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rename all instances of sample_stage -> spectroscopy_stage #38

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rename all instances of sample_stage -> spectroscopy_stage #38

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20 changes: 12 additions & 8 deletions src/dls_tiled/visr.py
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Original file line number Diff line number Diff line change
Expand Up @@ -196,7 +196,7 @@ def _channel_length(array: H5Dataset | numpy.ndarray | dict) -> int:


def _axis_letter(name: object) -> str | None:
"""Return "x", "y" or "z" if the axis name ends in one (e.g. "sample_stage-x")."""
"""Return "x", "y" or "z" if the name ends in one (e.g. "spectroscopy_stage-x")."""
if not isinstance(name, str):
return None
letter = re.split(r"[-_.]", name.lower())[-1]
Expand All @@ -211,7 +211,7 @@ def _axis_name(axis: object) -> str | None:
"""The device name of a spec axis, or None if the spec doesn't carry one.

A spec axis is whatever the plan passed in: a plain name, an ophyd-async
repr that carries the name (``Motor(name="sample_stage-x")``), or, in older
repr that carries the name (``Motor(name="spectroscopy_stage-x")``), or, in older
runs, an object repr with no name (``<... Motor object at 0x7f...>``).
"""
if not isinstance(axis, str):
Expand Down Expand Up @@ -486,11 +486,11 @@ async def get_setpoints(root, uid):

async def _fetch_readback_x(root, uid) -> tuple[H5Dataset | numpy.ndarray, ScanType]:
try:
x = await get_data(root, [uid, "primary", "internal", "sample_stage-x"])
x = await get_data(root, [uid, "primary", "internal", "spectroscopy_stage-x"])
scan_type = ScanType.FlyScan
except NoEntry:
try:
x = await get_data(root, [uid, "primary", "sample_stage-x"])
x = await get_data(root, [uid, "primary", "spectroscopy_stage-x"])
scan_type = ScanType.FlyScan
except NoEntry:
x = await get_data(root, [uid, "primary", "X"])
Expand All @@ -502,13 +502,17 @@ async def _fetch_readback_x(root, uid) -> tuple[H5Dataset | numpy.ndarray, ScanT
async def _fetch_readback_yz(root, uid, scan_type, x_shape):
if scan_type == ScanType.FlyScan:
try:
y = await get_data(root, [uid, "primary", "internal", "sample_stage-y"])
y = await get_data(
root, [uid, "primary", "internal", "spectroscopy_stage-y"]
)
except NoEntry:
y = await fill_data(root, [uid, "primary", "sample_stage-y"], x_shape)
y = await fill_data(root, [uid, "primary", "spectroscopy_stage-y"], x_shape)
try:
z = await get_data(root, [uid, "primary", "internal", "sample_stage-z"])
z = await get_data(
root, [uid, "primary", "internal", "spectroscopy_stage-z"]
)
except NoEntry:
z = await fill_data(root, [uid, "primary", "sample_stage-z"], x_shape)
z = await fill_data(root, [uid, "primary", "spectroscopy_stage-z"], x_shape)
else:
y = await fill_data(root, [uid, "primary", "Y"], x_shape)
z = await fill_data(root, [uid, "primary", "Z"], x_shape)
Expand Down
51 changes: 33 additions & 18 deletions tests/test_visr.py
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Original file line number Diff line number Diff line change
Expand Up @@ -167,7 +167,9 @@ async def lookup_adapter(path):

def test_setpoints_follow_axis_names_not_dimension_order():
# Raster scan: y is the outer dimension, x the inner one.
spec = Line("sample_stage-y", 0, 1, 2) * Line("sample_stage-x", 0, 10, 3)
spec = Line("spectroscopy_stage-y", 0, 1, 2) * Line(
"spectroscopy_stage-x", 0, 10, 3
)

x, y, z = _setpoints(spec)

Expand All @@ -181,7 +183,7 @@ def test_setpoints_of_runs_with_repr_axes_use_the_motors_list():
"<Motor object at 0x2>", 0, 10, 3
)

x, y, _ = _setpoints(spec, motors=["sample_stage-y", "sample_stage-x"])
x, y, _ = _setpoints(spec, motors=["spectroscopy_stage-y", "spectroscopy_stage-x"])

assert x.tolist() == [0, 5, 10, 0, 5, 10]
assert y.tolist() == [0, 0, 0, 1, 1, 1]
Expand Down Expand Up @@ -286,7 +288,9 @@ def _grid(spec, motors=None):


def test_grid_edges_sit_halfway_between_setpoints():
spec = Line("sample_stage-y", 0, 2, 3) * ~Line("sample_stage-x", 0, 10, 3)
spec = Line("spectroscopy_stage-y", 0, 2, 3) * ~Line(
"spectroscopy_stage-x", 0, 10, 3
)

x_edges, y_edges, n_total, *_ = _grid(spec)

Expand All @@ -300,7 +304,7 @@ def test_grid_of_runs_with_repr_axes_uses_the_motors_list():
"<Motor object at 0x2>", 0, 10, 3
)

x_edges, y_edges, *_ = _grid(spec, ["sample_stage-y", "sample_stage-x"])
x_edges, y_edges, *_ = _grid(spec, ["spectroscopy_stage-y", "spectroscopy_stage-x"])

assert len(x_edges) == 4 and len(y_edges) == 4

Expand Down Expand Up @@ -733,11 +737,14 @@ def test_binned_etag_changes_when_the_image_does(client):
@pytest.mark.parametrize(
("stored", "name"),
[
("sample_stage-x", "sample_stage-x"),
('Motor(name="sample_stage-x")', "sample_stage-x"),
("Motor(name='sample_stage-y')", "sample_stage-y"),
('Motor(device_name="stage", name="sample_stage-x")', "sample_stage-x"),
('Motor(prefix="BL01:", name="sample_stage-x")', "sample_stage-x"),
("spectroscopy_stage-x", "spectroscopy_stage-x"),
('Motor(name="spectroscopy_stage-x")', "spectroscopy_stage-x"),
("Motor(name='spectroscopy_stage-y')", "spectroscopy_stage-y"),
(
'Motor(device_name="stage", name="spectroscopy_stage-x")',
"spectroscopy_stage-x",
),
('Motor(prefix="BL01:", name="spectroscopy_stage-x")', "spectroscopy_stage-x"),
("<ophyd_async.epics.motor.Motor object at 0x7f797c058590>", None),
],
)
Expand All @@ -747,8 +754,8 @@ def test_axis_name_reads_the_name_out_of_the_forms_runs_store(stored, name):

def test_setpoints_of_runs_with_named_reprs_need_no_motors_list():
# recent runs store Motor(name=...) and fly scans have no motors list
spec = Line('Motor(name="sample_stage-y")', 0, 1, 2) * Line(
'Motor(name="sample_stage-x")', 0, 10, 3
spec = Line('Motor(name="spectroscopy_stage-y")', 0, 1, 2) * Line(
'Motor(name="spectroscopy_stage-x")', 0, 10, 3
)

x, y, _ = _setpoints(spec)
Expand All @@ -758,8 +765,8 @@ def test_setpoints_of_runs_with_named_reprs_need_no_motors_list():


def test_grid_of_runs_with_named_reprs_needs_no_motors_list():
spec = Line('Motor(name="sample_stage-y")', 0, 2, 3) * ~Line(
'Motor(name="sample_stage-x")', 0, 10, 3
spec = Line('Motor(name="spectroscopy_stage-y")', 0, 2, 3) * ~Line(
'Motor(name="spectroscopy_stage-x")', 0, 10, 3
)

x_edges, y_edges, n_total, *_ = _grid(spec)
Expand Down Expand Up @@ -906,7 +913,10 @@ def test_place_on_grid_without_points_is_the_bare_grid():

@pytest.mark.parametrize(
"motors",
[["sample_stage-y", "sample_stage-x"], ["sample_stage-x", "sample_stage-y"]],
[
["spectroscopy_stage-y", "spectroscopy_stage-x"],
["spectroscopy_stage-x", "spectroscopy_stage-y"],
],
)
def test_binned_lets_the_points_decide_x_and_y_when_only_the_motors_list_names_them(
client, motors
Expand Down Expand Up @@ -990,7 +1000,11 @@ def write_points(
target = primary if where == "primary" else primary.create_container(where)
names = {"X": "X", "Y": "Y", "Z": "Z"}
if where != "primary" or channels == "named":
names = {"X": "sample_stage-x", "Y": "sample_stage-y", "Z": "sample_stage-z"}
names = {
"X": "spectroscopy_stage-x",
"Y": "spectroscopy_stage-y",
"Z": "spectroscopy_stage-z",
}
target.write_array(numpy.asarray(x, dtype=float), key=names["X"])
target.write_array(numpy.asarray(y, dtype=float), key=names["Y"])
if z is not None:
Expand Down Expand Up @@ -1121,7 +1135,8 @@ def test_binned_swapping_the_dimension_indices_transposes_the_image(client):

@pytest.mark.parametrize("where", ["internal", "named"])
def test_binned_finds_positions_wherever_the_run_stores_them(client, where):
# older fly scans: primary/internal/sample_stage-x; others: primary/sample_stage-x
# older fly scans: primary/internal/spectroscopy_stage-x
# others: primary/spectroscopy_stage-x
x, y = [0.0, 1.0, 0.0, 1.0], [0.0, 0.0, 1.0, 1.0]
if where == "internal":
write_points(client, where, x, y, where="internal")
Expand Down Expand Up @@ -1284,8 +1299,8 @@ def test_binned_bins_a_step_scans_diodes_from_its_event_table(client):
primary.write_dataframe(
pandas.DataFrame(
{
"sample_stage-x": SQUARE_X,
"sample_stage-y": SQUARE_Y,
"spectroscopy_stage-x": SQUARE_X,
"spectroscopy_stage-y": SQUARE_Y,
**{f"spectroscopy_diodes-{c}": v for c, v in DIODES.items()},
}
),
Expand Down
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