junifer 0.0.6.dev227__py3-none-any.whl → 0.0.6.dev252__py3-none-any.whl

junifer/preprocess/warping/_ants_warper.py

@@ -6,7 +6,6 @@
 from typing import (
     Any,
     ClassVar,
-    Dict,
 )
 
 import nibabel as nib
@@ -15,7 +14,7 @@ import numpy as np
 from ...data import get_template, get_xfm
 from ...pipeline import WorkDirManager
 from ...typing import Dependencies, ExternalDependencies
-from ...utils import logger, run_ext_cmd
+from ...utils import logger, raise_error, run_ext_cmd
 
 
 __all__ = ["ANTsWarper"]
@@ -40,10 +39,10 @@ class ANTsWarper:
 
     def preprocess(
         self,
-        input: Dict[str, Any],
-        extra_input: Dict[str, Any],
+        input: dict[str, Any],
+        extra_input: dict[str, Any],
         reference: str,
-    ) -> Dict[str, Any]:
+    ) -> dict[str, Any]:
         """Preprocess using ANTs.
 
         Parameters
@@ -63,6 +62,11 @@ class ANTsWarper:
             values and new ``reference_path`` key whose value points to the
             reference file used for warping.
 
+        Raises
+        ------
+        RuntimeError
+            If warp file path could not be found in ``extra_input``.
+
         """
         # Create element-specific tempdir for storing post-warping assets
         element_tempdir = WorkDirManager().get_element_tempdir(
@@ -77,6 +81,17 @@ class ANTsWarper:
             # resolution
             resolution = np.min(input["data"].header.get_zooms()[:3])
 
+            # Get warp file path
+            warp_file_path = None
+            for entry in extra_input["Warp"]:
+                if entry["dst"] == "native":
+                    warp_file_path = entry["path"]
+            if warp_file_path is None:
+                raise_error(
+                    klass=RuntimeError,
+                    msg="Could not find correct warp file path",
+                )
+
             # Create a tempfile for resampled reference output
             resample_image_out_path = (
                 element_tempdir / "resampled_reference.nii.gz"
@@ -105,7 +120,7 @@ class ANTsWarper:
                 f"-i {input['path'].resolve()}",
                 # use resampled reference
                 f"-r {resample_image_out_path.resolve()}",
-                f"-t {extra_input['Warp']['path'].resolve()}",
+                f"-t {warp_file_path.resolve()}",
                 f"-o {apply_transforms_out_path.resolve()}",
             ]
             # Call antsApplyTransforms
@@ -115,6 +130,8 @@ class ANTsWarper:
             input["data"] = nib.load(apply_transforms_out_path)
             # Save resampled reference path
             input["reference_path"] = resample_image_out_path
+            # Keep pre-warp space for further operations
+            input["prewarp_space"] = input["space"]
             # Use reference input's space as warped input's space
             input["space"] = extra_input["T1w"]["space"]
 
@@ -163,6 +180,9 @@ class ANTsWarper:
 
             # Modify target data
             input["data"] = nib.load(warped_output_path)
+            # Keep pre-warp space for further operations
+            input["prewarp_space"] = input["space"]
+            # Update warped input's space
             input["space"] = reference
 
         return input

junifer/preprocess/warping/_fsl_warper.py

@@ -6,7 +6,6 @@
 from typing import (
     Any,
     ClassVar,
-    Dict,
 )
 
 import nibabel as nib
@@ -14,7 +13,7 @@ import numpy as np
 
 from ...pipeline import WorkDirManager
 from ...typing import Dependencies, ExternalDependencies
-from ...utils import logger, run_ext_cmd
+from ...utils import logger, raise_error, run_ext_cmd
 
 
 __all__ = ["FSLWarper"]
@@ -39,9 +38,9 @@ class FSLWarper:
 
     def preprocess(
         self,
-        input: Dict[str, Any],
-        extra_input: Dict[str, Any],
-    ) -> Dict[str, Any]:
+        input: dict[str, Any],
+        extra_input: dict[str, Any],
+    ) -> dict[str, Any]:
         """Preprocess using FSL.
 
         Parameters
@@ -59,6 +58,11 @@ class FSLWarper:
             values and new ``reference_path`` key whose value points to the
             reference file used for warping.
 
+        Raises
+        ------
+        RuntimeError
+            If warp file path could not be found in ``extra_input``.
+
         """
         logger.debug("Using FSL for space warping")
 
@@ -66,6 +70,16 @@ class FSLWarper:
         # resolution
         resolution = np.min(input["data"].header.get_zooms()[:3])
 
+        # Get warp file path
+        warp_file_path = None
+        for entry in extra_input["Warp"]:
+            if entry["dst"] == "native":
+                warp_file_path = entry["path"]
+        if warp_file_path is None:
+            raise_error(
+                klass=RuntimeError, msg="Could not find correct warp file path"
+            )
+
         # Create element-specific tempdir for storing post-warping assets
         element_tempdir = WorkDirManager().get_element_tempdir(
             prefix="fsl_warper"
@@ -93,7 +107,7 @@ class FSLWarper:
             "--interp=spline",
             f"-i {input['path'].resolve()}",
             f"-r {flirt_out_path.resolve()}",  # use resampled reference
-            f"-w {extra_input['Warp']['path'].resolve()}",
+            f"-w {warp_file_path.resolve()}",
             f"-o {applywarp_out_path.resolve()}",
         ]
         # Call applywarp
@@ -103,7 +117,8 @@ class FSLWarper:
         input["data"] = nib.load(applywarp_out_path)
         # Save resampled reference path
         input["reference_path"] = flirt_out_path
-
+        # Keep pre-warp space for further operations
+        input["prewarp_space"] = input["space"]
         # Use reference input's space as warped input's space
         input["space"] = extra_input["T1w"]["space"]
 

junifer/preprocess/warping/space_warper.py

@@ -3,7 +3,7 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, ClassVar, Dict, List, Optional, Tuple, Union
+from typing import Any, ClassVar, Optional, Union
 
 from templateflow import api as tflow
 
@@ -24,11 +24,12 @@ class SpaceWarper(BasePreprocessor):
 
     Parameters
     ----------
-    using : {"fsl", "ants"}
+    using : {"fsl", "ants", "auto"}
         Implementation to use for warping:
 
         * "fsl" : Use FSL's ``applywarp``
         * "ants" : Use ANTs' ``antsApplyTransforms``
+        * "auto" : Auto-select tool when ``reference="T1w"``
 
     reference : str
         The data type to use as reference for warping, can be either a data
@@ -56,10 +57,14 @@ class SpaceWarper(BasePreprocessor):
             "using": "ants",
             "depends_on": ANTsWarper,
         },
+        {
+            "using": "auto",
+            "depends_on": [FSLWarper, ANTsWarper],
+        },
     ]
 
     def __init__(
-        self, using: str, reference: str, on: Union[List[str], str]
+        self, using: str, reference: str, on: Union[list[str], str]
     ) -> None:
         """Initialize the class."""
         # Validate `using` parameter
@@ -89,7 +94,7 @@ class SpaceWarper(BasePreprocessor):
         else:
             raise_error(f"Unknown reference: {self.reference}")
 
-    def get_valid_inputs(self) -> List[str]:
+    def get_valid_inputs(self) -> list[str]:
         """Get valid data types for input.
 
         Returns
@@ -130,9 +135,9 @@ class SpaceWarper(BasePreprocessor):
 
     def preprocess(
         self,
-        input: Dict[str, Any],
-        extra_input: Optional[Dict[str, Any]] = None,
-    ) -> Tuple[Dict[str, Any], Optional[Dict[str, Dict[str, Any]]]]:
+        input: dict[str, Any],
+        extra_input: Optional[dict[str, Any]] = None,
+    ) -> tuple[dict[str, Any], Optional[dict[str, dict[str, Any]]]]:
         """Preprocess.
 
         Parameters
@@ -156,14 +161,16 @@ class SpaceWarper(BasePreprocessor):
             If ``extra_input`` is None when transforming to native space
             i.e., using ``"T1w"`` as reference.
         RuntimeError
-            If the data is in the correct space and does not require
+            If warper could not be found in ``extra_input`` when
+            ``using="auto"`` or
+            if the data is in the correct space and does not require
             warping or
-            if FSL is used for template space warping.
+            if FSL is used when ``reference="T1w"``.
 
         """
         logger.info(f"Warping to {self.reference} space using SpaceWarper")
         # Transform to native space
-        if self.using in ["fsl", "ants"] and self.reference == "T1w":
+        if self.using in ["fsl", "ants", "auto"] and self.reference == "T1w":
             # Check for extra inputs
             if extra_input is None:
                 raise_error(
@@ -182,6 +189,26 @@ class SpaceWarper(BasePreprocessor):
                     extra_input=extra_input,
                     reference=self.reference,
                 )
+            elif self.using == "auto":
+                warper = None
+                for entry in extra_input["Warp"]:
+                    if entry["dst"] == "native":
+                        warper = entry["warper"]
+                if warper is None:
+                    raise_error(
+                        klass=RuntimeError, msg="Could not find correct warper"
+                    )
+                if warper == "fsl":
+                    input = FSLWarper().preprocess(
+                        input=input,
+                        extra_input=extra_input,
+                    )
+                elif warper == "ants":
+                    input = ANTsWarper().preprocess(
+                        input=input,
+                        extra_input=extra_input,
+                        reference=self.reference,
+                    )
         # Transform to template space with ANTs possible
         elif self.using == "ants" and self.reference != "T1w":
             # Check pre-requirements for space manipulation

junifer/preprocess/warping/tests/test_space_warper.py

@@ -4,7 +4,6 @@
 # License: AGPL
 
 import socket
-from typing import Tuple, Type
 
 import pytest
 from numpy.testing import assert_array_equal, assert_raises
@@ -29,7 +28,7 @@ from junifer.typing import DataGrabberLike
 def test_SpaceWarper_errors(
     using: str,
     reference: str,
-    error_type: Type[Exception],
+    error_type: type[Exception],
     error_msg: str,
 ) -> None:
     """Test SpaceWarper errors.
@@ -96,7 +95,7 @@ def test_SpaceWarper_errors(
     reason="only for juseless",
 )
 def test_SpaceWarper_native(
-    datagrabber: DataGrabberLike, element: Tuple[str, ...], using: str
+    datagrabber: DataGrabberLike, element: tuple[str, ...], using: str
 ) -> None:
     """Test SpaceWarper for native space warping.
 
@@ -160,7 +159,7 @@ def test_SpaceWarper_native(
 )
 def test_SpaceWarper_multi_mni(
     datagrabber: DataGrabberLike,
-    element: Tuple[str, ...],
+    element: tuple[str, ...],
     space: str,
 ) -> None:
     """Test SpaceWarper for MNI space warping.

junifer/stats.py

@@ -4,7 +4,7 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, Callable, Dict, List, Optional
+from typing import Any, Callable, Optional
 
 import numpy as np
 from scipy.stats import mode, trim_mean
@@ -17,7 +17,7 @@ __all__ = ["get_aggfunc_by_name", "count", "winsorized_mean", "select"]
 
 
 def get_aggfunc_by_name(
-    name: str, func_params: Optional[Dict[str, Any]] = None
+    name: str, func_params: Optional[dict[str, Any]] = None
 ) -> Callable:
     """Get an aggregation function by its name.
 
@@ -169,8 +169,8 @@ def winsorized_mean(
 def select(
     data: np.ndarray,
     axis: int = 0,
-    pick: Optional[List[int]] = None,
-    drop: Optional[List[int]] = None,
+    pick: Optional[list[int]] = None,
+    drop: Optional[list[int]] = None,
 ) -> np.ndarray:
     """Select a subset of the data.
 

junifer/storage/base.py

@@ -5,8 +5,9 @@
 # License: AGPL
 
 from abc import ABC, abstractmethod
+from collections.abc import Iterable
 from pathlib import Path
-from typing import Any, Dict, Iterable, List, Optional, Union
+from typing import Any, Optional, Union
 
 import numpy as np
 import pandas as pd
@@ -43,7 +44,7 @@ class BaseFeatureStorage(ABC):
     def __init__(
         self,
         uri: Union[str, Path],
-        storage_types: Union[List[str], str],
+        storage_types: Union[list[str], str],
         single_output: bool = True,
     ) -> None:
         self.uri = uri
@@ -61,7 +62,7 @@ class BaseFeatureStorage(ABC):
         self._valid_inputs = storage_types
         self.single_output = single_output
 
-    def get_valid_inputs(self) -> List[str]:
+    def get_valid_inputs(self) -> list[str]:
         """Get valid storage types for input.
 
         Returns
@@ -76,7 +77,7 @@ class BaseFeatureStorage(ABC):
             klass=NotImplementedError,
         )
 
-    def validate(self, input_: List[str]) -> None:
+    def validate(self, input_: list[str]) -> None:
         """Validate the input to the pipeline step.
 
         Parameters
@@ -98,7 +99,7 @@ class BaseFeatureStorage(ABC):
             )
 
     @abstractmethod
-    def list_features(self) -> Dict[str, Dict[str, Any]]:
+    def list_features(self) -> dict[str, dict[str, Any]]:
         """List the features in the storage.
 
         Returns
@@ -119,8 +120,8 @@ class BaseFeatureStorage(ABC):
         self,
         feature_name: Optional[str] = None,
         feature_md5: Optional[str] = None,
-    ) -> Dict[
-        str, Union[str, List[Union[int, str, Dict[str, str]]], np.ndarray]
+    ) -> dict[
+        str, Union[str, list[Union[int, str, dict[str, str]]], np.ndarray]
     ]:
         """Read stored feature.
 
@@ -169,7 +170,7 @@ class BaseFeatureStorage(ABC):
         )
 
     @abstractmethod
-    def store_metadata(self, meta_md5: str, element: Dict, meta: Dict) -> None:
+    def store_metadata(self, meta_md5: str, element: dict, meta: dict) -> None:
         """Store metadata.
 
         Parameters
@@ -229,7 +230,7 @@ class BaseFeatureStorage(ABC):
     def store_matrix(
         self,
         meta_md5: str,
-        element: Dict,
+        element: dict,
         data: np.ndarray,
         col_names: Optional[Iterable[str]] = None,
         row_names: Optional[Iterable[str]] = None,
@@ -271,8 +272,8 @@ class BaseFeatureStorage(ABC):
     def store_vector(
         self,
         meta_md5: str,
-        element: Dict,
-        data: Union[np.ndarray, List],
+        element: dict,
+        data: Union[np.ndarray, list],
         col_names: Optional[Iterable[str]] = None,
     ) -> None:
         """Store vector.
@@ -297,7 +298,7 @@ class BaseFeatureStorage(ABC):
     def store_timeseries(
         self,
         meta_md5: str,
-        element: Dict,
+        element: dict,
         data: np.ndarray,
         col_names: Optional[Iterable[str]] = None,
     ) -> None:
@@ -323,7 +324,7 @@ class BaseFeatureStorage(ABC):
     def store_scalar_table(
         self,
         meta_md5: str,
-        element: Dict,
+        element: dict,
         data: np.ndarray,
         col_names: Optional[Iterable[str]] = None,
         row_names: Optional[Iterable[str]] = None,

junifer/storage/hdf5.py

@@ -6,8 +6,9 @@
 
 
 from collections import defaultdict
+from collections.abc import Iterable
 from pathlib import Path
-from typing import Any, Dict, Iterable, List, Optional, Union
+from typing import Any, Optional, Union
 
 import numpy as np
 import pandas as pd
@@ -30,7 +31,7 @@ __all__ = ["HDF5FeatureStorage"]
 
 
 def _create_chunk(
-    chunk_data: List[np.ndarray],
+    chunk_data: list[np.ndarray],
     kind: str,
     element_count: int,
     chunk_size: int,
@@ -164,7 +165,7 @@ class HDF5FeatureStorage(BaseFeatureStorage):
         self.force_float32 = force_float32
         self.chunk_size = chunk_size
 
-    def get_valid_inputs(self) -> List[str]:
+    def get_valid_inputs(self) -> list[str]:
         """Get valid storage types for input.
 
         Returns
@@ -176,7 +177,7 @@ class HDF5FeatureStorage(BaseFeatureStorage):
         """
         return ["matrix", "vector", "timeseries", "scalar_table"]
 
-    def _fetch_correct_uri_for_io(self, element: Optional[Dict]) -> str:
+    def _fetch_correct_uri_for_io(self, element: Optional[dict]) -> str:
         """Return proper URI for I/O based on `element`.
 
         If `element` is None, will return `self.uri`.
@@ -210,8 +211,8 @@ class HDF5FeatureStorage(BaseFeatureStorage):
         return f"{self.uri.parent}/{prefix}{self.uri.name}"  # type: ignore
 
     def _read_metadata(
-        self, element: Optional[Dict[str, str]] = None
-    ) -> Dict[str, Dict[str, Any]]:
+        self, element: Optional[dict[str, str]] = None
+    ) -> dict[str, dict[str, Any]]:
         """Read metadata (should not be called directly).
 
         Parameters
@@ -261,7 +262,7 @@ class HDF5FeatureStorage(BaseFeatureStorage):
 
         return metadata
 
-    def list_features(self) -> Dict[str, Dict[str, Any]]:
+    def list_features(self) -> dict[str, dict[str, Any]]:
         """List the features in the storage.
 
         Returns
@@ -281,8 +282,8 @@ class HDF5FeatureStorage(BaseFeatureStorage):
         return metadata
 
     def _read_data(
-        self, md5: str, element: Optional[Dict[str, str]] = None
-    ) -> Dict[str, Any]:
+        self, md5: str, element: Optional[dict[str, str]] = None
+    ) -> dict[str, Any]:
         """Read data (should not be called directly).
 
         Parameters
@@ -338,8 +339,8 @@ class HDF5FeatureStorage(BaseFeatureStorage):
         self,
         feature_name: Optional[str] = None,
         feature_md5: Optional[str] = None,
-    ) -> Dict[
-        str, Union[str, List[Union[int, str, Dict[str, str]]], np.ndarray]
+    ) -> dict[
+        str, Union[str, list[Union[int, str, dict[str, str]]], np.ndarray]
     ]:
         """Read stored feature.
 
@@ -562,7 +563,7 @@ class HDF5FeatureStorage(BaseFeatureStorage):
         return df
 
     def _write_processed_data(
-        self, fname: str, processed_data: Dict[str, Any], title: str
+        self, fname: str, processed_data: dict[str, Any], title: str
     ) -> None:
         """Write processed data to HDF5 (should not be called directly).
 
@@ -594,8 +595,8 @@ class HDF5FeatureStorage(BaseFeatureStorage):
     def store_metadata(
         self,
         meta_md5: str,
-        element: Dict[str, str],
-        meta: Dict[str, Any],
+        element: dict[str, str],
+        meta: dict[str, Any],
     ) -> None:
         """Store metadata.
 
@@ -655,7 +656,7 @@ class HDF5FeatureStorage(BaseFeatureStorage):
         self,
         kind: str,
         meta_md5: str,
-        element: List[Dict[str, str]],
+        element: list[dict[str, str]],
         data: np.ndarray,
         **kwargs: Any,
     ) -> None:
@@ -797,7 +798,7 @@ class HDF5FeatureStorage(BaseFeatureStorage):
     def store_matrix(
         self,
         meta_md5: str,
-        element: Dict[str, str],
+        element: dict[str, str],
         data: np.ndarray,
         col_names: Optional[Iterable[str]] = None,
         row_names: Optional[Iterable[str]] = None,
@@ -876,8 +877,8 @@ class HDF5FeatureStorage(BaseFeatureStorage):
     def store_vector(
         self,
         meta_md5: str,
-        element: Dict[str, str],
-        data: Union[np.ndarray, List],
+        element: dict[str, str],
+        data: Union[np.ndarray, list],
         col_names: Optional[Iterable[str]] = None,
     ) -> None:
         """Store vector.
@@ -919,7 +920,7 @@ class HDF5FeatureStorage(BaseFeatureStorage):
     def store_timeseries(
         self,
         meta_md5: str,
-        element: Dict[str, str],
+        element: dict[str, str],
         data: np.ndarray,
         col_names: Optional[Iterable[str]] = None,
     ) -> None:
@@ -949,7 +950,7 @@ class HDF5FeatureStorage(BaseFeatureStorage):
     def store_scalar_table(
         self,
         meta_md5: str,
-        element: Dict,
+        element: dict,
         data: np.ndarray,
         col_names: Optional[Iterable[str]] = None,
         row_names: Optional[Iterable[str]] = None,

junifer/storage/pandas_base.py

@@ -5,8 +5,9 @@
 # License: AGPL
 
 import json
+from collections.abc import Iterable
 from pathlib import Path
-from typing import Dict, Iterable, List, Optional, Union
+from typing import Optional, Union
 
 import numpy as np
 import pandas as pd
@@ -44,7 +45,7 @@ class PandasBaseFeatureStorage(BaseFeatureStorage):
     ) -> None:
         super().__init__(uri=uri, single_output=single_output, **kwargs)
 
-    def get_valid_inputs(self) -> List[str]:
+    def get_valid_inputs(self) -> list[str]:
         """Get valid storage types for input.
 
         Returns
@@ -56,7 +57,7 @@ class PandasBaseFeatureStorage(BaseFeatureStorage):
         """
         return ["matrix", "vector", "timeseries"]
 
-    def _meta_row(self, meta: Dict, meta_md5: str) -> pd.DataFrame:
+    def _meta_row(self, meta: dict, meta_md5: str) -> pd.DataFrame:
         """Convert the metadata to a pandas DataFrame.
 
         Parameters
@@ -80,7 +81,7 @@ class PandasBaseFeatureStorage(BaseFeatureStorage):
 
     @staticmethod
     def element_to_index(
-        element: Dict, n_rows: int = 1, rows_col_name: Optional[str] = None
+        element: dict, n_rows: int = 1, rows_col_name: Optional[str] = None
     ) -> Union[pd.Index, pd.MultiIndex]:
         """Convert the element metadata to index.
 
@@ -101,7 +102,7 @@ class PandasBaseFeatureStorage(BaseFeatureStorage):
 
         """
         # Make mapping between element access keys and values
-        elem_idx: Dict[str, Iterable[str]] = {
+        elem_idx: dict[str, Iterable[str]] = {
             k: [v] * n_rows for k, v in element.items()
         }
 
@@ -129,7 +130,7 @@ class PandasBaseFeatureStorage(BaseFeatureStorage):
         return index
 
     def store_df(
-        self, meta_md5: str, element: Dict, df: Union[pd.DataFrame, pd.Series]
+        self, meta_md5: str, element: dict, df: Union[pd.DataFrame, pd.Series]
     ) -> None:
         """Implement pandas DataFrame storing.
 
@@ -157,8 +158,8 @@ class PandasBaseFeatureStorage(BaseFeatureStorage):
     def _store_2d(
         self,
         meta_md5: str,
-        element: Dict,
-        data: Union[np.ndarray, List],
+        element: dict,
+        data: Union[np.ndarray, list],
         col_names: Optional[Iterable[str]] = None,
         rows_col_name: Optional[str] = None,
     ) -> None:
@@ -194,8 +195,8 @@ class PandasBaseFeatureStorage(BaseFeatureStorage):
     def store_vector(
         self,
         meta_md5: str,
-        element: Dict,
-        data: Union[np.ndarray, List],
+        element: dict,
+        data: Union[np.ndarray, list],
         col_names: Optional[Iterable[str]] = None,
     ) -> None:
         """Store vector.
@@ -232,7 +233,7 @@ class PandasBaseFeatureStorage(BaseFeatureStorage):
     def store_timeseries(
         self,
         meta_md5: str,
-        element: Dict,
+        element: dict,
         data: np.ndarray,
         col_names: Optional[Iterable[str]] = None,
     ) -> None: