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." _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits