Merge pull request #11 from sfarrens/testing

updated documentation
sfarrens · Feb 15, 2020 · 2a280dc · 2a280dc
2 parents 3094a15 + 1585591
commit 2a280dc
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Showing 7 changed files with 72 additions and 48 deletions.
diff --git a/requirements.txt b/requirements.txt
@@ -0,0 +1,2 @@
+numpy>=1.14.1
+modopt>=1.4.2
diff --git a/setup.py b/setup.py
@@ -10,6 +10,10 @@
 with open(infopath) as open_file:
     exec(open_file.read(), release_info)
 
+with open('requirements.txt') as open_file:
+    install_requires = open_file.read()
+
+
 setup(
     name='sf_tools',
     author='sfarrens',
@@ -18,7 +22,7 @@
     url='https://github.com/sfarrens/sf_tools',
     download_url='https://github.com/sfarrens/sf_tools',
     packages=find_packages(),
-    install_requires=['numpy>=1.14.1', 'future>=0.16.0', 'modopt>=1.1.4'],
+    install_requires=install_requires,
     license='MIT',
     description='Tools for image analysis, signal processing and statistics.',
     long_description=release_info["__about__"],

diff --git a/sf_tools/image/distort.py b/sf_tools/image/distort.py
@@ -26,14 +26,15 @@ def downsample(image, factor):
 
     Parameters
     ----------
-    image : np.ndarray
+    image : numpy.ndarray
         Input image array
     factor : int
         Downsampling factor
 
     Returns
     -------
-    np.ndarray downsampled image array
+    numpy.ndarray
+        Downsampled image array
 
     Raises
     ------
@@ -65,12 +66,13 @@ def resize_even_image(image):
 
     Parameters
     ----------
-    image : np.ndarray
+    image : numpy.ndarray
         Input image array
 
     Returns
     -------
-    np.ndarray resized image array
+    numpy.ndarray
+        Resized image array
 
     """
 
@@ -85,14 +87,15 @@ def roll_2d(data, roll_rad=(1, 1)):
 
     Parameters
     ----------
-    data : np.ndarray
+    data : numpy.ndarray
         Input 2D data array
     roll_rad : tuple
         Roll radius in each dimension
 
     Returns
     -------
-    np.ndarray rolled array
+    numpy.ndarray
+        Rolled array
 
     """
 
@@ -106,12 +109,13 @@ def rot_and_roll(data):
 
     Parameters
     ----------
-    data : np.ndarray
+    data : numpy.ndarray
         Input 2D data array
 
     Returns
     -------
-    np.ndarray rotated and rolled array
+    numpy.ndarray
+        Rotated and rolled array
 
     """
 
@@ -132,7 +136,8 @@ def gen_mask(kernel_shape, image_shape):
 
     Returns
     -------
-    np.ndarray boolean mask
+    numpy.ndarray
+        Boolean mask
 
     """
 
@@ -163,7 +168,8 @@ def roll_sequence(data_shape):
 
     Returns
     -------
-    list of roll radii
+    list
+        Roll radii
 
     """
 
@@ -183,12 +189,13 @@ def kernel_pattern(kernel_shape, mask):
     ----------
     kernel_shape : tuple
         Shape of kernel
-    mask : np.ndarray
+    mask : numpy.ndarray
         Boolean mask
 
     Returns
     -------
-    np.ndarray kernel pattern
+    numpy.ndarray
+        Kernel pattern
 
     """
 
@@ -231,7 +238,8 @@ def rearrange_kernel(kernel, data_shape=None):
 
     Returns
     -------
-    np.ndarray rearanged matrix of kernel elements
+    numpy.ndarray
+        Rearanged matrix of kernel elements
 
     """
 
@@ -275,14 +283,14 @@ def pad_shift(image, shift):
 
     Parameters
     ----------
-    image :  np.ndarray
+    image :  numpy.ndarray
         Input image
     shift : tuple
         Shift in x and y axes
 
     Returns
     -------
-    np.ndarray
+    numpy.ndarray
         Padded image
 
     """
@@ -300,14 +308,14 @@ def recentre(image, pos):
 
     Parameters
     ----------
-    image :  np.ndarray
+    image :  numpy.ndarray
         Input image
     pos : tuple
         Pos in x and y axes
 
     Returns
     -------
-    np.ndarray
+    numpy.ndarray
         Recentred image
 
     """

diff --git a/sf_tools/image/quality.py b/sf_tools/image/quality.py
@@ -30,16 +30,17 @@ def nmse(image1, image2, metric=np.mean):
 
     Parameters
     ----------
-    image1 : np.ndarray
+    image1 : numpy.ndarray
         First image (or stack of images) to be analysed (original image)
-    image2 : np.ndarray
+    image2 : numpy.ndarray
         Second image (or stack of images) to be analysed (reconstructed image)
     metric : function
-        Metric to be apllied to NMSE results (default is 'np.mean')
+        Metric to be apllied to NMSE results (default is 'numpy.mean')
 
     Returns
     -------
-    float NMSE value or metric value(s)
+    float
+        NMSE value or metric value(s)
 
     Raises
     ------
@@ -95,17 +96,18 @@ def e_error(image1, image2, metric=np.mean):
 
     Parameters
     ----------
-    image1 : np.ndarray
+    image1 : numpy.ndarray
         First image to be analysed (original image)
-    image2 : np.ndarray
+    image2 : numpy.ndarray
         Second image to be analysed (reconstructed image)
     metric : function
         Metric to be apllied to ellipticity error results (default is
-        'np.mean')
+        'numpy.mean')
 
     Returns
     -------
-    float ellipticity error value or metric value(s)
+    float
+        Ellipticity error value or metric value(s)
 
     Raises
     ------

diff --git a/sf_tools/image/shape.py b/sf_tools/image/shape.py
@@ -28,14 +28,15 @@ def ellipticity_atoms(data, offset=0):
 
     Parameters
     ----------
-    data : np.ndarray
+    data : numpy.ndarray
         Input data array, the image to be analysed
     offset : int, optional
         Shape projection offset (default is '0')
 
     Returns
     -------
-    np.ndarray of the image ellipticity components
+    numpy.ndarray
+        Image ellipticity components
 
     See Also
     --------
@@ -102,7 +103,7 @@ def shape_project(shape, offset=0, return_norm=False):
 
     Parameters
     ----------
-    shape : list, tuple or np.ndarray
+    shape : list, tuple or numpy.ndarray
         List of image dimensions
     offset : int, optional
         Shape projection offset (default is '0')
@@ -112,7 +113,8 @@ def shape_project(shape, offset=0, return_norm=False):
 
     Returns
     -------
-    np.ndarray of shape projection components
+    numpy.ndarray
+        Shape projection components
 
     See Also
     --------
@@ -185,16 +187,16 @@ class Ellipticity():
 
     Parameters
     ----------
-    data : np.ndarray
+    data : numpy.ndarray
         Input data array, the image to be analysed
     sigma : int, optional
         Estimation error (default is '1000')
-    centroid : np.ndarray, optional
+    centroid : numpy.ndarray, optional
         Centroid positions [x, y] of the input image (defualt is 'None')
-    moments : np.ndarray, optional
+    moments : numpy.ndarray, optional
         Quadrupole moments [[q00, q01], [q10, q11]] of the input image
         (defualt is 'None')
-    ellip_type : str {'chi', 'epsilon'}, optional
+    ellip_type : {'chi', 'epsilon'}, optional
         Ellipticity type (default is 'chi')
 
     Examples
@@ -284,7 +286,7 @@ def _update_weights(self):
                                (2 * self._sigma ** 2))
 
     def _update_centroid(self):
-        """Update the centroid
+        r"""Update the centroid
 
         This method updates the centroid value using the current weights.
 
@@ -349,7 +351,7 @@ def _get_centroid(self, n_iter=10):
         self._get_moments()
 
     def _get_moments(self):
-        """ Calculate the quadrupole moments
+        r""" Calculate the quadrupole moments
 
         This method calculates the quadrupole moments.
 
@@ -378,7 +380,7 @@ def _get_moments(self):
         self._get_ellipse()
 
     def _get_ellipse(self):
-        """Calculate the ellipticities
+        r"""Calculate the ellipticities
 
         This method cacluates ellipticities from quadrupole moments.
 

diff --git a/sf_tools/image/stamp.py b/sf_tools/image/stamp.py
@@ -31,7 +31,7 @@ def patch_centres(data_shape, layout):
 
     Returns
     -------
-    np.ndarray array of patch centres
+    numpy.ndarray array of patch centres
 
     """
 
@@ -57,7 +57,7 @@ def postage_stamp(data, pos, pixel_rad):
 
     Parameters
     ----------
-    data : np.ndarray
+    data : numpy.ndarray
         Input data array
     pos : tuple
         Position of postage stamp centre
@@ -66,7 +66,8 @@ def postage_stamp(data, pos, pixel_rad):
 
     Returns
     -------
-    np.ndarray rearanged matrix of kernel elements
+    numpy.ndarray
+        Rearanged matrix of kernel elements
 
     Notes
     -----
@@ -115,7 +116,8 @@ def pixel_pos(array_shape):
 
     Returns
     -------
-    list of pixel positions
+    list
+        Pixel positions
 
     """
 
@@ -131,7 +133,7 @@ class FetchStamps(object):
 
     Parameters
     ----------
-    data : np.ndarray
+    data : numpy.ndarray
         Input 2D data array
     pixel_rad : tuple
         Pixel radius in each dimension
@@ -248,7 +250,8 @@ def _stamp(self, pos, func=None, *args):
 
         Returns
         -------
-        np.ndarray postage stamp array or result of func
+        numpy.ndarray
+            Postage stamp array or result of func
 
         Raises
         ------
@@ -280,7 +283,8 @@ def scan(self, func=None, *args, **kwargs):
 
         Returns
         -------
-        np.ndarray postage stamp arrays or results of func
+        numpy.ndarray
+            Postage stamp arrays or results of func
 
         """