func TestGroup(t *testing.T) {
eatError := func(m ingest.Metadata, err error) ingest.Metadata {
if err != nil {
t.Fatal(err)
}
return m
}
format, err := ingest.ParseFormatString("$(slide) $(sample) $(region) $(stain).tif")
if err != nil {
t.Fatal(err)
}
images := []*ingest.Image{
{"path/a", eatError(format.Parse([]byte("slide-1 sample-1 L1 FFa.tif")))},
{"path/b", eatError(format.Parse([]byte("slide-2 sample-1 L2 FFa.tif")))},
{"path/c", eatError(format.Parse([]byte("slide-1 sample-1 L3 FFa.tif")))},
{"path/d", eatError(format.Parse([]byte("slide-2 sample-1 L1 FFb.tif")))},
{"path/e", eatError(format.Parse([]byte("slide-1 sample-1 L2 FFb.tif")))},
{"path/f", eatError(format.Parse([]byte("slide-2 sample-1 L3 FFb.tif")))},
{"path/g", eatError(format.Parse([]byte("slide-1 sample-1 L1 FFc.tif")))},
{"path/h", eatError(format.Parse([]byte("slide-2 sample-1 L2 FFc.tif")))},
{"path/i", eatError(format.Parse([]byte("slide-1 sample-1 L3 FFc.tif")))},
}
rows := MakeRows(images, []string{"slide", "region"}, []string{})
for _, row := range rows {
t.Log("row", row.Meta())
for _, img := range row.Images() {
t.Log(img)
}
t.Log()
}
paths := []string{
"path/a",
"path/g",
"path/e",
"path/c",
"path/i",
"path/d",
"path/b",
"path/h",
"path/f",
}
c := &Chart{rows: rows}
for i, img := range c.Images() {
if img.Path != paths[i] {
t.Fatal("img != paths[i]", img, paths[i])
}
}
}
func TestMakeCharts(t *testing.T) {
eatError := func(m ingest.Metadata, err error) ingest.Metadata {
if err != nil {
t.Fatal(err)
}
return m
}
format, err := ingest.ParseFormatString("$(slide) $(sample) $(region) $(stain).tif")
if err != nil {
t.Fatal(err)
}
images := []*ingest.Image{
{"path/a-1", eatError(format.Parse([]byte("slide-1 sample-1 L1 FFa.tif")))},
{"path/b-1", eatError(format.Parse([]byte("slide-1 sample-1 L2 FFa.tif")))},
{"path/c-1", eatError(format.Parse([]byte("slide-1 sample-1 L3 FFa.tif")))},
{"path/d-1", eatError(format.Parse([]byte("slide-1 sample-1 L1 FFb.tif")))},
{"path/e-1", eatError(format.Parse([]byte("slide-1 sample-1 L2 FFb.tif")))},
{"path/f-1", eatError(format.Parse([]byte("slide-1 sample-1 L3 FFb.tif")))},
{"path/g-1", eatError(format.Parse([]byte("slide-1 sample-1 L1 FFc.tif")))},
{"path/h-1", eatError(format.Parse([]byte("slide-1 sample-1 L2 FFc.tif")))},
{"path/i-1", eatError(format.Parse([]byte("slide-1 sample-1 L3 FFc.tif")))},
{"path/a-2", eatError(format.Parse([]byte("slide-2 sample-1 L1 FFa.tif")))},
{"path/b-2", eatError(format.Parse([]byte("slide-2 sample-1 L2 FFa.tif")))},
{"path/c-2", eatError(format.Parse([]byte("slide-2 sample-1 L3 FFa.tif")))},
{"path/d-2", eatError(format.Parse([]byte("slide-2 sample-1 L1 FFb.tif")))},
{"path/e-2", eatError(format.Parse([]byte("slide-2 sample-1 L2 FFb.tif")))},
{"path/f-2", eatError(format.Parse([]byte("slide-2 sample-1 L3 FFb.tif")))},
{"path/g-2", eatError(format.Parse([]byte("slide-2 sample-1 L1 FFc.tif")))},
{"path/h-2", eatError(format.Parse([]byte("slide-2 sample-1 L2 FFc.tif")))},
{"path/i-2", eatError(format.Parse([]byte("slide-2 sample-1 L3 FFc.tif")))},
{"path/a-3", eatError(format.Parse([]byte("slide-1 sample-2 L1 FFa.tif")))},
{"path/b-3", eatError(format.Parse([]byte("slide-1 sample-2 L2 FFa.tif")))},
{"path/c-3", eatError(format.Parse([]byte("slide-1 sample-2 L3 FFa.tif")))},
{"path/d-3", eatError(format.Parse([]byte("slide-1 sample-2 L1 FFb.tif")))},
{"path/e-3", eatError(format.Parse([]byte("slide-1 sample-2 L2 FFb.tif")))},
{"path/f-3", eatError(format.Parse([]byte("slide-1 sample-2 L3 FFb.tif")))},
{"path/g-3", eatError(format.Parse([]byte("slide-1 sample-2 L1 FFc.tif")))},
{"path/h-3", eatError(format.Parse([]byte("slide-1 sample-2 L2 FFc.tif")))},
{"path/i-3", eatError(format.Parse([]byte("slide-1 sample-2 L3 FFc.tif")))},
{"path/a-4", eatError(format.Parse([]byte("slide-2 sample-2 L1 FFa.tif")))},
{"path/b-4", eatError(format.Parse([]byte("slide-2 sample-2 L2 FFa.tif")))},
{"path/c-4", eatError(format.Parse([]byte("slide-2 sample-2 L3 FFa.tif")))},
{"path/d-4", eatError(format.Parse([]byte("slide-2 sample-2 L1 FFb.tif")))},
{"path/e-4", eatError(format.Parse([]byte("slide-2 sample-2 L2 FFb.tif")))},
{"path/f-4", eatError(format.Parse([]byte("slide-2 sample-2 L3 FFb.tif")))},
{"path/g-4", eatError(format.Parse([]byte("slide-2 sample-2 L1 FFc.tif")))},
{"path/h-4", eatError(format.Parse([]byte("slide-2 sample-2 L2 FFc.tif")))},
{"path/i-4", eatError(format.Parse([]byte("slide-2 sample-2 L3 FFc.tif")))},
}
charts := MakeCharts(images, []string{"sample", "slide"}, []string{"region"}, []string{"stain"})
for _, chart := range charts {
t.Log("chart", chart.Meta())
for _, row := range chart.rows {
t.Log("row", row.Meta())
for _, img := range row.Images() {
t.Log(img)
}
t.Log()
}
t.Log()
}
}
func main() {
args, optargs, err := getopt.GetOpt(
os.Args[1:],
"hl:d:o:f:s:r:c:",
[]string{"help", "directory=", "output=", "format=",
"column-sort=", "row-group=", "chart-group=",
"overlap-columns="},
)
if err != nil {
fmt.Fprintln(os.Stderr, "error parsing command line flags", err)
Usage(1)
}
if len(args) > 0 {
fmt.Fprintf(os.Stderr, "unexpected trailing args `%v`\n", strings.Join(args, " "))
Usage(1)
}
format, err := ingest.ParseFormatString("$(slide) $(subject) $(region) $(stain).tif")
if err != nil {
log.Fatal(err)
}
directory := ""
rowGroup := Vars("region")
chartGroup := Vars("subject,slide")
columnSort := Vars("stain")
overlapCols := Vars("")
for _, oa := range optargs {
switch oa.Opt() {
case "-h", "--help":
Usage(0)
os.Exit(0)
case "-f", "--format":
format, err = ingest.ParseFormatString(oa.Arg())
if err != nil {
fmt.Fprintf(os.Stderr, "Invalid format string (%v) '%v'\n", oa.Opt(), oa.Arg())
fmt.Fprintln(os.Stderr, err)
Usage(1)
}
case "-d", "--directory":
directory, err = filepath.Abs(oa.Arg())
if err != nil {
fmt.Fprintf(os.Stderr, "Bad directory (%v) '%v' supplied\n", oa.Opt(), oa.Arg())
Usage(1)
}
if _, err := os.Stat(directory); err != nil && os.IsNotExist(err) {
fmt.Fprintf(os.Stderr, "Bad directory (%v) '%v' supplied\n", oa.Opt(), oa.Arg())
Usage(1)
} else if err != nil {
fmt.Fprintln(os.Stderr, err)
fmt.Fprintf(os.Stderr, "Bad directory (%v) '%v' supplied\n", oa.Opt(), oa.Arg())
Usage(1)
}
case "-s", "--column-sort":
columnSort = Vars(oa.Arg())
case "-r", "--row-group":
rowGroup = Vars(oa.Arg())
case "-c", "--chart-group":
chartGroup = Vars(oa.Arg())
case "--overlap-columns":
overlapCols = Vars(oa.Arg())
default:
fmt.Fprintf(os.Stderr, "Unknown flag '%v'\n", oa.Opt())
Usage(1)
}
}
log.Println(directory)
files, err := ingest.Ingest(directory, format)
if err != nil {
log.Fatal(err)
}
log.Println(files)
for _, img := range files {
log.Println(img)
}
C := charts.MakeCharts(files, chartGroup, rowGroup, columnSort, overlapCols)
for _, chart := range C {
log.Println("chart", chart.Meta())
for _, row := range chart.Rows() {
log.Println("row", row.Meta())
for _, img := range row.Images() {
log.Println(img)
}
log.Println()
}
log.Println()
}
log.Println("done")
fmt.Println(charts.ChartsHTML(C))
}