Hi Jan The following might work for the create op -- it takes a java array not a python list....
from jarray import array blank=ops.createimg(array([100, 50], 'l')) Brian On Tue, Apr 28, 2015 at 11:53 AM, Jan Eglinger <jan.eglin...@gmail.com> wrote: > Hi all, > > some follow-up questions regarding imagej-ops: > > I tried to use some basic ops in python. From the 2014 wiki announcement > [1] and the python template [2], I assumed something like this would work > in python: > > # @OpService ops > # @DisplayService display > > blank = ops.create([100, 50]) > > display.createDisplay(blank) > > But a choice of candidate functions is listed in output: > > ********************************************** > Request: > - createimg( > Integer, > Integer) > > Candidates: > 1. (Img output) = > net.imagej.ops.create.DefaultCreateImg( > ==> Type outType?, > ImgFactory fac?, > long[] dims) > Inconvertible type: java.lang.Integer => > net.imglib2.type.Type<capture of ?> > 2. (ImgPlus output) = > net.imagej.ops.create.CreateEmptyImgCopy( > ImgPlus input) > Too many arguments: 2 > 1 > 3. (Img output) = > net.imagej.ops.create.CreateImgNativeType( > ImgFactory fac, > NativeType outType, > Dimensions dims) > Not enough arguments: 2 < 3 > 4. (Img output) = > net.imagej.ops.create.CreateImgDifferentNativeType( > ==> Img input, > NativeType type) > Inconvertible type: java.lang.Integer => > net.imglib2.img.Img<capture of ?> > 5. (ImgPlus output) = > net.imagej.ops.create.CreateEmptyImgPlusCopy( > ImgPlus input) > Too many arguments: 2 > 1 > ********************************************** > > and I am unsure if I have to provide image type and factory here. > > > Similarly, for the subtract op: > > # @OpService ops > # @StatisticsService stats > # @net.imagej.Dataset inData > # @OUTPUT net.imagej.Dataset outData > > outData = inData.duplicate() > > mean = stats.alphaTrimmedMean(inData, 0) > print mean > > ops.subtract(outData, inData, mean) > > I am getting the following list of candidates: > > ********************************************** > Request: > - math.subtract( > DefaultDataset, > DefaultDataset, > Double) > > Candidates: > 1. (Object result) = > net.imagej.ops.onthefly.ArithmeticOp$SubtractOp( > Object result, > Object a, > Object b) > Inputs do not conform to op rules > result = blobs.gif > a = blobs.gif > b = 103.26857775590551 > 2. (int result) = > net.imagej.ops.math.PrimitiveMath$IntegerSubtract( > int a, > int b) > Too many arguments: 3 > 2 > 3. (long result) = > net.imagej.ops.math.PrimitiveMath$LongSubtract( > long a, > long b) > Too many arguments: 3 > 2 > 4. (float result) = > net.imagej.ops.math.PrimitiveMath$FloatSubtract( > float a, > float b) > Too many arguments: 3 > 2 > 5. (double result) = > net.imagej.ops.math.PrimitiveMath$DoubleSubtract( > double a, > double b) > Too many arguments: 3 > 2 > 6. (RealType out) = > net.imagej.ops.arithmetic.real.RealSubtract( > ==> RealType out, > RealType in, > double constant) > Inconvertible type: net.imagej.DefaultDataset => capture of ? > ********************************************** > > is there a way with the type-unsafe scripting languages to get ops to use > the correct function? Or am I misunderstanding the concept of imagej-ops > here? > > Thanks again for any hints. > > Jan > > > [1] http://fiji.sc/2014-04-04_-_Announcing_ImageJ_OPS > [2] > https://github.com/imagej/imagej-legacy/blob/master/src/main/resources/script_templates/Python/OpsThresholdIJ1Analyze.py > > > > On 28.04.2015 09:03, Jan Eglinger wrote: > >> Dear Mark and Curtis, >> >> thank you very much for the quick replies and helpful pointers! >> >> Jan >> >> >> On 27.04.2015 20:42, Curtis Rueden wrote: >> >>> Hi Jan, >>> >>> Here is another version of the script, which avoids wrapping each >>> Dataset in another ImgPlus (which the framework would then wrap into yet >>> another Dataset....): >>> >>> # @DisplayService display >>> # @OpService ops >>> # @net.imagej.Dataset inputData1 >>> # @net.imagej.Dataset inputData2 >>> >>> inputData1.setName("my1") >>> inputData2.setName("my2") >>> display.createDisplay(inputData1) >>> display.createDisplay(inputData2) >>> >>> But note that you also don't need to explicitly call createDisplay. Any >>> output parameters of your script will automatically have displays >>> created for them. E.g.: >>> >>> # @OUTPUT net.imagej.Dataset outputData >>> >>> Will be shown at the conclusion of the script. >>> >>> Apologies for the appalling lack of documentation -- it would be great >>> to flesh out the wiki docs about all this. >>> >>> HTH, >>> Curtis >>> >>> On Mon, Apr 27, 2015 at 1:23 PM, Mark Hiner <hi...@wisc.edu >>> <mailto:hi...@wisc.edu>> wrote: >>> >>> Hi Jan, >>> >>> >an error message is displayed: "A Dataset is required but none >>> exist." >>> >>> This was due to limitations with the input preprocessor presenting >>> the list of datasets. Since ImagePluses aren't explicitly tracked by >>> the IJ2 framework, having an ImagePlus recognized as a Dataset >>> requires some extra layers. We had covered the single input case >>> (which is why your first script worked) but not the general >>> multi-input case. There is an issue tracking the multi-input >>> <https://github.com/imagej/imagej-legacy/issues/106> case, which I >>> resolved today. So this should work as intended in our next release >>> - and thank you for the motivation to wrap this up! >>> >>> You can also manually enable ImagePlus <> Dataset synchronization to >>> ensure ImagePluses always have a corresponding Dataset: >>> http://imagej.net/Compatibility#Translation_of_data_structures >>> >>> >(where can this title be set, by the way?) >>> >>> For the multiple choice input selection, the labels are based on the >>> name of the input type. Since the input type is Dataset, the Dataset >>> name is used (which delegates to the wrapped ImgPlus). In your code >>> you are applying labels to the Display, but not the underlying >>> dataset - if you name the ImgPlus, or explicitly create a Dataset >>> and set its name, that name will propagate up to the input chooser >>> (and the Display). As a side note, you should use the >>> net.imagej.ImgPlus instead of the net.imglib2.meta. >>> >>> An updated script would be: >>> >>> >>> # @DisplayService display >>> # @OpService ops >>> # @net.imagej.Dataset inputData1 >>> # @net.imagej.Dataset inputData2 >>> >>> from net.imagej import ImgPlus >>> >>> display.createDisplay(ImgPlus(inputData1, "my1")) >>> display.createDisplay(ImgPlus(inputData2, "my2")) >>> >>> Hope that helps. Let me know if you have any other questions. >>> >>> Best, >>> Mark >>> >>> On Mon, Apr 27, 2015 at 8:58 AM, Jan Eglinger >>> <jan.eglin...@gmail.com <mailto:jan.eglin...@gmail.com>> wrote: >>> >>> Dear all, >>> >>> *** TL;DR: >>> How do I proceed to get multiple input Datasets as ImageJ2 >>> parameters from open images in Fiji? >>> *** >>> >>> I was recently exploring ImageJ2 scripting in Fiji and found the >>> OpsThresholdIJ1Analyze template [1] in the script editor very >>> helpful. >>> >>> When trying to get more than one @net.imagej.Dataset input >>> parameter however, I noticed some inconsistencies. >>> Let me try to illustrate with the two following scripts: >>> >>> # @DisplayService display >>> # @OpService ops >>> # @net.imagej.Dataset inputData1 >>> >>> from net.imglib2.meta import ImgPlus >>> >>> display.createDisplay("my1", ImgPlus(inputData1)) >>> >>> >>> The above script re-displays the current image as expected (I >>> tried with the Blobs sample image open, which will be >>> re-displayed with a non-inverted LUT.) >>> >>> When I ask for two input datasets (right after a fresh start of >>> Fiji with only the Blobs sample image open): >>> >>> # @DisplayService display >>> # @OpService ops >>> # @net.imagej.Dataset inputData1 >>> # @net.imagej.Dataset inputData2 >>> >>> from net.imglib2.meta import ImgPlus >>> >>> display.createDisplay("my1", ImgPlus(inputData1)) >>> display.createDisplay("my2", ImgPlus(inputData2)) >>> >>> an error message is displayed: "A Dataset is required but none >>> exist." >>> The same error message is displayed when I open a second image >>> in Fiji before running the script. >>> >>> Now, when I run script #2 after script #1 was run at least once, >>> I get a dialog with two choices "InputData1" and "InputData2", >>> both choice fields containing "blobs.gif" and a number of >>> "Untitled" entries (where can this title be set, by the way?). >>> >>> I guess that a choice is only displayed if there are ImageJ2 >>> datasets (i.e. wrapped ImagePlus) already available. The single >>> input case seems to be special-cased as it auto-wraps the >>> currently open image. >>> >>> So how do I proceed to get more than one input in ImageJ2 >>> scripting from open (ImageJ1-)images? >>> >>> Thanks for your advice, >>> Regards, >>> Jan >>> >>> >>> [1]: >>> >>> >>> https://github.com/imagej/imagej-legacy/blob/master/src/main/resources/script_templates/Python/OpsThresholdIJ1Analyze.py >>> >>> >>> > _______________________________________________ > ImageJ-devel mailing list > ImageJ-devel@imagej.net > http://imagej.net/mailman/listinfo/imagej-devel >
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