def invert_epochs(epochs, end=None):
"""inverts epochs inverted
The first epoch will be mapped to [0, start] and the last will be mapped
to [end of last epoch, :end:]. Epochs that accidentally become negative
or zero-length will be omitted.
:type epochs: ndarray
:param epochs: epoch set to invert
:type end: int
:param end: If not None, it i taken for the end of the last epoch,
else max(index-dtype) is taken instead.
Default=None
:returns: ndarray - inverted epoch set
"""
# checks
if end is None:
end = sp.iinfo(INDEX_DTYPE).max
else:
end = INDEX_DTYPE.type(end)
# flip them
rval = sp.vstack((sp.concatenate(([0], epochs[:, 1])), sp.concatenate((epochs[:, 0], [end])))).T
return (rval[rval[:, 1] - rval[:, 0] > 0]).astype(INDEX_DTYPE)
def invert_epochs(epochs, end=None):
"""inverts epochs inverted
The first epoch will be mapped to [0, start] and the last will be mapped
to [end of last epoch, :end:]. Epochs that accidentally become negative
or zero-length will be omitted.
:type epochs: ndarray
:param epochs: epoch set to invert
:type end: int
:param end: If not None, it i taken for the end of the last epoch,
else max(index-dtype) is taken instead.
Default=None
:returns: ndarray - inverted epoch set
"""
# checks
if end is None:
end = sp.iinfo(INDEX_DTYPE).max
else:
end = INDEX_DTYPE.type(end)
# flip them
rval = sp.vstack((sp.concatenate(
([0], epochs[:, 1])), sp.concatenate((epochs[:, 0], [end])))).T
return (rval[rval[:, 1] - rval[:, 0] > 0]).astype(INDEX_DTYPE)
def _generate_masked_mesh(self, cell_mask=None):
r"""
Generates the mesh based on the cell mask provided
"""
#
if cell_mask is None:
cell_mask = sp.ones(self.data_map.shape, dtype=bool)
#
# initializing arrays
self._edges = sp.ones(0, dtype=str)
self._merge_patch_pairs = sp.ones(0, dtype=str)
self._create_blocks(cell_mask)
#
# building face arrays
mapper = sp.ravel(sp.array(cell_mask, dtype=int))
mapper[mapper == 1] = sp.arange(sp.count_nonzero(mapper))
mapper = sp.reshape(mapper, (self.nz, self.nx))
mapper[~cell_mask] = -sp.iinfo(int).max
#
boundary_dict = {
'bottom':
{'bottom': mapper[0, :][cell_mask[0, :]]},
'top':
{'top': mapper[-1, :][cell_mask[-1, :]]},
'left':
{'left': mapper[:, 0][cell_mask[:, 0]]},
'right':
{'right': mapper[:, -1][cell_mask[:, -1]]},
'front':
{'front': mapper[cell_mask]},
'back':
{'back': mapper[cell_mask]},
'internal':
{'bottom': [], 'top': [], 'left': [], 'right': []}
}
#
# determining cells linked to a masked cell
cell_mask = sp.where(~sp.ravel(cell_mask))[0]
inds = sp.in1d(self._field._cell_interfaces, cell_mask)
inds = sp.reshape(inds, (len(self._field._cell_interfaces), 2))
inds = inds[:, 0].astype(int) + inds[:, 1].astype(int)
inds = (inds == 1)
links = self._field._cell_interfaces[inds]
#
# adjusting order so masked cells are all on links[:, 1]
swap = sp.in1d(links[:, 0], cell_mask)
links[swap] = links[swap, ::-1]
#
# setting side based on index difference
sides = sp.ndarray(len(links), dtype='<U6')
sides[sp.where(links[:, 1] == links[:, 0]-self.nx)[0]] = 'bottom'
sides[sp.where(links[:, 1] == links[:, 0]+self.nx)[0]] = 'top'
sides[sp.where(links[:, 1] == links[:, 0]-1)[0]] = 'left'
sides[sp.where(links[:, 1] == links[:, 0]+1)[0]] = 'right'
#
# adding each block to the internal face dictionary
inds = sp.ravel(mapper)[links[:, 0]]
for side, block_id in zip(sides, inds):
boundary_dict['internal'][side].append(block_id)
self.set_boundary_patches(boundary_dict, reset=True)
def set_boundary_patches(self, boundary_blocks, reset=False):
r"""
Sets up boundary patches based on the dictionary passed in. Overlapping
declarations are overwritten by the last patch to use that face.
The boundary blocks dictionary contains a dictionary entry for
each patch name.
- boundary_blocks dictionary has the format of:
{patch_name: {
<side>: [ block-list ],
<side>: [ block-list ],
...
},
...
}
where <side> is left, right, bottom, top, front or back
and block list is a list of blocks to add that patch to the
side of.
- reset - boolean : if True then the face labels dictionary
and _faces array are re-initialized to default values
"""
#
offsets = {
'bottom': (0, (0, 1, 2, 3)),
'back': (1, (0, 1, 5, 4)),
'right': (2, (1, 2, 6, 5)),
'front': (3, (3, 2, 6, 7)),
'left': (4, (0, 3, 7, 4)),
'top': (5, (4, 5, 6, 7)),
}
#
# re-initializing all face labels
num_faces = 6 * len(self._blocks)
if reset:
self._faces = sp.ones(
(num_faces, 4), dtype=int) * -sp.iinfo(int).max
self.face_labels = {}
#
# adding any new face labels to the dictionary
for patch_name in boundary_blocks.keys():
key = 'boundary.' + patch_name
if key not in self.face_labels.keys():
self.face_labels[key] = sp.zeros(num_faces, dtype=bool)
#
# setting new face labels
for patch_name, side_dict in boundary_blocks.items():
for side, blocks in side_dict.items():
indices = sp.array(blocks, dtype=int) * 6 + offsets[side][0]
face_verts = self._blocks[blocks][:, offsets[side][1]]
self._faces[indices] = face_verts
self.face_labels['boundary.' + patch_name][indices] = True
#
# preventing overlapping face labels
for patch_name in boundary_blocks.keys():
indices = self.face_labels['boundary.' + patch_name]
reset = {key: indices for key in self.face_labels.keys()}
del reset['boundary.' + patch_name]
for key, indices in reset.items():
self.face_labels[key][indices] = False
def set_boundary_patches(self, boundary_blocks, reset=False):
r"""
Sets up boundary patches based on the dictionary passed in. Overlapping
declarations are overwritten by the last patch to use that face.
The boundary blocks dictionary contains a dictionary entry for
each patch name.
- boundary_blocks dictionary has the format of:
{patch_name: {
<side>: [ block-list ],
<side>: [ block-list ],
...
},
...
}
where <side> is left, right, bottom, top, front or back
and block list is a list of blocks to add that patch to the
side of.
- reset - boolean : if True then the face labels dictionary
and _faces array are re-initialized to default values
"""
#
offsets = {
'bottom': (0, (0, 1, 2, 3)),
'back': (1, (0, 1, 5, 4)),
'right': (2, (1, 2, 6, 5)),
'front': (3, (3, 2, 6, 7)),
'left': (4, (0, 3, 7, 4)),
'top': (5, (4, 5, 6, 7)),
}
#
# re-initializing all face labels
num_faces = 6 * len(self._blocks)
if reset:
self._faces = sp.ones((num_faces, 4), dtype=int)*-sp.iinfo(int).max
self.face_labels = {}
#
# adding any new face labels to the dictionary
for patch_name in boundary_blocks.keys():
key = 'boundary.'+patch_name
if key not in self.face_labels.keys():
self.face_labels[key] = sp.zeros(num_faces, dtype=bool)
#
# setting new face labels
for patch_name, side_dict in boundary_blocks.items():
for side, blocks in side_dict.items():
indices = sp.array(blocks, dtype=int) * 6 + offsets[side][0]
face_verts = self._blocks[blocks][:, offsets[side][1]]
self._faces[indices] = face_verts
self.face_labels['boundary.'+patch_name][indices] = True
#
# preventing overlapping face labels
for patch_name in boundary_blocks.keys():
indices = self.face_labels['boundary.'+patch_name]
reset = {key: indices for key in self.face_labels.keys()}
del reset['boundary.'+patch_name]
for key, indices in reset.items():
self.face_labels[key][indices] = False
def epochs_from_spiketrain(st, cut, end=None, with_corrected_st=False):
"""yields epoch set, given a spiketrain and cut parameter
:type st: ndarray
:param st: spiketrains as 1d array
:type cut: tuple
:param cut: 2-tuple of cutting parameters, (cut_left,cut_right) spike
epochs will be generated by using cut_left and cut_right on the spike
time. If an int is given, a symmetric cut tuple is assumed.
:type end: int
:param end: to determine potential problems with epochs overlapping data
boundaries. If an event in the spiketrain is closer to 0 than :cut[0]:
or closer to :end: than :cut[1]: the corresponding epoch will be
omitted. If None, :end: will be set to max(INDEX_DTYPE)
Default=None
:type with_corrected_st: bool
:param with_corrected_st: if True, return the corrected spiketrain by
omitting spike events that cannot generate valid spike epochs given
the passed cut settings.
Default=False
:returns: ndarray - epoch set of valid spike epochs, and if
:with_corrected_st: is True additionally the corrected spike train
"""
# checks
st = sp.asarray(st)
cut = get_cut(cut)
if end is None:
end = sp.iinfo(INDEX_DTYPE).max
else:
end = INDEX_DTYPE.type(end)
# return the epochs for the spiketrain
st_ok = (st >= cut[0]) * (st < end - cut[1])
rval = sp.vstack((
st[st_ok] - cut[0],
st[st_ok] + cut[1])).T.astype(INDEX_DTYPE)
## FIX: astype is handling float entries weird sometimes! take care to pass spiketrains as integer arrays!
## we are now correcting spike epochs to be of length sum(cut) by pruning the start of the epoch
tf = sum(cut)
for i in xrange(rval.shape[0]):
if rval[i, 1] - rval[i, 0] != tf:
rval[i, 0] = rval[i, 1] - tf
## XIF
if with_corrected_st is True:
return rval, st[st_ok]
else:
return rval
def epochs_from_spiketrain(st, cut, end=None, with_corrected_st=False):
"""yields epoch set, given a spiketrain and cut parameter
:type st: ndarray
:param st: spiketrains as 1d array
:type cut: tuple
:param cut: 2-tuple of cutting parameters, (cut_left,cut_right) spike
epochs will be generated by using cut_left and cut_right on the spike
time. If an int is given, a symmetric cut tuple is assumed.
:type end: int
:param end: to determine potential problems with epochs overlapping data
boundaries. If an event in the spiketrain is closer to 0 than :cut[0]:
or closer to :end: than :cut[1]: the corresponding epoch will be
omitted. If None, :end: will be set to max(INDEX_DTYPE)
Default=None
:type with_corrected_st: bool
:param with_corrected_st: if True, return the corrected spiketrain by
omitting spike events that cannot generate valid spike epochs given
the passed cut settings.
Default=False
:returns: ndarray - epoch set of valid spike epochs, and if
:with_corrected_st: is True additionally the corrected spike train
"""
# checks
st = sp.asarray(st)
cut = get_cut(cut)
if end is None:
end = sp.iinfo(INDEX_DTYPE).max
else:
end = INDEX_DTYPE.type(end)
# return the epochs for the spiketrain
st_ok = (st >= cut[0]) * (st < end - cut[1])
rval = sp.vstack(
(st[st_ok] - cut[0], st[st_ok] + cut[1])).T.astype(INDEX_DTYPE)
## FIX: astype is handling float entries weird sometimes! take care to pass spiketrains as integer arrays!
## we are now correcting spike epochs to be of length sum(cut) by pruning the start of the epoch
tf = sum(cut)
for i in xrange(rval.shape[0]):
if rval[i, 1] - rval[i, 0] != tf:
rval[i, 0] = rval[i, 1] - tf
## XIF
if with_corrected_st is True:
return rval, st[st_ok]
else:
return rval
def generate_offset_map(nonzero_locs, shape):
r"""
Creates a map storing the index of the lowest y-axis pixel in an
X-Z column.
"""
#
logger.info('creating initial offset map')
#
x_coords, y_coords, z_coords = sp.unravel_index(nonzero_locs, shape)
data = sp.ones(shape, dtype=sp.uint16)*sp.iinfo(sp.int16).max
data[x_coords, y_coords, z_coords] = y_coords
#
offset_map = sp.zeros((shape[0], shape[2]), dtype=sp.int16)
for z_index in range(shape[2]):
offset_map[:, z_index] = sp.amin(data[:, :, z_index], axis=1)
offset_map[:, z_index][offset_map[:, z_index] > shape[1]] = -1
#
return offset_map
def create_offset_map(self, no_data_fill=0):
r"""
Creates an offset map by storing the lowest voxel in each X-Z
column.
Parameters:
no_data_fill (numeric) - a value to use as the offset when a
column has no fracture voxels, sp.nan or sp.inf can be used.
"""
# getting coordinates of all fracture voxels
x_c, y_c, z_c = self.get_fracture_voxels(coordinates=True)
#
# recreating 3-D array with y coordinate as data values
data = sp.ones(self.shape, dtype=sp.uint16) * sp.iinfo(sp.int16).max
data[x_c, y_c, z_c] = y_c
del x_c, y_c, z_c
#
# generating offset map from data
offset_map = sp.zeros((self.nx, self.nz), dtype=float)
for z_ind in range(self.nz):
offset_map[:, z_ind] = sp.amin(data[:, :, z_ind], axis=1)
offset_map[:, z_ind][offset_map[:, z_ind] > self.ny] = no_data_fill
#
return offset_map.T
def generate_adjacency_matrix(conns, nonzero_locs):
r"""
generates a ajacency matrix based on connectivity array
"""
msg = 're-indexing connections array from absolute to relative indicies'
logger.info(msg)
mapper = sp.ones(nonzero_locs[-1] + 1, dtype=sp.uint32) * sp.iinfo(
sp.uint32).max
mapper[nonzero_locs] = sp.arange(nonzero_locs.size, dtype=sp.uint32)
conns[:, 0] = mapper[conns[:, 0]]
conns[:, 1] = mapper[conns[:, 1]]
del mapper
#
logger.info('creating adjacency matrix...')
num_blks = nonzero_locs.size
row = sp.append(conns[:, 0], conns[:, 1])
col = sp.append(conns[:, 1], conns[:, 0])
weights = sp.ones(conns.size) # using size automatically multiplies by 2
#
# Generate sparse adjacency matrix in 'coo' format and convert to csr
adj_mat = sprs.coo_matrix((weights, (row, col)), (num_blks, num_blks))
adj_mat = adj_mat.tocsr()
#
return adj_mat
def _setup_region(self, region_id, z_slice, x_slice, **kwargs):
r"""
sets up an individual mesh region
"""
#
sides = ['left', 'right', 'bottom', 'top']
patches = ['mergeLR{}', 'mergeRL{}', 'mergeBT{}', 'mergeTB{}']
labels = ['boundary.' + patch for patch in patches]
external_patches = {side: side for side in sides}
#
# setting offset values and region
x_offset = x_slice.start
z_offset = z_slice.start
region = DataFieldRegion(self.data_map[z_slice, x_slice],
self.point_data[z_slice, x_slice, :])
offset_reg = DataFieldRegion(self.offset_map[z_slice, x_slice],
self.offset_points[z_slice, x_slice, :])
#
# creating regional mesh
args = [
region, self.avg_fact, x_offset, z_offset, self.mesh_params,
offset_reg
]
region_mesh = BlockMeshRegion(*args)
region_mesh._generate_masked_mesh(cell_mask=self._mask[z_slice,
x_slice])
#
# need to test for holes on merge boundaries and change patch to internal
# creating map indexed 1:_blocks.size but with shape of (nz, nx)
mesh_map = sp.ones(region_mesh.data_vector.size, dtype=int)
mesh_map *= -sp.iinfo(int).max
inds = sp.where(region_mesh.data_vector > 0)[0]
mesh_map[inds] = sp.arange(inds.size)
mesh_map = sp.reshape(mesh_map, region_mesh.data_map.shape)
boundary_dict = {
'internal': {
'bottom': [],
'top': [],
'left': [],
'right': []
}
}
#
# updating patches
sides = {}
if x_slice.start != 0:
sides['left'] = 0
for iz in range(region_mesh.nz):
IZ = iz + z_offset
IX = x_offset
if self._mask[IZ, IX] and not self._mask[IZ, IX - 1]:
boundary_dict['internal']['left'].append(mesh_map[iz, 0])
#
if x_slice.stop != self.nx:
sides['right'] = 1
for iz in range(region_mesh.nz):
IZ = iz + z_offset
IX = x_offset + region_mesh.nx - 1
if self._mask[IZ, IX] and not self._mask[IZ, IX + 1]:
boundary_dict['internal']['right'].append(mesh_map[iz, -1])
#
if z_slice.start != 0:
sides['bottom'] = 2
for ix in range(region_mesh.nx):
IZ = z_offset
IX = ix + x_offset
if self._mask[IZ, IX] and not self._mask[IZ - 1, IX]:
boundary_dict['internal']['bottom'].append(mesh_map[0, ix])
#
if z_slice.stop != self.nz:
sides['top'] = 3
for ix in range(region_mesh.nx):
IZ = z_offset + region_mesh.nz - 1
IX = ix + x_offset
if self._mask[IZ, IX] and not self._mask[IZ + 1, IX]:
boundary_dict['internal']['top'].append(mesh_map[-1, ix])
#
face_labels = region_mesh.face_labels
for side, index in sides.items():
label = labels[index].format(region_id)
external_patches[side] = patches[index].format(region_id)
region_mesh.mesh_params[label + '.type'] = 'empty'
region_mesh.face_labels[label] = face_labels.pop('boundary.' +
side)
region_mesh.set_boundary_patches(boundary_dict)
#
# setting up initial MergeGroup as an individual region
group = MergeGroup(region_id, external_patches,
kwargs.get('path', '.'))
self.merge_groups.append(group)
#
return region_mesh
import logging
import scipy as sp
##---PACKAGE-LOGGING
logging.basicConfig(level=logging.DEBUG, format='')
log = logging.getLogger('BOTMpy')
##---CONSTANTS
## index type
INDEX_DTYPE = sp.dtype(sp.int64)
## integer max values
SI8MAX = sp.iinfo(sp.int8).max
SI16MAX = sp.iinfo(sp.int16).max
SI32MAX = sp.iinfo(sp.int32).max
SI64MAX = sp.iinfo(sp.int64).max
UI8MAX = sp.iinfo(sp.uint8).max
UI16MAX = sp.iinfo(sp.uint16).max
UI32MAX = sp.iinfo(sp.uint32).max
UI64MAX = sp.iinfo(sp.uint64).max
## CLASSES
class VERBOSE(object):
"""verbosity manager"""
# default modes
def __array_finalize__(self, obj):
#
# setting the type of integer that fits the flattened array index
itype = sp.uint32 if (self.size < sp.iinfo(sp.uint32).max) else sp.uint
self.index_int_type = itype
def _generate_masked_mesh(self, cell_mask=None):
r"""
Generates the mesh based on the cell mask provided
"""
#
if cell_mask is None:
cell_mask = sp.ones(self.data_map.shape, dtype=bool)
#
# initializing arrays
self._edges = sp.ones(0, dtype=str)
self._merge_patch_pairs = sp.ones(0, dtype=str)
self._create_blocks(cell_mask)
#
# building face arrays
mapper = sp.ravel(sp.array(cell_mask, dtype=int))
mapper[mapper == 1] = sp.arange(sp.count_nonzero(mapper))
mapper = sp.reshape(mapper, (self.nz, self.nx))
mapper[~cell_mask] = -sp.iinfo(int).max
#
boundary_dict = {
'bottom': {
'bottom': mapper[0, :][cell_mask[0, :]]
},
'top': {
'top': mapper[-1, :][cell_mask[-1, :]]
},
'left': {
'left': mapper[:, 0][cell_mask[:, 0]]
},
'right': {
'right': mapper[:, -1][cell_mask[:, -1]]
},
'front': {
'front': mapper[cell_mask]
},
'back': {
'back': mapper[cell_mask]
},
'internal': {
'bottom': [],
'top': [],
'left': [],
'right': []
}
}
#
# determining cells linked to a masked cell
cell_mask = sp.where(~sp.ravel(cell_mask))[0]
inds = sp.in1d(self._field._cell_interfaces, cell_mask)
inds = sp.reshape(inds, (len(self._field._cell_interfaces), 2))
inds = inds[:, 0].astype(int) + inds[:, 1].astype(int)
inds = (inds == 1)
links = self._field._cell_interfaces[inds]
#
# adjusting order so masked cells are all on links[:, 1]
swap = sp.in1d(links[:, 0], cell_mask)
links[swap] = links[swap, ::-1]
#
# setting side based on index difference
sides = sp.ndarray(len(links), dtype='<U6')
sides[sp.where(links[:, 1] == links[:, 0] - self.nx)[0]] = 'bottom'
sides[sp.where(links[:, 1] == links[:, 0] + self.nx)[0]] = 'top'
sides[sp.where(links[:, 1] == links[:, 0] - 1)[0]] = 'left'
sides[sp.where(links[:, 1] == links[:, 0] + 1)[0]] = 'right'
#
# adding each block to the internal face dictionary
inds = sp.ravel(mapper)[links[:, 0]]
for side, block_id in zip(sides, inds):
boundary_dict['internal'][side].append(block_id)
self.set_boundary_patches(boundary_dict, reset=True)
import logging
import scipy as sp
##---PACKAGE-LOGGING
logging.basicConfig(level=logging.DEBUG, format='')
log = logging.getLogger('BOTMpy')
##---CONSTANTS
## index type
INDEX_DTYPE = sp.dtype(sp.int64)
## integer max values
SI8MAX = sp.iinfo(sp.int8).max
SI16MAX = sp.iinfo(sp.int16).max
SI32MAX = sp.iinfo(sp.int32).max
SI64MAX = sp.iinfo(sp.int64).max
UI8MAX = sp.iinfo(sp.uint8).max
UI16MAX = sp.iinfo(sp.uint16).max
UI32MAX = sp.iinfo(sp.uint32).max
UI64MAX = sp.iinfo(sp.uint64).max
## CLASSES
class VERBOSE(object):
"""verbosity manager"""
# default modes
def _setup_region(self, region_id, z_slice, x_slice, **kwargs):
r"""
sets up an individual mesh region
"""
#
sides = ['left', 'right', 'bottom', 'top']
patches = ['mergeLR{}', 'mergeRL{}', 'mergeBT{}', 'mergeTB{}']
labels = ['boundary.'+patch for patch in patches]
external_patches = {side: side for side in sides}
#
# setting offset values and region
x_offset = x_slice.start
z_offset = z_slice.start
region = DataFieldRegion(self.data_map[z_slice, x_slice],
self.point_data[z_slice, x_slice, :])
offset_reg = DataFieldRegion(self.offset_map[z_slice, x_slice],
self.offset_points[z_slice, x_slice, :])
#
# creating regional mesh
args = [region, self.avg_fact, x_offset,
z_offset, self.mesh_params, offset_reg]
region_mesh = BlockMeshRegion(*args)
region_mesh._generate_masked_mesh(cell_mask=self._mask[z_slice, x_slice])
#
# need to test for holes on merge boundaries and change patch to internal
# creating map indexed 1:_blocks.size but with shape of (nz, nx)
mesh_map = sp.ones(region_mesh.data_vector.size, dtype=int)
mesh_map *= -sp.iinfo(int).max
inds = sp.where(region_mesh.data_vector > 0)[0]
mesh_map[inds] = sp.arange(inds.size)
mesh_map = sp.reshape(mesh_map, region_mesh.data_map.shape)
boundary_dict = {
'internal':
{'bottom': [], 'top': [], 'left': [], 'right': []}
}
#
# updating patches
sides = {}
if x_slice.start != 0:
sides['left'] = 0
for iz in range(region_mesh.nz):
IZ = iz + z_offset
IX = x_offset
if self._mask[IZ, IX] and not self._mask[IZ, IX-1]:
boundary_dict['internal']['left'].append(mesh_map[iz, 0])
#
if x_slice.stop != self.nx:
sides['right'] = 1
for iz in range(region_mesh.nz):
IZ = iz + z_offset
IX = x_offset + region_mesh.nx - 1
if self._mask[IZ, IX] and not self._mask[IZ, IX+1]:
boundary_dict['internal']['right'].append(mesh_map[iz, -1])
#
if z_slice.start != 0:
sides['bottom'] = 2
for ix in range(region_mesh.nx):
IZ = z_offset
IX = ix + x_offset
if self._mask[IZ, IX] and not self._mask[IZ-1, IX]:
boundary_dict['internal']['bottom'].append(mesh_map[0, ix])
#
if z_slice.stop != self.nz:
sides['top'] = 3
for ix in range(region_mesh.nx):
IZ = z_offset + region_mesh.nz - 1
IX = ix + x_offset
if self._mask[IZ, IX] and not self._mask[IZ+1, IX]:
boundary_dict['internal']['top'].append(mesh_map[-1, ix])
#
face_labels = region_mesh.face_labels
for side, index in sides.items():
label = labels[index].format(region_id)
external_patches[side] = patches[index].format(region_id)
region_mesh.mesh_params[label+'.type'] = 'empty'
region_mesh.face_labels[label] = face_labels.pop('boundary.'+side)
region_mesh.set_boundary_patches(boundary_dict)
#
# setting up initial MergeGroup as an individual region
group = MergeGroup(region_id, external_patches, kwargs.get('path', '.'))
self.merge_groups.append(group)
#
return region_mesh
