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sr #3043: Support for NMRPipe seriesTab format *.ser

Submitted by:  Troels E. Linnet <tlinnet>
Submitted on:  Tue 18 Jun 2013 11:16:58 AM UTC  
 
Category: NonePriority: 5 - Normal
Severity: 4 - ImportantStatus: Done
Assigned to: Troels E. Linnet <tlinnet>Open/Closed: Closed
Operating System: None

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Sat 03 Aug 2013 11:26:57 AM UTC, SVN revision 20523:

Merged revisions 20501-20522 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r20501 | bugman | 2013-08-02 13:39:53 +0200 (Fri, 02 Aug 2013) | 7 lines

Removed the flag for single_spectrum.

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

Troels E. Linnet provided this patch. Commit by: tlinnet aaattt gmail_dot_com

Signed-off-by: Edward d'Auvergne att nmr-relax dott com>
........
r20502 | bugman | 2013-08-02 13:40:28 +0200 (Fri, 02 Aug 2013) | 7 lines

Fixed wrong reference to Sparky format.

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

Troels E. Linnet provided this patch. Commit by: tlinset aaattt gmail_dot_com

Signed-off-by: Edward d'Auvergne att nmr-relax dott com>
........
r20503 | bugman | 2013-08-02 13:51:50 +0200 (Fri, 02 Aug 2013) | 7 lines

Modfied the intensity list to handle intensities for all spectra per spin.

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

Troels E. Linnet provided this patch. Commit by: tlinset aaattt gmail_dot_com

Signed-off-by: Edward d'Auvergne att nmr-relax dott com>
........
r20504 | bugman | 2013-08-02 13:52:16 +0200 (Fri, 02 Aug 2013) | 7 lines

Fixed the extraction of NMRPipe seriestab data in pipe_control.spectrum.read().

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

Troels E. Linnet provided this patch. Commit by: tlinset aaattt gmail_dot_com

Signed-off-by: Edward d'Auvergne att nmr-relax dott com>
........
r20505 | bugman | 2013-08-02 13:53:52 +0200 (Fri, 02 Aug 2013) | 7 lines

Fix for handling reading spin of type heteronuc='NE1' and proton='HE1'.

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

Troels E. Linnet provided this patch. Commit by: tlinset aaattt gmail_dot_com

[...]

[...] Signed-off-by: Edward d'Auvergne att nmr-relax dott com>

[...]........

[...] r20506 | bugman | 2013-08-02 14:00:20 +0200 (Fri, 02 Aug 2013) | 9 lines

[...]

[...] Adding NMR seriesTab data file for a multiple column / multiple spectrum formatted file.

[...]

[...] This file is from https://gna.org/support/download.php?file_id=18618 attached to the support request

[...] https://gna.org/support/?3043 by Troels Linnet.

[...]

[...] This is if the command:

[...] seriesTab -in ../../peaks.dat -out seriesTab_multi.ser -list nmrfiles.list -sum -dx 1 -dy 1

[...]

[...] where nmrfiles.list contains file reference to 10 .ft2 files.

[...]........

[...] r20507 | bugman | 2013-08-02 17:35:01 +0200 (Fri, 02 Aug 2013) | 7 lines

[...]

[...] Fix for unit test of nmrpipe.

[...]

[...] Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

[...]

[...] Troels E. Linnet provided this patch. Commit by: tlinset aaattt gmail_dot_com

[...]

[...] Signed-off-by: Edward d'Auvergne att nmr-relax dott com>

[...]........

[...] r20508 | bugman | 2013-08-02 17:35:57 +0200 (Fri, 02 Aug 2013) | 7 lines

[...]

[...] Replacing a pointer-reference structure to an empty creation of list of lists.

[...]

[...] Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

[...]

[...] Troels E. Linnet provided this patch. Commit by: tlinset aaattt gmail_dot_com

[...]

[...] Signed-off-by: Edward d'Auvergne att nmr-relax dott com>

[...]........

[...] r20509 | bugman | 2013-08-02 17:55:23 +0200 (Fri, 02 Aug 2013) | 7 lines

[...]

[...] The ID of spins in seriesTab_multi.ser was not formatted correctly to SPARKY format.

[...]

[...] Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

[...]

[...] Troels E. Linnet provided this patch. Commit by: tlinset aaattt gmail_dot_com

[...]

[...] Signed-off-by: Edward d'Auvergne att nmr-relax dott com>

[...]........

[...] r20510 | bugman | 2013-08-02 20:56:54 +0200 (Fri, 02 Aug 2013) | 14 lines

[...]

[...] Added system test for reading of a multi column formatted NMRPipe seriesTab file.

[...]

[...] Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

[...]

[...] Generated the reference data in Excell, for the system test.

[...] The spectrum ID's are auto generated by supplying the keyword spectrum_id='auto'.

[...] The first few tests was matched against integers rather than floats. Adding '.0' to the end of each number.

[...]

[...] Spaces added after the commas in the self.assertAlmostEqual() calls.

[...] The 2to3 conversion program (for Python 2 to Python 3 conversion) highlights this issue.

[...]

[...] Troels E. Linnet provided this patch. Commit by: tlinset aaattt gmail_dot_com

[...]

[...] Signed-off-by: Edward d'Auvergne

[...]........

[...] r20511 | bugman | 2013-08-02 20:58:55 +0200 (Fri, 02 Aug 2013) | 7 lines

[...]

[...] Added check for number of supplied spectra ID's and the number of returned intensity columns.

[...]

[...] Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

[...]

[...] Troels E. Linnet provided this patch. Commit by: tlinset aaattt gmail_dot_com

[...]

[...] Signed-off-by: Edward d'Auvergne

[...]........

[...] r20512 | bugman | 2013-08-02 20:58:57 +0200 (Fri, 02 Aug 2013) | 7 lines

[...]

[...] Made it possible to autogenerate spectrum ID's, if spectrum_id='auto'.

[...]

[...] Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

[...]

[...] Troels E. Linnet provided this patch. Commit by: tlinset aaattt gmail_dot_com

[...]

[...] Signed-off-by: Edward d'Auvergne

[...]........

[...] r20513 | bugman | 2013-08-02 20:58:59 +0200 (Fri, 02 Aug 2013) | 7 lines

[...]

[...] Remove from datalist where empty list starts. These are created where spins are skipped for ID = '?-?'.

[...]

[...] Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

[...]

[...] Troels E. Linnet provided this patch. Commit by: tlinset aaattt gmail_dot_com

[...]

[...] Signed-off-by: Edward d'Auvergne

[...]........

[...] r20514 | bugman | 2013-08-02 20:59:00 +0200 (Fri, 02 Aug 2013) | 7 lines

[...]

[...] Moved checks for matching length of spectrum IDs and intensities columns.

[...]

[...] Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

[...]

[...] Troels E. Linnet provided this patch. Commit by: tlinset aaattt gmail_dot_com

[...]

[...] Signed-off-by: Edward d'Auvergne

[...]........

[...] r20515 | bugman | 2013-08-02 20:59:02 +0200 (Fri, 02 Aug 2013) | 8 lines

[...]

[...] Moved the adding function of adding the spectrum id (and ncproc) to the relax data store.

[...]

[...] Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

[...]

[...] Shifting it to later will prevent the cdp.spectrum_ids list to be populated after the user calls the user function incorrectly.

[...] Troels E. Linnet provided this patch. Commit by: tlinnet aaattt gmail_dot_com

[...]

[...] Signed-off-by: Edward d'Auvergne

[...]........

[...] r20516 | bugman | 2013-08-02 21:29:16 +0200 (Fri, 02 Aug 2013) | 3 lines

[...]

[...] Fix for the spectrum.read_intensities user function in the GUI.

[...]

[...] The menu string was truncated to spectrum.read.

[...]........

[...] r20517 | bugman | 2013-08-02 22:07:49 +0200 (Fri, 02 Aug 2013) | 7 lines

[...]

[...] Added epydoc documentation in pipe_control\spectrum.py .read() when supplying keyword 'auto'.

[...]

[...] Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

[...]

[...] Troels E. Linnet provided this patch. Commit by: tlinnet aaattt gmail_dot_com

[...]

[...] Signed-off-by: Edward d'Auvergne

[...]........

[...] r20518 | bugman | 2013-08-02 22:07:51 +0200 (Fri, 02 Aug 2013) | 7 lines

[...]

[...] Added GUI description for when supplying 'auto' to the spectrum_id.

[...]

[...] Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

[...]

[...] Troels E. Linnet provided this patch. Commit by: tlinnet aaattt gmail_dot_com

[...]

[...] Signed-off-by: Edward d'Auvergne

[...]........

[...] r20519 | bugman | 2013-08-02 22:07:52 +0200 (Fri, 02 Aug 2013) | 7 lines

[...]

[...] Added a stub GUI describtion in the File formats, for NMRPipe seriesTab.

[...]

[...] Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

[...]

[...] Troels E. Linnet provided this patch. Commit by: tlinnet aaattt gmail_dot_com

[...]

[...] Signed-off-by: Edward d'Auvergne

[...]........

[...] r20520 | bugman | 2013-08-03 00:08:24 +0200 (Sat, 03 Aug 2013) | 8 lines

[...]

[...] Fix for two spaces are used after a period in documentation.

[...]

[...] Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

[...]

[...] relax uses the double space for easier for the eyes to pick up the sentence structure.

[...] Troels E. Linnet provided this patch. Commit by: tlinnet aaattt gmail_dot_com

[...]

[...] Signed-off-by: Edward d'Auvergne

[...]........

[...] r20521 | bugman | 2013-08-03 00:08:26 +0200 (Sat, 03 Aug 2013) | 8 lines

[...]

[...] Fix for two spaces are used after a period in documentation.

[...]

[...] Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

[...]

[...] relax uses the double space for easier for the eyes to pick up the sentence structure.

[...] Troels E. Linnet provided this patch. Commit by: tlinnet aaattt gmail_dot_com

[...]

[...] Signed-off-by: Edward d'Auvergne

[...]........

[...] r20522 | bugman | 2013-08-03 00:08:28 +0200 (Sat, 03 Aug 2013) | 8 lines

[...]

[...] Fix for two spaces are used after a period in documentation.

[...]

[...] Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

[...]

[...] relax uses the double space for easier for the eyes to pick up the sentence structure.

[...] Troels E. Linnet provided this patch. Commit by: tlinnet aaattt gmail_dot_com

[...]

[...] Signed-off-by: Edward d'Auvergne

[...]........

[...]

[...]

(Browse SVN revision 20523)

Edward d Auvergne <bugman>
Project Administrator
Sat 03 Aug 2013 07:22:02 AM UTC, comment #74:

The support for the NMRPipe seriesTab peak intensity file format is now complete and fully tested in the test suite. Closing the request.

Edward d Auvergne <bugman>
Project Administrator
Sat 03 Aug 2013 06:53:07 AM UTC, comment #73:

Should this be closed now, or wait until assurance that no bugs is introduced?

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 02 Aug 2013 10:08:28 PM UTC, SVN revision 20522:

Fix for two spaces are used after a period in documentation.

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

relax uses the double space for easier for the eyes to pick up the sentence structure.
Troels E. Linnet provided this patch. Commit by: tlinnet aaattt gmail_dot_com

Signed-off-by: Edward d'Auvergne

(Browse SVN revision 20522)

Edward d Auvergne <bugman>
Project Administrator
Fri 02 Aug 2013 10:08:26 PM UTC, SVN revision 20521:

Fix for two spaces are used after a period in documentation.

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

relax uses the double space for easier for the eyes to pick up the sentence structure.
Troels E. Linnet provided this patch. Commit by: tlinnet aaattt gmail_dot_com

Signed-off-by: Edward d'Auvergne

(Browse SVN revision 20521)

Edward d Auvergne <bugman>
Project Administrator
Fri 02 Aug 2013 10:08:24 PM UTC, SVN revision 20520:

Fix for two spaces are used after a period in documentation.

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

relax uses the double space for easier for the eyes to pick up the sentence structure.
Troels E. Linnet provided this patch. Commit by: tlinnet aaattt gmail_dot_com

Signed-off-by: Edward d'Auvergne

(Browse SVN revision 20520)

Edward d Auvergne <bugman>
Project Administrator
Fri 02 Aug 2013 09:55:07 PM UTC, comment #69:

Fix for two spaces are used after a period in documentation.

(file #18627)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 02 Aug 2013 08:07:52 PM UTC, SVN revision 20519:

Added a stub GUI describtion in the File formats, for NMRPipe seriesTab.

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

Troels E. Linnet provided this patch. Commit by: tlinnet aaattt gmail_dot_com

Signed-off-by: Edward d'Auvergne

(Browse SVN revision 20519)

Edward d Auvergne <bugman>
Project Administrator
Fri 02 Aug 2013 08:07:51 PM UTC, SVN revision 20518:

Added GUI description for when supplying 'auto' to the spectrum_id.

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

Troels E. Linnet provided this patch. Commit by: tlinnet aaattt gmail_dot_com

Signed-off-by: Edward d'Auvergne

(Browse SVN revision 20518)

Edward d Auvergne <bugman>
Project Administrator
Fri 02 Aug 2013 08:07:50 PM UTC, SVN revision 20517:

Added epydoc documentation in pipe_control\spectrum.py .read() when supplying keyword 'auto'.

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

Troels E. Linnet provided this patch. Commit by: tlinnet aaattt gmail_dot_com

Signed-off-by: Edward d'Auvergne

(Browse SVN revision 20517)

Edward d Auvergne <bugman>
Project Administrator
Fri 02 Aug 2013 07:49:58 PM UTC, comment #65:

Added documentation.

(file #18626)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 02 Aug 2013 06:59:11 PM UTC, comment #64:

Added the excell file, from which the test suite was formatted.

(file #18625)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 02 Aug 2013 06:59:02 PM UTC, SVN revision 20515:

Moved the adding function of adding the spectrum id (and ncproc) to the relax data store.

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

Shifting it to later will prevent the cdp.spectrum_ids list to be populated after the user calls the user function incorrectly.
Troels E. Linnet provided this patch. Commit by: tlinnet aaattt gmail_dot_com

Signed-off-by: Edward d'Auvergne

(Browse SVN revision 20515)

Edward d Auvergne <bugman>
Project Administrator
Fri 02 Aug 2013 06:59:00 PM UTC, SVN revision 20514:

Moved checks for matching length of spectrum IDs and intensities columns.

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

Troels E. Linnet provided this patch. Commit by: tlinset aaattt gmail_dot_com

Signed-off-by: Edward d'Auvergne

(Browse SVN revision 20514)

Edward d Auvergne <bugman>
Project Administrator
Fri 02 Aug 2013 06:58:59 PM UTC, SVN revision 20513:

Remove from datalist where empty list starts. These are created where spins are skipped for ID = '?-?'.

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

Troels E. Linnet provided this patch. Commit by: tlinset aaattt gmail_dot_com

Signed-off-by: Edward d'Auvergne

(Browse SVN revision 20513)

Edward d Auvergne <bugman>
Project Administrator
Fri 02 Aug 2013 06:58:57 PM UTC, SVN revision 20512:

Made it possible to autogenerate spectrum ID's, if spectrum_id='auto'.

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

Troels E. Linnet provided this patch. Commit by: tlinset aaattt gmail_dot_com

Signed-off-by: Edward d'Auvergne

(Browse SVN revision 20512)

Edward d Auvergne <bugman>
Project Administrator
Fri 02 Aug 2013 06:58:56 PM UTC, SVN revision 20511:

Added check for number of supplied spectra ID's and the number of returned intensity columns.

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

Troels E. Linnet provided this patch. Commit by: tlinset aaattt gmail_dot_com

Signed-off-by: Edward d'Auvergne

(Browse SVN revision 20511)

Edward d Auvergne <bugman>
Project Administrator
Fri 02 Aug 2013 06:56:56 PM UTC, SVN revision 20510:

Added system test for reading of a multi column formatted NMRPipe seriesTab file.

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

Generated the reference data in Excell, for the system test.
The spectrum ID's are auto generated by supplying the keyword spectrum_id='auto'.
The first few tests was matched against integers rather than floats. Adding '.0' to the end of each number.

Spaces added after the commas in the self.assertAlmostEqual() calls.
The 2to3 conversion program (for Python 2 to Python 3 conversion) highlights this issue.

Troels E. Linnet provided this patch. Commit by: tlinset aaattt gmail_dot_com

Signed-off-by: Edward d'Auvergne

(Browse SVN revision 20510)

Edward d Auvergne <bugman>
Project Administrator
Fri 02 Aug 2013 06:48:54 PM UTC, comment #57:

Made changes according to suggestions.

(file #18624)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 02 Aug 2013 03:55:23 PM UTC, SVN revision 20509:

The ID of spins in seriesTab_multi.ser was not formatted correctly to SPARKY format.

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

Troels E. Linnet provided this patch. Commit by: tlinset aaattt gmail_dot_com

Signed-off-by: Edward d'Auvergne att nmr-relax dott com>

(Browse SVN revision 20509)

Edward d Auvergne <bugman>
Project Administrator
Fri 02 Aug 2013 03:35:57 PM UTC, SVN revision 20508:

Replacing a pointer-reference structure to an empty creation of list of lists.

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

Troels E. Linnet provided this patch. Commit by: tlinset aaattt gmail_dot_com

Signed-off-by: Edward d'Auvergne att nmr-relax dott com>

(Browse SVN revision 20508)

Edward d Auvergne <bugman>
Project Administrator
Fri 02 Aug 2013 03:35:02 PM UTC, SVN revision 20507:

Fix for unit test of nmrpipe.

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

Troels E. Linnet provided this patch. Commit by: tlinset aaattt gmail_dot_com

Signed-off-by: Edward d'Auvergne att nmr-relax dott com>

(Browse SVN revision 20507)

Edward d Auvergne <bugman>
Project Administrator
Fri 02 Aug 2013 03:29:17 PM UTC, comment #53:

Multi colums import now supported.

Note, I made it possible to autogenerate spectrum ID's, if
spectrum_id='auto' for the function:

spectrum.read_intensities(file="seriesTab_multi.ser", dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'peak_lists', spectrum_id='auto', int_method='point sum')

(file #18619)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 02 Aug 2013 11:53:52 AM UTC, SVN revision 20505:

Fix for handling reading spin of type heteronuc='NE1' and proton='HE1'.

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

Troels E. Linnet provided this patch. Commit by: tlinset aaattt gmail_dot_com

Signed-off-by: Edward d'Auvergne att nmr-relax dott com>

(Browse SVN revision 20505)

Edward d Auvergne <bugman>
Project Administrator
Fri 02 Aug 2013 11:52:16 AM UTC, SVN revision 20504:

Fixed the extraction of NMRPipe seriestab data in pipe_control.spectrum.read().

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

Troels E. Linnet provided this patch. Commit by: tlinset aaattt gmail_dot_com

Signed-off-by: Edward d'Auvergne att nmr-relax dott com>

(Browse SVN revision 20504)

Edward d Auvergne <bugman>
Project Administrator
Fri 02 Aug 2013 11:51:50 AM UTC, SVN revision 20503:

Modfied the intensity list to handle intensities for all spectra per spin.

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

Troels E. Linnet provided this patch. Commit by: tlinset aaattt gmail_dot_com

Signed-off-by: Edward d'Auvergne att nmr-relax dott com>

(Browse SVN revision 20503)

Edward d Auvergne <bugman>
Project Administrator
Fri 02 Aug 2013 11:51:38 AM UTC, comment #49:

Adding NMR seriesTab data file for a multiple column / multiple spectrum formatted file. This is if the command:
seriesTab -in ../../peaks.dat -out seriesTab_multi.ser -list nmrfiles.list -sum -dx 1 -dy 1

where nmrfiles.list contains file reference to 10 .ft2 files.

The file should go into relax_trunk\test_suite\shared_data\peak_lists

(file #18618)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 02 Aug 2013 11:40:29 AM UTC, SVN revision 20502:

Fixed wrong reference to Sparky format.

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

Troels E. Linnet provided this patch. Commit by: tlinset aaattt gmail_dot_com

Signed-off-by: Edward d'Auvergne att nmr-relax dott com>

(Browse SVN revision 20502)

Edward d Auvergne <bugman>
Project Administrator
Fri 02 Aug 2013 11:39:53 AM UTC, SVN revision 20501:

Removed the flag for single_spectrum.

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

Troels E. Linnet provided this patch. Commit by: tlinnet aaattt gmail_dot_com

Signed-off-by: Edward d'Auvergne att nmr-relax dott com>

(Browse SVN revision 20501)

Edward d Auvergne <bugman>
Project Administrator
Fri 02 Aug 2013 11:37:35 AM UTC, comment #46:

Made changes according to suggestions.

(file #18617)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 02 Aug 2013 08:29:33 AM UTC, comment #45:

Patch for development of NMRPipe seriestab format.

Patch should be applied according to: http://wiki.nmr-relax.com/Git_patch

The reading of multiple columns still need testing.
An additional dataset will be provided shortly, and test will be setup.

(file #18616)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Mon 22 Jul 2013 10:01:35 AM UTC, SVN revision 20448:

Merged revisions 20439-20447 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r20439 | bugman | 2013-07-22 08:32:54 +0200 (Mon, 22 Jul 2013) | 6 lines

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

Completed NMRPipe SeriesTab reader for assignment according to SPARKY format. Changes implemented
according to: http://article.gmane.org/gmane.science.nmr.relax.devel/4120.
........
r20440 | bugman | 2013-07-22 08:34:04 +0200 (Mon, 22 Jul 2013) | 5 lines

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

The Extraction of NMRPipe SeriesTab data is changed in pipe_control/spectrum.py in the read() function.
........
r20441 | bugman | 2013-07-22 08:36:56 +0200 (Mon, 22 Jul 2013) | 8 lines

Reverted r20438 and r20439 as the commit messages were incomplete!!!

The command used was:
svn merge -r20440:20438 .

The commit messages need to be complete for the relax release announcements!
........
r20442 | bugman | 2013-07-22 08:37:58 +0200 (Mon, 22 Jul 2013) | 8 lines

Completed NMRPipe SeriesTab reader.

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

Completed NMRPipe SeriesTab reader for assignment according to SPARKY format. Changes implemented
according to: http://article.gmane.org/gmane.science.nmr.relax.devel/4120.
........
r20443 | bugman | 2013-07-22 08:45:50 +0200 (Mon, 22 Jul 2013) | 8 lines

Reverted the pipe_control/spectrum.py to r20438.

The command used was:
svn merge -rHEAD:r20439 pipe_control/spectrum.py

Somehow the file was in a bad state.
........
r20444 | bugman | 2013-07-22 08:47:33 +0200 (Mon, 22 Jul 2013) | 7 lines

Extraction of NMRPipe SeriesTab changed.

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

The Extraction of NMRPipe SeriesTab data is changed in pipe_control/spectrum.py in the read() function.

[...]........

[...] r20445 | bugman | 2013-07-22 08:48:21 +0200 (Mon, 22 Jul 2013) | 5 lines

[...]

[...] Added flag for single or multiple extraction of spectrum.

[...]

[...] Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

[...]........

[...] r20446 | bugman | 2013-07-22 08:49:41 +0200 (Mon, 22 Jul 2013) | 5 lines

[...]

[...] Flag change added to reading of NMRPipe SeriesTab.

[...]

[...] Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

[...]........

[...] r20447 | bugman | 2013-07-22 10:02:30 +0200 (Mon, 22 Jul 2013) | 7 lines

[...]

[...] Proper bug fix for the spin parameter array always being converted to lowercase (failed at r20421).

[...]

[...] The commit r20421 was causing failures in certain cases. One system test and one GUI test were

[...] failing because of r20421. Now the spin container is checked for the presence 'equation' variable

[...] to determine if this is a model free data pipe.

[...]........

[...]

[...]

(Browse SVN revision 20448)

Edward d Auvergne <bugman>
Project Administrator
Mon 22 Jul 2013 06:49:41 AM UTC, SVN revision 20446:

Flag change added to reading of NMRPipe SeriesTab.

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

(Browse SVN revision 20446)

Edward d Auvergne <bugman>
Project Administrator
Mon 22 Jul 2013 06:48:21 AM UTC, SVN revision 20445:

Added flag for single or multiple extraction of spectrum.

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

(Browse SVN revision 20445)

Edward d Auvergne <bugman>
Project Administrator
Mon 22 Jul 2013 06:47:34 AM UTC, SVN revision 20444:

Extraction of NMRPipe SeriesTab changed.

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

The Extraction of NMRPipe SeriesTab data is changed in pipe_control/spectrum.py in the read() function.

(Browse SVN revision 20444)

Edward d Auvergne <bugman>
Project Administrator
Mon 22 Jul 2013 06:37:59 AM UTC, SVN revision 20442:

Completed NMRPipe SeriesTab reader.

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

Completed NMRPipe SeriesTab reader for assignment according to SPARKY format. Changes implemented
according to: http://article.gmane.org/gmane.science.nmr.relax.devel/4120.

(Browse SVN revision 20442)

Edward d Auvergne <bugman>
Project Administrator
Mon 22 Jul 2013 06:34:05 AM UTC, SVN revision 20440:

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

The Extraction of NMRPipe SeriesTab data is changed in pipe_control/spectrum.py in the read() function.

(Browse SVN revision 20440)

Edward d Auvergne <bugman>
Project Administrator
Mon 22 Jul 2013 06:32:55 AM UTC, SVN revision 20439:

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for NMRPipe seriesTab format *.ser.

Completed NMRPipe SeriesTab reader for assignment according to SPARKY format. Changes implemented
according to: http://article.gmane.org/gmane.science.nmr.relax.devel/4120.

(Browse SVN revision 20439)

Edward d Auvergne <bugman>
Project Administrator
Sat 20 Jul 2013 04:39:56 PM UTC, comment #37:

Made corrections

(file #18372, file #18373)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Sat 20 Jul 2013 11:14:35 AM UTC, comment #36:

Made changes the reading of NMRPipe SeriesTab format.

Pathces created according to:
http://wiki.nmr-relax.com/Git_asynchronous_development

Suggestions for how to implement multiple spectrum loading would be appreciated.

(file #18366, file #18367)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Tue 09 Jul 2013 10:08:35 AM UTC, SVN revision 20262:

Merged revisions 20247-20257,20260-20261 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r20247 | bugman | 2013-06-21 17:28:04 +0200 (Fri, 21 Jun 2013) | 8 lines

Adding a test data file in NMRPipe SeriesTab format.

Progress sr #3043: (https://gna.org/support/index.php?3043) - Support for NMRPipe seriesTab format
*.ser.

A file in NMRPipe SeriesTab format is added to the test-suite for further development.
........
r20248 | bugman | 2013-06-21 18:23:24 +0200 (Fri, 21 Jun 2013) | 9 lines

Test function for NMRPipe SeriesTab format implemented.

Progress sr #3043: (https://gna.org/support/index.php?3043) - Support for NMRPipe seriesTab format
*.ser.

An assertEqual test is implemented for the reading of NMRPipe SeriesTab format. The standalone call
is: relax -s Peak_lists.test_read_peak_list_NMRPipe_seriesTab
........
r20249 | bugman | 2013-06-21 18:33:03 +0200 (Fri, 21 Jun 2013) | 9 lines

Adding a NMRPipe function file in the folder lib\software\nmrpipe.py.

Progress sr #3043: (https://gna.org/support/index.php?3043) - Support for NMRPipe seriesTab format
*.ser.

Initial file for: lib\software\nmrpipe.py. This file will hold the function calls handling NMRPipe
SeriesTab format.
........
r20250 | bugman | 2013-06-21 19:46:58 +0200 (Fri, 21 Jun 2013) | 9 lines

Fix for commit (http://article.gmane.org/gmane.science.nmr.relax.scm/18004). The spin naming was wrong.

Progress sr #3043: (https://gna.org/support/index.php?3043) - Support for NMRPipe seriesTab format
*.ser.

The spin naming was wrong. 'spin_id' keywords should be supplied different. Ex:
spin.name(name='NE1', spin_id=':62').
........
r20251 | bugman | 2013-06-21 20:01:06 +0200 (Fri, 21 Jun 2013) | 9 lines

Autodetect format implemented for NMRPipe SeriesTab format implemented.

Progress sr #3043: (https://gna.org/support/index.php?3043) - Support for NMRPipe seriesTab format
*.ser.

The file is determined a NMRPipe SeriesTab if the first two words of the first line is: REMARK

[...] SeriesTab.

[...]........

[...] r20252 | bugman | 2013-06-21 22:26:18 +0200 (Fri, 21 Jun 2013) | 6 lines

[...]

[...] Update of the rotation matrix example in the intro chapter of the user manual.

[...]

[...] The function is now in lib.geometry.rotations.euler_to_R_zyz(). The example has also been converted

[...] to the lstlisting environment for better formatting.

[...]........

[...] r20253 | bugman | 2013-06-21 22:48:44 +0200 (Fri, 21 Jun 2013) | 6 lines

[...]

[...] The relax prompt strings and help system are now keywords for the relax listings package definition.

[...]

[...] The prompt strings "relax>" and "relax|" are now recognised as keywords and are coloured blue. The

[...] help system has been added as a normal Python keyword for highlighting.

[...]........

[...] r20254 | bugman | 2013-06-21 23:40:55 +0200 (Fri, 21 Jun 2013) | 5 lines

[...]

[...] Converted all relax prompt examples in the intro chapter of the manual to the lstlisting environment.

[...]

[...] This is simply for a more colourful representation.

[...]........

[...] r20255 | bugman | 2013-06-22 00:45:10 +0200 (Sat, 22 Jun 2013) | 6 lines

[...]

[...] The prompt examples in the user function chapter of the manual now use the listing environment.

[...]

[...] This is via the fetch_docstrings.py script and results in much better formatting of these

[...] subsections.

[...]........

[...] r20256 | bugman | 2013-06-24 12:29:40 +0200 (Mon, 24 Jun 2013) | 9 lines

[...]

[...] Added function destination for auto-detected NMRPipe SeriesTab format.

[...]

[...] Progress sr #3043: (https://gna.org/support/index.php?3043) - Support for NMRPipe seriesTab format

[...] *.ser.

[...]

[...] Auto-detected NMRPipe SeriesTab format make function calls to the file: lib\software\nmrpipe.py in

[...] function nmrpipe.read_list_intensity_seriestab().

[...]........

[...] r20257 | bugman | 2013-06-24 14:58:23 +0200 (Mon, 24 Jun 2013) | 8 lines

[...]

[...] Imported the missing lib.software.nmrpipe module into pipe_control.spectrum.

[...]

[...] Progress sr #3043: (https://gna.org/support/index.php?3043) - Support for NMRPipe seriesTab format

[...] *.ser.

[...]

[...] Expected modules for use in lib\software\nmrpipe.py is imported.

[...]........

[...] r20260 | bugman | 2013-07-09 11:35:34 +0200 (Tue, 09 Jul 2013) | 6 lines

[...]

[...] Fix for the relax GUI splash screen.

[...]

[...] On certain systems, the GUI was failing due to the splash screen. It is now shown after the main

[...] wxPython window has been created.

[...]........

[...] r20261 | bugman | 2013-07-09 11:37:34 +0200 (Tue, 09 Jul 2013) | 6 lines

[...]

[...] Fix for the new analysis wizard when running the GUI tests.

[...]

[...] If the create_button() method is called without a function argument, the wizard is still created.

[...] This is triggered in the relax_disp branch on certain systems.

[...]........

[...]

[...]

(Browse SVN revision 20262)

Edward d Auvergne <bugman>
Project Administrator
Wed 26 Jun 2013 01:16:56 PM UTC, comment #34:

Now in zip format

(file #18176)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Tue 25 Jun 2013 05:06:43 PM UTC, comment #33:

Completed NMRPipe SeriesTab reader for assignment according to SPARKY format.

Progress sr #3043: (https://gna.org/support/index.php?3043) Support for NMRPipe seriesTab format *.ser

Multiple spectra and intensity reading for NMRPipe SeriesTab formatted file completed.

-----------
Zip file with 5 patches added

Completed according to:
http://nmr-relax.kimlinnet.dk/index.php?title=Git_asynchronous_development#Complete_test_suite

Patches should be applied with:
patch -p1 -i 0001-Imported-the-expected-used-modules-in-lib.software.n.patch

patch -p1 -i 0002-Imported-the-expected-used-modules-in-lib.software.n.patch

(file #18166)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Mon 24 Jun 2013 02:29:26 PM UTC, comment #32:

Imported expected used modules in lib.software.nmrpipe.py.

Progress sr #3043: (https://gna.org/support/index.php?3043) Support for NMRPipe seriesTab format *.ser

Expected modules for use in lib\software\nmrpipe.py is imported.

---------
Note, test patches with both svn diff and git diff is provided

(file #18158, file #18159)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Mon 24 Jun 2013 12:58:23 PM UTC, SVN revision 20257:

Imported the missing lib.software.nmrpipe module into pipe_control.spectrum.

Progress sr #3043: (https://gna.org/support/index.php?3043) - Support for NMRPipe seriesTab format
*.ser.

Expected modules for use in lib\software\nmrpipe.py is imported.

(Browse SVN revision 20257)

Edward d Auvergne <bugman>
Project Administrator
Mon 24 Jun 2013 12:46:24 PM UTC, comment #30:

Imported expected modules in nmrpipe.py

Progress sr #3043: (https://gna.org/support/index.php?3043) Support for NMRPipe seriesTab format *.ser

Expected modules for use in lib\software\nmrpipe.py is imported

(file #18157)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Mon 24 Jun 2013 10:45:21 AM UTC, comment #29:

Fix for missing import of nmrpipe.

Progress sr #3043: (https://gna.org/support/index.php?3043) Support for NMRPipe seriesTab format *.ser

Missed to make and import of nmrpipe: lib\software\nmrpipe.py

(file #18156)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Mon 24 Jun 2013 10:29:41 AM UTC, SVN revision 20256:

Added function destination for auto-detected NMRPipe SeriesTab format.

Progress sr #3043: (https://gna.org/support/index.php?3043) - Support for NMRPipe seriesTab format
*.ser.

Auto-detected NMRPipe SeriesTab format make function calls to the file: lib\software\nmrpipe.py in
function nmrpipe.read_list_intensity_seriestab().

(Browse SVN revision 20256)

Edward d Auvergne <bugman>
Project Administrator
Mon 24 Jun 2013 09:49:24 AM UTC, comment #27:

Added function destination for auto-detected NMRPipe SeriesTab format.

Progress sr #3043: (https://gna.org/support/index.php?3043) Support for NMRPipe seriesTab format *.ser

Auto-detected NMRPipe SeriesTab format make function calls to the file: lib\software\nmrpipe.py
in function nmrpipe.read_list_intensity_seriestab()

(file #18155)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 21 Jun 2013 06:04:16 PM UTC, comment #26:

Intensity column keyword added for NMRPipe SeriesTab format.

Progress sr #3043: (https://gna.org/support/index.php?3043) Support for NMRPipe seriesTab format *.ser

Added the keyword "col_mult":
""" The column which to multiply the peak intensity data (used by the SeriesTab intensity file format). """
If the file 'allplanes.list' contains several paths to .ft2 files, the call to:
seriesTab -in peaks.dat -out allplanes.ser -list allplanes.list
will give a result file where the the total intensity will be given by column: VOL x Z_A0 etc.

The result file contain the VARS keyword:
INDEX X_AXIS Y_AXIS X_PPM Y_PPM VOL ASS Z_A0 Z_A1 Z_A2 Z_A3
Where Z_A0 Z_A1 Z_A2 Z_A3 matches allplanes.list

An 'allplanes.list' is easily created by:

> ls -v -d -1 /.ft2 > allplanes.list

(file #18152)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 21 Jun 2013 06:01:06 PM UTC, SVN revision 20251:

Autodetect format implemented for NMRPipe SeriesTab format implemented.

Progress sr #3043: (https://gna.org/support/index.php?3043) - Support for NMRPipe seriesTab format
*.ser.

The file is determined a NMRPipe SeriesTab if the first two words of the first line is: REMARK
SeriesTab.

(Browse SVN revision 20251)

Edward d Auvergne <bugman>
Project Administrator
Fri 21 Jun 2013 05:58:36 PM UTC, comment #24:

Autodetect format implemented for NMRPipe SeriesTab format implemented.

Progress sr #3043: (https://gna.org/support/index.php?3043) Support for NMRPipe seriesTab format *.ser

The file is determined a NMRPipe SeriesTab if the first two words of the first line is: REMARK SeriesTab

(file #18151)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 21 Jun 2013 05:47:24 PM UTC, comment #23:

Autodetect format implemented for NMRPipe SeriesTab format implemented.

Progress sr #3043: (https://gna.org/support/index.php?3043) Support for NMRPipe seriesTab format *.ser

The file is determined a NMRPipe SeriesTab if the first two words of the first line is: REMARK SeriesTab

(file #18150)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 21 Jun 2013 05:46:58 PM UTC, SVN revision 20250:

Fix for commit (http://article.gmane.org/gmane.science.nmr.relax.scm/18004). The spin naming was wrong.

Progress sr #3043: (https://gna.org/support/index.php?3043) - Support for NMRPipe seriesTab format
*.ser.

The spin naming was wrong. 'spin_id' keywords should be supplied different. Ex:
spin.name(name='NE1', spin_id=':62').

(Browse SVN revision 20250)

Edward d Auvergne <bugman>
Project Administrator
Fri 21 Jun 2013 05:43:35 PM UTC, comment #21:

Fix for commit (http://article.gmane.org/gmane.science.nmr.relax.scm/18004). The spin naming was wrong.

Progress sr #3043: (https://gna.org/support/index.php?3043) Support for NMRPipe seriesTab format *.ser

The spin naming was wrong. 'spin_id' keywords should be supplied different. Ex. spin.name(name='NE1', spin_id=':62')

(file #18149)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 21 Jun 2013 05:30:06 PM UTC, comment #20:

Fix for commit (http://article.gmane.org/gmane.science.nmr.relax.scm/18004). The spin naming was wrong.

Progress sr #3043: (https://gna.org/support/index.php?3043) Support for NMRPipe seriesTab format *.ser

The spin naming was wrong. 'spin_id' keywords should be supplied different. Ex. spin.name(name='NE1', spin_id=':62@1')

(file #18148)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 21 Jun 2013 04:33:03 PM UTC, SVN revision 20249:

Adding a NMRPipe function file in the folder lib\software\nmrpipe.py.

Progress sr #3043: (https://gna.org/support/index.php?3043) - Support for NMRPipe seriesTab format
*.ser.

Initial file for: lib\software\nmrpipe.py. This file will hold the function calls handling NMRPipe
SeriesTab format.

(Browse SVN revision 20249)

Edward d Auvergne <bugman>
Project Administrator
Fri 21 Jun 2013 04:23:24 PM UTC, SVN revision 20248:

Test function for NMRPipe SeriesTab format implemented.

Progress sr #3043: (https://gna.org/support/index.php?3043) - Support for NMRPipe seriesTab format
*.ser.

An assertEqual test is implemented for the reading of NMRPipe SeriesTab format. The standalone call
is: relax -s Peak_lists.test_read_peak_list_NMRPipe_seriesTab

(Browse SVN revision 20248)

Edward d Auvergne <bugman>
Project Administrator
Fri 21 Jun 2013 04:14:50 PM UTC, comment #17:

Adding a nmrpipe function file in the folder: lib\software\nmrpipe.py

Progress sr #3043: (https://gna.org/support/index.php?3043) Support for NMRPipe seriesTab format *.ser

Initial file for: lib\software\nmrpipe.py . This file will hold the function calls handling NMRPipe SeriesTab format.

(file #18147)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 21 Jun 2013 04:10:55 PM UTC, comment #16:

Added function destination for auto-detected NMRPipe SeriesTab format.

Progress sr #3043: (https://gna.org/support/index.php?3043) Support for NMRPipe seriesTab format *.ser

Auto-detected NMRPipe SeriesTab format make function calls to the file: lib\software\nmrpipe.py

(file #18146)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 21 Jun 2013 04:02:44 PM UTC, comment #15:

Intensity column keyword added for NMRPipe SeriesTab format.

Progress sr #3043: (https://gna.org/support/index.php?3043) Support for NMRPipe seriesTab format *.ser

Added the keyword "col_mult":
""" The column which to multiply the peak intensity data (used by the SeriesTab intensity file format). """
If the file 'allplanes.list' contains several paths to .ft2 files, the call to:
seriesTab -in peaks.dat -out allplanes.ser -list allplanes.list

will give a result file where the the total intensity will be given by column: VOL x Z_A0 etc.

The result file contain the VARS keyword:
INDEX X_AXIS Y_AXIS X_PPM Y_PPM VOL ASS Z_A0 Z_A1 Z_A2 Z_A3
Where Z_A0 Z_A1 Z_A2 Z_A3 matches allplanes.list

An 'allplanes.list' is easily created by:

> ls -v -d -1 /.ft2 > allplanes.list

(file #18145)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 21 Jun 2013 03:54:45 PM UTC, comment #14:

Autodetect format implemented for NMRPipe SeriesTab format implemented.

Progress sr #3043: (https://gna.org/support/index.php?3043) Support for NMRPipe seriesTab format *.ser

The file is determined a NMRPipe SeriesTab if the first two words of the first line is: REMARK SeriesTab.

(file #18144)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 21 Jun 2013 03:50:28 PM UTC, comment #13:

Test function for NMRPipe SeriesTab format implemented.

Progress sr #3043: (https://gna.org/support/index.php?3043) Support for NMRPipe seriesTab format *.ser

An assertEqual test is implemented for the reading of NMRPipe SeriesTab format.
The standalone call is: relax -s Peak_lists.test_read_peak_list_NMRPipe_seriesTab

(file #18143)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 21 Jun 2013 03:29:18 PM UTC, comment #12:

Added the seriesTab.ser file to the repository. I modified the commit message to make the header line shorter, added full stops to all sentences, and fixed 'furhter'.

Edward d Auvergne <bugman>
Project Administrator
Fri 21 Jun 2013 03:28:04 PM UTC, SVN revision 20247:

Adding a test data file in NMRPipe SeriesTab format.

Progress sr #3043: (https://gna.org/support/index.php?3043) - Support for NMRPipe seriesTab format
*.ser.

A file in NMRPipe SeriesTab format is added to the test-suite for further development.

(Browse SVN revision 20247)

Edward d Auvergne <bugman>
Project Administrator
Fri 21 Jun 2013 03:26:21 PM UTC, comment #10:

Adding a test data file in NMRPipe SeriesTab format, in the folder:
test_suite\shared_data\peak_lists\seriesTab.ser

Progress sr #3043: (https://gna.org/support/index.php?3043) Support for NMRPipe seriesTab format *.ser

A file in NMRPipe SeriesTab format is added to the test-suite
for furhter development

(file #18142)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 21 Jun 2013 02:40:33 PM UTC, comment #9:

Troels, before I start committing the files, could you write a commit message for each? Cheers.

Edward d Auvergne <bugman>
Project Administrator
Fri 21 Jun 2013 02:38:14 PM UTC, comment #8:

Correction to the determination of SeriesTab.
The line consist of more than 2 entries.

(file #18141)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 21 Jun 2013 01:57:32 PM UTC, comment #7:

Created the nmrpipe file in : \lib\software

(file #18139)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 21 Jun 2013 01:47:34 PM UTC, comment #6:

Copyright information added

(file #18138)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 21 Jun 2013 01:36:24 PM UTC, comment #5:

Patch attached

(file #18137)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 21 Jun 2013 01:35:38 PM UTC, comment #4:

Added initial definitions for which file/function to call for the NMRPipe SeriesTab file format in the pipe_control/spectrum.py file.

Added the keyword "col_mult", which means:

"""
The column which to multiply the peak intensity data (used by the SeriesTab intensity file format).
"""

A call to: seriesTab -in ../../peaks.dat -out allplanes.ser -list allplanes.list

and if allplanes.list contains several file lines,

The intensity will be given by column: VOL x Z_A0 etc.
INDEX X_AXIS Y_AXIS X_PPM Y_PPM VOL ASS Z_A0 Z_A1 Z_A2 Z_A3

according to the allplanes.list
This is easily created by:

ls -v -d -1 /.ft2 > allplanes.list

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 21 Jun 2013 12:56:01 PM UTC, comment #3:

Added autodetect_format settings.

If file starts with: REMARK SeriesTab
it is a SeriesTab file

(file #18136)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 21 Jun 2013 11:03:26 AM UTC, comment #2:

Created test for the reading

(file #18131)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Fri 21 Jun 2013 10:48:36 AM UTC, comment #1:

Support file should be added in:

test_suite\shared_data\peak_lists\seriesTab.ser

(file #18130)

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.
Tue 18 Jun 2013 11:16:58 AM UTC, original submission:

seriesTab can extract Max Values or Sum of regions in an NMRPipe-format Spectral Series, using an NMRPipe-format Peak Table as Input.

A call to the function could be:
seriesTab -in peaks.dat -out peaks_0.ser -list files.list -sum -dx 1 -dy 1

peaks.dat contains the peak list with information of spectral position

VARS INDEX X_AXIS Y_AXIS X_PPM Y_PPM VOL ASS
FORMAT %5d %9.3f %9.3f %8.3f %8.3f %+e %s

1 246.658 18.268 9.932 128.374 +7.000000e+05 W62NE1-W62HE1
2 321.698 30.994 9.419 127.066 +7.000000e+05 L10N-L10HN
3 320.089 55.737 9.430 124.523 +7.000000e+05 V6N-V6HN
...

files.list contains
test.ft2

For folders [0,1,2..,22] with extracted CPMG interleaved spectra, containing test.ft2

A call to function could be:
#! /bin/csh -f
set x = 0;
while ( $x <= 22 )
cd $x
seriesTab -in ../peaks.dat -out ../peaks_${x}.ser -list ../files.list -sum -dx 1 -dy 1
cd ..
@ x = $x + 1
end

The output is:
REMARK SeriesTab Input: ../peaks.dat Output: ../peaks_0.ser
REMARK Mode: Summation Dimensions: 2
REMARK Input Region: X +/- 1 X-ZF: 3
REMARK Analysis Region: X +/- 1
REMARK Input Region: Y +/- 1 Y-ZF: 3
REMARK Analysis Region: Y +/- 1

VARS INDEX X_AXIS Y_AXIS X_PPM Y_PPM VOL ASS Z_A0
FORMAT %5d %9.3f %9.3f %8.3f %8.3f %+e %s %7.4f

NULLVALUE -666
NULLSTRING *

1 246.658 18.268 9.932 128.374 +1.851056e+06 W62NE1-W62HE1 1.0000
2 321.698 30.994 9.419 127.066 +3.224387e+05 L10N-L10HN 1.0000
3 320.089 55.737 9.430 124.523 +1.479366e+06 V6N-V6HN 1.0000

----------------------------
An input reader is wished, which is auto detected like a SPARKY list. The format is quite similar to this. This is an export from
CcpNmr Analysis

Assignment w1 w2 Height Volume
W62NE1-W62HE1 128.374 9.932 0.00E+00 0.00E+00 --
L10N-L10HN 127.066 9.419 0.00E+00 0.00E+00 --
V6N-V6HN 124.523 9.430 0.00E+00 0.00E+00 --

Test files are provided.

Troels E. Linnet <tlinnet>
Project MemberIn charge of this item.

 

(Note: upload size limit is set to 1024 kB, after insertion of the required escape characters.)

Attach File(s):
   
   
Comment:
   

Attached Files
file #18627:  fix.patch.tar.gz added by tlinnet (2kB - application/gzip)
file #18626:  fix.patch.tar.gz added by tlinnet (2kB - application/gzip)
file #18625:  make_test.xls added by tlinnet (55kB - application/vnd.ms-excel)
file #18624:  mtab.patch.tar.gz added by tlinnet (4kB - application/gzip)
file #18619:  stab.patch.tar.gz added by tlinnet (4kB - application/gzip)
file #18618:  seriesTab_multi.ser added by tlinnet (2kB - application/octet-stream)
file #18617:  seriestab2.patch.tar.gz added by tlinnet (4kB - application/gzip)
file #18616:  seriestab.patch added by tlinnet (24kB - application/octet-stream)
file #18372:  seriestab.tar.gz added by tlinnet (2kB - application/gzip)
file #18373:  spectrum.tar.gz added by tlinnet (1kB - application/gzip)
file #18366:  seriestab.tar.gz added by tlinnet (2kB - application/gzip)
file #18367:  spectrum.tar.gz added by tlinnet (1kB - application/gzip)
file #18176:  seriestab_patches_v1.zip added by tlinnet (5kB - application/octet-stream)
file #18166:  seriestab_patches_v1.rar added by tlinnet (5kB - application/octet-stream)
file #18158:  trunk_SeriesTab8 added by tlinnet (451B - application/octet-stream)
file #18159:  nmrpipe1 added by tlinnet (410B - application/octet-stream)
file #18157:  trunk_SeriesTab7_2 added by tlinnet (716B - application/octet-stream)
file #18156:  trunk_SeriesTab6 added by tlinnet (716B - application/octet-stream)
file #18155:  trunk_SeriesTab5 added by tlinnet (962B - application/octet-stream)
file #18152:  trunk_SeriesTab4_2 added by tlinnet (1kB - application/octet-stream)
file #18151:  trunk_SeriesTab3_2 added by tlinnet (1kB - application/octet-stream)
file #18150:  trunk_SeriesTab3 added by tlinnet (3kB - application/octet-stream)
file #18149:  trunk_SeriesTab2 added by tlinnet (2kB - application/octet-stream)
file #18148:  trunk_SeriesTab1 added by tlinnet (2kB - application/octet-stream)
file #18147:  nmrpipe.py added by tlinnet (2kB - text/plain)
file #18146:  seriesTab4 added by tlinnet (5kB - application/octet-stream)
file #18145:  seriesTab3 added by tlinnet (4kB - application/octet-stream)
file #18144:  seriesTab2 added by tlinnet (3kB - application/octet-stream)
file #18143:  seriesTab1 added by tlinnet (2kB - application/octet-stream)
file #18142:  seriesTab.ser added by tlinnet (618B - application/octet-stream)
file #18141:  patch6 added by tlinnet (9kB - application/octet-stream)
file #18139:  patch5 added by tlinnet (9kB - application/octet-stream)
file #18138:  patch4 added by tlinnet (6kB - application/octet-stream)
file #18137:  patch3 added by tlinnet (5kB - application/octet-stream)
file #18136:  patch2 added by tlinnet (3kB - application/octet-stream)
file #18131:  patch1 added by tlinnet (2kB - application/octet-stream)
file #18130:  seriesTab.ser added by tlinnet (618B - application/octet-stream)
file #18108:  peaks.dat added by tlinnet (297B - application/octet-stream)
file #18109:  peaks_0.ser added by tlinnet (603B - application/octet-stream)
file #18110:  files.list added by tlinnet (9B - application/octet-stream)

 

Depends on the following items: None found

Items that depend on this one: None found

 

Carbon-Copy List
  • -unavailable- added by bugman (Posted a comment)
  • -unavailable- added by tlinnet (Submitted the item)
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    Follow 25 latest changes.

    Date Changed By Updated Field Previous Value => Replaced By
    Mon 09 Dec 2013 01:07:00 PM UTCbugmanAssigned toNone=>tlinnet
    Sat 03 Aug 2013 07:22:02 AM UTCbugmanStatusIn Progress=>Done
      Open/ClosedOpen=>Closed
    Fri 02 Aug 2013 09:55:07 PM UTCtlinnetAttached File-=>Added fix.patch.tar.gz, #18627
    Fri 02 Aug 2013 07:49:58 PM UTCtlinnetAttached File-=>Added fix.patch.tar.gz, #18626
    Fri 02 Aug 2013 06:59:11 PM UTCtlinnetAttached File-=>Added make_test.xls, #18625
    Fri 02 Aug 2013 06:48:54 PM UTCtlinnetAttached File-=>Added mtab.patch.tar.gz, #18624
    Fri 02 Aug 2013 03:29:17 PM UTCtlinnetAttached File-=>Added stab.patch.tar.gz, #18619
    Fri 02 Aug 2013 11:51:38 AM UTCtlinnetAttached File-=>Added seriesTab_multi.ser, #18618
    Fri 02 Aug 2013 11:37:34 AM UTCtlinnetAttached File-=>Added seriestab2.patch.tar.gz, #18617
    Fri 02 Aug 2013 08:29:33 AM UTCtlinnetAttached File-=>Added seriestab.patch, #18616
    Sat 20 Jul 2013 04:39:56 PM UTCtlinnetAttached File-=>Added seriestab.tar.gz, #18372
      Attached File-=>Added spectrum.tar.gz, #18373
    Sat 20 Jul 2013 11:14:35 AM UTCtlinnetAttached File-=>Added seriestab.tar.gz, #18366
      Attached File-=>Added spectrum.tar.gz, #18367
    Wed 26 Jun 2013 01:16:56 PM UTCtlinnetAttached File-=>Added seriestab_patches_v1.zip, #18176
    Tue 25 Jun 2013 05:06:43 PM UTCtlinnetAttached File-=>Added seriestab_patches_v1.rar, #18166
    Mon 24 Jun 2013 02:29:26 PM UTCtlinnetAttached File-=>Added trunk_SeriesTab8, #18158
      Attached File-=>Added nmrpipe1, #18159
    Mon 24 Jun 2013 12:46:24 PM UTCtlinnetAttached File-=>Added trunk_SeriesTab7_2, #18157
    Mon 24 Jun 2013 10:45:21 AM UTCtlinnetAttached File-=>Added trunk_SeriesTab6, #18156
    Mon 24 Jun 2013 09:49:23 AM UTCtlinnetAttached File-=>Added trunk_SeriesTab5, #18155
    Fri 21 Jun 2013 06:04:16 PM UTCtlinnetAttached File-=>Added trunk_SeriesTab4_2, #18152
    Fri 21 Jun 2013 05:58:36 PM UTCtlinnetAttached File-=>Added trunk_SeriesTab3_2, #18151
    Fri 21 Jun 2013 05:47:24 PM UTCtlinnetAttached File-=>Added trunk_SeriesTab3, #18150
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