Adaptation of input and output file for the test

test/cli/test_cli_mask.py

@@ -0,0 +1,57 @@
+#!/usr/bin/env python3
+
+import pathlib
+import tempfile
+import os
+
+from click.testing import CliRunner
+from shimmingtoolbox.cli.mask import mask
+from shimmingtoolbox import __dir_testing__
+
+
+def test_cli_mask_cube():
+    with tempfile.TemporaryDirectory(prefix='st_' + pathlib.Path(__file__).stem) as tmp:
+        runner = CliRunner()
+
+        inp = os.path.join(__dir_testing__, 'sub-fieldmap/fmap/sub-fieldmap_phase1.nii.gz')
+        out = os.path.join(tmp, 'nifti1')
+        dim1 = 50
+        dim2 = 30
+        dim3 = 5
+
+        result = runner.invoke(mask, ['cube', '-input', inp, '-output', out, '-len_dim1', dim1, '-len_dim2', dim2,
+                                      '-len_dim3', dim3])
+
+        assert result.exit_code == 0
+        assert result is not None
+        assert len(os.listdir(out)) != 0
+
+
+def test_cli_mask_square():
+    with tempfile.TemporaryDirectory(prefix='st_' + pathlib.Path(__file__).stem) as tmp:
+        runner = CliRunner()
+
+        inp = os.path.join(__dir_testing__, 'sub-fieldmap/fmap/sub-fieldmap_phase1.nii.gz')
+        out = os.path.join(tmp, 'nifti2')
+        dim1 = 50
+        dim2 = 30
+
+        result = runner.invoke(mask, ['square', '-input', inp, '-output', out, '-len_dim1', dim1, '-len_dim2', dim2])
+
+        assert result.exit_code == 0
+        assert result is not None
+        assert len(os.listdir(out)) != 0
+
+
+def test_cli_mask_threshold():
+    with tempfile.TemporaryDirectory(prefix='st_' + pathlib.Path(__file__).stem) as tmp:
+        runner = CliRunner()
+
+        inp = os.path.join(__dir_testing__, 'sub-fieldmap/fmap/sub-fieldmap_phase1.nii.gz')
+        out = os.path.join(tmp, 'nifti3')
+        thr = 30
+        result = runner.invoke(mask, ['mask-threshold', '-input', inp, '-output', out, '-thr', thr])
+
+        assert result.exit_code == 0
+        assert result is not None
+        assert len(os.listdir(out)) != 0