[ImageJ-devel] Save/write image with SCIFIO/BF in python script
Hadrien Mary
hadrien.mary at gmail.com
Wed Jan 14 07:05:57 CST 2015
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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