[ImageJ-devel] Save/write image with SCIFIO/BF in python script
Hadrien Mary
hadrien.mary at gmail.com
Sat Jan 24 15:01:56 CST 2015
Quick update:
I tried to use another method to save cropped images using DatasetService:
---------------------------
# Create dataset
ds = data.create(imp)
# Save cropped image
data.save(ds, crop_fname)
-------------------------
And the error is exactly the same as before.
--
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 20, 2015 at 10:17 AM, Hadrien Mary <hadrien.mary at gmail.com> wrote:
> 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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