Author: bugman
Date: Fri Feb 6 19:24:16 2015
New Revision: 27604
URL: http://svn.gna.org/viewcvs/relax?rev=27604&view=rev
Log:
Merged revisions 27540-27551,27553-27569,27592-27603 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r27540 | bugman | 2015-02-05 12:03:31 +0100 (Thu, 05 Feb 2015) | 5 lines
Created the infrastructure for a Statistics system test class.
This will be used for checking statistics produced by relax.
........
r27541 | bugman | 2015-02-05 12:28:01 +0100 (Thu, 05 Feb 2015) | 20 lines
Reverted r27540, the Statistics system test class.
The command used was:
svn merge -r27540:r27539 .
Any statistics are specific to the different analysis types, therefore such
tests would be better
in the respective specific analysis system test classes.
.....
r27540 | bugman | 2015-02-05 12:03:31 +0100 (Thu, 05 Feb 2015) | 5 lines
Changed paths:
M /trunk/test_suite/system_tests/__init__.py
A /trunk/test_suite/system_tests/statistics.py
Created the infrastructure for a Statistics system test class.
This will be used for checking statistics produced by relax.
.....
........
r27542 | bugman | 2015-02-05 14:06:39 +0100 (Thu, 05 Feb 2015) | 7 lines
Created the N_state_model.test_statistics system test.
This system test will be used to implement the new statistics user function
class consisting of the
structure.model and structure.aic user functions for calculating and
storing the [chi2, n, k]
parameters and Akaike's Information Criterion statistic respectively.
........
r27543 | bugman | 2015-02-05 14:27:43 +0100 (Thu, 05 Feb 2015) | 6 lines
Added the structure.align user function to the renaming translation table.
This is so relax identifies structure.align user functions in scripts to
raise an error saying that
the structure.superimpose user function should be used instead.
........
r27544 | bugman | 2015-02-05 14:56:44 +0100 (Thu, 05 Feb 2015) | 3 lines
Added the office-chart-pie set of Oxygen icons for use in the new
statistics user function class.
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r27545 | bugman | 2015-02-05 14:59:36 +0100 (Thu, 05 Feb 2015) | 5 lines
Created the empty statistics user function class.
This adds the infrastructure for creating the statistics user functions.
........
r27546 | bugman | 2015-02-05 15:19:57 +0100 (Thu, 05 Feb 2015) | 3 lines
Small fix for the structure.add_model user function description.
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r27547 | bugman | 2015-02-05 15:26:04 +0100 (Thu, 05 Feb 2015) | 3 lines
Created the frontend for the statistics.model user function.
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r27548 | bugman | 2015-02-05 15:41:47 +0100 (Thu, 05 Feb 2015) | 5 lines
Created a wizard graphic for the statistics user functions.
This is based on a number of Oxygen icons, as labelled in the SVG layer
names.
........
r27549 | bugman | 2015-02-05 15:43:11 +0100 (Thu, 05 Feb 2015) | 3 lines
The statistics.model user function now uses the new statistics wizard
graphic.
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r27550 | bugman | 2015-02-05 15:45:47 +0100 (Thu, 05 Feb 2015) | 5 lines
Created the empty pipe_control.statistics module.
This will be used for the backend of all of the statistics user functions.
........
r27551 | bugman | 2015-02-05 17:14:08 +0100 (Thu, 05 Feb 2015) | 8 lines
Fixes for the EPS versions of some Oxygen icons used in the relax manual.
This is the actions.document-preview-archive and actions.office-chart-pie
Oxygen icons used for the
user function icons. The files were not created correctly in the Gimp.
The export to EPS requires
the width and height to be both set to 6 mm, and the X and Y offsets to
zero. This allows the icon
bounding boxes and sizes to match the other EPS icons.
........
r27553 | bugman | 2015-02-05 17:41:31 +0100 (Thu, 05 Feb 2015) | 7 lines
Implemented the backend of the statistics.model user function.
The implementation heavily uses the specific analysis API, calling the
calculate(), model_loop(),
print_model_title(), model_statistics() and get_model_container() methods
to do all of the work.
The last of these API methods is yet to be implemented.
........
r27554 | bugman | 2015-02-05 17:45:26 +0100 (Thu, 05 Feb 2015) | 6 lines
Fix for the statistics.model user function backend.
The API methods are now called with the model_info argument set to a
keyword argument so that it is
always passed in as the correct argument.
........
r27555 | bugman | 2015-02-05 17:47:03 +0100 (Thu, 05 Feb 2015) | 6 lines
Fix for the specific analysis API _print_model_title_global() common method.
This method was horribly broken, as it was never used. The new
statistics.model user function
together with the N-state model uncovers this breakage.
........
r27556 | bugman | 2015-02-05 18:24:03 +0100 (Thu, 05 Feb 2015) | 6 lines
Defined the get_model_container() specific analysis API method.
This base method raises a RelaxImplementError, therefore each analysis type
must implement its own
method (or use an API common method).
........
r27557 | bugman | 2015-02-05 18:29:00 +0100 (Thu, 05 Feb 2015) | 7 lines
Implemented the specific analysis API _get_model_container_cdp() commmon
method.
This is to be used for the get_model_container() for returning the current
data pipe object as the
model container. This is for the global models where the model information
is stored in the pipe
object rather than in spin containers.
........
r27558 | bugman | 2015-02-05 18:29:42 +0100 (Thu, 05 Feb 2015) | 5 lines
The N-state model now uses the _get_model_container_cdp() method.
This is aliased as the get_model_container() specific analysis API method.
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r27559 | bugman | 2015-02-05 18:31:57 +0100 (Thu, 05 Feb 2015) | 3 lines
Fix for the N_state_model.test_statistics system test - the probabilities
were missing from k.
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r27560 | bugman | 2015-02-05 18:38:43 +0100 (Thu, 05 Feb 2015) | 3 lines
Expanded the printouts from the statistics.model user function to include
the statistics.
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r27561 | bugman | 2015-02-05 18:47:41 +0100 (Thu, 05 Feb 2015) | 9 lines
Big bug fix for the N-state model num_data_points() function.
This is from the specific_analyses.n_state_model.data module. This code
was very much out of date.
It was expecting an ancient behaviour where the spin container 'pcs'
variable and interatomic data
container 'rdc' where lists of floats. However these were converted many
years ago to dictionaries
with keys set to the alignment IDs. The result was that no RDCs nor PCSs
were counted as a base
data point, so the function would in most cases return a value of zero.
........
r27562 | bugman | 2015-02-05 18:51:10 +0100 (Thu, 05 Feb 2015) | 3 lines
Updated the N-state model num_data_points() function to use more modern
integer incrementation.
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r27563 | bugman | 2015-02-05 18:58:26 +0100 (Thu, 05 Feb 2015) | 6 lines
Fixes for the printout from the pipe_control.pcs.return_pcs_data() function.
The number of PCSs printed out was including values of None when data was
missing for one alignment.
These values of None are no longer counted.
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r27564 | bugman | 2015-02-05 18:58:43 +0100 (Thu, 05 Feb 2015) | 6 lines
Fixes for the printout from the pipe_control.rdc.return_rdc_data() function.
The number of RDCs printed out was including values of None when data was
missing for one alignment.
These values of None are no longer counted.
........
r27565 | bugman | 2015-02-05 19:04:32 +0100 (Thu, 05 Feb 2015) | 6 lines
More fixes for the RDC and PCS count printouts from the corresponding data
assembly functions.
Sometimes the RDC or PCS value could be present as None. This is now
detected and the count is not
incremented.
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r27566 | bugman | 2015-02-05 19:10:44 +0100 (Thu, 05 Feb 2015) | 5 lines
More fixes for the PCS count printout from the
pipe_control.pcs.return_pcs_data() function.
The check for None values was incorrect.
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r27567 | bugman | 2015-02-05 19:12:57 +0100 (Thu, 05 Feb 2015) | 6 lines
Fixes for the N-state model num_data_points() function.
The deselected interatomic data containers are no longer used for counting
RDC data. And the
skipping of deselected spin containers for the PCS is now via the
spin_loop() skip_desel argument.
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r27568 | bugman | 2015-02-05 19:14:41 +0100 (Thu, 05 Feb 2015) | 6 lines
Fix for the N_state_model.test_statistics system test.
The deselected spins and interatomic data containers are now taken into
account for the RDC and PCS
data point counts.
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r27569 | bugman | 2015-02-05 19:26:32 +0100 (Thu, 05 Feb 2015) | 8 lines
Implementation of the statistics.aic user function.
This is very similar to the statistics.model user function - the code was
copied and only slightly
modified. The new user function will calculate the current chi-squared
value per model, obtain the
model statistics, calculate the AIC value per model, and store the AIC
value, chi-squared value and
number of parameters in the appropriate location for the model in the relax
data store.
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r27592 | bugman | 2015-02-06 12:05:31 +0100 (Fri, 06 Feb 2015) | 3 lines
Created the empty lib.plotting.veusz module for graphing using Veusz
(http://home.gna.org/veusz/).
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r27593 | bugman | 2015-02-06 14:29:35 +0100 (Fri, 06 Feb 2015) | 6 lines
Shifted the lib.software.grace module to lib.plotting.grace.
This follows from
http://thread.gmane.org/gmane.science.nmr.relax.devel/7532 and
http://thread.gmane.org/gmane.science.nmr.relax.devel/7536.
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r27594 | bugman | 2015-02-06 14:40:04 +0100 (Fri, 06 Feb 2015) | 3 lines
Copyright update.
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r27595 | bugman | 2015-02-06 14:42:20 +0100 (Fri, 06 Feb 2015) | 7 lines
Created XY-data functions for the plotting API of the relax library.
These are currently copies of the heads of the lib.plotting.grace functions
write_xy_data() and
write_xy_header(). These lib.plotting.api functions (write_xy_data() and
write_xy_header()) are set
up to use the grace functions.
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r27596 | bugman | 2015-02-06 14:47:10 +0100 (Fri, 06 Feb 2015) | 3 lines
Converted all of the Grace plotting in relax to use the plotting API of the
relax library.
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r27597 | bugman | 2015-02-06 14:58:01 +0100 (Fri, 06 Feb 2015) | 7 lines
Shifted the pipe_control.grace.write() function.
This is now the format independent pipe_control.plotting.write_xy()
function. The format argument
has been added and this defaults to 'grace'. The grace.write user function
has been updated to use
the new backend.
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r27598 | bugman | 2015-02-06 15:01:00 +0100 (Fri, 06 Feb 2015) | 3 lines
Updated the pcs.structural_noise user function to use the relax library
plotting API.
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r27599 | bugman | 2015-02-06 15:05:30 +0100 (Fri, 06 Feb 2015) | 6 lines
Fixes for the new pipe_control.plotting.write_xy() function.
This includes missing imports which should have moved from
pipe_control.grace, as well as shifting
the axis_setup() function from the pipe_control.grace module into the
pipe_control.plotting module.
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r27600 | bugman | 2015-02-06 15:14:15 +0100 (Fri, 06 Feb 2015) | 6 lines
The rdc.corr_plot user function backend now uses the relax library plotting
API.
The write_xy_data() and write_xy_header() functions from lib.plotting.api
are now uses instead of
the equivalent pipe_control.grace functions which no longer exist.
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r27601 | bugman | 2015-02-06 15:16:05 +0100 (Fri, 06 Feb 2015) | 3 lines
More import fixes for the new pipe_control.plotting.write_xy() function.
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r27602 | bugman | 2015-02-06 15:17:51 +0100 (Fri, 06 Feb 2015) | 5 lines
Fix for the backend of the relax_disp.plot_disp_curves user function.
The lib.plotting.api functions write_xy_data() and write_xy_header()
require the format argument.
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r27603 | bugman | 2015-02-06 15:32:12 +0100 (Fri, 06 Feb 2015) | 3 lines
Updated the relative stereochemistry auto-analysis to use the relax library
plotting API.
........
Added:
branches/frame_order_cleanup/graphics/oxygen_icons/128x128/actions/office-chart-pie.eps.gz
- copied unchanged from r27603,
trunk/graphics/oxygen_icons/128x128/actions/office-chart-pie.eps.gz
branches/frame_order_cleanup/graphics/oxygen_icons/128x128/actions/office-chart-pie.png
- copied unchanged from r27603,
trunk/graphics/oxygen_icons/128x128/actions/office-chart-pie.png
branches/frame_order_cleanup/graphics/oxygen_icons/16x16/actions/office-chart-pie.png
- copied unchanged from r27603,
trunk/graphics/oxygen_icons/16x16/actions/office-chart-pie.png
branches/frame_order_cleanup/graphics/oxygen_icons/22x22/actions/office-chart-pie.png
- copied unchanged from r27603,
trunk/graphics/oxygen_icons/22x22/actions/office-chart-pie.png
branches/frame_order_cleanup/graphics/oxygen_icons/32x32/actions/office-chart-pie.png
- copied unchanged from r27603,
trunk/graphics/oxygen_icons/32x32/actions/office-chart-pie.png
branches/frame_order_cleanup/graphics/oxygen_icons/48x48/actions/office-chart-pie.png
- copied unchanged from r27603,
trunk/graphics/oxygen_icons/48x48/actions/office-chart-pie.png
branches/frame_order_cleanup/graphics/wizards/statistics.png
- copied unchanged from r27603, trunk/graphics/wizards/statistics.png
branches/frame_order_cleanup/graphics/wizards/statistics.svg
- copied unchanged from r27603, trunk/graphics/wizards/statistics.svg
branches/frame_order_cleanup/lib/plotting/grace.py
- copied unchanged from r27603, trunk/lib/plotting/grace.py
branches/frame_order_cleanup/lib/plotting/veusz.py
- copied unchanged from r27603, trunk/lib/plotting/veusz.py
branches/frame_order_cleanup/pipe_control/statistics.py
- copied unchanged from r27603, trunk/pipe_control/statistics.py
branches/frame_order_cleanup/user_functions/statistics.py
- copied unchanged from r27603, trunk/user_functions/statistics.py
Removed:
branches/frame_order_cleanup/lib/software/grace.py
Modified:
branches/frame_order_cleanup/ (props changed)
branches/frame_order_cleanup/auto_analyses/relax_fit.py
branches/frame_order_cleanup/auto_analyses/stereochem_analysis.py
branches/frame_order_cleanup/graphics/oxygen_icons/128x128/actions/document-preview-archive.eps.gz
branches/frame_order_cleanup/lib/plotting/__init__.py
branches/frame_order_cleanup/lib/plotting/api.py
branches/frame_order_cleanup/lib/software/__init__.py
branches/frame_order_cleanup/pipe_control/__init__.py
branches/frame_order_cleanup/pipe_control/grace.py
branches/frame_order_cleanup/pipe_control/pcs.py
branches/frame_order_cleanup/pipe_control/plotting.py
branches/frame_order_cleanup/pipe_control/rdc.py
branches/frame_order_cleanup/specific_analyses/api_base.py
branches/frame_order_cleanup/specific_analyses/api_common.py
branches/frame_order_cleanup/specific_analyses/n_state_model/api.py
branches/frame_order_cleanup/specific_analyses/n_state_model/data.py
branches/frame_order_cleanup/specific_analyses/relax_disp/data.py
branches/frame_order_cleanup/test_suite/system_tests/n_state_model.py
branches/frame_order_cleanup/user_functions/__init__.py
branches/frame_order_cleanup/user_functions/grace.py
branches/frame_order_cleanup/user_functions/structure.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/frame_order_cleanup/auto_analyses/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/auto_analyses/relax_fit.py?rev=27604&r1=27603&r2=27604&view=diff
Modified: branches/frame_order_cleanup/auto_analyses/stereochem_analysis.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/auto_analyses/stereochem_analysis.py?rev=27604&r1=27603&r2=27604&view=diff
Modified:
branches/frame_order_cleanup/graphics/oxygen_icons/128x128/actions/document-preview-archive.eps.gz
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/graphics/oxygen_icons/128x128/actions/document-preview-archive.eps.gz?rev=27604&r1=27603&r2=27604&view=diff
Modified: branches/frame_order_cleanup/lib/plotting/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/plotting/__init__.py?rev=27604&r1=27603&r2=27604&view=diff
Modified: branches/frame_order_cleanup/lib/plotting/api.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/plotting/api.py?rev=27604&r1=27603&r2=27604&view=diff
Modified: branches/frame_order_cleanup/lib/software/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/software/__init__.py?rev=27604&r1=27603&r2=27604&view=diff
Removed: branches/frame_order_cleanup/lib/software/grace.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/software/grace.py?rev=27603&view=auto
Modified: branches/frame_order_cleanup/pipe_control/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/pipe_control/__init__.py?rev=27604&r1=27603&r2=27604&view=diff
Modified: branches/frame_order_cleanup/pipe_control/grace.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/pipe_control/grace.py?rev=27604&r1=27603&r2=27604&view=diff
Modified: branches/frame_order_cleanup/pipe_control/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/pipe_control/pcs.py?rev=27604&r1=27603&r2=27604&view=diff
Modified: branches/frame_order_cleanup/pipe_control/plotting.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/pipe_control/plotting.py?rev=27604&r1=27603&r2=27604&view=diff
Modified: branches/frame_order_cleanup/pipe_control/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/pipe_control/rdc.py?rev=27604&r1=27603&r2=27604&view=diff
Modified: branches/frame_order_cleanup/specific_analyses/api_base.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/api_base.py?rev=27604&r1=27603&r2=27604&view=diff
Modified: branches/frame_order_cleanup/specific_analyses/api_common.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/api_common.py?rev=27604&r1=27603&r2=27604&view=diff
Modified: branches/frame_order_cleanup/specific_analyses/n_state_model/api.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/n_state_model/api.py?rev=27604&r1=27603&r2=27604&view=diff
Modified: branches/frame_order_cleanup/specific_analyses/n_state_model/data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/n_state_model/data.py?rev=27604&r1=27603&r2=27604&view=diff
Modified: branches/frame_order_cleanup/specific_analyses/relax_disp/data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/relax_disp/data.py?rev=27604&r1=27603&r2=27604&view=diff
Modified:
branches/frame_order_cleanup/test_suite/system_tests/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/n_state_model.py?rev=27604&r1=27603&r2=27604&view=diff
Modified: branches/frame_order_cleanup/user_functions/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/user_functions/__init__.py?rev=27604&r1=27603&r2=27604&view=diff
Modified: branches/frame_order_cleanup/user_functions/grace.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/user_functions/grace.py?rev=27604&r1=27603&r2=27604&view=diff
Modified: branches/frame_order_cleanup/user_functions/structure.py
[... 2 lines stripped ...]
r27604 - in /branches/frame_order_cleanup: ./ auto_analyses/ graphics/oxygen_icons/128x128/actions/ graphics/oxygen_icons/16...