junifer 0.0.4.dev416__tar.gz → 0.0.4.dev425__tar.gz

{junifer-0.0.4.dev416 → junifer-0.0.4.dev425}/PKG-INFO

@@ -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.dev425/docs/changes/newsfragments/277.misc

@@ -0,0 +1 @@
+Add support for accessing ANTs via Docker wrapper along with ``antsApplyTransforms`` and ``antsApplyTransformsToPoints`` by `Synchon Mandal`_

junifer-0.0.4.dev425/docs/changes/newsfragments/278.bugfix

@@ -0,0 +1 @@
+Bypass FSL ``std2imgcoord`` stdin bug and use recommended piped input for coordinates transformation by `Synchon Mandal`_

{junifer-0.0.4.dev416 → junifer-0.0.4.dev425}/docs/installation.rst

@@ -152,3 +152,36 @@ Or, alternatively, you can execute this command which will update the
 .. code-block:: bash
 
   junifer setup fsl-docker | grep "PATH=" | xargs | >> ~/.bashrc
+
+ANTs
+----
+
+To install ANTs, you can always follow the `ANTs official instructions
+<https://github.com/ANTsX/ANTs>`_. Additionally, you can also follow the
+following steps to install and configure the ANTs Docker container in your
+local system.
+
+1. Install Docker. You can follow the
+   `Docker official instructions <https://docs.docker.com/get-docker/>`_.
+2. Pull the ANTs Docker image from
+   `Docker Hub ANTs <https://hub.docker.com/r/antsx/ants>`_:
+
+.. code-block:: bash
+
+  docker pull antsx/ants
+
+3. Add the Junifer ANTs scripts to your PATH environment variable. Run the
+   following command:
+
+.. code-block:: bash
+
+  junifer setup ants-docker
+
+Take the last line and copy it to your ``.bashrc`` or ``.zshrc`` file.
+
+Or, alternatively, you can execute this command which will update the
+``~/.bashrc`` for you:
+
+.. code-block:: bash
+
+  junifer setup ants-docker | grep "PATH=" | xargs | >> ~/.bashrc

{junifer-0.0.4.dev416 → junifer-0.0.4.dev425}/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-0.0.4.dev416 → junifer-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-0.0.4.dev425/junifer/api/res/ants/antsApplyTransforms

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

junifer-0.0.4.dev425/junifer/api/res/ants/antsApplyTransformsToPoints

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

junifer-0.0.4.dev425/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-0.0.4.dev416 → junifer-0.0.4.dev425}/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-0.0.4.dev416 → junifer-0.0.4.dev425}/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 → junifer-0.0.4.dev425}/junifer.egg-info/PKG-INFO

@@ -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 → junifer-0.0.4.dev425}/junifer.egg-info/SOURCES.txt

@@ -86,6 +86,8 @@ docs/changes/newsfragments/271.feature
 docs/changes/newsfragments/272.bugfix
 docs/changes/newsfragments/274.bugfix
 docs/changes/newsfragments/276.bugfix
+docs/changes/newsfragments/277.misc
+docs/changes/newsfragments/278.bugfix
 docs/extending/coordinates.rst
 docs/extending/datagrabber.rst
 docs/extending/extension.rst
@@ -140,6 +142,9 @@ junifer/api/res/afni/3dRSFC
 junifer/api/res/afni/3dReHo
 junifer/api/res/afni/afni
 junifer/api/res/afni/run_afni_docker.sh
+junifer/api/res/ants/antsApplyTransforms
+junifer/api/res/ants/antsApplyTransformsToPoints
+junifer/api/res/ants/run_ants_docker.sh
 junifer/api/res/fsl/applywarp
 junifer/api/res/fsl/flirt
 junifer/api/res/fsl/run_fsl_docker.sh