add caps_directory option in get-labels (#416)

* add caps_directory option in get-labels

* add block announce for clinicadl 1.3.0

* fix conflicts

clinicadl/tsvtools/get_labels/get_labels.py

@@ -249,6 +249,7 @@ def get_labels(
     missing_mods: Path = None,
     remove_unique_session: bool = False,
     output_dir: Path = None,
+    caps_directory: Path = None,
 ):
     """
     Writes one TSV file based on merged_tsv and missing_mods.
@@ -299,6 +300,7 @@ def get_labels(
             "missing_mods": missing_mods,
             "merged_tsv": merged_tsv,
             "remove_unique_session": remove_unique_session,
+            "caps_directory": caps_directory,
         },
         filename="labels.json",
     )
@@ -328,8 +330,8 @@ def get_labels(
         check_bids_folder(bids_directory)
         create_merge_file(
             bids_directory,
-            output_dir / "merged.tsv",
-            caps_dir=None,
+            merged_tsv,
+            caps_dir=caps_directory,
             pipelines=None,
             ignore_scan_files=None,
             ignore_sessions_files=None,

clinicadl/tsvtools/get_labels/get_labels_cli.py

@@ -11,6 +11,7 @@
 @cli_param.option.diagnoses
 @cli_param.option.modality
 @cli_param.option.variables_of_interest
+@cli_param.option.caps_directory
 @click.option(
     "--restriction_tsv",
     help="Path to a TSV file containing the sessions that can be included.",
@@ -54,6 +55,7 @@ def cli(
     missing_mods,
     merged_tsv,
     remove_unique_session,
+    caps_directory,
 ):
     """Get labels in a tsv file.
 
@@ -84,6 +86,7 @@ def cli(
         merged_tsv=merged_tsv,
         remove_unique_session=remove_unique_session,
         output_dir=results_tsv,
+        caps_directory=caps_directory,
     )
 
 

clinicadl/tsvtools/get_labels/old_get_labels_cli.py

@@ -10,6 +10,7 @@
 @cli_param.option.diagnoses
 @cli_param.option.modality
 @cli_param.option.variables_of_interest
+@cli_param.option.caps_directory
 @click.option(
     "--restriction_tsv",
     help="Path to a TSV file containing the sessions that can be included.",
@@ -52,6 +53,7 @@ def cli(
     missing_mods,
     merged_tsv,
     remove_unique_session,
+    caps_directory,
 ):
     """Get labels in a tsv file.
 
@@ -88,6 +90,7 @@ def cli(
         missing_mods=missing_mods,
         merged_tsv=merged_tsv,
         remove_unique_session=remove_unique_session,
+        caps_directory=caps_directory,
     )
 
 

docs/overrides/main.html

@@ -8,5 +8,5 @@
 {% endblock %}
 
 {% block announce %}
-<center> ClinicaDL 1.2.0 is now available 🎉! </center>
+<center> ClinicaDL 1.3.0 is now available 🎉! </center>
 {% endblock %}