Author: bugman
Date: Wed Jan 20 09:21:22 2010
New Revision: 10263
URL: http://svn.gna.org/viewcvs/relax?rev=10263&view=rev
Log:
Created feedback to relaxGUI Log Window during Rx calculation
This corresponds to the calc_rx_patch file attached to
https://gna.org/task/?6847 by
Michael Bieri (https://gna.org/users/michaelbieri), in the zip file
https://gna.org/support/download.php?file_id=7726.
added:
class RedirectText --> redirect the relax output to relaxGUI Log Window
# Number of Monte Carlo simulations
global montecarlo
montecarlo = int(global_setting[6])
--> set monte carlo value for updating progress bar in log window
# value for progress bar during monte carlo simulation
global progress
progress = 5.0
--> initial progress value before monte carlo simulation
# redirect relax output and errors to relaxGUI - log panel
redir=RedirectText(self)
sys.stdout=redir
sys.stderr=redir
redirecting system output and error to new created class that updates log
window
Modified:
branches/bieri_gui/gui_bieri/res/calc_rx.py
Modified: branches/bieri_gui/gui_bieri/res/calc_rx.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/gui_bieri/res/calc_rx.py?rev=10263&r1=10262&r2=10263&view=diff
==============================================================================
--- branches/bieri_gui/gui_bieri/res/calc_rx.py (original)
+++ branches/bieri_gui/gui_bieri/res/calc_rx.py Wed Jan 20 09:21:22 2010
@@ -29,24 +29,66 @@
import time
import sys
import os
+import wx
# relax module imports.
from float import floatAsByteArray
from generic_fns.mol_res_spin import generate_spin_id, spin_index_loop,
spin_loop
-from generic_fns import pipes
import generic_fns.structure.main
from relax_errors import RelaxError
from specific_fns.setup import relax_fit_obj
from generic_fns.state import save_state
-from generic_fns import monte_carlo
+from generic_fns import monte_carlo, results, minimise, pipes,
diffusion_tensor, fix, sequence, spectrum, relax_data, selection, value,
grace, eliminate
from minfx.generic import generic_minimise
# relaxGUI module import
from results_analysis import color_code_noe
-from message import relax_run_ok
-
+from message import relax_run_ok, question
+
+
+####### Class to redirect relax output to relaxGUI - log panel and progress
bar
+class RedirectText(object):
+ def __init__(self,aWxTextCtrl):
+ self.out=aWxTextCtrl
-def make_rx(target_dir, rx_list, relax_times, structure_pdb, nmr_freq,
r1_r2, freq_no, unres, self, freqno, global_setting, file_setting,
sequencefile):
+ def write(self,string):
+ global progress
+
+ wx.CallAfter(self.out.log_panel.WriteText, string)
+ time.sleep(0.001) # allow relaxGUI log panel to get refreshed
+
+ # split print out into list
+ a = str(string)
+ check = []
+ check = a.split()
+
+ # update progress bar
+ if 'Simulation' in string:
+ add = round(progress)
+ add_int = int(add)
+ wx.CallAfter(self.out.progress_bar.SetValue, add_int)
+ progress = ( (int(check[1]) * 100) / float(montecarlo + 6)) + 5
+ time.sleep(0.001) # allow relaxGUI progressbar to get refreshed
+
+
+
+########### Rx Calculation
+
+def make_rx(target_dir, rx_list, relax_times, structure_pdb, nmr_freq,
r1_r2, freq_no, unres, main, freqno, global_setting, file_setting,
sequencefile, self):
+
+ # Number of Monte Carlo simulations
+ global montecarlo
+ montecarlo = int(global_setting[6])
+
+ # value for progress bar during monte carlo simulation
+ global progress
+ progress = 5.0
+
+
+ # redirect relax output and errors to relaxGUI - log panel
+ redir=RedirectText(self)
+ sys.stdout=redir
+ sys.stderr=redir
hetero = global_setting[2]
prot = global_setting[3]
@@ -60,6 +102,9 @@
gracedir = str(target_dir) + sep + 'grace'
savefile = str(target_dir) + sep + 'r' + str(r1_r2) + '.' +
str(nmr_freq) + '.out'
+ wx.CallAfter(self.log_panel.AppendText, ('Starting R' + str(r1_r2) +
' calculation\n------------------------------------------\n\n') )
+ time.sleep(0.5)
+
# Select Peak Lists and Relaxation Times
peakfiles = rx_list
@@ -74,7 +119,8 @@
#create unresolved file
if not unres == '':
- print "\nCreating unresolved file"
+ wx.CallAfter(self.log_panel.AppendText, ('Creating unresolved
file\n\n'))
+ time.sleep(0.001)
unres = replace(unres, ",","\n")
unres = replace(unres, " ","")
filename2 = target_dir + sep + 'unresolved'
@@ -85,20 +131,29 @@
pipename = 'Rx ' + str(time.asctime(time.localtime()))
# Create the NOE data pipe.
+ wx.CallAfter(self.log_panel.AppendText, ("pipes.create("+pipename+",
'relax_fit')\n\n"))
+ time.sleep(0.001)
pipes.create(pipename, 'relax_fit')
+
+ # update progress bar
+ wx.CallAfter(self.progress_bar.SetValue, (1))
# Load Sequence
if str(structure_pdb) == '!!! Sequence file selected !!!':
# Read sequence file
- print "Reading Suquence from "+ sequencefile
+ wx.CallAfter(self.log_panel.AppendText, ("Reading Suquence from
"+ sequencefile+'\n\n'))
+ time.sleep(0.001)
sequence.read(sequencefile)
else:
# Load the backbone amide 15N spins from a PDB file.
- print "\nReading sequence from " + str(structure_pdb)
+ wx.CallAfter(self.log_panel.AppendText, ("Reading sequence from
" + str(structure_pdb) + '\n\n'))
generic_fns.structure.main.read_pdb(str(structure_pdb))
generic_fns.structure.main.load_spins(spin_id='@N')
+
+ # update progress bar
+ wx.CallAfter(self.progress_bar.SetValue, (2))
# Spectrum names.
names = peakfiles
@@ -110,7 +165,7 @@
print '\n'
for i in xrange(len(names)):
# Load the peak intensities.
- print "\nspectrum.read(file=str("+names[i]+"),
spectrum_id=str("+names[i]+"), int_method='height',
heteronuc="+str(hetero)+", proton="+str(prot)+")"
+ wx.CallAfter(self.log_panel.AppendText,
("spectrum.read(file=str("+names[i]+"), spectrum_id=str("+names[i]+"),
int_method='height', heteronuc="+str(hetero)+", proton="+str(prot)+")\n\n"))
spectrum.read(file=str(names[i]), spectrum_id=str(names[i]),
int_method='height', heteronuc=hetero, proton=prot)
# Set the relaxation times.
@@ -123,9 +178,11 @@
for j in range(i,(len(names))):
if times[i] == times[j]:
if not i == j:
- print "spectrum.replicated(spectrum_ids=[" + names[i] +
", "+names[j]+"])"
- spectrum.replicated(spectrum_ids=[names[i], names[j]])
-
+ print "spectrum.replicated(spectrum_ids=[" +
str(names[i]) + ", "+str(names[j])+"])"
+ spectrum.replicated(spectrum_ids= [ str(names[i]),
str(names[j])])
+
+ # update progress bar
+ wx.CallAfter(self.progress_bar.SetValue, (4))
# Peak intensity error analysis.
print "spectrum.error_analysis()"
@@ -136,6 +193,9 @@
print '\nDeselect Residues'
selection.desel_read(file=resultsdir + sep + 'unresolved',
res_num_col= 1)
+ # update progress bar
+ wx.CallAfter(self.progress_bar.SetValue, (5))
+
# Set the relaxation curve type.
print "\nrelax_fit_obj._select_model('exp')"
relax_fit_obj._select_model('exp')
@@ -149,8 +209,8 @@
minimise.minimise(min_algor='simplex', min_options=6,
func_tol=1e-25, grad_tol=None, max_iterations=10000000, constraints=False,
scaling=False, verbosity=1)
# Monte Carlo simulations.
- print "\nmonte_carlo.setup(number=500)"
- monte_carlo.setup(number=500)
+ print "\nmonte_carlo.setup(number="+str(montecarlo)+")"
+ monte_carlo.setup(number=montecarlo)
print "\nmonte_carlo.create_data('back_calc')"
monte_carlo.create_data('back_calc')
@@ -187,30 +247,37 @@
print ""
print ""
print ""
- print
"____________________________________________________________________________"
+ print
"________________________________________________________________________________"
print ""
print "calculation finished"
- print ""
+ print
"________________________________________________________________________________"
# list files to results
- self.list_rx.Append(target_dir + sep + 'grace' + sep + 'r' +
str(r1_r2)+'.' + str(nmr_freq) + '.agr')
- self.list_rx.Append(target_dir + sep + 'grace' + sep +
'intensities_norm.' + str(nmr_freq) + '.agr')
+ main.list_rx.Append(target_dir + sep + 'grace' + sep + 'r' +
str(r1_r2)+'.' + str(nmr_freq) + '.agr')
+ main.list_rx.Append(target_dir + sep + 'grace' + sep +
'intensities_norm.' + str(nmr_freq) + '.agr')
# add files to model-free tab
if r1_r2 == 1:
if freqno == 1:
- self.m_r1_1.SetValue(target_dir + sep + 'r1.' +
str(nmr_freq) + '.out')
+ main.m_r1_1.SetValue(target_dir + sep + 'r1.' +
str(nmr_freq) + '.out')
if freqno == 2:
- self.m_r1_2.SetValue(target_dir + sep + 'r1.' +
str(nmr_freq) + '.out')
+ main.m_r1_2.SetValue(target_dir + sep + 'r1.' +
str(nmr_freq) + '.out')
if freqno == 3:
- self.m_r1_3.SetValue(target_dir + sep + 'r1.' +
str(nmr_freq) + '.out')
+ main.m_r1_3.SetValue(target_dir + sep + 'r1.' +
str(nmr_freq) + '.out')
if r1_r2 == 2:
if freqno == 1:
- self.m_r2_1.SetValue(target_dir + sep + 'r2.' +
str(nmr_freq) + '.out')
+ main.m_r2_1.SetValue(target_dir + sep + 'r2.' +
str(nmr_freq) + '.out')
if freqno == 2:
- self.m_r2_2.SetValue(target_dir + sep + 'r2.' +
str(nmr_freq) + '.out')
+ main.m_r2_2.SetValue(target_dir + sep + 'r2.' +
str(nmr_freq) + '.out')
if freqno == 3:
- self.m_r2_3.SetValue(target_dir + sep + 'r2.' +
str(nmr_freq) + '.out')
-
- # Feedback
- relax_run_ok('T' + str(r1_r2) +' calculation was successful !')
+ main.m_r2_3.SetValue(target_dir + sep + 'r2.' +
str(nmr_freq) + '.out')
+
+ # update progress bar
+ wx.CallAfter(self.progress_bar.SetValue, (100))
+
+ # enable close button and disable cancel button
+ wx.CallAfter(self.close_button.Enable, True)
+ wx.CallAfter(self.cancel_button.Enable, False)
+
+ # close thread
+ return
r10263 - /branches/bieri_gui/gui_bieri/res/calc_rx.py