[ImageJ-devel] Save/write image with SCIFIO/BF in python script

[Hadrien Mary]

Hi,

I am writing a python macro which iterate over all rois in ROI Manager
and then use setCropRegion function from bioformat plugin to open a
cropped region of an image.

I tried to use SCIFIO to write cropped image on disk but it doesn not work.

(I am using an updated version of Fiji.)

Here is my script:

from ij.plugin.frame import RoiManager
from ij import IJ
from io.scif.img import ImgSaver

from loci.plugins import BF
from loci.plugins.in import ImporterOptions
from loci.common import Region

import os

# Get current image filename
imp = IJ.getImage()
f = imp.getOriginalFileInfo()
fname = os.path.join(f.directory, f.fileName)

IJ.log('Image filename is %s' % fname)

# Iterate over all ROIs from ROI Manager
rois = RoiManager.getInstance().getRoisAsArray()
for i, roi in enumerate(rois):

    crop_id = i +1
    IJ.log("Opening crop %i / %i" % (crop_id, len(rois)))

    bounds = roi.getBounds()

    x = bounds.x
    y = bounds.y
    w = bounds.width
    h = bounds.height

    # Import only cropped region of the image
    options = ImporterOptions()
    options.setCrop(True)
    options.setCropRegion(0, Region(x, y, w, h))
    options.setId(fname)
    imps = BF.openImagePlus(options)

    imp = imps[0]
    imp.show()

    crop_basename = "crop%i_%s" % (crop_id, f.fileName)
    crop_fname = os.path.join(f.directory, crop_basename)
    imp.setTitle(crop_basename)

    # Save image
    IJ.log("Saving crop to %s" % crop_fname)
    saver = ImgSaver()
    saver.saveImg(crop_basename, imp)

IJ.log('Done')

It fails with this error:

Traceback (most recent call last):
  File "/home/hadim/local/Fiji.app/plugins/Crop_Multi_Roi.py", line
49, in <module>
    saver.saveImg(crop_basename, imp)
TypeError: saveImg(): 1st arg can't be coerced to io.scif.Writer, String

at org.python.core.Py.TypeError(Py.java:235)
at org.python.core.PyReflectedFunction.throwError(PyReflectedFunction.java:209)
at org.python.core.PyReflectedFunction.throwBadArgError(PyReflectedFunction.java:312)
at org.python.core.PyReflectedFunction.throwError(PyReflectedFunction.java:321)
at org.python.core.PyReflectedFunction.__call__(PyReflectedFunction.java:167)
at org.python.core.PyReflectedFunction.__call__(PyReflectedFunction.java:204)
at org.python.core.PyObject.__call__(PyObject.java:422)
at org.python.core.PyObject.__call__(PyObject.java:426)
at org.python.core.PyMethod.__call__(PyMethod.java:139)
at org.python.pycode._pyx7.f$0(/home/hadim/local/Fiji.app/plugins/Crop_Multi_Roi.py:51)
at org.python.pycode._pyx7.call_function(/home/hadim/local/Fiji.app/plugins/Crop_Multi_Roi.py)
at org.python.core.PyTableCode.call(PyTableCode.java:165)
at org.python.core.PyCode.call(PyCode.java:18)
at org.python.core.Py.runCode(Py.java:1275)
at org.scijava.plugins.scripting.jython.JythonScriptEngine.eval(JythonScriptEngine.java:76)
at org.scijava.script.ScriptModule.run(ScriptModule.java:175)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
at org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:164)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)

Three questions:

how can I write cropped image (I need to write them as OME Tiff so I
need BF or SCIFIO).
Is there is any “easy” alternative to BF setCropRegion function in SCIFIO ?
I am currently using RoiManager.getInstance().getRoisAsArray() to
retrieve all rois. How can I directly get a ROIManager instance from
RoiSet.zip file ?

Any help would be very appreciated.

Thanks !

—
Hadrien Mary