Author: tlinnet
Date: Wed Jun 18 19:29:28 2014
New Revision: 24133
URL: http://svn.gna.org/viewcvs/relax?rev=24133&view=rev
Log:
Removal of junk, and implementing NO REX profiling script.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
Modified:
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_norex.py
Modified:
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_norex.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_norex.py?rev=24133&r1=24132&r2=24133&view=diff
==============================================================================
---
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_norex.py
(original)
+++
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_norex.py
Wed Jun 18 19:29:28 2014
@@ -55,7 +55,7 @@
from lib.physical_constants import g1H, g15N
from target_functions.chi2 import chi2
from target_functions.relax_disp import Dispersion
-from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_SQ,
MODEL_B14_FULL, MODEL_CR72, MODEL_CR72_FULL, MODEL_NS_CPMG_2SITE_3D_FULL,
MODEL_NS_CPMG_2SITE_STAR_FULL
+from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_SQ,
MODEL_NOREX, MODEL_B14_FULL, MODEL_CR72, MODEL_CR72_FULL,
MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_STAR_FULL
# Alter setup.
@@ -183,24 +183,6 @@
@return: The numpy array structures of the R2eff/R1rho values,
errors, missing data, and corresponding Larmor frequencies. For each
structure, the first dimension corresponds to the experiment types, the
second the spins of a spin block, the third to the spectrometer field
strength, and the fourth is the dispersion points. For the Larmor frequency
structure, the fourth dimension is omitted. For R1rho-type data, an offset
dimension is inserted between the spectrometer field strength and the
dispersion points.
@rtype: lists of numpy float arrays, lists of numpy float
arrays, lists of numpy float arrays, numpy rank-2 int array
"""
-
- # Unpack the parameter values.
- # Initialise the post spin parameter indices.
- end_index = []
- # The spin and frequency dependent R2 parameters.
- end_index.append(len(self.exp_type) * self.num_spins *
len(self.fields))
- if self.model in [MODEL_B14_FULL, MODEL_CR72_FULL,
MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_STAR_FULL]:
- end_index.append(2 * len(self.exp_type) * self.num_spins *
len(self.fields))
- # The spin and dependent parameters (phi_ex, dw, padw2).
- end_index.append(end_index[-1] + self.num_spins)
-
- # Unpack the parameter values.
- R20 = self.params[:end_index[1]].reshape(self.num_spins*2,
len(self.fields))
- R20A = R20[::2].flatten()
- R20B = R20[1::2].flatten()
- dw = self.params[end_index[1]:end_index[2]]
- pA = self.params[end_index[2]]
- kex = self.params[end_index[2]+1]
# Initialise the data structures for the target function.
exp_types = []
@@ -272,13 +254,6 @@
# Get the cpmg frq.
cpmg_frqs[ei][mi][oi] = self.points[mi]
- # Calculate how the value should be, so chi2 gets zero.
- # The R20 index.
- r20_index = mi + si*len(self.fields)
- # Convert dw from ppm to rad/s.
- dw_frq = dw[si] * frqs[ei][si][mi]
- r20a=R20A[r20_index]
- r20b=R20B[r20_index]
back_calc = array([0.0]*len(cpmg_frqs[ei][mi][oi]))
for oi in range(len(self.offset)):
@@ -424,11 +399,11 @@
"""
# Return chi2 value.
- chi2 = self.model.func_CR72_full(params)
+ chi2 = self.model.func_NOREX(params)
return chi2
-def single(num_spins=1, model=MODEL_CR72_FULL, iter=None):
+def single(num_spins=1, model=MODEL_NOREX, iter=None):
"""Calculate for a single spin.
@keyword num_spins: Number of spins in the cluster.
@@ -442,7 +417,7 @@
"""
# Instantiate class
- C1 = Profile(num_spins=num_spins, model=model, r2a=5.0, r2b=10.0,
dw=3.0, pA=0.9, kex=1000.0, spins_params=['r2a', 'r2b', 'dw', 'pA', 'kex'])
+ C1 = Profile(num_spins=num_spins, model=model, r2=5.0,
spins_params=['r2'])
# Loop 100 times for each spin in the clustered analysis (to make the
timing numbers equivalent).
for spin_index in xrange(100):
@@ -452,7 +427,7 @@
print("chi2 single:", chi2)
-def cluster(num_spins=100, model=MODEL_CR72_FULL, iter=None):
+def cluster(num_spins=100, model=MODEL_NOREX, iter=None):
"""Calculate for a number of clustered spins.
@keyword num_spins: Number of spins in the cluster.
@@ -466,7 +441,7 @@
"""
# Instantiate class
- C1 = Profile(num_spins=num_spins, model=model, r2a=5.0, r2b=10.0,
dw=3.0, pA=0.9, kex=1000.0, spins_params=['r2a', 'r2b', 'dw', 'pA', 'kex'])
+ C1 = Profile(num_spins=num_spins, model=model, r2=5.0,
spins_params=['r2'])
# Repeat the function call, to simulate minimisation.
for i in xrange(iter):
@@ -477,38 +452,3 @@
# Execute main function.
if __name__ == "__main__":
main()
-
-def test_reshape():
- C1 = Profile(num_spins=1, model=MODEL_CR72_FULL, r2a=5.0, r2b=10.0,
dw=3.0, pA=0.9, kex=1000.0, spins_params=['r2a', 'r2b', 'dw', 'pA', 'kex'])
- end_index = C1.model.end_index
- #print("end_index:", end_index)
- num_spins = C1.model.num_spins
- #print("num_spins:", num_spins)
- num_frq = C1.model.num_frq
- #print("num_frq:", num_frq)
- params = C1.params
- #print("params", params)
-
- R20 = params[:end_index[1]].reshape(num_spins*2, num_frq)
- R20A = R20[::2].flatten()
- R20B = R20[1::2].flatten()
- dw = params[end_index[1]:end_index[2]]
- pA = params[end_index[2]]
- kex = params[end_index[2]+1]
- print("R20A", R20A, len(R20A))
- print("R20B", R20B, len(R20B))
- print("dw", dw, len(dw))
- print("dw", pA)
- print("kex", kex)
-
- for si in range(num_spins):
- for mi in range(num_frq):
- r20_index = mi + si*num_frq
- r20a=R20A[r20_index]
- r20b=R20B[r20_index]
- print("r20a", r20a, "r20b", r20b)
-
- model = C1.calc(params)
- print(model)
-
-#test_reshape()
r24133 - /branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_norex.py