junifer 0.0.4.dev416__py3-none-any.whl → 0.0.4.dev425__py3-none-any.whl

junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.4.dev416'
-__version_tuple__ = version_tuple = (0, 0, 4, 'dev416')
+__version__ = version = '0.0.4.dev425'
+__version_tuple__ = version_tuple = (0, 0, 4, 'dev425')

junifer/api/cli.py

@@ -463,3 +463,26 @@ def fsl_docker() -> None:  # pragma: no cover
     export PATH="$PATH:{fsl_wrappers_path}"
     """
     click.secho(msg, fg="blue")
+
+
+@setup.command("ants-docker")
+def ants_docker() -> None:  # pragma: no cover
+    """Configure ANTs-Docker wrappers."""
+    import junifer
+
+    pkg_path = Path(junifer.__path__[0])  # type: ignore
+    ants_wrappers_path = pkg_path / "api" / "res" / "ants"
+    msg = f"""
+    Installation instructions for ANTs-Docker wrappers:
+
+    1. Install Docker: https://docs.docker.com/get-docker/
+
+    2. Get the ANTs-Docker image by running this on the command line:
+
+        docker pull antsx/ants
+
+    3. Add this line to the ~/.bashrc or ~/.zshrc file:
+
+    export PATH="$PATH:{ants_wrappers_path}"
+    """
+    click.secho(msg, fg="blue")

junifer/api/res/ants/antsApplyTransforms

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+run_ants_docker.sh antsApplyTransforms "$@"

junifer/api/res/ants/antsApplyTransformsToPoints

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+run_ants_docker.sh antsApplyTransformsToPoints "$@"

junifer/api/res/ants/run_ants_docker.sh

@@ -0,0 +1,39 @@
+#!/bin/bash
+
+corrected_args=()
+docker_args=()
+mounts=0
+for var in "$@"
+do
+if [ -d "${var}" ]; then
+        echo "$var is a directory"
+        var=$(realpath "${var}")
+        host_dir=$(dirname "${var}")
+        ((mounts+=1))
+        container_dir="/data/mount_${mounts}"
+        docker_args+=("-v ${host_dir}:${container_dir}")
+        var=${container_dir}
+    elif [ -f "${var}" ] || [[ "${var}" == /* ]]; then
+        if [ -f "${var}" ]; then
+            echo "$var is a file"
+            var=$(realpath "${var}")
+        else
+            echo "$var is a prefix"
+        fi
+        fname=$(basename "${var}")
+        host_dir=$(dirname "${var}")
+        ((mounts+=1))
+        container_dir="/data/mount_${mounts}"
+        docker_args+=("-v ${host_dir}:${container_dir}")
+        var=${container_dir}/${fname}
+    fi
+    corrected_args+=("${var}")
+done
+
+echo "Docker args: ${docker_args[*]}"
+echo "Corrected args for fsl: ${corrected_args[*]}"
+
+cwd=$(pwd)
+cmd="docker run --rm ${docker_args[*]} -v ${cwd}:${cwd} -w ${cwd} antsx/ants ${corrected_args[*]}"
+echo "Running command: ${cmd}"
+${cmd}

junifer/data/coordinates.py

@@ -260,11 +260,12 @@ def get_coordinates(
         std2imgcoord_out_path = element_tempdir / "coordinates_transformed.txt"
         # Set std2imgcoord command
         std2imgcoord_cmd = [
-            "std2imgcoord",
+            "cat",
+            f"{pretransform_coordinates_path.resolve()}",
+            "| std2imgcoord",
             f"-img {target_data['reference_path'].resolve()}",
             f"-warp {extra_input['Warp']['path'].resolve()}",
-            f"{pretransform_coordinates_path.resolve()}",
-            f"> {std2imgcoord_out_path.resolve()}",
+            f"- > {std2imgcoord_out_path.resolve()}",
         ]
         # Call std2imgcoord
         std2imgcoord_cmd_str = " ".join(std2imgcoord_cmd)

junifer/pipeline/utils.py

@@ -35,6 +35,9 @@ def check_ext_dependencies(name: str, optional: bool, **kwargs: Any) -> bool:
     # Check for fsl
     elif name == "fsl":
         found = _check_fsl(**kwargs)
+    # Check for ants
+    elif name == "ants":
+        found = _check_ants(**kwargs)
     # Went off the rails
     else:
         raise_error(
@@ -171,3 +174,63 @@ def _check_fsl(commands: Optional[List[str]] = None) -> bool:
                 f"{commands_found_results}"
             )
     return fsl_found
+
+
+def _check_ants(commands: Optional[List[str]] = None) -> bool:
+    """Check if ANTs is present in the system.
+
+    Parameters
+    ----------
+    commands : list of str, optional
+        The commands to specifically check for from ANTs. If None, only
+        the basic ANTS help would be looked up, else, would also
+        check for specific commands (default None).
+
+    Returns
+    -------
+    bool
+        Whether ANTs is found or not.
+
+    """
+    completed_process = subprocess.run(
+        "ANTS --help",
+        stdin=subprocess.DEVNULL,
+        stdout=subprocess.DEVNULL,
+        stderr=subprocess.STDOUT,
+        shell=True,  # is unsafe but kept for resolution via PATH
+        check=False,
+    )
+    ants_found = completed_process.returncode == 0
+
+    # Check for specific commands
+    if ants_found and commands is not None:
+        if not isinstance(commands, list):
+            commands = [commands]
+        # Store command found results
+        commands_found_results = {}
+        # Set all commands found flag to True
+        all_commands_found = True
+        # Check commands' existence
+        for command in commands:
+            command_process = subprocess.run(
+                [command],
+                stdin=subprocess.DEVNULL,
+                stdout=subprocess.DEVNULL,
+                stderr=subprocess.STDOUT,
+                shell=True,  # is unsafe but kept for resolution via PATH
+                check=False,
+            )
+            command_found = command_process.returncode == 0
+            commands_found_results[command] = (
+                "found" if command_found else "not found"
+            )
+            # Set flag to trigger warning
+            all_commands_found = all_commands_found and command_found
+        # One or more commands were missing
+        if not all_commands_found:
+            warn_with_log(
+                "ANTs is installed but some of the required commands "
+                "were not found. These are the results: "
+                f"{commands_found_results}"
+            )
+    return ants_found

{junifer-0.0.4.dev416.dist-info → junifer-0.0.4.dev425.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.4.dev416
+Version: 0.0.4.dev425
 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.dev416.dist-info → junifer-0.0.4.dev425.dist-info}/RECORD

@@ -1,8 +1,8 @@
 junifer/__init__.py,sha256=x1UR2jUcrUdm2HNl-3Qvyi4UUrU6ms5qm2qcmNY7zZk,391
-junifer/_version.py,sha256=oEiN87qcYMsn7tBFVlimnDizlVHV4f2oCFPPNYHlePw,428
+junifer/_version.py,sha256=p31cczSx2OSKphtDx6E2KUtMOHSLo8bDd0Eg7yeGf58,428
 junifer/stats.py,sha256=KUX4jJcLWnlE34coet8EkdFypFd-td4Vtpx5LvlomVs,5879
 junifer/api/__init__.py,sha256=YILu9M7SC0Ri4CVd90fELH2OnK_gvCYAXCoqBNCFE8E,257
-junifer/api/cli.py,sha256=606LWHcQjF5gv3rxAqmD8i2tCG1cnu7t1Tpej7yJzJs,12247
+junifer/api/cli.py,sha256=xScav2mF-Jr8JjVFt8kaHuLpX5l_jVTaQGPgQL3VNvA,12881
 junifer/api/decorators.py,sha256=8bnwHPAe7VgzKxl--M_e0umdAlTVSzaJQHEJZ5kof5k,2580
 junifer/api/functions.py,sha256=WPs0Yj10aWIOLh_1A12SBTdG0HK86si5fJ9qAfJJQO0,23057
 junifer/api/parser.py,sha256=a0IBvH3KN1PJaEpF3cnSv8g7VCVpDY1VsCvc8b8FFmE,3849
@@ -13,6 +13,9 @@ 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=Qw_yLv7GijmjPmmuiDA0qRmB2Kxuvsoerm5R7mjtzZo,1106
+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=svzsACUd1kh3C_ODL2fAUAY2fMKsjQ-MsCPOuxKxwW0,1095
 junifer/api/res/fsl/applywarp,sha256=DBgHfsn1yXWq0t-P7J0YvrjjJNgiblwDsh9L1hF9v_w,46
 junifer/api/res/fsl/flirt,sha256=tSjiUco8ui8AbHD7mTzChEwbR0Rf_4iJTgzYTPF_WuQ,42
 junifer/api/res/fsl/run_fsl_docker.sh,sha256=9y_9ehmVeflf0zfssXUNzaiS9FRPTXAd84XzyY5lmck,1098
@@ -37,7 +40,7 @@ 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=BVpiz9dkwTKwlAnPE8R44dIUD3gCjd9CZBDJHQR9kCY,10957
+junifer/data/coordinates.py,sha256=10bXVy94eZALfqdEbAbHTOuuF0Od9Zn2QbCFjAFSY5M,10980
 junifer/data/masks.py,sha256=chWSl-vyv5Nsd9GuQzydXPOY3AdhApOJq_42NSKpykQ,16952
 junifer/data/parcellations.py,sha256=wL8lkAYYvg7NDt160EA8N_xFjK8ZtDwoXYJQHNHwbDU,55805
 junifer/data/utils.py,sha256=K9quLIoWRmm2QFM8Rdy_5bYsWb_XhL0l5Uq_1Sie0kA,1274
@@ -178,7 +181,7 @@ junifer/pipeline/pipeline_step_mixin.py,sha256=fZtJa5NJ2_9r6dD_UOkXA5fOPtRjuPUbh
 junifer/pipeline/registry.py,sha256=PQq8D6DiHhSeh0tdHs9J6jv9L1WsfEUqJxzhlzAQDbE,3956
 junifer/pipeline/singleton.py,sha256=-BiiyFiEO1EItztBcAWI_eyApR-oJTAGVRXkV706rQ4,985
 junifer/pipeline/update_meta_mixin.py,sha256=WJhLdeIZQ3BjiEcPJM01wlH70ZNj0z5ZS2FfRTJG5oo,1532
-junifer/pipeline/utils.py,sha256=EnXtk7Nm7qacSoTiPbnERRhPzajD93d3-bvBgCvNv5U,5789
+junifer/pipeline/utils.py,sha256=f8vsROGdSb6tdA70TbA0CzT5yzRhhq2W5czkJRu0VP4,7936
 junifer/pipeline/workdir_manager.py,sha256=LxIAMyCBtJbYnDI_23_pAFAXQAeJY3cS06SY9aIUbZ8,7972
 junifer/pipeline/tests/test_pipeline_step_mixin.py,sha256=LMVMgc6e4ahhcQWL9VNL3IgxEEZ-phO7jhKae5-Mqns,5393
 junifer/pipeline/tests/test_registry.py,sha256=rYN0pO3gSueQ6XsasEM9VU5BkLyaNl8WaCZiaO8Rno0,4105
@@ -222,10 +225,10 @@ junifer/utils/fs.py,sha256=Jd9AoV2fIF7pT7KhXsn8T1O1fJ1_SFZgaFuOBAM7DG8,460
 junifer/utils/logging.py,sha256=4kH8j9X_J2bMdnBJMldVF95C5sURa5UAsLmSgRaD9Ig,9117
 junifer/utils/tests/test_fs.py,sha256=WQS7cKlKEZ742CIuiOYYpueeAhY9PqlastfDVpVVtvE,923
 junifer/utils/tests/test_logging.py,sha256=l8oo-AiBV7H6_IzlsNcj__cLeZBUvgIGoaMszD9VaJg,7754
-junifer-0.0.4.dev416.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
-junifer-0.0.4.dev416.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
-junifer-0.0.4.dev416.dist-info/METADATA,sha256=JaWqiW8qJ8I6veUVWU1lr_mYKkzCOLMrIbaxgmzMN8o,7569
-junifer-0.0.4.dev416.dist-info/WHEEL,sha256=Xo9-1PvkuimrydujYJAjF7pCkriuXBpUPEjma1nZyJ0,92
-junifer-0.0.4.dev416.dist-info/entry_points.txt,sha256=DxFvKq0pOqRunAK0FxwJcoDfV1-dZvsFDpD5HRqSDhw,48
-junifer-0.0.4.dev416.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
-junifer-0.0.4.dev416.dist-info/RECORD,,
+junifer-0.0.4.dev425.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
+junifer-0.0.4.dev425.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
+junifer-0.0.4.dev425.dist-info/METADATA,sha256=5u5z14ZMbrIE13ok_UGTzLaL4YQI2CHMOyegn6ifuS4,7569
+junifer-0.0.4.dev425.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
+junifer-0.0.4.dev425.dist-info/entry_points.txt,sha256=DxFvKq0pOqRunAK0FxwJcoDfV1-dZvsFDpD5HRqSDhw,48
+junifer-0.0.4.dev425.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
+junifer-0.0.4.dev425.dist-info/RECORD,,

{junifer-0.0.4.dev416.dist-info → junifer-0.0.4.dev425.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.41.3)
+Generator: bdist_wheel (0.42.0)
 Root-Is-Purelib: true
 Tag: py3-none-any