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
