fix sidecarChanges

UNFmontreal · Jul 5, 2023 · 62830c0 · 62830c0
1 parent a09a693
commit 62830c0
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Showing 8 changed files with 24 additions and 24 deletions.
diff --git a/dcm2bids/acquisition.py b/dcm2bids/acquisition.py
@@ -29,7 +29,7 @@ def __init__(
         custom_entities="",
         id=None,
         srcSidecar=None,
-        sidecarChanges=None,
+        sidecar_changes=None,
         **kwargs
     ):
         self.logger = logging.getLogger(__name__)
@@ -44,10 +44,10 @@ def __init__(
         self.custom_entities = custom_entities
         self.srcSidecar = srcSidecar
 
-        if sidecarChanges is None:
-            self.sidecarChanges = {}
+        if sidecar_changes is None:
+            self.sidecar_changes = {}
         else:
-            self.sidecarChanges = sidecarChanges
+            self.sidecar_changes = sidecar_changes
 
         if id is None:
             self.id = None
@@ -204,16 +204,16 @@ def dstSidecarData(self, idList):
         if 'TaskName' in self.srcSidecar.data:
             data["TaskName"] = self.srcSidecar.data["TaskName"]
 
-        # sidecarChanges
-        for key, value in self.sidecarChanges.items():
+        # sidecar_changes
+        for key, value in self.sidecar_changes.items():
             values = []
 
             if not isinstance(value, list):
                 value = [value]
 
             for val in value:
                 if isinstance(val, str):
-                    if val not in idList and key in DEFAULT.keyWithPathSidecarChanges:
+                    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}' "
                                         f"will be made "

diff --git a/dcm2bids/utils/utils.py b/dcm2bids/utils/utils.py
@@ -71,7 +71,7 @@ class DEFAULT(object):
                        "run", "mod", "echo", "flip", "inv", "mt", "part",
                        "recording"]
 
-    keyWithPathSidecarChanges = ['IntendedFor', 'Sources']
+    keyWithPathsidecar_changes = ['IntendedFor', 'Sources']
 
     # misc
     tmp_dir_name = "tmp_dcm2bids"

diff --git a/docs/how-to/create-config-file.md b/docs/how-to/create-config-file.md
@@ -12,7 +12,7 @@
         "SeriesDescription": "*T2*",
         "EchoTime": 0.1
       },
-      "sidecarChanges": {
+      "sidecar_changes": {
         "ProtocolName": "T2"
       }
     },
@@ -42,7 +42,7 @@
       "criteria": {
         "SeriesDescription": "bold_task-learning"
       },
-      "sidecarChanges": {
+      "sidecar_changes": {
         "TaskName": "learning"
       }
     },
@@ -53,7 +53,7 @@
         "SeriesDescription": "fmap_task-learning"
       },
       "IntendedFor": "id_task_learning",
-      "sidecarChanges": {
+      "sidecar_changes": {
         "TaskName": "learning"
       }
     }
@@ -148,7 +148,7 @@ custom_entities could also be combined with extractors.
 See [custom_entities combined with extractors](./use-advanced-commands.md#custom_entities-combined-with-extractors)
 
 
-## sidecarChanges
+## sidecar_changes
 
 Optional field to change or add information in a sidecar.
 
@@ -159,7 +159,7 @@ You will need to set an id to the corresponding description and put the same id
 
 Fo example, **`task_rest`** means it is intended for `task-rest_bold` 
 and **`id_task_learning`** is intended for `task-learning` which will be
-renamed to only `learning` because of the `"sidecarChanges": { "TaskName": "learning" }` field.
+renamed to only `learning` because of the `"sidecar_changes": { "TaskName": "learning" }` field.
 
 ## Multiple config files
 

diff --git a/docs/how-to/use-advanced-commands.md b/docs/how-to/use-advanced-commands.md
@@ -195,7 +195,7 @@ It means you don't have to add the field in the config file like this.
 
 ```
 {
-     "sidecarChanges": {
+     "sidecar_changes": {
         "TaskName": "learning"
     }
 }

diff --git a/docs/tutorial/first-steps.md b/docs/tutorial/first-steps.md
@@ -807,7 +807,7 @@ task name:
       "criteria": {
         "SeriesDescription": "Axial EPI-FMRI (Interleaved I to S)*"
       },
-      "sidecarChanges": {
+      "sidecar_changes": {
         "TaskName": "rest"
       }
     }
@@ -835,7 +835,7 @@ task name:
           "criteria": {
             "SeriesDescription": "*Axial EPI-FMRI (Interleaved I to S)*"
           },
-          "sidecarChanges": {
+          "sidecar_changes": {
             "TaskName": "rest"
           }
         }
@@ -892,7 +892,7 @@ file with the appropriate info.
       "criteria": {
         "SeriesDescription": "Axial EPI-FMRI (Interleaved I to S)*"
       },
-      "sidecarChanges": {
+      "sidecar_changes": {
         "TaskName": "rest"
       }
     },

diff --git a/example/config.json b/example/config.json
@@ -55,7 +55,7 @@
             "criteria": {
                 "SeriesDescription": "rs_fMRI"
             },
-            "sidecarChanges": {
+            "sidecar_changes": {
                 "SeriesDescription": "rsfMRI"
             }
         },

diff --git a/tests/data/config_test.json b/tests/data/config_test.json
@@ -8,7 +8,7 @@
             "criteria": {
                 "SeriesDescription": "locali*"
             },
-            "sidecarChanges": {
+            "sidecar_changes": {
                 "ProcedureStepDescription": "Modify by dcm2bids"
             }
         },
@@ -46,7 +46,7 @@
                 "EchoNumber": 1,
                 "EchoTime": 0.00492
             },
-            "sidecarChanges": {
+            "sidecar_changes": {
                 "IntendedFor": ["id_dwi", "T1", "dummy"]
             }
         },
@@ -59,7 +59,7 @@
                 "EchoTime": 0.00738,
                 "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND"]
             },
-            "sidecarChanges": {
+            "sidecar_changes": {
                 "IntendedFor": "id_dwi"
             }
         },
@@ -70,7 +70,7 @@
             "criteria": {
                 "SeriesDescription": "DTI_FA"
             },
-            "sidecarChanges": {
+            "sidecar_changes": {
                 "IntendedFor": ["id_dwi", "T1"]
             }
         },

diff --git a/tests/data/config_test_auto_extract.json b/tests/data/config_test_auto_extract.json
@@ -39,7 +39,7 @@
             "criteria": {
                 "SeriesDescription": "gre_field_mapping"
             },
-            "sidecarChanges": { 
+            "sidecar_changes": { 
                 "IntendedFor": ["id_dwi", "T1", "dummy"]
             }
         },
@@ -50,7 +50,7 @@
             "criteria": {
                 "SeriesDescription": "DTI_FA"
             },
-            "sidecarChanges": { 
+            "sidecar_changes": { 
                 "IntendedFor": ["id_dwi", "T1"] 
             }
         }
-Original file line number
+Diff line change
@@ Expand Up @@
     ```
     {
-         "sidecarChanges": {
+         "sidecar_changes": {
             "TaskName": "learning"
         }
     }
@@ Expand Down @@