fix #72

pyCHX/chx_generic_functions.py

@@ -4,7 +4,7 @@
 from scipy.special import erf
 
 from skimage.filters import  prewitt
-from skimage.draw import line_aa, line, polygon, ellipse, circle
+from skimage.draw import line_aa, line, polygon, ellipse, disk 
 
 from modest_image import imshow
 import matplotlib.cm as mcm
@@ -1918,9 +1918,9 @@ def create_ring_mask( shape, r1, r2, center, mask=None):
     '''
 
     m = np.zeros( shape, dtype= bool) 
-    rr,cc = circle(  center[1], center[0], r2, shape=shape  )
+    rr,cc = disk(  center[1], center[0], r2, shape=shape  )
     m[rr,cc] = 1
-    rr,cc = circle(  center[1], center[0], r1,shape=shape  )
+    rr,cc = disk(  center[1], center[0], r1,shape=shape  )
     m[rr,cc] = 0 
     if mask is not None:
         m += mask
@@ -2884,7 +2884,7 @@ def create_polygon_mask(  image, xcorners, ycorners   ):
 
 
     '''
-    from skimage.draw import line_aa, line, polygon, circle    
+    from skimage.draw import line_aa, line, polygon, disk    
     imy, imx = image.shape 
     bst_mask = np.zeros_like( image , dtype = bool)   
     rr, cc = polygon( ycorners,xcorners)
@@ -2906,7 +2906,7 @@ def create_rectangle_mask(  image, xcorners, ycorners   ):
 
 
     '''
-    from skimage.draw import line_aa, line, polygon, circle    
+    from skimage.draw import line_aa, line, polygon, disk    
     imy, imx = image.shape 
     bst_mask = np.zeros_like( image , dtype = bool)   
     rr, cc = polygon( ycorners,xcorners)
@@ -2954,18 +2954,18 @@ def create_multi_rotated_rectangle_mask(  image, center=None, length=100, width=
 
 def create_wedge(  image, center, radius, wcors,  acute_angle=True) :
     '''YG develop at June 18, 2017, @CHX
-        Create a wedge by a combination of circle and a triangle defined by center and wcors
+        Create a wedge by a combination of disk and a triangle defined by center and wcors
         wcors: [ [x1,x2,x3...], [y1,y2,y3..]
 
     '''
-    from skimage.draw import line_aa, line, polygon, circle
+    from skimage.draw import line_aa, line, polygon, disk
     imy, imx = image.shape   
     cy,cx = center
     x  = [cx] + list(wcors[0])
     y =  [cy] + list(wcors[1])
 
     maskc = np.zeros_like( image , dtype = bool) 
-    rr, cc = circle( cy, cx, radius, shape = image.shape)
+    rr, cc = disk( cy, cx, radius, shape = image.shape)
     maskc[rr,cc] =1  
 
     maskp = np.zeros_like( image , dtype = bool)
@@ -2982,20 +2982,20 @@ def create_wedge(  image, center, radius, wcors,  acute_angle=True) :
 
 
 def create_cross_mask(  image, center, wy_left=4, wy_right=4, wx_up=4, wx_down=4,
-                     center_circle = True, center_radius=10
+                     center_disk = True, center_radius=10
                      ):
     '''
     Give image and the beam center to create a cross-shaped mask
     wy_left: the width of left h-line
     wy_right: the width of rigth h-line
     wx_up: the width of up v-line
     wx_down: the width of down v-line
-    center_circle: if True, create a circle with center and center_radius
+    center_disk: if True, create a disk with center and center_radius
 
     Return:
     the cross mask
     '''
-    from skimage.draw import line_aa, line, polygon, circle
+    from skimage.draw import line_aa, line, polygon, disk
 
     imy, imx = image.shape   
     cx,cy = center
@@ -3033,7 +3033,7 @@ def create_cross_mask(  image, center, wy_left=4, wy_right=4, wx_up=4, wx_down=4
     bst_mask[rr,cc] =1   
 
     if center_radius!=0:
-        rr, cc = circle( cy, cx, center_radius, shape = bst_mask.shape)
+        rr, cc = disk( cy, cx, center_radius, shape = bst_mask.shape)
         bst_mask[rr,cc] =1   
 
 
@@ -3370,22 +3370,22 @@ def create_hot_pixel_mask(img, threshold, center=None, center_radius=300, outer_
            threshold: the threshold above which will be considered as hot pixels
            center: optional, default=None
                              else, as a two-element list (beam center), i.e., [center_x, center_y]
-           if center is not None, the hot pixel will not include a circle region 
+           if center is not None, the hot pixel will not include a disk region 
                            which is defined by center and center_radius ( in unit of pixel)
        Output:
            a bool types numpy array (mask), 1 is good and 0 is excluded   
 
     '''
     bst_mask = np.ones_like( img , dtype = bool)    
     if center is not None:    
-        from skimage.draw import  circle    
+        from skimage.draw import  disk   
         imy, imx = img.shape   
         cy,cx = center        
-        rr, cc = circle( cy, cx, center_radius,shape=img.shape )
+        rr, cc = disk( cy, cx, center_radius,shape=img.shape )
         bst_mask[rr,cc] =0 
         if outer_radius:
             bst_mask = np.zeros_like( img , dtype = bool)   
-            rr2, cc2 = circle( cy, cx, outer_radius,shape=img.shape )
+            rr2, cc2 = disk( cy, cx, outer_radius,shape=img.shape )
             bst_mask[rr2,cc2] =1
             bst_mask[rr,cc] =0 
     hmask = np.ones_like( img )

pyCHX/chx_libs.py

@@ -5,7 +5,7 @@
 """
 from IPython.core.magics.display import Javascript
 from skbeam.core.utils import multi_tau_lags
-from skimage.draw import line_aa, line, polygon, ellipse, circle
+from skimage.draw import line_aa, line, polygon, ellipse, disk
 from modest_image import imshow
 # edit handlers here to switch to PIMS or dask
 # this does the databroker import

pyCHX/v2/_commonspeckle/chx_generic_functions.py

@@ -5,7 +5,7 @@
 from scipy.special import erf
 
 from skimage.filters import prewitt
-from skimage.draw import line_aa, line, polygon, ellipse, circle
+from skimage.draw import line_aa, line, polygon, ellipse, disk
 
 # from modest_image import imshow #common
 import matplotlib.cm as mcm
@@ -2259,9 +2259,9 @@ def create_ring_mask(shape, r1, r2, center, mask=None):
     """
 
     m = np.zeros(shape, dtype=bool)
-    rr, cc = circle(center[1], center[0], r2, shape=shape)
+    rr, cc = disk(center[1], center[0], r2, shape=shape)
     m[rr, cc] = 1
-    rr, cc = circle(center[1], center[0], r1, shape=shape)
+    rr, cc = disk(center[1], center[0], r1, shape=shape)
     m[rr, cc] = 0
     if mask is not None:
         m += mask
@@ -3356,7 +3356,7 @@ def create_polygon_mask(image, xcorners, ycorners):
 
 
     """
-    from skimage.draw import line_aa, line, polygon, circle
+    from skimage.draw import line_aa, line, polygon, disk
 
     imy, imx = image.shape
     bst_mask = np.zeros_like(image, dtype=bool)
@@ -3379,7 +3379,7 @@ def create_rectangle_mask(image, xcorners, ycorners):
 
 
     """
-    from skimage.draw import line_aa, line, polygon, circle
+    from skimage.draw import line_aa, line, polygon, disk
 
     imy, imx = image.shape
     bst_mask = np.zeros_like(image, dtype=bool)
@@ -3441,19 +3441,19 @@ def create_multi_rotated_rectangle_mask(
 
 def create_wedge(image, center, radius, wcors, acute_angle=True):
     """YG develop at June 18, 2017, @CHX
-    Create a wedge by a combination of circle and a triangle defined by center and wcors
+    Create a wedge by a combination of disk and a triangle defined by center and wcors
     wcors: [ [x1,x2,x3...], [y1,y2,y3..]
 
     """
-    from skimage.draw import line_aa, line, polygon, circle
+    from skimage.draw import line_aa, line, polygon, disk
 
     imy, imx = image.shape
     cy, cx = center
     x = [cx] + list(wcors[0])
     y = [cy] + list(wcors[1])
 
     maskc = np.zeros_like(image, dtype=bool)
-    rr, cc = circle(cy, cx, radius, shape=image.shape)
+    rr, cc = disk(cy, cx, radius, shape=image.shape)
     maskc[rr, cc] = 1
 
     maskp = np.zeros_like(image, dtype=bool)
@@ -3475,7 +3475,7 @@ def create_cross_mask(
     wy_right=4,
     wx_up=4,
     wx_down=4,
-    center_circle=True,
+    center_disk=True,
     center_radius=10,
 ):
     """
@@ -3484,12 +3484,12 @@ def create_cross_mask(
     wy_right: the width of rigth h-line
     wx_up: the width of up v-line
     wx_down: the width of down v-line
-    center_circle: if True, create a circle with center and center_radius
+    center_disk: if True, create a disk with center and center_radius
 
     Return:
     the cross mask
     """
-    from skimage.draw import line_aa, line, polygon, circle
+    from skimage.draw import line_aa, line, polygon, disk
 
     imy, imx = image.shape
     cx, cy = center
@@ -3527,7 +3527,7 @@ def create_cross_mask(
     bst_mask[rr, cc] = 1
 
     if center_radius != 0:
-        rr, cc = circle(cy, cx, center_radius, shape=bst_mask.shape)
+        rr, cc = disk(cy, cx, center_radius, shape=bst_mask.shape)
         bst_mask[rr, cc] = 1
 
     full_mask = ~bst_mask
@@ -3848,23 +3848,23 @@ def create_hot_pixel_mask(
         threshold: the threshold above which will be considered as hot pixels
         center: optional, default=None
                           else, as a two-element list (beam center), i.e., [center_x, center_y]
-        if center is not None, the hot pixel will not include a circle region
+        if center is not None, the hot pixel will not include a disk region
                         which is defined by center and center_radius ( in unit of pixel)
     Output:
         a bool types numpy array (mask), 1 is good and 0 is excluded
 
     """
     bst_mask = np.ones_like(img, dtype=bool)
     if center is not None:
-        from skimage.draw import circle
+        from skimage.draw import disk
 
         imy, imx = img.shape
         cy, cx = center
-        rr, cc = circle(cy, cx, center_radius, shape=img.shape)
+        rr, cc = disk(cy, cx, center_radius, shape=img.shape)
         bst_mask[rr, cc] = 0
         if outer_radius:
             bst_mask = np.zeros_like(img, dtype=bool)
-            rr2, cc2 = circle(cy, cx, outer_radius, shape=img.shape)
+            rr2, cc2 = disk(cy, cx, outer_radius, shape=img.shape)
             bst_mask[rr2, cc2] = 1
             bst_mask[rr, cc] = 0
     hmask = np.ones_like(img)

pyCHX/v2/_commonspeckle/chx_libs.py

@@ -5,7 +5,7 @@
 """
 from IPython.core.magics.display import Javascript
 from skbeam.core.utils import multi_tau_lags
-from skimage.draw import line_aa, line, polygon, ellipse, circle
+from skimage.draw import line_aa, line, polygon, ellipse, disk
 
 # from modest_image import imshow #common
 # edit handlers here to switch to PIMS or dask

pyCHX/v2/_futurepyCHX/chx_generic_functions.py

@@ -5,7 +5,7 @@
 from scipy.special import erf
 
 from skimage.filters import prewitt
-from skimage.draw import line_aa, line, polygon, ellipse, circle
+from skimage.draw import line_aa, line, polygon, ellipse, disk
 
 from modest_image import imshow
 import matplotlib.cm as mcm
@@ -2259,9 +2259,9 @@ def create_ring_mask(shape, r1, r2, center, mask=None):
     """
 
     m = np.zeros(shape, dtype=bool)
-    rr, cc = circle(center[1], center[0], r2, shape=shape)
+    rr, cc = disk(center[1], center[0], r2, shape=shape)
     m[rr, cc] = 1
-    rr, cc = circle(center[1], center[0], r1, shape=shape)
+    rr, cc = disk(center[1], center[0], r1, shape=shape)
     m[rr, cc] = 0
     if mask is not None:
         m += mask
@@ -3356,7 +3356,7 @@ def create_polygon_mask(image, xcorners, ycorners):
 
 
     """
-    from skimage.draw import line_aa, line, polygon, circle
+    from skimage.draw import line_aa, line, polygon, disk
 
     imy, imx = image.shape
     bst_mask = np.zeros_like(image, dtype=bool)
@@ -3379,7 +3379,7 @@ def create_rectangle_mask(image, xcorners, ycorners):
 
 
     """
-    from skimage.draw import line_aa, line, polygon, circle
+    from skimage.draw import line_aa, line, polygon, disk
 
     imy, imx = image.shape
     bst_mask = np.zeros_like(image, dtype=bool)
@@ -3441,19 +3441,19 @@ def create_multi_rotated_rectangle_mask(
 
 def create_wedge(image, center, radius, wcors, acute_angle=True):
     """YG develop at June 18, 2017, @CHX
-    Create a wedge by a combination of circle and a triangle defined by center and wcors
+    Create a wedge by a combination of disk and a triangle defined by center and wcors
     wcors: [ [x1,x2,x3...], [y1,y2,y3..]
 
     """
-    from skimage.draw import line_aa, line, polygon, circle
+    from skimage.draw import line_aa, line, polygon, disk
 
     imy, imx = image.shape
     cy, cx = center
     x = [cx] + list(wcors[0])
     y = [cy] + list(wcors[1])
 
     maskc = np.zeros_like(image, dtype=bool)
-    rr, cc = circle(cy, cx, radius, shape=image.shape)
+    rr, cc = disk(cy, cx, radius, shape=image.shape)
     maskc[rr, cc] = 1
 
     maskp = np.zeros_like(image, dtype=bool)
@@ -3475,7 +3475,7 @@ def create_cross_mask(
     wy_right=4,
     wx_up=4,
     wx_down=4,
-    center_circle=True,
+    center_disk=True,
     center_radius=10,
 ):
     """
@@ -3484,12 +3484,12 @@ def create_cross_mask(
     wy_right: the width of rigth h-line
     wx_up: the width of up v-line
     wx_down: the width of down v-line
-    center_circle: if True, create a circle with center and center_radius
+    center_disk: if True, create a disk with center and center_radius
 
     Return:
     the cross mask
     """
-    from skimage.draw import line_aa, line, polygon, circle
+    from skimage.draw import line_aa, line, polygon, disk
 
     imy, imx = image.shape
     cx, cy = center
@@ -3527,7 +3527,7 @@ def create_cross_mask(
     bst_mask[rr, cc] = 1
 
     if center_radius != 0:
-        rr, cc = circle(cy, cx, center_radius, shape=bst_mask.shape)
+        rr, cc = disk(cy, cx, center_radius, shape=bst_mask.shape)
         bst_mask[rr, cc] = 1
 
     full_mask = ~bst_mask
@@ -3848,23 +3848,23 @@ def create_hot_pixel_mask(
         threshold: the threshold above which will be considered as hot pixels
         center: optional, default=None
                           else, as a two-element list (beam center), i.e., [center_x, center_y]
-        if center is not None, the hot pixel will not include a circle region
+        if center is not None, the hot pixel will not include a disk region
                         which is defined by center and center_radius ( in unit of pixel)
     Output:
         a bool types numpy array (mask), 1 is good and 0 is excluded
 
     """
     bst_mask = np.ones_like(img, dtype=bool)
     if center is not None:
-        from skimage.draw import circle
+        from skimage.draw import disk
 
         imy, imx = img.shape
         cy, cx = center
-        rr, cc = circle(cy, cx, center_radius, shape=img.shape)
+        rr, cc = disk(cy, cx, center_radius, shape=img.shape)
         bst_mask[rr, cc] = 0
         if outer_radius:
             bst_mask = np.zeros_like(img, dtype=bool)
-            rr2, cc2 = circle(cy, cx, outer_radius, shape=img.shape)
+            rr2, cc2 = disk(cy, cx, outer_radius, shape=img.shape)
             bst_mask[rr2, cc2] = 1
             bst_mask[rr, cc] = 0
     hmask = np.ones_like(img)

pyCHX/v2/_futurepyCHX/chx_libs.py

@@ -5,7 +5,7 @@
 """
 from IPython.core.magics.display import Javascript
 from skbeam.core.utils import multi_tau_lags
-from skimage.draw import line_aa, line, polygon, ellipse, circle
+from skimage.draw import line_aa, line, polygon, ellipse, disk
 from modest_image import imshow
 
 # edit handlers here to switch to PIMS or dask