__author__ = 'jcorrea'
from tako.arms.correction import Correction
from tako.head import head
correction = Correction(setup={"algorithm": "ijmacro",
"data": "/Users/DOE6903584/NERSC/tako/examples/data/Lenna.png",
"params": {'macro': "/Users/DOE6903584/NERSC/tako/bin/correction/imagej-macro.ijm"}
}
)
do = head.do_workflow(setup=[correction])
__author__ = 'jcorrea'
import sys
sys.path.append("/Users/DOE6903584/NERSC/tako/")
sys.path.append("/Users/DOE6903584/NERSC/tako/tako/util")
from tako.arms.alignment import Alignment
from tako.arms.correction import Correction
from tako.arms.segmentation import Segmentation
from tako.arms.visualization import Visualization
import tako.arms
from tako.head import head
# Alignment block
alignment = Alignment(setup={"algorithm": "method1",
"data": "/Users/DOE6903584/NERSC/tako/examples/data/Lenna.png",
"params": {'macro': "/Users/DOE6903584/NERSC/tako/bin/alignment/imagej-macro.ijm"}
}
)
do = head.do_workflow(setup=[alignment])
alignment = Correction(
setup={
"algorithm": "ijmacro",
"data": "/Users/DOE6903584/NERSC/tako/examples/data/myxo-small.tif",
"output": "/Users/DOE6903584/NERSC/tako/examples/demo/myxo-small_align.tif",
"params": {"macro": "/Users/DOE6903584/NERSC/tako/bin/correction/alignment.ijm"},
}
)
segmentation = Correction(
setup={
"algorithm": "ijmacro",
"data": alignment.output,
"output": "/Users/DOE6903584/NERSC/tako/examples/demo/myxo-small_seg.tif",
"params": {"macro": "/Users/DOE6903584/NERSC/tako/bin/segmentation/segmentation.ijm"},
}
)
visualization = Correction(
setup={
"algorithm": "ijmacro",
"data": segmentation.output,
"output": "/Users/DOE6903584/NERSC/tako/examples/demo/myxo-small_vis.tif",
"params": {"macro": "/Users/DOE6903584/NERSC/tako/bin/visualization/visualization.ijm"},
}
)
do = head.do_workflow(setup=[alignment, segmentation, visualization])