diff --git a/openflexure_microscope/api/default_extensions/scan.py b/openflexure_microscope/api/default_extensions/scan.py index 544d8017..5a8eba27 100644 --- a/openflexure_microscope/api/default_extensions/scan.py +++ b/openflexure_microscope/api/default_extensions/scan.py @@ -33,7 +33,7 @@ def construct_grid(initial, step_sizes, n_steps, style="raster"): if style == "spiral": # deal with the centre image immediately coord = initial - arr.append(initial) + arr.append([initial]) # for spiral, n_steps is the number of shells, and so only requires n_steps[0] for i in range(2, n_steps[0] + 1): arr.append([]) @@ -66,16 +66,6 @@ def construct_grid(initial, step_sizes, n_steps, style="raster"): return arr -def flatten_grid(grid): - """ - Convert a 3D list of scan positions into a flat list - of sequential positions. - """ - - grid = list(itertools.chain(*grid)) - return grid - - ### Capturing diff --git a/openflexure_microscope/utilities.py b/openflexure_microscope/utilities.py index e0756303..0d0d0a65 100644 --- a/openflexure_microscope/utilities.py +++ b/openflexure_microscope/utilities.py @@ -26,7 +26,7 @@ class Timer(object): def deserialise_array_b64(b64_string, dtype, shape): - flat_arr = np.fromstring(base64.b64decode(b64_string), dtype) + flat_arr = np.frombuffer(base64.b64decode(b64_string), dtype) return flat_arr.reshape(shape) @@ -106,16 +106,6 @@ def axes_to_array( return base_array -def filter_dict(dictionary: dict, keys: list): - # Get value by recursively applying getitem - val = reduce(operator.getitem, keys, dictionary) - - # Create new dictionary by running reduce on key, val pairs - out = reduce(lambda x, y: {y: x}, reversed(keys), val) - - return out - - def entry_by_uuid(entry_id: str, object_list: list): """Return an object from a list, if .id matches id argument.""" found = None @@ -132,26 +122,3 @@ def entry_by_uuid(entry_id: str, object_list: list): if converter(o.id) == converter(entry_id): found = o return found - - -def recursively_apply(data, func): - """ - Recursively apply a function to a dictionary, list, array, or tuple - - Args: - data: Input iterable data - func: Function to apply to all non-iterable values - """ - # If the object is a dictionary - if isinstance(data, abc.Mapping): - return {key: recursively_apply(val, func) for key, val in data.items()} - # If the object is iterable but NOT a dictionary or a string - elif ( - isinstance(data, abc.Iterable) - and not isinstance(data, abc.Mapping) - and not isinstance(data, str) - ): - return [recursively_apply(x, func) for x in data] - # if the object is neither a map nor iterable - else: - return func(data) diff --git a/poetry.lock b/poetry.lock index 982ef0d1..26facc8a 100644 --- a/poetry.lock +++ b/poetry.lock @@ -63,6 +63,14 @@ six = ">=1.12,<2.0" typed-ast = {version = ">=1.4.0,<1.5", markers = "implementation_name == \"cpython\" and python_version < \"3.8\""} wrapt = ">=1.11,<2.0" +[[package]] +name = "atomicwrites" +version = "1.4.0" 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mode 100644 index 00000000..c3a86004 --- /dev/null +++ b/tests/test_extension_scan.py @@ -0,0 +1,59 @@ +from pprint import pprint + +from openflexure_microscope.api.default_extensions import scan + + +def test_construct_grid_raster(): + grid = scan.construct_grid((0, 0), (100, 100), (3, 3), style="raster") + assert grid == [ + [(0, 0), (0, 100), (0, 200)], + [(100, 0), (100, 100), (100, 200)], + [(200, 0), (200, 100), (200, 200)], + ] + + +def test_construct_grid_snake(): + grid = scan.construct_grid((0, 0), (100, 100), (3, 3), style="snake") + assert grid == [ + [(0, 0), (0, 100), (0, 200)], + [(100, 200), (100, 100), (100, 0)], + [(200, 0), (200, 100), (200, 200)], + ] + + +def test_construct_grid_spiral(): + grid = scan.construct_grid((0, 0), (100, 100), (3, 0), style="spiral") + assert grid == [ + [(0, 0)], + [ + (0, 100), + (100, 100), + (100, 0), + (100, -100), + (0, -100), + (-100, -100), + (-100, 0), + (-100, 100), + ], + [ + (-100, 200), + (0, 200), + (100, 200), + (200, 200), + (200, 100), + (200, 0), + (200, -100), + (200, -200), + (100, -200), + (0, -200), + (-100, -200), + (-200, -200), + (-200, -100), + (-200, 0), + (-200, 100), + (-200, 200), + ], + ] + + # Ensure second n_steps value makes no difference + assert grid == scan.construct_grid((0, 0), (100, 100), (3, 3), style="spiral") diff --git a/tests/test_utilities.py b/tests/test_utilities.py new file mode 100644 index 00000000..95ae1fcd --- /dev/null +++ b/tests/test_utilities.py @@ -0,0 +1,31 @@ +import numpy as np + +from openflexure_microscope import utilities + + +def test_serialise_array_b64(): + shape_in = (3, 2) + arr_in = np.random.randint(100, size=shape_in, dtype=np.int) + + b64_string, dtype, shape = utilities.serialise_array_b64(arr_in) + assert b64_string + assert dtype == "int32" + assert shape == shape_in + + arr_out = utilities.deserialise_array_b64(b64_string, dtype, shape) + assert np.array_equal(arr_out, arr_in) + + +def test_ndarray_to_json(): + shape_in = (3, 2) + arr_in = np.random.randint(100, size=shape_in, dtype=np.int) + + json_out = utilities.ndarray_to_json(arr_in) + + arr_out = utilities.json_to_ndarray(json_out) + assert np.array_equal(arr_out, arr_in) + + +def test_axes_to_array(): + dict_in = {"x": 1, "y": 2, "z": 3} + assert utilities.axes_to_array(dict_in) == [1, 2, 3]