New upstream version 0.4.20

.gitignore

@@ -54,3 +54,6 @@ Icon?
 
 # Emacs backup files
 *~
+
+# Virtual Studio Code
+.vscode

conda-recipe/meta.yaml

 package:
   name: nexusformat
-  version: "0.4.18"
+  version: "0.4.19"
 
 source:
   git_url: https://github.com/nexpy/nexusformat.git
-  git_tag: v0.4.18
+  git_tag: v0.4.19
 
 build:
   entry_points:

src/nexusformat/_version.py

@@ -20,8 +20,8 @@ def get_keywords():
     # setup.py/versioneer.py will grep for the variable names, so they must
     # each be defined on a line of their own. _version.py will just call
     # get_keywords().
-    git_refnames = " (HEAD -> master, tag: v0.4.18)"
-    git_full = "b9de7f7dba7e2b4c623aa05f19bee12fbc4ec3a9"
+    git_refnames = " (tag: v0.4.20)"
+    git_full = "e1e6689b1651b8b7217158528336b80d8f126113"
     keywords = {"refnames": git_refnames, "full": git_full}
     return keywords
 

src/nexusformat/nexus/plot.py

@@ -71,7 +71,8 @@ class PylabPlotter(object):
     Matplotlib plotter class for NeXus data.
     """
 
-    def plot(self, data_group, fmt, xmin, xmax, ymin, ymax, zmin, zmax, **opts):
+    def plot(self, data_group, fmt='', xmin=None, xmax=None, ymin=None, ymax=None, 
+             vmin=None, vmax=None, **opts):
         """
         Plot the data entry.
 
@@ -159,18 +160,18 @@ class PylabPlotter(object):
                     y = boundaries(axes[-2], data.shape[-2])
                     xlabel, ylabel = label(axes[-1]), label(axes[-2])
 
-                if not zmin: 
-                    zmin = np.nanmin(data[data>-np.inf])
-                if not zmax: 
-                    zmax = np.nanmax(data[data<np.inf])
+                if not vmin: 
+                    vmin = np.nanmin(data[data>-np.inf])
+                if not vmax: 
+                    vmax = np.nanmax(data[data<np.inf])
             
                 if not image:
                     if log:
-                        zmin = max(zmin, 0.01)
-                        zmax = max(zmax, 0.01)
-                        opts["norm"] = LogNorm(zmin, zmax)
+                        vmin = max(vmin, 0.01)
+                        vmax = max(vmax, 0.01)
+                        opts["norm"] = LogNorm(vmin, vmax)
                     else:
-                        opts["norm"] = Normalize(zmin, zmax)
+                        opts["norm"] = Normalize(vmin, vmax)
 
                 ax = plt.gca()
                 if image:

src/nexusformat/nexus/tree.py

@@ -28,7 +28,7 @@ data.
 Example 1: Loading a NeXus file
 -------------------------------
 The following commands loads NeXus data from a file, displays (some of) the
-contents as a tree, and then accesses individual data items.
+contents as a tree, and then accesses individual data items
 
     >>> from nexusformat import nexus as nx
     >>> a=nx.load('sns/data/ARCS_7326.nxs')
@@ -83,7 +83,7 @@ file. The data are first created as Numpy arrays
     >>> z=np.sin(X)*np.sin(Y)
 
 Then, a NeXus data group is created and the data inserted to produce a
-NeXus-compliant structure that can be saved to a file.
+NeXus-compliant structure that can be saved to a file
 
     >>> root=nx.NXroot(NXentry())
     >>> print root.tree
@@ -369,7 +369,7 @@ class NXFile(object):
         elif not os.path.exists(os.path.dirname(name)):
             raise NeXusError("'%s/' does not exist"
                              % os.path.dirname(name))
-        elif mode == 'w' or mode == 'w-' or mode == 'w5':
+        elif mode == 'w' or mode == 'w-' or mode == 'w5' or mode == 'a':
             if mode == 'w5':
                 mode = 'w'
             self._file = self.h5.File(name, mode, **opts)
@@ -892,7 +892,7 @@ def _getvalue(value, dtype=None, shape=None):
                 _dtype = _getdtype(dtype)
                 if _dtype.kind == 'S':
                     value = text(value).encode('utf-8')
-                return np.asscalar(np.array(value, dtype=_dtype)), _dtype, ()
+                return np.array(value, dtype=_dtype).item(), _dtype, ()
             except Exception:
                 raise NeXusError("The value is incompatible with the dtype")
         else:
@@ -909,7 +909,14 @@ def _getvalue(value, dtype=None, shape=None):
         else:
             _value = np.asarray(value) #convert subclasses of ndarray
     else:
-        _value = np.asarray(value)
+        try:
+            _value = [np.asarray(v) for v in value]
+            if len(set([v.shape for v in _value])) > 1:
+                raise NeXusError(
+                    "Cannot assign an iterable with items of multiple shapes")
+            _value = np.asarray(_value)
+        except TypeError:
+            _value = np.asarray(value)
         if _value.dtype.kind == 'S' or _value.dtype.kind == 'U':
             _value = _value.astype(string_dtype)
     if dtype is not None:
@@ -927,7 +934,7 @@ def _getvalue(value, dtype=None, shape=None):
         except ValueError:
             raise NeXusError("The value is incompatible with the shape")
     if _value.shape == ():
-        return np.asscalar(_value), _value.dtype, _value.shape
+        return _value.item(), _value.dtype, _value.shape
     else:
         return _value, _value.dtype, _value.shape
 
@@ -1161,7 +1168,7 @@ class NXattr(object):
             else:
                 return [text(value) for value in self._value[()]]
         elif self.shape == (1,):
-            return np.asscalar(self._value)
+            return self._value.item()
         else:
             return self._value
 
@@ -1967,7 +1974,7 @@ class NXfield(NXobject):
         """
         idx = convert_index(idx, self)
         if len(self) == 1:
-            result = self
+            result = self.nxvalue
         elif self._value is None:
             if self._uncopied_data:
                 self._get_uncopied_data()
@@ -2320,8 +2327,10 @@ class NXfield(NXobject):
     def __long__(self):
         """
         Casts a scalar field as a long integer
+
+        The use of the 'long' function is not valid in Python 3 and no longer useful in Python 2
         """
-        return long(self.nxvalue)
+        return int(self.nxvalue)
 
     def __float__(self):
         """
@@ -2723,7 +2732,7 @@ class NXfield(NXobject):
             else:
                 return [text(value) for value in _value[()]]
         elif self.shape == (1,):
-            return np.asscalar(_value)
+            return _value.item()
         else:
             return _value
 
@@ -2931,7 +2940,9 @@ class NXfield(NXobject):
 
     @property
     def maxshape(self):
-        if self.nxfilemode:
+        if self._maxshape is not None:
+            return self._maxshape
+        elif self.nxfilemode:
             with self.nxfile as f:
                 _maxshape = f[self.nxfilepath].maxshape
         elif self._memfile:
@@ -2992,7 +3003,7 @@ class NXfield(NXobject):
             return False
 
     def plot(self, fmt='', xmin=None, xmax=None, ymin=None, ymax=None,
-             zmin=None, zmax=None, **opts):
+             vmin=None, vmax=None, **opts):
         """
         Plot data if the signal attribute is defined.
 
@@ -3031,7 +3042,8 @@ class NXfield(NXobject):
             else:
                 signal_path = self.nxpath
             data.nxsignal.attrs['signal_path'] = signal_path
-            plotview.plot(data, fmt, xmin, xmax, ymin, ymax, zmin, zmax, **opts)
+            plotview.plot(data, fmt, xmin=None, xmax=None, ymin=None, ymax=None,
+                          vmin=None, vmax=None, **opts)
         else:
             raise NeXusError("NXfield not plottable")
     
@@ -3042,23 +3054,23 @@ class NXfield(NXobject):
         self.plot(fmt=fmt, over=True, **opts)
 
     def logplot(self, fmt='', xmin=None, xmax=None, ymin=None, ymax=None,
-                zmin=None, zmax=None, **opts):
+                vmin=None, vmax=None, **opts):
         """
         Plots the data intensity contained within the group on a log scale.
         """
         self.plot(fmt=fmt, log=True,
                   xmin=xmin, xmax=xmax, ymin=ymin, ymax=ymax,
-                  zmin=zmin, zmax=zmax, **opts)
+                  vmin=vmin, vmax=vmax, **opts)
 
     def implot(self, fmt='', xmin=None, xmax=None, ymin=None, ymax=None,
-                zmin=None, zmax=None, **opts):
+                vmin=None, vmax=None, **opts):
         """
         Plots the data intensity as an RGB(A) image.
         """
         if self.plot_rank > 2 and (self.shape[-1] == 3 or self.shape[-1] == 4):
             self.plot(fmt=fmt, image=True,
                       xmin=xmin, xmax=xmax, ymin=ymin, ymax=ymax,
-                      zmin=zmin, zmax=zmax, **opts)
+                      vmin=vmin, vmax=vmax, **opts)
         else:
             raise NeXusError("Invalid shape for RGB(A) image")
 
@@ -3595,7 +3607,7 @@ class NXgroup(NXobject):
         """
         Returns true if a NeXus object with the specified name is in the group.
         """
-        return self.entries.has_key(name)    
+        return name in self.entries   
 
     def copy(self):
         """
@@ -3741,30 +3753,30 @@ class NXgroup(NXobject):
         """
         return self.sum(axis, averaged=True)
 
-    def moment(self, order=1):
+    def moment(self, order=1, center=None):
         """
-        Returns an NXfield containing the moments of the NXdata group
+        Returns an NXfield containing the central moments of the NXdata group
         assuming the signal is one-dimensional.
-
-        Currently, the first two moments have been defined (order =1 or 2).
         """
-        if self.nxsignal is None:
+        signal, axes = self.nxsignal, self.nxaxes
+        if signal is None:
             raise NeXusError("No signal to calculate")
-        elif len(self.nxsignal.shape) > 1:
+        elif len(signal.shape) > 1:
             raise NeXusError(
                 "Operation only possible on one-dimensional signals")
-        elif order > 2:
-            raise NeXusError("Higher moments not yet implemented")
-        if not hasattr(self,"nxclass"):
+        if not hasattr(self, "nxclass"):
             raise NeXusError(
                 "Operation not allowed for groups of unknown class")
-        y = self.nxsignal
-        x = centers(y, self.nxaxes)[0]
-        mean = (y * x).sum() / y.sum()
+        y = signal / signal.sum()
+        x = centers(y, axes)[0]
+        if center:
+            c = center
+        else:
+            c = (y * x).sum()
         if order == 1:
-            return mean
-        elif order == 2:
-            return ((y * x**2).sum() / y.sum()) - mean**2
+            return c
+        else:
+            return (y * (x - c)**order).sum()
 
     def mean(self):
         """
@@ -4618,7 +4630,7 @@ class NXdata(NXgroup):
             idx, axes = self.slab(key)
             removed_axes = []
             for axis in axes:
-                if axis.shape == () or axis.shape == (1,):
+                if axis.shape == () or axis.shape == (0,) or axis.shape == (1,):
                     removed_axes.append(axis)
             axes = [ax for ax in axes if ax not in [rax for rax in removed_axes 
                                                     if rax is ax]]            
@@ -4877,8 +4889,8 @@ class NXdata(NXgroup):
             else:
                 ind = convert_index(ind, axes[i])
                 slices.append(ind)
-                if (signal.shape[i] < axes[i].shape[0] and
-                       isinstance(ind, slice) and ind.stop is not None):
+                if (isinstance(ind, slice) and ind.stop is not None
+                    and signal.shape[i] < axes[i].shape[0]):
                     ind = slice(ind.start, ind.stop+1, ind.step)
                 axes[i] = axes[i][ind]
         return tuple(slices), axes
@@ -4924,7 +4936,7 @@ class NXdata(NXgroup):
             return None
 
     def plot(self, fmt='', xmin=None, xmax=None, ymin=None, ymax=None,
-             zmin=None, zmax=None, **opts):
+             vmin=None, vmax=None, **opts):
         """
         Plot data contained within the group.
 
@@ -4966,7 +4978,8 @@ class NXdata(NXgroup):
         except ImportError:
             from .plot import plotview
             
-        plotview.plot(self, fmt, xmin, xmax, ymin, ymax, zmin, zmax, **opts)
+        plotview.plot(self, fmt, xmin=xmin, xmax=xmax, ymin=ymin, ymax=ymax, 
+                      vmin=vmin, vmax=vmax, **opts)
     
     def oplot(self, fmt='', **opts):
         """
@@ -4975,16 +4988,16 @@ class NXdata(NXgroup):
         self.plot(fmt=fmt, over=True, **opts)
 
     def logplot(self, fmt='', xmin=None, xmax=None, ymin=None, ymax=None,
-                zmin=None, zmax=None, **opts):
+                vmin=None, vmax=None, **opts):
         """
         Plots the data intensity contained within the group on a log scale.
         """
         self.plot(fmt=fmt, log=True,
                   xmin=xmin, xmax=xmax, ymin=ymin, ymax=ymax,
-                  zmin=zmin, zmax=zmax, **opts)
+                  vmin=vmin, vmax=vmax, **opts)
 
     def implot(self, fmt='', xmin=None, xmax=None, ymin=None, ymax=None,
-                zmin=None, zmax=None, **opts):
+                vmin=None, vmax=None, **opts):
         """
         Plots the data intensity as an image.
         """
@@ -4992,7 +5005,7 @@ class NXdata(NXgroup):
             (self.nxsignal.shape[-1] == 3 or self.nxsignal.shape[-1] == 4)):
             self.plot(fmt=fmt, image=True,
                       xmin=xmin, xmax=xmax, ymin=ymin, ymax=ymax,
-                      zmin=zmin, zmax=zmax, **opts)
+                      vmin=vmin, vmax=vmax, **opts)
         else:
             raise NeXusError("Invalid shape for RGB(A) image")