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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