junifer 0.0.4.dev493__py3-none-any.whl → 0.0.4.dev530__py3-none-any.whl

junifer/preprocess/fsl/tests/test_apply_warper.py

@@ -3,12 +3,16 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
+import socket
+from pathlib import Path
 from typing import List
 
+import nibabel as nib
 import pytest
 
-# from junifer.datareader import DefaultDataReader
-# from junifer.pipeline.utils import _check_fsl
+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
 
 
@@ -47,27 +51,54 @@ def test_ApplyWarper_get_output_type(input_: List[str]) -> None:
     assert apply_warper.get_output_type(input_) == input_
 
 
-@pytest.mark.skip(reason="requires testing dataset")
-# @pytest.mark.skipif(
-#     _check_fsl() is False, reason="requires fsl to be in PATH"
-# )
+@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__run_applywarp() -> None:
     """Test ApplyWarper _run_applywarp."""
-    # Initialize datareader
-    # reader = DefaultDataReader()
-    # Initialize preprocessor
-    # bold_warper = _ApplyWarper(reference="T1w", on="BOLD")
-    # TODO(synchon): setup datagrabber and run pipeline
-
-
-@pytest.mark.skip(reason="requires testing dataset")
-# @pytest.mark.skipif(
-#     _check_fsl() is False, reason="requires fsl to be in PATH"
-# )
+    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
+        warped_data, resampled_ref_path = _ApplyWarper(
+            reference="T1w", on="BOLD"
+        )._run_applywarp(
+            input_data=element_data["BOLD"],
+            ref_path=element_data["T1w"]["path"],
+            warp_path=element_data["Warp"]["path"],
+        )
+        assert isinstance(warped_data, nib.Nifti1Image)
+        assert isinstance(resampled_ref_path, Path)
+
+
+@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."""
-    # Initialize datareader
-    # reader = DefaultDataReader()
-    # Initialize preprocessor
-    # bold_warper = _ApplyWarper(reference="T1w", on="BOLD")
-    # TODO(synchon): setup datagrabber and run pipeline
+    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)

junifer/preprocess/tests/test_bold_warper.py

@@ -3,15 +3,21 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import List
+import socket
+from typing import TYPE_CHECKING, List, Tuple
 
 import pytest
 
-# from junifer.datareader import DefaultDataReader
-# from junifer.pipeline.utils import _check_fsl
+from junifer.datagrabber import DataladHCP1200, DMCC13Benchmark
+from junifer.datareader import DefaultDataReader
+from junifer.pipeline.utils import _check_ants, _check_fsl
 from junifer.preprocess import BOLDWarper
 
 
+if TYPE_CHECKING:
+    from junifer.datagrabber import BaseDataGrabber
+
+
 def test_BOLDWarper_init() -> None:
     """Test BOLDWarper init."""
     bold_warper = BOLDWarper(reference="T1w")
@@ -45,14 +51,58 @@ def test_BOLDWarper_get_output_type(input_: List[str]) -> None:
     assert bold_warper.get_output_type(input_) == input_
 
 
-@pytest.mark.skip(reason="requires testing dataset")
-# @pytest.mark.skipif(
-#     _check_fsl() is False, reason="requires fsl to be in PATH"
-# )
-def test_BOLDWarper_preprocess() -> None:
-    """Test BOLDWarper preprocess."""
-    # Initialize datareader
-    # reader = DefaultDataReader()
-    # Initialize preprocessor
-    # bold_warper = BOLDWarper(reference="T1w")
-    # TODO(synchon): setup datagrabber and run pipeline
+@pytest.mark.parametrize(
+    "datagrabber, element",
+    [
+        [
+            DMCC13Benchmark(
+                types=["BOLD", "T1w", "Warp"],
+                sessions=["wave1bas"],
+                tasks=["Rest"],
+                phase_encodings=["AP"],
+                runs=["1"],
+                native_t1w=True,
+            ),
+            ("f9057kp", "wave1bas", "Rest", "AP", "1"),
+        ],
+        [
+            DataladHCP1200(
+                tasks=["REST1"],
+                phase_encodings=["LR"],
+                ica_fix=True,
+            ),
+            ("100206", "REST1", "LR"),
+        ],
+    ],
+)
+@pytest.mark.skipif(_check_fsl() is False, reason="requires FSL to be in PATH")
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
+@pytest.mark.skipif(
+    socket.gethostname() != "juseless",
+    reason="only for juseless",
+)
+def test_BOLDWarper_preprocess(
+    datagrabber: "BaseDataGrabber", element: Tuple[str, ...]
+) -> None:
+    """Test BOLDWarper preprocess.
+
+    Parameters
+    ----------
+    datagrabber : DataGrabber-like object
+        The parametrized DataGrabber objects.
+    element : tuple of str
+        The parametrized elements.
+
+    """
+    with datagrabber as dg:
+        # Read data
+        element_data = DefaultDataReader().fit_transform(dg[element])
+        # Preprocess data
+        data_type, data = BOLDWarper(reference="T1w").preprocess(
+            input=element_data["BOLD"],
+            extra_input=element_data,
+        )
+        assert data_type == "BOLD"
+        assert isinstance(data, dict)

junifer/utils/__init__.py

@@ -6,3 +6,4 @@
 
 from .fs import make_executable
 from .logging import configure_logging, logger, raise_error, warn_with_log
+from .helpers import run_ext_cmd

junifer/utils/helpers.py

@@ -0,0 +1,53 @@
+"""Provide helper functions for the package."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+import subprocess
+from typing import List
+
+from .logging import logger, raise_error
+
+
+def run_ext_cmd(name: str, cmd: List[str]) -> None:
+    """Run external command via subprocess.
+
+    Parameters
+    ----------
+    name : str
+        The name of the command.
+    cmd : list of str
+        The command to run as list of string.
+
+    Raises
+    ------
+    RuntimeError
+        If command fails.
+
+    """
+    # Convert list to str
+    cmd_str = " ".join(cmd)
+    logger.info(f"{name} command to be executed:\n{cmd_str}")
+    # Run command via subprocess
+    process = subprocess.run(
+        cmd_str,  # string needed with shell=True
+        stdin=subprocess.DEVNULL,
+        stdout=subprocess.PIPE,
+        stderr=subprocess.STDOUT,
+        shell=True,  # needed for respecting $PATH
+        check=False,
+    )
+    # Check for success or failure
+    if process.returncode == 0:
+        logger.info(
+            f"{name} command succeeded with the following output:\n"
+            f"{process.stdout}"
+        )
+    else:
+        raise_error(
+            msg=(
+                f"{name} command failed with the following error:\n"
+                f"{process.stdout}"
+            ),
+            klass=RuntimeError,
+        )

junifer/utils/tests/test_helpers.py

@@ -0,0 +1,35 @@
+"""Provide tests for helper functions."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+import logging
+
+import pytest
+
+from junifer.utils.helpers import run_ext_cmd
+
+
+def test_run_ext_cmd_success(caplog: pytest.LogCaptureFixture) -> None:
+    """Test external command run success.
+
+    Parameters
+    ----------
+    caplog : pytest.LogCaptureFixture
+        The pytest.LogCaptureFixture object.
+
+    """
+    # Set log capturing at INFO
+    with caplog.at_level(logging.INFO):
+        # Run external command
+        run_ext_cmd(name="pwd", cmd=["pwd"])
+        # Check logging message
+        assert "executed" in caplog.text
+        assert "succeeded" in caplog.text
+
+
+def test_run_ext_cmd_failure() -> None:
+    """Test external command run failure."""
+    with pytest.raises(RuntimeError, match="failed"):
+        # Run external command
+        run_ext_cmd(name="flymetothemoon", cmd=["flymetothemoon"])

{junifer-0.0.4.dev493.dist-info → junifer-0.0.4.dev530.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.4.dev493
+Version: 0.0.4.dev530
 Summary: JUelich NeuroImaging FEature extractoR
 Author-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
 Maintainer-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>

{junifer-0.0.4.dev493.dist-info → junifer-0.0.4.dev530.dist-info}/RECORD

@@ -1,5 +1,5 @@
 junifer/__init__.py,sha256=x1UR2jUcrUdm2HNl-3Qvyi4UUrU6ms5qm2qcmNY7zZk,391
-junifer/_version.py,sha256=s3b4obIT6-Dm0gw7Hf_6VelPhsN39hihLhhrnI_A6sU,428
+junifer/_version.py,sha256=UAZSywn04AiXQwVQkUu_X6dPMnW5TVCTZAN98gzqfqU,428
 junifer/stats.py,sha256=sU5IZ2qFZWbzgSutQS_z42miIVItpSGmQYBn6KkD5fA,6162
 junifer/api/__init__.py,sha256=YILu9M7SC0Ri4CVd90fELH2OnK_gvCYAXCoqBNCFE8E,257
 junifer/api/cli.py,sha256=xScav2mF-Jr8JjVFt8kaHuLpX5l_jVTaQGPgQL3VNvA,12881
@@ -13,6 +13,7 @@ junifer/api/res/afni/3dRSFC,sha256=MkPtS_nKEoJOHDAT3ZP9IA-SvMdhyzZDiyxObV_XI3g,4
 junifer/api/res/afni/3dReHo,sha256=Jb5B97iPPPQ14zAz7tK5BVG4jPZyOe9c6kgM6ixKaY8,44
 junifer/api/res/afni/afni,sha256=idLvNWHwd6P4jWXfk6hMXQckdpcTJYbvnLC3uNP6sBg,42
 junifer/api/res/afni/run_afni_docker.sh,sha256=_MHr4oEfnjvFEegx8VWl3S0Js0KioySvtJfdxyea0JE,1130
+junifer/api/res/ants/ResampleImage,sha256=oJKZ31rBAW20ETozB8Ub5SbXMuhmZfrerpJTnRu-hOY,51
 junifer/api/res/ants/antsApplyTransforms,sha256=SqlQEJ2RMMw_qGyDaNTXKzQqO7Bvrm6y5SEPmyqHiYc,57
 junifer/api/res/ants/antsApplyTransformsToPoints,sha256=lqyvQGo8oI-RNpNlRqz-BvLHh7Th5HQgsDZjHF6nEeI,65
 junifer/api/res/ants/run_ants_docker.sh,sha256=d6lZ9CCPP3nsCALhW4T4tI67gyUSiM4AuXj5JPKTLtA,1119
@@ -41,9 +42,9 @@ junifer/configs/juseless/datagrabbers/tests/test_ixi_vbm.py,sha256=8jxpNZelXwpJG
 junifer/configs/juseless/datagrabbers/tests/test_ucla.py,sha256=e-jdvcZ9B0mka6_573JJU_cGwSaUV54U8X_n0UadtJY,3351
 junifer/configs/juseless/datagrabbers/tests/test_ukb_vbm.py,sha256=b9hjc1mgO--PSRC3id2EzzfE2yWNsuZ2UI47a6sfGZU,1025
 junifer/data/__init__.py,sha256=oUjOs8_M6fitNb44izxpXf3su1e4pG_vCdjwVYkjZjQ,550
-junifer/data/coordinates.py,sha256=rwjPb6hYlCpxqM73UNatl7bLtXEF9o8nIEwXz1iwERE,11317
-junifer/data/masks.py,sha256=gsA8_1l011uq2E0hRZvQvfk3_ER8HFsmWd3h6o5qPxE,17311
-junifer/data/parcellations.py,sha256=wL8lkAYYvg7NDt160EA8N_xFjK8ZtDwoXYJQHNHwbDU,55805
+junifer/data/coordinates.py,sha256=GcL95_wzW5t4iNNmRbgD6IwwH-ERMChJK3kWfZ3ORDc,12701
+junifer/data/masks.py,sha256=81v3GhAf9lc_CobV9f6n_vMK1jWZCbeANmopa02XZOQ,17744
+junifer/data/parcellations.py,sha256=72Gv7Rn5Ppyi2z7m9t9cuwS62yocXEL_bG2uoFUyWww,56211
 junifer/data/utils.py,sha256=K9quLIoWRmm2QFM8Rdy_5bYsWb_XhL0l5Uq_1Sie0kA,1274
 junifer/data/VOIs/meta/CogAC_VOIs.txt,sha256=Sr5_E712OLdeQRyUcDNM0wLBvZIyO6gc9Q7KkyJHX1A,398
 junifer/data/VOIs/meta/CogAR_VOIs.txt,sha256=t3NLwEVUZTPP34p15SaB3UInLrQyK-7Qc4iLBuQlZu8,189
@@ -134,7 +135,7 @@ junifer/markers/complexity/tests/test_sample_entropy.py,sha256=3IeDnDgSeFNmUoPxQ
 junifer/markers/complexity/tests/test_weighted_perm_entropy.py,sha256=M7Qt_SFZSmptMi0cBGh5Merd1_3hPieIddl_pz7MWbs,2088
 junifer/markers/falff/__init__.py,sha256=QAUIVtaOFWDL7B8xFrDgsmRum7Q0DCENyDYD1cPMJmM,197
 junifer/markers/falff/falff_base.py,sha256=isHD643TvDFg7YJxpopHSrpJlgUwx2fW0tzJeSio6c8,6323
-junifer/markers/falff/falff_estimator.py,sha256=ayXdQWHUyYyeR7NulOPZpYXkjQ2V8HlbHhy-jDKtZI0,12869
+junifer/markers/falff/falff_estimator.py,sha256=U56sp9wfo5T-MOQN79XSiwj3113x-z8wFIMIwrP5KME,11905
 junifer/markers/falff/falff_parcels.py,sha256=UTADrIl96eO_xZ90LtOIt7tuN2eLDPnfIJghr9HAO88,4550
 junifer/markers/falff/falff_spheres.py,sha256=XR2pcBRxjyTZ-J7j_HOjL20_2IHgYO0dI9x4LlQFoVE,5086
 junifer/markers/falff/tests/test_falff_estimator.py,sha256=aVnkFvPqA5mTb9dXegwAJPku8Tf-1jWtDkfXhdcjDj8,8259
@@ -155,7 +156,7 @@ junifer/markers/functional_connectivity/tests/test_functional_connectivity_parce
 junifer/markers/functional_connectivity/tests/test_functional_connectivity_spheres.py,sha256=KOaMkLf7CEd1H8A92WpZAy6X6VNf6TADzYqsqXqvV4Q,4278
 junifer/markers/reho/__init__.py,sha256=9IfeAxKEVgMWbhud-8T54Le07I4pR6A29sMKeFtvEPg,189
 junifer/markers/reho/reho_base.py,sha256=d6oxynZ41EGd7f3zorRww6vMtFYF0PjD6RdAVlLq9BA,3932
-junifer/markers/reho/reho_estimator.py,sha256=88Ki-Ysq7MfmODynA_wk-7tvYdggmB_Z5HDa3gaZeoM,19692
+junifer/markers/reho/reho_estimator.py,sha256=vLGQDBs9QMT7E7Oc9e8Jz70CScQ9JmlrDdxbEMAz8WA,17996
 junifer/markers/reho/reho_parcels.py,sha256=Q-gkB9aO0ncxgEQ68XEQKekpLLu_kXiYC6Xqkv8cdvY,6048
 junifer/markers/reho/reho_spheres.py,sha256=ng5JzYorEnYmFVlxRMOMwkLNFsq2FlMN4o95B_BBVo0,6565
 junifer/markers/reho/tests/test_reho_estimator.py,sha256=V_584X3I5a-XXAIs8YtR4TMuSqhMvGd5E1vcoDj8gQA,10168
@@ -190,14 +191,17 @@ junifer/pipeline/tests/test_update_meta_mixin.py,sha256=KiMqiTthXP24NMSyHJKKRhRG
 junifer/pipeline/tests/test_workdir_manager.py,sha256=E1WY4C-GDsx2c49sePqr1WR_Y3nZ1kiRn4Veu506uTs,2801
 junifer/preprocess/__init__.py,sha256=-3exohZnw-gJ-MjVM63WcXzBW1mbSetEVozcDfs5etc,342
 junifer/preprocess/base.py,sha256=syiNqI8pUjoGyShZSjs_RTsd5VHhwoqzIfPfFstr4f4,6230
-junifer/preprocess/bold_warper.py,sha256=Sia8mCdluYNrFkYsRx0vP-z_RNF7x-dwHcEDkmpvnHo,3277
+junifer/preprocess/bold_warper.py,sha256=KOYCPCTJE92yI1juXK-3yl7VUxUhbzqqQxJrCYgk-0E,4572
+junifer/preprocess/ants/__init__.py,sha256=Uobmbhh6_gOowkF2hQNSQOh3AYeaXzarBXEcLJzhERE,112
+junifer/preprocess/ants/ants_apply_transforms_warper.py,sha256=V3y9EIGdIeJhJpnEVi123fHTK3R0sv_-OmWY7R_DC1M,6627
+junifer/preprocess/ants/tests/test_ants_apply_transforms_warper.py,sha256=ibLLISss0o0wg3lqpLhL1oO7MfU_bZF5PBqY3OOd9sg,3737
 junifer/preprocess/confounds/__init__.py,sha256=EDlcD9jy8O9xluJr6XOnFXtjGCDVqwg6sDIRDMbM8ZU,235
 junifer/preprocess/confounds/fmriprep_confound_remover.py,sha256=23UJ6miqX0iE3dUMsZ1hzWoJDnMLl6WMlT-k9GFmAAU,21904
 junifer/preprocess/confounds/tests/test_fmriprep_confound_remover.py,sha256=OKACXAHytNrOAFZ5I2UcyfcYz5s2qeu31MZ9K71rWGc,22167
 junifer/preprocess/fsl/__init__.py,sha256=DerGFQ-dIuX5PT9a_BH6QkIXkJZVymjYy-woXF7tYGc,111
-junifer/preprocess/fsl/apply_warper.py,sha256=QTls4z2oF0qVqZ_S1yc-uYNUE9MeJZR4Lesv98SnJrc,7915
-junifer/preprocess/fsl/tests/test_apply_warper.py,sha256=qDDGeWGkxuthDB7y5f1MBMMMOKco2oz4GIcF6sJli44,2101
-junifer/preprocess/tests/test_bold_warper.py,sha256=PQ0Sg4pwciJFDus4Y-Kt6kGu1w1ETPiqVIa7IlYbd0A,1494
+junifer/preprocess/fsl/apply_warper.py,sha256=_HU1-63A32cSQw9eNdgpKN52BFivn6cZaDa0_at-4UY,6215
+junifer/preprocess/fsl/tests/test_apply_warper.py,sha256=b--MMPlaJw284gJWw-QV8rz6Rb2zmcBjYaY-cb6-uNU,3024
+junifer/preprocess/tests/test_bold_warper.py,sha256=X4rs-IBu_Oe9wF81Xlh6ih9BCu8SUyDm64lXKk-l9Q8,2831
 junifer/preprocess/tests/test_preprocess_base.py,sha256=UHuH_YOK7AU3AfApWqgB6YLG-J669BgztuxNSWCtmtI,2560
 junifer/storage/__init__.py,sha256=QlzBw9UrRhmg_f7zQVas9h313u3sfZIBicA3_0Skm4M,337
 junifer/storage/base.py,sha256=ocFuP2M6ot8EticAc2wZZvp16mKXIYxHFYicSn1d-zE,9653
@@ -221,15 +225,17 @@ junifer/testing/tests/test_spmauditory_datagrabber.py,sha256=1G1emk-Ze59HiNLaYsy
 junifer/testing/tests/test_testing_registry.py,sha256=oerticBaPRaRZm3yANzInLac0Mqph3Y0aZPQFayu7xA,827
 junifer/tests/test_main.py,sha256=GMff7jlisGM9_FsiUwWDte43j-KQJGFRYZpwRRqTkd8,373
 junifer/tests/test_stats.py,sha256=3vPMgYYpWxk8ECDFOMm3-dFBlh4XxjL83SwRBSBAHok,4155
-junifer/utils/__init__.py,sha256=ZDPU9ezSKawAJhb-3T67jDf-16QEyF6e7ONyu-lnBtQ,277
+junifer/utils/__init__.py,sha256=sFpsDKbPPtoU3Db3OSO9Vo45u4yE7UfocNaBtD-qvdk,310
 junifer/utils/fs.py,sha256=Jd9AoV2fIF7pT7KhXsn8T1O1fJ1_SFZgaFuOBAM7DG8,460
+junifer/utils/helpers.py,sha256=Hp3yGZa9x659BCqFTd4keEU1gbHXNAbJ1_lHG1M6lwI,1338
 junifer/utils/logging.py,sha256=4kH8j9X_J2bMdnBJMldVF95C5sURa5UAsLmSgRaD9Ig,9117
 junifer/utils/tests/test_fs.py,sha256=WQS7cKlKEZ742CIuiOYYpueeAhY9PqlastfDVpVVtvE,923
+junifer/utils/tests/test_helpers.py,sha256=k5qqfxK8dFyuewTJyR1Qn6-nFaYNuVr0ysc18bfPjyU,929
 junifer/utils/tests/test_logging.py,sha256=l8oo-AiBV7H6_IzlsNcj__cLeZBUvgIGoaMszD9VaJg,7754
-junifer-0.0.4.dev493.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
-junifer-0.0.4.dev493.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
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