[BF] fix intendedFor

dcm2bids/dcm2bids.py

@@ -124,6 +124,7 @@ def run(self):
             sidecars.append(
                 Sidecar(filename, self.config.get("compKeys", DEFAULT.compKeys))
             )
+
         sidecars = sorted(sidecars)
 
         parser = SidecarPairing(
@@ -137,15 +138,18 @@ def run(self):
         parser.find_runs()
 
         self.logger.info("moving acquisitions into BIDS folder")
+
+        intendedForList = [[] for i in range(len(parser.descriptions))]
         for acq in parser.acquisitions:
-            self.move(acq)
+            intendedForList = self.move(acq, intendedForList)
 
         check_latest()
         check_latest("dcm2niix")
 
-    def move(self, acquisition):
+    def move(self, acquisition, intendedForList):
         """Move an acquisition to BIDS format"""
         for srcFile in glob(acquisition.srcRoot + ".*"):
+
             _, ext = splitext_(srcFile)
             dstFile = os.path.join(self.bidsDir, acquisition.dstRoot + ext)
 
@@ -177,18 +181,25 @@ def move(self, acquisition):
                     pass
                 defaceTpl = self.config.get("defaceTpl")
                 cmd = defaceTpl.format(srcFile=srcFile, dstFile=dstFile)
+
                 run_shell_command(cmd)
+                intendedForList[acquisition.indexSidecar].append(acquisition.dstIntendedFor + ext)
 
-            # use
             elif ext == ".json":
-                data = acquisition.dstSidecarData(self.config["descriptions"])
+                data = acquisition.dstSidecarData(self.config["descriptions"],
+                                                  intendedForList)
                 save_json(dstFile, data)
                 os.remove(srcFile)
 
             # just move
             else:
                 os.rename(srcFile, dstFile)
 
+            intendedFile = acquisition.dstIntendedFor + ".nii.gz"
+            if not intendedFile in intendedForList[acquisition.indexSidecar]:
+                intendedForList[acquisition.indexSidecar].append(intendedFile)
+
+        return intendedForList
 
 def get_arguments():
     """Load arguments for main"""

dcm2bids/sidecar.py

@@ -95,7 +95,7 @@ def __init__(self, sidecars, descriptions, searchMethod=DEFAULT.searchMethod,
 
         self._searchMethod = ""
         self.graph = OrderedDict()
-        self.aquisitions = []
+        self.acquisitions = []
 
         self.sidecars = sidecars
         self.descriptions = descriptions
@@ -154,14 +154,14 @@ def build_graph(self):
             A graph (OrderedDict)
         """
         graph = OrderedDict((_, []) for _ in self.sidecars)
-
         possibleLinks = itertools.product(self.sidecars, self.descriptions)
         for sidecar, description in possibleLinks:
             criteria = description.get("criteria", None)
             if criteria and self.isLink(sidecar.data, criteria):
-                graph[sidecar].append(description)
+                    graph[sidecar].append(description)
 
         self.graph = graph
+
         return graph
 
     def isLink(self, data, criteria):
@@ -213,32 +213,42 @@ def build_acquisitions(self, participant):
             A list of acquisition objects
         """
         acquisitions = []
+        acquisitions_intendedFor = []
 
         self.logger.info("Sidecars pairing:")
-        for sidecar, descriptions in iteritems(self.graph):
+        for sidecar, valid_descriptions in iteritems(self.graph):
+        #for sidecar, descriptions in iteritems(self.graph):
             sidecarName = os.path.basename(sidecar.root)
 
             # only one description for the sidecar
-            if len(descriptions) == 1:
-                desc = descriptions[0]
-                acq = Acquisition(participant, srcSidecar=sidecar, **desc)
-                acquisitions.append(acq)
+            if len(valid_descriptions) == 1:
+                desc = valid_descriptions[0]
+                acq = Acquisition(participant,
+                                  srcSidecar=sidecar, **desc)
+                acq.indexSidecar = self.descriptions.index(desc)
+
+                if acq.intendedFor != [None]:
+                    acquisitions_intendedFor.append(acq)
+                else:
+                    acquisitions.append(acq)
 
                 self.logger.info("%s  <-  %s", acq.suffix, sidecarName)
 
             # sidecar with no link
-            elif len(descriptions) == 0:
+            elif len(valid_descriptions) == 0:
                 self.logger.info("No Pairing  <-  %s", sidecarName)
 
             # sidecar with several links
             else:
                 self.logger.warning("Several Pairing  <-  %s", sidecarName)
-                for desc in descriptions:
-                    acq = Acquisition(participant, **desc)
+                for desc in valid_descriptions:
+                    acq = Acquisition(participant, indexSidecar=self.descriptions.index(desc),
+                                      **desc)
                     self.logger.warning("    ->  %s", acq.suffix)
 
-        self.acquisitions = acquisitions
-        return acquisitions
+        self.acquisitions = acquisitions + acquisitions_intendedFor
+
+        return acquisitions + acquisitions_intendedFor
 
     def find_runs(self):
         """

dcm2bids/structure.py

@@ -113,6 +113,7 @@ def __init__(
         participant,
         dataType,
         modalityLabel,
+        indexSidecar=None,
         customLabels="",
         srcSidecar=None,
         sidecarChanges=None,
@@ -123,16 +124,19 @@ def __init__(
         self._modalityLabel = ""
         self._customLabels = ""
         self._intendedFor = None
+        self._indexSidecar = None
 
         self.participant = participant
         self.dataType = dataType
         self.modalityLabel = modalityLabel
         self.customLabels = customLabels
         self.srcSidecar = srcSidecar
+
         if sidecarChanges is None:
             self.sidecarChanges = {}
         else:
             self.sidecarChanges = sidecarChanges
+
         if intendedFor is None:
             self.intendedFor = IntendedFor
         else:
@@ -206,6 +210,18 @@ def dstRoot(self):
             self.participant.prefix + self.suffix,
         )
 
+    @property
+    def dstIntendedFor(self):
+        """
+        Return:
+            The destination root inside the BIDS structure for intendedFor
+        """
+        return opj(
+            self.participant.session,
+            self.dataType,
+            self.participant.prefix + self.suffix,
+        )
+
     @property
     def intendedFor(self):
         return self._intendedFor
@@ -217,27 +233,36 @@ def intendedFor(self, value):
         else:
             self._intendedFor = [value]
 
-    def dstSidecarData(self, descriptions):
+    @property
+    def indexSidecar(self):
+        """
+        Returns:
+            A int '_<indexSidecar>'
+        """
+        return self._indexSidecar
+
+    @indexSidecar.setter
+    def indexSidecar(self, value):
+        """
+        Returns:
+            A int '_<indexSidecar>'
+        """
+        self._indexSidecar = value
+
+
+    def dstSidecarData(self, descriptions, intendedForList):
         """
         """
         data = self.srcSidecar.origData
         data["Dcm2bidsVersion"] = __version__
 
+
         # intendedFor key
         if self.intendedFor != [None]:
             intendedValue = []
-            for index in self.intendedFor:
-                intendedDesc = descriptions[index]
 
-                session = self.participant.session
-                dataType = intendedDesc["dataType"]
-
-                niiFile = self.participant.prefix
-                niiFile += self.prepend(intendedDesc.get("customLabels", ""))
-                niiFile += self.prepend(intendedDesc["modalityLabel"])
-                niiFile += ".nii.gz"
-
-                intendedValue.append(opj(session, dataType, niiFile).replace("\\", "/"))
+            for index in self.intendedFor:
+                intendedValue = intendedValue + intendedForList[index]
 
             if len(intendedValue) == 1:
                 data["IntendedFor"] = intendedValue[0]

tests/test_dcm2bids.py

@@ -57,7 +57,7 @@ def test_dcm2bids():
     fmapFile = os.path.join(bidsDir.name, "sub-01", "fmap", "sub-01_echo-492_fmap.json")
     data = load_json(fmapFile)
     fmapMtime = os.stat(fmapFile).st_mtime
-    assert data["IntendedFor"] == "dwi/sub-01_dwi.nii.gz"
+    assert data["IntendedFor"] == os.path.join("dwi", "sub-01_dwi.nii.gz")
 
     data = load_json(
         os.path.join(

tests/test_structure.py

@@ -29,5 +29,5 @@
 )
 def test_acquisition_get_dst_path(name, session, modality, custom, expected):
     participant = Participant(name, session)
-    acquisition = Acquisition(participant, "anat", modality, custom)
+    acquisition = Acquisition(participant, "anat", modality, customLabels=custom)
     assert acquisition.dstRoot == expected