Develop Reference

any existing code/library for image sharpness or blurriness estimation in python?

I would like to find some existing code/library for sharpness/blurriness estimation on normal images. (prefer in Python) I will need to compare the performance of different algorithms later.
I have 10000+ MRI scan images with different "quality"(sharpness/blurriness). I need to write code to filter images with certain "quality"(sharpness/blurriness) which is up to user. Hence, I am trying to research about image sharpness/blurriness estimation on medical images. My supervisor told me there are lots of existing code for sharpness/blurriness estimation on normal images(maybe it is no-reference sharpness metric) on internet. She asked me to search about them and try them on normal images first. Then try to learn about their algorithms.
I have searched about this on internet and found some pages which are relevant. However, lots of them are out of date.
For example:
On
Image sharpness metric
page,
Cumulative probability of blur detection (CPBD) https://ivulab.asu.edu/software/quality/cpbd
seems not working anymore. I guess the reason is that "imread" function is removed from new "scipy" library. (please see later code and error message) I think I can try the old version of "scipy" later. However, I would like to find some more currently available code/library about image sharpness/blurriness estimation.
Also, my working environment will be in Windows 10 or CentOS-7.
I have tried the following code with CPBD:
import sys, cpbd
from scipy import ndimage
input_image1 = ndimage.imread('D:\Work\Project\scripts\test_images\blur1.png', mode='L')
input_image2 = ndimage.imread('D:\Work\Project\scripts\test_images\clr1.png', mode='L')
print("blurry image sharpness:")
cpbd.compute(input_image1)
print("clear image sharpness:")
cpbd.compute(input_image2)
Error message from Python 3.7 shell (ran in Window 10):
Traceback (most recent call last):
File "D:\Work\Project\scripts\try_cpbd.py", line 1, in <module>
import sys, cpbd
File "D:\Program_Files_2\Python\lib\site-packages\cpbd\__init__.py", line 3, in <module>
from .compute import compute
File "D:\Program_Files_2\Python\lib\site-packages\cpbd\compute.py", line 14, in <module>
from scipy.misc import imread #Original: from scipy.ndimage import imread
ImportError: cannot import name 'imread' from 'scipy.misc' (D:\Program_Files_2\Python\lib\site-packages\scipy\misc\__init__.py)

Seems that cpbd package has not been updated from some time.
It worked for me with the following steps:
Edit "D:\Program_Files_2\Python\lib\site-packages\cpbd\compute.py":
Comment the last 4 lines starting with:
#if __name__ == '__main__':
Use the python code:
import cpbd
import cv2
input_image1 = cv2.imread('blur1.png')
if input_image1 is None:
print("error opening image")
exit()
input_image1 = cv2.cvtColor(input_image1, cv2.COLOR_BGR2GRAY)
print("blurry image sharpness:")
cpbd.compute(input_image1)

Since scipy.misc.imread is deprecated since 1.0.0, and removed in 1.2.0, I would use skimage.io.imread instead (which is in most ways a drop-in replacement).
Edit the code in cpbd/compute.py
import skimage.io
input_image1 = skimage.io.imread('blur1.png')
cv2 also works (or other options: imageio, PIL, ...) but skimage tends to be a bit easier to install/use.

The following steps worked for me:
Open the compute.py from C:\ProgramData\Anaconda3\Lib\site-packages\cpbd\compute.py or wherever you have installed it. You will find the following code:
from scipy.ndimage import imread
replace it with:
from skimage.io import imread
If you can't save the compute.py file, then copy it to desktop, edit it in the above mentioned way and replace the file in C:\ProgramData\Anaconda3\Lib\site-packages\cpbd\compute.py with it.

Following the answer from Baj Mile, I did the following and it worked for me.
opened the cpbd\compute.py file
commented the line : from scipy.ndimage import imread
Added the line: import cv2
Made the following changes to the main section:
if __name__ == '__main__':
#input_image = imread(argv[1], mode='L')
input_image=cv2.imread(argv[1])
sharpness = compute(input_image)
print('CPBD sharpness for %s: %f' % (argv[1], sharpness))
close the compute.py file.
In the main code:
import cpbd
import cv2
input_image1 = cv2.imread('testimage.jpg')
input_image1 = cv2.cvtColor(input_image1, cv2.COLOR_BGR2GRAY)
cpbd.compute(input_image1)

Name error when calculating the average error between two data sets

I want to calculate the average error between two data sets and write the result to a file but my code gives this error:
NameError: name 'first1' is not defined
Could you please tell me how to fix this error?
The command I use to run the code is here:
python script.py input1.txt input2.txt > output.txt
My code:
import numpy
from numpy import *
import scipy
import scipy.stats
import matplotlib. pyplot as plt
import matplotlib.patches as patches
from pylab import *
import scipy.integrate
from operator import itemgetter, attrgetter
import sys
def main(argv):
t = open(sys.argv[1])
first1 = t.readline()
tt = open(argv[2])
second2 = tt.readline()
return [first1], [second2]
def analysis(first1, second2):
first = np.array(first1, dtype = np.float64)
second = np.array(second2, dtype = np.float64)
#Average error
avgerr = (first - second).mean()
return [avgerr]
analysis(first1, second2)
if __name__ == '__main__':
sys.exit(main(sys.argv))
input1.txt:
2.5
2.8
3.9
4.2
5.8
input2.txt:
0.8
2.5
3.2
5.8
6.3

Where are you stuck on this? The first active statement executed in your main program is
analysis(first1, second2)
Neither of those variables is defined anywhere in the main program.
That's why you get the error. The sequence you have is something like this:
import stuff
define (but don't execute) main function
define (but don't execute) analysis function
call analysis, giving it variables first1 & second2
Again, those variables are not defined yet.

Your line:
analysis(first1, second2)
Is causing the error. This is because you are calling the function without providing values.
The way you have structured your code is it's expected to be run via command line.
If you want to test your script without using command line, you could change your code line above to..
analysis('input1.txt', 'input2.txt')

Python Import Error + DLL load failed + sys.path

in Python 2.7.10 Anaconda 2.3.0 (64-bit), if I write
sys.path.append('C:\\Anaconda\\sms-tools-master\\software\\models\\utilFunctions_C\\')
print sys.path
I get
C:\Anaconda\sms-tools-master\workspace\A1>python A1Part1.py
['C:\Anaconda\sms-tools-master\workspace\A1', 'C:\Anaconda\python27.zip',
'C:\Anaconda\DLLs', 'C:\Anaconda\lib', 'C:\Anaconda\lib\plat-win', 'C:\A
naconda\lib\lib-tk', 'C:\Anaconda', 'C:\Anaconda\lib\site-packages', 'C:\
Anaconda\lib\site-packages\Sphinx-1.3.1-py2.7.egg', 'C:\Anaconda\lib\site-
packages\cryptography-0.9.1-py2.7-win-amd64.egg', 'C:\Anaconda\lib\site-pack
ages\win32', 'C:\Anaconda\lib\site-packages\win32\lib', 'C:\Anaconda\lib
\site-packages\Pythonwin', 'C:\Anaconda\lib\site-packages\setuptools-17.1.
1-py2.7.egg', 'C:\Anaconda\sms-tools-master\software\models\utilFunctions_C
\']
Is this absolute way of adding to sys.path correct? Is there a relative way?
In the next line of python code I wrote
from utilFunctions_C import wavread
I instantly get
ImportError: cannot import name wavread
if I run the code in cmd but if I run the code inside IDLE I get:
['C:\Anaconda\sms-tools-master\workspace\A1',
'C:\Python27\Lib\idlelib', 'C:\Windows\system32\python27.zip',
'C:\Python27\DLLs', 'C:\Python27\lib',
'C:\Python27\lib\plat-win', 'C:\Python27\lib\lib-tk',
'C:\Python27', 'C:\Python27\lib\site-packages',
'C:\Anaconda\sms-tools-master\software\models\utilFunctions_C\']
Traceback (most recent call last): File
"C:\Anaconda\sms-tools-master\workspace\A1\A1Part1.py", line 8, in
from utilFunctions_C import wavread ImportError: DLL load failed: %1 is not a valid Win32 application.
So why there is a difference and how to tackle this issue? Thnx!

I commented
from utilFunctions_C import wavread
and used
from scipy.io.wavfile import read
Now my code is okay. I found that
utiLFunctions.wavread() is a wrapper that uses scipy.io.wavfile.read()
and scales the data to floating point between -1 and 1. If you open up
utilFunctions.py you will see that.
You can use scipy.io.wavfile.read as well, as long you scale the data
correctly looking at the datatype in the wav file. Due to scaling, for
wav files that store samples as int16, you will see that
scipy.io.wavfile.read returns values will be 32767 times the values
returned by utilFunctions.wavread
Lectures used the function to explain the process more explicitly.
Once you have got it, you can use the wrapper utilFunctions.wavread
for the rest of the course and in practical applications.
Scroll in
https://class.coursera.org/audio-002/forum/search?q=Cannot+import+name+wavread#15-state-query=wavread&15-state-page_num=1
for more details.

Cython import works once - and then gives a gcc.bat error

I am writing a Python program in Anaconda/Spyder on a 64-bit Windows 8 machine. I'm getting all the know issues with gcc.bat ("gcc.bat' failed with exit status 1") and I have it fixed - almost. My pyx file (called testFunc.pyx) has the following code:
import numpy as np
cimport numpy as np
def funcMatUtility(np.ndarray[np.float64_t, ndim=1] vecX,
np.ndarray[np.float64_t, ndim=1] vecE):
cdef np.ndarray[np.float64_t, ndim=2] out = \
np.zeros((len(vecX),len(vecE)),dtype=np.float64)
for iX, valX in enumerate(vecX):
for iE, valE in enumerate(vecE):
out[iX,iE] = valX + valE
return out
I call this function by running the following py file in Spyder:
import os
import numpy as np
import pyximport
os.environ['CPATH'] = np.get_include()
mingw_setup_args = { 'options': { 'build_ext': { 'compiler': 'mingw32' } } }
pyximport.install(setup_args=mingw_setup_args)
import testFunc
x = testFunc.funcMatUtility(np.array([0.0,1.0,2.0]),np.array([0.0,1.0,2.0,3.0]))
Without the line os.environ['CPATH'] = np.get_include() I get the gcc.bat error message immediately. Without the setup arguments in install() I get another error message: Unable to find vcvarsall.bat.
So with these lines I can compile my Cython code, which suggests that this is what I needed to run the Cython compiler on my Windows machine in the first place. The problem, however, is that I can only do this once. If want to import it again, for example because I am still developing my code and I only did a test run, I get the gcc.bat error message again (gcc.bat failed with exit status 1) unless I close and re-open Spyder. I tried the second import with just the import statement (i.e. not importing pyximport again), to no avail. What could be the reason that I can only compile the Cython code once?

I think I found the problem (and hence, the solution): I need to tell the compiler I'm using numpy. I found the explanation here: https://github.com/cython/cython/wiki/InstallingOnWindows
So the py file should be
import numpy
import pyximport
pyximport.install(
setup_args={"script_args":["--compiler=mingw32"],
"include_dirs":numpy.get_include()},reload_support=True)
import testFunc
x = testFunc.funcMatUtility(np.array([0.0,1.0,2.0]),np.array([0.0,1.0,2.0,3.0]))
The 'include_dirs' part tells the compiler I'm using numpy. This works in Spyder, also in repeated runs.

Why am I getting NameError: name 'array' is not defined

I'm using spyder and have written the following class:
class Ray:
def __init__(self, r, p, k):
if r.shape == (3,):
self.r = r
if p.shape == (3,):
self.p = p
if k.shape == (3,):
self.k = k
r = array(range(3))
p = array(range(3))
k = array(range(3))
It is stored in /home/user/workspace/spyder/project and the console working directory is that one. In the console I can run an array(range(3)) and it returns an array with values 0,1,2. However when doing
import ray
I get the following error
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "ray.py", line 8, in <module>
class Ray:
File "ray.py", line 20, in ray
r = array(range(3));
NameError: name 'array' is not defined
EDIT:
by default spyder has the following behaviour, don't really understand why array() works by default I thought it was only part of numpy.
import numpy as np # NumPy (multidimensional arrays, linear algebra, ...)
import scipy as sp # SciPy (signal and image processing library)
import matplotlib as mpl # Matplotlib (2D/3D plotting library)
import matplotlib.pyplot as plt # Matplotlib's pyplot: MATLAB-like syntax
from mayavi import mlab # 3D plotting functions
from pylab import * # Matplotlib's pylab interface
ion() # Turned on Matplotlib's interactive mode
Within Spyder, this intepreter also provides:
* special commands (e.g. %ls, %pwd, %clear)
* system commands, i.e. all commands starting with '!' are subprocessed
(e.g. !dir on Windows or !ls on Linux, and so on)

You need from numpy import array.
This is done for you by the Spyder console. But in a program, you must do the necessary imports; the advantage is that your program can be run by people who do not have Spyder, for instance.
I am not sure of what Spyder imports for you by default. array might be imported through from pylab import * or equivalently through from numpy import *. If you want to directly copy code from the Spyder console to a program, you might need from numpy import * or even from pylab import *. It is officially not recommended to do this in a program, though, as this pollutes the program's namespace; doing import numpy as np and then np.array(…) is customary.