Author: bugman
Date: Wed Feb 4 13:57:37 2015
New Revision: 27506
URL: http://svn.gna.org/viewcvs/relax?rev=27506&view=rev
Log:
Created the new devel_scripts/memory_management/ directory.
This will be used for holding all of the memory C module leak detection, GUI
object leak detection,
memory management, etc. development scripts.
Added:
trunk/devel_scripts/GUI_uf_minimise_execute.py
- copied unchanged from r27505,
trunk/devel_scripts/memory_leak_test_GUI_uf.py
trunk/devel_scripts/memory_management/
trunk/devel_scripts/memory_management/leak_test_relax_fit.py
- copied unchanged from r27504,
trunk/devel_scripts/memory_leak_test_relax_fit.py
Removed:
trunk/devel_scripts/memory_leak_test_GUI_uf.py
trunk/devel_scripts/memory_leak_test_relax_fit.py
Removed: trunk/devel_scripts/memory_leak_test_GUI_uf.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/devel_scripts/memory_leak_test_GUI_uf.py?rev=27505&view=auto
==============================================================================
--- trunk/devel_scripts/memory_leak_test_GUI_uf.py (original)
+++ trunk/devel_scripts/memory_leak_test_GUI_uf.py (removed)
@@ -1,276 +0,0 @@
-###############################################################################
-#
#
-# Copyright (C) 2013-2015 Edward d'Auvergne
#
-#
#
-# This file is part of the program relax (http://www.nmr-relax.com).
#
-#
#
-# This program is free software: you can redistribute it and/or modify
#
-# it under the terms of the GNU General Public License as published by
#
-# the Free Software Foundation, either version 3 of the License, or
#
-# (at your option) any later version.
#
-#
#
-# This program is distributed in the hope that it will be useful,
#
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
#
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
-# GNU General Public License for more details.
#
-#
#
-# You should have received a copy of the GNU General Public License
#
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
-#
#
-###############################################################################
-
-"""Script for relaxation curve fitting.
-
-Run with a normal version of Python, i.e. a debugging version is not needed,
with:
-
-$ ./relax devel_scripts/memory_leak_test_GUI_uf.py
-"""
-
-# Python module imports.
-from os import sep
-from pympler import muppy
-import sys
-import wx
-
-# relax module imports.
-from data_store import Relax_data_store; ds = Relax_data_store()
-from gui import relax_gui
-from gui.controller import Controller
-from gui.fonts import font
-from gui.interpreter import Interpreter
-from gui.uf_objects import Uf_storage; uf_store = Uf_storage()
-from lib.errors import RelaxError
-from status import Status; status = Status()
-from user_functions.data import Uf_info; uf_info = Uf_info()
-
-
-
-class Controller:
- """Dummy relax controller."""
-
- def __init__(self):
- self.log_panel = Log_panel()
-
-
-
-class Log_panel:
- """Dummy relax controller log panel."""
-
- def on_goto_end(self, arg1):
- """Dummy function."""
-
-
-
-class Testing_frame(wx.Frame):
- """Testing frame."""
-
- def __init__(self, parent, title):
- """Set up a minimal relax GUI."""
-
- # Initialise the frame.
- wx.Frame.__init__(self, parent, title=title, size=(200,100))
-
- # Set up a pseudo-relax GUI.
- app = wx.GetApp()
- app.gui = self
-
- # Set up some standard interface-wide fonts.
- font.setup()
-
- # Initialise the special interpreter thread object.
- self.interpreter = Interpreter()
-
- # Build the controller, but don't show it.
- self.controller = Controller()
-
- self.test()
- self.Show(True)
-
-
- def _execute_uf(self, *args, **kargs):
- """Execute the given user function.
-
- @keyword uf_name: The name of the user function.
- @type uf_name: str
- """
-
- # Checks.
- if 'uf_name' not in kargs:
- raise RelaxError("The user function name argument 'uf_name' has
not been supplied.")
-
- # Process the user function name.
- uf_name = kargs.pop('uf_name')
-
- # Get the user function data object.
- uf_data = uf_info.get_uf(uf_name)
-
- # Convert the args into keyword args.
- for i in range(len(args)):
- # The keyword name for this arg.
- name = uf_data.kargs[i]['name']
-
- # Check.
- if name in kargs:
- raise RelaxError("The argument '%s' clashes with the %s
keyword argument of '%s'." % (arg[i], name, kargs[name]))
-
- # Set the keyword arg.
- kargs[name] = args[i]
-
- # Add the keyword args not supplied, using the default value.
- for i in range(len(uf_data.kargs)):
- # Alias.
- arg = uf_data.kargs[i]
-
- # Already set.
- if arg['name'] in kargs:
- continue
-
- # Set the default.
- kargs[arg['name']] = arg['default']
-
- # Merge the file and directory args, as needed.
- for i in range(len(uf_data.kargs)):
- # Alias.
- arg = uf_data.kargs[i]
-
- # File selection and associated directory arg.
- if arg['arg_type'] == 'dir' and arg['name'] in kargs:
- # Find the associated file selection arg name.
- for j in range(len(uf_data.kargs)):
- if uf_data.kargs[j]['arg_type'] == 'file sel':
- file_sel_name = uf_data.kargs[j]['name']
-
- # Prepend the directory to the file, if needed and supplied.
- if file_sel_name in kargs and kargs[arg['name']]:
- kargs[file_sel_name] = kargs[arg['name']] + sep +
kargs[file_sel_name]
-
- # Remove the directory argument.
- kargs.pop(arg['name'])
-
- # The user function object.
- uf = uf_store[uf_name]
-
- # Force synchronous operation of the user functions.
- status.gui_uf_force_sync = True
-
- # Call the GUI user function object with all keyword args, but do
not execute the wizard.
- uf(wx_wizard_run=False, **kargs)
-
- # Execute the user function, by mimicking a click on 'ok'.
- uf.wizard._ok()
-
- # Restore the synchronous or asynchronous operation of the user
functions so the GUI can return to normal.
- status.gui_uf_force_sync = False
-
- # Destroy the user function object.
- uf.Destroy()
-
-
- def show_controller(self, arg1):
- """Dummy function."""
-
-
- def test(self):
- """Run the tests."""
-
- # Minimise via the GUI user function.
- file = open('muppy_log', 'w')
- for i in range(10000):
- self._execute_uf(uf_name='minimise.execute',
min_algor='simplex', constraints=False)
- if not i % 100:
- file.write("Iteration %i\n" % i)
- file.write("Muppy heap:\n")
- for line in
muppy.summary.format_(muppy.summary.summarize(muppy.get_objects())):
- file.write("%s\n" % line)
- file.write("\n\n\n")
- file.flush()
-
- print("Finished!")
-
-
-# Missing intensity type (allow this script to run outside of the system
test framework).
-if not hasattr(ds, 'int_type'):
- ds.int_type = 'height'
-
-# Missing temporary directory.
-if not hasattr(ds, 'tmpdir'):
- ds.tmpdir = 'temp'
-
-# Create the data pipe.
-pipe.create('rx', 'relax_fit')
-
-# The path to the data files.
-data_path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'curve_fitting'
-
-# Load the sequence.
-sequence.read('Ap4Aase.seq', dir=status.install_path +
sep+'test_suite'+sep+'shared_data', res_num_col=1, res_name_col=2)
-
-# Deselect unresolved spins.
-deselect.read(file='unresolved', dir=data_path, res_num_col=1)
-
-# Name the spins so they can be matched to the assignments.
-spin.name(name='N')
-
-# Spectrum names.
-names = [
- 'T2_ncyc1_ave',
- 'T2_ncyc1b_ave',
- 'T2_ncyc2_ave',
- 'T2_ncyc4_ave',
- 'T2_ncyc4b_ave',
- 'T2_ncyc6_ave',
- 'T2_ncyc9_ave',
- 'T2_ncyc9b_ave',
- 'T2_ncyc11_ave',
- 'T2_ncyc11b_ave'
-]
-
-# Relaxation times (in seconds).
-times = [
- 0.0176,
- 0.0176,
- 0.0352,
- 0.0704,
- 0.0704,
- 0.1056,
- 0.1584,
- 0.1584,
- 0.1936,
- 0.1936
-]
-
-# Load the data twice to test data deletion.
-for iter in range(2):
- # Loop over the spectra.
- for i in range(len(names)):
- # Load the peak intensities.
- spectrum.read_intensities(file=names[i]+'.list', dir=data_path,
spectrum_id=names[i], int_method=ds.int_type)
-
- # Set the relaxation times.
- relax_fit.relax_time(time=times[i], spectrum_id=names[i])
-
- # Specify the duplicated spectra.
- spectrum.replicated(spectrum_ids=['T2_ncyc1_ave', 'T2_ncyc1b_ave'])
- spectrum.replicated(spectrum_ids=['T2_ncyc4_ave', 'T2_ncyc4b_ave'])
- spectrum.replicated(spectrum_ids=['T2_ncyc9b_ave', 'T2_ncyc9_ave'])
- spectrum.replicated(spectrum_ids=['T2_ncyc11_ave', 'T2_ncyc11b_ave'])
-
- # Peak intensity error analysis.
- spectrum.error_analysis()
-
- # Delete the data.
- if iter == 0:
- for i in range(len(names)):
- spectrum.delete(names[i])
-
-# Set the relaxation curve type.
-relax_fit.select_model('exp')
-
-# Grid search.
-minimise.grid_search(inc=11)
-
-# Set up and execute the GUI.
-app = wx.App(False)
-frame = Testing_frame(None, "GUI memory test")
-frame.Show(True)
-app.MainLoop()
Removed: trunk/devel_scripts/memory_leak_test_relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/devel_scripts/memory_leak_test_relax_fit.py?rev=27505&view=auto
==============================================================================
--- trunk/devel_scripts/memory_leak_test_relax_fit.py (original)
+++ trunk/devel_scripts/memory_leak_test_relax_fit.py (removed)
@@ -1,147 +0,0 @@
-###############################################################################
-#
#
-# Copyright (C) 2013-2015 Edward d'Auvergne
#
-#
#
-# This file is part of the program relax (http://www.nmr-relax.com).
#
-#
#
-# This program is free software: you can redistribute it and/or modify
#
-# it under the terms of the GNU General Public License as published by
#
-# the Free Software Foundation, either version 3 of the License, or
#
-# (at your option) any later version.
#
-#
#
-# This program is distributed in the hope that it will be useful,
#
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
#
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
-# GNU General Public License for more details.
#
-#
#
-# You should have received a copy of the GNU General Public License
#
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
-#
#
-###############################################################################
-
-"""Script for relaxation curve fitting.
-
-Run with a debugging compiled version of Python, eg:
-
-/data/python/pydebug/bin/python relax
devel_scripts/memory_leak_test_relax_fit.py
-
-and build the C module with:
-
-gcc -o target_functions/c_chi2.os -c
-I/data/python/pydebug/include/python2.7/ -fPIC target_functions/c_chi2.c
-gcc -o target_functions/exponential.os -c
-I/data/python/pydebug/include/python2.7/ -fPIC target_functions/exponential.c
-gcc -o target_functions/exponential_inv.os -c
-I/data/python/pydebug/include/python2.7/ -fPIC
target_functions/exponential_inv.c
-gcc -o target_functions/exponential_sat.os -c
-I/data/python/pydebug/include/python2.7/ -fPIC
target_functions/exponential_sat.c
-gcc -o target_functions/relax_fit.os -c
-I/data/python/pydebug/include/python2.7/ -fPIC target_functions/relax_fit.c
-gcc -o target_functions/relax_fit.so -shared target_functions/c_chi2.os
target_functions/exponential.os target_functions/exponential_inv.os
target_functions/exponential_sat.os target_functions/relax_fit.os
-"""
-
-
-# Python module imports.
-from os import sep
-import sys
-
-# Check.
-if not hasattr(sys, 'gettotalrefcount'):
- print("This is not a debugging compiled version of Python, quitting!")
- sys.exit()
-
-# relax module imports.
-from data_store import Relax_data_store; ds = Relax_data_store()
-from status import Status; status = Status()
-
-
-# Missing intensity type (allow this script to run outside of the system
test framework).
-if not hasattr(ds, 'int_type'):
- ds.int_type = 'height'
-
-# Missing temporary directory.
-if not hasattr(ds, 'tmpdir'):
- ds.tmpdir = 'temp'
-
-# Create the data pipe.
-pipe.create('rx', 'relax_fit')
-
-# The path to the data files.
-data_path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'curve_fitting'
-
-# Load the sequence.
-sequence.read('Ap4Aase.seq', dir=status.install_path +
sep+'test_suite'+sep+'shared_data', res_num_col=1, res_name_col=2)
-
-# Deselect unresolved spins.
-deselect.read(file='unresolved', dir=data_path, res_num_col=1)
-
-# Name the spins so they can be matched to the assignments.
-spin.name(name='N')
-
-# Spectrum names.
-names = [
- 'T2_ncyc1_ave',
- 'T2_ncyc1b_ave',
- 'T2_ncyc2_ave',
- 'T2_ncyc4_ave',
- 'T2_ncyc4b_ave',
- 'T2_ncyc6_ave',
- 'T2_ncyc9_ave',
- 'T2_ncyc9b_ave',
- 'T2_ncyc11_ave',
- 'T2_ncyc11b_ave'
-]
-
-# Relaxation times (in seconds).
-times = [
- 0.0176,
- 0.0176,
- 0.0352,
- 0.0704,
- 0.0704,
- 0.1056,
- 0.1584,
- 0.1584,
- 0.1936,
- 0.1936
-]
-
-# Load the data twice to test data deletion.
-for iter in range(2):
- # Loop over the spectra.
- for i in range(len(names)):
- # Load the peak intensities.
- spectrum.read_intensities(file=names[i]+'.list', dir=data_path,
spectrum_id=names[i], int_method=ds.int_type)
-
- # Set the relaxation times.
- relax_fit.relax_time(time=times[i], spectrum_id=names[i])
-
- # Specify the duplicated spectra.
- spectrum.replicated(spectrum_ids=['T2_ncyc1_ave', 'T2_ncyc1b_ave'])
- spectrum.replicated(spectrum_ids=['T2_ncyc4_ave', 'T2_ncyc4b_ave'])
- spectrum.replicated(spectrum_ids=['T2_ncyc9b_ave', 'T2_ncyc9_ave'])
- spectrum.replicated(spectrum_ids=['T2_ncyc11_ave', 'T2_ncyc11b_ave'])
-
- # Peak intensity error analysis.
- spectrum.error_analysis()
-
- # Delete the data.
- if iter == 0:
- for i in range(len(names)):
- spectrum.delete(names[i])
-
-# Set the relaxation curve type.
-relax_fit.select_model('exp')
-
-# Grid search.
-minimise.grid_search(inc=11)
-
-# Minimise.
-from guppy import hpy
-file = open('guppy_log', 'w')
-for i in range(10000):
- minimise.execute('simplex', constraints=False)
- if not i % 100:
- file.write("Iteration %i\n" % i)
- file.write("Reference counts:\n%s\n\n" % sys.gettotalrefcount())
- h = hpy()
- file.write("Guppy heap:\n%s\n\n\n" % h.heap())
- file.flush()
-
-
-print("Finished :)")
r27506 - in /trunk/devel_scripts: ./ memory_management/