From 1f0baf92375c3e942c85f0a899cdbc1a1025c5da Mon Sep 17 00:00:00 2001 From: ZoeLi0525 <1558079116@qq.com> Date: Thu, 26 Oct 2023 16:29:15 +0200 Subject: [PATCH 1/4] add peak velocity and peak acceleration --- src/vstt/display.py | 4 +++ src/vstt/stats.py | 67 +++++++++++++++++++++++++++++++++++++++++++ src/vstt/vis.py | 7 ++++- src/vstt/vtypes.py | 2 ++ tests/test_display.py | 2 ++ tests/test_stats.py | 38 ++++++++++++++++++++++++ tests/test_vis.py | 4 +++ 7 files changed, 123 insertions(+), 1 deletion(-) diff --git a/src/vstt/display.py b/src/vstt/display.py index fcf80e6b..3bc7d572 100644 --- a/src/vstt/display.py +++ b/src/vstt/display.py @@ -25,6 +25,8 @@ def default_display_options() -> vstt.vtypes.DisplayOptions: "to_center_success": False, "area": False, "normalized_area": False, + "peak_velocity": False, + "peak_acceleration": False, "averages": True, } @@ -49,6 +51,8 @@ def display_options_labels() -> Dict[str, str]: "to_center_success": "Statistic: successful movement to center", "area": "Statistic: the area formed by the paths connecting the target and the center", "normalized_area": "Statistic: (the area formed by paths) / (length of the paths)²", + "peak_velocity": "Statistic: maximum velocity during cursor movement", + "peak_acceleration": "Statistic: maximum acceleration during cursor movement", "averages": "Also show statistics averaged over all targets", } diff --git a/src/vstt/stats.py b/src/vstt/stats.py index e479f4f2..32114b30 100644 --- a/src/vstt/stats.py +++ b/src/vstt/stats.py @@ -9,6 +9,7 @@ import numpy as np import pandas as pd +from numpy import linalg as LA from psychopy.data import TrialHandlerExt from psychopy.event import xydist from shapely.geometry import LineString @@ -32,6 +33,8 @@ def list_dest_stat_label_units() -> List[Tuple[str, List[Tuple[str, str, str]]]] list_dest_stats.append((destination, stats)) list_dest_stats.append(("", [("area", "Area", "")])) list_dest_stats.append(("", [("normalized_area", "Normalized Area", "")])) + list_dest_stats.append(("", [("peak_velocity", "Peak Velocity", "")])) + list_dest_stats.append(("", [("peak_acceleration", "Peak Acceleration", "")])) return list_dest_stats @@ -174,6 +177,34 @@ def stats_dataframe(trial_handler: TrialHandlerExt) -> pd.DataFrame: ), axis=1, ) + df["peak_velocity"] = df.apply( + lambda x: _peak_velocity( + np.concatenate((x["to_target_timestamps"], x["to_center_timestamps"])), + np.concatenate( + ( + x["to_target_mouse_positions"], + x["to_center_mouse_positions"].reshape( + x["to_center_mouse_positions"].shape[0], 2 + ), + ) + ), + ), + axis=1, + ) + df["peak_acceleration"] = df.apply( + lambda x: _peak_acceleration( + np.concatenate((x["to_target_timestamps"], x["to_center_timestamps"])), + np.concatenate( + ( + x["to_target_mouse_positions"], + x["to_center_mouse_positions"].reshape( + x["to_center_mouse_positions"].shape[0], 2 + ), + ) + ), + ), + axis=1, + ) return df @@ -493,3 +524,39 @@ def preprocess_mouse_positions(mouse_positions: np.ndarray) -> np.ndarray: mouse_positions.reshape(0, 2) if mouse_positions.size == 0 else mouse_positions ) return mouse_positions + + +def _peak_velocity(mouse_times: np.ndarray, mouse_positions: np.ndarray) -> float: + velocity = get_velocity(mouse_times, mouse_positions) + peak_velocity = np.amax(velocity) + return peak_velocity + + +def _peak_acceleration(mouse_times: np.ndarray, mouse_positions: np.ndarray) -> float: + acceleration = get_acceleration(mouse_times, mouse_positions) + peak_acceleration = np.amax(acceleration) + return peak_acceleration + + +def get_derivative(y: np.ndarray, x: np.ndarray) -> np.ndarray: + dy_dx = np.diff(y) / np.diff(x) + return dy_dx + + +def get_velocity(mouse_times: np.ndarray, mouse_positions: np.ndarray) -> np.ndarray: + if mouse_times.size == 0 or mouse_positions.size == 0: + return np.array([0]) + first_order_derivative = get_derivative(mouse_positions.transpose(), mouse_times) + velocity = LA.norm(first_order_derivative, axis=0) + return velocity + + +def get_acceleration( + mouse_times: np.ndarray, mouse_positions: np.ndarray +) -> np.ndarray: + if mouse_times.size == 0 or mouse_positions.size == 0: + return np.array([0]) + first_order_derivative = get_derivative(mouse_positions.transpose(), mouse_times) + second_order_derivative = get_derivative(first_order_derivative, mouse_times[:-1]) + acceleration = LA.norm(second_order_derivative, axis=0) + return acceleration diff --git a/src/vstt/vis.py b/src/vstt/vis.py index 3cbbba7b..c59fd938 100644 --- a/src/vstt/vis.py +++ b/src/vstt/vis.py @@ -163,7 +163,12 @@ def _make_stats_txt( stat_str = f"{stats[stat]: .0%}" else: stat_str = f"{stats[stat] == 1}" - if stat == "area" or stat == "normalized_area": + if ( + stat == "area" + or stat == "normalized_area" + or stat == "peak_velocity" + or stat == "peak_acceleration" + ): txt_stats += f"{label}: {stat_str}\n" else: txt_stats += f"{label} (to {destination}): {stat_str}\n" diff --git a/src/vstt/vtypes.py b/src/vstt/vtypes.py index 15b272b0..0319bcea 100644 --- a/src/vstt/vtypes.py +++ b/src/vstt/vtypes.py @@ -68,6 +68,8 @@ class DisplayOptions(TypedDict): averages: bool area: bool normalized_area: bool + peak_velocity: bool + peak_acceleration: bool class Metadata(TypedDict): diff --git a/tests/test_display.py b/tests/test_display.py index b6c5eb2e..bf2162a8 100644 --- a/tests/test_display.py +++ b/tests/test_display.py @@ -35,6 +35,8 @@ def test_import_display_options(caplog: pytest.LogCaptureFixture) -> None: "to_center_success": False, "area": False, "normalized_area": False, + "peak_velocity": False, + "peak_acceleration": False, } for key in default_display_options: assert key in display_options_dict diff --git a/tests/test_stats.py b/tests/test_stats.py index 132c7540..7160cc1d 100644 --- a/tests/test_stats.py +++ b/tests/test_stats.py @@ -168,3 +168,41 @@ def test_normalized_area() -> None: ), [1 / (24 + 16 * math.sqrt(2))], ) + + +def test_peak_velocity() -> None: + assert np.allclose(vstt.stats._peak_velocity(np.array([]), np.array([])), [0]) + assert np.allclose( + vstt.stats._peak_velocity(np.array([0, 0.5, 0.6, 1]), np.array([])), [0] + ) + assert np.allclose( + vstt.stats._peak_velocity( + np.array([]), np.array([[0, 0], [0, 1], [1, 1], [1, 0]]) + ), + [0], + ) + assert np.allclose( + vstt.stats._peak_velocity( + np.array([0, 0.5, 0.6, 1]), np.array([[0, 0], [0, 1], [1, 1], [1, 0]]) + ), + [10], + ) + + +def test_peak_acceleration() -> None: + assert np.allclose(vstt.stats._peak_acceleration(np.array([]), np.array([])), [0]) + assert np.allclose( + vstt.stats._peak_acceleration(np.array([0, 0.5, 0.6, 1]), np.array([])), [0] + ) + assert np.allclose( + vstt.stats._peak_acceleration( + np.array([]), np.array([[0, 0], [0, 1], [1, 1], [1, 0]]) + ), + [0], + ) + assert np.allclose( + vstt.stats._peak_acceleration( + np.array([0, 0.5, 0.6, 1]), np.array([[0, 0], [0, 1], [1, 1], [1, 0]]) + ), + [103.07764], + ) diff --git a/tests/test_vis.py b/tests/test_vis.py index 0c87f848..7b924ef6 100644 --- a/tests/test_vis.py +++ b/tests/test_vis.py @@ -231,6 +231,8 @@ def test_display_results_nothing( "to_center_success": False, "area": False, "normalized_area": False, + "peak_velocity": False, + "peak_acceleration": False, } for all_trials_for_this_condition in [False, True]: # trial 0: 0,1,2 are trials without auto-move to center @@ -296,6 +298,8 @@ def test_display_results_everything( "to_center_success": True, "area": True, "normalized_area": True, + "peak_velocity": True, + "peak_acceleration": True, } for all_trials_for_this_condition in [False, True]: # trial 0: 0,1,2 are trials without auto-move to center From f71aa3dcea69e28a10266b91e13131a1e6bb3fcb Mon Sep 17 00:00:00 2001 From: ZoeLi0525 <1558079116@qq.com> Date: Mon, 6 Nov 2023 17:09:10 +0100 Subject: [PATCH 2/4] add velocity and acceleration information in docs/reference/statistics.rst and fix a bug --- docs/reference/images/acceleration.svg | 31 ++++++++++++++++++++++ docs/reference/images/velocity.svg | 31 ++++++++++++++++++++++ docs/reference/statistics.rst | 36 ++++++++++++++++++++++++++ src/vstt/stats.py | 6 ++--- tests/test_stats.py | 24 +++++++++++++++++ 5 files changed, 124 insertions(+), 4 deletions(-) create mode 100644 docs/reference/images/acceleration.svg create mode 100644 docs/reference/images/velocity.svg diff --git a/docs/reference/images/acceleration.svg b/docs/reference/images/acceleration.svg new file mode 100644 index 00000000..c20ef08d --- /dev/null +++ b/docs/reference/images/acceleration.svg @@ -0,0 +1,31 @@ + +{\displaystyle {\bar {\mathbf {a} }}={\frac {\Delta \mathbf {v} }{\Delta t}}.} + + + diff --git a/docs/reference/images/velocity.svg b/docs/reference/images/velocity.svg new file mode 100644 index 00000000..6ecd2144 --- /dev/null +++ b/docs/reference/images/velocity.svg @@ -0,0 +1,31 @@ + +{\displaystyle {\boldsymbol {\bar {v}}}={\frac {\Delta {\boldsymbol {x}}}{\Delta t}}.} + + + diff --git a/docs/reference/statistics.rst b/docs/reference/statistics.rst index 3c48254f..58eea95d 100644 --- a/docs/reference/statistics.rst +++ b/docs/reference/statistics.rst @@ -80,3 +80,39 @@ Given pairs of :math:`(x, y)` cursor locations, the following statistics are cal * Normalized Area * (the area formed by paths) / (length of the paths)² + +Velocity +-------- + +.. figure:: images/velocity.svg + :alt: Velocity is defined as the rate of change of position with respect to time + +The cursor location at a timestamp is given by a pair of :math:`(x, y)` coordinates, +where :math:`(0, 0)` corresponds to the center of the screen, and 1 in these units is equal to the height of the screen. + +Given pairs of :math:`(x, y)` cursor locations, and pairs of :math:`t` timestamp, the following statistics are calculated, all in units of screen height: + + * Velocity + * :math:`\frac{\sqrt{(x_{i+1}-x_i)^2+(y_{i+1}-y_i)^2}}{t_{i+1}-t_i}` + * the rate of change of position with respect to time + + * Peak Velocity + * maximum velocity + +Acceleration +----------- + +.. figure:: images/acceleration.png + :alt: Acceleration is the rate of change of the velocity of an object with respect to time + +The cursor location at a timestamp is given by a pair of :math:`(x, y)` coordinates, +where :math:`(0, 0)` corresponds to the center of the screen, and 1 in these units is equal to the height of the screen. + +Given pairs of :math:`(x, y)` cursor locations, and pairs of :math:`t` timestamp, the following statistics are calculated, all in units of screen height: + + * Acceleration + * :math:`\frac{\sqrt{(\frac{x_{i+2}-x_{i+1}}{t_{i+2}-t_{i+1}}-\frac{x_{i+1}-x_{i}}{t_{i+1}-t_{i}})^2+(\frac{y_{i+2}-y_{i+1}}{t_{i+2}-t_{i+1}}-\frac{y_{i+1}-y`_{i}}{t_{i+1}-t_{i}})^2}}{t_{i+1}-t_i}` + * the rate of change of the velocity of an object with respect to time + + * Peak Acceleration + * maximum Acceleration diff --git a/src/vstt/stats.py b/src/vstt/stats.py index 32114b30..a5a0f1be 100644 --- a/src/vstt/stats.py +++ b/src/vstt/stats.py @@ -539,13 +539,13 @@ def _peak_acceleration(mouse_times: np.ndarray, mouse_positions: np.ndarray) -> def get_derivative(y: np.ndarray, x: np.ndarray) -> np.ndarray: + if x.size <= 1 or y.size <= 1: + return np.array([0]) dy_dx = np.diff(y) / np.diff(x) return dy_dx def get_velocity(mouse_times: np.ndarray, mouse_positions: np.ndarray) -> np.ndarray: - if mouse_times.size == 0 or mouse_positions.size == 0: - return np.array([0]) first_order_derivative = get_derivative(mouse_positions.transpose(), mouse_times) velocity = LA.norm(first_order_derivative, axis=0) return velocity @@ -554,8 +554,6 @@ def get_velocity(mouse_times: np.ndarray, mouse_positions: np.ndarray) -> np.nda def get_acceleration( mouse_times: np.ndarray, mouse_positions: np.ndarray ) -> np.ndarray: - if mouse_times.size == 0 or mouse_positions.size == 0: - return np.array([0]) first_order_derivative = get_derivative(mouse_positions.transpose(), mouse_times) second_order_derivative = get_derivative(first_order_derivative, mouse_times[:-1]) acceleration = LA.norm(second_order_derivative, axis=0) diff --git a/tests/test_stats.py b/tests/test_stats.py index 7160cc1d..5344b85b 100644 --- a/tests/test_stats.py +++ b/tests/test_stats.py @@ -187,6 +187,18 @@ def test_peak_velocity() -> None: ), [10], ) + assert np.allclose( + vstt.stats._peak_velocity(np.array([0.5]), np.array([[0, 0]])), + [0], + ) + assert np.allclose( + vstt.stats._peak_velocity(np.array([0.5]), np.array([])), + [0], + ) + assert np.allclose( + vstt.stats._peak_velocity(np.array([]), np.array([[0, 0]])), + [0], + ) def test_peak_acceleration() -> None: @@ -206,3 +218,15 @@ def test_peak_acceleration() -> None: ), [103.07764], ) + assert np.allclose( + vstt.stats._peak_acceleration(np.array([0.5]), np.array([[0, 0]])), + [0], + ) + assert np.allclose( + vstt.stats._peak_acceleration(np.array([0.5]), np.array([])), + [0], + ) + assert np.allclose( + vstt.stats._peak_acceleration(np.array([]), np.array([[0, 0]])), + [0], + ) From 48bf7c4480021dc0ad2d2fce0fc6f2a9dd582e32 Mon Sep 17 00:00:00 2001 From: ZoeLi0525 <1558079116@qq.com> Date: Fri, 10 Nov 2023 15:31:47 +0100 Subject: [PATCH 3/4] corrrect docs/reference/statistics.rst --- docs/reference/statistics.rst | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/docs/reference/statistics.rst b/docs/reference/statistics.rst index 58eea95d..080682d4 100644 --- a/docs/reference/statistics.rst +++ b/docs/reference/statistics.rst @@ -88,9 +88,9 @@ Velocity :alt: Velocity is defined as the rate of change of position with respect to time The cursor location at a timestamp is given by a pair of :math:`(x, y)` coordinates, -where :math:`(0, 0)` corresponds to the center of the screen, and 1 in these units is equal to the height of the screen. +where :math:`(0, 0)` corresponds to the center of the screen, and 1 in these units is equal to the height of the screen per second. -Given pairs of :math:`(x, y)` cursor locations, and pairs of :math:`t` timestamp, the following statistics are calculated, all in units of screen height: +Given pairs of :math:`(x, y)` cursor locations, and pairs of :math:`t` timestamp, the following statistics are calculated, all in units of screen height per second: * Velocity * :math:`\frac{\sqrt{(x_{i+1}-x_i)^2+(y_{i+1}-y_i)^2}}{t_{i+1}-t_i}` @@ -102,16 +102,16 @@ Given pairs of :math:`(x, y)` cursor locations, and pairs of :math:`t` timestamp Acceleration ----------- -.. figure:: images/acceleration.png +.. figure:: images/acceleration.svg :alt: Acceleration is the rate of change of the velocity of an object with respect to time The cursor location at a timestamp is given by a pair of :math:`(x, y)` coordinates, -where :math:`(0, 0)` corresponds to the center of the screen, and 1 in these units is equal to the height of the screen. +where :math:`(0, 0)` corresponds to the center of the screen, and 1 in these units is equal to the screen height per second squared. -Given pairs of :math:`(x, y)` cursor locations, and pairs of :math:`t` timestamp, the following statistics are calculated, all in units of screen height: +Given pairs of :math:`(x, y)` cursor locations, and pairs of :math:`t` timestamp, the following statistics are calculated, all in units of screen height per second squared: * Acceleration - * :math:`\frac{\sqrt{(\frac{x_{i+2}-x_{i+1}}{t_{i+2}-t_{i+1}}-\frac{x_{i+1}-x_{i}}{t_{i+1}-t_{i}})^2+(\frac{y_{i+2}-y_{i+1}}{t_{i+2}-t_{i+1}}-\frac{y_{i+1}-y`_{i}}{t_{i+1}-t_{i}})^2}}{t_{i+1}-t_i}` + * :math:`\frac{\sqrt{(\frac{x_{i+2}-x_{i+1}}{t_{i+2}-t_{i+1}}-\frac{x_{i+1}-x_{i}}{t_{i+1}-t_{i}})^2+(\frac{y_{i+2}-y_{i+1}}{t_{i+2}-t_{i+1}}-\frac{y_{i+1}-y_{i}}{t_{i+1}-t_{i}})^2}}{t_{i+1}-t_i}` * the rate of change of the velocity of an object with respect to time * Peak Acceleration From 8f29c0cf8a188aea3cb79542b059e0e933450075 Mon Sep 17 00:00:00 2001 From: Liam Keegan Date: Fri, 10 Nov 2023 15:44:04 +0100 Subject: [PATCH 4/4] don't fail readthedocs build for warnings --- .readthedocs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.readthedocs.yml b/.readthedocs.yml index c2b5e7ba..2841dc6d 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -45,7 +45,7 @@ build: sphinx: builder: html configuration: docs/conf.py - fail_on_warning: true + fail_on_warning: false formats: - pdf