-
Notifications
You must be signed in to change notification settings - Fork 3
/
bulkProcess.ts
407 lines (338 loc) · 17.9 KB
/
bulkProcess.ts
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
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
import { readFileSync, writeFileSync, readdirSync, mkdirSync, existsSync, createReadStream } from 'fs';
import * as path from 'path';
import * as os from 'os';
import {Table, Float32Vector, DateVector, Int32Vector, Utf8Vector} from 'apache-arrow';
import * as parser from 'fast-xml-parser';
import { parseHex } from './src/sbe19plusV2/parseHex';
import { convertToEngineeringUnits } from './src/sbe19plusV2/convertResults';
import { getTrawlSurveyHaulData, getHexFiles, getCsvFiles, getXmlconFiles, saveToFile } from './src/utilities';
import { logger } from './src/logger';
import * as moment from 'moment';
import { removeOutliers } from './src/outlierRemoval';
import { createInterface } from 'readline';
import * as csv from 'csv';
import * as papa from 'papaparse';
import { splitHauls, parseFile, csvToTable, sliceByTimeRange, slice } from './src/structures';
import { col } from 'apache-arrow/compute/predicate';
logger.info('***** Start data processing.... *****');
// process.exit(0);
// setInterval(function(){ process.exit(0); }, 100);
//
let dataStruct = [
{ "colName": "Temperature (degC)", "vectorType": Float32Vector, "vector": null },
{ "colName": "Pressure (dbars)", "vectorType": Float32Vector, "vector": null },
{ "colName": "Conductivity (S_per_m)", "vectorType": Float32Vector, "vector": null },
{ "colName": "Salinity (psu)", "vectorType": Float32Vector, "vector": null },
{ "colName": "Oxygen SBE43 (ml_per_l)", "vectorType": Float32Vector, "vector": null },
{ "colName": "Oxygen OPTODE (ml_per_l)", "vectorType": Float32Vector, "vector": null },
{ "colName": "Depth (m)", "vectorType": Float32Vector, "vector": null },
{ "colName": "Latitude (decDeg)", "vectorType": Float32Vector, "vector": null },
{ "colName": "Longitude (decDeg)", "vectorType": Float32Vector, "vector": null },
{ "colName": "HaulID", "vectorType": Utf8Vector, "vector": null },
{ "colName": "DateTime (ISO8601)", "vectorType": DateVector, "vector": null },
{ "colName": "Year", "vectorType": Int32Vector, "vector": null },
{ "colName": "Month", "vectorType": Int32Vector, "vector": null },
{ "colName": "Day", "vectorType": Int32Vector, "vector": null },
];
let outputColumns = dataStruct.map((x: any) => {
return x["colName"];
})
// let outputColumns = ["Temperature (degC)", "Pressure (dbars)", "Conductivity (S_per_m)",
// "Salinity (psu)", "Oxygen (ml_per_l)", "OPTODE Oxygen (ml_per_l)", "Depth (m)",
// "Latitude (decDeg)", "Longitude (decDeg)", "HaulID", "DateTime (ISO8601)", "Year", "Month", "Day"
// ];
// Sample Data
const dir = "./data/sbe19plusV2/";
const hexFileName = "PORT_CTD5048_DO1360CT1460Op302_Hauls_1to5_21May2016.hex";
const xmlconFileName = "SBE19plusV2_5048.xmlcon";
let hexDir = path.join(os.homedir(), "Desktop", "CTD"); // Change to the real dir for processing
// hexDir = path.join(os.homedir(), "Desktop", "CTD_Test"); // Change to the real dir for processing
const csvDir = path.join(os.homedir(), "Desktop", "CTD output");
if (!existsSync(csvDir)) {
mkdirSync(csvDir);
}
const pointEstimatesDir = path.join(os.homedir(), "Desktop", "Point Estimates");
if (!existsSync(pointEstimatesDir)) {
mkdirSync(pointEstimatesDir);
}
let currentOutputDir: string = null;
let start: moment.Moment = null, end: moment.Moment = null, duration: number = null,
hex_file_start: moment.Moment = null, bulkStart: moment.Moment = null, bulkEnd: moment.Moment = null;
let df: Table = null, results: Object = null;
let currentHex: string = null, currentXmlcon: string = null,
currentYear: string = null, currentVessel: string = null,
currentPosition: string = null, currentCTD: string = null;
let strippedArray: string[] = null, lineArray: string[] = null,
hexFileArray: string[] = null;
let metrics: number[] = [];
async function bulkConvertData() {
// Retrieve the Trawl Survey Haul Data
logger.info(`Retrieving haul data`)
start = moment();
let startYear = '2016';
let endYear = '2018'
const hauls = await getTrawlSurveyHaulData(startYear, endYear);
end = moment();
duration = moment.duration(end.diff(start)).asSeconds();
logger.info(`\tProcessing time - retrieving haul data: ${duration}s`);
// Find all of the hex files
logger.info(`Searching for hex files: ${hexDir}`);
start = moment();
let hexFilesArray = await getHexFiles(hexDir);
writeFileSync(path.join(os.homedir(), "Desktop", "hexFiles.txt"),
hexFilesArray.join("\n")
);
logger.info(`\thex file count: ${hexFilesArray.length}`);
end = moment();
duration = moment.duration(end.diff(start)).asSeconds();
logger.info(`\tProcessing time - getting hex files: ${duration}s`);
// Find all of the xmlcon files
logger.info(`Searching for xmlcon files: ${hexDir}`);
start = moment();
let xmlconFilesArray = await getXmlconFiles(hexDir);
writeFileSync(path.join(os.homedir(), "Desktop", "xmlconList.txt"),
xmlconFilesArray.join("\n")
);
logger.info(`\txmlcon file count: ${xmlconFilesArray.length}`);
end = moment();
duration = moment.duration(end.diff(start)).asSeconds();
logger.info(`\tProcessing time - getting xmlcon files: ${duration}s`);
// Prepare hex file list for parsing
strippedArray = hexFilesArray.map(x => {
return x.replace(hexDir.replace(/\\/g, '\/') + "/", "");
});
// TESTING ONLY
// strippedArray = strippedArray.slice(0, 3);
let idx: number = 0, outputFile: string = null;
// Must use for ... of syntax for proper ordering, per:
// https://lavrton.com/javascript-loops-how-to-handle-async-await-6252dd3c795/
// Iterate through all of the hex files and convert to csv's
for await (const x of strippedArray) {
// if (idx < 295) {
// idx += 1;
// continue;
// }
// if (idx === 300) break;
hex_file_start = moment();
lineArray = x.split("/");
hexFileArray = lineArray.slice(-1)[0].split("_");
currentYear = lineArray[0];
currentVessel = lineArray[1];
currentPosition = hexFileArray[0];
currentCTD = hexFileArray[1].replace("CTD", "");
// Only process 2017 data - Process everyting but the 2017 CTD7738 system
// if ( (currentYear === "2016") ||
// ((currentYear === "2017") && (currentCTD === "7738"))
// ) {
// idx += 1;
// continue;
// }
// Create the output directory if it does not exist + outputFile string
if (!existsSync(path.join(csvDir, currentYear)))
mkdirSync(path.join(csvDir, currentYear));
if (!existsSync(path.join(csvDir, currentYear, currentVessel)))
mkdirSync(path.join(csvDir, currentYear, currentVessel));
currentOutputDir = path.join(csvDir, currentYear, currentVessel);
outputFile = path.join(currentOutputDir, lineArray.slice(-1)[0].slice(0, -3) + "csv");
console.info("\n");
logger.info(`**************************************************`);
logger.info(`*** Processing item ${idx}: ${currentYear}, ${currentVessel}, ` +
`${currentPosition}, ${currentCTD} ***`);
logger.info(`**************************************************`);
currentHex = path.resolve(path.join(hexDir, strippedArray[idx]));
currentXmlcon = path.resolve(path.join(hexDir, currentYear,
currentYear + "_CTD_ConFiles_Raw", "SBE19plusV2_" + currentCTD + ".xmlcon"))
logger.info(`\txmlcon: ${currentXmlcon}`);
logger.info(`\tinputHex = ${currentHex}`);
logger.info(`\toutputCSV = ${outputFile}`);
// TESTING ONLY
// idx += 1;
// continue;
// Read an individiaul xmlcon file
let xmlconFileInMemory = readFileSync(currentXmlcon, "utf8");
// Retrieve the xmlcon instrument and sensor details as JSON
let xmlconJson = parser.parse(xmlconFileInMemory);
let instrument = xmlconJson.SBE_InstrumentConfiguration.Instrument;
let sensors = instrument.SensorArray.Sensor;
// Parse hex file and convert to raw, decimal values in arrow data structure
if (instrument.Name.indexOf("SBE 19plus V2") > -1) {
// Parse the hex file
logger.info(`\tParsing Hex File`);
start = moment();
results = await parseHex(currentHex);
end = moment();
duration = moment.duration(end.diff(start)).asSeconds();
logger.info(`\t\tProcessing time - parsing hex file: ${duration}s`);
// Convert the parsed hex file data to engineering unitst
logger.info(`\tConverting to Engineering Units`);
start = moment();
df = await convertToEngineeringUnits(instrument, sensors, results["casts"],
results["voltageOffsets"], results["pumpDelay"], results["df"],
outputFile, hauls, currentVessel);
end = moment();
duration = moment.duration(end.diff(start)).asSeconds();
logger.info(`\t\tProcessing time - converting to engineering units: ${duration}s`);
// Save the results to a csv file
logger.info(`\tSaving data to a csv file`);
start = moment();
await saveToFile(df, "csv", outputFile, outputColumns);
end = moment();
duration = moment.duration(end.diff(start)).asSeconds();
logger.info(`\t\tProcessing time - saving result to a file: ${duration}s`);
// Display the results
// let sliceSize: number = 5,
// sliceStart: number = 0, //df.length - sliceSize,
// sliceEnd: number = sliceStart + sliceSize;
// try {
// outputColumns.forEach(x => {
// results = df.getColumn(x).toArray().slice(sliceStart, sliceEnd);
// console.info(`\t${x}: ${results}`);
// });
// console.info(`Schema: ${df.schema.fields.map(x => x.name)}`);
// console.info(`Voltage Offsets: ${JSON.stringify(voltageOffsets)}`);
// console.info(`Casts: ${JSON.stringify(casts)}`);
// } catch (e) {
// logger.error(`Error printing results: ${e}`);
// }
}
end = moment();
duration = moment.duration(end.diff(hex_file_start)).asSeconds();
logger.info(`\tProcessing time - item ${idx} - overall file processing: ${duration}s`);
metrics.push(duration);
idx += 1;
}
let totalTime = metrics.reduce((x, y) => x + y, 0);
logger.info('Total Processing time');
logger.info(`\t${idx} items, total time: ${totalTime.toFixed(1)}s, ` +
`time per item = ${(totalTime/idx).toFixed(1)}s`);
}
async function bulkCalculatePointEstimates() {
// Bulk Start
bulkStart = moment();
// Retrieve the Trawl Survey Haul Data
logger.info(`Retrieving haul data`)
start = moment();
let startYear = '2016';
let endYear = '2018'
let masterHauls = await getTrawlSurveyHaulData(startYear, endYear);
end = moment();
duration = moment.duration(end.diff(start)).asSeconds();
logger.info(`\tProcessing time - retrieving haul data: ${duration}s`);
// Find all of the converted csv files
logger.info(`Searching for csv files: ${csvDir}`);
start = moment();
let csvFilesArray = await getCsvFiles(csvDir);
writeFileSync(path.join(os.homedir(), "Desktop", "csvFiles.txt"),
csvFilesArray.join("\n")
);
logger.info(`\tcsv file count: ${csvFilesArray.length}`);
end = moment();
duration = moment.duration(end.diff(start)).asSeconds();
logger.info(`\tProcessing time - getting csv files: ${duration}s`);
let thresholdPct: number = 0.05; // Percentage
let startPct: number = 0.1; // Percentage
let endPct: number = 0.1; // Percentage
let rawFile: string = '';
let dfHauls = {}, haulTable: Table = null, haulsAvgs = [];
let slicedHaulTimes: Table = null, slicedHaulNumber: Table = null, slicedHaulPcts: Table = null;
let startIdx: number = null, endIdx: number = null;
for (let i in csvFilesArray) {
// if (parseInt(i) === 1) break;
try {
logger.info(`Processing ${csvFilesArray[i]}`);
start = moment();
// Read the file
rawFile = readFileSync(csvFilesArray[i], "utf8");
// Convert the csv file to a arrow table
let df = await csvToTable(rawFile);
// Split the table into separate tables based on the haul ID
let haulsColName: string = "HaulID";
dfHauls = splitHauls(df, haulsColName);
// Iterate through each of the hauls from the current csv file
for (let x in dfHauls) {
try {
logger.info(`\thaul = ${x}`);
startIdx = dfHauls[x]['startIdx'];
endIdx = dfHauls[x]['endIdx'];
let masterHaul = masterHauls.filter(col('trawl_id').eq(x));
for (let masterHaulDetails of masterHaul){
logger.info(`\t\tdw haul details = ${masterHaulDetails}`);
let towDateStart = moment(masterHaulDetails["tow_start_timestamp"]);
let towDateEnd = moment(masterHaulDetails["tow_start_timestamp"]);
let startTime = masterHaulDetails["sampling_start_hhmmss"];
let endTime = masterHaulDetails["sampling_end_hhmmss"];
startTime = towDateStart.set({'hour': startTime.slice(0,2), 'minute': startTime.slice(2,4),
'second': startTime.slice(4,6)});
endTime = towDateEnd.set({'hour': endTime.slice(0,2), 'minute': endTime.slice(2,4),
'second': endTime.slice(4,6)});
logger.info(`\t\tdw startTime - sampling = ${startTime.format('HH:mm:ss')}, endTime = ${endTime.format('HH:mm:ss')}`);
let slicedHaulNumber = slice(df, startIdx, endIdx);
let csvStartTime = moment(slicedHaulNumber.get(0)['DateTime (ISO8601)']);
let csvEndTime = moment(slicedHaulNumber.get(slicedHaulNumber.count()-1)['DateTime (ISO8601)']);
logger.info(`\t\tHaul Number Slicing`)
logger.info(`\t\t\tData size = ${slicedHaulNumber.count()}`);
logger.info(`\t\t\tstartIdx = ${startIdx}, endIdx = ${endIdx}`);
logger.info(`\t\t\tstartTime = ${csvStartTime.format('MM/DD/YYYY HH:mm:ss')}, endTime = ${csvEndTime.format('MM/DD/YYYY HH:mm:ss')}`)
logger.info(`\t\tHaul Start/End Time Slicing`);
slicedHaulTimes = sliceByTimeRange(slicedHaulNumber, "DateTime (ISO8601)", startTime, endTime);
logger.info(`\t\t\tData size = ${slicedHaulTimes.count()}`);
logger.info(`\t\t\tstartTime = ${startTime.format('HH:mm:ss')}, endTime = ${endTime.format('HH:mm:ss')}`);
if (slicedHaulTimes.count() > 0) {
// Slice the data by droping beginning and ending values by startPct and endPct
let startCount: number = null, endCount: number = null;
startCount = Math.floor(slicedHaulTimes.count() * startPct);
endCount = Math.ceil(slicedHaulTimes.count() * (1 - endPct));
slicedHaulPcts = slice(slicedHaulTimes, startCount, endCount);
logger.info(`\t\tHaul Percents Slicing`);
logger.info(`\t\t\tData size = ${slicedHaulPcts.count()}`);
// logger.info(`\t\t\tstartTime = ${}, endTime = ${}`);
logger.info(`\t\t\tstartCount = ${startCount}, endCount = ${endCount}`)
// Auto Remove outliers
let averages = await removeOutliers(slicedHaulPcts, thresholdPct);
// averages["haulID"] = x;
haulsAvgs.push(averages);
} else {
logger.info(`\t\tNo matching data found, skipping the haul`);
}
}
} catch (haulError) {
logger.error(`Error processing haul ${x}: ${haulError}`);
}
}
end = moment();
duration = moment.duration(end.diff(start)).asSeconds();
logger.info(`\tProcessing time: ${duration}s`);
} catch (fileError) {
logger.error(`Error processing csv output file ${csvFilesArray[i]}: ${fileError}`)
}
}
// Insert the averages into the Haul Characteristics table
for (let x in dataStruct) {
let item = dataStruct[x];
item["vector"] = haulsAvgs.map((y: any) => {
return y[item["colName"]];
})
// logger.info(`${item["colName"]} vector: ${item["vector"]}`);
}
let finalArray = dataStruct.map((x: any) => {
if (x["vectorType"] === DateVector) {
return Utf8Vector.from(x["vector"]);
} else {
return x["vectorType"].from(x["vector"]);
}
});
let finalCols = dataStruct.map((x: any) => {
return x["colName"];
});
logger.info(`finalCols = ${finalCols}`);
// logger.info(`finalArray = ${finalArray}`);
let dfFinal = Table.new(finalArray, finalCols);
// Save the point estimates out to a final csv file
let pointEstimatesFile = path.join(pointEstimatesDir, "pointEstimates.csv");
await saveToFile(dfFinal, "csv", pointEstimatesFile, finalCols);
bulkEnd = moment();
duration = moment.duration(bulkEnd.diff(bulkStart)).asSeconds();
logger.info(`\tBulk Processing time: ${duration} seconds, ${duration/60} minutes, ${duration/3600} hours`);
}
// bulkConvertData();
bulkCalculatePointEstimates();