first commit

clinicadl/resources/config/train_config.toml

@@ -61,6 +61,7 @@ use_extracted_features = false
 multi_cohort = false
 diagnoses = ["AD", "CN"]
 baseline = false
+valid_longitudinal = false
 normalize = true
 data_augmentation = false
 sampler = "random"

clinicadl/train/tasks/classification_cli.py

@@ -31,6 +31,7 @@
 @train_option.multi_cohort
 @train_option.diagnoses
 @train_option.baseline
+@train_option.valid_longitudinal
 @train_option.normalize
 @train_option.data_augmentation
 @train_option.sampler

clinicadl/train/tasks/reconstruction_cli.py

@@ -31,6 +31,7 @@
 @train_option.multi_cohort
 @train_option.diagnoses
 @train_option.baseline
+@train_option.valid_longitudinal
 @train_option.normalize
 @train_option.data_augmentation
 @train_option.sampler

clinicadl/train/tasks/regression_cli.py

@@ -31,6 +31,7 @@
 @train_option.multi_cohort
 @train_option.diagnoses
 @train_option.baseline
+@train_option.valid_longitudinal
 @train_option.normalize
 @train_option.data_augmentation
 @train_option.sampler

clinicadl/train/tasks/task_utils.py

@@ -61,6 +61,7 @@ def task_launcher(network_task: str, task_options_list: List[str], **kwargs):
         "track_exp",
         "transfer_path",
         "transfer_selection_metric",
+        "valid_longitudinal",
         "weight_decay",
         "sampler",
         "seed",

clinicadl/tsvtools/kfold/kfold.py

@@ -60,6 +60,7 @@ def write_splits(
         test_df = baseline_df.iloc[test_index]
         train_df = baseline_df.iloc[train_index]
         long_train_df = retrieve_longitudinal(train_df, diagnosis_df)
+        long_test_df = retrieve_longitudinal(test_df, diagnosis_df)
 
         train_df.reset_index(inplace=True, drop=True)
         test_df.reset_index(inplace=True, drop=True)
@@ -86,6 +87,11 @@ def write_splits(
             sep="\t",
             index=False,
         )
+        long_test_df.to_csv(
+            results_directory / f"split-{i}" / f"{subset_name}.tsv",
+            sep="\t",
+            index=False,
+        )
 
 
 def split_diagnoses(

clinicadl/utils/cli_param/train_option.py

@@ -171,6 +171,12 @@
     default=None,
     help="If provided, only the baseline sessions are used for training.",
 )
+valid_longitudinal = cli_param.option_group.data_group.option(
+    "--valid_longitudinal/--not_valid_longitudinal",
+    type=bool,
+    default=None,
+    help="If provided, not only the baseline sessions are used for validation (careful with this bad habits).",
+)
 normalize = cli_param.option_group.data_group.option(
     "--normalize/--unnormalize",
     type=bool,

clinicadl/utils/split_manager/kfold.py

@@ -11,6 +11,7 @@ def __init__(
         diagnoses,
         n_splits,
         baseline=False,
+        valid_longitudinal=False,
         multi_cohort=False,
         split_list=None,
     ):
@@ -19,6 +20,7 @@ def __init__(
             tsv_path,
             diagnoses,
             baseline,
+            valid_longitudinal,
             multi_cohort,
             split_list,
         )

clinicadl/utils/split_manager/single_split.py

@@ -10,6 +10,7 @@ def __init__(
         tsv_path,
         diagnoses,
         baseline=False,
+        valid_longitudinal=False,
         multi_cohort=False,
         split_list=None,
     ):
@@ -18,6 +19,7 @@ def __init__(
             tsv_path,
             diagnoses,
             baseline,
+            valid_longitudinal,
             multi_cohort,
             split_list,
         )

clinicadl/utils/split_manager/split_manager.py

@@ -21,6 +21,7 @@ def __init__(
         tsv_path: Path,
         diagnoses,
         baseline=False,
+        valid_longitudinal=False,
         multi_cohort=False,
         split_list=None,
     ):
@@ -36,6 +37,8 @@ def __init__(
             List of diagnosis
         baseline: bool
             if True, split only on baseline sessions
+        valid_longitudinal: bool
+            if True, split validation on longitudinal sessions
         multi-cohort: bool
         split_list: List[str]
 
@@ -46,6 +49,7 @@ def __init__(
         self.multi_cohort = multi_cohort
         self.diagnoses = diagnoses
         self.baseline = baseline
+        self.valid_longitudinal = valid_longitudinal
         self.split_list = split_list
 
     @abc.abstractmethod
@@ -139,8 +143,10 @@ def concatenate_diagnoses(
             train_path = train_path / "train_baseline.tsv"
         else:
             train_path = train_path / "train.tsv"
-
-        valid_path = valid_path / "validation_baseline.tsv"
+        if self.valid_longitudinal:
+            valid_path = valid_path / "validation.tsv"
+        else:
+            valid_path = valid_path / "validation_baseline.tsv"
 
         train_df = pd.read_csv(train_path, sep="\t")
         valid_df = pd.read_csv(valid_path, sep="\t")