update import for trainer and generate

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

@@ -8,15 +8,14 @@
 
 from clinicadl.generate import generate_param
 from clinicadl.generate.generate_config import GenerateArtifactsConfig
-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.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.artifacts")
 

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

@@ -9,6 +9,12 @@
 
 from clinicadl.generate import generate_param
 from clinicadl.generate.generate_config import GenerateHypometabolicConfig
+from clinicadl.generate.generate_utils import (
+    find_file_type,
+    load_and_check_tsv,
+    mask_processing,
+    write_missing_mods,
+)
 from clinicadl.tsvtools.tsvtools_utils import extract_baseline
 from clinicadl.utils.caps_dataset.data import CapsDataset
 from clinicadl.utils.clinica_utils import (
@@ -24,13 +30,6 @@
 from clinicadl.utils.exceptions import DownloadError
 from clinicadl.utils.maps_manager.iotools import commandline_to_json
 
-from .....generate.generate_utils import (
-    find_file_type,
-    load_and_check_tsv,
-    mask_processing,
-    write_missing_mods,
-)
-
 logger = getLogger("clinicadl.generate.hypometabolic")
 
 

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

@@ -8,13 +8,12 @@
 
 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 .....generate.generate_utils import (
+from clinicadl.generate.generate_utils import (
     generate_shepplogan_phantom,
     write_missing_mods,
 )
+from clinicadl.preprocessing.preprocessing import write_preprocessing
+from clinicadl.utils.maps_manager.iotools import check_and_clean, commandline_to_json
 
 logger = getLogger("clinicadl.generate.shepplogan")
 

clinicadl/commandline/pipelines/train/from_json/cli.py

@@ -24,7 +24,7 @@ def cli(**kwargs):
 
     OUTPUT_MAPS_DIRECTORY is the path to the MAPS folder where outputs and results will be saved.
     """
-    from clinicadl.train.trainer import Trainer
+    from clinicadl.trainer.trainer import Trainer
     from clinicadl.utils.maps_manager.maps_manager_utils import read_json
 
     logger = getLogger("clinicadl")

clinicadl/commandline/pipelines/train/regression/regression_cli.py

@@ -20,8 +20,8 @@
     transforms,
     validation,
 )
-from clinicadl.train.trainer import Trainer
 from clinicadl.train.utils import merge_cli_and_config_file_options
+from clinicadl.trainer.trainer import Trainer
 from clinicadl.utils.enum import Task
 
 

clinicadl/commandline/pipelines/train/resume/cli.py

@@ -14,6 +14,6 @@ def cli(input_maps_directory, split):
 
     INPUT_MAPS_DIRECTORY is the path to the MAPS folder where training job has started.
     """
-    from ....train.resume.resume import automatic_resume
+    from clinicadl.train.resume.resume import automatic_resume
 
     automatic_resume(input_maps_directory, user_split_list=split)

clinicadl/random_search/random_search.py

@@ -4,7 +4,7 @@
 
 from pathlib import Path
 
-from clinicadl.train.trainer import Trainer
+from clinicadl.trainer.trainer import Trainer
 
 from .random_search_config import RandomSearchConfig, create_training_config
 from .random_search_utils import get_space_dict, random_sampling

clinicadl/random_search/random_search_config.py

@@ -14,7 +14,7 @@
 from clinicadl.utils.enum import Normalization, Pooling, Task
 
 if TYPE_CHECKING:
-    from clinicadl.train.trainer import TrainConfig
+    from clinicadl.trainer.trainer import TrainConfig
 
 
 class RandomSearchConfig(