From 03500ab321489db1aecef5b3f64de64b31c7d66c Mon Sep 17 00:00:00 2001 From: "Kaustubh R. Mote" Date: Thu, 25 Jan 2024 09:28:57 +0530 Subject: [PATCH 1/2] return tuples instead of lists for compatibility in 'thres' and 'thres-fast' segment finders --- nmrglue/analysis/peakpick.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nmrglue/analysis/peakpick.py b/nmrglue/analysis/peakpick.py index 8eeda0d3..17e46f57 100644 --- a/nmrglue/analysis/peakpick.py +++ b/nmrglue/analysis/peakpick.py @@ -535,7 +535,7 @@ def find_pseg_slice(data, location, thres): stop = stop + 1 al[dim] = stop seg_slice.append(slice(start + 1, stop)) - return seg_slice + return tuple(seg_slice) def find_nseg_slice(data, location, thres): @@ -558,4 +558,4 @@ def find_nseg_slice(data, location, thres): stop = stop + 1 al[dim] = stop seg_slice.append(slice(start + 1, stop)) - return seg_slice + return tuple(seg_slice) From 92f4193047468782e2e3d46bcc3af7cdff8afcd0 Mon Sep 17 00:00:00 2001 From: "Kaustubh R. Mote" Date: Thu, 25 Jan 2024 09:29:27 +0530 Subject: [PATCH 2/2] tests for detecting 1D, 2D, and 3D peaks using all available algorithms improved docs for the peak picking tests and added pytest marks --- tests/test_peakpick.py | 245 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 245 insertions(+) create mode 100644 tests/test_peakpick.py diff --git a/tests/test_peakpick.py b/tests/test_peakpick.py new file mode 100644 index 00000000..5895715b --- /dev/null +++ b/tests/test_peakpick.py @@ -0,0 +1,245 @@ +import nmrglue as ng +import numpy as np +import pytest + + +_ONE_D_PEAKS = { + "shape": (1024,), + "positions": [100, 200, 300, 400, 500], + "lws": [10, 20, 10, 20, 10], + "amps": [100, 200, 300, 300, 150], + "vparams": [0.2, 0.4, 0.2, 0.5, 1.0], +} + +_TWO_D_PEAKS = { + "shape": (512, 128), + "positions": [(100, 100), (200, 53), (300, 110), (400, 75)], + "lws": [(10, 5), (20, 5), (10, 5), (20, 5)], + "amps": [100, 200, 300, 300], + "vparams": [(0.2, 0.2), (0.4, 0.4), (0.2, 0.2), (0.5, 0.4)], +} + + +_THREE_D_PEAKS = { + "shape": (256, 64, 64), + "positions": [(150, 24, 22), (200, 10, 50), (210, 50, 10), (77, 30, 15)], + "lws": [(5, 5, 5), (3, 8, 5), (7, 5, 5), (7, 6, 5)], + "amps": [100, 200, 300, 300], + "vparams": [(0.2, 0.2, 0.3), (0.5, 0.4, 0.4), (0.1, 0.2, 0.2), (0.3, 0.5, 0.4)], +} + + +def _generate_1d_data(shape, positions, lws, amps, vparams): + """ + Generates a test 1d dataset with multiple peaks + + Parameters + ---------- + shape : Iterable[int] + shape of the numpy array to be created + positions : Iterable[int] + a list of the positions of the peaks + lws : Iterable[float|int] + a list of linewidths for each peak + amps : Iterable[float|int] + a list of amplitudes for each peak + vparams : Iterable[float|int] + a list of list containing the eta parameter + for the pseudo voigt lineshape + + Returns + ------- + numpy.ndarray + simulated one-d dataset + + """ + data = ng.linesh.sim_NDregion( + shape=shape, + lineshapes=["pv"], + params=[[(pos, lws, vp)] for pos, lws, vp in zip(positions, lws, vparams)], + amps=amps, + ) + return data + + +def _generate_2d_data(dataset): + """ + Generates a test 2d dataset with multiple peaks + + Parameters + ---------- + shape : Iterable[Iterable[int, int]] + shape of the numpy array to be created + positions : Iterable[Iterable[int, int]] + a list of list of two positions for each peak + lws : Iterable[Iterable[float, float]] + a list of list of two linewidths for each peak + amps : Iterable[Iterable[float, float]] + a list of list of two amplitudes for each peak + vparams : Iterable[Iterable[float, float]] + a list of list containing 2 values for the + eta parameter for the pseud-voigt lineshape + + Returns + ------- + numpy.ndarray + simulated two-d dataset + + """ + params = [] + for i in range(len(dataset["positions"])): + d = [[], []] + for j in range(2): + d[j] = ( + dataset["positions"][i][j], + dataset["lws"][i][j], + dataset["vparams"][i][j], + ) + + params.append(d) + + data = ng.linesh.sim_NDregion( + shape=(512, 128), lineshapes=["pv", "pv"], params=params, amps=dataset["amps"] + ) + + return data + + +def _generate_3d_data(dataset): + """ + Generates a test 3d dataset with multiple peaks + + Parameters + ---------- + shape : Iterable[Iterable[int, int, int]] + shape of the numpy array to be created + positions : Iterable[Iterable[int, int, int]] + a list of list of three positions for each peak + lws : Iterable[Iterable[float, float, float]] + a list of list of three linewidths for each peak + amps : Iterable[Iterable[float, float, float]] + a list of list of three amplitudes for each peak + vparams : Iterable[Iterable[float, float, float]] + a list of list containing three values for the + eta parameter for the pseud-voigt lineshape + + Returns + ------- + numpy.ndarray + simulated three-d dataset + + """ + params = [] + for i in range(len(dataset["positions"])): + d = [[], [], []] + for j in range(3): + d[j] = ( + dataset["positions"][i][j], + dataset["lws"][i][j], + dataset["vparams"][i][j], + ) + + params.append(d) + + data = ng.linesh.sim_NDregion( + shape=(256, 64, 64), + lineshapes=["pv", "pv", "pv"], + params=params, + amps=dataset["amps"], + ) + + return data + + +def _test_1d(dataset, algorithm, msep=None, rtol=1): + """test 1d peak picking""" + + data = _generate_1d_data(**dataset) + peaks = ng.peakpick.pick(data, pthres=50, algorithm=algorithm, msep=msep) + assert np.allclose(peaks.X_AXIS, dataset["positions"], rtol=1) + + +def _test_2d(dataset, algorithm, msep=None, rtol=1): + """test 2d peak picking""" + + data = _generate_2d_data(dataset) + peaks = ng.peakpick.pick(data, pthres=50, algorithm=algorithm, msep=msep) + assert np.allclose(peaks.X_AXIS, [i[1] for i in dataset["positions"]], rtol=1) + assert np.allclose(peaks.Y_AXIS, [i[0] for i in dataset["positions"]], rtol=1) + + +def _test_3d(dataset, algorithm, msep=None, rtol=1): + """test 3d peak picking""" + + data = _generate_3d_data(dataset) + peaks = ng.peakpick.pick(data, pthres=50, algorithm=algorithm, msep=msep) + + assert np.allclose( + sorted(peaks.X_AXIS), sorted([i[2] for i in dataset["positions"]]), rtol=rtol + ) + assert np.allclose( + sorted(peaks.Y_AXIS), sorted([i[1] for i in dataset["positions"]]), rtol=rtol + ) + assert np.allclose( + sorted(peaks.Z_AXIS), sorted([i[0] for i in dataset["positions"]]), rtol=rtol + ) + + +@pytest.mark.fast +def test_1d_connected(): + _test_1d(dataset=_ONE_D_PEAKS, algorithm="connected") + + +@pytest.mark.fast +def test_1d_downward(): + _test_1d(dataset=_ONE_D_PEAKS, algorithm="downward") + + +@pytest.mark.fast +def test_1d_thres(): + _test_1d(dataset=_ONE_D_PEAKS, algorithm="thres", msep=(5,)) + + +@pytest.mark.fast +def test_1d_thres_fast(): + _test_1d(dataset=_ONE_D_PEAKS, algorithm="thres-fast", msep=(5,)) + + +@pytest.mark.fast +def test_2d_connected(): + _test_2d(dataset=_TWO_D_PEAKS, algorithm="connected") + + +@pytest.mark.fast +def test_2d_downward(): + _test_2d(dataset=_TWO_D_PEAKS, algorithm="downward") + + +@pytest.mark.fast +def test_2d_thres(): + _test_2d(dataset=_TWO_D_PEAKS, algorithm="thres", msep=(5, 5)) + + +@pytest.mark.fast +def test_2d_thres_fast(): + _test_2d(dataset=_TWO_D_PEAKS, algorithm="thres-fast", msep=(5, 5)) + + +@pytest.mark.fast +def test_3d_connected(): + _test_3d(dataset=_THREE_D_PEAKS, algorithm="connected") + + +@pytest.mark.fast +def test_3d_downward(): + _test_3d(dataset=_THREE_D_PEAKS, algorithm="downward") + + +@pytest.mark.fast +def test_3d_thres(): + _test_3d(dataset=_THREE_D_PEAKS, algorithm="thres", msep=(2, 2, 2)) + + +@pytest.mark.fast +def test_3d_thres_fast(): + _test_3d(dataset=_THREE_D_PEAKS, algorithm="thres-fast", msep=(2, 2, 2))