[WIP] Fix Entity Table Order

dcm2bids/structure.py

@@ -2,7 +2,7 @@
 
 """k"""
 
-
+import logging
 from os.path import join as opj
 from future.utils import iteritems
 from .utils import DEFAULT
@@ -132,6 +132,8 @@ def __init__(
         self.customLabels = customLabels
         self.srcSidecar = srcSidecar
 
+        self.logger = logging.getLogger(__name__)
+
         if sidecarChanges is None:
             self.sidecarChanges = {}
         else:
@@ -207,7 +209,7 @@ def dstRoot(self):
         return opj(
             self.participant.directory,
             self.dataType,
-            self.participant.prefix + self.suffix,
+            self.set_order_entity_table(),
         )
 
     @property
@@ -219,9 +221,36 @@ def dstIntendedFor(self):
         return opj(
             self.participant.session,
             self.dataType,
-            self.participant.prefix + self.suffix,
+            self.set_order_entity_table(),
         )
 
+    def set_order_entity_table(self):
+        """
+        Return:
+            The destination filename formated following BIDS entity key table
+            https://bids-specification.readthedocs.io/en/latest/99-appendices/04-entity-table.html#appendix-iv-entity-table
+        """
+        curr_name = self.participant.prefix + self.suffix
+        new_name = ''
+        curr_dict = dict(x.split("-") for x in curr_name.split("_") if len(x.split('-')) == 2)
+        ext = [x for x in curr_name.split("_") if len(x.split('-')) == 1]
+
+        for curr_key in DEFAULT.entityTableKeys:
+            if curr_key in curr_dict.keys():
+                new_name = '_'.join([new_name, curr_key + '-' +
+                                    curr_dict[curr_key]])
+                curr_dict.pop(curr_key, None)
+
+        for curr_key in curr_dict.keys():
+            self.logger.warning(
+                "Entity \"%s\" is not a valid BIDS entity.", curr_key
+            )
+            new_name = '_'.join([new_name, curr_key + '-' +
+                                 curr_dict[curr_key]])
+        new_name = new_name[1:]
+        new_name = '_'.join([new_name, ext[0]])
+        return new_name
+
     @property
     def intendedFor(self):
         return self._intendedFor
@@ -249,14 +278,12 @@ 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/latest/99-appendices/04-entity-table.html#appendix-iv-entity-table
+    entityTableKeys = ["sub", "ses", "task", "acq", "ce", "rec", "dir",
+                       "run", "mod", "echo", "flip", "inv", "mt", "part",
+                       "recording"]
+
     # misc
     tmpDirName = "tmp_dcm2bids"
     helperDir = "helper"