junifer 0.0.3.dev186__py3-none-any.whl → 0.0.4__py3-none-any.whl

junifer/preprocess/confounds/tests/test_fmriprep_confound_remover.py

@@ -5,9 +5,8 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-import typing
+from typing import List
 
-import nibabel as nib
 import numpy as np
 import pandas as pd
 import pytest
@@ -40,39 +39,62 @@ def test_fMRIPrepConfoundRemover_init() -> None:
         fMRIPrepConfoundRemover(strategy={"motion": "wrong"})
 
 
-def test_fMRIPrepConfoundRemover_validate_input() -> None:
-    """Test fMRIPrepConfoundRemover validate_input."""
-    confound_remover = fMRIPrepConfoundRemover()
+@pytest.mark.parametrize(
+    "input_",
+    [
+        ["T1w"],
+        ["BOLD"],
+        ["T1w", "BOLD"],
+    ],
+)
+def test_fMRIPrepConfoundRemover_validate_input_errors(
+    input_: List[str],
+) -> None:
+    """Test errors for fMRIPrepConfoundRemover validate_input.
 
-    # Input is valid when both BOLD and BOLD_confounds are present
+    Parameters
+    ----------
+    input_ : list of str
+        The input data types.
 
-    input = ["T1w"]
-    with pytest.raises(ValueError, match="not have the required data"):
-        confound_remover.validate_input(input)
+    """
+    confound_remover = fMRIPrepConfoundRemover()
 
-    input = ["BOLD"]
     with pytest.raises(ValueError, match="not have the required data"):
-        confound_remover.validate_input(input)
+        confound_remover.validate_input(input_)
 
-    input = ["BOLD", "T1w"]
-    with pytest.raises(ValueError, match="not have the required data"):
-        confound_remover.validate_input(input)
 
-    input = ["BOLD", "T1w", "BOLD_confounds"]
-    confound_remover.validate_input(input)
+@pytest.mark.parametrize(
+    "input_",
+    [
+        ["BOLD", "BOLD_confounds"],
+        ["T1w", "BOLD", "BOLD_confounds"],
+    ],
+)
+def test_fMRIPrepConfoundRemover_validate_input(input_: List[str]) -> None:
+    """Test fMRIPrepConfoundRemover validate_input.
+
+    Parameters
+    ----------
+    input_ : list of str
+        The input data types.
+
+    """
+    confound_remover = fMRIPrepConfoundRemover()
+    confound_remover.validate_input(input_)
+
+
+def test_fMRIPrepConfoundRemover_get_valid_inputs() -> None:
+    """Test fMRIPrepConfoundRemover get_valid_inputs."""
+    confound_remover = fMRIPrepConfoundRemover()
+    assert confound_remover.get_valid_inputs() == ["BOLD"]
 
 
 def test_fMRIPrepConfoundRemover_get_output_type() -> None:
-    """Test fMRIPrepConfoundRemover validate_input."""
+    """Test fMRIPrepConfoundRemover get_output_type."""
     confound_remover = fMRIPrepConfoundRemover()
-    inputs = [
-        ["BOLD", "T1w", "BOLD_confounds"],
-        ["BOLD", "VBM_GM", "BOLD_confounds"],
-        ["BOLD", "BOLD_confounds"],
-    ]
     # Confound remover works in place
-    for input in inputs:
-        assert confound_remover.get_output_type(input) == input
+    assert confound_remover.get_output_type("BOLD") == "BOLD"
 
 
 def test_fMRIPrepConfoundRemover__map_adhoc_to_fmriprep() -> None:
@@ -259,7 +281,7 @@ def test_fMRIPrepConfoundRemover__pick_confounds_adhoc() -> None:
     assert set(out.columns) == set(fmriprep_all_vars)
 
 
-def test_FMRIPRepConfoundRemover__pick_confounds_fmriprep() -> None:
+def test_fMRIPRepConfoundRemover__pick_confounds_fmriprep() -> None:
     """Test fMRIPrepConfoundRemover pick confounds on fmriprep confounds."""
     confound_remover = fMRIPrepConfoundRemover(
         strategy={"wm_csf": "full"}, spike=0.2
@@ -292,7 +314,7 @@ def test_FMRIPRepConfoundRemover__pick_confounds_fmriprep() -> None:
     assert_frame_equal(out1, out2)
 
 
-def test_FMRIPRepConfoundRemover__pick_confounds_fmriprep_compute() -> None:
+def test_fMRIPRepConfoundRemover__pick_confounds_fmriprep_compute() -> None:
     """Test if fmriprep returns the same derivatives/power2 as we compute."""
 
     confound_remover = fMRIPrepConfoundRemover(strategy={"wm_csf": "full"})
@@ -326,78 +348,80 @@ def test_FMRIPRepConfoundRemover__pick_confounds_fmriprep_compute() -> None:
 def test_fMRIPrepConfoundRemover__validate_data() -> None:
     """Test fMRIPrepConfoundRemover validate data."""
     confound_remover = fMRIPrepConfoundRemover(strategy={"wm_csf": "full"})
-    reader = DefaultDataReader()
+
     with OasisVBMTestingDataGrabber() as dg:
-        input = dg["sub-01"]
-        input = reader.fit_transform(input)
-        new_input = input["VBM_GM"]
+        element_data = DefaultDataReader().fit_transform(dg["sub-01"])
+        vbm = element_data["VBM_GM"]
         with pytest.raises(
             DimensionError, match="incompatible dimensionality"
         ):
-            confound_remover._validate_data(new_input, None)
+            confound_remover._validate_data(vbm, None)
 
     with PartlyCloudyTestingDataGrabber(reduce_confounds=False) as dg:
-        input = dg["sub-01"]
-        input = reader.fit_transform(input)
-        new_input = input["BOLD"]
+        element_data = DefaultDataReader().fit_transform(dg["sub-01"])
+        bold = element_data["BOLD"]
 
         with pytest.raises(ValueError, match="No extra input"):
-            confound_remover._validate_data(new_input, None)
-        with pytest.raises(ValueError, match="No BOLD_confounds provided"):
-            confound_remover._validate_data(new_input, {})
+            confound_remover._validate_data(bold, None)
+        with pytest.raises(
+            ValueError, match="`BOLD_confounds` data type not provided"
+        ):
+            confound_remover._validate_data(bold, {})
         with pytest.raises(
-            ValueError, match="No BOLD_confounds data provided"
+            ValueError, match="`BOLD_confounds.data` not provided"
         ):
-            confound_remover._validate_data(new_input, {"BOLD_confounds": {}})
+            confound_remover._validate_data(bold, {"BOLD_confounds": {}})
 
         extra_input = {
             "BOLD_confounds": {"data": "wrong"},
         }
-        msg = "must be a pandas dataframe"
+        msg = "must be a `pandas.DataFrame`"
         with pytest.raises(ValueError, match=msg):
-            confound_remover._validate_data(new_input, extra_input)
+            confound_remover._validate_data(bold, extra_input)
 
         extra_input = {"BOLD_confounds": {"data": pd.DataFrame()}}
         with pytest.raises(ValueError, match="Image time series and"):
-            confound_remover._validate_data(new_input, extra_input)
+            confound_remover._validate_data(bold, extra_input)
 
         extra_input = {
-            "BOLD_confounds": {"data": input["BOLD_confounds"]["data"]}
+            "BOLD_confounds": {"data": element_data["BOLD_confounds"]["data"]}
         }
-        with pytest.raises(ValueError, match="format must be specified"):
-            confound_remover._validate_data(new_input, extra_input)
+        with pytest.raises(
+            ValueError, match="`BOLD_confounds.format` not provided"
+        ):
+            confound_remover._validate_data(bold, extra_input)
 
         extra_input = {
             "BOLD_confounds": {
-                "data": input["BOLD_confounds"]["data"],
+                "data": element_data["BOLD_confounds"]["data"],
                 "format": "wrong",
             }
         }
-        with pytest.raises(ValueError, match="Invalid confounds format wrong"):
-            confound_remover._validate_data(new_input, extra_input)
+        with pytest.raises(ValueError, match="Invalid confounds format"):
+            confound_remover._validate_data(bold, extra_input)
 
         extra_input = {
             "BOLD_confounds": {
-                "data": input["BOLD_confounds"]["data"],
+                "data": element_data["BOLD_confounds"]["data"],
                 "format": "adhoc",
             }
         }
-        with pytest.raises(ValueError, match="variables names mappings"):
-            confound_remover._validate_data(new_input, extra_input)
+        with pytest.raises(ValueError, match="need to be set"):
+            confound_remover._validate_data(bold, extra_input)
 
         extra_input = {
             "BOLD_confounds": {
-                "data": input["BOLD_confounds"]["data"],
+                "data": element_data["BOLD_confounds"]["data"],
                 "format": "adhoc",
                 "mappings": {},
             }
         }
-        with pytest.raises(ValueError, match="mappings to fmriprep"):
-            confound_remover._validate_data(new_input, extra_input)
+        with pytest.raises(ValueError, match="need to be set"):
+            confound_remover._validate_data(bold, extra_input)
 
         extra_input = {
             "BOLD_confounds": {
-                "data": input["BOLD_confounds"]["data"],
+                "data": element_data["BOLD_confounds"]["data"],
                 "format": "adhoc",
                 "mappings": {
                     "fmriprep": {
@@ -409,11 +433,11 @@ def test_fMRIPrepConfoundRemover__validate_data() -> None:
             }
         }
         with pytest.raises(ValueError, match=r"names: \['wrong'\]"):
-            confound_remover._validate_data(new_input, extra_input)
+            confound_remover._validate_data(bold, extra_input)
 
         extra_input = {
             "BOLD_confounds": {
-                "data": input["BOLD_confounds"]["data"],
+                "data": element_data["BOLD_confounds"]["data"],
                 "format": "adhoc",
                 "mappings": {
                     "fmriprep": {
@@ -425,11 +449,11 @@ def test_fMRIPrepConfoundRemover__validate_data() -> None:
             }
         }
         with pytest.raises(ValueError, match=r"Missing columns: \['wrong'\]"):
-            confound_remover._validate_data(new_input, extra_input)
+            confound_remover._validate_data(bold, extra_input)
 
         extra_input = {
             "BOLD_confounds": {
-                "data": input["BOLD_confounds"]["data"],
+                "data": element_data["BOLD_confounds"]["data"],
                 "format": "adhoc",
                 "mappings": {
                     "fmriprep": {
@@ -440,51 +464,25 @@ def test_fMRIPrepConfoundRemover__validate_data() -> None:
                 },
             }
         }
-        confound_remover._validate_data(new_input, extra_input)
-
-
-def test_fMRIPrepConfoundRemover__remove_confounds() -> None:
-    """Test fMRIPrepConfoundRemover remove confounds."""
-    confound_remover = fMRIPrepConfoundRemover(
-        strategy={"wm_csf": "full"}, spike=0.2
-    )
-    reader = DefaultDataReader()
-    with PartlyCloudyTestingDataGrabber(reduce_confounds=False) as dg:
-        input = dg["sub-01"]
-        input = reader.fit_transform(input)
-        raw_bold = input["BOLD"]["data"]
-        extra_input = {k: v for k, v in input.items() if k != "BOLD"}
-        clean_bold = confound_remover._remove_confounds(
-            input=input["BOLD"], extra_input=extra_input
-        )
-        clean_bold = typing.cast(nib.Nifti1Image, clean_bold)
-        # TODO: Find a better way to test functionality here
-        assert (
-            clean_bold.header.get_zooms()  # type: ignore
-            == raw_bold.header.get_zooms()  # type: ignore
-        )
-        assert clean_bold.get_fdata().shape == raw_bold.get_fdata().shape
-    # TODO: Test confound remover with mask, needs #79 to be implemented
+        confound_remover._validate_data(bold, extra_input)
 
 
 def test_fMRIPrepConfoundRemover_preprocess() -> None:
     """Test fMRIPrepConfoundRemover with all confounds present."""
-
-    # need reader for the data
-    reader = DefaultDataReader()
     # All strategies full, no spike
     confound_remover = fMRIPrepConfoundRemover()
 
     with PartlyCloudyTestingDataGrabber(reduce_confounds=False) as dg:
-        input = dg["sub-01"]
-        input = reader.fit_transform(input)
-        orig_bold = input["BOLD"]["data"].get_fdata().copy()
-        pre_input = input["BOLD"]
-        pre_extra_input = {"BOLD_confounds": input["BOLD_confounds"]}
-        key, output = confound_remover.preprocess(pre_input, pre_extra_input)
+        element_data = DefaultDataReader().fit_transform(dg["sub-01"])
+        orig_bold = element_data["BOLD"]["data"].get_fdata().copy()
+        pre_input = element_data["BOLD"]
+        pre_extra_input = {"BOLD_confounds": element_data["BOLD_confounds"]}
+        output, _ = confound_remover.preprocess(pre_input, pre_extra_input)
         trans_bold = output["data"].get_fdata()
         # Transformation is in place
-        assert_array_equal(trans_bold, input["BOLD"]["data"].get_fdata())
+        assert_array_equal(
+            trans_bold, element_data["BOLD"]["data"].get_fdata()
+        )
 
         # Data should have the same shape
         assert orig_bold.shape == trans_bold.shape
@@ -493,25 +491,22 @@ def test_fMRIPrepConfoundRemover_preprocess() -> None:
         assert_raises(
             AssertionError, assert_array_equal, orig_bold, trans_bold
         )
-        assert key == "BOLD"
 
 
 def test_fMRIPrepConfoundRemover_fit_transform() -> None:
     """Test fMRIPrepConfoundRemover with all confounds present."""
-
-    # need reader for the data
-    reader = DefaultDataReader()
     # All strategies full, no spike
     confound_remover = fMRIPrepConfoundRemover()
 
     with PartlyCloudyTestingDataGrabber(reduce_confounds=False) as dg:
-        input = dg["sub-01"]
-        input = reader.fit_transform(input)
-        orig_bold = input["BOLD"]["data"].get_fdata().copy()
-        output = confound_remover.fit_transform(input)
+        element_data = DefaultDataReader().fit_transform(dg["sub-01"])
+        orig_bold = element_data["BOLD"]["data"].get_fdata().copy()
+        output = confound_remover.fit_transform(element_data)
         trans_bold = output["BOLD"]["data"].get_fdata()
         # Transformation is in place
-        assert_array_equal(trans_bold, input["BOLD"]["data"].get_fdata())
+        assert_array_equal(
+            trans_bold, element_data["BOLD"]["data"].get_fdata()
+        )
 
         # Data should have the same shape
         assert orig_bold.shape == trans_bold.shape
@@ -535,6 +530,8 @@ def test_fMRIPrepConfoundRemover_fit_transform() -> None:
         assert t_meta["t_r"] is None
         assert t_meta["masks"] is None
 
+        assert "BOLD_mask" not in output
+
         assert "dependencies" in output["BOLD"]["meta"]
         dependencies = output["BOLD"]["meta"]["dependencies"]
         assert dependencies == {"numpy", "nilearn"}
@@ -542,22 +539,20 @@ def test_fMRIPrepConfoundRemover_fit_transform() -> None:
 
 def test_fMRIPrepConfoundRemover_fit_transform_masks() -> None:
     """Test fMRIPrepConfoundRemover with all confounds present."""
-
-    # need reader for the data
-    reader = DefaultDataReader()
     # All strategies full, no spike
     confound_remover = fMRIPrepConfoundRemover(
         masks={"compute_brain_mask": {"threshold": 0.2}}
     )
 
     with PartlyCloudyTestingDataGrabber(reduce_confounds=False) as dg:
-        input = dg["sub-01"]
-        input = reader.fit_transform(input)
-        orig_bold = input["BOLD"]["data"].get_fdata().copy()
-        output = confound_remover.fit_transform(input)
+        element_data = DefaultDataReader().fit_transform(dg["sub-01"])
+        orig_bold = element_data["BOLD"]["data"].get_fdata().copy()
+        output = confound_remover.fit_transform(element_data)
         trans_bold = output["BOLD"]["data"].get_fdata()
         # Transformation is in place
-        assert_array_equal(trans_bold, input["BOLD"]["data"].get_fdata())
+        assert_array_equal(
+            trans_bold, element_data["BOLD"]["data"].get_fdata()
+        )
 
         # Data should have the same shape
         assert orig_bold.shape == trans_bold.shape

junifer/preprocess/fsl/__init__.py

@@ -0,0 +1,4 @@
+"""Provide imports for fsl sub-package."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL

junifer/preprocess/fsl/apply_warper.py

@@ -0,0 +1,179 @@
+"""Provide class for warping via FSL FLIRT."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+from pathlib import Path
+from typing import (
+    TYPE_CHECKING,
+    Any,
+    ClassVar,
+    Dict,
+    List,
+    Optional,
+    Tuple,
+    Union,
+)
+
+import nibabel as nib
+import numpy as np
+
+from ...pipeline import WorkDirManager
+from ...utils import logger, raise_error, run_ext_cmd
+
+
+if TYPE_CHECKING:
+    from nibabel import Nifti1Image
+
+
+class _ApplyWarper:
+    """Class for warping NIfTI images via FSL FLIRT.
+
+    Wraps FSL FLIRT ``applywarp``.
+
+    Parameters
+    ----------
+    reference : str
+        The data type to use as reference for warping.
+    on : str
+        The data type to use for warping.
+
+    Raises
+    ------
+    ValueError
+        If a list was passed for ``on``.
+
+    """
+
+    _EXT_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, List[str]]]]] = [
+        {
+            "name": "fsl",
+            "commands": ["flirt", "applywarp"],
+        },
+    ]
+
+    def __init__(self, reference: str, on: str) -> None:
+        """Initialize the class."""
+        self.ref = reference
+        # Check only single data type is passed
+        if isinstance(on, list):
+            raise_error("Can only work on single data type, list was passed.")
+        self.on = on
+
+    def _run_applywarp(
+        self,
+        input_data: Dict,
+        ref_path: Path,
+        warp_path: Path,
+    ) -> Tuple["Nifti1Image", Path]:
+        """Run ``applywarp``.
+
+        Parameters
+        ----------
+        input_data : dict
+            The input data.
+        ref_path : pathlib.Path
+            The path to the reference file.
+        warp_path : pathlib.Path
+            The path to the warp file.
+
+        Returns
+        -------
+        Niimg-like object
+            The warped input image.
+        pathlib.Path
+            The path to the resampled reference image.
+
+        """
+        # Get the min of the voxel sizes from input and use it as the
+        # resolution
+        resolution = np.min(input_data["data"].header.get_zooms()[:3])
+
+        # Create element-specific tempdir for storing post-warping assets
+        tempdir = WorkDirManager().get_element_tempdir(prefix="applywarp")
+
+        # Create a tempfile for resampled reference output
+        flirt_out_path = tempdir / "reference_resampled.nii.gz"
+        # Set flirt command
+        flirt_cmd = [
+            "flirt",
+            "-interp spline",
+            f"-in {ref_path.resolve()}",
+            f"-ref {ref_path.resolve()}",
+            f"-applyisoxfm {resolution}",
+            f"-out {flirt_out_path.resolve()}",
+        ]
+        # Call flirt
+        run_ext_cmd(name="flirt", cmd=flirt_cmd)
+
+        # Create a tempfile for warped output
+        applywarp_out_path = tempdir / "input_warped.nii.gz"
+        # Set applywarp command
+        applywarp_cmd = [
+            "applywarp",
+            "--interp=spline",
+            f"-i {input_data['path'].resolve()}",
+            f"-r {flirt_out_path.resolve()}",  # use resampled reference
+            f"-w {warp_path.resolve()}",
+            f"-o {applywarp_out_path.resolve()}",
+        ]
+        # Call applywarp
+        run_ext_cmd(name="applywarp", cmd=applywarp_cmd)
+
+        # Load nifti
+        output_img = nib.load(applywarp_out_path)
+
+        return output_img, flirt_out_path  # type: ignore
+
+    def preprocess(
+        self,
+        input: Dict[str, Any],
+        extra_input: Optional[Dict[str, Any]] = None,
+    ) -> Tuple[str, Dict[str, Any]]:
+        """Preprocess.
+
+        Parameters
+        ----------
+        input : dict
+            A single input from the Junifer Data object in which to preprocess.
+        extra_input : dict, optional
+            The other fields in the Junifer Data object. Must include the
+            ``Warp`` and ``ref`` value's keys.
+
+        Returns
+        -------
+        str
+            The key to store the output in the Junifer Data object.
+        dict
+            The computed result as dictionary. This will be stored in the
+            Junifer Data object under the key ``data`` of the data type.
+
+        Raises
+        ------
+        ValueError
+            If ``extra_input`` is None.
+
+        """
+        logger.debug("Warping via FSL using ApplyWarper")
+        # Check for extra inputs
+        if extra_input is None:
+            raise_error(
+                f"No extra input provided, requires `Warp` and `{self.ref}` "
+                "data types in particular."
+            )
+        # Retrieve data type info to warp
+        to_warp_input = input
+        # Retrieve data type info to use as reference
+        ref_input = extra_input[self.ref]
+        # Retrieve Warp data
+        warp = extra_input["Warp"]
+        # Replace original data with warped data and add resampled reference
+        # path
+        input["data"], input["reference_path"] = self._run_applywarp(
+            input_data=to_warp_input,
+            ref_path=ref_input["path"],
+            warp_path=warp["path"],
+        )
+        # Use reference input's space as warped input's space
+        input["space"] = ref_input["space"]
+        return self.on, input

junifer/preprocess/fsl/tests/test_apply_warper.py

@@ -0,0 +1,45 @@
+"""Provide tests for ApplyWarper."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+import socket
+
+import pytest
+
+from junifer.datagrabber import DataladHCP1200
+from junifer.datareader import DefaultDataReader
+from junifer.pipeline.utils import _check_fsl
+from junifer.preprocess.fsl.apply_warper import _ApplyWarper
+
+
+def test_ApplyWarper_init() -> None:
+    """Test ApplyWarper init."""
+    apply_warper = _ApplyWarper(reference="T1w", on="BOLD")
+    assert apply_warper.ref == "T1w"
+    assert apply_warper.on == "BOLD"
+
+
+@pytest.mark.skipif(_check_fsl() is False, reason="requires FSL to be in PATH")
+@pytest.mark.skipif(
+    socket.gethostname() != "juseless",
+    reason="only for juseless",
+)
+def test_ApplyWarper_preprocess() -> None:
+    """Test ApplyWarper preprocess."""
+    with DataladHCP1200(
+        tasks=["REST1"],
+        phase_encodings=["LR"],
+        ica_fix=True,
+    ) as dg:
+        # Read data
+        element_data = DefaultDataReader().fit_transform(
+            dg[("100206", "REST1", "LR")]
+        )
+        # Preprocess data
+        data_type, data = _ApplyWarper(reference="T1w", on="BOLD").preprocess(
+            input=element_data["BOLD"],
+            extra_input=element_data,
+        )
+        assert isinstance(data_type, str)
+        assert isinstance(data, dict)