Ejemplo n.º 1
0
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)
Ejemplo n.º 2
0
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)
Ejemplo n.º 4
0
    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
Ejemplo n.º 6
0
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
Ejemplo n.º 7
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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
Ejemplo n.º 9
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 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
Ejemplo n.º 11
0
 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
Ejemplo n.º 12
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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
Ejemplo n.º 13
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 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
Ejemplo n.º 14
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 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)
Ejemplo n.º 15
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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