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

Hadrien Mary hadrien.mary at gmail.com
Thu Jan 8 15:22:51 CST 2015


Thank you Curtis for the answer.

I tried to apply what you told me and the code now works without
error. However the saved cropped image is not cropped (same size as
original) and pixel values are modified).

Script:

from io.scif.config import SCIFIOConfig
from io.scif.img import ImageRegion
from io.scif.img import ImgOpener
from io.scif.img import ImgSaver

fname = "/home/hadim/original.ome.tif"
target = "/home/hadim/cropped.ome.tif"

config = SCIFIOConfig()
region = ImageRegion(dict(x=2, y=2, width=10, height=10))
config.imgOpenerSetRegion(region)

opener = ImgOpener()
imps = opener.openImgs(fname, config)
imp = imps[0]

print(imps)

saver = ImgSaver()
saver.saveImg(target, imp)

Thanks again for your time. Don't be sorry if you don't have time to
write an example.

I will be happy to provide some python/scifio examples scripts.


--
Hadrien Mary

Ph.D student in Biology
Tournier-Gachet Team
CNRS - LBCMCP - UMR 5088

Université de Toulouse - Bât. 4R3B1
118, route de Narbonne - 31062 Toulouse


On Thu, Jan 8, 2015 at 9:56 PM, Curtis Rueden <ctrueden at wisc.edu> wrote:
> Hi Hadrien,
>
>> I tried to use SCIFIO to write cropped image on disk but it doesn not
>> work.
>
> The error you see is because SCIFIO operates on ImgLib2 data structures, not
> ImagePlus objects.
>
>> Is there is any “easy” alternative to BF setCropRegion function in
>> SCIFIO ?
>
> Yes: you create a SCIFIOConfig, calling imgOpenerSetRegion [1] on it, then
> pass it as an argument to the ImgOpener. You'll get back an ImgLib2 data
> object which can then be fed to the SCIFIO ImgSaver.
>
> I'm sorry that I don't have time to whip up an example for you right now. It
> would be great to add more SCIFIO tutorials [2] that use the ImgOpener and
> ImgSaver, since they are much higher level APIs akin to the Bio-Formats "BF"
> functionality... please feel welcome to contribute some!
>
> Regards,
> Curtis
>
> [1]
> http://javadoc.imagej.net/SCIFIO/io/scif/config/SCIFIOConfig.html#imgOpenerSetRegion(io.scif.img.ImageRegion)
> [2] https://github.com/scifio/scifio-tutorials
>
> On Thu, Jan 8, 2015 at 2:18 PM, Hadrien Mary <hadrien.mary at gmail.com> wrote:
>>
>> 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
>>
>> _______________________________________________
>> ImageJ-devel mailing list
>> ImageJ-devel at imagej.net
>> http://imagej.net/mailman/listinfo/imagej-devel
>
>



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