Author: tlinnet
Date: Wed Dec 3 18:38:19 2014
New Revision: 26929
URL: http://svn.gna.org/viewcvs/relax?rev=26929&view=rev
Log:
Added the pipe_control.io module.
This is for storing the return of different io operations.
This could be accessing a file list in a directory, and be used to call a
list of peak files, and its associated ID.
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/io.py
Modified: branches/nmrglue/pipe_control/io.py
URL:
http://svn.gna.org/viewcvs/relax/branches/nmrglue/pipe_control/io.py?rev=26929&r1=26928&r2=26929&view=diff
==============================================================================
--- branches/nmrglue/pipe_control/io.py (original)
+++ branches/nmrglue/pipe_control/io.py Wed Dec 3 18:38:19 2014
@@ -20,81 +20,28 @@
###############################################################################
# Module docstring.
-"""Module for the using of nmrglue."""
+"""Module for the using of pipe_control.io."""
# relax module imports.
from lib.errors import RelaxError
-from lib.software.nmrglue import contour_plot, read_spectrum
from pipe_control.pipes import check_pipe
-from pipe_control.spectrum import add_spectrum_id, check_spectrum_id, delete
-def add_nmrglue_data(spectrum_id=None, nmrglue_data=None):
- """Add the nmrglue_data to the data store.
+def add_io_data(object_name=None, io_id=None, io_data=None):
+ """Add the io data to the data store under the the given object_name
within a dictionary with io_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 io_id: The dictionary key, to access the data. As As
cdp.object_name['io_id']
+ @type io_id: str
+ @keyword io_data: The type of data depending on called function.
+ @type io_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]
-
-
-def read(file=None, dir=None, spectrum_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
- """
-
- # Data checks.
- check_pipe()
-
- # Check the file name.
- if file == None:
- raise RelaxError("The file name must be supplied.")
-
- # Add spectrum ID.
- add_spectrum_id(spectrum_id)
-
- # Read the spectrum, and get it back as a class instance object.
- nmrglue_data = read_spectrum(file=file, dir=dir)
-
- # Store the data.
- add_nmrglue_data(spectrum_id=spectrum_id, nmrglue_data=nmrglue_data)
-
-
-def plot_contour(spectrum_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 contour_start: Contour level start value
- @type contour_start: float
- @keyword contour_num: Number of contour levels
- @type contour_num: int
- @keyword contour_factor: Scaling factor between contour levels
- @type contour_factor: float
- @keyword ppm: A flag which if True will make the plot in
ppm scale. Else it is in points.
- @type ppm: bool
- @keyword show: A flag which if True will make a call to
matplotlib.pyplot.show().
- @type show: bool
- @return: The matplotlib.axes.AxesSubplot class, which
can be manipulated to add additional text to the axis.
- @rtype: matplotlib.axes.AxesSubplot
- """
-
- # 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)
-
- return ax
-
+ # Add the data under the dictionary key.
+ obj_dict = getattr(cdp, object_name)
+ obj_dict[io_id] = io_data
r26929 - /branches/nmrglue/pipe_control/io.py