quantification

package

v4.32.0 Latest Latest Go to latest Published: Sep 3, 2024 License: Apache-2.0 Imports: 36 Imported by: 0

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Repository

github.com/pixlise/core

Links

Open Source Insights

Documentation ¶

Overview ¶

Example (CalculateTotals_AB_NeedsCombined) ¶

q, err := readQuantificationFile("./testdata/AB.bin")
fmt.Printf("%v\n", err)

if err == nil {
	result, err := calculateTotals(q, []int{90, 91, 95})

	fmt.Printf("%v|%v\n", result, err)
}

Output:

<nil>
map[]|Quantification must be for Combined detectors

Example (CalculateTotals_NoPMC) ¶

q, err := readQuantificationFile("./testdata/combined.bin")
fmt.Printf("%v\n", err)

if err == nil {
	result, err := calculateTotals(q, []int{68590, 68591, 68595})

	fmt.Printf("%v|%v\n", result, err)
}

Output:

<nil>
map[]|Quantification had no valid data for ROI PMCs

Example (CalculateTotals_Success) ¶

q, err := readQuantificationFile("./testdata/combined.bin")
fmt.Printf("%v\n", err)

if err == nil {
	result, err := calculateTotals(q, []int{90, 91, 95})

	fmt.Printf("%v|%v\n", result, err)
}

Output:

<nil>
map[CaO_%:7.5057006 FeO-T_%:10.621034 SiO2_%:41.48377 TiO2_%:0.7424]|<nil>

Example (CleanLogName) ¶

// Don't fix it...
fmt.Println(cleanLogName("node00001_data.log"))
// Do fix it...
fmt.Println(cleanLogName("node00001.pmcs_stdout.log"))
// Do fix it...
fmt.Println(cleanLogName("NODE00001.PMCS_stdout.log"))

Output:

node00001_data.log
node00001_stdout.log
NODE00001_stdout.log

Example (CombineQuantOutputs_BadPMC) ¶

var mockS3 awsutil.MockS3Client
defer mockS3.FinishTest()

const jobsBucket = "jobs-bucket"

// Some of our files are empty, not there, have content
// and they're meant to end up combined into one response...
mockS3.ExpGetObjectInput = []s3.GetObjectInput{
	{
		Bucket: aws.String(jobsBucket), Key: aws.String("JobData/abc123/output/node001.pmcs_result.csv"),
	},
	{
		Bucket: aws.String(jobsBucket), Key: aws.String("JobData/abc123/output/node002.pmcs_result.csv"),
	},
}
mockS3.QueuedGetObjectOutput = []*s3.GetObjectOutput{
	{
		Body: io.NopCloser(bytes.NewReader([]byte(`Header row1
PMC, CaO_%, CaO_int, RTT
30, 5.1, 400, 7890
12, 6.1, 405, 7800
`))),
	},
	{
		Body: io.NopCloser(bytes.NewReader([]byte(`Header row2
PMC, CaO_%, CaO_int, RTT
NaN, 7.1, 415, 7840
`))),
	},
}

fs := fileaccess.MakeS3Access(&mockS3)
combinedCSV, err := combineQuantOutputs(fs, jobsBucket, "JobData/abc123", "The custom header", []string{"node001.pmcs", "node002.pmcs", "node003.pmcs"})

fmt.Printf("%v\n", err)
fmt.Println(combinedCSV)

Output:

Failed to combine map segment: JobData/abc123/output/node002.pmcs_result.csv, invalid PMC NaN at line 3

Example (CombineQuantOutputs_DownloadError) ¶

var mockS3 awsutil.MockS3Client
defer mockS3.FinishTest()

const jobsBucket = "jobs-bucket"

// Some of our files are empty, not there, have content
// and they're meant to end up combined into one response...
mockS3.ExpGetObjectInput = []s3.GetObjectInput{
	{
		Bucket: aws.String(jobsBucket), Key: aws.String("JobData/abc123/output/node001.pmcs_result.csv"),
	},
	{
		Bucket: aws.String(jobsBucket), Key: aws.String("JobData/abc123/output/node002.pmcs_result.csv"),
	},
}
mockS3.QueuedGetObjectOutput = []*s3.GetObjectOutput{
	{
		Body: io.NopCloser(bytes.NewReader([]byte(`Header row1
PMC, CaO_%, CaO_int, RTT
30, 5.1, 400, 7890
12, 6.1, 405, 7800
`))),
	},
	nil,
}

fs := fileaccess.MakeS3Access(&mockS3)
combinedCSV, err := combineQuantOutputs(fs, jobsBucket, "JobData/abc123", "The custom header", []string{"node001.pmcs", "node002.pmcs", "node003.pmcs"})

fmt.Printf("%v\n", err)
fmt.Println(combinedCSV)

Output:

Failed to combine map segment: JobData/abc123/output/node002.pmcs_result.csv

Example (CombineQuantOutputs_DuplicatePMC) ¶

var mockS3 awsutil.MockS3Client
defer mockS3.FinishTest()

const jobsBucket = "jobs-bucket"

// Some of our files are empty, not there, have content
// and they're meant to end up combined into one response...
mockS3.ExpGetObjectInput = []s3.GetObjectInput{
	{
		Bucket: aws.String(jobsBucket), Key: aws.String("JobData/abc123/output/node001.pmcs_result.csv"),
	},
	{
		Bucket: aws.String(jobsBucket), Key: aws.String("JobData/abc123/output/node002.pmcs_result.csv"),
	},
	{
		Bucket: aws.String(jobsBucket), Key: aws.String("JobData/abc123/output/node003.pmcs_result.csv"),
	},
}
mockS3.QueuedGetObjectOutput = []*s3.GetObjectOutput{
	{
		Body: io.NopCloser(bytes.NewReader([]byte(`Header row1
PMC, CaO_%, CaO_int, RTT
30, 5.1, 400, 7890
12, 6.1, 405, 7800
`))),
	},
	{
		Body: io.NopCloser(bytes.NewReader([]byte(`Header row2
PMC, CaO_%, CaO_int, RTT
18, 7.1, 415, 7840
`))),
	},
	{
		Body: io.NopCloser(bytes.NewReader([]byte(`Header row3
PMC, CaO_%, CaO_int, RTT
3, 1.1, 450, 7830
30, 1.3, 451, 7833
40, 8.1, 455, 7870
`))),
	},
}

fs := fileaccess.MakeS3Access(&mockS3)
combinedCSV, err := combineQuantOutputs(fs, jobsBucket, "JobData/abc123", "The custom header", []string{"node001.pmcs", "node002.pmcs", "node003.pmcs"})

fmt.Printf("%v\n", err)
fmt.Println(combinedCSV)

Output:

<nil>
The custom header
PMC, CaO_%, CaO_int, RTT
3, 1.1, 450, 7830
12, 6.1, 405, 7800
18, 7.1, 415, 7840
30, 5.1, 400, 7890
30, 1.3, 451, 7833
40, 8.1, 455, 7870

Example (CombineQuantOutputs_LastLineCutOff) ¶

var mockS3 awsutil.MockS3Client
defer mockS3.FinishTest()

const jobsBucket = "jobs-bucket"

// Some of our files are empty, not there, have content
// and they're meant to end up combined into one response...
mockS3.ExpGetObjectInput = []s3.GetObjectInput{
	{
		Bucket: aws.String(jobsBucket), Key: aws.String("JobData/abc123/output/node001.pmcs_result.csv"),
	},
	{
		Bucket: aws.String(jobsBucket), Key: aws.String("JobData/abc123/output/node002.pmcs_result.csv"),
	},
}
mockS3.QueuedGetObjectOutput = []*s3.GetObjectOutput{
	{
		Body: io.NopCloser(bytes.NewReader([]byte(`Header row1
PMC, CaO_%, CaO_int, RTT
30, 5.1, 400, 7890
12, 6.1, 405, 7800
`))),
	},
	{
		Body: io.NopCloser(bytes.NewReader([]byte(`Header row2
PMC, CaO_%, CaO_int, RTT
31
`))),
	},
}

fs := fileaccess.MakeS3Access(&mockS3)
combinedCSV, err := combineQuantOutputs(fs, jobsBucket, "JobData/abc123", "The custom header", []string{"node001.pmcs", "node002.pmcs", "node003.pmcs"})

fmt.Printf("%v\n", err)
fmt.Println(combinedCSV)

Output:

Failed to combine map segment: JobData/abc123/output/node002.pmcs_result.csv, no PMC at line 3

Example (CombineQuantOutputs_OK) ¶

var mockS3 awsutil.MockS3Client
defer mockS3.FinishTest()

const jobsBucket = "jobs-bucket"

// Some of our files are empty, not there, have content
// and they're meant to end up combined into one response...
mockS3.ExpGetObjectInput = []s3.GetObjectInput{
	{
		Bucket: aws.String(jobsBucket), Key: aws.String("JobData/abc123/output/node001.pmcs_result.csv"),
	},
	{
		Bucket: aws.String(jobsBucket), Key: aws.String("JobData/abc123/output/node002.pmcs_result.csv"),
	},
	{
		Bucket: aws.String(jobsBucket), Key: aws.String("JobData/abc123/output/node003.pmcs_result.csv"),
	},
}
mockS3.QueuedGetObjectOutput = []*s3.GetObjectOutput{
	{
		Body: io.NopCloser(bytes.NewReader([]byte(`Header row1
PMC, CaO_%, CaO_int, RTT
30, 5.1, 400, 7890
12, 6.1, 405, 7800
`))),
	},
	{
		Body: io.NopCloser(bytes.NewReader([]byte(`Header row2
PMC, CaO_%, CaO_int, RTT
18, 7.1, 415, 7840
`))),
	},
	{
		Body: io.NopCloser(bytes.NewReader([]byte(`Header row3
PMC, CaO_%, CaO_int, RTT
3, 1.1, 450, 7830
40, 8.1, 455, 7870
`))),
	},
}

fs := fileaccess.MakeS3Access(&mockS3)
combinedCSV, err := combineQuantOutputs(fs, jobsBucket, "JobData/abc123", "The custom header", []string{"node001.pmcs", "node002.pmcs", "node003.pmcs"})

fmt.Printf("%v\n", err)
fmt.Println(combinedCSV)

Output:

<nil>
The custom header
PMC, CaO_%, CaO_int, RTT
3, 1.1, 450, 7830
12, 6.1, 405, 7800
18, 7.1, 415, 7840
30, 5.1, 400, 7890
40, 8.1, 455, 7870

Example (ConvertQuantificationData) ¶

data := csvData{
	[]string{"PMC", "Ca_%", "Ca_int", "SCLK", "Ti_%", "filename", "RTT"},
	[][]string{
		[]string{"23", "1.5", "5", "11111", "4", "fileA.msa", "44"},
		[]string{"70", "3.4", "32", "12345", "4.21", "fileB.msa", "45"},
	},
}

result, err := convertQuantificationData(data, []string{"PMC", "RTT", "SCLK", "filename"})
fmt.Printf("%v|%v\n", result, err)

Output:

{[Ca_% Ca_int Ti_%] [F I F] [{23 44 11111 fileA.msa [1.5 5 4]} {70 45 12345 fileB.msa [3.4 32 4.21]}]}|<nil>

Example (DecodeMapFileNameColumn) ¶

rt, det, err := decodeMapFileNameColumn("file.txt")
fmt.Printf("%v|%v|%v\n", rt, det, err)

rt, det, err = decodeMapFileNameColumn("Normal_A")
fmt.Printf("%v|%v|%v\n", rt, det, err)

rt, det, err = decodeMapFileNameColumn("Normal_A_MyRoiID")
fmt.Printf("%v|%v|%v\n", rt, det, err)

rt, det, err = decodeMapFileNameColumn("Dwell_B")
fmt.Printf("%v|%v|%v\n", rt, det, err)

rt, det, err = decodeMapFileNameColumn("Normal_C")
fmt.Printf("%v|%v|%v\n", rt, det, err)

rt, det, err = decodeMapFileNameColumn("LongRead_B")
fmt.Printf("%v|%v|%v\n", rt, det, err)

rt, det, err = decodeMapFileNameColumn("Scotland_something_00012.msa")
fmt.Printf("%v|%v|%v\n", rt, det, err)

rt, det, err = decodeMapFileNameColumn("Scotland_something_00012_10keV_33.msa")
fmt.Printf("%v|%v|%v\n", rt, det, err)

rt, det, err = decodeMapFileNameColumn("Normal_A_0123456789_873495_455.msa")
fmt.Printf("%v|%v|%v\n", rt, det, err)

Output:

||decodeMapFileNameColumn: Invalid READTYPE in filename: "file.txt"
Normal|A|<nil>
Normal|A|<nil>
Dwell|B|<nil>
||decodeMapFileNameColumn: Invalid DETECTOR_ID in filename: "Normal_C"
||decodeMapFileNameColumn: Invalid READTYPE in filename: "LongRead_B"
||decodeMapFileNameColumn: Invalid READTYPE in filename: "Scotland_something_00012.msa"
||decodeMapFileNameColumn: Invalid READTYPE in filename: "Scotland_something_00012_10keV_33.msa"
Normal|A|<nil>

Example (FilterListItems) ¶

// Should just filter indexes that are valid
idxToIgnoreMap := map[int]bool{
	-9: true,
	1:  true,
	2:  true,
	5:  true,
	6:  true,
}

fmt.Println(filterListItems([]string{"snowboarding", "is", "awesome", "says", "Peter", "Nemere"}, idxToIgnoreMap))

Output:

[snowboarding says Peter]

Example (GetElements) ¶

fmt.Printf("%v", getElements([]string{"PMC", "SCLK", "Ca_%", "Ti_%", "Ca_int", "Ti_int", "livetime", "Mg_%", "chisq"}))

Output:

[Ca Ti Mg]

Example (GetExistingAutoQuants) ¶

db := wstestlib.GetDB()

// Ensure none
ctx := context.TODO()
coll := db.Collection(dbCollections.QuantificationsName)
fmt.Printf("Drop: %v\n", coll.Drop(ctx))

names := []string{"AutoQuant-PDS(AB)", "AutoQuant-PIXL(AB)", "AutoQuant-PDS(Combined)", "AutoQuant-PIXL(Combined)"}
existing, err := getExistingAutoQuants("123", names, db)
fmt.Println("Test missing")
fmt.Printf("%v\n", err)
fmt.Printf("Read:%v\n\n", strings.Join(existing, ","))

autoQuant := &protos.QuantificationSummary{
	Id:     "PIXLAB123",
	ScanId: "123",
	Params: &protos.QuantStartingParameters{
		UserParams: &protos.QuantCreateParams{
			Command:        "map",
			Name:           "AutoQuant-PIXL(AB)",
			ScanId:         "123",
			Elements:       []string{"Na", "Mg"},
			DetectorConfig: "PIXL/PiquantConfigs/v7",
			Parameters:     "-Fe,1",
			QuantMode:      "Combined",
		},
		PmcCount:     51,
		ScanFilePath: "Datasets/104202753/dataset.bin",
	},
	Elements: []string{"Na2O", "MgO"},
	Status: &protos.JobStatus{
		JobId:          "PIXLAB123",
		Status:         5,
		Message:        "Nodes ran: 1",
		EndUnixTimeSec: 1670988052,
		OutputFilePath: "Quantifications/104202753/auth0|62eda29040fd995f305e2322",
		OtherLogFiles:  []string{"node00001_piquant.log", "node00001_stdout.log"},
	},
}

_, err = coll.InsertOne(ctx, autoQuant, options.InsertOne())
fmt.Printf("Insert: %v\n", err)

//names := []string{"AutoQuant-PIXL(AB)"}
existing, err = getExistingAutoQuants("123", names, db)
fmt.Println("Test exists")
fmt.Printf("%v\n", err)
fmt.Printf("%v\n", strings.Join(existing, ","))

Output:

Drop: <nil>
Test missing
<nil>
Read:

Insert: <nil>
Test exists
<nil>
AutoQuant-PIXL(AB) (id: PIXLAB123)

Example (GetInterestingColIndexes) ¶

header := []string{"PMC", "K_%", "Ca_%", "Fe_%", "K_int", "Ca_int", "Fe_int", "K_err", "Ca_err", "Fe_err", "total_counts", "livetime", "chisq", "eVstart", "eV/ch", "res", "iter", "filename", "Events", "Triggers", "SCLK", "RTT"}
interesting, err := getInterestingColIndexes(header, []string{"PMC", "filename", "SCLK", "RTT"})
fmt.Printf("\"%v\" \"%v\"\n", interesting, err)
interesting, err = getInterestingColIndexes(header, []string{"K_%", "total_counts"})
fmt.Printf("\"%v\" \"%v\"\n", interesting, err)

// Bad cases
interesting, err = getInterestingColIndexes(header, []string{"PMC", "TheFileName", "SCLK", "RTT"})
fmt.Printf("\"%v\" \"%v\"\n", interesting, err)
header[5] = "SCLK"
interesting, err = getInterestingColIndexes(header, []string{"PMC", "TheFileName", "SCLK", "RTT"})
fmt.Printf("\"%v\" \"%v\"\n", interesting, err)

// 22 header items...

Output:

"map[PMC:0 RTT:21 SCLK:20 filename:17]" "<nil>"
"map[K_%:1 total_counts:10]" "<nil>"
"map[]" "CSV column missing: TheFileName"
"map[]" "Duplicate CSV column: SCLK"

Example (MakeColumnTypeList) ¶

data := csvData{[]string{"a", "b", "c", "d", "e"}, [][]string{[]string{"1.11111", "2", "3.1415962", "5", "6"}}}
result, err := makeColumnTypeList(data, map[int]bool{2: true, 3: true})
fmt.Printf("%v|%v\n", result, err)
result, err = makeColumnTypeList(data, map[int]bool{})
fmt.Printf("%v|%v\n", result, err)

// Bad type
data = csvData{[]string{"a", "b", "c", "d", "e"}, [][]string{[]string{"1.11111", "Wanaka", "3.1415962", "5"}}}
result, err = makeColumnTypeList(data, map[int]bool{2: true, 3: true})
fmt.Printf("%v|%v\n", result, err)

// Skipping the string 1 should make it work...
result, err = makeColumnTypeList(data, map[int]bool{1: true, 3: true})
fmt.Printf("%v|%v\n", result, err)

Output:

[F I I]|<nil>
[F I F I I]|<nil>
[F]|Failed to parse "Wanaka" as float or int at col 1/row 0
[F F]|<nil>

Example (MakeIndividualPMCListFileContents_AB) ¶

fmt.Println(makeIndividualPMCListFileContents([]int32{15, 7, 388}, "5x11dataset.bin", false, false, map[int32]bool{}))

Output:

5x11dataset.bin
15|Normal|A
15|Normal|B
7|Normal|A
7|Normal|B
388|Normal|A
388|Normal|B
 <nil>

Example (MakeIndividualPMCListFileContents_AB_Dwell) ¶

fmt.Println(makeIndividualPMCListFileContents([]int32{15, 7, 388}, "5x11dataset.bin", false, true, map[int32]bool{15: true}))

Output:

5x11dataset.bin
15|Normal|A,15|Dwell|A
15|Normal|B,15|Dwell|B
7|Normal|A
7|Normal|B
388|Normal|A
388|Normal|B
 <nil>

Example (MakeIndividualPMCListFileContents_Combined) ¶

fmt.Println(makeIndividualPMCListFileContents([]int32{15, 7, 388}, "5x11dataset.bin", true, false, map[int32]bool{}))

Output:

5x11dataset.bin
15|Normal|A,15|Normal|B
7|Normal|A,7|Normal|B
388|Normal|A,388|Normal|B
 <nil>

Example (MakeIndividualPMCListFileContents_Combined_Dwell) ¶

fmt.Println(makeIndividualPMCListFileContents([]int32{15, 7, 388}, "5x11dataset.bin", true, true, map[int32]bool{15: true}))

Output:

5x11dataset.bin
15|Normal|A,15|Normal|B,15|Dwell|A,15|Dwell|B
7|Normal|A,7|Normal|B
388|Normal|A,388|Normal|B
 <nil>

Example (MakeQuantJobPMCLists) ¶

fmt.Println(makeQuantJobPMCLists([]int32{1, 2, 3, 4, 5, 6, 7, 8}, 3))
fmt.Println(makeQuantJobPMCLists([]int32{1, 2, 3, 4, 5, 6, 7, 8, 9}, 3))
fmt.Println(makeQuantJobPMCLists([]int32{1, 2, 3, 4, 5, 6, 7, 8, 9, 10}, 3))

Output:

[[1 2 3] [4 5 6] [7 8]]
[[1 2 3] [4 5 6] [7 8 9]]
[[1 2 3] [4 5 6] [7 8 9] [10]]

Example (MakeQuantedLocation) ¶

// Should just filter indexes that are valid
fmt.Println(makeQuantedLocation([]string{"Ca_%", "PMC", "Ti_%", "RTT", "filename", "Ca_int"}, []string{"1.11111", "2", "3.1415962", "5", "FileA.msa", "6"}, map[int]bool{1: true, 3: true, 4: true}))

Output:

{2 5 0 FileA.msa [1.11111 3.1415962 6]} <nil>

Example (MakeROIPMCListFileContents_AB) ¶

fmt.Println(makeROIPMCListFileContents(testROIs, "5x11dataset.bin", false, false, map[int32]bool{}))

Output:

5x11dataset.bin
roi1-id:7|Normal|A,15|Normal|A,388|Normal|A
roi1-id:7|Normal|B,15|Normal|B,388|Normal|B
roi2-id:7|Normal|A,450|Normal|A
roi2-id:7|Normal|B,450|Normal|B
 <nil>

Example (MakeROIPMCListFileContents_AB_Dwells) ¶

fmt.Println(makeROIPMCListFileContents(testROIs, "5x11dataset.bin", false, true, map[int32]bool{15: true}))

Output:

5x11dataset.bin
roi1-id:7|Normal|A,15|Normal|A,15|Dwell|A,388|Normal|A
roi1-id:7|Normal|B,15|Normal|B,15|Dwell|B,388|Normal|B
roi2-id:7|Normal|A,450|Normal|A
roi2-id:7|Normal|B,450|Normal|B
 <nil>

Example (MakeROIPMCListFileContents_Combined) ¶

fmt.Println(makeROIPMCListFileContents(testROIs, "5x11dataset.bin", true, false, map[int32]bool{}))

Output:

5x11dataset.bin
roi1-id:7|Normal|A,7|Normal|B,15|Normal|A,15|Normal|B,388|Normal|A,388|Normal|B
roi2-id:7|Normal|A,7|Normal|B,450|Normal|A,450|Normal|B
 <nil>

Example (MakeROIPMCListFileContents_Combined_Dwells) ¶

fmt.Println(makeROIPMCListFileContents(testROIs, "5x11dataset.bin", true, true, map[int32]bool{15: true}))

Output:

5x11dataset.bin
roi1-id:7|Normal|A,7|Normal|B,15|Normal|A,15|Normal|B,15|Dwell|A,15|Dwell|B,388|Normal|A,388|Normal|B
roi2-id:7|Normal|A,7|Normal|B,450|Normal|A,450|Normal|B
 <nil>

Example (MatchPMCsWithDataset) ¶

l := &logger.StdOutLogger{}
data := csvData{[]string{"X", "Y", "Z", "filename", "Ca_%"}, [][]string{[]string{"1", "0.40", "0", "Roastt_Laguna_Salinas_28kV_230uA_03_03_2020_111.msa", "4.5"}}}

exp, err := readDatasetFile("./testdata/LagunaSalinasdataset.bin")
fmt.Printf("Test file read: %v\n", err)
fmt.Printf("%v, header[%v]=%v, data[%v]=%v\n", matchPMCsWithDataset(&data, exp, true, l), len(data.header)-1, data.header[5], len(data.data[0])-1, data.data[0][5])

data = csvData{[]string{"X", "Y", "Z", "filename", "Ca_%"}, [][]string{[]string{"1", "930.40", "0", "Roastt_Laguna_Salinas_28kV_230uA_03_03_2020_111.msa", "4.5"}}}
fmt.Println(matchPMCsWithDataset(&data, exp, true, l))

data = csvData{[]string{"X", "Y", "Z", "filename", "Ca_%"}, [][]string{[]string{"1", "0.40", "0", "Roastt_Laguna_Salinas_28kV_230uA_03_03_2020_116.msa", "4.5"}}}
fmt.Printf("%v, header[%v]=%v, data[%v]=%v\n", matchPMCsWithDataset(&data, exp, false, l), len(data.header)-1, data.header[5], len(data.data[0])-1, data.data[0][5])

Output:

Test file read: <nil>
<nil>, header[5]=PMC, data[5]=111
matchPMCsWithDataset Failed to match 1.00,930.40,0.00 to a PMC in dataset file
<nil>, header[5]=PMC, data[5]=116

Example (ParseFloatColumnValue) ¶

fVal, err := parseFloatColumnValue("3.1415926")
fmt.Printf("%v|%v\n", fVal, err)

fVal, err = parseFloatColumnValue("-3.15")
fmt.Printf("%v|%v\n", fVal, err)

fVal, err = parseFloatColumnValue("1.234e02")
fmt.Printf("%v|%v\n", fVal, err)

fVal, err = parseFloatColumnValue("")
fmt.Printf("%v|%v\n", fVal, err)

fVal, err = parseFloatColumnValue("nan")
fmt.Printf("%v|%v\n", fVal, err)

fVal, err = parseFloatColumnValue("-nan")
fmt.Printf("%v|%v\n", fVal, err)

Output:

3.1415925|<nil>
-3.15|<nil>
123.4|<nil>
0|strconv.ParseFloat: parsing "": invalid syntax
NaN|<nil>
NaN|<nil>

Example (ProcessQuantROIsToPMCs_Combined_CSVRowCountROICountMismatch) ¶

var mockS3 awsutil.MockS3Client
defer mockS3.FinishTest()

const jobsBucket = "jobs-bucket"

// Some of our files are empty, not there, have content
// and they're meant to end up combined into one response...
mockS3.ExpGetObjectInput = []s3.GetObjectInput{
	{
		Bucket: aws.String(jobsBucket), Key: aws.String("JobData/abc123/output/node001.pmcs_result.csv"),
	},
}
mockS3.QueuedGetObjectOutput = []*s3.GetObjectOutput{
	{
		Body: io.NopCloser(bytes.NewReader([]byte(`Header row1
PMC, CaO_%, CaO_int, RTT, filename
15, 5.1, 400, 7890, Normal_A_roi1-id
7, 6.1, 405, 7800, Normal_A_roi1-id
12, 6.7, 407, 7700, Normal_A_roi1-id
`))),
	},
}

fs := fileaccess.MakeS3Access(&mockS3)
outputCSV, err := processQuantROIsToPMCs(fs, jobsBucket, "JobData/abc123", "The custom header", "node001.pmcs", true, testROIs)

fmt.Printf("%v\n", err)
fmt.Println(outputCSV)

Output:

PMC 12 in CSV: JobData/abc123/output/node001.pmcs_result.csv doesn't exist in ROI: roi1

Example (ProcessQuantROIsToPMCs_Combined_DownloadError) ¶

var mockS3 awsutil.MockS3Client
defer mockS3.FinishTest()

const jobsBucket = "jobs-bucket"

// Some of our files are empty, not there, have content
// and they're meant to end up combined into one response...
mockS3.ExpGetObjectInput = []s3.GetObjectInput{
	{
		Bucket: aws.String(jobsBucket), Key: aws.String("JobData/abc123/output/node001.pmcs_result.csv"),
	},
}
mockS3.QueuedGetObjectOutput = []*s3.GetObjectOutput{
	nil,
}

fs := fileaccess.MakeS3Access(&mockS3)
outputCSV, err := processQuantROIsToPMCs(fs, jobsBucket, "JobData/abc123", "The custom header", "node001.pmcs", true, testROIs)

fmt.Printf("%v\n", err)
fmt.Println(outputCSV)

Output:

Failed to read map CSV: JobData/abc123/output/node001.pmcs_result.csv

Example (ProcessQuantROIsToPMCs_Combined_InvalidPMC) ¶

var mockS3 awsutil.MockS3Client
defer mockS3.FinishTest()

const jobsBucket = "jobs-bucket"

// Some of our files are empty, not there, have content
// and they're meant to end up combined into one response...
mockS3.ExpGetObjectInput = []s3.GetObjectInput{
	{
		Bucket: aws.String(jobsBucket), Key: aws.String("JobData/abc123/output/node001.pmcs_result.csv"),
	},
}
mockS3.QueuedGetObjectOutput = []*s3.GetObjectOutput{
	{
		Body: io.NopCloser(bytes.NewReader([]byte(`Header row1
PMC, CaO_%, CaO_int, filename, RTT
15, 5.1, 400, Normal_A_roi1-id, 7890
Qwerty, 6.1, 405, Normal_A_roi1-id, 7800
`))),
	},
}

fs := fileaccess.MakeS3Access(&mockS3)
outputCSV, err := processQuantROIsToPMCs(fs, jobsBucket, "JobData/abc123", "The custom header", "node001.pmcs", true, testROIs)

fmt.Printf("%v\n", err)
fmt.Println(outputCSV)

Output:

Failed to process map CSV: JobData/abc123/output/node001.pmcs_result.csv, invalid PMC Qwerty at line 4

Example (ProcessQuantROIsToPMCs_Combined_NoFileNameCol) ¶

var mockS3 awsutil.MockS3Client
defer mockS3.FinishTest()

const jobsBucket = "jobs-bucket"

// Some of our files are empty, not there, have content
// and they're meant to end up combined into one response...
mockS3.ExpGetObjectInput = []s3.GetObjectInput{
	{
		Bucket: aws.String(jobsBucket), Key: aws.String("JobData/abc123/output/node001.pmcs_result.csv"),
	},
}
mockS3.QueuedGetObjectOutput = []*s3.GetObjectOutput{
	{
		Body: io.NopCloser(bytes.NewReader([]byte(`Header row1
PMC, CaO_%, CaO_int, RTT
15, 5.1, 400, 7890
7, 6.1, 405, 7800
`))),
	},
}

fs := fileaccess.MakeS3Access(&mockS3)
outputCSV, err := processQuantROIsToPMCs(fs, jobsBucket, "JobData/abc123", "The custom header", "node001.pmcs", true, testROIs)

fmt.Printf("%v\n", err)
fmt.Println(outputCSV)

Output:

Map csv: JobData/abc123/output/node001.pmcs_result.csv, does not contain a filename column (used to match up ROIs)

Example (ProcessQuantROIsToPMCs_Combined_OK) ¶

var mockS3 awsutil.MockS3Client
defer mockS3.FinishTest()

const jobsBucket = "jobs-bucket"

// Some of our files are empty, not there, have content
// and they're meant to end up combined into one response...
mockS3.ExpGetObjectInput = []s3.GetObjectInput{
	{
		Bucket: aws.String(jobsBucket), Key: aws.String("JobData/abc123/output/node001.pmcs_result.csv"),
	},
}
mockS3.QueuedGetObjectOutput = []*s3.GetObjectOutput{
	{
		Body: io.NopCloser(bytes.NewReader([]byte(`Header row1
PMC, CaO_%, filename, CaO_int, RTT
15, 5.1, Normal_A_roi1-id, 400, 7890
7, 6.1, Normal_B_roi2-id, 405, 7800
`))),
	},
}

fs := fileaccess.MakeS3Access(&mockS3)
outputCSV, err := processQuantROIsToPMCs(fs, jobsBucket, "JobData/abc123", "The custom header", "node001.pmcs", true, testROIs)

fmt.Printf("%v\n", err)
fmt.Println(outputCSV)

Output:

<nil>
The custom header
PMC, CaO_%, filename, CaO_int, RTT
7, 5.1, Normal_A_roi1-id, 400, 7890
15, 5.1, Normal_A_roi1-id, 400, 7890
388, 5.1, Normal_A_roi1-id, 400, 7890
7, 6.1, Normal_B_roi2-id, 405, 7800
450, 6.1, Normal_B_roi2-id, 405, 7800

Example (ProcessQuantROIsToPMCs_SeparateAB_InvalidFileName) ¶

var mockS3 awsutil.MockS3Client
defer mockS3.FinishTest()

const jobsBucket = "jobs-bucket"

// Some of our files are empty, not there, have content
// and they're meant to end up combined into one response...
mockS3.ExpGetObjectInput = []s3.GetObjectInput{
	{
		Bucket: aws.String(jobsBucket), Key: aws.String("JobData/abc123/output/node001.pmcs_result.csv"),
	},
}
mockS3.QueuedGetObjectOutput = []*s3.GetObjectOutput{
	{
		Body: io.NopCloser(bytes.NewReader([]byte(`Header row1
PMC, CaO_%, CaO_int, filename, RTT
15, 5.1, 400, Normal_A_roi1-id, 7890
15, 5.2, 401, Normal_B, 7890
7, 6.1, 405, Normal_A, 7800
7, 6.2, 406, Normal_B, 7800
`))),
	},
}

fs := fileaccess.MakeS3Access(&mockS3)
outputCSV, err := processQuantROIsToPMCs(fs, jobsBucket, "JobData/abc123", "The custom header", "node001.pmcs", false, testROIs)

fmt.Printf("%v\n", err)
fmt.Println(outputCSV)

Output:

Invalid file name read: Normal_B from map CSV: JobData/abc123/output/node001.pmcs_result.csv, line 4

Example (ProcessQuantROIsToPMCs_SeparateAB_OK) ¶

var mockS3 awsutil.MockS3Client
defer mockS3.FinishTest()

const jobsBucket = "jobs-bucket"

// Some of our files are empty, not there, have content
// and they're meant to end up combined into one response...
mockS3.ExpGetObjectInput = []s3.GetObjectInput{
	{
		Bucket: aws.String(jobsBucket), Key: aws.String("JobData/abc123/output/node001.pmcs_result.csv"),
	},
}
mockS3.QueuedGetObjectOutput = []*s3.GetObjectOutput{
	{
		Body: io.NopCloser(bytes.NewReader([]byte(`Header row1
PMC, CaO_%, CaO_int, filename, RTT
15, 5.1, 400, Normal_A_roi1-id, 7890
15, 5.2, 401, Normal_B_roi1-id, 7890
7, 6.1, 405, Normal_A_roi2-id, 7800
7, 6.2, 406, Normal_B_roi2-id, 7800
`))),
	},
}

fs := fileaccess.MakeS3Access(&mockS3)
outputCSV, err := processQuantROIsToPMCs(fs, jobsBucket, "JobData/abc123", "The custom header", "node001.pmcs", false, testROIs)

fmt.Printf("%v\n", err)
fmt.Println(outputCSV)

Output:

<nil>
The custom header
PMC, CaO_%, CaO_int, filename, RTT
7, 5.1, 400, Normal_A_roi1-id, 7890
7, 5.2, 401, Normal_B_roi1-id, 7890
15, 5.1, 400, Normal_A_roi1-id, 7890
15, 5.2, 401, Normal_B_roi1-id, 7890
388, 5.1, 400, Normal_A_roi1-id, 7890
388, 5.2, 401, Normal_B_roi1-id, 7890
7, 6.1, 405, Normal_A_roi2-id, 7800
7, 6.2, 406, Normal_B_roi2-id, 7800
450, 6.1, 405, Normal_A_roi2-id, 7800
450, 6.2, 406, Normal_B_roi2-id, 7800

Example (ReadCSV) ¶

csv := `something header
more header
col 1,"col, 2",  col_3
"value one",123, 456
value two,444,555
`
d, err := readCSV(csv, 2)
fmt.Printf("%v|%v", d, err)

Output:

{[col 1 col, 2 col_3] [[value one 123 456] [value two 444 555]]}|<nil>

Example (ReadQuantifiablePMCs) ¶

expr, err := readDatasetFile("./testdata/LagunaSalinasdataset.bin")
fmt.Printf("Read Laguna: %v\n", err)
pmcs, err := readQuantifiablePMCs(expr, "123", &logger.StdOutLoggerForTest{})
fmt.Printf("PMCRead: %v\n", err)
fmt.Printf("PMCs: %v\n", pmcs)

expr, err = readDatasetFile("./testdata/Naltsosdataset.bin")
fmt.Printf("Read Naltsos: %v\n", err)
pmcs, err = readQuantifiablePMCs(expr, "123", &logger.StdOutLoggerForTest{})
fmt.Printf("PMCRead: %v\n", err)
fmt.Printf("PMCs: %v\n", pmcs)

Output:

Read Laguna: <nil>
PMCRead: <nil>
PMCs: []
Read Naltsos: <nil>
PMCRead: <nil>
PMCs: [93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 216]

Example (ValidateParameters) ¶

fmt.Printf("%v\n", validateParameters("-b,0,50,2,10 -f"))
fmt.Printf("%v\n", validateParameters("-b,0,50,2,10.55 -o \"filename.whatever\" -f -Fe,1"))
fmt.Printf("%v\n", validateParameters("-b,0,50,2,10;ls -al;echo -f"))
fmt.Printf("%v\n", validateParameters("-b,0,50,2,10&&rm -rf ~/; -f"))

Output:

<nil>
<nil>
Invalid parameters passed: -b,0,50,2,10;ls -al;echo -f
Invalid parameters passed: -b,0,50,2,10&&rm -rf ~/; -f

Index ¶

Constants
func ConvertQuantificationCSV(logger logger.ILogger, data string, expectMetaColumns []string, ...) ([]byte, []string, error)
func CreateJob(createParams *protos.QuantCreateParams, requestorUserId string, ...) (*protos.JobStatus, error)
func FormCombinedCSV(quantIDs []string, dataPerDetectorPerPMC map[string]map[int32]quantItem, ...) string
func FormMultiQuantSummary(dataPerDetectorPerPMC map[string]map[int32]quantItem, ...) *protos.QuantCombineSummary
func ImportQuantCSV(hctx wsHelpers.HandlerContext, scanId string, importUser *protos.UserInfo, ...) (string, error)
func IsValidCreateParam(createParams *protos.QuantCreateParams, hctx wsHelpers.HandlerContext) error
func ListUserQuants(searchParams *protos.SearchParams, hctx wsHelpers.HandlerContext) ([]*protos.QuantificationSummary, map[string]*protos.OwnershipItem, error)
func MultiQuantCombinedCSV(name string, scanId string, roiZStack []*protos.QuantCombineItem, ...) (combinedQuantData, error)
func MultiQuantCompare(reqRoiId string, roiPMCs []int32, quantIds []string, exprPB *protos.Experiment, ...) ([]*protos.QuantComparisonTable, error)
func RunAutoQuantifications(scanId string, svcs *services.APIServices, onlyIfNotExists bool)
type QuantJobUpdater
- func MakeQuantJobUpdater(params *protos.QuantCreateParams, session *melody.Session, ...) QuantJobUpdater
- func (i *QuantJobUpdater) SendEphemeralQuantJobUpdate(status *protos.JobStatus)
- func (i *QuantJobUpdater) SendQuantJobUpdate(status *protos.JobStatus)

Examples ¶

Package (CalculateTotals_AB_NeedsCombined)
Package (CalculateTotals_NoPMC)
Package (CalculateTotals_Success)
Package (CleanLogName)
Package (CombineQuantOutputs_BadPMC)
Package (CombineQuantOutputs_DownloadError)
Package (CombineQuantOutputs_DuplicatePMC)
Package (CombineQuantOutputs_LastLineCutOff)
Package (CombineQuantOutputs_OK)
Package (ConvertQuantificationData)
Package (DecodeMapFileNameColumn)
Package (FilterListItems)
Package (GetElements)
Package (GetExistingAutoQuants)
Package (GetInterestingColIndexes)
Package (MakeColumnTypeList)
Package (MakeIndividualPMCListFileContents_AB)
Package (MakeIndividualPMCListFileContents_AB_Dwell)
Package (MakeIndividualPMCListFileContents_Combined)
Package (MakeIndividualPMCListFileContents_Combined_Dwell)
Package (MakeQuantJobPMCLists)
Package (MakeQuantedLocation)
Package (MakeROIPMCListFileContents_AB)
Package (MakeROIPMCListFileContents_AB_Dwells)
Package (MakeROIPMCListFileContents_Combined)
Package (MakeROIPMCListFileContents_Combined_Dwells)
Package (MatchPMCsWithDataset)
Package (ParseFloatColumnValue)
Package (ProcessQuantROIsToPMCs_Combined_CSVRowCountROICountMismatch)
Package (ProcessQuantROIsToPMCs_Combined_DownloadError)
Package (ProcessQuantROIsToPMCs_Combined_InvalidPMC)
Package (ProcessQuantROIsToPMCs_Combined_NoFileNameCol)
Package (ProcessQuantROIsToPMCs_Combined_OK)
Package (ProcessQuantROIsToPMCs_SeparateAB_InvalidFileName)
Package (ProcessQuantROIsToPMCs_SeparateAB_OK)
Package (ReadCSV)
Package (ReadQuantifiablePMCs)
Package (ValidateParameters)

Constants ¶

View Source

const JobParamsFileName = "params.json"

JobParamsFileName - File name of job params file

View Source

const QuantModeABManualUpload = "ABManual"

View Source

const QuantModeABMultiQuant = "ABMultiQuant"

View Source

const QuantModeCombinedManualUpload = "ABManual"

View Source

const QuantModeCombinedMultiQuant = "CombinedMultiQuant"

Variables ¶

This section is empty.

Functions ¶

func ConvertQuantificationCSV ¶

func ConvertQuantificationCSV(logger logger.ILogger, data string, expectMetaColumns []string, exprPB *protos.Experiment, matchPMCByCoord bool, detectorIDOverride string, detectorDuplicateAB bool) ([]byte, []string, error)

ConvertQuantificationCSV - converts from incoming string CSV data to serialised binary data. exprPB if nil means we wont match to dataset PMCs Returns the serialised quantification bytes and the elements that were quantified

func CreateJob ¶

func CreateJob(createParams *protos.QuantCreateParams, requestorUserId string, svcs *services.APIServices, sessUser *wsHelpers.SessionUser, sendUpdate func(*protos.JobStatus)) (*protos.JobStatus, error)

CreateJob - creates a new quantification job

func FormCombinedCSV ¶

func FormCombinedCSV(quantIDs []string, dataPerDetectorPerPMC map[string]map[int32]quantItem, allColumns map[string]bool) string

func FormMultiQuantSummary ¶

func FormMultiQuantSummary(dataPerDetectorPerPMC map[string]map[int32]quantItem, allColumns map[string]bool, totalPMCCount int) *protos.QuantCombineSummary

func ImportQuantCSV ¶

func ImportQuantCSV(
	hctx wsHelpers.HandlerContext,
	scanId string,
	importUser *protos.UserInfo,
	csvBody string,
	csvOrigin string,
	idPrefix string,
	quantName string,
	quantModeEnum string,
	comments string) (string, error)

func IsValidCreateParam ¶

func IsValidCreateParam(createParams *protos.QuantCreateParams, hctx wsHelpers.HandlerContext) error

Validates the create parameters. Side-effect of modifying PmcsEncoded to just be an array of decoded PMCs

func ListUserQuants ¶

func ListUserQuants(searchParams *protos.SearchParams, hctx wsHelpers.HandlerContext) ([]*protos.QuantificationSummary, map[string]*protos.OwnershipItem, error)

func MultiQuantCombinedCSV ¶

func MultiQuantCombinedCSV(
	name string,
	scanId string,
	roiZStack []*protos.QuantCombineItem,
	exprPB *protos.Experiment,
	hctx wsHelpers.HandlerContext) (combinedQuantData, error)

func MultiQuantCompare ¶

func MultiQuantCompare(reqRoiId string, roiPMCs []int32, quantIds []string, exprPB *protos.Experiment, hctx wsHelpers.HandlerContext) ([]*protos.QuantComparisonTable, error)

func RunAutoQuantifications ¶

func RunAutoQuantifications(scanId string, svcs *services.APIServices, onlyIfNotExists bool)

Types ¶

type QuantJobUpdater ¶

type QuantJobUpdater struct {
	// contains filtered or unexported fields
}

func MakeQuantJobUpdater ¶

func MakeQuantJobUpdater(
	params *protos.QuantCreateParams,
	session *melody.Session,

	notifier services.INotifier,
	db *mongo.Database,
	fs fileaccess.FileAccess,
	usersBucket string,
) QuantJobUpdater

func (*QuantJobUpdater) SendEphemeralQuantJobUpdate ¶ added in v4.31.4

func (i *QuantJobUpdater) SendEphemeralQuantJobUpdate(status *protos.JobStatus)

We send updates for ephemeral quant jobs (that are short running) this way...

func (*QuantJobUpdater) SendQuantJobUpdate ¶

func (i *QuantJobUpdater) SendQuantJobUpdate(status *protos.JobStatus)

We send updates for quant jobs (that are long running, have names, stick around) this way...

Directories ¶

Path	Synopsis
quantRunner Exposes interfaces and structures required to run PIQUANT in the Kubernetes cluster along with functions to access quantification files, logs, results and summaries of quant jobs.	Exposes interfaces and structures required to run PIQUANT in the Kubernetes cluster along with functions to access quantification files, logs, results and summaries of quant jobs.

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Documentation ¶

Overview ¶

Index ¶

Examples ¶

Constants ¶

Variables ¶

Functions ¶

func ConvertQuantificationCSV ¶

func CreateJob ¶

func FormCombinedCSV ¶

func FormMultiQuantSummary ¶

func ImportQuantCSV ¶

func IsValidCreateParam ¶

func ListUserQuants ¶

func MultiQuantCombinedCSV ¶

func MultiQuantCompare ¶

func RunAutoQuantifications ¶

Types ¶

type QuantJobUpdater ¶

func MakeQuantJobUpdater ¶

func (*QuantJobUpdater) SendEphemeralQuantJobUpdate ¶ added in v4.31.4

func (*QuantJobUpdater) SendQuantJobUpdate ¶

Source Files ¶

Directories ¶