Author: bugman
Date: Wed Apr 10 17:30:41 2013
New Revision: 19435
URL: http://svn.gna.org/viewcvs/relax?rev=19435&view=rev
Log:
Merged revisions 19401-19409,19428-19430,19433-19434 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r19401 | bugman | 2013-04-08 15:07:50 +0200 (Mon, 08 Apr 2013) | 7 lines
Created the pipe_control.plotting module.
This will be used as a base for the plotting of all types of data. This
includes the current OpenDX
and Grace modules, as well as future modules. The determine_functions()
function has been added and
is used to simplify the pipe_control.grace.get_data() function.
........
r19402 | bugman | 2013-04-08 16:45:13 +0200 (Mon, 08 Apr 2013) | 6 lines
The grace.write user function data type argument sequence values have
changed.
Instead of 'spin', this can now be 'res_num' or 'spin_num' to specify that
either the residue number
or spin number should be plotted on the desired axis. The x_data_type now
defaults to 'res_num'.
........
r19403 | bugman | 2013-04-08 16:46:14 +0200 (Mon, 08 Apr 2013) | 5 lines
Created the pipe_control.mol_res_spin.count_max_spins_per_residue()
function.
This will be used by the plotting module to determine if more than one spin
per residue exists.
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r19404 | bugman | 2013-04-08 16:49:17 +0200 (Mon, 08 Apr 2013) | 3 lines
Fixes for the change of the grace.write user function data type 'spin' to
'res_num'.
........
r19405 | bugman | 2013-04-08 16:55:19 +0200 (Mon, 08 Apr 2013) | 3 lines
Updated the pipe_control.plotting.determine_functions() function.
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r19406 | bugman | 2013-04-09 15:40:58 +0200 (Tue, 09 Apr 2013) | 7 lines
Added the skip_desel flag to the important
pipe_control.mol_res_spin.spin_loop() generator function.
This is used to skip deselected spins within the loop. As must of the code
in relax using the
spin_loop() does this anyway, this can be used to simplify many of the spin
looping elements in
relax.
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r19407 | bugman | 2013-04-09 18:21:18 +0200 (Tue, 09 Apr 2013) | 5 lines
Fix for the new pipe_control.mol_res_spin.count_max_spins_per_residue()
function.
The data pipe container was missing.
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r19408 | bugman | 2013-04-09 18:54:26 +0200 (Tue, 09 Apr 2013) | 5 lines
Fix for the analysis specific API common _return_value_general() method.
The value of None is now handled properly when a simulation value is asked
for.
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r19409 | bugman | 2013-04-09 21:53:41 +0200 (Tue, 09 Apr 2013) | 5 lines
Restored the default behaviour of the spin_loop().
The skip_desel flag is now functional and defaults to False.
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r19428 | bugman | 2013-04-10 15:53:44 +0200 (Wed, 10 Apr 2013) | 5 lines
Fix for the relax_times and intensities parameter definitions for
specific_analyses.relax_fit.
These are dictionaries, not lists.
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r19429 | bugman | 2013-04-10 16:21:16 +0200 (Wed, 10 Apr 2013) | 5 lines
Expanded the relax_fit system test script to produce all types of currently
supported Grace graphs.
This is to more extensively test the grace.write user function.
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r19430 | bugman | 2013-04-10 16:28:27 +0200 (Wed, 10 Apr 2013) | 16 lines
Large redesign of the 2D graphing code in relax.
This currently affects only the grace.write user function, but the new
infrastructure will make it
much easier to expand the graphing abilities and to support other 2D
graphing software. The
plotting code has also been significantly simplified.
The pipe_control.grace.get_data() function has been shifted into the
pipe_control.plotting module.
It has been split up into the base assemble_data() function with the data
assembly shifted to
assemble_data_scatter(), assemble_data_seq_value() and
assemble_data_series_series(). This split
massively simplifies the code by not packing all different graph and set
combinations into one.
In addition the auxiliary functions classify_graph_2D(), fetch_1D_data(),
get_functions(), and
get_data_type() have been created to maximise code sharing between the
different assemble_*()
functions.
........
r19433 | bugman | 2013-04-10 17:28:21 +0200 (Wed, 10 Apr 2013) | 6 lines
Modified the relax_fit system test script to generate a new type of graph.
This is the residue number sequence verses the peak intensity series data
(and vice versa) via the
grace.write user function. This is to help in the implementation of this
graph type.
........
r19434 | bugman | 2013-04-10 17:29:36 +0200 (Wed, 10 Apr 2013) | 6 lines
Created the pipe_control.plotting.assemble_data_seq_series() function.
This is to allow the residue or spin numbering to be plotted against any
series type data (lists or
dictionaries), or vice versa.
........
Added:
branches/relax_disp/pipe_control/plotting.py
- copied unchanged from r19434, trunk/pipe_control/plotting.py
Modified:
branches/relax_disp/ (props changed)
branches/relax_disp/auto_analyses/dauvergne_protocol.py
branches/relax_disp/pipe_control/__init__.py
branches/relax_disp/pipe_control/grace.py
branches/relax_disp/pipe_control/mol_res_spin.py
branches/relax_disp/sample_scripts/model_free/final_data_extraction.py
branches/relax_disp/specific_analyses/api_common.py
branches/relax_disp/specific_analyses/relax_fit.py
branches/relax_disp/test_suite/system_tests/grace.py
branches/relax_disp/test_suite/system_tests/model_free.py
branches/relax_disp/test_suite/system_tests/scripts/relax_fit.py
branches/relax_disp/user_functions/grace.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/relax_disp/auto_analyses/dauvergne_protocol.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/auto_analyses/dauvergne_protocol.py?rev=19435&r1=19434&r2=19435&view=diff
Modified: branches/relax_disp/pipe_control/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/pipe_control/__init__.py?rev=19435&r1=19434&r2=19435&view=diff
Modified: branches/relax_disp/pipe_control/grace.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/pipe_control/grace.py?rev=19435&r1=19434&r2=19435&view=diff
Modified: branches/relax_disp/pipe_control/mol_res_spin.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/pipe_control/mol_res_spin.py?rev=19435&r1=19434&r2=19435&view=diff
Modified:
branches/relax_disp/sample_scripts/model_free/final_data_extraction.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/sample_scripts/model_free/final_data_extraction.py?rev=19435&r1=19434&r2=19435&view=diff
Modified: branches/relax_disp/specific_analyses/api_common.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/api_common.py?rev=19435&r1=19434&r2=19435&view=diff
Modified: branches/relax_disp/specific_analyses/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_fit.py?rev=19435&r1=19434&r2=19435&view=diff
Modified: branches/relax_disp/test_suite/system_tests/grace.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/grace.py?rev=19435&r1=19434&r2=19435&view=diff
Modified: branches/relax_disp/test_suite/system_tests/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/model_free.py?rev=19435&r1=19434&r2=19435&view=diff
Modified: branches/relax_disp/test_suite/system_tests/scripts/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/scripts/relax_fit.py?rev=19435&r1=19434&r2=19435&view=diff
Modified: branches/relax_disp/user_functions/grace.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/user_functions/grace.py?rev=19435&r1=19434&r2=19435&view=diff
r19435 - in /branches/relax_disp: ./ auto_analyses/ pipe_control/ sample_scripts/model_free/ specific_analyses/ test_suite/s...