def test_generate_mask_with_untrusted_polygon_and_pixels(
experiments_masks, tmpdir):
experiments, masks = experiments_masks
params = phil_scope.fetch(
phil.parse("""
untrusted {
polygon = 100 100 100 200 200 200 200 100
}
untrusted {
pixel = 0 0
}
untrusted {
pixel = 1 1
}""")).extract()
with tmpdir.as_cwd():
generate_mask(experiments, params)
assert all(tmpdir.join(mask).check() for mask in masks)
with tmpdir.join(masks[0]).open("rb") as fh:
mask = pickle.load(fh)
assert not mask[0][0, 0]
assert not mask[0][1, 1]
assert mask[0][0, 1]
def test_generate_mask_with_resolution_range(input_experiment_list, tmpdir):
params = phil_scope.fetch().extract()
params.resolution_range = [(2, 3)]
with tmpdir.as_cwd():
generate_mask(input_experiment_list, params)
assert tmpdir.join("pixels.mask").check()
def test_generate_mask_with_untrusted_polygon_and_pixels(input_experiment_list, tmpdir):
params = phil_scope.fetch(
phil.parse(
"""
untrusted {
polygon = 100 100 100 200 200 200 200 100
}
untrusted {
pixel = 0 0
}
untrusted {
pixel = 1 1
}"""
)
).extract()
with tmpdir.as_cwd():
generate_mask(input_experiment_list, params)
assert tmpdir.join("pixels.mask").check()
with tmpdir.join("pixels.mask").open("rb") as fh:
mask = pickle.load(fh)
assert not mask[0][0, 0]
assert not mask[0][1, 1]
assert mask[0][0, 1]
def test_generate_mask(experiments_masks, tmpdir):
experiments, masks = experiments_masks
params = phil_scope.fetch().extract()
with tmpdir.as_cwd():
generate_mask(experiments, params)
assert all(tmpdir.join(mask).check() for mask in masks)
def test_generate_mask_with_ice_rings(input_experiment_list, tmpdir):
params = phil_scope.fetch().extract()
params.ice_rings.filter = True
params.ice_rings.d_min = 2
with tmpdir.as_cwd():
generate_mask(input_experiment_list, params)
assert tmpdir.join("pixels.mask").check()
def test_generate_mask_with_d_min_d_max(input_experiment_list, tmpdir):
params = phil_scope.fetch().extract()
params.d_min = 3
params.d_max = 2
with tmpdir.as_cwd():
generate_mask(input_experiment_list, params)
assert tmpdir.join("pixels.mask").check()
def test_generate_mask_with_untrusted_circle(experiments_masks, tmpdir):
experiments, masks = experiments_masks
params = phil_scope.fetch(phil.parse("untrusted.circle=100,100,10")).extract()
with tmpdir.as_cwd():
generate_mask(experiments, params)
assert all(tmpdir.join(mask).check() for mask in masks)
def test_generate_mask_with_resolution_range(experiments_masks, tmpdir):
experiments, masks = experiments_masks
params = phil_scope.fetch().extract()
params.resolution_range = [(2, 3)]
with tmpdir.as_cwd():
generate_mask(experiments, params)
assert all(tmpdir.join(mask).check() for mask in masks)
def test_generate_mask_with_ice_rings(experiments_masks, tmpdir):
experiments, masks = experiments_masks
params = phil_scope.fetch().extract()
params.ice_rings.filter = True
params.ice_rings.d_min = 2
with tmpdir.as_cwd():
generate_mask(experiments, params)
assert all(tmpdir.join(mask).check() for mask in masks)
def test_generate_mask_with_untrusted_rectangle(input_experiment_list, tmpdir):
params = phil_scope.fetch(
phil.parse("untrusted.rectangle=100,200,100,200")
).extract()
params.output.experiments = "masked.expt"
with tmpdir.as_cwd():
generate_mask(input_experiment_list, params)
assert tmpdir.join("pixels.mask").check()
assert tmpdir.join("masked.expt").check()
experiments = load.experiment_list(tmpdir.join("masked.expt").strpath)
imageset = experiments.imagesets()[0]
assert imageset.external_lookup.mask.filename == tmpdir.join("pixels.mask").strpath
def test_generate_mask_with_untrusted_rectangle(experiments_masks, tmpdir):
experiments, masks = experiments_masks
params = phil_scope.fetch(
phil.parse("untrusted.rectangle=100,200,100,200")).extract()
params.output.experiments = "masked.expt"
with tmpdir.as_cwd():
generate_mask(experiments, params)
assert all(tmpdir.join(mask).check() for mask in masks)
assert tmpdir.join("masked.expt").check()
experiments = ExperimentList.from_file(tmpdir.join("masked.expt").strpath)
imageset = experiments.imagesets()[0]
assert imageset.external_lookup.mask.filename == tmpdir.join(
masks[0]).strpath
def test_generate_whole_panel_mask(experiments_masks, tmpdir):
experiments, masks = experiments_masks
params = phil_scope.fetch(phil.parse("""
untrusted {
panel = 0
}
""")).extract()
with tmpdir.as_cwd():
generate_mask(experiments, params)
assert all(tmpdir.join(mask).check() for mask in masks)
with tmpdir.join(masks[0]).open("rb") as fh:
mask = pickle.load(fh)
assert mask[0].count(False) == len(mask[0])
def test_generate_mask_function_with_untrusted_rectangle(input_experiment_list, tmpdir):
params = phil_scope.fetch().extract()
params.output.mask = tmpdir.join("pixels4.mask").strpath
params.output.experiments = tmpdir.join("masked.expt").strpath
params.untrusted.rectangle = [100, 200, 100, 200]
generate_mask(input_experiment_list, params)
assert tmpdir.join("pixels4.mask").check() or all(
tmpdir.join("pixels4_{:d}.mask".format(i + 1)).check() for i in range(4)
)
assert tmpdir.join("masked.expt").check()
experiments = load.experiment_list(tmpdir.join("masked.expt").strpath)
imageset = experiments.imagesets()[0]
associated_masks = [
tmpdir.join(f).strpath for f in ("pixels4.mask", "pixels4_1.mask")
]
assert imageset.external_lookup.mask.filename in associated_masks
def test_generate_mask_function_with_untrusted_rectangle(experiments_masks, tmpdir):
experiments, masks = experiments_masks
masks = [tmpdir.join(mask.replace("pixels", "pixels4")) for mask in masks]
params = phil_scope.fetch().extract()
params.output.mask = tmpdir.join("pixels4.mask").strpath
params.output.experiments = tmpdir.join("masked.expt").strpath
params.untrusted.rectangle = [100, 200, 100, 200]
generate_mask(experiments, params)
assert all(mask.check() for mask in masks)
assert tmpdir.join("masked.expt").check()
experiments = ExperimentList.from_file(tmpdir.join("masked.expt").strpath)
associated_masks = [
imageset.external_lookup.mask.filename for imageset in experiments.imagesets()
]
assert all(assoc_mask == mask for assoc_mask, mask in zip(associated_masks, masks))
def test_generate_mask_trusted_range(dials_data, tmpdir):
# https://github.com/dials/dials/issues/978
image_files = [
f.strpath for f in dials_data("x4wide").listdir("*.cbf", sort=True)
]
with tmpdir.as_cwd():
# Import as usual
importer = ImageImporter(import_phil_scope)
importer.import_image(["output.experiments=no-overloads.expt"] +
image_files)
experiments = ExperimentList.from_file(
tmpdir.join("no-overloads.expt").strpath)
params = phil_scope.fetch(
phil.parse("untrusted.rectangle=100,200,100,200")).extract()
params.output.mask = "pixels1.mask"
generate_mask(experiments, params)
# Import with narrow trusted range to produce overloads
importer = ImageImporter(import_phil_scope)
importer.import_image(
["trusted_range=-1,100", "output.experiments=overloads.expt"] +
image_files)
experiments = ExperimentList.from_file(
tmpdir.join("overloads.expt").strpath)
params = phil_scope.fetch(
phil.parse("untrusted.rectangle=100,200,100,200")).extract()
params.output.mask = "pixels2.mask"
generate_mask(experiments, params)
with tmpdir.join("pixels1.mask").open("rb") as fh:
mask1 = pickle.load(fh)
with tmpdir.join("pixels2.mask").open("rb") as fh:
mask2 = pickle.load(fh)
# Overloads should not be included in the mask
assert (mask1[0] == mask2[0]).all_eq(True)
def test_generate_mask_with_untrusted_circle(input_experiment_list, tmpdir):
params = phil_scope.fetch(phil.parse("untrusted.circle=100,100,10")).extract()
with tmpdir.as_cwd():
generate_mask(input_experiment_list, params)
assert tmpdir.join("pixels.mask").check()
