def test_show_draw_and_pickup_segmentation_label(self):
"""
just run editor to see what is new
Returns:
"""
app = QApplication(sys.argv)
data = (np.random.rand(30, 31, 32) * 100).astype(np.int)
data[15:40, 13:20, 10:18] += 50
segmentation = np.zeros_like(data)
segmentation[15:40, 13:20, 10:18] = 1
se = seededitorqt.QTSeedEditor(data, contours=segmentation)
se.selectSlice(20)
se.slice_box.seed_mark = 3 # seed 3
se.slice_box.last_position = [1, 3]
se.slice_box.drawSeeds([10, 5])
se.slice_box.seed_mark = 2 # left mouse button
se.slice_box.last_position = [8, 1]
se.slice_box.drawSeeds([7, 5])
# try to pick up seed from slice
se.slice_box._pick_up_segmentation_label([16, 16])
# self.assertEqual(se.textFocusedSeedLabel, "3", "Pickuped value")
idx = se.combo_segmentation_label.currentIndex()
logger.debug("idx {}".format(idx))
self.assertEqual(idx, 1, "Picked up value")
se.change_focus_segmentation_label(0)
idx = se.combo_segmentation_label.currentIndex()
logger.debug("idx {}".format(idx))
self.assertEqual(idx, 0, "Changed value")
def test_devel_vein_basin_segmentation(self):
pth = r"E:\data\medical\processed\mik2018 para\P09_paraall_cropped.pklz"
datap = io3d.read(pth)
labels = {
"1": 1,
"2": 2,
"3": 3,
"4": 4,
"5": 5,
"6": 6,
}
from PyQt4.QtGui import QApplication, QPushButton
app = QApplication(sys.argv)
import seededitorqt
se = seededitorqt.QTSeedEditor(datap["data3d"],
contours=datap["segmentation"])
def split(obj):
import lisa.virtual_resection as vr
print(np.max(datap["data3d"]))
print(np.unique(se.seeds))
out, sepobj = vr.split_vessel(datap,
se.seeds,
method="separate labels",
input_seeds_label2=2)
print(np.unique(out))
se.seeds = out
se.contours = out
se.setView(se.actual_view)
qpb = QPushButton("Ahoj")
qpb.clicked.connect(split)
wg = se.my_layout.layout().itemAt(0).itemAt(2).addWidget(qpb)
se.exec_()
def test_show_editor_with_seeds(self):
"""
just run editor to see what is new
Returns:
"""
img, segm, seeds = self.make_data()
app = QApplication(sys.argv)
se = seededitorqt.QTSeedEditor(img, seeds=seeds)
# se.exec_()
assert np.max(se.seeds) > 0
def test_show_editor_with_too_much_wide_data(self):
"""
just run editor to see what is new
Returns:
"""
app = QApplication(sys.argv)
data = (np.random.rand(30, 31, 150) * 100).astype(np.int)
data[15:40, 13:20, 10:18] += 50
se = seededitorqt.QTSeedEditor(data)
se.exec_()
def test_addplugin(self):
"""
just run editor to see what is new
Returns:
"""
app = QApplication(sys.argv)
data = (np.random.rand(30, 31, 32) * 100).astype(np.int)
data[15:40, 13:20, 10:18] += 50
se = seededitorqt.QTSeedEditor(data)
wg0 = seededitorqt.plugin.SampleThresholdPlugin()
se.addPlugin(wg0)
def test_draw_seed_function(self):
"""
just run editor to see what is new
Returns:
"""
app = QApplication(sys.argv)
data = (np.random.rand(30, 31, 32) * 100).astype(np.int)
data[15:40, 13:20, 10:18] += 50
se = seededitorqt.QTSeedEditor(data)
se.slice_box.seed_mark = 1 # left mouse button
se.slice_box.last_position = [1, 3]
se.slice_box.drawSeeds([10, 5])
se.slice_box.seed_mark = 2 # left mouse button
se.slice_box.last_position = [8, 1]
se.slice_box.drawSeeds([7, 5])
def test_show_editor_with_seeds_custom_colors(self):
"""
just run editor to see what is new
Returns:
"""
img, segm, seeds = self.make_data()
app = QApplication(sys.argv)
seeds_colortable = seededitorqt.seed_editor_qt.SEEDS_COLORTABLE.copy()
# BGRA
seeds_colortable[0] = [255, 0, 0, 64]
seeds_colortable[1] = [0, 255, 0, 64]
seeds_colortable[2] = [0, 0, 255, 64]
seeds_colortable[3] = [0, 255, 255, 64]
seeds_colortable[4] = [255, 0, 255, 64]
seeds_colortable[5] = [255, 255, 0, 64]
se = seededitorqt.QTSeedEditor(img, seeds=seeds, contours=segm.astype(np.uint8), seeds_colortable=seeds_colortable)
# se.exec_()
assert se.slice_box.seeds_colortable[1][1] == 255
assert np.max(se.seeds) > 0
def test_show_draw_and_pickup_seed(self):
"""
just run editor to see what is new
Returns:
"""
app = QApplication(sys.argv)
data = (np.random.rand(30, 31, 32) * 100).astype(np.int)
data[15:40, 13:20, 10:18] += 50
se = seededitorqt.QTSeedEditor(data)
se.slice_box.seed_mark = 3 # seed 3
se.slice_box.last_position = [1, 3]
se.slice_box.drawSeeds([10, 5])
se.slice_box.seed_mark = 2 # left mouse button
se.slice_box.last_position = [8, 1]
se.slice_box.drawSeeds([7, 5])
# try to pick up seed from slice
se.slice_box._pick_up_seed_label([1, 3])
self.assertEqual(se.textFocusedSeedLabel, "3", "Pickuped value")
se.change_focus_seed_label(2)
self.assertEqual(se.textFocusedSeedLabel, "2", "Changed value")
def vesselSegmentation(data,
segmentation=-1,
threshold=None,
voxelsize_mm=[1, 1, 1],
inputSigma=-1,
aoi_dilation_iterations=0,
aoi_dilation_structure=None,
nObj=10,
biggestObjects=False,
useSeedsOfCompactObjects=False,
seeds=None,
interactivity=True,
binaryClosingIterations=2,
binaryOpeningIterations=0,
smartInitBinaryOperations=False,
returnThreshold=False,
binaryOutput=True,
returnUsedData=False,
qapp=None,
auto_method='',
aoi_label=1,
forbidden_label=None,
slab=None,
old_gui=False,
debug=False):
"""
Vessel segmentation z jater.
Input:
:param data: - CT (nebo MRI) 3D data
:param segmentation: - zakladni oblast pro segmentaci, oznacena struktura se
:param stejnymi: rozmery jako "data",
kde je oznaceni (label) jako:
1 jatra,
-1 zajimava tkan (kosti, ...)
0 jinde
:param threshold: - prah
:param voxelsize_mm: - (vektor o hodnote 3) rozmery jednoho voxelu
:param inputSigma: - pocatecni hodnota pro prahovani
:param aoi_dilation_iterations: - pocet operaci dilation nad zakladni oblasti pro
segmentaci ("segmantation")
:param aoi_dilation_structure: - struktura pro operaci dilation
:param nObj: - oznacuje, kolik nejvetsich objektu se ma vyhledat - pokud je
rovno 0 (nule), vraci cela data
:param biggestObjects: - moznost, zda se maji vracet nejvetsi objekty nebo ne
:param seeds: - moznost zadat pocatecni body segmentace na vstupu. Je to matice
o rozmerech jako data. Vsude nuly, tam kde je oznaceni jsou jednicky
It can be same shape like data, or it can be
indexes e.g. from np.nonzero(seeds)
:param interactivity: - nastavi, zda ma nebo nema byt pouzit interaktivni mod
upravy dat
:param binaryClosingIterations: - vstupni binary closing operations
:param binaryOpeningIterations: - vstupni binary opening operations
:param smartInitBinaryOperations: - logicka hodnota pro smart volbu pocatecnich
hodnot binarnich operaci (bin. uzavreni a bin. otevreni)
:param returnThreshold: - jako druhy parametr funkce vrati posledni hodnotu
prahu
:param binaryOutput: - zda ma byt vystup vracen binarne nebo ne (binarnim
vystupem se rozumi: cokoliv jineho nez hodnota 0 je hodnota 1)
:param returnUsedData: - vrati pouzita data
:param aoi_label: label of organ where is the target vessel
:param forbidden_label: int or list of ints. Labels of areas which are not used for segmentation.
Output:
filtrovana data
"""
# self.qapp = qapp
dim = numpy.ndim(data)
logger.debug('Dimenze vstupnich dat: ' + str(dim))
if (dim < 2) or (dim > 3):
logger.debug('Nepodporovana dimenze dat!')
logger.debug('Ukonceni funkce!')
return None
if seeds is None:
logger.debug('Funkce spustena bez prioritnich objektu!')
if biggestObjects:
logger.debug(
'Funkce spustena s vracenim nejvetsich objektu => nebude mozne\
vybrat prioritni objekty!')
if (nObj < 1):
nObj = 1
if biggestObjects:
logger.debug('Vybrano objektu k vraceni: ' + str(nObj))
logger.debug('Pripravuji data...')
voxel = numpy.array(voxelsize_mm)
# Kalkulace objemove jednotky (voxel) (V = a*b*c).
voxel1 = voxel[0] # [0]
voxel2 = voxel[1] # [0]
voxel3 = voxel[2] # [0]
voxelV = voxel1 * voxel2 * voxel3
# number je zaokrohleny 2x nasobek objemove jednotky na 2 desetinna mista.
# number stanovi doporucenou horni hranici parametru gauss. filtru.
number = (numpy.round((2 * voxelV**(1.0 / 3.0)), 2))
if aoi_label is None:
target_organ_segmentation = np.ones(segmentation.shape)
else:
target_organ_segmentation = image_manipulation.select_labels(
segmentation, aoi_label, slab)
# Operace dilatace (dilation) nad samotnymi jatry ("segmentation").
if (aoi_dilation_iterations > 0.0):
target_organ_segmentation = scipy.ndimage.binary_dilation(
input=target_organ_segmentation,
structure=aoi_dilation_structure,
iterations=aoi_dilation_iterations)
# remove forbidden areas from segmentation
if forbidden_label is not None:
forbidden_organ_segmentation = image_manipulation.select_labels(
segmentation, forbidden_label, slab)
target_organ_segmentation[forbidden_organ_segmentation] = 0
del (forbidden_organ_segmentation)
# Ziskani datove oblasti jater (bud pouze jater nebo i jejich okoli -
# zalezi, jakym zpusobem bylo nalozeno s operaci dilatace dat).
preparedData = (data * (target_organ_segmentation)) # .astype(numpy.float)
logger.debug('Typ vstupnich dat: ' + str(preparedData.dtype))
# if preparedData.dtype != numpy.uint8:
# print 'Data nejsou typu numpy.uint8 => muze dojit k errorum'
if not numpy.can_cast(preparedData.dtype, numpy.float):
logger.debug(
'ERROR: (debug message) Data nejsou takoveho typu, aby se daly \
prevest na typ "numpy.float" => muze dojit k errorum')
logger.debug('Ukoncuji funkci!')
raise ValueError("Cannot cast input data to numpy.float")
return None
if (preparedData == False).all():
logger.debug(
'ERROR: (debug message) Jsou spatna data nebo segmentacni matice: \
all is true == data is all false == bad segmentation matrix (if data matrix is \
ok)')
logger.debug('Ukoncuji funkci!')
raise ValueError(
"Wrong input data. All is true == data is all false == bad segmentation matrix (if data matrix is ok)"
)
return None
# del(data)
# del(segmentation)
# Nastaveni rozmazani a prahovani dat.
if (inputSigma == -1):
inputSigma = number
if (inputSigma > number):
inputSigma = number
# seeds = None
if biggestObjects == False and\
seeds is None and interactivity == True and threshold is None:
if old_gui:
logger.debug((
'Nyni si levym nebo pravym tlacitkem mysi (klepnutim nebo tazenim)\
oznacte specificke oblasti k vraceni.'))
import sed3
pyed = sed3.sed3qt(preparedData,
contour=segmentation,
windowW=400,
windowC=50)
# pyed.show()
pyed.exec_()
# from PyQt4.QtCore import pyqtRemoveInputHook
# pyqtRemoveInputHook()
# import ipdb; ipdb.set_trace() # noqa BREAKPOINT
seeds = pyed.seeds
# Zkontrolovat, jestli uzivatel neco vybral - nejaky item musi byt
# ruzny od nuly.
if (seeds != 0).any() == False:
seeds = None
logger.debug(
'Zadne seedy nezvoleny => nejsou prioritni objekty.')
else:
# seeds * (seeds != 0) ## seeds je n-tice poli indexu nenulovych
# prvku => item krychle je == krychle[ seeds[0][x], seeds[1][x],
# seeds[2][x] ]
seeds = seeds.nonzero()
logger.debug('Seedu bez nul: ' + str(len(seeds[0])))
closing = binaryClosingIterations
opening = binaryOpeningIterations
if (smartInitBinaryOperations and interactivity):
if (seeds == None): # noqa
closing = 5
opening = 1
else:
closing = 2
opening = 0
# Samotne filtrovani
if interactivity:
if old_gui:
uiT = uiThreshold.uiThresholdQt(
preparedData,
voxel=voxel,
threshold=threshold,
interactivity=interactivity,
number=number,
inputSigma=inputSigma,
nObj=nObj,
biggestObjects=biggestObjects,
useSeedsOfCompactObjects=useSeedsOfCompactObjects,
binaryClosingIterations=closing,
binaryOpeningIterations=opening,
seeds=seeds,
threshold_auto_method=auto_method,
)
output = uiT.run()
else:
# TODO use all parameters
import seededitorqt
se = seededitorqt.QTSeedEditor(preparedData, voxelSize=voxel)
import imtools.threshold_qsed_plugin
wg0 = imtools.threshold_qsed_plugin.QtSEdThresholdPlugin(
nObj=nObj, debug=debug)
se.addPlugin(wg0)
se.exec_()
output = se.getContours()
else:
uiT = uiThreshold.uiThreshold(
preparedData,
voxel=voxel,
threshold=threshold,
interactivity=interactivity,
number=number,
inputSigma=inputSigma,
nObj=nObj,
biggestObjects=biggestObjects,
useSeedsOfCompactObjects=useSeedsOfCompactObjects,
binaryClosingIterations=closing,
binaryOpeningIterations=opening,
seeds=seeds,
threshold_auto_method=auto_method,
)
output = uiT.run()
# Vypocet binarni matice.
if output is None: # noqa
logger.debug('Zadna data k vraceni! (output == None)')
elif binaryOutput:
output[output != 0] = 1
# Vraceni matice.
if returnThreshold:
if returnUsedData:
return preparedData, output, uiT.returnLastThreshold()
else:
return output, uiT.returnLastThreshold()
else:
if returnUsedData:
return preparedData, output
else:
return output
