Author: tlinnet
Date: Wed Dec 3 20:40:53 2014
New Revision: 26941
URL: http://svn.gna.org/viewcvs/relax?rev=26941&view=rev
Log:
Added the user function io.file_list.
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/
Documentation: http://nmrglue.readthedocs.org/en/latest/index.html
Modified:
branches/nmrglue/user_functions/io.py
Modified: branches/nmrglue/user_functions/io.py
URL:
http://svn.gna.org/viewcvs/relax/branches/nmrglue/user_functions/io.py?rev=26941&r1=26940&r2=26941&view=diff
==============================================================================
--- branches/nmrglue/user_functions/io.py (original)
+++ branches/nmrglue/user_functions/io.py Wed Dec 3 20:40:53 2014
@@ -1,6 +1,7 @@
###############################################################################
#
#
# Copyright (C) 2013-2014 Edward d'Auvergne
#
+# Copyright (C) 2014 Troels E. Linnet
#
#
#
# This file is part of the program relax (http://www.nmr-relax.com).
#
#
#
@@ -20,7 +21,7 @@
###############################################################################
# Module docstring.
-"""The chemical_shift user function definitions."""
+"""The io user function definitions."""
# Python module imports.
import dep_check
@@ -32,112 +33,53 @@
# relax module imports.
from graphics import WIZARD_IMAGE_PATH
-from pipe_control import chemical_shift
+from pipe_control import io
from user_functions.data import Uf_info; uf_info = Uf_info()
from user_functions.objects import Desc_container
from user_functions.wildcards import WILDCARD_SPECTRUM_PEAKLIST
# The user function class.
-uf_class = uf_info.add_class('chemical_shift')
-uf_class.title = "Class for handling chemical shifts."
-uf_class.menu_text = "&chemical_shift"
-uf_class.gui_icon = "relax.chemical_shift"
+uf_class = uf_info.add_class('io')
+uf_class.title = "Class for handling IO operations."
+uf_class.menu_text = "&io"
+uf_class.gui_icon = "relax.relax"
-# The chemical_shift.read user function.
-uf = uf_info.add_uf('chemical_shift.read')
-uf.title = "Read chemical shifts from a file."
+# The io.file_list user function.
+uf = uf_info.add_uf('io.file_list')
+uf.title = "Store a file list matching a file pattern in a directory."
uf.title_short = "Chemical shift reading."
uf.add_keyarg(
- name = "file",
+ name = "glob",
py_type = "str",
- arg_type = "file sel",
- desc_short = "file name",
- desc = "The name of the peak list of generic formatted file containing
the chemical shifts.",
- wiz_filesel_wildcard = WILDCARD_SPECTRUM_PEAKLIST,
- wiz_filesel_style = FD_OPEN
+ desc_short = "file pattern",
+ desc = "The pattern that may contain simple shell-style wildcards.",
)
uf.add_keyarg(
name = "dir",
py_type = "str",
- arg_type = "dir",
+ arg_type = "dir sel",
desc_short = "directory name",
desc = "The directory where the file is located.",
can_be_none = True
)
uf.add_keyarg(
- name = "spin_id_col",
- py_type = "int",
- arg_type = "free format",
- desc_short = "spin ID string column",
- desc = "The spin ID string column used by the generic file format (an
alternative to the mol, res, and spin name and number columns).",
- can_be_none = True
-)
-uf.add_keyarg(
- name = "mol_name_col",
- py_type = "int",
- arg_type = "free format",
- desc_short = "molecule name column",
- desc = "The molecule name column used by the generic file format
(alternative to the spin ID column).",
- can_be_none = True
-)
-uf.add_keyarg(
- name = "res_num_col",
- py_type = "int",
- arg_type = "free format",
- desc_short = "residue number column",
- desc = "The residue number column used by the generic file format
(alternative to the spin ID column).",
- can_be_none = True
-)
-uf.add_keyarg(
- name = "res_name_col",
- py_type = "int",
- arg_type = "free format",
- desc_short = "residue name column",
- desc = "The residue name column used by the generic file format
(alternative to the spin ID column).",
- can_be_none = True
-)
-uf.add_keyarg(
- name = "spin_num_col",
- py_type = "int",
- arg_type = "free format",
- desc_short = "spin number column",
- desc = "The spin number column used by the generic file format
(alternative to the spin ID column).",
- can_be_none = True
-)
-uf.add_keyarg(
- name = "spin_name_col",
- py_type = "int",
- arg_type = "free format",
- desc_short = "spin name column",
- desc = "The spin name column used by the generic file format
(alternative to the spin ID column).",
- can_be_none = True
-)
-uf.add_keyarg(
- name = "sep",
+ name = "id",
py_type = "str",
- arg_type = "free format",
- desc_short = "column separator",
- desc = "The column separator used by the generic format (the default
is white space).",
- can_be_none = True
-)
-uf.add_keyarg(
- name = "spin_id",
- py_type = "str",
- desc_short = "spin ID string",
- desc = "The spin ID string used to restrict the loading of data to
certain spin subsets.",
+ desc_short = "IO ID string",
+ desc = "The IO ID string used to store the filelist under.",
can_be_none = True
)
# Description.
uf.desc.append(Desc_container())
-uf.desc[-1].add_paragraph("This will read chemical shifts from a peak list
or a generic column formatted file.")
+uf.desc[-1].add_paragraph("This will store a list of file basenames and
fileroot matching the file pattern. These are stored in cdp.io_basename
and cdp.io_file_root.")
# Prompt examples.
uf.desc.append(Desc_container("Prompt examples"))
-uf.desc[-1].add_paragraph("The following commands will read the chemical
shifts out of the Sparky peak list '10ms.list':")
-uf.desc[-1].add_prompt("relax> chemical_shift.read('10ms.list')")
-uf.backend = chemical_shift.read
+uf.desc[-1].add_paragraph("The following commands will store a filelist to
cdp:")
+uf.desc[-1].add_prompt("relax> io.file_list(glob='128_*_FT.ft2',
dir='/path/to/foolder', id='750MHz_128_NI')")
+uf.backend = io.file_list
uf.menu_text = "&read"
-uf.gui_icon = "oxygen.actions.document-open"
+uf.gui_icon = "oxygen.actions.document-preview"
uf.wizard_size = (800, 500)
-uf.wizard_image = WIZARD_IMAGE_PATH + 'spectrum' + sep + 'spectrum_200.png'
+uf.wizard_image = WIZARD_IMAGE_PATH + 'document-preview.png'
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Re: r26941 - /branches/nmrglue/user_functions/io.py