AFM-MINER

Tech Review

Garrett, Jessica, and Wesley



In [3]:

    
import cv2
import numpy as np
import scipy.io
import scipy.optimize
from scipy import stats
import matplotlib.pyplot as plt
from matplotlib import gridspec 
import pandas
#import magni
import math
from PIL import Image
#import seaborn as sns; sns.set()
from sklearn.cross_validation import train_test_split
from sklearn import metrics
from sklearn.tree import DecisionTreeRegressor
from sklearn.ensemble import RandomForestRegressor
%matplotlib inline

Finding objects in the data: Using the Canny edge detector in OpenCV

Edge vs region based techniques:

Edge detection based methods of finding objects focus on the expectation of a gradient at the object's edge and the background
Region based methods focus on the object itself

How the Canny edge dection algorithm works:

Use a convolution operator to remove noise. In this case we apply a 5x5 guassian operator/filter.
- The idea behind filter-based approaches to reducing noise is to consider a window of surrounding pixels and use a combination of their values to replace the current pixel.
Use a convolution method to find edge gradients and angles. That is, weight the discrete sum of the image with another discrete function, the spatial mask. In this case, the Sobel operator is the spatial mask. OpenCV rounds this angle as one of four directions; the gradient is always perpendicular to the edge direction
Use non-maximum suppression to turn pixel values to zero if they don't exist at a local maximum in its neighborhood in the direction of the gradient. An effective method of thinning the edge
Perform hysteresis thresholding. Rather than instatiating a cut off for gradients values, pixels greater than a max value are binned as edges, pixels less than a min value are binned as not edges, and anything between is classified as an edge it is connected to max value binned edges.



In [5]:

    
img = cv2.imread('height.jpg',0)

#Python: cv.Canny(image, edges, threshold1, threshold2, aperture_size=3) → None
edges = cv2.Canny(img,0,20,3)

plt.subplot(121),plt.imshow(img,cmap = 'gray')
plt.title('Original Image'), plt.xticks([]), plt.yticks([])
plt.subplot(122),plt.imshow(edges,cmap = 'gray')
plt.title('Edge Image'), plt.xticks([]), plt.yticks([])

plt.show()

Cons of the edge-based method and the OpenCV Canny edge dector:

Success is dependent on how well the object is separated from the background (the severity of the generated pixel gradient at the edge)
Can't adjust the gaussian filter, where there is a trade-off between size of the filter and reduction in noise. Actually, Canny had first suggested using different values of sigma and resulting edge images be integrated for the final result. Larger sigmas capture coarser details in the image.
Can't employ other filters such as the wavelet-based approaches

Pros

Can adjust the size of the sobel kernel, high and low pass filters

Widgets for GUI-type thing

module : ipywidgets

can create a bunch of sliders or buttons to manipulate and vary different parameters

Pros

- Looks clean
- Easy to implement
- Many different options and functions

We haven't found a ton of drawbacks for it as of now.



In [6]:

    
%matplotlib inline
import numpy as np
import matplotlib.pyplot as plt
from ipywidgets import interact, FloatSlider, RadioButtons

amplitude_slider = FloatSlider(min=0.1, max=1.0, step=0.1, value=0.2)

color_buttons = RadioButtons(options=['blue', 'green', 'red'])

@interact(amplitude=amplitude_slider, color=color_buttons)

def plot(amplitude, color):
    
    fig, ax = plt.subplots(figsize=(4, 3),
                       subplot_kw={'axisbg':'#EEEEEE',
                                   'axisbelow':True})

    ax.grid(color='w', linewidth=2, linestyle='solid')
    x = np.linspace(0, 10, 1000)
    ax.plot(x, amplitude * np.sin(x), color=color,
        lw=5, alpha=0.4)
    ax.set_xlim(0, 10)
    ax.set_ylim(-1.1, 1.1)



In [7]:

    
import numpy as np
import scipy.io
import scipy.optimize
from scipy import stats
import matplotlib.pyplot as plt
from matplotlib import gridspec
from ipywidgets import interact, FloatSlider, RadioButtons, IntSlider
import pandas
import math
from sklearn.cross_validation import train_test_split
from sklearn import metrics
from sklearn.tree import DecisionTreeRegressor
from sklearn.ensemble import RandomForestRegressor
%matplotlib inline
def myround(x, base):
    return (float(base) * round(float(x)/float(base)))
params = {
    'lines.markersize' : 3,
    'axes.labelsize': 10,
    'font.size': 10,
    'legend.fontsize': 10,
    'xtick.labelsize': 10,
    'ytick.labelsize': 10,
    'text.usetex': False,
   }
#plp.rcParams.update(params)
plt.rcParams.update(params)
Ht2 = np.loadtxt('./data/MABr.1.Ht.txt',skiprows=0, dtype=np.float64)
Po2 = np.loadtxt('./data/MABr.1.Po.txt',skiprows=0, dtype=np.float64)
Ph2 = np.loadtxt('./data/MABr.1.Ph.txt',skiprows=0, dtype=np.float64)
Am2 = np.loadtxt('./data/MABr.1.Am.txt',skiprows=0, dtype=np.float64)
Pl2 = np.loadtxt('./data/MABr.1.Pl.txt',skiprows=0, dtype=np.float64)
# flatten the images
Ht2_flat = Ht2.flatten()
Po2_flat = Po2.flatten()
Ph2_flat = Ph2.flatten()
Am2_flat = Am2.flatten()
Pl2_flat = Pl2.flatten()
plt.show()
X = [Ht2_flat, Po2_flat, Ph2_flat, Am2_flat]
X = np.array(X).T
Y = np.array(Pl2_flat).T
Xtrain = np.array([Ht2_flat[0:31625], Po2_flat[0:31625], Ph2_flat[0:31625], Am2_flat[0:31625]]).T
Xtest = np.array([Ht2_flat[31625:], Po2_flat[31625:], Ph2_flat[31625:], Am2_flat[31625:]]).T
Ytrain = np.array(Pl2_flat[0:31625])
Ytest = np.array(Pl2_flat[31625:])



depth_slider = IntSlider(min=1, max=20, step=1, value=2)

@interact(Depth=depth_slider,continuous_update=False)

def plot(Depth):
    
    clf = DecisionTreeRegressor(max_depth=Depth)
    
    clf.fit(Xtrain, Ytrain)
    Ypred = clf.predict(Xtest)
    x = Ht2.shape[0]
    y = Ht2.shape[1]
    k=0
    merge = np.concatenate((Ytrain,Ypred))
    Pl_predict = np.zeros((x,y))
    for i in range(x):
        for j in range (y):
            Pl_predict[i,j] = merge[k]
            k = k + 1 
    fig = plt.figure(figsize=(8,6))
    pl_ax = fig.add_subplot(121)
    pl_ax.imshow(Pl_predict, cmap='viridis')
    pl_ax.set_title('Photoluminescence')
    pl_ax.axis('off')
    pl_ax = fig.add_subplot(122)
    cax = pl_ax.imshow(Pl2, cmap='viridis')
    pl_ax.set_title('Photoluminescence')
    pl_ax.axis('off')
    fig.colorbar(cax)

Correlating two 2-D arrays

Does as the name suggests

Use

Helpful if you are working with images that are generated from 2-D arrays.

Drawbacks

Not sure: how np.unravel_index or np.argmax do/work what is a "flax index" or "array of flat indices?" what is an integer array? Argmax "returns indices of maximum values along an axis," what does this mean? Why do you specifcy an axis with an integer? How are axes assigned in arrays?



In [1]:

    
from scipy import signal
from scipy import misc
import matplotlib.pyplot as plt
import numpy as np

#get racoon face
face=misc.face(gray=True) - misc.face(gray=True).mean()
#plt.imshow(face)
#plt.show()
#copy right eye of racoom face
template=np.copy(face[300:365, 670:750])
template-=template.mean()
#adds noise to face
#np.random.randn returns samples from the standard normal distribution with the the same shape as face.shape.
face=face+np.random.randn(*face.shape)*50
#correlate the face and the eye
corr=signal.correlate2d(face, template, boundary='symm', mode='same')
#finds where the two images match
#np.argmax gives indices of the maximum value along a specified axes
#np.unravel_index converts a flat index or array of flat indices into a tuple of coordinate arrays. ?
y,x=np.unravel_index(np.argmax(corr), corr.shape)



In [2]:

    
#show the match
%matplotlib inline
fig, (ax_orig, ax_template, ax_corr)=plt.subplots(3,1,figsize=(6,15))

ax_orig.imshow(face, cmap='gray')
ax_orig.set_title('Original')
ax_template.set_axis_off()
ax_template.imshow(template, cmap='gray')
ax_template.set_title('Template')
ax_template.set_axis_off()
ax_corr.imshow(corr, cmap='gray')
ax_corr.set_title('Cross-correlation')
ax_corr.set_axis_off()
ax_orig.plot(x,y,'ro')









    Out[2]:





[<matplotlib.lines.Line2D at 0x112272690>]