Changes between Version 8 and Version 9 of barSoftwareGUI

Timestamp:

10/12/11 08:18:44 (13 years ago)

Author:

pmajka

Comment:

--

barSoftwareGUI

@@ -13 +13 @@
 
 To facilitate reconstruction process a simple graphical user interface was prepared.
+Below, the 3dBAR reconstruction GUI with an exemplary CAF dataset loaded (`Johnson et. al., 2010 <http://www.ncbi.nlm.nih.gov/pubmed/20600960>`_) it presented.
 
-+------------+------------+
-| |figA|     |  |figB|    | 
-+------------+------------+ 
+|figA|
+
+**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).
+
+|figB|
+
+**Figure 2:** The *model customization tab*. Reconstructions of *Striatum*, *Amygdala* and *Hippocampus* are presented.
 
 
-**Figure 1:** The 3dBAR reconstruction GUI with an exemplary CAF dataset loaded (`Johnson et. al., 2010 <http://www.ncbi.nlm.nih.gov/pubmed/20600960>`_). The *Striatum* selected for reconstruction (gray highlight); and *Hippocampus* loaded as context models (red font). The reconstruction of `Hypothalamus` is cached and available for loading (bold font). A) The structure selection tab B) The model customization tab.
+Selecting structures
+====================
 
-
-The left panel contains ontology tree loaded from CAF index file.  One
+The left panel contains *ontology tree* loaded from CAF index file. One
 can browse through structures, select them for reconstruction or
-load already reconstructed, cached models.  The right panel contains
-two tabs. *Structure selection* tab displays detailed
+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
@@ -35 +40 @@
 
 
+Viewing and customizing the reconstructions
+===========================================
+
+The model customization tab.
 Reconstructed models can be viewed in the *Model customization tab*
-(Fig. B) which also
-provides access to parameters of VTK customization pipeline.  The
+(Fig. 2) which also
+provides access to parameters of VTK pipeline.  The
 preview is displayed in the form of triangular mesh although the
 actual model is still stored in volumetric form.
@@ -59 +68 @@
 
 
+Generating multiple reconstructions
+===================================
+
 Multiple reconstructions can be performed one by one as described
 above.  However, this is convenient only when few models are required.
@@ -69 +81 @@
 reconstructed they are loaded into preview window as context models.
 
+Exporting the models
+====================
 
 By default models are cached in the directory where CAF dataset is
@@ -77 +91 @@
 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
+(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.
-
+may be exported into VRML_ (Virtual Reality Modelling Language) or X3D_ format.
+ 
 -------------------------------
 |3dBAR| CLI reconstruction tool
@@ -96 +109 @@
 
 .. |3dBAR| replace:: 3D Brain Atlas Reconstructor
+
+.. _vtkImageData: http://vtk.org/doc/nightly/html/classvtkImageData.html
+.. _vtkPolyData: http://vtk.org/doc/nightly/html/classvtkPolyData.html
+.. _NIfTI: http://nifti.nimh.nih.gov/nifti-1/
+.. _VRML: http://en.wikipedia.org/wiki/VRML
+.. _X3D: 
 }}}