Merge pull request #243 from UNFmontreal/fix_sidecars

[BF] fix sidecars suggested by Sam

dcm2bids/acquisition.py

@@ -212,7 +212,7 @@ def dstSidecarData(self, idList):
                 value = [value]
 
             for val in value:
-                if isinstance(val, str):
+                if isinstance(val, str) or isinstance(val, bool):
                     if val not in idList and key in DEFAULT.keyWithPathsidecar_changes:
                         logging.warning(f"No id found for '{key}' value '{val}'.")
                         logging.warning(f"No sidecar changes for field '{key}' "
@@ -221,6 +221,11 @@ def dstSidecarData(self, idList):
                                         "with this id.")
                     else:
                         values.append(idList.get(val, val))
+                        if values[-1] != val:
+                            if isinstance(values[-1], list):
+                                values[-1] = "bids::" + values[-1][0]
+                            else:
+                                 values[-1] = "bids::" + values[-1]
 
             # handle if nested list vs str
             flat_value_list = []
@@ -229,10 +234,11 @@ def dstSidecarData(self, idList):
                     flat_value_list += item
                 else:
                     flat_value_list.append(item)
+
             if len(flat_value_list) == 1:
-                flat_value_list = flat_value_list[0]
-
-            data[key] = flat_value_list
+                data[key] = flat_value_list[0]
+            else:
+                data[key] = flat_value_list
 
         return data
 

dcm2bids/dcm2bids_gen.py

@@ -155,9 +155,11 @@ def move(self, acquisition, idList, post_op):
             # Populate idList
             if '.nii' in ext:
                 if acquisition.id in idList:
-                    idList[acquisition.id].append(acquisition.dstId + "".join(ext))
+                    idList[acquisition.id].append(os.path.join(acquisition.participant.name,
+                                                               acquisition.dstId + "".join(ext)))
                 else:
-                    idList[acquisition.id] = [acquisition.dstId + "".join(ext)]
+                    idList[acquisition.id] = [os.path.join(acquisition.participant.name,
+                                                           acquisition.dstId + "".join(ext))]
 
                 for curr_post_op in post_op:
                     if acquisition.datatype in curr_post_op['datatype'] or 'any' in curr_post_op['datatype']:

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

@@ -1,4 +1,6 @@
-# How to use advanced configuration
+# Advanced configuration and commands
+
+## How to use advanced configuration
 
 These optional configurations can be inserted in the configuration file at the
 same level as the `"description"` entry.
@@ -43,7 +45,7 @@ same level as the `"description"` entry.
 }
 ```
 
-## custom_entities combined with extractors
+### `custom_entities` combined with extractors
 
 default: None
 
@@ -57,15 +59,15 @@ entities directly into the final filename. custom_entities can be a list that
 combined extractor keys and regular entities. If key is `task` it will
 automatically add the field "TaskName" inside the sidecase file.
 
-## search_method
+### `search_method`
 
 default: `"search_method": "fnmatch"`
 
 fnmatch is the behaviour (See criteria) by default and the fall back if this
 option is set incorrectly. `re` is the other choice if you want more flexibility
 to match criteria.
 
-## dup_method
+### `dup_method`
 
 default: `"dup_method": "run"`
 
@@ -77,14 +79,14 @@ customEntities of the other acquisitions. This behavior is a
 [heudiconv](https://heudiconv.readthedocs.io/en/latest/changes.html) inspired
 feature.
 
-## case_sensitive
+### `case_sensitive`
 
 default: `"case_sensitive": "true"`
 
 If false, comparisons between strings/lists will be not case sensitive. It's
 only disabled when used with `"search_method": "fnmatch"`.
 
-## post_op
+### `post_op`
 
 default: `"post_op": []`
 
@@ -130,23 +132,23 @@ which datatype is fmap.
 Finally, this is a template string and dcm2bids will replace `src_file` and
 `dst_file` by the source file (input) and the destination file (output).
 
-## dcm2niixOptions
+### `dcm2niixOptions`
 
 default: `"dcm2niixOptions": "-b y -ba y -z y -f '%3s_%f_%p_%t'"`
 
 Arguments for dcm2niix
 
-## compKeys
+### `compKeys`
 
 default: `"compKeys": ["SeriesNumber", "AcquisitionTime", "SidecarFilename"]`
 
 Acquisitions are sorted using the sidecar data. The default behaviour is to sort
 by `SeriesNumber` then by `AcquisitionTime` then by the `SidecarFilename`. You
 can change this behaviour setting this key inside the configuration file.
 
-## criteria
+### `criteria`
 
-### Handle multi site filtering
+#### Handle multi site filtering
 
 As mentionned in the [first-steps tutorial](../tutorial/first-steps.md),
 criteria is the way to filter specific acquisitions. If you work with dicoms
@@ -160,7 +162,7 @@ feature where for a specific criteria you can get multiple descriptions.
 }
 ```
 
-### Enhanced float/int comparison
+#### Enhanced float/int comparison
 
 Criteria can help you filter acquisitions by comparing float/int sidecar.
 
@@ -196,9 +198,9 @@ If you want to use btw or btwe you will need to give an ordered list like this.
 }
 ```
 
-# How to use advanced commands
+## How to use advanced commands
 
-## dcm2bids advanced options
+### dcm2bids advanced options
 
 By now, you should be used to getting the `--help` information before running a
 command.
@@ -236,7 +238,7 @@ command.
                             depending on the suffix and datatype. [False]
     --bids_validate       If set, once your conversion is done it will check if your output folder is BIDS valid. [False]
                           bids-validator needs to be installed check: https://github.com/bids-standard/bids-validator#quickstart
-    --forceDcm2niix       Overwrite previous temporary dcm2niix output if it exists
+    --force_dcm2niix       Overwrite previous temporary dcm2niix output if it exists
     --clobber             Overwrite output if it exists
     -l {DEBUG,INFO,WARNING,ERROR,CRITICAL}, --log_level {DEBUG,INFO,WARNING,ERROR,CRITICAL}
                             Set logging level
@@ -245,7 +247,7 @@ command.
 
     ```
 
-## --auto_extract_entities
+### `--auto_extract_entities`
 
 This option will automatically try to find 3 entities (task, dir and echo) for
 specific datatype/suffix.
@@ -310,7 +312,7 @@ like this.
 :radioactive: You can find more detailed information by looking at the file [`dcm2bids/utils/utils.py`](../dcm2bids/utils/utils/) and
 more specifically *`auto_extractors`* and *`auto_entities`* variables.
 
-## --bids_validate
+### `--bids_validate`
 
 By default, dcm2bids will not validate your final BIDS structure. If needed, you
 can install

tests/data/config_test_sidecar.json

@@ -0,0 +1,92 @@
+{
+    "descriptions": [
+      {
+        "datatype": "localizer",
+        "suffix": "localizer",
+        "criteria": {
+          "SeriesDescription": "locali*"
+        },
+        "sidecar_changes": {
+          "ProcedureStepDescription": "Modified by dcm2bids"
+        }
+      },
+      {
+        "id": "T1",
+        "datatype": "anat",
+        "suffix": "T1w",
+        "criteria": {
+          "SidecarFilename": "*MPRAGE*"
+        },
+        "sidecar_changes": {
+          "new_field": "new value"
+        }
+      },
+      {
+        "id": "id_dwi",
+        "datatype": "dwi",
+        "suffix": "dwi",
+        "criteria": {
+          "SeriesDescription": "DTI"
+        }
+      },
+      {
+        "datatype": "fmap",
+        "suffix": "fmap",
+        "custom_entities": "echo-492",
+        "criteria": {
+          "EchoNumber": 1,
+          "EchoTime": 0.00492
+        },
+        "sidecar_changes": {
+          "MTState": true
+        }
+      },
+      {
+        "datatype": "fmap",
+        "suffix": "fmap",
+        "custom_entities": "echo-738",
+        "criteria": {
+          "EchoNumber": 2,
+          "EchoTime": 0.00738,
+          "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND"]
+        },
+        "sidecar_changes": {
+          "MTState": "false"
+        }
+      },
+      {
+        "datatype": "dwi",
+        "suffix": "dwi",
+        "custom_entities": "desc-fa01",
+        "criteria": {
+          "SeriesDescription": "DTI_FA"
+        },
+        "sidecar_changes": {
+          "IntendedFor": [
+            "id_dwi",
+            "T1"
+          ],
+          "Sources": [
+            "T1",
+            "id_dwi"
+          ]
+        }
+      },
+      {
+        "datatype": "dwi",
+        "suffix": "dwi",
+        "custom_entities": "desc-trace",
+        "criteria": {
+          "SeriesDescription": "DTI_TRACEW"
+        },
+        "sidecar_changes": {
+          "IntendedFor": [
+            "id_dwi"
+          ],
+          "Sources": [
+            "T1"
+          ]
+        }
+      }
+    ]
+  }