Merge #1030 from pc494/deperecating_utils

Deprecation of {pyfai,segment,virtual_images} utils

CHANGELOG.rst

@@ -33,6 +33,7 @@ Deprecated
 - Deprecated `CalibrationGenerator` in favour of `pyxem.utils.calibration_utils.Calibration` class (#1000)
 - Deprecated `pyxem.generators.virtual_image_generator.VirtualImageGenerator` in
   favor of `pyxem.signals.CommonDiffraction.get_virtual_image` (#1014)
+- Several utility modules have been deprecated: utils.{pyfai,segement,virtual_images,background_utils,cluster_tools} (#1060 & #1030).
 
 Deleted
 -------

pyxem/utils/pyfai_utils.py

@@ -3,7 +3,10 @@
 from pyFAI.detectors import Detector
 from pyFAI.units import register_radial_unit, eq_q
 
+from pyxem.utils._deprecated import deprecated
 
+
+@deprecated(since="0.18.0", removal="1.0.0")
 def get_azimuthal_integrator(
     detector,
     detector_distance,
@@ -60,6 +63,7 @@ def get_azimuthal_integrator(
     return ai
 
 
+@deprecated(since="0.18.0", removal="1.0.0")
 def _get_radial_extent(ai, shape=None, unit=None):
     """Takes an Azimuthal Integrator and calculates the domain of the output.
 
@@ -78,6 +82,7 @@ def _get_radial_extent(ai, shape=None, unit=None):
     return [np.min(postions), np.max(postions)]
 
 
+@deprecated(since="0.18.0", removal="1.0.0")
 def _get_displacements(center, shape, affine):
     """Gets the displacements for a set of points based on some affine transformation
     about some center point.
@@ -114,6 +119,7 @@ def _get_displacements(center, shape, affine):
     return dx, dy
 
 
+@deprecated(since="0.18.0", removal="1.0.0")
 def _get_setup(wavelength, pyxem_unit, pixel_scale, radial_range=None):
     """Returns a generic set up for a flat detector with accounting for Ewald sphere effects."""
     units_table = {

pyxem/utils/segment_utils.py

@@ -28,7 +28,10 @@
 from skimage.segmentation import watershed
 from sklearn.cluster import DBSCAN
 
+from pyxem.utils._deprecated import deprecated
 
+
+@deprecated(since="0.18.0", removal="1.0.0")
 def norm_cross_corr(image, template):
     """Calculates the normalised cross-correlation between an image
     and a template at zero displacement.
@@ -59,6 +62,7 @@ def norm_cross_corr(image, template):
     return corr
 
 
+@deprecated(since="0.18.0", removal="1.0.0")
 def separate_watershed(
     vdf_temp,
     min_distance=1,
@@ -286,6 +290,7 @@ def separate_watershed(
     return vdf_sep
 
 
+@deprecated(since="0.18.0", removal="1.0.0")
 def get_gaussian2d(a, xo, yo, x, y, sigma):
     """Obtain a 2D Gaussian of amplitude a and standard deviation
     sigma, centred at (xo, yo), on a grid given by x and y.

pyxem/utils/virtual_images_utils.py

@@ -17,8 +17,10 @@
 # along with pyXem.  If not, see <http://www.gnu.org/licenses/>.
 
 import numpy as np
+from pyxem.utils._deprecated import deprecated
 
 
+@deprecated(since="0.18.0", removal="1.0.0")
 def normalize_virtual_images(im):
     """Normalizes image intensity by dividing by maximum value.
 
@@ -37,6 +39,7 @@ def normalize_virtual_images(im):
     return imn
 
 
+@deprecated(since="0.18.0", removal="1.0.0")
 def get_vectors_mesh(g1_norm, g2_norm, g_norm_max, angle=0.0, shear=0.0):
     """
     Calculate vectors coordinates of a mesh defined by a norm, a rotation and