Hi Troels,
Could you remind me later (after branch merger) to expand the target
function docstring to include descriptions of {NE, NS, NM, NO, ND}?
Cheers,
Edward
On 11 June 2014 10:08, <[email protected]> wrote:
> Author: tlinnet
> Date: Wed Jun 11 10:08:05 2014
> New Revision: 23819
>
> URL: http://svn.gna.org/viewcvs/relax?rev=23819&view=rev
> Log:
> Replaced self.(ei,si,mi,oi,di) with self.(NE,NS,NM,NO,ND).
>
> These numbers represents the maximum number of dimensions, instead of index.
>
> Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
> models for Clustered analysis.
>
> Modified:
> branches/disp_spin_speed/target_functions/relax_disp.py
>
> Modified: branches/disp_spin_speed/target_functions/relax_disp.py
> URL:
> http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/target_functions/relax_disp.py?rev=23819&r1=23818&r2=23819&view=diff
> ==============================================================================
> --- branches/disp_spin_speed/target_functions/relax_disp.py (original)
> +++ branches/disp_spin_speed/target_functions/relax_disp.py Wed Jun 11
> 10:08:05 2014
> @@ -409,11 +409,12 @@
> self.numpy_array_shape = back_calc_shape +
> [self.max_num_disp_points]
>
> # Set the dimensions to paramater.
> - self.ei = self.numpy_array_shape[0]
> - self.si = self.numpy_array_shape[1]
> - self.mi = self.numpy_array_shape[2]
> - self.oi = self.numpy_array_shape[3]
> - self.di = self.numpy_array_shape[4]
> + # The total numbers of experiments, number of spins, number of
> magnetic field strength, number of offsets, maximum number of dispersion
> point.
> + self.NE = self.numpy_array_shape[0]
> + self.NS = self.numpy_array_shape[1]
> + self.NM = self.numpy_array_shape[2]
> + self.NO = self.numpy_array_shape[3]
> + self.ND = self.numpy_array_shape[4]
>
> # Create zero and one numpy structure.
> zeros_a = zeros(self.numpy_array_shape, float64)
> @@ -439,17 +440,17 @@
> self.dw_struct = deepcopy(zeros_a)
>
> # Temporary storage to avoid memory allocations and garbage
> collection.
> - self.dw_temp = zeros([self.si] + self.numpy_array_shape, float64)
> + self.dw_temp = zeros([self.NS] + self.numpy_array_shape, float64)
>
> # The structure for multiplication with dw to piecewise build up
> the full dw structure.
> self.dw_mask = deepcopy(self.dw_temp)
>
> # Loop over the experiment types.
> - for ei in range(self.num_exp):
> + for ei in range(self.NE):
> # Loop over the spins.
> - for si in range(self.num_spins):
> + for si in range(self.NS):
> # Loop over the spectrometer frequencies.
> - for mi in range(self.num_frq):
> + for mi in range(self.NM):
> # Fill dw_mask with frequencies.
> self.dw_mask[si, :, si, mi] = self.frqs[ei][si][mi]
>
> @@ -558,7 +559,7 @@
> """
>
> # Loop over the dw elements (one per spin).
> - for si in range(self.si):
> + for si in range(self.NS):
> # First multiply the spin specific dw with the spin specific
> frequency mask, using temporary storage.
> multiply(dw[si], self.dw_mask[si], self.dw_temp[si])
>
> @@ -566,13 +567,13 @@
> add(self.dw_struct, self.dw_temp[si], self.dw_struct)
>
> # Reshape dw to per experiment and nr spins.
> - dw_axis = asarray(dw).reshape(self.ei, self.si)
> + dw_axis = asarray(dw).reshape(self.NE, self.NS)
>
> # Expand dw to number of axis for frequency, offset and dispersion
> points.
> dw_axis = dw_axis[:,:,None,None,None]
>
> # Tile dw according to dimensions.
> - dw_axis = tile(dw_axis, (1, 1, self.mi, self.oi, self.di))
> + dw_axis = tile(dw_axis, (1, 1, self.NM, self.NO, self.ND))
>
> # Convert dw from ppm to rad/s.
> dw_frq_a = dw_axis*self.disp_struct*self.frqs_a
> @@ -585,16 +586,16 @@
> #sys.exit()
>
> # Reshape R20A and R20B to per experiment, spin and frequency.
> - R20A_axis = R20A.reshape(self.ei, self.si, self.mi)
> - R20B_axis = R20B.reshape(self.ei, self.si, self.mi)
> + R20A_axis = R20A.reshape(self.NE, self.NS, self.NM)
> + R20B_axis = R20B.reshape(self.NE, self.NS, self.NM)
>
> # Expand R20A and R20B axis to offset and dispersion points.
> R20A_axis = R20A_axis[:,:,:,None,None]
> R20B_axis = R20B_axis[:,:,:,None,None]
>
> # Tile R20A and R20B according to maximum of dispersion points.
> Multiply with spin structure array.
> - R20A_axis = tile(R20A_axis, (1, 1, 1, self.oi, self.di)) *
> self.disp_struct
> - R20B_axis = tile(R20B_axis, (1, 1, 1, self.oi, self.di)) *
> self.disp_struct
> + R20A_axis = tile(R20A_axis, (1, 1, 1, self.NO, self.ND)) *
> self.disp_struct
> + R20B_axis = tile(R20B_axis, (1, 1, 1, self.NO, self.ND)) *
> self.disp_struct
>
> ## Back calculate the R2eff values.
> r2eff_CR72(r20a=R20A_axis, r20b=R20B_axis, pA=pA, dw=dw_frq_a,
> kex=kex, cpmg_frqs=self.cpmg_frqs_a, back_calc=self.back_calc_a,
> num_points=self.num_disp_points_a)
>
>
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