Author: bugman
Date: Thu Jul 24 13:26:12 2014
New Revision: 24703
URL: http://svn.gna.org/viewcvs/relax?rev=24703&view=rev
Log:
Merged revisions
24542,24545-24548,24552-24559,24564-24584,24587-24595,24597-24611,24616-24618,24640,24649,24671,24674-24678,24680-24683,24688-24701
via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/zooming_grid_search
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r24542 | bugman | 2014-07-16 17:35:02 +0200 (Wed, 16 Jul 2014) | 7 lines
Added a new set of icons for use with the minimisation user functions.
These are of the Rosenbrock function and are much better suited for small
icons than the current
OpenDX 3D isosurface plots. The matplotlib figure originates from public
domain code at
http://commons.wikimedia.org/wiki/File:Rosenbrock_function.svg.
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r24545 | bugman | 2014-07-16 20:57:03 +0200 (Wed, 16 Jul 2014) | 12 lines
Redesign of the optimisation user functions calculate, grid_search, and
minimise.
In preparation for expanding the number of optimisation user functions,
these three current user
functions have been shifted into the new minimise user function class. The
calculate user function
is now accessed as minimise.calculate. The grid search as
minimise.grid_search. And minimisation
is via the minimise.execute user function. The icon used for the new user
function class is the
Rosenbrock function or the banana optimisation problem.
As this is such a radical change, a huge number of changes in the relax
source code, the sample
scripts, the user manual, and the test suite were required.
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r24546 | bugman | 2014-07-17 14:27:50 +0200 (Thu, 17 Jul 2014) | 6 lines
Created the new minimise.grid_zoom user function.
This allows the grid zoom level to be set. The value is stored in the
current data pipe and will be
used later by the minimise.grid_search user function.
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r24547 | bugman | 2014-07-17 14:36:15 +0200 (Thu, 17 Jul 2014) | 3 lines
The minimise.grid_zoom user function now uses the zoom-in Oxygen icon.
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r24548 | bugman | 2014-07-17 14:46:53 +0200 (Thu, 17 Jul 2014) | 6 lines
Created the Relax_fit.test_zooming_grid_search system test.
This will be used to test the implementation of the zooming grid search.
The relaxation
curve-fitting analysis should be one of the fastest for testing this.
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r24552 | bugman | 2014-07-17 16:22:36 +0200 (Thu, 17 Jul 2014) | 5 lines
Added the print_model_title() method to the specific analysis base API
class.
This will be used to format and print out the information returned by the
model_info() API method.
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r24553 | bugman | 2014-07-17 16:29:14 +0200 (Thu, 17 Jul 2014) | 3 lines
Implemented the print_model_title() specific analysis API method for the
dispersion analysis.
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r24554 | bugman | 2014-07-17 16:45:06 +0200 (Thu, 17 Jul 2014) | 6 lines
Modified the specific analysis API _model_loop_spin() common method.
This now additionally returns the spin ID string to allow the corresponding
spin container to be
identified.
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r24555 | bugman | 2014-07-17 16:46:57 +0200 (Thu, 17 Jul 2014) | 6 lines
Implemented the specific analysis API common method
_print_model_title_spin().
This is for the corresponding _model_loop_spin() method. It can be aliased
in the specific analyses
to provide the print_model_title() API method.
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r24556 | bugman | 2014-07-17 16:49:26 +0200 (Thu, 17 Jul 2014) | 6 lines
Aliased the _print_model_title_spin() specific analysis API common method
in a few analyses.
This provides the print_model_title() API method for the J(w) mapping,
consistency testing, and
relaxation curve fitting analyses.
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r24557 | bugman | 2014-07-17 17:13:34 +0200 (Thu, 17 Jul 2014) | 6 lines
Updated all the specific analysis methods affected by the
_model_info_spin() API method change.
This is for the change whereby the common API method now returns the spin
ID string as well
(r24554).
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r24558 | bugman | 2014-07-17 17:24:09 +0200 (Thu, 17 Jul 2014) | 3 lines
Fix for a number of docstring typos from r24557.
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r24559 | bugman | 2014-07-17 17:31:50 +0200 (Thu, 17 Jul 2014) | 5 lines
Implemented get_param_names() and get_param_values() for the relaxation
curve-fitting analysis.
These are part of the specific analysis API.
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r24564 | bugman | 2014-07-18 11:02:52 +0200 (Fri, 18 Jul 2014) | 6 lines
Created the specific analysis API return_parameter_object() function.
This is used by the non-specific analysis code to obtain the parameter
object (a singleton object).
It will allow for more direct access to the parameter information.
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r24565 | bugman | 2014-07-18 11:05:51 +0200 (Fri, 18 Jul 2014) | 8 lines
Created the parameter object infrastructure for adding the grid search
lower and upper bounds.
The _add() method now accepts the grid_lower and grid_upper keyword
arguments, which can be either
values or functions. These are then stored in the _grid_lower and
_grid_upper class dictionaries.
The public methods grid_lower() and grid_upper() have been added to return
the value corresponding
to the given parameter.
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r24566 | bugman | 2014-07-18 11:51:54 +0200 (Fri, 18 Jul 2014) | 8 lines
Modified the specific analysis parameter object grid_lower() and
grid_upper() methods.
These now accept the model information from the model_loop() API method and
send that into an grid
lower and upper functions. These functions will require the information to
pull out the correct
spin, spin cluster, or other information from the current data pipe to
determine what the bounds
should be.
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r24567 | bugman | 2014-07-18 13:47:59 +0200 (Fri, 18 Jul 2014) | 12 lines
Implemented infrastructure in the grid_search user function in preparation
for the zooming grid.
The grid search backend now calls the new grid_bounds() function. This
takes the lower and upper
bounds as arguments, uses the specific API to determine the per-model
parameter grid search bounds,
and then returns a per model list of lower and upper bounds. The specific
API get_param_names() and
get_param_values() are called to obtain the current model parameter names
and values, and then the
parameter names and model info are used in the new parameter object
grid_lower() and grid_upper()
methods to obtain the bounds. This shifts all of the grid search bounds
logic out of the specific
analyses and into the grid search backend, so it should allow the specific
analysis code to be
simplified.
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r24568 | bugman | 2014-07-18 14:43:07 +0200 (Fri, 18 Jul 2014) | 11 lines
More modifications of the minimise.grid_search user function backend.
The grid_bounds() function has been renamed to grid_setup(), and it now
accepts and processes the
inc user function argument. The error checking code of the relaxation
curve-fitting
grid_search_setup() optimisation function has been shifted into this
analysis independent
grid_setup() function to shift the minimise.grid_search user function error
checking out of the
specific analyses. The function now scales the parameter bounds, using the
yet-to-be implemented
scaling() method of the parameter object. And the grid search increments
are converted into a
per-model list of lists.
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r24569 | bugman | 2014-07-18 15:03:54 +0200 (Fri, 18 Jul 2014) | 7 lines
Created the parameter object infrastructure for registering parameter
scalings.
The _add() method now accepts the scaling keyword argument, which can be
either a value or function.
This is then stored in the _scaling dictionary. The public method
scaling() has been added to
return the scaling factor corresponding to the given parameter.
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r24570 | bugman | 2014-07-18 15:51:10 +0200 (Fri, 18 Jul 2014) | 12 lines
Modified the analysis specific API optimisation method.
The base calculate(), grid_search() and minimise() methods now all accept
the scaling_matrix
argument, and the minimise() scaling argument has been removed. This
scaling_matrix argument should
be a per-model list of scaling matrices.
To handle the change, the pipe_control.minimise.assemble_scaling_matrix()
function has been created.
This uses the new parameter object scaling values to create the list of
scaling matrices. This will
in the end replace all of the analysis specific assemble_scaling_matrix()
functions and simplify
their optimisation code paths.
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r24571 | bugman | 2014-07-18 16:13:11 +0200 (Fri, 18 Jul 2014) | 7 lines
Changed the order of operations in the minimisation user function backends.
The specific analysis API overfit_deselect() method needs to be called
before any grid bounds,
increments, or the scaling matrices are assembled. This is for the cases
when the grid bounds or
scaling factors are functions rather than values.
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r24572 | bugman | 2014-07-18 16:26:29 +0200 (Fri, 18 Jul 2014) | 15 lines
Converted the relaxation curve-fitting analysis to the new grid bounds and
scaling factor design.
The parameter object now registers the grid bounds and scaling factors for
all of the curve-fitting
parameters. This includes three functions i_scaling(), i0() and iinf() in
the
specific_analyses.relax_fit.parameter_object module for calculating some of
these values.
The specific_analyses.relax_fit.parameters.assemble_scaling_matrix()
function has been deleted as
this is now provided by the upstream code in pipe_control.minimise. And
the API methods
grid_search() and minimise() has been modified to accept the list of
scaling matrices.
As the grid bounds and increments are now handled by the upstream
pipe_control.minimise.grid_setup()
function, the specific_analyses.relax_fit.optimisation.grid_search_setup()
function was redundant
and was deleted.
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r24573 | bugman | 2014-07-18 16:43:39 +0200 (Fri, 18 Jul 2014) | 7 lines
Created the consistency testing specific API method get_param_names().
This is now required for the minimise.calculate user function, specifically
for the analysis
independent assemble_scaling_matrix() function. The get_param_names()
method simply returns the
fixed list of parameter names.
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r24574 | bugman | 2014-07-18 19:43:23 +0200 (Fri, 18 Jul 2014) | 7 lines
Standardisation of the specific analysis API with respect to the
model_loop() and base_data_loop().
The model information arguments for the data returned by model_loop(), and
the data arguments for
the data arguments for the data returned by base_data_loop() have been
standardised throughout the
API.
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r24575 | bugman | 2014-07-21 08:57:55 +0200 (Mon, 21 Jul 2014) | 3 lines
Epydoc parameter order rearrangement in the specific analysis API base
class.
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r24576 | bugman | 2014-07-21 09:01:54 +0200 (Mon, 21 Jul 2014) | 3 lines
Updated the specific analysis API common methods for the recent model_info
argument changes.
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r24577 | bugman | 2014-07-21 09:07:47 +0200 (Mon, 21 Jul 2014) | 7 lines
Updated all of the specific API calculate() methods to accept the
scaling_matrix argument.
The list of per-model scaling matrices is now created independently of the
analysis type by the
pipe_control.minimise methods for the minimise.calculate,
minimise.grid_search and minimise.execute
user functions and sent into the specific analysis backend.
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r24578 | bugman | 2014-07-21 09:14:00 +0200 (Mon, 21 Jul 2014) | 10 lines
Updated all of the specific API grid_search() methods to accept the
scaling_matrix argument.
The list of per-model scaling matrices is now created independently of the
analysis type by the
pipe_control.minimise methods for the minimise.calculate,
minimise.grid_search and minimise.execute
user functions and sent into the specific analysis backend.
The argument is also passed into the minimise() API method from the
grid_search() method when that
is used.
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r24579 | bugman | 2014-07-21 09:17:44 +0200 (Mon, 21 Jul 2014) | 7 lines
Updated all of the specific API minimise() methods to accept the
scaling_matrix argument.
The list of per-model scaling matrices is now created independently of the
analysis type by the
pipe_control.minimise methods for the minimise.calculate,
minimise.grid_search and minimise.execute
user functions and sent into the specific analysis backend.
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r24580 | bugman | 2014-07-21 09:23:37 +0200 (Mon, 21 Jul 2014) | 3 lines
Fix for the Monte Carlo simulations for the model_info argument changes in
the specific API.
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r24581 | bugman | 2014-07-21 09:28:44 +0200 (Mon, 21 Jul 2014) | 5 lines
Fixes for the consistency testing and J(w) mapping calculate() methods.
This is for the changes to the data_init() specific analysis API method.
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r24582 | bugman | 2014-07-21 09:30:43 +0200 (Mon, 21 Jul 2014) | 3 lines
More fixes for the Monte Carlo simulations for the model_info argument
changes in the specific API.
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r24583 | bugman | 2014-07-21 09:50:45 +0200 (Mon, 21 Jul 2014) | 3 lines
Updated all of the data_init() specific API calls where the spin ID is
expected.
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r24584 | bugman | 2014-07-21 09:59:34 +0200 (Mon, 21 Jul 2014) | 6 lines
Fixes for the _data_init_spin() specific API common method.
The data returned from _base_data_loop_spin() is just the spin ID, the spin
container is not
included.
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r24587 | bugman | 2014-07-21 18:57:56 +0200 (Mon, 21 Jul 2014) | 3 lines
Updated the elminate user function backend to work with the model_info
argument changes in the specific API.
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r24588 | bugman | 2014-07-21 18:59:58 +0200 (Mon, 21 Jul 2014) | 6 lines
The new pipe_control.minimise module functions can now handle models with
no parameters.
The new assemble_scaling_matrix() and grid_setup() functions will now
handle models with no
parameters, as this is required for the relaxation dispersion analysis.
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r24589 | bugman | 2014-07-21 19:18:06 +0200 (Mon, 21 Jul 2014) | 6 lines
More fixes for the elminate user function backend.
This is for the model_info argument changes in the specific API.
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r24590 | bugman | 2014-07-22 10:15:15 +0200 (Tue, 22 Jul 2014) | 9 lines
Fixes for the grid search backend for a recent breakage and expansion of
its capabilities.
The user supplied lower and upper bounds for the grid search were no longer
being scaled via the
scaling matrix.
In addition, the code has been refactored to be simpler and more flexible.
The user can now supply
just the lower or just the upper bounds and the grid search will work.
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r24591 | bugman | 2014-07-22 10:43:19 +0200 (Tue, 22 Jul 2014) | 7 lines
The grid search setup function now prints out the grid search bounds to be
used.
This is in the pipe_control.minimise.grid_setup() function, hence it is
analysis independent. This
is useful feedback for the user to know what the grid search is doing. And
it will be even more
useful for the zooming grid search to understand what is happening.
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r24592 | bugman | 2014-07-22 10:45:28 +0200 (Tue, 22 Jul 2014) | 3 lines
The grid search setup printout now also included the number of increments
for each parameter.
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r24593 | bugman | 2014-07-22 10:49:33 +0200 (Tue, 22 Jul 2014) | 6 lines
Modified the new print_model_title() specific analysis API method.
This now accepts the prefix argument for creating different titles
independently of the specific
analysis.
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r24594 | bugman | 2014-07-22 10:51:23 +0200 (Tue, 22 Jul 2014) | 5 lines
The grid search setup function now uses the prefix argument to the
print_model_title() API function.
This is simply set to 'Grid search setup:'.
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r24595 | bugman | 2014-07-22 11:22:56 +0200 (Tue, 22 Jul 2014) | 3 lines
The relaxation dispersion API now uses the MODEL_R2EFF variable for
identifying the R2eff model.
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r24597 | bugman | 2014-07-22 13:06:50 +0200 (Tue, 22 Jul 2014) | 5 lines
Changes to the minimise.grid_search user function front end.
The Boolean constraints argument has been shifted to the end, and empty
lines have been removed.
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r24598 | bugman | 2014-07-22 13:11:50 +0200 (Tue, 22 Jul 2014) | 3 lines
Epydoc docstring fixes for the keyword arguments of the
pipe_control.minimise module.
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r24599 | bugman | 2014-07-22 13:12:40 +0200 (Tue, 22 Jul 2014) | 3 lines
Shifted the constraints boolean argument to the end of the grid_search()
function argument list.
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r24600 | bugman | 2014-07-22 13:36:33 +0200 (Tue, 22 Jul 2014) | 12 lines
Major change to the grid search user function.
The minimise.grid_search user function now accepts the skip_preset flag.
When True, the grid search
will skip any parameters with a preset value. This allows the user to set
parameters via the
value.set user function and then have these parameters skipped in the grid
search.
The new skip_preset argument is passed into the
pipe_control.minimise.grid_setup() function in the
backend. This then sets both the grid lower and upper bounds to the preset
parameter value and sets
the number of increments to 1 for that parameter so that it is essentially
skipped in the grid
search.
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r24601 | bugman | 2014-07-22 13:44:40 +0200 (Tue, 22 Jul 2014) | 7 lines
Increased the amount of user feedback for the minimise.grid_search user
function.
Now a comment for each parameter is included in the printed grid search
setup table. This includes
if the lower or upper bounds, or both, have been supplied by the user and
if a preset value has been
used instead.
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r24602 | bugman | 2014-07-22 13:46:27 +0200 (Tue, 22 Jul 2014) | 3 lines
Small change to the table printed out during the minimise.grid_search setup.
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r24603 | bugman | 2014-07-22 14:22:48 +0200 (Tue, 22 Jul 2014) | 5 lines
Fix for the skipping of preset parameters in the grid search.
Dictionary and list type parameters are now handled correctly.
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r24604 | bugman | 2014-07-22 14:30:48 +0200 (Tue, 22 Jul 2014) | 24 lines
Converted the relaxation dispersion analysis to the new grid bounds and
scaling factor design.
The parameter object now registers the grid bounds and scaling factors for
all of the dispersion
parameters. This includes the functions dw_lower(), dwH_lower(),
pA_lower() and i0_upper() in the
specific_analyses.relax_disp.parameter_object module for calculating some
of these values.
The specific_analyses.relax_disp.parameters.assemble_scaling_matrix()
function has been deleted as
this is now provided by the upstream code in pipe_control.minimise. And
the API methods
grid_search() and minimise() has been modified to accept the list of
scaling matrices.
As the grid bounds and increments are now handled by the upstream
pipe_control.minimise.grid_setup()
function, the specific_analyses.relax_disp.optimisation.grid_search_setup()
function was redundant
and was deleted.
The specific_analyses.relax_disp.parameters.get_param_names() function was
also modified with the
full argument added, to allow either the base parameter names or an
augmented form with the
dictionary key for presenting to the user to be returned.
Importantly to allow the changes to be operational, the model_loop() API
method was redesigned so
that, for the R2eff base model, the individual spins rather than spin
clusters will be looped over.
This allows the specific_analyses.relax_disp.optimisation.minimise_r2eff()
function to continue to
operate correctly.
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r24605 | bugman | 2014-07-22 14:33:18 +0200 (Tue, 22 Jul 2014) | 6 lines
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r24703 - in /trunk: ./ auto_analyses/ devel_scripts/ docs/ docs/latex/ graphics/misc/Rosenbrock_function/ graphics/relax_ico...