Changes between Initial Version and Version 1 of barSoftwareGUI

Timestamp:

10/11/11 13:29:19 (13 years ago)

Author:

pmajka

Comment:

--

barSoftwareGUI

@@ +1 @@
+{{{
+#!rst
+==============================================
+3d Brain Atlas Reconstructor standalone manual
+==============================================
+
+================================================
+Description of GUI of the 3D model building tool
+================================================
+
+To facilitate reconstruction process a simple graphical user interface was
+prepared Fig.
+`Python <http://www.python.org/>`_.
+    
+The 3dBAR reconstruction GUI with an exemplary CAF dataset loaded `Johnson2010`. The *Striatum* selected for reconstruction (gray highlight); and *Hippocampus* loaded as context models 
+font). The reconstruction of `Hypothalamus` is cache available for loading (bold font). A) The structure
+selection tab B) The model customization tab. 
+
+ChapterRendering-interface
+
+
+The left panel contains ontology tree loaded from CAF index file.  One
+can browse through structures, select them for reconstruction and also
+load already reconstructed, cached models.  The right panel contains
+two tabs. *Structure selection* tab displays detailed
+information about the currently selected structure for reconstruction.
+This includes abbreviated and full name of the structure, span of
+slides on which it is defined as well as color assigned to this
+structure.  Here one can also set the resolution, the depth of
+decomposition of the structure into substructures according to
+ontology tree, and mirroring of brain hemisphere may be enabled if
+needed.
+
+Reconstructed models can be viewed in the *Model customization tab*
+(Fig. B) which also
+provides access to parameters of VTK customization pipeline.  The
+preview is displayed in the form of triangular mesh although the
+actual model is still stored in volumetric form.
+The model can be rotated by pressing and holding left mouse button,
+zoomed in or out by pressing and holding the right button. Pressing
+the middle button allows one to pan the model over the scene. One can
+switch between wireframe and surface representations of the model by
+pressing `w` or `s` keys.
+
+After changing VTK pipeline parameters, mesh may be recalculated by
+pressing *Refresh* button and cached by pressing *Save model*.
+Models are cached in form of polygonal meshes
+(*vtkPolyData*). *Clear scene* button removes all models
+from preview window.  When a model is cached, the corresponding
+element of the ontology tree is displayed with bold font.  Cached
+models can be loaded in the preview window as *context models*}
+alongside the model being presently reconstructed, however they cannot
+be modified. When a cached model is loaded into context, the
+corresponding element in ontology tree is displayed in red.
+
+Multiple reconstructions can be performed one by one as described
+above.  However, this is convenient only when few models are required.
+To reconstruct multiple structures one can choose a parent structure
+containing desired substructures and reconstruct them down to a
+desired level of detail.  All substructures are generated using the
+same set of reconstruction parameters provided in `Structure selection`
+tab and the same VTK pipeline.  Models are generated one
+by one and automatically cached. When all the substructures are
+reconstructed they are loaded into preview window as context models.
+
+By default models are cached in the directory where CAF dataset is
+located. One may choose another export directory by selecting
+*Set cache directory* from *Edit* menu. When cache directory
+is changed, all currently loaded structures are removed from preview
+and ontology tree updates information about availability of cached
+models from the new directory.
+
+3d Brain Atlas Reconstructor GUI offers three ways of exporting three dimensional
+models. Single reconstructions may be cached as polygonal data
+(*vtkPolyData*) or exported as volumetric datasets in the native
+VTK *vtkImageData* or NIfTI (Neuroimaging Informatics Technology
+Initiative) formats. Complex scenes containing numerous context models
+may be exported into VRML (Virtual Reality Modelling Language) format.
+}}}