"""Support Disperse I/O.

The reader is based on a description of the structure using Kaitai (https://kaitai.io/).
"""

import numpy as np
import pandas as pd

from ..utilities.decorators import read_files
from ..utilities.types import FloatArrayType, PathType
from .disperse_reader import DisperseReader


class Disperse:
    """Read a disperse NDskl file.

    Parameters
    ----------
    fname : str, filename
    """

    @read_files(1)
    def __init__(self, fname: PathType):
        self.fname = fname
        self.read()

    def read(self):
        ds = DisperseReader.from_file(self.fname)

        # Gather data
        nnode, nnode_data, ndim = ds.header.nnode, ds.header.nnode_data, ds.header.ndim
        node_pos = np.asarray(ds.data.node_pos).reshape((nnode, ndim))
        node_data = np.asarray(ds.data.node_data).reshape((nnode, nnode_data))

        nseg, nseg_data = ds.header.nseg, ds.header.nseg_data
        seg_data = np.asarray(ds.data.seg_data).reshape((nseg, nseg_data))

        #  # Gather information about nodes
        _v1 = pd.DataFrame(
            [
                (*node_pos[s0.pos_index], s0.index, s0.flags, s0.type)
                for s0 in ds.data.node_data_int
            ],
            columns=["x", "y", "z", "index", "flags", "type"],
        ).set_index("index")

        _v2 = pd.DataFrame(
            node_data,
            columns=[_.replace("\x00", "") for _ in ds.header.node_data_info],
            index=_v1.index,
        )
        # Parse what's integer as integer
        int_columns = ["parent_index", "persistence_pair"]
        for c in int_columns:
            _v2[c] = _v2[c].astype(int)

        node_ds = pd.concat((_v1, _v2), axis=1)
        node_ds["type_s"] = [
            ("void", "wall", "filament", "peak")[_] for _ in node_ds.type
        ]

        #  # Gather information about segments
        _v1 = pd.DataFrame(
            [
                (s0.index, s0.node_ids[0], s0.node_ids[1], s0.prev_seg, s0.next_seg)
                for s0 in ds.data.seg_data_int
            ],
            columns=["index", "node_start", "node_end", "seg_prev", "seg_next"],
        )
        _v1 = _v1.set_index("index")
        _v2 = pd.DataFrame(
            seg_data,
            columns=[_.replace("\x00", "") for _ in ds.header.seg_data_info],
            index=_v1.index,
        )
        # Parse what's integer as integer
        int_columns = ["type", "orientation"]
        for c in int_columns:
            _v2[c] = _v2[c].astype(int)
        # Replace off-bound values by dummy values
        _v1.loc[_v1["seg_prev"] > ds.header.nseg, "seg_prev"] = ds.header.nseg
        _v1.loc[_v1["seg_next"] > ds.header.nseg, "seg_next"] = ds.header.nseg

        seg_ds = pd.concat((_v1, _v2), axis=1)

        seg_ds["node_start_type"] = node_ds["type"].iloc[seg_ds["node_start"]].values
        seg_ds["node_end_type"] = node_ds["type"].iloc[seg_ds["node_end"]].values

        self.nodes = node_ds
        self.segments = seg_ds
        self.disperse_source = ds

    def segment_positions(self) -> FloatArrayType:
        """Compute the segment position.

        Returns
        -------
        pos : np.ndarray, shape (nsegment, 2, ndim)
            The start/end of all segments.
        """
        nseg = self.disperse_source.header.nseg
        ndim = self.disperse_source.header.ndim
        pos = np.asarray(self.disperse_source.data.seg_pos).reshape(nseg, 2, ndim)
        return pos

"""Support Disperse I/O.

The reader is based on a description of the structure using Kaitai (https://kaitai.io/).
"""

import numpy as np
import pandas as pd

from ..utilities.decorators import read_files
from ..utilities.types import FloatArrayType, PathType
from .disperse_reader import DisperseReader


class Disperse:
    """Read a disperse NDskl file.

    Parameters
    ----------
    fname : str, filename
    """

    @read_files(1)
    def __init__(self, fname: PathType):
        self.fname = fname
        self.read()

    def read(self):
        ds = DisperseReader.from_file(self.fname)

        # Gather data
        nnode, nnode_data, ndim = ds.header.nnode, ds.header.nnode_data, ds.header.ndim
        node_pos = np.asarray(ds.data.node_pos).reshape((nnode, ndim))
        node_data = np.asarray(ds.data.node_data).reshape((nnode, nnode_data))

        nseg, nseg_data = ds.header.nseg, ds.header.nseg_data
        seg_data = np.asarray(ds.data.seg_data).reshape((nseg, nseg_data))

        #  # Gather information about nodes
        _v1 = pd.DataFrame(
            [
                (*node_pos[s0.pos_index], s0.index, s0.flags, s0.type)
                for s0 in ds.data.node_data_int
            ],
            columns=["x", "y", "z", "index", "flags", "type"],
        ).set_index("index")

        _v2 = pd.DataFrame(
            node_data,
            columns=[_.replace("\x00", "") for _ in ds.header.node_data_info],
            index=_v1.index,
        )
        # Parse what's integer as integer
        int_columns = ["parent_index", "persistence_pair"]
        for c in int_columns:
            _v2[c] = _v2[c].astype(int)

        node_ds = pd.concat((_v1, _v2), axis=1)
        node_ds["type_s"] = [
            ("void", "wall", "filament", "peak")[_] for _ in node_ds.type
        ]

        #  # Gather information about segments
        _v1 = pd.DataFrame(
            [
                (s0.index, s0.node_ids[0], s0.node_ids[1], s0.prev_seg, s0.next_seg)
                for s0 in ds.data.seg_data_int
            ],
            columns=["index", "node_start", "node_end", "seg_prev", "seg_next"],
        )
        _v1 = _v1.set_index("index")
        _v2 = pd.DataFrame(
            seg_data,
            columns=[_.replace("\x00", "") for _ in ds.header.seg_data_info],
            index=_v1.index,
        )
        # Parse what's integer as integer
        int_columns = ["type", "orientation"]
        for c in int_columns:
            _v2[c] = _v2[c].astype(int)
        # Replace off-bound values by dummy values
        _v1.loc[_v1["seg_prev"] > ds.header.nseg, "seg_prev"] = ds.header.nseg
        _v1.loc[_v1["seg_next"] > ds.header.nseg, "seg_next"] = ds.header.nseg

        seg_ds = pd.concat((_v1, _v2), axis=1)

        seg_ds["node_start_type"] = node_ds["type"].iloc[seg_ds["node_start"]].values
        seg_ds["node_end_type"] = node_ds["type"].iloc[seg_ds["node_end"]].values

        self.nodes = node_ds
        self.segments = seg_ds
        self.disperse_source = ds

    def segment_positions(self) -> FloatArrayType:
        """Compute the segment position.

        Returns
        -------
        pos : np.ndarray, shape (nsegment, 2, ndim)
            The start/end of all segments.
        """
        nseg = self.disperse_source.header.nseg
        ndim = self.disperse_source.header.ndim
        pos = np.asarray(self.disperse_source.data.seg_pos).reshape(nseg, 2, ndim)
        return pos

Support Disperse I/O.  The reader is based on a description of the structure using Kaitai (https://kaitai.io/). Read a disperse NDskl file.      Parameters     ----------     fname : str, filename # Gather data #  # Gather information about nodes # Parse what's integer as integer #  # Gather information about segments # Parse what's integer as integer # Replace off-bound values by dummy values Compute the segment position.          Returns         -------         pos : np.ndarray, shape (nsegment, 2, ndim)             The start/end of all segments.