Added support for NIfTI and refactored DICOM reader (#29)

Co-authored-by: phuctt <[email protected]>

.gitignore

@@ -13,5 +13,4 @@
 
 # Dependency directories (remove the comment below to include it)
 # vendor/
-test_data
 .idea

README.md

@@ -1,35 +1,23 @@
-# go2com (DICOM image parser)
+# go2com (DICOM and NIFTI image parser)
+
+** This package is under active development and can be in a very broken state. Please use the latest released version **
+
+## TODO
+- [ ] Improve NIfTI reader for large file size
+- [ ] Improve NIfTI writer to export as NIfTI-2 format
+- [ ] Improve DICOM frame parser
+- [ ] Support for additional medical image formats
+- [ ] Support changing value in NIfTI frame
 
 ## Example
-To parse a DICOM file, import the package as `github.com/okieraised/go2com`
+To parse a DICOM file
 ```go
-package main
-
-import (
-	"log"
-	"os"
 
-	"github.com/okieraised/go2com"
-)
+```
 
-func main() {
-	file, err := os.Open("/path_to_dcm_file")
-	if err != nil {
-		log.Fatal(err)
-	}
-	defer file.Close()
-	info, err := file.Stat()
-	if err != nil {
-		log.Fatal(err)
-	}
-	fileSize := info.Size()
+To parse a single NIfTI file:
+```go
 
-	parser, err := go2com.NewParser(file, fileSize, false, false)
-	if err != nil {
-		log.Fatal(err)
-	}
-	err = parser.Parse()
-}
 ```
 
 ## Supported Transfer Syntaxes

dicom_reader_test.go

@@ -0,0 +1,150 @@
+package go2com
+
+import (
+	"bufio"
+	"fmt"
+	"github.com/okieraised/go2com/internal/utils"
+	"github.com/okieraised/go2com/pkg/dicom/dcm_io"
+	"github.com/stretchr/testify/assert"
+	_ "image/jpeg"
+	"os"
+	"strings"
+	"testing"
+)
+
+func Test_ReaderProfiling(t *testing.T) {
+	assert := assert.New(t)
+	f, err := os.Open("./test_data/01.dcm")
+	assert.NoError(err)
+
+	fInfo, err := f.Stat()
+	assert.NoError(err)
+
+	fn := func() {
+		dcmReader := dcm_io.NewDICOMReader(bufio.NewReader(f), dcm_io.WithSkipPixelData(false), dcm_io.WithSkipDataset(false), dcm_io.WithSetFileSize(fInfo.Size()))
+		err = dcmReader.Parse()
+		assert.NoError(err)
+	}
+
+	err = utils.CPUProfilingFunc(fn, "./cpu1.pprof")
+	assert.NoError(err)
+}
+
+func Test_NewParser1(t *testing.T) {
+	assert := assert.New(t)
+	filePaths, err := utils.ReadDirRecursively("/home/tripg/workspace/dicom/test_data")
+	assert.NoError(err)
+	for _, fPath := range filePaths {
+		fmt.Println("process:", fPath)
+
+		f, err := os.Open(fPath)
+		assert.NoError(err)
+
+		fInfo, err := f.Stat()
+		assert.NoError(err)
+
+		dcmReader := dcm_io.NewDICOMReader(bufio.NewReader(f), dcm_io.WithSetFileSize(fInfo.Size()))
+
+		err = dcmReader.Parse()
+		if err != nil {
+			fmt.Println(err)
+			return
+		}
+		assert.NoError(err)
+	}
+}
+
+func Test_NewParser2(t *testing.T) {
+	assert := assert.New(t)
+	filePaths, err := utils.ReadDirRecursively("/home/tripg/workspace/dicom/test_full")
+	assert.NoError(err)
+	for _, fPath := range filePaths {
+		fmt.Println("process:", fPath)
+		f, err := os.Open(fPath)
+		assert.NoError(err)
+
+		fInfo, err := f.Stat()
+		assert.NoError(err)
+
+		dcmReader := dcm_io.NewDICOMReader(bufio.NewReader(f), dcm_io.WithSetFileSize(fInfo.Size()))
+
+		err = dcmReader.Parse()
+		if err != nil {
+			if strings.Contains(err.Error(), "not in valid dicom format") {
+				continue
+			}
+		}
+		assert.NoError(err)
+	}
+}
+
+func Test_NewParser3(t *testing.T) {
+	assert := assert.New(t)
+	filePaths, err := utils.ReadDirRecursively("/home/tripg/workspace/dicom/mammo_dicoms")
+	assert.NoError(err)
+	for _, fPath := range filePaths {
+		fmt.Println("process:", fPath)
+
+		f, err := os.Open(fPath)
+		assert.NoError(err)
+
+		fInfo, err := f.Stat()
+		assert.NoError(err)
+
+		dcmReader := dcm_io.NewDICOMReader(bufio.NewReader(f), dcm_io.WithSetFileSize(fInfo.Size()))
+
+		err = dcmReader.Parse()
+		assert.NoError(err)
+
+		_ = dcmReader.ExportDatasetTags(false)
+	}
+}
+
+func Test_NewParser4(t *testing.T) {
+	assert := assert.New(t)
+	fPath := "/home/tripg/workspace/dicom/mammo_dicoms/1.2.840.113619.2.255.10452022879169.3670200508103440.2701.dicom"
+	f, err := os.Open(fPath)
+	assert.NoError(err)
+
+	fInfo, err := f.Stat()
+	assert.NoError(err)
+
+	parser := dcm_io.NewDICOMReader(bufio.NewReader(f), dcm_io.WithSkipPixelData(true), dcm_io.WithSkipDataset(true), dcm_io.WithSetFileSize(fInfo.Size()))
+	err = parser.Parse()
+	assert.NoError(err)
+
+	for _, elem := range parser.GetDataset().Elements {
+		fmt.Println(elem)
+	}
+}
+
+func Test_NewParser5(t *testing.T) {
+	assert := assert.New(t)
+	fPath := "/home/tripg/workspace/10142022/ALI_Technologies/UltraPACS/studies/w0019837/view0001"
+	f, err := os.Open(fPath)
+	assert.NoError(err)
+
+	fInfo, err := f.Stat()
+	assert.NoError(err)
+
+	parser := dcm_io.NewDICOMReader(bufio.NewReader(f), dcm_io.WithSkipPixelData(false), dcm_io.WithSkipDataset(false), dcm_io.WithSetFileSize(fInfo.Size()))
+	err = parser.Parse()
+	assert.NoError(err)
+
+}
+
+func Test_NewParser6(t *testing.T) {
+	assert := assert.New(t)
+	f, err := os.Open("/home/tripg/workspace/10142022/ALI_Technologies/UltraPACS/studies/w0055053/view0013")
+	//f, err = os.Open("/home/tripg/workspace/10142022/Acuson/Sequoia/EXAMS/EXAM0000/CLIPS/CLIP0031")
+	f, err = os.Open("/home/tripg/workspace/10142022/Hamamatsu/Dog_15x15_20x.dcm")
+	//f, err = os.Open("/home/tripg/workspace/dicom2/PrivateGEImplicitVRBigEndianTransferSyntax16Bits.dcm")
+	assert.NoError(err)
+
+	fInfo, err := f.Stat()
+	assert.NoError(err)
+
+	parser := dcm_io.NewDICOMReader(bufio.NewReader(f), dcm_io.WithSkipPixelData(false), dcm_io.WithSkipDataset(false), dcm_io.WithSetFileSize(fInfo.Size()))
+	err = parser.Parse()
+	assert.NoError(err)
+}

example/example1.go

@@ -1,38 +1,31 @@
 package main
 
-import (
-	"fmt"
-	"github.com/okieraised/go2com"
-	"log"
-	"os"
-)
-
 func main() {
-	go2com.InitTagDict()
-	file, err := os.Open("./test_data/01.dcm")
-	if err != nil {
-		fmt.Println(err)
-		return
-	}
-	defer file.Close()
-	info, err := file.Stat()
-	if err != nil {
-		fmt.Println(err)
-		return
-	}
-	fileSize := info.Size()
-
-	parser, err := go2com.NewParser(file, fileSize, true, false)
-	if err != nil {
-		log.Fatal(err)
-		return
-	}
-	err = parser.Parse()
-	if err != nil {
-		log.Fatal(err)
-		return
-	}
-	for _, elem := range parser.GetDataset().Elements {
-		fmt.Println(elem)
-	}
+	//go2com.InitTagDict()
+	//file, err := os.Open("./test_data/01.dcm")
+	//if err != nil {
+	//	fmt.Println(err)
+	//	return
+	//}
+	//defer file.Close()
+	//info, err := file.Stat()
+	//if err != nil {
+	//	fmt.Println(err)
+	//	return
+	//}
+	//fileSize := info.Size()
+	//
+	//parser, err := go2com.NewParser(file, fileSize, true, false)
+	//if err != nil {
+	//	log.Fatal(err)
+	//	return
+	//}
+	//err = parser.Parse()
+	//if err != nil {
+	//	log.Fatal(err)
+	//	return
+	//}
+	//for _, elem := range parser.GetDataset().Elements {
+	//	fmt.Println(elem)
+	//}
 }

internal/system/system.go

@@ -15,6 +15,7 @@ func init() {
 	switch buf {
 	case [2]byte{0xCD, 0xAB}:
 		NativeEndian = binary.LittleEndian
+
 	case [2]byte{0xAB, 0xCD}:
 		NativeEndian = binary.BigEndian
 	default:

main.py

@@ -44,6 +44,15 @@
 fpath = '/home/tripg/Documents/dicom/test_full/023.dcm'
 fpath = '/home/tripg/Documents/dicom/10142022/ALI_Technologies/UltraPACS/studies/w0019837/view0001'
 fpath = '/home/tripg/Documents/dicom/vinlab/Mini-batch0/1.3.12.2.1107.5.1.7.112561.30000019122607094739800003704/DICOM/1.3.12.2.1107.5.1.7.112561.30000019122622575003400000100.dcm'
+fpath = '/home/tripg/Downloads/123.241606668321866.1722978010541148/DICOM/1.2.840.113619.2.427.84108138632.1643160910.120.dicom'
+fpath = '/home/tripg/workspace/1 0142022/ALI_Technologies/UltraPACS/studies/w0055053/view0013'
+fpath = '/home/tripg/workspace/10142022/Acuson/Sequoia/EXAMS/EXAM0000/CLIPS/CLIP0031'
+fpath = '/home/tripg/workspace/10142022/Hamamatsu/Dog_15x15_20x.dcm'
+fpath = '/home/tripg/Downloads/N2D0027.dcm'
+fpath = '/home/tripg/Downloads/123.241606668321866.1724728615648318_en.dcm'
+fpath = '/home/tripg/Downloads/1-1.dcm'
+fpath = '/home/tripg/workspace/dicom3/winter.dcm'
+fpath = '/home/tripg/Downloads/PrivateGEImplicitVRBigEndianTransferSyntax16Bits.dcm'
 
 ds = dcmread(fpath, force=True)
 print(ds)