Revision history [back]

Dear all,

I have problems to call scipy.ndimage.binary_opening. Code, output and error messages in sage are as follows...

SAGE:

from numpy import *

import scipy.ndimage

import matplotlib.image

import matplotlib.pyplot

img=matplotlib.image.imread(DATA+'NbW-STEM.png')

type(img)

print "Image dtype: %s"%(img.dtype)

print "Image size: %6d"%(img.size)

print "Image shape: %3dx%3d"%(img.shape[0],img.shape[1])

print "Max value %1.2f at pixel %6d"%(img.max(),img.argmax())

print "Min value %1.2f at pixel %6d"%(img.min(),img.argmin())

print "Variance: %1.5f\nStandard deviation: %1.5f"%(img.var(),img.std())

OUTPUT:

Image dtype: float32

Image size: 261075

Image shape: 295x295

Max value 1.00 at pixel 226320

Min value 0.00 at pixel 17109

Variance: 0.02580

Standard deviation: 0.16062

SAGE:

BWatoms=img>0.62

BWatoms=scipy.ndimage.binary_opening(BWatoms,structure=ones((2,2)))

ERROR MESSAGE:

Traceback (most recent call last): File "<stdin>", line 1, in <module>

File "_sage_input_27.py", line 10, in <module> exec compile(u'open("___code___.py","w").write("# -- coding: utf-8 --\n" + _support_.preparse_worksheet_cell(base64.b64decode("QldhdG9tcz1pbWc+MC42MgpCV2F0b21zPXNjaXB5Lm5kaW1hZ2UuYmluYXJ5X29wZW5pbmcoQldhdG9tcyxzdHJ1Y3R1cmU9b25lcygoMiwyKSkp"),globals())+"\n"); execfile(os.path.abspath("___code___.py"))

File "", line 1, in <module>

File "/tmp/tmpaXpo0G/___code___.py", line 4, in <module> exec compile(u'BWatoms=scipy.ndimage.binary_opening(BWatoms,structure=ones((_sage_const_2 ,_sage_const_2 )))

File "", line 1, in <module>

File "/home/ottom/Documents/sage_build/sage-4.6.1/local/lib/python2.6/site-packages/scipy/ndimage/morphology.py", line 646, in binary_opening origin)

File "/home/ottom/Documents/sage_build/sage-4.6.1/local/lib/python2.6/site-packages/scipy/ndimage/morphology.py", line 394, in binary_erosion output, border_value, origin, 0, brute_force)

File "/home/ottom/Documents/sage_build/sage-4.6.1/local/lib/python2.6/site-packages/scipy/ndimage/morphology.py", line 229, in _binary_erosion raise RuntimeError, 'structure rank must equal input rank'

RuntimeError: structure rank must equal input ran

This code was also tested on the sage-online server (alpha), which failed as well. The code worked fine with Enthought 6.2-2 (pylab-mode). Any suggestions are welcome.

All the best Otto

Dear all,

I have problems to call scipy.ndimage.binary_opening. scipy.ndimage.binary_opening. Code, output and error messages in sage are as follows...

SAGE:

from numpy import *
 
*
import scipy.ndimage
 
scipy.ndimage
import matplotlib.image
 
matplotlib.image
import matplotlib.pyplot
 
img=matplotlib.image.imread(DATA+'NbW-STEM.png')
 
type(img)
 
matplotlib.pyplot
img=matplotlib.image.imread(DATA+'NbW-STEM.png')
type(img)
print "Image dtype: %s"%(img.dtype)
 
%s"%(img.dtype)
print "Image size: %6d"%(img.size)
 
%6d"%(img.size)
print "Image shape: %3dx%3d"%(img.shape[0],img.shape[1])
 
%3dx%3d"%(img.shape[0],img.shape[1])
print "Max value %1.2f at pixel %6d"%(img.max(),img.argmax())
 
%6d"%(img.max(),img.argmax())
print "Min value %1.2f at pixel %6d"%(img.min(),img.argmin())
 
%6d"%(img.min(),img.argmin())
print "Variance: %1.5f\nStandard deviation: %1.5f"%(img.var(),img.std())%1.5f"%(img.var(),img.std())

Image dtype: float32
 
float32
Image size: 261075
 
261075
Image shape: 295x295
 
295x295
Max value 1.00 at pixel 226320
 
226320
Min value 0.00 at pixel  17109
 
17109
Variance: 0.02580
 
0.02580
Standard deviation: 0.160620.16062

BWatoms=img>0.62
BWatoms=scipy.ndimage.binary_opening(BWatoms,structure=ones((2,2)))

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
 
<module>

  File "_sage_input_27.py", line 10, in <module>
    exec compile(u'open("___code___.py","w").write("# -- -*- coding: utf-8 --\n" -*-\\n" + _support_.preparse_worksheet_cell(base64.b64decode("QldhdG9tcz1pbWc+MC42MgpCV2F0b21zPXNjaXB5Lm5kaW1hZ2UuYmluYXJ5X29wZW5pbmcoQldhdG9tcyxzdHJ1Y3R1cmU9b25lcygoMiwyKSkp"),globals())+"\n"); execfile(os.path.abspath("___code___.py"))
 
_support_.preparse_worksheet_cell(base64.b64decode("QldhdG9tcz1pbWc+MC42MgpCV2F0b21zPXNjaXB5Lm5kaW1hZ2UuYmluYXJ5X29wZW5pbmcoQldhdG9tcyxzdHJ1Y3R1cmU9b25lcygoMiwyKSkp"),globals())+"\\n"); execfile(os.path.abspath("___code___.py"))

  File "", line 1, in <module>
 
<module>

  File "/tmp/tmpaXpo0G/___code___.py", line 4, in <module>
    exec compile(u'BWatoms=scipy.ndimage.binary_opening(BWatoms,structure=ones((_sage_const_2 ,_sage_const_2 )))
 
)))

  File "", line 1, in <module>
 
<module>

  File "/home/ottom/Documents/sage_build/sage-4.6.1/local/lib/python2.6/site-packages/scipy/ndimage/morphology.py", line 646, in binary_opening
    origin)
 
origin)

  File "/home/ottom/Documents/sage_build/sage-4.6.1/local/lib/python2.6/site-packages/scipy/ndimage/morphology.py", line 394, in binary_erosion
    output, border_value, origin, 0, brute_force)
 
brute_force)

  File "/home/ottom/Documents/sage_build/sage-4.6.1/local/lib/python2.6/site-packages/scipy/ndimage/morphology.py", line 229, in _binary_erosion
    raise RuntimeError, 'structure rank must equal input rank'
 
rank'

RuntimeError: structure rank must equal input ran
 
rank