Author: bugman
Date: Wed Dec 4 09:42:18 2013
New Revision: 21762
URL: http://svn.gna.org/viewcvs/relax?rev=21762&view=rev
Log:
Huge speed ups of the relaxation dispersion analysis.
This is due to the removal of huge inefficiencies in the loop_point(),
return_cpmg_frqs() and
return_spin_lock_nu1() functions of the
specific_analysis.relax_disp.disp_data module. Two new
functions return_cpmg_frqs_single() and return_spin_lock_nu1_single() have
been introduces to pull
out the nu_CPMG and spin-lock field strengths for a given experiment and
spectrometer frequency.
This avoids calling the loop_exp() and loop_frq() functions from within
loop_point() which itself
is often called inside a loop_exp() and loop_frq() sequence.
Modified:
trunk/specific_analyses/relax_disp/disp_data.py
Modified: trunk/specific_analyses/relax_disp/disp_data.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/disp_data.py?rev=21762&r1=21761&r2=21762&view=diff
==============================================================================
--- trunk/specific_analyses/relax_disp/disp_data.py (original)
+++ trunk/specific_analyses/relax_disp/disp_data.py Wed Dec 4 09:42:18 2013
@@ -908,14 +908,11 @@
# Assemble the dispersion data.
ref_flag = not skip_ref
if cdp.exp_type_list[exp_type_index] in EXP_TYPE_LIST_CPMG:
- fields = return_cpmg_frqs(ref_flag=ref_flag)
+ fields =
return_cpmg_frqs_single(exp_type=cdp.exp_type_list[exp_type_index],
frq=return_value_from_frq_index(frq_index=frq_index), ref_flag=ref_flag)
elif cdp.exp_type_list[exp_type_index] in EXP_TYPE_LIST_R1RHO:
- fields = return_spin_lock_nu1(ref_flag=ref_flag)
+ fields =
return_spin_lock_nu1_single(exp_type=cdp.exp_type_list[exp_type_index],
frq=return_value_from_frq_index(frq_index=frq_index), ref_flag=ref_flag)
else:
raise RelaxError("The experiment type '%s' is unknown." %
cdp.exp_type_list[exp_type_index])
-
- # Alias the correct structure.
- fields = fields[exp_type_index][frq_index]
# Initialise the index.
point_index = -1
@@ -1967,14 +1964,31 @@
# Loop over the frequencies.
for point in cdp.cpmg_frqs_list:
+ # Skip reference points.
if (not ref_flag) and point == None:
continue
- # Fetch all of the matching intensity keys.
- keys = find_intensity_keys(exp_type=exp_type, frq=frq,
point=point, raise_error=False)
+ # Find a matching experiment ID.
+ found = False
+ for id in cdp.exp_type.keys():
+ # Skip non-matching experiments.
+ if cdp.exp_type[id] != exp_type:
+ continue
+
+ # Skip non-matching spectrometer frequencies.
+ if hasattr(cdp, 'spectrometer_frq') and
cdp.spectrometer_frq[id] != frq:
+ continue
+
+ # Skip non-matching points.
+ if cdp.cpmg_frqs[id] != point:
+ continue
+
+ # Found.
+ found = True
+ break
# No data.
- if not len(keys):
+ if not found:
continue
# Add the data.
@@ -1985,6 +1999,62 @@
# Return the data.
return cpmg_frqs
+
+
+def return_cpmg_frqs_single(exp_type=None, frq=None, ref_flag=True):
+ """Return the list of nu_CPMG frequencies.
+
+ @keyword exp_type: The experiment type.
+ @type exp_type: str
+ @keyword frq: The spectrometer frequency in Hz.
+ @type frq: float
+ @keyword ref_flag: A flag which if False will cause the reference
spectrum frequency of None to be removed from the list.
+ @type ref_flag: bool
+ @return: The list of nu_CPMG frequencies in Hz.
+ @rtype: numpy rank-1 float64 array
+ """
+
+ # No data.
+ if not hasattr(cdp, 'cpmg_frqs_list'):
+ return None
+
+ # Initialise.
+ cpmg_frqs = []
+
+ # Loop over the points.
+ for point in cdp.cpmg_frqs_list:
+ # Skip reference points.
+ if (not ref_flag) and point == None:
+ continue
+
+ # Find a matching experiment ID.
+ found = False
+ for id in cdp.exp_type.keys():
+ # Skip non-matching experiments.
+ if cdp.exp_type[id] != exp_type:
+ continue
+
+ # Skip non-matching spectrometer frequencies.
+ if hasattr(cdp, 'spectrometer_frq') and cdp.spectrometer_frq[id]
!= frq:
+ continue
+
+ # Skip non-matching points.
+ if cdp.cpmg_frqs[id] != point:
+ continue
+
+ # Found.
+ found = True
+ break
+
+ # No data.
+ if not found:
+ continue
+
+ # Add the data.
+ cpmg_frqs.append(point)
+
+ # Return the data as a numpy array.
+ return array(cpmg_frqs, float64)
def return_index_from_disp_point(value, exp_type=None):
@@ -2596,11 +2666,27 @@
if (not ref_flag) and point == None:
continue
- # Fetch all of the matching intensity keys.
- keys = find_intensity_keys(exp_type=exp_type, frq=frq,
point=point, raise_error=False)
+ # Find a matching experiment ID.
+ found = False
+ for id in cdp.exp_type.keys():
+ # Skip non-matching experiments.
+ if cdp.exp_type[id] != exp_type:
+ continue
+
+ # Skip non-matching spectrometer frequencies.
+ if hasattr(cdp, 'spectrometer_frq') and
cdp.spectrometer_frq[id] != frq:
+ continue
+
+ # Skip non-matching points.
+ if cdp.spin_lock_nu1[id] != point:
+ continue
+
+ # Found.
+ found = True
+ break
# No data.
- if not len(keys):
+ if not found:
continue
# Add the data.
@@ -2611,6 +2697,62 @@
# Return the data.
return nu1
+
+
+def return_spin_lock_nu1_single(exp_type=None, frq=None, ref_flag=True):
+ """Return the list of spin-lock field strengths.
+
+ @keyword exp_type: The experiment type.
+ @type exp_type: str
+ @keyword frq: The spectrometer frequency in Hz.
+ @type frq: float
+ @keyword ref_flag: A flag which if False will cause the reference
spectrum frequency of None to be removed from the list.
+ @type ref_flag: bool
+ @return: The list of spin-lock field strengths in Hz.
+ @rtype: numpy rank-1 float64 array
+ """
+
+ # No data.
+ if not hasattr(cdp, 'spin_lock_nu1_list'):
+ return None
+
+ # Initialise.
+ nu1 = []
+
+ # Loop over the points.
+ for point in cdp.spin_lock_nu1_list:
+ # Skip reference points.
+ if (not ref_flag) and point == None:
+ continue
+
+ # Find a matching experiment ID.
+ found = False
+ for id in cdp.exp_type.keys():
+ # Skip non-matching experiments.
+ if cdp.exp_type[id] != exp_type:
+ continue
+
+ # Skip non-matching spectrometer frequencies.
+ if hasattr(cdp, 'spectrometer_frq') and cdp.spectrometer_frq[id]
!= frq:
+ continue
+
+ # Skip non-matching points.
+ if cdp.spin_lock_nu1[id] != point:
+ continue
+
+ # Found.
+ found = True
+ break
+
+ # No data.
+ if not found:
+ continue
+
+ # Add the data.
+ nu1.append(point)
+
+ # Return the data as a numpy array.
+ return array(nu1, float64)
def return_value_from_frq_index(frq_index=None):
r21762 - /trunk/specific_analyses/relax_disp/disp_data.py