[ImageJ-devel] Save/write image with SCIFIO/BF in python script

Hadrien Mary hadrien.mary at gmail.com
Sat Jan 10 05:13:26 CST 2015 

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 <hiner at 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.mary at 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.mary at 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.mary at 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 <ctrueden at 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.mary at 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.mary at 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 <ctrueden at 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.mary at 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 at imagej.net
>> >>>> >>> http://imagej.net/mailman/listinfo/imagej-devel
>> >>>> >>
>> >>>> >>
>> >>>
>> >>>
>>
>> _______________________________________________
>> ImageJ-devel mailing list
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