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Add test
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@keller-mark
keller-mark committed Oct 7, 2024
1 parent 5d95665 commit 3f10a28
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Showing 4 changed files with 96 additions and 22 deletions.
66 changes: 62 additions & 4 deletions tests/test_wrappers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -394,13 +394,71 @@ def test_multivec_zarr_with_base_dir(self):
def test_spatial_data_with_base_dir(self):

spatial_data_path = 'test.spatialdata.zarr'
w = SpatialDataWrapper(sdata_path=spatial_data_path, image_path="images/picture", obs_set_paths=['obs/CellType'], obs_set_names=['Cell Type'], obs_embedding_paths=[
'obsm/X_umap'], obs_embedding_names=['UMAP'])
w = SpatialDataWrapper(
sdata_path=spatial_data_path,
image_path="images/picture",
obs_set_paths=['obs/CellType'],
obs_set_names=['Cell Type'],
obs_embedding_paths=['obsm/X_umap'],
obs_embedding_names=['UMAP']
)
w.base_dir = data_path
w.local_dir_uid = 'spatialdata.zarr'

file_def_creator = w.make_file_def_creator('A', 0)
file_def = file_def_creator('http://localhost:8000')
print(file_def)
self.assertEqual(file_def,
{'fileType': 'spatialdata.zarr', 'url': 'http://localhost:8000/test.spatialdata.zarr', 'options': {'obsSets': {'obsSets': [{'name': 'Cell Type', 'path': 'obs/CellType'}], 'tablePath': 'tables/table'}, 'image': {'path': 'images/picture'}}})
self.assertEqual(file_def, {
'fileType': 'spatialdata.zarr',
'url': 'http://localhost:8000/test.spatialdata.zarr',
'options': {
'obsSets': {
'obsSets': [{'name': 'Cell Type', 'path': 'obs/CellType'}],
'tablePath': 'tables/table'
},
'image': {'path': 'images/picture'}
}})

def test_spatial_data_with_base_dir_2(self):

spatial_data_path = 'test.spatialdata.zarr'
w = SpatialDataWrapper(
sdata_path=spatial_data_path,
image_path='images/CytAssist_FFPE_Human_Breast_Cancer_full_image',
coordinate_system='aligned',
region='CytAssist_FFPE_Human_Breast_Cancer',
obs_feature_matrix_path='tables/table/X',
obs_spots_path='shapes/CytAssist_FFPE_Human_Breast_Cancer',
table_path='tables/table',
coordination_values={
"obsType": "spot"
}
)
w.base_dir = data_path
w.local_dir_uid = 'spatialdata.zarr'

file_def_creator = w.make_file_def_creator('A', 0)
file_def = file_def_creator('http://localhost:8000')
self.assertDictEqual(file_def, {
'fileType': 'spatialdata.zarr',
'url': 'http://localhost:8000/test.spatialdata.zarr',
'options': {
'image': {
'path': 'images/CytAssist_FFPE_Human_Breast_Cancer_full_image',
'coordinateSystem': 'aligned',
},
'obsFeatureMatrix': {
'path': 'tables/table/X',
'region': 'CytAssist_FFPE_Human_Breast_Cancer'
},
'obsSpots': {
'path': 'shapes/CytAssist_FFPE_Human_Breast_Cancer',
'tablePath': 'tables/table',
'region': 'CytAssist_FFPE_Human_Breast_Cancer',
'coordinateSystem': 'aligned',
}
},
'coordinationValues': {
"obsType": "spot"
}
})
21 changes: 18 additions & 3 deletions vitessce/file_def_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -142,13 +142,28 @@ def gen_sdata_labels_schema(options, path: str, table_path: str = "tables/table"
return options


def gen_sdata_obs_spots_schema(options: dict, shapes_path: Optional[str] = None, table_path: str = "tables/table", region: Optional[str] = None, coordinate_system: Optional[str] = None) -> dict:
def gen_sdata_obs_spots_schema(options: dict, shapes_path: str, table_path: str = "tables/table", region: Optional[str] = None, coordinate_system: Optional[str] = None) -> dict:
if shapes_path is not None:
options['obsSpots'] = {
"path": shapes_path,
"tablePath": table_path,
"region": region
"tablePath": table_path
}
if region is not None:
options['obsSpots']['region'] = region
if coordinate_system is not None:
options['obsSpots']['coordinateSystem'] = coordinate_system
return options


def gen_sdata_obs_feature_matrix_schema(options: dict, matrix_path: Optional[str] = None, var_filter_path: Optional[str] = None, init_var_filter_path: Optional[str] = None, region: Optional[str] = None):
if matrix_path is not None:
options["obsFeatureMatrix"] = {
"path": matrix_path
}
if region is not None:
options['obsFeatureMatrix']['region'] = region
if var_filter_path is not None:
options["obsFeatureMatrix"]["featureFilterPath"] = var_filter_path
if init_var_filter_path is not None:
options["obsFeatureMatrix"]["initialFeatureFilterPath"] = init_var_filter_path
return options
6 changes: 3 additions & 3 deletions vitessce/widget.py
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Original file line number Diff line number Diff line change
Expand Up @@ -454,7 +454,7 @@ class VitessceWidget(anywidget.AnyWidget):

next_port = DEFAULT_PORT

js_package_version = Unicode('3.4.12').tag(sync=True)
js_package_version = Unicode('3.4.13').tag(sync=True)
js_dev_mode = Bool(False).tag(sync=True)
custom_js_url = Unicode('').tag(sync=True)
plugin_esm = List(trait=Unicode(''), default_value=[]).tag(sync=True)
Expand All @@ -463,7 +463,7 @@ class VitessceWidget(anywidget.AnyWidget):

store_urls = List(trait=Unicode(''), default_value=[]).tag(sync=True)

def __init__(self, config, height=600, theme='auto', uid=None, port=None, proxy=False, js_package_version='3.4.12', js_dev_mode=False, custom_js_url='', plugins=None, remount_on_uid_change=True, invoke_timeout=30000):
def __init__(self, config, height=600, theme='auto', uid=None, port=None, proxy=False, js_package_version='3.4.13', js_dev_mode=False, custom_js_url='', plugins=None, remount_on_uid_change=True, invoke_timeout=30000):
"""
Construct a new Vitessce widget.
Expand Down Expand Up @@ -576,7 +576,7 @@ def _plugin_command(self, params, buffers):
# Launch Vitessce using plain HTML representation (no ipywidgets)


def ipython_display(config, height=600, theme='auto', base_url=None, host_name=None, uid=None, port=None, proxy=False, js_package_version='3.4.12', js_dev_mode=False, custom_js_url='', plugin_esm=DEFAULT_PLUGIN_ESM, remount_on_uid_change=True):
def ipython_display(config, height=600, theme='auto', base_url=None, host_name=None, uid=None, port=None, proxy=False, js_package_version='3.4.13', js_dev_mode=False, custom_js_url='', plugin_esm=DEFAULT_PLUGIN_ESM, remount_on_uid_change=True):
from IPython.display import display, HTML
uid_str = "vitessce" + get_uid_str(uid)

Expand Down
25 changes: 13 additions & 12 deletions vitessce/wrappers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,8 @@
gen_sdata_image_schema,
gen_sdata_labels_schema,
gen_sdata_obs_spots_schema,
gen_sdata_obs_sets_schema
gen_sdata_obs_sets_schema,
gen_sdata_obs_feature_matrix_schema,
)

from .constants import (
Expand Down Expand Up @@ -1289,7 +1290,7 @@ def auto_view_config(self, vc):

class SpatialDataWrapper(AnnDataWrapper):

def __init__(self, sdata_path: Optional[str] = None, sdata_url: Optional[str] = None, sdata_store: Optional[Union[str, zarr.storage.StoreLike]] = None, sdata_artifact: Optional[ln.Artifact] = None, image_path: Optional[str] = None, region: Optional[str] = None, coordinate_system: Optional[str] = None, affine_transformation: Optional[np.ndarray] = None, spot_shapes_path: Optional[str] = None, labels_path: Optional[str] = None, table_path: str = "tables/table", **kwargs):
def __init__(self, sdata_path: Optional[str] = None, sdata_url: Optional[str] = None, sdata_store: Optional[Union[str, zarr.storage.StoreLike]] = None, sdata_artifact: Optional[ln.Artifact] = None, image_path: Optional[str] = None, region: Optional[str] = None, coordinate_system: Optional[str] = None, affine_transformation: Optional[np.ndarray] = None, obs_spots_path: Optional[str] = None, labels_path: Optional[str] = None, table_path: str = "tables/table", **kwargs):
"""
Wrap a SpatialData object.
Expand All @@ -1301,16 +1302,16 @@ def __init__(self, sdata_path: Optional[str] = None, sdata_url: Optional[str] =
:type sdata_store: Optional[Union[str, zarr.storage.StoreLike]]
:param sdata_artifact: Artifact that corresponds to a SpatialData object.
:type sdata_artifact: Optional[ln.Artifact]
:param image_elem: Name of the image element of interest. By default, None.
:type image_elem: Optional[str]
:param image_path: Path to the image element of interest. By default, None.
:type image_path: Optional[str]
:param coordinate_system: Name of a target coordinate system.
:type coordinate_system: Optional[str]
:param affine_transformation: Transformation to be applied to the image. By default, None. Prefer coordinate_system.
:type affine_transformation: Optional[np.ndarray]
:param shapes_elem: location of the shapes, by default None
:type shapes_elem: Optional[str]
:param labels_elem: location of the labels, by default None
:type labels_elem: Optional[str]
:param obs_spots_path: Location of shapes that should be interpreted as spot observations, by default None
:type obs_spots_path: Optional[str]
:param labels_path: Location of the labels (segmentation bitmask image), by default None
:type labels_path: Optional[str]
"""
raise_error_if_zero_or_more_than_one([
sdata_path,
Expand All @@ -1331,7 +1332,7 @@ def __init__(self, sdata_path: Optional[str] = None, sdata_url: Optional[str] =
self._coordinate_system = coordinate_system
self._affine_transformation = affine_transformation
self._kwargs = kwargs
self._spot_shapes_path = spot_shapes_path
self._obs_spots_path = obs_spots_path
self._labels_path = labels_path
if self._adata_path is not None:
self.zarr_folder = 'spatialdata.zarr'
Expand Down Expand Up @@ -1402,7 +1403,7 @@ def from_object(cls: Type[SpatialDataWrapperType], sdata: SpatialData, table_key
image_path=str(image_elem) if image_elem is not None else None,
labels_path=str(labels_elem) if labels_elem is not None else None,
obs_feature_matrix_path=str(obs_feature_matrix_elem),
spot_shapes_path=str(spot_shapes_elem) if spot_shapes_elem is not None else None,
obs_spots_path=str(spot_shapes_elem) if spot_shapes_elem is not None else None,
initial_feature_filter_path=initial_feature_filter_elem,
obs_set_paths=obs_set_elems,
coordination_values={"obsType": "spot"} # TODO: should we remove?
Expand All @@ -1414,9 +1415,9 @@ def make_file_def_creator(self, dataset_uid: str, obj_i: str) -> Optional[Callab
def generator(base_url):
options = {}
options = gen_obs_labels_schema(options, self._obs_labels_elems, self._obs_labels_names)
options = gen_obs_feature_matrix_schema(options, self._expression_matrix, self._gene_var_filter, self._matrix_gene_var_filter)
options = gen_sdata_obs_feature_matrix_schema(options, self._expression_matrix, self._gene_var_filter, self._matrix_gene_var_filter, self._region)
options = gen_sdata_obs_sets_schema(options, self._obs_set_elems, self._obs_set_names, self._table_path, self._region)
options = gen_sdata_obs_spots_schema(options, self._spot_shapes_path, self._table_path, self._region, self._coordinate_system)
options = gen_sdata_obs_spots_schema(options, self._obs_spots_path, self._table_path, self._region, self._coordinate_system)
options = gen_sdata_image_schema(options, self._image_path, self._coordinate_system, self._affine_transformation)
options = gen_sdata_labels_schema(options, self._labels_path, self._table_path, self._coordinate_system, self._affine_transformation)
options = gen_feature_labels_schema(self._feature_labels, options)
Expand Down

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