def initTrakem(path, nbLayers, mipmaps = False): #initialize a project
path = cleanLinuxPath(path)
ControlWindow.setGUIEnabled(False)
project = Project.newFSProject("blank", None, path)
project.getLoader().setMipMapsRegeneration(mipmaps)
layerset = project.getRootLayerSet()
for i in range(nbLayers): # create the layers
layerset.getLayer(i, 1, True)
project.getLayerTree().updateList(layerset) #update the LayerTree
Display.updateLayerScroller(layerset) # update the display slider
IJ.log('TrakEM project initialized with ' + str(nbLayers) + ' layers and stored in ' + path + ' (but not saved yet)')
return project
ControlWindow.setGUIEnabled(False)
# 1. Create a TrakEM2 project
project = Project.newFSProject("blank", None, out_folder)
loader = project.getLoader()
loader.setMipMapsRegeneration(True) # disable mipmaps
layerset = project.getRootLayerSet()
# 2. Create 10 layers (or as many as you need)
for i in range(num_sections):
layerset.getLayer(i, 1, True)
layerset.setDimensions(im_width, im_height, LayerSet.NORTHWEST)
# ... and update the LayerTree:
project.getLayerTree().updateList(layerset)
# ... and the display slider
Display.updateLayerScroller(layerset)
filenames = sorted(os.listdir(storm_merged_folder))
filenames1 = sorted(os.listdir(conv_561_folder))
filenames2 = sorted(os.listdir(conv_merged_folder))
filenames3 = sorted(os.listdir(conv_align_folder))
#3 Load in images
for i, layer in enumerate(layerset.getLayers()):
#i = i +150 #use this to start in the middle of a dataset
filepath = os.path.join(storm_merged_folder, filenames[i])
patch = Patch.createPatch(project, filepath)
# patch.updateMipMaps()
layer.add(patch, False)
#
filepath = os.path.join(conv_merged_folder, filenames2[i])
patch = Patch.createPatch(project, filepath)
# patch.updateMipMaps()