def test_read_image():
"""
Tests functionality of read_image from cervical.py
"""
# Create and save an image that is just four pixels as such:
# [RED] [YELLOW]
# [GREEN] [BLUE]
test_image = ones((2, 2, 3), uint8)
test_image[0][0] = helps.colorDict["red"]
test_image[0][1] = helps.colorDict["yellow"]
test_image[1][0] = helps.colorDict["green"]
test_image[1][1] = helps.colorDict["blue"]
cv2.imwrite("test.png", test_image)
# Read color image and verify values
clone_image = cer.read_image("./test.png")
assert_equal(clone_image, test_image)
# Read grayscale image
gray_image = cer.read_image("./test.png", False)
assert_raises(AssertionError, assert_equal, gray_image, test_image)
assert_raises(AssertionError, assert_equal, gray_image, clone_image)
for i in range(2):
for j in range(2):
try:
len(gray_image[i][j])
assert False
except TypeError:
assert gray_image[i][j] >= 0
assert gray_image[i][j] < 256
def main():
# 1. Parse CLA for image name and init logfile
main_args = cer.parse_critical_CLA()
imgname = main_args.img_name
helps.init_log_file(abnormal, "Abnormal cervix images", "INFO")
info(imgname)
# 2. Read in image
rgbimage = cer.read_image(imgname)
gsimage = cer.read_image(imgname, False)
if rgbimage is None or gsimage is None:
info("EXIT_FAILURE")
return
# 3. Blackout glare (i.e. white portions of image)
rgbimage = cer.blackout_glare(rgbimage)
# 4. Extract RGB + grayscale
channels = cer.extract_RGB(rgbimage)
channels["gray"] = cer.create_grayscale_channel(gsimage)
# 5. Run stats on each color component
redstats = cer.channel_stats(channels["red"])
info("RED")
helps.print_channel_stats(redstats, True)
greenstats = cer.channel_stats(channels["green"])
info("GREEN")
helps.print_channel_stats(greenstats, True)
bluestats = cer.channel_stats(channels["blue"])
info("BLUE")
helps.print_channel_stats(bluestats, True)
graystats = cer.channel_stats(channels["gray"])
info("GRAY")
helps.print_channel_stats(graystats, True)
# 6. Write the critical boundaries for RGB to output file
with open(abnormal+".txt", 'w') as f:
f.write("red ")
f.write("%d %d\n" % (redstats["median"], cer.COLORMAX-1))
f.write("green ")
f.write("%d %d\n" % (greenstats["median"], cer.COLORMAX-1))
f.write("blue ")
f.write("%d %d\n" % (bluestats["firstQrt"], bluestats["median"]))
def main():
# 1. Parse Command Line arguments
main_args = cer.parse_main()
imagename = main_args.full_img_path
svmfile = main_args.svm_file
loglevel = main_args.log_level
# 2. Init log file
helps.init_log_file("cervical", "Cervical Imaging Classification",
loglevel)
# 3. Read input image (in color)
image = cer.read_image(imagename)
if image is None:
cer.error("Unable to read the provided input image: %r\n" % imagename)
cer.info(fail)
return
# 4. Determine x-axis parameter (critical pixel density)
criticalvalues = cer.parse_critical("abnormal.txt")
if criticalvalues == {}:
cer.info(fail)
return
x = cer.critical_pixel_density(image, criticalvalues)
if x is None:
cer.info(fail)
return
cer.info("Calculated critical pixel density: %.5f" % x)
# 5. Determine y-axis parameter (blue mean)
channels = cer.extract_RGB(image)
if channels == {}:
cer.info(fail)
return
bluestats = cer.channel_stats(channels["blue"])
if bluestats == {}:
cer.info(fail)
return
y = bluestats["mean"]
cer.info("Calculated blue channel mean: %.2f" % y)
# 6. Package x and y into one variable
unknown = [x, y]
# 7. Use both calculated parameters to classify image from svmfile data
svmdata = jl.load(svmfile)
classification = svmdata.predict(unknown)[0]
# 8. Print to terminal & log file
cer.print_diagnosis(imagename, classification, True)
# DONE
cer.info(success)
def test_critical_pixel_density():
"""
Tests functionality of critical_pixel_density from cervical.py
"""
testCritVals = {"red": (240, 255), # these values are looking for yellow
"green": (240, 255),
"blue": (0, 25)}
# Test case 1 - 1/4 pixels match
img1 = cer.read_image("./test.png")
output1 = cer.critical_pixel_density(img1, testCritVals)
assert output1 == 0.25
# Test case 2 - 0/4 pixels match
img2 = ones((2, 2, 3), uint8)
img2[0][0] = helps.colorDict["blue"]
img2[0][1] = helps.colorDict["blue"]
img2[1][0] = helps.colorDict["blue"]
img2[1][1] = helps.colorDict["blue"]
output2 = cer.critical_pixel_density(img2, testCritVals)
assert output2 == 0
def svm_param1():
# Parse CLA & init log file always comes first!
main_args = cer.parse_SVM_CLA()
dirname = main_args.directory
critfile = main_args.crit_file
helps.init_log_file(training, "Moss", "INFO")
# 1. Initialize empty lists for both dysplasia and healthy images
# These lists will contain counts for each image of how many critical
# pixels each contains
allDysplasia = []
allHealthy = []
# 2. Parse critical values file
critVals = cer.parse_critical(critfile)
# 3. Cylce through all dysplasia images in TrainingData directory
dys_n = 0
while True:
imgname = helps.create_image_name(dysplasia, dys_n)
filename = dirname + imgname
# 3a. Read in image
rgbimage = cer.read_image(filename)
if rgbimage is None:
break
# 3b. Count how many pixels are in critical range
density = cer.critical_pixel_density(rgbimage, critVals)
# 3c. Log count for image and append list
allDysplasia.append(density)
info(filename)
info("Critical p: %.5f\n" % density)
# 3d. Extract RGB channels
channels = cer.extract_RGB(rgbimage)
# 3e. Calculate stats on each channel
redstats = cer.channel_stats(channels["red"])
greenstats = cer.channel_stats(channels["green"])
bluestats = cer.channel_stats(channels["blue"])
# 3f. Print stats
helps.print_channel_stats(redstats, True)
helps.print_channel_stats(greenstats, True)
helps.print_channel_stats(bluestats, True)
dys_n += 1
# 4. Cycle through all healthy images in TrainingData and repeat 2a-g
hea_n = 0
while True:
imgname = helps.create_image_name(healthy, hea_n)
filename = dirname + imgname
# 4a. Read in image
rgbimage = cer.read_image(filename)
if rgbimage is None:
break
# 4b. Count how many pixels are in critical range
density = cer.critical_pixel_density(rgbimage, critVals)
# 4c. Log count for image and append list
allHealthy.append(density)
info(filename)
info("Critical p: %.5f\n" % density)
# 4d. Extract RGB channels
channels = cer.extract_RGB(rgbimage)
# 4e. Calculate stats on each channel
redstats = cer.channel_stats(channels["red"])
greenstats = cer.channel_stats(channels["green"])
bluestats = cer.channel_stats(channels["blue"])
# 4f. Print stats
helps.print_channel_stats(redstats, True)
helps.print_channel_stats(greenstats, True)
helps.print_channel_stats(bluestats, True)
hea_n += 1
# 5. Save parameter
with open('svm_param1.txt', 'w') as f:
json.dump({"dysplasia": allDysplasia, "healthy": allHealthy}, f)
info("EXIT_SUCCESS")
def svm_param2():
# parse CLA & init log file always comes first!
main_args = cer.parse_SVM_CLA()
dirname = main_args.directory
helps.init_log_file(training, "Moss", "INFO")
# 1. Initialize empty lists for both dysplasia and healthy images
# These lists will have elements that are dictionaries to dictionaries to
# dictionaries (this maps an image number to four channels (RGB and
# grayscale), which map to a statistical value)
allDysplasia = []
allHealthy = []
# 2. Cylce through all dysplasia images in TrainingData directory
dys_n = 0
while True:
imgname = helps.create_image_name(dysplasia, dys_n)
filename = dirname + imgname
# 2a. extract RGB + grayscale
rgbimage = cer.read_image(filename)
gsimage = cer.read_image(filename, False)
if rgbimage is None or gsimage is None:
break
info(filename)
channels = cer.extract_RGB(rgbimage)
channels["gray"] = cer.create_grayscale_channel(gsimage)
# 2b. Blue channel analysis
blue_channels = cer.remove_glare(channels["blue"], 240)
bluestats = cer.channel_stats(blue_channels)
info("BLUE")
helps.print_channel_stats(bluestats, True)
# 2c. Green channel analysis
greenstats = cer.channel_stats(channels["green"])
info("GREEN")
helps.print_channel_stats(greenstats, True)
# 2d. Red channel analysis
redstats = cer.channel_stats(channels["red"])
info("RED")
helps.print_channel_stats(redstats, True)
# 2e. Grayscale channel analysis
graystats = cer.channel_stats(channels["gray"])
info("GRAYSCALE")
helps.print_channel_stats(graystats, True)
# 2f. Create dictionary of dictionary of dictionary
allstats = {
"red": redstats,
"green": greenstats,
"blue": bluestats,
"gray": graystats
}
imagestats = {dys_n: allstats}
# 2g. Update/append list for dysplasia images
allDysplasia.append(imagestats)
dys_n += 1
# 3. Cycle through all healthy images in TrainingData and repeat 2a-g
hea_n = 0
while True:
imgname = helps.create_image_name(healthy, hea_n)
filename = dirname + imgname
# 3a. extract RGB + grayscale
rgbimage = cer.read_image(filename)
gsimage = cer.read_image(filename, False)
if rgbimage is None or gsimage is None:
break
info(filename)
channels = cer.extract_RGB(rgbimage)
channels["gray"] = cer.create_grayscale_channel(gsimage)
# 3b. Blue channel analysis
blue_channels = cer.remove_glare(channels["blue"], 240)
bluestats = cer.channel_stats(blue_channels)
info("BLUE")
helps.print_channel_stats(bluestats, True)
# 3c. Green channel analysis
greenstats = cer.channel_stats(channels["green"])
info("GREEN")
helps.print_channel_stats(greenstats, True)
# 3d. Red channel analysis
redstats = cer.channel_stats(channels["red"])
info("RED")
helps.print_channel_stats(redstats, True)
# 3e. Grayscale channel analysis
graystats = cer.channel_stats(channels["gray"])
info("GRAYSCALE")
helps.print_channel_stats(graystats, True)
# 3f. Create dictionary of dictionary of dictionary
allstats = {
"red": redstats,
"green": greenstats,
"blue": bluestats,
"gray": graystats
}
imagestats = {hea_n: allstats}
# 3g. Update/append list for healthy images
allHealthy.append(imagestats)
hea_n += 1
# 4. Save parameter
with open('svm_param2.txt', 'w') as f:
json.dump({"dysplasia": allDysplasia, "healthy": allHealthy}, f)
info("EXIT_SUCCESS")