Merge pull request #541 from chrisbll971/master

Infer Media Storage SOP Class UID and Media Storage SOP Instance UID from the SOP Class UID and SOP Instance UID when missing

object/src/lib.rs

@@ -225,6 +225,12 @@ pub enum ReadError {
         #[snafu(backtrace)]
         source: crate::meta::Error,
     },
+    #[snafu(display("Could not parse sop attribute"))]
+    ParseSopAttribute {
+        #[snafu(source(from(dicom_core::value::ConvertValueError, Box::from)))]
+        source: Box<dicom_core::value::ConvertValueError>,
+        backtrace: Backtrace,
+    },
     #[snafu(display("Could not create data set parser"))]
     CreateParser {
         #[snafu(backtrace)]

object/src/mem.rs

@@ -58,8 +58,8 @@ use crate::{
     CreatePrinterSnafu, DicomObject, ElementNotFoundSnafu, FileDicomObject, InvalidGroupSnafu,
     MissingElementValueSnafu, MissingLeafElementSnafu, NoSpaceSnafu, NoSuchAttributeNameSnafu,
     NoSuchDataElementAliasSnafu, NoSuchDataElementTagSnafu, NotASequenceSnafu, OpenFileSnafu,
-    ParseMetaDataSetSnafu, PrematureEndSnafu, PrepareMetaTableSnafu, PrintDataSetSnafu,
-    PrivateCreatorNotFoundSnafu, PrivateElementError, ReadError, ReadFileSnafu,
+    ParseMetaDataSetSnafu, ParseSopAttributeSnafu, PrematureEndSnafu, PrepareMetaTableSnafu,
+    PrintDataSetSnafu, PrivateCreatorNotFoundSnafu, PrivateElementError, ReadError, ReadFileSnafu,
     ReadPreambleBytesSnafu, ReadTokenSnafu, ReadUnsupportedTransferSyntaxSnafu,
     UnexpectedTokenSnafu, WithMetaError, WriteError,
 };
@@ -365,22 +365,42 @@ where
         }
 
         // read metadata header
-        let meta = FileMetaTable::from_reader(&mut file).context(ParseMetaDataSetSnafu)?;
+        let mut meta = FileMetaTable::from_reader(&mut file).context(ParseMetaDataSetSnafu)?;
 
         // read rest of data according to metadata, feed it to object
         if let Some(ts) = ts_index.get(&meta.transfer_syntax) {
             let mut dataset = DataSetReader::new_with_ts(file, ts).context(CreateParserSnafu)?;
+            let obj = InMemDicomObject::build_object(
+                &mut dataset,
+                dict,
+                false,
+                Length::UNDEFINED,
+                read_until,
+            )?;
 
-            Ok(FileDicomObject {
-                meta,
-                obj: InMemDicomObject::build_object(
-                    &mut dataset,
-                    dict,
-                    false,
-                    Length::UNDEFINED,
-                    read_until,
-                )?,
-            })
+            // if Media Storage SOP Class UID is empty attempt to infer from SOP Class UID
+            if meta.media_storage_sop_class_uid().is_empty() {
+                if let Some(elem) = obj.get(tags::SOP_CLASS_UID) {
+                    meta.media_storage_sop_class_uid = elem
+                        .value()
+                        .to_str()
+                        .context(ParseSopAttributeSnafu)?
+                        .to_string();
+                }
+            }
+
+            // if Media Storage SOP Instance UID is empty attempt to infer from SOP Instance UID
+            if meta.media_storage_sop_instance_uid().is_empty() {
+                if let Some(elem) = obj.get(tags::SOP_INSTANCE_UID) {
+                    meta.media_storage_sop_instance_uid = elem
+                        .value()
+                        .to_str()
+                        .context(ParseSopAttributeSnafu)?
+                        .to_string();
+                }
+            }
+
+            Ok(FileDicomObject { meta, obj })
         } else {
             ReadUnsupportedTransferSyntaxSnafu {
                 uid: meta.transfer_syntax,
@@ -2447,6 +2467,54 @@ mod tests {
         assert_eq!(elem1, &another_patient_name);
     }
 
+    #[test]
+    fn infer_media_sop_from_dataset_sop_elements() {
+        let sop_instance_uid = "1.4.645.313131";
+        let sop_class_uid = "1.2.840.10008.5.1.4.1.1.2";
+        let mut obj = InMemDicomObject::new_empty();
+
+        obj.put(DataElement::new(
+            Tag(0x0008, 0x0018),
+            VR::UI,
+            dicom_value!(Strs, [sop_instance_uid]),
+        ));
+        obj.put(DataElement::new(
+            Tag(0x0008, 0x0016),
+            VR::UI,
+            dicom_value!(Strs, [sop_class_uid]),
+        ));
+
+        let file_object = obj.with_exact_meta(
+            FileMetaTableBuilder::default()
+                .transfer_syntax("1.2.840.10008.1.2.1")
+                // Media Storage SOP Class and Instance UIDs are missing and set to an empty string
+                .media_storage_sop_class_uid("")
+                .media_storage_sop_instance_uid("")
+                .build()
+                .unwrap(),
+        );
+
+        // create temporary file path and write object to that file
+        let dir = tempfile::tempdir().unwrap();
+        let mut file_path = dir.into_path();
+        file_path.push(format!("{}.dcm", sop_instance_uid));
+
+        file_object.write_to_file(&file_path).unwrap();
+
+        // read the file back to validate the outcome
+        let saved_object = open_file(file_path).unwrap();
+
+        // verify that the empty string media storage sop instance and class UIDs have been inferred from the sop instance and class UID
+        assert_eq!(
+            saved_object.meta().media_storage_sop_instance_uid(),
+            sop_instance_uid
+        );
+        assert_eq!(
+            saved_object.meta().media_storage_sop_class_uid(),
+            sop_class_uid
+        );
+    }
+
     #[test]
     fn inmem_object_get_opt() {
         let another_patient_name = DataElement::new(

object/src/meta.rs

@@ -972,16 +972,17 @@ impl FileMetaTableBuilder {
             // Missing information version, will assume (00H, 01H). See #28
             [0, 1],
         );
-        let media_storage_sop_class_uid =
-            self.media_storage_sop_class_uid
-                .context(MissingElementSnafu {
-                    alias: "MediaStorageSOPClassUID",
-                })?;
+        let media_storage_sop_class_uid = self.media_storage_sop_class_uid.unwrap_or_else(|| {
+            tracing::warn!("MediaStorageSOPClassUID is missing. Defaulting to empty string.");
+            String::default()
+        });
         let media_storage_sop_instance_uid =
-            self.media_storage_sop_instance_uid
-                .context(MissingElementSnafu {
-                    alias: "MediaStorageSOPInstanceUID",
-                })?;
+            self.media_storage_sop_instance_uid.unwrap_or_else(|| {
+                tracing::warn!(
+                    "MediaStorageSOPInstanceUID is missing. Defaulting to empty string."
+                );
+                String::default()
+            });
         let transfer_syntax = self.transfer_syntax.context(MissingElementSnafu {
             alias: "TransferSyntax",
         })?;