def search(self, searchId, query, searchPoint=None):
"""Trigger an asynchronous search (specified by search id)
for the given term
:param str query: search query
"""
online = self.gui.m.get("onlineServices", None)
if online:
# construct result handling callback
callback = lambda x: self._searchCB(searchId, x)
# get search function corresponding to the search id
searchFunction = self._getSearchFunction(searchId)
# start the search and remember the search thread id
# so we can use it to track search progress
# (there might be more searches in progress so we
# need to know the unique search thread id)
if searchId == "local" and searchPoint:
pointInstance = point.Point(searchPoint.latitude,
searchPoint.longitude)
threadId = searchFunction(query,
callback,
around=pointInstance)
else:
threadId = searchFunction(query, callback)
self._threadsInProgress[threadId] = searchId
return threadId
def createMeshHomo(self, name, chem, init_conc, coord_x_start,
coord_y_start):
""" Create mesh for this compartment with homogeneous properties,
i.e. the partition and diffusion properties are all uniform
Args:
name: two-letter string to indicate the name of this compartment
coord_x_start, coord_y_start: starting coordinates
"""
dx = self.x_length / self.nx
dy = self.y_length / self.ny
self.meshes = [mesh.Mesh() for i in range(self.nx * self.ny)
] # organised in row dominant
coord_x = coord_x_start
coord_y = coord_y_start
current_point = point.Point(coord_x, coord_y, dx, dy, name, name)
for i in range(self.nx): # verticle direction up to down
for j in range(self.ny): # lateral direction left to right
idx = i * self.ny + j
self.meshes[idx].setup(name, chem, init_conc, self.Kw, self.D,
current_point.x_coord,
current_point.y_coord, current_point.dx,
current_point.dy, self.dz_dtheta)
if j == self.ny - 1: # last element in the lateral direction, move down
coord_x += dx
coord_y = coord_y_start
else: # not the last element in the lateral direction, thus move to the right
coord_y += dy
current_point.setPoint(coord_x, coord_y, dx, dy, name, name)
plt.subplot(131)
plt.plot(range(len(x)), x, 'o-')
plt.title("x(t)")
plt.subplot(132)
plt.plot(range(len(y)), y, 'o-')
plt.title("y(t)")
plt.subplot(133)
plt.plot(x, y, 'o-')
plt.title("(x,y)")
plt.subplots_adjust(top=0.8)
plt.show()
def add_point(self, point):
last_point = self.trajectory.pop()
self.trajectory.append(point)
self.trajectory.append(last_point)
if __name__ == '__main__':
start = pt.Point(0, 0)
middle = pt.Point(1, 5)
end = pt.Point(10, 10)
tr = Trajectory(start, end)
tr.add_point(middle)
tr.plot_trajectory()
def createMesh(self,
chem,
coord_x_start,
coord_y_start,
water_frac_surface=.55):
""" Create mesh for this compartment
Args:
coord_x_start, coord_y_start: starting coordinates
water_frac_surface : water content (w/w); saturation at .55; dry skin at .25
"""
# some initial settings
bOffset = False
cc_subtype = 0 # 0 = d_n; 1 = s; 2 = d_m, 3 = s;
dx_lipid = self.geom_g / self.nx_grids_lipid
dx_cc = self.geom_t / self.nx_grids_cc
dy_lipid = self.geom_s / self.ny_grids_lipid
dy_cc = self.geom_dn / self.ny_grids_cc_dn
self.meshes = [mesh.Mesh() for i in range(self.nx * self.ny)
] # organised in row dominant
# work out the starting point from given offset
length = self.geom_d + self.geom_s
len_vec = [self.geom_dn, self.geom_s, self.geom_dm, self.geom_s]
while self.offset_y > length:
self.offset_y -= length
length = .0
for i in range(4):
length += len_vec[i]
if self.offset_y < length:
break
cc_subtype_offset = i
length = self.offset_y - length + len_vec[i]
if cc_subtype_offset == 0 or cc_subtype_offset == 2:
# corneocyte width
idx_y_offset = int(length / dy_cc)
dy_offset = dy_cc
elif cc_subtype_offset == 1 or cc_subtype_offset == 3:
# lipid width
idx_y_offset = int(length / dy_lipid)
dy_offset = dy_lipid
else:
raise ValueError('Invalid subtype name')
# Now prepare values for the loop to create meshes
water_frac_sat = 0.55 # saturated water content (w/w)
water_increment_per_x = (water_frac_sat -
water_frac_surface) / self.x_length
idx_x = 0
idx_y = idx_y_offset
cc_subtype = cc_subtype_offset
coord_x = coord_x_start
coord_y = coord_y_start
# starting from lipid on the top layer
current_point = point.Point(coord_x, coord_y, dx_lipid, dy_offset,
'LP', 'LP')
init_conc = 0
for i in range(self.nx): # verticle direction up to down
water_frac = water_frac_surface + (
current_point.x_coord - coord_x_start) * water_increment_per_x
for j in range(self.ny): # lateral direction left to right
idx = i * self.ny + j
# assign type
if current_point.x_type == 'LP' or current_point.y_type == 'LP':
# Entire lipid layer (1st ==) or lateral lipid between two coreneocytes (2nd ==)
name = 'LP'
else: # corneocyte
name = 'CC'
# and then create meshes
Kw, D = self.compParDiff(name, chem, water_frac,
water_frac_sat, self.V_mortar,
self.V_brick, self.V_all, self.eta)
self.meshes[idx].setup(name, chem, init_conc, Kw, D,
current_point.x_coord,
current_point.y_coord, current_point.dx,
current_point.dy, self.dz_dtheta)
### update current_point, fairly complicated
if j == self.ny - 1: # last element in the lateral direction, move down
idx_x += 1
coord_y = coord_y_start
if current_point.x_type == 'LP':
coord_x += dx_lipid
if idx_x == self.nx_grids_lipid: # reaching end of lateral lipid layer
if cc_subtype_offset == 0 or cc_subtype_offset == 2:
current_point.setPoint(coord_x, coord_y, dx_cc,
dy_offset, 'CC', 'CC')
elif cc_subtype_offset == 1:
if not bOffset:
current_point.setPoint(
coord_x, coord_y, dx_cc, dy_offset,
'CC', 'CC')
else:
current_point.setPoint(
coord_x, coord_y, dx_cc, dy_offset,
'CC', 'LP')
elif cc_subtype_offset == 3:
if not bOffset:
current_point.setPoint(
coord_x, coord_y, dx_cc, dy_offset,
'CC', 'LP')
else:
current_point.setPoint(
coord_x, coord_y, dx_cc, dy_offset,
'CC', 'CC')
else:
raise ValueError('Invalid subtype name')
idx_x = 0
else: # NOT reaching end of lateral lipid layer
current_point.setPoint(coord_x, coord_y, dx_lipid,
dy_offset, 'LP', 'LP')
elif current_point.x_type == 'CC':
coord_x += dx_cc
if idx_x == self.nx_grids_cc: # reaching end of lateral corneocyte layer
current_point.setPoint(coord_x, coord_y, dx_lipid,
dy_offset, 'LP', 'LP')
idx_x = 0
bOffset = not bOffset
else: # NOT reaching end of lateral corneocyte layer
if cc_subtype_offset == 0 or cc_subtype_offset == 2:
current_point.setPoint(coord_x, coord_y, dx_cc,
dy_offset, 'CC', 'CC')
elif cc_subtype_offset == 1:
if not bOffset:
current_point.setPoint(
coord_x, coord_y, dx_cc, dy_offset,
'CC', 'CC')
else:
current_point.setPoint(
coord_x, coord_y, dx_cc, dy_offset,
'CC', 'LP')
elif cc_subtype_offset == 3:
if not bOffset:
current_point.setPoint(
coord_x, coord_y, dx_cc, dy_offset,
'CC', 'LP')
else:
current_point.setPoint(
coord_x, coord_y, dx_cc, dy_offset,
'CC', 'CC')
else:
raise ValueError('Invalid subtype name')
else:
raise ValueError('Invalid current_point.x_type')
idx_y = idx_y_offset
cc_subtype = cc_subtype_offset
else: # not the last element in the lateral direction, thus move to the right
idx_y += 1
if current_point.x_type == 'LP': # current row is lipid
if cc_subtype == 0: # now within dh
coord_y += dy_cc
if idx_y == self.ny_grids_cc_dn:
current_point.setPoint(coord_x, coord_y,
dx_lipid, dy_lipid,
'LP', 'LP')
idx_y = 0
cc_subtype += 1
else:
current_point.setPoint(coord_x, coord_y,
dx_lipid, dy_cc, 'LP',
'LP')
elif cc_subtype == 1: # now within s
coord_y += dy_lipid
if idx_y == self.ny_grids_lipid:
current_point.setPoint(coord_x, coord_y,
dx_lipid, dy_cc, 'LP',
'LP')
idx_y = 0
cc_subtype += 1
else:
current_point.setPoint(coord_x, coord_y,
dx_lipid, dy_lipid,
'LP', 'LP')
elif cc_subtype == 2: # now wtihin dm
coord_y += dy_cc
if idx_y == self.ny_grids_cc_dn * self.w:
current_point.setPoint(coord_x, coord_y,
dx_lipid, dy_lipid,
'LP', 'LP')
idx_y = 0
cc_subtype += 1
else:
current_point.setPoint(coord_x, coord_y,
dx_lipid, dy_cc, 'LP',
'LP')
elif cc_subtype == 3: # now within the 2nd s
coord_y += dy_lipid
if idx_y == self.ny_grids_lipid:
current_point.setPoint(coord_x, coord_y,
dx_lipid, dy_cc, 'LP',
'LP')
idx_y = 0
cc_subtype = 0
else:
current_point.setPoint(coord_x, coord_y,
dx_lipid, dy_lipid,
'LP', 'LP')
else:
raise ValueError('Invalid cc_subtype')
elif current_point.x_type == 'CC': # current row is corneocyte
if cc_subtype == 0: # now within dh
coord_y += dy_cc
if idx_y == self.ny_grids_cc_dn:
if bOffset:
current_point.setPoint(
coord_x, coord_y, dx_cc, dy_lipid,
'CC', 'LP')
else:
current_point.setPoint(
coord_x, coord_y, dx_cc, dy_lipid,
'CC', 'CC')
idx_y = 0
cc_subtype += 1
else:
current_point.setPoint(coord_x, coord_y, dx_cc,
dy_cc, 'CC', 'CC')
elif cc_subtype == 1: # now within s
coord_y += dy_lipid
if idx_y == self.ny_grids_lipid:
current_point.setPoint(coord_x, coord_y, dx_cc,
dy_cc, 'CC', 'CC')
idx_y = 0
cc_subtype += 1
else:
if bOffset:
current_point.setPoint(
coord_x, coord_y, dx_cc, dy_lipid,
'CC', 'LP')
else:
current_point.setPoint(
coord_x, coord_y, dx_cc, dy_lipid,
'CC', 'CC')
elif cc_subtype == 2: # now wtihin dm
coord_y += dy_cc
if idx_y == self.ny_grids_cc_dn * self.w:
if bOffset:
current_point.setPoint(
coord_x, coord_y, dx_cc, dy_lipid,
'CC', 'CC')
else:
current_point.setPoint(
coord_x, coord_y, dx_cc, dy_lipid,
'CC', 'LP')
idx_y = 0
cc_subtype += 1
else:
current_point.setPoint(coord_x, coord_y, dx_cc,
dy_cc, 'CC', 'CC')
elif cc_subtype == 3: # now within the 2nd s
coord_y += dy_lipid
if idx_y == self.ny_grids_lipid:
current_point.setPoint(coord_x, coord_y, dx_cc,
dy_cc, 'CC', 'CC')
idx_y = 0
cc_subtype = 0
else:
if bOffset:
current_point.setPoint(
coord_x, coord_y, dx_cc, dy_lipid,
'CC', 'CC')
else:
current_point.setPoint(
coord_x, coord_y, dx_cc, dy_lipid,
'CC', 'LP')
else:
raise ValueError('Invalid cc_subtype')
else:
raise ValueError('Invalid current_point.x_type')