Re: [Fwd: Re: [Animl-develop] Update to JCAMP Converter]

[Prof. R. J. L. <rob...@uw...>]

Burkhard,

this suggests processing the file twice or holding info in temp variables until I get
down to the ExperimentStep to find the role to then try to find out which of the
sampleIDs correspond to the actual sample?

In my case lets say I am trying to read the file to fill in JCAMP-DX header items so that if
I export as JCAMP-DX I know whether I have found the MP of the sample or the
MP of the reference (for which there is NO JCAMP-DX label).

That is, I've read in the sampleID's and the information given for each but don't know
how to fill in the header labels until I reach the Role under ExperimentStep.

It seems to me to be MUCH better to have the SampleID say exactly
that this is the sample the reference or blank etc. There can't be too
many alternatives to deal with. There can be another attribute that
gives the info like "polystyrene_IR" but at least it is clear when
processing the Sample section when I find a MP or Temp or refractive index
whatever that the value is related to the SAMPLE and not the BLANK or
REFERENCE.

Doesn't this sound less confusing?

Thanks
Robert



on 11/04/2006 07:16 PM Burkhard Schaefer said the following:
> Robert,
> 
>> in conversion of JCAMP-DX files to AnIML I am concerned about
>> RESOLUTION as well since this is NOT required in JCAMP-DX
>> so will not be present in thousands of files already in existence.
>>
>> Our PE FTIR machines can be set at 1,2 or 4 cm-1 resolution so
>> even then I am not always sure what was the setting when the
>> info was recorded.
>>
>> What should go into the field in the AnIML file exported
>> from a JCAMP-DX file when it is given as REQUIRED?
> 
> This is probably an error in the technique definition. I've filed a bug 
> for this (#1468925).
> 
> 
> 
>> Another problem I have....
>> I am attaching a section of a file from Anh Dao
> 
> I'm snipping out a few things for brevity.
> 
>>
>> ==============================================================
>> <AnIML xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" 
>> xsi:noNamespaceSchemaLocation="animl-core.xsd"
>> xmlns:ds="http://www.w3.org/2000/09/xmldsig#" version="1.0">
>>     <SampleSet>
>>         <Sample sampleID="Polystyrene_IR" derived="false"> [...]
>>         </Sample>
>>         <Sample sampleID="Reference_IR" derived="false"> [...]
>>         </Sample>
>>     </SampleSet>
>>     <MeasurementData>
>>         <ExperimentStep name="Measurement_Polystyrene_IR">
>>             <Author type="device">
>>                 <Name>Magna System 550</Name>
>>             </Author>
>>             <Timestamp>2002-11-06T13:03:04</Timestamp>
>>             <SamplesUsed>
>>                 <SampleRef sampleID="Polystyrene_IR" 
>> role="MeasurementSample" purpose="consumed"/>
>>             </SamplesUsed>
>> =========================================================================================== 
> 
> 
>> I can not understand how (without human intervention) it will be 
>> possible to decide
>> which of the sample sampleID labels refers to a SAMPLE or BACKGROUND 
>> or REFERENCE.
> 
> This is determined by the Sample Role, as given in the role attribute of 
> the SampleRef element. Note that this happens inside the ExperimentStep, 
> not within the sample definition itself.
> 
> At this point I am not sure if the list of sample roles for the IR 
> technique is sufficient. [This is something where the technique NDRs 
> will come into play.]
> 
> 
>> The labels used above are "polytyrene_ir" and "reference_ir" which can 
>> be anything
>> the user puts there and not specific for a SAMPLE or REFERENCE.
> 
> True. The sampleId does not contain any semantics. It is just an 
> identifier.
> 
> 
>> How do I decide what the sample state is for the SAMPLE when I don't 
>> know if it
>> is the SAMPLE or REFERENCE tag that I have just read??
> 
> You can have multiple SampleRef elements inside the ExperimentStep (as 
> declared in the Technique Definition). For example, you could have a 
> measured sample (role: Run Sample) and a sample used for background 
> subtraction (role: Background Sample).
> 
> The names of these roles will be standardized in the Technique NDRs.
> 
> Best regards,
> Burkhard
> 


-- 
Prof. Robert J. Lancashire   mailto:rob...@uw...
Department of Chemistry                           Tel (876) 512 3026
University of the West Indies, Kingston 7     Fax (876) 9771835
Mona Campus, JAMAICA.  http://wwwchem.uwimona.edu.jm/chrl.html