[REF] Adapt Stat Volume to SPM25 (aramis-lab#1626)

* todos

* Adapt to spm standalone

* No GUI question

* Fix unit tests

* Fix unit tests 2

* Fix unit test spm

Author: AliceJoubert

.github/workflows/test_non_regression_fast.yml

@@ -49,7 +49,7 @@ jobs:
           source /builds/miniconda/etc/profile.d/conda.sh
           conda activate "${{ github.workspace }}"/env
           source /usr/local/Modules/init/profile.sh
-          module load clinica.all
+          module load clinica_standalone.all
           make install
           cd test
           poetry run pytest --verbose \

clinica/pipelines/statistics_volume/info.json

@@ -8,7 +8,7 @@
         {
             "type": "software",
             "name": "spm",
-            "version": ">=12"
+            "version": ">=25"
         }
     ]
-}
+}

clinica/pipelines/statistics_volume/statistics_volume_utils.py

@@ -406,9 +406,7 @@ def run_m_script(m_file: str) -> str:
     """
     from pathlib import Path
 
-    from clinica.pipelines.statistics_volume.statistics_volume_utils import (  # noqa
-        _delete_last_line,
-        _run_matlab_script_with_matlab,
+    from clinica.pipelines.statistics_volume.statistics_volume_utils import (
         _run_matlab_script_with_spm_standalone,
     )
     from clinica.utils.spm import use_spm_standalone_if_available
@@ -420,53 +418,14 @@ def run_m_script(m_file: str) -> str:
         raise ValueError(
             f"[Error] {m_file} is not a Matlab file (extension must be .m)"
         )
-    if use_spm_standalone_if_available():
-        _delete_last_line(m_file)
-        _run_matlab_script_with_spm_standalone(m_file)
-    else:
-        _run_matlab_script_with_matlab(str(m_file))
+    use_spm_standalone_if_available()
+    _run_matlab_script_with_spm_standalone(m_file)
     output_mat_file = (m_file.parent.parent / "2_sample_t_test" / "SPM.mat").resolve()
     if not output_mat_file.is_file():
         raise RuntimeError(f"Output matrix {output_mat_file} was not produced")
     return str(output_mat_file)
 
 
-def _delete_last_line(filename: Path) -> None:
-    """Removes the last line of the provided file.
-
-    Used to remove the call to spm jobman if the MATLAB file
-    is used with SPM standalone.
-
-    Parameters
-    ----------
-    filename: Path
-        Path to filename
-    """
-    import os
-
-    with open(filename, "r+", encoding="utf-8") as file:
-        # Move the pointer (similar to a cursor in a text editor) to the end of the file
-        file.seek(0, os.SEEK_END)
-
-        # This code means the following code skips the very last character in the file -
-        # i.e. in the case the last line is null we delete the last line
-        # and the penultimate one
-        pos = file.tell() - 1
-
-        # Read each character in the file one at a time from the penultimate
-        # character going backwards, searching for a newline character
-        # If we find a new line, exit the search
-        while pos > 0 and file.read(1) != "\n":
-            pos -= 1
-            file.seek(pos, os.SEEK_SET)
-
-        # So long as we're not at the start of the file, delete all the characters ahead
-        # of this position
-        if pos > 0:
-            file.seek(pos, os.SEEK_SET)
-            file.truncate()
-
-
 def _run_matlab_script_with_spm_standalone(m_file: Path) -> None:
     """Runs a matlab script spm_standalone
 
@@ -492,56 +451,10 @@ def _get_matlab_standalone_command(m_file: Path) -> str:
     SystemError
         If this is run on unsupported platforms.
     """
-    if _is_running_on_mac():
-        return f"cd $SPMSTANDALONE_HOME && ./run_spm12.sh $MCR_HOME batch {m_file}"
-    if _is_running_on_linux():
-        return f"$SPMSTANDALONE_HOME/run_spm12.sh $MCR_HOME batch {m_file}"
-    raise SystemError("Clinica only support Mac OS and Linux")
-
-
-def _is_running_on_os(os: str) -> bool:
-    import platform
-
-    return platform.system().lower().startswith(os)
-
-
-_is_running_on_mac = functools.partial(_is_running_on_os, os="darwin")
-_is_running_on_linux = functools.partial(_is_running_on_os, os="linux")
-
-
-def _run_matlab_script_with_matlab(m_file: str) -> None:
-    """Runs a matlab script using matlab
-
-    Parameters
-    ----------
-    m_file: str
-        Path to the script
-    """
-    import platform
-    from os.path import abspath
-
-    from nipype.interfaces.matlab import MatlabCommand, get_matlab_command
-
-    _add_spm_path_to_matlab_script(m_file)
-    MatlabCommand.set_default_matlab_cmd(get_matlab_command())
-    matlab = MatlabCommand()
-    if platform.system().lower().startswith("linux"):
-        matlab.inputs.args = "-nosoftwareopengl"
-    matlab.inputs.paths = Path(m_file).parent
-    matlab.inputs.script = Path(m_file).stem
-    matlab.inputs.single_comp_thread = False
-    matlab.inputs.logfile = abspath("./matlab_output.log")
-    matlab.run()
-
-
-def _add_spm_path_to_matlab_script(m_file: str) -> None:
-    from clinica.utils.check_dependency import get_spm_home
+    from clinica.utils.check_dependency import get_spm_standalone_home
+    from clinica.utils.spm import _get_real_spm_standalone_file
 
-    with open(m_file, "r") as fp:
-        lines = fp.readlines()
-    lines.insert(0, f"addpath('{get_spm_home()}');")
-    with open(m_file, "w") as fp:
-        fp.writelines(lines)
+    return f"$SPMSTANDALONE_HOME/{_get_real_spm_standalone_file(get_spm_standalone_home())} $MCR_HOME batch {m_file}"
 
 
 def clean_template_file(mat_file: str, template_file: str) -> str:

clinica/pipelines/statistics_volume/template_model_contrast.m

@@ -18,4 +18,5 @@
 matlabbatch{1}.spm.stats.con.consess{2}.tcon.weights = weights2;
 matlabbatch{1}.spm.stats.con.consess{2}.tcon.sessrep = 'none';
 
+% run batch
 spm_jobman('run', matlabbatch)

clinica/pipelines/statistics_volume/template_model_creation.m

@@ -3,6 +3,7 @@
 % Then View > Show m-code
 
 spm('defaults','pet');
+spm_get_defaults('cmdline',true);
 spm_jobman('initcfg');
 
 matlabbatch{1}.spm.stats.factorial_design.dir = {@OUTPUTDIR};
@@ -19,3 +20,6 @@
 matlabbatch{1}.spm.stats.factorial_design.globalc.g_omit = 1;
 matlabbatch{1}.spm.stats.factorial_design.globalm.gmsca.gmsca_no = 1;
 matlabbatch{1}.spm.stats.factorial_design.globalm.glonorm = 1;
+
+
+% no need run batch bc things will be added here by spm

clinica/pipelines/statistics_volume/template_model_estimation.m

@@ -8,4 +8,6 @@
 matlabbatch{1}.spm.stats.fmri_est.spmmat = {@SPMMAT};
 matlabbatch{1}.spm.stats.fmri_est.write_residuals = 0;
 matlabbatch{1}.spm.stats.fmri_est.method.Classical = 1;
-spm_jobman('run', matlabbatch)
+
+% run batch
+spm_jobman('run', matlabbatch)

test/unittests/pipelines/statistics_volume/test_statistics_volume_utils.py

@@ -199,52 +199,6 @@ def test_is_number(input_number, expected):
     assert _is_number(input_number) == expected
 
 
-@pytest.mark.parametrize(
-    "input_data,expected",
-    [
-        ("", ""),
-        ("foo bar baz", "foo bar baz"),
-        ("foo bar baz\n", "foo bar baz\n"),
-        ("foo bar\nbaz", "foo bar"),
-        ("foo bar\nbaz\n", "foo bar"),
-        (
-            _get_tsv_data_two_classes(),
-            "\n".join(_get_tsv_data_two_classes().split("\n")[:-1]),
-        ),
-    ],
-    ids=(
-        "empty content",
-        "one line",
-        "one line with new line",
-        "two lines",
-        "two lines with new line",
-        "multiple lines",
-    ),
-)
-def test_delete_last_line(tmp_path, input_data, expected):
-    from clinica.pipelines.statistics_volume.statistics_volume_utils import (
-        _delete_last_line,
-    )
-
-    (tmp_path / "foo.tsv").write_text(input_data)
-
-    _delete_last_line(tmp_path / "foo.tsv")
-
-    assert (tmp_path / "foo.tsv").read_text() == expected
-
-
-def test_delete_last_line_empty(tmp_path):
-    from clinica.pipelines.statistics_volume.statistics_volume_utils import (
-        _delete_last_line,
-    )
-
-    (tmp_path / "foo.tsv").touch()
-
-    _delete_last_line(tmp_path / "foo.tsv")
-
-    assert (tmp_path / "foo.tsv").read_text() == ""
-
-
 def test_write_covariate_lines_error(tmp_path):
     from clinica.pipelines.statistics_volume.statistics_volume_utils import (
         _write_covariate_lines,
@@ -303,7 +257,7 @@ def test_run_m_script_no_output_file_error(tmp_path, mocker):
     m_file = tmp_path / "script.m"
     m_file.touch()
     mocker.patch(
-        "clinica.pipelines.statistics_volume.statistics_volume_utils._run_matlab_script_with_matlab",
+        "clinica.pipelines.statistics_volume.statistics_volume_utils._run_matlab_script_with_spm_standalone",
         return_value=None,
     )
     (tmp_path / "spm_home_folder").mkdir()
@@ -330,7 +284,7 @@ def test_run_m_script(tmp_path, mocker):
     expected_output_file = expected_output_folder / "SPM.mat"
     expected_output_file.touch()
     mocker.patch(
-        "clinica.pipelines.statistics_volume.statistics_volume_utils._run_matlab_script_with_matlab",
+        "clinica.pipelines.statistics_volume.statistics_volume_utils._run_matlab_script_with_spm_standalone",
         return_value=None,
     )
     (tmp_path / "spm_home_folder").mkdir()
@@ -339,51 +293,21 @@ def test_run_m_script(tmp_path, mocker):
         assert run_m_script(m_file) == str(expected_output_file)
 
 
-@pytest.mark.parametrize(
-    "mocked_values,expected",
-    [
-        (
-            [True, False],
-            "cd $SPMSTANDALONE_HOME && ./run_spm12.sh $MCR_HOME batch script.m",
-        ),
-        ([False, True], "$SPMSTANDALONE_HOME/run_spm12.sh $MCR_HOME batch script.m"),
-    ],
-    ids=("running on MAC OS", "running on Linux"),
-)
-def test_get_matlab_standalone_command(mocker, mocked_values, expected):
-    from clinica.pipelines.statistics_volume.statistics_volume_utils import (
-        _get_matlab_standalone_command,
-    )
-
-    for func, return_value in zip(
-        ["_is_running_on_mac", "_is_running_on_linux"], mocked_values
-    ):
-        mocker.patch(
-            f"clinica.pipelines.statistics_volume.statistics_volume_utils.{func}",
-            return_value=return_value,
-        )
-
-    assert _get_matlab_standalone_command(Path("script.m")) == expected
-
-
-def test_get_matlab_standalone_command_system_error(mocker):
+def test_get_matlab_standalone_command():
+    import clinica.utils.check_dependency as check_dep
+    import clinica.utils.spm as spm_utils
     from clinica.pipelines.statistics_volume.statistics_volume_utils import (
         _get_matlab_standalone_command,
     )
 
-    for func, return_value in zip(
-        ["_is_running_on_mac", "_is_running_on_linux"], [False, False]
-    ):
-        mocker.patch(
-            f"clinica.pipelines.statistics_volume.statistics_volume_utils.{func}",
-            return_value=return_value,
-        )
-
-    with pytest.raises(
-        SystemError,
-        match="Clinica only support Mac OS and Linux",
-    ):
-        _get_matlab_standalone_command(Path("script.m"))
+    with mock.patch.object(spm_utils, "_get_real_spm_standalone_file") as mock_get_real:
+        with mock.patch.object(check_dep, "get_spm_standalone_home") as mock_get_spm:
+            mock_get_real.return_value = "run_spm12.sh"
+            assert (
+                _get_matlab_standalone_command(Path("script.m"))
+                == f"$SPMSTANDALONE_HOME/run_spm12.sh $MCR_HOME batch script.m"
+            )
+            mock_get_spm.assert_called_once()
 
 
 @pytest.mark.parametrize(