Author: bugman
Date: Sat Mar 23 23:17:20 2013
New Revision: 19092
URL: http://svn.gna.org/viewcvs/relax?rev=19092&view=rev
Log:
Converted the OpenDX package pipe_control.opendx into a module.
As most code was shifted to lib.opendx, the code was small enough to merge
into one module.
Added:
trunk/pipe_control/opendx.py
- copied, changed from r19091, trunk/pipe_control/opendx/base_map.py
Removed:
trunk/pipe_control/opendx/
trunk/test_suite/unit_tests/_pipe_control/_opendx/
Modified:
trunk/user_functions/dx.py
Copied: trunk/pipe_control/opendx.py (from r19091,
trunk/pipe_control/opendx/base_map.py)
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/opendx.py?p2=trunk/pipe_control/opendx.py&p1=trunk/pipe_control/opendx/base_map.py&r1=19091&r2=19092&rev=19092&view=diff
==============================================================================
--- trunk/pipe_control/opendx/base_map.py (original)
+++ trunk/pipe_control/opendx.py Sat Mar 23 23:17:20 2013
@@ -30,15 +30,70 @@
# relax module imports.
from pipe_control import diffusion_tensor
from pipe_control import pipes
+from pipe_control import value
from lib.errors import RelaxError, RelaxUnknownParamError
from lib.io import open_write_file
from lib.opendx.files import write_config, write_general, write_point,
write_program
from specific_analyses.setup import get_specific_fn
-
-
-class Base_Map:
+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.
+ Map(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.")
+
+
+
+class Map:
"""The space mapping base class."""
def __init__(self, params, spin_id, inc, lower, upper, axis_incs,
file_prefix, dir, point, point_file, remap):
@@ -152,7 +207,7 @@
map_file = open_write_file(file_name=self.file_prefix, dir=self.dir,
force=True)
# Generate and write the text of the map.
- self.map_text(map_file)
+ self.map_3D_text(map_file)
# Close the file.
map_file.close()
@@ -193,6 +248,80 @@
# Append the parameter name.
self.param_names.append(name)
+
+
+ def map_3D_text(self, map_file):
+ """Function for creating the text of a 3D map."""
+
+ # Initialise.
+ values = zeros(3, float64)
+ percent = 0.0
+ percent_inc = 100.0 / (self.inc + 1.0)**(self.n - 1.0)
+ print("%-10s%8.3f%-1s" % ("Progress:", percent, "%"))
+
+ # Fix the diffusion tensor.
+ unfix = False
+ if hasattr(cdp, 'diff_tensor') and not cdp.diff_tensor.fixed:
+ cdp.diff_tensor.fixed = True
+ unfix = True
+
+ # Initial value of the first parameter.
+ values[0] = self.bounds[0, 0]
+
+ # The model identifier.
+
+ # Loop over the first parameter.
+ for i in range((self.inc + 1)):
+ # Initial value of the second parameter.
+ values[1] = self.bounds[1, 0]
+
+ # Loop over the second parameter.
+ for j in range((self.inc + 1)):
+ # Initial value of the third parameter.
+ values[2] = self.bounds[2, 0]
+
+ # Loop over the third parameter.
+ for k in range((self.inc + 1)):
+ # Set the parameter values.
+ if self.spin_id:
+ value.set(val=values, param=self.params,
spin_id=self.spin_id, force=True)
+ else:
+ value.set(val=values, param=self.params, force=True)
+
+ # Calculate the function values.
+ if self.spin_id:
+ self.calculate(spin_id=self.spin_id, verbosity=0)
+ else:
+ self.calculate(verbosity=0)
+
+ # Get the minimisation statistics for the model.
+ if self.spin_id:
+ k, n, chi2 = self.model_stats(spin_id=self.spin_id)
+ else:
+ k, n, chi2 = self.model_stats(model_info=0)
+
+ # Set maximum value to 1e20 to stop the OpenDX server
connection from breaking.
+ if chi2 > 1e20:
+ map_file.write("%30f\n" % 1e20)
+ else:
+ map_file.write("%30f\n" % chi2)
+
+ # Increment the value of the third parameter.
+ values[2] = values[2] + self.step_size[2]
+
+ # Progress incrementation and printout.
+ percent = percent + percent_inc
+ print("%-10s%8.3f%-8s%-8g" % ("Progress:", percent, "%, " +
repr(values) + ", f(x): ", chi2))
+
+ # Increment the value of the second parameter.
+ values[1] = values[1] + self.step_size[1]
+
+ # Increment the value of the first parameter.
+ values[0] = values[0] + self.step_size[0]
+
+ # Unfix the diffusion tensor.
+ if unfix:
+ cdp.diff_tensor.fixed = False
def map_axes(self):
Modified: trunk/user_functions/dx.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/user_functions/dx.py?rev=19092&r1=19091&r2=19092&view=diff
==============================================================================
--- trunk/user_functions/dx.py (original)
+++ trunk/user_functions/dx.py Sat Mar 23 23:17:20 2013
@@ -26,7 +26,7 @@
from pipe_control import diffusion_tensor
from graphics import WIZARD_IMAGE_PATH
import lib.opendx.execute
-import pipe_control.opendx.main
+import pipe_control.opendx
from prompt.doc_string import regexp_doc
from specific_analyses.model_free import Model_free
from user_functions.data import Uf_info; uf_info = Uf_info()
@@ -204,7 +204,7 @@
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 = pipe_control.opendx.main.map
+uf.backend = pipe_control.opendx.map
uf.menu_text = "&map"
uf.gui_icon = "relax.grid_search"
uf.wizard_height_desc = 280
r19092 - in /trunk: pipe_control/ pipe_control/opendx/ test_suite/unit_tests/_pipe_control/_opendx/ user_functions/