generalization of defaceTpl to postOp

dcm2bids/dcm2bids_gen.py

@@ -97,7 +97,8 @@ def run(self):
             self.auto_extract_entities,
             self.config.get("searchMethod", DEFAULT.searchMethod),
             self.config.get("caseSensitive", DEFAULT.caseSensitive),
-            self.config.get("dupMethod", DEFAULT.dupMethod)
+            self.config.get("dupMethod", DEFAULT.dupMethod),
+            self.config.get("postOp",  DEFAULT.postOp)
         )
         parser.build_graph()
         parser.build_acquisitions(self.participant)
@@ -107,7 +108,7 @@ def run(self):
 
         idList = {}
         for acq in parser.acquisitions:
-            idList = self.move(acq, idList)
+            idList = self.move(acq, idList, parser.postOp)
 
         if self.bids_validate:
             try:
@@ -121,7 +122,7 @@ def run(self):
                                   "computer. Please check: "
                                   "https://github.com/bids-standard/bids-validator.")
 
-    def move(self, acquisition, idList):
+    def move(self, acquisition, idList, postOp):
         """Move an acquisition to BIDS format"""
         for srcFile in glob(acquisition.srcRoot + ".*"):
             ext = Path(srcFile).suffixes
@@ -151,18 +152,15 @@ def move(self, acquisition, idList):
                 else:
                     idList[acquisition.id] = [acquisition.dstId + "".join(ext)]
 
-            if (self.config.get("defaceTpl") and acquisition.datatype == "anat" and ".nii" in ext):
-                try:
-                    os.remove(dstFile)
-                except FileNotFoundError:
-                    pass
-                defaceTpl = self.config.get("defaceTpl")
+                for curr_postOp in postOp:
+                    if acquisition.datatype in curr_postOp['datatype'] or 'any' in curr_postOp['datatype']:
+                        if acquisition.suffix in curr_postOp['suffix'] or '_any' in curr_postOp['suffix']:
+                            cmd = curr_postOp['cmd'].replace('srcFile', str(srcFile))
+                            cmd = cmd.replace('dstFile', str(dstFile))
+                            run_shell_command(cmd.split())
+                            break
 
-                cmd = [w.replace('srcFile', srcFile) for w in defaceTpl]
-                cmd = [w.replace('dstFile', dstFile) for w in defaceTpl]
-                run_shell_command(cmd)
-
-            elif ".json" in ext:
+            if ".json" in ext:
                 data = acquisition.dstSidecarData(idList)
                 save_json(dstFile, data)
                 os.remove(srcFile)

dcm2bids/sidecar.py

@@ -96,10 +96,12 @@ def __init__(self,
                  auto_extractor=DEFAULT.auto_extract_entities,
                  searchMethod=DEFAULT.searchMethod,
                  caseSensitive=DEFAULT.caseSensitive,
-                 dupMethod=DEFAULT.dupMethod):
+                 dupMethod=DEFAULT.dupMethod,
+                 postOp=DEFAULT.postOp):
         self.logger = logging.getLogger(__name__)
         self._searchMethod = ""
         self._dupMethod = ""
+        self._postOp = ""
         self.graph = OrderedDict()
         self.acquisitions = []
         self.extractors = extractors
@@ -109,6 +111,7 @@ def __init__(self,
         self.searchMethod = searchMethod
         self.caseSensitive = caseSensitive
         self.dupMethod = dupMethod
+        self.postOp = postOp
 
     @property
     def searchMethod(self):
@@ -150,6 +153,48 @@ def dupMethod(self, value):
             self.logger.warning(f"{value} is not a duplicate method implemented.")
             self.logger.warning(f"Falling back to default: {DEFAULT.dupMethod}.")
 
+    @property
+    def postOp(self):
+        return self._postOp
+
+    @postOp.setter
+    def postOp(self, value):
+        """
+        Checks if postOp commands don't overlap
+        """
+        postOp = []
+        try:
+            pairs = []
+            for curr_postOp in value:
+                postOp.append(curr_postOp)
+                datatype = curr_postOp['datatype']
+                suffix = curr_postOp['suffix']
+
+                if isinstance(datatype, str):
+                    postOp[-1]['datatype'] = [datatype]
+                    datatype = [datatype]
+                if isinstance(suffix, str):
+                    # It will be compare with acq.suffix which has a `_` character
+                    postOp[-1]['suffix'] = ['_' + suffix]
+                    suffix = [suffix]
+                else:
+                    postOp[-1]['suffix'] = ['_' + curr_suffix for curr_suffix in suffix]
+
+                pairs = pairs + list(itertools.product(datatype, suffix))
+
+            res = list(set([ele for ele in pairs if pairs.count(ele) > 1]))
+            if res:
+                raise ValueError("Some post operations apply on "
+                                 "the same combination of datatype/suffix."
+                                 "Please fix postOp key in your config file."
+                                 f"{pairs}")
+
+            self._postOp = postOp
+
+        except Exception:
+            raise ValueError("postOp is not defined correctly."
+                             "Please check the documentation.")
+
     @property
     def caseSensitive(self):
         return self._caseSensitive

dcm2bids/utils/utils.py

@@ -28,7 +28,7 @@ class DEFAULT(object):
     auto_extract_entities = False
     clobber = False
     force_dcm2niix = False
-    defaceTpl = None
+    postOp = []
     logLevel = "WARNING"
 
     entity_dir = {"j-": "AP",

docs/get-started/install.md

@@ -300,9 +300,6 @@ options:
   --clobber             Overwrite output if it exists
   -l {DEBUG,INFO,WARNING,ERROR,CRITICAL}, --log_level {DEBUG,INFO,WARNING,ERROR,CRITICAL}
                         Set logging level
-  -a, --anonymizer      This option no longer exists from the script in this
-                        release. See:https://github.com/unfmontreal/Dcm2Bids/blob/m
-                        aster/README.md#defaceTpl
 
             Documentation at https://github.com/unfmontreal/Dcm2Bids
 ```

docs/how-to/use-advanced-commands.md

@@ -9,7 +9,9 @@ same level as the `"descriptions"` entry.
                    "BodyPartExamined": ["(?P<bodypart>[a-zA-Z]+)"]},
     "searchMethod": "fnmatch",
     "caseSensitive": true,
-    "defaceTpl": ["pydeface", "--outfile", "dstFile", "srcFile"],
+    "postOp": {"cmd": "pydeface --outfile dstFile srcFile",
+               "datatype": "anat",
+               "suffix": ["T1w", "MP2RAGE"]},
     "description": [
     {
       "datatype": "anat",
@@ -48,18 +50,37 @@ default: `"caseSensitive": "true"`
 If false, comparisons between strings/lists will be not case sensitive. It's
 only disabled when used with `"searchMethod": "fnmatch"`.
 
-## defaceTpl
+## postOp
 
-default: `"defaceTpl": None`
+default: `"postOp": []`
 
-!!! danger The anonymizer option no longer exists from `v2.0.0`. It is still
-possible to deface the anatomical nifti images.
+postOp key allows you to run any post-processing analyses just before being moved 
+to there respective folders. 
 
-For example, if you use the last version of pydeface, add:
+For example, if you want to deface your T1w images you could use pydeface by adding:
+```
+    "postOp": [{"cmd": "pydeface --outfile dstFile srcFile",
+               "datatype": "anat",
+               "suffix": ["T1w", "MP2RAGE"]}],
+```
+
+It will specifically run the corresponding `cmd` to any image that follow the combinations
+datatype/suffix: `(anat, T1w) or (anat, MP2RAGE)`.
+
+Although you can add multiple commands the combination datatype/suffix has to be unique.
+
+```
+    "postOp": [{"cmd": "pydeface --outfile dstFile srcFile",
+               "datatype": "anat",
+               "suffix": ["T1w", "MP2RAGE"]},
+               {"cmd": "my_new_script --input srcFile --output dstFile ",
+               "datatype": "fmap",
+               "suffix": ["any"]}],
+```
 
-`"defaceTpl": "pydeface --outfile {dstFile} {srcFile}"`
+In this example the second command "my_new_script" will be running on any image which datatype is fmap.
 
-It is a template string and dcm2bids will replace {srcFile} and {dstFile} by the
+Finally, this is a template string and dcm2bids will replace srcFile and dstFile by the
 source file (input) and the destination file (output).
 
 ## dcm2niixOptions
@@ -120,7 +141,6 @@ command.
     --clobber             Overwrite output if it exists
     -l {DEBUG,INFO,WARNING,ERROR,CRITICAL}, --log_level {DEBUG,INFO,WARNING,ERROR,CRITICAL}
                             Set logging level
-    -a, --anonymizer      This option no longer exists from the script in this release. See:https://github.com/unfmontreal/Dcm2Bids/blob/master/README.md#defaceTpl
 
                 Documentation at https://github.com/unfmontreal/Dcm2Bids
 

docs/tutorial/first-steps.md

@@ -106,12 +106,8 @@ You can test it with any command but a safe way is to use the `--help` command.
     --clobber             Overwrite output if it exists
     -l {DEBUG,INFO,WARNING,ERROR,CRITICAL}, --log_level {DEBUG,INFO,WARNING,ERROR,CRITICAL}
                             Set logging level
-    -a, --anonymizer      This option no longer exists from the script in this
-                            release. See:https://github.com/unfmontreal/Dcm2Bids/blob/m
-                            aster/README.md#defaceTpl
 
                 Documentation at https://github.com/unfmontreal/Dcm2Bids
-
     ```
 
 ??? bug "What you can do if you did not get this output"
@@ -978,7 +974,6 @@ command.
     --clobber             Overwrite output if it exists
     -l {DEBUG,INFO,WARNING,ERROR,CRITICAL}, --log_level {DEBUG,INFO,WARNING,ERROR,CRITICAL}
                             Set logging level
-    -a, --anonymizer      This option no longer exists from the script in this release. See:https://github.com/unfmontreal/Dcm2Bids/blob/master/README.md#defaceTpl
 
                 Documentation at https://github.com/unfmontreal/Dcm2Bids
 

example/config.json

@@ -1,6 +1,8 @@
 {
     "searchMethod": "fnmatch",
-    "defaceTpl": "pydeface --outfile {dstFile} {srcFile}",
+    "postOp": [{"cmd" : "pydeface --outfile dstFile srcFile",
+                "datatype": "anat",
+                "suffix": ["T1w", "MP2RAGE"]}],
     "descriptions": [
         {
             "datatype": "anat",