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Move checking and prepping of some kwargs in NDCubeSequencePlotMixin …
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…plot and and plot_as_cube methods to external function. Also added more comments.
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@DanRyanIrish
DanRyanIrish committed Mar 23, 2018
1 parent 5910439 commit cae5a0e
Showing 1 changed file with 124 additions and 83 deletions.
207 changes: 124 additions & 83 deletions ndcube/mixins/sequence_plotting.py
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Original file line number Diff line number Diff line change
Expand Up @@ -83,48 +83,33 @@ def plot(self, cubesequence, axes=None, plot_axis_indices=None,
ax: ???
"""
# If plot_axis_indices, axes_coordinates, axes_units are not None and not lists,
# convert to lists for consistent indexing behaviour.
if (not isinstance(plot_axis_indices, list)) and (plot_axis_indices is not None):
plot_axis_indices = [plot_axis_indices]
if (not isinstance(axes_coordinates, list)) and (axes_coordinates is not None):
axes_coordinates = [axes_coordinates]
if (not isinstance(axes_units, list)) and (axes_units is not None):
axes_units = [axes_units]
# Ensure length of kwargs is consistent with dimensionality of sequence
# and setting of plot_as_cube.
# Check kwargs are in consistent formats and set default values if not done so by user.
naxis = len(cubesequence.dimensions)
_check_kwargs_dimensions(naxis, plot_axis_indices, axes_coordinates, axes_units)
# Set default values of kwargs is not det by user.
if plot_axis_indices is None:
plot_axis_indices = [-1, -2]
plot_axis_indices, axes_coordinates, axes_units = _prep_axes_kwargs(
naxis, plot_axis_indices, axes_coordinates, axes_units)
if naxis == 1:
x_axis_coordinates, unit_x_axis = _derive_1D_coordinates_and_units(axes_coordinates,
axes_units)
# Make 1D line plot.
ax = self._plot_1D_sequence(
cubesequence, x_axis_coordinates=x_axis_coordinates,
unit_x_axis=unit_x_axis, data_unit=data_unit, **kwargs)
ax = self._plot_1D_sequence(cubesequence, x_axis_coordinates,
unit_x_axis, data_unit, **kwargs)
else:
if len(plot_axis_indices) == 1:
# Since sequence has more than 1 dimension and number of plot axes is 1,
# produce a 1D line animation.
if axes_units is not None:
unit_x_axis = axes_units[plot_axis_indices[0]]
else:
unit_x_axis = None
ax = LineAnimatorNDCubeSequence(
cubesequence, plot_axis_index=plot_axis_indices[0],
axis_ranges=axes_coordinates,
unit_x_axis=unit_x_axis,
data_unit=data_unit, **kwargs)
ax = LineAnimatorNDCubeSequence(cubesequence, plot_axis_indices[0], axes_coordinates,
unit_x_axis, data_unit, **kwargs)
elif len(plot_axis_indices) == 2:
if plot_axis_indices is None:
plot_axis_indices = [-1, -2]
if naxis == 2:
ax = self._plot_2D_sequence(
cubesequence, plot_axis_indices=plot_axis_indices,
axes_coordinates=axes_coordinates, axes_units=axes_units,
data_unit=data_unit, **kwargs)
# Since sequence has 2 dimensions and number of plot axes is 2,
# produce a 2D image.
ax = self._plot_2D_sequence(cubesequence, plot_axis_indices, axes_coordinates,
axes_units, data_unit, **kwargs)
else:
# Since sequence has more than 2 dimensions and number of plot axes is 2,
# produce a 2D animation.
if axes_units is None:
axes_units = [None] * naxis
ax = ImageAnimatorNDCubeSequence(
Expand Down Expand Up @@ -209,68 +194,63 @@ def plot_as_cube(self, cubesequence, axes=None, plot_axis_indices=None,
# Verify common axis is set.
if cubesequence._common_axis is None:
raise TypeError("Common axis must be set.")
# If plot_axis_indices, axes_coordinates, axes_units are not None and not lists,
# convert to lists for consistent indexing behaviour.
if (not isinstance(plot_axis_indices, list)) and (plot_axis_indices is not None):
plot_axis_indices = [plot_axis_indices]
if (not isinstance(axes_coordinates, list)) and (axes_coordinates is not None):
axes_coordinates = [axes_coordinates]
if (not isinstance(axes_units, list)) and (axes_units is not None):
axes_units = [axes_units]
# Ensure length of kwargs is consistent with dimensionality of sequence
# and setting of plot_as_cube.
# Check kwargs are in consistent formats and set default values if not done so by user.
naxis = len(cubesequence.cube_like_dimensions)
_check_kwargs_dimensions(naxis, plot_axis_indices, axes_coordinates, axes_units)
# Set default values of kwargs is not det by user.
if plot_axis_indices is None:
plot_axis_indices = [-1, -2]
plot_axis_indices, axes_coordinates, axes_units = _prep_axes_kwargs(
naxis, plot_axis_indices, axes_coordinates, axes_units)
# Produce plot/image/animation based on cube-like dimensions of sequence.
if naxis == 1:
x_axis_coordinates, unit_x_axis = _derive_1D_coordinates_and_units(
axes_coordinates, axes_units)
# Since sequence has 1 cube-like dimension, produce a 1D line plot.
ax = self._plot_2D_sequence_as_1Dline(
cubesequence, x_axis_coordinates=x_axis_coordinates,
unit_x_axis=unit_x_axis, data_unit=data_unit, **kwargs)
else:
if len(plot_axis_indices) == 1:
ax = LineAnimatorCubeLikeNDCubeSequence(
cubesequence, plot_axis_index=plot_axis_indices[0],
axis_ranges=axes_coordinates,
unit_x_axis=unit_x_axis,
data_unit=data_unit, xlabel=xlabel, ylabel=ylabel,
xlim=xlim, ylim=ylim)
# Since sequence has more than 1 cube-like dimension and
# number of plot axes is 1, produce a 1D line animation.
if axes_units is not None:
unit_x_axis = axes_units[plot_axis_indices[0]]
else:
unit_x_axis = None
ax = LineAnimatorCubeLikeNDCubeSequence(cubesequence, plot_axis_indices[0],
axes_coordinates, unit_x_axis,
data_unit=data_unit, **kwargs)
elif len(plot_axis_indices) == 2:
if naxis == 2:
ax = self._plot_3D_sequence_as_2Dimage(
axes=axes, plot_axis_indices=plot_axis_indices,
axes_coordinates=axes_coordinates, axes_units=axes_units,
data_unit=data_unit, **kwargs)
# Since sequence has 2 cube-like dimensions and
# number of plot axes is 2, produce a 2D image.
ax = self._plot_3D_sequence_as_2Dimage(axes, plot_axis_indices,
axes_coordinates, axes_units,
data_unit, **kwargs)
else:
ax = ImageAnimatorCubeLikeNDCubeSequence(
cubesequence, image_axes=plot_axis_indices,
axis_ranges=axes_coordinates, unit_x_axis=axes_units[plot_axis_indices[0]],
unit_y_axis=axes_units[plot_axis_indices[1]], **kwargs)

# Since sequence has more than 2 cube-like dimensions and
# number of plot axes is 2, produce a 2D animation.
ax = ImageAnimatorCubeLikeNDCubeSequence(cubesequence, plot_axis_indices,
axes_coordinates,
axes_units[plot_axis_indices[0]],
axes_units[plot_axis_indices[1]],
**kwargs)
return ax

def _plot_1D_sequence(self, cubesequence, x_axis_coordinates=None,
unit_x_axis=None, data_unit=None, **kwargs):
def _plot_1D_sequence(self, cubesequence, axes_coordinates=None,
axes_units=None, data_unit=None, **kwargs):
"""
Visualizes an NDCubeSequence of scalar NDCubes as a line plot.
A scalar NDCube is one whose NDCube.data is a scalar rather than an array.
Parameters
----------
x_axis_coordinates: `numpy.ndarray` or `astropy.unit.Quantity` or `str` or `None`
axes_coordinates: `numpy.ndarray` `astropy.unit.Quantity` `str` `None` or length 1 `list`
Denotes the physical coordinates of the x-axis.
If list, must be of length 1 containing one object of one of the other allowed types.
If None, coordinates are derived from the WCS objects.
If an `astropy.units.Quantity` or a `numpy.ndarray` gives the coordinates for
each pixel along the x-axis.
If a `str`, denotes the extra coordinate to be used. The extra coordinate must
correspond to the sequence axis.
unit_x_axis: `astropy.unit.Unit` or valid unit `str`
axes_units: `astropy.unit.Unit` or valid unit `str` or length 1 `list` of those types.
Unit in which X-axis should be displayed. Must be compatible with the unit of
the coordinate denoted by x_axis_range. Not used if x_axis_range is a
`numpy.ndarray` or the designated extra coordinate is a `numpy.ndarray`
Expand All @@ -280,8 +260,11 @@ def _plot_1D_sequence(self, cubesequence, x_axis_coordinates=None,
the sub-cubes must be compatible to set this kwarg.
"""
unit_y_axis = data_unit
# Derive x-axis coordinates and unit from inputs.
x_axis_coordinates, unit_x_axis = _derive_1D_coordinates_and_units(axes_coordinates,
axes_units)
# Check that the unit attribute is a set in all cubes and derive unit_y_axis if not set.
unit_y_axis = data_unit
sequence_units, unit_y_axis = _determine_sequence_units(cubesequence.data, unit_y_axis)
# If all cubes have unit set, create a data quantity from cubes' data.
if sequence_units is not None:
Expand Down Expand Up @@ -322,7 +305,7 @@ def _plot_1D_sequence(self, cubesequence, x_axis_coordinates=None,
return ax

def _plot_2D_sequence_as_1Dline(self, cubesequence, x_axis_coordinates=None,
axes_units=None, **kwargs):
axes_units=None, data_unit=None, **kwargs):
"""
Visualizes an NDCubeSequence of 1D NDCubes with a common axis as a line plot.
Expand All @@ -333,13 +316,11 @@ def _plot_2D_sequence_as_1Dline(self, cubesequence, x_axis_coordinates=None,
Same as _plot_1D_sequence
"""
if axes_units is None:
unit_x_axis = None
unit_y_axis = None
else:
unit_x_axis = axes_units[0]
unit_y_axis = axes_units[1]
# Derive x-axis coordinates and unit from inputs.
x_axis_coordinates, unit_x_axis = _derive_1D_coordinates_and_units(axes_coordinates,
axes_units)
# Check that the unit attribute is set of all cubes and derive unit_y_axis if not set.
unit_y_axis = data_unit
sequence_units, unit_y_axis = _determine_sequence_units(cubesequence.data, unit_y_axis)
# If all cubes have unit set, create a y data quantity from cube's data.
if sequence_units is not None:
Expand Down Expand Up @@ -387,6 +368,7 @@ def _plot_2D_sequence_as_1Dline(self, cubesequence, x_axis_coordinates=None,
fig, ax = _make_1D_sequence_plot(xdata, ydata, yerror, unit_y_axis, default_xlabel, kwargs)
return ax


def _plot_2D_sequence(self, cubesequence, plot_axis_indices=None, axes_coordinates=None,
axes_units=None, data_unit=None, **kwargs):
"""
Expand Down Expand Up @@ -1254,26 +1236,85 @@ def _get_all_cube_units(sequence_data):
return sequence_units


def _check_kwargs_dimensions(naxis, plot_axis_indices, axes_coordinates, axes_units):
if (plot_axis_indices is not None) and (naxis > 1):
if len(plot_axis_indices) not in [1, 2]:
raise ValueError("plot_axis_indices can have at most length 2.")
def _prep_axes_kwargs(naxis, plot_axis_indices, axes_coordinates, axes_units):
"""
Checks input values are correct based on number of sequence dimensions and sets defaults.
Parameters
----------
plot_axis_indices: As for NDCubeSequencePlotMixin.plot or NDCubeSequencePlotMixin.plot_as_cube
axes_coordinates: As for NDCubeSequencePlotMixin.plot or NDCubeSequencePlotMixin.plot_as_cube
axes_units: As for NDCubeSequencePlotMixin.plot or NDCubeSequencePlotMixin.plot_as_cube
Returns
-------
plot_axis_indices: None or `list` of `int` of length 1 or 2.
axes_coordinates: `None` or `list` of `None` `astropy.units.Quantity` `numpy.ndarray` `str`
Length of list equals number of sequence axes.
axes_units: None or `list` of `None` `astropy.units.Unit` or `str`
Length of list equals number of sequence axes.
"""
# If plot_axis_indices, axes_coordinates, axes_units are not None and not lists,
# convert to lists for consistent indexing behaviour.
if (not isinstance(plot_axis_indices, list)) and (plot_axis_indices is not None):
plot_axis_indices = [plot_axis_indices]
if (not isinstance(axes_coordinates, list)) and (axes_coordinates is not None):
axes_coordinates = [axes_coordinates]
if (not isinstance(axes_units, list)) and (axes_units is not None):
axes_units = [axes_units]
# Set default value of plot_axis_indices if not set by user.
if plot_axis_indices is None:
plot_axis_indices = [-1, -2]
# If number of sequence dimensions is greater than 1,
# ensure length of plot_axis_indices is 1 or 2.
# No need to check case where number of sequence dimensions is 1
# as plot_axis_indices is ignored in that case.
if naxis > 1:
len(plot_axis_indices) not in [1, 2]:
raise ValueError("plot_axis_indices can have at most length 2.")
# If convention of axes_coordinates and axes_units being length of
# plot_axis_index is being used, convert to convention where their
# length equals sequence dimensions. Only do this if number of dimensions if
# greater than 1 as the conventions are equivalent if there is only one dimension.
if axes_coordinates is not None:
if len(axes_coordinates) == len(plot_axis_indices):
none_axes_coordinates = np.array([None] * naxis)
none_axes_coordinates[plot_axis_indices] = plot_axis_indices
axes_coordinates = list(none_axes_coordinates)
if axes_units is not None:
if len(axes_units) == len(plot_axis_indices):
none_axes_units = np.array([None] * naxis)
none_axes_units[plot_axis_indices] = plot_axis_indices
axes_units = list(none_axes_units)
if axes_coordinates is not None:
if len(axes_coordinates) != naxis:
# Now axes_coordinates have been converted to a consistent convention,
# ensure their length equals the number of sequence dimensions.
len(axes_coordinates) != naxis:
raise ValueError("length of axes_coordinates must be {0}.".format(naxis))
# Ensure all elements in axes_coordinates are of correct types.
ax_coord_types = (u.Quantity, np.ndarray, str)
for axis_coordinate in axes_coordinates:
if not instance(axis_coordinate, ax_coord_types):
if axis_coordinate is not None and not instance(axis_coordinate, ax_coord_types):
raise TypeError("axes_coordinates must be one of {0} or list of {0}.".format(
ax_coord_types))
[None] + list(ax_coord_types)))
if axes_units is not None:
# Now axes_units have been converted to a consistent convention,
# ensure their length equals the number of sequence dimensions.
if len(axes_units) != naxis:
raise ValueError("length of axes_units must be {0}.".format(naxis))
# Ensure all elements in axes_units are of correct types.
ax_unit_types = (u.Unit, str)
for axis_coordinate in axes_units:
if not instance(axis_coordinate, ax_coord_types):
for axis_unit in axes_units:
if axis_unit is not None and not instance(axis_unit, ax_unit_types):
raise TypeError("axes_units must be one of {0} or list of {0}.".format(
ax_coord_types))
ax_unit_types))

return plot_axis_indices, axes_coordinates, axes_units


def _derive_1D_coordinates_and_units(axes_coordinates, axes_units):
Expand Down

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