Author: bugman
Date: Sat Mar 23 23:06:29 2013
New Revision: 19090
URL: http://svn.gna.org/viewcvs/relax?rev=19090&view=rev
Log:
Shifted some more OpenDX code from pipe_control.opendx.main into the new
module lib.opendx.execute.
Added:
trunk/lib/opendx/execute.py
- copied, changed from r19089, trunk/pipe_control/opendx/main.py
Modified:
trunk/lib/opendx/__init__.py
trunk/pipe_control/opendx/main.py
trunk/user_functions/dx.py
Modified: trunk/lib/opendx/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/opendx/__init__.py?rev=19090&r1=19089&r2=19090&view=diff
==============================================================================
--- trunk/lib/opendx/__init__.py (original)
+++ trunk/lib/opendx/__init__.py Sat Mar 23 23:06:29 2013
@@ -23,5 +23,6 @@
"""The relax-lib NMR package - a library of functions for interacting with
the OpenDX software."""
__all__ = [
+ 'execute',
'files'
]
Copied: trunk/lib/opendx/execute.py (from r19089,
trunk/pipe_control/opendx/main.py)
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/opendx/execute.py?p2=trunk/lib/opendx/execute.py&p1=trunk/pipe_control/opendx/main.py&r1=19089&r2=19090&rev=19090&view=diff
==============================================================================
--- trunk/pipe_control/opendx/main.py (original)
+++ trunk/lib/opendx/execute.py Sat Mar 23 23:06:29 2013
@@ -20,71 +20,14 @@
###############################################################################
# Module docsting.
-"""Module containing the functions which interface relax with OpenDX."""
+"""Module for executing OpenDX."""
# Python module imports.
from os import system
# relax module imports.
-from pipe_control.opendx import isosurface_3D
-from lib.errors import RelaxError
from lib.io import test_binary
-
-
-def map(params=None, map_type='Iso3D', spin_id=None, inc=20, lower=None,
upper=None, axis_incs=10, file_prefix="map", dir="dx", point=None,
point_file="point", remap=None):
- """Map the space corresponding to the spin identifier and create the
OpenDX files.
-
- @keyword params:
- @type params:
- @keyword map_type: The type of map to create. The available
options are:
- - 'Iso3D', a 3D isosurface visualisation of
the space.
- @type map_type: str
- @keyword spin_id: The spin identification string.
- @type spin_id: str
- @keyword inc: The resolution of the plot. This is the number
of increments per
- dimension.
- @type inc: int
- @keyword lower: The lower bounds of the space to map. If
supplied, this should be a
- list of floats, its length equal to the number
of parameters in the
- model.
- @type lower: None or list of float
- @keyword upper: The upper bounds of the space to map. If
supplied, this should be a
- list of floats, its length equal to the number
of parameters in the
- model.
- @type upper: None or list of float
- @keyword axis_incs: The number of tick marks to display in the
OpenDX plot in each
- dimension.
- @type axis_incs: int
- @keyword file_prefix: The file prefix for all the created files.
- @type file_prefix: str
- @keyword dir: The directory to place the files into.
- @type dir: str or None
- @keyword point: If supplied, a red sphere will be placed at
these coordinates.
- @type point: None or list of float
- @keyword point_file: The file prefix for the point output files.
- @type point_file: str or None
- @keyword remap: A function which is used to remap the space.
The function should accept
- the parameter array (list of float) and return
an array of equal length
- (again list of float).
- @type remap: None or func
- """
-
- # Check the args.
- if inc <= 1:
- raise RelaxError("The increment value needs to be greater than 1.")
- if axis_incs <= 1:
- raise RelaxError("The axis increment value needs to be greater than
1.")
-
- # Space type.
- if map_type.lower() == "iso3d":
- if len(params) != 3:
- raise RelaxError("The 3D isosurface map requires a 3 parameter
model.")
-
- # Create the map.
- isosurface_3D.Iso3D(params, spin_id, inc, lower, upper, axis_incs,
file_prefix, dir, point, point_file, remap)
- else:
- raise RelaxError("The map type '" + map_type + "' is not supported.")
def run(file_prefix="map", dir="dx", dx_exe="dx", vp_exec=True):
Modified: trunk/pipe_control/opendx/main.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/opendx/main.py?rev=19090&r1=19089&r2=19090&view=diff
==============================================================================
--- trunk/pipe_control/opendx/main.py (original)
+++ trunk/pipe_control/opendx/main.py Sat Mar 23 23:06:29 2013
@@ -23,13 +23,9 @@
"""Module containing the functions which interface relax with OpenDX."""
-# Python module imports.
-from os import system
-
# relax module imports.
from pipe_control.opendx import isosurface_3D
from lib.errors import RelaxError
-from lib.io import test_binary
def map(params=None, map_type='Iso3D', spin_id=None, inc=20, lower=None,
upper=None, axis_incs=10, file_prefix="map", dir="dx", point=None,
point_file="point", remap=None):
@@ -85,34 +81,3 @@
isosurface_3D.Iso3D(params, spin_id, inc, lower, upper, axis_incs,
file_prefix, dir, point, point_file, remap)
else:
raise RelaxError("The map type '" + map_type + "' is not supported.")
-
-
-def run(file_prefix="map", dir="dx", dx_exe="dx", vp_exec=True):
- """Execute OpenDX.
-
- @keyword file_prefix: The file prefix for all the created files.
- @type file_prefix: str
- @keyword dir: The directory to place the files into.
- @type dir: str or None
- @keyword dx_exe: The path to the OpenDX executable file. This
can be changed if the
- binary 'dx' is not located in the system path.
- @type dx_exe: str
- @keyword vp_exec: If True, then the OpenDX visual program will be
launched.
- @type vp_exec: bool
- """
-
- # Text for changing to the directory dir.
- dir_text = ""
- if dir != None:
- dir_text = " -directory " + dir
-
- # Text for executing OpenDX.
- execute_text = ""
- if vp_exec:
- execute_text = " -execute"
-
- # Test the binary file string corresponds to a valid executable.
- test_binary(dx_exe)
-
- # Run OpenDX.
- system(dx_exe + dir_text + " -program " + file_prefix + ".net" +
execute_text + " &")
Modified: trunk/user_functions/dx.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/user_functions/dx.py?rev=19090&r1=19089&r2=19090&view=diff
==============================================================================
--- trunk/user_functions/dx.py (original)
+++ trunk/user_functions/dx.py Sat Mar 23 23:06:29 2013
@@ -25,6 +25,7 @@
# relax module imports.
from pipe_control import diffusion_tensor
from graphics import WIZARD_IMAGE_PATH
+import lib.opendx.execute
import pipe_control.opendx.main
from prompt.doc_string import regexp_doc
from specific_analyses.model_free import Model_free
@@ -77,7 +78,7 @@
# 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.backend = pipe_control.opendx.main.run
+uf.backend = lib.opendx.execute.run
uf.menu_text = "&execute"
uf.gui_icon = "oxygen.categories.applications-education"
uf.wizard_size = (700, 500)
r19090 - in /trunk: lib/opendx/__init__.py lib/opendx/execute.py pipe_control/opendx/main.py user_functions/dx.py