def extract(self, experiment, variant, indiv):
filepath = experiment[2] + os.path.sep + PathConfig.populationFolderNormal + os.path.sep + indiv[0] + "_vox.vxa"
if not os.path.isfile(filepath):
return ['NA'] * 3
vd = VoxelData(filepath)
dnaMatrix = vd.getDNAmatrix()
if type(dnaMatrix) == types.BooleanType and not dnaMatrix:
return ['NA'] * 3
toCheck = []
for x in range(10):
for y in range(10):
for z in range(10):
if int(dnaMatrix[z, y, x]) in [3, 4]:
val = int(dnaMatrix[z, y, x])
mirrors = [
(x, y, z),
(9 - x, y, z),
(x, 9 - y, z),
(x, y, 9 - z),
(y, x, z),
(x, z, y),
(z, y, x),
(9 - y, 9 - x, z),
(x, 9 - z, 9 - y),
(9 - z, y, 9 - x)
]
mirrors = list(set(mirrors))
cellHash = str(x) + '-' + str(y) + '-' + str(z)
toCheck += zip(mirrors, [val] * len(mirrors), [cellHash] * len(mirrors))
sameExisting = 0
missing = 0
counterExisting = 0
musclesChecked = []
for toCheckLocation in toCheck:
val = toCheckLocation[1]
knownMuscle = False
if toCheckLocation[2] in musclesChecked:
knownMuscle = True
opposite = 4
if val == 4:
opposite = 3
x, y, z = toCheckLocation[0]
if int(dnaMatrix[x, y, z]) == val:
sameExisting += 1
elif int(dnaMatrix[x, y, z]) == opposite:
counterExisting += 1
else:
if not knownMuscle:
missing += 1
if not knownMuscle:
musclesChecked.append(toCheckLocation[2])
return [sameExisting, counterExisting, missing]
def extract(self, experiment, type, indiv):
filepath = experiment[2] + os.path.sep + PathConfig.populationFolderNormal + os.path.sep + indiv[0] + "_vox.vxa"
if os.path.isfile(filepath):
vd = VoxelData(filepath)
lifetime = vd.getLifeTime()
if not lifetime:
return ['NA']
return [lifetime]
else:
return ['NA']
def extract(self, experiment, type, indiv):
noResultVal = ['NA', 'NA', 'NA']
filepath = experiment[2] + os.path.sep + PathConfig.populationFolderNormal + os.path.sep + indiv[0] + "_vox.vxa"
if os.path.isfile(filepath):
vd = VoxelData(filepath)
relCounts = vd.getRelCounts()
if not relCounts:
return noResultVal
return [relCounts["fat"], relCounts["muscle"], relCounts["bone"]]
else:
return noResultVal
def extract(self, experiment, type, indiv):
noResultVal = ["NA", "NA", "NA"]
filepath = GetAltFile.getAltPopFile(experiment, type, indiv)
if filepath != False:
vd = VoxelData(filepath)
relCounts = vd.getRelCounts()
if not relCounts:
return noResultVal
return [relCounts["fat"], relCounts["muscle"], relCounts["bone"]]
else:
return noResultVal
def extract(self, experiment, type, indiv):
filepath = experiment[2] + os.path.sep + PathConfig.populationFolderNormal + os.path.sep + indiv[0] + "_vox.vxa"
if os.path.isfile(filepath):
vd = VoxelData(filepath)
absCounts = vd.getAbsCounts()
if not absCounts:
return ['NA']
probability = (absCounts["fat"] / 1000.0) * 0.5
return [probability]
else:
return ['NA']
def extract(self, experiment, type, indiv):
noResultVal = ['NA'] * 4
filepath = GetAltFile.getAltPopFile(experiment, type, indiv)
if filepath != False:
vd = VoxelData(filepath)
absCounts = vd.getAbsCounts()
if not absCounts:
return noResultVal
return [absCounts["fat"], absCounts["muscle"], absCounts["bone"], sum(absCounts.values())]
else:
return noResultVal
def extract(self, experiment, type, indiv):
noResultVal = ['NA'] * 4
filepath = experiment[2] + os.path.sep + PathConfig.populationFolderNormal + os.path.sep + indiv[0] + "_vox.vxa"
if os.path.isfile(filepath):
vd = VoxelData(filepath)
absCounts = vd.getAbsCounts()
if not absCounts:
return noResultVal
return [absCounts["fat"], absCounts["muscle"], absCounts["bone"], sum(absCounts.values())]
else:
return noResultVal
def extract(self, experiment, variant, indiv):
filepath = experiment[2] + os.path.sep + PathConfig.populationFolderNormal + os.path.sep + indiv[0] + "_vox.vxa"
if not os.path.isfile(filepath):
return ['NA'] * 6
vd = VoxelData(filepath)
dnaMatrix = vd.getDNAmatrix()
if type(dnaMatrix) == types.BooleanType and not dnaMatrix:
return ['NA'] * 6
muscleBottom = 0
for x in range(10):
for y in range(10):
for z in range(3):
if int(dnaMatrix[z, y, x]) in [3, 4]:
muscleBottom += 1
muscleTop = 0
for x in range(10):
for y in range(10):
for z in range(3):
if int(dnaMatrix[z + 7, y, x]) in [3, 4]:
muscleTop += 1
muscleCenter = 0
for x in range(4):
for y in range(4):
for z in range(4):
if int(dnaMatrix[z + 3, y + 3, x + 3]) in [3, 4]:
muscleCenter += 1
muscleOuter = 0
for x in [0, 1, 8, 9]:
for y in [0, 1, 8, 9]:
for z in [0, 1, 8, 9]:
if int(dnaMatrix[z, y, x]) in [3, 4]:
muscleOuter += 1
muscleTotal = vd.dna.count("3") + vd.dna.count("4")
if muscleTotal > 0:
muscleCenterRel = float(muscleCenter) / muscleTotal
muscleOuterRel = float(muscleOuter) / muscleTotal
else:
muscleCenterRel = 0.0
muscleOuterRel = 0.0
return [muscleBottom, muscleTop, muscleCenter, muscleOuter, muscleCenterRel, muscleOuterRel]
def extract(self, experiment, type, indiv):
filepath = experiment[2] + os.path.sep + PathConfig.populationFolderNormal + os.path.sep + indiv[0] + "_vox.vxa"
if not os.path.isfile(filepath):
return ['NA']
vd = VoxelData(filepath)
dnaMatrix = vd.getDNAmatrix().astype(int)
H = 0
total = 1000
for i in range(5):
count = (dnaMatrix == i).sum()
p_i = count/total
if p_i == 0:
H -= 0
else:
H -= p_i * math.log(p_i,2)
return [H]
def extract(self, experiment, type, indiv):
filepath = experiment[2] + os.path.sep + PathConfig.populationFolderNormal + os.path.sep + indiv[0] + "_vox.vxa"
if not os.path.isfile(filepath):
return ["NA"] * 4
vd = VoxelData(filepath)
dnaMatrix = vd.getDNAmatrix()
if isinstance(dnaMatrix, bool):
return ["NA"] * 4
dnaMatrix = dnaMatrix.astype(int)
ratio, triangles = self.calc_complexity(dnaMatrix)
limbs = self.calc_limbs(dnaMatrix)
ratio_norm = ratio # No normalization because values are already 0..1
triangles_norm = (triangles - 12) / (70 - 12) # Normalization according to the data used to generate PCAvector
limbs_norm = (limbs - 1) / (5 - 1) # Normalization according to the data used to generate PCAvector
shapeComplexity = np.dot(self.PCAvector, np.array([ratio_norm, triangles_norm, limbs_norm]))
return [ratio, triangles, limbs, shapeComplexity]
def extract(self, experiment, variant, indiv):
filepath = experiment[2] + os.path.sep + PathConfig.populationFolderNormal + os.path.sep + indiv[0] + "_vox.vxa"
if os.path.isfile(filepath):
vd = VoxelData(filepath)
dnaMatrix = vd.getDNAmatrix()
if type(dnaMatrix) == types.BooleanType and not dnaMatrix:
return ['NA'] * 6
zMin = 9999
zMax = 0
for x in range(10):
for y in range(10):
zColumn = [cell for cell in dnaMatrix[:, y, x] if cell != "0"]
zMax = max(len(zColumn), zMax)
zMin = min(len(zColumn), zMin)
yMin = 9999
yMax = 0
for x in range(10):
for z in range(10):
yColumn = [cell for cell in dnaMatrix[z, :, x] if cell != "0"]
yMax = max(len(yColumn), yMax)
yMin = min(len(yColumn), yMin)
xMin = 9999
xMax = 0
for z in range(10):
for y in range(10):
xColumn = [cell for cell in dnaMatrix[z, y, :] if cell != "0"]
xMax = max(len(xColumn), xMax)
xMin = min(len(xColumn), xMin)
return [xMax, yMax, zMax, xMin, yMin, zMin]
else:
return ['NA'] * 6
