def test_project_creation_mode(mode, tmp_path2, new_project):
# test creating in empty dir
cm = pytest.raises(FileNotFoundError) if "r" in mode else nullcontext()
with cm:
QuPathProject(tmp_path2, mode=mode).save()
# prepare an existing proj
p = new_project.path
new_project.save()
del new_project
assert not p.with_suffix('.qpproj.backup').is_file()
assert not any(p.parent.parent.glob('*.backup'))
# test creating in existing dir
if "x" in mode:
cm = pytest.raises(FileExistsError)
elif "r" == mode:
cm = pytest.raises(IOError) # can't save!
else:
cm = nullcontext()
with cm:
QuPathProject(p, mode=mode).save()
assert p.is_file()
backups = list(p.parent.parent.glob('*.backup'))
if 'w' in mode:
assert len(backups) == 1
assert backups[0].is_file()
else:
assert len(backups) == 0
def project_with_removed_image_without_image_data(removable_svs_small):
with tempfile.TemporaryDirectory(prefix='paquo-') as tmpdir:
qp = QuPathProject(tmpdir, mode='x')
_ = qp.add_image(removable_svs_small)
qp.save()
removable_svs_small.unlink()
yield qp.path
def project_with_removed_image(removable_svs_small):
with tempfile.TemporaryDirectory(prefix='paquo-') as tmpdir:
qp = QuPathProject(tmpdir, mode='x')
_ = qp.add_image(removable_svs_small,
image_type=QuPathImageType.BRIGHTFIELD_H_E)
qp.save()
removable_svs_small.unlink()
yield qp.path
def list_project(path):
"""print information about the project"""
from paquo.projects import QuPathProject
with QuPathProject(path, mode='r') as qp:
print("Project:", qp.name)
print("Classes: #", len(qp.path_classes), sep='')
for path_class in qp.path_classes:
color = path_class.color
color_str = f" [{color.to_hex()}]" if color else ""
print(f"- {path_class.id}{color_str}")
_md_keys = set()
_md_value_len = defaultdict(int)
print("Images: #", len(qp.images), sep='')
for idx, image in enumerate(qp.images):
print(f"- [{idx}] {image.image_name}")
for k, v in image.metadata.items():
_md_keys.add(k)
_md_value_len[k] = max(_md_value_len[k], len(v), len(k))
print("Project Metadata: #", len(_md_keys), sep='')
if len(_md_keys):
_md_keys = list(sorted(_md_keys))
hdr = ["# "]
for _key in _md_keys:
hdr.append(f"{_key:<{_md_value_len[_key]}}")
print(" ".join(hdr))
for idx, image in enumerate(qp.images):
line = [f"- [{idx}]"]
for _key in _md_keys:
val = image.metadata.get(_key, '')
line.append(f"{val:<{_md_value_len[_key]}}")
print(" ".join(line))
def test_imagedata_saving_for_removed_images_without_type(
project_with_removed_image_without_image_data):
with QuPathProject(project_with_removed_image_without_image_data,
mode='r+') as qp:
entry = qp.images[0]
# todo: check if we actually want this behavior.
# at least it's documented now
assert not (entry.entry_path / "data.qpdata").is_file()
def test_project_version(new_project):
from paquo.java import GeneralTools
new_project.save()
qp_version = str(GeneralTools.getVersion())
assert new_project.version == qp_version
with QuPathProject(new_project.path, mode='r+') as qp:
assert qp.version == qp_version
def project_and_changes(svs_small):
with tempfile.TemporaryDirectory(prefix='paquo-') as tmpdir:
qp = QuPathProject(tmpdir, mode='x')
entry = qp.add_image(svs_small)
entry.hierarchy.add_annotation(
roi=shapely.geometry.Point(1, 2)
)
qp.save()
project_path = qp.path.parent
del qp
last_changes = {}
for file in project_path.glob("**/*.*"):
p = str(file.absolute())
last_changes[p] = file.stat().st_mtime
yield project_path, last_changes
def test_project_creation_input_error(tmp_path):
p = tmp_path / Path('somewhere')
p.mkdir()
with pytest.raises(TypeError):
# noinspection PyTypeChecker
QuPathProject(p, image_provider=object())
with pytest.raises(ValueError):
QuPathProject(p / 'myproject.proj') # needs .qpproj
with pytest.raises(FileNotFoundError):
QuPathProject(p / 'myproject.qpproj', mode='r+')
with open(p / 'should-not-be-here', 'w') as f:
f.write('project directories need to be empty')
with pytest.raises(ValueError):
QuPathProject(p, mode='x')
def test_project_image_uri_update(tmp_path, svs_small):
project_path = tmp_path / "paquo-project"
new_svs_small = tmp_path / "images" / f"image_be_gone{svs_small.suffix}"
new_svs_small.parent.mkdir(parents=True, exist_ok=True)
shutil.copy(svs_small, new_svs_small)
assert new_svs_small.is_file()
# create a project
with QuPathProject(project_path, mode='x') as qp:
entry = qp.add_image(new_svs_small)
assert entry.is_readable()
assert all(qp.is_readable().values())
# cleanup
del entry
del qp
# remove image
os.unlink(new_svs_small)
# reload the project
with QuPathProject(project_path, mode='r+') as qp:
entry, = qp.images
assert not entry.is_readable()
assert not all(qp.is_readable().values())
# test if there's no remapping
qp.update_image_paths(uri2uri={})
# test if we remap to same
qp.update_image_paths(uri2uri={entry.uri: entry.uri})
# create mapping for uris
uri2uri = {
entry.uri: ImageProvider.uri_from_path(svs_small),
}
# update the uris
qp.update_image_paths(uri2uri=uri2uri)
# test that entry can be read
assert entry.is_readable()
assert all(qp.is_readable().values())
def test_project_image_uri_update_try_relative(tmp_path, svs_small):
# prepare initial location
location_0 = tmp_path / "location_0"
location_0.mkdir()
# prepare a project and images at location_0
image_path = location_0 / "images" / "image0.svs"
image_path.parent.mkdir(parents=True)
shutil.copy(svs_small, image_path)
assert image_path.is_file()
# create a project
with QuPathProject(location_0 / "project", mode='x') as qp:
entry = qp.add_image(image_path)
assert entry.is_readable()
assert all(qp.is_readable().values())
# cleanup
del entry
del qp
# NOW move the location
location_1 = tmp_path / "location_1"
shutil.move(location_0, location_1)
with QuPathProject(location_1 / "project", mode='r') as qp:
entry, = qp.images
assert not entry.is_readable()
assert not all(qp.is_readable().values())
assert 'location_1' in str(qp.path)
assert 'location_0' in entry.uri # still points to the old location
# fixme: testing private api
assert 'location_0' in str(qp.java_object.getPreviousURI().toString())
qp.update_image_paths(try_relative=True)
# test that entry can be read
assert entry.is_readable()
assert all(qp.is_readable().values())
def export_annotations(path, image_idx, pretty=False):
"""print annotations as geojson"""
import pprint
from paquo.projects import QuPathProject
with QuPathProject(path, mode='r') as qp:
image = qp.images[image_idx]
data = image.hierarchy.to_geojson()
if pretty:
pprint.pprint(data)
else:
print(data)
def test_readonly_recovery_image_server(project_with_removed_image):
from paquo.java import compatibility
if not compatibility.supports_image_server_recovery():
pytest.skip(f"unsupported in {compatibility.version}")
with QuPathProject(project_with_removed_image, mode='r') as qp:
image_entry = qp.images[0]
assert image_entry.height
assert image_entry.width
assert image_entry.num_channels
assert image_entry.num_timepoints
assert image_entry.num_z_slices
assert image_entry.downsample_levels
assert repr(image_entry.hierarchy)
def project_with_data(svs_small):
from shapely.geometry import Point
from paquo.classes import QuPathPathClass
from paquo.images import QuPathImageType
from paquo.projects import QuPathProject
with tempfile.TemporaryDirectory(prefix='paquo-') as tmp_path:
with QuPathProject(tmp_path, mode='x') as qp:
entry = qp.add_image(svs_small,
image_type=QuPathImageType.BRIGHTFIELD_OTHER)
entry.hierarchy.add_annotation(roi=Point(500, 500))
pcs = list(qp.path_classes)
pcs.append(QuPathPathClass("myclass"))
qp.path_classes = pcs
entry.metadata["mykey"] = "myval"
qp.save()
yield qp.path
def test_add_duplicate_to_hierarchy(project_with_annotations):
"""adding duplicate annotations works"""
# create a project with an image and annotations
from paquo.projects import QuPathProject
p = project_with_annotations.path
num_annotations = len(project_with_annotations.images[0].hierarchy)
annotation = next(iter(project_with_annotations.images[0].hierarchy.annotations))
del project_with_annotations
# read project
with QuPathProject(p, mode="a") as qp:
entry1 = qp.images[0]
entry1.hierarchy.add_annotation(
roi=annotation.roi
)
assert len(entry1.hierarchy) == num_annotations + 1
def test_add_to_existing_hierarchy(project_with_annotations):
# create a project with an image and annotations
from shapely.geometry import Point
from paquo.projects import QuPathProject
p = project_with_annotations.path
num_annotations = len(project_with_annotations.images[0].hierarchy)
del project_with_annotations
# read project
with QuPathProject(p, mode="a") as qp:
entry1 = qp.images[0]
assert len(entry1.hierarchy) == num_annotations
entry1.hierarchy.add_annotation(
roi=Point(2, 2)
)
assert len(entry1.hierarchy) == num_annotations + 1
def create_project(project_path,
class_names_colors,
images,
annotations_json_func=None,
remove_default_classes=False,
force_write=False):
"""create a qupath project"""
from paquo._logging import get_logger
from paquo._utils import load_json_from_path
from paquo.classes import QuPathPathClass
from paquo.images import QuPathImageType
from paquo.projects import QuPathProject
_logger = get_logger(__name__)
mode = 'x' if not force_write else 'w'
if annotations_json_func is not None and not callable(
annotations_json_func):
raise ValueError("annotations_json_func should be callable")
# noinspection PyTypeChecker
with QuPathProject(project_path, mode=mode) as qp:
if remove_default_classes:
qp.path_classes = ()
path_classes = list(qp.path_classes)
for name, color in class_names_colors:
path_classes.append(QuPathPathClass(name, color=color))
qp.path_classes = path_classes
for image in images:
qp_image = qp.add_image(image,
image_type=QuPathImageType.BRIGHTFIELD_H_E)
if annotations_json_func:
annotations_jsons = annotations_json_func(Path(image).name)
for annotations_json in annotations_jsons:
_logger.info(f"loading '{annotations_json}'")
geojson = load_json_from_path(annotations_json)
qp_image.hierarchy.load_geojson(geojson["annotations"])
name = qp.name
return name
def test_hierarchy_update_on_annotation_update(project_with_annotations):
"""updating annotation or detection objects triggers is_changed on hierarchy"""
# create a project with an image and annotations
from paquo.projects import QuPathProject
from paquo.classes import QuPathPathClass
p = project_with_annotations.path
num_annotations = len(project_with_annotations.images[0].hierarchy)
del project_with_annotations
# test update
with QuPathProject(p, mode="a") as qp:
entry1 = qp.images[0]
assert len(entry1.hierarchy) == num_annotations
for annotation in entry1.hierarchy.annotations:
annotation.update_path_class(QuPathPathClass("new"))
assert entry1.is_changed() # every update changes
assert len(entry1.hierarchy) == num_annotations
assert all(a.path_class.name == "new" for a in entry1.hierarchy.annotations)
def prepare_example_resources():
"""build an example project"""
from paquo.projects import QuPathProject
from paquo.images import QuPathImageType
from paquo.classes import QuPathPathClass
from shapely.geometry import Polygon
# download all images
print(">>> downloading images...")
images = list(download_image(copies=3))
# remove the example_project
example_project_dir = PROJECTS_DIR / "example_01_project"
shutil.rmtree(example_project_dir, ignore_errors=True)
print(">>> creating project...")
with QuPathProject(example_project_dir, mode="x") as qp:
for img_fn in images:
qp.add_image(img_fn, image_type=QuPathImageType.BRIGHTFIELD_H_E)
qp.path_classes = map(QuPathPathClass,
["myclass_0", "myclass_1", "myclass_2"])
for idx, image in enumerate(qp.images):
image.metadata['image_number'] = str(1000 + idx)
def _get_bounds(idx_x, idx_y):
cx = 200 * idx_x + 100
cy = 200 * idx_y + 100
return cx - 50, cy - 50, cx + 50, cy + 50
image_0 = qp.images[0]
for x, y in itertools.product(range(4), repeat=2):
roi = Polygon.from_bounds(*_get_bounds(x, y))
image_0.hierarchy.add_annotation(
roi, path_class=QuPathPathClass("myclass_1"))
with open(DATA_DIR / "annotations.geojson", "w") as f:
json.dump(image_0.hierarchy.to_geojson(), f)
print(">>> done.")
def image_entry(svs_small):
with tempfile.TemporaryDirectory(prefix='paquo-') as tmpdir:
qp = QuPathProject(tmpdir, mode='x')
entry = qp.add_image(svs_small)
yield entry
def new_project(tmp_path):
yield QuPathProject(tmp_path / "paquo-project", mode='x')
def readonly_project(project_and_changes):
project_path, changes = project_and_changes
qp = QuPathProject(project_path, mode="r")
qp.__changes = changes
yield qp
"""example showing how to create a empty project with classes"""
from pathlib import Path
from paquo.projects import QuPathProject
from paquo.classes import QuPathPathClass
EXAMPLE_PROJECT = Path(
__file__).parent.absolute() / "projects" / "example_03_project"
MY_CLASSES_AND_COLORS = [
("My Class 1", "#ff0000"),
("Some Other Class", "#0000ff"),
("Nothing*", "#00ff00"),
]
# create a the new project
with QuPathProject(EXAMPLE_PROJECT, mode='x') as qp:
print("created", qp.name)
new_classes = []
for class_name, class_color in MY_CLASSES_AND_COLORS:
new_classes.append(QuPathPathClass(name=class_name, color=class_color))
# setting QuPathProject.path_class always replaces all classes
qp.path_classes = new_classes
print("project classes:")
for path_class in qp.path_classes:
print(">", f"'{path_class.name}'", path_class.color.to_hex())
print(f"done. Please look at {qp.name} in QuPath.")
def test_unsupported_mode(tmp_path):
with pytest.raises(ValueError):
QuPathProject(tmp_path, mode="???")
def test_project_name(tmp_path):
p = Path(tmp_path) / "my_project_123"
p.mkdir()
qp = QuPathProject(p, mode='x')
assert qp.name == "my_project_123"
def test_project_open_with_filename(new_project):
new_project.save()
# this points to path/project.qpproj
proj_fn = new_project.path
QuPathProject(proj_fn, mode='r+')
def test_readonly_recovery_hierarchy(
project_with_removed_image_without_image_data):
with QuPathProject(project_with_removed_image_without_image_data,
mode='r+') as qp:
entry = qp.images[0]
assert repr(entry.hierarchy)
def test_project_add_image_writes_project(tmp_path, svs_small):
qp = QuPathProject(tmp_path, mode='x')
qp.add_image(svs_small)
assert qp.path.is_file()
def test_imagedata_saving_for_removed_images(project_with_removed_image):
with QuPathProject(project_with_removed_image, mode='r+') as qp:
entry = qp.images[0]
assert (entry.entry_path / "data.qpdata").is_file()
def test_project_instance():
with tempfile.TemporaryDirectory(prefix='paquo-') as tmpdir:
q = QuPathProject(tmpdir, mode='x')
repr(q)
q.save()
def test_project_create_no_dir():
with tempfile.TemporaryDirectory(prefix='paquo-') as tmpdir:
project_path = Path(tmpdir) / "new_project"
q = QuPathProject(project_path, mode='x')
q.save()