of Plots and Graphs

2017-06-26T09:24:21Z

Davide: /* Background and References */

Project Week 25/Interactive Manipulation of Plots and Graphs

2017-06-26T09:24:09Z

Davide: /* Background and References */

Project Week 25/Interactive Manipulation of Plots and Graphs

2017-06-26T09:23:37Z

Davide:

Project Week 25/Interactive Manipulation of Plots and Graphs

2017-06-26T09:22:47Z

Davide:

File:SlicerAstroLogo.png

2017-06-26T09:21:30Z

Davide:

Project Week 25/Interactive Manipulation of Plots and Graphs

2017-06-26T09:20:58Z

Davide:

Project Week 25/Interactive Manipulation of Plots and Graphs

2017-06-26T08:37:48Z

Davide:

Project Week 25/Interactive Manipulation of Plots and Graphs

2017-06-26T08:30:57Z

Davide:

Project Week 25/Interactive Manipulation of Plots and Graphs

2017-06-26T08:29:56Z

Davide:

Project Week 25/Interactive Manipulation of Plots and Graphs

2017-06-20T08:41:28Z

Davide: /* Key Investigators */

Project Week 25/Interactive Manipulation of Plots and Graphs

2017-06-09T14:10:28Z

Davide:

__NOTOC__

Back to [[Project_Week_25#Projects|Projects List]]

==Key Investigators==

*[http://www.rug.nl/staff/davide.punzo/ Davide Punzo] (Kapteyn Astronomical Institute)
*[https://lmi.med.harvard.edu/people/steve-pieper Steve Piper] (Isomics)
*[https://www.kitware.com/jean-christophe-fillion-robin/ Jean-Christophe Fillion-Robin] (Kitware)

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|
Implementing the following plotting and graphs infrastructure enhancement:
* Panning a zoomed section of the graphs;
* Click and Drag a point;
* Data selection (select many points at once).
|
* Review if jqPlot can satisfy our requirements
* Implement them
|

|}

==Illustrations==
The idea is to be able to modify the parameters (in the table) of a model (blue object in the 3D View) directly from the plotting window.

[[File:SlicerAstroWiki13.png|1000px]]

==Background and References==
*https://www.slicer.org/wiki/Developer_Meetings/20170425
*http://www.jqplot.com/examples/customHighlighterCursorTrendline.php
*http://www.jqplot.com/examples/zooming.php

Project Week 25/Interactive Manipulation of Plots and Graphs

2017-06-09T14:08:48Z

Davide:

__NOTOC__

Back to [[Project_Week_25#Projects|Projects List]]

==Key Investigators==

*[http://www.rug.nl/staff/davide.punzo/ Davide Punzo] (Kapteyn Astronomical Institute)
*[https://lmi.med.harvard.edu/people/steve-pieper Steve Piper] (Isomics)
*[https://www.kitware.com/jean-christophe-fillion-robin/ Jean-Christophe Fillion-Robin] (Kitware)

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|
Implementing the following plotting and graphs infrastructure enhancement:
* Panning a zoomed section of the graphs;
* Click and Drag a point;
* Data selection (select many points at once).
|
* Review if jqPlot can satisfy our requirements
* Implement them
|

|}

==Illustrations==
The idea is to be able to modify the parameters (in the table) of a model (cyan surface) directly from the plotting window.

[[File:SlicerAstroWiki13.png|1000px]]

==Background and References==
*https://www.slicer.org/wiki/Developer_Meetings/20170425
*http://www.jqplot.com/examples/customHighlighterCursorTrendline.php
*http://www.jqplot.com/examples/zooming.php

Project Week 25/Interactive Manipulation of Plots and Graphs

2017-06-09T14:08:18Z

Davide: /* Key Investigators */

__NOTOC__

Back to [[Project_Week_25#Projects|Projects List]]

==Key Investigators==

*[http://www.rug.nl/staff/davide.punzo/ Davide Punzo] (Kapteyn Astronomical Institute)
*[https://lmi.med.harvard.edu/people/steve-pieper Steve Piper] (Isomics)
*[https://www.kitware.com/jean-christophe-fillion-robin/ Jean-Christophe Fillion-Robin] (Kitware)

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|
Implementing the following plotting and graphs infrastructure enhancement:
* Panning a zoomed section of the graphs;
* Click and Drag a point;
* Data selection (select many points at once).
|
* Review if jqPlot can satisfy our requirements
* Implement them
|

|}

==Illustrations==
The idea is to be able to modify the parameters (in the table) of a model (cyan surface) directly from the plotting window.

[[File:SlicerAstroWiki13.png|1000px]]

==Background and References==
https://www.slicer.org/wiki/Developer_Meetings/20170425
http://www.jqplot.com/examples/customHighlighterCursorTrendline.php
http://www.jqplot.com/examples/zooming.php

Project Week 25/Interactive Manipulation of Plots and Graphs

2017-06-09T13:59:51Z

Davide: /* Key Investigators */

__NOTOC__

Back to [[Project_Week_25#Projects|Projects List]]

==Key Investigators==

*[ Davide Punzo] (Kapteyn Astronomical Institute)
*[https://lmi.med.harvard.edu/people/steve-pieper Steve Piper] (Isomics)
*[https://www.kitware.com/jean-christophe-fillion-robin/ Jean-Christophe Fillion-Robin] (Kitware)

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|
Implementing the following plotting and graphs infrastructure enhancement:
* Panning a zoomed section of the graphs;
* Click and Drag a point;
* Data selection (select many points at once).
|
* Review if jqPlot can satisfy our requirements
* Implement them
|

|}

==Illustrations==
The idea is to be able to modify the parameters (in the table) of a model (cyan surface) directly from the plotting window.

[[File:SlicerAstroWiki13.png|1000px]]

==Background and References==
https://www.slicer.org/wiki/Developer_Meetings/20170425
http://www.jqplot.com/examples/customHighlighterCursorTrendline.php
http://www.jqplot.com/examples/zooming.php

File:SlicerAstroWiki13.png

2017-06-09T13:51:41Z

Davide:

Project Week 25/Interactive Manipulation of Plots and Graphs

2017-06-09T13:50:29Z

Davide: /* Illustrations */

__NOTOC__

Back to [[Project_Week_25#Projects|Projects List]]

==Key Investigators==

*Davide Punzo (Kapteyn Astronomical Institute)
*Steve Piper (Isomics)
*Jean-Christophe Fillion-Robin (Kitware)

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|
Implementing the following plotting and graphs infrastructure enhancement:
* Panning a zoomed section of the graphs;
* Click and Drag a point;
* Data selection (select many points at once).
|
* Review if jqPlot can satisfy our requirements
* Implement them
|

|}

==Illustrations==
The idea is to be able to modify the parameters (in the table) of a model (cyan surface) directly from the plotting window.

[[File:SlicerAstroWiki13.png|1000px]]

==Background and References==
https://www.slicer.org/wiki/Developer_Meetings/20170425
http://www.jqplot.com/examples/customHighlighterCursorTrendline.php
http://www.jqplot.com/examples/zooming.php

Project Week 25/Interactive Manipulation of Plots and Graphs

2017-06-09T13:49:37Z

Davide: /* Illustrations */

__NOTOC__

Back to [[Project_Week_25#Projects|Projects List]]

==Key Investigators==

*Davide Punzo (Kapteyn Astronomical Institute)
*Steve Piper (Isomics)
*Jean-Christophe Fillion-Robin (Kitware)

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|
Implementing the following plotting and graphs infrastructure enhancement:
* Panning a zoomed section of the graphs;
* Click and Drag a point;
* Data selection (select many points at once).
|
* Review if jqPlot can satisfy our requirements
* Implement them
|

|}

==Illustrations==
The idea is to be able to modify the parameters (in the table) of a model (cyan surface) directly from the plotting window.

https://raw.githubusercontent.com/Punzo/SlicerAstroWikiImages/master/SlicerAstroWiki13.png

==Background and References==
https://www.slicer.org/wiki/Developer_Meetings/20170425
http://www.jqplot.com/examples/customHighlighterCursorTrendline.php
http://www.jqplot.com/examples/zooming.php

Project Week 25/Interactive Manipulation of Plots and Graphs

2017-06-09T13:49:06Z

Davide: /* Illustrations */

__NOTOC__

Back to [[Project_Week_25#Projects|Projects List]]

==Key Investigators==

*Davide Punzo (Kapteyn Astronomical Institute)
*Steve Piper (Isomics)
*Jean-Christophe Fillion-Robin (Kitware)

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|
Implementing the following plotting and graphs infrastructure enhancement:
* Panning a zoomed section of the graphs;
* Click and Drag a point;
* Data selection (select many points at once).
|
* Review if jqPlot can satisfy our requirements
* Implement them
|

|}

==Illustrations==
The idea is to be able to modify the parameters (in the table) of a model (cyan surface) directly from the plotting window.

[[https://raw.githubusercontent.com/Punzo/SlicerAstroWikiImages/master/SlicerAstroWiki13.png|1000px]]

==Background and References==
https://www.slicer.org/wiki/Developer_Meetings/20170425
http://www.jqplot.com/examples/customHighlighterCursorTrendline.php
http://www.jqplot.com/examples/zooming.php

Project Week 25/Interactive Manipulation of Plots and Graphs

2017-06-09T13:48:46Z

Davide: /* Illustrations */

__NOTOC__

Back to [[Project_Week_25#Projects|Projects List]]

==Key Investigators==

*Davide Punzo (Kapteyn Astronomical Institute)
*Steve Piper (Isomics)
*Jean-Christophe Fillion-Robin (Kitware)

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|
Implementing the following plotting and graphs infrastructure enhancement:
* Panning a zoomed section of the graphs;
* Click and Drag a point;
* Data selection (select many points at once).
|
* Review if jqPlot can satisfy our requirements
* Implement them
|

|}

==Illustrations==
The idea is to be able to modify the parameters (in the table) of a model (cyan surface) directly from the plotting window.

[[https://raw.githubusercontent.com/Punzo/SlicerAstroWikiImages/master/SlicerAstroWiki13.png | 1000px]]

==Background and References==
https://www.slicer.org/wiki/Developer_Meetings/20170425
http://www.jqplot.com/examples/customHighlighterCursorTrendline.php
http://www.jqplot.com/examples/zooming.php

Project Week 25/Interactive Manipulation of Plots and Graphs

2017-06-09T13:47:37Z

Davide:

__NOTOC__

Back to [[Project_Week_25#Projects|Projects List]]

==Key Investigators==

*Davide Punzo (Kapteyn Astronomical Institute)
*Steve Piper (Isomics)
*Jean-Christophe Fillion-Robin (Kitware)

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|
Implementing the following plotting and graphs infrastructure enhancement:
* Panning a zoomed section of the graphs;
* Click and Drag a point;
* Data selection (select many points at once).
|
* Review if jqPlot can satisfy our requirements
* Implement them
|

|}

==Illustrations==
The idea is to be able to modify the parameters (in the table) of a model (cyan surface) directly from the plotting window.

[https://raw.githubusercontent.com/Punzo/SlicerAstroWikiImages/master/SlicerAstroWiki13.png | 1000px]

==Background and References==
https://www.slicer.org/wiki/Developer_Meetings/20170425
http://www.jqplot.com/examples/customHighlighterCursorTrendline.php
http://www.jqplot.com/examples/zooming.php

Project Week 25

2017-06-09T13:46:42Z

Davide: /* Projects */

__NOTOC__
Back to [[Events]]

A summary of all past [[Project_Events#Past_Project_Weeks|Project Events]].

[[image:PW25.png|300px]] [[image:IEL_logo.png|225px]]
<br>

=Welcome to the web page for the 25th Project Week!=
It is a pleasure to announce that the 25th Project week will be held in [https://goo.gl/maps/b9CpkFxNyWN2 Catanzaro Lido] (Calabria, Italy) on June 26-30, 2017. This is the first time in Italy for the Slicer Community, and the event is organized in cooperation with [http://www.imagenglab.com ImagEngLab]. Catanzaro Lido is a city on the Ionian Sea, in the middle of Squillace Gulf where, according to the ancient legend, Odysseus started his journey back to Ithaca. Of course bring your swimsuit...the conference room and the hotel are 20 meters far away from the beach!

This project week is an event [[Post-NCBC-2014|endorsed]] by the MICCAI society.

Please make sure that you are on the NA-MIC Project Week [http://public.kitware.com/mailman/listinfo/na-mic-project-week mailing list].

===Local Organizing Committee===
*[http://www.imagenglab.com/newsite/mf_spadea/ Maria Francesca Spadea, PhD]
*[http://www.imagenglab.com/newsite/paolo_zaffino/ Paolo Zaffino, PhD].

==Videoconferences for preparation==
Time: Wednesday 9am EDT (GMT -4), April 15 to June 21, 2017
URL: [https://zoom.us/j/879371330 click here] to join the videoconference (zoom is the tool as of May 31)

#(Tina Kapur) Hangout #1: April 5 ([[PW25 Hangouts Notes|Notes]])
#(Steve Pieper) Hangout #2: April 12: Web browser based computing: Dockerized Slicer with remote computing and GPU computing; Cornerstone/LesionTracker OHIF; XTK->AMI (threejs); ePad; vtk.js; QWebEngine;
#(Andras Lasso) Hangout #3: April 19: Connecting devices such as surgical navigation, ultrasound, 3D Slicer, PLUS, OpenIGTLink, Augmented reality;
#(Tina Kapur) Hangout #4: April 26: Deep Learning for Detection of Cancer and Instruments;
#(Simon Drouin) Hangout #5: May 3: Volume Rendering, Augmented Reality, and Virtual Reality. [https://docs.google.com/document/d/1UwdSzjnDm1yEeQ44OEhXWbH6V83Uo1Cd4KngxoyrRdI/edit Notes];
#(Tina Kapur) Hangout #6: May 10: For new participants: What is project week and how to get the most out of participating in it?
#(Andrey Fedorov) Hangout #7: May 17:DICOM for Quantitative Imaging and integration with processing applications. ([http://bit.ly/2017NSPW-DICOM notes])
#(Tina Kapur) Hangout #8: May 24:Discussion of Projects and teams that have been provided on the wiki page by participants, internationalization strategy for Slicer.
#(Francesca Spadea) Hangout #9: May 31: Review of local logistics -- all registered attendees should join
#(Tina Kapur) Hangout #10: June 7: Discussion of Projects, Project Pages
#(TBD) Hangout #11: June 14: Review of Project Pages
#(Francesca Spadea) Hangout #12: June 21: Review of local logistics -- all registered attendees with questions should join

==Logistics==
*'''Dates:''' June 26-30, 2017. Consider staying for one more day (leaving Sunday morning), as a day off in a gorgeous sea place is planned on July 1st. More details in the calendar below.
*'''Location:''' [http://www.hotelperladelporto.it/en/home-page.aspx Perla del Porto Hotel]
**[mailto:prenotazioni@hotelperladelporto.it Booking]. Subject line: "Slicer Summer Project Week 2017".
***Special rates are:
****Single room, full bed, 79 € per night (1 person)
****Single room, queen bed 89 € per night (1 person)
****Double room, queen bed 99 € per night (2 people)
****Triple room, 110 € (3 people)
*'''Registration:''' To register please visit this [http://www.imagenglab.com/newsite/project-week page]
*'''Registration Fee:''' 320€ and it includes lunches, coffee breaks and airport connections
*'''Hotel:''' [http://www.hotelperladelporto.it/en/home-page.aspx Perla del Porto Hotel]. The closest airport is [http://www.lameziaairport.it/english/ Lamezia Terme Airport (IATA: SUF)].
*'''Transportation from Airport to Hotel:''' Your registration fee includes ground transportation [https://www.google.com/maps/dir/Lamezia+Terme+International+Airport,+Via+Aeroporto,+88046+Lamezia+Terme+CZ,+Italy/BEST+WESTERN+PLUS+Hotel+Perla+Del+Porto,+Via+Martiri+di+Cefalonia,+64,+88100+Catanzaro,+Italy/@38.868758,16.1564814,10z/data=!3m1!4b1!4m14!4m13!1m5!1m1!1s0x133fe15a3cbed47f:0x544ab120c3de78a6!2m2!1d16.2434017!2d38.9065845!1m5!1m1!1s0x134003d668252a13:0x2989caf676f45a72!2m2!1d16.6312407!2d38.827712!3e0 to/from the hotel and airport].
** Please fill out this [https://goo.gl/forms/7vmhxZSHy8Z1A62z2 form] to request transportation
*'''Local points of interest (pubs, restaurants, bar):''' [https://www.google.com/maps/d/viewer?mid=1FU63ik9Do3zzP6K2kvLVTtM2at8&ll=38.86221979925013%2C16.44292274999998&z=12 map] (constantly updated)

==Calendar==
{{#widget:Google Calendar
|id=kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com
|timezone=America/New_York&dates=20170108%2F20170114
|title=NA-MIC Project Week (Timezone is Italy / GMT+02.)
|view=WEEK
|dates=20170626/20170701
}}

iCal (.ics) link: https://calendar.google.com/calendar/ical/kitware.com_sb07i171olac9aavh46ir495c4%40group.calendar.google.com/public/basic.ics

=Projects=

<big>Please duplicate [https://na-mic.org/wiki/Project_Week_Template this template] to create a page for your project. </big>

Please put a brief preliminary title for your project here with some names in parenthesis for potential team members

#[[Project_Week_25/NeedleSegmentation | Needle Segmentation]]
#[[Project_Week_25/Human-Computer_Interaction_under_sterile_conditions |Human-Computer Interaction under Sterile Conditions]]
# [[Project_Week_25/Next_Generation_GPU_Volume_Rendering | Next Generation of Volume Rendering in VTK ]]
# [[Project_Week_25/Tracked-Ultrasound-Standardization-IV | Tracked Ultrasound Standardization IV: Controlling US Acquisition]]
#[[Project_Week_25/Intra-operative deformable_registration_based_on_dense_point_cloud_reconstruction |Intra-operative Deformable Registration Based on Dense Point Cloud Reconstruction]]
#[[Project_Week_25/Segmentation for improving image registration of preoperative MRI with intraoperative ultrasound images for neuro-navigation |Segmentation for Improving Image Registration of Preoperative MRI with Intraoperative Ultrasound Images for Neuro-navigation]]
#[[Project_Week_25/Deep_Learning_Data_augmentation_for_prostate_segmentation | Deep Learning: Data Augmentation for Prostate Segmentation]]
#DICOM Segmentation Support for Cornerstone / OHIF Viewer (Erik Ziegler, Steve Pieper, Marco Nolden, Tina Kapur)
#[[Project_Week_25/Conversion of DICOM Single Frame MR to Enhanced Multiframe | Conversion of DICOM Single Frame MR to Enhanced Multiframe]] (Michael Onken, Steve Pieper, Andras Lasso, Csaba Pinter)
#[[Project_Week_25/Development_and_Evaluation_of_New_AR_Visualization_Techniques_to_Support_Radiological_Interventions | Development and Evaluation of New AR Visualization Techniques to Support Radiological Interventions]]
#[[Project_Week_25/Interactive_Manipulation_of_Plots_and_Graphs | Interactive Manipulation of Plots and Graphs (Davide Punzo, Steve Pieper, Jean-Christophe Fillion-Robin)]]
#Steerable Catheters Path Planner Extension for Brain Surgery Applications (Alberto Favaro, Marlene Pinzi)
#Improving Depth Perception in Interventional Augmented Reality Visualization/(+Sonification?) (Simon Drouin, Christian Hansen, David Black)
#DICOM for Quantitative Imaging and Integration with Processing Applications (Jasmin Metzger, Marco Nolden, Steve Pieper)
#CNN for PseudoCT Generation from T1/T2 MRI (Giampaolo Pileggi, Paolo Zaffino, Salvatore Scaramuzzino, Maria Francesca Spadea, Gino Gulamhussene, Anneke Meyer)
#Internationalizing Slicer Modules (Juan Ruiz Alzola)
#Interfacing Slicer to Mobile Phone-controlled Sensors (Juan Ruiz Alzola)
#Slicer and 3D Printing (Juan Ruiz Alzola, Mike Halle, Christian Hansen)
#Slicer Export to VR (Juan Ruiz Alzola, Mike Halle,)
#2D Slice to 3D Volume Registration to Support Radiologic Interventions (Gino Gulamhussene)

=Registrants=

Do not add your name to this list - it is maintained by the organizers based on your paid registration. To register, visit this [http://www.imagenglab.com/newsite/project-week/ registration site].

# Kikinis, Ron :: Brigham and Women's Hospital, Harvard Medical School, USA
# Pieper, Steve :: Isomics, Inc., USA
# Kapur, Tina :: Brigham and Women's Hospital, Harvard Medical School, USA
# Spadea, Maria Francesca :: Magna Graecia University, Italy
# Zaffino, Paolo :: Magna Graecia University, Italy
# Scaramuzzino, Salvatore :: Magna Graecia University/ASL Vercelli, Italy
# Pileggi, Giampaolo :: Magna Graecia University, Italy/DKFZ, Germany
# Rackerseder, Julia :: Technische Universität München, Germany
# Pinter, Csaba :: Queen's University, Canada
# Kraß, Scheherazade :: University of Bremen, Germany
# Gerig, Guido :: NYU Tandon School of Engineering, USA
# Punzo, Davide :: Kapteyn Astronomical Institute, Netherlands
# Drouin, Simon :: NeuroImaging and Surgical Technologies (NIST) Lab, Canada
# Lasso, Andras :: School of Computing, Queen's University, Canada
# Favaro, Alberto :: Politecnico di Milano, Italy
# Leger, Etienne :: Concordia University, Canada
# Ziegler, Erik :: Ziegler Consult SAS
# Onken, Michael :: Open Connections GmbH, Germany
# Pinzi, Marlene :: Imperial College, UK
# Nitsch, Jennifer :: University Of Bremen, Germany
# Moccia, Sara :: Politecnico di Milano, Italy
# Black, David :: Fraunhofer Institute for Medical Image Computing MEVIS, Bremen, Germany
# Penzkofer, Tobias :: Charité Universitätsmedizin, Berlin, Germany
# Hansen, Christian :: Universität Magdeburg, Germany
# Vegard Solberg, Ole :: Norway
# Heinrich, Florian :: Universität Magdeburg, Germany
# Mewes, André :: Universität Magdeburg, Germany
# Hatscher, Benjamin :: Universität Magdeburg, Germany
# Hettig, Julian :: Universität Magdeburg, Germany
# Meyer, Anneke :: Universität Magdeburg, Germany
# Gulamhussene, Gino :: Universität Magdeburg, Germany
# Cassetta, Roberto :: Politecnico di Milano, Italy
# Fillion-Robin, Jean-Christophe :: Kitware, USA
# Metzger, Jasmin :: DKFZ, Germany
# Fishbaugh, James :: NYU Tandon School of Engineering, USA
# Nolden, Marco :: DKFZ, Germany
# Jorge Quintero Nehrkorn :: Canary Islands, Spain

Project Week 25/Interactive Manipulation of Plots and Graphs

2017-06-09T13:45:58Z

Davide: Created page with "__NOTOC__ Back to Projects List ==Key Investigators==  *Davide Punzo (Kapteyn Astronomical Institute) *S..."

__NOTOC__

Back to [[Project_Week_25#Projects|Projects List]]

==Key Investigators==

*Davide Punzo (Kapteyn Astronomical Institute)
*Steve Piper (Isomics)
*Jean-Christophe Fillion-Robin (Kitware)

==Project Description==
{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|
Implementing the following plotting and graphs infrastructure enhancement:
* Panning a zoomed section of the graphs;
* Click and Drag a point;
* Data selection (select many points at once).
|
* Review if jqPlot can satisfy our requirements
* Implement them
|

|}

==Illustrations==
The idea is to be able to modify the parameters (in the table) of a model (cyan surface) directly from the plotting window.

https://raw.githubusercontent.com/Punzo/SlicerAstroWikiImages/master/SlicerAstroWiki13.png

==Background and References==
https://www.slicer.org/wiki/Developer_Meetings/20170425
http://www.jqplot.com/examples/customHighlighterCursorTrendline.php
http://www.jqplot.com/examples/zooming.php

Project Week 25

2017-06-09T13:36:16Z

Davide: /* Projects */

__NOTOC__
Back to [[Events]]

A summary of all past [[Project_Events#Past_Project_Weeks|Project Events]].

[[image:PW25.png|300px]] [[image:IEL_logo.png|225px]]
<br>

=Welcome to the web page for the 25th Project Week!=
It is a pleasure to announce that the 25th Project week will be held in [https://goo.gl/maps/b9CpkFxNyWN2 Catanzaro Lido] (Calabria, Italy) on June 26-30, 2017. This is the first time in Italy for the Slicer Community, and the event is organized in cooperation with [http://www.imagenglab.com ImagEngLab]. Catanzaro Lido is a city on the Ionian Sea, in the middle of Squillace Gulf where, according to the ancient legend, Odysseus started his journey back to Ithaca. Of course bring your swimsuit...the conference room and the hotel are 20 meters far away from the beach!

This project week is an event [[Post-NCBC-2014|endorsed]] by the MICCAI society.

Please make sure that you are on the NA-MIC Project Week [http://public.kitware.com/mailman/listinfo/na-mic-project-week mailing list].

===Local Organizing Committee===
*[http://www.imagenglab.com/newsite/mf_spadea/ Maria Francesca Spadea, PhD]
*[http://www.imagenglab.com/newsite/paolo_zaffino/ Paolo Zaffino, PhD].

==Videoconferences for preparation==
Time: Wednesday 9am EDT (GMT -4), April 15 to June 21, 2017
URL: [https://zoom.us/j/879371330 click here] to join the videoconference (zoom is the tool as of May 31)

#(Tina Kapur) Hangout #1: April 5 ([[PW25 Hangouts Notes|Notes]])
#(Steve Pieper) Hangout #2: April 12: Web browser based computing: Dockerized Slicer with remote computing and GPU computing; Cornerstone/LesionTracker OHIF; XTK->AMI (threejs); ePad; vtk.js; QWebEngine;
#(Andras Lasso) Hangout #3: April 19: Connecting devices such as surgical navigation, ultrasound, 3D Slicer, PLUS, OpenIGTLink, Augmented reality;
#(Tina Kapur) Hangout #4: April 26: Deep Learning for Detection of Cancer and Instruments;
#(Simon Drouin) Hangout #5: May 3: Volume Rendering, Augmented Reality, and Virtual Reality. [https://docs.google.com/document/d/1UwdSzjnDm1yEeQ44OEhXWbH6V83Uo1Cd4KngxoyrRdI/edit Notes];
#(Tina Kapur) Hangout #6: May 10: For new participants: What is project week and how to get the most out of participating in it?
#(Andrey Fedorov) Hangout #7: May 17:DICOM for Quantitative Imaging and integration with processing applications. ([http://bit.ly/2017NSPW-DICOM notes])
#(Tina Kapur) Hangout #8: May 24:Discussion of Projects and teams that have been provided on the wiki page by participants, internationalization strategy for Slicer.
#(Francesca Spadea) Hangout #9: May 31: Review of local logistics -- all registered attendees should join
#(Tina Kapur) Hangout #10: June 7: Discussion of Projects, Project Pages
#(TBD) Hangout #11: June 14: Review of Project Pages
#(Francesca Spadea) Hangout #12: June 21: Review of local logistics -- all registered attendees with questions should join

==Logistics==
*'''Dates:''' June 26-30, 2017. Consider staying for one more day (leaving Sunday morning), as a day off in a gorgeous sea place is planned on July 1st. More details in the calendar below.
*'''Location:''' [http://www.hotelperladelporto.it/en/home-page.aspx Perla del Porto Hotel]
**[mailto:prenotazioni@hotelperladelporto.it Booking]. Subject line: "Slicer Summer Project Week 2017".
***Special rates are:
****Single room, full bed, 79 € per night (1 person)
****Single room, queen bed 89 € per night (1 person)
****Double room, queen bed 99 € per night (2 people)
****Triple room, 110 € (3 people)
*'''Registration:''' To register please visit this [http://www.imagenglab.com/newsite/project-week page]
*'''Registration Fee:''' 320€ and it includes lunches, coffee breaks and airport connections
*'''Hotel:''' [http://www.hotelperladelporto.it/en/home-page.aspx Perla del Porto Hotel]. The closest airport is [http://www.lameziaairport.it/english/ Lamezia Terme Airport (IATA: SUF)].
*'''Transportation from Airport to Hotel:''' Your registration fee includes ground transportation [https://www.google.com/maps/dir/Lamezia+Terme+International+Airport,+Via+Aeroporto,+88046+Lamezia+Terme+CZ,+Italy/BEST+WESTERN+PLUS+Hotel+Perla+Del+Porto,+Via+Martiri+di+Cefalonia,+64,+88100+Catanzaro,+Italy/@38.868758,16.1564814,10z/data=!3m1!4b1!4m14!4m13!1m5!1m1!1s0x133fe15a3cbed47f:0x544ab120c3de78a6!2m2!1d16.2434017!2d38.9065845!1m5!1m1!1s0x134003d668252a13:0x2989caf676f45a72!2m2!1d16.6312407!2d38.827712!3e0 to/from the hotel and airport].
** Please fill out this [https://goo.gl/forms/7vmhxZSHy8Z1A62z2 form] to request transportation
*'''Local points of interest (pubs, restaurants, bar):''' [https://www.google.com/maps/d/viewer?mid=1FU63ik9Do3zzP6K2kvLVTtM2at8&ll=38.86221979925013%2C16.44292274999998&z=12 map] (constantly updated)

==Calendar==
{{#widget:Google Calendar
|id=kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com
|timezone=America/New_York&dates=20170108%2F20170114
|title=NA-MIC Project Week (Timezone is Italy / GMT+02.)
|view=WEEK
|dates=20170626/20170701
}}

iCal (.ics) link: https://calendar.google.com/calendar/ical/kitware.com_sb07i171olac9aavh46ir495c4%40group.calendar.google.com/public/basic.ics

=Projects=

<big>Please duplicate [https://na-mic.org/wiki/Project_Week_Template this template] to create a page for your project. </big>

Please put a brief preliminary title for your project here with some names in parenthesis for potential team members

#[[Project_Week_25/NeedleSegmentation | Needle Segmentation]]
#[[Project_Week_25/Human-Computer_Interaction_under_sterile_conditions |Human-Computer Interaction under Sterile Conditions]]
# [[Project_Week_25/Next_Generation_GPU_Volume_Rendering | Next Generation of Volume Rendering in VTK ]]
# [[Project_Week_25/Tracked-Ultrasound-Standardization-IV | Tracked Ultrasound Standardization IV: Controlling US Acquisition]]
#[[Project_Week_25/Intra-operative deformable_registration_based_on_dense_point_cloud_reconstruction |Intra-operative Deformable Registration Based on Dense Point Cloud Reconstruction]]
#[[Project_Week_25/Segmentation for improving image registration of preoperative MRI with intraoperative ultrasound images for neuro-navigation |Segmentation for Improving Image Registration of Preoperative MRI with Intraoperative Ultrasound Images for Neuro-navigation]]
#[[Project_Week_25/Deep_Learning_Data_augmentation_for_prostate_segmentation | Deep Learning: Data Augmentation for Prostate Segmentation]]
#DICOM Segmentation Support for Cornerstone / OHIF Viewer (Erik Ziegler, Steve Pieper, Marco Nolden, Tina Kapur)
#Conversion of DICOM Single Frame MR to Enhanced Multiframe (Michael Onken, Steve Pieper, Andras Lasso, Csaba Pinter)
#[[Project_Week_25/Development_and_Evaluation_of_New_AR_Visualization_Techniques_to_Support_Radiological_Interventions | Development and Evaluation of New AR Visualization Techniques to Support Radiological Interventions]]
#[[Project_Week_25/Interactive_Manipulation_of_Plots_and_Graphs | Interactive Manipulation of Plots and Graphs: i) Panning; ii) Click and Drag; iii) Data Selection (Davide Punzo, Steve Pieper, Jean-Christophe Fillion-Robin)]]
#Steerable Catheters Path Planner Extension for Brain Surgery Applications (Alberto Favaro, Marlene Pinzi)
#Improving Depth Perception in Interventional Augmented Reality Visualization/(+Sonification?) (Simon Drouin, Christian Hansen, David Black)
#DICOM for Quantitative Imaging and Integration with Processing Applications (Jasmin Metzger, Marco Nolden, Steve Pieper)
#CNN for PseudoCT Generation from T1/T2 MRI (Giampaolo Pileggi, Paolo Zaffino, Salvatore Scaramuzzino, Maria Francesca Spadea, Gino Gulamhussene, Anneke Meyer)
#Internationalizing Slicer Modules (Juan Ruiz Alzola)
#Interfacing Slicer to Mobile Phone-controlled Sensors (Juan Ruiz Alzola)
#Slicer and 3D Printing (Juan Ruiz Alzola, Mike Halle, Christian Hansen)
#Slicer Export to VR (Juan Ruiz Alzola, Mike Halle,)
#2D Slice to 3D Volume Registration to Support Radiologic Interventions (Gino Gulamhussene)

=Registrants=

Do not add your name to this list - it is maintained by the organizers based on your paid registration. To register, visit this [http://www.imagenglab.com/newsite/project-week/ registration site].

# Kikinis, Ron :: Brigham and Women's Hospital, Harvard Medical School, USA
# Pieper, Steve :: Isomics, Inc., USA
# Kapur, Tina :: Brigham and Women's Hospital, Harvard Medical School, USA
# Spadea, Maria Francesca :: Magna Graecia University, Italy
# Zaffino, Paolo :: Magna Graecia University, Italy
# Scaramuzzino, Salvatore :: Magna Graecia University/ASL Vercelli, Italy
# Pileggi, Giampaolo :: Magna Graecia University, Italy/DKFZ, Germany
# Rackerseder, Julia :: Technische Universität München, Germany
# Pinter, Csaba :: Queen's University, Canada
# Kraß, Scheherazade :: University of Bremen, Germany
# Gerig, Guido :: NYU Tandon School of Engineering, USA
# Punzo, Davide :: Kapteyn Astronomical Institute, Netherlands
# Drouin, Simon :: NeuroImaging and Surgical Technologies (NIST) Lab, Canada
# Lasso, Andras :: School of Computing, Queen's University, Canada
# Favaro, Alberto :: Politecnico di Milano, Italy
# Leger, Etienne :: Concordia University, Canada
# Ziegler, Erik :: Ziegler Consult SAS
# Onken, Michael :: Open Connections GmbH, Germany
# Pinzi, Marlene :: Imperial College, UK
# Nitsch, Jennifer :: University Of Bremen, Germany
# Moccia, Sara :: Politecnico di Milano, Italy
# Black, David :: Fraunhofer Institute for Medical Image Computing MEVIS, Bremen, Germany
# Penzkofer, Tobias :: Charité Universitätsmedizin, Berlin, Germany
# Hansen, Christian :: Universität Magdeburg, Germany
# Vegard Solberg, Ole :: Norway
# Heinrich, Florian :: Universität Magdeburg, Germany
# Mewes, André :: Universität Magdeburg, Germany
# Hatscher, Benjamin :: Universität Magdeburg, Germany
# Hettig, Julian :: Universität Magdeburg, Germany
# Meyer, Anneke :: Universität Magdeburg, Germany
# Gulamhussene, Gino :: Universität Magdeburg, Germany
# Cassetta, Roberto :: Politecnico di Milano, Italy
# Fillion-Robin, Jean-Christophe :: Kitware, USA
# Metzger, Jasmin :: DKFZ, Germany
# Fishbaugh, James :: NYU Tandon School of Engineering, USA
# Nolden, Marco :: DKFZ, Germany
# Jorge Quintero Nehrkorn :: Canary Islands, Spain

Project Week 25

2017-05-28T12:36:34Z

Davide: /* Projects */

__NOTOC__
Back to [[Events]]

A summary of all past [[Project_Events#Past_Project_Weeks|Project Events]].

[[image:PW-Summer2017.png|300px]] [[image:IEL_logo.png|225px]]
<br>

=Welcome to the web page for the 25th Project Week!=

It is a pleasure to announce that the 25th Project week will be held in [https://goo.gl/maps/b9CpkFxNyWN2 Catanzaro Lido] (Calabria, Italy) on June 26-30, 2017. This is the first time in Italy for the Slicer Community, and the event is organized in cooperation with [http://www.imagenglab.com ImagEngLab]. Catanzaro Lido is a city on the Ionian Sea, in the middle of Squillace Gulf where, according to the ancient legend, Odysseus started his journey back to Ithaca. Of course bring your swimsuit...the conference room and the hotel are 20 meters far away from the beach!

This project week is an event [[Post-NCBC-2014|endorsed]] by the MICCAI society.

Please make sure that you are on the NA-MIC Project Week [http://public.kitware.com/mailman/listinfo/na-mic-project-week mailing list].

===Local Organizing Committee===
*[http://www.imagenglab.com/newsite/mf_spadea/ Maria Francesca Spadea, PhD]
*[http://www.imagenglab.com/newsite/paolo_zaffino/ Paolo Zaffino, PhD].

==Hangouts for preparation==
#(Tina Kapur) Hangout #1: April 5th, 2017 - 9.00 AM Boston time: [https://plus.google.com/events/cjh9ag37hm1e7peplatphl7kh2g?authkey=COWc5cKc77jymgE event page] ([[PW25 Hangouts Notes|Notes]])
#(Steve Pieper) Hangout #2: Wednesday April 12, 2017, 9am EDT (GMT-4): Web browser based computing: Dockerized Slicer with remote computing and GPU computing; Cornerstone/LesionTracker OHIF; XTK->AMI (threejs); ePad; vtk.js; QWebEngine; [https://plus.google.com/hangouts/_/kitware.com/pw-25?hceid=a2l0d2FyZS5jb21fc2IwN2kxNzFvbGFjOWFhdmg0NmlyNDk1YzRAZ3JvdXAuY2FsZW5kYXIuZ29vZ2xlLmNvbQ.fffs75fitbu0mvpl3vvmrcqf3s&authuser=0 hangout page]
#(Andras Lasso) Hangout #3: Wednesday April 19, 2017, 9am EDT (GMT-4) Connecting devices such as surgical navigation, ultrasound, 3D Slicer, PLUS, OpenIGTLink, Augmented reality; [https://hangouts.google.com/hangouts/_/kitware.com/pw-25?authuser=0 hangout page]
#(Tina Kapur) Hangout #4: Wednesday April 26, 2017, 9am EDT (GMT-4) Deep Learning for Detection of Cancer and Instruments; [https://hangouts.google.com/hangouts/_/kitware.com/pw-25?authuser=0 hangout page];
#(Simon Drouin) Hangout #5: Wednesday May 3, 2017, 9am EDT (GMT-4)Volume Rendering, Augmented Reality, and Virtual Reality. [https://docs.google.com/document/d/1UwdSzjnDm1yEeQ44OEhXWbH6V83Uo1Cd4KngxoyrRdI/edit Notes];[https://plus.google.com/hangouts/_/kitware.com/pw-25?hceid=a2l0d2FyZS5jb21fc2IwN2kxNzFvbGFjOWFhdmg0NmlyNDk1YzRAZ3JvdXAuY2FsZW5kYXIuZ29vZ2xlLmNvbQ.fffs75fitbu0mvpl3vvmrcqf3s&authuser=0 hangout page]
#(Tina Kapur) Hangout #6: Wednesday May 10, 2017, 9am EDT (GMT-4) For new participants: What is project week and how to get the most out of participating in it? [https://hangouts.google.com/hangouts/_/kitware.com/pw-25?authuser=0 hangout page]
#(Andrey Fedorov) Hangout #7: Wednesday May 17, 2017, 9am EDT (GMT-4) DICOM for Quantitative Imaging and integration with processing applications. [https://hangouts.google.com/hangouts/_/kitware.com/pw-25?authuser=0 hangout page] ([http://bit.ly/2017NSPW-DICOM notes])
#(Tina Kapur) Hangout #8: Wednesday May 24, 2017, 9am EDT (GMT-4) Review of Projects and teams that have been provided on the wiki page by participants, internationalization strategy for Slicer. [https://hangouts.google.com/hangouts/_/kitware.com/pw-25?authuser=0 hangout page]
#(Francesca Spadea) Hangout #9: Wednesday May 31, 2017, 9am EDT (GMT-4) Review of local logistics -- all registered attendees should join [https://zoom.us/j/879371330 zoom "hangout" page]
#(TBD) Hangout #10: Wednesday June 7, 2017, 9am EDT (GMT-4) TBD [https://zoom.us/j/879371330 zoom "hangout" page]
#(TBD) Hangout #11: Wednesday June 14, 2017, 9am EDT (GMT-4) TBD [https://zoom.us/j/879371330 zoom "hangout" page]
#(Francesca Spadea) Hangout #12: Wednesday June 21, 2017, 9am EDT (GMT-4) Review of local logistics -- all registered attendees with questions should join [https://zoom.us/j/879371330 zoom "hangout" page]

==Logistics==

*'''Dates:''' June 26-30, 2017. Consider staying for one more day (leaving Sunday morning), as a day off in a gorgeous sea place is planned on July 1st. More details in the calendar below.
*'''Location:''' [http://www.hotelperladelporto.it/en/home-page.aspx Perla del Porto Hotel]
**[mailto:prenotazioni@hotelperladelporto.it Booking]. Subject line: "Slicer Summer Project Week 2017".
***Special rates are:
****Single room, full bed, 79 € per night (1 person)
****Single room, queen bed 89 € per night (1 person)
****Double room, queen bed 99 € per night (2 people)
****Triple room, 110 € (3 people)
*'''REGISTRATION:''' To register please visit this [http://www.imagenglab.com/newsite/project-week page]
*'''Registration Fee:''' 320€ and it includes lunches, coffee breaks and airport connections
*'''Hotel:''' [http://www.hotelperladelporto.it/en/home-page.aspx Perla del Porto Hotel]. The closest airport is [http://www.lameziaairport.it/english/ Lamezia Terme Airport (IATA: SUF)].
*'''Transportation from Airport to Hotel''' Your registration fee includes ground transportation [https://www.google.com/maps/dir/Lamezia+Terme+International+Airport,+Via+Aeroporto,+88046+Lamezia+Terme+CZ,+Italy/BEST+WESTERN+PLUS+Hotel+Perla+Del+Porto,+Via+Martiri+di+Cefalonia,+64,+88100+Catanzaro,+Italy/@38.868758,16.1564814,10z/data=!3m1!4b1!4m14!4m13!1m5!1m1!1s0x133fe15a3cbed47f:0x544ab120c3de78a6!2m2!1d16.2434017!2d38.9065845!1m5!1m1!1s0x134003d668252a13:0x2989caf676f45a72!2m2!1d16.6312407!2d38.827712!3e0 to/from the hotel and airport].
** Please fill out this form to request transportation https://goo.gl/forms/7vmhxZSHy8Z1A62z2
*'''Local points of interest (pubs, restaurants, bar):''' [https://www.google.com/maps/d/viewer?mid=1FU63ik9Do3zzP6K2kvLVTtM2at8&ll=38.86221979925013%2C16.44292274999998&z=12 map (constantly updated)]

==Calendar==

{{#widget:Google Calendar
|id=kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com
|timezone=America/New_York&dates=20170108%2F20170114
|title=NA-MIC Project Week (Timezone is EDT, Will change to Italy time during that week.)
|view=WEEK
|dates=20170626/20170701
}}

iCal (.ics) link: https://calendar.google.com/calendar/ical/kitware.com_sb07i171olac9aavh46ir495c4%40group.calendar.google.com/public/basic.ics

=Projects=

Please put a brief preliminary title for your project here with some names in parenthesis for potential team members

#Needle segmentation Project 1 (Guillaume Pernelle, Tina Kapur, Paolo Zaffino, Salvatore Scaramuzzino, Francesca Spadea)
#Needle segmentation Project 2 (Paolo Zaffino, Salvatore Scaramuzzino, Francesca Spadea, Guillaume Pernelle, Tina Kapur)
#DICOM Segmentation support for Cornerstone / OHIF Viewer (Erik Ziegler, Steve Pieper, Marco Nolden, Tina Kapur)
#Conversion of DICOM single frame MR to Enhanced Multiframe (Michael Onken, Steve Pieper, Andras Lasso, Csaba Pinter)
#Human-Computer Interaction under sterile conditions (Christian Hansen, Julian Hettig, Benjamin Hatscher, David Black, Marco Nolden, Juan Ruiz)
#Development and evaluation of new AR visualization techniques to support radiological interventions (Christian Hansen, Florian Heinrich, Andrè Mewes, Juan Ruiz, Marco Nolden)
#Interactive manipulation of plots and graphs: i) panning; ii) click and drag; iii) data selection (Davide Punzo, Steve Pieper, Jean-Christophe Fillion-Robin)
#Next generation of volume rendering in VTK (Simon Drouin, Steve Pieper, Ole Vegard Solberg, Andras Lasso)
#Tracked Ultrasound Standardization IV: Controlling US acquisition (Simon Drouin, Ole Vegard Solberg, Andras Lasso [electronically: Longquan Chen, Adam Rankin])
#Steerable catheters path planner extension for brain surgery applications (Alberto Favaro, Marlene Pinzi)
#Improving depth perception in interventional Augmented Reality visualization/(+sonification?) (Simon Drouin, Christian Hansen, David Black)
#DICOM for Quantitative Imaging and integration with processing applications (Jasmin Metzger, Marco Nolden, Steve Pieper)
#Tissue deformation estimation based on dense points cloud reconstruction using stereo images (Sara Moccia)
#Segmentation for improving image registration of preoperative MRI/intraoperative ultrasound images for neuro-navigation (Jennifer Nitsch, Scheherazade Kraß)
#CNN for pseudoCT generation from T1/T2 MRI (Giampaolo Pileggi, Paolo Zaffino, Salvatore Scaramuzzino, Maria Francesca Spadea)
#Internationalizing Slicer modules (Juan Ruiz Alzola, )
#Interfacing Slicer to mobile phone-controlled sensors (Juan Ruiz Alzola, )
#Slicer and 3D Printing (Juan Ruiz Alzola, Mike Halle, )
#Slicer export to VR (Juan Ruiz Alzola, Mike Halle, )

=Registrants=

Do not add your name to this list - it is maintained by the organizers based on your paid registration. To register, visit this [http://www.imagenglab.com/newsite/project-week/ registration site].

# Kikinis, Ron :: Brigham and Women's Hospital, Harvard Medical School, USA
# Pieper, Steve :: Isomics, Inc., USA
# Kapur, Tina :: Brigham and Women's Hospital, Harvard Medical School, USA
# Spadea, Maria Francesca :: Magna Graecia University, Italy
# Zaffino, Paolo :: Magna Graecia University, Italy
# Scaramuzzino, Salvatore :: Magna Graecia University/ASL Vercelli, Italy
# Pileggi, Giampaolo :: Magna Graecia University, Italy/DKFZ, Germany
# Rackerseder, Julia :: Technische Universität München, Germany
# Pinter, Csaba :: Queen's University, Canada
# Kraß, Scheherazade :: University of Bremen, Germany
# Gerig, Guido :: NYU Tandon School of Engineering, USA
# Punzo, Davide :: Kapteyn Astronomical Institute, Netherlands
# Drouin, Simon :: NeuroImaging and Surgical Technologies (NIST) Lab, Canada
# Lasso, Andras :: School of Computing, Queen's University, Canada
# Favaro, Alberto :: Politecnico di Milano, Italy
# Leger, Etienne :: Concordia University, Canada
# Ziegler, Erik :: Ziegler Consult SAS
# Onken, Michael :: Open Connections GmbH, Germany
# Pinzi, Marlene :: Imperial College, UK
# Nitsch, Jennifer :: University Of Bremen, Germany
# Moccia, Sara :: Politecnico di Milano, Italy
# Black, David :: Fraunhofer Institute for Medical Image Computing MEVIS, Bremen, Germany
# Penzkofer, Tobias :: Charité Universitätsmedizin, Berlin, Germany
# Hansen, Christian :: Universität Magdeburg, Germany
# Vegard Solberg, Ole :: Norway
# Heinrich, Florian :: Universität Magdeburg, Germany
# Mewes, André :: Universität Magdeburg, Germany
# Hatscher, Benjamin :: Universität Magdeburg, Germany
# Hettig, Julian :: Universität Magdeburg, Germany
# Meyer, Anneke :: Universität Magdeburg, Germany
# Gulamhussene, Gino :: Universität Magdeburg, Germany

Project Week 25

2017-05-10T17:53:27Z

Davide:

__NOTOC__
Back to [[Events]]

A summary of all past [[Project_Events#Past_Project_Weeks|Project Events]].

[[image:PW-Summer2017.png|300px]] [[image:IEL_logo.png|225px]]
<br>

=Welcome to the web page for the 25th Project Week!=

It is a pleasure to announce that the 25th Project week will be held in [https://goo.gl/maps/b9CpkFxNyWN2 Catanzaro Lido] (Calabria, Italy) on June 26-30, 2017. This is the first time in Italy for the Slicer Community, and the event is organized in cooperation with [http://www.imagenglab.com ImagEngLab]. Catanzaro Lido is a city on the Ionian Sea, in the middle of Squillace Gulf where, according to the ancient legend, Odysseus started his journey back to Ithaca. Of course bring your swimsuit...the conference room and the hotel are 20 meters far away from the beach!

This project week is an event [[Post-NCBC-2014|endorsed]] by the MICCAI society.

Please make sure that you are on the NA-MIC Project Week [http://public.kitware.com/mailman/listinfo/na-mic-project-week mailing list].

===Local Organizing Committee===
*[http://www.imagenglab.com/newsite/mf_spadea/ Maria Francesca Spadea, PhD]
*[http://www.imagenglab.com/newsite/paolo_zaffino/ Paolo Zaffino, PhD].

==Hangouts for preparation==
#(Tina Kapur) Hangout #1: April 5th, 2017 - 9.00 AM Boston time: [https://plus.google.com/events/cjh9ag37hm1e7peplatphl7kh2g?authkey=COWc5cKc77jymgE event page] ([[PW25 Hangouts Notes|Notes]])
#(Steve Pieper) Hangout #2: Wednesday April 12, 2017, 9am EDT (GMT-4): Web browser based computing: Dockerized Slicer with remote computing and GPU computing; Cornerstone/LesionTracker OHIF; XTK->AMI (threejs); ePad; vtk.js; QWebEngine; [https://plus.google.com/hangouts/_/kitware.com/pw-25?hceid=a2l0d2FyZS5jb21fc2IwN2kxNzFvbGFjOWFhdmg0NmlyNDk1YzRAZ3JvdXAuY2FsZW5kYXIuZ29vZ2xlLmNvbQ.fffs75fitbu0mvpl3vvmrcqf3s&authuser=0 hangout page]
#(Andras Lasso) Hangout #3: Wednesday April 19, 2017, 9am EDT (GMT-4) Connecting devices such as surgical navigation, ultrasound, 3D Slicer, PLUS, OpenIGTLink, Augmented reality; [https://hangouts.google.com/hangouts/_/kitware.com/pw-25?authuser=0 hangout page]
#(Tina Kapur) Hangout #4: Wednesday April 26, 2017, 9am EDT (GMT-4) Deep Learning for Detection of Cancer and Instruments; [https://hangouts.google.com/hangouts/_/kitware.com/pw-25?authuser=0 hangout page];
#(Simon Drouin) Hangout #5: Wednesday May 3, 2017, 9am EDT (GMT-4)Volume Rendering, Augmented Reality, and Virtual Reality. [https://docs.google.com/document/d/1UwdSzjnDm1yEeQ44OEhXWbH6V83Uo1Cd4KngxoyrRdI/edit Notes];[https://plus.google.com/hangouts/_/kitware.com/pw-25?hceid=a2l0d2FyZS5jb21fc2IwN2kxNzFvbGFjOWFhdmg0NmlyNDk1YzRAZ3JvdXAuY2FsZW5kYXIuZ29vZ2xlLmNvbQ.fffs75fitbu0mvpl3vvmrcqf3s&authuser=0 hangout page]
#(Tina Kapur) Hangout #6: Wednesday May 10, 2017, 9am EDT (GMT-4) For new participants: What is project week and how to get the most out of participating in it? [https://hangouts.google.com/hangouts/_/kitware.com/pw-25?authuser=0 hangout page]
#(Andrey Fedorov) Hangout #7: Wednesday May 17, 2017, 9am EDT (GMT-4) DICOM for Quantitative Imaging and integration with processing applications.
#(Tina Kapur) Hangout #8: Wednesday May 24, 2017, 9am EDT (GMT-4) Review of Projects and teams that have been provided on the wiki page by participants
#(Francesca Spadea) Hangout #9: Wednesday May 31, 2017, 9am EDT (GMT-4) Review of local logistics -- all registered attendees should join
#(TBD) Hangout #10: Wednesday June 7, 2017, 9am EDT (GMT-4) TBD
#(TBD) Hangout #11: Wednesday June 14, 2017, 9am EDT (GMT-4) TBD
#(Francesca Spadea) Hangout #12: Wednesday June 21, 2017, 9am EDT (GMT-4) Review of local logistics -- all registered attendees with questions should join

==Logistics==

*'''Dates:''' June 26-30, 2017. Consider staying for one more day (leaving Sunday morning), as a day off in a gorgeous sea place is planned on July 1st. More details will be posted soon.
*'''Location:''' [http://www.hotelperladelporto.it/en/home-page.aspx Perla del Porto Hotel]
**[mailto:prenotazioni@hotelperladelporto.it Booking]. Subject line: "Slicer Summer Project Week 2017".
***Special rates are:
****Single room, full bed, 79 € per night (1 person)
****Single room, queen bed 89 € per night (1 person)
****Double room, queen bed 99 € per night (2 people)
****Triple room, 110 € (3 people)
*'''REGISTRATION:''' To register please visit this [http://www.imagenglab.com/newsite/project-week page]
*'''Registration Fee:''' 320€ and it includes lunches, coffee breaks and airport connections
*'''Hotel:''' [http://www.hotelperladelporto.it/en/home-page.aspx Perla del Porto Hotel]. The closest airport is [http://www.lameziaairport.it/english/ Lamezia Terme Airport (IATA: SUF)].
*'''Transportation from Airport to Hotel''' Your registration fee includes ground transportation [https://www.google.com/maps/dir/Lamezia+Terme+International+Airport,+Via+Aeroporto,+88046+Lamezia+Terme+CZ,+Italy/BEST+WESTERN+PLUS+Hotel+Perla+Del+Porto,+Via+Martiri+di+Cefalonia,+64,+88100+Catanzaro,+Italy/@38.868758,16.1564814,10z/data=!3m1!4b1!4m14!4m13!1m5!1m1!1s0x133fe15a3cbed47f:0x544ab120c3de78a6!2m2!1d16.2434017!2d38.9065845!1m5!1m1!1s0x134003d668252a13:0x2989caf676f45a72!2m2!1d16.6312407!2d38.827712!3e0 to/from the hotel and airport].
** Please fill out this form to request transportation https://goo.gl/forms/7vmhxZSHy8Z1A62z2
*'''Local points of interest (pubs, restaurants, bar):''' [https://www.google.com/maps/d/viewer?mid=1FU63ik9Do3zzP6K2kvLVTtM2at8&ll=38.86221979925013%2C16.44292274999998&z=12 map (constantly updated)]

==Calendar==

'''''<font color="maroon">The events are listed in the calendar below. Note that due to a current known limitation of our infrastructure, you will need to manually navigate to the week of June 26, 2017 to see the relevant events.</font>'''''<br>

{{#widget:Google Calendar
|id=kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com
|timezone=America/New_York&dates=20170108%2F20170114
|title=NA-MIC Project Week
|view=WEEK
|dates=20170626/20170701
}}

iCal (.ics) link: https://calendar.google.com/calendar/ical/kitware.com_sb07i171olac9aavh46ir495c4%40group.calendar.google.com/public/basic.ics

=Projects=

Please put a brief preliminary title for your project here with some names in parenthesis for potential team members

#Needle segmentation Project 1 (Guillaume Pernelle, Tina Kapur, Paolo Zaffino, Salvatore, Francesca Spadea)
#Needle segmentation Project 2 (Paolo Zaffino, Salvatore, Francesca Spadea, Guillaume Pernelle, Tina Kapur)
#DICOM Segmentation support for Cornerstone / OHIF Viewer (Erik Ziegler)
#Human-Computer Interaction under sterile conditions (Christian Hansen, Julian Hettig, Benjamin Hatscher)
#Development and evaluation of new AR visualization technniques to support radiological interventions (Christian Hansen, Florian Heinrich, Andrè Mewes)
#Interactive manipulation of plots and graphs: i) panning; ii) click and drag; iii) data selection (Davide Punzo, Steve Pieper)

=Registrants=

Do not add your name to this list - it is maintained by the organizers based on your paid registration. To register, visit this [http://www.imagenglab.com/newsite/project-week/ registration site].

# Kikinis, Ron :: Brigham and Women's Hospital, Harvard Medical School, USA
# Pieper, Steve :: Isomics, Inc., USA
# Kapur, Tina :: Brigham and Women's Hospital, Harvard Medical School, USA
# Spadea, Maria Francesca :: Magna Graecia University, Italy
# Zaffino, Paolo :: Magna Graecia University, Italy
# Scaramuzzino, Salvatore :: Magna Graecia University/ASL Vercelli, Italy
# Pileggi, Giampaolo :: Magna Graecia University, Italy/DKFZ, Germany
# Rackerseder, Julia :: Technische Universität München, Germany
# Pinter, Csaba :: Queen's University, Canada
# Scheherazade, Kraß :: University of Bremen, Germany
# Gerig, Guido :: NYU Tandon School of Engineering, USA
# Punzo, Davide :: Kapteyn Astronomical Institute, Netherlands
# Drouin, Simon :: NeuroImaging and Surgical Technologies (NIST) Lab, Canada
# Andras Lasso :: School of Computing, Queen's University, Canada
# Alberto Favaro :: Politecnico di Milano, Italy
# Etienne Leger :: Concordia University, Canada
# Erik Ziegler :: Ziegler Consult SAS

Project Week 25

2017-05-10T17:51:37Z

Davide:

__NOTOC__
Back to [[Events]]

A summary of all past [[Project_Events#Past_Project_Weeks|Project Events]].

[[image:PW-Summer2017.png|300px]] [[image:IEL_logo.png|225px]]
<br>

=Welcome to the web page for the 25th Project Week!=

It is a pleasure to announce that the 25th Project week will be held in [https://goo.gl/maps/b9CpkFxNyWN2 Catanzaro Lido] (Calabria, Italy) on June 26-30, 2017. This is the first time in Italy for the Slicer Community, and the event is organized in cooperation with [http://www.imagenglab.com ImagEngLab]. Catanzaro Lido is a city on the Ionian Sea, in the middle of Squillace Gulf where, according to the ancient legend, Odysseus started his journey back to Ithaca. Of course bring your swimsuit...the conference room and the hotel are 20 meters far away from the beach!

This project week is an event [[Post-NCBC-2014|endorsed]] by the MICCAI society.

Please make sure that you are on the NA-MIC Project Week [http://public.kitware.com/mailman/listinfo/na-mic-project-week mailing list].

===Local Organizing Committee===
*[http://www.imagenglab.com/newsite/mf_spadea/ Maria Francesca Spadea, PhD]
*[http://www.imagenglab.com/newsite/paolo_zaffino/ Paolo Zaffino, PhD].

==Hangouts for preparation==
#(Tina Kapur) Hangout #1: April 5th, 2017 - 9.00 AM Boston time: [https://plus.google.com/events/cjh9ag37hm1e7peplatphl7kh2g?authkey=COWc5cKc77jymgE event page] ([[PW25 Hangouts Notes|Notes]])
#(Steve Pieper) Hangout #2: Wednesday April 12, 2017, 9am EDT (GMT-4): Web browser based computing: Dockerized Slicer with remote computing and GPU computing; Cornerstone/LesionTracker OHIF; XTK->AMI (threejs); ePad; vtk.js; QWebEngine; [https://plus.google.com/hangouts/_/kitware.com/pw-25?hceid=a2l0d2FyZS5jb21fc2IwN2kxNzFvbGFjOWFhdmg0NmlyNDk1YzRAZ3JvdXAuY2FsZW5kYXIuZ29vZ2xlLmNvbQ.fffs75fitbu0mvpl3vvmrcqf3s&authuser=0 hangout page]
#(Andras Lasso) Hangout #3: Wednesday April 19, 2017, 9am EDT (GMT-4) Connecting devices such as surgical navigation, ultrasound, 3D Slicer, PLUS, OpenIGTLink, Augmented reality; [https://hangouts.google.com/hangouts/_/kitware.com/pw-25?authuser=0 hangout page]
#(Tina Kapur) Hangout #4: Wednesday April 26, 2017, 9am EDT (GMT-4) Deep Learning for Detection of Cancer and Instruments; [https://hangouts.google.com/hangouts/_/kitware.com/pw-25?authuser=0 hangout page];
#(Simon Drouin) Hangout #5: Wednesday May 3, 2017, 9am EDT (GMT-4)Volume Rendering, Augmented Reality, and Virtual Reality. [https://docs.google.com/document/d/1UwdSzjnDm1yEeQ44OEhXWbH6V83Uo1Cd4KngxoyrRdI/edit Notes];[https://plus.google.com/hangouts/_/kitware.com/pw-25?hceid=a2l0d2FyZS5jb21fc2IwN2kxNzFvbGFjOWFhdmg0NmlyNDk1YzRAZ3JvdXAuY2FsZW5kYXIuZ29vZ2xlLmNvbQ.fffs75fitbu0mvpl3vvmrcqf3s&authuser=0 hangout page]
#(Tina Kapur) Hangout #6: Wednesday May 10, 2017, 9am EDT (GMT-4) For new participants: What is project week and how to get the most out of participating in it? [https://hangouts.google.com/hangouts/_/kitware.com/pw-25?authuser=0 hangout page]
#(Andrey Fedorov) Hangout #7: Wednesday May 17, 2017, 9am EDT (GMT-4) DICOM for Quantitative Imaging and integration with processing applications.
#(Tina Kapur) Hangout #8: Wednesday May 24, 2017, 9am EDT (GMT-4) Review of Projects and teams that have been provided on the wiki page by participants
#(Francesca Spadea) Hangout #9: Wednesday May 31, 2017, 9am EDT (GMT-4) Review of local logistics -- all registered attendees should join
#(TBD) Hangout #10: Wednesday June 7, 2017, 9am EDT (GMT-4) TBD
#(TBD) Hangout #11: Wednesday June 14, 2017, 9am EDT (GMT-4) TBD
#(Francesca Spadea) Hangout #12: Wednesday June 21, 2017, 9am EDT (GMT-4) Review of local logistics -- all registered attendees with questions should join

==Logistics==

*'''Dates:''' June 26-30, 2017. Consider staying for one more day (leaving Sunday morning), as a day off in a gorgeous sea place is planned on July 1st. More details will be posted soon.
*'''Location:''' [http://www.hotelperladelporto.it/en/home-page.aspx Perla del Porto Hotel]
**[mailto:prenotazioni@hotelperladelporto.it Booking]. Subject line: "Slicer Summer Project Week 2017".
***Special rates are:
****Single room, full bed, 79 € per night (1 person)
****Single room, queen bed 89 € per night (1 person)
****Double room, queen bed 99 € per night (2 people)
****Triple room, 110 € (3 people)
*'''REGISTRATION:''' To register please visit this [http://www.imagenglab.com/newsite/project-week page]
*'''Registration Fee:''' 320€ and it includes lunches, coffee breaks and airport connections
*'''Hotel:''' [http://www.hotelperladelporto.it/en/home-page.aspx Perla del Porto Hotel]. The closest airport is [http://www.lameziaairport.it/english/ Lamezia Terme Airport (IATA: SUF)].
*'''Transportation from Airport to Hotel''' Your registration fee includes ground transportation [https://www.google.com/maps/dir/Lamezia+Terme+International+Airport,+Via+Aeroporto,+88046+Lamezia+Terme+CZ,+Italy/BEST+WESTERN+PLUS+Hotel+Perla+Del+Porto,+Via+Martiri+di+Cefalonia,+64,+88100+Catanzaro,+Italy/@38.868758,16.1564814,10z/data=!3m1!4b1!4m14!4m13!1m5!1m1!1s0x133fe15a3cbed47f:0x544ab120c3de78a6!2m2!1d16.2434017!2d38.9065845!1m5!1m1!1s0x134003d668252a13:0x2989caf676f45a72!2m2!1d16.6312407!2d38.827712!3e0 to/from the hotel and airport].
** Please fill out this form to request transportation https://goo.gl/forms/7vmhxZSHy8Z1A62z2
*'''Local points of interest (pubs, restaurants, bar):''' [https://www.google.com/maps/d/viewer?mid=1FU63ik9Do3zzP6K2kvLVTtM2at8&ll=38.86221979925013%2C16.44292274999998&z=12 map (constantly updated)]

==Calendar==

'''''<font color="maroon">The events are listed in the calendar below. Note that due to a current known limitation of our infrastructure, you will need to manually navigate to the week of June 26, 2017 to see the relevant events.</font>'''''<br>

{{#widget:Google Calendar
|id=kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com
|timezone=America/New_York&dates=20170108%2F20170114
|title=NA-MIC Project Week
|view=WEEK
|dates=20170626/20170701
}}

iCal (.ics) link: https://calendar.google.com/calendar/ical/kitware.com_sb07i171olac9aavh46ir495c4%40group.calendar.google.com/public/basic.ics

=Projects=

Please put a brief preliminary title for your project here with some names in parenthesis for potential team members

#Needle segmentation Project 1 (Guillaume Pernelle, Tina Kapur, Paolo Zaffino, Salvatore, Francesca Spadea)
#Needle segmentation Project 2 (Paolo Zaffino, Salvatore, Francesca Spadea, Guillaume Pernelle, Tina Kapur)
#DICOM Segmentation support for Cornerstone / OHIF Viewer (Erik Ziegler)
#Human-Computer Interaction under sterile conditions (Christian Hansen, Julian Hettig, Benjamin Hatscher)
#Development and evaluation of new AR visualization technniques to support radiological interventions (Christian Hansen, Florian Heinrich, Andrè Mewes)
#Interactive manipulation of plots and graphs (e.g., panning; click and drag; data selection) (Davide Punzo, Steve Pieper)

=Registrants=

Do not add your name to this list - it is maintained by the organizers based on your paid registration. To register, visit this [http://www.imagenglab.com/newsite/project-week/ registration site].

# Kikinis, Ron :: Brigham and Women's Hospital, Harvard Medical School, USA
# Pieper, Steve :: Isomics, Inc., USA
# Kapur, Tina :: Brigham and Women's Hospital, Harvard Medical School, USA
# Spadea, Maria Francesca :: Magna Graecia University, Italy
# Zaffino, Paolo :: Magna Graecia University, Italy
# Scaramuzzino, Salvatore :: Magna Graecia University/ASL Vercelli, Italy
# Pileggi, Giampaolo :: Magna Graecia University, Italy/DKFZ, Germany
# Rackerseder, Julia :: Technische Universität München, Germany
# Pinter, Csaba :: Queen's University, Canada
# Scheherazade, Kraß :: University of Bremen, Germany
# Gerig, Guido :: NYU Tandon School of Engineering, USA
# Punzo, Davide :: Kapteyn Astronomical Institute, Netherlands
# Drouin, Simon :: NeuroImaging and Surgical Technologies (NIST) Lab, Canada
# Andras Lasso :: School of Computing, Queen's University, Canada
# Alberto Favaro :: Politecnico di Milano, Italy
# Etienne Leger :: Concordia University, Canada
# Erik Ziegler :: Ziegler Consult SAS

2016 Summer Project Week/3D Lasso Selection

2016-06-25T08:40:20Z

Davide:

__NOTOC__
<gallery>
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]
Image:SlicerAstro3DSelection1.pdf|3-D selection
</gallery>

==Key Investigators==
* Davide Punzo
* Csaba Pinter
* Andras Lasso
* Steve Pieper

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Adding a CloudLasso selection tool in the Segmentation editor for grid data. The Segmetation editor already works on 3-D View. Therefore, it should streightforward to implement a draw effect on the 3-D and apply a grid CloudLasso selection.
* Example of CloudLasso selection on particles https://www.youtube.com/watch?v=xqUkXol6oX8&hd=1
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Discuss with Csaba, Andras and Steve the implementation.
* Do it!
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Design and Implementation discussed with Andras, Steve and Csaba.
* Collected feedback from some users on the desired feature (e.g. an "eraser" 3-D Lasso is also requested).
* Generalized qSlicerSegmentEditorAbstractLabelEffect::appendPolyMask to work also in 3-DView (i.e. It will be easier for developer to implement editor effect working in 3-D).
* The project it is not finished, however in this week we created a solid base (many useful implementation feedback and coding sharing by Andras, Steve and Csaba). The project will continued/finished next week.
* Implementing Rectangular effect in the 3-D View, STATUS: still not working, but in good progress.
* Implementing Lasso effect in 3-D View, STATUS: I'll start to implement it on next week and it will be built on the basis of the rectangular effect.
</div>
</div>