Seriesgrouping

heudiconv/convert.py

@@ -46,6 +46,7 @@
     set_readonly,
     treat_infofile,
     write_config,
+    has_deprecated_seriesid,
 )
 
 if TYPE_CHECKING:
@@ -172,7 +173,8 @@ def prep_conversion(
     # if conversion table(s) do not exist -- we need to prepare them
     # (the *prepare* stage in https://github.com/nipy/heudiconv/issues/134)
     # if overwrite - recalculate this anyways
-    reuse_conversion_table = op.exists(edit_file)
+    # MD: a check for the deprecated series_id is added here to avoid reusing the conversion table
+    reuse_conversion_table = op.exists(edit_file) and not has_deprecated_seriesid(edit_file)
     # We also might need to redo it if changes in the heuristic file
     # detected
     # ref: https://github.com/nipy/heudiconv/issues/84#issuecomment-330048609

heudiconv/dicoms.py

@@ -12,6 +12,7 @@
 from typing import TYPE_CHECKING, Any, Dict, List, NamedTuple, Optional, Union, overload
 from unittest.mock import patch
 import warnings
+import hashlib
 
 import pydicom as dcm
 
@@ -114,7 +115,7 @@ def create_seqinfo(mw: dw.Wrapper, series_files: list[str], series_id: str) -> S
 
 def validate_dicom(
     fl: str, dcmfilter: Optional[Callable[[dcm.dataset.Dataset], Any]]
-) -> Optional[tuple[dw.Wrapper, tuple[int, str], Optional[str]]]:
+) -> Optional[tuple[dw.Wrapper, tuple[int, str, str], Optional[str]]]:
     """
     Parse DICOM attributes. Returns None if not valid.
     """
@@ -135,7 +136,7 @@ def validate_dicom(
     try:
         protocol_name = mw.dcm_data.ProtocolName
         assert isinstance(protocol_name, str)
-        series_id = (int(mw.dcm_data.SeriesNumber), protocol_name)
+        series_id = (int(mw.dcm_data.SeriesNumber), protocol_name, mw.dcm_data.SeriesInstanceUID)
     except AttributeError as e:
         lgr.warning('Ignoring %s since not quite a "normal" DICOM: %s', fl, e)
         return None
@@ -159,10 +160,13 @@ def validate_dicom(
 class SeriesID(NamedTuple):
     series_number: int
     protocol_name: str
+    series_uid: str
     file_studyUID: Optional[str] = None
 
     def __str__(self) -> str:
-        s = f"{self.series_number}-{self.protocol_name}"
+        len_hash_hex = 8
+        suid_hex = hashlib.md5(self.series_uid.encode('utf-8')).hexdigest()[:len_hash_hex]
+        s = f"{self.series_number}-{self.protocol_name}-{suid_hex}"
         if self.file_studyUID is not None:
             s += f"-{self.file_studyUID}"
         return s
@@ -285,7 +289,7 @@ def group_dicoms_into_seqinfos(
             removeidx.append(idx)
             continue
         mw, series_id_, file_studyUID = mwinfo
-        series_id = SeriesID(series_id_[0], series_id_[1])
+        series_id = SeriesID(series_id_[0], series_id_[1], series_id_[2])
         if per_studyUID:
             series_id = series_id._replace(file_studyUID=file_studyUID)
 
@@ -320,6 +324,7 @@ def group_dicoms_into_seqinfos(
                 series_id = SeriesID(
                     mwgroup[idx].dcm_data.SeriesNumber,
                     mwgroup[idx].dcm_data.ProtocolName,
+                    mwgroup[idx].dcm_data.SeriesInstanceUID,
                 )
                 if per_studyUID:
                     series_id = series_id._replace(file_studyUID=file_studyUID)

heudiconv/parser.py

@@ -278,15 +278,9 @@ def infotoids(
             )
             lgr.info("Study session for %r", study_session_info)
 
-            if study_session_info in study_sessions:
-                if grouping != "all":
-                    # MG - should this blow up to mimic -d invocation?
-                    lgr.warning(
-                        "Existing study session with the same values (%r)."
-                        " Skipping DICOMS %s",
-                        study_session_info,
-                        seqinfo.values(),
-                    )
-                    continue
+            if grouping != "all":
+                assert (study_session_info not in study_sessions), (
+                    f"Existing study session {study_session_info} "
+                    f"already in analyzed sessions {study_sessions.keys()}")
             study_sessions[study_session_info] = seqinfo
     return study_sessions

heudiconv/utils.py

@@ -18,6 +18,7 @@
 import stat
 from subprocess import check_output
 import sys
+import string
 import tempfile
 from time import sleep
 from types import ModuleType
@@ -222,6 +223,41 @@
     return data
 
 
+def is_deprecated_seriesid(series_id: str, len_hash_hex: int = 8) -> bool:
+    """Return True if series_id is in deprecated format.
+    A deprecated series ID is in the format "series_number-protocol_name".
+    A non-deprecated series ID is in the format "series_number-protocol_name-seriesUID_hash_hex"
+    """
+    # Check at least two '-' in the series_id
+    if series_id.count('-') <= 1:
+        return True
+    # Check the first part of the series_id is a number
+    series_number = series_id.split('-')[0]
+    if not series_number.isdigit():
+        return True
+    # Check the last part of the series_id is a hash in hexadecimal format of length len_hash_hex
+    hash_hex = series_id.split('-')[-1]
+    hex_digits = set(string.hexdigits)
+    if len(hash_hex) != len_hash_hex or not all(c in hex_digits for c in hash_hex):
+        return True
+    # If all previous tests passed, then the series_id is not deprecated
+    return False
+
+
+def has_deprecated_seriesid(info_file: str) -> bool:
+    """Return True if any series_id in the info_file is in deprecated format."""
+    info = read_config(info_file)
+    series_ids = [series_id for sublist in info.values() for series_id in sublist]
+    if any(is_deprecated_seriesid(series_id) for series_id in series_ids):
+        lgr.warning(
+            "Found deprecated series identifier in info file in the format"
+            "<series num>-<protocol name> instead of <series num>-<protocol name>-<UID hash>"
+            "The existing conversion table will be ignored."
+        )
+        return True
+    return False
+
+
 def assure_no_file_exists(path: str | Path) -> None:
     """Check if file or symlink (git-annex?) exists, and if so -- remove"""
     if os.path.lexists(path):