cansas1d casestudy collagen - Revision history

Jemian at 03:38, 23 March 2008

2008-03-23T03:38:46Z

← Older revision		Revision as of 03:38, 23 March 2008
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	Now close the macro editing window and return to the SAXS data in the spreadsheet.		Now close the macro editing window and return to the SAXS data in the spreadsheet.

	~~=== Estimation of Qdev ===~~

	~~Part of the standard requires an estimate of '''Qdev'''~~
	~~(from the [[cansas1d_definition_of_terms\|documentation]],~~
	''Estimated standard deviation of Q. Must specify the unit as an attribute.'') and that was not provided in the data. Best we can do is to estimate it by subtracting adjacent Q values. On inspection, these are all about 0.00055(6) 1/A so we'll pick the value Qdev = 0.00055 1/A.

	~~Q unit is '''1/A'''. We don't know what the intensities are so use '''a.u.''' (arbitrary unit)~~

	=== construct the Idata lines in XML ===		=== construct the Idata lines in XML ===

	move to spreadsheet cell '''E5''' and enter this formula		move to spreadsheet cell '''E5''' and enter this formula
	<pre>=IDATA_tag(A5,$A$4,B5,$B~~$4,0.00055,$A~~$4,C5,$C$4)</pre>		<pre>=IDATA_tag(A5,$A$4,B5,$B$4,C5,$C$4)</pre>

	Copy it down through cell '''E335'''		Copy it down through cell '''E335'''

Jemian: /* Excel macros used */

2008-03-23T03:37:52Z

Excel macros used

← Older revision		Revision as of 03:37, 23 March 2008
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	End Function		End Function

	Function Idata_tag(Q, Q_unit, I, I_unit~~, Qdev, Qdev_unit~~, Idev, Idev_unit) As String		Function Idata_tag(Q, Q_unit, I, I_unit, Idev, Idev_unit) As String
	XML = SAS_Idata_tag("Q", Q_unit, Q)		XML = SAS_Idata_tag("Q", Q_unit, Q)
	XML = XML & SAS_Idata_tag("I", I_unit, I)		XML = XML & SAS_Idata_tag("I", I_unit, I)
	~~XML = XML & SAS_Idata_tag("Qdev", Qdev_unit, Qdev)~~
	XML = XML & SAS_Idata_tag("Idev", Idev_unit, Idev)		XML = XML & SAS_Idata_tag("Idev", Idev_unit, Idev)
	Idata_tag = XML_tag("Idata", "", XML)		Idata_tag = XML_tag("Idata", "", XML)

Jemian: point to TRAC

2008-03-22T18:32:21Z

point to TRAC

← Older revision		Revision as of 18:32, 22 March 2008
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	The only metadata available for this data (without resorting to digging through piles of old notebooks) was obtained from two file headers:		The only metadata available for this data (without resorting to digging through piles of old notebooks) was obtained from two file headers:

	[~~[Media~~:COLLAGEN.ASC~~.txt\|~~ collagen.asc ]]		[http://svn.smallangles.net/trac/canSAS/browser/1dwg/trunk/examples/collagen/COLLAGEN.ASC collagen.asc]
	<pre>		<pre>
	Sep 19 1994 01:41:02 am Elt: 00090 Seconds		Sep 19 1994 01:41:02 am Elt: 00090 Seconds
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	</pre>		</pre>

	[~~[Media~~:~~Cs-Collagen~~.saxs~~.txt\|~~ collagen.saxs ]]		[http://svn.smallangles.net/trac/canSAS/browser/1dwg/trunk/examples/collagen/collagen.saxs collagen.saxs]
	<pre>		<pre>
	dry chick collagen, d = 673 A		dry chick collagen, d = 673 A
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	It is easiest to copy a template rather than start from an empty file.		It is easiest to copy a template rather than start from an empty file.
	Copy the [[cansas1d.xml]] file into your working directory and rename it to '''collagen.xml'''.		Copy the [http://svn.smallangles.net/svn/canSAS/1dwg/trunk/cansas1d.xml cansas1d.xml] file into your working directory and rename it to '''collagen.xml'''.

	==modify collagen.xml==		==modify collagen.xml==
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	=== Excel macros used ===		=== Excel macros used ===

	Within Excel, with the SAXS data in columns as shown above ([[Media:Cs-collagen-data-table-Excel.jpg]]), let's define the macros for our use. ~~Type~~ '''<alt><F11>''' to open the macro editing window.		Within Excel, with the SAXS data in columns as shown above ([[Media:Cs-collagen-data-table-Excel.jpg]]), let's define the macros for our use. In Excel, type '''<alt><F11>''' to open the macro editing window.

	<pre>		<pre>
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	So you think you have an XML file. Let's validate it using the procedure from the [[cansas1d_documentation#Validation_of_XML_against_the_Schema\|documentation]].		So you think you have an XML file. Let's validate it using the procedure from the [[cansas1d_documentation#Validation_of_XML_against_the_Schema\|documentation]].
	All the instructions are on the documentation page. No sense in repeating them here.		All the instructions are on the documentation page. No sense in repeating them here.

			= References =

			All files are available at [http://svn.smallangles.net/trac/canSAS/browser/1dwg/trunk/examples/collagen/ http://svn.smallangles.net/trac/canSAS/browser/1dwg/trunk/examples/collagen/]

Jemian: point to subversion

2008-03-22T18:20:19Z

point to subversion

Show changes

Jemian: /* Final Result */

2008-02-25T18:51:40Z

Final Result

← Older revision		Revision as of 18:51, 25 February 2008
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	xmlns="http://www.smallangles.net/cansas1d"		xmlns="http://www.smallangles.net/cansas1d"
	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"		xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
	xsi:schemaLocation="http://www.smallangles.net/cansas1d/ http://www.smallangles.net/cansas1d/1.0/cansas1d.xsd"		xsi:schemaLocation="
			http://www.smallangles.net/cansas1d/
			http://www.smallangles.net/cansas1d/1.0/cansas1d.xsd
			"
	>		>
	<SASentry>		<SASentry>

Jemian: /* Estimation of Qdev */

2008-02-25T18:50:48Z

Estimation of Qdev

← Older revision		Revision as of 18:50, 25 February 2008
Line 135:		Line 135:
	''Estimated standard deviation of Q. Must specify the unit as an attribute.'') and that was not provided in the data. Best we can do is to estimate it by subtracting adjacent Q values. On inspection, these are all about 0.00055(6) 1/A so we'll pick the value Qdev = 0.00055 1/A.		''Estimated standard deviation of Q. Must specify the unit as an attribute.'') and that was not provided in the data. Best we can do is to estimate it by subtracting adjacent Q values. On inspection, these are all about 0.00055(6) 1/A so we'll pick the value Qdev = 0.00055 1/A.

	Q unit is '''1/A''. We don't know what the intensities are so use '''a.u.''' (arbitrary unit)		Q unit is '''1/A'''. We don't know what the intensities are so use '''a.u.''' (arbitrary unit)

	=== construct the Idata lines in XML ===		=== construct the Idata lines in XML ===

Jemian: /* Estimation of Qdev */

2008-02-25T18:50:28Z

Estimation of Qdev

← Older revision		Revision as of 18:50, 25 February 2008
Line 135:		Line 135:
	''Estimated standard deviation of Q. Must specify the unit as an attribute.'') and that was not provided in the data. Best we can do is to estimate it by subtracting adjacent Q values. On inspection, these are all about 0.00055(6) 1/A so we'll pick the value Qdev = 0.00055 1/A.		''Estimated standard deviation of Q. Must specify the unit as an attribute.'') and that was not provided in the data. Best we can do is to estimate it by subtracting adjacent Q values. On inspection, these are all about 0.00055(6) 1/A so we'll pick the value Qdev = 0.00055 1/A.

			Q unit is '''1/A''. We don't know what the intensities are so use '''a.u.''' (arbitrary unit)

	=== construct the Idata lines in XML ===		=== construct the Idata lines in XML ===

Jemian: /* Excel macros used */

2008-02-25T18:48:17Z

Excel macros used

← Older revision		Revision as of 18:48, 25 February 2008
Line 95:		Line 95:
	=== Excel macros used ===		=== Excel macros used ===

	Within Excel, with the SAXS data in columns, let's define the macros for our use. Type '''<alt><F11>'' to open the macro editing window.		Within Excel, with the SAXS data in columns as shown above ([[Media:Cs-collagen-data-table-Excel.jpg]]), let's define the macros for our use. Type '''<alt><F11>''' to open the macro editing window.

	<pre>		<pre>

	Function XML_tag(tag, attr, content) As String		Function XML_tag(tag, attr, content) As String
	If attr = "" Then		If attr = "" Then

Jemian: /* Overview */

2008-02-25T18:45:29Z

Overview

← Older revision		Revision as of 18:45, 25 February 2008
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	To demonstrate how to get SAS data into the XML standard format, consider this set of SAXS data collected at the National Synchrotron Light Source, Brookhaven National Laboratory, using a SAXS camera set up temporarily at beam line X6B (operated by the Materials Science Division, Argonne National Lab).		To demonstrate how to get SAS data into the XML standard format, consider this set of SAXS data collected at the National Synchrotron Light Source, Brookhaven National Laboratory, using a SAXS camera set up temporarily at beam line X6B (operated by the Materials Science Division, Argonne National Lab).

	The sample was '''dry chick collagen.'''		The sample was '''dry chick collagen.''' (Thanks to Malcolm Capel, NSLS beam line X12C for the sample.)

	The raw data was collected on a linear position-sensitive detector and reduced to columns of '''Q''', '''I''', and '''Iesd''' (estimated standard deviation of '''I''').		The raw data was collected on a linear position-sensitive detector and reduced to columns of '''Q''', '''I''', and '''Iesd''' (estimated standard deviation of '''I''').

Jemian: /* Overview */

2008-02-25T18:39:58Z

Overview

← Older revision		Revision as of 18:39, 25 February 2008
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	</pre>		</pre>

	But, ~~that will~~ fulfill the minimum requirements of the 1D standard file format		But, the data can fulfill the minimum requirements of the 1D standard file format
	and make an excellent example of a minimal		and also make an excellent example of a minimal
	[[cansas1d_documentation\|canSAS reduced 1-D SAS data file in XML]].		[[cansas1d_documentation\|canSAS reduced 1-D SAS data file in XML]].