Author: tlinnet
Date: Sun Dec 7 23:43:00 2014
New Revision: 27004
URL: http://svn.gna.org/viewcvs/relax?rev=27004&view=rev
Log:
Several fixes to pipe_control.nmrglue functions.
This is mainly the change from spectrum_id to nmrglue_id, and how data is
stored.
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/pipe_control/nmrglue.py
Modified: branches/nmrglue/pipe_control/nmrglue.py
URL:
http://svn.gna.org/viewcvs/relax/branches/nmrglue/pipe_control/nmrglue.py?rev=27004&r1=27003&r2=27004&view=diff
==============================================================================
--- branches/nmrglue/pipe_control/nmrglue.py (original)
+++ branches/nmrglue/pipe_control/nmrglue.py Sun Dec 7 23:43:00 2014
@@ -26,35 +26,57 @@
from lib.errors import RelaxError
from lib.software.nmrglue import contour_plot, hist_plot, read_spectrum
from pipe_control.pipes import check_pipe
-from pipe_control.spectrum import add_spectrum_id, check_spectrum_id, delete
+from pipe_control.spectrum import check_spectrum_id, delete
-def add_nmrglue_data(spectrum_id=None, nmrglue_data=None):
- """Add the nmrglue_data to the data store.
+def add_nmrglue_data(object_name=None, nmrglue_id=None, nmrglue_data=None):
+ """Add the nmrglue data to the data store under the the given
object_name within a dictionary with nmrglue_id key.
- @keyword spectrum_id: The spectrum ID string.
- @type spectrum_id: str
- @keyword nmrglue_data: The nmrglue data as class instance object.
- @type nmrglue_data: lib.spectrum.objects.Nmrglue_data instance
+ @keyword object_name: The object name for where to store the data.
As cdp.object_name.
+ @type object_name: str
+ @keyword nmrglue_id: The dictionary key, to access the data. As
As cdp.object_name['nmrglue_id']
+ @type nmrglue_id: str
+ @keyword nmrglue_data: The type of data depending on called
function.
+ @type nmrglue_data: depend on function
"""
# Initialise the structure, if needed.
- if not hasattr(cdp, 'ngdata'):
- cdp.ngdata = {}
+ if not hasattr(cdp, object_name):
+ setattr(cdp, object_name, {})
- # Add the data under the spectrum ID.
- cdp.ngdata[spectrum_id] = nmrglue_data[0]
+ # Add the data under the dictionary key.
+ obj_dict = getattr(cdp, object_name)
+ obj_dict[nmrglue_id] = nmrglue_data
-def read(file=None, dir=None, spectrum_id=None):
+def add_nmrglue_id(nmrglue_id=None):
+ """Add the nmrglue ID to the data store.
+
+ @keyword nmrglue_id: The nmrglue ID string.
+ @type nmrglue_id: str
+ """
+
+ # Initialise the structure, if needed.
+ if not hasattr(cdp, 'nmrglue_ids'):
+ cdp.nmrglue_ids = []
+
+ # The ID already exists.
+ if nmrglue_id in cdp.nmrglue_ids:
+ return
+
+ # Add the ID.
+ cdp.nmrglue_ids.append(nmrglue_id)
+
+
+def read(file=None, dir=None, nmrglue_id=None):
"""Read the spectrum file.
@keyword file: The name of the file(s) containing the spectrum.
@type file: str or list of str
@keyword dir: The directory where the file is located.
@type dir: str
- @keyword spectrum_id: The spectrum identification string.
- @type spectrum_id: str or list of str
+ @keyword nmrglue_id: The spectrum identification string.
+ @type nmrglue_id: str or list of str
"""
# Data checks.
@@ -67,7 +89,7 @@
# Multiple ID flags.
flag_multi = False
flag_multi_file = False
- if isinstance(spectrum_id, list):
+ if isinstance(nmrglue_id, list):
flag_multi = True
if isinstance(file, list):
flag_multi_file = True
@@ -79,8 +101,8 @@
raise RelaxError("The file and spectrum ID must both be of list
type.")
# List lengths for multiple files.
- if flag_multi_file and len(spectrum_id) != len(file):
- raise RelaxError("The file list %s and spectrum ID list %s do
not have the same number of elements." % (file, spectrum_id))
+ if flag_multi_file and len(nmrglue_id) != len(file):
+ raise RelaxError("The file list %s and spectrum ID list %s do
not have the same number of elements." % (file, nmrglue_id))
# More list argument checks (when only one spectrum ID is supplied).
else:
@@ -92,30 +114,32 @@
if not isinstance(file, list):
file = [file]
- # Convert the spectrum_id argument to a list if necessary.
- if not isinstance(spectrum_id, list):
- spectrum_id = [spectrum_id]
+ # Convert the nmrglue_id argument to a list if necessary.
+ if not isinstance(nmrglue_id, list):
+ nmrglue_id = [nmrglue_id]
# Loop over the files.
for i, file_i in enumerate(file):
# Assign spectrum id.
- spectrum_id_i = spectrum_id[i]
+ nmrglue_id_i = nmrglue_id[i]
# Add spectrum ID.
- add_spectrum_id(spectrum_id_i)
+ add_nmrglue_id(nmrglue_id_i)
- # Read the spectrum, and get it back as a class instance object.
- nmrglue_data = read_spectrum(file=file_i, dir=dir)
+ # Read the spectrum, and get it back two dictionaries, and a numpy
array.
+ dic, udic, data = read_spectrum(file=file_i, dir=dir)
# Store the data.
- add_nmrglue_data(spectrum_id=spectrum_id_i,
nmrglue_data=nmrglue_data)
+ add_nmrglue_data(object_name='nmrglue_dic', nmrglue_id=nmrglue_id_i,
nmrglue_data=dic)
+ add_nmrglue_data(object_name='nmrglue_udic',
nmrglue_id=nmrglue_id_i, nmrglue_data=udic)
+ add_nmrglue_data(object_name='nmrglue_data',
nmrglue_id=nmrglue_id_i, nmrglue_data=data)
-def plot_contour(spectrum_id=None, contour_start=30000., contour_num=20,
contour_factor=1.20, ppm=True, show=False):
+def plot_contour(nmrglue_id=None, contour_start=30000., contour_num=20,
contour_factor=1.20, ppm=True, show=False):
"""Plot the spectrum as contour plot.
- @keyword spectrum_id: The spectrum identification string.
- @type spectrum_id: str or list of str
+ @keyword nmrglue_id: The spectrum identification string.
+ @type nmrglue_id: str or list of str
@keyword contour_start: Contour level start value
@type contour_start: float
@keyword contour_num: Number of contour levels
@@ -131,7 +155,7 @@
"""
# Call the contour plot.
- ax = contour_plot(spectrum_id=spectrum_id, contour_start=contour_start,
contour_num=contour_num, contour_factor=contour_factor, ppm=ppm, show=show)
+ ax = contour_plot(nmrglue_id=nmrglue_id, contour_start=contour_start,
contour_num=contour_num, contour_factor=contour_factor, ppm=ppm, show=show)
# Return the axis instance, for possibility for additional decoration.
return ax
r27004 - /branches/nmrglue/pipe_control/nmrglue.py