junifer 0.0.5.dev24__tar.gz → 0.0.5.dev33__tar.gz

{junifer-0.0.5.dev24 → junifer-0.0.5.dev33}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.5.dev24
+Version: 0.0.5.dev33
 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-0.0.5.dev33/docs/changes/newsfragments/323.feature

@@ -0,0 +1 @@
+Add ``junifer list-elements`` to list out available elements for a DataGrabber based on filtering via ``--element`` by `Synchon Mandal`_

junifer-0.0.5.dev33/docs/changes/newsfragments/324.bugfix

@@ -0,0 +1 @@
+Remove extra dimension from parcellations warped via ANTs to other template spaces by `Synchon Mandal`_

{junifer-0.0.5.dev24 → junifer-0.0.5.dev33}/junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.5.dev24'
-__version_tuple__ = version_tuple = (0, 0, 5, 'dev24')
+__version__ = version = '0.0.5.dev33'
+__version_tuple__ = version_tuple = (0, 0, 5, 'dev33')

{junifer-0.0.5.dev24 → junifer-0.0.5.dev33}/junifer/api/cli.py

@@ -8,7 +8,7 @@ import pathlib
 import subprocess
 import sys
 from pathlib import Path
-from typing import Dict, List, Tuple, Union
+from typing import Dict, List, Optional, Tuple, Union
 
 import click
 import pandas as pd
@@ -20,6 +20,7 @@ from ..utils.logging import (
     warn_with_log,
 )
 from .functions import collect as api_collect
+from .functions import list_elements as api_list_elements
 from .functions import queue as api_queue
 from .functions import reset as api_reset
 from .functions import run as api_run
@@ -451,6 +452,69 @@ def reset(
     api_reset(config)
 
 
+@cli.command()
+@click.argument(
+    "filepath",
+    type=click.Path(
+        exists=True, readable=True, dir_okay=False, path_type=pathlib.Path
+    ),
+)
+@click.option("--element", type=str, multiple=True)
+@click.option(
+    "-o",
+    "--output-file",
+    type=click.Path(dir_okay=False, writable=True, path_type=pathlib.Path),
+)
+@click.option(
+    "-v",
+    "--verbose",
+    type=click.UNPROCESSED,
+    callback=_validate_verbose,
+    default="info",
+)
+def list_elements(
+    filepath: click.Path,
+    element: Tuple[str],
+    output_file: Optional[click.Path],
+    verbose: Union[str, int],
+) -> None:
+    """Element listing command for CLI.
+
+    \f
+
+    Parameters
+    ----------
+    filepath : click.Path
+        The filepath to the configuration file.
+    element : tuple of str
+        The element to operate on.
+    output_file : click.Path or None
+        The path to write the output to. If not None, writing to
+        stdout is not performed.
+    verbose : click.Choice
+        The verbosity level: warning, info or debug (default "info").
+
+    """
+    configure_logging(level=verbose)
+    # Parse YAML
+    config = parse_yaml(filepath)  # type: ignore
+    # Fetch datagrabber
+    datagrabber = config["datagrabber"]
+    # Parse elements
+    elements = _parse_elements(element, config)
+    # Perform operation
+    listed_elements = api_list_elements(
+        datagrabber=datagrabber,
+        elements=elements,
+    )
+    # Check if output file is provided
+    if output_file is not None:
+        output_file.touch()
+        output_file.write_text(listed_elements)
+    else:
+        click.secho(listed_elements, fg="blue")
+
+
 @cli.group()
 def setup() -> None:  # pragma: no cover
     """Configure commands for Junifer."""

{junifer-0.0.5.dev24 → junifer-0.0.5.dev33}/junifer/api/functions.py

@@ -361,3 +361,44 @@ def reset(config: Dict) -> None:
             shutil.rmtree(job_dir)
             # Remove directory
             job_dir.parent.rmdir()
+
+
+def list_elements(
+    datagrabber: Dict,
+    elements: Union[str, List[Union[str, Tuple]], Tuple, None] = None,
+) -> str:
+    """List elements of the datagrabber filtered using `elements`.
+
+    Parameters
+    ----------
+    datagrabber : dict
+        DataGrabber to index. Must have a key ``kind`` with the kind of
+        DataGrabber to use. All other keys are passed to the DataGrabber
+        constructor.
+    elements : str or tuple or list of str or tuple, optional
+        Element(s) to filter using. Will be used to index the DataGrabber
+        (default None).
+
+    """
+    # Get datagrabber to use
+    datagrabber_object = _get_datagrabber(datagrabber)
+
+    # Fetch elements
+    raw_elements_to_list = []
+    with datagrabber_object:
+        if elements is not None:
+            for element in datagrabber_object.filter(elements):
+                raw_elements_to_list.append(element)
+        else:
+            for element in datagrabber_object:
+                raw_elements_to_list.append(element)
+
+    elements_to_list = []
+    for element in raw_elements_to_list:
+        # Stringify elements if tuple for operation
+        str_element = (
+            ",".join(element) if isinstance(element, tuple) else element
+        )
+        elements_to_list.append(str_element)
+
+    return "\n".join(elements_to_list)

{junifer-0.0.5.dev24 → junifer-0.0.5.dev33}/junifer/api/tests/test_cli.py

@@ -14,6 +14,7 @@ from ruamel.yaml import YAML
 from junifer.api.cli import (
     _parse_elements_file,
     collect,
+    list_elements,
     queue,
     reset,
     run,
@@ -297,6 +298,88 @@ def test_reset(
         assert reset_result.exit_code == 0
 
 
+@pytest.mark.parametrize(
+    "elements",
+    [
+        ("sub-01", "sub-02"),
+        ("sub-03", "sub-04"),
+    ],
+)
+def test_list_elements_stdout(
+    elements: Tuple[str, ...],
+) -> None:
+    """Test elements listing to stdout.
+
+    Parameters
+    ----------
+    elements : tuple of str
+        The parametrized elements for filtering.
+
+    """
+    # Get test config
+    infile = Path(__file__).parent / "data" / "partly_cloudy_agg_mean_tian.yml"
+    # List elements command arguments
+    list_elements_args = [
+        str(infile.absolute()),
+        "--verbose",
+        "debug",
+        "--element",
+        elements[0],
+        "--element",
+        elements[1],
+    ]
+    # Invoke list elements command
+    list_elements_result = runner.invoke(list_elements, list_elements_args)
+    # Check
+    assert list_elements_result.exit_code == 0
+    assert f"{elements[0]}\n{elements[1]}" in list_elements_result.stdout
+
+
+@pytest.mark.parametrize(
+    "elements",
+    [
+        ("sub-01", "sub-02"),
+        ("sub-03", "sub-04"),
+    ],
+)
+def test_list_elements_output_file(
+    tmp_path: Path,
+    elements: Tuple[str, ...],
+) -> None:
+    """Test elements listing to output file.
+
+    Parameters
+    ----------
+    tmp_path : pathlib.Path
+        The path to the test directory.
+    elements : tuple of str
+        The parametrized elements for filtering.
+
+    """
+    # Get test config
+    infile = Path(__file__).parent / "data" / "partly_cloudy_agg_mean_tian.yml"
+    # Output file
+    output_file = tmp_path / "elements.txt"
+    # List elements command arguments
+    list_elements_args = [
+        str(infile.absolute()),
+        "--verbose",
+        "debug",
+        "--element",
+        elements[0],
+        "--element",
+        elements[1],
+        "--output-file",
+        str(output_file.resolve()),
+    ]
+    # Invoke list elements command
+    list_elements_result = runner.invoke(list_elements, list_elements_args)
+    # Check
+    assert list_elements_result.exit_code == 0
+    with open(output_file) as f:
+        assert f"{elements[0]}\n{elements[1]}" == f.read()
+
+
 def test_wtf_short() -> None:
     """Test short version of wtf command."""
     # Invoke wtf command

{junifer-0.0.5.dev24 → junifer-0.0.5.dev33}/junifer/api/tests/test_functions.py

@@ -7,13 +7,13 @@
 
 import logging
 from pathlib import Path
-from typing import Dict, List, Tuple, Union
+from typing import Dict, List, Optional, Tuple, Union
 
 import pytest
 from ruamel.yaml import YAML
 
 import junifer.testing.registry  # noqa: F401
-from junifer.api.functions import collect, queue, reset, run
+from junifer.api.functions import collect, list_elements, queue, reset, run
 from junifer.datagrabber.base import BaseDataGrabber
 from junifer.pipeline.registry import build
 
@@ -637,3 +637,28 @@ def test_reset_queue(
 
         assert not Path(storage["uri"]).exists()
         assert not (tmp_path / "junifer_jobs" / job_name).exists()
+
+
+@pytest.mark.parametrize(
+    "elements",
+    [
+        ["sub-01"],
+        None,
+    ],
+)
+def test_list_elements(
+    datagrabber: Dict[str, str],
+    elements: Optional[List[str]],
+) -> None:
+    """Test elements listing.
+
+    Parameters
+    ----------
+    datagrabber : dict
+        Testing datagrabber as dictionary.
+    elements : str of list of str
+        The parametrized elements for filtering.
+
+    """
+    listed_elements = list_elements(datagrabber, elements)
+    assert "sub-01" in listed_elements

{junifer-0.0.5.dev24 → junifer-0.0.5.dev33}/junifer/markers/parcel_aggregation.py

@@ -195,7 +195,9 @@ class ParcelAggregation(BaseMarker):
         )
 
         # Get binarized parcellation image for masking
-        parcellation_bin = math_img("img != 0", img=parcellation_img)
+        parcellation_bin = math_img(
+            "np.squeeze(img) != 0", img=parcellation_img
+        )
 
         # Load mask
         if self.masks is not None:

{junifer-0.0.5.dev24 → junifer-0.0.5.dev33}/junifer.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.5.dev24
+Version: 0.0.5.dev33
 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-0.0.5.dev24 → junifer-0.0.5.dev33}/junifer.egg-info/SOURCES.txt

@@ -59,6 +59,8 @@ docs/changes/contributors.inc
 docs/changes/newsfragments/.gitignore
 docs/changes/newsfragments/161.feature
 docs/changes/newsfragments/273.feature
+docs/changes/newsfragments/323.feature
+docs/changes/newsfragments/324.bugfix
 docs/extending/coordinates.rst
 docs/extending/datagrabber.rst
 docs/extending/dependencies.rst