Author: bugman
Date: Wed Mar 4 14:48:39 2015
New Revision: 27775
URL: http://svn.gna.org/viewcvs/relax?rev=27775&view=rev
Log:
Merged revisions 27771-27774 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r27771 | bugman | 2015-03-04 14:28:46 +0100 (Wed, 04 Mar 2015) | 6 lines
Created the Align_tensor.test_copy_pipes system test.
This is to show a problem in the align_tensor.copy user function when
copying all tensors between
data pipes.
........
r27772 | bugman | 2015-03-04 14:30:30 +0100 (Wed, 04 Mar 2015) | 5 lines
The align_tensor.copy user function 'tensor_from' argument can now be None.
This is to enable the copying of all alignment tensors from one data pipe
to another.
........
r27773 | bugman | 2015-03-04 14:34:07 +0100 (Wed, 04 Mar 2015) | 5 lines
Modified the pipe_control.align_tensor.align_data_exists() function to
handle no tensor IDs.
If no tensor ID is supplied, this will then return True if any alignment
data exists.
........
r27774 | bugman | 2015-03-04 14:47:21 +0100 (Wed, 04 Mar 2015) | 6 lines
Improvement for the align_tensor.copy user function.
The user function has been modified to allow all alignment tensors to be
copied between two data
pipes. This allows the Align_tensor.test_copy_pipes system test to pass.
........
Modified:
branches/frame_order_cleanup/ (props changed)
branches/frame_order_cleanup/pipe_control/align_tensor.py
branches/frame_order_cleanup/test_suite/system_tests/align_tensor.py
branches/frame_order_cleanup/user_functions/align_tensor.py
Propchange: branches/frame_order_cleanup/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Wed Mar 4 14:48:39 2015
@@ -1 +1 @@
-/trunk:1-27769
+/trunk:1-27774
Modified: branches/frame_order_cleanup/pipe_control/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/pipe_control/align_tensor.py?rev=27775&r1=27774&r2=27775&view=diff
==============================================================================
--- branches/frame_order_cleanup/pipe_control/align_tensor.py (original)
+++ branches/frame_order_cleanup/pipe_control/align_tensor.py Wed Mar 4
14:48:39 2015
@@ -44,15 +44,15 @@
from pipe_control.pipes import check_pipe
-def align_data_exists(tensor, pipe=None):
+def align_data_exists(tensor=None, pipe=None):
"""Function for determining if alignment data exists in the current data
pipe.
- @param tensor: The alignment tensor identification string.
- @type tensor: str
- @param pipe: The data pipe to search for data in.
- @type pipe: str
- @return: The answer to the question.
- @rtype: bool
+ @keyword tensor: The alignment tensor ID string. If not supplied,
then any alignment data will result in the function returning True.
+ @type tensor: str or None
+ @keyword pipe: The data pipe to search for data in. This defaults
to the current data pipe if not supplied.
+ @type pipe: str or None
+ @return: The answer to the question.
+ @rtype: bool
"""
# The data pipe to check.
@@ -64,6 +64,8 @@
# Test if an alignment tensor corresponding to the arg 'tensor' exists.
if hasattr(pipe, 'align_tensors'):
+ if tensor == None:
+ return True
for data in pipe.align_tensors:
if data.name == tensor:
return True
@@ -134,29 +136,49 @@
dp_to.align_tensors = AlignTensorList()
# Add the tensor if it doesn't already exist.
- if tensor_to not in dp_to.align_tensors.names():
+ if tensor_to != None and tensor_to not in dp_to.align_tensors.names():
dp_to.align_tensors.add_item(tensor_to)
- # Find the tensor index.
- index_from = get_tensor_index(tensor=tensor_from, pipe=pipe_from)
- index_to = get_tensor_index(tensor=tensor_to, pipe=pipe_to)
-
- # Copy the data.
- if index_to == None:
-
dp_to.align_tensors.append(deepcopy(dp_from.align_tensors[index_from]))
- index_to = len(dp_to.align_tensors) - 1
+ # Copy all data.
+ if tensor_from == None:
+ # Check.
+ if tensor_to != tensor_from:
+ raise RelaxError("The tensor_to argument '%s' should not be
supplied when tensor_from is None." % tensor_to)
+
+ # The align IDs.
+ align_ids = []
+
+ # Loop over and copy all tensors.
+ for i in range(len(dp_from.align_tensors)):
+ dp_to.align_tensors.append(deepcopy(dp_from.align_tensors[i]))
+ align_ids.append(dp_from.align_tensors[i].align_id)
+
+ # Copy a single tensor.
else:
- dp_to.align_tensors[index_to] =
deepcopy(dp_from.align_tensors[index_from])
-
- # Update the tensor's name.
- dp_to.align_tensors[index_to].set('name', tensor_to)
-
- # Add the align ID to the target data pipe if needed.
- align_id = dp_from.align_tensors[index_from].align_id
+ # Find the tensor index.
+ index_from = get_tensor_index(tensor=tensor_from, pipe=pipe_from)
+ index_to = get_tensor_index(tensor=tensor_to, pipe=pipe_to)
+
+ # Copy the tensor.
+ tensor = deepcopy(dp_from.align_tensors[index_from])
+ if index_to == None:
+ dp_to.align_tensors.append(tensor)
+ index_to = len(dp_to.align_tensors) - 1
+ else:
+ dp_to.align_tensors[index_to] = tensor
+
+ # Update the tensor's name.
+ dp_to.align_tensors[index_to].set('name', tensor_to)
+
+ # The align IDs.
+ align_ids = [dp_from.align_tensors[index_from].align_id]
+
+ # Add the align IDs to the target data pipe if needed.
if not hasattr(dp_to, 'align_ids'):
dp_to.align_ids = []
- if align_id not in dp_to.align_ids:
- dp_to.align_ids.append(align_id)
+ for align_id in align_ids:
+ if align_id not in dp_to.align_ids:
+ dp_to.align_ids.append(align_id)
def delete(tensor=None):
Modified: branches/frame_order_cleanup/test_suite/system_tests/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/align_tensor.py?rev=27775&r1=27774&r2=27775&view=diff
==============================================================================
--- branches/frame_order_cleanup/test_suite/system_tests/align_tensor.py
(original)
+++ branches/frame_order_cleanup/test_suite/system_tests/align_tensor.py
Wed Mar 4 14:48:39 2015
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2006-2013 Edward d'Auvergne
#
+# Copyright (C) 2006-2015 Edward d'Auvergne
#
#
#
# This file is part of the program relax (http://www.nmr-relax.com).
#
#
#
@@ -288,6 +288,28 @@
self.assertEqual(cdp.align_tensors[1].name, 'new')
+ def test_copy_pipes(self):
+ """Test the copying of alignment tensors between data pipes."""
+
+ # First reset.
+ self.interpreter.reset()
+
+ # Create two data pipes.
+ self.interpreter.pipe.create('target', 'N-state')
+ self.interpreter.pipe.create('source', 'N-state')
+
+ # Initialise one tensor.
+ self.interpreter.align_tensor.init(tensor='orig', align_id='test',
params=self.tensors_full[0], param_types=0)
+
+ # Copy the tensor.
+ self.interpreter.align_tensor.copy(pipe_from='source',
pipe_to='target')
+
+ # Checks.
+ self.interpreter.pipe.switch('target')
+ self.assertEqual(len(cdp.align_tensors), 1)
+ self.assertEqual(cdp.align_tensors[0].name, 'orig')
+
+
def test_fix(self):
"""Test the align_tensor.fix user function."""
Modified: branches/frame_order_cleanup/user_functions/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/user_functions/align_tensor.py?rev=27775&r1=27774&r2=27775&view=diff
==============================================================================
--- branches/frame_order_cleanup/user_functions/align_tensor.py (original)
+++ branches/frame_order_cleanup/user_functions/align_tensor.py Wed Mar 4
14:48:39 2015
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2007-2014 Edward d'Auvergne
#
+# Copyright (C) 2007-2015 Edward d'Auvergne
#
#
#
# This file is part of the program relax (http://www.nmr-relax.com).
#
#
#
@@ -45,7 +45,8 @@
default = None,
py_type = "str",
desc_short = "source tensor ID",
- desc = "The identification string of the alignment tensor to copy the
data from."
+ desc = "The identification string of the alignment tensor to copy the
data from.",
+ can_be_none = True
)
uf.add_keyarg(
name = "pipe_from",
r27775 - in /branches/frame_order_cleanup: ./ pipe_control/ test_suite/system_tests/ user_functions/