[ImageJ-devel] Save/write image with SCIFIO/BF in python script
Hadrien Mary
hadrien.mary at gmail.com
Fri Jan 9 11:49:14 CST 2015
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
>>>> >>
>>>> >>
>>>
>>>
More information about the ImageJ-devel
mailing list