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 > >> >> > > >> >> > > >> > > >> > > > > > >
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