Version 3.1.1

3.1.1

.gitignore

@@ -2,6 +2,9 @@
 __pycache__/
 *.py[cod]
 
+# direnv
+*.envrc
+
 # distribution / packaging
 .Python
 env/

readthedocs.yml → .readthedocs.yml

@@ -1,6 +1,10 @@
 requirements_file: requirements.txt
 
+build:
+    image: latest
+
 python:
+  version: 3.6
   pip_install: true
   extra_requirements: [docs]
 

.travis.yml

@@ -6,8 +6,6 @@ addons:
     apt:
         packages:
             - libfreetype6-dev
-            - hdf5-tools
-            - libhdf5-dev
             - libopenblas-dev
 install:
   - python setup.py install

WrightTools/VERSION

@@ -1 +1 @@
-3.1.0
+3.1.1

WrightTools/__main__.py

@@ -0,0 +1,29 @@
+# --- import --------------------------------------------------------------------------------------
+
+
+import WrightTools as wt
+import argparse
+
+
+# --- define --------------------------------------------------------------------------------------
+
+
+def wt_tree():
+    parser = argparse.ArgumentParser(description="Print a given data tree.")
+
+    # Add arguments
+    parser.add_argument("path", type=str)
+    parser.add_argument("--verbose", "-v", action="store_true", help="Verbose? False by default")
+    parser.add_argument("--depth", "-d", "-L", type=int, default=9, help="depth to print (int)")
+    parser.add_argument("internal_path", nargs="?", default="/")
+    args = parser.parse_args()
+
+    # Create the data/collection object
+    obj = wt.open(args.path, edit_local=True)[args.internal_path]
+
+    # Print the tree
+    # If the object is a data object, it doesn't take depth as a parameter
+    if isinstance(obj, wt.Data):
+        obj.print_tree(verbose=args.verbose)
+    else:
+        obj.print_tree(verbose=args.verbose, depth=args.depth)

WrightTools/artists/__init__.py

@@ -6,3 +6,4 @@
 from ._colors import *
 from ._helpers import *
 from ._quick import *
+from ._interact import *

WrightTools/artists/_base.py

@@ -99,13 +99,67 @@ def _parse_limits(self, zi=None, data=None, channel_index=None, dynamic_range=Fa
             else:
                 vmin = data.channels[channel_index].null
                 vmax = data.channels[channel_index].max()
-            # don't overwrite
-            if "vmin" not in kwargs.keys():
-                kwargs["vmin"] = vmin
-            if "vmax" not in kwargs.keys():
-                kwargs["vmax"] = vmax
+        # don't overwrite
+        if "vmin" not in kwargs.keys():
+            kwargs["vmin"] = vmin
+        if "vmax" not in kwargs.keys():
+            kwargs["vmax"] = vmax
         return kwargs
 
+    def _parse_plot_args(self, *args, **kwargs):
+        plot_type = kwargs.pop("plot_type")
+        if plot_type not in ["pcolor", "pcolormesh"]:
+            raise NotImplementedError
+        args = list(args)  # offer pop, append etc
+        dynamic_range = kwargs.pop("dynamic_range", False)
+        if isinstance(args[0], Data):
+            data = args.pop(0)
+            if plot_type in ["pcolor", "pcolormesh"]:
+                ndim = 2
+            if not data.ndim == ndim:
+                raise wt_exceptions.DimensionalityError(ndim, data.ndim)
+            # arrays
+            channel = kwargs.pop("channel", 0)
+            channel_index = wt_kit.get_index(data.channel_names, channel)
+            zi = data.channels[channel_index][:]
+            xi = data.axes[0].full
+            yi = data.axes[1].full
+            if plot_type in ["pcolor", "pcolormesh"]:
+                X, Y = pcolor_helper(xi, yi)
+            else:
+                X, Y = xi, yi
+            args = [X, Y, zi] + args
+            # limits
+            kwargs = self._parse_limits(
+                data=data, channel_index=channel_index, dynamic_range=dynamic_range, **kwargs
+            )
+            # cmap
+            kwargs = self._parse_cmap(data=data, channel_index=channel_index, **kwargs)
+        else:
+            xi, yi, zi = args[:3]
+            if plot_type in ["pcolor", "pcolormesh"]:
+                # only apply pcolor_helper if it looks like it hasn't been applied
+                if (xi.ndim == 1 and xi.size == zi.shape[1]) or (
+                    xi.ndim == 2 and xi.shape == zi.shape
+                ):
+                    xi, yi = pcolor_helper(xi, yi)
+                    args[:3] = [xi.T.copy(), yi.T.copy(), zi]
+            data = None
+            channel_index = 0
+            kwargs = self._parse_limits(zi=args[2], **kwargs)
+            kwargs = self._parse_cmap(**kwargs)
+        # labels
+        self._apply_labels(
+            autolabel=kwargs.pop("autolabel", False),
+            xlabel=kwargs.pop("xlabel", None),
+            ylabel=kwargs.pop("ylabel", None),
+            data=data,
+            channel_index=channel_index,
+        )
+        # decoration
+        self.set_facecolor([0.75] * 3)
+        return args, kwargs
+
     def add_sideplot(self, along, pad=0, height=0.75, ymin=0, ymax=1.1):
         """Add a side axis.
 
@@ -210,9 +264,6 @@ def contour(self, *args, **kwargs):
                 channel_index=channel_index,
             )
         else:
-            data = None
-            channel_index = 0
-            signed = False
             kwargs = self._parse_limits(zi=args[2], dynamic_range=dynamic_range, **kwargs)
         # call parent
         return super().contour(*args, **kwargs)
@@ -362,50 +413,43 @@ def pcolor(self, *args, **kwargs):
         -------
         matplotlib.collections.PolyCollection
         """
-        args = list(args)  # offer pop, append etc
-        channel = kwargs.pop("channel", 0)
-        dynamic_range = kwargs.pop("dynamic_range", False)
-        # unpack data object, if given
-        if isinstance(args[0], Data):
-            data = args.pop(0)
-            if not data.ndim == 2:
-                raise wt_exceptions.DimensionalityError(2, data.ndim)
-            # arrays
-            channel_index = wt_kit.get_index(data.channel_names, channel)
-            xi = data.axes[0].full
-            yi = data.axes[1].full
-            zi = data.channels[channel_index][:]
-            X, Y, Z = pcolor_helper(xi, yi, zi)
-            args = [X, Y, Z] + args
-            # limits
-            kwargs = self._parse_limits(
-                data=data, channel_index=channel_index, dynamic_range=dynamic_range, **kwargs
-            )
-            # cmap
-            kwargs = self._parse_cmap(data=data, channel_index=channel_index, **kwargs)
-        else:
-            xi, yi, zi = args[:3]
-            if xi.ndim == 1 and xi.size == zi.shape[1]:
-                xi, yi, zi = pcolor_helper(xi, yi, zi)
-            elif xi.ndim == 2 and xi.shape == zi.shape:
-                xi, yi, zi = pcolor_helper(xi, yi, zi)
-            data = None
-            channel_index = 0
-            kwargs = self._parse_limits(zi=args[2], **kwargs)
-            kwargs = self._parse_cmap(**kwargs)
-        # labels
-        self._apply_labels(
-            autolabel=kwargs.pop("autolabel", False),
-            xlabel=kwargs.pop("xlabel", None),
-            ylabel=kwargs.pop("ylabel", None),
-            data=data,
-            channel_index=channel_index,
-        )
-        # decoration
-        self.set_facecolor([0.75] * 3)
-        # call parent
+        args, kwargs = self._parse_plot_args(*args, **kwargs, plot_type="pcolor")
         return super().pcolor(*args, **kwargs)
 
+    def pcolormesh(self, *args, **kwargs):
+        """Create a pseudocolor plot of a 2-D array.
+
+        Uses pcolor_helper to ensure that color boundaries are drawn
+        bisecting point positions, when possible.
+        Quicker than pcolor
+
+        Parameters
+        ----------
+        data : 2D WrightTools.data.Data object
+            Data to plot.
+        channel : int or string (optional)
+            Channel index or name. Default is 0.
+        dynamic_range : boolean (optional)
+            Force plotting of all contours, overloading for major extent. Only applies to signed
+            data. Default is False.
+        autolabel : {'none', 'both', 'x', 'y'}  (optional)
+            Parameterize application of labels directly from data object. Default is none.
+        xlabel : string (optional)
+            xlabel. Default is None.
+        ylabel : string (optional)
+            ylabel. Default is None.
+        **kwargs
+            matplotlib.axes.Axes.pcolormesh__ optional keyword arguments.
+
+            __ https://matplotlib.org/api/_as_gen/matplotlib.pyplot.pcolormesh.html
+
+        Returns
+        -------
+        matplotlib.collections.QuadMesh
+        """
+        args, kwargs = self._parse_plot_args(*args, **kwargs, plot_type="pcolormesh")
+        return super().pcolormesh(*args, **kwargs)
+
     def plot(self, *args, **kwargs):
         """Plot lines and/or markers.
 

WrightTools/artists/_colors.py

@@ -105,7 +105,7 @@ def make_colormap(seq, name="CustomMap", plot=False):
     name : string (optional)
         A name for the colormap
     plot : boolean (optional)
-        Use to generate a plot of the colormap (Defalut is False).
+        Use to generate a plot of the colormap (Default is False).
 
     Returns
     -------

WrightTools/artists/_helpers.py

@@ -5,7 +5,6 @@
 
 
 import os
-import sys
 
 import numpy as np
 
@@ -17,7 +16,9 @@
 from mpl_toolkits.axes_grid1 import make_axes_locatable
 
 import imageio
+import warnings
 
+from .. import exceptions as wt_exceptions
 from .. import kit as wt_kit
 from ._base import Figure, GridSpec
 from ._colors import colormaps
@@ -147,8 +148,10 @@ def add_sideplot(
     # beautify
     if along == "x":
         axCorr.set_ylim(ymin, ymax)
+        axCorr.tick_params(axis="x", which="both", length=0)
     elif along == "y":
         axCorr.set_xlim(ymin, ymax)
+        axCorr.tick_params(axis="y", which="both", length=0)
     plt.grid(grid)
     if zero_line:
         if along == "x":
@@ -485,7 +488,7 @@ def get_scaled_bounds(ax, position, *, distance=0.1, factor=200):
     return [h_scaled, v_scaled], [va, ha]
 
 
-def pcolor_helper(xi, yi, zi):
+def pcolor_helper(xi, yi, zi=None):
     """Prepare a set of arrays for plotting using `pcolor`.
 
     The return values are suitable for feeding directly into ``matplotlib.pcolor``
@@ -497,28 +500,27 @@ def pcolor_helper(xi, yi, zi):
         Array of X-coordinates.
     yi : 1D or 2D array-like
         Array of Y-coordinates.
-    zi : 2D array-like
-        Rectangular array of Z-coordinates.
+    zi : 2D array (optional, deprecated)
+        If zi is not None, it is returned unchanged in the output.
 
     Returns
     -------
     X : 2D ndarray
         X dimension for pcolor
     Y : 2D ndarray
         Y dimension for pcolor
-    Z : 2D ndarray
-        Z dimension for pcolor
+    zi : 2D ndarray
+        if zi parameter is not None, returns zi parameter unchanged
     """
     xi = xi.copy()
     yi = yi.copy()
-    zi = zi.copy()
     if xi.ndim == 1:
         xi.shape = (xi.size, 1)
     if yi.ndim == 1:
         yi.shape = (1, yi.size)
     shape = wt_kit.joint_shape(xi, yi)
-    # full
 
+    # full
     def full(arr):
         for i in range(arr.ndim):
             if arr.shape[i] == 1:
@@ -546,7 +548,14 @@ def full(arr):
             ll = orig[idx[0] + 0, idx[1] + 0]
             lr = orig[idx[0] + 0, idx[1] + 1]
             out[idx] = np.mean([ul, ur, ll, lr])
-    return X, Y, zi
+    if zi is not None:
+        warnings.warn(
+            "zi argument is not used in pcolor_helper and is not required",
+            wt_exceptions.VisibleDeprecationWarning,
+        )
+        return X, Y, zi.copy()
+    else:
+        return X, Y
 
 
 def plot_colorbar(
@@ -634,6 +643,8 @@ def plot_colorbar(
     # parse clim
     if vlim is None:
         vlim = clim
+    if max(vlim) == min(vlim):
+        vlim[-1] += 1e-1
     # parse format
     if isinstance(decimals, int):
         format = "%.{0}f".format(decimals)
@@ -1011,17 +1022,13 @@ def stitch_to_animation(images, outpath=None, *, duration=0.5, palettesize=256,
     if outpath is None:
         outpath = os.path.splitext(images[0])[0] + ".gif"
     # write
-    try:
-        t = wt_kit.Timer(verbose=False)
-        with t, imageio.get_writer(
-            outpath, mode="I", duration=duration, palettesize=palettesize
-        ) as writer:
-            for p in images:
-                image = imageio.imread(p)
-                writer.append_data(image)
-    except BaseException:
-        print("Error: {0}".format(sys.exc_info()[0]))
-        return None
+    t = wt_kit.Timer(verbose=False)
+    with t, imageio.get_writer(
+        outpath, mode="I", duration=duration, palettesize=palettesize
+    ) as writer:
+        for p in images:
+            image = imageio.imread(p)
+            writer.append_data(image)
     # finish
     if verbose:
         interval = np.round(t.interval, 2)