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Fixes the bug associated with axes_coordinates #189

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merged 13 commits into from
Aug 8, 2019
Merged

Fixes the bug associated with axes_coordinates #189

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3a020b5
Solved the bug of ``axes_coordinates``.
yashrsharma44 Jul 28, 2019
81f8c04
PEP8 fixes
yashrsharma44 Jul 28, 2019
1360ae0
Removed the rewriting of None values along the slider_axes
yashrsharma44 Aug 2, 2019
3ef2284
Added a check for reduction of data into 1D if data is not 1D or of s…
yashrsharma44 Aug 2, 2019
7b7a5ae
Changed xdata with new_axes_coordinate
yashrsharma44 Aug 5, 2019
7ea20e3
Remove redundant numpy array conversion
yashrsharma44 Aug 5, 2019
3d6f250
Modified the explanation for downscaling the dimension of the data an…
yashrsharma44 Aug 5, 2019
b3cdea6
Added docstrings for the changes
yashrsharma44 Aug 5, 2019
bfbb391
nitpickings for docstrings
yashrsharma44 Aug 5, 2019
eedb321
Reinitiate CI
yashrsharma44 Aug 7, 2019
1b1a79c
Added docstring for str values in axes_coordinates
yashrsharma44 Aug 7, 2019
9daf4ed
PEP8 fixes
yashrsharma44 Aug 7, 2019
da6c451
Removed incorrect docstrings from sequence_plotting.py
yashrsharma44 Aug 7, 2019
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69 changes: 51 additions & 18 deletions ndcube/mixins/plotting.py
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Original file line number Diff line number Diff line change
Expand Up @@ -61,6 +61,12 @@ def plot(self, axes=None, plot_axis_indices=None, axes_coordinates=None,
same length as the axis which will provide all values for that slider.
If None is specified for an axis then the array indices will be used
for that axis.
The physical coordinates expected by axes_coordinates should be an array of
pixel_edges.
A str entry in axes_coordinates signifies that an extra_coord will be used for the axis's coordinates.
The str must be a valid name of an extra_coord that corresponds to the same axis to which it is applied in the plot.



"""
# If old API is used, convert to new API.
Expand Down Expand Up @@ -237,7 +243,7 @@ def _plot_2D_cube(self, axes=None, plot_axis_indices=None, axes_coordinates=None
else:
# Else manually set axes x and y values based on user's input for axes_coordinates.
new_axes_coordinates, new_axis_units, default_labels = \
self._derive_axes_coordinates(axes_coordinates, axes_units)
self._derive_axes_coordinates(axes_coordinates, axes_units, data.shape)
# Initialize axes object and set values along axis.
fig, ax = plt.subplots(1, 1)
# Since we can't assume the x-axis will be uniform, create NonUniformImage
Expand Down Expand Up @@ -291,6 +297,10 @@ def _plot_3D_cube(self, plot_axis_indices=None, axes_coordinates=None,
same length as the axis which will provide all values for that slider.
If None is specified for an axis then the array indices will be used
for that axis.
The physical coordinates expected by axes_coordinates should be an array of
pixel_edges.
A str entry in axes_coordinates signifies that an extra_coord will be used for the axis's coordinates.
The str must be a valid name of an extra_coord that corresponds to the same axis to which it is applied in the plot.

"""
# For convenience in inserting dummy variables later, ensure
Expand All @@ -311,16 +321,20 @@ def _plot_3D_cube(self, plot_axis_indices=None, axes_coordinates=None,
data = np.ma.masked_array(data, self.mask)
# If axes_coordinates not provided generate an ImageAnimatorWCS plot
# using NDCube's wcs object.
new_axes_coordinates, new_axes_units, default_labels = \
self._derive_axes_coordinates(axes_coordinates, axes_units, data.shape, edges=True)

if (axes_coordinates[plot_axis_indices[0]] is None and
axes_coordinates[plot_axis_indices[1]] is None):

# If there are missing axes in WCS object, add corresponding dummy axes to data.
if data.ndim < self.wcs.naxis:
new_shape = list(data.shape)
for i in np.arange(self.wcs.naxis)[self.missing_axes[::-1]]:
new_shape.insert(i, 1)
# Also insert dummy coordinates and units.
axes_coordinates.insert(i, None)
axes_units.insert(i, None)
new_axes_coordinates.insert(i, None)
new_axes_units.insert(i, None)
# Iterate plot_axis_indices if neccessary
for j, pai in enumerate(plot_axis_indices):
if pai >= i:
Expand All @@ -329,16 +343,23 @@ def _plot_3D_cube(self, plot_axis_indices=None, axes_coordinates=None,
data = data.reshape(new_shape)
# Generate plot
ax = ImageAnimatorWCS(data, wcs=self.wcs, image_axes=plot_axis_indices,
unit_x_axis=axes_units[plot_axis_indices[0]],
unit_y_axis=axes_units[plot_axis_indices[1]],
axis_ranges=axes_coordinates, **kwargs)
unit_x_axis=new_axes_units[plot_axis_indices[0]],
unit_y_axis=new_axes_units[plot_axis_indices[1]],
axis_ranges=new_axes_coordinates, **kwargs)

# Set the labels of the plot
ax.axes.coords[0].set_axislabel(self.wcs.world_axis_physical_types[plot_axis_indices[0]])
ax.axes.coords[1].set_axislabel(self.wcs.world_axis_physical_types[plot_axis_indices[1]])

# If one of the plot axes is set manually, produce a basic ImageAnimator object.
else:
new_axes_coordinates, new_axes_units, default_labels = \
self._derive_axes_coordinates(axes_coordinates, axes_units)
# If axis labels not set by user add to kwargs.
ax = ImageAnimator(data, image_axes=plot_axis_indices,
axis_ranges=new_axes_coordinates, **kwargs)

# Add the labels of the plot
ax.axes.set_xlabel(default_labels[plot_axis_indices[0]])
ax.axes.set_ylabel(default_labels[plot_axis_indices[1]])
return ax

def _animate_cube_1D(self, plot_axis_index=-1, axes_coordinates=None,
Expand Down Expand Up @@ -371,9 +392,7 @@ def _animate_cube_1D(self, plot_axis_index=-1, axes_coordinates=None,
else:
unit_x_axis = None
# Put xdata back into axes_coordinates as a masked array.

if len(xdata.shape) > 1:

# Since LineAnimator currently only accepts 1-D arrays for the x-axis, collapse xdata
# to single dimension by taking mean along non-plotting axes.
index = utils.wcs.get_dependent_data_axes(self.wcs, plot_axis_index, self.missing_axes)
Expand All @@ -382,7 +401,6 @@ def _animate_cube_1D(self, plot_axis_index=-1, axes_coordinates=None,
index = np.delete(index, reduce_axis)
# Reduce the data by taking mean
xdata = np.mean(xdata, axis=tuple(index))

axes_coordinates[plot_axis_index] = xdata
# Set default x label
default_xlabel = "{0} [{1}]".format(xname, unit_x_axis)
Expand All @@ -406,21 +424,35 @@ def _animate_cube_1D(self, plot_axis_index=-1, axes_coordinates=None,
ylabel="Data [{0}]".format(data_unit), **kwargs)
return ax

def _derive_axes_coordinates(self, axes_coordinates, axes_units):
def _derive_axes_coordinates(self, axes_coordinates, axes_units, data_shape, edges=False):
new_axes_coordinates = []
new_axes_units = []
default_labels = []
default_label_text = ""
for i, axis_coordinate in enumerate(axes_coordinates):
# If axis coordinate is None, derive axis values from WCS.
if axis_coordinate is None:
# N.B. This assumes axes are independent. Fix this before merging!!!
new_axis_coordinate = self.axis_world_coords(i)

# If the new_axis_coordinate is not independent, i.e. dimension is >2D
# and not equal to dimension of data, then the new_axis_coordinate must
# be reduced to a 1D ndarray by taking the mean along all non-plotting axes.
new_axis_coordinate = self.axis_world_coords(i, edges=edges)
axis_label_text = self.world_axis_physical_types[i]
# If the shape of the data is not 1, or all the axes are not dependent
if new_axis_coordinate.ndim != 1 and new_axis_coordinate.ndim != len(data_shape):
index = utils.wcs.get_dependent_data_axes(self.wcs, i, self.missing_axes)
reduce_axis = np.where(index == np.array([i]))[0]

index = np.delete(index, reduce_axis)
# Reduce the data by taking mean
new_axis_coordinate = np.mean(new_axis_coordinate, axis=tuple(index))

elif isinstance(axis_coordinate, str):
# If axis coordinate is a string, derive axis values from
# corresponding extra coord.
new_axis_coordinate = self.extra_coords[axis_coordinate]["value"]
# Calculate edge value if required
new_axis_coordinate = _get_extra_coord_edges(self.extra_coords[axis_coordinate]["value"]) if edges else \
self.extra_coords[axis_coordinate]["value"]
axis_label_text = axis_coordinate
else:
# Else user must have manually set the axis coordinates.
Expand All @@ -445,13 +477,14 @@ def _derive_axes_coordinates(self, axes_coordinates, axes_units):
new_axis_unit = None
else:
raise TypeError(INVALID_UNIT_SET_MESSAGE)

# Derive default axis label
if type(new_axis_coordinate[0]) is datetime.datetime:
if type(new_axis_coordinate) is datetime.datetime:
if axis_label_text == default_label_text:
default_label = "{0}".format(new_axis_coordinate[0].strftime("%Y/%m/%d %H:%M"))
default_label = "{0}".format(new_axis_coordinate.strftime("%Y/%m/%d %H:%M"))
else:
default_label = "{0} [{1}]".format(
axis_label_text, new_axis_coordinate[0].strftime("%Y/%m/%d %H:%M"))
axis_label_text, new_axis_coordinate.strftime("%Y/%m/%d %H:%M"))
else:
default_label = "{0} [{1}]".format(axis_label_text, new_axis_unit)
# Append new coordinates, units and labels to output list.
Expand Down
22 changes: 22 additions & 0 deletions ndcube/mixins/sequence_plotting.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -62,6 +62,10 @@ def plot(self, axes=None, plot_axis_indices=None,
`None` (implies derive the coordinates from the WCS objects),
an `astropy.units.Quantity` or a `numpy.ndarray` of coordinates for each pixel,
or a `str` denoting a valid extra coordinate.
The physical coordinates expected by axes_coordinates should be an array of
pixel_edges.
A str entry in axes_coordinates signifies that an extra_coord will be used for the axis's coordinates.
The str must be a valid name of an extra_coord that corresponds to the same axis to which it is applied in the plot.

axes_units: `None or `list` of `None`, `astropy.units.Unit` and/or `str`
If None units derived from the WCS objects will be used for all axes.
Expand Down Expand Up @@ -168,6 +172,10 @@ def plot_as_cube(self, axes=None, plot_axis_indices=None,
`None` (implies derive the coordinates from the WCS objects),
an `astropy.units.Quantity` or a `numpy.ndarray` of coordinates for each pixel,
or a `str` denoting a valid extra coordinate.
The physical coordinates expected by axes_coordinates should be an array of
pixel_edges.
A str entry in axes_coordinates signifies that an extra_coord will be used for the axis's coordinates.
The str must be a valid name of an extra_coord that corresponds to the same axis to which it is applied in the plot.

axes_units: `None or `list` of `None`, `astropy.units.Unit` and/or `str`
If None units derived from the WCS objects will be used for all axes.
Expand Down Expand Up @@ -254,6 +262,10 @@ def _plot_1D_sequence(self, axes_coordinates=None,
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.
The physical coordinates expected by axes_coordinates should be an array of
pixel_edges.
A str entry in axes_coordinates signifies that an extra_coord will be used for the axis's coordinates.
The str must be a valid name of an extra_coord that corresponds to the same axis to which it is applied in the plot.

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
Expand Down Expand Up @@ -683,6 +695,8 @@ class ImageAnimatorNDCubeSequence(ImageAnimatorWCS):
same length as the axis which will provide all values for that slider.
If None is specified for an axis then the array indices will be used
for that axis.
The physical coordinates expected by axis_ranges should be an array of
pixel_edges.

interval: `int`
Animation interval in ms
Expand Down Expand Up @@ -778,6 +792,8 @@ class ImageAnimatorCubeLikeNDCubeSequence(ImageAnimatorWCS):
same length as the axis which will provide all values for that slider.
If None is specified for an axis then the array indices will be used
for that axis.
The physical coordinates expected by axis_ranges should be an array of
pixel_edges.

interval: `int`
Animation interval in ms
Expand Down Expand Up @@ -895,6 +911,8 @@ class LineAnimatorNDCubeSequence(LineAnimator):
same length as the axis which will provide all values for that slider.
If None is specified for an axis then the array indices will be used
for that axis.
The physical coordinates expected by axis_ranges should be an array of
pixel_edges.

interval: `int`
Animation interval in ms
Expand Down Expand Up @@ -1129,6 +1147,8 @@ class LineAnimatorCubeLikeNDCubeSequence(LineAnimator):
same length as the axis which will provide all values for that slider.
If None is specified for an axis then the array indices will be used
for that axis.
The physical coordinates expected by axis_ranges should be an array of
pixel_edges.

interval: `int`
Animation interval in ms
Expand Down Expand Up @@ -1349,6 +1369,8 @@ def _prep_axes_kwargs(naxis, plot_axis_indices, axes_coordinates, axes_units):

axes_coordinates: `None` or `list` of `None` `astropy.units.Quantity` `numpy.ndarray` `str`
Length of list equals number of sequence axes.
The physical coordinates expected by axes_coordinates should be an array of
pixel_edges.

axes_units: None or `list` of `None` `astropy.units.Unit` or `str`
Length of list equals number of sequence axes.
Expand Down
1 change: 1 addition & 0 deletions ndcube/tests/test_plotting.py
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Original file line number Diff line number Diff line change
Expand Up @@ -33,6 +33,7 @@

data = np.array([[[1, 2, 3, 4], [2, 4, 5, 3], [0, -1, 2, 3]],
[[2, 4, 5, 1], [10, 5, 2, 2], [10, 3, 3, 0]]])

uncertainty = np.sqrt(data)
mask_cube = data < 0

Expand Down