def translate_line(steno3d_resource, view, _lookup_dict=None):
"""Translate Steno3D line into LineSet Element and Arrays"""
vertices = files.Array(steno3d_resource.mesh.vertices)
segments = files.Array(steno3d_resource.mesh.segments)
data = [
translate_binder(dat, view, _lookup_dict=_lookup_dict)
for dat in steno3d_resource.data
]
element = spatial.ElementLineSet(
name=steno3d_resource.title or '',
description=steno3d_resource.description or '',
vertices=vertices,
segments=segments,
data=data,
)
if steno3d_resource.mesh.opts.view_type == 'tube':
opts = spatial.OptionsTubes(radius={'value': 10})
else:
opts = spatial.OptionsLines()
opts.visible = True
opts.color.value = 'random'
opts.opacity.value = 1.
if steno3d_resource.opts.color is not None:
opts.color.value = steno3d_resource.opts.color
if steno3d_resource.opts.opacity is not None:
opts.opacity.value = steno3d_resource.opts.opacity
element.defaults = opts
view.contents += [vertices, segments, element]
view.elements += [element]
if _lookup_dict is not None and hasattr(steno3d_resource, '_upload_data'):
_lookup_dict.update({steno3d_resource._upload_data['uid']: element})
return element
def translate_data_array(steno3d_data, location, view, _lookup_dict=None):
"""Translate Steno3D array data into Data, Mapping, and Arrays"""
arr = files.Array(steno3d_data.array)
data = spatial.DataBasic(
name=steno3d_data.title or '',
description=steno3d_data.description or '',
array=arr,
location=location,
)
if steno3d_data.colormap is not None:
gradient = files.Array(steno3d_data.colormap)
mapping = spatial.MappingContinuous(
gradient=gradient,
data_controls=[
np.nanmin(steno3d_data.array),
np.nanmax(steno3d_data.array),
],
gradient_controls=[0., 1.],
visibility=[True, True, True],
)
data.mappings = [mapping]
view.contents += [mapping, gradient]
view.contents += [arr, data]
if _lookup_dict is not None and hasattr(steno3d_data, '_upload_data'):
_lookup_dict.update({steno3d_data._upload_data['uid']: data})
return data
def translate_data_category(steno3d_data, location, view, _lookup_dict=None):
"""Translate Steno3D category data into Data, Mappings, and Array"""
arr = files.Array(steno3d_data.array)
data = spatial.DataCategory(
name=steno3d_data.title or '',
description=steno3d_data.description or '',
array=arr,
location=location,
)
if steno3d_data.categories is not None:
mapping = spatial.MappingCategory(
values=steno3d_data.categories,
indices=list(range(len(steno3d_data.categories))),
visibility=[True] * len(steno3d_data.categories),
)
data.categories = mapping
view.contents.append(mapping)
if steno3d_data.colormap is not None:
mapping = spatial.MappingCategory(
values=steno3d_data.colormap,
indices=list(range(len(steno3d_data.colormap))),
visibility=[True] * len(steno3d_data.colormap),
)
if not data.categories:
data.categories = mapping
else:
data.mappings = [mapping]
view.contents.append(mapping)
view.contents += [arr, data]
if _lookup_dict is not None and hasattr(steno3d_data, '_upload_data'):
_lookup_dict.update({steno3d_data._upload_data['uid']: data})
return data
def translate_point(steno3d_resource, view, _lookup_dict=None):
"""Translate Steno3D point into PointSet Element and Array"""
vertices = files.Array(steno3d_resource.mesh.vertices)
data = [
translate_binder(dat, view, _lookup_dict=_lookup_dict)
for dat in steno3d_resource.data
] + [
translations[tex.__class__](tex, view, _lookup_dict=_lookup_dict)
for tex in steno3d_resource.textures
]
element = spatial.ElementPointSet(
name=steno3d_resource.title or '',
description=steno3d_resource.description or '',
vertices=vertices,
data=data,
)
if steno3d_resource.opts.color is not None:
element.defaults.color.value = steno3d_resource.opts.color
if steno3d_resource.opts.opacity is not None:
element.defaults.opacity.value = steno3d_resource.opts.opacity
view.contents += [vertices, element]
view.elements += [element]
if _lookup_dict is not None and hasattr(steno3d_resource, '_upload_data'):
_lookup_dict.update({steno3d_resource._upload_data['uid']: element})
return element
def translate_data_discrete(steno3d_data, location, view, _lookup_dict=None):
"""Translate Steno3D discrete data into Data, Mapping, and Array"""
arr = files.Array(steno3d_data.array)
if steno3d_data.range_visibility is not None:
visibility = [bool(rv) for rv in steno3d_data.range_visibility]
else:
visibility = [True] * (len(steno3d_data.end_values) + 1)
if steno3d_data.end_inclusive is not None:
end_inclusive = [bool(ei) for ei in steno3d_data.end_inclusive]
else:
end_inclusive = [True] * len(steno3d_data.end_values)
mapping = spatial.MappingDiscrete(
end_points=steno3d_data.end_values,
visibility=visibility,
end_inclusive=end_inclusive,
values=steno3d_data.colormap
or [''] * (len(steno3d_data.end_values) + 1),
)
data = spatial.DataBasic(name=steno3d_data.title or '',
description=steno3d_data.description or '',
array=arr,
location=location,
mappings=[mapping])
view.contents += [arr, mapping, data]
if _lookup_dict is not None and hasattr(steno3d_data, '_upload_data'):
_lookup_dict.update({steno3d_data._upload_data['uid']: data})
return data
def translate_surface(steno3d_resource, view, _lookup_dict=None):
"""Translate Steno3D surface into Surface Element and Arrays"""
data = [
translate_binder(dat, view, _lookup_dict=_lookup_dict)
for dat in steno3d_resource.data
] + [
translations[tex.__class__](tex, view, _lookup_dict=_lookup_dict)
for tex in steno3d_resource.textures
]
if isinstance(steno3d_resource.mesh, steno3d.Mesh2D):
vertices = files.Array(steno3d_resource.mesh.vertices)
triangles = files.Array(steno3d_resource.mesh.triangles)
element = spatial.ElementSurface(
name=steno3d_resource.title or '',
description=steno3d_resource.description or '',
vertices=vertices,
triangles=triangles,
data=data,
)
view.contents += [vertices, triangles]
else:
element = spatial.ElementSurfaceGrid(
name=steno3d_resource.title or '',
description=steno3d_resource.description or '',
tensor_u=list(steno3d_resource.mesh.h1),
tensor_v=list(steno3d_resource.mesh.h2),
axis_u=steno3d_resource.mesh.U,
axis_v=steno3d_resource.mesh.V,
origin=steno3d_resource.mesh.O,
data=data,
)
if (steno3d_resource.mesh.Z is not None
and len(steno3d_resource.mesh.Z)):
offset_w = files.Array(steno3d_resource.mesh.Z)
element.offset_w = offset_w
view.contents.append(offset_w)
if steno3d_resource.opts.color is not None:
element.defaults.color.value = steno3d_resource.opts.color
if steno3d_resource.opts.opacity is not None:
element.defaults.opacity.value = steno3d_resource.opts.opacity
if steno3d_resource.mesh.opts.wireframe is not None:
element.defaults.wireframe.active = steno3d_resource.mesh.opts.wireframe
view.contents.append(element)
view.elements += [element]
if _lookup_dict is not None and hasattr(steno3d_resource, '_upload_data'):
_lookup_dict.update({steno3d_resource._upload_data['uid']: element})
return element
def test_array_init(input_arr):
arr = files.Array(input_arr)
assert arr.validate()
assert isinstance(arr.array, np.ndarray)
assert np.array_equal(arr.array, np.array([1, 2, 3]))
assert arr.dtype.startswith('Int')
assert arr.shape == [3]
assert arr.content_type == 'application/octet-stream'
assert arr.content_length == np.dtype(arr.array.dtype).itemsize * 3
assert arr.is_1d()
def test_array_serialize():
arr = files.Array([[1]])
arr.validate()
serial_arr = arr.serialize()
assert serial_arr == {
'__class__': 'Array',
'content_length': np.dtype(arr.array.dtype).itemsize,
'content_type': 'application/octet-stream',
'dtype': 'Int32Array',
'shape': [1, 1],
}
def test_upload(mock_regex, mock_upload_image, mock_upload_array, mock_put,
mock_patch, mock_post, verbose, workers, parallel, session):
mock_resp = mock.MagicMock()
mock_resp.json.return_value = {
'links': {
'self': 'https://example.com/api/self',
'location': 'https://example.com/api/location',
'thumbnail': 'https://example.com/api/self/thumbnail'
},
}
mock_resp.ok = True
mock_post.return_value = mock_resp
mock_patch.return_value = mock_resp
mock_put.return_value = mock_resp
mock_file_resp = mock.MagicMock()
mock_file_resp.json.return_value = {}
mock_file_resp.ok = True
mock_upload_array.return_value = mock_file_resp
mock_upload_image.return_value = mock_file_resp
mock_regex.return_value = re.compile(r'^https://example\.com/api/')
mapping_uploaded = spatial.MappingDiscrete(
values=[(255, 0, 0), (0, 255, 0), (0, 0, 255)],
end_points=[10., 20.],
end_inclusive=[True, True],
visibility=[True, True, True],
)
mapping_uploaded._links = {
'self': 'https://example.com/api/mapping_uploaded'
}
array_data = files.Array([0., 10, 20])
img = io.BytesIO()
s = [[0, 1, 0, 1], [1, 0, 1, 0], [0, 1, 0, 1], [1, 0, 1, 0]]
w = png.Writer(4, 4, greyscale=True, bitdepth=16)
w.write(img, s)
view = manifests.View(
name='Test View',
elements=[
spatial.ElementPointSet(
vertices=files.Array([[0., 0, 0], [1, 1, 1], [2, 2, 2]]),
data=[
spatial.DataBasic(
name='Dataset 1',
location='n',
array=array_data,
uid='local_id',
),
spatial.DataBasic(
name='Dataset 2',
description='Same array as dataset 1',
location='n',
array=array_data,
mappings=[
spatial.MappingContinuous(
gradient='https://example.com/api/my_colormap',
data_controls=[0., 10., 20., 30.],
),
mapping_uploaded,
]),
spatial.TextureProjection(
origin=[0., 0, 0],
axis_u=[1., 0, 0],
axis_v=[0., 1, 0],
image=img,
),
],
defaults={
'color': {
'value': '#FF0000'
},
'opacity': {
'value': 1
},
'size': {
'value': 10
},
'shape': 'square'
},
),
'https://example.com/api/my_element',
])
try:
dirname, _ = os.path.split(os.path.abspath(__file__))
png_file = os.path.sep.join(dirname.split(os.path.sep) + ['temp.png'])
s = ['110010010011', '101011010100', '110010110101', '100010010011']
s = [[int(v) for v in val] for val in s]
f = open(png_file, 'wb')
w = png.Writer(len(s[0]), len(s), greyscale=True, bitdepth=16)
w.write(f, s)
f.close()
session.upload(
view,
verbose=verbose,
thumbnail=png_file,
parallel=parallel,
workers=workers,
)
finally:
os.remove(png_file)
assert mock_post.call_count == 9
assert mock_patch.call_count == 1
assert mock_put.call_count == 1
assert mock_upload_array.call_count == 2
assert mock_upload_image.call_count == 2
mock_post.assert_has_calls(
[
mock.call(
'https://example.com/api/v1/project/myorg/myproj/files/array',
json={
'shape': [3, 3],
'dtype': 'Float64Array',
'content_type': 'application/octet-stream',
'content_length': 31,
'content_encoding': 'gzip'
},
),
mock.call(
'https://example.com/api/v1/project/myorg/myproj/files/array',
json={
'shape': [3],
'dtype': 'Float64Array',
'content_type': 'application/octet-stream',
'content_length':
24, # this file is 29 bytes when compressed
},
),
mock.call(
'https://example.com/api/v1/project/myorg/myproj/files/image',
json={
'content_type': 'image/png',
'content_length': img.seek(0, 2),
},
),
mock.call(
'https://example.com/api/v1/project/myorg/myproj/mappings/continuous',
json={
'gradient': 'https://example.com/api/my_colormap',
'data_controls': [0., 10., 20., 30.],
'gradient_controls': [0., 0., 1., 1.],
'visibility': [False, True, True, True, False],
'interpolate': False,
},
),
mock.call(
'https://example.com/api/v1/project/myorg/myproj/data/basic',
json={
'name': 'Dataset 1',
'location': 'nodes',
'array': 'https://example.com/api/self',
'mappings': [],
},
),
mock.call(
'https://example.com/api/v1/project/myorg/myproj/data/basic',
json={
'name':
'Dataset 2',
'description':
'Same array as dataset 1',
'location':
'nodes',
'array':
'https://example.com/api/self',
'mappings': [
'https://example.com/api/self',
'https://example.com/api/mapping_uploaded',
],
},
),
mock.call(
'https://example.com/api/v1/project/myorg/myproj/textures/projection',
json={
'origin': [0., 0, 0],
'axis_u': [1., 0, 0],
'axis_v': [0., 1, 0],
'image': 'https://example.com/api/self',
},
),
mock.call(
'https://example.com/api/v1/project/myorg/myproj/elements/pointset',
json={
'vertices':
'https://example.com/api/self',
'data': [
'https://example.com/api/self',
'https://example.com/api/self',
'https://example.com/api/self',
],
'defaults': {
'visible': True,
'color': {
'value': '#FF0000'
},
'opacity': {
'value': 1
},
'size': {
'value': 10
},
'shape': 'square'
},
},
),
mock.call(
'https://example.com/api/v1/project/myorg/myproj/views',
json={
'name':
'Test View',
'elements': [
'https://example.com/api/self',
'https://example.com/api/my_element',
],
'contents': [
'https://example.com/api/self',
'https://example.com/api/self',
'https://example.com/api/my_colormap',
'https://example.com/api/self',
'https://example.com/api/mapping_uploaded',
'https://example.com/api/self',
'https://example.com/api/self',
'https://example.com/api/self',
'https://example.com/api/self',
'https://example.com/api/self',
'https://example.com/api/my_element',
],
},
),
],
any_order=True)
mock_patch.assert_called_with(
'https://example.com/api/mapping_uploaded',
json={
'values': ['#FF0000', '#00FF00', '#0000FF'],
'end_points': [10., 20.],
'end_inclusive': [True, True],
'visibility': [True, True, True],
},
)
mock_put.assert_called_with(
'https://example.com/api/self/thumbnail',
json={
'content_type': 'image/png',
'content_length': 88,
},
)
def test_array_assignment(input_arr):
arr = files.Array()
with pytest.raises(ValueError):
arr.array = input_arr
def test_object_without_array():
arr = files.Array()
arr.content_length = 64
arr.dtype = 'Int8Array'
arr.shape = [64]
assert arr.validate()
def test_is_1d(input, is_1d):
assert files.Array(input).is_1d() == is_1d
def test_bad_input():
with pytest.raises(properties.ValidationError):
files.Array(dtype='bad')
arr = files.Array(dtype='Int32Array', shape=[1])
with pytest.raises(properties.ValidationError):
arr.content_length = 100
def test_empty_init():
arr = files.Array()
with pytest.raises(properties.ValidationError):
arr.validate()
import properties
from lfview.resources import files, spatial
def test_types():
assert spatial.DataBasic.BASE_TYPE == 'data'
assert spatial.DataBasic.SUB_TYPE == 'basic'
assert spatial.DataCategory.BASE_TYPE == 'data'
assert spatial.DataCategory.SUB_TYPE == 'category'
@pytest.mark.parametrize('array', [
'https://example.com/api/files/array/abc123',
[10., 20, 15.],
files.Array(shape=[3], dtype='Float32Array', content_length=12),
])
@pytest.mark.parametrize('location', ['nodes', 'cells', 'N', 'CC'])
@pytest.mark.parametrize(
'mappings', [[
'https://example.com/api/mappings/continuous/abc123',
'https://example.com/api/mappings/discrete/def456'
],
[{
'gradient': 'https://example.com/api/files/array/ghi789',
'data_controls': [1., 2., 3., 4.]
}, {
'values': ['a', 'b'],
'end_points': [1.],
'end_inclusive': [True],
'visibility': [True, True]
def test_unsupported_array():
with pytest.raises(ValueError):
files.Array('bad array')
int64array = np.array([100000000000])
with pytest.raises(ValueError):
files.Array(int64array)
def test_types():
assert spatial.MappingContinuous.BASE_TYPE == 'mappings'
assert spatial.MappingDiscrete.BASE_TYPE == 'mappings'
assert spatial.MappingCategory.BASE_TYPE == 'mappings'
assert spatial.MappingContinuous.SUB_TYPE == 'continuous'
assert spatial.MappingDiscrete.SUB_TYPE == 'discrete'
assert spatial.MappingCategory.SUB_TYPE == 'category'
@pytest.mark.parametrize(
'gradient', [
'https://example.com/api/files/array/abc123',
[[0, 0, 0], [255, 255, 255]],
files.Array(shape=[5, 3], dtype='Int16Array', content_length=30)
]
)
@pytest.mark.parametrize('data_controls', [[-1., 2., 3.], [1., 1., 1.]])
@pytest.mark.parametrize('gradient_controls', [[0., 0.5, 1], [0., 0., 0.]])
@pytest.mark.parametrize(
'visibility', [[True, True, True, True], [0, 0, 1, 0]]
)
@pytest.mark.parametrize('interpolate', [0, 1])
def test_good_continuous(
gradient, data_controls, gradient_controls, visibility, interpolate
):
mc = spatial.MappingContinuous(
gradient=gradient,
data_controls=data_controls,
gradient_controls=gradient_controls,
session.upload_feedback(feedback, slide=slide_url, verbose=verbose)
if isinstance(feedback, scene.Feedback):
mock_upload.assert_called_once_with(
resource=feedback,
verbose=verbose,
chunk_size=None,
json_dict=expected_json_dict,
post_url=expected_post_url,
executor=mock_executor,
)
else:
mock_upload.assert_called_once()
@pytest.mark.parametrize(('feedback', 'slide_url'), [
(files.Array([1., 2.]),
'https://example.com/api/v1/view/org1/proj1/view1/slides/slide1'),
(None, None),
(None,
'https://example.com/api/v1/view/org1/proj1/view1/slides/slide1/feedback'
),
])
@pytest.mark.parametrize('verbose', [True, False])
def test_bad_upload_feedback(feedback, slide_url, verbose, session):
if not feedback:
feedback = scene.Feedback(comment='bad')
with pytest.raises(ValueError):
session.upload_feedback(feedback, slide=slide_url, verbose=verbose)
@pytest.fixture