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from pathlib import Path
import numpy as np
import zarr
from vcelldata.mesh import CartesianMesh
from vcelldata.simdata_models import PdeDataSet, DataBlockHeader, DataFunctions, NamedFunction, VariableType
def write_zarr(pde_dataset: PdeDataSet, data_functions: DataFunctions, mesh: CartesianMesh, zarr_dir: Path) -> None:
volume_data_vars: list[DataBlockHeader] = [v for v in pde_dataset.variables_block_headers()
if v.variable_type == VariableType.VOLUME]
volume_functions: list[NamedFunction] = [f for f in data_functions.named_functions
if f.variable_type == VariableType.VOLUME]
num_channels = len(volume_data_vars) + len(volume_functions) + 1
num_t: int = len(pde_dataset.times())
times: list[float] = pde_dataset.times()
header = pde_dataset.first_data_zip_file_metadata().file_header
num_x: int = header.sizeX
num_y: int = header.sizeY
num_z: int = header.sizeZ
z1 = zarr.open(str(zarr_dir.absolute()), mode='w', shape=(num_t, num_channels, num_z, num_y, num_x), chunks=(1,1,num_z,num_y,num_x), dtype=float)
channel_metadata: list[dict] = []
for t in range(num_t):
bindings = {}
# add region map
region_map = mesh.volume_region_map.reshape((num_z, num_y, num_x))
z1[t, 0, :, :, :] = region_map
if t == 0:
channel_metadata.append({"index": 0,
"label": "region_mask",
"domain_name": "all",
"min_value": np.min(region_map),
"max_value": np.max(region_map)})
# add volumetric state variables
for i, v in enumerate(volume_data_vars):
var_data: np.ndarray = pde_dataset.get_data(v.var_name, times[t]).reshape((num_z, num_y, num_x))
c = i + 1
z1[t, c, :, :, :] = var_data
domain_name = v.var_name.split("::")[0]
var_name = v.var_name.split("::")[1]
bindings[var_name] = var_data
if t == 0:
channel_metadata.append({"index": c,
"label": var_name,
"domain_name": domain_name,
"min_values": [],
"max_values": [],
"mean_values": []})
channel_metadata[c]["min_values"].append(np.min(var_data))
channel_metadata[c]["max_values"].append(np.max(var_data))
channel_metadata[c]["mean_values"].append(np.mean(var_data))
# add volumetric functions
for j, f in enumerate(volume_functions):
func_data = f.evaluate(variable_bindings=bindings).reshape((num_z, num_y, num_x))
c = i + j + 2
z1[t, c, :, :, :] = func_data
domain_name = f.name.split("::")[0]
function_name = f.name.split("::")[1]
if t == 0:
channel_metadata.append({"index": (i + j + 2),
"label": function_name,
"domain_name": domain_name,
"min_values": [],
"max_values": [],
"mean_values": []})
channel_metadata[c]["min_values"].append(np.min(func_data))
channel_metadata[c]["max_values"].append(np.max(func_data))
channel_metadata[c]["mean_values"].append(np.mean(func_data))
z1.attrs["metadata"] = {
"axes": [
{"name": "t", "type": "time", "unit": "second"},
{"name": "c", "type": "channel", "unit": None},
{"name": "z", "type": "space", "unit": "micrometer"},
{"name": "y", "type": "space", "unit": "micrometer"},
{"name": "x", "type": "space", "unit": "micrometer"}
],
"channels": channel_metadata,
"times": times,
"mesh": {
"size": mesh.size,
"extent": mesh.extent,
"origin": mesh.origin,
"volume_regions": [{"region_index": mesh.volume_regions[i][0],
"domain_type_index": mesh.volume_regions[i][1],
"volume": mesh.volume_regions[i][2],
"domain_name": mesh.volume_regions[i][3]} for i in range(len(mesh.volume_regions))],
}
}
z1.attrs["metadata"]["mesh"] = {
"size": mesh.size,
"extent": mesh.extent,
"origin": mesh.origin,
"volume_regions": [{"region_index": mesh.volume_regions[i][0],
"domain_type_index": mesh.volume_regions[i][1],
"volume": mesh.volume_regions[i][2],
"domain_name": mesh.volume_regions[i][3]} for i in range(len(mesh.volume_regions))],
}
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