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TrakEM2 Scripting

1,615 bytes added, 20:07, 2 February 2011
Save the project while running a task
Of course it may be easier to set that autosaving interval <b>before</b> running the long task!
 
= Create a TrakEM2 project for fast visualization, without mipmaps =
 
Create a TrakEM2 project that avoids generating mipmaps, then import lots of images from a text file that has four columns: the file path, the X, the Y, and the section index of each image tile. Then acquire a snapshot of the first section.
 
<source lang="python">
# Albert Cardona 2011-02-02
# At Madison, Wisconsin, with Erwin Frise
from ini.trakem2 import Project
from ij.gui import Toolbar
from java.awt import Color
from ij import ImagePlus
 
project = Project.newFSProject("blank", None, "/home/albert/Desktop/t2/")
loader = project.getLoader()
loader.setMipMapsRegeneration(False) # disable mipmaps
layerset = project.getRootLayerSet()
layerset.setSnapshotsMode(1) # outlines
 
task = loader.importImages(
layerset.getLayers().get(0), # the first layer
"/home/albert/Desktop/t2/example-data/images/list.txt", # the absolute file path to the text file with absolute image file paths
" ", # the column separator <path> <x> <y> <section index>
1.0, # section thickness, defaults to 1
1.0, # calibration, defaults to 1
False, # whether to homogenize contrast, avoid
1.0) # scaling factor, default to 1
 
task.join() # Optional: wait until all images have been imported
 
# Export a snapshot of the layer at 25% magnification
 
scale = 0.25
layer = layerset.getLayers().get(0)
flat = loader.makeFlatImage(ImagePlus.COLOR_RGB, layer, layerset.get2DBounds(), scale, layer.getAll(Patch), Color.black)
 
imp = ImagePlus("snap " + str(scale), flat).show()
 
print "done!"
</source>
= Enrich the GUI of TrakEM =
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