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Astronomy (HI) extension for 3DSlicer (https://www.slicer.org/)

License: BSD 3-Clause "New" or "Revised" License

C++ 92.19% CMake 3.38% Python 4.18% HTML 0.19% CSS 0.01% Shell 0.01% C 0.04%

astronomy 3d visualization 3dslicer image-processing visual-analytics c-plus-plus

slicerastro's Introduction

SlicerAstro

Astronomy (HI) extension for 3DSlicer

Upcoming HI (neutral Hydrogen) surveys will deliver large datasets, and automated processing using the full 3D 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 3D data, helping the astronomer to deal with the analysis of complex sources. 3D visualization, coupled to modeling, provides additional capabilities helping the discovery and analysis of subtle structures in the 3D domain.

Objective: general description

1) Proper visualization of astronomical data cubes: using data astronomical data formats, such as FITS, and astronomical world coordinates system (WCS);
2) Quantification: visualization of the beam, interactive histograms, contours, statistics linked with the 2D/3D views, masking volumes with segmentations, flux density profiles, moment maps and position-velocity diagrams;
3) Enabling interactive smoothing in all three dimensions;
4) Interactive HI data modeling coupled to visualization;
5) Skill to overlay observations at different wavelength and to plot catalogs info on data;
6) Interoperability with Topcat, and other virtual observatory (VO) tools and catalogs.

For more information regarding the project, its status and License, please check the following links:

slicerastro's People

Contributors

Stargazers

Watchers

Forkers

jcfr slahabdellaoui juandesant lunarplugins karenleewaddell afizik

slicerastro's Issues

ENH: recalculate RMS and display parameters in a ROI

BUG: multipass GPU OpenGL filtering not working with VTK8

COMP: Qt4 binaries crash

Qt5 version of the Slicer and SlicerAstro binaries will be soon released. Therefore, this won't be fixed.

COMP: macosx packing

cmakeLists.txt should be updated to use the macosx packing issue fixed in Slicer r25182

ENH: updating SlicerAstro to VTK7

Slicer/Slicer#540

BUG: numpy utilities (python wrapping) do not work on AstroVolume data

improve cloudLasso selection tool perfomance

see
Slicer/Slicer@b2bfa60

ENH: investigate how to add astropy in 3DSlicer or SlicerAstro binaries

ENH: updating Modeling module to new plotting infrastructure

https://www.slicer.org/wiki/Documentation/Nightly/Developers/Plots

ENH: add the X3D file format for Models

BUG: check and mask NAN values for input datacubes

vtkMRMLAstroVolumeNode::UpdateNoiseAttributes and UpdateRangeAttributes do not mask for NAN values.

BUG: issue with the degree code (\u00B0) in QT5

COMP: update gcc compiler linux kitware factory machine

Hi @jcfr, would be possible to update the linux factory machine gcc from 4.6 to 4.7 to support OpenMP call reduction max and min? gcc 4.7 supports OpenMP 3.1 which is the one I need.

Or may you keep in mind this when setting up the new infrastructure to compile the Qt5/VTK9 version?

build Error:
#pragma omp parallel for schedule(static) reduction(max : max_val), reduction(min : min_val)
http://slicer.cdash.org/viewBuildError.php?buildid=1186462

Update metadata

See

SlicerAstro/CMakeLists.txt

Lines 5 to 14 in 2817670

 #----------------------------------------------------------------------------- 

 # Extension meta-information 

 set(EXTENSION_HOMEPAGE "http://www.example.com/Slicer/Extensions/SlicerAstro") 

 set(EXTENSION_CATEGORY "Astronomy") 

 set(EXTENSION_CONTRIBUTORS "Davide Punzo (Kapteyn Astronomical Institute)") 

 set(EXTENSION_DESCRIPTION "Extension for enabling Astronomical visualization in Slicer") 

 set(EXTENSION_ICONURL "http://www.example.com/Slicer/Extensions/SlicerAstro.png") 

 set(EXTENSION_SCREENSHOTURLS "http://www.example.com/Slicer/Extensions/SlicerAstro/Screenshots/1.png") 

 set(EXTENSION_DEPENDS "NA") # Specified as a space separated list or 'NA' if any 

 set(EXTENSION_BUILD_SUBDIRECTORY inner-build)

ENH: update SlicerAstro branch of BBAROLO

This https://github.com/Punzo/Bbarolo needs this update
editeodoro/Bbarolo@55b0dd5

(Then let's merge to https://github.com/editeodoro/Bbarolo/)

BUG: CloudLasso selection tool fires No Input Data Warning.

COMP: automatic procedure for "deafult" settings

// Setup Home Module
cout<app->settings()->value("Modules/HomeModule").toString().toStdString()<<endl;
d->app->settings()->setValue("Modules/HomeModule", "AstroWelcome");
cout<app->settings()->value("Modules/HomeModule").toString().toStdString()<<endl;
// Setup modules to ignore
qSlicerCoreApplication * coreApp = qSlicerCoreApplication::application();
qSlicerAbstractModuleFactoryManager* factoryManager = coreApp->moduleManager()->factoryManager();
QStringList modulesNames;
modulesNames << "DICOM";
factoryManager->setModulesToIgnore(modulesNames);

tried this in qSlicerAstroVolumeModule::setup()

it was changing the value to the AstroWelcome, but then the Home Module loaded was still the SlicerWelcome
using this Slicer get completely stucked.

another way can be setting up in slicerExtension a script after the installation of the extension
http://na-mic.org/Mantis/view.php?id=2920#c13958

Remove directory SlicerAstro.git

BUG: crash loading a scene

If in a scene there is an AstroVolumeNode and the import scene has an AstroVolumeNode as well (with same IDs), it results in a crash. The crash seems connected with AstroVolumeDisplayNode. It appears to be a reference issue.

COMP: update to VTK8/Qt5

https://www.slicer.org/wiki/Documentation/Labs/Qt5-and-VTK8
some classes will need to be updated

ENH: add widget for the recalculation of RMS and 2D/3D color functions

In the astroVolume GUI

ENH: reading and writing compressed fits file

reported Anja Schroeder (PHISCC 2017)

BUG: crash when using clone node from SubjectHierarch

The copy method works, most likley the bug is in the SubjectHierarch classes

BUG: crush when smoothing with Gaussian or Box kernels on GPU with kernels parameters set to zero

crush if one of the FWHMx,y,z or Nx,y,z are set to zero (on GPU).

ENH: add modeling GUI to make the normalization optional

COMP: OpenGL2 not compatible with vtkOpenGLAstroShaderComputation and vtkOpenGLAstroTextureImage

The classes vtkOpenGLAstroShaderComputation and vtkOpenGLAstroTextureImage will not work with OpenGL2 (VTK7) (vtkgl classes not available anymore). Working on new version for the GPU filters based on Kitware/VTK@c3a6dfa

ENH: masking NaN numbers

Three options:

Change the NaN values to zeroes at the loading of the datacube
Change the NaN values to zeroes before applying any operations (such as smoothing)
Masking all the values during the operations (expensive)
Provide a module and leave the conversion to the user

BUG: astro colorNodes erased when closing scene

ENH: making generation of masks optional in AstroSmoothing module

BUG: Barolo does not update NV (number of clouds) after the estimation of the parameter

if NV is zero, barolo estimates it and it will use the new value in the fit. However, the value of the NV variable in the Param class is not updated. Therefore, SlicerAstro will show in the interface always zero, even if NV has been calculated internally.

BUG: vtkLeaks

vtkDebugLeaks has detected LEAKS!
Class "vtkXOpenGLRenderWindow" has 1 instance still around.
Class "vtkCellData" has 1 instance still around.
Class "vtkOpenGLPainterDeviceAdapter" has 1 instance still around.
Class "vtkOpenGLAstroShaderComputation" has 1 instance still around.
Class "vtkPointData" has 1 instance still around.
Class "vtkInformation" has 1 instance still around.
Class "vtkInformationIntegerPointerValue" has 1 instance still around.
Class "vtkOpenGLAstroTextureImage" has 2 instances still around.
Class "vtkOpenGLExtensionManager" has 1 instance still around.
Class "vtkIdList" has 1 instance still around.
Class "vtkInformationIntegerValue" has 1 instance still around.
Class "vtkRendererCollection" has 1 instance still around.
Class "vtkImageData" has 1 instance still around.
Class "vtkFieldData" has 1 instance still around.
Class "vtkCommand or subclass" has 1 instance still around.

CloudLasso selection not working inside the datacube extents

When the 3D rendering is zoomed inside the extent of the datacube (pink frame) the cloud lasso selection tool does not work.

selection tool does not work on datacube translated

reported by @Fil8

BUG+COMP: Python wrapping of vtkFITS does not work both on VTK7 and VTK8 build

ENH: color box 3-D View

different box color along the velocity axis (reported by Marc).

ENH: Improved node saving and loading #574

check if any updated is needed

WCS fail: stack smashing when NAXIS = 4 and NAXIS4 = 1

It is not clear if it is due to a patch to the wcs 5.11 to 5.14.

Fixing the header, removing all the fourth keywords may fix it.

fits_delete_key
https://heasarc.gsfc.nasa.gov/docs/software/fitsio/c/c_user/node39.html

and modify NAXIS:
https://heasarc.gsfc.nasa.gov/docs/software/fitsio/cexamples/modhead.c

vtkFITSReader.cxx: Fix -Wmulticha warning

/Users/kitware/Dashboards/Experimental/SlicerAstro/vtkFits/vtkFITSReader.cxx:415:43: warning: multi-character
      character constant [-Wmultichar]
     std::replace(str.begin(), str.end(), 'D+', 'E+');
                                          ^
/Users/kitware/Dashboards/Experimental/SlicerAstro/vtkFits/vtkFITSReader.cxx:415:49: warning: multi-character
      character constant [-Wmultichar]
     std::replace(str.begin(), str.end(), 'D+', 'E+');
                                                ^
2 warnings generated.

Create Config.cmake files for external dependencies

See https://github.com/SBU-BMI/SlicerOpenCV/ for example

BUG: bad memory allocation in 2DWCSdisplaymanager

https://github.com/Punzo/SlicerAstro/blob/master/AstroVolume/MRML/vtkMRMLAstroTwoDAxesDisplayableManager.cxx#L315

crush when loading a scene

BUG: WCS on 2-D view controller wrong if image spacing is changed

Before calculating the WCS, the offset has to converted properly from RAS to IJK

BUG+COMP: Python wrapping of MRML nodes does not work with VTK8 build

BUG: 3DBarolo fitting in the AstroModeling generate random segmentation fault on MacOS

ENH: adding a second 3D view for the cloudlasso selection

Adding a button to set a second 3D view (camera perpendicular) that shows the depth coordinate of the selection.

ENH: add multiply widget for 3d color function

ENH: adding astropy in 3DSlicer or SlicerAstro binaries

Compatibility with https://github.com/Slicer/Slicer/pull/450

Part of the code regarding the ruler has shifted from Python to C++. This means that SlicerAstro WCS axis has to be refactorized in C++.

COMP: update and test cfitsio 3.41

ENH: add GUI for setting BBarolo normalization on AZIM

COMP: MacOS binaries are not compiling on Kitware factory machine

loading initial cache file /.../SlicerAstro-build/inner-prefix/tmp/inner-cache-Release.cmake
-- Setting OSX_ARCHITECTURES to 'x86_64' as none was specified.
-- Setting OSX_SYSROOT to latest '/Developer/SDKs/MacOSX10.6.sdk' as none was specified.
-- Configuring incomplete, errors occurred!

CMAKE_OSX_DEPLOYMENT_TARGET must be 10.6 or greater.
Call Stack (most recent call first):
/Users/kitware/Dashboards/Nightly/Slicer-0-build/Slicer-build/SlicerConfig.cmake:106 (include)
CMakeLists.txt:28 (find_package)

	#-----------------------------------------------------------------------------
	# Extension meta-information
	set(EXTENSION_HOMEPAGE "http://www.example.com/Slicer/Extensions/SlicerAstro")
	set(EXTENSION_CATEGORY "Astronomy")
	set(EXTENSION_CONTRIBUTORS "Davide Punzo (Kapteyn Astronomical Institute)")
	set(EXTENSION_DESCRIPTION "Extension for enabling Astronomical visualization in Slicer")
	set(EXTENSION_ICONURL "http://www.example.com/Slicer/Extensions/SlicerAstro.png")
	set(EXTENSION_SCREENSHOTURLS "http://www.example.com/Slicer/Extensions/SlicerAstro/Screenshots/1.png")
	set(EXTENSION_DEPENDS "NA") # Specified as a space separated list or 'NA' if any
	set(EXTENSION_BUILD_SUBDIRECTORY inner-build)