[ImageJ-devel] Save/write image with SCIFIO/BF in python script
Hadrien Mary
hadrien.mary at gmail.com
Tue Jan 20 03:17:52 CST 2015
Another thing I noticed, it's that histogram is different when
cropping manually inside Fiji (select area and do "Duplicate") or when
it has been cropped with the python script (SCIFIO crop).
See screenshot attachment.
--
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 Mon, Jan 19, 2015 at 10:29 AM, Hadrien Mary <hadrien.mary at gmail.com> wrote:
> Hi again,
>
> The script works well for small images (OME Tiff or normal Tiff) with
> the recent Fiji update. However when I run it on large movies (13GB),
> I have the following error.
>
> ----------------------------------------------------------
> -- Classpath of ClassLoader --
> /home/hadim/local/Fiji.app/plugins/
>
> at org.scijava.Context.inject(Context.java:431)
> at org.scijava.Context.inject(Context.java:363)
> at org.scijava.plugin.DefaultPluginService.createInstance(DefaultPluginService.java:237)
> at org.scijava.ui.DefaultUIService.discoverUIs(DefaultUIService.java:500)
> at org.scijava.ui.DefaultUIService.uiList(DefaultUIService.java:479)
> at org.scijava.ui.DefaultUIService.getAvailableUIs(DefaultUIService.java:231)
> at org.scijava.ui.DefaultUIService.onEvent(DefaultUIService.java:457)
> at sun.reflect.GeneratedMethodAccessor5.invoke(Unknown Source)
> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:606)
> at org.scijava.event.DefaultEventService$ProxySubscriber.onEvent(DefaultEventService.java:280)
> at org.scijava.event.DefaultEventService$ProxySubscriber.onEvent(DefaultEventService.java:254)
> at org.bushe.swing.event.ThreadSafeEventService.publish(ThreadSafeEventService.java:971)
> at org.scijava.event.DefaultEventBus.access$201(DefaultEventBus.java:56)
> at org.scijava.event.DefaultEventBus$2.run(DefaultEventBus.java:223)
> at org.scijava.thread.DefaultThreadService$1.run(DefaultThreadService.java:147)
> at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
> at java.util.concurrent.FutureTask.run(FutureTask.java:262)
> at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
> at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
> at java.lang.Thread.run(Thread.java:745)
> Traceback (most recent call last):
> File "/home/hadim/local/Fiji.app/plugins/Scripts/Plugins/Crop_Multi_Roi.py",
> line 50, in <module>
> saver.saveImg(crop_fname, imp)
> at io.scif.img.cell.loaders.AbstractArrayLoader.loadArray(AbstractArrayLoader.java:156)
> at io.scif.img.cell.SCIFIOCellCache.load(SCIFIOCellCache.java:144)
> at io.scif.img.cell.SCIFIOImgCells$CachedCells.get(SCIFIOImgCells.java:122)
> at io.scif.img.cell.SCIFIOImgCells$CachedCells.get(SCIFIOImgCells.java:101)
> at net.imglib2.img.list.ListCursor.get(ListCursor.java:80)
> at net.imglib2.img.cell.CellCursor.getCell(CellCursor.java:92)
> at net.imglib2.img.cell.CellCursor.moveToNextCell(CellCursor.java:180)
> at net.imglib2.img.cell.CellCursor.reset(CellCursor.java:150)
> at net.imglib2.img.cell.CellCursor.<init>(CellCursor.java:86)
> at net.imglib2.img.cell.AbstractCellImg.cursor(AbstractCellImg.java:113)
> at net.imglib2.img.cell.AbstractCellImg.cursor(AbstractCellImg.java:47)
> at net.imglib2.img.AbstractImg.firstElement(AbstractImg.java:81)
> at net.imagej.ImgPlus.firstElement(ImgPlus.java:261)
> at io.scif.img.ImgSaver.populateMeta(ImgSaver.java:894)
> at io.scif.img.ImgSaver.writeImg(ImgSaver.java:514)
> at io.scif.img.ImgSaver.writeImg(ImgSaver.java:495)
> at io.scif.img.ImgSaver.writeImg(ImgSaver.java:457)
> at io.scif.img.ImgSaver.saveImg(ImgSaver.java:174)
> at io.scif.img.ImgSaver.saveImg(ImgSaver.java:158)
> at io.scif.img.ImgSaver.saveImg(ImgSaver.java:128)
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:606)
>
> java.lang.NullPointerException: java.lang.NullPointerException
> -------------------------------------------------------------------
>
> The associated script is below.
>
> ------------------------------------------------------------------------
> from ij import IJ
> from ij.plugin.frame import RoiManager
>
> 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.imagej.axis import Axes
>
> 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)))
>
> # Get ROI bounds
> bounds = roi.getBounds()
> x = bounds.x
> y = bounds.y
> w = bounds.width
> h = bounds.height
>
> # Import only cropped region of the image
> axes = [Axes.X, Axes.Y]
> ranges = ["%i-%i" % (x, x+w), "%i-%i" % (y, y+h)]
> config = SCIFIOConfig()
> config.imgOpenerSetRegion(ImageRegion(axes, ranges))
>
> opener = ImgOpener()
> imps = opener.openImgs(fname, config)
> imp = imps[0]
>
> # Get filename and basename of the current cropped image
> crop_basename = "crop%i_%s" % (crop_id, f.fileName)
> crop_fname = os.path.join(f.directory, crop_basename)
> IJ.log("Saving crop to %s" % crop_fname)
>
> # Save cropped image
> saver = ImgSaver()
> saver.saveImg(crop_fname, imp)
>
> IJ.log('Done')
> ----------------------------------------------------------------------------
>
> Does opener.openImgs() wait for the image to open ? If it does not I
> guess that saver.saveImg() is called on an image that does not exist
> in memory.
>
> Thanks
>
> --
> 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 4:35 PM, Hadrien Mary <hadrien.mary at gmail.com> wrote:
>> I confirm it works !
>>
>> Thanks again
>>
>> --
>> 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 3:32 PM, Mark Hiner <hiner at wisc.edu> wrote:
>>> 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
>>>> >> >> >
>>>> >> >> >
>>>> >> >
>>>> >> >
>>>> >
>>>> >
>>>
>>>
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