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
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