relax SVN archive

Completion of the C code for the fitting of relaxation curves and preparation for Monte Carlo sims.

The 'chi2()' C function is now declared in the 'func()' function as returning a double. Previously
it was interpreting it the result as an int!

The exponential back calculation function has been debugged. The function is I0 * exp(-t * Rx) and
not I0 * exp(-t / Rx)!

In 'maths_fns/c_chi2.c' the function 'square()' has been defined.

The makefile 'maths_fns/Makefile' has been modified so that changes to 'maths_fns/relax_fit.h' will
now cause recompilation of all C code.

The spectral density function 'num_instances()' in 'specific_fns/jw_mapping.py' has been debugged.

In 'specific_fns/relax_fit.py', the function 'ave_and_sd()' has been renamed to 'mean_and_error()'.
The user function 'mean_and_error()' has been added to 'prompt/relax_fit.py'. Previously this was
being called by the minimise function of 'specific_fns/relax_fit.py', ie both during the grid search
and the minimisation. This function has to be called prior to optimisation.

For Monte Carlo simulations, the function 'back_calc_I()' has been added to 'maths_fns/relax_fit.c'.
This simply converts the C external variable 'back_calc[]' to a Numeric array and returns it. The
code isn't fully functional yet. In addition, in the file 'specific_fns/relax_fit.py', the
functions 'num_instances()', 'return_data()', 'set_selected_sim()', and 'sim_pack_data()' have been
added for MC sims.

The error function 'RelaxNoMfModelError' has been changed to 'RelaxNoModelError' to generalise it
for both model-free analysis and relaxation curve fitting.

The function 'sim_set_selected()' has been renamed to 'set_selected_sim()' in
'specific_fns/model_free.py'.

Fix bug where Ri values of None were read from results files

Added a catch for zero Rx values.

Fixed the chi-squared function and 'func' now calls it.

Assigned the back calculated intensity to the external array 'back_calc'.

Added some sanity to the PyArrayObjects in the C code.

Pointers, eg 'relax_times' have been created to 'numpy_relax_times->data' and recast as double. Now
the elements of the array are refered to as 'relax_times[2]' rather than
'relax_times->data + 2*relax_times->strides[0]'. This should remove much pain.

Improved the makefile rules for compiling the C code.

Started to code the exponential back calculation function.

Added the C file for the back calculation of peak intensities in relaxation curve fitting.

More modifications to the relaxation curve fitting C modules.

The external variable *num_times, the number of relaxation times, has been added and is part of the
setup function argument list. The statement '#define MAXTIMES 30' has been added to the header.

The 'func' function has been updated.

The variables in the header have been sorted.

The compilation of the module has changed. Now the C files are compiled into object code *.o and
all the relaxation curve fitting code is linked into a single *.so file. These changes have been to
'maths_fns/Makefile'.

The base directory makefile has had it's goal modified to properly handle recursive making.