Author: bugman
Date: Wed Apr 16 16:35:50 2008
New Revision: 5762
URL: http://svn.gna.org/viewcvs/relax?rev=5762&view=rev
Log:
Converted the map_space() base class method into the __init__() method.
Modified:
1.3/opendx/base_map.py
Modified: 1.3/opendx/base_map.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/opendx/base_map.py?rev=5762&r1=5761&r2=5762&view=diff
==============================================================================
--- 1.3/opendx/base_map.py (original)
+++ 1.3/opendx/base_map.py Wed Apr 16 16:35:50 2008
@@ -32,226 +32,10 @@
class Base_Map:
- def __init__(self):
- """The space mapping base class."""
-
-
- def create_config(self):
- """Function for creating the OpenDX .cfg program configuration
file."""
-
- # Print out.
- print "\nCreating the OpenDX .cfg program configuration file."
-
- # Open the file.
- config_file =
self.relax.IO.open_write_file(file_name=self.file+".cfg", dir=self.dir,
force=1)
-
- # Get the text of the configuration file.
- text = self.config_text()
-
- # Write the text.
- config_file.write(text)
-
- # Close the file.
- config_file.close()
-
-
- def create_general(self):
- """Function for creating the OpenDX .general file."""
-
- # Print out.
- print "\nCreating the OpenDX .general file."
-
- # Open the file.
- general_file =
self.relax.IO.open_write_file(file_name=self.file+".general", dir=self.dir,
force=1)
-
- # Get the text of the configuration file.
- text = self.general_text()
-
- # Write the text.
- general_file.write(text)
-
- # Close the file.
- general_file.close()
-
-
- def create_map(self):
- """Function for creating the map."""
-
- # Print out.
- print "\nCreating the map."
-
- # Open the file.
- map_file = self.relax.IO.open_write_file(file_name=self.file,
dir=self.dir, force=1)
-
- # Generate and write the text of the map.
- self.map_text(map_file)
-
- # Close the file.
- map_file.close()
-
-
- def create_point(self):
- """Function for creating a sphere at a given position within the 3D
map.
-
- The formula used to calculate the coordinate position is:
-
- V - L
- coord = Inc * -----
- U - L
-
- where:
- V is the coordinate or parameter value.
- L is the lower bound value.
- U is the upper bound value.
- Inc is the number of increments.
-
- Both a data file and .general file will be created.
- """
-
- # Print out.
- print "\nCreating the OpenDX .general and data files for the given
point."
-
- # Open the files.
- point_file =
self.relax.IO.open_write_file(file_name=self.point_file, dir=self.dir,
force=1)
- point_file_general =
self.relax.IO.open_write_file(file_name=self.point_file+".general",
dir=self.dir, force=1)
-
- # Calculate the coordinate values.
- coords = self.inc * (self.point - self.bounds[:, 0]) /
(self.bounds[:, 1] - self.bounds[:, 0])
- for i in xrange(self.n):
- point_file.write("%-15.5g" % coords[i])
- point_file.write("1\n")
-
- # Get the text of the point .general file.
- text = self.point_text()
-
- # Write the text.
- point_file_general.write(text)
-
- # Close the data and .general files.
- point_file.close()
- point_file_general.close()
-
-
- def create_program(self):
- """Function for creating the OpenDX .net program file."""
-
- # Print out.
- print "\nCreating the OpenDX .net program file."
-
- # Open the file.
- program_file =
self.relax.IO.open_write_file(file_name=self.file+".net", dir=self.dir,
force=1)
-
- # Create the strings associated with the map axes.
- self.map_axes()
-
- # Corners.
- self.corners = "{[0"
- for i in xrange(self.n - 1):
- self.corners = self.corners + " 0"
- self.corners = self.corners + "] [" + `self.inc`
- for i in xrange(self.n - 1):
- self.corners = self.corners + " " + `self.inc`
- self.corners = self.corners + "]}"
-
- # Sphere size.
- self.sphere_size = `0.025 * (self.inc + 1.0)`
-
- # Get the text of the program.
- text = self.program_text()
-
- # Write the text.
- program_file.write(text)
-
- # Close the file.
- program_file.close()
-
-
- def get_date(self):
- """Function for creating a date string."""
-
- self.date = asctime(localtime())
-
-
- def get_param_names(self):
- """Function for retrieving the parameter names."""
-
- # Initialise.
- self.param_names = []
-
- # Loop over the parameters.
- for i in xrange(self.n):
- # Get the parameter name.
- name = self.return_data_name(self.params[i])
-
- # Diffusion tensor parameter.
- if self.function_type == 'mf':
- # The diffusion tensor parameter name.
- diff_name =
self.relax.generic.diffusion_tensor.return_data_name(self.params[i])
-
- # Replace the model-free parameter with the diffusion tensor
parameter if it exists.
- if diff_name:
- name = diff_name
-
- # Set the flag indicating if there are diffusion tensor
parameters.
- self.diff_params[i] = 1
-
- # Bad parameter name.
- if not name:
- raise RelaxUnknownParamError, self.params[i]
-
- # Append the parameter name.
- self.param_names.append(name)
-
-
- def map_axes(self):
- """Function for creating labels, tick locations, and tick values for
an OpenDX map."""
-
- # Initialise.
- self.labels = "{"
- self.tick_locations = []
- self.tick_values = []
- loc_inc = float(self.inc) / float(self.axis_incs)
-
- # Loop over the parameters
- for i in xrange(self.n):
- # Parameter conversion factors.
- factor = self.return_conversion_factor[i](self.param_names[i])
-
- # Parameter units.
- units = self.return_units[i](self.param_names[i])
-
- # Labels.
- if units:
- self.labels = self.labels + "\"" + self.params[i] + " (" +
units + ")\""
- else:
- self.labels = self.labels + "\"" + self.params[i] + "\""
-
- if i < self.n - 1:
- self.labels = self.labels + " "
- else:
- self.labels = self.labels + "}"
-
- # Tick values.
- vals = self.bounds[i, 0] / factor
- val_inc = (self.bounds[i, 1] - self.bounds[i, 0]) /
(self.axis_incs * factor)
-
- string = ""
- for j in xrange(self.axis_incs + 1):
- string = string + "\"" + "%.2f" % vals + "\" "
- vals = vals + val_inc
- self.tick_values.append("{" + string + "}")
-
- # Tick locations.
- string = ""
- val = 0.0
- for j in xrange(self.axis_incs + 1):
- string = string + " " + `val`
- val = val + loc_inc
- self.tick_locations.append("{" + string + " }")
-
-
- def map_space(self, run, params, res_num, index, inc, lower, upper,
axis_incs, file, dir, point, point_file, remap):
- """Generic function for mapping a space."""
+ """The space mapping base class."""
+
+ def __init__(self, run, params, res_num, index, inc, lower, upper,
axis_incs, file, dir, point, point_file, remap):
+ """Map the space upon class instantiation."""
# Initialise.
#############
@@ -351,3 +135,217 @@
# Generate the map.
self.create_map()
+
+
+ def create_config(self):
+ """Function for creating the OpenDX .cfg program configuration
file."""
+
+ # Print out.
+ print "\nCreating the OpenDX .cfg program configuration file."
+
+ # Open the file.
+ config_file =
self.relax.IO.open_write_file(file_name=self.file+".cfg", dir=self.dir,
force=1)
+
+ # Get the text of the configuration file.
+ text = self.config_text()
+
+ # Write the text.
+ config_file.write(text)
+
+ # Close the file.
+ config_file.close()
+
+
+ def create_general(self):
+ """Function for creating the OpenDX .general file."""
+
+ # Print out.
+ print "\nCreating the OpenDX .general file."
+
+ # Open the file.
+ general_file =
self.relax.IO.open_write_file(file_name=self.file+".general", dir=self.dir,
force=1)
+
+ # Get the text of the configuration file.
+ text = self.general_text()
+
+ # Write the text.
+ general_file.write(text)
+
+ # Close the file.
+ general_file.close()
+
+
+ def create_map(self):
+ """Function for creating the map."""
+
+ # Print out.
+ print "\nCreating the map."
+
+ # Open the file.
+ map_file = self.relax.IO.open_write_file(file_name=self.file,
dir=self.dir, force=1)
+
+ # Generate and write the text of the map.
+ self.map_text(map_file)
+
+ # Close the file.
+ map_file.close()
+
+
+ def create_point(self):
+ """Function for creating a sphere at a given position within the 3D
map.
+
+ The formula used to calculate the coordinate position is:
+
+ V - L
+ coord = Inc * -----
+ U - L
+
+ where:
+ V is the coordinate or parameter value.
+ L is the lower bound value.
+ U is the upper bound value.
+ Inc is the number of increments.
+
+ Both a data file and .general file will be created.
+ """
+
+ # Print out.
+ print "\nCreating the OpenDX .general and data files for the given
point."
+
+ # Open the files.
+ point_file =
self.relax.IO.open_write_file(file_name=self.point_file, dir=self.dir,
force=1)
+ point_file_general =
self.relax.IO.open_write_file(file_name=self.point_file+".general",
dir=self.dir, force=1)
+
+ # Calculate the coordinate values.
+ coords = self.inc * (self.point - self.bounds[:, 0]) /
(self.bounds[:, 1] - self.bounds[:, 0])
+ for i in xrange(self.n):
+ point_file.write("%-15.5g" % coords[i])
+ point_file.write("1\n")
+
+ # Get the text of the point .general file.
+ text = self.point_text()
+
+ # Write the text.
+ point_file_general.write(text)
+
+ # Close the data and .general files.
+ point_file.close()
+ point_file_general.close()
+
+
+ def create_program(self):
+ """Function for creating the OpenDX .net program file."""
+
+ # Print out.
+ print "\nCreating the OpenDX .net program file."
+
+ # Open the file.
+ program_file =
self.relax.IO.open_write_file(file_name=self.file+".net", dir=self.dir,
force=1)
+
+ # Create the strings associated with the map axes.
+ self.map_axes()
+
+ # Corners.
+ self.corners = "{[0"
+ for i in xrange(self.n - 1):
+ self.corners = self.corners + " 0"
+ self.corners = self.corners + "] [" + `self.inc`
+ for i in xrange(self.n - 1):
+ self.corners = self.corners + " " + `self.inc`
+ self.corners = self.corners + "]}"
+
+ # Sphere size.
+ self.sphere_size = `0.025 * (self.inc + 1.0)`
+
+ # Get the text of the program.
+ text = self.program_text()
+
+ # Write the text.
+ program_file.write(text)
+
+ # Close the file.
+ program_file.close()
+
+
+ def get_date(self):
+ """Function for creating a date string."""
+
+ self.date = asctime(localtime())
+
+
+ def get_param_names(self):
+ """Function for retrieving the parameter names."""
+
+ # Initialise.
+ self.param_names = []
+
+ # Loop over the parameters.
+ for i in xrange(self.n):
+ # Get the parameter name.
+ name = self.return_data_name(self.params[i])
+
+ # Diffusion tensor parameter.
+ if self.function_type == 'mf':
+ # The diffusion tensor parameter name.
+ diff_name =
self.relax.generic.diffusion_tensor.return_data_name(self.params[i])
+
+ # Replace the model-free parameter with the diffusion tensor
parameter if it exists.
+ if diff_name:
+ name = diff_name
+
+ # Set the flag indicating if there are diffusion tensor
parameters.
+ self.diff_params[i] = 1
+
+ # Bad parameter name.
+ if not name:
+ raise RelaxUnknownParamError, self.params[i]
+
+ # Append the parameter name.
+ self.param_names.append(name)
+
+
+ def map_axes(self):
+ """Function for creating labels, tick locations, and tick values for
an OpenDX map."""
+
+ # Initialise.
+ self.labels = "{"
+ self.tick_locations = []
+ self.tick_values = []
+ loc_inc = float(self.inc) / float(self.axis_incs)
+
+ # Loop over the parameters
+ for i in xrange(self.n):
+ # Parameter conversion factors.
+ factor = self.return_conversion_factor[i](self.param_names[i])
+
+ # Parameter units.
+ units = self.return_units[i](self.param_names[i])
+
+ # Labels.
+ if units:
+ self.labels = self.labels + "\"" + self.params[i] + " (" +
units + ")\""
+ else:
+ self.labels = self.labels + "\"" + self.params[i] + "\""
+
+ if i < self.n - 1:
+ self.labels = self.labels + " "
+ else:
+ self.labels = self.labels + "}"
+
+ # Tick values.
+ vals = self.bounds[i, 0] / factor
+ val_inc = (self.bounds[i, 1] - self.bounds[i, 0]) /
(self.axis_incs * factor)
+
+ string = ""
+ for j in xrange(self.axis_incs + 1):
+ string = string + "\"" + "%.2f" % vals + "\" "
+ vals = vals + val_inc
+ self.tick_values.append("{" + string + "}")
+
+ # Tick locations.
+ string = ""
+ val = 0.0
+ for j in xrange(self.axis_incs + 1):
+ string = string + " " + `val`
+ val = val + loc_inc
+ self.tick_locations.append("{" + string + " }")
r5762 - /1.3/opendx/base_map.py