def convert_mouse_pos(self, x, y, min_x, min_y):
# Original position zoom corrected
ex, ey = x, y
# Correct for zoom
px_width, px_height = self.anat_image.pixelSize()
x /= px_width
y /= px_height
# Inverse transformation from display to data
coords = np.intp(pg.transformCoordinates(self.anat_image.inverseDataTransform(), np.array([x, y])))
dx = min_x + coords[0]
dy = min_y + coords[1]
# Divide dx and dy by the number of the atlas scale (here, 10)
dx = dx
dy = dy
return dx, dy
def map(self, obj):
"""
Extends QMatrix4x4.map() to allow mapping (3, ...) arrays of coordinates
"""
if isinstance(obj, np.ndarray) and obj.ndim >= 2 and obj.shape[0] in (2,3):
return pg.transformCoordinates(self, obj)
else:
return QtGui.QMatrix4x4.map(self, obj)
def test_pyqtgraph_conversion(self):
if not HAVE_PYQTGRAPH:
self.skipTest("pyqtgraph could not be imported")
pts2 = np.random.normal(size=(100, 2))
qtr1 = pyqtgraph.QtGui.QTransform()
qtr1.scale(1.1, -9)
qtr1.translate(3, -30)
qtr1.rotate(32)
t_atr = linear.STTransform.convert_from(qtr1, 'pyqtgraph')
qtr2 = t_atr.convert_to('pyqtgraph')
assert np.allclose(
pyqtgraph.transformCoordinates(qtr1, pts2, transpose=True),
t_atr.map(pts2))
assert np.allclose(
pyqtgraph.transformCoordinates(qtr2, pts2, transpose=True),
t_atr.map(pts2))
pts3 = np.random.normal(size=(100, 3))
qtr1 = pyqtgraph.Transform3D()
qtr1.scale(1.1, -9, 1e4)
qtr1.translate(3, -30, 0)
qtr1.rotate(32, 0, 1, 2)
t_atr = linear.AffineTransform.convert_from(qtr1, 'pyqtgraph')
print(t_atr)
qtr2 = t_atr.convert_to('pyqtgraph')
assert np.allclose(
pyqtgraph.transformCoordinates(qtr1, pts3, transpose=True),
t_atr.map(pts3))
assert np.allclose(
pyqtgraph.transformCoordinates(qtr2, pts3, transpose=True),
t_atr.map(pts3))
def __init__(self, h):
self.h = h
verts, edges = h.get_geometry()
meshes = []
sec_ids = []
for edge in edges:
ends = verts['pos'][edge]
dia = verts['dia'][edge]
sec_id = verts['sec_index'][edge[0]]
dif = ends[1]-ends[0]
length = (dif**2).sum() ** 0.5
mesh = gl.MeshData.cylinder(rows=1, cols=8, radius=[dia[0]/2., dia[1]/2.], length=length)
mesh_verts = mesh.vertexes(indexed='faces')
# Rotate cylinder vertexes to match segment
p1 = pg.Vector(*ends[0])
p2 = pg.Vector(*ends[1])
z = pg.Vector(0,0,1)
axis = pg.QtGui.QVector3D.crossProduct(z, p2-p1)
ang = z.angle(p2-p1)
tr = pg.Transform3D()
tr.translate(ends[0][0], ends[0][1], ends[0][2]) # move into position
tr.rotate(ang, axis.x(), axis.y(), axis.z())
mesh_verts = pg.transformCoordinates(tr, mesh_verts, transpose=True)
sec_id_array = np.empty(mesh_verts.shape[0]*3, dtype=int)
sec_id_array[:] = sec_id
meshes.append(mesh_verts)
sec_ids.append(sec_id_array)
self.vertex_sec_ids = np.concatenate(sec_ids, axis=0)
mesh_verts = np.concatenate(meshes, axis=0)
md = gl.MeshData(vertexes=mesh_verts)
gl.GLMeshItem.__init__(self, meshdata=md, shader='shaded')
def correctCoordinates(node, item):
## Remove transformation matrices from <g> tags by applying matrix to coordinates inside.
## Each item is represented by a single top-level group with one or more groups inside.
## Each inner group contains one or more drawing primitives, possibly of different types.
groups = node.getElementsByTagName('g')
## Since we leave text unchanged, groups which combine text and non-text primitives must be split apart.
## (if at some point we start correcting text transforms as well, then it should be safe to remove this)
groups2 = []
for grp in groups:
subGroups = [grp.cloneNode(deep=False)]
textGroup = None
for ch in grp.childNodes[:]:
if isinstance(ch, xml.Element):
if textGroup is None:
textGroup = ch.tagName == 'text'
if ch.tagName == 'text':
if textGroup is False:
subGroups.append(grp.cloneNode(deep=False))
textGroup = True
else:
if textGroup is True:
subGroups.append(grp.cloneNode(deep=False))
textGroup = False
subGroups[-1].appendChild(ch)
groups2.extend(subGroups)
for sg in subGroups:
node.insertBefore(sg, grp)
node.removeChild(grp)
groups = groups2
for grp in groups:
matrix = grp.getAttribute('transform')
match = re.match(r'matrix\((.*)\)', matrix)
if match is None:
vals = [1,0,0,1,0,0]
else:
vals = [float(a) for a in match.groups()[0].split(',')]
tr = np.array([[vals[0], vals[2], vals[4]], [vals[1], vals[3], vals[5]]])
removeTransform = False
for ch in grp.childNodes:
if not isinstance(ch, xml.Element):
continue
if ch.tagName == 'polyline':
removeTransform = True
coords = np.array([[float(a) for a in c.split(',')] for c in ch.getAttribute('points').strip().split(' ')])
coords = pg.transformCoordinates(tr, coords, transpose=True)
ch.setAttribute('points', ' '.join([','.join([str(a) for a in c]) for c in coords]))
elif ch.tagName == 'path':
removeTransform = True
newCoords = ''
oldCoords = ch.getAttribute('d').strip()
if oldCoords == '':
continue
for c in oldCoords.split(' '):
x,y = c.split(',')
if x[0].isalpha():
t = x[0]
x = x[1:]
else:
t = ''
nc = pg.transformCoordinates(tr, np.array([[float(x),float(y)]]), transpose=True)
newCoords += t+str(nc[0,0])+','+str(nc[0,1])+' '
ch.setAttribute('d', newCoords)
elif ch.tagName == 'text':
removeTransform = False
## leave text alone for now. Might need this later to correctly render text with outline.
#c = np.array([
#[float(ch.getAttribute('x')), float(ch.getAttribute('y'))],
#[float(ch.getAttribute('font-size')), 0],
#[0,0]])
#c = pg.transformCoordinates(tr, c, transpose=True)
#ch.setAttribute('x', str(c[0,0]))
#ch.setAttribute('y', str(c[0,1]))
#fs = c[1]-c[2]
#fs = (fs**2).sum()**0.5
#ch.setAttribute('font-size', str(fs))
## Correct some font information
families = ch.getAttribute('font-family').split(',')
if len(families) == 1:
font = QtGui.QFont(families[0].strip('" '))
if font.style() == font.SansSerif:
families.append('sans-serif')
elif font.style() == font.Serif:
families.append('serif')
elif font.style() == font.Courier:
families.append('monospace')
ch.setAttribute('font-family', ', '.join([f if ' ' not in f else '"%s"'%f for f in families]))
## correct line widths if needed
if removeTransform and ch.getAttribute('vector-effect') != 'non-scaling-stroke':
w = float(grp.getAttribute('stroke-width'))
s = pg.transformCoordinates(tr, np.array([[w,0], [0,0]]), transpose=True)
w = ((s[0]-s[1])**2).sum()**0.5
ch.setAttribute('stroke-width', str(w))
if removeTransform:
grp.removeAttribute('transform')
def correctCoordinates(node, item):
## Remove transformation matrices from <g> tags by applying matrix to coordinates inside.
groups = node.getElementsByTagName("g")
for grp in groups:
matrix = grp.getAttribute("transform")
match = re.match(r"matrix\((.*)\)", matrix)
if match is None:
vals = [1, 0, 0, 1, 0, 0]
else:
vals = map(float, match.groups()[0].split(","))
tr = np.array([[vals[0], vals[2], vals[4]], [vals[1], vals[3], vals[5]]])
removeTransform = False
for ch in grp.childNodes:
if not isinstance(ch, xml.Element):
continue
if ch.tagName == "polyline":
removeTransform = True
coords = np.array([map(float, c.split(",")) for c in ch.getAttribute("points").strip().split(" ")])
coords = pg.transformCoordinates(tr, coords, transpose=True)
ch.setAttribute("points", " ".join([",".join(map(str, c)) for c in coords]))
elif ch.tagName == "path":
removeTransform = True
newCoords = ""
oldCoords = ch.getAttribute("d").strip()
if oldCoords == "":
continue
for c in oldCoords.split(" "):
x, y = c.split(",")
if x[0].isalpha():
t = x[0]
x = x[1:]
else:
t = ""
nc = pg.transformCoordinates(tr, np.array([[float(x), float(y)]]), transpose=True)
newCoords += t + str(nc[0, 0]) + "," + str(nc[0, 1]) + " "
ch.setAttribute("d", newCoords)
elif ch.tagName == "text":
removeTransform = False
## leave text alone for now. Might need this later to correctly render text with outline.
# c = np.array([
# [float(ch.getAttribute('x')), float(ch.getAttribute('y'))],
# [float(ch.getAttribute('font-size')), 0],
# [0,0]])
# c = pg.transformCoordinates(tr, c, transpose=True)
# ch.setAttribute('x', str(c[0,0]))
# ch.setAttribute('y', str(c[0,1]))
# fs = c[1]-c[2]
# fs = (fs**2).sum()**0.5
# ch.setAttribute('font-size', str(fs))
## Correct some font information
families = ch.getAttribute("font-family").split(",")
if len(families) == 1:
font = QtGui.QFont(families[0].strip('" '))
if font.style() == font.SansSerif:
families.append("sans-serif")
elif font.style() == font.Serif:
families.append("serif")
elif font.style() == font.Courier:
families.append("monospace")
ch.setAttribute("font-family", ", ".join([f if " " not in f else '"%s"' % f for f in families]))
## correct line widths if needed
if removeTransform and ch.getAttribute("vector-effect") != "non-scaling-stroke":
w = float(grp.getAttribute("stroke-width"))
s = pg.transformCoordinates(tr, np.array([[w, 0], [0, 0]]), transpose=True)
w = ((s[0] - s[1]) ** 2).sum() ** 0.5
ch.setAttribute("stroke-width", str(w))
if removeTransform:
grp.removeAttribute("transform")
def correctCoordinates(node, item):
## Remove transformation matrices from <g> tags by applying matrix to coordinates inside.
groups = node.getElementsByTagName('g')
for grp in groups:
matrix = grp.getAttribute('transform')
match = re.match(r'matrix\((.*)\)', matrix)
if match is None:
vals = [1, 0, 0, 1, 0, 0]
else:
vals = map(float, match.groups()[0].split(','))
tr = np.array([[vals[0], vals[2], vals[4]],
[vals[1], vals[3], vals[5]]])
removeTransform = False
for ch in grp.childNodes:
if not isinstance(ch, xml.Element):
continue
if ch.tagName == 'polyline':
removeTransform = True
coords = np.array([
map(float, c.split(','))
for c in ch.getAttribute('points').strip().split(' ')
])
coords = pg.transformCoordinates(tr, coords, transpose=True)
ch.setAttribute(
'points',
' '.join([','.join(map(str, c)) for c in coords]))
elif ch.tagName == 'path':
removeTransform = True
newCoords = ''
oldCoords = ch.getAttribute('d').strip()
if oldCoords == '':
continue
for c in oldCoords.split(' '):
x, y = c.split(',')
if x[0].isalpha():
t = x[0]
x = x[1:]
else:
t = ''
nc = pg.transformCoordinates(tr,
np.array(
[[float(x),
float(y)]]),
transpose=True)
newCoords += t + str(nc[0, 0]) + ',' + str(nc[0, 1]) + ' '
ch.setAttribute('d', newCoords)
elif ch.tagName == 'text':
removeTransform = False
## leave text alone for now. Might need this later to correctly render text with outline.
#c = np.array([
#[float(ch.getAttribute('x')), float(ch.getAttribute('y'))],
#[float(ch.getAttribute('font-size')), 0],
#[0,0]])
#c = pg.transformCoordinates(tr, c, transpose=True)
#ch.setAttribute('x', str(c[0,0]))
#ch.setAttribute('y', str(c[0,1]))
#fs = c[1]-c[2]
#fs = (fs**2).sum()**0.5
#ch.setAttribute('font-size', str(fs))
## Correct some font information
families = ch.getAttribute('font-family').split(',')
if len(families) == 1:
font = QtGui.QFont(families[0].strip('" '))
if font.style() == font.SansSerif:
families.append('sans-serif')
elif font.style() == font.Serif:
families.append('serif')
elif font.style() == font.Courier:
families.append('monospace')
ch.setAttribute(
'font-family', ', '.join([
f if ' ' not in f else '"%s"' % f for f in families
]))
## correct line widths if needed
if removeTransform and ch.getAttribute(
'vector-effect') != 'non-scaling-stroke':
w = float(grp.getAttribute('stroke-width'))
s = pg.transformCoordinates(tr,
np.array([[w, 0], [0, 0]]),
transpose=True)
w = ((s[0] - s[1])**2).sum()**0.5
ch.setAttribute('stroke-width', str(w))
if removeTransform:
grp.removeAttribute('transform')
def correctCoordinates(node, item):
## Remove transformation matrices from <g> tags by applying matrix to coordinates inside.
## Each item is represented by a single top-level group with one or more groups inside.
## Each inner group contains one or more drawing primitives, possibly of different types.
groups = node.getElementsByTagName('g')
## Since we leave text unchanged, groups which combine text and non-text primitives must be split apart.
## (if at some point we start correcting text transforms as well, then it should be safe to remove this)
groups2 = []
for grp in groups:
subGroups = [grp.cloneNode(deep=False)]
textGroup = None
for ch in grp.childNodes[:]:
if isinstance(ch, xml.Element):
if textGroup is None:
textGroup = ch.tagName == 'text'
if ch.tagName == 'text':
if textGroup is False:
subGroups.append(grp.cloneNode(deep=False))
textGroup = True
else:
if textGroup is True:
subGroups.append(grp.cloneNode(deep=False))
textGroup = False
subGroups[-1].appendChild(ch)
groups2.extend(subGroups)
for sg in subGroups:
node.insertBefore(sg, grp)
node.removeChild(grp)
groups = groups2
for grp in groups:
matrix = grp.getAttribute('transform')
match = re.match(r'matrix\((.*)\)', matrix)
if match is None:
vals = [1, 0, 0, 1, 0, 0]
else:
vals = [float(a) for a in match.groups()[0].split(',')]
tr = np.array([[vals[0], vals[2], vals[4]],
[vals[1], vals[3], vals[5]]])
removeTransform = False
for ch in grp.childNodes:
if not isinstance(ch, xml.Element):
continue
if ch.tagName == 'polyline':
removeTransform = True
coords = np.array(
[[float(a) for a in c.split(',')]
for c in ch.getAttribute('points').strip().split(' ')])
coords = pg.transformCoordinates(tr, coords, transpose=True)
ch.setAttribute(
'points',
' '.join([','.join([str(a) for a in c]) for c in coords]))
elif ch.tagName == 'path':
removeTransform = True
newCoords = ''
oldCoords = ch.getAttribute('d').strip()
if oldCoords == '':
continue
for c in oldCoords.split(' '):
x, y = c.split(',')
if x[0].isalpha():
t = x[0]
x = x[1:]
else:
t = ''
nc = pg.transformCoordinates(tr,
np.array(
[[float(x),
float(y)]]),
transpose=True)
newCoords += t + str(nc[0, 0]) + ',' + str(nc[0, 1]) + ' '
ch.setAttribute('d', newCoords)
elif ch.tagName == 'text':
removeTransform = False
## leave text alone for now. Might need this later to correctly render text with outline.
#c = np.array([
#[float(ch.getAttribute('x')), float(ch.getAttribute('y'))],
#[float(ch.getAttribute('font-size')), 0],
#[0,0]])
#c = pg.transformCoordinates(tr, c, transpose=True)
#ch.setAttribute('x', str(c[0,0]))
#ch.setAttribute('y', str(c[0,1]))
#fs = c[1]-c[2]
#fs = (fs**2).sum()**0.5
#ch.setAttribute('font-size', str(fs))
## Correct some font information
families = ch.getAttribute('font-family').split(',')
if len(families) == 1:
font = QtGui.QFont(families[0].strip('" '))
if font.style() == font.SansSerif:
families.append('sans-serif')
elif font.style() == font.Serif:
families.append('serif')
elif font.style() == font.Courier:
families.append('monospace')
ch.setAttribute(
'font-family', ', '.join([
f if ' ' not in f else '"%s"' % f for f in families
]))
## correct line widths if needed
if removeTransform and ch.getAttribute(
'vector-effect') != 'non-scaling-stroke':
w = float(grp.getAttribute('stroke-width'))
s = pg.transformCoordinates(tr,
np.array([[w, 0], [0, 0]]),
transpose=True)
w = ((s[0] - s[1])**2).sum()**0.5
ch.setAttribute('stroke-width', str(w))
if removeTransform:
grp.removeAttribute('transform')
