test: update serdes tests (#71)

.pre-commit-config.yaml

@@ -18,6 +18,8 @@ repos:
  - id: check-docstring-first
  - id: end-of-file-fixer
  - id: trailing-whitespace
+ - id: pretty-format-json
+ args: ["--autofix"]
 
  - repo: https://github.com/charliermarsh/ruff-pre-commit
  rev: v0.0.226

tests/conftest.py

@@ -0,0 +1,31 @@
+import pytest
+
+from useq import MDASequence
+
+
+@pytest.fixture
+def mda1() -> MDASequence:
+ return MDASequence(
+ axis_order="tpcz",
+ metadata={"some info": "something"},
+ stage_positions=[
+ (10, 20),
+ {
+ "x": 10,
+ "y": 20,
+ "z": 50,
+ "name": "test_name",
+ "z_plan": {"above": 10, "below": 0, "step": 1},
+ },
+ ],
+ channels=[
+ {"config": "Cy5", "exposure": 50},
+ {"config": "FITC", "exposure": 100.0},
+ {"config": "DAPI", "do_stack": False, "acquire_every": 3},
+ ],
+ time_plan=[
+ {"interval": 3, "loops": 3},
+ {"duration": {"minutes": 40}, "interval": 10},
+ ],
+ z_plan={"range": 1.0, "step": 0.5},
+ )

tests/fixtures/mda.json

@@ -0,0 +1,78 @@
+{
+ "axis_order": "tpcz",
+ "channels": [
+ {
+ "acquire_every": 1,
+ "camera": null,
+ "config": "Cy5",
+ "do_stack": true,
+ "exposure": 50.0,
+ "group": "Channel",
+ "z_offset": 0.0
+ },
+ {
+ "acquire_every": 1,
+ "camera": null,
+ "config": "FITC",
+ "do_stack": true,
+ "exposure": 100.0,
+ "group": "Channel",
+ "z_offset": 0.0
+ },
+ {
+ "acquire_every": 3,
+ "camera": null,
+ "config": "DAPI",
+ "do_stack": false,
+ "exposure": null,
+ "group": "Channel",
+ "z_offset": 0.0
+ }
+ ],
+ "metadata": {
+ "some info": "something"
+ },
+ "stage_positions": [
+ {
+ "name": null,
+ "x": 10.0,
+ "y": 20.0,
+ "z": null,
+ "z_plan": {
+ "go_up": true
+ }
+ },
+ {
+ "name": "test_name",
+ "x": 10.0,
+ "y": 20.0,
+ "z": 50.0,
+ "z_plan": {
+ "above": 10.0,
+ "below": 0.0,
+ "go_up": true,
+ "step": 1.0
+ }
+ }
+ ],
+ "time_plan": {
+ "phases": [
+ {
+ "interval": 3.0,
+ "loops": 3,
+ "prioritize_duration": false
+ },
+ {
+ "duration": 2400.0,
+ "interval": 10.0,
+ "prioritize_duration": true
+ }
+ ],
+ "prioritize_duration": false
+ },
+ "z_plan": {
+ "go_up": true,
+ "range": 1.0,
+ "step": 0.5
+ }
+}

tests/fixtures/mda.yaml

@@ -0,0 +1,31 @@
+axis_order: tpcz
+channels:
+- config: Cy5
+ exposure: 50.0
+- config: FITC
+ exposure: 100.0
+- acquire_every: 3
+ config: DAPI
+ do_stack: false
+metadata:
+ some info: something
+stage_positions:
+- x: 10.0
+ y: 20.0
+- name: test_name
+ x: 10.0
+ y: 20.0
+ z: 50.0
+ z_plan:
+ above: 10.0
+ below: 0.0
+ step: 1.0
+time_plan:
+ phases:
+ - interval: 0:00:03
+ loops: 3
+ - duration: 0:40:00
+ interval: 0:00:10
+z_plan:
+ range: 1.0
+ step: 0.5

tests/test_serialization.py

@@ -0,0 +1,18 @@
+import json
+from pathlib import Path
+
+import pytest
+
+from useq import MDASequence
+
+
+@pytest.mark.parametrize("ext", ["json", "yaml"])
+def test_serialization(mda1: MDASequence, ext: str) -> None:
+ FILE = Path(__file__).parent / "fixtures" / f"mda.{ext}"
+ text = FILE.read_text()
+ mda = MDASequence.parse_file(str(FILE))
+ assert mda == mda1
+ if ext == "json":
+ assert json.loads(mda.json(exclude={"uid"})) == json.loads(text)
+ else:
+ assert mda.yaml() == text