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feature focus on 3d viewer, add copy/paste

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This commit is contained in:
matei jordache
2026-03-26 21:25:35 -07:00
parent de0b49acc5
commit 30671a5362
24 changed files with 1680 additions and 320 deletions
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331
tests/test_nodes.py
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@@ -1107,9 +1107,13 @@ def test_annotations():
print("=== Test: Annotations ===")
from backend.nodes.annotations import Annotations
from backend.nodes.font_node import Font
from backend.data_types import ImageData
node = Annotations()
font_node = Font()
warnings = []
Annotations._broadcast_warning_fn = lambda nid, msg: warnings.append(msg)
Annotations._current_node_id = "test"
field = DataField(
data=np.linspace(0.0, 1.0, 64 * 64, dtype=np.float64).reshape(64, 64),
xreal=1e-6,
@@ -1123,7 +1127,7 @@ def test_annotations():
plain_preview = render_datafield_preview(field, "viridis")
assert np.array_equal(plain_preview, base)
plain_field, = node.render(field, colormap="auto", show_scale_bar=False, show_color_map=False)
plain_field, = node.render(input=field, colormap="auto", show_scale_bar=False, show_color_map=False)
assert isinstance(plain_field, DataField)
assert np.array_equal(plain_field.data, field.data)
assert plain_field.colormap == "viridis"
@@ -1132,19 +1136,19 @@ def test_annotations():
assert plain.shape == base.shape
assert np.array_equal(plain, base)
with_scale_field, = node.render(field, colormap="auto", show_scale_bar=True, show_color_map=False)
with_scale_field, = node.render(input=field, colormap="auto", show_scale_bar=True, show_color_map=False)
with_scale = render_datafield_preview(with_scale_field, with_scale_field.colormap)
assert with_scale.shape == base.shape
assert not np.array_equal(with_scale, base)
with_legend_field, = node.render(field, colormap="auto", show_scale_bar=False, show_color_map=True)
with_legend_field, = node.render(input=field, colormap="auto", show_scale_bar=False, show_color_map=True)
with_legend = render_datafield_preview(with_legend_field, with_legend_field.colormap)
assert with_legend.shape[0] == base.shape[0]
assert with_legend.shape[1] > base.shape[1]
assert with_legend.shape[2] == 3
larger_legend_field, = node.render(
field,
input=field,
colormap="auto",
show_scale_bar=False,
show_color_map=True,
@@ -1156,7 +1160,7 @@ def test_annotations():
annotation_font, = font_node.build("Arial")
with_font_field, = node.render(
field,
input=field,
colormap="auto",
show_scale_bar=False,
show_color_map=True,
@@ -1167,18 +1171,62 @@ def test_annotations():
with_font = render_datafield_preview(with_font_field, with_font_field.colormap)
assert with_font.shape == with_legend.shape
with_both_field, = node.render(field, colormap="auto", show_scale_bar=True, show_color_map=True)
with_both_field, = node.render(input=field, colormap="auto", show_scale_bar=True, show_color_map=True)
with_both = render_datafield_preview(with_both_field, with_both_field.colormap)
assert with_both.shape == with_legend.shape
assert not np.array_equal(with_both[:, :base.shape[1]], base)
viewport_image = ImageData(
np.zeros((48, 64, 3), dtype=np.uint8),
metadata={
"annotation_context": {
"xreal": 2e-6,
"si_unit_xy": "m",
"legend_min": -1.5,
"legend_mid": 0.0,
"legend_max": 1.5,
"legend_unit": "V",
"colormap": "viridis",
},
},
)
annotated_image, = node.render(
input=viewport_image,
colormap="auto",
show_scale_bar=True,
show_color_map=True,
text_size=18.0,
)
assert isinstance(annotated_image, ImageData)
assert annotated_image.shape[0] == viewport_image.shape[0]
assert annotated_image.shape[1] > viewport_image.shape[1]
assert annotated_image.metadata["annotation_context"]["legend_unit"] == "V"
assert not np.array_equal(np.asarray(annotated_image)[:, :viewport_image.shape[1]], np.asarray(viewport_image))
assert warnings == []
plain_image = ImageData(np.zeros((32, 40, 3), dtype=np.uint8))
passthrough_image, = node.render(
input=plain_image,
colormap="auto",
show_scale_bar=True,
show_color_map=True,
text_size=18.0,
)
assert isinstance(passthrough_image, ImageData)
assert passthrough_image.shape == plain_image.shape
assert np.array_equal(np.asarray(passthrough_image), np.asarray(plain_image))
assert len(warnings) == 1
assert "no scale metadata" in warnings[0]
Annotations._broadcast_warning_fn = None
print(" PASS\n")
def test_markup():
print("=== Test: Markup ===")
from backend.nodes.markup import Markup
from backend.data_types import _preview_markup_stroke_width
from backend.data_types import ImageData, _preview_markup_stroke_width
node = Markup()
field = make_field(data=np.linspace(0.0, 1.0, 48 * 48, dtype=np.float64).reshape(48, 48))
@@ -1192,7 +1240,7 @@ def test_markup():
Markup._current_node_id = "test"
plain_field, = node.process(
field=field,
input=field,
shape="line",
stroke_color="#ffd54f",
stroke_width=3,
@@ -1212,7 +1260,7 @@ def test_markup():
{"kind": "arrow", "x1": 0.15, "y1": 0.85, "x2": 0.85, "y2": 0.2, "width": 4, "color": "#ffffff"},
])
marked_field, = node.process(
field=field,
input=field,
shape="arrow",
stroke_color="#ffffff",
stroke_width=4,
@@ -1222,6 +1270,23 @@ def test_markup():
assert marked.shape == base.shape
assert not np.array_equal(marked, base)
viewport_image = ImageData(
np.zeros((48, 48, 3), dtype=np.uint8),
metadata={"annotation_context": {"xreal": 1e-6, "si_unit_xy": "m"}},
)
image_markup, = node.process(
input=viewport_image,
shape="line",
stroke_color="#ff0000",
stroke_width=4,
markup_shapes=json.dumps([
{"kind": "line", "x1": 0.1, "y1": 0.2, "x2": 0.9, "y2": 0.8, "width": 4, "color": "#ff0000"},
]),
)
assert isinstance(image_markup, ImageData)
assert image_markup.metadata["annotation_context"]["si_unit_xy"] == "m"
assert not np.array_equal(np.asarray(image_markup), np.asarray(viewport_image))
Markup._broadcast_overlay_fn = None
print(" PASS\n")
@@ -1326,6 +1391,36 @@ def test_load_file_npz():
print(" PASS\n")
def test_load_file_cache():
print("=== Test: Image cache ===")
from unittest.mock import patch
from backend.nodes.image import Image
node = Image()
Image._load_fields_cached.cache_clear()
with tempfile.TemporaryDirectory() as tmpdir:
data = np.arange(16, dtype=np.float64).reshape(4, 4)
path = os.path.join(tmpdir, "cached.npy")
np.save(path, data)
with patch.object(Image, "_load_image_or_array", wraps=Image._load_image_or_array) as loader:
first, = node.load(filename=path)
second, = node.load(filename=path)
assert loader.call_count == 1
assert np.allclose(first.data, data)
assert np.allclose(second.data, data)
assert first is not second
first.data[0, 0] = -999.0
third, = node.load(filename=path)
assert third.data[0, 0] == data[0, 0]
Image._load_fields_cached.cache_clear()
print(" PASS\n")
def test_load_file_not_found():
print("=== Test: Image not found ===")
from backend.nodes.image import Image
@@ -1487,6 +1582,31 @@ def test_load_demo():
print(" PASS\n")
def test_load_demo_cache():
print("=== Test: ImageDemo cache ===")
from unittest.mock import patch
from backend.nodes.image import Image
from backend.nodes.image_demo import ImageDemo
node = ImageDemo()
Image._load_fields_cached.cache_clear()
with patch.object(Image, "_load_image_or_array", wraps=Image._load_image_or_array) as loader:
first, = node.load(name="nanoparticles.npy")
second, = node.load(name="nanoparticles.npy")
assert loader.call_count == 1
assert np.allclose(first.data, second.data)
assert first is not second
first.data[0, 0] = -999.0
third, = node.load(name="nanoparticles.npy")
assert third.data[0, 0] != -999.0
Image._load_fields_cached.cache_clear()
print(" PASS\n")
def test_load_demo_multi_layer_preview_payload():
print("=== Test: ImageDemo multi-layer preview payload ===")
from backend.execution import ExecutionEngine
@@ -1849,6 +1969,10 @@ def test_stats():
def test_view3d():
print("=== Test: View3D ===")
from backend.nodes.view_3d import View3D
from backend.data_types import ImageData, MeshModel
import base64
import io
from PIL import Image
node = View3D()
field = make_field()
@@ -1857,8 +1981,25 @@ def test_view3d():
View3D._broadcast_mesh_fn = lambda nid, mesh: captured.append(mesh)
View3D._current_node_id = "test"
result = node.render(field, colormap="viridis", z_scale=2.0, resolution=64)
assert result == ()
preview_image = Image.new("RGB", (12, 10), (255, 0, 0))
preview_buffer = io.BytesIO()
preview_image.save(preview_buffer, format="PNG")
viewport_snapshot = "data:image/png;base64," + base64.b64encode(preview_buffer.getvalue()).decode()
result = node.render(
field,
colormap="viridis",
z_scale=2.0,
resolution=64,
make_solid=False,
viewport_snapshot=viewport_snapshot,
)
assert len(result) == 2
assert isinstance(result[0], MeshModel)
assert isinstance(result[1], ImageData)
assert result[1].shape == (10, 12, 3)
assert np.all(result[1][0, 0] == np.array([255, 0, 0], dtype=np.uint8))
assert result[1].metadata["annotation_context"]["si_unit_xy"] == field.si_unit_xy
assert len(captured) == 1
mesh = captured[0]
@@ -1873,7 +2014,6 @@ def test_view3d():
assert mesh["z_min"] < mesh["z_max"]
# Verify base64 data can be decoded
import base64
z_bytes = base64.b64decode(mesh["z_data"])
assert len(z_bytes) == mesh["width"] * mesh["height"] * 4 # float32
@@ -1883,14 +2023,178 @@ def test_view3d():
# High-res input should be downsampled
big_field = make_field(shape=(256, 256))
captured.clear()
node.render(big_field, colormap="hot", z_scale=1.0, resolution=64)
node.render(big_field, colormap="hot", z_scale=1.0, resolution=64, make_solid=False)
assert captured[0]["width"] <= 64
assert captured[0]["height"] <= 64
# Separate map input should affect colors without changing mesh geometry
mesh_field = make_field(data=np.zeros((64, 64), dtype=np.float64), xreal=2.0, yreal=3.0)
map_field = make_field(data=np.tile(np.linspace(0.0, 1.0, 64, dtype=np.float64), (64, 1)), xreal=2.0, yreal=3.0)
captured.clear()
mapped_result = node.render(mesh_field, map_field=map_field, colormap="viridis", z_scale=1.0, resolution=32, make_solid=False)
mapped_mesh = captured[0]
assert mapped_mesh["x_range"] == [float(mesh_field.xoff), float(mesh_field.xoff + mesh_field.xreal)]
assert mapped_mesh["y_range"] == [float(mesh_field.yoff), float(mesh_field.yoff + mesh_field.yreal)]
mapped_z = np.frombuffer(base64.b64decode(mapped_mesh["z_data"]), dtype=np.float32)
assert np.allclose(mapped_z, 0.0)
mapped_colors = np.frombuffer(base64.b64decode(mapped_mesh["colors"]), dtype=np.uint8)
captured.clear()
node.render(mesh_field, colormap="viridis", z_scale=1.0, resolution=32, make_solid=False)
mesh_only = captured[0]
mesh_only_colors = np.frombuffer(base64.b64decode(mesh_only["colors"]), dtype=np.uint8)
assert not np.array_equal(mapped_colors, mesh_only_colors)
# make_solid should add extra geometry beyond the top surface grid
solid_mesh = mapped_result[0]
assert isinstance(solid_mesh, MeshModel)
captured.clear()
solid_result = node.render(mesh_field, colormap="viridis", z_scale=1.0, resolution=16, make_solid=True)
assert len(solid_result[0].vertices) > 16 * 16
assert len(solid_result[0].faces) > (15 * 15 * 2)
solid_payload = captured[0]
assert solid_payload["make_solid"] is True
assert "positions" in solid_payload
assert "indices" in solid_payload
assert "vertex_colors" in solid_payload
View3D._broadcast_mesh_fn = None
print(" PASS\n")
def test_save_generic():
print("=== Test: Save ===")
from backend.nodes.save import Save
from backend.data_types import DataField, LineData, MeasureTable, MeshModel, RecordTable
import tifffile
from PIL import Image as PILImage
node = Save()
with tempfile.TemporaryDirectory() as tmpdir:
# Save scalar as TXT and JSON
node.save(filename="scalar", directory_path=tmpdir, format="TXT", value=3.5)
assert Path(tmpdir, "scalar.txt").read_text(encoding="utf-8").strip() == "3.5"
node.save(filename="scalar_json", directory_path=tmpdir, format="JSON", value=3.5)
assert json.loads(Path(tmpdir, "scalar_json.json").read_text(encoding="utf-8")) == {"value": 3.5}
# Save line as CSV, NPZ, and JSON
line = LineData(data=np.array([1.0, 2.0, 3.0]), x_axis=np.array([0.0, 0.5, 1.0]), x_unit="um", y_unit="nm")
node.save(filename="profile", directory_path=tmpdir, format="CSV", value=line)
csv_text = Path(tmpdir, "profile.csv").read_text(encoding="utf-8")
assert "x,y,x_unit,y_unit" in csv_text
assert "um" in csv_text and "nm" in csv_text
node.save(filename="profile_npz", directory_path=tmpdir, format="NPZ", value=line)
line_npz = np.load(Path(tmpdir, "profile_npz.npz"))
assert np.allclose(line_npz["x"], line.x_axis)
assert np.allclose(line_npz["y"], line.data)
node.save(filename="profile_json", directory_path=tmpdir, format="JSON", value=line)
line_json = json.loads(Path(tmpdir, "profile_json.json").read_text(encoding="utf-8"))
assert line_json["x_unit"] == "um"
assert line_json["y_unit"] == "nm"
assert line_json["x"] == [0.0, 0.5, 1.0]
assert line_json["y"] == [1.0, 2.0, 3.0]
# Save DATA_FIELD as TIFF, PNG, and NPZ
field = DataField(
data=np.array([[1.0, 2.0], [3.0, 4.5]], dtype=np.float64),
xreal=2e-6,
yreal=1e-6,
si_unit_xy="m",
si_unit_z="m",
colormap="viridis",
)
node.save(filename="field_tiff", directory_path=tmpdir, format="TIFF", value=field)
field_tiff = tifffile.imread(Path(tmpdir, "field_tiff.tiff"))
assert field_tiff.shape == field.data.shape
assert field_tiff.dtype == np.float32
assert np.allclose(field_tiff, field.data.astype(np.float32))
node.save(filename="field_png", directory_path=tmpdir, format="PNG", value=field)
field_png = np.asarray(PILImage.open(Path(tmpdir, "field_png.png")))
assert field_png.shape == (2, 2, 3)
assert field_png.dtype == np.uint8
node.save(filename="field_npz", directory_path=tmpdir, format="NPZ", value=field)
field_npz = np.load(Path(tmpdir, "field_npz.npz"))
assert np.allclose(field_npz["field"], field.data)
# Save IMAGE as PNG, TIFF, and NPZ
image = np.array(
[
[[255, 0, 0], [0, 255, 0]],
[[0, 0, 255], [255, 255, 0]],
],
dtype=np.uint8,
)
node.save(filename="image_png", directory_path=tmpdir, format="PNG", value=image)
image_png = np.asarray(PILImage.open(Path(tmpdir, "image_png.png")))
assert image_png.shape == image.shape
assert np.array_equal(image_png, image)
node.save(filename="image_tiff", directory_path=tmpdir, format="TIFF", value=image)
image_tiff = tifffile.imread(Path(tmpdir, "image_tiff.tiff"))
assert image_tiff.shape == image.shape
assert image_tiff.dtype == np.uint8
assert np.array_equal(image_tiff, image)
node.save(filename="image_npz", directory_path=tmpdir, format="NPZ", value=image)
image_npz = np.load(Path(tmpdir, "image_npz.npz"))
assert np.array_equal(image_npz["image"], image)
# Save tables as CSV and JSON
measure_table = MeasureTable([
{"quantity": "Rq", "value": 1.23, "unit": "nm"},
{"quantity": "Ra", "value": 0.98, "unit": "nm"},
])
node.save(filename="measurements_csv", directory_path=tmpdir, format="CSV", value=measure_table)
measure_csv = Path(tmpdir, "measurements_csv.csv").read_text(encoding="utf-8")
assert "quantity,value,unit" in measure_csv
assert "Rq,1.23,nm" in measure_csv
node.save(filename="measurements_json", directory_path=tmpdir, format="JSON", value=measure_table)
assert json.loads(Path(tmpdir, "measurements_json.json").read_text(encoding="utf-8")) == list(measure_table)
record_table = RecordTable([
{"label": "particle-1", "height": 12.0, "area": 44.0},
{"label": "particle-2", "height": 8.0, "area": 21.0},
])
node.save(filename="records_csv", directory_path=tmpdir, format="CSV", value=record_table)
record_csv = Path(tmpdir, "records_csv.csv").read_text(encoding="utf-8")
assert "label,height,area" in record_csv
assert "particle-1,12.0,44.0" in record_csv
node.save(filename="records_json", directory_path=tmpdir, format="JSON", value=record_table)
assert json.loads(Path(tmpdir, "records_json.json").read_text(encoding="utf-8")) == list(record_table)
# Save mesh as OBJ and STL
mesh = MeshModel(
vertices=np.array([[0, 0, 0], [1, 0, 0], [0, 1, 0]], dtype=np.float32),
faces=np.array([[0, 1, 2]], dtype=np.int32),
)
node.save(filename="triangle", directory_path=tmpdir, format="OBJ", value=mesh)
obj_text = Path(tmpdir, "triangle.obj").read_text(encoding="utf-8")
assert "v 0.0 0.0 0.0" in obj_text
assert "f 1 2 3" in obj_text
node.save(filename="triangle", directory_path=tmpdir, format="STL", value=mesh)
stl_text = Path(tmpdir, "triangle.stl").read_text(encoding="utf-8")
assert stl_text.startswith("solid argonode")
assert "facet normal" in stl_text
try:
node.save(filename="triangle", directory_path=tmpdir, format="PNG", value=mesh)
assert False, "Mesh should only be saveable as OBJ or STL"
except ValueError:
pass
try:
node.save(filename="field_bad", directory_path=tmpdir, format="CSV", value=field)
assert False, "DATA_FIELD should reject unsupported save formats"
except ValueError:
pass
print(" PASS\n")
# =========================================================================
# Run all tests
# =========================================================================
@@ -1940,6 +2244,7 @@ if __name__ == "__main__":
test_load_demo()
test_coordinate()
test_range_slider()
test_save_generic()
test_save_image()
# Display