junifer 0.0.5.dev62__py3-none-any.whl → 0.0.5.dev68__py3-none-any.whl

junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.5.dev62'
-__version_tuple__ = version_tuple = (0, 0, 5, 'dev62')
+__version__ = version = '0.0.5.dev68'
+__version_tuple__ = version_tuple = (0, 0, 5, 'dev68')

junifer/api/cli.py

@@ -588,3 +588,29 @@ def ants_docker() -> None:  # pragma: no cover
     export PATH="$PATH:{ants_wrappers_path}"
     """
     click.secho(msg, fg="blue")
+
+
+@setup.command("freesurfer-docker")
+def freesurfer_docker() -> None:  # pragma: no cover
+    """Configure FreeSurfer-Docker wrappers."""
+    import junifer
+
+    pkg_path = Path(junifer.__path__[0])  # type: ignore
+    fs_wrappers_path = pkg_path / "api" / "res" / "freesurfer"
+    msg = f"""
+    Installation instructions for FreeSurfer-Docker wrappers:
+
+    1. Install Docker: https://docs.docker.com/get-docker/
+
+    2. Get the FreeSurfer-Docker image by running this on the command line:
+
+        docker pull freesurfer/freesurfer
+
+    3. Get license from: https://surfer.nmr.mgh.harvard.edu/registration.html .
+       You can skip this step if you already have one.
+
+    4. Add this line to the ~/.bashrc or ~/.zshrc file:
+
+    export PATH="$PATH:{fs_wrappers_path}"
+    """
+    click.secho(msg, fg="blue")

junifer/api/res/freesurfer/mri_binarize

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

junifer/api/res/freesurfer/mri_mc

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

junifer/api/res/freesurfer/mri_pretess

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

junifer/api/res/freesurfer/mris_convert

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

junifer/api/res/freesurfer/run_freesurfer_docker.sh

@@ -0,0 +1,61 @@
+#!/bin/bash
+
+corrected_args=()
+docker_args=()
+mounts=0
+
+FS_LICENSE="${FS_LICENSE:=$HOME/freesurfer_license.txt}"
+
+if [ -f "${FS_LICENSE}" ]; then
+    >&2 echo "Using freesurfer license from ${FS_LICENSE}"
+else
+    >&2 echo "Freesurfer license not found at ${FS_LICENSE}. You can either set FS_LICENSE to the path of the license file or place the license file at
+${FS_LICENSE}"
+    exit 1
+fi
+
+# Map the license path to the container by binding
+license_path=$(realpath "${FS_LICENSE}")
+license_path_fname=$(basename "${FS_LICENSE}")
+host_dir=$(dirname "${license_path}")
+((mounts+=1))
+container_dir="/data/mount_${mounts}"
+docker_args+=("-v ${host_dir}:${container_dir}")
+export DOCKERENV_FS_LICENSE=${container_dir}/${license_path_fname}
+
+for var in "$@"
+do
+if [ -d "${var}" ]; then
+        echo "$var is a directory" >&2
+        var=$(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 "$var is a file" >&2
+            var=$(realpath "${var}")
+        else
+            echo "$var is a prefix" >&2
+        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[*]}" >&2
+echo "Corrected args for FreeSurfer: ${corrected_args[*]}" >&2
+
+cwd=$(pwd)
+cmd="docker run --rm ${docker_args[*]} -v ${cwd}:${cwd} -w ${cwd} freesurfer/freesurfer ${corrected_args[*]}"
+echo "Running command: ${cmd}" >&2
+${cmd}
+
+unset DOCKERENV_FS_LICENSE

junifer/pipeline/utils.py

@@ -37,7 +37,7 @@ def check_ext_dependencies(
         If ``name`` is mandatory and is not found.
 
     """
-    valid_ext_dependencies = ("afni", "fsl", "ants")
+    valid_ext_dependencies = ("afni", "fsl", "ants", "freesurfer")
     if name not in valid_ext_dependencies:
         raise_error(
             "Invalid value for `name`, should be one of: "
@@ -52,6 +52,9 @@ def check_ext_dependencies(
     # Check for ants
     elif name == "ants":
         found = _check_ants(**kwargs)
+    # Check for freesurfer
+    elif name == "freesurfer":
+        found = _check_freesurfer(**kwargs)
 
     # Check if the dependency is mandatory in case it's not found
     if not found and not optional:
@@ -245,3 +248,63 @@ def _check_ants(commands: Optional[List[str]] = None) -> bool:
                 f"{commands_found_results}"
             )
     return ants_found
+
+
+def _check_freesurfer(commands: Optional[List[str]] = None) -> bool:
+    """Check if FreeSurfer is present in the system.
+
+    Parameters
+    ----------
+    commands : list of str, optional
+        The commands to specifically check for from FreeSurfer. If None, only
+        the basic FreeSurfer help would be looked up, else, would also
+        check for specific commands (default None).
+
+    Returns
+    -------
+    bool
+        Whether FreeSurfer is found or not.
+
+    """
+    completed_process = subprocess.run(
+        "recon-all -help",
+        stdin=subprocess.DEVNULL,
+        stdout=subprocess.DEVNULL,
+        stderr=subprocess.STDOUT,
+        shell=True,  # is unsafe but kept for resolution via PATH
+        check=False,
+    )
+    fs_found = completed_process.returncode == 0
+
+    # Check for specific commands
+    if fs_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(
+                "FreeSurfer is installed but some of the required commands "
+                "were not found. These are the results: "
+                f"{commands_found_results}"
+            )
+    return fs_found

{junifer-0.0.5.dev62.dist-info → junifer-0.0.5.dev68.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.5.dev62
+Version: 0.0.5.dev68
 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.dev62.dist-info → junifer-0.0.5.dev68.dist-info}/RECORD

@@ -1,8 +1,8 @@
 junifer/__init__.py,sha256=x1UR2jUcrUdm2HNl-3Qvyi4UUrU6ms5qm2qcmNY7zZk,391
-junifer/_version.py,sha256=hgHhCEpD3JpS1CgIK8NxTVb-Oy5VWX6RF9_cs92ZylU,426
+junifer/_version.py,sha256=PBqSCqCS6ZvtB0pHoCsVMEJ5SO6mMY2-aeQleSYHyog,426
 junifer/stats.py,sha256=jN22_qFvWYBU9ZIMnCSzN4iOscWnWrcrUPIdLeDkV64,6163
 junifer/api/__init__.py,sha256=pSj8V8tmwOAQ3sshWJfRfB-n3z5bcJj3pHOBX4-8ONc,251
-junifer/api/cli.py,sha256=wtU7Rv9tDIT-4KQAkG6WxiE6mop3cuz6XxGDewceHPs,15329
+junifer/api/cli.py,sha256=53pews3mXkJ7DUDSkV51PbitYnuVAdQRkWG-gjO08Uw,16142
 junifer/api/decorators.py,sha256=8bnwHPAe7VgzKxl--M_e0umdAlTVSzaJQHEJZ5kof5k,2580
 junifer/api/functions.py,sha256=zCWLXDZ_cAqRZ5bFeky0KeqBztuoa6L3-djI65tqtpY,13055
 junifer/api/parser.py,sha256=a3SSC2xO-PF1pqXZXFq8Sh9aVd-dmHolJbCkGyOUTAM,4416
@@ -26,6 +26,11 @@ junifer/api/res/ants/ResampleImage,sha256=oJKZ31rBAW20ETozB8Ub5SbXMuhmZfrerpJTnR
 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
+junifer/api/res/freesurfer/mri_binarize,sha256=d6tjwyOTvLxaMcmUMaeYdR6gE0aI0Bj7ITnDLO3eNdk,56
+junifer/api/res/freesurfer/mri_mc,sha256=sTVbj27M_rjs1RIj6dyp_OTSN4ZB3Q_7f2A5z-ri1QA,50
+junifer/api/res/freesurfer/mri_pretess,sha256=BxhyeD8M3jxIpA_1i6sMAHcsaBQQtvfPu2i1u_nGFBg,55
+junifer/api/res/freesurfer/mris_convert,sha256=7r6L2nQlBNUMJwtsRiIicU_LvKi5GQ9pQUkbDP__p_Q,56
+junifer/api/res/freesurfer/run_freesurfer_docker.sh,sha256=zn6fa0lNAMx3KNZqLcjUYhabpCmcqSETBtqqiqiRQAY,1848
 junifer/api/res/fsl/applywarp,sha256=DBgHfsn1yXWq0t-P7J0YvrjjJNgiblwDsh9L1hF9v_w,46
 junifer/api/res/fsl/flirt,sha256=tSjiUco8ui8AbHD7mTzChEwbR0Rf_4iJTgzYTPF_WuQ,42
 junifer/api/res/fsl/img2imgcoord,sha256=Zmaw3oJYrEltcXiPyEubXry9ppAq3SND52tdDWGgeZk,49
@@ -196,7 +201,7 @@ junifer/pipeline/pipeline_step_mixin.py,sha256=kU0Wut_chlT-iTUb8NP72c7YEoHAECbp7
 junifer/pipeline/registry.py,sha256=12tRsFeDz_kj9D1nzy9SAkBpchu5IyRH7U2h7eqPDZA,4260
 junifer/pipeline/singleton.py,sha256=-BiiyFiEO1EItztBcAWI_eyApR-oJTAGVRXkV706rQ4,985
 junifer/pipeline/update_meta_mixin.py,sha256=WJhLdeIZQ3BjiEcPJM01wlH70ZNj0z5ZS2FfRTJG5oo,1532
-junifer/pipeline/utils.py,sha256=qlDUPOFfAq53EDtyHK-klliUwgQBiFDsFghAJO2iHUQ,8039
+junifer/pipeline/utils.py,sha256=70LPMyitmr4d1IiboajI6mo6zPQg6oolYWJIvenYtnA,10252
 junifer/pipeline/workdir_manager.py,sha256=s2I1I4vjxxqAVAT12ZrZx9KW0WxNMtxRTozB4Xcnh9M,8019
 junifer/pipeline/tests/test_pipeline_step_mixin.py,sha256=_ykZzyNzREXy-r_yv1gY_jquLZzVBl8qwYrVORCKY_k,7807
 junifer/pipeline/tests/test_registry.py,sha256=rYN0pO3gSueQ6XsasEM9VU5BkLyaNl8WaCZiaO8Rno0,4105
@@ -248,10 +253,10 @@ junifer/utils/logging.py,sha256=furcU3XIUpUvnpe4PEwzWWIWgmH4j2ZA4MQdvSGWjj0,9216
 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-0.0.5.dev62.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
-junifer-0.0.5.dev62.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
-junifer-0.0.5.dev62.dist-info/METADATA,sha256=iK9h-P28t4ysBf_C97-FNWO5jaU8uFIFE6nyEN5aiiw,8234
-junifer-0.0.5.dev62.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-junifer-0.0.5.dev62.dist-info/entry_points.txt,sha256=DxFvKq0pOqRunAK0FxwJcoDfV1-dZvsFDpD5HRqSDhw,48
-junifer-0.0.5.dev62.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
-junifer-0.0.5.dev62.dist-info/RECORD,,
+junifer-0.0.5.dev68.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
+junifer-0.0.5.dev68.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
+junifer-0.0.5.dev68.dist-info/METADATA,sha256=2B8FVputNlxRR-ehtPjaLIxf9zzOnQh0UqDe-sbTndI,8234
+junifer-0.0.5.dev68.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+junifer-0.0.5.dev68.dist-info/entry_points.txt,sha256=DxFvKq0pOqRunAK0FxwJcoDfV1-dZvsFDpD5HRqSDhw,48
+junifer-0.0.5.dev68.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
+junifer-0.0.5.dev68.dist-info/RECORD,,