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 <hi...@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.m...@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 <hi...@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.m...@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 <hi...@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.m...@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 <hi...@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.m...@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.m...@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.m...@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 >> >> >> >> >> <ctrue...@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.m...@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.m...@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 >> >> >> >> >>>> > <ctrue...@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.m...@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@imagej.net >> >> >> >> >>>> >>> http://imagej.net/mailman/listinfo/imagej-devel >> >> >> >> >>>> >> >> >> >> >> >>>> >> >> >> >> >> >>> >> >> >> >> >>> >> >> >> >> >> >> >> >> _______________________________________________ >> >> >> >> ImageJ-devel mailing list >> >> >> >> ImageJ-devel@imagej.net >> >> >> >> http://imagej.net/mailman/listinfo/imagej-devel >> >> >> > >> >> >> > >> >> > >> >> > >> > >> > > > _______________________________________________ ImageJ-devel mailing list ImageJ-devel@imagej.net http://imagej.net/mailman/listinfo/imagej-devel
