Documentation: http → https (#249)

* chmod -x

* Documentation: http → https

README.md

@@ -90,5 +90,5 @@ For __v1__ I rewrote and redesigned the core library essentially from scratch, a
 * Grailbio [go-dicom](https://github.com/grailbio/go-dicom) -- commits from their fork were applied to ours
 * GradientHealth for supporting work I did on this while there [gradienthealth/dicom](https://github.com/gradienthealth/dicom)
 * Innolitics [DICOM browser](https://dicom.innolitics.com/ciods)
-* [DICOM Specification](http://dicom.nema.org/medical/dicom/current/output/pdf/part05.pdf)
-* <div>Icons made by <a href="https://www.freepik.com/?__hstc=57440181.48e262e7f01bcb2b41259e2e5a8103b3.1557697512782.1557697512782.1557697512782.1&__hssc=57440181.4.1557697512783&__hsfp=2768524783" title="Freepik">Freepik</a> from <a href="https://www.flaticon.com/" 			    title="Flaticon">www.flaticon.com</a> is licensed by <a href="http://creativecommons.org/licenses/by/3.0/" 			    title="Creative Commons BY 3.0" target="_blank">CC 3.0 BY</a></div>
+* [DICOM Specification](https://dicom.nema.org/medical/dicom/current/output/pdf/part05.pdf)
+* <div>Icons made by <a href="https://www.freepik.com/?__hstc=57440181.48e262e7f01bcb2b41259e2e5a8103b3.1557697512782.1557697512782.1557697512782.1&__hssc=57440181.4.1557697512783&__hsfp=2768524783" title="Freepik">Freepik</a> from <a href="https://www.flaticon.com/" title="Flaticon">www.flaticon.com</a> is licensed by <a href="https://creativecommons.org/licenses/by/3.0/" title="Creative Commons BY 3.0" target="_blank">CC 3.0 BY</a></div>

dataset.go

@@ -15,7 +15,7 @@ import (
 var ErrorElementNotFound = errors.New("element not found")
 
 // Dataset represents a DICOM dataset, see
-// http://dicom.nema.org/medical/dicom/current/output/html/part05.html#chapter_7.
+// https://dicom.nema.org/medical/dicom/current/output/html/part05.html#chapter_7.
 //
 // This Dataset representation is JSON serializable out of the box
 // (implements json.Marshaler) and will also pretty print as a string nicely (see String example).

element.go

@@ -14,7 +14,7 @@ import (
 var ErrorUnexpectedDataType = errors.New("the type of the data was unexpected or not allowed")
 
 // Element represents a standard DICOM data element (see the DICOM standard:
-// http://dicom.nema.org/medical/dicom/current/output/html/part05.html#sect_7.1 ).
+// https://dicom.nema.org/medical/dicom/current/output/html/part05.html#sect_7.1 ).
 // This Element can be serialized to JSON out of the box and pretty printed as a string via the String() method.
 type Element struct {
 	Tag                    tag.Tag    `json:"tag"`
@@ -251,7 +251,7 @@ func (s *floatsValue) MarshalJSON() ([]byte, error) {
 
 // SequenceItemValue is a Value that represents a single Sequence Item. Learn
 // more about Sequences at
-// http://dicom.nema.org/medical/dicom/current/output/chtml/part05/sect_7.5.html.
+// https://dicom.nema.org/medical/dicom/current/output/chtml/part05/sect_7.5.html.
 type SequenceItemValue struct {
 	elements []*Element
 }

parse.go

@@ -1,5 +1,5 @@
 // Package dicom provides a set of tools to read, write, and generally
-// work with DICOM (http://dicom.nema.org/) medical image files in Go.
+// work with DICOM (https://dicom.nema.org/) medical image files in Go.
 //
 // dicom.Parse and dicom.Write provide the core functionality to read and write
 // DICOM Datasets. This package provides Go data structures that represent

pkg/charset/charset.go

@@ -77,7 +77,7 @@ var htmlEncodingNames = map[string]string{
 // ParseSpecificCharacterSet converts DICOM character encoding names, such as
 // "ISO-IR 100" to encoding.Decoder(s). It will return nil, nil for the default (7bit
 // ASCII) encoding. Cf. P3.2
-// D.6.2. http://dicom.nema.org/medical/dicom/2016d/output/chtml/part02/sect_D.6.2.html
+// D.6.2. https://dicom.nema.org/medical/dicom/2016d/output/chtml/part02/sect_D.6.2.html
 func ParseSpecificCharacterSet(encodingNames []string) (CodingSystem, error) {
 	var decoders []*encoding.Decoder
 	for _, name := range encodingNames {

pkg/dcmtime/errors.go

@@ -6,20 +6,20 @@ import "errors"
 var ErrParseDA = errors.New(
 	"error parsing dicom DA (date) value -- expected format is 'YYYYMMDD'. " +
 		"for more details on proper DA value formatting, see here: " +
-		"http://dicom.nema.org/medical/dicom/current/output/html/part05.html#table_6.2-1",
+		"https://dicom.nema.org/medical/dicom/current/output/html/part05.html#table_6.2-1",
 )
 
 // ErrParseDA is a sentinel error returned from ParseDatetime.
 var ErrParseDT = errors.New(
 	"error parsing dicom DT (datetime) value -- expected format is" +
 		" 'YYYYMMDDHHMMSS.FFFFFF&ZZXX'. " +
 		"for more details on proper DT value formatting, see here: " +
-		"http://dicom.nema.org/medical/dicom/current/output/html/part05.html#table_6.2-1",
+		"https://dicom.nema.org/medical/dicom/current/output/html/part05.html#table_6.2-1",
 )
 
 // ErrParseTM is a sentinel error returned from ParseTime.
 var ErrParseTM = errors.New(
 	"error parsing dicom TM (time) value, but expected format is 'HHMMSS.FFFFFF'. " +
 		"for more details on proper TM value formatting, see here: " +
-		"http://dicom.nema.org/medical/dicom/current/output/html/part05.html#table_6.2-1",
+		"https://dicom.nema.org/medical/dicom/current/output/html/part05.html#table_6.2-1",
 )

pkg/personname/doc.go

@@ -2,6 +2,6 @@
 The personname package provides methods and data types for inspecting Person Name (PN)
 DICOM Value Representations, as defined here:
 
-http://dicom.nema.org/dicom/2013/output/chtml/part05/sect_6.2.html
+https://dicom.nema.org/dicom/2013/output/chtml/part05/sect_6.2.html
 */
 package personname

pkg/personname/errs.go

@@ -40,7 +40,7 @@ var ErrNullSepLevelInvalid = fmt.Errorf("TrailingNullLevel exceeded maximum")
 func newErrTooManyGroups(groupsFound int) error {
 	return fmt.Errorf(
 		"%w: value contains %v groups. see 'PN' entry in official dicom spec: "+
-			"http://dicom.nema.org/medical/dicom/current/output/html/part05.html#sect_6.2",
+			"https://dicom.nema.org/medical/dicom/current/output/html/part05.html#sect_6.2",
 		ErrParseGroupCount,
 		groupsFound,
 	)
@@ -51,7 +51,7 @@ func newErrTooManyGroups(groupsFound int) error {
 func newErrTooManyGroupSegments(group pnGroup, segmentsFound int) error {
 	return fmt.Errorf(
 		"%w: value group %v contains %v segments. see 'PN' entry in official "+
-			"dicom spec: http://dicom.nema.org/medical/dicom/current/output/html/part05.html#sect_6.2",
+			"dicom spec: https://dicom.nema.org/medical/dicom/current/output/html/part05.html#sect_6.2",
 		ErrParseGroupSegmentCount,
 		group,
 		segmentsFound,

pkg/personname/groupInfo_test.go

@@ -436,7 +436,7 @@ func TestNewPersonNameFromDicom_Err(t *testing.T) {
 	expectedString := "error parsing PN value: no more than 5 segments with " +
 		"'[Last]^[First]^[Middle]^[Prefix]^[Suffix]' format are allowed: value group " +
 		"Alphabetic contains 6 segments. see 'PN' entry in official dicom spec: " +
-		"http://dicom.nema.org/medical/dicom/current/output/html/part05.html#sect_6.2"
+		"https://dicom.nema.org/medical/dicom/current/output/html/part05.html#sect_6.2"
 
 	if err.Error() != expectedString {
 		t.Errorf("unexpected error text: %v", err.Error())

pkg/personname/info.go

@@ -80,7 +80,7 @@ func validateInfoNullSepLevel(level InfoTrailingNullLevel) error {
 }
 
 // Info holds information from an element with a "PN" VR. See the "PN"
-// entry at: http://dicom.nema.org/dicom/2013/output/chtml/part05/sect_6.2.html
+// entry at: https://dicom.nema.org/dicom/2013/output/chtml/part05/sect_6.2.html
 //
 // PN values are split into three groups which represent three different ways to
 // represent a name:

pkg/personname/info_test.go

@@ -400,31 +400,31 @@ func TestParse_Err(t *testing.T) {
 			ErrString: "error parsing PN value: no more than 3 groups with " +
 				"'[Alphabetic]=[Ideographic]=[Phonetic]' format are allowed: value " +
 				"contains 4 groups. see 'PN' entry in official dicom spec: " +
-				"http://dicom.nema.org/medical/dicom/current/output/html/part05.html#sect_6.2",
+				"https://dicom.nema.org/medical/dicom/current/output/html/part05.html#sect_6.2",
 		},
 		{
 			Raw: "^^^^^",
 			ErrString: "error parsing PN value: no more than 5 segments with " +
 				"'[Last]^[First]^[Middle]^[Prefix]^[Suffix]' format are allowed: " +
 				"value group Alphabetic contains 6 segments. see 'PN' entry in " +
 				"official dicom spec: " +
-				"http://dicom.nema.org/medical/dicom/current/output/html/part05.html#sect_6.2",
+				"https://dicom.nema.org/medical/dicom/current/output/html/part05.html#sect_6.2",
 		},
 		{
 			Raw: "=^^^^^",
 			ErrString: "error parsing PN value: no more than 5 segments with " +
 				"'[Last]^[First]^[Middle]^[Prefix]^[Suffix]' format are allowed: " +
 				"value group Ideographic contains 6 segments. see 'PN' entry in " +
 				"official dicom spec: " +
-				"http://dicom.nema.org/medical/dicom/current/output/html/part05.html#sect_6.2",
+				"https://dicom.nema.org/medical/dicom/current/output/html/part05.html#sect_6.2",
 		},
 		{
 			Raw: "==^^^^^",
 			ErrString: "error parsing PN value: no more than 5 segments with " +
 				"'[Last]^[First]^[Middle]^[Prefix]^[Suffix]' format are allowed: " +
 				"value group Phonetic contains 6 segments. see 'PN' entry in " +
 				"official dicom spec: " +
-				"http://dicom.nema.org/medical/dicom/current/output/html/part05.html#sect_6.2",
+				"https://dicom.nema.org/medical/dicom/current/output/html/part05.html#sect_6.2",
 		},
 	}
 

pkg/vrraw/vrraw.go

@@ -1,6 +1,6 @@
 // Package vrraw offers aliases to all VR abbreviations as defined here:
 //
-// http://dicom.nema.org/medical/dicom/current/output/html/part05.html#table_6.2-1
+// https://dicom.nema.org/medical/dicom/current/output/html/part05.html#table_6.2-1
 //
 // Deprecated VRs from older editions are also included
 package vrraw

read.go

@@ -63,7 +63,7 @@ func readVL(r dicomio.Reader, isImplicit bool, t tag.Tag, vr string) (uint32, er
 	}
 
 	// Explicit Transfer Syntax
-	// More details here: http://dicom.nema.org/medical/dicom/current/output/html/part05.html#sect_7.1.2
+	// More details here: https://dicom.nema.org/medical/dicom/current/output/html/part05.html#sect_7.1.2
 	switch vr {
 	// TODO: Parsed VR should be an enum. Will require refactors of tag pkg.
 	case "NA", vrraw.OtherByte, vrraw.OtherDouble, vrraw.OtherFloat,
@@ -380,7 +380,7 @@ func readNativeFrames(d dicomio.Reader, parsedData *Dataset, fc chan<- *frame.Fr
 
 // readSequence reads a sequence element (VR = SQ) that contains a subset of Items. Each item contains
 // a set of Elements.
-// See http://dicom.nema.org/medical/dicom/current/output/chtml/part05/sect_7.5.2.html#table_7.5-1
+// See https://dicom.nema.org/medical/dicom/current/output/chtml/part05/sect_7.5.2.html#table_7.5-1
 func readSequence(r dicomio.Reader, t tag.Tag, vr string, vl uint32, d *Dataset) (Value, error) {
 	var sequences sequencesValue
 

testdata/data_details.md

@@ -35,7 +35,7 @@ be mentioned in one of them for brevity.
 ### Relevant Citations
 #### For files 1.dcm, 2.dcm:
 ##### Data Citation:
-Kinahan, Paul; Muzi, Mark; Bialecki, Brian; Coombs, Laura. (2017). Data from ACRIN-FLT-Breast. The Cancer Imaging Archive. http://doi.org/10.7937/K9/TCIA.2017.ol20zmxg
+Kinahan, Paul; Muzi, Mark; Bialecki, Brian; Coombs, Laura. (2017). Data from ACRIN-FLT-Breast. The Cancer Imaging Archive. https://doi.org/10.7937/K9/TCIA.2017.ol20zmxg
 
 ##### Publication Citation
 Kostakoglu L ,  Duan F ,  Idowu MO ,  Jolles PR ,  Bear HD ,  Muzi M ,  Cormack J ,  Muzi JP ,  Pryma DA ,  Specht JM ,  Hovanessian-Larsen L ,  Miliziano J ,  Mallett S ,  Shields AF ,  Mankoff DA ;  ACRIN 668 Investigative Team . A Phase II Study of 3'-Deoxy-3'-18F-Fluorothymidine PET in the Assessment of Early Response of Breast Cancer to Neoadjuvant Chemotherapy: Results from ACRIN 6688. J Nucl Med. 2015 Nov;56(11):1681-9. doi: 10.2967/jnumed.115.160663. Epub 2015 Sep 10. 
@@ -44,7 +44,7 @@ Kostakoglu L ,  Duan F ,  Idowu MO ,  Jolles PR ,  Bear HD ,  Muzi M ,  Cormack
 #### For file 3.dcm
 
 ##### Data Citation:
-Choyke P, Turkbey B, Pinto P, Merino M, Wood B. (2016). Data From PROSTATE-MRI. The Cancer Imaging Archive. http://doi.org/10.7937/K9/TCIA.2016.6046GUDv
+Choyke P, Turkbey B, Pinto P, Merino M, Wood B. (2016). Data From PROSTATE-MRI. The Cancer Imaging Archive. https://doi.org/10.7937/K9/TCIA.2016.6046GUDv
 
 
 #### TCIA Citation

write.go

@@ -473,7 +473,7 @@ func writeStrings(w dicomio.Writer, values []string, vr string) error {
 			vrraw.ShortString, vrraw.ShortText, vrraw.UnlimitedText,
 			vrraw.DecimalString, vrraw.CodeString, vrraw.Time,
 			vrraw.IntegerString, vrraw.Unknown:
-			if err := w.WriteString(" "); err != nil { // http://dicom.nema.org/medical/dicom/current/output/html/part05.html#sect_6.2
+			if err := w.WriteString(" "); err != nil { // https://dicom.nema.org/medical/dicom/current/output/html/part05.html#sect_6.2
 				return err
 			}
 		default:
@@ -610,7 +610,7 @@ func writeSequence(w dicomio.Writer, t tag.Tag, values []*SequenceItemValue, vr
 	// Note: we currently don't validate that the length of the sequence matches
 	// the VL if it's not undefined VL.
 	// More details about the sequence structure can be found at:
-	// http://dicom.nema.org/medical/dicom/current/output/chtml/part05/sect_7.5.html
+	// https://dicom.nema.org/medical/dicom/current/output/chtml/part05/sect_7.5.html
 
 	// Write out the items.
 	for _, seqItem := range values {