def gazePointsToHeatmaps(self):
self.XYHeatmap = []
self.XZHeatmap = []
for sx in range(self.gaze_points.shape[2]):
XYG = []
XZG = []
for f in range(self.gaze_points.shape[0]):
d = self.gaze_points[f, :, sx]
xyg = self.gaussian(mu=d[0], max=self.frame_size[0])
xzg = self.gaussian(mu=d[1], max=self.frame_size[1])
XYG.append(xyg)
XZG.append(xzg)
self.XYHeatmap.append(np.array(XYG))
self.XZHeatmap.append(np.array(XZG))
self.XYHeatmap = np.sum(self.XYHeatmap, 0)
self.XZHeatmap = np.sum(self.XZHeatmap, 0)
self.XYHeatmap = gl.GLImageItem(self.getColors(self.XYHeatmap, cm.jet))
self.XZHeatmap = gl.GLImageItem(self.getColors(self.XZHeatmap, cm.jet))
self.XYHeatmap.scale(self.image_spacing, 1, 1)
self.XZHeatmap.scale(self.image_spacing, 1, 1)
self.XYHeatmap.rotate(90, -1, 0, 0)
self.XYHeatmap.translate(0, -50 * self.scaling_factor, 0)
self.XZHeatmap.translate(
0, 0, -self.frame_size[0] - 50 * self.scaling_factor)
def mkTexture(w, img, T):
W = img.shape[1]
if img.shape[2] == 3:
obj = gl.GLImageItem(data=img2tex(img.transpose(1, 0, 2)))
else:
obj = gl.GLImageItem(data=img2texA(img.transpose(1, 0, 2)))
w.addItem(obj)
S = scale((1 / W, 1 / W, 1))
D = desp((0, 0, -DC))
def update(H):
transform(D @ H @ T @ S, obj)
return update
def loadFrameByNumber(self,
number,
rotation=[90, 0, 1, 0],
x_shift=0,
y_shift=0,
option='translucent'):
# list and sort all frames in folder
frame_paths = sorted(listdir(self.image_path))
frame_paths = [path.join(self.image_path, p) for p in frame_paths]
if number >= len(frame_paths):
return None
frame = misc.imread(frame_paths[number])
if not self.scaling_factor == 1.:
frame = misc.imresize(frame, self.scaling_factor)
if self.frame_size is None:
self.frame_size = frame.shape[:2]
self.z_shift = 0 #self.frame_size[0]
# convert frame into RGBA image
frame = pg.makeRGBA(frame, levels=[frame.min(), frame.max()])[0]
frame = gl.GLImageItem(frame)
frame.rotate(rotation[0], rotation[1], rotation[2], rotation[3])
frame.translate(number * self.image_spacing + x_shift, y_shift,
self.z_shift)
frame.setGLOptions(option)
return frame
def _initialize_planes(self):
""" Create the xy plane, the arbitrary cut plane and the view in the
selector panel.
"""
# xy
super()._initialize_planes()
# selector
xy = self.get_xy_slice(0)
self.selector.set_image(xy, lut=self.lut)
# cutline in selector
if not hasattr(self, 'cutline'):
self.cutline = Cutline(self.selector)
self.cutline.initialize()
# cut plane
if hasattr(self, 'cutplane'):
self.glview.removeItem(self.cutplane)
cut, coords = self.get_cutline_cut()
cut_texture = self.make_texture(cut)
self.cutplane = gl.GLImageItem(cut_texture, glOptions=self.gloptions)
# Scale and move to origin in upright position
self.cutplane.scale(self.xscale, self.zscale, 1)
self.cutplane.rotate(90, 1, 0, 0)
self.cutplane.translate(T, 0, T)
self.transform0 = self.cutplane.transform()
self.glview.addItem(self.cutplane)
self.cutline.sig_region_changed.connect(self.update_cut)
def prepare_RA(w, size, fov, dist=20):
WIDTH, HEIGHT = size
# Ponemos el punto de vista de la visualización gráfica en el origen del sistema
# de referencia, con elevación y azimuth de modo que el eje x apunte hacia la
# derecha, el eje y hacia abajo y el eje z mirando hacia delante.
# Es la posición "inicial" de una cámara en el origen.
# (ponemos distancia > 0 que luego se compensa porque cero da problemas)
setCameraPosition(w, distance=DC, elevation=-90, azimuth=-90, fov=fov)
# Preparamos el objeto textura que contendrá la imagen de cámara en vivo. La vamos
# a situar centrada delante del punto de vista del visor gráfico, a la distancia
# justa para que ocupe toda la ventana, teniendo en cuenta el FOV. Es el fondo
# de la escena, delante pondremos los objetos virtuales.
W2 = WIDTH / 2
d = dist
s = (d + DC) / W2 * np.tan(np.radians(fov) / 2)
camera_image = gl.GLImageItem(data=np.zeros([100, 100, 4]))
transform(
scale((s, s, 1)) @ desp((-WIDTH // 2, -HEIGHT // 2, d)), camera_image)
w.addItem(camera_image)
def update(frame):
camera_image.setData(data=img2tex(frame.transpose(1, 0, 2)))
return update
def updateXY(self):
try:
self.w.removeItem(self.v3)
except:
pass
tex3 = pg.makeRGBA(self.data[:,:,self.slice3], levels=self.levels)[0] # xy plane
self.v3 = gl.GLImageItem(tex3)
self.v3.translate(-self.slice1, -self.slice2, 0)
self.w.addItem(self.v3)
return
def updateXZ(self):
try:
self.w.removeItem(self.v2)
except:
pass
tex2 = pg.makeRGBA(self.data[:,self.slice2], levels=self.levels)[0] # xz plane
self.v2 = gl.GLImageItem(tex2)
self.v2.translate(-self.slice1, -self.slice3, 0)
self.v2.rotate(-90, 1,0,0)
self.w.addItem(self.v2)
return
def updateYZ(self):
try:
self.w.removeItem(self.v1)
except:
pass
tex1 = pg.makeRGBA(self.data[self.slice1], levels=self.levels)[0] # yz plane
self.v1 = gl.GLImageItem(tex1)
self.v1.translate(-self.slice2, -self.slice3, 0)
self.v1.rotate(90, 0,0,1)
self.v1.rotate(-90, 0,1,0)
self.w.addItem(self.v1)
return
def slice(self):
if( len(self.mesh) == 0):
self.message('Load mesh first!')
return
self.slices.clear()
curdir = os.getcwd()
if(path.isdir("images")):
#remove all files in images
filelist = [ f for f in os.listdir("./images") if f.endswith(".png") ]
for f in filelist:
os.remove(os.path.join(curdir+"/images", f))
else:
os.mkdir("images")
self.out_path = os.path.join(curdir, "images/slice-%d.png")
self.message('Slicing mesh...')
self.update_var()
self.mesh_info.first_layer_thicknes = self.conf.get("first_layer_thickness")
self.mesh_info.layer_thickness = self.conf.get("layer_thickness")
nLayer = self.mesh_info.get_layers()
z_list = self.mesh_info.get_z_list()
str_layers = str(nLayer)
x_pixel_size, y_pixel_size, x0, y0 = stl2pngfunc.stl2png(self.mesh_info.path,
z_list,
self.mesh_info.image_width, self.mesh_info.image_height,
self.out_path,
self.mesh_info.border_size,
func = lambda i: self.message("slicing layer " + str(i+1) + "/" + str_layers, False)
)
self.mesh_info.real_pixel_size, self.mesh_info.real_pixel_size, self.gcode_minx, self.gcode_miny = x_pixel_size, y_pixel_size, x0, y0
self.message('Slicing mesh into ' + self.out_path)
self.message(self.mesh_info.get_info() )
im = cv2.imread(self.out_path % 0)
tex1 = cv2.cvtColor(im, cv2.COLOR_BGR2RGBA)
v1 = gl.GLImageItem(tex1)
v1.translate(0, 0, 0)
self.view_slice.addItem(v1)
# activate slider
self.sl.setMinimum(0)
self.sl.setMaximum(self.mesh_info.get_layers() - 1)
self.sl.setValue(0)
self.sl.setTickPosition(QSlider.TicksBelow)
self.sl.setTickInterval(1)
self.sl.valueChanged.connect(self.show_slice)
return
def show_slice(self):
i = self.sl.value()
self.message("Show slice {}.".format(i+1), False)
curdir = os.getcwd()
im = cv2.imread(self.out_path % i)
#self.slices[i] = im
tex1 = cv2.cvtColor(im, cv2.COLOR_BGR2RGBA)
v1 = gl.GLImageItem(tex1)
v1.translate(0, 0, i * self.mesh_info.layer_thickness)
self.view_slice.items = []
self.view_slice.addItem(v1)
def updateXZ(self):
try:
self.w.removeItem(self.v2)
except:
pass
tex2 = pg.makeRGBA(self.data[:,self.slice2], levels=self.levels)[0] # xz plane
self.v2 = gl.GLImageItem(tex2)
#self.v2.translate(-self.slice1, -self.slice3, int(self.shape[1]/2)-self.slice2)
self.v2.translate(-self.slice1, -self.slice3, -int(self.shape[1]/2)+self.slice2)
self.v2.rotate(-90, 1,0,0)
#self.v2.scale(-1, 1, 1, local=False) #fliplr
self.w.addItem(self.v2)
return
def loadKeyFrames(self, key_frame_list, rotation=[90, 0, 1, 0], scale=.5):
self.keyFrames = []
for kf in key_frame_list:
if kf >= len(self.frames) or kf < 0:
print('key frame value not in list: {0}'.format(kf))
continue
data = self.frames[kf].data.copy()
keyFrame = gl.GLImageItem(data)
keyFrame.rotate(*rotation)
keyFrame.scale(scale, scale, 1)
keyFrame.translate(self.image_spacing * kf,
self.frame_size[1] * 1.15, 0)
#-self.frame_size[0]*1.15)
self.keyFrames.append(keyFrame)
def img2glimage(img_path, gloptions):
imgarr, sizex, sizey, xcols, yrows, midpt = image2array(img_path)
v1 = gl.GLImageItem(imgarr)
sx = sizex / xcols
sy = sizey / yrows
v1.scale(sx, sy, 0)
dx = sizex / 2 #sizex/2
dy = sizey / 2 #sizey/2
v1.translate(-1 * dx, -1 * dy, 0)
v1.rotate(180, 0, 1, 0)
v1.rotate(180, 0, 0, 1)
v1.translate(midpt[0], midpt[1], 0)
v1.setGLOptions(gloptions)
return v1
def fill(self):
try:
i = self.sl.value()
self.message("Show slice {}.".format(i + 1), False)
curdir = os.getcwd()
filepath = self.out_path % i
offset = self.conf.get("infill_offset")
line_width = 1 # int(abs(offset)/2)
pe = pathengine.pathEngine()
pe.generate_contours_from_img(filepath, True)
pe.im = cv2.cvtColor(pe.im, cv2.COLOR_GRAY2BGR)
contour_tree = pe.convert_hiearchy_to_PyPolyTree()
group_contour = pe.get_contours_from_each_connected_region(
contour_tree, '0')
# draw boundaries
#################################
# Generate N color list
#################################
def generate_RGB_list(N):
import colorsys
HSV_tuples = [(x * 1.0 / N, 0.8, 0.9) for x in range(N)]
RGB_tuples = map(lambda x: colorsys.hsv_to_rgb(*x), HSV_tuples)
rgb_list = tuple(RGB_tuples)
return np.array(rgb_list) * 255
N = 50
colors = generate_RGB_list(N)
bg_img = pe.im.copy()
bg_img = np.full(bg_img.shape, 255, dtype=np.uint8)
for boundary in group_contour.values():
spiral = mkspiral.spiral(pe, boundary, offset)
pathengine.suPath2D.draw_line(
spiral, bg_img, colors[0], line_width)
# for show
cv2.imwrite(filepath, bg_img)
tex1 = cv2.cvtColor(bg_img, cv2.COLOR_BGR2RGBA)
v1 = gl.GLImageItem(tex1)
v1.translate(0, 0, i * self.mesh_info.layer_thickness)
self.view_slice.items = []
self.view_slice.addItem(v1)
except Exception as e:
self.message(str(e))
return
def initialize_xy(self):
""" Create the xy plane. """
# Get out if no data is present
if self.data.get_value() is None: return
# Remove any old planes
if hasattr(self, 'xy'):
self.glview.removeItem(self.xy)
# Get the data and texture to create the GLImageItem object
cut = self.get_xy_slice(self.slider_xy.pos.get_value())
texture = self.make_texture(cut)
self.xy = gl.GLImageItem(texture, glOptions=self.gloptions)
# Scale and translate to origin and add to glview
self.xy.scale(self.xscale, self.yscale, 1)
self.xy.translate(T, T, T)
# Put to position in accordance with slider
self.old_z = 0 #self.slider_xy.pos.get_value()
self.update_xy()
# Add to GLView
self.glview.addItem(self.xy)
def initialize_zx(self):
""" Create the zx plane. """
# Get out if no data is present
if self.data.get_value() is None: return
# Remove any old planes
if hasattr(self, 'zx'):
self.glview.removeItem(self.zx)
# Get the data and texture to create the GLImageItem object
cut = self.get_zx_slice(0)
texture = self.make_texture(cut)
self.zx = gl.GLImageItem(texture, glOptions=self.gloptions)
# Scale and translate to origin and add to glview (this plane has
# shape (x, z))
self.zx.scale(self.xscale, self.zscale, 1)
self.zx.translate(T, T, 0)
self.zx.rotate(90, 1, 0, 0)
self.zx.translate(0, T, 0)
# Put to position in accordance with slider
self.update_zx()
# Add to GLView
self.glview.addItem(self.zx)
def gazePointsToGaussians(self,
sigma=20,
rotation=[90, 0, 1, 0],
x_shift=0,
y_shift=0,
option='additive'):
'''
Transforms the csv data into a list of GLImageItems. Each item contains the
viewpoints (AOIs) of every subject represented as Gaussians
'''
self.gaussians = []
self.XYHeatmap = []
self.XZHeatmap = []
for frame_idx in range(self.gaze_points.shape[0]):
print('computing gaussian overlay #{0}'.format(frame_idx))
frame_data = self.gaze_points[frame_idx, :2, :]
gaussians = []
for subject in range(self.gaze_points.shape[2]):
# mus are simply pixel indices of eye tracking
subject_data = frame_data[:, subject]
#
gaussian = self.gaussian2d([subject_data[0], subject_data[1]],
self.sigma)
gaussians.append(gaussian)
# add all gaussians
gaussians = np.sum(gaussians, 0)
# divide by number of subjects to renormalize gaussians (0,1)
gaussians /= (subject + 1)
# transform to RGBA
gaussians = self.getColors(gaussians, cm.jet)
# transform into GLImageItem
gaussians = gl.GLImageItem(gaussians)
# rotate, translate, scale, set option
gaussians.rotate(rotation[0], rotation[1], rotation[2],
rotation[3])
gaussians.translate(frame_idx * self.image_spacing + x_shift + 1,
y_shift, 0)
gaussians.setGLOptions(option)
self.gaussians.append(gaussians)
def __init__(self, w, path, sensor_no):
super().__init__()
a = self._anchor = gl.GLGraphicsItem.GLGraphicsItem()
self._gizmo = gl.GLAxisItem(size=self.SIZE)
self._gizmo.setParentItem(a)
name = "{} {}".format(path[1:], sensor_no)
sd_font = ImageFont.truetype(str(SQUARE_DEAL), 20)
temp_image = Image.new('RGBA', (2, 2), (0, 0, 0, 0))
width, height = ImageDraw.Draw(temp_image).textsize(name, sd_font)
txt_image = Image.new('RGBA', (width + 2, height + 2), (0, 0, 0, 0))
draw = ImageDraw.Draw(txt_image)
draw.text((1, 1), name, font=sd_font, fill=(255, 255, 255, 128))
tex1 = np.asarray(txt_image)
v1 = gl.GLImageItem(tex1)
v1.setParentItem(a)
v1.scale(0.05, 0.05, 0.05)
w.addItem(a)
w.addItem(v1)
w.addItem(self._gizmo)
self._sensor_no = sensor_no
self.update(QtGui.QQuaternion())
## create volume data set to slice three images from shape = (100, 100, 70) data = pg.gaussianFilter(np.random.normal(size=shape), (4, 4, 4)) data += pg.gaussianFilter(np.random.normal(size=shape), (15, 15, 15)) * 15 ## slice out three planes, convert to RGBA for OpenGL texture levels = (-0.08, 0.08) tex1 = pg.makeRGBA(data[shape[0] // 2], levels=levels)[0] # yz plane tex2 = pg.makeRGBA(data[:, shape[1] // 2], levels=levels)[0] # xz plane tex3 = pg.makeRGBA(data[:, :, shape[2] // 2], levels=levels)[0] # xy plane #tex1[:,:,3] = 128 #tex2[:,:,3] = 128 #tex3[:,:,3] = 128 ## Create three image items from textures, add to view v1 = gl.GLImageItem(tex1) v1.translate(-shape[1] / 2, -shape[2] / 2, 0) v1.rotate(90, 0, 0, 1) v1.rotate(-90, 0, 1, 0) w.addItem(v1) v2 = gl.GLImageItem(tex2) v2.translate(-shape[0] / 2, -shape[2] / 2, 0) v2.rotate(-90, 1, 0, 0) w.addItem(v2) v3 = gl.GLImageItem(tex3) v3.translate(-shape[0] / 2, -shape[1] / 2, 0) w.addItem(v3) ax = gl.GLAxisItem() w.addItem(ax)
if show_time:
w.addItem(make_grid_item((-radius, 0, time_length/2), (90, 0, 1, 0), (time_length/20, radius/10, radius/10)))
w.addItem(make_grid_item((-radius, 0, time_length*3/2), (90, 0, 1, 0), (time_length/20, radius/10, radius/10)))
w.addItem(make_grid_item((0, -radius, time_length/2), (90, 1, 0, 0), (radius/10, time_length/20, radius/10)))
w.addItem(make_grid_item((0, -radius, time_length*3/2), (90, 1, 0, 0), (radius/10, time_length/20, radius/10)))
w.addItem(make_grid_item((0, 0, 0), (0, 0, 0, 0), (radius/10, radius/10, radius/10)))
# Make Image Base
# Determine the background image according to meta phase
bg_path = 'maze.png'
img = imread(os.path.join(local_directory, bg_path))
image_scale = (radius * 2.0) / float(img.shape[0])
tex1 = pg.makeRGBA(img)[0]
base_image = gl.GLImageItem(tex1)
base_image.translate(-radius, -radius, 0)
base_image.rotate(270, 0, 0, 1)
base_image.scale(image_scale, image_scale, image_scale)
w.addItem(base_image)
# Generate Path Line
color = (255, 255, 255, 255)
line_color = np.empty((len(iterations), 4))
line_color_state = np.empty((len(iterations), 4))
x = []
y = []
z = []
for idx, i in enumerate(iterations):
x.append(float(i['x']))
ax = gl.GLAxisItem(glOptions='opaque')
ax.setSize(2, 2, 2)
win.addItem(ax)
ax.setTransform(
QtGui.QMatrix4x4(*(rotation((1, 0, 0), 0.0001, homog=True).flatten())))
ax.translate(0, 0, -0.02)
axc = gl.GLAxisItem(glOptions='opaque')
axc.setSize(1, 1, 1)
#axc.translate(0,0,0.02)
win.addItem(axc)
# imagen
view = gl.GLImageItem(data=np.zeros([100, 100, 4]))
win.addItem(view)
# marker
gmark = gl.GLLinePlotItem(pos=np.vstack([marker, marker[0]]),
color=(255, 0, 0, 1),
antialias=True,
width=3)
gmark.setGLOptions('opaque')
gmark.translate(0, 0, 0.01)
win.addItem(gmark)
# camera
cam = gl.GLLinePlotItem(pos=np.array([[0, 0, 0]]),
color=(255, 255, 255, 1),
antialias=True,
def fill(self):
try:
i = self.sl.value()
self.message("Show slice {}.".format(i + 1), False)
curdir = os.getcwd()
filepath = self.out_path % i
offset = -6
line_width = 1 #int(abs(offset)/2)
pe = pathengine.pathEngine()
pe.generate_contours_from_img(filepath, True)
pe.im = cv2.cvtColor(pe.im, cv2.COLOR_GRAY2BGR)
contour_tree = pe.convert_hiearchy_to_PyPolyTree()
group_contour = pe.get_contours_from_each_connected_region(
contour_tree, '0')
#draw boundaries
#################################
# Generate N color list
#################################
def generate_RGB_list(N):
import colorsys
HSV_tuples = [(x * 1.0 / N, 0.8, 0.9) for x in range(N)]
RGB_tuples = map(lambda x: colorsys.hsv_to_rgb(*x), HSV_tuples)
rgb_list = tuple(RGB_tuples)
return np.array(rgb_list) * 255
N = 50
colors = generate_RGB_list(N)
for boundary in group_contour.values():
iso_contours = pe.fill_closed_region_with_iso_contours(
boundary, offset)
idx = 0
for cs in iso_contours:
for c in cs:
pathengine.suPath2D.draw_line(np.vstack([c,
c[0]]), pe.im,
colors[idx], line_width)
idx += 1
cv2.imwrite(filepath, pe.im)
tex1 = cv2.cvtColor(pe.im, cv2.COLOR_BGR2RGBA)
v1 = gl.GLImageItem(tex1)
v1.translate(0, 0, i * self.mesh_info.layer_thickness)
self.view_slice.items = []
self.view_slice.addItem(v1)
except Exception as e:
self.message(str(e))
# gen fermat's curve
# gen 3d point n*3 matrix
#n = 51
#y = np.linspace(-10,10,n)
#x = np.linspace(-10,10,100)
#for i in range(n):
#yi = np.array([y[i]]*100)
#d = (x**2 + yi**2)**0.5
#z = 10 * np.cos(d) / (d+1)
#pts = np.vstack([x,yi,z]).transpose()
#plt = gl.GLLinePlotItem(pos=pts, color=pg.glColor((i,n*1.3)), width=(i+1)/10., antialias=True)
#self.view_slice.addItem(plt)
return
def init_ui(self):
self.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
self.setMinimumSize(250, 250)
layout = QGridLayout()
layout.setContentsMargins(0, 0, 0, 0)
self.setLayout(layout)
positions = np.vstack([self.x_points, self.y_points,
self.z_points]).transpose()
self.view = GLViewWidgetFix.GLViewWidgetFix()
self.view.setBackgroundColor(119, 181, 254)
self.view.setCameraPosition(distance=1950, elevation=90, azimuth=0)
self.plot = opengl.GLLinePlotItem(pos=positions,
color=[1, 0, 0, 1],
width=3)
self.plot.setGLOptions("opaque")
self.view.addItem(self.plot)
# self.grid = opengl.GLGridItem(color="white")
# self.grid.setSize(x=(self.lon_max-self.lon_min)*self.meters_per_lon,
# y=(self.lat_max-self.lat_min)*self.meters_per_lat)
# self.grid.setSpacing(x=100, y=100)
# self.view.addItem(self.grid)
self.image_file = Image.open(self.image_name)
self.image = opengl.GLImageItem(np.asarray(self.image_file))
self.view.addItem(self.image)
self.image.scale((self.lat_max - self.lat_min) * self.meters_per_lat /
self.image_file.size[1],
(self.lon_max - self.lon_min) * self.meters_per_lon /
self.image_file.size[0], 1)
self.image.translate(
-(self.lat_max - self.lat_min) * self.meters_per_lat / 2,
-(self.lon_max - self.lon_min) * self.meters_per_lon / 2, 0)
flat_earth = opengl.GLMeshItem(meshdata=opengl.MeshData.cylinder(
1, 64, [6371000, 0], 0),
color=[84 / 255, 89 / 255, 72 / 255, 1],
smooth=True)
flat_earth.translate(0, 0, -10000)
flat_earth.setGLOptions("opaque")
self.view.addItem(flat_earth)
crosshair_mesh = mesh.Mesh.from_file("DisplayModels/Crosshairs.stl")
crosshair_mesh_data = opengl.MeshData(vertexes=crosshair_mesh.vectors)
self.crosshair = opengl.GLMeshItem(meshdata=crosshair_mesh_data,
color=[1, 0, 0, 1])
self.set_crosshair_pos(0, 0, 0)
self.view.addItem(self.crosshair)
self.view_btn = QPushButton("2D")
self.view_btn.clicked.connect(self.switch_3d)
self.view_btn.setMaximumWidth(30)
self.coords_label = QLineEdit("0,0")
self.coords_label.setAlignment(Qt.AlignCenter)
self.coords_label.setReadOnly(True)
self.clear_btn = QPushButton("CLR")
self.clear_btn.setSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed)
self.clear_btn.setToolTip("Clear Data")
self.clear_btn.setFixedWidth(35)
self.clear_btn.setParent(self.view)
self.clear_btn.clicked.connect(self.clear_plot)
self.sats_label = QLineEdit("0")
self.sats_label.setAlignment(Qt.AlignCenter)
self.sats_label.setReadOnly(True)
self.sats_label.setToolTip("Number of Satellites")
self.sats_label.setMaximumWidth(50)
layout.addWidget(self.view, 0, 0, 1, 4)
layout.addWidget(self.clear_btn, 1, 3)
layout.addWidget(self.view_btn, 1, 0)
layout.addWidget(self.coords_label, 1, 1)
layout.addWidget(self.sats_label, 1, 2)
data = pickle.load(f)
nx, ny, nz = data.shape
print(nx, ny, nz)
x0, y0, z0 = 0, 0, 0
x0, y0, z0 = [int(2 * n / 5) for n in [nx, ny, nz]]
# Create Textures
levels = [data.min(), data.max()]
cmap = cmaps[cmap]
lut = cmap.getLookupTable()
textures = [
pg.makeRGBA(d, levels=levels, lut=lut)[0]
for d in [data[x0], data[:, y0], data[:, :, z0]]
]
planes = [gl.GLImageItem(texture, glOptions=gloption) for texture in textures]
## Apply transformations to get lanes where they need to go
xscale, yscale, zscale = 1 / nx, 1 / ny, 1 / nz
# xy plane
xy = planes[2]
xy.scale(xscale, yscale, 1)
xy.translate(-1 / 2, -1 / 2, -1 / 2 + z0 * zscale)
main.addItem(xy)
# yz plane (appears in the coordinate system along xy)
yz = planes[0]
yz.scale(yscale, zscale, 1)
yz.rotate(90, 0, 0, 1)
yz.rotate(90, 0, 1, 0)
yz.translate(-1 / 2 + x0 * xscale, -1 / 2, -1 / 2)
def __init__(self):
super(MyView, self).__init__()
self.opts['distance'] = 10
self.opts['center'].setX(floor_sz[0] * 0.5)
self.opts['center'].setY(floor_sz[1] * 0.5)
self.opts['center'].setZ(wall_height * 0.5)
self.opts['elevation'] = 0
self.show()
self.setWindowTitle('Hack4Sweden')
# Floor
floor_tex = scipy.ndimage.imread('textures/wood.jpeg', mode='RGBA')
floor_tex = tile(floor_tex, floor_sz)
floor = gl.GLImageItem(floor_tex)
self.addItem(floor)
# Walls
wall1_tex = scipy.ndimage.imread('textures/wall_tex.jpg', mode='RGBA')
wall1_tex = tile(wall1_tex, [floor_sz[0], wall_height])
wall1 = gl.GLImageItem(wall1_tex)
wall1.rotate(90, 1, 0, 0)
self.addItem(wall1)
wall2 = gl.GLImageItem(wall1_tex)
wall2.rotate(90, 1, 0, 0)
wall2.translate(0, floor_sz[1], 0)
self.addItem(wall2)
# Lighting
globAmb = [0.3, 0.3, 0.3, 1.0]
lightAmb = [0.75, 0.75, 0.75, 1.0]
lightDifAndSpec = [0.7, 0.7, 0.7, 1.0]
# glEnable(GL_LIGHTING)
# glLightfv(GL_LIGHT0, GL_AMBIENT, lightAmb)
# glLightfv(GL_LIGHT0, GL_DIFFUSE, lightDifAndSpec)
# glLightfv(GL_LIGHT0, GL_SPECULAR, lightDifAndSpec)
# # glLightfv(GL_LIGHT0, GL_POSITION, [500, 250, 100, 0])
# glEnable(GL_LIGHT0)
# glLightModelfv(GL_LIGHT_MODEL_AMBIENT, globAmb)
# glLightModeli(GL_LIGHT_MODEL_LOCAL_VIEWER, GL_TRUE)
# glEnable(GL_DEPTH_TEST)
# Load paintings
db = TinyDB('paintings/db.json')
# db.insert({'name': 'Captain Planet', 'img': 'test.jpg'})
added = 0
for item in db.all():
painting_tex = scipy.ndimage.imread('paintings/' + item['img'], mode='RGBA')
painting = gl.GLImageItem(painting_tex, smooth=True)
scale = painting_width * 1.0 / painting_tex.shape[1]
painting.rotate(90, 0, 1, 0)
painting.rotate(90, 0, 0, 1)
painting.scale(scale, scale, scale)
added += painting_spacing + painting_width
painting.translate(added, 5, painting_tex.shape[0] * scale / 2 + wall_height / 2)
self.addItem(painting)
def visualize(path=None):
"""
This function visualizes data for the virtual morris water maze task.
:param path: a path to a log file from the virtual morris water maze task
:return: Nothing
"""
# noinspection PyGlobalUndefined
global path_line, idx, timer, iterations, num_points_to_update, line_color_state, line_color
####################################################################################################################
# Setup
####################################################################################################################
show_time = False
if path is None:
path = easygui.fileopenbox()
if path is '':
logging.info('No file selected. Closing.')
exit()
if not os.path.exists(path):
logging.error('File not found. Closing.')
exit()
meta = None
# noinspection PyBroadException
try:
meta = get_filename_meta_data(os.path.basename(path)) # The meta filename information for convenience
except:
logging.error('There was an error reading the filename meta-information. Please confirm this is a valid log '
'file.')
exit()
logging.info("Parsing file (" + str(path) + ")...")
# First we populate a list of each iteration's data
# This section of code contains some custom binary parser data which won't be explained here
iterations = read_binary_file(path)
# Output the iterations count for debugging purposes
logging.info("Plotting " + str(len(iterations)) + " iterations.")
# Generate UI Window and Set Camera Settings
app = QtGui.QApplication([])
w = gl.GLViewWidget()
w.opts['center'] = pg.Qt.QtGui.QVector3D(0, 0, 0)
w.opts['elevation'] = 90
w.opts['azimuth'] = 0
w.opts['distance'] = 200
w.setWindowTitle('MSL Virtual Morris Water Maze Visualizer' + ' - Subject {0}, Trial {1}, iteration {2}'.format(
meta['subid'],
meta['trial'],
trial_num_to_str(meta['iteration'])))
####################################################################################################################
# Generate static graphical items
####################################################################################################################
# Make Grid
grid_items = []
def make_grid_item(loc, rot, scale):
g = gl.GLGridItem()
g.scale(scale[0], scale[1], scale[2])
g.rotate(rot[0], rot[1], rot[2], rot[3])
g.translate(loc[0], loc[1], loc[2])
return g
radius = 60
time_length = 60
if show_time:
g0 = make_grid_item((-radius, 0, time_length/2), (90, 0, 1, 0), (time_length/20, radius/10, radius/10))
g1 = make_grid_item((-radius, 0, time_length*3/2), (90, 0, 1, 0), (time_length/20, radius/10, radius/10))
g2 = make_grid_item((0, -radius, time_length/2), (90, 1, 0, 0), (radius/10, time_length/20, radius/10))
g3 = make_grid_item((0, -radius, time_length*3/2), (90, 1, 0, 0), (radius/10, time_length/20, radius/10))
grid_items.append(g0)
grid_items.append(g1)
grid_items.append(g2)
grid_items.append(g3)
w.addItem(g0)
w.addItem(g1)
w.addItem(g2)
w.addItem(g3)
gn = make_grid_item((0, 0, 0), (0, 0, 0, 0), (radius/10, radius/10, radius/10))
grid_items.append(gn)
w.addItem(gn)
# Make Image Base
# Determine the background image according to meta phase
bg_path = 'maze.png'
img = imread(os.path.join('./media/virtual_morris_water_maze', bg_path))
image_scale = (radius * 2.0) / float(img.shape[0])
tex1 = pg.makeRGBA(img)[0]
base_image = gl.GLImageItem(tex1)
base_image.translate(-radius, -radius, 0)
base_image.rotate(270, 0, 0, 1)
base_image.scale(image_scale, image_scale, image_scale)
w.addItem(base_image)
# Generate Path Line
color = (255, 255, 255, 255)
line_color = np.empty((len(iterations), 4))
line_color_state = np.empty((len(iterations), 4))
x = []
y = []
z = []
for idx, i in enumerate(iterations):
x.append(float(i['x']))
y.append(float(i['z']))
if show_time:
z.append(float(i['time']))
else:
z.append(0.0)
line_color[idx] = pg.glColor(color)
line_color_state[idx] = pg.glColor((0, 0, 0, 0))
pts = np.vstack([x, y, z]).transpose()
path_line = gl.GLLinePlotItem(pos=pts, color=line_color_state, mode='line_strip', antialias=True)
w.addItem(path_line)
####################################################################################################################
# Show UI
####################################################################################################################
w.show()
logging.info("Showing plot. Close plot to exit program.")
####################################################################################################################
# Custom Keyboard Controls
####################################################################################################################
# These variables are modified by the keyboard controls
idx = 0
num_points_to_update = 5
saved_points_to_update = 0
paused = False
# GUI Callbacks
def speed_up():
global num_points_to_update, paused
if not paused:
num_points_to_update += 5
logging.info("Setting speed to " + str(num_points_to_update) + " points per tick.")
def speed_down():
global num_points_to_update, paused
if not paused:
num_points_to_update -= 5
logging.info("Setting speed to " + str(num_points_to_update) + " points per tick.")
def pause():
global num_points_to_update, saved_points_to_update, paused
if not paused:
logging.info("Paused.")
saved_points_to_update = num_points_to_update
num_points_to_update = 0
paused = True
else:
logging.info("Unpaused.")
num_points_to_update = saved_points_to_update
saved_points_to_update = -0.5
paused = False
def reset():
global idx, line_color_state
logging.info("Resetting to time zero.")
idx = 0
for index in range(0, len(line_color_state) - 1):
line_color_state[index] = (0, 0, 0, 0)
def go_to_end():
global idx, line_color_state, line_color
logging.info("Going to end.")
idx = len(line_color_state) - 1
for index in range(0, len(line_color_state) - 1):
line_color_state[index] = line_color[index]
def close_all():
global timer, app
logging.info("User Shutdown Via Button Press")
timer.stop()
app.closeAllWindows()
# Visibility Variables
grid_visible = True
base_visible = True
path_line_visible = True
def toggle_grid_visible():
global grid_visible
if grid_visible:
for g in grid_items:
g.hide()
grid_visible = False
else:
for g in grid_items:
g.show()
grid_visible = True
def toggle_base_visible():
global base_visible
if base_visible:
base_image.hide()
base_visible = False
else:
base_image.show()
base_visible = True
def toggle_path_line_visible():
global path_line_visible
if path_line_visible:
path_line.hide()
path_line_visible = False
else:
path_line.show()
path_line_visible = True
# GUI Initialization
sh = QtGui.QShortcut(QtGui.QKeySequence("+"), w, speed_up)
sh.setContext(QtCore.Qt.ApplicationShortcut)
sh = QtGui.QShortcut(QtGui.QKeySequence("-"), w, speed_down)
sh.setContext(QtCore.Qt.ApplicationShortcut)
sh = QtGui.QShortcut(QtGui.QKeySequence(" "), w, pause)
sh.setContext(QtCore.Qt.ApplicationShortcut)
sh = QtGui.QShortcut(QtGui.QKeySequence("R"), w, reset)
sh.setContext(QtCore.Qt.ApplicationShortcut)
sh = QtGui.QShortcut(QtGui.QKeySequence("E"), w, go_to_end)
sh.setContext(QtCore.Qt.ApplicationShortcut)
sh = QtGui.QShortcut(QtGui.QKeySequence("Escape"), w, close_all)
sh.setContext(QtCore.Qt.ApplicationShortcut)
sh = QtGui.QShortcut(QtGui.QKeySequence("1"), w, toggle_grid_visible)
sh.setContext(QtCore.Qt.ApplicationShortcut)
sh = QtGui.QShortcut(QtGui.QKeySequence("2"), w, toggle_base_visible)
sh.setContext(QtCore.Qt.ApplicationShortcut)
sh = QtGui.QShortcut(QtGui.QKeySequence("5"), w, toggle_path_line_visible)
sh.setContext(QtCore.Qt.ApplicationShortcut)
####################################################################################################################
# Animation Loop
####################################################################################################################
timer = QtCore.QTimer()
# noinspection PyUnresolvedReferences
timer.timeout.connect(update)
timer.start(1)
####################################################################################################################
# PyQtGraph Initialization
####################################################################################################################
if (sys.flags.interactive != 1) or not hasattr(QtCore, 'PYQT_VERSION'):
# noinspection PyArgumentList
QtGui.QApplication.instance().exec_()
plt_yaxis = gl.GLLinePlotItem(pos=pts_yaxis, width=linewidth, antialias=True)
w.addItem(plt_yaxis)
## make x-axis
xaxis = np.linspace(-x_length, x_length, 10)
y_xaxis = np.zeros(10)
z_xaxis = np.zeros(10)
pts_xaxis = np.vstack([y_xaxis, z_xaxis, xaxis]).transpose()
plt_xaxis = gl.GLLinePlotItem(pos=pts_xaxis, width=linewidth, antialias=True)
w.addItem(plt_xaxis)
## make images
image_shape = (8, 8)
uniform_values = np.ones(image_shape) * 255
uniform_image_transparent = pg.makeARGB(uniform_values)[0]
uniform_image_transparent[:, :, 3] = 65
v1 = gl.GLImageItem(uniform_image_transparent)
v1.translate(-image_shape[0] / 2, -image_shape[1] / 2, 0)
v1.rotate(90, 1, 0, 0)
#w.addItem(v1)
v = []
for i in range(0, 20):
vtemp = gl.GLImageItem(uniform_image_transparent)
vtemp.translate(-image_shape[0] / 2, -image_shape[1] / 2, 0)
vtemp.rotate(90, 1, 0, 0)
dz = float(i - 10)
vtemp.translate(0, dz, 0)
v.append(vtemp)
w.addItem(v[i])
# Set up some animation parameters
frametime = 50 # frame refresh time in ms
def make_color_bar(rgb, p, r, s):
v = gl.GLImageItem(np.array([[rgb + (255,)]]))
v.translate(p[0], p[1], p[2])
v.scale(s[0], s[1], s[2])
v.rotate(r[0], r[1], r[2], r[3])
return v
def visualize_time_travel_data(path=None, automatically_rotate=True):
"""
This function visualizes data from the Time Travel Task in 3D.
:param path: the path to a data file to visualize
:param automatically_rotate: If True, the figure will automatically rotate in an Abs(Sin(x)) function shape,
otherwise the user can interact with the figure.
:return: Nothing
"""
# noinspection PyGlobalUndefined
global path_line, idx, timer, iterations, click_scatter, click_pos, click_color, click_size, window, meta, \
reconstruction_items, num_points_to_update, line_color, line_color_state, auto_rotate
auto_rotate = automatically_rotate
####################################################################################################################
# Setup
####################################################################################################################
# Get Log File Path and Load File
local_directory = os.path.dirname(os.path.realpath(__file__)) # The directory of this script
# filename = '001_1_1_1_2016-08-29_10-26-03.dat' # The relative path to the data file (CHANGE ME)
# path = os.path.join(local_directory, filename)
if path is None:
path = easygui.fileopenbox()
if path is '':
logging.info('No file selected. Closing.')
exit()
if not os.path.exists(path):
logging.error('File not found. Closing.')
exit()
meta = None
# noinspection PyBroadException
try:
meta = get_filename_meta_data(os.path.basename(path)) # The meta filename information for convenience
except:
logging.error('There was an error reading the filename meta-information. Please confirm this is a valid log '
'file.')
exit()
logging.info("Parsing file (" + str(path) + ")...")
# First we populate a list of each iteration's data
# This section of code contains some custom binary parser data which won't be explained here
iterations = read_binary_file(path)
# Output the iterations count for debugging purposes
logging.info("Plotting " + str(len(iterations)) + " iterations.")
# Generate UI Window and Set Camera Settings
app = QtGui.QApplication([])
window = gl.GLViewWidget()
window.opts['center'] = pg.Qt.QtGui.QVector3D(0, 0, 30)
window.opts['distance'] = 200
window.setWindowTitle('Timeline Visualizer' +
' - Subject {0}, Trial {1}, Phase {2}'.format(meta['subID'], meta['trial'],
phase_num_to_str(int(meta['phase']))))
####################################################################################################################
# Generate static graphical items
####################################################################################################################
# Make Grid
grid_items = []
def make_grid_item(loc, rot, scale):
g = gl.GLGridItem()
g.scale(scale[0], scale[1], scale[2])
g.rotate(rot[0], rot[1], rot[2], rot[3])
g.translate(loc[0], loc[1], loc[2])
return g
if meta['phase'] == '0' or meta['phase'] == '3' or meta['phase'] == '6':
g0 = make_grid_item((-19, 0, 15), (90, 0, 1, 0), (1.5, 1.9, 1.9))
g1 = make_grid_item((0, -19, 15), (90, 1, 0, 0), (1.9, 1.5, 1.9))
grid_items.append(g0)
grid_items.append(g1)
window.addItem(g0)
window.addItem(g1)
else:
g0 = make_grid_item((-19, 0, 15), (90, 0, 1, 0), (1.5, 1.9, 1.9))
g1 = make_grid_item((-19, 0, 45), (90, 0, 1, 0), (1.5, 1.9, 1.9))
g2 = make_grid_item((0, -19, 15), (90, 1, 0, 0), (1.9, 1.5, 1.9))
g3 = make_grid_item((0, -19, 45), (90, 1, 0, 0), (1.9, 1.5, 1.9))
grid_items.append(g0)
grid_items.append(g1)
grid_items.append(g2)
grid_items.append(g3)
window.addItem(g0)
window.addItem(g1)
window.addItem(g2)
window.addItem(g3)
gn = make_grid_item((0, 0, 0), (0, 0, 0, 0), (1.9, 1.9, 1.9))
grid_items.append(gn)
window.addItem(gn)
# Make Image Base
# Determine the background image according to meta phase
img_location = './media/time_travel_task/'
bg_path = 'studyBG.png'
if meta['phase'] == '0' or meta['phase'] == '3':
bg_path = 'practiceBG.png'
elif meta['phase'] == '6':
bg_path = 'practiceBG.png'
elif meta['phase'] == '7' or meta['phase'] == '8':
bg_path = 'studyBG.png'
img = imread(os.path.abspath(os.path.join(img_location, bg_path)))
image_scale = (19.0 * 2.0) / float(img.shape[0])
tex1 = pg.makeRGBA(img)[0]
base_image = gl.GLImageItem(tex1)
base_image.translate(-19, -19, 0)
base_image.rotate(270, 0, 0, 1)
base_image.scale(image_scale, image_scale, image_scale)
window.addItem(base_image)
# Make Timeline Colored Bars
color_bars = []
def make_color_bar(rgb, p, r, s):
v = gl.GLImageItem(np.array([[rgb + (255,)]]))
v.translate(p[0], p[1], p[2])
v.scale(s[0], s[1], s[2])
v.rotate(r[0], r[1], r[2], r[3])
return v
color_bar_length = 15
if meta['phase'] == '0' or meta['phase'] == '3' or meta['phase'] == '6':
times = [0, 7.5, 15, 22.5]
color_bar_length = 7.5
else:
times = [0, 15, 30, 45]
if meta['inverse'] == '1':
times.reverse()
v0 = make_color_bar((255, 255, 0), (19, times[0], 19), (90, 1, 0, 0), (5, color_bar_length, 0))
v1 = make_color_bar((255, 0, 0), (19, times[1], 19), (90, 1, 0, 0), (5, color_bar_length, 0))
v2 = make_color_bar((0, 255, 0), (19, times[2], 19), (90, 1, 0, 0), (5, color_bar_length, 0))
v3 = make_color_bar((0, 0, 255), (19, times[3], 19), (90, 1, 0, 0), (5, color_bar_length, 0))
color_bars.append(v0)
color_bars.append(v1)
color_bars.append(v2)
color_bars.append(v3)
window.addItem(v0)
window.addItem(v1)
window.addItem(v2)
window.addItem(v3)
# Generate Path Line
forwardColor = (255, 255, 255, 255)
backwardColor = (255, 0, 255, 255)
line_color = np.empty((len(iterations), 4))
line_color_state = np.empty((len(iterations), 4))
x = []
y = []
z = []
for idx, i in enumerate(iterations):
x.append(float(i['x']))
y.append(float(i['z']))
z.append(float(i['time_val']))
c = forwardColor
if i['timescale'] <= 0:
c = backwardColor
line_color[idx] = pg.glColor(c)
line_color_state[idx] = pg.glColor((0, 0, 0, 0))
pts = np.vstack([x, y, z]).transpose()
path_line = gl.GLLinePlotItem(pos=pts, color=line_color_state, mode='line_strip', antialias=True)
window.addItem(path_line)
# Generate Item Lines (ground truth)
# noinspection PyUnusedLocal
items, times, directions = get_items_solutions(meta)
if meta['phase'] == '0' or meta['phase'] == '3' or meta['phase'] == '6':
times = [2, 12, 18, 25]
directions = [2, 1, 2, 1] # Fall = 2, Fly = 1, Stay = 0
if meta['inverse'] == '1':
times.reverse()
directions.reverse()
items = [{'direction': directions[0], 'pos': (2, -12, times[0]), 'color': (255, 255, 0)},
{'direction': directions[1], 'pos': (2, 13, times[1]), 'color': (255, 0, 0)},
{'direction': directions[2], 'pos': (-13, 2, times[2]), 'color': (0, 255, 0)},
{'direction': directions[3], 'pos': (-12, -17, times[3]), 'color': (0, 0, 255)},
{'direction': 0, 'pos': (13, 5, 0), 'color': (128, 0, 128)}]
# elif meta['phase'] == '7' or meta['phase'] == '8':
# times = [2, 8, 17, 23]
# directions = [2, 1, 1, 2] # Fall = 2, Fly = 1, Stay = 0
# if meta['inverse'] == '1':
# times.reverse()
# directions.reverse()
# items = [{'direction': directions[0], 'pos': (16, -14, times[0]), 'color': (255, 255, 0)},
# {'direction': directions[1], 'pos': (-10, -2, times[1]), 'color': (255, 0, 0)},
# {'direction': directions[2], 'pos': (15, -8, times[2]), 'color': (0, 255, 0)},
# {'direction': directions[3], 'pos': (-15, -15, times[3]), 'color': (0, 0, 255)},
# {'direction': 0, 'pos': (-2, 10, 0), 'color': (128, 0, 128)}]
else:
times = [4, 10, 16, 25, 34, 40, 46, 51]
directions = [2, 1, 1, 2, 2, 1, 2, 1] # Fall = 2, Fly = 1, Stay = 0
if meta['inverse'] == '1':
times.reverse()
directions.reverse()
items = [{'direction': directions[0], 'pos': (18, -13, times[0]), 'color': (255, 255, 0)},
{'direction': directions[1], 'pos': (-13, 9, times[1]), 'color': (255, 255, 0)},
{'direction': directions[2], 'pos': (-10, -2, times[2]), 'color': (255, 0, 0)},
{'direction': directions[3], 'pos': (6, -2, times[3]), 'color': (255, 0, 0)},
{'direction': directions[4], 'pos': (17, -8, times[4]), 'color': (0, 255, 0)},
{'direction': directions[5], 'pos': (-2, -7, times[5]), 'color': (0, 255, 0)},
{'direction': directions[6], 'pos': (-15, -15, times[6]), 'color': (0, 0, 255)},
{'direction': directions[7], 'pos': (6, 18, times[7]), 'color': (0, 0, 255)},
{'direction': 0, 'pos': (14, 6, 0), 'color': (128, 0, 128)},
{'direction': 0, 'pos': (-2, 10, 0), 'color': (128, 0, 128)}]
item_lines = []
pos = np.empty((len(items), 3))
size = np.empty((len(items)))
color = np.empty((len(items), 4))
end_time = 60
if meta['phase'] == '0' or meta['phase'] == '3' or meta['phase'] == '6':
end_time = 30
for idx, i in enumerate(items):
pos[idx] = i['pos']
size[idx] = 2
if i['direction'] == 0:
size[idx] = 0
color[idx] = (i['color'][0] / 255, i['color'][1] / 255, i['color'][2] / 255, 1)
idx += 1
end = i['pos']
if i['direction'] == 1:
end = (end[0], end[1], 0)
elif i['direction'] == 2 or i['direction'] == 0:
end = (end[0], end[1], end_time)
line = gl.GLLinePlotItem(pos=np.vstack([[i['pos'][0], end[0]],
[i['pos'][1], end[1]],
[i['pos'][2], end[2]]]).transpose(),
color=pg.glColor(i['color']), width=3, antialias=True)
item_lines.append(line)
window.addItem(line)
item_scatter_plot = gl.GLScatterPlotItem(pos=pos, size=size, color=color, pxMode=False)
window.addItem(item_scatter_plot)
####################################################################################################################
# Generate data graphical items
####################################################################################################################
# If Study/Practice, label click events
'''click_pos = np.empty((len(items), 3))
click_size = np.zeros((len(iterations), len(items)))
click_color = np.empty((len(items), 4))
if meta['phase'] == '0' or meta['phase'] == '1' or meta['phase'] == '3' or meta['phase'] == '4' \
or meta['phase'] == '6' or meta['phase'] == '7':
for idx, i in enumerate(iterations):
if idx + 1 < len(iterations):
for idxx, (i1, i2) in enumerate(zip(i['itemsclicked'], iterations[idx + 1]['itemsclicked'])):
if i['itemsclicked'][idxx]:
click_size[idx][idxx] = 0.5
if not i1 == i2:
click_pos[idxx] = (i['x'], i['z'], i['time_val'])
click_color[idxx] = (128, 128, 128, 255)
else:
for idxx, i1 in enumerate(i['itemsclicked']):
if i['itemsclicked'][idxx]:
click_size[idx][idxx] = 0.5
'''
click_pos, _, click_size, click_color = get_click_locations_and_indicies(iterations, items, meta)
click_scatter = gl.GLScatterPlotItem(pos=click_pos, size=click_size[0], color=click_color, pxMode=False)
window.addItem(click_scatter)
# If Test, Generate Reconstruction Items
event_state_labels, item_number_label, item_label_filename, cols = get_item_details()
# if meta['phase'] == '7' or meta['phase'] == '8':
# item_number_label = ['bottle', 'clover', 'boot', 'bandana', 'guitar']
# item_label_filename = ['bottle.jpg', 'clover.jpg', 'boot.jpg', 'bandana.jpg', 'guitar.jpg']
# cols = [(255, 255, pastel_factor), (255, pastel_factor, pastel_factor), (pastel_factor, 255, pastel_factor),
# (pastel_factor, pastel_factor, 255), (128, pastel_factor / 2, 128)]
reconstruction_item_scatter_plot = None
reconstruction_item_lines = []
if meta['phase'] == '2' or meta['phase'] == '5' or meta['phase'] == '8':
reconstruction_items, order = parse_test_items(iterations, cols,
item_number_label, event_state_labels)
pos = np.empty((len(reconstruction_items), 3))
size = np.empty((len(reconstruction_items)))
color = np.empty((len(reconstruction_items), 4))
# Iterate through the reconstruction items and visualize them
for idx, i in enumerate(reconstruction_items):
pos[idx] = i['pos']
size[idx] = 2
if i['direction'] == 0:
size[idx] = 0
color[idx] = (i['color'][0] / 255, i['color'][1] / 255, i['color'][2] / 255, 1)
end = pos[idx]
if i['direction'] == 1:
end = (end[0], end[1], 0)
elif i['direction'] == 2 or i['direction'] == 0:
end = (end[0], end[1], end_time)
line = gl.GLLinePlotItem(pos=np.vstack([[pos[idx][0], end[0]],
[pos[idx][1], end[1]],
[pos[idx][2], end[2]]]).transpose(),
color=pg.glColor(i['color']), width=3, antialias=True)
reconstruction_item_lines.append(line)
window.addItem(line)
img_path = item_label_filename[idx]
img = imread(os.path.join(local_directory, img_path))
expected_size = 2.0
image_scale = expected_size / float(img.shape[0])
offset_param = 0.0 - image_scale / 2 - expected_size / 2
tex = pg.makeRGBA(img)[0]
label_image = gl.GLImageItem(tex)
t = pos[idx][2]
if i['direction'] == 0:
t = end_time
label_image.translate(pos[idx][0] + offset_param, pos[idx][1] + offset_param, t)
label_image.scale(image_scale, image_scale, image_scale)
window.addItem(label_image)
billboard_item_labels.append(label_image)
reconstruction_item_scatter_plot = gl.GLScatterPlotItem(pos=pos, size=size, color=color, pxMode=False)
window.addItem(reconstruction_item_scatter_plot)
####################################################################################################################
# Show UI
####################################################################################################################
window.show()
logging.info("Showing plot. Close plot to exit program.")
####################################################################################################################
# Custom Keyboard Controls
####################################################################################################################
# These variables are modified by the keyboard controls
idx = 0
num_points_to_update = 5
saved_points_to_update = 0
paused = False
# GUI Callbacks
def speed_up():
global num_points_to_update, paused
if not paused:
num_points_to_update += 5
logging.info("Setting speed to " + str(num_points_to_update) + " points per tick.")
def speed_down():
global num_points_to_update, paused
if not paused:
num_points_to_update -= 5
logging.info("Setting speed to " + str(num_points_to_update) + " points per tick.")
def pause():
global num_points_to_update, saved_points_to_update, paused
if not paused:
logging.info("Paused.")
saved_points_to_update = num_points_to_update
num_points_to_update = 0
paused = True
else:
logging.info("Unpaused.")
num_points_to_update = saved_points_to_update
saved_points_to_update = -0.5
paused = False
def reset():
global idx, line_color_state
logging.info("Resetting to time zero.")
idx = 0
for index in range(0, len(line_color_state) - 1):
line_color_state[index] = (0, 0, 0, 0)
def go_to_end():
global idx, line_color_state, line_color
logging.info("Going to end.")
idx = len(line_color_state) - 1
for index in range(0, len(line_color_state) - 1):
line_color_state[index] = line_color[index]
def close_all():
global timer, app
logging.info("User Shutdown Via Button Press")
timer.stop()
app.closeAllWindows()
# Visibility Variables
grid_visible = True
base_visible = True
color_bars_visible = True
items_visible = True
path_line_visible = True
reconstruction_item_lines_visible = True
billboard_item_labels_visible = True
def toggle_grid_visible():
global grid_visible
if grid_visible:
for g in grid_items:
g.hide()
grid_visible = False
else:
for g in grid_items:
g.show()
grid_visible = True
def toggle_base_visible():
global base_visible
if base_visible:
base_image.hide()
base_visible = False
else:
base_image.show()
base_visible = True
def toggle_color_bars_visible():
global color_bars_visible
if color_bars_visible:
for bar in color_bars:
bar.hide()
color_bars_visible = False
else:
for bar in color_bars:
bar.show()
color_bars_visible = True
def toggle_items_visible():
global items_visible
if items_visible:
item_scatter_plot.hide()
for il in item_lines:
il.hide()
items_visible = False
else:
item_scatter_plot.show()
for il in item_lines:
il.show()
items_visible = True
def toggle_path_line_visible():
global path_line_visible
if path_line_visible:
path_line.hide()
click_scatter.hide()
path_line_visible = False
else:
path_line.show()
click_scatter.show()
path_line_visible = True
def toggle_reconstruction_item_lines_visible():
global reconstruction_item_lines_visible
if reconstruction_item_lines_visible:
if reconstruction_item_scatter_plot is not None:
reconstruction_item_scatter_plot.hide()
for ril in reconstruction_item_lines:
ril.hide()
reconstruction_item_lines_visible = False
else:
if reconstruction_item_scatter_plot is not None:
reconstruction_item_scatter_plot.show()
for ril in reconstruction_item_lines:
ril.show()
reconstruction_item_lines_visible = True
def toggle_billboard_item_labels_visible():
global billboard_item_labels_visible
if billboard_item_labels_visible:
for il in billboard_item_labels:
il.hide()
billboard_item_labels_visible = False
else:
for il in billboard_item_labels:
il.show()
billboard_item_labels_visible = True
# GUI Initialization
sh = QtGui.QShortcut(QtGui.QKeySequence("+"), window, speed_up)
sh.setContext(QtCore.Qt.ApplicationShortcut)
sh = QtGui.QShortcut(QtGui.QKeySequence("-"), window, speed_down)
sh.setContext(QtCore.Qt.ApplicationShortcut)
sh = QtGui.QShortcut(QtGui.QKeySequence(" "), window, pause)
sh.setContext(QtCore.Qt.ApplicationShortcut)
sh = QtGui.QShortcut(QtGui.QKeySequence("R"), window, reset)
sh.setContext(QtCore.Qt.ApplicationShortcut)
sh = QtGui.QShortcut(QtGui.QKeySequence("E"), window, go_to_end)
sh.setContext(QtCore.Qt.ApplicationShortcut)
sh = QtGui.QShortcut(QtGui.QKeySequence("Escape"), window, close_all)
sh.setContext(QtCore.Qt.ApplicationShortcut)
sh = QtGui.QShortcut(QtGui.QKeySequence("1"), window, toggle_grid_visible)
sh.setContext(QtCore.Qt.ApplicationShortcut)
sh = QtGui.QShortcut(QtGui.QKeySequence("2"), window, toggle_base_visible)
sh.setContext(QtCore.Qt.ApplicationShortcut)
sh = QtGui.QShortcut(QtGui.QKeySequence("3"), window, toggle_color_bars_visible)
sh.setContext(QtCore.Qt.ApplicationShortcut)
sh = QtGui.QShortcut(QtGui.QKeySequence("4"), window, toggle_items_visible)
sh.setContext(QtCore.Qt.ApplicationShortcut)
sh = QtGui.QShortcut(QtGui.QKeySequence("5"), window, toggle_path_line_visible)
sh.setContext(QtCore.Qt.ApplicationShortcut)
sh = QtGui.QShortcut(QtGui.QKeySequence("6"), window, toggle_reconstruction_item_lines_visible)
sh.setContext(QtCore.Qt.ApplicationShortcut)
sh = QtGui.QShortcut(QtGui.QKeySequence("7"), window, toggle_billboard_item_labels_visible)
sh.setContext(QtCore.Qt.ApplicationShortcut)
####################################################################################################################
# Animation Loop
####################################################################################################################
timer = QtCore.QTimer()
# noinspection PyUnresolvedReferences
timer.timeout.connect(update)
timer.start(1)
####################################################################################################################
# PyQtGraph Initialization
####################################################################################################################
if (sys.flags.interactive != 1) or not hasattr(QtCore, 'PYQT_VERSION'):
# noinspection PyArgumentList
QtGui.QApplication.instance().exec_()
def make_freeslice():
#_Parameters________________________________________________________________
DATA_PATH = pkg_resources.resource_filename('data_slicer', 'data/')
datafile = DATA_PATH + 'pit.p'
## Visual
gloption = 'translucent'
cmap = 'ocean'
#_GUI_setup_________________________________________________________________
# Set up the main window and set a central widget
window = QtGui.QMainWindow()
window.resize(800, 800)
central_widget = QtGui.QWidget()
window.setCentralWidget(central_widget)
# Create a layout
layout = QtGui.QGridLayout()
central_widget.setLayout(layout)
# Add the selector view
selector = ImagePlot()
#selector = gl.GLViewWidget()
layout.addWidget(selector, 1, 0, 1, 1)
# Set up the main 3D view widget
main = gl.GLViewWidget()
layout.addWidget(main, 0, 0, 1, 1)
# Somehow this is needed for both widets to be visible
layout.setRowStretch(0, 1)
layout.setRowStretch(1, 1)
#_Data_loading_and_presenting_______________________________________________
# Load data
with open(datafile, 'rb') as f:
data = pickle.load(f)
nx, ny, nz = data.shape
x0, y0, z0 = 0, 0, 0
x0, y0, z0 = [int(2 * n / 5) for n in [nx, ny, nz]]
# Create Textures
levels = [data.min(), data.max()]
cmap = load_cmap(cmap)
lut = cmap.getLookupTable()
cuts = [data[x0], data[:, y0], data[:, :, z0]]
textures = [pg.makeRGBA(d, levels=levels, lut=lut)[0] for d in cuts]
planes = [
gl.GLImageItem(texture, glOptions=gloption) for texture in textures
]
## Apply transformations to get lanes where they need to go
xscale, yscale, zscale = 1 / nx, 1 / ny, 1 / nz
# xy plane
xy = planes[2]
xy.scale(xscale, yscale, 1)
xy.translate(-1 / 2, -1 / 2, -1 / 2 + z0 * zscale)
main.addItem(xy)
#_Selector__________________________________________________________________
# Set an image in the selector plot
selector.set_image(cuts[2], lut=lut)
cutline = Cutline(selector)
cutline.initialize()
# A plane representing the cutline
cut, coords = cutline.get_array_region(data,
selector.image_item,
returnMappedCoords=True)
cut_texture = pg.makeRGBA(cut, levels=levels, lut=lut)[0]
cutplane = gl.GLImageItem(cut_texture, glOptions=gloption)
# Scale and move it to origin in upright position
# Upon initialization, this is like an xz plane
cutplane.scale(xscale, zscale, 1)
cutplane.rotate(90, 1, 0, 0)
cutplane.translate(-1 / 2, 0, -1 / 2)
transform0 = cutplane.transform()
main.addItem(cutplane)
# Conversion from ROI coordinates to Scene coordinates
roi_coords = cutline.roi.getLocalHandlePositions()
# also usefule for later
original_roi_x0 = roi_coords[0][1].x()
original_roi_x1 = roi_coords[1][1].x()
# length in ROI coordinates
length_in_roi = np.abs(original_roi_x1 - original_roi_x0)
# length in data coordinates
length_in_data = np.abs(coords[0, 0] - coords[0, -1])
# conversion in units of "roi/data"
roi_data_conversion = length_in_roi / length_in_data
# distance from left handle to M in data coords
distance_p0_m = length_in_data / 2
print('Distance: ', distance_p0_m)
def update_texture():
print('==')
print('LocalHandles: ', cutline.roi.getLocalHandlePositions())
print('Scene: ', cutline.roi.getSceneHandlePositions())
print('++')
transform = cutline.roi.getArraySlice(data, selector.image_item)[1]
cut, coords = cutline.get_array_region(data,
selector.image_item,
returnMappedCoords=True)
texture = pg.makeRGBA(cut, levels=levels, lut=lut)[0]
cutplane.setData(texture)
## Find the original center of mass (if no length changes would have been applied)
# The current handle positions in data coordinates are in p0 and p1
p0 = coords[[0, 1], [0, 0]]
p1 = coords[[0, 1], [-1, -1]]
# Find how much they have been stretched or compressed with respect to
# the original handles
new_roi_coords = cutline.roi.getLocalHandlePositions()
delta0 = (original_roi_x0 -
new_roi_coords[0][1].x()) / roi_data_conversion
# Construct a unit vector pointing from P0 to P1
diff = p1 - p0
e_pp = diff / np.sqrt(diff.dot(diff))
print('p0: ', p0)
print('p1: ', p1)
print('diff', diff)
print('e_pp: ', e_pp)
# Now the original midpoint is at p0 + e_pp*(distance_p0_m+delta0)
print('delta0: ', delta0)
M = p0
tx, ty = M[0], M[1]
print('tx, ty: {}, {}'.format(tx, ty))
tx *= xscale
ty *= yscale
print('tx, ty: {}, {}'.format(tx, ty))
# Rotate around origin
try:
alpha = np.arctan((p1[1] - p0[1]) / (p1[0] - p0[0]))
except ZeroDivisionError:
alpha = np.sign(p1[1] - p0[1]) * np.pi / 2
# Correct for special cases
if p1[0] < p0[0]:
alpha -= np.sign(p1[1] - p0[1]) * np.pi
alpha_deg = alpha * 180 / np.pi
print('alpha_deg: {}'.format(alpha_deg))
nt = QtGui.QMatrix4x4()
nt.translate(tx - 1 / 2, ty - 1 / 2, -1 / 2)
nt.scale(xscale, yscale, 1)
nt.rotate(alpha_deg, 0, 0, 1)
nt.rotate(90, 1, 0, 0)
nt.scale(1, zscale, 1)
cutplane.setTransform(nt)
cutline.sig_region_changed.connect(update_texture)
# Draw a coordinate system
axis = gl.GLAxisItem()
main.addItem(axis)
return window
