def get1DobjectsSmooth(vals,
xPos,
xText='x',
yPosDelta=0.5,
size=0.3,
vMax=None,
vMin=None,
highlight=None):
if vMin is None:
minVal = min(vals)
else:
minVal = vMin
if vMax is None:
maxVal = max(vals)
else:
maxVal = vMax
size1 = 0.2 + 0.8 * (np.array(vals) - minVal) / (maxVal - minVal)
colors = plt.cm.Blues(size1)[:, :-1]
allObj = []
for i, color in enumerate(colors):
if (highlight is not None) and (highlight != i):
color = cl.rgb_to_hsv(color)
# color[0] = 0
color[1] = 0
color = cl.hsv_to_rgb(color)
obj = sO.Cube()
obj.source.SetCenter(xPos, i * yPosDelta, 0)
obj.setSize(size * size1[i])
obj.setColor(color)
if (highlight is not None) and (highlight != i):
obj.actor.GetProperty().SetOpacity(0.2)
allObj.append(obj)
xLabel = sO.Text(f'{xText}')
xLabel.actor.SetScale(0.1, 0.1, 0.1)
xLabel.actor.SetPosition(xPos - 0.2, -1, 0)
xLabel.actor.GetProperty().SetColor(0, 0, 0)
allObj.append(xLabel)
ax1 = sO.Line((xPos, -0.4, 0), (xPos, -0.6, 0))
allObj.append(ax1)
return allObj
def createSphere():
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
allSpheres = []
allVoxels = []
for x in range(10):
for y in range(10):
for z in range(3):
sphere = sO.Sphere()
sphere.source.SetCenter(x, y, z)
sphere.source.SetRadius(0.1)
sphere.setColor([1,0,0])
sphere.setResolution(10)
allSpheres.append(sphere)
voxel = sO.Voxel()
voxel.actor.SetPosition( x-0.5, y-0.5, z-0.5 )
allVoxels.append( voxel )
myText = sO.Text('Some Text')
myText.actor.SetScale( 0.1, 0.1, 0.1 )
ren.AddActor( myText.actor )
for sphere in allSpheres:
ren.AddActor(sphere.actor)
for voxel in allVoxels:
ren.AddViewProp( voxel.actor )
renWin.SetSize(1500, 1500)
renWin.SetWindowName('Cylinder')
iren.Initialize()
ren.ResetCamera()
# ren.GetActiveCamera().Zoom(1.5)
renWin.Render()
# Start the event loop.
iren.Start()
return
def listToBin(forBin,
type='sphere',
posDelta=0.2,
vPosDelta=0.5,
startPos=0,
startStr=''):
distinct = sorted(list(set(forBin)))
distinctPos = {
k: (i * posDelta + startPos)
for i, k in enumerate(distinct)
}
NDist = len(distinct)
objects = []
for i, d in enumerate(distinct):
myText = sO.Text(f'{startStr}[{d}]')
myText.actor.SetScale(0.1, 0.1, 0.1)
myText.actor.SetPosition(startPos + i * posDelta, -1, 0)
myText.actor.GetProperty().SetColor(0, 0, 0)
myText.actor.RotateZ(-90)
objects.append(myText)
vLine = sO.Line((startPos + i * posDelta, -.4, 0),
(startPos + i * posDelta, -.6, 0))
objects.append(vLine)
vLine = sO.Line((startPos, -.5, 0),
(startPos + (NDist - 1) * posDelta, -.5, 0))
objects.append(vLine)
for i, k in enumerate(forBin):
s = sO.Sphere()
s.actor.SetScale(posDelta * 0.5)
s.actor.SetPosition(distinctPos[k], i * vPosDelta, 0)
s.actor.GetProperty().SetColor(0, 1, 0)
objects.append(s)
for j in range(NDist):
v = sO.Voxel()
v.actor.SetPosition(startPos + (j - 0.5) * posDelta,
(i - 0.5) * vPosDelta, -0.5 * posDelta)
v.actor.SetScale(posDelta, vPosDelta, posDelta)
objects.append(v)
return objects
def get2DObjects(colors2D,
sizes2D,
xPos,
xText='x',
yPosDelta=0.5,
zPosDelta=0.5,
size=0.3,
maxNz=10,
highlight=None):
allObj = []
for i, (colors, sizes) in enumerate(zip(colors2D, sizes2D)):
for j, (c, s) in enumerate(zip(colors, sizes)):
if j > maxNz:
break
if (highlight is not None) and (highlight != i):
c = cl.rgb_to_hsv(c)
# color[0] = 0
c[1] = 0
c = cl.hsv_to_rgb(c)
obj = sO.Cube()
obj.source.SetCenter(xPos, i * yPosDelta, -j * zPosDelta)
obj.setSize(size * s)
obj.setColor(c)
if (highlight is not None) and (highlight != i):
obj.actor.GetProperty().SetOpacity(0.1)
allObj.append(obj)
xLabel = sO.Text(f'{xText}')
xLabel.actor.SetScale(0.1, 0.1, 0.1)
xLabel.actor.SetPosition(xPos - 0.2, -1, 0)
xLabel.actor.GetProperty().SetColor(0, 0, 0)
allObj.append(xLabel)
ax1 = sO.Line((xPos, -0.4, 0), (xPos, -0.6, 0))
allObj.append(ax1)
return allObj
def getPatients(nPatients, xPos, yPosDelta):
allObj = []
for p in range(nPatients):
patientText = sO.Text(f'p_{p:03d}')
patientText.actor.SetScale(0.1, 0.1, 0.1)
patientText.actor.SetPosition(xPos, p * yPosDelta, 0)
patientText.actor.GetProperty().SetColor(0, 0, 0)
allObj.append(patientText)
ax = sO.Line((xPos - 0.3 - 0.1, p * yPosDelta, 0),
(xPos - 0.3 + 0.1, p * yPosDelta, 0))
allObj.append(ax)
ax = sO.Line((xPos - 0.3, 0, 0),
(xPos - 0.3, (nPatients - 1) * yPosDelta, 0))
allObj.append(ax)
return allObj
def get1Dobjects(colors,
xPos,
xText='x',
yPosDelta=0.5,
size=0.3,
highlight=None):
allObj = []
for i, color in enumerate(colors):
if (highlight is not None) and (highlight != i):
color = cl.rgb_to_hsv(color)
# color[0] = 0
color[1] = 0
color = cl.hsv_to_rgb(color)
obj = sO.Cube()
obj.source.SetCenter(xPos, i * yPosDelta, 0)
obj.setSize(size)
obj.setColor(color)
if (highlight is not None) and (highlight != i):
obj.actor.GetProperty().SetOpacity(0.2)
allObj.append(obj)
xLabel = sO.Text(f'{xText}')
xLabel.actor.SetScale(0.1, 0.1, 0.1)
xLabel.actor.SetPosition(xPos - 0.2, -1, 0)
xLabel.actor.GetProperty().SetColor(0, 0, 0)
allObj.append(xLabel)
ax1 = sO.Line((xPos, -0.4, 0), (xPos, -0.6, 0))
allObj.append(ax1)
return allObj
def getDiagnObjs(diagn,
xPos,
xText='x',
yPosDelta=0.5,
zPosDelta=0.5,
size=0.3,
highlight=None):
uniques = set([])
for ds in diagn:
for d in ds:
uniques.update(d)
uniques = sorted(list(uniques))
nUniq = len(uniques)
colors = {m: plt.cm.tab20b(i / nUniq)[:-1] for i, m in enumerate(uniques)}
poss = {m: i for i, m in enumerate(uniques)}
allObj = []
for i, patient in enumerate(diagn):
for j, day in enumerate(patient):
for k, disease in enumerate(uniques):
if disease in day:
c = colors[disease]
if (highlight is not None) and (highlight != i):
c = cl.rgb_to_hsv(c)
c[1] = 0
c = cl.hsv_to_rgb(c)
obj = sO.Cube()
obj.source.SetCenter(xPos - k * size / (nUniq),
i * yPosDelta, -j * zPosDelta)
obj.setSize(size / (nUniq + 1))
obj.setColor(c)
if (highlight is not None) and (highlight != i):
obj.actor.GetProperty().SetOpacity(0.1)
allObj.append(obj)
for i, u in enumerate(uniques):
xTick = sO.Line((xPos - i * size / (nUniq), -0.4, 0),
(xPos - i * size / (nUniq), -0.6, 0))
allObj.append(xTick)
xLabel = sO.Text(f'[{xText}]-{u}')
xLabel.actor.SetScale(0.1, 0.1, 0.1)
xLabel.actor.SetPosition(xPos - i * size / (nUniq), -1, 0)
xLabel.actor.GetProperty().SetColor(0, 0, 0)
xLabel.actor.RotateZ(-90)
allObj.append(xLabel)
xLabel = sO.Text(f'{xText}')
xLabel.actor.SetScale(0.1, 0.1, 0.1)
xLabel.actor.SetPosition(xPos - 0.6, -0.8, 0)
xLabel.actor.GetProperty().SetColor(0, 0, 0)
allObj.append(xLabel)
ax = sO.Line((xPos, -0.5, 0),
(xPos - (nUniq - 1) * size / (nUniq), -0.5, 0))
allObj.append(ax)
return allObj
def plot2D(config):
bgColor = [217 / 255, 211 / 255, 232 / 255]
# bgColor = [219/255, 225/255, 235/255]
Npatients = 10
data = getData()[:Npatients + 1]
header = data[0]
data = data[1:]
site, patient, sex, race = zip(*data)
N = len(site)
ren.SetBackground(bgColor)
renWin.AddRenderer(ren)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
sexColors = colorMapper(sex)
raceColors = colorMapper(race)
siteColors = colorMapper(site)
if config['ohe']:
for m in listToBin(sex, posDelta=0.4, startPos=4, startStr='sex'):
ren.AddActor(m.actor)
for m in listToBin(race, posDelta=0.4, startPos=5, startStr='race'):
ren.AddActor(m.actor)
# Render the x-axes
ax1 = sO.Line((1, -0.5, 0), (3, -0.5, 0))
ren.AddActor(ax1.actor)
for i in range(3):
ax1 = sO.Line((i + 1, -0.4, 0), (i + 1, -0.6, 0))
ren.AddActor(ax1.actor)
# Render the y-axes
ax1 = sO.Line((0, 0, 0), (0, (Npatients - 1) * 0.5, 0))
ren.AddActor(ax1.actor)
for i in range(Npatients):
ax1 = sO.Line((-0.1, i * 0.5, 0), (0.1, i * 0.5, 0))
ren.AddActor(ax1.actor)
for patient in range(Npatients):
# Set the names for the patients
myText = sO.Text(f'p_{patient:04d}')
myText.actor.SetScale(0.1, 0.1, 0.1)
myText.actor.SetPosition(-1, patient * 0.5, 0)
myText.actor.GetProperty().SetColor(0, 0, 0)
ren.AddActor(myText.actor)
# set the cohort values
cohort = sO.Sphere()
cohort.actor.SetScale(0.3)
cohort.actor.SetPosition(1, patient * 0.5, 0)
cohort.setColor((0, 1, 0))
ren.AddActor(cohort.actor)
# set the sex values
sex = sO.Cube()
sex.source.SetCenter(2, patient * 0.5, 0)
sex.setSize(0.3)
sex.setColor(sexColors[patient])
ren.AddActor(sex.actor)
# set the race values
race = sO.Cube()
race.source.SetCenter(3, patient * 0.5, 0)
race.setSize(0.3)
race.setColor(raceColors[patient])
ren.AddActor(race.actor)
# Set the names for the axes
for pos, dataType in enumerate(['cohort', 'sex ', 'race']):
myText = sO.Text(f'{dataType}')
myText.actor.SetScale(0.1, 0.1, 0.1)
myText.actor.SetPosition(pos + 0.8, -1, 0)
myText.actor.GetProperty().SetColor(0, 0, 0)
ren.AddActor(myText.actor)
renWin.SetSize(900, 900)
renWin.SetWindowName('Cylinder')
iren.AddObserver("KeyPressEvent", Keypress)
iren.Initialize()
ren.ResetCamera()
restoreCammeraSpecs('../results/cameraPos/latest2D.json')
renWin.Render()
# Start the event loop.
iren.Start()
return