Merge pull request #334 from metrumresearchgroup/summary-more-nan

nmparser: guard against NaN for all incoming floats

integration/nmless/bbi_summary_test.go

@@ -44,7 +44,7 @@ func TestSummaryHappyPath(tt *testing.T) {
 		"example2_bayes",   // Bayes (5 est methods, from NONMEM examples)
 		"iovmm",            // Mixture model. Also has parameter_near_boundary and final_zero_gradient heuristics.
 		"acop-iov",         // fake model with 62 OMEGAS (fake iov)
-		"acop-nan",         // NaN values for objective function
+		"acop-nan",         // NaN values in several spots
 		"onlysim",          // $SIM with ONLYSIM.
 		"chain",            // CHAIN method that lacks estimation data.
 		"12-empty-problem", // $PROBLEM is an empty string

integration/nmless/testdata/bbi_summary/aa_golden_files/acop-nan.golden.json

@@ -49,12 +49,12 @@
 				"theta": [
 					2.31034,
 					54.9596,
-					464.659,
+					-999999999,
 					-0.0805722,
 					4.1303
 				],
 				"omega": [
-					0.0964407,
+					-999999999,
 					0,
 					0.153571
 				],
@@ -65,14 +65,14 @@
 			"std_err": {
 				"theta": [
 					0.086147,
-					3.32914,
+					-999999999,
 					29.6177,
 					0.0555149,
 					1.35989
 				],
 				"omega": [
 					0.0200146,
-					10000000000,
+					-999999999,
 					0.026733
 				],
 				"sigma": [
@@ -105,7 +105,7 @@
 					0,
 					0,
 					0,
-					0
+					-999999999
 				],
 				"omega": [
 					0,

integration/nmless/testdata/bbi_summary/aa_golden_files/acop-nan.golden.txt

@@ -8,14 +8,14 @@ No Heuristic Problems Detected
 | THETA |  NAME  |  ESTIMATE  |   STDERR (RSE)    |
 +-------+--------+------------+-------------------+
 | TH 1  | THETA1 | 2.31034    | 0.086147 (3.7%)   |
-| TH 2  | THETA2 | 54.9596    | 3.32914 (6.1%)    |
-| TH 3  | THETA3 | 464.659    | 29.6177 (6.4%)    |
+| TH 2  | THETA2 | 54.9596    | -                 |
+| TH 3  | THETA3 | -999999999 | 29.6177 (0.0%)    |
 | TH 4  | THETA4 | -0.0805722 | 0.0555149 (68.9%) |
 | TH 5  | THETA5 | 4.1303     | 1.35989 (32.9%)   |
 +-------+--------+------------+-------------------+
-+------------+------+----------+---------------+
-|   OMEGA    | ETA  | ESTIMATE | SHRINKAGE (%) |
-+------------+------+----------+---------------+
-| OMEGA(1,1) | ETA1 | 0.096441 | 17.511500     |
-| OMEGA(2,2) | ETA2 | 0.153571 | 2.059620      |
-+------------+------+----------+---------------+
++------------+------+-------------------+---------------+
+|   OMEGA    | ETA  |     ESTIMATE      | SHRINKAGE (%) |
++------------+------+-------------------+---------------+
+| OMEGA(1,1) | ETA1 | -999999999.000000 | 17.511500     |
+| OMEGA(2,2) | ETA2 | 0.153571          | 2.059620      |
++------------+------+-------------------+---------------+

integration/nmless/testdata/bbi_summary/acop-nan/acop-nan.ext

@@ -7,10 +7,10 @@ TABLE NO.     1: First Order Conditional Estimation with Interaction: Goal Funct
            20  2.30528E+00  5.58065E+01  4.72255E+02 -8.05144E-02  4.12591E+00  1.00000E+00  9.09862E-02  0.00000E+00  2.06974E-01    2638.5029836424560
            25  2.31302E+00  5.44961E+01  4.65370E+02 -8.07920E-02  4.13612E+00  1.00000E+00  9.61335E-02  0.00000E+00  1.57375E-01    2636.8778706340345
            28  2.31034E+00  5.49596E+01  4.64659E+02 -8.05722E-02  4.13030E+00  1.00000E+00  9.64407E-02  0.00000E+00  1.53571E-01    2636.8457703290751
-  -1000000000  2.31034E+00  5.49596E+01  4.64659E+02 -8.05722E-02  4.13030E+00  1.00000E+00  9.64407E-02  0.00000E+00  1.53571E-01    2636.8457703290751
-  -1000000001  8.61470E-02  3.32914E+00  2.96177E+01  5.55149E-02  1.35989E+00  1.00000E+10  2.00146E-02  1.00000E+10  2.67330E-02    0.0000000000000000
-  -1000000004  0.00000E+00  0.00000E+00  0.00000E+00  0.00000E+00  0.00000E+00  1.00000E+00  3.10549E-01  0.00000E+00  3.91882E-01    0.0000000000000000
-  -1000000005  0.00000E+00  0.00000E+00  0.00000E+00  0.00000E+00  0.00000E+00  1.00000E+10  3.22245E-02  1.00000E+10  3.41085E-02    0.0000000000000000
-  -1000000006  0.00000E+00  0.00000E+00  0.00000E+00  0.00000E+00  0.00000E+00  1.00000E+00  0.00000E+00  1.00000E+00  0.00000E+00    0.0000000000000000
-  -1000000007  0.00000E+00  3.70000E+01  0.00000E+00  0.00000E+00  0.00000E+00  0.00000E+00  0.00000E+00  0.00000E+00  0.00000E+00    0.0000000000000000
-  -1000000008 -3.39427E-03  1.00007E-04 -7.27007E-04 -1.46088E-01  2.43350E-03  0.00000E+00  4.84108E-02  0.00000E+00 -5.58021E-03    0.0000000000000000
+  -1000000000  2.31034E+00  5.49596E+01     NaN      -8.05722E-02  4.13030E+00  1.00000E+00     NaN       0.00000E+00  1.53571E-01    2636.8457703290751
+  -1000000001  8.61470E-02      NaN      2.96177E+01  5.55149E-02  1.35989E+00  1.00000E+10  2.00146E-02      NaN      2.67330E-02    0.0000000000000000
+  -1000000004     NaN       0.00000E+00  0.00000E+00  0.00000E+00  0.00000E+00  1.00000E+00  3.10549E-01  0.00000E+00  3.91882E-01    0.0000000000000000
+  -1000000005  0.00000E+00  0.00000E+00  0.00000E+00     NaN       0.00000E+00  1.00000E+10  3.22245E-02  1.00000E+10  3.41085E-02    0.0000000000000000
+  -1000000006  0.00000E+00  0.00000E+00  0.00000E+00  0.00000E+00      NaN      1.00000E+00  0.00000E+00  1.00000E+00  0.00000E+00    0.0000000000000000
+  -1000000007  0.00000E+00  3.70000E+01  0.00000E+00  0.00000E+00  0.00000E+00     NaN       0.00000E+00  0.00000E+00  0.00000E+00    0.0000000000000000
+  -1000000008 -3.39427E-03  1.00007E-04 -7.27007E-04 -1.46088E-01  2.43350E-03  0.00000E+00  4.84108E-02  0.00000E+00     NaN         0.0000000000000000

parsers/nmparser/get_model_output.go

@@ -4,7 +4,6 @@ import (
 	"errors"
 	"fmt"
 	"path/filepath"
-	"strconv"
 	"strings"
 
 	"github.com/metrumresearchgroup/bbi/utils"
@@ -90,7 +89,7 @@ func GetModelOutput(lstPath string, ext ModelOutputFile, grd bool, shk bool) (Su
 		log.Trace("error reading cpu file: ", err)
 	} else {
 		results.RunDetails.OutputFilesUsed = append(results.RunDetails.OutputFilesUsed, filepath.Base(cpuFilePath))
-		cpuTime, err := strconv.ParseFloat(strings.TrimSpace(cpuLines[0]), 64)
+		cpuTime, err := parseFloatReplaceNaN(strings.TrimSpace(cpuLines[0]))
 		if err != nil {
 			// this is set to trace as don't want it to log normally as could screw up json output that
 			log.Trace("error parsing cpu time: ", err)

parsers/nmparser/parse_lst_file.go

@@ -105,7 +105,7 @@ func getMatrixData(lines []string, start int) MatrixData {
 		// populate matrix
 		for j, row := range rows {
 			for k, cell := range strings.Fields(row) {
-				value, err := strconv.ParseFloat(cell, 64)
+				value, err := parseFloatReplaceNaN(cell)
 				if err == nil {
 					matrix[j][k] = value
 				} else {
@@ -418,7 +418,7 @@ func mustCalculateConditionNumber(lines []string, start int) float64 {
 
 		eigenstarted = true
 		for _, s := range strings.Fields(line) {
-			eigenvalue, err := strconv.ParseFloat(s, 64)
+			eigenvalue, err := parseFloatReplaceNaN(s)
 			if err != nil {
 				panic(fmt.Sprintf("Attempting to calculate condition number but could not parse eigenvalues -- %v", err))
 			}

parsers/nmparser/parse_run_details.go

@@ -58,7 +58,7 @@ func ParseRunDetails(lines []string) RunDetails {
 		case strings.Contains(line, "NO. OF FUNCTION EVALUATIONS USED"):
 			runDetails.FunctionEvaluations, _ = strconv.ParseInt(replaceTrim(line, "NO. OF FUNCTION EVALUATIONS USED:"), 10, 64)
 		case strings.Contains(line, "NO. OF SIG. DIGITS IN FINAL EST.:"):
-			runDetails.SignificantDigits, _ = strconv.ParseFloat(replaceTrim(line, "NO. OF SIG. DIGITS IN FINAL EST.:"), 64)
+			runDetails.SignificantDigits = strToFloat(replaceTrim(line, "NO. OF SIG. DIGITS IN FINAL EST.:"))
 		case strings.Contains(line, "Elapsed estimation"):
 			runDetails.EstimationTime = append(runDetails.EstimationTime,
 				parseFinalTime(line))
@@ -68,7 +68,7 @@ func ParseRunDetails(lines []string) RunDetails {
 		case strings.Contains(line, "Elapsed postprocess"):
 			runDetails.PostprocessTime = parseFinalTime(line)
 		case strings.Contains(line, " #CPUT: Total CPU Time in Seconds,"):
-			runDetails.CpuTime, _ = strconv.ParseFloat(replaceTrim(line, " #CPUT: Total CPU Time in Seconds,"), 64)
+			runDetails.CpuTime = strToFloat(replaceTrim(line, " #CPUT: Total CPU Time in Seconds,"))
 		case strings.Contains(line, "Started"):
 			runDetails.RunStart = replaceTrim(line, "Started")
 		case strings.HasPrefix(lineTrimmed, "Finished "):

parsers/nmparser/read_cov.go

@@ -1,7 +1,6 @@
 package parser
 
 import (
-	"strconv"
 	"strings"
 )
 
@@ -51,7 +50,7 @@ func getThetaMatrix(lines []string) [][]float64 {
 			thetas := make([]float64, len)
 
 			for n := 1; n <= len; n++ {
-				if f, err := strconv.ParseFloat(fields[n], 64); err == nil {
+				if f, err := parseFloatReplaceNaN(fields[n]); err == nil {
 					thetas[n-1] = f
 				} else {
 					panic("error converting value in cov file to number: " + fields[n])

parsers/nmparser/read_ext.go

@@ -98,7 +98,7 @@ func ParseParamsExt(ed ExtData) ([]ParametersData, ParameterNames) {
 					// this is the OBJ which we've gotten elsewhere
 					continue
 				}
-				if n, err := strconv.ParseFloat(val, 64); err == nil {
+				if n, err := parseFloatReplaceNaN(val); err == nil {
 					result[i-1] = n
 				} else {
 					log.Println("Did you use a non-default format parameter? bbi does not support non-default format parameters.")
@@ -163,7 +163,7 @@ func ParseConditionNumberExt(ed ExtData) []ConditionNumDetails {
 			fields := strings.Fields(line)
 			step, _ := strconv.Atoi(fields[0])
 			if step == -1000000003 {
-				condNum, _ = strconv.ParseFloat(fields[1], 64)
+				condNum = strToFloat(fields[1])
 
 				break
 			} else {

parsers/nmparser/read_grd.go

@@ -1,7 +1,6 @@
 package parser
 
 import (
-	"strconv"
 	"strings"
 )
 
@@ -64,7 +63,7 @@ func ParseGrdData(ed ExtData) ([]ParametersData, ParameterNames) {
 					if i == 0 {
 						continue
 					}
-					if n, err := strconv.ParseFloat(val, 64); err == nil {
+					if n, err := parseFloatReplaceNaN(val); err == nil {
 						result[i-1] = n
 					} else {
 						panic("error converting value in grd file to number: " + val)

parsers/nmparser/utils.go

@@ -63,6 +63,8 @@ func CheckIfBayesian(results SummaryOutput) bool {
 	return isBayesian
 }
 
+// strToFloat converts s to a float64.  If the result is NaN or any error is
+// encountered, DefaultFloat64 is returned as the value.
 func strToFloat(s string) float64 {
 	f, err := strconv.ParseFloat(s, 64)
 	if err != nil || math.IsNaN(f) {
@@ -71,3 +73,15 @@ func strToFloat(s string) float64 {
 
 	return f
 }
+
+// parseFloatReplaceNaN converts s to a float64.  If the result is NaN,
+// DefaultFloat64 is returned as the value.  Any errors are relayed as is from
+// strconv.ParseFloat.
+func parseFloatReplaceNaN(s string) (float64, error) {
+	f, err := strconv.ParseFloat(s, 64)
+	if math.IsNaN(f) {
+		f = DefaultFloat64
+	}
+
+	return f, err
+}