[ENH] Allow user to use relative path for bids uri

dcm2bids/acquisition.py

@@ -4,6 +4,7 @@
 
 import logging
 from os.path import join as opj
+from os import sep
 
 from dcm2bids.utils.utils import DEFAULT
 from dcm2bids.version import __version__
@@ -30,6 +31,7 @@ def __init__(
         id=None,
         src_sidecar=None,
         sidecar_changes=None,
+        bids_uri=None,
         do_not_reorder_entities=None,
         **kwargs
     ):
@@ -44,6 +46,7 @@ def __init__(
         self.suffix = suffix
         self.custom_entities = custom_entities
         self.src_sidecar = src_sidecar
+        self.bids_uri = bids_uri
         self.do_not_reorder_entities = do_not_reorder_entities
 
         if sidecar_changes is None:
@@ -284,10 +287,16 @@ def dstSidecarData(self, idList):
                     else:
                         values.append(idList.get(val, val))
                         if values[-1] != val:
-                            if isinstance(values[-1], list):
-                                values[-1] = ["bids::" + img_dest for img_dest in values[-1]]
+                            if self.bids_uri == DEFAULT.bids_uri:
+                                if isinstance(values[-1], list):
+                                    values[-1] = ["bids::" + img_dest for img_dest in values[-1]]
+                                else:
+                                    values[-1] = "bids::" + values[-1]
                             else:
-                                values[-1] = "bids::" + values[-1]
+                                if isinstance(values[-1], list):
+                                    values[-1] = [img_dest.replace(self.participant.name + sep, "") for img_dest in values[-1]]
+                                else:
+                                    values[-1] = values[-1].replace(self.participant.name + sep, "")
 
             # handle if nested list vs str
             flat_value_list = []

dcm2bids/dcm2bids_gen.py

@@ -110,7 +110,8 @@ def run(self):
             self.config.get("search_method", DEFAULT.search_method),
             self.config.get("case_sensitive", DEFAULT.case_sensitive),
             self.config.get("dup_method", DEFAULT.dup_method),
-            self.config.get("post_op",  DEFAULT.post_op)
+            self.config.get("post_op",  DEFAULT.post_op),
+            self.config.get("bids_uri",  DEFAULT.bids_uri)
         )
         parser.build_graph()
         parser.build_acquisitions(self.participant)

dcm2bids/sidecar.py

@@ -11,7 +11,8 @@
 
 from dcm2bids.acquisition import Acquisition
 from dcm2bids.utils.io import load_json
-from dcm2bids.utils.utils import DEFAULT, convert_dir, combine_dict_extractors, splitext_
+from dcm2bids.utils.utils import (DEFAULT, convert_dir, combine_dict_extractors,
+                                  splitext_)
 
 compare_float_keys = ["lt", "gt", "le", "ge", "btw", "btwe"]
 
@@ -100,11 +101,13 @@ def __init__(self,
                  search_method=DEFAULT.search_method,
                  case_sensitive=DEFAULT.case_sensitive,
                  dup_method=DEFAULT.dup_method,
-                 post_op=DEFAULT.post_op):
+                 post_op=DEFAULT.post_op,
+                 bids_uri=DEFAULT.bids_uri):
         self.logger = logging.getLogger(__name__)
         self._search_method = ""
         self._dup_method = ""
         self._post_op = ""
+        self._bids_uri = ""
         self.graph = OrderedDict()
         self.acquisitions = []
         self.extractors = extractors
@@ -116,6 +119,7 @@ def __init__(self,
         self.case_sensitive = case_sensitive
         self.dup_method = dup_method
         self.post_op = post_op
+        self.bids_uri = bids_uri
 
     @property
     def search_method(self):
@@ -220,6 +224,25 @@ def post_op(self, value):
             raise ValueError("post_op is not defined correctly. "
                              "Please check the documentation.")
 
+    @property
+    def bids_uri(self):
+        return self._bids_uri
+
+    @bids_uri.setter
+    def bids_uri(self, value):
+        """
+        Checks if the method bids_uri is using is implemented
+        Warns the user if not and fall back to default
+        """
+        if value in DEFAULT.bids_uri_choices:
+            self._bids_uri = value
+        else:
+            self.bids_uri = DEFAULT.bids_uri
+            self.logger.warning(
+                "BIDS URI methods implemented: %s", DEFAULT.bids_uri_choices)
+            self.logger.warning(f"{value} is not a bids URI method implemented.")
+            self.logger.warning(f"Falling back to default: {DEFAULT.bids_uri}.")
+
     @property
     def case_sensitive(self):
         return self._case_sensitive
@@ -396,8 +419,10 @@ def build_acquisitions(self, participant):
                 desc = valid_descriptions[0]
                 desc, sidecar = self.searchDcmTagEntity(sidecar, desc)
                 acq = Acquisition(participant,
+                                  src_sidecar=sidecar,
+                                  bids_uri=self.bids_uri,
                                   do_not_reorder_entities=self.do_not_reorder_entities,
-                                  src_sidecar=sidecar, **desc)
+                                  **desc)
                 acq.setDstFile()
 
                 if acq.id:
@@ -416,6 +441,7 @@ def build_acquisitions(self, participant):
                 self.logger.warning(f"Several Pairing  <-  {sidecarName}")
                 for desc in valid_descriptions:
                     acq = Acquisition(participant,
+                                      bids_uri=self.bids_uri,
                                       do_not_reorder_entities=self.do_not_reorder_entities,
                                       **desc)
                     self.logger.warning(f"    ->  {acq.suffix}")

dcm2bids/utils/utils.py

@@ -83,6 +83,8 @@ class DEFAULT(object):
     dup_method = "run"
     runTpl = "_run-{:02d}"
     dupTpl = "_dup-{:02d}"
+    bids_uri_choices = ["URI", "relative"]
+    bids_uri = "URI"
     case_sensitive = True
 
     # Entity table:

requirements-doc.txt

@@ -1,5 +1,5 @@
 Babel==2.12.1
-certifi==2023.7.22
+certifi==2024.7.4
 charset-normalizer==3.2.0
 click==8.1.4
 colorama==0.4.6
@@ -33,6 +33,6 @@ regex==2023.6.3
 requests==2.32.0
 six==1.16.0
 smmap==5.0.0
-urllib3==2.0.7
+urllib3==2.2.2
 verspec==0.1.0
 watchdog==3.0.0

tests/data/config_test_multiple_intendedfor_uri_relative.json

@@ -0,0 +1,34 @@
+{
+    "search_method": "fnmatch",
+    "extractors": {"SeriesDescription": ["task-(?P<task>[a-zA-Z0-9]+)"]},
+    "bids_uri": "relative",
+    "descriptions": [
+        {
+            "id": "localizer",
+            "datatype": "localizer",
+            "suffix": "localizer",
+            "criteria": {
+                "SeriesDescription": "locali*"
+            }
+        },
+        {
+            "id": "T1",
+            "datatype": "anat",
+            "suffix": "T1w",
+            "criteria": {
+                "SidecarFilename": "*MPRAGE*"
+            }
+        },
+        {
+            "datatype": "fmap",
+            "suffix": "fmap",
+            "criteria": {
+                "EchoNumber": 1,
+                "EchoTime": 0.00492
+            },
+            "sidecar_changes": {
+                "IntendedFor": ["localizer", "T1"]
+            }
+        }
+    ]
+}

tests/test_dcm2bids.py

@@ -591,4 +591,31 @@ def test_dcm2bids_no_reorder_entities():
     func_json = os.path.join(bids_dir.name, "sub-01",
                              "func",
                              "sub-01_acq-highres_task-rest_bold.json")
-    assert os.path.exists(func_json)
+    assert os.path.exists(func_json)
+
+
+def test_dcm2bids_multiple_intendedFor():
+    bids_dir = TemporaryDirectory()
+
+    tmp_sub_dir = os.path.join(bids_dir.name, DEFAULT.tmp_dir_name, "sub-01")
+    shutil.copytree(os.path.join(TEST_DATA_DIR, "sidecars"), tmp_sub_dir)
+
+    app = Dcm2BidsGen(TEST_DATA_DIR, "01",
+                      os.path.join(TEST_DATA_DIR,
+                                   "config_test_multiple_intendedfor_uri_relative.json"),
+                      bids_dir.name,
+                      auto_extract_entities=True)
+    app.run()
+
+    epi_file = os.path.join(bids_dir.name, "sub-01", "fmap", "sub-01_fmap.json")
+    data = load_json(epi_file)
+
+    assert os.path.exists(epi_file)
+    assert data["IntendedFor"] == [os.path.join("localizer",
+                                                "sub-01_run-01_localizer.nii"),
+                                   os.path.join("localizer",
+                                                "sub-01_run-02_localizer.nii"),
+                                   os.path.join("localizer",
+                                                "sub-01_run-03_localizer.nii"),
+                                   os.path.join("anat",
+                                                "sub-01_T1w.nii")]