DPQ/dataset.py at main · Biomedical-Simulation-Lab/DPQ · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
import sys
import os
from pathlib import Path
import numpy as np
#import scipy.linalg as la
import math
import h5py
import pyvista as pv
import vtk

class Dataset():
    """ Load BSL-specific data and common ops.
    """
    def __init__(self, folder, mesh_folder = None, file_glob_key=None, file_stride=1, case_name=None, wss_files=False):
        self.folder = Path(folder)
        if case_name is not None:
            self.case_name=case_name

        if file_glob_key is None:
            file_glob_key = '*_curcyc_*up.h5'

        mesh_glob_key = '*h5'
        if mesh_folder is None:
            #get from data path instead of results path
            self.folder_data=self.folder.parents[0] / ('data')
            print(self.folder_data)
            self.mesh_file = sorted(self.folder_data.glob(mesh_glob_key), key=lambda x: len(x.stem))[0]
            self.ts = '_ts='
            self.tssplit = '_'
            self.different_folders=False
        else:
            self.mesh_file = sorted(mesh_folder.glob(mesh_glob_key), key=lambda x: len(x.stem))[0]
            self.ts='_tstep='
            self.tssplit='.'
            self.different_folders=True

        self.up_files = sorted(self.folder.glob(file_glob_key), key=self._get_ts)[::int(file_stride)]
        self.tsteps = len(sorted(self.folder.glob(file_glob_key), key=self._get_ts)[::int(file_stride)])
        self.times = sorted(self.folder.glob(file_glob_key), key=self._get_time)[::int(file_stride)]
        if wss_files:
            wss_folder = folder / ('wss_files')
            self.wss_files = sorted(self.folder.glob(file_glob_key), key=self._get_ts)[::int(file_stride)]


    def __call__(self, idx=0, array='u', file=None):
        """ Return velocity in u_file. """
        if array in ['u', 'p']:
            if file==None:
                h5_file = self.up_files[idx]
            else:
                h5_file=file
            with h5py.File(h5_file, 'r') as hf:
                if self.different_folders:
                    val = np.array(hf[array])
                else:
                    val = np.array(hf['Solution'][array])
        else:
            if array in ['wss', 'qcriterion']:
                if file==None:
                    h5_file = self.wss_files[idx]
                else:
                    h5_file=file
                with h5py.File(h5_file, 'r') as hf:
                    val = np.array(hf['Computed'][array])
            else:
                h5_file = file
                with h5py.File(h5_file, 'r') as hf:
                    val = np.array(hf[array])
        return val

    def _get_ts(self, h5_file):
        """ Given a simulation h5_file, get ts. """
        return int(h5_file.stem.split(self.ts)[1].split(self.tssplit)[0])

    def _get_ts_swirl(self, h5_file):
        """ Given a different h5_file, get ts. """
        return int(h5_file.stem.split('_')[1].split('.')[0])

    def _get_time(self, h5_file):
        """ Given a simulation h5_file, get time. """
        return float(h5_file.stem.split('_t=')[1].split('_')[0]) / 1000.0

    def check_cells(self):
        #print(self.mesh.n_cells)
        cellsize=self.mesh.compute_cell_sizes().cell_data['Volume']
        neg=np.flatnonzero(cellsize<0)
        #mark the boundary cells:
        self.mesh.cell_data['boundary']=np.zeros(self.mesh.n_cells)
        self.mesh.cell_data['boundary'][neg]=1
        #print(np.sum(self.mesh.cell_data['boundary']))
        self.mesh=self.mesh.cell_data_to_point_data()
        #now swap the last two indices of those cells:
        n3=5*neg+2
        n4=5*neg+3
        cells = self.mesh.cells.copy()
        cells_n3=cells[n3].copy()
        cells_n4=cells[n4].copy()
        cells[n3]=cells_n4
        cells[n4]=cells_n3
        self.mesh.cells = cells
        cellsize=self.mesh.compute_cell_sizes().cell_data['Volume']
        new_neg=np.flatnonzero(cellsize<0)
        if len(new_neg)>0:
            print("check_cells didn't work!")
            sys.exit()
        return self

    def assemble_mesh(self):
        """ Create UnstructuredGrid from h5 mesh file. """
        assert self.mesh_file.exists(), 'mesh_file does not exist.'
        #self.mesh_file='../mesh_rez/cases/case_C/case_106_ultraultralow/data/PTSeg106_ultraultralow.h5'

        with h5py.File(self.mesh_file, 'r') as hf:
            points = np.array(hf['Mesh']['coordinates'])*(10**-3)
            cells = np.array(hf['Mesh']['topology'])

            celltypes = np.empty(cells.shape[0], dtype=np.uint8)
            celltypes[:] = vtk.VTK_TETRA
            cell_type = np.ones((cells.shape[0], 1), dtype=int) * 4
            cells = np.concatenate([cell_type, cells], axis = 1)
            self.mesh = pv.UnstructuredGrid(cells.ravel(), celltypes, points)
            self=self.check_cells()

            w_points = np.array(hf['Mesh']['Wall']['coordinates'])*(10**-3)
            w_cells = np.array(hf['Mesh']['Wall']['topology'])

            w_cell_type = np.ones((w_cells.shape[0], 1), dtype=int) * 3
            w_cells = np.concatenate([w_cell_type, w_cells], axis = 1)
            self.surf = pv.PolyData(w_points, w_cells)

        # self.assemble_surface()
        return self