Author: bugman
Date: Tue Oct 14 19:21:53 2014
New Revision: 26282
URL: http://svn.gna.org/viewcvs/relax?rev=26282&view=rev
Log:
Renaming of the 'dx' user function class to 'mapping'.
In addition, the dx.map user function is now called mapping.setup and the
dx.execute user function
is now mapping.dx_execute.
Added:
branches/space_mapping_refactor/user_functions/mapping.py
- copied, changed from r26280,
branches/space_mapping_refactor/user_functions/dx.py
Removed:
branches/space_mapping_refactor/user_functions/dx.py
Modified:
branches/space_mapping_refactor/user_functions/__init__.py
Modified: branches/space_mapping_refactor/user_functions/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/user_functions/__init__.py?rev=26282&r1=26281&r2=26282&view=diff
==============================================================================
--- branches/space_mapping_refactor/user_functions/__init__.py (original)
+++ branches/space_mapping_refactor/user_functions/__init__.py Tue Oct 14
19:21:53 2014
@@ -43,7 +43,6 @@
'deselect',
'diffusion_tensor',
'domain',
- 'dx',
'eliminate',
'error_analysis',
'fix',
@@ -52,6 +51,7 @@
'interatom',
'j_coupling',
'jw_mapping',
+ 'mapping',
'minimisation',
'model_free',
'model_selection',
@@ -101,7 +101,6 @@
import user_functions.deselect
import user_functions.diffusion_tensor
import user_functions.domain
- import user_functions.dx
import user_functions.eliminate
import user_functions.error_analysis
import user_functions.fix
@@ -110,6 +109,7 @@
import user_functions.interatom
import user_functions.j_coupling
import user_functions.jw_mapping
+ import user_functions.mapping
import user_functions.minimisation
import user_functions.model_free
import user_functions.model_selection
Removed: branches/space_mapping_refactor/user_functions/dx.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/user_functions/dx.py?rev=26281&view=auto
==============================================================================
--- branches/space_mapping_refactor/user_functions/dx.py (original)
+++ branches/space_mapping_refactor/user_functions/dx.py (removed)
@@ -1,235 +0,0 @@
-###############################################################################
-#
#
-# Copyright (C) 2003-2014 Edward d'Auvergne
#
-# Copyright (C) 2014 Troels E. Linnet
#
-#
#
-# 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/>.
#
-#
#
-###############################################################################
-
-# Module docstring.
-"""The dx user function definitions for controlling the OpenDX visualisation
software."""
-
-# Python module imports.
-import dep_check
-if dep_check.wx_module:
- from wx import FD_OPEN
-else:
- FD_OPEN = -1
-
-# relax module imports.
-from graphics import WIZARD_IMAGE_PATH
-from lib.software.opendx.execute import run
-from pipe_control.opendx import map
-from specific_analyses.frame_order.parameter_object import
Frame_order_params; frame_order_params = Frame_order_params()
-from specific_analyses.model_free.parameter_object import Model_free_params;
model_free_params = Model_free_params()
-from specific_analyses.n_state_model.parameter_object import N_state_params;
n_state_params = N_state_params()
-from specific_analyses.relax_disp.parameter_object import Relax_disp_params;
relax_disp_params = Relax_disp_params()
-from user_functions.data import Uf_info; uf_info = Uf_info()
-from user_functions.data import Uf_tables; uf_tables = Uf_tables()
-from user_functions.objects import Desc_container
-
-
-# The user function class.
-uf_class = uf_info.add_class("dx")
-uf_class.title = "Class for interfacing with OpenDX."
-uf_class.menu_text = "&dx"
-uf_class.gui_icon = "relax.opendx"
-
-
-# The dx.execute user function.
-uf = uf_info.add_uf("dx.execute")
-uf.title = "Execute an OpenDX program."
-uf.title_short = "OpenDX execution."
-uf.add_keyarg(
- name = "file_prefix",
- default = "map",
- py_type = "str",
- desc_short = "file name",
- desc = "The file name prefix. For example if file is set to 'temp',
then the OpenDX program temp.net will be loaded."
-)
-uf.add_keyarg(
- name = "dir",
- default = "dx",
- py_type = "str",
- arg_type = "dir sel",
- desc_short = "directory name",
- desc = "The directory to change to for running OpenDX. If this is set
to None, OpenDX will be run in the current directory.",
- can_be_none = True
-)
-uf.add_keyarg(
- name = "dx_exe",
- default = "dx",
- py_type = "str",
- arg_type = "file sel",
- desc_short = "OpenDX executable file name",
- desc = "The OpenDX executable file.",
- wiz_filesel_style = FD_OPEN,
- wiz_filesel_preview = False
-)
-uf.add_keyarg(
- name = "vp_exec",
- default = True,
- py_type = "bool",
- desc_short = "visual program execution flag",
- desc = "A flag specifying whether to execute the visual program
automatically at start-up. The default of True causes the program to be
executed."
-)
-# Description.
-uf.desc.append(Desc_container())
-uf.desc[-1].add_paragraph("This will execute OpenDX to display the space
maps created previously by the dx.map user function. This will work for any
type of OpenDX map.")
-uf.backend = run
-uf.menu_text = "&execute"
-uf.gui_icon = "oxygen.categories.applications-education"
-uf.wizard_size = (700, 500)
-uf.wizard_apply_button = False
-uf.wizard_image = WIZARD_IMAGE_PATH + 'opendx.png'
-
-
-# The dx.map user function.
-uf = uf_info.add_uf("dx.map")
-uf.title = "Create a map of the given space in OpenDX format."
-uf.title_short = "OpenDX map creation."
-uf.display = True
-uf.add_keyarg(
- name = "params",
- py_type = "str_list",
- desc_short = "parameters",
- desc = "The parameters to be mapped. This should be an array of
strings, the meanings of which are described below."
-)
-uf.add_keyarg(
- name = "map_type",
- default = "Iso3D",
- py_type = "str",
- desc_short = "map type",
- desc = "The type of map to create. For example the default, a 3D
isosurface, the type is 'Iso3D'. See below for more details.",
- wiz_element_type = "combo",
- wiz_combo_choices = ["Iso3D"],
- wiz_read_only = True,
-)
-uf.add_keyarg(
- name = "spin_id",
- py_type = "str",
- desc_short = "spin ID string",
- desc = "The spin ID string.",
- can_be_none = True
-)
-uf.add_keyarg(
- name = "inc",
- default = 20,
- py_type = "int",
- desc_short = "number of increments",
- desc = "The number of increments to map in each dimension. This value
controls the resolution of the map.",
- wiz_element_type = "spin"
-)
-uf.add_keyarg(
- name = "lower",
- py_type = "num_list",
- desc_short = "lower bounds",
- desc = "The lower bounds of the space. If you wish to change the lower
bounds of the map then supply an array of length equal to the number of
parameters in the model. A lower bound for each parameter must be supplied.
If nothing is supplied then the defaults will be used.",
- can_be_none = True
-)
-uf.add_keyarg(
- name = "upper",
- py_type = "num_list",
- desc_short = "upper bounds",
- desc = "The upper bounds of the space. If you wish to change the upper
bounds of the map then supply an array of length equal to the number of
parameters in the model. A upper bound for each parameter must be supplied.
If nothing is supplied then the defaults will be used.",
- can_be_none = True
-)
-uf.add_keyarg(
- name = "axis_incs",
- default = 5,
- py_type = "int",
- desc_short = "axis increments",
- desc = "The number of increments or ticks displaying parameter values
along the axes of the OpenDX plot.",
- wiz_element_type = "spin"
-)
-uf.add_keyarg(
- name = "file_prefix",
- default = "map",
- py_type = "str",
- desc_short = "file prefix",
- desc = "The file name. All the output files are prefixed with this
name. The main file containing the data points will be called the value of
'file'. The OpenDX program will be called 'file.net' and the OpenDX import
file will be called 'file.general'."
-)
-uf.add_keyarg(
- name = "dir",
- default = "dx",
- py_type = "str",
- arg_type = "dir sel",
- desc_short = "directory name",
- desc = "The directory to output files to. Set this to 'None' if you do
not want the files to be placed in subdirectory. If the directory does not
exist, it will be created.",
- can_be_none = True
-)
-uf.add_keyarg(
- name = "point",
- py_type = "list_val_or_list_of_list_val",
- dim = (None, 3),
- desc_short = "highlight points in the space",
- desc = "This argument allows specific points in the optimisation space
to be displayed as coloured spheres. This can be used to highlight a minimum
or other any other feature of the space. Either a single point or a list of
points can be supplied. Each point is a list of floating point numbers in
the form [x, y, z]",
- list_titles = ['X coordinate', 'Y coordinate', 'Z coordinate'],
- can_be_none = True
-)
-uf.add_keyarg(
- name = "point_file",
- default = "point",
- py_type = "str",
- desc_short = "point file name prefix",
- desc = "The name of that the point output files will be prefixed with.",
- can_be_none = True
-)
-uf.add_keyarg(
- name = "chi_surface",
- default = None,
- py_type = "float_array",
- desc_short = "Set the chi2 surface level for the Innermost, Inner,
Middle and Outer Isosurface.",
- desc = "A list of 4 numbers, setting the level for the 4 isosurfaces.
Useful in scripting if you create a set of OpenDX maps with all the same
contour levels. Ideal for comparisons.",
- can_be_none = True,
- dim = 4
-)
-uf.add_keyarg(
- name = "create_par_file",
- default = False,
- py_type = "bool",
- desc_short = "creation of file with parameter and calculated chi2",
- desc = "A flag specifying whether to create a file with parameters and
associated chi2 value. The default of False causes the file not to be
created."
-)
-# Description.
-uf.desc.append(Desc_container())
-uf.desc[-1].add_paragraph("This will map the space corresponding to the spin
identifier and create the OpenDX files. The map type can be changed to one
of the following supported map types:")
-table = uf_tables.add_table(label="table: opendx map", caption="OpenDx
mapping types.")
-table.add_headings(["Surface type", "Name"])
-table.add_row(["3D isosurface", "'Iso3D'"])
-uf.desc[-1].add_table(table.label)
-# Additional.
-uf.desc.append(model_free_params.uf_doc(label="table: all model-free
parameters"))
-uf.desc.append(n_state_params.uf_doc(label="table: N-state parameters"))
-uf.desc.append(relax_disp_params.uf_doc(label="table: dispersion
parameters"))
-uf.desc.append(frame_order_params.uf_doc(label="table: frame order
parameters"))
-# Prompt examples.
-uf.desc.append(Desc_container("Prompt examples"))
-uf.desc[-1].add_paragraph("The following commands will generate a map of the
extended model-free space for model 'm5' consisting of the parameters {S2,
S2f, ts}. Files will be output into the directory 'dx' and will be prefixed
by 'map'. In this case, the system is a protein and residue number 6 will be
mapped.")
-uf.desc[-1].add_prompt("relax> dx.map(['s2', 's2f', 'ts'], spin_id=':6')")
-uf.desc[-1].add_prompt("relax> dx.map(['s2', 's2f', 'ts'], spin_id=':6',
file_prefix='map', dir='dx')")
-uf.desc[-1].add_prompt("relax> dx.map(params=['s2', 's2f', 'ts'],
spin_id=':6', inc=20, file_prefix='map', dir='dx')")
-uf.desc[-1].add_prompt("relax> dx.map(params=['s2', 's2f', 'ts'],
spin_id=':6', map_type='Iso3D', inc=20, file_prefix='map', dir='dx')")
-uf.desc[-1].add_paragraph("To map the model-free space 'm4' for residue 2,
spin N6 defined by the parameters {S2, te, Rex}, name the results 'test', and
to place the files in the current directory, use one of the following
commands:")
-uf.desc[-1].add_prompt("relax> dx.map(['s2', 'te', 'rex'], spin_id=':2@N6',
file_prefix='test', dir=None)")
-uf.desc[-1].add_prompt("relax> dx.map(params=['s2', 'te', 'rex'],
spin_id=':2@N6', inc=100, file_prefix='test', dir=None)")
-uf.backend = map
-uf.menu_text = "&map"
-uf.gui_icon = "relax.grid_search"
-uf.wizard_height_desc = 280
-uf.wizard_size = (1000, 750)
-uf.wizard_image = WIZARD_IMAGE_PATH + 'opendx.png'
Copied: branches/space_mapping_refactor/user_functions/mapping.py (from
r26280, branches/space_mapping_refactor/user_functions/dx.py)
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/user_functions/mapping.py?p2=branches/space_mapping_refactor/user_functions/mapping.py&p1=branches/space_mapping_refactor/user_functions/dx.py&r1=26280&r2=26282&rev=26282&view=diff
==============================================================================
--- branches/space_mapping_refactor/user_functions/dx.py (original)
+++ branches/space_mapping_refactor/user_functions/mapping.py Tue Oct 14
19:21:53 2014
@@ -21,7 +21,7 @@
###############################################################################
# Module docstring.
-"""The dx user function definitions for controlling the OpenDX visualisation
software."""
+"""The mapping user function definitions for mapping the chi-squared
parameter space."""
# Python module imports.
import dep_check
@@ -44,14 +44,14 @@
# The user function class.
-uf_class = uf_info.add_class("dx")
+uf_class = uf_info.add_class("mapping")
uf_class.title = "Class for interfacing with OpenDX."
-uf_class.menu_text = "&dx"
+uf_class.menu_text = "&mapping"
uf_class.gui_icon = "relax.opendx"
-# The dx.execute user function.
-uf = uf_info.add_uf("dx.execute")
+# The mapping.dx_execute user function.
+uf = uf_info.add_uf("mapping.dx_execute")
uf.title = "Execute an OpenDX program."
uf.title_short = "OpenDX execution."
uf.add_keyarg(
@@ -89,7 +89,7 @@
)
# Description.
uf.desc.append(Desc_container())
-uf.desc[-1].add_paragraph("This will execute OpenDX to display the space
maps created previously by the dx.map user function. This will work for any
type of OpenDX map.")
+uf.desc[-1].add_paragraph("This will execute OpenDX to display the space
maps created previously by the mapping.setup user function. This will work
for any type of OpenDX map.")
uf.backend = run
uf.menu_text = "&execute"
uf.gui_icon = "oxygen.categories.applications-education"
@@ -98,8 +98,8 @@
uf.wizard_image = WIZARD_IMAGE_PATH + 'opendx.png'
-# The dx.map user function.
-uf = uf_info.add_uf("dx.map")
+# The mapping.setup user function.
+uf = uf_info.add_uf("mapping.setup")
uf.title = "Create a map of the given space in OpenDX format."
uf.title_short = "OpenDX map creation."
uf.display = True
@@ -220,13 +220,13 @@
# Prompt examples.
uf.desc.append(Desc_container("Prompt examples"))
uf.desc[-1].add_paragraph("The following commands will generate a map of the
extended model-free space for model 'm5' consisting of the parameters {S2,
S2f, ts}. Files will be output into the directory 'dx' and will be prefixed
by 'map'. In this case, the system is a protein and residue number 6 will be
mapped.")
-uf.desc[-1].add_prompt("relax> dx.map(['s2', 's2f', 'ts'], spin_id=':6')")
-uf.desc[-1].add_prompt("relax> dx.map(['s2', 's2f', 'ts'], spin_id=':6',
file_prefix='map', dir='dx')")
-uf.desc[-1].add_prompt("relax> dx.map(params=['s2', 's2f', 'ts'],
spin_id=':6', inc=20, file_prefix='map', dir='dx')")
-uf.desc[-1].add_prompt("relax> dx.map(params=['s2', 's2f', 'ts'],
spin_id=':6', map_type='Iso3D', inc=20, file_prefix='map', dir='dx')")
+uf.desc[-1].add_prompt("relax> mapping.setup(['s2', 's2f', 'ts'],
spin_id=':6')")
+uf.desc[-1].add_prompt("relax> mapping.setup(['s2', 's2f', 'ts'],
spin_id=':6', file_prefix='map', dir='dx')")
+uf.desc[-1].add_prompt("relax> mapping.setup(params=['s2', 's2f', 'ts'],
spin_id=':6', inc=20, file_prefix='map', dir='dx')")
+uf.desc[-1].add_prompt("relax> mapping.setup(params=['s2', 's2f', 'ts'],
spin_id=':6', map_type='Iso3D', inc=20, file_prefix='map', dir='dx')")
uf.desc[-1].add_paragraph("To map the model-free space 'm4' for residue 2,
spin N6 defined by the parameters {S2, te, Rex}, name the results 'test', and
to place the files in the current directory, use one of the following
commands:")
-uf.desc[-1].add_prompt("relax> dx.map(['s2', 'te', 'rex'], spin_id=':2@N6',
file_prefix='test', dir=None)")
-uf.desc[-1].add_prompt("relax> dx.map(params=['s2', 'te', 'rex'],
spin_id=':2@N6', inc=100, file_prefix='test', dir=None)")
+uf.desc[-1].add_prompt("relax> mapping.setup(['s2', 'te', 'rex'],
spin_id=':2@N6', file_prefix='test', dir=None)")
+uf.desc[-1].add_prompt("relax> mapping.setup(params=['s2', 'te', 'rex'],
spin_id=':2@N6', inc=100, file_prefix='test', dir=None)")
uf.backend = map
uf.menu_text = "&map"
uf.gui_icon = "relax.grid_search"
r26282 - in /branches/space_mapping_refactor/user_functions: __init__.py dx.py mapping.py