Add requirements

Add examples

examples/pipeline_hbm_analysis.py

@@ -0,0 +1,25 @@
+import os
+
+from gaitalytics import api
+from gaitalytics import utils
+
+
+def main():
+    settings_file = "settings/hbm_pig.yaml"
+    buffered_path = "./raw"
+    out_path = "./spatio_temp"
+
+    configs = utils.ConfigProvider(settings_file)
+
+    loaded_cycles = api.extract_cycles_buffered(buffered_path, configs)
+    cycle_data = loaded_cycles.get_raw_cycle_points()
+
+    results = api.analyse_data(cycle_data, configs)
+
+    if not os.path.exists(out_path):
+        os.mkdir(out_path)
+    results.to_csv(f"{out_path}/spatio_temp.csv")
+
+
+if __name__ == "__main__":
+    main()

examples/pipeline_hbm_events.py

@@ -0,0 +1,17 @@
+from gaitalytics import api
+from gaitalytics import utils
+
+
+def main():
+    settings_file = "settings/hbm_pig.yaml"
+    file_path = "./test/data/Baseline.3.c3d"
+    out_path = "./test/data/"
+
+    # load configs
+    configs = utils.ConfigProvider(settings_file)
+
+    api.detect_gait_events(file_path, out_path, configs, show_plot=False)
+
+
+if __name__ == "__main__":
+    main()

examples/pipeline_hbm_extraction_normalisation.py

@@ -0,0 +1,27 @@
+import os
+
+from gaitalytics import api
+from gaitalytics import utils
+
+
+def main():
+    settings_file = "settings/hbm_pig.yaml"
+    file_path = "./test/data/Baseline.5.c3d"
+    buffered_path_raw = "./raw"
+    buffered_path_norm = "./norm"
+
+    configs = utils.ConfigProvider(settings_file)
+    if not os.path.exists(buffered_path_raw):
+        os.mkdir(buffered_path_raw)
+        cycle_data = api.extract_cycles(file_path, configs, buffer_output_path=buffered_path_raw)
+    else:
+        cycle_data = api.extract_cycles_buffered(buffered_path_raw, configs).get_raw_cycle_points()
+
+    if not os.path.exists(buffered_path_norm):
+        os.mkdir(buffered_path_norm)
+    api.normalise_cycles(file_path, cycle_data, buffer_output_path=buffered_path_norm)
+
+
+# __name__
+if __name__ == "__main__":
+    main()

examples/pipeline_hbm_modelling.py

@@ -0,0 +1,16 @@
+from gaitalytics import utils, api
+
+
+def main():
+    settings_file = "settings/hbm_pig.yaml"
+    file_path = "./tests/data/Baseline.4.c3d"
+    out_path = "./tests/data/"
+
+    # load configs
+    configs = utils.ConfigProvider(settings_file)
+
+    api.model_data(file_path, out_path, configs, methode=api.MODELLING_CMOS, belt_speed=0.8, dominant_leg_length=998)
+
+
+if __name__ == "__main__":
+    main()

examples/pipline_coherence.py

@@ -0,0 +1,28 @@
+from gaitalytics import emg, files
+
+# This is an example pipeline #
+###############################
+
+# Define paths
+DATA_PATH = "test/data/"
+TEST_ORIGIN_FILE_NAME = "1min_emg_walk.c3d"
+SETTINGS_PATH = "settings/"
+SETTINGS_FILE = "CGM2_5-pyCGM2.settings"
+
+
+def main():
+    acq_trial = c3d.read_btk(f"{DATA_PATH}{TEST_ORIGIN_FILE_NAME}")
+
+    # Instanciate EMGCoherenceAnalysis objects
+    coh_left = emg.EMGCoherenceAnalysis(1, 2, "Left")  # Verify if good channel indexs
+    coh_right = emg.EMGCoherenceAnalysis(3, 4, "Right")  # Verify if good channel indexs
+
+    # Results stored in a tuple of frequencies and coherences
+    coherence_result_left = coh_left.calculate_coherence(acq_trial)
+    coherence_result_right = coh_right.calculate_coherence(acq_trial)
+
+
+# Using the special variable
+# __name__
+if __name__ == "__main__":
+    main()

settings/hbm_pig.yaml

@@ -0,0 +1,99 @@
+# Environment: Motek Caren
+# Marker set: HBM2 Lower Body Trunk
+# Modelling: PIG
+environment_setting:
+  progression_axes: y
+  progression_values: negativ
+
+marker_set_mapping:
+  left_back_hip: LASIS
+  right_back_hip: RASIS
+  left_front_hip: LPSIS
+  right_front_hip: RPSIS
+
+  left_lat_upper_leg: LLTHI
+  right_lat_upper_leg: RLTHI
+
+  left_lat_knee: LLEK
+  right_lat_knee: RLEK
+  left_med_knee: LMEK
+  right_med_knee: RMEK
+
+  left_lat_lower_leg: LLSHA
+  right_lat_lower_leg: RLSHA
+
+  left_lat_malleoli: LLM
+  right_lat_malleoli: RLM
+  left_med_malleoli: LMM
+  right_med_malleoli: RMM
+
+  right_heel: RHEE
+  left_heel: LHEE
+  right_meta_2: RMT2
+  left_meta_2: LMT2
+  right_meta_5: RMT5
+  left_meta_5: LMT5
+
+  neck: C7
+  back: T10
+  jugularis: JN
+  xyphoideus: XIPH
+
+  # Additional markers which will be modelled in modelling.py
+  com: COM
+  xcom: XCOM
+  cmos: CMOS
+
+model_mapping:
+  #Angles
+  left_thorax_angles: LThoraxAngles
+  right_thorax_angles: RThoraxAngles
+  left_spine_angles: LSpineAngles
+  right_spine_angles: RSpineAngles
+  left_pelvis_angles: LPelvisAngles
+  right_pelvis_angles: RPelvisAngles
+  left_foot_progression_angles: LFootProgressAngles
+  right_foot_progression_angles: RFootProgressAngles
+  left_hip_angles: LHipAngles
+  right_hip_angles: RHipAngles
+  left_knee_angles: LKneeAngles
+  right_knee_angles: RKneeAngles
+  left_ankle_angles: LAnkleAngles
+  right_ankle_angles: RAnkleAngles
+
+  #Forces
+  left_GRF: LGroundReactionForce
+  right_GRF: RGroundReactionForce
+  left_nGRF: LNormalisedGRF
+  right_nGRF: RNormalisedGRF
+  left_waist_force: LWaistForce
+  right_waist_force: RWaistForce
+  left_hip_force: LHipForce
+  right_hip_force: RHipForce
+  left_knee_force: LKneeForce
+  right_knee_force: RKneeForce
+  left_ankle_force: LAnkleForce
+  right_ankle_force: RAnkleForce
+
+  #Moments
+  left_GRM: LGroundReactionMoment
+  right_GRM: RGroundReactionMoment
+  left_waist_moment: LWaistMoment
+  right_waist_moment: RWaistMoment
+  left_hip_moment: LHipMoment
+  right_hip_moment: RHipMoment
+  left_knee_moment: LKneeMoment
+  right_knee_moment: RKneeMoment
+  left_ankle_moment: LAnkleMoment
+  right_ankle_moment: RAnkleMoment
+
+  #Powers
+  left_waist_power: LWaistPower
+  right_waist_power: RWaistPower
+  left_hip_power: LHipPower
+  right_hip_power: RHipPower
+  left_knee_power: LKneePower
+  right_knee_power: RKneePower
+  left_ankle_power: LAnklePower
+  right_ankle_power: RAnklePower
+

setup.py

@@ -10,7 +10,6 @@ def read(*names, **kwargs):
     with Path(__file__).parent.joinpath(*names).open(encoding=kwargs.get("encoding", "utf8")) as fh:
         return fh.read()
 
-
 setup(
     name="gaitalytics",
     version="0.0.0",
@@ -63,6 +62,11 @@ def read(*names, **kwargs):
     python_requires=">=3.8",
     install_requires=[
         "click",
+        "pandas==2.1.4",
+        "numpy==1.26.4",
+        "scipy==1.11.3",
+        "pyyaml==6.0.1",
+        "matplotlib==3.8.0",
         # eg: "aspectlib==1.1.1", "six>=1.7",
     ],
     extras_require={
@@ -76,3 +80,4 @@ def read(*names, **kwargs):
         ]
     },
 )
+