[WIP] Fix Entity Table Order

dcm2bids/dcm2bids.py

@@ -141,20 +141,16 @@ def run(self):
 
         intendedForList = [[] for i in range(len(parser.descriptions))]
         for acq in parser.acquisitions:
+            acq.setDstFile()
             intendedForList = self.move(acq, intendedForList)
 
-        check_latest()
-        check_latest("dcm2niix")
-
     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)
 
-            # os.makedirs(os.path.dirname(dstFile), exist_ok=True)
-            # python2 compatibility
             if not os.path.exists(os.path.dirname(dstFile)):
                 os.makedirs(os.path.dirname(dstFile))
 
@@ -196,11 +192,12 @@ def move(self, acquisition, intendedForList):
                 os.rename(srcFile, dstFile)
 
             intendedFile = acquisition.dstIntendedFor + ".nii.gz"
-            if not intendedFile in intendedForList[acquisition.indexSidecar]:
+            if intendedFile not in intendedForList[acquisition.indexSidecar]:
                 intendedForList[acquisition.indexSidecar].append(intendedFile)
 
         return intendedForList
 
+
 def get_arguments():
     """Load arguments for main"""
     parser = argparse.ArgumentParser(
@@ -298,6 +295,9 @@ def main():
         )
         return 1
 
+    check_latest()
+    check_latest("dcm2niix")
+
     app = Dcm2bids(**vars(args))
     return app.run()
 

dcm2bids/sidecar.py

@@ -158,7 +158,7 @@ def build_graph(self):
         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
 
@@ -189,7 +189,7 @@ def compare(name, pattern):
         result = []
 
         for tag, pattern in iteritems(criteria):
-            name = data.get(tag, '')# or ''
+            name = data.get(tag, '')
 
             if isinstance(name, list):
                 try:
@@ -217,7 +217,6 @@ def build_acquisitions(self, participant):
 
         self.logger.info("Sidecars pairing:")
         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
@@ -226,6 +225,7 @@ def build_acquisitions(self, participant):
                 acq = Acquisition(participant,
                                   srcSidecar=sidecar, **desc)
                 acq.indexSidecar = self.descriptions.index(desc)
+                acq.setDstFile()
 
                 if acq.intendedFor != [None]:
                     acquisitions_intendedFor.append(acq)
@@ -242,13 +242,14 @@ def build_acquisitions(self, participant):
             else:
                 self.logger.warning("Several Pairing  <-  %s", sidecarName)
                 for desc in valid_descriptions:
-                    acq = Acquisition(participant, indexSidecar=self.descriptions.index(desc),
+                    acq = Acquisition(participant,
+                                      indexSidecar=self.descriptions.index(desc),
                                       **desc)
                     self.logger.warning("    ->  %s", acq.suffix)
 
         self.acquisitions = acquisitions + acquisitions_intendedFor
 
-        return acquisitions + acquisitions_intendedFor
+        return self.acquisitions
 
     def find_runs(self):
         """

dcm2bids/structure.py

@@ -1,8 +1,8 @@
 # -*- coding: utf-8 -*-
 
-"""k"""
-
+"""Participant class"""
 
+import logging
 from os.path import join as opj
 from future.utils import iteritems
 from .utils import DEFAULT
@@ -121,6 +121,8 @@ def __init__(
         IntendedFor=None,
         **kwargs
     ):
+        self.logger = logging.getLogger(__name__)
+
         self._modalityLabel = ""
         self._customLabels = ""
         self._intendedFor = None
@@ -142,6 +144,8 @@ def __init__(
         else:
             self.intendedFor = intendedFor
 
+        self.dstFile = ''
+
     def __eq__(self, other):
         return (
             self.dataType == other.dataType
@@ -207,7 +211,7 @@ def dstRoot(self):
         return opj(
             self.participant.directory,
             self.dataType,
-            self.participant.prefix + self.suffix,
+            self.dstFile,
         )
 
     @property
@@ -219,9 +223,50 @@ def dstIntendedFor(self):
         return opj(
             self.participant.session,
             self.dataType,
-            self.participant.prefix + self.suffix,
+            self.dstFile,
         )
 
+    def setDstFile(self):
+        """
+        Return:
+            The destination filename formatted following the v1.7.0 BIDS entity key table
+            https://bids-specification.readthedocs.io/en/v1.7.0/99-appendices/04-entity-table.html
+        """
+        current_name = self.participant.prefix + self.suffix
+        new_name = ''
+        current_dict = dict(x.split("-") for x in current_name.split("_") if len(x.split('-')) == 2)
+        suffix_list = [x for x in current_name.split("_") if len(x.split('-')) == 1]
+
+        for current_key in DEFAULT.entityTableKeys:
+            if current_key in current_dict and new_name != '':
+                new_name += f"_{current_key}-{current_dict[current_key]}"
+            elif current_key in current_dict:
+                new_name = f"{current_key}-{current_dict[current_key]}"
+            current_dict.pop(current_key, None)
+
+        for current_key in current_dict:
+            new_name += f"_{current_key}-{current_dict[current_key]}"
+
+        if current_dict:
+            self.logger.warning("Entity \"{}\"".format(list(current_dict.keys())) +
+                                " is not a valid BIDS entity.")
+
+        new_name += f"_{'_'.join(suffix_list)}"  # Allow multiple single key (without value)
+
+        if len(suffix_list) != 1:
+            self.logger.warning("There was more than one suffix found "
+                                f"({suffix_list}). this is not BIDS "
+                                "compliant. Make sure you know what"
+                                "you are doing.")
+
+        if current_name != new_name:
+            self.logger.warning(
+                f"""✅ Filename was reordered according to BIDS entity table order:
+                from:   {current_name}
+                to:     {new_name}""")
+
+        self.dstFile = new_name
+
     @property
     def intendedFor(self):
         return self._intendedFor
@@ -249,14 +294,12 @@ def indexSidecar(self, value):
         """
         self._indexSidecar = value
 
-
     def dstSidecarData(self, descriptions, intendedForList):
         """
         """
         data = self.srcSidecar.origData
         data["Dcm2bidsVersion"] = __version__
 
-
         # intendedFor key
         if self.intendedFor != [None]:
             intendedValue = []

dcm2bids/utils.py

@@ -37,6 +37,12 @@ class DEFAULT(object):
     runTpl = "_run-{:02d}"
     caseSensitive = True
 
+    # Entity table:
+    # https://bids-specification.readthedocs.io/en/v1.7.0/99-appendices/04-entity-table.html
+    entityTableKeys = ["sub", "ses", "task", "acq", "ce", "rec", "dir",
+                       "run", "mod", "echo", "flip", "inv", "mt", "part",
+                       "recording"]
+
     # misc
     tmpDirName = "tmp_dcm2bids"
     helperDir = "helper"

tests/test_dcm2bids.py

@@ -96,8 +96,7 @@ def test_caseSensitive_false():
     app.run()
 
     layout = BIDSLayout(bidsDir.name,
-                        validate=False,
-                        ignore='tmp_dcm2bids')
+                        validate=False)
 
     path_dwi = os.path.join(bidsDir.name,
                             "sub-01",

tests/test_structure.py

@@ -30,4 +30,5 @@
 def test_acquisition_get_dst_path(name, session, modality, custom, expected):
     participant = Participant(name, session)
     acquisition = Acquisition(participant, "anat", modality, customLabels=custom)
+    acquisition.setDstFile()
     assert acquisition.dstRoot == expected