def test_invalid_image():
fake_im = "fake.nii"
if os.path.exists(fake_im):
os.remove(fake_im)
qv = QuickViewer(["data/ct.nii", fake_im], show=False)
assert len(qv.viewer) == 1
qv = QuickViewer(fake_im, show=False)
assert not len(qv.viewer)
def test_dose():
opacity = 0.3
cmap = "gray"
qv = QuickViewer("data/MI_BSpline30/result.0.nii",
dose="data/MI_BSpline30/spatialJacobian.nii",
dose_kwargs={"cmap": cmap},
dose_opacity=opacity, show=False)
assert qv.viewer[0].ui_dose.value == opacity
def test_struct_colours():
colour = 'cyan'
# Test with wildcard filename
qv = QuickViewer("data/ct.nii", structs="data/structs/*parotid*",
struct_colours={"*parotid*": colour},
show=False)
assert len(qv.viewer[0].im.structs) == 2
assert qv.viewer[0].im.structs[0].color == to_rgba(colour)
# Test with structure name
qv = QuickViewer("data/ct.nii", structs="data/structs/*right_parotid*",
struct_colours={"right parotid": colour},
show=False)
assert qv.viewer[0].im.structs[0].color == to_rgba(colour)
# Test with wildcard structure name
qv = QuickViewer("data/ct.nii", structs="data/structs/*right_parotid*",
struct_colours={"*parotid": colour}, show=False)
assert qv.viewer[0].im.structs[0].color == to_rgba(colour)
def test_structs():
# Test directory
qv = QuickViewer("data/ct.nii", structs="data/structs", show=False)
assert len(qv.viewer[0].im.structs) == len(os.listdir("data/structs")) - 1
# Test list of files
qv = QuickViewer(
"data/ct.nii",
structs=[
"data/structs/RTSTRUCT_CT_20140715_113632_002_mpc.nii.gz",
"data/structs/RTSTRUCT_CT_20140715_113632_002_right_smg.nii.gz"
], show=False)
assert len(qv.viewer[0].im.structs) == 2
# Test wildcard directory
qv = QuickViewer("data/ct.nii", structs="data/str*", show=False)
assert len(qv.viewer[0].im.structs) == len(os.listdir("data/structs")) - 1
# Test wildcard files
qv = QuickViewer("data/ct.nii", show=False,
structs=["data/structs/*parotid*", "data/structs/*mpc*"])
assert len(qv.viewer[0].im.structs) == 3
def view(self, **kwargs):
'''View with QuickViewer.'''
from quickviewer import QuickViewer
qv_kwargs = {
'hu': [self.min_hu, self.max_hu],
'title': '',
'origin': self.origin,
'voxel_size': self.voxel_size,
'mpl_kwargs': {'interpolation': 'none'},
}
qv_kwargs.update(kwargs)
structs = self.get_struct_data()
QuickViewer(self.get_data(), structs=structs, **qv_kwargs)
def view(self, **kwargs):
"""View with QuickViewer."""
from quickviewer import QuickViewer
qv_kwargs = {
"hu": [self.min_hu, self.max_hu],
"title": "",
"origin": self.origin,
"voxel_sizes": self.voxel_sizes,
"mpl_kwargs": {"interpolation": "none"},
}
qv_kwargs.update(kwargs)
structs = self.get_struct_data()
QuickViewer(self.get_data(), structs=structs, **qv_kwargs)
def test_plots_per_row():
qv = QuickViewer(["data/ct.nii", "data/ct.nii"], plots_per_row=1,
show=False)
def test_orthog_view():
qv = QuickViewer("data/ct.nii", orthog_view=True, show=False)
assert isinstance(qv.viewer[0], OrthogViewer)
def test_share_slider():
qv = QuickViewer(['data/MI_Translation/ct_relapse.nii',
'data/MI_Translation/result.0.nii'], share_slider=False,
show=False)
assert len(qv.viewer) == 2
assert len(qv.slider_boxes) == 2
def test_translation():
QuickViewer(['data/MI_Translation/ct_relapse.nii',
'data/MI_Translation/result.0.nii'],
translation=True, show=False)
def test_init_views():
QuickViewer("data/ct.nii", init_view="x-y", show=False)
QuickViewer("data/ct.nii", init_view="x-z", show=False)
QuickViewer("data/ct.nii", init_view="y-z", show=False)
def test_custom_hu():
v = (-500, 100)
qv = QuickViewer("data/ct.nii", hu=v, show=False)
assert qv.viewer[0].ui_hu.value == v
def test_different_size_images():
qv = QuickViewer(['data/MI_Translation/ct_planning.nii',
'data/MI_Translation/result.0.nii'], show=False)
assert len(qv.viewer) == 2
assert len(qv.slider_boxes) == 2
def test_downsample():
QuickViewer("data/ct.ni", downsample=(5, 4, 2), show=False)
def test_zoom():
QuickViewer("data/ct.nii", zoom=2, show=False)
def test_struct_mask():
opacity = 0.6
qv = QuickViewer("data/ct.nii", structs="data/structs/*mpc*",
struct_plot_type="mask", struct_opacity=opacity,
show=False)
assert qv.viewer[0].ui_struct_opacity.value == opacity
def test_comparison_only():
qv = QuickViewer(['data/MI_Translation/ct_relapse.nii',
'data/MI_Translation/result.0.nii'],
show_cb=True, show_diff=True, show_overlay=True,
comparison_only=True, show=False)
assert len(qv.comparison) == 3
def test_single_image():
qv = QuickViewer("data/ct.nii", show=False)
assert len(qv.viewer) == 1
def test_titles():
title = ["test1", "test2"]
qv = QuickViewer(["data/ct.nii", "data/ct.nii"], title=title, show=False)
assert qv.viewer[0].im.title == title[0]
assert qv.viewer[1].im.title == title[1]
def test_duplicate_image():
qv = QuickViewer(["data/ct.nii", "data/ct.nii"], show=False)
assert len(qv.viewer) == 2
assert not len(qv.slider_boxes)
def test_multiple_images():
qv = QuickViewer(['data/MI_Translation/ct_relapse.nii',
'data/MI_Translation/result.0.nii'], show=False)
assert len(qv.viewer) == 2
assert not len(qv.slider_boxes)
def test_jacobian():
opacity = 0.2
qv = QuickViewer("data/MI_BSpline30/result.0.nii",
jacobian="data/MI_BSpline30/spatialJacobian.nii",
jacobian_opacity=opacity, show=False)
assert qv.viewer[0].ui_jac_opacity.value == opacity
def test_init_idx():
init_sl = 50
qv = QuickViewer("data/ct.nii", init_sl=init_sl, scale_in_mm=False,
show=False)
assert qv.viewer[0].ui_slice.value == init_sl
def test_df_grid():
qv = QuickViewer("data/MI_BSpline30/result.0.nii",
df="data/MI_BSpline30/deformationField.nii", show=False)
assert qv.viewer[0].ui_df.value == "grid"
def test_figsize():
QuickViewer("data/ct.nii", figsize=10, show=False)
def test_df_quiver():
qv = QuickViewer("data/MI_BSpline30/result.0.nii",
df="data/MI_BSpline30/deformationField.nii",
df_plot_type="quiver", show=False)
assert qv.viewer[0].ui_df.value == "quiver"
def test_suptitle():
title = "test"
qv = QuickViewer("data/ct.nii", suptitle=title, show=False)
assert qv.suptitle == title
def test_save():
output = "data/test_march2.pdf"
# if os.path.isfile(output):
# os.remove(output)
QuickViewer("data/ct.nii", save_as=output, show=False)
kwargs = {k: v for k, v in kwargs.items() if v is not None}
# Swap negative booleans for positive
swaps = {
"no_share_slider": "share_slider",
"no_struct_legend": "struct_legend",
"no_mm": "scale_in_mm",
"no_show": "show"
}
for sw1, sw2 in swaps.items():
if sw1 in kwargs:
kwargs[sw2] = kwargs[sw1]
del kwargs[sw1]
# Parse structure colours
if "struct_colours" in kwargs:
sc = kwargs["struct_colours"]
if len(sc) % 2 != 0:
raise SyntaxError("Please provide a colour for every structure name!")
new_sc = {sc[2 * i]: sc[2 * i + 1] for i in range(0, int(len(sc) / 2))}
kwargs["struct_colours"] = new_sc
# Set downsample and zoom to be single values
for opt in ["zoom", "downsample"]:
if opt in kwargs:
if len(kwargs[opt]) == 1:
kwargs[opt] = kwargs[opt][0]
# Launch QuickViewer
QuickViewer(**kwargs)
def test_mask():
QuickViewer("data/ct.nii", mask=("data/structs/RTSTRUCT_CT_20140715_113632"
"_002_alterio_pcs.nii.gz"), show=False)