animl-develop — Discussions regarding development

[Animl-develop] JCAMP -> AnIML converter 2.0 beta available

[Chalk, S. <sc...@un...>]

I have a new version of the JCAMP to AnIML converter for everyone to  
try out.

Go to http://fad.coas.unf.edu/animl/jcampconversion2.php

The code for generation of the XML has been completely rewritten  
(available upon request)
and now formats XML elements uniformly using a class file.  Other new  
features are an
example UV/Vis file, and the option to have AnIML specification  
comments in the output XML file.
The format is version 1.26 of the animl-core.xsd and version 1.2 of  
the uv-vis.atdd.

Please test with files (if you have time before PittCon ;)) and let  
me know of problems.

This is only available for UV/Vis data but after PittCon I will add  
more techniques as definition files are available.


Stuart Chalk, Ph.D.
Associate Professor of Chemistry
Department of Chemistry and Physics
University of North Florida
P: 904-620-1938
F: 904-620-1989
E: sc...@un...

Re: [Animl-develop] Validation

[Burkhard S. <bur...@bu...>]

Hi everybody,

> Gary, the technique document I believe is being overstated and causing
> too much grief for AnIML. I believe AnIML needs to use technique
> documents to clearly define the minimum requirement for an instances
> document. This actually is good, because it requires good
> documentation. 

Technique definitions are the key concept that ensures interoperability.
They also permit the combination of multiple techniques within the same
experiment. Example: LC+UV, GC+MS.

The main benefit for software vendors is that they can reuse the same
set of tools (or libraries) for any instrument they make.

> I don’t feel we should worry about extensions, if it meets the minimum
> requirement of the technique document, it is valid AnIML.

The extensions are one of the unique selling points for AnIML. After
all, this is (to my knowledge) the first standard that permits vendors
to extend it in a well-defined manner without adversely affecting
compatibility. If we were to take that out, we'd just be an XMLified
JCAMP -- with all the consequences.

> I also believe you can have a valid AnIML file without a technique,
> not useful but allowable.

Do you have an example for that?

> A webservice should be created that has the validation tool and all
> registered technique documents. When validating a system the
> Webservice can be used.

Validators can take a number of shapes. A webservice could certainly be
one of them. Do you think Agilent might provide one / contribute
resources to create one?

Technique definition documents will be freely available on the web
anyway, so I don't see the need to encapsulate these in a web service.

> This means, no one is required to worry about the validator, technique
> tools, or technique documents. 

The complexity of the validator might be overrated. It is actually not a
difficult piece of software, if properly designed. (I was involved in
writing one.)

> The core schema allows the companies to confirm at a minimum they have
> valid AnIML.

Won't this adversely impact interoperability? You could then no longer
rely on things (Vectors, Parameters, ...) having the proper names and
being laid out the way they are intended.

> Additions to a technique can be made to as time passes.

Certainly. As long as the new versions of the documents are stored at a
different URL, that won't cause problems.

> I believe we should simplify AnIML and its requirements as much as
> possible. Keeping it simple will help get acceptance in the industry.

I'm all for simplification as long as we don't sacrifice essential
functionality.

>  The validator is a liability and a non standard tool. 

The validator is a tool that I believe will be most useful to software
developers that want to make sure their products are creating valid
AnIML files. If every software developer uses one, no end user will have
to. Think of it as your QA department.

My €0.02...

Burkhard

[Animl-develop] More animl questions

[Chalk, S. <sc...@un...>]

I am going through writing up an example UV/Vis document that has  
everything in it so I can see how it looks and I have come
across some issues that I think need to be looked at.  They are...

1) For consistency I think we should change sampleIDUsage keyref to  
sampleIDRef (animl-core)
2) For ease of use I think we should not use the DSIG id attribute  
for the Reference element in the AuditTrail
      Doesn't it make more sense to make the Reference element  
contain an absolute xpath to the part of the document?
3) It would be helpful to have other actions for the entries in the  
auditTrial.  For dealing with transformation of legacy
      data I propose "converted" and "usedDefault".  Entries in the  
auditTrial could then identify where default values were
      used to fill required elements where no definitive value is  
present in the legacy data.

In addition, there is no way right now in the UV-Vis atdd to insert a  
page of replicate data.  e.g. the absorbance of a solution
is measured five times at one wavelength.  How do I store that in an  
animl file?  Five different vectors that have each have a length of 1?
How do I indicate they are replicates?  Trivial but important.

Finally, I wonder if the ParentDataPointReference element should be  
added at the page level (as well as the ExperimentStep level?).
I seems that references inside a pageset are more likely?

Stuart

Re: [Animl-develop] Contributing to AnIML

[Chalk, S. <sc...@un...>]

Hopefully its OK if I speak for the other animl developers...

My thought is the best contribution you could make is to identify the  
following pieces of information for
the "analysis technique" of raman spectrography.

1) What are the typical data representations? (i.e. is it 2D raman  
shift v's intensity, 3D shift v's intensity v's position etc)
2) What are the data types of the vectors that make up the data  
representations? (e.g. integers, floats etc)
3) What are the critical instrument parameters that would be used to  
describe how the data was taken?
4) What are the other metadata fields that would be expected to be  
with the data that is gather?
      (this could be time, location inside/outside the body, surgeon,  
surgery, reason for use of the instrument, patient conditions, etc...)

Doing a thorough analysis of the topics above will give you a sense  
of all the information that might need to be captured.
Then you can look at AnIML and decide where and how it can be  
included and (very important) which parameters are required.
Finally, you can then write a technique definition file for raman  
spectrography and propose it to the group.

Hope this helps.

Stuart Chalk, Ph.D.
Associate Professor of Chemistry
Department of Chemistry and Physics
University of North Florida
P: 904-620-1938
F: 904-620-1989
E: sc...@un...


On Dec 1, 2006, at 11:35 AM, Jan Oosthoek wrote:

> A bit off topic perhaps, but how can we contribute to
> the project? We are trying to implement AnIML with
> DSIG for Raman Spectrography medical devices.
>
> Best regards,
>   Jan Izaak Oosthoek.
>
>
>
> ______________________________________________________________________ 
> ______________
> Cheap talk?
> Check out Yahoo! Messenger's low PC-to-Phone call rates.
> http://voice.yahoo.com
>
> ---------------------------------------------------------------------- 
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> _______________________________________________
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> Ani...@li...
> https://lists.sourceforge.net/lists/listinfo/animl-develop
>

[Animl-develop] Contributing to AnIML

[Jan O. <the...@ya...>]

A bit off topic perhaps, but how can we contribute to
the project? We are trying to implement AnIML with
DSIG for Raman Spectrography medical devices.

Best regards,
  Jan Izaak Oosthoek.


 
____________________________________________________________________________________
Cheap talk?
Check out Yahoo! Messenger's low PC-to-Phone call rates.
http://voice.yahoo.com

Re: [Animl-develop] Element XML in animl-core

[Burkhard S. <bur...@bu...>]

Miloslav,

thanks for your message. Indeed, this is a mistake. It should now be 
fixed. A new version of the Core schema (1.23) is available in the CVS.

Changes made:
- XMLType complex type renamed to EmbeddedXMLType
- XML element renamed to EmbeddedXML
- references updated

Thanks again for reporting the bug.

Best regards,
Burkhard



Miloslav Nic wrote:
> Hello,
>    today I have looked at animal-core schema and I have found there a 
> declaration for element "XML".
> 
> Element names starting with xml are prohibited by XML specification:
> 
>    http://www.w3.org/TR/2006/REC-xml-20060816/#sec-logical-struct
> 
> -----------------------------
> This specification does not constrain the application semantics, use, or 
> (beyond syntax) names of the element types and attributes, except that 
> names beginning with a match to (('X'|'x')('M'|'m')('L'|'l')) are 
> reserved for standardization in this or future versions of this 
> specification.
> ---------------------------------
> 
> I would advice to change the name - while some XML parsers ignore this 
> rule at this moment it is not reasonable to have an element in 
> specification which can cause well-formedness error.
> 
> 
>                             Miloslav Nic  (founder of Zvon.org)
> 
> -------------------------------------------------------------------------
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with pre-integrated technology to make your job easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
> _______________________________________________
> Animl-develop mailing list
> Ani...@li...
> https://lists.sourceforge.net/lists/listinfo/animl-develop

[Animl-develop] Element XML in animl-core

[Miloslav N. <Mil...@vs...>]

Hello,
   today I have looked at animal-core schema and I have found there a 
declaration for element "XML".

Element names starting with xml are prohibited by XML specification:

   http://www.w3.org/TR/2006/REC-xml-20060816/#sec-logical-struct

-----------------------------
This specification does not constrain the application semantics, use, or 
(beyond syntax) names of the element types and attributes, except that 
names beginning with a match to (('X'|'x')('M'|'m')('L'|'l')) are 
reserved for standardization in this or future versions of this 
specification.
---------------------------------

I would advice to change the name - while some XML parsers ignore this 
rule at this moment it is not reasonable to have an element in 
specification which can cause well-formedness error.


                            Miloslav Nic  (founder of Zvon.org)

[Animl-develop] Thought you might be interested in...

[Chalk, S. <sc...@un...>]

I came across some interesting material on the web that I thought  
everyone should hear about

SensorML		http://vast.uah.edu/SensorML/

Also have we thought about non-traditional instrumentation enough in  
AnIML spec?  See...
http://www.instrumentmiddleware.org/metadot/index.pl? 
iid=2119&isa=Category

Stuart Chalk, Ph.D.
Associate Professor of Chemistry
Department of Chemistry and Physics
University of North Florida
P: 904-620-1938
F: 904-620-1989
E: sc...@un...

Re: [Animl-develop] Application

[<dal...@ag...>]

I believe the only piece of software to leave its mark should be the =
creator of the file. If additional pieces of software change or modify =
any part of the original file, then an audit trail entry would suffice.

Dale.

-----Original Message-----
From: Burkhard Schaefer [mailto:b.s...@bs...]=20
Sent: Wednesday, September 06, 2006 3:38 PM
To: dal...@ag...
Cc: gar...@ni...; mar...@wa...; mar...@gs...; =
ani...@li...; Alexander Roth
Subject: Re: Application

I'm not sure if we need to completely break down the name of the=20
generator software into Vendor/Product/Version. Perhaps a "generator"=20
attribute would suffice?

<AnIML version=3D"..." generator=3D"Burkhard Inc.'s MyShinyProduct 1.0">
...
</AnIML>

On the other hand, an application could always store this as XML=20
comments. If at all needed.

However, perhaps it opens another ugly can of worms: If we introduce a=20
systematic mechanism to add generator information, we need a policy=20
which software is allowed to leave its marks in the file:

- the software that created the file?
- the software that performed the most recent modification?

What if multiple pieces of software were involved?
I'd like to not open this can of worms too wide. Other thoughts?

Burkhard



dal...@ag... wrote:
> To all:
>=20
> AnIML is used primarily as an Archive and interchange mechanism. One=20
> item that seems should be there in the core is an Application element =
or=20
> complex type. The string or complex type would describing the =
generating=20
> Application.  The information contained would include manufacturer,=20
> program name and revision. ie "Scientific Software; Elite; 3.2" =20
>=20
> =20
>=20
> The complex type could have the following elements:
>=20
>             Manufacturer
>=20
>             Program name
>=20
>             Program revision
>=20
> =20
>=20
> =20
>=20
> Dale.
>=20

--=20
Burkhard A. Sch=E4fer
BSSN Software

Tel: +49 (6136) 7527-64 (direct)
Fax: +49 (6136) 7527-68
USA: +1 (888) 674-0047 (toll free)
EMail: b.s...@bs...

Re: [Animl-develop] Application

[<dal...@ag...>]

Add IntegrityValue

DocumentInfo
	CreatedBY
	CreationDate
	Description
	LastModifiedBy
	LastModifiedDate
	ApplicationVersion
	IntegrityValue - Value to confirm integrity of this document.
	AuditTrail - Entries

-----Original Message-----
From: O'NEILL,DALE (A-USA,ex1)=20
Sent: Wednesday, September 06, 2006 4:26 PM
To: O'NEILL,DALE (A-USA,ex1); 'Burkhard Schaefer'
Cc: 'gar...@ni...'; 'mar...@wa...'; =
'mar...@gs...'; 'ani...@li...'; 'Alexander =
Roth'
Subject: RE: Application

Maybe instead of Application element it could be called DocumentInfo and =
had elements such as=20

	CreatedBY
	CreationDate
	Description
	LastModifiedBy
	LastModifiedDate
	ApplicationVersion
	AuditTrail - Entries

Dale.

-----Original Message-----
From: O'NEILL,DALE (A-USA,ex1)=20
Sent: Wednesday, September 06, 2006 4:16 PM
To: 'Burkhard Schaefer'; O'NEILL,DALE (A-USA,ex1)
Cc: gar...@ni...; mar...@wa...; mar...@gs...; =
ani...@li...; Alexander Roth
Subject: RE: Application

I believe the only piece of software to leave its mark should be the =
creator of the file. If additional pieces of software change or modify =
any part of the original file, then an audit trail entry would suffice.

Dale.

-----Original Message-----
From: Burkhard Schaefer [mailto:b.s...@bs...]=20
Sent: Wednesday, September 06, 2006 3:38 PM
To: dal...@ag...
Cc: gar...@ni...; mar...@wa...; mar...@gs...; =
ani...@li...; Alexander Roth
Subject: Re: Application

I'm not sure if we need to completely break down the name of the=20
generator software into Vendor/Product/Version. Perhaps a "generator"=20
attribute would suffice?

<AnIML version=3D"..." generator=3D"Burkhard Inc.'s MyShinyProduct 1.0">
...
</AnIML>

On the other hand, an application could always store this as XML=20
comments. If at all needed.

However, perhaps it opens another ugly can of worms: If we introduce a=20
systematic mechanism to add generator information, we need a policy=20
which software is allowed to leave its marks in the file:

- the software that created the file?
- the software that performed the most recent modification?

What if multiple pieces of software were involved?
I'd like to not open this can of worms too wide. Other thoughts?

Burkhard



dal...@ag... wrote:
> To all:
>=20
> AnIML is used primarily as an Archive and interchange mechanism. One=20
> item that seems should be there in the core is an Application element =
or=20
> complex type. The string or complex type would describing the =
generating=20
> Application.  The information contained would include manufacturer,=20
> program name and revision. ie "Scientific Software; Elite; 3.2" =20
>=20
> =20
>=20
> The complex type could have the following elements:
>=20
>             Manufacturer
>=20
>             Program name
>=20
>             Program revision
>=20
> =20
>=20
> =20
>=20
> Dale.
>=20

--=20
Burkhard A. Sch=E4fer
BSSN Software

Tel: +49 (6136) 7527-64 (direct)
Fax: +49 (6136) 7527-68
USA: +1 (888) 674-0047 (toll free)
EMail: b.s...@bs...

Re: [Animl-develop] Application

[<dal...@ag...>]

Maybe instead of Application element it could be called DocumentInfo and =
had elements such as=20

	CreatedBY
	CreationDate
	Description
	LastModifiedBy
	LastModifiedDate
	ApplicationVersion
	AuditTrail - Entries

Dale.

-----Original Message-----
From: O'NEILL,DALE (A-USA,ex1)=20
Sent: Wednesday, September 06, 2006 4:16 PM
To: 'Burkhard Schaefer'; O'NEILL,DALE (A-USA,ex1)
Cc: gar...@ni...; mar...@wa...; mar...@gs...; =
ani...@li...; Alexander Roth
Subject: RE: Application

I believe the only piece of software to leave its mark should be the =
creator of the file. If additional pieces of software change or modify =
any part of the original file, then an audit trail entry would suffice.

Dale.

-----Original Message-----
From: Burkhard Schaefer [mailto:b.s...@bs...]=20
Sent: Wednesday, September 06, 2006 3:38 PM
To: dal...@ag...
Cc: gar...@ni...; mar...@wa...; mar...@gs...; =
ani...@li...; Alexander Roth
Subject: Re: Application

I'm not sure if we need to completely break down the name of the=20
generator software into Vendor/Product/Version. Perhaps a "generator"=20
attribute would suffice?

<AnIML version=3D"..." generator=3D"Burkhard Inc.'s MyShinyProduct 1.0">
...
</AnIML>

On the other hand, an application could always store this as XML=20
comments. If at all needed.

However, perhaps it opens another ugly can of worms: If we introduce a=20
systematic mechanism to add generator information, we need a policy=20
which software is allowed to leave its marks in the file:

- the software that created the file?
- the software that performed the most recent modification?

What if multiple pieces of software were involved?
I'd like to not open this can of worms too wide. Other thoughts?

Burkhard



dal...@ag... wrote:
> To all:
>=20
> AnIML is used primarily as an Archive and interchange mechanism. One=20
> item that seems should be there in the core is an Application element =
or=20
> complex type. The string or complex type would describing the =
generating=20
> Application.  The information contained would include manufacturer,=20
> program name and revision. ie "Scientific Software; Elite; 3.2" =20
>=20
> =20
>=20
> The complex type could have the following elements:
>=20
>             Manufacturer
>=20
>             Program name
>=20
>             Program revision
>=20
> =20
>=20
> =20
>=20
> Dale.
>=20

--=20
Burkhard A. Sch=E4fer
BSSN Software

Tel: +49 (6136) 7527-64 (direct)
Fax: +49 (6136) 7527-68
USA: +1 (888) 674-0047 (toll free)
EMail: b.s...@bs...

Re: [Animl-develop] Application

[Burkhard S. <b.s...@bs...>]

I'm not sure if we need to completely break down the name of the 
generator software into Vendor/Product/Version. Perhaps a "generator" 
attribute would suffice?

<AnIML version="..." generator="Burkhard Inc.'s MyShinyProduct 1.0">
...
</AnIML>

On the other hand, an application could always store this as XML 
comments. If at all needed.

However, perhaps it opens another ugly can of worms: If we introduce a 
systematic mechanism to add generator information, we need a policy 
which software is allowed to leave its marks in the file:

- the software that created the file?
- the software that performed the most recent modification?

What if multiple pieces of software were involved?
I'd like to not open this can of worms too wide. Other thoughts?

Burkhard



dal...@ag... wrote:
> To all:
> 
> AnIML is used primarily as an Archive and interchange mechanism. One 
> item that seems should be there in the core is an Application element or 
> complex type. The string or complex type would describing the generating 
> Application.  The information contained would include manufacturer, 
> program name and revision. ie “Scientific Software; Elite; 3.2”  
> 
>  
> 
> The complex type could have the following elements:
> 
>             Manufacturer
> 
>             Program name
> 
>             Program revision
> 
>  
> 
>  
> 
> Dale.
> 

-- 
Burkhard A. Schäfer
BSSN Software

Tel: +49 (6136) 7527-64 (direct)
Fax: +49 (6136) 7527-68
USA: +1 (888) 674-0047 (toll free)
EMail: b.s...@bs...

Re: [Animl-develop] AnIML first last delta

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

Burkhard,

For feeling is that.....

In a number of cases the first and last may be integers
for example in IR when you scan from 4400 - 400 cm-1 or
in Vis spec when you scan from 950 - 350 nm or GC
traces when time is 0 - 1000 seconds etc.
For NMR the scan may be integer in ppm but since data
is stored in Hz then they will never be integer but
depend on the frequency of the instrument.

So first and last may suffer less from truncation
errors than deltaX which is why I am suggesting
not enforcing deltax but rather first and last.

This sound reasonable?

Thanks
Robert




on 15/08/2006 07:02 PM Burkhard Schaefer said the following:
>   Robert,
>=20
> that's a tricky issue. The only bullet-proof way to get this right is=20
> *not* to use floating point arithmetics when calculating the=20
> auto-incremented values.
>=20
> The problem is that in IEEE floating point, the neither of the followin=
g=20
> equations hold:
>=20
> (x_max - x_min ) / (endOffset-startOffset) =3D D x
>=20
> So no matter if we give x_min , x_max or x_min and _ D x, we'll have=20
> rounding problems. Consider this:
>=20
> S _i=3DstartOffset...endOffset D x =3D (endOffset-startOffset) =B7 D x
>=20
> Even this does not hold in floating point arithmetics. However, to=20
> calculate a value x_i , it's more precise to use multiplication (like i=
n=20
> the right hand part of the equation) rather than adding things up in a=20
> for loop. It avoids adding up the rounding errors. That's why I opted=20
> for storing the D x value.
>=20
> The best practice when implementing it would of course be not to use=20
> floating point arithmetics. Most programming languages offer a concept=20
> of precise arithmetics. In Java, there's the BigDecimal class to do thi=
s.
>=20
> Of course, it's important that applications write these values into the=
=20
> AniML document without truncating them. If they truncate, there's very=20
> little we can do.
>=20
> Best regards,
> Burkhard
>=20
>=20
> Prof. Robert J. Lancashire wrote:
>> Hi,
>>
>> I have been working through some coding for reading and writing CML
>> documents and noticed that like JCAMP-DX they have followed the
>> arrangement that for auto-generated X values the approach is
>> provide the firstX, lastX and the number of points.
>>  From this deltaX is calculated.
>>
>> With AnIML, firstx and deltax is provided and I wonder whether this
>> introduces a problem with respect to rounding errors.
>> When packages give deltax in an output routine they may truncate
>> to a set number of figures which would then lead to innaccuracies.
>>
>> I suggest it would be better to give first last and number of points
>> so that deltaX is not truncated.
>>
>> In the case of JCAMP-DX though, I must admit to having seen numerous
>> files where the ##FIRSTX=3D and ##LASTX=3D values were significantly
>> trunacted by comparison to the actual values listed in the data sectio=
n
>> so there may be still be an issue with rounding that affects the
>> calculation of delta.
>>
>> Any thoughts.
>> Excuse me if this was covered long ago!!
>>
>> Robert
>>
>>
>> ----------------------------------------------------------------------=
---
>> Using Tomcat but need to do more? Need to support web services, securi=
ty?
>> Get stuff done quickly with pre-integrated technology to make your job=
 easier
>> Download IBM WebSphere Application Server v.1.0.1 based on Apache Gero=
nimo
>> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&da=
t=3D121642 <http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D=
263057&dat=3D121642>
>> _______________________________________________
>> Animl-develop mailing list
>> Ani...@li... <mailto:Ani...@li...urce=
forge.net>
>> https://lists.sourceforge.net/lists/listinfo/animl-develop
>>  =20

Re: [Animl-develop] AnIML first last delta

[Burkhard S. <bur...@bu...>]

Robert,

that's a tricky issue. The only bullet-proof way to get this right is=20
*not* to use floating point arithmetics when calculating the=20
auto-incremented values.

The problem is that in IEEE floating point, the neither of the following=20
equations hold:

(x_max - x_min ) / (endOffset-startOffset) =3D Dx

So no matter if we give x_min , x_max or x_min and _ Dx, we'll have=20
rounding problems. Consider this:

S_i=3DstartOffset...endOffset Dx =3D (endOffset-startOffset) =B7 Dx

Even this does not hold in floating point arithmetics. However, to=20
calculate a value x_i , it's more precise to use multiplication (like in=20
the right hand part of the equation) rather than adding things up in a=20
for loop. It avoids adding up the rounding errors. That's why I opted=20
for storing the Dx value.

The best practice when implementing it would of course be not to use=20
floating point arithmetics. Most programming languages offer a concept=20
of precise arithmetics. In Java, there's the BigDecimal class to do this.

Of course, it's important that applications write these values into the=20
AniML document without truncating them. If they truncate, there's very=20
little we can do.

Best regards,
Burkhard


Prof. Robert J. Lancashire wrote:
> Hi,
>
> I have been working through some coding for reading and writing CML
> documents and noticed that like JCAMP-DX they have followed the
> arrangement that for auto-generated X values the approach is
> provide the firstX, lastX and the number of points.
>  From this deltaX is calculated.
>
> With AnIML, firstx and deltax is provided and I wonder whether this
> introduces a problem with respect to rounding errors.
> When packages give deltax in an output routine they may truncate
> to a set number of figures which would then lead to innaccuracies.
>
> I suggest it would be better to give first last and number of points
> so that deltaX is not truncated.
>
> In the case of JCAMP-DX though, I must admit to having seen numerous
> files where the ##FIRSTX=3D and ##LASTX=3D values were significantly
> trunacted by comparison to the actual values listed in the data section
> so there may be still be an issue with rounding that affects the
> calculation of delta.
>
> Any thoughts.
> Excuse me if this was covered long ago!!
>
> Robert
>
>
> -----------------------------------------------------------------------=
--
> Using Tomcat but need to do more? Need to support web services, securit=
y?
> Get stuff done quickly with pre-integrated technology to make your job =
easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geron=
imo
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&dat=
=3D121642
> _______________________________________________
> Animl-develop mailing list
> Ani...@li...
> https://lists.sourceforge.net/lists/listinfo/animl-develop
>  =20

[Animl-develop] AnIML first last delta

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

Hi,

I have been working through some coding for reading and writing CML
documents and noticed that like JCAMP-DX they have followed the
arrangement that for auto-generated X values the approach is
provide the firstX, lastX and the number of points.
 From this deltaX is calculated.

With AnIML, firstx and deltax is provided and I wonder whether this
introduces a problem with respect to rounding errors.
When packages give deltax in an output routine they may truncate
to a set number of figures which would then lead to innaccuracies.

I suggest it would be better to give first last and number of points
so that deltaX is not truncated.

In the case of JCAMP-DX though, I must admit to having seen numerous
files where the ##FIRSTX= and ##LASTX= values were significantly
trunacted by comparison to the actual values listed in the data section
so there may be still be an issue with rounding that affects the
calculation of delta.

Any thoughts.
Excuse me if this was covered long ago!!

Robert

Re: [Animl-develop] [Fwd: Re: AnIML sequence]

[<Mar...@wa...>]

Hi Robert,

I have entered this as a bug into the tracking system on Sourceforge,

Mit freundlichen Gr=FC=DFen / Best regards

Maren.=20


Dr. Maren Fiege
Senior Product Manager
=20
Waters GmbH
Europaallee 27, D-50226 Frechen, Germany
Tel.+49 2234 9207 - 0  Fax +49 2234 9207-99

http://www.waters.com/informatics=20





"Prof. Robert John Lancashire" <rob...@uw...>=20
Sent by: ani...@li...
29.05.2006 20:01

To
ani...@li..., Maren=5F...@wa...
cc

Subject
[Animl-develop] [Fwd: Re: AnIML sequence]






Maren,

I was checking on a sample file generated by Anh Dao called something like
ADNIR to see why it was crashing my read routine and realised
that it did not have an attribute labelled IDENTIFIER under=20
MeasurementData.
StAX routines fail if you try to read an attribute that is absent!

I was using this attribute as the equivalent of the JCAMP-DX ##TITLE=3D=20
label
since based on the discussion about SampleSet where the sample could
be reference or sample simultaneously in 1 aml document then it would
seem that the SampleName label could NOT be used as the title equivalent.

Does this make sense and thus should not IDENTIFIER be a required label?

Thanks
Robert



-------- Original Message --------
Subject: Re: AnIML sequence
Date: Wed, 24 May 2006 10:36:50 +0200
From: Maren=5F...@wa...
To: Prof. Robert John Lancashire <rob...@uw...>
CC: Prof. Tony Davies <Ant...@gm...>, Maren=5F...@wa...

Hi Robert,

> Can you give me an example of what you are thinking of here?
>
> I think at the time you are creating the document it is known
> what it is you have taken the measurement on! Hence you know
> what is the sample and what may be blanks or references!
The idea is that there could be a case where you store multiple
measurements in an AnIML file, and the same physical sample is a reference
in one, but a run sample in another. In order to not have to waste a lot
of space with redundant sample information, each one is only stored once
and can assume different roles.


Mit freundlichen Gr=FC=DFen / Best regards

Maren.


Dr. Maren Fiege
Senior Product Manager

Waters GmbH
Europaallee 27, D-50226 Frechen, Germany
Tel.+49 2234 9207 - 0  Fax +49 2234 9207-99

http://www.waters.com/informatics





"Prof. Robert John Lancashire" <rob...@uw...>
09.05.2006 13:01

To
Maren=5F...@wa...
cc
"Prof. Tony Davies" <Ant...@gm...>
Subject
Re: AnIML sequence






Maren,

I think I get the concept that a sample can be a sample in one experiment
and a reference in a different experiment but are you suggesting that
within the same AnIML document it could change role.

Can you give me an example of what you are thinking of here?

I think at the time you are creating the document it is known
what it is you have taken the measurement on! Hence you know
what is the sample and what may be blanks or references!

I continually run across this problem of trying to envisage when
the document is being generated but figure that the instrument
can generate the spectrum section and the user generate the
sample section at a later stage.

I have tried 2 different approaches to reading the document,
1 using DOM and the other using StAX. StAX fits exactly
with the lazy load concept.

I think the lazy load idea is OK and in fact for a spectrum display
I could totally IGNORE the sample section altogether and never read
anything in there, if all I want is an XY plot.

It is only when I want to associate sample info with spectrum info that
I run into difficulty unless I store all sample info and then
read spectrum info and try to work backwards to do the association having
eventually found out which is the sample.

bear with me while I get this sorted out...
Thanks
Robert



on 09/05/2006 04:04 AM Maren=5F...@wa... said the following:
> Hi Robert,
>=20
> catching up on my email...
>=20
>> I think this is inefficient and whilst there may be benefits to having
>> sample separate to measurement I believe it would be easy enough to
>> add an attribute at the sample stage to declare which of the
>> samplesets was the actual sample and which was the blank etc.
>> The sampleID seems at present to be anything you want to call it
>> so if that is to stay the same then a new attribute is needed.
>> It could be a simple Boolean (isSample or isReference) and would
>> only be required if the sample was part of the measurement.
> The samples defined in AnIML can be re-used and may change roles, so you =



> cannot flag them in the sample definition as you suggest.
> You are trying to stream in the AnIML file and keep it in memory=20
> altogether. The idea when designing the format was that you should use=20
> something called "lazy load", meaning that you would only read what you=20
> need at a given time. This is an entirely different paradigm.
>=20
> Mit freundlichen Gr=FC=DFen / Best regards
>=20
> Maren.=20
>=20
>=20
> Dr. Maren Fiege
> Senior Product Manager
>=20
> Waters GmbH
> Europaallee 27, D-50226 Frechen, Germany
> Tel.+49 2234 9207 - 0  Fax +49 2234 9207-99
>=20
> http://www.waters.com/informatics=20
>=20
>=20
>=20


--=20
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






--=20
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


=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=
=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F
Animl-develop mailing list
Ani...@li...
https://lists.sourceforge.net/lists/listinfo/animl-develop

Re: [Animl-develop] AnIML query

[<Mar...@wa...>]

Hi Robert,

I had intended to bring this up at the developers' meeting on Tuesday, but =

unfortunately I could not attend.
When I create a sample XML file based on the AnIML core schema in XMLSpy,=20
it starts like this:

---------------------------------------------------------------------------=
------------------------------------------------------
<?xml version=3D"1.0" encoding=3D"UTF-8"?>
<!--Sample XML file generated by XMLSpy v2005 sp1 U=20
(http://www.xmlspy.com)-->
<AnIML xmlns=3D"urn:org:astm:animl:schema:core:draft:0.2" xmlns:ds=3D"
http://www.w3.org/2000/09/xmldsig#" xmlns:xsi=3D"
http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation=3D"
urn:org:astm:animl:schema:core:draft:0.2:\DOCUME~1\MARENF~1.CLC\LOCALS~1\Te=
mp\notes6030C8\animl-core.xsd
" version=3D"0.2">
        <SampleSet id=3D"ID000000">
---------------------------------------------------------------------------=
------------------------------------------------------

A CML file created the same way starts with:

---------------------------------------------------------------------------=
------------------------------------------------------
<?xml version=3D"1.0" encoding=3D"UTF-8"?>
<!--Sample XML file generated by XMLSpy v2005 sp1 U=20
(http://www.xmlspy.com)-->
<cml xmlns=3D"http://www.xml-cml.org/schema/cml2/core" xmlns:val=3D"
http://www.w3.org/1999/XSL/TransformX" xmlns:xlink=3D"
http://www.w3.org/1999/xlink" xmlns:stm=3D"
http://www.xml-cml.org/schema/stmml" xmlns:xsi=3D"
http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation=3D"
http://www.xml-cml.org/schema/cml2/core:\DOCUME~1\MarenF.CLCDOM\MYDOCU~1\Pr=
ojekte\AnIML\OTHERR~1\CML\cmlCore.xsd
" dictRef=3D"AA:AA" title=3D"String" convention=3D"AA:AA" id=3D"AA:AA"/>
---------------------------------------------------------------------------=
------------------------------------------------------

So the root element actually is <AnIML...> as you requested.

Mit freundlichen Gr=FC=DFen / Best regards

Maren.=20


Dr. Maren Fiege
Senior Product Manager
=20
Waters GmbH
Europaallee 27, D-50226 Frechen, Germany
Tel.+49 2234 9207 - 0  Fax +49 2234 9207-99

http://www.waters.com/informatics=20





"Prof. Robert John Lancashire" <rob...@uw...>=20
Sent by: ani...@li...
12.06.2006 22:37

To
"Burkhard Schaefer" <bur...@bu...>
cc
Maren=5F...@wa..., ani...@li...
Subject
[Animl-develop] AnIML query






Maren and Burkhard,

I have released an update to JSpecView where MeasurementData is
replaced by ExperimentStepSet and generated a dozen or so files
with the revised tags. I can email them to you if you want to put
them on sourceforge.

I have another query for you...

In CML they use
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D
<spectrum id=3D"$ident" title=3D"$title" convention=3D"jcamp:DX4.24"
    xmlns=3D"http://www.xml-cml.org/schema"
    xsi:schemaLocation=3D"http://www.xml-cml.org/schema ../../schema.xsd"
    xmlns:xsi=3D"http://www.w3.org/2001/XMLSchema-instance"
    xmlns:siUnits=3D"http://www.xml-cml.org/units/siUnits"
    xmlns:units=3D"http://www.xml-cml.org/units/units"
    xmlns:nmr=3D"http://www.nmrshiftdb.org/dict"
    xmlns:cml=3D"http://www.xml-cml.org/dict/cmlDict"
    xmlns:dc=3D"http://purl.org/dc/elements/1.1/" type=3D"$specinits">


or it may be contained in a CML wrapper like...

<cml xmlns=3D"http://www.xml-cml.org/schema"
    xsi:schemaLocation=3D"http://www.xml-cml.org/schema ../../schema.xsd"
    xmlns:xsi=3D"http://www.w3.org/2001/XMLSchema-instance"
    xmlns:siUnits=3D"http://www.xml-cml.org/units/siUnits"
    xmlns:units=3D"http://www.xml-cml.org/units/units"
    xmlns:nmr=3D"http://www.nmrshiftdb.org/dict"
    xmlns:cml=3D"http://www.xml-cml.org/dict/cmlDict"
    xmlns:dc=3D"http://purl.org/dc/elements/1.1/">
<spectrum id =3D......>

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D


For AnIML, why is it necessary to have an XML container?

Why can't it start with

<ANIML ......

I want to be able to easily distinguish the two forms by something
other than file extension since xml could be either.
I suspect that aml extensions may go the same way as cml and so I need
to be able to recognise them from the namespaces or something simple.

any suggestions

Robert




=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=
=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F
Animl-develop mailing list
Ani...@li...
https://lists.sourceforge.net/lists/listinfo/animl-develop

[Animl-develop] AnIML query

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

Maren and Burkhard,

I have released an update to JSpecView where MeasurementData is
replaced by ExperimentStepSet and generated a dozen or so files
with the revised tags. I can email them to you if you want to put
them on sourceforge.

I have another query for you...

In CML they use
=========================================================
<spectrum id="$ident" title="$title" convention="jcamp:DX4.24"
    xmlns="http://www.xml-cml.org/schema"
    xsi:schemaLocation="http://www.xml-cml.org/schema ../../schema.xsd"
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xmlns:siUnits="http://www.xml-cml.org/units/siUnits"
    xmlns:units="http://www.xml-cml.org/units/units"
    xmlns:nmr="http://www.nmrshiftdb.org/dict"
    xmlns:cml="http://www.xml-cml.org/dict/cmlDict"
    xmlns:dc="http://purl.org/dc/elements/1.1/" type="$specinits">


or it may be contained in a CML wrapper like...

<cml xmlns="http://www.xml-cml.org/schema"
    xsi:schemaLocation="http://www.xml-cml.org/schema ../../schema.xsd"
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xmlns:siUnits="http://www.xml-cml.org/units/siUnits"
    xmlns:units="http://www.xml-cml.org/units/units"
    xmlns:nmr="http://www.nmrshiftdb.org/dict"
    xmlns:cml="http://www.xml-cml.org/dict/cmlDict"
    xmlns:dc="http://purl.org/dc/elements/1.1/">
<spectrum id =......>

==========================================================


For AnIML, why is it necessary to have an XML container?

Why can't it start with

<ANIML ......

I want to be able to easily distinguish the two forms by something
other than file extension since xml could be either.
I suspect that aml extensions may go the same way as cml and so I need
to be able to recognise them from the namespaces or something simple.

any suggestions

Robert

[Animl-develop] [Fwd: Re: AnIML sequence]

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

Maren,

I was checking on a sample file generated by Anh Dao called something lik=
e
ADNIR to see why it was crashing my read routine and realised
that it did not have an attribute labelled IDENTIFIER under MeasurementDa=
ta.
StAX routines fail if you try to read an attribute that is absent!

I was using this attribute as the equivalent of the JCAMP-DX ##TITLE=3D l=
abel
since based on the discussion about SampleSet where the sample could
be reference or sample simultaneously in 1 aml document then it would
seem that the SampleName label could NOT be used as the title equivalent.

Does this make sense and thus should not IDENTIFIER be a required label?

Thanks
Robert



-------- Original Message --------
Subject: Re: AnIML sequence
Date: Wed, 24 May 2006 10:36:50 +0200
From: Mar...@wa...
To: Prof. Robert John Lancashire <rob...@uw...>
CC: Prof. Tony Davies <Ant...@gm...>, Mar...@wa...

Hi Robert,

> Can you give me an example of what you are thinking of here?
>
> I think at the time you are creating the document it is known
> what it is you have taken the measurement on! Hence you know
> what is the sample and what may be blanks or references!
The idea is that there could be a case where you store multiple
measurements in an AnIML file, and the same physical sample is a referenc=
e
in one, but a run sample in another. In order to not have to waste a lot
of space with redundant sample information, each one is only stored once
and can assume different roles.


Mit freundlichen Gr=FC=DFen / Best regards

Maren.


Dr. Maren Fiege
Senior Product Manager

Waters GmbH
Europaallee 27, D-50226 Frechen, Germany
Tel.+49 2234 9207 - 0  Fax +49 2234 9207-99

http://www.waters.com/informatics





"Prof. Robert John Lancashire" <rob...@uw...>
09.05.2006 13:01

To
Mar...@wa...
cc
"Prof. Tony Davies" <Ant...@gm...>
Subject
Re: AnIML sequence






Maren,

I think I get the concept that a sample can be a sample in one experiment
and a reference in a different experiment but are you suggesting that
within the same AnIML document it could change role.

Can you give me an example of what you are thinking of here?

I think at the time you are creating the document it is known
what it is you have taken the measurement on! Hence you know
what is the sample and what may be blanks or references!

I continually run across this problem of trying to envisage when
the document is being generated but figure that the instrument
can generate the spectrum section and the user generate the
sample section at a later stage.

I have tried 2 different approaches to reading the document,
1 using DOM and the other using StAX. StAX fits exactly
with the lazy load concept.

I think the lazy load idea is OK and in fact for a spectrum display
I could totally IGNORE the sample section altogether and never read
anything in there, if all I want is an XY plot.

It is only when I want to associate sample info with spectrum info that
I run into difficulty unless I store all sample info and then
read spectrum info and try to work backwards to do the association having
eventually found out which is the sample.

bear with me while I get this sorted out...
Thanks
Robert



on 09/05/2006 04:04 AM Mar...@wa... said the following:
> Hi Robert,
>=20
> catching up on my email...
>=20
>> I think this is inefficient and whilst there may be benefits to having
>> sample separate to measurement I believe it would be easy enough to
>> add an attribute at the sample stage to declare which of the
>> samplesets was the actual sample and which was the blank etc.
>> The sampleID seems at present to be anything you want to call it
>> so if that is to stay the same then a new attribute is needed.
>> It could be a simple Boolean (isSample or isReference) and would
>> only be required if the sample was part of the measurement.
> The samples defined in AnIML can be re-used and may change roles, so yo=
u=20

> cannot flag them in the sample definition as you suggest.
> You are trying to stream in the AnIML file and keep it in memory=20
> altogether. The idea when designing the format was that you should use=20
> something called "lazy load", meaning that you would only read what you=
=20
> need at a given time. This is an entirely different paradigm.
>=20
> Mit freundlichen Gr=FC=DFen / Best regards
>=20
> Maren.=20
>=20
>=20
> Dr. Maren Fiege
> Senior Product Manager
>=20
> Waters GmbH
> Europaallee 27, D-50226 Frechen, Germany
> Tel.+49 2234 9207 - 0  Fax +49 2234 9207-99
>=20
> http://www.waters.com/informatics=20
>=20
>=20
>=20


--=20
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






--=20
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

[Animl-develop] [Fwd: SUBJECT: SourceForge.net: CVS service offering changes]

[Burkhard S. <b_...@us...>]

Hi folks,

just passing this message along. This is of interest to everybody who 
uses the SourceForge CVS system.

Best regards,
Burkhard

Re: [Animl-develop] Indication of error of measurements

[<Mar...@wa...>]

Hi Robert,

> I wonder if I am missing something (still/again) since I see all sorts=20
of
> element tags for MP, BP refractive index etc which are represented as
> a single value. There is nothing to indicate to me that invariably what
> is quoted is a range, rather than a single figure or some idea of what
> the error range is. For an Analytical document it would seem appropriate
> to have this information, e.g M.P 122-123.5 or=20
This question also came up at the ACS meeting. ThermoML has provisions for =

errors and uncertainties (in fact, about a third of the ThermoML schema=20
deals with this). We had a brief discussion about this in the committee=20
and judged that at least for the spectroscopic data we do not want to open =

that can of worms (and besides, it is often hard to tell the precision of=20
an instrument anyway).
For parameters, the situations might be different. What do the others=20
think?

> magnetic moment 3.83 +/- 0.15 Bohr Magneton (not yet listed as a=20
possible data type).
Where would this go? NNMR?

Mit freundlichen Gr=FC=DFen / Best regards

Maren.=20


Dr. Maren Fiege
Senior Product Manager
=20
Waters GmbH
Europaallee 27, D-50226 Frechen, Germany
Tel.+49 2234 9207 - 0  Fax +49 2234 9207-99

http://www.waters.com/informatics=20

Re: [Animl-develop] Update to JCAMP Converter

[<Mar...@wa...>]

Hi Robert,

> Information for IR that should be required is whether the spectrum=20
> was recorded as gas phase, KBr disc/k, parafin/nujol mull, solution, etc =

including the
> techniques mentioned by Peter below. If ATR, IRRAS, then there may well
> be other parameters that should be recorded and set as required as well.
I added this as a to do in the bug tracker.

> In JCAMP-DX there is a distinction made between TEXT and STRING
> values.
> TEXT essentially says it can be anything
> STRING represents pre-defined key words
We depict this in the technique definitions using enumerations. The=20
principle is the same.

Mit freundlichen Gr=FC=DFen / Best regards

Maren.=20


Dr. Maren Fiege
Senior Product Manager
=20
Waters GmbH
Europaallee 27, D-50226 Frechen, Germany
Tel.+49 2234 9207 - 0  Fax +49 2234 9207-99

http://www.waters.com/informatics=20

Re: [Animl-develop] Update to JCAMP Converter

[Burkhard S. <bur...@bu...>]

Hi,

it's true, in XML you need to escape the < and > characters so that the 
parser won't confuse them with element boundaries.

In Java, you can use two calls to the String.replaceAll method to do 
this. See here:

http://java.sun.com/j2se/1.4.2/docs/api/java/lang/String.html#replaceAll(java.lang.String,%20java.lang.String)

Best regards,
Burkhard

Mar...@wa... wrote:
> Hi Robert,
> 
> sorry for the delay in replying. I've been on the road too much...
> "V6" is a special flavor of JCAMP that doesn't always follow the original 
> specs, so I guess it needs some special treatment.
> Maybe Brkhard has an idea for a less clumsy way to treat the <>s?
> 
> Mit freundlichen Grüßen / Best regards
> 
> Maren. 
> 
> 
> Dr. Maren Fiege
> Senior Product Manager
>  
> Waters GmbH
> Europaallee 27, D-50226 Frechen, Germany
> Tel.+49 2234 9207 - 0  Fax +49 2234 9207-99
> 
> http://www.waters.com/informatics 
> 
> 
> 
> "Prof. Robert John Lancashire" <rob...@uw...> wrote on 
> 11.04.2006 15:58:18:
> 
>> Maren
>>
>> it is true that you can add a $$ and a comment at the end of a header 
> value
>> but also true that you can put in a $$ at the start of a line with a 
> comment.
>> In the first case it is perhaps easy enough to identify what the comment
>> referred to but not so in the second case.
>>
>> In fact the IR protocol had suggested that after the ##JCAMP-DX=
>> label that a comment was inserted that gave the software and
>> version that created the file. This is not always done.
>>
>> I note that in the Bruker "vs 6" NMR files that they have things like
>> ##TITLE=
>> ##JCAMP-DX=
>> ##DATA TYPE=
>>
>>
>> and further down may have
>> $$ ##TITLE=
>> $$ ##JCAMP-DX=
>> $$ ##DATA TYPE=
>>
>>
>> which is something I was not expecting!
>>
>> To try to read every JCAMP comment line and convert < and >
>> to XML/HTML &lt; and &gt; is a possibility but clumsy!?
>>
>> Robert
>>
>>
>>
>> on 11/04/2006 09:31 AM Mar...@wa... said the following:
>>> Hi, 
>>>
>>>> Yes. There's no explicit relation between an XML comment and the 
>>>> associated element. The same problem exists in JCAMP. It's hard to 
>>>> determine which data item a JCAMP comment belongs to.
>>> Is that so? I thought you could put a JCAMP comment into a line that 
>>> already has a JCAMP label in it. Robert?
>>>
>>> Mit freundlichen Grüßen / Best regards
>>>
>>> Maren. 
>>>
>>>
>>> Dr. Maren Fiege
>>> Product Manager
>>>
>>> Waters GmbH
>>> Europaallee 27, D-50226 Frechen, Germany
>>> Tel.+49 2234 9207 - 0 Fax. +49 2234 9207-99
>>>
>>> http://www.waters.com/informatics 
>>>
>>>
>>>
>>>
>>
>> -- 
>> 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
>>
> 
> 

[Animl-develop] Indication of error of measurements

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

Hi all,

I wonder if I am missing something (still/again) since I see all sorts of
element tags for MP, BP refractive index etc which are represented as
a single value. There is nothing to indicate to me that invariably what
is quoted is a range, rather than a single figure or some idea of what
the error range is. For an Analytical document it would seem appropriate
to have this information, e.g M.P 122-123.5 or magnetic moment
3.83 +/- 0.15 Bohr Magneton (not yet listed as a possible data type).

regards
Robert

-- 
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

Re: [Animl-develop] Update to JCAMP Converter

[<Mar...@wa...>]

Hi Robert,

sorry for the delay in replying. I've been on the road too much...
"V6" is a special flavor of JCAMP that doesn't always follow the original=20
specs, so I guess it needs some special treatment.
Maybe Brkhard has an idea for a less clumsy way to treat the <>s?

Mit freundlichen Gr=FC=DFen / Best regards

Maren.=20


Dr. Maren Fiege
Senior Product Manager
=20
Waters GmbH
Europaallee 27, D-50226 Frechen, Germany
Tel.+49 2234 9207 - 0  Fax +49 2234 9207-99

http://www.waters.com/informatics=20



"Prof. Robert John Lancashire" <rob...@uw...> wrote on =

11.04.2006 15:58:18:

> Maren
>=20
> it is true that you can add a $$ and a comment at the end of a header=20
value
> but also true that you can put in a $$ at the start of a line with a=20
comment.
>=20
> In the first case it is perhaps easy enough to identify what the comment
> referred to but not so in the second case.
>=20
> In fact the IR protocol had suggested that after the ##JCAMP-DX=3D
> label that a comment was inserted that gave the software and
> version that created the file. This is not always done.
>=20
> I note that in the Bruker "vs 6" NMR files that they have things like
> ##TITLE=3D
> ##JCAMP-DX=3D
> ##DATA TYPE=3D
>=20
>=20
> and further down may have
> $$ ##TITLE=3D
> $$ ##JCAMP-DX=3D
> $$ ##DATA TYPE=3D
>=20
>=20
> which is something I was not expecting!
>=20
> To try to read every JCAMP comment line and convert < and >
> to XML/HTML &lt; and &gt; is a possibility but clumsy!?
>=20
> Robert
>=20
>=20
>=20
> on 11/04/2006 09:31 AM Maren=5F...@wa... said the following:
> > Hi,=20
> >=20
> >> Yes. There's no explicit relation between an XML comment and the=20
> >> associated element. The same problem exists in JCAMP. It's hard to=20
> >> determine which data item a JCAMP comment belongs to.
> > Is that so? I thought you could put a JCAMP comment into a line that=20
> > already has a JCAMP label in it. Robert?
> >=20
> > Mit freundlichen Gr=FC=DFen / Best regards
> >=20
> > Maren.=20
> >=20
> >=20
> > Dr. Maren Fiege
> > Product Manager
> >=20
> > Waters GmbH
> > Europaallee 27, D-50226 Frechen, Germany
> > Tel.+49 2234 9207 - 0 Fax. +49 2234 9207-99
> >=20
> > http://www.waters.com/informatics=20
> >=20
> >=20
> >=20
> >=20
>=20
>=20
> --=20
> 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
>=20