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

Mark Hiner hiner at wisc.edu
Wed Jan 14 08:32:52 CST 2015 

Hi Hadrien,

>Exception in thread "DrawAndDrop" java.lang.NoSuchMethodError:
>io.scif.ImageMetadata.setAxisLength(Lnet/imglib2/meta/AxisType;J)V

Ah sorry - my fault again for responding too quickly. ImageJ.git doesn't
have a dependency on scifio-ome-xml; it's a dependency in Fiji itself[1].
So when you installed ImageJ into your Fiji, it updated all the
dependencies but didn't actually update scifio-ome-xml.

You can either manually copy scifio-ome-xml[2] over, or try installing from
the latest Fiji master[3] which I just updated to have the latest
dependencies.

[1]
https://github.com/fiji/fiji/blob/2bc6266ff5ad5dfa155db9c0631db9baae396062/pom.xml#L608-612
[2]
https://github.com/scifio/scifio-ome-xml/releases/tag/scifio-ome-xml-0.12.0
[3]
https://github.com/fiji/fiji/commit/2bc6266ff5ad5dfa155db9c0631db9baae396062

On Wed, Jan 14, 2015 at 7:05 AM, Hadrien Mary <hadrien.mary at gmail.com>
wrote:

> Ok it makes sense now !
>
> So I did what you told me about cloning imagej repo, building and
> install it with maven inside my local Fiji.app/. I don't know if it's
> a bug or a missing dependency but I am now unable to open OME Tiff
> files (other kind of file works well) wether it is by drag and drop or
> with my script. The error is the following:
>
> -------------------------------------------------
> Exception in thread "DrawAndDrop" java.lang.NoSuchMethodError:
> io.scif.ImageMetadata.setAxisLength(Lnet/imglib2/meta/AxisType;J)V
> at
> io.scif.ome.formats.OMETIFFFormat$Metadata.populateImageMetadata(OMETIFFFormat.java:273)
> at io.scif.AbstractParser.parse(AbstractParser.java:254)
> at io.scif.ome.formats.OMETIFFFormat$Parser.parse(OMETIFFFormat.java:609)
> at io.scif.ome.formats.OMETIFFFormat$Parser.parse(OMETIFFFormat.java:552)
> at io.scif.AbstractParser.parse(AbstractParser.java:335)
> at io.scif.AbstractParser.parse(AbstractParser.java:52)
> at io.scif.AbstractReader.setSource(AbstractReader.java:270)
> at
> io.scif.services.DefaultInitializeService.initializeReader(DefaultInitializeService.java:90)
> at io.scif.img.ImgOpener.createReader(ImgOpener.java:542)
> at io.scif.img.ImgOpener.openImgs(ImgOpener.java:144)
> at io.scif.io.DatasetIOPlugin.open(DatasetIOPlugin.java:133)
> at io.scif.io.DatasetIOPlugin.open(DatasetIOPlugin.java:109)
> at io.scif.io.DatasetIOPlugin.open(DatasetIOPlugin.java:63)
> at
> net.imagej.legacy.plugin.DefaultLegacyOpener.open(DefaultLegacyOpener.java:134)
> at
> net.imagej.legacy.DefaultLegacyHooks.interceptDragAndDropFile(DefaultLegacyHooks.java:358)
> at ij.plugin.DragAndDrop.openFile(DragAndDrop.java)
> at ij.plugin.DragAndDrop.run(DragAndDrop.java:152)
> at java.lang.Thread.run(Thread.java:745)
> -----------------------------------------------
>
> I guess something in scifio has not been updated to use the new
> net.imagej.axis or maybe the update is not built/downloaded when I run
> maven on my imagej clone.
>
>
> --
> 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 Wed, Jan 14, 2015 at 12:58 PM, Mark Hiner <hiner at wisc.edu> wrote:
> > Hi Hadrien,
> >
> >>Sorry if it's off topic but I tried to run my script and I got a python
> >> error
> >
> > Oh no! This is totally my fault. I had to update your script for the new
> > dependencies I mentioned and forgot to paste the new version in my
> response
> > yesterday:
> >
> >>from net.imglib2.meta import Axes
> >
> > This import needs to change to:
> >
> > from net.imagej.axis import Axes
> >
> > Sorry about that!
> >
> > Best,
> > Mark
> >
> >
> > On Tue, Jan 13, 2015 at 3:59 PM, Hadrien Mary <hadrien.mary at gmail.com>
> > wrote:
> >>
> >> Thank you Mark !
> >>
> >> Sorry if it's off topic but I tried to run my script and I got a
> >> python error probably related to type difference between python and
> >> java. It's not the first time I saw this kind of message and I'd like
> >> to know how to resolve it. Note that for python script I mainly use
> >> javadoc as documentation.
> >>
> >> The error is below coming from almost the same script as before in this
> >> thread.
> >>
> >> ********************************
> >> Started test_open_save.py at Tue Jan 13 22:54:36 CET 2015
> >> Traceback (most recent call last):
> >>   File
> >>
> "/home/hadim/Documents/phd/dev/scripts/imagej_scripts/test_open_save.py",
> >> line 17, in <module>
> >>     config.imgOpenerSetRegion(ImageRegion(axes, ranges))
> >> TypeError: io.scif.img.ImageRegion(): 1st arg can't be coerced to
> >> net.imagej.axis.AxisType[]
> >>
> >> 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.PyReflectedConstructor.__call__(PyReflectedConstructor.java:176)
> >> at org.python.core.PyObject.__call__(PyObject.java:345)
> >> at org.python.core.PyMethod.instancemethod___call__(PyMethod.java:220)
> >> at org.python.core.PyMethod.__call__(PyMethod.java:211)
> >> at org.python.core.PyMethod.__call__(PyMethod.java:206)
> >> at org.python.core.Deriveds.dispatch__init__(Deriveds.java:19)
> >> at
> >>
> org.python.core.PyObjectDerived.dispatch__init__(PyObjectDerived.java:1057)
> >> at org.python.core.PyType.type___call__(PyType.java:1565)
> >> at org.python.core.PyType.__call__(PyType.java:1548)
> >> at org.python.core.PyObject.__call__(PyObject.java:404)
> >> at org.python.core.PyObject.__call__(PyObject.java:408)
> >> at
> >>
> org.python.pycode._pyx0.f$0(/home/hadim/Documents/phd/dev/scripts/imagej_scripts/test_open_save.py:26)
> >> at
> >>
> org.python.pycode._pyx0.call_function(/home/hadim/Documents/phd/dev/scripts/imagej_scripts/test_open_save.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)
> >> ************************************
> >>
> >> --
> >> 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 Tue, Jan 13, 2015 at 10:20 PM, Mark Hiner <hiner at wisc.edu> wrote:
> >> > Hi Hadrien,
> >> >
> >> >  Unsurprisingly, cropping and writing OME-TIFFs was quite broken.
> >> >
> >> >  It's working for me now, as of the latest SCIFIO[1] and
> >> > SCIFIO-OME-XML[2].
> >> > Note that these libraries have updated dependencies compared to what's
> >> > currently on Fiji, so you can't just drop these .jars into your Fiji
> >> > installation if you want to test locally; you need to update the
> >> > dependencies as well. The easiest way to do this would be to just
> clone
> >> > Imagej.git[3] and install it into your Fiji.app directory by running:
> >> >
> >> > mvn -Dimagej.app.directory=/path/to/Fiji.app/
> >> > -Ddelete.other.versions=true
> >> >
> >> > We'll push these changes up to Fiji this week, and I will find or
> write
> >> > better instructions for local testing.
> >> >
> >> > Hope this helps. Let us know if you have any questions/problems.
> Thanks
> >> > again for finding this issue!
> >> >
> >> > Best,
> >> > - Mark
> >> >
> >> > [1] https://github.com/scifio/scifio/releases/tag/scifio-0.19.0
> >> > [2]
> >> >
> >> >
> https://github.com/scifio/scifio-ome-xml/releases/tag/scifio-ome-xml-0.12.0
> >> > [3] https://github.com/imagej/imagej
> >> >
> >> > On Sat, Jan 10, 2015 at 5:13 AM, Hadrien Mary <hadrien.mary at gmail.com
> >
> >> > wrote:
> >> >>
> >> >> Ok. Let me know when you want me to test your changes. I also tested
> >> >> fix-writing branch and I didn't notice any changes.
> >> >>
> >> >> --
> >> >> 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 Fri, Jan 9, 2015 at 10:14 PM, Mark Hiner <hiner at wisc.edu> wrote:
> >> >> > Hi Hadrien,
> >> >> >
> >> >> > I've identified at least two bugs that could be affecting you here.
> >> >> >
> >> >> > First of all, there was a bug in the OME-TIFF format writing out
> >> >> > multi-dimensional images. That's fixed on a branch but not uploaded
> >> >> > to
> >> >> > Fiji
> >> >> > yet [1].
> >> >> >
> >> >> > Second, it seems like cropping is restricting pixel reads to the
> >> >> > correct
> >> >> > region but then doesn't change the image size.
> >> >> >
> >> >> > I'm hoping when I fix the second issue writing cropped regions will
> >> >> > be
> >> >> > fixed.
> >> >> >
> >> >> > Thanks for the great feedback!
> >> >> > - Mark
> >> >> >
> >> >> > [1] https://github.com/scifio/scifio-ome-xml/tree/fix-writing
> >> >> >
> >> >> > On Fri, Jan 9, 2015 at 11:49 AM, Hadrien Mary
> >> >> > <hadrien.mary at gmail.com>
> >> >> > wrote:
> >> >> >>
> >> >> >> I also confirm the same behaviour when replacing original file by
> >> >> >> OME
> >> >> >> sample data :
> >> >> >>
> >> >> >>
> >> >> >>
> http://www.openmicroscopy.org/Schemas/Samples/2013-06/bioformats-artificial/multi-channel-4D-series.ome.tif.zip
> .
> >> >> >>
> >> >> >> --
> >> >> >> 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 Fri, Jan 9, 2015 at 6:46 PM, Hadrien Mary
> >> >> >> <hadrien.mary at gmail.com>
> >> >> >> wrote:
> >> >> >> > After some investigations I think there is a bug with ImgSaver.
> In
> >> >> >> > the
> >> >> >> > following script, X, Y crop is fine but axes informations (T and
> >> >> >> > Z)
> >> >> >> > are lost and all frames appears on the same axes. Now if I
> replace
> >> >> >> > "target = "/home/hadim/cropped.tif" by "target =
> >> >> >> > "/home/hadim/cropped.ome.tif" on line 9. X, Y crop fails,
> cropped
> >> >> >> > image has the same dimensions than original however axes
> >> >> >> > informations
> >> >> >> > (T and Z) are ok. Note that in cropped.ome.tif, pixel values are
> >> >> >> > totally incoherent which is not the case in cropped.tif.
> >> >> >> >
> >> >> >> > Files can be found here :
> >> >> >> >
> >> >> >> >
> >> >> >> >
> >> >> >> >
> https://arwen.hadim.fr/public.php?service=files&t=71aa17336dcccb3437d9a3dff789d2c0
> >> >> >> >
> >> >> >> > Archive contains cropped.tif, cropped.ome.tif and
> >> >> >> > original.ome.tif.
> >> >> >> >
> >> >> >> > The script:
> >> >> >> >
> >> >> >> > ---------------------------------------------------
> >> >> >> > from io.scif import SCIFIO
> >> >> >> > from io.scif.config import SCIFIOConfig
> >> >> >> > from io.scif.img import ImageRegion
> >> >> >> > from io.scif.img import ImgOpener
> >> >> >> > from io.scif.img import ImgSaver
> >> >> >> > from net.imglib2.meta import Axes
> >> >> >> >
> >> >> >> > fname = "/home/hadim/original.ome.tif"
> >> >> >> > target = "/home/hadim/cropped.tif"
> >> >> >> >
> >> >> >> > axes = [Axes.X, Axes.Y]
> >> >> >> > ranges = ["%i-%i" % (0, 15), "%i-%i" % (0, 25)]
> >> >> >> > config = SCIFIOConfig()
> >> >> >> > config.imgOpenerSetRegion(ImageRegion(axes, ranges))
> >> >> >> >
> >> >> >> > opener = ImgOpener()
> >> >> >> > imps = opener.openImgs(fname, config)
> >> >> >> > imp = imps[0]
> >> >> >> >
> >> >> >> > saver = ImgSaver()
> >> >> >> > saver.saveImg(target, imp)
> >> >> >> >
> >> >> >> > print('Done')
> >> >> >> > ---------------------------------------------------
> >> >> >> >
> >> >> >> >
> >> >> >> > --
> >> >> >> > Hadrien Mary
> >> >> >> >
> >> >> >> >
> >> >> >> > On Fri, Jan 9, 2015 at 12:25 AM, Hadrien Mary
> >> >> >> > <hadrien.mary at gmail.com>
> >> >> >> > wrote:
> >> >> >> >> Thanks for the tip (reminder to me: always look for example in
> >> >> >> >> tests!).
> >> >> >> >>
> >> >> >> >> Unfortunately crop does not work... I will try to do more tests
> >> >> >> >> tomorrow or wait for you or someone else to have a look.
> >> >> >> >>
> >> >> >> >> Updated code:
> >> >> >> >>
> >> >> >> >> from ij import IJ
> >> >> >> >> from ij import ImagePlus
> >> >> >> >>
> >> >> >> >> from io.scif import SCIFIO
> >> >> >> >> from io.scif.config import SCIFIOConfig
> >> >> >> >> from io.scif.img import ImageRegion
> >> >> >> >> from io.scif.img import ImgOpener
> >> >> >> >> from io.scif.img import ImgSaver
> >> >> >> >> from net.imglib2.meta import Axes
> >> >> >> >>
> >> >> >> >> fname = "/home/hadim/original.ome.tif"
> >> >> >> >> target = "/home/hadim/cropped.ome.tif"
> >> >> >> >>
> >> >> >> >> axes = [Axes.X, Axes.Y]
> >> >> >> >> ranges = ["%i-%i" % (2, 15), "%i-%i" % (2, 25)]
> >> >> >> >> config = SCIFIOConfig()
> >> >> >> >> config.imgOpenerSetRegion(ImageRegion(axes, ranges))
> >> >> >> >>
> >> >> >> >> opener = ImgOpener()
> >> >> >> >> imps = opener.openImgs(fname, config)
> >> >> >> >> imp = imps[0]
> >> >> >> >>
> >> >> >> >> saver = ImgSaver()
> >> >> >> >> saver.saveImg(target, imp)
> >> >> >> >>
> >> >> >> >> print('Done')
> >> >> >> >>
> >> >> >> >> --
> >> >> >> >> Hadrien Mary
> >> >> >> >>
> >> >> >> >>
> >> >> >> >> On Fri, Jan 9, 2015 at 12:09 AM, Curtis Rueden
> >> >> >> >> <ctrueden at wisc.edu>
> >> >> >> >> wrote:
> >> >> >> >>> Hi Hadrien,
> >> >> >> >>>
> >> >> >> >>>> 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).
> >> >> >> >>>
> >> >> >> >>> Here's some Java:
> >> >> >> >>>
> >> >> >> >>>     int minX = 128, maxX = 255, minY = 128, minY = 255;
> >> >> >> >>>     AxisType[] axes = { Axes.X, Axes.Y };
> >> >> >> >>>     String[] ranges = { minX + "-" + maxX, minY + "-" + maxY
> };
> >> >> >> >>>     config.imgOpenerSetRegion(new ImageRegion(axes, ranges));
> >> >> >> >>>
> >> >> >> >>> Adapted from here:
> >> >> >> >>>
> >> >> >> >>>
> >> >> >> >>>
> >> >> >> >>>
> https://github.com/scifio/scifio/blob/scifio-0.18.0/src/test/java/io/scif/img/utests/ImgOpenerTest.java#L189-L191
> >> >> >> >>>
> >> >> >> >>> And untested.
> >> >> >> >>>
> >> >> >> >>> HTH,
> >> >> >> >>> Curtis
> >> >> >> >>>
> >> >> >> >>> On Thu, Jan 8, 2015 at 4:47 PM, Hadrien Mary
> >> >> >> >>> <hadrien.mary at gmail.com>
> >> >> >> >>> wrote:
> >> >> >> >>>>
> >> >> >> >>>> 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
> >> >> >> >>>> >>
> >> >> >> >>>> >>
> >> >> >> >>>
> >> >> >> >>>
> >> >> >>
> >> >> >> _______________________________________________
> >> >> >> ImageJ-devel mailing list
> >> >> >> ImageJ-devel at imagej.net
> >> >> >> http://imagej.net/mailman/listinfo/imagej-devel
> >> >> >
> >> >> >
> >> >
> >> >
> >
> >
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://imagej.net/pipermail/imagej-devel/attachments/20150114/55c2b0a0/attachment-0001.html>

More information about the ImageJ-devel mailing list