reorganize architecture

clinicadl/utils/callbacks/callbacks.py → clinicadl/callbacks/callbacks.py

@@ -127,14 +127,14 @@ def on_train_end(self, parameters, **kwargs):
 class Tracker(Callback):
     def on_train_begin(self, parameters, **kwargs):
         if parameters["track_exp"] == "wandb":
-            from clinicadl.utils.tracking_exp import WandB_handler
+            from clinicadl.callbacks.tracking_exp import WandB_handler
 
             self.run = WandB_handler(
                 kwargs["split"], parameters, kwargs["maps_path"].name
             )
 
         if parameters["track_exp"] == "mlflow":
-            from clinicadl.utils.tracking_exp import Mlflow_handler
+            from clinicadl.callbacks.tracking_exp import Mlflow_handler
 
             self.run = Mlflow_handler(
                 kwargs["split"], parameters, kwargs["maps_path"].name

clinicadl/config/config/callbacks.py → clinicadl/callbacks/config.py

@@ -7,8 +7,8 @@
 from pydantic import BaseModel, ConfigDict, computed_field, field_validator
 from pydantic.types import NonNegativeFloat, NonNegativeInt, PositiveFloat, PositiveInt
 
+from clinicadl.preprocessing.preprocessing import read_preprocessing
 from clinicadl.utils.enum import ExperimentTracking
-from clinicadl.utils.preprocessing import read_preprocessing
 
 logger = getLogger("clinicadl.callbacks_config")
 

clinicadl/cmdline.py

@@ -1,17 +1,19 @@
 # coding: utf8
 import click
 
-from clinicadl.generate.generate_cli import cli as generate_cli
-from clinicadl.hugging_face.hugging_face_cli import cli as hf_cli
-from clinicadl.interpret.interpret_cli import cli as interpret_cli
-from clinicadl.predict.predict_cli import cli as predict_cli
-from clinicadl.prepare_data.prepare_data_cli import cli as prepare_data_cli
-from clinicadl.prepare_data.prepare_data_from_bids_cli import (
+from clinicadl.commandline.pipelines.generate.cli import cli as generate_cli
+from clinicadl.commandline.pipelines.interpret.cli import cli as interpret_cli
+from clinicadl.commandline.pipelines.predict.cli import cli as predict_cli
+from clinicadl.commandline.pipelines.prepare_data.prepare_data_cli import (
+    cli as prepare_data_cli,
+)
+from clinicadl.commandline.pipelines.prepare_data.prepare_data_from_bids_cli import (
     cli as prepare_data_from_bids_cli,
 )
+from clinicadl.commandline.pipelines.train.cli import cli as train_cli
+from clinicadl.hugging_face.hugging_face_cli import cli as hf_cli
 from clinicadl.quality_check.qc_cli import cli as qc_cli
 from clinicadl.random_search.random_search_cli import cli as random_search_cli
-from clinicadl.train.train_cli import cli as train_cli
 from clinicadl.tsvtools.cli import cli as tsvtools_cli
 from clinicadl.utils.logger import setup_logging
 

clinicadl/config/options/callbacks.py → clinicadl/commandline/modules_options/callbacks.py

@@ -1,8 +1,8 @@
 import click
 
-from clinicadl.config.config.callbacks import CallbacksConfig
-from clinicadl.utils.config_utils import get_default_from_config_class as get_default
-from clinicadl.utils.config_utils import get_type_from_config_class as get_type
+from clinicadl.callbacks.config import CallbacksConfig
+from clinicadl.config.config_utils import get_default_from_config_class as get_default
+from clinicadl.config.config_utils import get_type_from_config_class as get_type
 
 emissions_calculator = click.option(
     "--calculate_emissions/--dont_calculate_emissions",

clinicadl/config/options/computational.py → clinicadl/commandline/modules_options/computational.py

@@ -1,8 +1,8 @@
 import click
 
 from clinicadl.config.config.computational import ComputationalConfig
-from clinicadl.utils.config_utils import get_default_from_config_class as get_default
-from clinicadl.utils.config_utils import get_type_from_config_class as get_type
+from clinicadl.config.config_utils import get_default_from_config_class as get_default
+from clinicadl.config.config_utils import get_type_from_config_class as get_type
 
 # Computational
 amp = click.option(

clinicadl/config/options/cross_validation.py → clinicadl/commandline/modules_options/cross_validation.py

@@ -1,8 +1,8 @@
 import click
 
 from clinicadl.config.config.cross_validation import CrossValidationConfig
-from clinicadl.utils.config_utils import get_default_from_config_class as get_default
-from clinicadl.utils.config_utils import get_type_from_config_class as get_type
+from clinicadl.config.config_utils import get_default_from_config_class as get_default
+from clinicadl.config.config_utils import get_type_from_config_class as get_type
 
 # Cross Validation
 n_splits = click.option(

clinicadl/config/options/data.py → clinicadl/commandline/modules_options/data.py

@@ -1,8 +1,8 @@
 import click
 
 from clinicadl.config.config.data import DataConfig
-from clinicadl.utils.config_utils import get_default_from_config_class as get_default
-from clinicadl.utils.config_utils import get_type_from_config_class as get_type
+from clinicadl.config.config_utils import get_default_from_config_class as get_default
+from clinicadl.config.config_utils import get_type_from_config_class as get_type
 
 # Data
 baseline = click.option(

clinicadl/config/options/dataloader.py → clinicadl/commandline/modules_options/dataloader.py

@@ -1,8 +1,8 @@
 import click
 
 from clinicadl.config.config.dataloader import DataLoaderConfig
-from clinicadl.utils.config_utils import get_default_from_config_class as get_default
-from clinicadl.utils.config_utils import get_type_from_config_class as get_type
+from clinicadl.config.config_utils import get_default_from_config_class as get_default
+from clinicadl.config.config_utils import get_type_from_config_class as get_type
 
 # DataLoader
 batch_size = click.option(

clinicadl/config/options/early_stopping.py → clinicadl/commandline/modules_options/early_stopping.py

@@ -1,8 +1,8 @@
 import click
 
 from clinicadl.config.config.early_stopping import EarlyStoppingConfig
-from clinicadl.utils.config_utils import get_default_from_config_class as get_default
-from clinicadl.utils.config_utils import get_type_from_config_class as get_type
+from clinicadl.config.config_utils import get_default_from_config_class as get_default
+from clinicadl.config.config_utils import get_type_from_config_class as get_type
 
 # Early Stopping
 patience = click.option(

clinicadl/config/options/maps_manager.py → clinicadl/commandline/modules_options/maps_manager.py

@@ -1,7 +1,7 @@
 import click
 
 from clinicadl.config.config.maps_manager import MapsManagerConfig
-from clinicadl.utils.config_utils import get_type_from_config_class as get_type
+from clinicadl.config.config_utils import get_type_from_config_class as get_type
 
 maps_dir = click.argument("maps_dir", type=get_type("maps_dir", MapsManagerConfig))
 data_group = click.option("data_group", type=get_type("data_group", MapsManagerConfig))

clinicadl/config/options/modality.py → clinicadl/commandline/modules_options/modality.py

@@ -5,8 +5,8 @@
     DTIModalityConfig,
     PETModalityConfig,
 )
-from clinicadl.utils.config_utils import get_default_from_config_class as get_default
-from clinicadl.utils.config_utils import get_type_from_config_class as get_type
+from clinicadl.config.config_utils import get_default_from_config_class as get_default
+from clinicadl.config.config_utils import get_type_from_config_class as get_type
 
 tracer = click.option(
     "--tracer",

clinicadl/commandline/modules_options/network.py

@@ -0,0 +1,20 @@
+import click
+
+from clinicadl.config.config_utils import get_default_from_config_class as get_default
+from clinicadl.config.config_utils import get_type_from_config_class as get_type
+from clinicadl.network.config import NetworkConfig
+
+# Model
+multi_network = click.option(
+    "--multi_network/--single_network",
+    default=get_default("multi_network", NetworkConfig),
+    help="If provided uses a multi-network framework.",
+    show_default=True,
+)
+dropout = click.option(
+    "--dropout",
+    type=get_type("dropout", NetworkConfig),
+    default=get_default("dropout", NetworkConfig),
+    help="Rate value applied to dropout layers in a CNN architecture.",
+    show_default=True,
+)

clinicadl/config/options/optimization.py → clinicadl/commandline/modules_options/optimization.py

@@ -1,8 +1,8 @@
 import click
 
-from clinicadl.config.config.optimization import OptimizationConfig
-from clinicadl.utils.config_utils import get_default_from_config_class as get_default
-from clinicadl.utils.config_utils import get_type_from_config_class as get_type
+from clinicadl.config.config_utils import get_default_from_config_class as get_default
+from clinicadl.config.config_utils import get_type_from_config_class as get_type
+from clinicadl.optimizer.optimization import OptimizationConfig
 
 # Optimization
 accumulation_steps = click.option(

clinicadl/config/options/optimizer.py → clinicadl/commandline/modules_options/optimizer.py

@@ -1,8 +1,8 @@
 import click
 
-from clinicadl.config.config.optimizer import OptimizerConfig
-from clinicadl.utils.config_utils import get_default_from_config_class as get_default
-from clinicadl.utils.config_utils import get_type_from_config_class as get_type
+from clinicadl.config.config_utils import get_default_from_config_class as get_default
+from clinicadl.config.config_utils import get_type_from_config_class as get_type
+from clinicadl.optimizer.optimizer import OptimizerConfig
 
 # Optimizer
 learning_rate = click.option(

clinicadl/config/options/preprocessing.py → clinicadl/commandline/modules_options/preprocessing.py

@@ -1,8 +1,8 @@
 import click
 
-from clinicadl.config.config.preprocessing import PreprocessingConfig
-from clinicadl.utils.config_utils import get_default_from_config_class as get_default
-from clinicadl.utils.config_utils import get_type_from_config_class as get_type
+from clinicadl.config.config_utils import get_default_from_config_class as get_default
+from clinicadl.config.config_utils import get_type_from_config_class as get_type
+from clinicadl.preprocessing.config import PreprocessingConfig
 
 extract_json = click.option(
     "-ej",

clinicadl/config/options/reproducibility.py → clinicadl/commandline/modules_options/reproducibility.py

@@ -1,8 +1,8 @@
 import click
 
 from clinicadl.config.config.reproducibility import ReproducibilityConfig
-from clinicadl.utils.config_utils import get_default_from_config_class as get_default
-from clinicadl.utils.config_utils import get_type_from_config_class as get_type
+from clinicadl.config.config_utils import get_default_from_config_class as get_default
+from clinicadl.config.config_utils import get_type_from_config_class as get_type
 
 # Reproducibility
 compensation = click.option(

clinicadl/config/options/ssda.py → clinicadl/commandline/modules_options/ssda.py

@@ -1,8 +1,8 @@
 import click
 
 from clinicadl.config.config.ssda import SSDAConfig
-from clinicadl.utils.config_utils import get_default_from_config_class as get_default
-from clinicadl.utils.config_utils import get_type_from_config_class as get_type
+from clinicadl.config.config_utils import get_default_from_config_class as get_default
+from clinicadl.config.config_utils import get_type_from_config_class as get_type
 
 # SSDA
 caps_target = click.option(

clinicadl/config/options/transforms.py → clinicadl/commandline/modules_options/transforms.py

@@ -1,8 +1,8 @@
 import click
 
-from clinicadl.config.config.transforms import TransformsConfig
-from clinicadl.utils.config_utils import get_default_from_config_class as get_default
-from clinicadl.utils.config_utils import get_type_from_config_class as get_type
+from clinicadl.config.config_utils import get_default_from_config_class as get_default
+from clinicadl.config.config_utils import get_type_from_config_class as get_type
+from clinicadl.transforms.config import TransformsConfig
 
 # Transform
 data_augmentation = click.option(

clinicadl/config/options/validation.py → clinicadl/commandline/modules_options/validation.py

@@ -1,8 +1,8 @@
 import click
 
 from clinicadl.config.config.validation import ValidationConfig
-from clinicadl.utils.config_utils import get_default_from_config_class as get_default
-from clinicadl.utils.config_utils import get_type_from_config_class as get_type
+from clinicadl.config.config_utils import get_default_from_config_class as get_default
+from clinicadl.config.config_utils import get_type_from_config_class as get_type
 
 # Validation
 valid_longitudinal = click.option(

clinicadl/commandline/pipelines/generate/__init__.py

@@ -0,0 +1,7 @@
+from . import (
+    random,
+    shepplogan,
+    trivial,
+)
+from .artifacts import options
+from .hypometabolic import options

clinicadl/generate/generate_artifacts_cli.py → clinicadl/commandline/pipelines/generate/artifacts/cli.py

@@ -12,7 +12,7 @@
 from clinicadl.utils.clinica_utils import clinicadl_file_reader
 from clinicadl.utils.maps_manager.iotools import commandline_to_json
 
-from .generate_utils import (
+from .....generate.generate_utils import (
     find_file_type,
     load_and_check_tsv,
     write_missing_mods,

clinicadl/config/options/generate/artifacts.py → clinicadl/commandline/pipelines/generate/artifacts/options.py

@@ -1,8 +1,8 @@
 import click
 
+from clinicadl.config.config_utils import get_default_from_config_class as get_default
+from clinicadl.config.config_utils import get_type_from_config_class as get_type
 from clinicadl.generate.generate_config import GenerateArtifactsConfig
-from clinicadl.utils.config_utils import get_default_from_config_class as get_default
-from clinicadl.utils.config_utils import get_type_from_config_class as get_type
 
 contrast = click.option(
     "--contrast/--no-contrast",

clinicadl/generate/generate_cli.py → clinicadl/commandline/pipelines/generate/cli.py

@@ -1,10 +1,20 @@
 import click
 
-from clinicadl.generate.generate_artifacts_cli import cli as generate_artifacts_cli
-from clinicadl.generate.generate_hypometabolic_cli import cli as generate_hypo_cli
-from clinicadl.generate.generate_random_cli import cli as generate_random_cli
-from clinicadl.generate.generate_shepplogan_cli import cli as generate_shepplogan_cli
-from clinicadl.generate.generate_trivial_cli import cli as generate_trivial_cli
+from clinicadl.commandline.pipelines.generate.artifacts.cli import (
+    cli as generate_artifacts_cli,
+)
+from clinicadl.commandline.pipelines.generate.hypometabolic.cli import (
+    cli as generate_hypo_cli,
+)
+from clinicadl.commandline.pipelines.generate.random.cli import (
+    cli as generate_random_cli,
+)
+from clinicadl.commandline.pipelines.generate.shepplogan.cli import (
+    cli as generate_shepplogan_cli,
+)
+from clinicadl.commandline.pipelines.generate.trivial.cli import (
+    cli as generate_trivial_cli,
+)
 
 
 class RegistrationOrderGroup(click.Group):

clinicadl/generate/generate_hypometabolic_cli.py → clinicadl/commandline/pipelines/generate/hypometabolic/cli.py

@@ -9,6 +9,7 @@
 
 from clinicadl.generate import generate_param
 from clinicadl.generate.generate_config import GenerateHypometabolicConfig
+from clinicadl.tsvtools.tsvtools_utils import extract_baseline
 from clinicadl.utils.caps_dataset.data import CapsDataset
 from clinicadl.utils.clinica_utils import (
     RemoteFileStructure,
@@ -22,9 +23,8 @@
 )
 from clinicadl.utils.exceptions import DownloadError
 from clinicadl.utils.maps_manager.iotools import commandline_to_json
-from clinicadl.utils.tsvtools_utils import extract_baseline
 
-from .generate_utils import (
+from .....generate.generate_utils import (
     find_file_type,
     load_and_check_tsv,
     mask_processing,

clinicadl/config/options/generate/hypometabolic.py → clinicadl/commandline/pipelines/generate/hypometabolic/options.py

@@ -1,8 +1,8 @@
 import click
 
+from clinicadl.config.config_utils import get_default_from_config_class as get_default
+from clinicadl.config.config_utils import get_type_from_config_class as get_type
 from clinicadl.generate.generate_config import GenerateHypometabolicConfig
-from clinicadl.utils.config_utils import get_default_from_config_class as get_default
-from clinicadl.utils.config_utils import get_type_from_config_class as get_type
 
 pathology = click.option(
     "--pathology",

clinicadl/generate/generate_random_cli.py → clinicadl/commandline/pipelines/generate/random/cli.py

@@ -9,15 +9,14 @@
 
 from clinicadl.generate import generate_param
 from clinicadl.generate.generate_config import GenerateRandomConfig
-from clinicadl.utils.caps_dataset.data import CapsDataset
-from clinicadl.utils.clinica_utils import clinicadl_file_reader
-from clinicadl.utils.maps_manager.iotools import commandline_to_json
-
-from .generate_utils import (
+from clinicadl.generate.generate_utils import (
     find_file_type,
     load_and_check_tsv,
     write_missing_mods,
 )
+from clinicadl.utils.caps_dataset.data import CapsDataset
+from clinicadl.utils.clinica_utils import clinicadl_file_reader
+from clinicadl.utils.maps_manager.iotools import commandline_to_json
 
 logger = getLogger("clinicadl.generate.random")
 

clinicadl/config/options/generate/random.py → clinicadl/commandline/pipelines/generate/random/options.py

@@ -1,8 +1,8 @@
 import click
 
+from clinicadl.config.config_utils import get_default_from_config_class as get_default
+from clinicadl.config.config_utils import get_type_from_config_class as get_type
 from clinicadl.generate.generate_config import GenerateRandomConfig
-from clinicadl.utils.config_utils import get_default_from_config_class as get_default
-from clinicadl.utils.config_utils import get_type_from_config_class as get_type
 
 mean = click.option(
     "--mean",

clinicadl/generate/generate_shepplogan_cli.py → clinicadl/commandline/pipelines/generate/shepplogan/cli.py

@@ -8,10 +8,10 @@
 
 from clinicadl.generate import generate_param
 from clinicadl.generate.generate_config import GenerateSheppLoganConfig
+from clinicadl.preprocessing.preprocessing import write_preprocessing
 from clinicadl.utils.maps_manager.iotools import check_and_clean, commandline_to_json
-from clinicadl.utils.preprocessing import write_preprocessing
 
-from .generate_utils import (
+from .....generate.generate_utils import (
     generate_shepplogan_phantom,
     write_missing_mods,
 )

clinicadl/config/options/generate/shepplogan.py → clinicadl/commandline/pipelines/generate/shepplogan/options.py

@@ -2,9 +2,9 @@
 
 import click
 
+from clinicadl.config.config_utils import get_default_from_config_class as get_default
+from clinicadl.config.config_utils import get_type_from_config_class as get_type
 from clinicadl.generate.generate_config import GenerateSheppLoganConfig
-from clinicadl.utils.config_utils import get_default_from_config_class as get_default
-from clinicadl.utils.config_utils import get_type_from_config_class as get_type
 
 extract_json = click.option(
     "-ej",