Filtering by instrument

[James Wettenhall]

Hi,

I know it's possible to have data sets spanning multiple instruments (microscopes), but our users have indicated that they would prefer to keep each data set as being associated with a single microscope.

So how can a user filter by instrument in the MyTardis web interface, i.e. only show experiments from microscope 1?

We are using the "tardis:instrument" field in the atom feed template: 

<tardis:instrument>Microscope 1</tardis:instrument> 

to identify the instrument. Do we need a filter on the MyTardis server to add meta-data to experiments saying which instrument they came from, so that users can filter for experiments from one particular instrument?

Does a filter like this already exist?

Hopefully it's clear that I'm using the term "filter" to refer to two different things:

1. A user wanting to display only experiments / data sets which match some given meta data (the instrument where the data was collected), and

2. Some Python functionality which automatically runs after data is ingested to tag it with meta data for the instrument it was collected from.

Thanks,

James

[Steve Bennett]

On Mon, Oct 7, 2013 at 10:54 PM, James Wettenhall <james.we...@monash.edu> wrote:

Hi,

I know it's possible to have data sets spanning multiple instruments (microscopes), but our users have indicated that they would prefer to keep each data set as being associated with a single microscope.

So how can a user filter by instrument in the MyTardis web interface, i.e. only show experiments from microscope 1?

We are using the "tardis:instrument" field in the atom feed template: 

<tardis:instrument>Microscope 1</tardis:instrument> 

to identify the instrument.

From memory, I added that field to the provider template but it's not actually used by the ingest. It should be: the instrument that produced a dataset is obviously pretty fundamental. It tends to be recorded implicitly in other ways (like the file source..., or by the parameter schema that gets applied - assuming you only have one instrument of a given type)

 

Do we need a filter on the MyTardis server to add meta-data to experiments saying which instrument they came from, so that users can filter for experiments from one particular instrument?

I have a feeling we incorporated that into the parameter set schema as a constant field - but I'm probably making this up.

 

Does a filter like this already exist?

(not that I know of - there's search, of course) 

Hopefully it's clear that I'm using the term "filter" to refer to two different things:

1. A user wanting to display only experiments / data sets which match some given meta data (the instrument where the data was collected), and

2. Some Python functionality which automatically runs after data is ingested to tag it with meta data for the instrument it was collected from.

More precisely, "...to tag it with metadata for the filetype it matches". Unless something has changed since I last looked, metadata filters are pretty dumb - Tardis throws every filter at every file to see what sticks. It doesn't use any extra context like the instrument name to help decide which filter to apply. (And it should...)

Steve

[James Wettenhall]

Hi Steve and others,

Perhaps what I'm looking for is a new "instrument" parameter in my "Atom Import - Experiment" schema record.

Currently, when I search for experiments, I can select "ATOM-IMPORT-EXPERIMENT" from the combo-box, but the only field I see is "Filename".

I would like to see an "Instrument" field there, but as you say, even if I enable searching by Instrument in MyTardis, I would still need to ensure that the Instrument gets recorded in MyTardis when each experiment is ingested by the atom ingest app.

My ideal user interface for "filtering by instrument" would be something like a an iTunes quick search box in the top-right corner, where I could start typing "Hitachi microscope" and then reduce my list of experiments to those which match the search text on one of the main experiments pages - "Mine", "Shared" and "Public".  But that would probably require a lot of AJAX programming, and could get messy if/when you allow the search text to match multiple fields.

Cheers,

James

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[Steve Bennett]

On Tue, Oct 8, 2013 at 2:38 PM, James Wettenhall <james.we...@monash.edu> wrote:

Perhaps what I'm looking for is a new "instrument" parameter in my "Atom Import - Experiment" schema record.

Sounds good. Bear in mind that the term 'instrument' is a bit ambiguous. It could mean:

- the manufacturer and model number (eg, FEI Quanta 200) (If there was a standard of some kind, it would be great to use that), but what do you do if there are two identical instruments (as is the case at RMIT HIRi, I believe)

- the shorthand string used to refer to an instrument (eg, "Confocal"), in directory settings etc

- the file format, or something related to the software that saves the data rather than the instrument itself

And don't forget that some "instruments" have additional detectors which produce completely different kinds of data. They're effectively all different instruments, but users will informally call the instrument plus additional detectors all one "instrument".

(Not to discourage you - just something to bear in mind.)

 

My ideal user interface for "filtering by instrument" would be something like a an iTunes quick search box in the top-right corner, where I could start typing "Hitachi microscope" and then reduce my list of experiments to those which match the search text on one of the main experiments pages - "Mine", "Shared" and "Public".  But that would probably require a lot of AJAX programming, and could get messy if/when you allow the search text to match multiple fields.

If this gets implemented, it would be just as applicable to any other kind of metadata, especially user-added fields.

Steve