Cleanup

shimmingtoolbox/cli/prepare_fieldmap.py

@@ -26,19 +26,13 @@
 @click.option('-unwrapper', type=click.Choice(['prelude']), default='prelude', help="Algorithm for unwrapping")
 @click.option('-output', 'fname_output', type=click.Path(), default=os.curdir, help="Output filename for the fieldmap")
 @click.option('-mask', 'fname_mask', type=click.Path(), help="Input path for a mask. Used for PRELUDE")
-@click.option('-threshold', 'threshold', type=int, help="Threshold for masking. Used for: PRELUDE")
+@click.option('-threshold', 'threshold', type=float, help="Threshold for masking. Used for: PRELUDE")
 def prepare_fieldmap_cli(phase, fname_mag, unwrapper, fname_output, fname_mask, threshold):
     """Creates fieldmap from phase and magnitude images
 
-    Args:
-        phase: Input path of phase nifti file, oredered in ascending order i.e. echo1, echo2, etc...
+    phase: Input path of phase nifti file, oredered in ascending order i.e. echo1, echo2, etc...
     """
 
-    # flag: -unwrapper DEFAULT prelude, -method DEFAULT, mask fname
-    # Make sure we have a mag input, make sure we have a phase input
-    # Look for method, compare to number of inputs (look in header to make sure #inputs work with given input)
-    # for phase (phasediff or echoes)
-
     # Get the time between echoes and calculate phase difference depending on number of echoes
     if len(phase) == 1:
         # phase should be a phasediff
@@ -91,6 +85,7 @@ def prepare_fieldmap_cli(phase, fname_mag, unwrapper, fname_output, fname_mask,
 
     else:
         # TODO: More echoes
+        # TODO: Add method once multiple methods are implemented
         raise RuntimeError(" Number of phase filenames not supported")
 
     # Import mask

test/cli/test_prepare_fieldmap.py

@@ -5,12 +5,13 @@
 import os
 import pathlib
 import tempfile
+import pytest
 
 from shimmingtoolbox.cli.prepare_fieldmap import prepare_fieldmap_cli
 from shimmingtoolbox import __dir_testing__
 
 
-# Add pytest prelude dependency
+@pytest.mark.prelude
 def test_cli_prepare_fieldmap_1_echo():
     with tempfile.TemporaryDirectory(prefix='st_' + pathlib.Path(__file__).stem) as tmp:
         runner = CliRunner()
@@ -28,7 +29,7 @@ def test_cli_prepare_fieldmap_1_echo():
         assert os.path.isfile(fname_output)
 
 
-# Add pytest prelude dependency
+@pytest.mark.prelude
 def test_cli_prepare_fieldmap_2_echos():
     with tempfile.TemporaryDirectory(prefix='st_' + pathlib.Path(__file__).stem) as tmp:
         runner = CliRunner()