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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