Release 0.7b2 having fixed breakages from mixin re-ordering

Author: gb119

Stoner/Analysis.py

@@ -1573,7 +1573,7 @@ def action(i,column,row):
                 action(i, column, self.data[i])
         return self
 
-    def peaks(self, ycol=None, width=None, significance=None, xcol=None, peaks=True, troughs=False, poly=2, sort=False,modify=False):
+    def peaks(self, ycol=None, width=None, significance=None, xcol=None, peaks=True, troughs=False, poly=2, sort=False,modify=False,full_data=True):
         """Locates peaks and/or troughs in a column of data by using SG-differentiation.
 
         Args:
@@ -1592,6 +1592,8 @@ def peaks(self, ycol=None, width=None, significance=None, xcol=None, peaks=True,
             troughs (bool): select whether to measure troughs in data (default False)
             sort (bool): Sor the results by significance of peak
             modify (book): If true, then the returned object is a copy of self with only the peaks/troughs left in the data.
+            full_data (bool): If True (default) then all columns of the data at which peaks in the *ycol* column are found. *modify* true implies
+                      *full_data* is also true. If *full_data* is False, then only the x-column values of the peaks are returned.
 
         Returns:
             If *modify* is true, then returns a the AnalysisMixin with the data set to just the peaks/troughs. If *modify* is false (default),
@@ -1604,7 +1606,9 @@ def peaks(self, ycol=None, width=None, significance=None, xcol=None, peaks=True,
             """
 
         _=self._col_args(scalar=False,xcol=xcol,ycol=ycol)
-        xcol,ycol=_.xcol,_.ycol[0]
+        xcol,ycol=_.xcol,_.ycol
+        if isinstance(ycol,Iterable):
+            ycol=ycol[0]
         if width is None:  # Set Width to be length of data/20
             width = len(self) / 20
         assert poly >= 2, "poly must be at least 2nd order in peaks for checking for significance of peak or trough"
@@ -1624,20 +1628,13 @@ def peaks(self, ycol=None, width=None, significance=None, xcol=None, peaks=True,
         elif isinstance(significance, int): # integer significance is inverse to floating
             significance = _np_.max(_np_.abs(d2))/significance # Base an apriori significance on max d2y/dx2 / 20
 
-        i = _np_.arange(len(self))
         d2_interp = interp1d(_np_.arange(len(d2)), d2,kind='cubic')
         # Ensure we have some X-data
-        if xcol == None:
-            full_data=True
-            xdata = i
-
-        elif isinstance(xcol,bool) and not xcol:
-            full_data=False
-            xdata = i
+        if xcol is None:
+            xdata = _np_.arange(len(self))
         else:
-            full_data=False
             xdata = self.column(xcol)
-        xdata = interp1d(i, xdata,kind="cubic")
+        xdata = interp1d(_np_.arange(len(self)), xdata,kind="cubic")
 
 
         possible_peaks = _np_.array(_threshold(0, d1, rising=troughs, falling=peaks))
@@ -1657,9 +1654,8 @@ def peaks(self, ycol=None, width=None, significance=None, xcol=None, peaks=True,
         elif full_data:
             ret=self.interpolate(xdat,kind="cubic",xcol=False)
         else:
-            ret=xdata(possible_peaks+index_offset)
+            ret=xdat
         self.setas=setas
-        print(setas)
         # Return - but remembering to add back on the offset that we took off due to differentials not working at start and end
         return ret
 

Stoner/Core.py

@@ -1067,6 +1067,8 @@ def __new__(cls, input_array, *args,**kargs):
         # Finally, we must return the newly created object:
         obj.i=i
         obj.setas._row=_row and len(obj.shape)==1
+        #Set shared mask - stops some deprication warnings
+        obj._shared_mask=True
         return obj
 
     def __array_finalize__(self, obj):
@@ -1401,6 +1403,7 @@ class DataFile(metadataObject):
                            already saved to disc. This is the default filename used by the :py:meth:`Stoner.Core.DataFile.load`
                            and :py:meth:`Stoner.Core.DataFile.save`.
         mask (array of booleans): Returns the current mask applied to the numerical data equivalent to self.data.mask.
+        mime_type (list of str): The possible mime-types of data files represented by each matching filename pattern in :py:attr:`Datafile.pattern`. 
         patterns (list): A list of filename extenion glob patterns that matrches the expected filename patterns for a DataFile (*.txt and *.dat")
         priority (int): Used to indicathe order in which subclasses of :py:class:`DataFile` are tried when loading data. A higher number means a lower
                             priority (!)
@@ -1413,7 +1416,7 @@ class DataFile(metadataObject):
         dtype (numpoy dtype): Returns the datatype stored in the :py:attr:`DataFile.data` attribute.
         T (:py:class:`DataArray`): Transposed version of the data.
         subclasses (list): Returns a list of all the subclasses of DataFile currently in memory, sorted by
-                           their py:attr:`Stoner.Core.DataFile.priority. Each entry in the list consists of the
+                           their py:attr:`Stoner.Core.DataFile.priority`. Each entry in the list consists of the
                            string name of the subclass and the class object.
     """
 

Stoner/Image/core.py

@@ -161,7 +161,7 @@ def __array_finalize__(self, obj):
         more info and examples
         """
         if obj is None: return
-        self.metadata = getattr(obj, 'metadata', None)
+        self.metadata = getattr(obj, 'metadata', {})
         self.filename = getattr(obj, 'filename', None)
 
     def __array_wrap__(self, out_arr, context=None):

Stoner/Util.py

@@ -140,11 +140,12 @@ def annotate_fit(self,model,x=None,y=None,z=None,prefix=None,text_only=False,**k
             y (float): y co-ordinate of the label
             z (float): z co-ordinbate of the label if the current axes are 3D
             prefix (str): The prefix placed ahead of the model parameters in the metadata.
-            text_only (bool): If False (default), add the text to the plot and return the current object, otherwise,
-                return just the text and don't add to a plot.
+            text_only (bool): If False (default), add the text to the plot and return the current object, otherwise, 
+                      return just the text and don't add to a plot.
 
         Returns:
-            A copy of the current Data instance if text_only is False, otherwise returns the text.
+            
+            (Datam, str): A copy of the current Data instance if text_only is False, otherwise returns the text.
 
         If *prefix* is not given, then the first prefix in the metadata lmfit.prefix is used if present,
         otherwise a prefix is generated from the model.prefix attribute. If *x* and *y* are not specified then they
@@ -271,8 +272,11 @@ def split_up_down(data, col=None, folder=None):
     width = len(a) / 10
     if width % 2 == 0:  # Ensure the window for Satvisky Golay filter is odd
         width += 1
-    peaks = list(a.peaks(col, width,xcol=False, peaks=True, troughs=False))
-    troughs = list(a.peaks(col, width, xcol=False, peaks=False, troughs=True))
+    setas=a.setas.clone
+    a.setas=""
+    peaks = list(a.peaks(col, width,xcol=None, peaks=True, troughs=False,full_data=False))
+    troughs = list(a.peaks(col, width, xcol=None, peaks=False, troughs=True,full_data=False))
+    a.setas=setas
     if len(peaks) > 0 and len(troughs) > 0:  #Ok more than up down here
         order = peaks[0] < troughs[0]
     elif len(peaks) > 0:  #Rise then fall

Stoner/__init__.py

@@ -10,5 +10,5 @@
 from .Util import Data
 from .Folders import DataFolder
 
-__version_info__ = ('0', '7', 'b1')
+__version_info__ = ('0', '7', 'b2')
 __version__ = '.'.join(__version_info__)

doc/Stoner.rst

@@ -90,7 +90,7 @@ Instrument Formats
 
     BigBlueFile
     FmokeFile
-    QDSquidVSMFile
+    QDFile
     RigakuFile
     VSMFile
     MokeFile

doc/UserGuide/datafile.rst

@@ -55,8 +55,8 @@ Base Classes and Generic Formats
         but has not been extensively tested.
     :py:class:`Stoner.FileFormats.TDMSFile`
         Loads a file saved in the National Instruments TDMS format
-    :py:class:`Stoner.FileFormats.QDSquidVSMFile`
-        Loads data from a Quantum Design SQUID VSM as used on the I10 Beamline in Diamond and in our labs.
+    :py:class:`Stoner.FileFormats.QDFile`
+        Loads data from various Quantum Design instruments, cincluding PPMS, MPMS and  SQUID VSM.
     :py:class:`Stoner.FileFormats.OVFFile`
         OVF files are output by a variety of micomagnetics simulators. The standard was designed for the OOMMF code. This class will handle rectangualr mesh files with text or binary formats, versions 1.0 and 2.0
 
@@ -144,8 +144,8 @@ from disk::
 
    data=Stoner.Core.DataFile()<<open("File on Disk.txt")
 
-Constructing :py:class:`DataFile`s from Scratch
------------------------------------------------
+Constructing :py:class:`DataFile` s from Scratch
+------------------------------------------------------------
 
 The constructor :py:class:`DataFile`, :py:meth:`DataFile.__init__` will try its best to guess what your intention
 was in constructing a new instance of a DataFile. First of all a constructor function is called based on the number of positional

doc/UserGuide/plotfile.rst

@@ -10,7 +10,7 @@ publication ready figures. The :py:class:`PlotMixin` is included as apart of the
 Quick Plots
 ===========
 
-:py:class:`PlotMixin` is intended to help you make plots that look reasonably good with as little hassle as possible.
+The :py:class:`PlotMixin` class is intended to help you make plots that look reasonably good with as little hassle as possible.
 In common with many graph plotting programmes, it has a concept of declaring columns of data to be used for 'x', 'y' axes and
 for containing error bars. This is done with the :py:attr:`DataFile.setas` attribute (see :ref:`setas` for full details). Once this is done, the plotting
 methods will use these to try to make a sensible plot.::

tests/Stoner/test_Folders.py

@@ -64,7 +64,7 @@ def test_Operators(self):
         print("Starting....")
         self.assertEqual((fl+1)*2,len(fldr2),"Failed + operator with DataFolder on DataFolder")
         print("Passed 2")
-        fldr-="Untitled-0"
+        fldr-="Untitled"
         self.assertEqual(len(fldr),fl,"Failed to remove Untitled-0 from DataFolder by name.")
         print("Passed 3")
         fldr-="New-XRay-Data.dql"