working version

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,
         **kwargs
     ):
         self.logger = logging.getLogger(__name__)
@@ -43,6 +45,7 @@ def __init__(
         self.suffix = suffix
         self.custom_entities = custom_entities
         self.src_sidecar = src_sidecar
+        self.bids_uri = bids_uri
 
         if sidecar_changes is None:
             self.sidecar_changes = {}
@@ -277,10 +280,16 @@ 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

@@ -102,7 +102,8 @@ 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"]
 
@@ -99,11 +100,13 @@ 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
@@ -114,6 +117,7 @@ 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):
@@ -218,6 +222,25 @@ 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
@@ -393,9 +416,10 @@ def build_acquisitions(self, participant):
             if len(valid_descriptions) == 1:
                 desc = valid_descriptions[0]
                 desc, sidecar = self.searchDcmTagEntity(sidecar, desc)
-
                 acq = Acquisition(participant,
-                                  src_sidecar=sidecar, **desc)
+                                  src_sidecar=sidecar,
+                                  bids_uri=self.bids_uri,
+                                  **desc)
                 acq.setDstFile()
 
                 if acq.id:
@@ -414,6 +438,7 @@ 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,
                                       **desc)
                     self.logger.warning(f"    ->  {acq.suffix}")
 
@@ -438,7 +463,6 @@ def searchDcmTagEntity(self, sidecar, desc):
             if self.auto_extract_entities:
                 self.extractors = combine_dict_extractors(self.extractors, DEFAULT.auto_extractors)
 
-
             for dcmTag in self.extractors:
                 if dcmTag in sidecar.data.keys():
                     dcmInfo = sidecar.data.get(dcmTag)
@@ -473,12 +497,11 @@ def searchDcmTagEntity(self, sidecar, desc):
                     if left_auto_entities:
                         self.logger.warning(f"{left_auto_entities} have not been found for datatype '{descWithTask['datatype']}' "
                                             f"and suffix '{descWithTask['suffix']}'.")
-                    
+
                     entities = list(entities) + list(auto_entities)
                     entities = list(set(entities))
                     descWithTask["custom_entities"] = entities
 
-
             for curr_entity in entities:
                 if curr_entity in concatenated_matches.keys():
                     if curr_entity == 'dir':

dcm2bids/utils/utils.py

@@ -59,14 +59,16 @@ class DEFAULT(object):
                      "func_bold": ["task"],
                      "func_sbref": ["task"],
                      "fmap_epi": ["dir"]}
-    
+
     compKeys = ["AcquisitionTime", "SeriesNumber", "SidecarFilename"]
     search_methodChoices = ["fnmatch", "re"]
     search_method = "fnmatch"
     dup_method_choices = ["dup", "run"]
     dup_method = "run"
     runTpl = "_run-{:02d}"
     dupTpl = "_dup-{:02d}"
+    bids_uri_choices = ["URI", "relative"]
+    bids_uri = "URI"
     case_sensitive = True
 
     # Entity table:
@@ -143,15 +145,15 @@ def convert_dir(dir):
 
 
 def combine_dict_extractors(d1, d2):
-    """ combine dict 
+    """ combine dict
     Args:
         d1 (dic): dictionary
         d2 (dic): dictionary
-    
+
     Returns:
         dict: dictionary with combined information
               if d1 d2 use the same keys, return dict will return a list of items.
-    """    
+    """
     return {
             k: [d[k][0] for d in (d1, d2) if k in d]
             for k in set(d1.keys()) | set(d2.keys())