Merge branch 'master' into adding_signed

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/psf/black
-    rev: 23.12.1 # Replace by any tag/version: https://github.com/psf/black/tags
+    rev: 24.1.1 # Replace by any tag/version: https://github.com/psf/black/tags
     hooks:
       - id: black
         language_version: python3 # Should be a command that runs python3.6+

.readthedocs.yml

@@ -1,12 +1,20 @@
-requirements_file: requirements.txt
+version: 2
 
 build:
-    image: latest
+  os: ubuntu-22.04
+  tools:
+    python: "3.9"
 
 python:
-  version: 3.8
-  pip_install: true
-  extra_requirements: [docs]
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: docs/conf.py
 
 formats:
   - epub

CHANGELOG.md

@@ -7,9 +7,15 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/).
 
 ### Added
 - `kit.guess_signed` for empirically guessing channel sign (useful for automated workflows)
+- `Data.squeeze`: squeezing the data object to the shape of the axes.
 
 ### Fixed
 - `interact2D`: fixed bug where use_imshow broke the sliders
+- `artists.stitch_to_animation`: use imageio v3 api and declare pillow plugin
+- `data.join` ensures valid `method` is selected
+
+### Changed
+- `data.join` no longer supports `sum` method
 
 ## [3.5.0]
 

WrightTools/__init__.py

@@ -1,4 +1,5 @@
 """WrightTools init."""
+
 # flake8: noqa
 
 

WrightTools/__version__.py

@@ -1,6 +1,5 @@
 """Define WrightTools version."""
 
-
 # --- import --------------------------------------------------------------------------------------
 
 

WrightTools/__wt5_version__.py

@@ -1,6 +1,5 @@
 """Define wt5 version."""
 
-
 # --- import --------------------------------------------------------------------------------------
 
 

WrightTools/_close.py

@@ -1,6 +1,5 @@
 """Function to close all open wt5 files."""
 
-
 # --- import -------------------------------------------------------------------------------------
 
 

WrightTools/_dataset.py

@@ -1,6 +1,5 @@
 """Dataset base class."""
 
-
 # --- import --------------------------------------------------------------------------------------
 
 

WrightTools/_group.py

@@ -1,6 +1,5 @@
 """Group base class."""
 
-
 # --- import --------------------------------------------------------------------------------------
 
 

WrightTools/_open.py

@@ -1,6 +1,5 @@
 """Generic open method for wt5 files."""
 
-
 # --- import -------------------------------------------------------------------------------------
 
 

WrightTools/artists/__init__.py

@@ -1,4 +1,5 @@
 """Artists."""
+
 # flake8: noqa
 
 

WrightTools/artists/_base.py

@@ -1,6 +1,5 @@
 """Base tools for visualizing data."""
 
-
 # --- import --------------------------------------------------------------------------------------
 
 

WrightTools/artists/_colors.py

@@ -1,6 +1,5 @@
 """Colormaps."""
 
-
 # --- import --------------------------------------------------------------------------------------
 
 import copy

WrightTools/artists/_helpers.py

@@ -1,6 +1,5 @@
 """Functions to help with plotting."""
 
-
 # --- import --------------------------------------------------------------------------------------
 
 
@@ -15,7 +14,7 @@
 import matplotlib.patheffects as PathEffects
 from mpl_toolkits.axes_grid1 import make_axes_locatable
 
-import imageio
+import imageio.v3 as iio
 import warnings
 
 from .. import exceptions as wt_exceptions
@@ -1082,14 +1081,14 @@ def subplots_adjust(fig=None, inches=1):
         fig.subplots_adjust(top=top, right=right, bottom=bottom, left=left)
 
 
-def stitch_to_animation(images, outpath=None, *, duration=0.5, palettesize=256, verbose=True):
+def stitch_to_animation(paths, outpath=None, *, duration=0.5, palettesize=256, verbose=True):
     """Stitch a series of images into an animation.
 
     Currently supports animated gifs, other formats coming as needed.
 
     Parameters
     ----------
-    images : list of strings
+    paths : list of strings
         Filepaths to the images to stitch together, in order of apperence.
     outpath : string (optional)
         Path of output, including extension. If None, bases output path on path
@@ -1098,22 +1097,21 @@ def stitch_to_animation(images, outpath=None, *, duration=0.5, palettesize=256,
         Duration of (each) frame in seconds. Default is 0.5.
     palettesize : int (optional)
         The number of colors in the resulting animation. Input is rounded to
-        the nearest power of 2. Default is 1024.
+        the nearest power of 2. Default is 256.
     verbose : bool (optional)
         Toggle talkback. Default is True.
     """
     # parse filename
     if outpath is None:
-        outpath = os.path.splitext(images[0])[0] + ".gif"
+        outpath = os.path.splitext(paths[0])[0] + ".gif"
     # write
     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
+    with t, iio.imopen(outpath, "w") as gif:
+        for p in paths:
+            frame = iio.imread(p)
+            gif.write(
+                frame, plugin="pillow", duration=duration * 1e3, loop=0, palettesize=palettesize
+            )
     if verbose:
         interval = np.round(t.interval, 2)
         print("gif generated in {0} seconds - saved at {1}".format(interval, outpath))

WrightTools/artists/_quick.py

@@ -1,6 +1,5 @@
 """Quick plotting."""
 
-
 # --- import --------------------------------------------------------------------------------------
 
 

WrightTools/artists/_turbo.py

@@ -1,6 +1,5 @@
 """Define turbo colormap."""
 
-
 # Copyright 2019 Google LLC.
 # SPDX-License-Identifier: Apache-2.0
 

WrightTools/collection/__init__.py

@@ -1,4 +1,5 @@
 """Collection class and associated."""
+
 # flake8: noqa
 
 

WrightTools/collection/_cary.py

@@ -1,6 +1,5 @@
 """Cary."""
 
-
 # --- import --------------------------------------------------------------------------------------
 
 

WrightTools/collection/_collection.py

@@ -1,6 +1,5 @@
 """Collection."""
 
-
 # --- import --------------------------------------------------------------------------------------
 
 

WrightTools/collection/_directory.py

@@ -1,6 +1,5 @@
 """Cary."""
 
-
 # --- import --------------------------------------------------------------------------------------
 
 

WrightTools/data/__init__.py

@@ -1,4 +1,5 @@
 """Data class and associated."""
+
 # flake8: noqa
 
 

WrightTools/data/_aramis.py

@@ -1,6 +1,5 @@
 """Aramis."""
 
-
 # --- import --------------------------------------------------------------------------------------
 
 

WrightTools/data/_axis.py

@@ -1,6 +1,5 @@
 """Axis class and associated."""
 
-
 # --- import --------------------------------------------------------------------------------------
 
 

WrightTools/data/_brunold.py

@@ -1,6 +1,5 @@
 """Brunold."""
 
-
 # --- import --------------------------------------------------------------------------------------
 
 

WrightTools/data/_channel.py

@@ -1,6 +1,5 @@
 """Channel class and associated."""
 
-
 # --- import --------------------------------------------------------------------------------------
 
 
@@ -225,3 +224,13 @@ def trim(self, neighborhood, method="ztest", factor=3, replace="nan", verbose=Tr
         if verbose:
             print("%i outliers removed" % len(outliers))
         return outliers
+
+    def _to_dict(self):
+        out = {}
+        out["name"] = self.natural_name
+        out["values"] = self[:]
+        out["units"] = self.units
+        out["label"] = self.label
+        out["signed"] = self.signed
+        out.update(self.attrs)
+        return out

WrightTools/data/_colors.py

@@ -1,6 +1,5 @@
 """COLORS."""
 
-
 # --- import --------------------------------------------------------------------------------------
 
 

WrightTools/data/_constant.py

@@ -1,6 +1,5 @@
 """Constant class and associated."""
 
-
 # --- import --------------------------------------------------------------------------------------
 
 

WrightTools/data/_data.py

@@ -1,6 +1,5 @@
 """Central data class and associated."""
 
-
 # --- import --------------------------------------------------------------------------------------
 
 from __future__ import annotations
@@ -360,6 +359,78 @@ def at(self, parent=None, name=None, **at) -> Data:
         idx = self._at_to_slice(**at)
         return self._from_slice(idx, name=name, parent=parent)
 
+    def squeeze(self, name=None, parent=None):
+        """Reduce the data to the dimensionality of the (non-trivial) span of the axes.
+        i.e. if the joint shape of the axes has an array dimension with length 1, this
+        array dimension is squeezed.
+
+        channels and variables that span beyond the axes are removed.
+
+        Parameters
+        ----------
+        name : string (optional)
+            name of the new Data.
+        parent : WrightTools Collection instance (optional)
+            Collection to place the new "chop" collection within. Default is
+            None (new parent).
+
+        Returns
+        -------
+        out : wt.Data
+            new data object.  The new data object has dimensions of the
+            (non-trivial) span of the current axes
+
+        Examples
+        --------
+        >>> ...
+
+        See also
+        --------
+        Data.chop: Divide the dataset into its lower-dimensionality components.
+        ...
+        """
+        new = Data(name=name, parent=parent)
+
+        attrs = {
+            k: v
+            for k, v in self.attrs.items()
+            if k
+            not in [
+                "axes",
+                "channel_names",
+                "constants",
+                "name",
+                "source",
+                "item_names",
+                "variable_names",
+            ]
+        }
+        new.attrs.update(attrs)
+
+        joint_shape = wt_kit.joint_shape(*[ai[:] for ai in self.axes])
+        cull_dims = [j == 1 for j in joint_shape]
+        sl = [0 if cull else slice(None) for cull in cull_dims]
+        matches_broadcast_axes = lambda a: all(
+            [a.shape[i] == 1 for i in range(self.ndim) if cull_dims[i]]
+        )
+
+        for v in filter(matches_broadcast_axes, self.variables):
+            kwargs = v._to_dict()
+            kwargs["values"] = v[sl]
+            new.create_variable(**kwargs)
+
+        for c in filter(matches_broadcast_axes, self.channels):
+            kwargs = c._to_dict()
+            kwargs["values"] = c[sl]
+            new.create_channel(**kwargs)
+
+        # inherit constants
+        for c in self.constants:
+            new.create_constant(c.expression)
+
+        new.transform(*self.axis_expressions)
+        return new
+
     def chop(self, *args, at=None, parent=None, verbose=True) -> wt_collection.Collection:
         """Divide the dataset into its lower-dimensionality components.
 
@@ -509,21 +580,12 @@ def _from_slice(self, idx, name=None, parent=None) -> Data:
             out = parent.create_data(name=name)
 
         for v in self.variables:
-            kwargs = {}
-            kwargs["name"] = v.natural_name
+            kwargs = v._to_dict()
             kwargs["values"] = v[idx]
-            kwargs["units"] = v.units
-            kwargs["label"] = v.label
-            kwargs.update(v.attrs)
             out.create_variable(**kwargs)
         for c in self.channels:
-            kwargs = {}
-            kwargs["name"] = c.natural_name
+            kwargs = c._to_dict()
             kwargs["values"] = c[idx]
-            kwargs["units"] = c.units
-            kwargs["label"] = c.label
-            kwargs["signed"] = c.signed
-            kwargs.update(c.attrs)
             out.create_channel(**kwargs)
 
         new_axes = [a.expression for a in self.axes if a[idx].size > 1]