def watershedSegment(image, diskSize=20):
gradmag = gradientMagnitudue(image)
## compute foreground markers
# open image to create flat regions at cell centers
se_disk = pymorph.sedisk(diskSize)
image_opened = mahotas.open(image, se_disk);
# define foreground markers as regional maxes of cells
# this step is slow!
foreground_markers = mahotas.regmax(image_opened)
## compute background markers
# Threshold the image, cast it to the right datatype, and then calculate the distance image
image_black_white = image_opened > mahotas.otsu(image_opened)
image_black_white = image_black_white.astype('uint16')
# note the inversion here- a key difference from the matlab algorithm
# matlab distance is to nearest non-zero pixel
# python distance is to nearest 0 pixel
image_distance = pymorph.to_uint16(nd.distance_transform_edt(np.logical_not(image_black_white)))
eight_conn = pymorph.sebox()
distance_markers = mahotas.label(mahotas.regmin(image_distance, eight_conn))[0]
image_dist_wshed, image_dist_wshed_lines =mahotas.cwatershed(image_distance, distance_markers, eight_conn, return_lines=True)
background_markers = image_distance_watershed_lines - image_black_white
all_markers = np.logical_or(foreground_markers, background_markers)
# impose a min on the gradient image. assumes int64
gradmag2 = imimposemin(gradmag.astype(int), all_markers, eight_conn)
# call watershed
segmented_cells, segmented_cell_lines = mahotas.cwatershed(gradmag2, mahotas.label(all_markers)[0], eight_conn, return_lines=True)
# seperate watershed regions
segmented_cells[gradientMagnitudue(segmented_cells) > 0] = 0
return segmented_cells > 0, segmented_cells
def addCell(self, eventTuple):
if self.maskOn:
if self.data.ndim == 2:
self.aveData = self.data.copy()
else:
self.aveData = self.data.mean(axis=2)
x, y = eventTuple
localValue = self.currentMask[x, y]
print str(self.mode) + " " + "x: " + str(x) + ", y: " + str(y) + ", mask val: " + str(localValue)
# ensure mask is uint16
self.currentMask = self.currentMask.astype("uint16")
sys.stdout.flush()
########## NORMAL MODE
if self.mode is None:
if localValue > 0 and localValue != self.currentMaskNumber:
print "we are altering mask at at %d, %d" % (x, y)
# copy the old mask
newMask = self.currentMask.copy()
# make a labeled image of the current mask
labeledCurrentMask = mahotas.label(newMask)[0]
roiNumber = labeledCurrentMask[x, y]
# set that ROI to zero
newMask[labeledCurrentMask == roiNumber] = self.currentMaskNumber
newMask = newMask.astype("uint16")
self.listOfMasks.append(newMask)
self.currentMask = self.listOfMasks[-1]
elif localValue > 0 and self.data.ndim == 3:
# update info panel
labeledCurrentMask = mahotas.label(self.currentMask.copy())[0]
roiNumber = labeledCurrentMask[x, y]
self.updateInfoPanel(ROI_number=roiNumber)
elif localValue == 0:
xmin = int(x - self.diskSize)
xmax = int(x + self.diskSize)
ymin = int(y - self.diskSize)
ymax = int(y + self.diskSize)
sub_region_image = self.aveData[xmin:xmax, ymin:ymax].copy()
# threshold = mahotas.otsu(self.data[xmin:xmax, ymin:ymax].astype('uint16'))
# do a gaussian_laplacian filter to find the edges and the center
g_l = nd.gaussian_laplace(
sub_region_image, 1
) # second argument is a free parameter, std of gaussian
g_l = mahotas.dilate(mahotas.erode(g_l >= 0))
g_l = mahotas.label(g_l)[0]
center = g_l == g_l[g_l.shape[0] / 2, g_l.shape[0] / 2]
# edges = mahotas.dilate(mahotas.dilate(mahotas.dilate(center))) - center
newCell = np.zeros_like(self.currentMask)
newCell[xmin:xmax, ymin:ymax] = center
newCell = mahotas.dilate(newCell)
if self.useNMF:
modes, thresh_modes, fit_data, this_cell, is_cell, nmf_limits = self.doLocalNMF(x, y, newCell)
for mode, mode_thresh, t, i in zip(modes, thresh_modes, this_cell, is_cell):
# need to place it in the right place
# have x and y
mode_width, mode_height = mode_thresh.shape
mode_thresh_fullsize = np.zeros_like(newCell)
mode_thresh_fullsize[
nmf_limits[0] : nmf_limits[1], nmf_limits[2] : nmf_limits[3]
] = mode_thresh
# need to add all modes belonging to this cell first,
# then remove the ones nearby.
if i:
if t:
valid_area = np.logical_and(
mahotas.dilate(
mahotas.dilate(mahotas.dilate(mahotas.dilate(newCell.astype(bool))))
),
mode_thresh_fullsize,
)
newCell = np.logical_or(newCell.astype(bool), valid_area)
else:
newCell = np.logical_and(
newCell.astype(bool), np.logical_not(mahotas.dilate(mode_thresh_fullsize))
)
newCell = mahotas.close_holes(newCell.astype(bool))
self.excludePixels(newCell, 2)
newCell = newCell.astype(self.currentMask.dtype)
# remove all pixels in and near current mask and filter for ROI size
newCell[mahotas.dilate(self.currentMask > 0)] = 0
newCell = self.excludePixels(newCell, 10)
newMask = (newCell * self.currentMaskNumber) + self.currentMask
newMask = newMask.astype("uint16")
self.listOfMasks.append(newMask.copy())
self.currentMask = newMask.copy()
elif self.mode is "OGB":
# build structuring elements
se = pymorph.sebox()
se2 = pymorph.sedisk(self.cellRadius, metric="city-block")
seJunk = pymorph.sedisk(max(np.floor(self.cellRadius / 4.0), 1), metric="city-block")
seExpand = pymorph.sedisk(self.diskSize, metric="city-block")
# add a disk around selected point, non-overlapping with adjacent cells
dilatedOrignal = mahotas.dilate(self.currentMask.astype(bool), Bc=se)
safeUnselected = np.logical_not(dilatedOrignal)
# tempMask is
tempMask = np.zeros_like(self.currentMask, dtype=bool)
tempMask[x, y] = True
tempMask = mahotas.dilate(tempMask, Bc=se2)
tempMask = np.logical_and(tempMask, safeUnselected)
# calculate the area we should add to this disk based on % of a threshold
cellMean = self.aveData[tempMask == 1.0].mean()
allMeanBw = self.aveData >= (cellMean * float(self.contrastThreshold))
tempLabel = mahotas.label(np.logical_and(allMeanBw, safeUnselected).astype(np.uint16))[0]
connMeanBw = tempLabel == tempLabel[x, y]
connMeanBw = np.logical_and(np.logical_or(connMeanBw, tempMask), safeUnselected).astype(np.bool)
# erode and then dilate to remove sharp bits and edges
erodedMean = mahotas.erode(connMeanBw, Bc=seJunk)
dilateMean = mahotas.dilate(erodedMean, Bc=seJunk)
dilateMean = mahotas.dilate(dilateMean, Bc=seExpand)
modes, thresh_modes, fit_data, this_cell, is_cell, limits = self.doLocaNMF(x, y)
newCell = np.logical_and(dilateMean, safeUnselected)
newMask = (newCell * self.currentMaskNumber) + self.currentMask
newMask = newMask.astype("uint16")
self.listOfMasks.append(newMask.copy())
self.currentMask = newMask.copy()
########## SQUARE MODE
elif self.mode is "square":
self.modeData.append((x, y))
if len(self.modeData) == 2:
square_mask = np.zeros_like(self.currentMask)
xstart = self.modeData[0][0]
ystart = self.modeData[0][1]
xend = self.modeData[1][0]
yend = self.modeData[1][1]
square_mask[xstart:xend, ystart:yend] = 1
# check if square_mask interfers with current mask, if so, abort
if np.any(np.logical_and(square_mask, self.currentMask)):
return None
# add square_mask to mask
newMask = (square_mask * self.currentMaskNumber) + self.currentMask
newMask = newMask.astype("uint16")
self.listOfMasks.append(newMask)
self.currentMask = self.listOfMasks[-1]
# clear current mode data
self.clearModeData()
########## CIRCLE MODE
elif self.mode is "circle":
# make a strel and move it in place to make circle_mask
if self.diskSize < 1:
return None
if self.diskSize is 1:
se = np.ones((1, 1))
elif self.diskSize is 2:
se = pymorph.secross(r=1)
else:
se = pymorph.sedisk(r=(self.diskSize - 1))
se_extent = int(se.shape[0] / 2)
circle_mask = np.zeros_like(self.currentMask)
circle_mask[x - se_extent : x + se_extent + 1, y - se_extent : y + se_extent + 1] = se * 1.0
circle_mask = circle_mask.astype(bool)
# check if circle_mask interfers with current mask, if so, abort
if np.any(np.logical_and(circle_mask, mahotas.dilate(self.currentMask.astype(bool)))):
return None
# add circle_mask to mask
newMask = (circle_mask * self.currentMaskNumber) + self.currentMask
newMask = newMask.astype("uint16")
self.listOfMasks.append(newMask)
self.currentMask = self.listOfMasks[-1]
########## POLY MODE
elif self.mode is "poly":
self.modeData.append((x, y))
sys.stdout.flush()
self.makeNewMaskAndBackgroundImage()
def tentDetection_wt_mm(strInputFile, maxTentArea, strOutputFile, strShape='box', iThresh_coeff=0):
import pywt
import pymorph as pymm
objImg = osgeo.gdal.Open(strInputFile, GA_ReadOnly)
nRasterCount = objImg.RasterCount
poDataset = objImg.ReadAsArray().astype(np.float)
geotransform = objImg.GetGeoTransform()
pixelWidth = np.fabs(geotransform[1])
pixelHeight = np.fabs(geotransform[5])
resolution = pixelWidth * pixelHeight
# NoDataValue = objImg.GetRasterBand(1).GetNoDataValue()
# gray scale image
if (nRasterCount == 1):
objnImg = pymm.to_int32(poDataset)
# RGB image
elif(nRasterCount == 3):
objnImg = pymm.to_gray(poDataset)
else:
print 'it only supports gray-scale or RGB image'
sys.exit(1)
# determine the structure element
iNum = int(np.sqrt(maxTentArea) / resolution) + 1
if (strShape == 'box'):
objStructureElement = pymm.sebox(iNum)
elif (strShape == 'cross'):
objStructureElement = pymm.secross(iNum)
else:
objStructureElement = pymm.sedisk(iNum)
# decomposition until 1 level
wp = pywt.WaveletPacket2D(data=objnImg, wavelet='db4', mode='sym', maxlevel=1)
# iMaxLevel = wp.maxlevel()
# top-hat
wp['h'].data = pymm.openrecth(pymm.to_int32(wp['h'].data), objStructureElement, objStructureElement)
wp['v'].data = pymm.openrecth(pymm.to_int32(wp['v'].data), objStructureElement, objStructureElement)
wp['d'].data = pymm.openrecth(pymm.to_int32(wp['d'].data), objStructureElement, objStructureElement)
wp['a'].data = 0.5 * wp['a'].data
# reconstruction
wp.reconstruct(update=True)
# top-hat for reconstructed image
objtophat = pymm.openrecth(pymm.to_int32(wp.data), objStructureElement, objStructureElement)
# y = mean + k*std
(minValue, maxValue, meanValue, stdValue) = objImg.GetRasterBand(1).GetStatistics(0, 1)
if (nRasterCount == 3):
(minValue2, maxValue2, meanValue2, stdValue2) = objImg.GetRasterBand(2).GetStatistics(0, 1)
(minValue3, maxValue3, meanValue3, stdValue3) = objImg.GetRasterBand(3).GetStatistics(0, 1)
meanValue = 0.2989 * meanValue + 0.5870 * meanValue2 + 0.1140 * meanValue3
maxValue = 0.2989 * maxValue + 0.5870 * maxValue2 + 0.1140 * maxValue3
# meanValue = 438
# maxValue = 2047
threshad = meanValue + iThresh_coeff * stdValue
objTent = pymm.threshad(objtophat, stdValue, maxValue)
data_list = []
data_list.append(objTent)
WriteOutputImage(strOutputFile, 1, data_list, 0, 0, 0, strInputFile)
def tentDetection_MM(strInputFile, maxTentArea, strOutputFile, strShape='box', iThresh_coeff=0):
# five step to do this
# 1. opening-determine the square structure element (6-60 m2/resolution)
# 2. opening by reconstruction
# 3. top-hat by reconstruction
# 4. lower threshold
# 5. double threshold
import pymorph as pymm
objImg = osgeo.gdal.Open(strInputFile, GA_ReadOnly)
nRasterCount = objImg.RasterCount
poDataset = objImg.ReadAsArray().astype(np.float)
geotransform = objImg.GetGeoTransform()
pixelWidth = np.fabs(geotransform[1])
pixelHeight = np.fabs(geotransform[5])
resolution = pixelWidth * pixelHeight
# NoDataValue = objImg.GetRasterBand(1).GetNoDataValue()
# gray scale image
if (nRasterCount == 1):
objnImg = pymm.to_int32(poDataset)
# RGB image
elif(nRasterCount == 3):
objnImg = pymm.to_gray(poDataset)
else:
print 'it only supports gray-scale or RGB image'
sys.exit(1)
# determine the structure element
iNum = int(np.sqrt(maxTentArea) / resolution) + 1
if (strShape == 'box'):
objStructureElement = pymm.sebox(iNum)
elif (strShape == 'cross'):
objStructureElement = pymm.secross(iNum)
else:
objStructureElement = pymm.sedisk(iNum)
# opening
objOpen = pymm.open(objnImg, objStructureElement)
# opening by reconstruction
objOpenRec = pymm.openrec(objOpen, objStructureElement, objStructureElement)
objtophat = pymm.openrecth(objnImg, objStructureElement, objStructureElement)
# objtophat = pymm.subm(objnImg, objOpenRec)
# objTent = pymm.threshad(objtophat, 0.25 * objnImg, 0.40 * objnImg)
# y = mean + k*std
(minValue, maxValue, meanValue, stdValue) = objImg.GetRasterBand(1).GetStatistics(0, 1)
if (nRasterCount == 3):
(minValue2, maxValue2, meanValue2, stdValue2) = objImg.GetRasterBand(2).GetStatistics(0, 1)
(minValue3, maxValue3, meanValue3, stdValue3) = objImg.GetRasterBand(3).GetStatistics(0, 1)
meanValue = 0.2989 * meanValue + 0.5870 * meanValue2 + 0.1140 * meanValue3
maxValue = 0.2989 * maxValue + 0.5870 * maxValue2 + 0.1140 * maxValue3
# meanValue = 438
# maxValue = 2047
threshad = meanValue + iThresh_coeff * stdValue
objTent = pymm.threshad(objtophat, threshad, maxValue)
data_list = []
data_list.append(objTent)
WriteOutputImage(strOutputFile, 1, data_list, 0, 0, 0, strInputFile)
'''
def watershedSegment(image, diskSize=20):
"""This routine implements the watershed example from
http://www.mathworks.com/help/images/examples/marker-controlled-watershed-segmentation.html,
but using pymorph and mahotas.
:param image: an image (2d numpy array) to be segemented
:param diskSize: an integer used as a size for a structuring element used
for morphological preprocessing.
:returns: tuple of binarized and labeled segmention masks
"""
def gradientMagnitudue(image):
sobel_x = nd.sobel(image.astype('double'), 0)
sobel_y = nd.sobel(image.astype('double'), 1)
return np.sqrt((sobel_x * sobel_x) + (sobel_y * sobel_y))
def imimposemin(image, mask, connectivity):
fm = image.copy()
fm[mask] = -9223372036854775800
fm[np.logical_not(mask)] = 9223372036854775800
fp1 = image + 1
g = np.minimum(fp1, fm)
j = infrec(fm, g)
return j
def infrec(f, g, Bc=None):
if Bc is None: Bc = pymorph.secross()
n = f.size
return fast_conditional_dilate(f, g, Bc, n)
def fast_conditional_dilate(f, g, Bc=None, n=1):
if Bc is None:
Bc = pymorph.secross()
f = pymorph.intersec(f, g)
for i in xrange(n):
prev = f
f = pymorph.intersec(mahotas.dilate(f, Bc), g)
if pymorph.isequal(f, prev):
break
return f
gradmag = gradientMagnitudue(image)
## compute foreground markers
# open image to create flat regions at cell centers
se_disk = pymorph.sedisk(diskSize)
image_opened = mahotas.open(image, se_disk)
# define foreground markers as regional maxes of cells
# this step is slow!
foreground_markers = mahotas.regmax(image_opened)
## compute background markers
# Threshold the image, cast it to the right datatype, and then calculate the distance image
image_black_white = image_opened > mahotas.otsu(image_opened)
image_black_white = image_black_white.astype('uint16')
# note the inversion here- a key difference from the matlab algorithm
# matlab distance is to nearest non-zero pixel
# python distance is to nearest 0 pixel
image_distance = pymorph.to_uint16(
nd.distance_transform_edt(np.logical_not(image_black_white)))
eight_conn = pymorph.sebox()
distance_markers = mahotas.label(mahotas.regmin(image_distance,
eight_conn))[0]
image_dist_wshed, image_dist_wshed_lines = mahotas.cwatershed(
image_distance, distance_markers, eight_conn, return_lines=True)
background_markers = image_dist_wshed_lines - image_black_white
all_markers = np.logical_or(foreground_markers, background_markers)
# impose a min on the gradient image. assumes int64
gradmag2 = imimposemin(gradmag.astype(int), all_markers, eight_conn)
# call watershed
segmented_cells, segmented_cell_lines = mahotas.cwatershed(
gradmag2, mahotas.label(all_markers)[0], eight_conn, return_lines=True)
segmented_cells -= 1
# seperate watershed regions
segmented_cells[gradientMagnitudue(segmented_cells) > 0] = 0
return segmented_cells > 0, segmented_cells
def test_sebox():
assert np.all(pymorph.sebox(0) == np.array([1]))
assert np.all(pymorph.sebox(1) == np.ones((3,3)))
assert np.all(pymorph.sebox(9) == np.ones((2*9+1,2*9+1)))
def watershedSegment(image, diskSize=20):
def gradientMagnitudue(image):
sobel_x = nd.sobel(image.astype('double'), 0)
sobel_y = nd.sobel(image.astype('double'), 1)
return np.sqrt((sobel_x * sobel_x) + (sobel_y * sobel_y))
def imimposemin(image, mask, connectivity):
fm = image.copy()
fm[mask] = -9223372036854775800
fm[np.logical_not(mask)] = 9223372036854775800
fp1 = image + 1
g = np.minimum(fp1, fm)
j = infrec(fm, g)
return j
def infrec(f, g, Bc=None):
if Bc is None: Bc = pymorph.secross()
n = f.size
return fast_conditional_dilate(f, g, Bc, n);
def fast_conditional_dilate(f, g, Bc=None, n=1):
if Bc is None:
Bc = pymorph.secross()
f = pymorph.intersec(f,g)
for i in xrange(n):
prev = f
f = pymorph.intersec(mahotas.dilate(f, Bc), g)
if pymorph.isequal(f, prev):
break
return f
gradmag = gradientMagnitudue(image)
## compute foreground markers
# open image to create flat regions at cell centers
se_disk = pymorph.sedisk(diskSize)
image_opened = mahotas.open(image, se_disk);
# define foreground markers as regional maxes of cells
# this step is slow!
foreground_markers = mahotas.regmax(image_opened)
## compute background markers
# Threshold the image, cast it to the right datatype, and then calculate the distance image
image_black_white = image_opened > mahotas.otsu(image_opened)
image_black_white = image_black_white.astype('uint16')
# note the inversion here- a key difference from the matlab algorithm
# matlab distance is to nearest non-zero pixel
# python distance is to nearest 0 pixel
image_distance = pymorph.to_uint16(nd.distance_transform_edt(np.logical_not(image_black_white)))
eight_conn = pymorph.sebox()
distance_markers = mahotas.label(mahotas.regmin(image_distance, eight_conn))[0]
image_dist_wshed, image_dist_wshed_lines = mahotas.cwatershed(image_distance, distance_markers, eight_conn, return_lines=True)
background_markers = image_dist_wshed_lines - image_black_white
all_markers = np.logical_or(foreground_markers, background_markers)
# impose a min on the gradient image. assumes int64
gradmag2 = imimposemin(gradmag.astype(int), all_markers, eight_conn)
# call watershed
segmented_cells, segmented_cell_lines = mahotas.cwatershed(gradmag2, mahotas.label(all_markers)[0], eight_conn, return_lines=True)
segmented_cells -= 1
# seperate watershed regions
segmented_cells[gradientMagnitudue(segmented_cells) > 0] = 0
return segmented_cells > 0, segmented_cells
def tentDetection_wt_mm(strInputFile,
maxTentArea,
strOutputFile,
strShape='box',
iThresh_coeff=0):
import pywt
import pymorph as pymm
objImg = osgeo.gdal.Open(strInputFile, GA_ReadOnly)
nRasterCount = objImg.RasterCount
poDataset = objImg.ReadAsArray().astype(np.float)
geotransform = objImg.GetGeoTransform()
pixelWidth = np.fabs(geotransform[1])
pixelHeight = np.fabs(geotransform[5])
resolution = pixelWidth * pixelHeight
# NoDataValue = objImg.GetRasterBand(1).GetNoDataValue()
# gray scale image
if (nRasterCount == 1):
objnImg = pymm.to_int32(poDataset)
# RGB image
elif (nRasterCount == 3):
objnImg = pymm.to_gray(poDataset)
else:
print 'it only supports gray-scale or RGB image'
sys.exit(1)
# determine the structure element
iNum = int(np.sqrt(maxTentArea) / resolution) + 1
if (strShape == 'box'):
objStructureElement = pymm.sebox(iNum)
elif (strShape == 'cross'):
objStructureElement = pymm.secross(iNum)
else:
objStructureElement = pymm.sedisk(iNum)
# decomposition until 1 level
wp = pywt.WaveletPacket2D(data=objnImg,
wavelet='db4',
mode='sym',
maxlevel=1)
# iMaxLevel = wp.maxlevel()
# top-hat
wp['h'].data = pymm.openrecth(pymm.to_int32(wp['h'].data),
objStructureElement, objStructureElement)
wp['v'].data = pymm.openrecth(pymm.to_int32(wp['v'].data),
objStructureElement, objStructureElement)
wp['d'].data = pymm.openrecth(pymm.to_int32(wp['d'].data),
objStructureElement, objStructureElement)
wp['a'].data = 0.5 * wp['a'].data
# reconstruction
wp.reconstruct(update=True)
# top-hat for reconstructed image
objtophat = pymm.openrecth(pymm.to_int32(wp.data), objStructureElement,
objStructureElement)
# y = mean + k*std
(minValue, maxValue, meanValue,
stdValue) = objImg.GetRasterBand(1).GetStatistics(0, 1)
if (nRasterCount == 3):
(minValue2, maxValue2, meanValue2,
stdValue2) = objImg.GetRasterBand(2).GetStatistics(0, 1)
(minValue3, maxValue3, meanValue3,
stdValue3) = objImg.GetRasterBand(3).GetStatistics(0, 1)
meanValue = 0.2989 * meanValue + 0.5870 * meanValue2 + 0.1140 * meanValue3
maxValue = 0.2989 * maxValue + 0.5870 * maxValue2 + 0.1140 * maxValue3
# meanValue = 438
# maxValue = 2047
threshad = meanValue + iThresh_coeff * stdValue
objTent = pymm.threshad(objtophat, stdValue, maxValue)
data_list = []
data_list.append(objTent)
WriteOutputImage(strOutputFile, 1, data_list, 0, 0, 0, strInputFile)
def tentDetection_MM(strInputFile,
maxTentArea,
strOutputFile,
strShape='box',
iThresh_coeff=0):
# five step to do this
# 1. opening-determine the square structure element (6-60 m2/resolution)
# 2. opening by reconstruction
# 3. top-hat by reconstruction
# 4. lower threshold
# 5. double threshold
import pymorph as pymm
objImg = osgeo.gdal.Open(strInputFile, GA_ReadOnly)
nRasterCount = objImg.RasterCount
poDataset = objImg.ReadAsArray().astype(np.float)
geotransform = objImg.GetGeoTransform()
pixelWidth = np.fabs(geotransform[1])
pixelHeight = np.fabs(geotransform[5])
resolution = pixelWidth * pixelHeight
# NoDataValue = objImg.GetRasterBand(1).GetNoDataValue()
# gray scale image
if (nRasterCount == 1):
objnImg = pymm.to_int32(poDataset)
# RGB image
elif (nRasterCount == 3):
objnImg = pymm.to_gray(poDataset)
else:
print 'it only supports gray-scale or RGB image'
sys.exit(1)
# determine the structure element
iNum = int(np.sqrt(maxTentArea) / resolution) + 1
if (strShape == 'box'):
objStructureElement = pymm.sebox(iNum)
elif (strShape == 'cross'):
objStructureElement = pymm.secross(iNum)
else:
objStructureElement = pymm.sedisk(iNum)
# opening
objOpen = pymm.open(objnImg, objStructureElement)
# opening by reconstruction
objOpenRec = pymm.openrec(objOpen, objStructureElement,
objStructureElement)
objtophat = pymm.openrecth(objnImg, objStructureElement,
objStructureElement)
# objtophat = pymm.subm(objnImg, objOpenRec)
# objTent = pymm.threshad(objtophat, 0.25 * objnImg, 0.40 * objnImg)
# y = mean + k*std
(minValue, maxValue, meanValue,
stdValue) = objImg.GetRasterBand(1).GetStatistics(0, 1)
if (nRasterCount == 3):
(minValue2, maxValue2, meanValue2,
stdValue2) = objImg.GetRasterBand(2).GetStatistics(0, 1)
(minValue3, maxValue3, meanValue3,
stdValue3) = objImg.GetRasterBand(3).GetStatistics(0, 1)
meanValue = 0.2989 * meanValue + 0.5870 * meanValue2 + 0.1140 * meanValue3
maxValue = 0.2989 * maxValue + 0.5870 * maxValue2 + 0.1140 * maxValue3
# meanValue = 438
# maxValue = 2047
threshad = meanValue + iThresh_coeff * stdValue
objTent = pymm.threshad(objtophat, threshad, maxValue)
data_list = []
data_list.append(objTent)
WriteOutputImage(strOutputFile, 1, data_list, 0, 0, 0, strInputFile)
'''
def alternative_solution(self,
a,
orientation='coronal',
linethickness=10,
outimg=False):
'''
Paramenters
-----------
a: original image in graylevel
'''
H, W = a.shape
if orientation == 'coronal':
# UL = mm.limits(a)[1] # upper limit
UL = 255
b = 1 - iacircle(a.shape, H / 3, (1.4 * H / 3, W / 2)) # Circle
b = b[0:70, W / 2 - 80:W / 2 + 80] # Rectangle
# if outimg:
# b_ = 0 * a; b_[0:70, W / 2 - 80:W / 2 + 80] = UL * b # b_ only for presentation
# b_[:, W / 2 - linethickness / 2:W / 2 + linethickness / 2] = UL # b_ only for presentation
c = a + 0
c[:, W / 2 - linethickness / 2:W / 2 + linethickness / 2] = UL
c[0:70, W / 2 - 80:W / 2 +
80] = (1 - b) * c[0:70, W / 2 - 80:W / 2 + 80] + b * UL
c[0:40, W / 2 - 70:W / 2 + 70] = UL
d = mm.open(c, mm.img2se(mm.binary(np.ones((20, 10)))))
e = mm.close(d, mm.seline(5))
f = mm.close_holes(e)
g = mm.subm(f, d)
h = mm.close_holes(g)
i = mm.areaopen(h, 1000)
j1, j2 = iaotsu(i)
# j = i > j1
ret, j = cv2.threshold(cv2.GaussianBlur(i, (7, 7), 0), j1, 255,
cv2.THRESH_BINARY)
k = mm.open(j, mm.seline(20, 90))
l = mm.areaopen(k, 1000)
# m = mm.label(l)
res = np.vstack(
[np.hstack([c, d, e, f, g]),
np.hstack([h, i, j, k, l])])
cv2.imshow('Result', res)
cv2.waitKey(0)
cv2.destroyAllWindows()
################################
# l_ = mm.blob(k,'AREA','IMAGE')
# l = l_ == max(ravel(l_))
# m = mm.open(l, mm.sedisk(3)) # VERIFICAR O MELHOR ELEMENTO ESTRUTURANTE AQUI
# n = mm.label(m)
if outimg:
if not os.path.isdir('outimg'):
os.mkdir('outimg')
def N(x):
# y = uint8(ianormalize(x, (0, 255)) + 0.5)
y = (ianormalize(x, (0, 255)) + 0.5).astype(np.uint8)
return y
adwrite('outimg/a.png', N(a))
adwrite('outimg/b.png', N(b_))
adwrite('outimg/c.png', N(c))
adwrite('outimg/d.png', N(d))
adwrite('outimg/e.png', N(e))
adwrite('outimg/f.png', N(f))
adwrite('outimg/g.png', N(g))
adwrite('outimg/h.png', N(h))
adwrite('outimg/i.png', N(i))
adwrite('outimg/j.png', N(j))
adwrite('outimg/k.png', N(k))
adwrite('outimg/l.png', N(l))
adwrite('outimg/m.png', N(m))
# adwrite('outimg/n.png', N(n))
return m
else:
b = mm.areaopen(a, 500)
c = mm.close(b, mm.sebox(3))
d = mm.close_holes(c)
e = mm.subm(d, c)
f = mm.areaopen(e, 1000)
# g = f > 5
ret, g = cv2.threshold(cv2.GaussianBlur(f, (5, 5), 0), 3, 255,
cv2.THRESH_BINARY)
# ret, g = cv2.threshold(
# cv2.GaussianBlur(f, (7, 7), 0),
# 5, 255,
# cv2.THRESH_BINARY_INV)
h = mm.asf(g, 'CO', mm.sedisk(5))
i = mm.close_holes(h)
res = np.vstack(
[np.hstack([a, b, c, d, e]),
np.hstack([f, g, h, i, a])])
cv2.imshow('Result', res)
cv2.waitKey(0)
cv2.destroyAllWindows()
if outimg:
if not os.path.isdir('outimg'):
os.mkdir('outimg')
def N(x):
y = (ianormalize(x, (0, 255)) + 0.5).astype(np.uint8)
return y
adwrite('outimg/a.png', N(a))
adwrite('outimg/b.png', N(b))
adwrite('outimg/c.png', N(c))
adwrite('outimg/d.png', N(d))
adwrite('outimg/e.png', N(e))
adwrite('outimg/f.png', N(f))
adwrite('outimg/g.png', N(g))
adwrite('outimg/h.png', N(h))
adwrite('outimg/i.png', N(i))
return i