Spaces:
Sleeping
Sleeping
File size: 12,018 Bytes
6ee917b | 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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 | import Foundation
import Vapor
import OmFileFormat
/**
Upgrade legacy om-files to new version. Transposes data to proper 3d context.
*/
struct MigrationCommand: AsyncCommand {
struct Signature: CommandSignature {
@Flag(name: "execute", help: "Perform file moves")
var execute: Bool
}
var help: String {
"Perform database migration"
}
func run(using context: CommandContext, signature: Signature) async throws {
let logger = context.application.logger
// loop over data directory
let execute = signature.execute
let pathUrl = URL(fileURLWithPath: OpenMeteo.dataDirectory, isDirectory: true)
let resourceKeys = Set<URLResourceKey>([.nameKey, .isDirectoryKey, .contentModificationDateKey, .fileSizeKey])
guard let directoryEnumerator = FileManager.default.enumerator(at: pathUrl, includingPropertiesForKeys: Array(resourceKeys), options: [.skipsHiddenFiles, .skipsSubdirectoryDescendants]) else {
logger.warning("No files at \(pathUrl)")
return
}
for case let fileURL as URL in directoryEnumerator {
guard let resourceValues = try? fileURL.resourceValues(forKeys: resourceKeys),
let isDirectory = resourceValues.isDirectory,
let name = resourceValues.name,
!name.contains("~"),
isDirectory
else {
continue
}
guard let domain = DomainRegistry(rawValue: name) else {
logger.warning("Skipping \(name)")
continue
}
let grid = domain == .copernicus_dem90 ? nil : domain.getDomain().grid
guard let directoryEnumerator = FileManager.default.enumerator(at: URL(fileURLWithPath: "\(OpenMeteo.dataDirectory)\(name)", isDirectory: true), includingPropertiesForKeys: Array(resourceKeys), options: [.skipsHiddenFiles, .skipsSubdirectoryDescendants]) else {
logger.warning("No files at \(OpenMeteo.dataDirectory)\(name)")
continue
}
for case let fileURL as URL in directoryEnumerator {
guard let resourceValues = try? fileURL.resourceValues(forKeys: resourceKeys),
let isDirectory = resourceValues.isDirectory,
let variable = resourceValues.name,
!variable.contains("~"),
isDirectory
else {
continue
}
let path = "\(OpenMeteo.dataDirectory)\(name)/\(variable)"
guard let directoryEnumerator = FileManager.default.enumerator(at: URL(fileURLWithPath: path, isDirectory: true), includingPropertiesForKeys: Array(resourceKeys), options: [.skipsHiddenFiles, .skipsSubdirectoryDescendants]) else {
logger.warning("No files at \(path)")
continue
}
for case let fileURL as URL in directoryEnumerator {
guard let resourceValues = try? fileURL.resourceValues(forKeys: resourceKeys),
let isDirectory = resourceValues.isDirectory,
let file = resourceValues.name,
!file.contains("~"),
file.suffix(3) == ".om",
!isDirectory
else {
continue
}
//logger.info("Processing \(domain)/\(variable)/\(file)")
try await convertToNewFormat(logger: logger, file: "\(path)/\(file)", grid: grid, execute: execute)
}
}
}
}
/// Read om file and write it as version 3 and reshape data to proper 3d files
/// If no grid is given, assume that files are converted 1:1. This is the case for the DEM model
func convertToNewFormat(logger: Logger, file: String, grid: Gridable?, execute: Bool) async throws {
let temporary = "\(file)~"
FileManager.default.waitIfFileWasRecentlyModified(at: temporary)
try FileManager.default.removeItemIfExists(at: temporary)
// Read data from the input OM file
guard let readfile = try? OmFileReader(file: file) else {
logger.warning("Failed to open file: \(file)")
return
}
guard let reader = readfile.asArray(of: Float.self), readfile.isLegacyFormat() else {
logger.info("File already in new format \(file)")
return
}
let dimensions = Array(reader.getDimensions())
let chunks = Array(reader.getChunkDimensions())
guard dimensions.count == 2 else {
logger.warning("Invalid dimension count \(file)")
return
}
let ny = UInt64(grid?.ny ?? Int(dimensions[0]))
let nx = UInt64(grid?.nx ?? Int(dimensions[1]))
// Simple file like surface elevation
// No need to re-chunk data. Just 1:1 migration
if dimensions.count == 2 && ny == dimensions[0] && nx == dimensions[1] {
logger.info("Migrate simple \(file) dimensions=\(dimensions) chunks=\(chunks)")
guard execute else {
return
}
let writeFn = try FileHandle.createNewFile(file: temporary)
let fileWriter = OmFileWriter(fn: writeFn, initialCapacity: 1024 * 1024 * 10)
let writer = try fileWriter.prepareArray(
type: Float.self,
dimensions: dimensions,
chunkDimensions: chunks,
compression: reader.compression,
scale_factor: reader.scaleFactor,
add_offset: reader.addOffset
)
let data = try reader.read()
try writer.writeData(array: data)
let variable = try fileWriter.write(
array: try writer.finalise(),
name: "",
children: []
)
try fileWriter.writeTrailer(rootVariable: variable)
try writeFn.close()
/// Read data again to ensure the written data matches exactly
guard let verify = try OmFileReader(file: temporary).asArray(of: Float.self)?.read() else {
fatalError("Could not read temporary file")
}
guard data.isSimilar(verify) else {
fatalError("Data does not match")
}
try FileManager.default.moveFileOverwrite(from: temporary, to: file)
return
}
guard dimensions.count == 2, nx * ny == dimensions[0] else {
logger.warning("Dimensions do not agree \(file). E.g. no support for ensemble files")
return
}
let nt = dimensions[1]
let dimensionsOut = [ny, nx, nt]
let chunksOut = [1,chunks[0],chunks[1]]
logger.info("Migrate \(file) new dimensions=\(dimensionsOut) chunks=\(chunksOut)")
guard execute else {
return
}
let writeFn = try FileHandle.createNewFile(file: temporary)
let fileWriter = OmFileWriter(fn: writeFn, initialCapacity: 1024 * 1024 * 10)
let writer = try fileWriter.prepareArray(
type: Float.self,
dimensions: dimensionsOut,
chunkDimensions: chunksOut,
compression: reader.compression,
scale_factor: reader.scaleFactor,
add_offset: reader.addOffset
)
let progress = TransferAmountTracker(logger: logger, totalSize: 4 * Int(dimensions.reduce(1, *)), name: "Convert")
/// Reshape data from flattened 2D to 3D context
for yStart in stride(from: 0, to: ny, by: UInt64.Stride(chunksOut[0])) {
for xStart in stride(from: 0, to: nx, by: UInt64.Stride(chunksOut[1])) {
for tStart in stride(from: 0, to: nt, by: UInt64.Stride(chunksOut[2])) {
let yRange = yStart ..< min(yStart + chunksOut[0], ny)
let xRange = xStart ..< min(xStart + chunksOut[1], nx)
let tRange = tStart ..< min(tStart + chunksOut[2], nt)
//print("chunk y=\(yRange) x=\(xRange) t=\(tRange)")
var chunk = [Float](repeating: .nan, count: yRange.count * xRange.count * tRange.count)
for (row, y) in yRange.enumerated() {
try reader.read(
into: &chunk,
range: [y * nx + xRange.startIndex ..< y * nx + xRange.endIndex, tRange],
intoCubeOffset: [UInt64(row * xRange.count), 0],
intoCubeDimension: [UInt64(yRange.count * xRange.count), UInt64(tRange.count)]
)
}
try writer.writeData(
array: chunk,
arrayDimensions: [UInt64(yRange.count), UInt64(xRange.count), UInt64(tRange.count)],
arrayOffset: nil,
arrayCount: nil
)
progress.add(chunk.count * 4)
}
}
}
progress.finish()
let variable = try fileWriter.write(
array: try writer.finalise(),
name: "",
children: []
)
try fileWriter.writeTrailer(rootVariable: variable)
try writeFn.close()
/// Read data again to ensure the written data matches exactly
guard let verify = try OmFileReader(file: temporary).asArray(of: Float.self) else {
fatalError("Could not read temporary file")
}
let progressVerify = TransferAmountTracker(logger: logger, totalSize: 4 * Int(dimensions.reduce(1, *)), name: "Verify")
for yStart in stride(from: 0, to: ny, by: UInt64.Stride(chunksOut[0])) {
for xStart in stride(from: 0, to: nx, by: UInt64.Stride(chunksOut[1])) {
for tStart in stride(from: 0, to: nt, by: UInt64.Stride(chunksOut[2])) {
let yRange = yStart ..< min(yStart + chunksOut[0], ny)
let xRange = xStart ..< min(xStart + chunksOut[1], nx)
let tRange = tStart ..< min(tStart + chunksOut[2], nt)
var chunk = [Float](repeating: .nan, count: yRange.count * xRange.count * tRange.count)
for (row, y) in yRange.enumerated() {
try reader.read(
into: &chunk,
range: [y * nx + xRange.startIndex ..< y * nx + xRange.endIndex, tRange],
intoCubeOffset: [UInt64(row * xRange.count), 0],
intoCubeDimension: [UInt64(yRange.count * xRange.count), UInt64(tRange.count)]
)
}
let verifyData = try verify.read(range: [yRange, xRange, tRange])
guard chunk.isSimilar(verifyData) else {
fatalError("Data does not match \(yRange) \(xRange) \(tRange)")
}
progressVerify.add(chunk.count * 4)
}
}
}
progressVerify.finish()
try FileManager.default.moveFileOverwrite(from: temporary, to: file)
}
}
public extension Array where Element == Float {
func isSimilar(_ b: [Float], accuracy: Float = 0.0001) -> Bool {
let a = self
guard a.count == b.count else {
return false
}
for (a1,b1) in zip(a,b) {
if a1.isNaN && b1.isNaN {
continue
}
if a1.isNaN || b1.isNaN || abs(a1 - b1) > accuracy {
return false
}
}
return true
}
}
|