Author: tlinnet
Date: Thu Nov 27 16:43:24 2014
New Revision: 26787
URL: http://svn.gna.org/viewcvs/relax?rev=26787&view=rev
Log:
Added the user funcion spectrum.nmrglue_read to read spectrum files via
nmrglue.
Task #7873 (https://gna.org/task/index.php?7873): Write wrapper function to
nmrglue, to read .ft2 files and process them.
Homepage: http://www.nmrglue.com/
Link to nmrglue discussion:
https://groups.google.com/forum/#!forum/nmrglue-discuss
The code is develop at Github: https://github.com/jjhelmus/nmrglue/
Google code: https://code.google.com/p/nmrglue/
Documentation: http://nmrglue.readthedocs.org/en/latest/index.html
Modified:
branches/nmrglue/user_functions/spectrum.py
Modified: branches/nmrglue/user_functions/spectrum.py
URL:
http://svn.gna.org/viewcvs/relax/branches/nmrglue/user_functions/spectrum.py?rev=26787&r1=26786&r2=26787&view=diff
==============================================================================
--- branches/nmrglue/user_functions/spectrum.py (original)
+++ branches/nmrglue/user_functions/spectrum.py Thu Nov 27 16:43:24 2014
@@ -33,7 +33,7 @@
# relax module imports.
from graphics import WIZARD_IMAGE_PATH
-from pipe_control import spectrum
+from pipe_control import nmrglue, spectrum
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
@@ -213,6 +213,52 @@
uf.wizard_image = WIZARD_IMAGE_PATH + 'spectrum' + sep + 'spectrum_200.png'
+# The spectrum.nmrglue_read user function.
+uf = uf_info.add_uf('spectrum.nmrglue_read')
+uf.title = "Read spectrum with nmrglue."
+uf.title_short = "spectrum reading."
+uf.add_keyarg(
+ name = "file",
+ py_type = "str_or_str_list",
+ arg_type = "file sel multi",
+ desc_short = "file name(s)",
+ desc = "The name of the file or the list of files containing the
intensity data.",
+ wiz_filesel_wildcard = WILDCARD_SPECTRUM_PEAKLIST,
+ wiz_filesel_style = FD_OPEN
+)
+uf.add_keyarg(
+ name = "dir",
+ py_type = "str",
+ arg_type = "dir",
+ desc_short = "directory name",
+ desc = "The directory where the file is located.",
+ can_be_none = True
+)
+uf.add_keyarg(
+ name = "spectrum_id",
+ py_type = "str_or_str_list",
+ desc_short = "spectrum ID string",
+ desc = "The unique spectrum ID string or list of strings to associate
with the peak intensity values. If multiple files are given, then each
file should have a corresponding spectrum ID string. If 'auto' is provided
for a NMRPipe seriesTab formatted file, the IDs are auto generated in form
of Z_A{i}."
+)
+# Description.
+uf.desc.append(Desc_container())
+uf.desc[-1].add_paragraph("Read spectrum with nmrglue.")
+## File formats.
+#uf.desc.append(Desc_container("File formats"))
+#uf.desc[-1].add_paragraph("The peak list or intensity file will be
automatically determined.")
+#uf.desc.append(Desc_container("Multiple files"))
+#uf.desc[-1].add_paragraph("The data from multiple files can be loaded
simultaneously if a list of files is supplied. In this case, a list of
spectrum ID strings of equal length must be supplied.")
+## Prompt examples.
+#uf.desc.append(Desc_container("Prompt examples"))
+#uf.desc[-1].add_paragraph("To read the reference and saturated spectra
peak heights from the Sparky formatted files 'ref.list' and 'sat.list',
type:")
+uf.backend = nmrglue.read
+uf.menu_text = "&nmrglue_read"
+uf.gui_icon = "oxygen.actions.document-open"
+uf.wizard_height_desc = 300
+uf.wizard_size = (1000, 750)
+uf.wizard_image = WIZARD_IMAGE_PATH + 'spectrum' + sep + 'spectrum_200.png'
+
+
# The spectrum.read_intensities user function.
uf = uf_info.add_uf('spectrum.read_intensities')
uf.title = "Read peak intensities from a file."
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Re: r26787 - /branches/nmrglue/user_functions/spectrum.py