Merge pull request #723 from wright-group/development

3.1.2

.travis.yml

@@ -1,14 +1,23 @@
 language: python
-python:
-  - "3.5"
-  - "3.6"
+matrix:
+    include:
+        - python: 3.5
+          dist: trusty
+          sudo: false
+        - python: 3.6
+          dist: trusty
+          sudo: false
+        - python: 3.7
+          dist: xenial
+          sudo: true
 addons:
     apt:
         packages:
             - libfreetype6-dev
             - libopenblas-dev
 install:
-  - python setup.py install
+  - pip install cython
+  - pip install .
   - pip install -U pytest pytest-mp
 before_script:
 - "export DISPLAY=:99.0"

WrightTools/VERSION

@@ -1 +1 @@
-3.1.1
+3.1.2

WrightTools/_dataset.py

@@ -22,7 +22,7 @@
 class Dataset(h5py.Dataset):
     """Array-like data container."""
 
-    instances = {}
+    _instances = {}
     class_name = "Dataset"
 
     def __getitem__(self, index):
@@ -88,12 +88,12 @@ def __init__(self, *args, **kwargs):
     def __new__(cls, parent, id, **kwargs):
         """New object formation handler."""
         fullpath = parent.fullpath + h5py.h5i.get_name(id).decode()
-        if fullpath in cls.instances.keys():
-            return cls.instances[fullpath]
+        if fullpath in cls._instances.keys():
+            return cls._instances[fullpath]
         else:
             instance = super(Dataset, cls).__new__(cls)
             cls.__init__(instance, parent, id, **kwargs)
-            cls.instances[fullpath] = instance
+            cls._instances[fullpath] = instance
             return instance
 
     def __repr__(self):
@@ -363,7 +363,7 @@ def max(self):
             def f(dataset, s):
                 return np.nanmax(dataset[s])
 
-            self.attrs["max"] = max(self.chunkwise(f).values())
+            self.attrs["max"] = np.nanmax(list(self.chunkwise(f).values()))
         return self.attrs["max"]
 
     def min(self):
@@ -373,7 +373,7 @@ def min(self):
             def f(dataset, s):
                 return np.nanmin(dataset[s])
 
-            self.attrs["min"] = min(self.chunkwise(f).values())
+            self.attrs["min"] = np.nanmin(list(self.chunkwise(f).values()))
         return self.attrs["min"]
 
     def slices(self):

WrightTools/_group.py

@@ -40,7 +40,7 @@ def __call__(cls, *args, **kwargs):
 class Group(h5py.Group, metaclass=MetaClass):
     """Container of groups and datasets."""
 
-    instances = {}
+    _instances = {}
     class_name = "Group"
 
     def __init__(self, file=None, parent=None, name=None, **kwargs):
@@ -154,11 +154,11 @@ def __new__(cls, *args, **kwargs):
         elif edit_local and filepath:
             p = filepath
         p = str(p)
-        for i in cls.instances.keys():
+        for i in cls._instances.keys():
             if i.startswith(os.path.abspath(p) + "::"):
-                file = cls.instances[i].file
-                if hasattr(cls.instances[i], "_tmpfile"):
-                    tmpfile = cls.instances[i]._tmpfile
+                file = cls._instances[i].file
+                if hasattr(cls._instances[i], "_tmpfile"):
+                    tmpfile = cls._instances[i]._tmpfile
                 break
         if file is None:
             file = h5py.File(p, "a")
@@ -171,14 +171,14 @@ def __new__(cls, *args, **kwargs):
         fullpath = p + "::" + parent + name
         # create and/or return
         try:
-            instance = cls.instances[fullpath]
+            instance = cls._instances[fullpath]
         except KeyError:
             kwargs["file"] = file
             kwargs["parent"] = parent
             kwargs["name"] = natural_name
             instance = super(Group, cls).__new__(cls)
             cls.__init__(instance, **kwargs)
-            cls.instances[fullpath] = instance
+            cls._instances[fullpath] = instance
             if tmpfile:
                 setattr(instance, "_tmpfile", tmpfile)
                 weakref.finalize(instance, instance.close)
@@ -232,27 +232,28 @@ def parent(self):
             from .collection import Collection
 
             key = posixpath.dirname(self.fullpath) + posixpath.sep
-            self._parent = Collection.instances[key]
+            self._parent = Collection._instances[key]
         finally:
             return self._parent
 
     def close(self):
         """Close the file that contains the Group.
 
-        All groups which are in the file will be closed and removed from the instances dictionaries.
-        Tempfiles, if they exist, will be removed.
+        All groups which are in the file will be closed and removed from the
+        _instances dictionaries.
+        Tempfiles, if they exist, will be removed
         """
         from .collection import Collection
         from .data._data import Channel, Data, Variable
 
         path = os.path.abspath(self.filepath) + "::"
         for kind in (Collection, Channel, Data, Variable, Group):
             rm = []
-            for key in kind.instances.keys():
+            for key in kind._instances.keys():
                 if key.startswith(path):
                     rm.append(key)
             for key in rm:
-                kind.instances.pop(key, None)
+                kind._instances.pop(key, None)
 
         if self.fid.valid > 0:
             # for some reason, the following file operations sometimes fail

WrightTools/artists/_base.py

@@ -574,7 +574,7 @@ def add_subplot(self, *args, **kwargs):
         self._axstack.add(key, a)
         self.sca(a)
         if int(matplotlib.__version__.split(".")[0]) > 1:
-            a._remove_method = self.__remove_ax
+            a._remove_method = lambda ax: self.delaxes(ax)
             self.stale = True
             a.stale_callback = matplotlib.figure._stale_figure_callback
         # finish

WrightTools/artists/_interact.py

@@ -82,10 +82,14 @@ def get_clim(channel, current_state):
     return clim
 
 
-def gen_ticklabels(points):
+def gen_ticklabels(points, signed=None):
     step = np.nanmin(np.diff(points))
-    if step == 0:
-        ticklabels = ["NaN" for point in points]
+    if step == 0:  # zeros everywhere
+        ticklabels = ['' for i in range(11)]
+        if signed:
+            ticklabels[5] = '0'
+        else:
+            ticklabels[0] = '0'
         return ticklabels
     ordinal = np.log10(np.abs(step))
     ndigits = -int(np.floor(ordinal))
@@ -216,6 +220,9 @@ def interact2D(data, xaxis=0, yaxis=1, channel=0, local=False, verbose=True):
         verbose=False,
     )[0]
     clim = get_clim(channel, current_state)
+    ticklabels = gen_ticklabels(np.linspace(*clim, 11), channel.signed)
+    if clim[0] == clim[1]:
+        clim = [-1 if channel.signed else 0, 1]
     obj2D = ax0.pcolormesh(
         current_state.dat,
         cmap=cmap,
@@ -229,6 +236,8 @@ def interact2D(data, xaxis=0, yaxis=1, channel=0, local=False, verbose=True):
     colorbar = plot_colorbar(
         cax, cmap=cmap, label=channel.natural_name, ticks=np.linspace(clim[0], clim[1], 11)
     )
+    colorbar.set_ticklabels(ticklabels)
+    fig.canvas.draw_idle()
 
     def draw_sideplot_projections():
         arr = current_state.dat[channel.natural_name][:]
@@ -353,9 +362,10 @@ def update_local(index):
             print("normalization:", index)
         current_state.local = radio.value_selected[1:] == "local"
         clim = get_clim(channel, current_state)
-        colorbar = plot_colorbar(
-            cax, cmap=cmap, label=channel.natural_name, ticks=np.linspace(clim[0], clim[1], 11)
-        )
+        ticklabels = gen_ticklabels(np.linspace(*clim, 11), channel.signed)
+        colorbar.set_ticklabels(ticklabels)
+        if clim[0] == clim[1]:
+            clim = [-1 if channel.signed else 0, 1]
         obj2D.set_clim(*clim)
         fig.canvas.draw_idle()
 
@@ -378,11 +388,11 @@ def update(info):
                 )
             obj2D.set_array(current_state.dat[channel.natural_name][:].ravel())
             clim = get_clim(channel, current_state)
+            ticklabels = gen_ticklabels(np.linspace(*clim, 11), channel.signed)
+            if clim[0] == clim[1]:
+                clim = [-1 if channel.signed else 0, 1]
             obj2D.set_clim(*clim)
-            ticklabels = gen_ticklabels(np.linspace(*clim, 11))
-            colorbar = plot_colorbar(
-                cax, cmap=cmap, label=channel.natural_name, ticks=np.linspace(clim[0], clim[1], 11)
-            )
+            colorbar.set_ticklabels(ticklabels)
             sp_x.collections.clear()
             sp_y.collections.clear()
             draw_sideplot_projections()

WrightTools/data/_axis.py

@@ -11,6 +11,7 @@
 
 import numpy as np
 
+from ._variable import Variable
 from .. import exceptions as wt_exceptions
 from .. import kit as wt_kit
 from .. import units as wt_units
@@ -63,7 +64,7 @@ def __getitem__(self, index):
             vs[variable.natural_name] = wt_units.converter(arr, variable.units, self.units)
         return numexpr.evaluate(self.expression.split("=")[0], local_dict=vs)
 
-    def __repr__(self):
+    def __repr__(self) -> str:
         return "<WrightTools.Axis {0} ({1}) at {2}>".format(
             self.expression, str(self.units), id(self)
         )
@@ -72,50 +73,49 @@ def __repr__(self):
     def _leaf(self):
         out = self.expression
         if self.units is not None:
-            out += " ({0}) {1}".format(self.units, self.shape)
+            out += " ({0})".format(self.units)
+        out += " {0}".format(self.shape)
         return out
 
     @property
-    def full(self):
+    def full(self) -> np.ndarray:
         arr = self[:]
         for i in range(arr.ndim):
             if arr.shape[i] == 1:
                 arr = np.repeat(arr, self.parent.shape[i], axis=i)
         return arr
 
     @property
-    def identity(self):
+    def identity(self) -> str:
         """Complete identifier written to disk in data.attrs['axes']."""
         return self.natural_name + " {%s}" % self.units
 
     @property
-    def label(self):
-        symbol = wt_units.get_symbol(self.units)
-        label = self.expression
-        for v in self.variables:
-            vl = "%s_{%s}" % (symbol, v.label)
-            vl = vl.replace("_{}", "")  # label can be empty, no empty subscripts
-            label = label.replace(v.natural_name, vl)
+    def label(self) -> str:
+        label = self.expression.replace("_", "\\;")
         if self.units_kind:
+            symbol = wt_units.get_symbol(self.units)
+            for v in self.variables:
+                vl = "%s_{%s}" % (symbol, v.label)
+                vl = vl.replace("_{}", "")  # label can be empty, no empty subscripts
+                label = label.replace(v.natural_name, vl)
             units_dictionary = getattr(wt_units, self.units_kind)
             label += r"\,"
             label += r"\left("
             label += units_dictionary[self.units][2]
             label += r"\right)"
-        else:
-            pass
         label = r"$\mathsf{%s}$" % label
         return label
 
     @property
-    def natural_name(self):
+    def natural_name(self) -> str:
         name = self.expression.strip()
         for op in operators:
             name = name.replace(op, operator_to_identifier[op])
         return wt_kit.string2identifier(name)
 
     @property
-    def ndim(self):
+    def ndim(self) -> int:
         """Get number of dimensions."""
         try:
             assert self._ndim is not None
@@ -125,27 +125,27 @@ def ndim(self):
             return self._ndim
 
     @property
-    def points(self):
+    def points(self) -> np.ndarray:
         """Squeezed array."""
         return np.squeeze(self[:])
 
     @property
-    def shape(self):
+    def shape(self) -> tuple:
         """Shape."""
         return wt_kit.joint_shape(*self.variables)
 
     @property
-    def size(self):
+    def size(self) -> int:
         """Size."""
         return functools.reduce(operator.mul, self.shape)
 
     @property
-    def units_kind(self):
+    def units_kind(self) -> str:
         """Units kind."""
         return wt_units.kind(self.units)
 
     @property
-    def variables(self):
+    def variables(self) -> list:
         """Variables."""
         try:
             assert self._variables is not None
@@ -170,9 +170,10 @@ def convert(self, destination_units, *, convert_variables=False):
         convert_variables : boolean (optional)
             Toggle conversion of stored arrays. Default is False.
         """
+        if self.units is None and (destination_units is None or destination_units == "None"):
+            return
         if not wt_units.is_valid_conversion(self.units, destination_units):
-            kind = wt_units.kind(self.units)
-            valid = list(wt_units.dicts[kind].keys())
+            valid = wt_units.get_valid_conversions(self.units)
             raise wt_exceptions.UnitsError(valid, destination_units)
         if convert_variables:
             for v in self.variables:
@@ -181,8 +182,8 @@ def convert(self, destination_units, *, convert_variables=False):
 
     def max(self):
         """Axis max."""
-        return np.max(self[:])
+        return np.nanmax(self[:])
 
     def min(self):
         """Axis min."""
-        return np.min(self[:])
+        return np.nanmin(self[:])

WrightTools/data/_brunold.py

@@ -21,7 +21,7 @@
 # --- from function -------------------------------------------------------------------------------
 
 
-def from_BrunoldrRaman(filepath, name=None, parent=None, verbose=True):
+def from_BrunoldrRaman(filepath, name=None, parent=None, verbose=True) -> Data:
     """Create a data object from the Brunold rRaman instrument.
 
     Expects one energy (in wavenumbers) and one counts value.