public abstract class MainSpatial extends Object implements ij.plugin.PlugIn
Modifier and Type | Field and Description |
---|---|
protected org.sbml.jsbml.SBMLDocument |
document
The SBML document.
|
protected HashMap<String,Integer> |
hashSampledValue
The hashmap of sampled value of spatial image.
|
protected ImageExplorer |
imgexp
The ImageExplorer.
|
protected org.sbml.jsbml.Model |
model
The SBML model.
|
protected org.sbml.jsbml.ext.spatial.SpatialModelPlugin |
spatialplugin
The SBML spatialplugin.
|
protected SpatialImage |
spImg
The SpatialImage, which is a class for handling spatial image in XitoSBML.
|
protected Viewer |
viewer
The viewer.
|
Constructor and Description |
---|
MainSpatial() |
Modifier and Type | Method and Description |
---|---|
protected void |
addSBases()
Create a tabbed table which allows users to add the SBases to the model through GUI.
|
protected void |
computeImg()
Following process is performed to an image:
Interpolate an image if it is a Z-stack image (3D image) and the voxel size of each axis (x, y and z) is not equal
Fill holes (blank pixels) in the image by morphology operation if exists
Add a membrane between two different domains if exists
The converted image will be generated as
SpatialImage ,
which is a base class for representing spatial image in XitoSBML. |
protected void |
gui()
Create a GUI which allows users to specify the correspondence between each image
and the region in the cell.
|
protected void |
print()
Prints the SBML document to stdout.
|
protected void |
showDomainStructure()
Show inclusion relationship of domains as a graph.
|
protected void |
showStep(SpatialImage spImg)
Visualize SpatialImage.
|
protected void |
visualize(SpatialImage spImg)
Visualize the spatial model with ImageJ 3D Viewer.
|
protected org.sbml.jsbml.SBMLDocument document
protected org.sbml.jsbml.Model model
protected org.sbml.jsbml.ext.spatial.SpatialModelPlugin spatialplugin
protected ImageExplorer imgexp
protected HashMap<String,Integer> hashSampledValue
protected Viewer viewer
protected SpatialImage spImg
protected void gui()
protected void computeImg()
SpatialImage
,
which is a base class for representing spatial image in XitoSBML.protected void visualize(SpatialImage spImg)
spImg
- the SpatialImage, which is a class for handling spatial image in XitoSBML.protected void addSBases()
protected void showDomainStructure()
protected void showStep(SpatialImage spImg)
spImg
- the SpatialImage, which is a class for handling spatial image in XitoSBML.protected void print()
Copyright © 2017–2019 Funahashi Lab.. All rights reserved.