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

Thu Jan 8 16:47:34 CST 2015

After some investigations, I'm pretty sure I don't instanciate
ImageRegion correctly. Doc and source code didn't help me... I would
like to be able to crop a region in X and Y while keeping any other
dimensions which could exist (C, Z, T).

--
Hadrien Mary

On Thu, Jan 8, 2015 at 10:22 PM, Hadrien Mary <hadrien.mary at gmail.com> wrote:
> 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
>>
>>