def imshow(im, windowName='Image', histogram=False, bitDepth=8, dpi=128.5):
# Determine the numnber of grey levels
numberLevels = 2**bitDepth
# Normalize the image so that it falls in the range [0, 1]
normalizedImage = (im / float(numberLevels-1)).astype(numpy.float32)
# Reverse the channel order (BGR to RGB) for color images (assumption is
# that OpenCV-style color images are provided)
if len(im.shape) == 3:
normalizedImage = cv2.cvtColor(normalizedImage, cv2.COLOR_BGR2RGB)
# Determine the current screen size and set the figure size appropriately
scale = 0.85
screenSize = hardware.get_screen_size(dpi=dpi)
if histogram:
figureSize = [screenSize[3]*scale, screenSize[2]*scale]
else:
figureSize = [screenSize[2]*scale, screenSize[2]*scale]
# Create a Matplotlib figure with the given title and a canvas to contain
# this figure
figure = matplotlib.pyplot.figure(windowName,
figsize=[figureSize[0],
figureSize[1]])
canvas = matplotlib.backends.backend_agg.FigureCanvasAgg(figure)
# Add one or two subplot axes to the figure depending on whether or not
# the histogram is to be displayed
if histogram:
figureRows = 2
figureCols = 1
axes1 = figure.add_subplot(figureRows, figureCols, 1)
axes2 = figure.add_subplot(figureRows, figureCols, 2)
else:
figureRows = 1
figureCols = 1
axes1 = figure.add_subplot(figureRows, figureCols, 1)
# Add the image and the histogram (if requested) to the figure
if len(im.shape) == 2:
axes1.imshow(normalizedImage, cmap=matplotlib.cm.Greys_r)
else:
axes1.imshow(normalizedImage)
axes1.axis('off')
if histogram:
h, pdf, cdf = ipcv.histogram(im, maxCount=numberLevels-1)
axes2.set_xlim([0, numberLevels-1])
axes2.set_xlabel('DC')
axes2.set_ylabel('PDF')
if len(h) == 1:
axes2.plot(range(numberLevels), pdf[0], 'k')
else:
for band in range(len(h)):
axes2.plot(range(numberLevels), pdf[band])
# Display the figure to the screen
matplotlib.pyplot.show()
def histogram_enhancement(im, etype='linear2', target=None, maxCount=255): """ Title: histogram_enhancement Author: Molly Hill, [email protected] Description: Returns given image quantized at set number of levels, using either a uniform or IGS method. Attributes: im - ndarray, can be grayscale or color of any size etype - enhancement type, of the following options: - 'linearX' where X is an integer percent of the area to be clipped/crushed with contrast increas - 'match' where the image is to be matched to a provided target image or PDF - 'equalize' where the image's histogram is to be spread equally across digital count target - if etype = 'match', then target must be provided as either an image (3D array) or PDF (1D array) maxCount - maximum code value of pixel; must be positive integer Requires: histogram.py, author: Carl Salvaggio dimensions.py, author: Carl Salvaggio """ if maxCount <= 0 or type(maxCount) is not int: msg = "Specified maximum digital count must be a positive integer." raise ValueError(msg) if type(im) is not numpy.ndarray: msg = "Specified image type must be ndarray." raise TypeError(msg) if etype[:6] != 'linear' and etype != 'match' and etype != 'equalize': msg = "Enhancement types available are linear, match, and equalize. Defaulting to linear2." print(msg) if etype == 'match': if type(target) == None: etype = 'equalize' msg = "If using match, target must be provided." print(msg) elif target.ndim !=1 and target.ndim !=2: print(target.ndim) msg = "Provided target must be PDF (1-D array) or image (3-D array)" raise TypeError(msg) enhIm = numpy.copy(im) srcCDF = ipcv.histogram(enhIm)[2] DCout = [] tgtCDF = [] tgtPDF = target if etype == 'match' or etype == 'equalize': if etype == 'match' and target.ndim != 1: #is image tgtCDF = ipcv.histogram(target)[2][0] #create CDF of target, currently does red channel if color else: #equalize or PDF passed in as target for matching if etype == 'equalize': tgtPDF = numpy.ones(maxCount+1)/(maxCount+1) tgtCDF = numpy.cumsum(tgtPDF) #convert PDF to CDF for i in range(ipcv.dimensions(srcCDF)[1]): #createLUT difference = numpy.fabs(numpy.subtract(tgtCDF,srcCDF[0][i])) #red channel only DCout.extend([int(maxCount*tgtCDF[numpy.argmin(difference)])]) for j in range(im.size): #apply LUT enhIm.flat[j] = DCout[enhIm.flat[j]] #uses original code value to assign new output from LUT else: #linear pct = (int(etype[6:])/2) / 100 #extract percent from etype and halve difference = numpy.fabs(numpy.subtract(srcCDF[0],pct)) DCmin = numpy.argmin(difference) difference = numpy.fabs(numpy.subtract(srcCDF[0],(1-pct))) DCmax = numpy.argmin(difference) slope = (maxCount+1)/(DCmax-DCmin) intercept = -slope * DCmin for j in range(enhIm.size): px = enhIm.flat[j] if px >= DCmax: px = maxCount elif px <= DCmin: px = 0 else: px = slope * px + intercept enhIm.flat[j] = int(px) return enhIm
# A greyscale test image
filename = 'crowd.jpg'
# A 3-channel color test image
filename = 'lenna.tif'
im = cv2.imread(filename, cv2.IMREAD_UNCHANGED)
print('Data type = {0}'.format(type(im)))
print('Image shape = {0}'.format(im.shape))
print('Image size = {0}'.format(im.size))
dataType = str(im.dtype)
imType = {'uint8':8, 'uint16':16, 'uint32':32}
startTime = time.time()
h, pdf, cdf = ipcv.histogram(im, bitDepth=imType[dataType])
print('Elasped time = {0} [s]'.format(time.time() - startTime))
# The follow will produce a figure containing color-coded plots of the
# computed histogram, probability function (PDF), and cumulative density
# function (CDF)
import matplotlib.pyplot
import matplotlib.backends.backend_agg
maxCount = 2**imType[dataType]
bins = list(range(maxCount))
figure = matplotlib.pyplot.figure('Histogram')
canvas = matplotlib.backends.backend_agg.FigureCanvas(figure)
import cv2
import ipcv
import time
# A greyscale test image
#filename = 'crowd.jpg'
# A 3-channel color test image
filename = 'lenna.tiff'
im = cv2.imread(filename, cv2.IMREAD_UNCHANGED)
print('Data type = {0}'.format(type(im)))
print('Image shape = {0}'.format(im.shape))
print('Image size = {0}'.format(im.size))
startTime = time.time()
h, pdf, cdf = ipcv.histogram(im)
print('Elapsed time = {0} [s]'.format(time.time() - startTime))
Max = range(256)
if len(im.shape) == 3:
[histR, histG, histB] = h
[pdfR, pdfG, pdfB] = pdf
[cdfR, cdfG, cdfB] = cdf
matplotlib.pyplot.figure(1)
matplotlib.pyplot.subplot(3, 1, 1)
matplotlib.pyplot.ylabel('number of pixels')
matplotlib.pyplot.xlabel('Digital Count')
matplotlib.pyplot.plot(Max, histR, 'r-')
def histogram_enhancement(img,
etype='linear2',
target=None,
maxCount=255,
pool=False):
"""
:NAME:
histogram_enchancement
:PURPOSE:
This method modifies an image using basic histogram enhancement techniques:
linear -- removes removes extranesous pixels on outer edge of histogram and stretches
histogram to fill entire DC range
equalization -- a technique to even out peaks on the histogram and product a near-flat
histogram curve
match -- modifies an image such that it's pixel distribution mimics that of a target
image or distribution
:CATEGORY:
ipcv -- histogram enchancement tool
:CALLING SEQUENCE:
quantizedImage = histogram_enchancement(img,\
etype=etype,\
target=targer,\
maxCount = maxCount,\
pool = pool)
:INPUTS:
img
[numpy.ndarray] input image
etype
[string] type of histogram enhancement to perform
target
[numpy.ndarray] target image or distribution using in histogram matching
maxCount
[int] the largest possible DC value in the image
pool
[boolean] whether or not to pool all colors into one cdf or loop by band
:RETURN VALUE:
a numpy array containing the enhanced image
:SIDE EFFECTS:
removes possibly pertinent data in an image
:ERROR CHECKING:
ValueError
TypeError
:REQUIRES:
numpy
sys.exc_info
os.path.split
:MODIFICATION HISTORY:
Engineer: Jeff Maggio
original: 09/09/16
"""
#ERROR CHECKING
if etype == "match":
if (isinstance(target, np.ndarray) == False):
print(
"-------------------------------------------------------------------"
)
print(
"input 'target' must by a valid numpy.ndarray, currently {0}".
format(type(target)))
print(
"-------------------------------------------------------------------"
)
print("raising TypeError...")
raise TypeError
if isinstance(maxCount, int) == False:
print(
"-------------------------------------------------------------------"
)
print("input 'maxCount' must be an int type, currently is {0}".format(
type(target)))
print(
"-------------------------------------------------------------------"
)
elif maxCount < 0:
print(
"-------------------------------------------------------------------"
)
print("maxCount must be greater than 0, currently is {0}".format(
maxCount))
print(
"-------------------------------------------------------------------"
)
if isinstance(img, np.ndarray) == True:
img = img.reshape(img.shape[0], img.shape[1], 1) if (len(img.shape)
== 2) else img
bands = img.shape[2]
if isinstance(target, np.ndarray) == True:
target = target.reshape(target.shape[0], target.shape[1], 1) if (len(
target.shape) == 2) else target
if etype == "match":
if (len(target.shape) != 1) and (target.shape[2] != img.shape[2]):
print(
"-------------------------------------------------------------------"
)
print(
"original and target images must both be of the same type (grayscale or color"
)
print("raising TypeError...")
print(
"-------------------------------------------------------------------"
)
raise TypeError
#BEGIN ACTUAL WORK
try:
#2 is index of cdf from return tuple
if "linear" in etype:
for band in range(bands):
#cdf is recalculated by band
cdf = ipcv.histogram(img=img,channels=band,histSize=(maxCount+1),\
ranges=[0,maxCount+1],returnType=1)[2]
# generating components of the line
lowerBound = (float(etype.replace("linear", "")) / 200.0
) #1/2 input on each side
upperbound = (1 - lowerBound)
dcLow = np.where(cdf >= lowerBound)[0][0]
dcHigh = np.where(cdf <= upperbound)[0][-1]
m = (maxCount / (dcHigh - dcLow))
b = maxCount - (m * dcHigh)
#generating the lookup table by applying a linear transform
LUT = (m * np.arange(maxCount + 1)) + b
LUT = np.clip(LUT, 0, 255)
print(img[:, :, band].shape)
img[:, :, band] = LUT[img[:, :, band]]
elif etype == 'equalize':
for band in range(bands):
cdf = ipcv.histogram(img=img,channels=band,histSize=(maxCount+1),\
ranges=[0,maxCount+1],returnType=1)[2]
LUT = (cdf * maxCount).flatten()
print(LUT.shape)
img[:, :, band] = LUT[img[:, :, band]]
elif etype == "match":
#Generating the target CDFs
tCdf = []
if len(target.shape) == 1:
for band in range(bands):
tCdf.append(np.cumsum(target))
else:
for band in range(bands):
tCdf.append(ipcv.histogram(img=target,channels=band,histSize=(maxCount+1),\
ranges=[0,maxCount+1],returnType=1)[2]) #only return the cdf here
for band in range(bands):
cdf = ipcv.histogram(img=img,channels=band,histSize=(maxCount+1),\
ranges=[0,maxCount+1],returnType=1)[2]
LUT = np.zeros(maxCount + 1)
index = 0
for percentage in cdf:
upperValues = np.where(tCdf[band] >= percentage)
if upperValues[0].size != 0:
dc = upperValues[0][0]
else:
dc = 0
LUT[index] = dc
index += 1
img[:, :, band] = LUT[img[:, :, band]]
return img.astype(np.uint8)
except Exception as e:
print(
"==================================================================="
)
exc_type, exc_obj, exc_tb = exc_info()
fname = split(exc_tb.tb_frame.f_code.co_filename)[1]
print("\nfile: {0}\n\nline: {1} \n\n{2}\n".format(
fname, exc_tb.tb_lineno, e))
print(
"==================================================================="
)
def otsu_threshold(img, maxCount=255, verbose=False):
"""
:NAME:
otsu_threshold
:PURPOSE:
this method generates a binary thresholded image based off of
Otsu's class discrimination method
:CATEGORY:
ipcv -- object recognition and thresholding tool
:CALLING SEQUENCE:
quantizedImage = quantize(img = inputImage,\
maxCount = max display level\
verbose = true or false)
:INPUTS:
img
[numpy.ndarray] input image to be quanitized
maxCount
[int] maximum pixel value in the output array
verbose
[boolean] whether or not to graph the histogram
:RETURN VALUE:
tuple containing:
returnTuple[0] -- binary numpy.array of the same shape as the input image
returnTuple[1] -- threshold determined by otsu's method
:ERROR CHECKING:
TypeError
ValueError
RuntimeError
:REQUIRES:
np
sys.exc_info
os.path.split
ipcv
:MODIFICATION HISTORY:
Engineer: Jeff Maggio
08/25/16: otsu code
"""
###################### BEGIN ERROR CHECKING #######################
if isinstance(img,np.ndarray) == True:
dims = ipcv.dimensions(img,"dictionary")
if dims["bands"] == 1:
if len(img.shape) == 3:
#making the array two dimensional if it only has 1 band
img = img.reshape(dims['rows'],dims['cols'])
else:
print("")
print("input 'img' must be grayscale or single-banded")
print("")
raise RuntimeError
else:
print("")
print("input 'img' must be a valid 2 dimensional numpy array, currently {0}".format(type(img)))
print("")
raise TypeError
if isinstance(maxCount,int) == False:
print("")
print("input 'maxCount' must be an int, currently {0}".format(type(maxCount)))
print("")
raise TypeError
elif maxCount <= 0:
print("")
print("input 'maxCount' must be greater than zero")
print("")
raise ValueError
if isinstance(verbose,bool) == False:
print("")
print("input 'verbose' must be integer boolean , currently {0}".format(verbose))
print("")
raise TypeError
###################### END ERROR CHECKING #######################
try:
numberCounts = maxCount + 1
#generating the pdf and cdf
hist,pdf,cdf = ipcv.histogram(img,histSize=numberCounts,ranges=[0,numberCounts])
meanLevelArray = np.cumsum( np.arange(0,numberCounts) * pdf )
muTotal = meanLevelArray[-1]
sigmaSquaredBValues = np.zeros(numberCounts)
startingK = np.where(cdf>0.0)[0][0]
endingK = np.where(cdf<1.0)[0][-1]
for k in range(startingK, endingK):
muK = meanLevelArray[k]
omegaK = cdf[k]
sigmaSquaredB = ( ( (muTotal * omegaK) - muK )**2 ) / ( omegaK * (1-omegaK) )
sigmaSquaredBValues[k] = sigmaSquaredB
threshold = np.argmax(sigmaSquaredBValues)
LUT = np.zeros( numberCounts )
LUT[threshold+1:] = 1
img = LUT[img]
if verbose == True:
values = (pdf,)
colors = ('r',)
filename = "image_pdf_wOtsu.eps"
thresholdMarker = (threshold,)
labels = ("pdf",)
graph = ipcv.quickplot(values,colors,labels,filename=filename,verticalMarkers=thresholdMarker,\
xLabel="Digital Counts",yLabel="probability",display=False)
graph.annotate("otsu's Threshold", xy=(threshold, .01), xytext=(3, 1.5),arrowprops=dict(facecolor='black', shrink=0.05))
graph.show()
return img.astype(np.uint8), threshold
except Exception as e:
print("===============================================================")
exc_type, exc_obj, tb = exc_info()
fname = split(tb.tb_frame.f_code.co_filename)[1]
print("\r\nfile: {0}\r\n\r\nline: {1} \r\n\r\n{2}\r\n\r\n".format(fname,tb.tb_lineno,exc_obj,e))
print("===============================================================")
def otsu_threshold(im, maxCount=255, verbose=False):
"""
Title: otsu_threshold
Author: Molly Hill, [email protected]
Description:
Finds threshold for foreground/background in given image
Returns:
matte - binary image indicating areas above/below threshold
kOpt - optimum threshold for given image
Attributes:
im - source image; ndarray, must be grayscale
maxCount - maximum code value of pixel; must be positive integer
verbose - if True, plots histogram of image, marked with optimum threshold
Requires:
histogram.py, author: Carl Salvaggio
"""
if maxCount <= 0 or type(maxCount) is not int:
msg = "Specified maximum digital count must be a positive integer."
raise ValueError(msg)
if type(im) is not numpy.ndarray:
msg = "Specified image type must be ndarray."
raise TypeError(msg)
if type(verbose) is not bool:
msg = "Verbose must be a boolean. Defaulting to False."
print(msg)
#initialize variables
srcIm = numpy.copy(im)
histo = ipcv.histogram(srcIm)[0]
srcPDF = ipcv.histogram(srcIm)[1][0]
matte = []
stdDev = []
kOpt = 0
firstMtot = []
indices = numpy.arange(maxCount + 1)
for i in range(numpy.size(indices)):
firstMtot.extend([srcPDF[i] * indices[i]
]) #pre-sum first moment across image
meanLvl = numpy.sum(firstMtot) #mean level of image
for k in range(0, maxCount):
zeroM = numpy.sum(srcPDF[0:k]) #zero moment
if zeroM == 0 or zeroM == 1:
stdDev.extend([0])
else:
firstM = numpy.sum(firstMtot[:k]) #first moment up to k
stdDev.extend([
(((meanLvl * zeroM) - firstM)**2) // (zeroM * (1 - zeroM))
])
kOpt = numpy.argmax(stdDev) + 1
matte = numpy.uint8(1 *
(im >= kOpt)) #get as Booleans and convert to integers
if verbose == True: #plot histogram and threshold
#NOTE THIS SLOWS EVERYTHING DOWN BY A LOT
matplotlib.pyplot.plot(indices, histo[0])
matplotlib.pyplot.ylabel('Number of Pixels')
matplotlib.pyplot.xlabel('Digital Count')
matplotlib.pyplot.ylim([0, max(histo[0])])
matplotlib.pyplot.xlim([0, maxCount])
matplotlib.pyplot.axvline(x=kOpt,
label='Threshold' + str(kOpt),
color='r')
matplotlib.pyplot.show()
return matte, kOpt
