Author: bugman
Date: Wed Sep 4 19:03:17 2013
New Revision: 20817
URL: http://svn.gna.org/viewcvs/relax?rev=20817&view=rev
Log:
Redesigned the relax_disp.exp_type user function to be associated with
spectrum IDs.
This follows from http://thread.gmane.org/gmane.science.nmr.relax.devel/4530,
the thread about
supporting multiple data types such as SQ+MQ data simultaneously.
The user function backend has been moved from
specific_analyses.relax_disp.api to
specific_analyses.relax_disp.disp_data. A few temporary code additions have
been made to keep the
user function functional with the current dispersion code.
Modified:
branches/relax_disp/specific_analyses/relax_disp/api.py
branches/relax_disp/specific_analyses/relax_disp/disp_data.py
branches/relax_disp/user_functions/relax_disp.py
Modified: branches/relax_disp/specific_analyses/relax_disp/api.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/api.py?rev=20817&r1=20816&r2=20817&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/api.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/api.py Wed Sep 4
19:03:17 2013
@@ -278,36 +278,6 @@
# Return the IDs.
return ids
-
-
- def _exp_type(self, exp_type='cpmg fixed'):
- """Select the relaxation dispersion experiment type performed.
-
- @keyword exp: The relaxation dispersion experiment type. Can be one
of 'cpmg fixed', 'cpmg exponential', 'r1rho fixed' or 'r1rho exponential'.
- @type exp: str
- """
-
- # Test if the current pipe exists.
- pipes.test()
-
- # Printouts.
- if exp_type == 'cpmg fixed':
- print("The fixed relaxation time period CPMG-type experiments.")
- elif exp_type == 'cpmg exponential':
- print("The CPMG-type experiments consisting of full exponential
curves for each dispersion point.")
- elif exp_type == 'r1rho fixed':
- print("The fixed relaxation time period R1rho-type experiments.")
- elif exp_type == 'r1rho exponential':
- print("The R1rho-type experiments consisting of full exponential
curves for each dispersion point.")
- else:
- raise RelaxError("The relaxation dispersion experiment '%s' is
invalid." % exp_type)
-
- # Sanity check.
- if exp_type not in EXP_TYPE_LIST_FIXED_TIME and exp_type not in
EXP_TYPE_LIST_VAR_TIME:
- raise RelaxError("The experiment type '%s' is neither a fixed
relaxation time period or variable relaxation time period experiment." %
exp_type)
-
- # Store the value.
- cdp.exp_type = exp_type
def _grid_search_setup(self, spins=None, param_vector=None, lower=None,
upper=None, inc=None, scaling_matrix=None):
Modified: branches/relax_disp/specific_analyses/relax_disp/disp_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/disp_data.py?rev=20817&r1=20816&r2=20817&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/disp_data.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/disp_data.py Wed Sep 4
19:03:17 2013
@@ -46,7 +46,8 @@
from pipe_control import pipes
from pipe_control.mol_res_spin import exists_mol_res_spin_data, return_spin,
spin_loop
from pipe_control.result_files import add_result_file
-from specific_analyses.relax_disp.variables import EXP_TYPE_LIST_CPMG,
EXP_TYPE_LIST_FIXED_TIME, EXP_TYPE_LIST_R1RHO
+from pipe_control.spectrum import check_spectrum_id
+from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_FIXED,
EXP_TYPE_CPMG_EXP, EXP_TYPE_DESC_CPMG_FIXED, EXP_TYPE_DESC_CPMG_EXP,
EXP_TYPE_DESC_R1RHO_FIXED, EXP_TYPE_DESC_R1RHO_EXP, EXP_TYPE_LIST,
EXP_TYPE_LIST_CPMG, EXP_TYPE_LIST_FIXED_TIME, EXP_TYPE_LIST_R1RHO,
EXP_TYPE_R1RHO_FIXED, EXP_TYPE_R1RHO_EXP
from stat import S_IRWXU, S_IRGRP, S_IROTH
from os import chmod, path, sep
@@ -181,6 +182,55 @@
print("Setting the '%s' spectrum CPMG frequency %s Hz." % (spectrum_id,
cdp.cpmg_frqs[spectrum_id]))
+def exp_type(spectrum_id=None, exp_type=None):
+ """Select the relaxation dispersion experiment type performed.
+
+ @keyword spectrum_id: The spectrum ID string.
+ @type spectrum_id: str
+ @keyword exp: The relaxation dispersion experiment type. It
can be one of 'cpmg fixed', 'cpmg exponential', 'r1rho fixed' or 'r1rho
exponential'.
+ @type exp: str
+ """
+
+ # Data checks.
+ pipes.test()
+ check_spectrum_id(spectrum_id)
+
+ # Check the experiment type.
+ if exp_type not in EXP_TYPE_LIST:
+ raise RelaxError("The relaxation dispersion experiment '%s' is
invalid." % exp_type)
+
+ # FIXME: Temporary solution to keep the branch functional.
+ cdp.exp_type = {}
+
+ # Initialise the experiment type data structures if needed.
+ if not hasattr(cdp, 'exp_type'):
+ cdp.exp_type = {}
+ if not hasattr(cdp, 'exp_type_list'):
+ cdp.exp_type_list = []
+
+ # Store the value.
+ cdp.exp_type[spectrum_id] = exp_type
+
+ # Unique experiments.
+ if cdp.exp_type[spectrum_id] not in cdp.exp_type_list:
+ cdp.exp_type_list.append(cdp.exp_type[spectrum_id])
+
+ # Printout.
+ text = "Setting the '%s' spectrum to" % spectrum_id
+ if exp_type == EXP_TYPE_CPMG_FIXED:
+ text += EXP_TYPE_DESC_CPMG_FIXED + "."
+ elif exp_type == EXP_TYPE_CPMG_EXP:
+ text += EXP_TYPE_DESC_CPMG_EXP + "."
+ elif exp_type == EXP_TYPE_R1RHO_FIXED:
+ text += EXP_TYPE_DESC_R1RHO_FIXED + "."
+ elif exp_type == EXP_TYPE_R1RHO_EXP:
+ text += EXP_TYPE_DESC_R1RHO_EXP + "."
+ print(text)
+
+ # FIXME: Temporary solution to keep the branch functional.
+ cdp.exp_type = exp_type
+
+
def find_intensity_keys(frq=None, point=None, time=None):
"""Return the key corresponding to the spectrometer frequency,
dispersion point, and relaxation time.
Modified: branches/relax_disp/user_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/user_functions/relax_disp.py?rev=20817&r1=20816&r2=20817&view=diff
==============================================================================
--- branches/relax_disp/user_functions/relax_disp.py (original)
+++ branches/relax_disp/user_functions/relax_disp.py Wed Sep 4 19:03:17 2013
@@ -37,7 +37,7 @@
from pipe_control.mol_res_spin import get_spin_ids
from graphics import ANALYSIS_IMAGE_PATH, WIZARD_IMAGE_PATH
from specific_analyses.relax_disp.cpmgfit import cpmgfit_execute,
cpmgfit_input
-from specific_analyses.relax_disp.disp_data import cpmg_frq,
plot_disp_curves, plot_exp_curves, relax_time, spin_lock_field,
spin_lock_offset
+from specific_analyses.relax_disp.disp_data import cpmg_frq, exp_type,
plot_disp_curves, plot_exp_curves, relax_time, spin_lock_field,
spin_lock_offset
from specific_analyses.relax_disp.nessy import nessy_input
from specific_analyses.relax_disp.parameters import copy
from specific_analyses.relax_disp.sherekhan import sherekhan_input
@@ -224,8 +224,17 @@
# The relax_disp.exp_type user function.
uf = uf_info.add_uf('relax_disp.exp_type')
-uf.title = "Select the type of relaxation dispersion experiments to be
analysed."
+uf.title = "Select the relaxation dispersion experiment type."
uf.title_short = "Relaxation dispersion experiment type selection."
+uf.add_keyarg(
+ name = "spectrum_id",
+ py_type = "str",
+ desc_short = "spectrum ID string",
+ desc = "The spectrum ID string to associate the spin-lock field strength
to.",
+ wiz_element_type = 'combo',
+ wiz_combo_iter = spectrum.get_ids,
+ wiz_read_only = True
+)
uf.add_keyarg(
name = "exp_type",
default = "cpmg fixed",
@@ -236,8 +245,8 @@
wiz_combo_choices = [
"CPMG, fixed time",
"CPMG, full exponential",
- "R1rho, fixed time",
- "R1rho, full exponential"
+ u("R\u2081\u1D68, fixed time"),
+ u("R\u2081\u1D68, full exponential")
],
wiz_combo_data = [
"cpmg fixed",
@@ -249,6 +258,7 @@
)
# Description.
uf.desc.append(Desc_container())
+uf.desc[-1].add_paragraph("Peak intensities should already be loaded using
the spectrum.read_intensities user function. The intensity values will then
be associated with a spectrum ID. To allow for different data types to be
analysed together, each spectrum ID must be associated an experiment type.")
uf.desc[-1].add_paragraph("The currently supported experiments include:")
uf.desc[-1].add_item_list_element("'cpmg fixed'", "The fixed relaxation time
period CPMG-type experiments,")
uf.desc[-1].add_item_list_element("'cpmg exponential'", "The full
exponential curve CPMG-type experiments,")
@@ -275,7 +285,7 @@
uf.desc[-1].add_paragraph("To pick the experiment type 'cpmg fixed' for all
selected spins, type one of:")
uf.desc[-1].add_prompt("relax> relax_disp.exp_type('cpmg fixed')")
uf.desc[-1].add_prompt("relax> relax_disp.exp_type(exp_type='cpmg fixed')")
-uf.backend = relax_disp_obj._exp_type
+uf.backend = exp_type
uf.menu_text = "&exp_type"
uf.wizard_height_desc = 500
uf.wizard_size = (1000, 700)
r20817 - in /branches/relax_disp: specific_analyses/relax_disp/ user_functions/