Python do_workflow Examples

Example #1

File: imagej_macro.py Project: jjcorreao/tako

__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])

Example #2

File: small_workflow.py Project: jjcorreao/tako

__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])

Example #3

File: demo.py Project: jjcorreao/tako

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])