junifer 0.0.6.dev422__py3-none-any.whl → 0.0.6.dev445__py3-none-any.whl

junifer/data/template_spaces.py

@@ -6,22 +6,18 @@
 from pathlib import Path
 from typing import Any, Optional, Union
 
-import datalad.api as dl
 import nibabel as nib
 import numpy as np
-from datalad.support.exceptions import IncompleteResultsError
 from templateflow import api as tflow
 
 from ..utils import logger, raise_error
-from .utils import closest_resolution
+from .utils import check_dataset, closest_resolution, fetch_file_via_datalad
 
 
 __all__ = ["get_template", "get_xfm"]
 
 
-def get_xfm(
-    src: str, dst: str, xfms_dir: Union[str, Path, None] = None
-) -> Path:  # pragma: no cover
+def get_xfm(src: str, dst: str) -> Path:  # pragma: no cover
     """Fetch warp files to convert from ``src`` to ``dst``.
 
     Parameters
@@ -30,94 +26,24 @@ def get_xfm(
         The template space to transform from.
     dst : str
         The template space to transform to.
-    xfms_dir : str or pathlib.Path, optional
-        Path where the retrieved transformation files are stored.
-        The default location is "$HOME/junifer/data/xfms" (default None).
 
     Returns
     -------
     pathlib.Path
         The path to the transformation file.
 
-    Raises
-    ------
-    RuntimeError
-        If there is a problem cloning the xfm dataset or
-        if there is a problem fetching the xfm file.
-
     """
-    # Set default path for storage
-    if xfms_dir is None:
-        xfms_dir = Path().home() / "junifer" / "data" / "xfms"
-
-    # Convert str to Path
-    if not isinstance(xfms_dir, Path):
-        xfms_dir = Path(xfms_dir)
-
-    # Check if the template xfms dataset is installed at storage path
-    is_installed = dl.Dataset(xfms_dir).is_installed()
-    # Use existing dataset
-    if is_installed:
-        logger.debug(
-            f"Found existing template xfms dataset at: {xfms_dir.resolve()}"
-        )
-        # Set dataset
-        dataset = dl.Dataset(xfms_dir)
-    # Clone a fresh copy
-    else:
-        logger.debug(f"Cloning template xfms dataset to: {xfms_dir.resolve()}")
-        # Clone dataset
-        try:
-            dataset = dl.clone(
-                "https://github.com/juaml/human-template-xfms.git",
-                path=xfms_dir,
-                result_renderer="disabled",
-            )
-        except IncompleteResultsError as e:
-            raise_error(
-                msg=f"Failed to clone dataset: {e.failed}",
-                klass=RuntimeError,
-            )
-        else:
-            logger.debug(
-                f"Successfully cloned template xfms dataset to: "
-                f"{xfms_dir.resolve()}"
-            )
-
+    # Get dataset
+    dataset = check_dataset()
     # Set file path to retrieve
     xfm_file_path = (
-        xfms_dir / "xfms" / f"{src}_to_{dst}" / f"{src}_to_{dst}_Composite.h5"
+        dataset.pathobj
+        / "xfms"
+        / f"{src}_to_{dst}"
+        / f"{src}_to_{dst}_Composite.h5"
     )
-
     # Retrieve file
-    try:
-        got = dataset.get(xfm_file_path, result_renderer="disabled")
-    except IncompleteResultsError as e:
-        raise_error(
-            msg=f"Failed to get file from dataset: {e.failed}",
-            klass=RuntimeError,
-        )
-    else:
-        file_path = Path(got[0]["path"])
-        # Conditional logging based on file fetch
-        status = got[0]["status"]
-        if status == "ok":
-            logger.info(
-                f"Successfully fetched xfm file for {src} to {dst} at "
-                f"{file_path.resolve()}"
-            )
-            return file_path
-        elif status == "notneeded":
-            logger.info(
-                f"Found existing xfm file for {src} to {dst} at "
-                f"{file_path.resolve()}"
-            )
-            return file_path
-        else:
-            raise_error(
-                f"Failed to fetch xfm file for {src} to {dst} at "
-                f"{file_path.resolve()}"
-            )
+    return fetch_file_via_datalad(dataset=dataset, file_path=xfm_file_path)
 
 
 def get_template(
@@ -190,7 +116,7 @@ def get_template(
 
     logger.info(
         f"Downloading template {space} ({template_type} in "
-        f"resolution {resolution}"
+        f"resolution {resolution})"
     )
     # Retrieve template
     try:
@@ -224,9 +150,11 @@ def get_template(
         )
     except Exception:  # noqa: BLE001
         raise_error(
-            f"Template {space} ({template_type}) with resolution {resolution} "
-            "not found",
+            msg=(
+                f"Template {space} ({template_type}) with resolution "
+                f"{resolution}) not found"
+            ),
             klass=RuntimeError,
         )
     else:
-        return nib.load(template_path)  # type: ignore
+        return nib.load(template_path)

junifer/data/utils.py

@@ -5,14 +5,22 @@
 # License: AGPL
 
 from collections.abc import MutableMapping
+from pathlib import Path
 from typing import Optional, Union
 
+import datalad.api as dl
 import numpy as np
+from datalad.support.exceptions import IncompleteResultsError
 
-from ..utils import logger, raise_error
+from ..utils import config, logger, raise_error
 
 
-__all__ = ["closest_resolution", "get_native_warper"]
+__all__ = [
+    "check_dataset",
+    "closest_resolution",
+    "fetch_file_via_datalad",
+    "get_native_warper",
+]
 
 
 def closest_resolution(
@@ -114,3 +122,96 @@ def get_native_warper(
         )
 
     return possible_warpers[0]
+
+
+def check_dataset() -> dl.Dataset:
+    """Get or install junifer-data dataset.
+
+    Returns
+    -------
+    datalad.api.Dataset
+        The junifer-data dataset.
+
+    Raises
+    ------
+    RuntimeError
+        If there is a problem cloning the dataset.
+
+    """
+    # Check config and set default if not passed
+    data_dir = config.get("data.location")
+    if data_dir is not None:
+        data_dir = Path(data_dir)
+    else:
+        data_dir = Path().home() / "junifer_data"
+
+    # Check if the dataset is installed at storage path;
+    # else clone a fresh copy
+    if dl.Dataset(data_dir).is_installed():
+        logger.debug(f"Found existing junifer-data at: {data_dir.resolve()}")
+        return dl.Dataset(data_dir)
+    else:
+        logger.debug(f"Cloning junifer-data to: {data_dir.resolve()}")
+        # Clone dataset
+        try:
+            dataset = dl.clone(
+                "https://github.com/juaml/junifer-data.git",
+                path=data_dir,
+                result_renderer="disabled",
+            )
+        except IncompleteResultsError as e:
+            raise_error(
+                msg=f"Failed to clone junifer-data: {e.failed}",
+                klass=RuntimeError,
+            )
+        else:
+            logger.debug(
+                f"Successfully cloned junifer-data to: "
+                f"{data_dir.resolve()}"
+            )
+            return dataset
+
+
+def fetch_file_via_datalad(dataset: dl.Dataset, file_path: Path) -> Path:
+    """Fetch `file_path` from `dataset` via datalad.
+
+    Parameters
+    ----------
+    dataset : datalad.api.Dataset
+        The datalad dataset to fetch files from.
+    file_path : pathlib.Path
+        The file path to fetch.
+
+    Returns
+    -------
+    pathlib.Path
+        Resolved fetched file path.
+
+    Raises
+    ------
+    RuntimeError
+        If there is a problem fetching the file.
+
+    """
+    try:
+        got = dataset.get(file_path, result_renderer="disabled")
+    except IncompleteResultsError as e:
+        raise_error(
+            msg=f"Failed to get file from dataset: {e.failed}",
+            klass=RuntimeError,
+        )
+    else:
+        got_path = Path(got[0]["path"])
+        # Conditional logging based on file fetch
+        status = got[0]["status"]
+        if status == "ok":
+            logger.info(f"Successfully fetched file: {got_path.resolve()}")
+            return got_path
+        elif status == "notneeded":
+            logger.debug(f"Found existing file: {got_path.resolve()}")
+            return got_path
+        else:
+            raise_error(
+                msg=f"Failed to fetch file: {got_path.resolve()}",
+                klass=RuntimeError,
+            )

{junifer-0.0.6.dev422.dist-info → junifer-0.0.6.dev445.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: junifer
-Version: 0.0.6.dev422
+Version: 0.0.6.dev445
 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>
@@ -38,7 +38,6 @@ Requires-Dist: nilearn<=0.10.4,>=0.10.3
 Requires-Dist: sqlalchemy<=2.1.0,>=2.0.25
 Requires-Dist: ruamel.yaml<0.19,>=0.17
 Requires-Dist: h5py>=3.10
-Requires-Dist: httpx[http2]<0.28.0,>=0.26.0
 Requires-Dist: tqdm<4.67.0,>=4.66.1
 Requires-Dist: templateflow>=23.0.0
 Requires-Dist: lapy<2.0.0,>=1.0.0

{junifer-0.0.6.dev422.dist-info → junifer-0.0.6.dev445.dist-info}/RECORD

@@ -1,6 +1,6 @@
 junifer/__init__.py,sha256=2McgH1yNue6Z1V26-uN_mfMjbTcx4CLhym-DMBl5xA4,266
 junifer/__init__.pyi,sha256=SsTvgq2Dod6UqJN96GH1lCphH6hJQQurEJHGNhHjGUI,508
-junifer/_version.py,sha256=0SUPdERo7s4t4XnU8IbLMWhY77f3A5mTiz_zmLl7P0w,428
+junifer/_version.py,sha256=BvD--u8WQlVv5BSuYt8l4VpOAPHUHWapEY83eY04RtE,428
 junifer/conftest.py,sha256=PWYkkRDU8ly2lYwv7VBKMHje4et6HX7Yey3Md_I2KbA,613
 junifer/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 junifer/stats.py,sha256=e9aaagMGtgpRfW3Wdpz9ocpnYld1IWylCDcjFUgX9Mk,6225
@@ -48,7 +48,7 @@ junifer/cli/parser.py,sha256=jLinKVcZeuyTnxjB2p5sj8555DO5rcPcWKgZCtgFARY,8498
 junifer/cli/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 junifer/cli/utils.py,sha256=AbPQC0Kl-tHMNKiPxp_01gLAGD3IGoLbsq3rXyPMM-c,3116
 junifer/cli/tests/test_cli.py,sha256=AYL4my12GmFRCbI3JV7-rju32heYxAqbXNwnV8PwqVY,10982
-junifer/cli/tests/test_cli_utils.py,sha256=orbBhWaaIxTgB_JzURYH8CvAYqrwle043zHWoVaj6cM,2746
+junifer/cli/tests/test_cli_utils.py,sha256=f_x0IIzZD8GGnZtVp8vSMywl-BNVdenl2pT79dWqchs,2712
 junifer/cli/tests/test_parser.py,sha256=5A6yI2t9Ou5w--wpEzXY7mdcVMWWFZaTNLPQ6yLU9gI,6113
 junifer/cli/tests/data/gmd_mean.yaml,sha256=Ohb_C5cfQMK-59U9O1ZhejXyBtzLc5Y4cv8QyYq2azg,330
 junifer/cli/tests/data/gmd_mean_htcondor.yaml,sha256=f7NLv_KIJXTiPNFmOWl2Vw8EfwojhfkGtwbh5prbd6w,417
@@ -75,12 +75,12 @@ junifer/data/__init__.pyi,sha256=qYszjUYcbFi_2zO23MnbA2HhTW-Ad2oh1pqPQYd6yt0,542
 junifer/data/_dispatch.py,sha256=O524U1R4MtbGhGJsL0HSh9EqisapBFJWK7uupXrJuMg,6158
 junifer/data/pipeline_data_registry_base.py,sha256=G8bE3WTj4D_rKC4ZKZe6E48Sd96CGea1PS3SxmTgGK4,2010
 junifer/data/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-junifer/data/template_spaces.py,sha256=wkxaDA_I_W5FB42GPxOKrl_A_fp0Crdrh6wFux27_NA,7147
-junifer/data/utils.py,sha256=5r-0QGQCNZvDM1tVcl9xyrIdgAO85mww0plpM1RUaGA,3247
+junifer/data/template_spaces.py,sha256=qa-qPDVF0TqyeY1KnOD5bQ6EY4V5jUBloRn52KIy7s0,4690
+junifer/data/utils.py,sha256=u35ni7lSD5PxmhpHPjZBzzLuYSZQ0Q7lJBdTfWjcgzI,6093
 junifer/data/coordinates/__init__.py,sha256=ffM8rwcHLgHAWixJbKrATrbUKzX940V1UF6RAxZdUMg,186
 junifer/data/coordinates/__init__.pyi,sha256=Z-Ti5XD3HigkZ8uYN6oYsLqw40-F1GvTVQ5QAy08Wng,88
 junifer/data/coordinates/_ants_coordinates_warper.py,sha256=5RWDC-nI3VG9lkSJ-_y_hlDtjPctKSJokQOp3v8ozwY,2956
-junifer/data/coordinates/_coordinates.py,sha256=fBXVvuTxYLTNBSrQiTCiQsxpT0SdbQze3DYuGGgz_mY,12501
+junifer/data/coordinates/_coordinates.py,sha256=khgX0wYThgWGqvkTfVqFkgMtnp3AN9-Lyt5oovAcW_w,13386
 junifer/data/coordinates/_fsl_coordinates_warper.py,sha256=5h7rwiPMYBQlA3sMZUImcpnNLLWvIp2-bAEaaHtzX9c,2409
 junifer/data/coordinates/VOIs/meta/AutobiographicalMemory_VOIs.txt,sha256=9af38naeL18Tlt_gy_ep6vyTAxOB336JYjbo5FvP8PQ,686
 junifer/data/coordinates/VOIs/meta/CogAC_VOIs.txt,sha256=Sr5_E712OLdeQRyUcDNM0wLBvZIyO6gc9Q7KkyJHX1A,398
@@ -101,13 +101,13 @@ junifer/data/coordinates/VOIs/meta/WM_VOIs.txt,sha256=6uyH5nsv9i5bKS_aEYCgg3wgE7
 junifer/data/coordinates/VOIs/meta/eMDN_VOIs.txt,sha256=p5D4GdBuGl1d5IbXhsuj3XIU6UGMxhzCR-T8Dwfxz30,382
 junifer/data/coordinates/VOIs/meta/eSAD_VOIs.txt,sha256=DwgDEFSZoAojG5RP6HpSvlRPpXItBzx8ms-1zoSxKRk,268
 junifer/data/coordinates/VOIs/meta/extDMN_VOIs.txt,sha256=Ogx1QvqZcnXDM3ncF2ha78br8xwQ5wklSjHygtoLpyI,317
-junifer/data/coordinates/tests/test_coordinates.py,sha256=_c2P4oaDGpsmui5gJBe_jN6HLGiKxONkYPR69sRBUlU,4219
+junifer/data/coordinates/tests/test_coordinates.py,sha256=mjHm90Fgytv47F2vPQHW58jRy6LLbAttizEeg1zjxmA,4196
 junifer/data/masks/__init__.py,sha256=eEEhHglyVEx1LrqwXjq3cOmjf4sTsgBstRx5-k7zIQU,180
 junifer/data/masks/__init__.pyi,sha256=lcgr8gmWDPibC4RxnWBXb8DDpIkO73Aax09u6VXiJJI,114
 junifer/data/masks/_ants_mask_warper.py,sha256=JLK2Jh2AOAiv_NoUGhRoTBEhRFXPRXTDPmQGH9vBSok,5805
 junifer/data/masks/_fsl_mask_warper.py,sha256=YZOMlRgQ7_4shnXNc_05tmwDk5xHI-1wqle-RdNsJ34,2857
-junifer/data/masks/_masks.py,sha256=K-A1cr9TAeVzFPGgn4FUmwIo6LBP0xQb1Q4NW6WTWVo,28166
-junifer/data/masks/tests/test_masks.py,sha256=W0bzRB5Bp-iGO44VtEmaf7BuT-joe_2tQI0lma5NQHA,16090
+junifer/data/masks/_masks.py,sha256=ykspETk2nBVMuIU9eLynIRKcSgDg42CEFUsAhCWcxek,28971
+junifer/data/masks/tests/test_masks.py,sha256=T-WpJvBlAqMIRWF8ODkQBmmBSj-7XUNeTdH3qlsWJC8,16207
 junifer/data/masks/ukb/UKB_15K_GM_template.nii.gz,sha256=jcX1pDOrDsoph8cPMNFVKH5gZYio5G4rJNpOFXm9wJI,946636
 junifer/data/masks/vickery-patil/CAT12_IXI555_MNI152_TMP_GS_GMprob0.2_clean.nii.gz,sha256=j6EY8EtRnUuRxeKgD65Q6B0GPEPIALKDJEIje1TfnAU,88270
 junifer/data/masks/vickery-patil/CAT12_IXI555_MNI152_TMP_GS_GMprob0.2_clean_3mm.nii.gz,sha256=crb_y7YO1vjjf2PwbRJUm8KamPK6fx1y0B_l-E3g8FY,12862
@@ -116,8 +116,8 @@ junifer/data/parcellations/__init__.py,sha256=6-Ysil3NyZ69V6rWx4RO15_d-iDKizfbHu
 junifer/data/parcellations/__init__.pyi,sha256=lhBHTbMDizzqUqVHrx2eyfPFodrTBgMFeTgxfESSkQ8,140
 junifer/data/parcellations/_ants_parcellation_warper.py,sha256=YUCJC0_wutGw7j_n9JRU3LCwm9Ttg5PIlJUgqejfRhs,5806
 junifer/data/parcellations/_fsl_parcellation_warper.py,sha256=JfJ022flg5OR48P4OAALVHHQgTVxdMBXT-fAqBl3nUM,2679
-junifer/data/parcellations/_parcellations.py,sha256=JUUglL0ZM_UKL5jTG1q-3x6Fd3CUO6Hl4YAGAUsGtmI,67019
-junifer/data/parcellations/tests/test_parcellations.py,sha256=ESQI-KWsepmgKB2BWWWUxjkpjOWeIZhhlKxNuTsRPJg,39268
+junifer/data/parcellations/_parcellations.py,sha256=a3Z1Ygb9AYOZC9FuB7Aj32eeaB2eDI-F6KSebo_zoak,50121
+junifer/data/parcellations/tests/test_parcellations.py,sha256=bDoIYC8XAcHI3vEPPMkf7Gex7apnvEqNGRhUENaPgho,36699
 junifer/data/tests/test_data_utils.py,sha256=136iGPjGecCxyqgUwU8VZMHoE6imcYJ0WNC32PDGK4g,1063
 junifer/data/tests/test_template_spaces.py,sha256=ZEicEcLqOJ-NpuBZ5SYh4yZ0xZRkhYHnYXiC_YSxjrY,3219
 junifer/datagrabber/__init__.py,sha256=EHIK-lbjuvkt0V8ypFvLSt85OAAXSkaxBmVlCbNNz8M,323
@@ -341,10 +341,10 @@ junifer/utils/tests/test_config.py,sha256=7ltIXuwb_W4Mv_1dxQWyiyM10XgUAfsWKV6D_i
 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=duO4ou365hxwa_kwihFtKPLaL6LC5XHiyhOijrrngbA,8009
-junifer-0.0.6.dev422.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
-junifer-0.0.6.dev422.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
-junifer-0.0.6.dev422.dist-info/METADATA,sha256=PS2Llw7XCBtnS2KNkImOgWiT2RgUZ0Gshu2u1Z8F9VM,8429
-junifer-0.0.6.dev422.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-junifer-0.0.6.dev422.dist-info/entry_points.txt,sha256=6O8ru0BP-SP7YMUZiizFNoaZ2HvJpadO2G7nKk4PwjI,48
-junifer-0.0.6.dev422.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
-junifer-0.0.6.dev422.dist-info/RECORD,,
+junifer-0.0.6.dev445.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
+junifer-0.0.6.dev445.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
+junifer-0.0.6.dev445.dist-info/METADATA,sha256=HR2aD6lGERZB17sq9_WuyV_IDv_zm3Q0TuPxj3M3YpQ,8385
+junifer-0.0.6.dev445.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+junifer-0.0.6.dev445.dist-info/entry_points.txt,sha256=6O8ru0BP-SP7YMUZiizFNoaZ2HvJpadO2G7nKk4PwjI,48
+junifer-0.0.6.dev445.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
+junifer-0.0.6.dev445.dist-info/RECORD,,