From 04c797c8c0994fe42e8d778e126488fedb146b3f Mon Sep 17 00:00:00 2001
From: Alexandre D'Astous <po09i@hotmail.com>
Date: Mon, 9 Nov 2020 20:21:07 -0500
Subject: [PATCH] Initial set up for CLI and test

---
 shimmingtoolbox/cli/prepare_fieldmap.py | 19 ++++++++++++++++
 test/cli/test_prepare_fieldmap.py       | 29 +++++++++++++++++++++++++
 2 files changed, 48 insertions(+)
 create mode 100644 shimmingtoolbox/cli/prepare_fieldmap.py
 create mode 100644 test/cli/test_prepare_fieldmap.py

diff --git a/shimmingtoolbox/cli/prepare_fieldmap.py b/shimmingtoolbox/cli/prepare_fieldmap.py
new file mode 100644
index 000000000..1afecc036
--- /dev/null
+++ b/shimmingtoolbox/cli/prepare_fieldmap.py
@@ -0,0 +1,19 @@
+#!/usr/bin/python3
+# -*- coding: utf-8 -*
+
+import click
+import os
+
+CONTEXT_SETTINGS = dict(help_option_names=['-h', '--help'])
+
+
+@click.command(
+    context_settings=CONTEXT_SETTINGS,
+)
+@click.option('-phase', 'fname_phase', type=click.Path(), required=True, help="Input path of phase nifti file")
+@click.option('-mag', 'fname_mag', type=click.Path(), required=True, help="Input path of mag nifti file")
+@click.option('-output', 'path_output', type=click.Path(), default=os.curdir, help="Output path for the fieldmap")
+def prepare_fieldmap_cli(fname_phase, fname_mag, path_output):
+    """Creates fieldmap from phase and magnitute images"""
+    
+    pass
diff --git a/test/cli/test_prepare_fieldmap.py b/test/cli/test_prepare_fieldmap.py
new file mode 100644
index 000000000..cb4402a4c
--- /dev/null
+++ b/test/cli/test_prepare_fieldmap.py
@@ -0,0 +1,29 @@
+#!/usr/bin/python3
+# -*- coding: utf-8 -*
+
+from click.testing import CliRunner
+import os
+import pathlib
+import tempfile
+
+from shimmingtoolbox.cli.prepare_fieldmap import prepare_fieldmap_cli
+from shimmingtoolbox import __dir_testing__
+
+
+def test_cli_prepare_fieldmap():
+    with tempfile.TemporaryDirectory(prefix='st_' + pathlib.Path(__file__).stem) as tmp:
+        runner = CliRunner()
+
+        # TODO: use phase 1 and phase 2 from sub_fieldmap
+        fname_phasediff = os.path.join(__dir_testing__, 'realtime_zshimming_data', 'nifti', 'sub-example', 'fmap',
+                                       'sub-example_phasediff.nii.gz')
+        fname_mag = os.path.join(__dir_testing__, 'realtime_zshimming_data', 'nifti', 'sub-example', 'fmap',
+                                 'sub-example_magnitude1.nii.gz')
+        # fname_phase1 = os.path.join(__dir_testing__, 'sub-fieldmap', 'fmap', 'sub-fieldmap_phase1.nii.gz')
+        # fname_phase2 = os.path.join(__dir_testing__, 'sub-fieldmap', 'fmap', 'sub-fieldmap_phase2.nii.gz')
+        # fname_mag = os.path.join(__dir_testing__, 'sub-fieldmap', 'fmap', 'sub-fieldmap_magnitude1.nii.gz')
+
+        result = runner.invoke(prepare_fieldmap_cli, ['-phase', fname_phasediff, '-mag', fname_mag,
+                                                      '-output', tmp])
+
+    assert result.exit_code == 0