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Ticket #1978 (closed defect: moved)

Opened 2013-08-08T16:51:17-05:00

Last modified 2014-12-09T17:02:39-06:00

Create a measurement service

Reported by:	bdezonia	Owned by:	bdezonia
Priority:	major	Milestone:	imagej2-b8-analysis
Component:	ImgLib2	Version:
Severity:	serious	Keywords:
Cc:	christian.dietz@…, leek	Blocked By:
Blocking:	#1519

Description

We could use a service in Imglib that facilitates the creation and reuse of measurements of data sources. For example the mean value of an Img, or the convex hull of a RegionOfInterest. The service should cache some commonly used measures, recalc measures when underlying data changes (optional), allow one to name and retrieve and forget measures, etc. It should also define a protocol for other developers to create new measures that can be easily slotted in. Ideally it would pass over input data a minimum number of times in calcing values.

The Knime developers want to see this also and have contributed their feature measurement code (in the knip_features branch of imglib) as example code to support in some fashion and to inform the design of this service.

Barry played with some ideas on the measure-engine branch too some time ago. There were related fiji-devel emails too. And there was the creation of the measure2-experiments branch to begin fleshing out something going forward.

For a partial history see ticket #1384.

Change History

comment:1 Changed 2013-08-09T09:37:02-05:00 by bdezonia

In a private email with Christian Dietz I asked what he is looking for in a measurement facility. Below is his response.

For us a feature measurement service is the following:
Compute on a certain IterableInterval/RandomAccessibleInterval (which may result from a labeling, segmentation, certain roi definition, overlay) a set of numerical features:

First order statistics like mean, std. dev, kurtosis, etc.
Texture features like Haralick, Tamura
Zernike Features
Shape Descriptors
Geometrical Features (Circularity, Convexity, Extend, Size, Perimeter etc)
... many more out there

If you for example take a labeling and calculate these feature for each region of interest (or the resulting iterableinterval), you in the end get a table, each row containing all features (or measurements) for a certain region of interest (see Image Segment Features in KNIME, e.g. example flow HCS on tech.knime.org/community/image-processing).

What would be cool (dreaming):

Avoid redundant computations (e.g. if you compute the mean on a certain iterable interval you don't need to recompute the mean again for std. dev. or if you compute convexhull, you dont need to recomute this again etc).
Easy extendible (maybe with a service?)
Annotatable classes (Simply write a class against a certain interface and this class could be a "FeatureFactory" then you annotate some methods/attributes which then will be used as features like

@Feature(Name="Mean", Dependency="none")
double mean = 0.0;

We use these features (as well as CellProfiler for example) for classification/clustering/measurements/statistic issues afterwards.
I think how we define such FeatureFactories/MeasurementServices also heavily depend on the definition of ROIs in ImgLib2 (e.g. RandomAccessibleInterval vs. IterableInterval).

comment:2 Changed 2013-08-09T09:37:54-05:00 by bdezonia

Cc leek added

comment:3 Changed 2014-12-09T17:02:39-06:00 by curtis

Status changed from new to closed
Resolution set to moved

Migrated to https://github.com/imagej/imagej-ops/issues/67