File size: 6,794 Bytes
9d54b72 |
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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 |
import numpy as np
from pathlib import Path
import zlib
class CartesianMesh:
"""
reads the .mesh file and extracts the mesh information
Example .mesh file:
Version 1.2
CartesianMesh {
// X Y Z
Size 71 71 25
Extent 74.239999999999995 74.239999999999995 26
Origin 0 0 0
VolumeRegionsMapSubvolume {
6
//VolRegID SubvolID Volume
0 0 124767.54117864356 //ec
1 1 14855.904388351477 //cytosol
2 1 1.2185460680272107 //cytosol
3 1 1.2185460680272107 //cytosol
4 1 1.2185460680272107 //cytosol
5 2 3673.9163951019395 //Nucleus
}
MembraneRegionsMapVolumeRegion {
5
//MemRegID VolReg1 VolReg2 Surface
0 1 0 4512.8782874369472
1 2 0 1.7113582585034091
2 3 0 1.7113582585033937
3 4 0 1.711358258503394
4 5 1 1306.5985272332098
}
VolumeElementsMapVolumeRegion {
126025 Compressed
789CEDDD8D72DBC81100612389DFFF9573572A5912B9BF2066A66176B32A57B12CE22B8022E5DD11
F5EB9799999999999999999999999999999999999999999999999999999999999999999999999999
...
"""
mesh_file: Path
size: list[int] # [x, y, z]
extent: list[float] # [x, y, z]
origin: list[float] # [x, y, z]
volume_regions: list[tuple[int, int, float, str]] # list of tuples (vol_reg_id, subvol_id, volume, region_name)
membrane_regions: list[tuple[int, int, int, float]] # list of tuples (mem_reg_id, vol_reg1, vol_reg2, surface)
# membrane_element[m,:] = [idx, vol1, vol2, conn0, conn1, conn2, conn3, mem_reg_id]
membrane_elements: np.ndarray # shape (num_membrane_elements, 8)
# volume_region_map[m] = vol_reg_id
volume_region_map: np.ndarray # shape (size[0] * size[1] * size[2],)
def __init__(self, mesh_file: Path) -> None:
self.mesh_file = mesh_file
self.size = []
self.extent = []
self.origin = []
self.volume_regions = []
self.membrane_regions = []
# self.membrane_elements
self.volume_region_map = np.array([], dtype=np.uint8)
def read(self) -> None:
# read file as lines and parse
with (self.mesh_file.open('r') as f):
# get line enumerator from f
iter_lines = iter(f.readlines())
assert next(iter_lines) == "Version 1.2\n"
assert next(iter_lines) == "CartesianMesh {\n"
assert next(iter_lines) == "\t// X Y Z\n"
size_line = next(iter_lines).split()
if size_line[0] == "Size":
self.size = [int(size_line[1]), int(size_line[2]), int(size_line[3])]
extent_line = next(iter_lines).split()
if extent_line[0] == "Extent":
self.extent = [float(extent_line[1]), float(extent_line[2]), float(extent_line[3])]
origin_line = next(iter_lines).split()
if origin_line[0] == "Origin":
self.origin = [float(origin_line[1]), float(origin_line[2]), float(origin_line[3])]
while next(iter_lines) != "\tVolumeRegionsMapSubvolume {\n":
pass
num_volume_regions = int(next(iter_lines))
header_line = next(iter_lines)
self.volume_regions = []
for i in range(num_volume_regions):
parts = next(iter_lines).split()
self.volume_regions.append((int(parts[0]), int(parts[1]), float(parts[2]), parts[3].strip("//")))
while next(iter_lines) != "\tMembraneRegionsMapVolumeRegion {\n":
pass
num_membrane_regions = int(next(iter_lines))
header_line = next(iter_lines)
self.membrane_regions = []
for i in range(num_membrane_regions):
parts = next(iter_lines).split()
self.membrane_regions.append((int(parts[0]), int(parts[1]), int(parts[2]), float(parts[3])))
while next(iter_lines) != "\tVolumeElementsMapVolumeRegion {\n":
pass
compressed_line = next(iter_lines).split()
num_volume_elements = int(compressed_line[0])
assert compressed_line[1] == "Compressed"
# read HEX lines until "}" line, and concatenate into one string, then convert to bytes and decompress
hex_lines = []
while True:
line = next(iter_lines)
if line.strip() == "}":
break
hex_lines.append(line.strip())
hex_string: str = "".join(hex_lines).strip()
compressed_bytes = bytes.fromhex(hex_string)
# assert len(compressed_bytes) == num_compressed_bytes
uncompressed_bytes: bytes = zlib.decompress(compressed_bytes)
self.volume_region_map = np.frombuffer(uncompressed_bytes, dtype='<u2') # unsigned 2-byte integers
assert self.volume_region_map.shape[0] == self.size[0] * self.size[1] * self.size[2]
assert num_volume_elements == self.volume_region_map.shape[0]
assert set(np.unique(self.volume_region_map)) == set([v[0] for v in self.volume_regions])
while next(iter_lines).strip() != "MembraneElements {":
pass
num_membrane_elements = int(next(iter_lines))
self.membrane_elements = np.zeros((num_membrane_elements, 8), dtype=np.int32)
header_line = next(iter_lines).split()
mem_index = 0
while True:
line = next(iter_lines)
if line.strip() == "}":
break
parts = line.split()
idx = int(parts[0])
vol1 = int(parts[1])
vol2 = int(parts[2])
conn0 = int(parts[3])
conn1 = int(parts[4])
conn2 = int(parts[5])
conn3 = int(parts[6])
mem_reg_id = int(parts[7])
self.membrane_elements[mem_index, :] = [idx, vol1, vol2, conn0, conn1, conn2, conn3, mem_reg_id]
mem_index += 1
assert self.membrane_elements.shape == (num_membrane_elements, 8)
assert set(np.unique(self.membrane_elements[:, 7])) == set([v[0] for v in self.membrane_regions])
|