feat: init

test/model/metadata_sources/test_metadata.py

@@ -0,0 +1,154 @@
+import pytest
+import random
+
+
+def test_metadata_voxel_size(dummy_model):
+    from navigate.model.metadata_sources.metadata import Metadata
+
+    md = Metadata()
+
+    md.configuration = dummy_model.configuration
+
+    zoom = dummy_model.configuration["experiment"]["MicroscopeState"]["zoom"]
+    active_microscope = dummy_model.configuration["experiment"]["MicroscopeState"][
+        "microscope_name"
+    ]
+    pixel_size = float(
+        dummy_model.configuration["configuration"]["microscopes"][active_microscope][
+            "zoom"
+        ]["pixel_size"][zoom]
+    )
+
+    dx, dy, dz = md.voxel_size
+
+    assert (
+        (dx == pixel_size)
+        and (dy == pixel_size)
+        and (
+            dz
+            == float(
+                dummy_model.configuration["experiment"]["MicroscopeState"]["step_size"]
+            )
+        )
+    )
+
+
+def test_metadata_shape(dummy_model):
+    from navigate.model.metadata_sources.metadata import Metadata
+
+    dummy_model.configuration["experiment"]["MicroscopeState"]["image_mode"] = "z-stack"
+
+    md = Metadata()
+
+    md.configuration = dummy_model.configuration
+
+    microscope_name = dummy_model.configuration["experiment"]["MicroscopeState"][
+        "microscope_name"
+    ]
+    txs = dummy_model.configuration["experiment"]["CameraParameters"][microscope_name][
+        "img_x_pixels"
+    ]
+    tys = dummy_model.configuration["experiment"]["CameraParameters"][microscope_name][
+        "img_y_pixels"
+    ]
+    tzs = dummy_model.configuration["experiment"]["MicroscopeState"]["number_z_steps"]
+    tts = dummy_model.configuration["experiment"]["MicroscopeState"]["timepoints"]
+    tcs = sum(
+        [
+            v["is_selected"] is True
+            for k, v in dummy_model.configuration["experiment"]["MicroscopeState"][
+                "channels"
+            ].items()
+        ]
+    )
+
+    xs, ys, cs, zs, ts = md.shape
+
+    assert (xs == txs) and (ys == tys) and (zs == tzs) and (ts == tts) and (cs == tcs)
+
+
+@pytest.mark.parametrize(
+    "image_mode",
+    [
+        "single",
+        "Confocal Projection",
+        "z-stack",
+    ],
+)
+@pytest.mark.parametrize("stack_cycling_mode", ["per_stack", "per_z"])
+@pytest.mark.parametrize("conpro_cycling_mode", ["per_stack", "per_plane"])
+def test_metadata_set_stack_order_from_configuration_experiment(
+    dummy_model, image_mode, stack_cycling_mode, conpro_cycling_mode
+):
+    from navigate.model.metadata_sources.metadata import Metadata
+
+    dummy_model.configuration["experiment"]["MicroscopeState"][
+        "image_mode"
+    ] = image_mode
+    dummy_model.configuration["experiment"]["MicroscopeState"][
+        "stack_cycling_mode"
+    ] = stack_cycling_mode
+    dummy_model.configuration["experiment"]["MicroscopeState"][
+        "conpro_cycling_mode"
+    ] = conpro_cycling_mode
+
+    md = Metadata()
+
+    md.configuration = dummy_model.configuration
+
+    if image_mode == "z-stack" and stack_cycling_mode == "per_stack":
+        assert md._per_stack is True
+    elif image_mode == "Confocal Projection" and stack_cycling_mode == "per_stack":
+        assert md._per_stack is True
+    else:
+        assert md._per_stack is False
+
+def set_shape_from_configuration_experiment(dummy_model):
+    from navigate.model.metadata_sources.metadata import Metadata
+
+    md = Metadata()
+
+    md.configuration = dummy_model.configuration.copy()
+
+
+    # set up experiment with multiposition
+    # no position
+    md.configuration["experiment"]["MicroscopeState"]["image_mode"] = "z-stack"
+    md.configuration["multi_positions"] = [
+        ["X", "Y", "Z", "THETA", "F"]
+    ]
+    md.configuration["expriment"]["MicroscopeState"]["is_multiposition"] = False
+
+    md._set_shape_from_configuration_experiment()
+
+    assert md._multiposition is False
+    assert md.positions == 1
+
+    # customized mode
+    md.configuration["experiment"]["MicroscopeState"]["image_mode"] = "customized"
+    assert md._multiposition is True
+    assert md.positions == 1
+
+    # random multiposition
+    md.configuration["experiment"]["MicroscopeState"]["image_mode"] = "z-stack"
+    for i in range(5):
+        num_positions = random.randint(2, 10)
+        md.configuration["multi_positions"] = [["X", "Y", "Z", "THETA", "F"]]
+        for p in range(num_positions):
+            pos = [
+                random.uniform(0, 100),  # X
+                random.uniform(0, 100),  # Y
+                random.uniform(0, 100),  # Z
+                random.uniform(0, 360),  # THETA
+                random.uniform(0, 10),  # F
+            ]
+            md.configuration["multi_positions"].append(pos)
+
+        md.configuration["experiment"]["MicroscopeState"]["is_multiposition"] = True
+
+        md._set_shape_from_configuration_experiment()
+
+        assert md._multiposition is True
+        assert md.positions == num_positions
+
+