Changes between Version 21 and Version 22 of barSoftwareGUI
- Timestamp:
- 12/15/11 13:45:16 (13 years ago)
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barSoftwareGUI
v21 v22 1 {{{ 2 #!rst 1 = Description of GUI of the 3D model building tool = 3 2 4 ------------------------------------------------5 Description of GUI of the 3D model building tool6 ------------------------------------------------7 3 8 4 To facilitate reconstruction process a simple graphical user interface was prepared. 9 Below, the 3dBAR reconstruction GUI with an exemplary CAF dataset loaded ( `Johnson et. al., 2010 <http://www.ncbi.nlm.nih.gov/pubmed/20600960>`_) is presented.5 Below, the 3dBAR reconstruction GUI with an exemplary CAF dataset loaded ([http://www.ncbi.nlm.nih.gov/pubmed/20600960 Johnson et. al., 2010].) 10 6 11 |figA| 7 [[Image(wiki:barSoftwareGUI:3dbar_interface_strucure_selection.png,100%)]] 12 8 13 **Figure 1:** The `structure selection tab`. The *Striatum* selected for reconstruction (gray highlight); *Amygdala* and *Hippocampus*loaded as context models (red font). The reconstruction of `Hypothalamus` is cached and available for loading (bold font).9 **Figure 1:** The ''structure selection tab''. The ''Striatum'' selected for reconstruction (gray highlight); ''Amygdala'' and ''Hippocampus'' loaded as context models (red font). The reconstruction of `Hypothalamus` is cached and available for loading (bold font). 14 10 15 Selecting structures 16 ==================== 11 == Selecting structures == 17 12 18 The left panel contains *ontology tree*loaded from CAF index file. One13 The left panel contains ''ontology tree'' loaded from CAF index file. One 19 14 can browse through structures, select them for reconstruction or 20 15 load already reconstructed, cached models. The right panel contains 21 two tabs. *Structure selection tab*displays detailed16 two tabs. ''Structure selection tab'' displays detailed 22 17 information about the currently selected structure for reconstruction. 23 18 This includes abbreviated and full name of the structure, span of … … 29 24 30 25 26 [[Image(wiki:barSoftwareGUI:3dbar_interface_strucure_selection.png,100%)]] 31 27 32 |figB| 33 34 **Figure 2:** The *model customization tab*. Reconstructions of *Striatum*, *Amygdala* and *Hippocampus* are presented. 28 **Figure 2:** The ''model customization tab''. Reconstructions of ''Striatum'', ''Amygdala'' and ''Hippocampus'' are presented. 35 29 36 30 37 Viewing and customizing the reconstructions 38 =========================================== 31 == Viewing and customizing the reconstructions == 39 32 40 Reconstructed models can be viewed in the *Model customization tab*33 Reconstructed models can be viewed in the ''Model customization tab'' 41 34 (Fig. 2) which also 42 35 provides access to parameters of VTK pipeline. The … … 51 44 52 45 After changing VTK pipeline parameters, mesh may be recalculated by 53 pressing *Refresh* button and cached by pressing *Save model*.46 pressing ''Refresh'' button and cached by pressing ''Save model''. 54 47 Models are cached in form of polygonal meshes 55 ( *vtkPolyData*). *Clear scene*button removes all models48 ([http://vtk.org/doc/nightly/html/classvtkPolyData.html vtkPolyData]). ''Clear scene'' button removes all models 56 49 from preview window. When a model is cached, the corresponding 57 50 element of the ontology tree is displayed with bold font. Cached 58 models can be loaded in the preview window as *context models*51 models can be loaded in the preview window as ''context models'' 59 52 alongside the model being presently reconstructed, however they cannot 60 53 be modified. When a cached model is loaded into context, the … … 62 55 63 56 64 Generating multiple reconstructions 65 =================================== 57 == Generating multiple reconstructions == 66 58 67 59 Multiple reconstructions can be performed one by one as described … … 75 67 reconstructed they are loaded into preview window as context models. 76 68 77 Exporting the models 78 ==================== 69 == Exporting the models == 79 70 80 71 By default models are cached in the directory where CAF dataset is 81 72 located. One may choose another export directory by selecting 82 *Set cache directory* from *Edit*menu. When cache directory73 ''Set cache directory'' from ''Edit'' menu. When cache directory 83 74 is changed, all currently loaded structures are removed from preview 84 75 and ontology tree updates information about availability of cached … … 87 78 3d Brain Atlas Reconstructor GUI offers three ways of exporting three dimensional 88 79 models. Single reconstructions may be cached as polygonal data 89 (vtkPolyData_) or exported as volumetric datasets in the native 90 VTK vtkImageData_ or NIfTI_ (Neuroimaging Informatics Technology 91 Initiative) formats. Complex scenes containing numerous context models 92 may be exported into VRML_ (Virtual Reality Modelling Language) or X3D_ format. 93 94 .. |figA| image:: http://www.3dbar.org/raw-attachment/wiki/barSoftwareGUI/3dbar_interface_strucure_selection.png 95 :height: 400px 96 97 .. |figB| image:: http://www.3dbar.org/raw-attachment/wiki/barSoftwareGUI/interface_reconstruction.png 98 :height: 400px 99 100 .. |3dBAR| replace:: 3D Brain Atlas Reconstructor 101 102 .. _vtkImageData: http://vtk.org/doc/nightly/html/classvtkImageData.html 103 .. _vtkPolyData: http://vtk.org/doc/nightly/html/classvtkPolyData.html 104 .. _NIfTI: http://nifti.nimh.nih.gov/nifti-1/ 105 .. _VRML: http://en.wikipedia.org/wiki/VRML 106 .. _X3D: http://en.wikipedia.org/wiki/X3D 107 }}} 80 ([http://vtk.org/doc/nightly/html/classvtkPolyData.html vtkPolyData]) or exported as volumetric datasets in the native 81 VTK ([http://vtk.org/doc/nightly/html/classvtkImageData.html vtkImageData]) or (Neuroimaging Informatics Technology 82 Initiative, [http://nifti.nimh.nih.gov/nifti-1/ NIfTI]) formats. Complex scenes containing numerous context models 83 may be exported into (Virtual Reality Modelling Language, [http://en.wikipedia.org/wiki/VRML VRML]) or [http://en.wikipedia.org/wiki/X3D X3D] format.
