def __init__(self, data, voxel, threshold = -1, interactivity = True, number = 100.0, inputSigma = -1,
nObj = 10, biggestObjects = True, binaryClosingIterations = 2, binaryOpeningIterations = 0,
seeds = None, cmap = matplotlib.cm.Greys_r):
"""
Inicialitacni metoda.
Input:
data - data pro prahovani, se kterymi se pracuje
voxel - velikost voxelu
threshold
interactivity - zapnuti / vypnuti gui
number - maximalni hodnota slideru pro gauss. filtrovani (max sigma)
inputSigma - pocatecni hodnota pro gauss. filtr
nObj - pocet nejvetsich objektu k vraceni
biggestObjects - oznacuje, zda se maji vracet nejvetsi objekty
binaryClosingIterations - iterace binary closing
binaryOpeningIterations - iterace binary opening
seeds - matice s kliknutim uzivatele- pokud se maji vracet specifikce objekty
cmap - grey
"""
logger.debug('Spoustim prahovani dat...')
self.inputDimension = numpy.ndim(data)
if(self.inputDimension != 3):
logger.debug('Vstup nema 3 dimenze! Ma jich ' + str(self.inputDimension) + '.')
self.errorsOccured = True
return
else:
self.errorsOccured = False
self.interactivity = interactivity
self.cmap = cmap
self.number = number
self.inputSigma = inputSigma
self.threshold = threshold
self.nObj = nObj
self.biggestObjects = biggestObjects
self.ICBinaryClosingIterations = binaryClosingIterations
self.ICBinaryOpeningIterations = binaryOpeningIterations
self.seeds = seeds
if (sys.version_info[0] < 3):
import copy
self.data = copy.copy(data)
self.voxel = copy.copy(voxel)
else:
self.data = data.copy()
self.voxel = voxel.copy()
## Kalkulace objemove jednotky (voxel) (V = a*b*c)
voxel1 = self.voxel[0]
voxel2 = self.voxel[1]
voxel3 = self.voxel[2]
self.voxelV = voxel1 * voxel2 * voxel3
self.numpyAMaxKeepDims = False
self.arrSeed = None
if self.interactivity == True:
self.fig = matpyplot.figure()
## Maximalni a minimalni pouzita hodnota prahovani v datech (bud v
## celych datech nebo vybranych seedu)
self.min0 = numpy.amin(numpy.amin(self.data, axis = 0))
if self.seeds == None:
self.max0 = numpy.amax(numpy.amax(self.data, axis = 0))
self.max0 = self.max0 + abs(abs(self.min0) - abs(self.max0)) / 10
else:
self.arrSeed = thresholding_functions.getSeeds(data, self.seeds)
## Pokud existuji vhodne labely, vytvori se nova data k
## vraceni.
## Pokud ne, vrati se "None" typ. { Deprecated: Pokud ne,
## vrati se cela nafiltrovana data, ktera do funkce prisla
## (nedojde k vraceni specifickych objektu). }
if len(self.arrSeed) > 0:
## Zbaveni se duplikatu.
self.arrSeed = list(set(self.arrSeed))
logger.debug( 'Hodnoty seedu: ')
logger.debug( self.arrSeed)
self.max0 = max(self.arrSeed)
self.max0 = self.max0 + abs(abs(self.min0) - abs(self.max0)) / 10
# Prahy
logger.debug( '')
logger.debug( 'Minimalni doporucena hodnota prahu: ' + str(min(self.arrSeed)))
logger.debug( 'Maximalni doporucena hodnota prahu: ' + str(max(self.arrSeed)))
logger.debug( '')
else:
self.max0 = numpy.amax(numpy.amax(self.data, axis = 0))
self.max0 = self.max0 + abs(abs(self.min0) - abs(self.max0)) / 10
## Pridani subplotu do okna (do figure)
self.ax1 = self.fig.add_subplot(131)
self.ax2 = self.fig.add_subplot(132)
self.ax3 = self.fig.add_subplot(133)
## Upraveni subplotu
self.fig.subplots_adjust(left = 0.1, bottom = 0.3)
## Vykreslit obrazek
self.ax1.imshow(numpy.amax(self.data, axis = 0, keepdims = self.numpyAMaxKeepDims), self.cmap)
self.ax2.imshow(numpy.amax(self.data, axis = 1, keepdims = self.numpyAMaxKeepDims), self.cmap)
self.ax3.imshow(numpy.amax(self.data, axis = 2, keepdims = self.numpyAMaxKeepDims), self.cmap)
## Zalozeni mist pro slidery
self.axcolor = 'white' # lightgoldenrodyellow
self.axmin = self.fig.add_axes([0.20, 0.24, 0.55, 0.03], axisbg = self.axcolor)
self.axmax = self.fig.add_axes([0.20, 0.20, 0.55, 0.03], axisbg = self.axcolor)
self.axclosing = self.fig.add_axes([0.20, 0.16, 0.55, 0.03], axisbg = self.axcolor)
self.axopening = self.fig.add_axes([0.20, 0.12, 0.55, 0.03], axisbg = self.axcolor)
self.axsigma = self.fig.add_axes([0.20, 0.08, 0.55, 0.03], axisbg = self.axcolor)
## Vlastni vytvoreni slideru
minBinaryClosing = 0
minBinaryOpening = 0
minSigma = 0.00
self.firstRun = True
thres = self.threshold
if thres == -1:
thres = thresholding_functions.calculateAutomaticThreshold(self.data, self.arrSeed)
self.smin = Slider(self.axmin, 'Minimal threshold ' + str(self.min0),
self.min0, self.max0, valinit = thres, dragging = True)
self.smax = Slider(self.axmax, 'Maximal threshold ' + str(self.min0),
self.min0, self.max0, valinit = self.max0, dragging = True)
if(self.ICBinaryClosingIterations >= 1):
self.sclose = Slider(self.axclosing, 'Binary closing', minBinaryClosing, 100, valinit = self.ICBinaryClosingIterations, dragging = False)
else:
self.sclose = Slider(self.axclosing, 'Binary closing', minBinaryClosing, 100, valinit = 0, dragging = False)
if(self.ICBinaryOpeningIterations >= 1):
self.sopen = Slider(self.axopening, 'Binary opening',minBinaryOpening, 100, valinit = self.ICBinaryOpeningIterations, dragging = False)
else:
self.sopen = Slider(self.axopening, 'Binary opening', minBinaryOpening, 100, valinit = 0, dragging = False)
self.ssigma = Slider(self.axsigma, 'Sigma', 0.00, self.number, valinit = self.inputSigma, dragging = False)
## Funkce slideru pri zmene jeho hodnoty
self.smin.on_changed(self.updateImage)
self.smax.on_changed(self.updateImage)
self.sclose.on_changed(self.updateImage)
self.sopen.on_changed(self.updateImage)
self.ssigma.on_changed(self.updateImage)
## Zalozeni mist pro tlacitka
self.axbuttnext1 = self.fig.add_axes([0.86, 0.24, 0.04, 0.03], axisbg = self.axcolor)
self.axbuttprev1 = self.fig.add_axes([0.81, 0.24, 0.04, 0.03], axisbg = self.axcolor)
self.axbuttnext2 = self.fig.add_axes([0.86, 0.20, 0.04, 0.03], axisbg = self.axcolor)
self.axbuttprev2 = self.fig.add_axes([0.81, 0.20, 0.04, 0.03], axisbg = self.axcolor)
self.axbuttnextclosing = self.fig.add_axes([0.86, 0.16, 0.04, 0.03], axisbg = self.axcolor)
self.axbuttprevclosing = self.fig.add_axes([0.81, 0.16, 0.04, 0.03], axisbg = self.axcolor)
self.axbuttnextopening = self.fig.add_axes([0.86, 0.12, 0.04, 0.03], axisbg = self.axcolor)
self.axbuttprevopening = self.fig.add_axes([0.81, 0.12, 0.04, 0.03], axisbg = self.axcolor)
self.axbuttreset = self.fig.add_axes([0.79, 0.08, 0.06, 0.03], axisbg = self.axcolor)
self.axbuttcontinue = self.fig.add_axes([0.86, 0.08, 0.06, 0.03], axisbg = self.axcolor)
## Zalozeni tlacitek
self.bnext1 = Button(self.axbuttnext1, '+1.0')
self.bprev1 = Button(self.axbuttprev1, '-1.0')
self.bnext2 = Button(self.axbuttnext2, '+1.0')
self.bprev2 = Button(self.axbuttprev2, '-1.0')
self.bnextclosing = Button(self.axbuttnextclosing, '+1.0')
self.bprevclosing = Button(self.axbuttprevclosing, '-1.0')
self.bnextopening = Button(self.axbuttnextopening, '+1.0')
self.bprevopening = Button(self.axbuttprevopening, '-1.0')
self.breset = Button(self.axbuttreset, 'Reset')
self.bcontinue = Button(self.axbuttcontinue, 'Next UI')
## Funkce tlacitek pri jejich aktivaci
self.bnext1.on_clicked(self.buttonMinNext)
self.bprev1.on_clicked(self.buttonMinPrev)
self.bnext2.on_clicked(self.buttonMaxNext)
self.bprev2.on_clicked(self.buttonMaxPrev)
self.bnextclosing.on_clicked(self.buttonNextClosing)
self.bprevclosing.on_clicked(self.buttonPrevClosing)
self.bnextopening.on_clicked(self.buttonNextOpening)
self.bprevopening.on_clicked(self.buttonPrevOpening)
self.breset.on_clicked(self.buttonReset)
self.bcontinue.on_clicked(self.buttonContinue)
self.smin.valtext.set_text('{}'.format(self.smin.val))
self.smax.valtext.set_text('{}'.format(self.smax.val))
def updateImage(self, val):
"""
Hlavni update metoda.
Cinny kod pro gaussovske filtrovani, prahovani, binarni uzavreni a otevreni a vraceni nejvetsich nebo oznacenych objektu.
"""
if (sys.version_info[0] < 3):
import copy
self.imgFiltering = copy.copy(self.data)
else:
self.imgFiltering = self.data.copy()
## Filtrovani
## Zjisteni jakou sigmu pouzit
if(self.firstRun == True and self.inputSigma >= 0):
sigma = numpy.round(self.inputSigma, 2)
else:
sigma = numpy.round(self.ssigma.val, 2)
sigmaNew = thresholding_functions.calculateSigma(self.voxel, sigma)
self.imgFiltering = thresholding_functions.gaussFilter(self.imgFiltering, sigmaNew)
del(sigmaNew)
## Prahovani (smin, smax)
max_threshold = -1
min_threshold = self.threshold
if self.interactivity:
self.smin.val = (numpy.round(self.smin.val, 2))
self.smin.valtext.set_text('{}'.format(self.smin.val))
self.smax.val = (numpy.round(self.smax.val, 2))
self.smax.valtext.set_text('{}'.format(self.smax.val))
min_threshold = self.smin.val
max_threshold = self.smax.val
self.threshold = min_threshold
if (self.threshold == -1) and self.firstRun:
min_threshold = thresholding_functions.calculateAutomaticThreshold(self.imgFiltering, self.arrSeed)
self.imgFiltering = thresholding_functions.thresholding(self.imgFiltering, min_threshold, max_threshold, True, self.interactivity)
## Operace binarni otevreni a uzavreni.
## Nastaveni hodnot slideru.
if (self.interactivity == True) :
closeNum = int(numpy.round(self.sclose.val, 0))
openNum = int(numpy.round(self.sopen.val, 0))
self.sclose.valtext.set_text('{}'.format(closeNum))
self.sopen.valtext.set_text('{}'.format(openNum))
else:
closeNum = self.ICBinaryClosingIterations
openNum = self.ICBinaryOpeningIterations
self.imgFiltering = thresholding_functions.binaryClosingOpening(self.imgFiltering, closeNum, openNum, True)
## Zjisteni nejvetsich objektu.
self.getBiggestObjects()
## Vykresleni dat
if (self.interactivity == True):
self.drawVisualization()
## Nastaveni kontrolnich hodnot
self.firstRun = False
garbage.collect()
self.debugInfo()