Looking at output, I get:
This means that all calculated R2eff is 1.0 ???
relax> relax_disp.r2eff_read_spin(id='CPMG_599.9', spin_id=':1@N',
file='CPMG_599.9_1_N.txt',
dir='/var/folders/ww/1jkhkh315x57jglgxnr9g24w0000gp/T/tmpVtMOA1',
disp_point_col=1, offset_col=None, data_col=2, error_col=3, sep=None)
Opening the file
'/var/folders/ww/1jkhkh315x57jglgxnr9g24w0000gp/T/tmpVtMOA1/CPMG_599.9_1_N.txt'
for reading.
The following R2eff/R1rho data has been loaded into the relax data store:
# R2eff_key Disp_point R2eff
R2eff_error
sq_cpmg_599.89086170_0.000_33.333 33.333333333333336
1.000000000000000 0.100000000000000
sq_cpmg_599.89086170_0.000_66.667 66.666666666666671
1.000000000000000 0.100000000000000
sq_cpmg_599.89086170_0.000_133.333 133.333333333333343
1.000000000000000 0.100000000000000
sq_cpmg_599.89086170_0.000_166.667 166.666666666666686
1.000000000000000 0.100000000000000
sq_cpmg_599.89086170_0.000_333.333 333.333333333333371
1.000000000000000 0.100000000000000
sq_cpmg_599.89086170_0.000_500.000 500.000000000000000
1.000000000000000 0.100000000000000
sq_cpmg_599.89086170_0.000_666.667 666.666666666666742
1.000000000000000 0.100000000000000
sq_cpmg_599.89086170_0.000_1000.000 1000.000000000000000
1.000000000000000 0.100000000000000
Opening the file
'/var/folders/ww/1jkhkh315x57jglgxnr9g24w0000gp/T/tmpVtMOA1/CPMG_499.9_1_N.txt'
for writing.
relax> relax_disp.r2eff_read_spin(id='CPMG_499.9', spin_id=':1@N',
file='CPMG_499.9_1_N.txt',
dir='/var/folders/ww/1jkhkh315x57jglgxnr9g24w0000gp/T/tmpVtMOA1',
disp_point_col=1, offset_col=None, data_col=2, error_col=3, sep=None)
Opening the file
'/var/folders/ww/1jkhkh315x57jglgxnr9g24w0000gp/T/tmpVtMOA1/CPMG_499.9_1_N.txt'
for reading.
The following R2eff/R1rho data has been loaded into the relax data store:
# R2eff_key Disp_point R2eff
R2eff_error
sq_cpmg_499.89086170_0.000_40.000 40.000000000000000
1.000000000000000 0.100000000000000
sq_cpmg_499.89086170_0.000_80.000 80.000000000000000
1.000000000000000 0.100000000000000
sq_cpmg_499.89086170_0.000_160.000 160.000000000000000
1.000000000000000 0.100000000000000
sq_cpmg_499.89086170_0.000_200.000 200.000000000000000
1.000000000000000 0.100000000000000
sq_cpmg_499.89086170_0.000_600.000 600.000000000000000
1.000000000000000 0.100000000000000
sq_cpmg_499.89086170_0.000_700.000 700.000000000000000
1.000000000000000 0.100000000000000
sq_cpmg_499.89086170_0.000_800.000 800.000000000000000
1.000000000000000 0.100000000000000
sq_cpmg_499.89086170_0.000_1000.000 1000.000000000000000
1.000000000000000 0.100000000000000
Generating data with MODEL:CR72, for spin id::1@N
Opening the file
'/var/folders/ww/1jkhkh315x57jglgxnr9g24w0000gp/T/tmpVtMOA1/CPMG_599.9_1_N.txt'
for writing.
relax> relax_disp.r2eff_read_spin(id='CPMG_599.9', spin_id=':1@N',
file='CPMG_599.9_1_N.txt',
dir='/var/folders/ww/1jkhkh315x57jglgxnr9g24w0000gp/T/tmpVtMOA1',
disp_point_col=1, offset_col=None, data_col=2, error_col=3, sep=None)
Opening the file
'/var/folders/ww/1jkhkh315x57jglgxnr9g24w0000gp/T/tmpVtMOA1/CPMG_599.9_1_N.txt'
for reading.
The following R2eff/R1rho data has been loaded into the relax data store:
# R2eff_key Disp_point R2eff
R2eff_error
sq_cpmg_599.89086170_0.000_33.333 33.333333333333336
1.000000000000000 0.100000000000000
sq_cpmg_599.89086170_0.000_66.667 66.666666666666671
1.000000000000000 0.100000000000000
sq_cpmg_599.89086170_0.000_133.333 133.333333333333343
1.000000000000000 0.100000000000000
sq_cpmg_599.89086170_0.000_166.667 166.666666666666686
1.000000000000000 0.100000000000000
sq_cpmg_599.89086170_0.000_333.333 333.333333333333371
1.000000000000000 0.100000000000000
sq_cpmg_599.89086170_0.000_500.000 500.000000000000000
1.000000000000000 0.100000000000000
sq_cpmg_599.89086170_0.000_666.667 666.666666666666742
1.000000000000000 0.100000000000000
sq_cpmg_599.89086170_0.000_1000.000 1000.000000000000000
1.000000000000000 0.100000000000000
Generating data with MODEL:CR72, for spin id::1@N
Opening the file
'/var/folders/ww/1jkhkh315x57jglgxnr9g24w0000gp/T/tmpVtMOA1/CPMG_499.9_1_N.txt'
for writing.
relax> relax_disp.r2eff_read_spin(id='CPMG_499.9', spin_id=':1@N',
file='CPMG_499.9_1_N.txt',
dir='/var/folders/ww/1jkhkh315x57jglgxnr9g24w0000gp/T/tmpVtMOA1',
disp_point_col=1, offset_col=None, data_col=2, error_col=3, sep=None)
Opening the file
'/var/folders/ww/1jkhkh315x57jglgxnr9g24w0000gp/T/tmpVtMOA1/CPMG_499.9_1_N.txt'
for reading.
The following R2eff/R1rho data has been loaded into the relax data store:
# R2eff_key Disp_point R2eff
R2eff_error
sq_cpmg_499.89086170_0.000_40.000 40.000000000000000
1.000000000000000 0.100000000000000
sq_cpmg_499.89086170_0.000_80.000 80.000000000000000
1.000000000000000 0.100000000000000
sq_cpmg_499.89086170_0.000_160.000 160.000000000000000
1.000000000000000 0.100000000000000
sq_cpmg_499.89086170_0.000_200.000 200.000000000000000
1.000000000000000 0.100000000000000
sq_cpmg_499.89086170_0.000_600.000 600.000000000000000
1.000000000000000 0.100000000000000
sq_cpmg_499.89086170_0.000_700.000 700.000000000000000
1.000000000000000 0.100000000000000
sq_cpmg_499.89086170_0.000_800.000 800.000000000000000
1.000000000000000 0.100000000000000
2014-06-13 17:54 GMT+02:00 Troels Emtekær Linnet <[email protected]>:
> Or in:
> r2effs = optimisation.back_calc_r2eff(spin=cur_spin, spin_id=cur_spin_id)
>
>
> 2014-06-13 17:52 GMT+02:00 Troels Emtekær Linnet <[email protected]>:
>
> Hi Ed.
>>
>> I think I have broken something somewhere?
>>
>> It must be something with:
>> specific_analyses.relax_disp.data
>> loop_offset_point
>>
>> Best
>> Troels
>>
>>
>> ---------- Forwarded message ----------
>> From: <[email protected]>
>> Date: 2014-06-13 17:31 GMT+02:00
>> Subject: r23942 - /branches/disp_spin_speed/target_functions/relax_disp.py
>> To: [email protected]
>>
>>
>> Author: tlinnet
>> Date: Fri Jun 13 17:31:40 2014
>> New Revision: 23942
>>
>> URL: http://svn.gna.org/viewcvs/relax?rev=23942&view=rev
>> Log:
>> Replaced target function for model ns_cpmg_2site_expanded, to use higher
>> dimensional numpy array structures.
>>
>> That makes the model much faster.
>>
>> I cannot get system test: Relax_disp.test_cpmg_synthetic_dx_map_points
>> to pass.
>>
>> -------
>> File
>> "/Users/tlinnet/software/disp_spin_speed/test_suite/system_tests/relax_disp.py",
>> line 1671, in test_cpmg_synthetic_dx_map_points
>> self.assertEqual(res_file[i], lines[i])
>> AssertionError: '0.76981 3.9169 0.41353 1\n' !=
>> '0.0098838 1.4654 18.661 1\n'
>> -------
>>
>> 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=23942&r1=23941&r2=23942&view=diff
>>
>> ==============================================================================
>> --- branches/disp_spin_speed/target_functions/relax_disp.py (original)
>> +++ branches/disp_spin_speed/target_functions/relax_disp.py Fri Jun
>> 13 17:31:40 2014
>> @@ -396,7 +396,7 @@
>>
>>
>> # Setup special numpy array structures, for higher dimensional
>> computation.
>> - test_models = [MODEL_B14, MODEL_B14_FULL, MODEL_CR72,
>> MODEL_CR72_FULL, MODEL_DPL94, MODEL_IT99, MODEL_LM63, MODEL_M61,
>> MODEL_M61B, MODEL_MP05, MODEL_TAP03, MODEL_TP02, MODEL_TSMFK01]
>> + test_models = [MODEL_B14, MODEL_B14_FULL, MODEL_CR72,
>> MODEL_CR72_FULL, MODEL_DPL94, MODEL_IT99, MODEL_LM63, MODEL_M61,
>> MODEL_M61B, MODEL_MP05, MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_TAP03,
>> MODEL_TP02, MODEL_TSMFK01]
>>
>> if model in test_models + [MODEL_NOREX]:
>> # Get the shape of back_calc structure.
>> @@ -457,10 +457,10 @@
>> self.phi_ex_struct = deepcopy(zeros_a)
>>
>> if model in [MODEL_B14, MODEL_B14_FULL, MODEL_MMQ_CR72,
>> MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL,
>> MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_CPMG_2SITE_STAR,
>> MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_MMQ_2SITE, MODEL_NS_MMQ_3SITE,
>> MODEL_NS_MMQ_3SITE_LINEAR, MODEL_TSMFK01, MODEL_NS_R1RHO_2SITE,
>> MODEL_NS_R1RHO_3SITE, MODEL_NS_R1RHO_3SITE_LINEAR]:
>> - # Expand relax times.
>> - self.inv_relax_times_a = 1.0 / multiply.outer(
>> tile(self.relax_times[:,None],(1, 1, self.NS)).reshape(self.NE, self.NS,
>> self.NM), self.no_nd_struct )
>> - self.power_a = ones(self.numpy_array_shape, int16)
>> + self.relax_times_a = deepcopy(zeros_a)
>> + self.inv_relax_times_a = deepcopy(zeros_a)
>> self.tau_cpmg_a = deepcopy(zeros_a)
>> + self.power_a = zeros(self.numpy_array_shape, int16)
>>
>> # For R1rho data.
>> if model in MODEL_LIST_R1RHO_FULL:
>> @@ -501,8 +501,13 @@
>> self.has_missing = True
>> missing_a[ei][si][mi][oi][di] = 1.0
>> if model in [MODEL_B14, MODEL_B14_FULL,
>> MODEL_MMQ_CR72, MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL,
>> MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_CPMG_2SITE_STAR,
>> MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_MMQ_2SITE, MODEL_NS_MMQ_3SITE,
>> MODEL_NS_MMQ_3SITE_LINEAR, MODEL_TSMFK01, MODEL_NS_R1RHO_2SITE,
>> MODEL_NS_R1RHO_3SITE, MODEL_NS_R1RHO_3SITE_LINEAR]:
>> - self.power_a[ei][si][mi][oi][di] =
>> int(round(self.cpmg_frqs[ei][mi][0][di] * self.relax_times[ei][mi]))
>> - self.tau_cpmg_a[ei][si][mi][oi][di]
>> = 0.25 / self.cpmg_frqs[ei][mi][0][di]
>> +
>> self.relax_times_a[ei][si][mi][oi][di] = self.relax_times[ei][mi]
>> + self.tau_cpmg_a[ei][si][mi][oi][di]
>> = self.tau_cpmg[ei][mi][di]
>> + self.power_a[ei][si][mi][oi][di] =
>> self.power[ei][mi][di]
>> +
>> + if model != MODEL_TSMFK01:
>> +
>> self.inv_relax_times_a[ei][si][mi][oi][di] = self.inv_relax_times[ei][mi]
>> +
>> # For R1rho data.
>> if model in MODEL_LIST_R1RHO_FULL and
>> model != MODEL_NOREX:
>> self.disp_struct[ei][si][mi][oi][di]
>> = 1.0
>> @@ -1500,37 +1505,25 @@
>> pA = params[self.end_index[1]]
>> kex = params[self.end_index[1]+1]
>>
>> - # Once off parameter conversions.
>> - pB = 1.0 - pA
>> - k_BA = pA * kex
>> - k_AB = pB * kex
>> -
>> - # Chi-squared initialisation.
>> - chi2_sum = 0.0
>> -
>> - # Loop over the spins.
>> - for si in range(self.num_spins):
>> - # Loop over the spectrometer frequencies.
>> - for mi in range(self.num_frq):
>> - # The R20 index.
>> - r20_index = mi + si*self.num_frq
>> -
>> - # Convert dw from ppm to rad/s.
>> - dw_frq = dw[si] * self.frqs[0][si][mi]
>> -
>> - # Back calculate the R2eff values.
>> - r2eff_ns_cpmg_2site_expanded(r20=R20[r20_index], pA=pA,
>> dw=dw_frq, k_AB=k_AB, k_BA=k_BA, relax_time=self.relax_times[0][mi],
>> inv_relax_time=self.inv_relax_times[0][mi], tcp=self.tau_cpmg[0][mi],
>> back_calc=self.back_calc[0][si][mi][0],
>> num_points=self.num_disp_points[0][si][mi][0], num_cpmg=self.power[0][mi])
>> -
>> - # For all missing data points, set the back-calculated
>> value to the measured values so that it has no effect on the chi-squared
>> value.
>> - for di in range(self.num_disp_points[0][si][mi][0]):
>> - if self.missing[0][si][mi][0][di]:
>> - self.back_calc[0][si][mi][0][di] =
>> self.values[0][si][mi][0][di]
>> -
>> - # Calculate and return the chi-squared value.
>> - chi2_sum += chi2(self.values[0][si][mi][0],
>> self.back_calc[0][si][mi][0], self.errors[0][si][mi][0])
>> -
>> - # Return the total chi-squared value.
>> - return chi2_sum
>> + # Convert dw from ppm to rad/s. Use the out argument, to pass
>> directly to structure.
>> + multiply( multiply.outer( dw.reshape(self.NE, self.NS),
>> self.nm_no_nd_struct ), self.frqs_a, out=self.dw_struct )
>> +
>> + # Reshape R20A and R20B to per experiment, spin and frequency.
>> + self.r20_struct[:] = multiply.outer( R20.reshape(self.NE,
>> self.NS, self.NM), self.no_nd_struct )
>> +
>> + # Back calculate the R2eff values.
>> + r2eff_ns_cpmg_2site_expanded(r20=self.r20_struct, pA=pA,
>> dw=self.dw_struct, dw_orig=dw, kex=kex, relax_time=self.relax_times_a,
>> inv_relax_time=self.inv_relax_times_a, tcp=self.tau_cpmg_a,
>> back_calc=self.back_calc_a, num_cpmg=self.power_a)
>> +
>> + # Clean the data for all values, which is left over at the end
>> of arrays.
>> + self.back_calc_a = self.back_calc_a*self.disp_struct
>> +
>> + ## For all missing data points, set the back-calculated value to
>> the measured values so that it has no effect on the chi-squared value.
>> + if self.has_missing:
>> + # Replace with values.
>> + self.back_calc_a[self.mask_replace_blank.mask] =
>> self.values_a[self.mask_replace_blank.mask]
>> +
>> + ## Calculate the chi-squared statistic.
>> + return chi2_rankN(self.values_a, self.back_calc_a, self.errors_a)
>>
>>
>> def func_ns_cpmg_2site_star(self, params):
>>
>>
>> _______________________________________________
>> relax (http://www.nmr-relax.com)
>>
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>>
>
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