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TST: Validate nib-diff dtype command-line option #672

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Merged
merged 4 commits into from
Oct 12, 2018
Merged

TST: Validate nib-diff dtype command-line option #672

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7315931
storing changes for main testing
chrispycheng Oct 10, 2018
974a3a9
cmdline test added for dtype access
chrispycheng Oct 11, 2018
5361c7f
ENH: adjusted some strings etc to fit the width and avoid duplicate s…
yarikoptic Oct 11, 2018
edb72bc
Merge branch 'master' into enh-diff-dtype
effigies Oct 11, 2018
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22 changes: 13 additions & 9 deletions nibabel/cmdline/diff.py
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Original file line number Diff line number Diff line change
Expand Up @@ -38,22 +38,25 @@ def get_opt_parser():

Option("-H", "--header-fields",
dest="header_fields", default='all',
help="Header fields (comma separated) to be printed as well (if present)"),
help="Header fields (comma separated) to be printed as well"
" (if present)"),

Option("--ma", "--data-max-abs-diff",
dest="data_max_abs_diff",
type=float,
default=0.0,
help="Maximal absolute difference in data between files to tolerate."),
help="Maximal absolute difference in data between files"
" to tolerate."),

Option("--mr", "--data-max-rel-diff",
dest="data_max_rel_diff",
type=float,
default=0.0,
help="Maximal relative difference in data between files to tolerate."
" If --data-max-abs-diff is also specified, only the data points "
" with absolute difference greater than that value would be "
" considered for relative difference check."),
help="Maximal relative difference in data between files to"
" tolerate. If --data-max-abs-diff is also specified,"
" only the data points with absolute difference greater"
" than that value would be considered for relative"
" difference check."),
Option("--dt", "--datatype",
dest="dtype",
default=np.float64,
Expand Down Expand Up @@ -302,15 +305,16 @@ def display_diff(files, diff):
return output


def diff(files, header_fields='all', data_max_abs_diff=None, data_max_rel_diff=None,
dtype=np.float64):
def diff(files, header_fields='all', data_max_abs_diff=None,
data_max_rel_diff=None, dtype=np.float64):
assert len(files) >= 2, "Please enter at least two files"

file_headers = [nib.load(f).header for f in files]

# signals "all fields"
if header_fields == 'all':
# TODO: header fields might vary across file types, thus prior sensing would be needed
# TODO: header fields might vary across file types,
# thus prior sensing would be needed
header_fields = file_headers[0].keys()
else:
header_fields = header_fields.split(',')
Expand Down
4 changes: 4 additions & 0 deletions nibabel/tests/test_scripts.py
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Original file line number Diff line number Diff line change
Expand Up @@ -95,6 +95,10 @@ def check_nib_diff_examples():
code, stdout, stderr = run_command(['nib-diff'] + fnames4, check_code=False)
assert_equal(stdout, "These files are identical.")

code, stdout, stderr = run_command(['nib-diff', '--dt', 'float64'] + fnames, check_code=False)
for item in checked_fields:
assert_true(item in stdout)



@script_test
Expand Down