added script_paths and python files

Author: jpsnir

DEVELOPER.md

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+# Developer instructions
+
+This document is to describe the rules of developing for this repository.
+It also discusses the features and changes which will be in pipeline.
+
+# Development plan
+- [] Merge the code into main branch after making all changes in the current
+    model.
+    - [] Implement AR model process to highlight the choice of coefficients. Get
+        a plot out of it marked with important parameters.
+    - [] Write a script to highlight the values of tau and error associated with
+        the choice.
+    - [] Do simulation to highlight the relevance of value of pink noise
+        B parameter, range of taus and tau1 highlighting the error
+        contribution from each setting.
+    - [] Simulate the effect of new parameters for each IMU.
+- [] Tag the released branch and update documentation.
+- [] Then create another branch for packaging the project.
+- []

config_files

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+from scipy.io import savemat
+import numpy as np
+import zarr
+import argparse
+import os
+import sys
+import matplotlib.pyplot as plt
+
+SECONDS_IN_HR = 3600
+# Save large numpy file as a mat file.  Save smaller segments of the numpy file as mat file.
+
+
+class TUM_npy2mat:
+    def __init__(self, config):
+        self.config = config
+
+    def slice_accelerometer_data(self, data, offset_time, duration):
+        rows, col = stationary_acclerometer_data.shape
+        tot_time = stationary_acclerometer_data[-1,
+                                                0] - stationary_acclerometer_data[0, 0]
+        print("No. of hrs %f" % (tot_time/3600))
+        self.avg_fs = int(np.round(rows/tot_time))
+        self.offset_in_hr = offset_time
+        self.duration_in_hr = duration
+        sample_num_start = self.offset_in_hr*self.avg_fs*SECONDS_IN_HR
+        sample_num_end = sample_num_start + self.duration_in_hr*self.avg_fs*SECONDS_IN_HR
+        return data[sample_num_start:sample_num_end, :]
+
+    def visualize_accelerometer_data(self, data):
+        fig, axes = plt.subplots(nrows=3, ncols=2)
+        for i, ax in enumerate(axes):
+            ax[0].plot(data[:, 0]/3600, data[:, i+1])
+            ax[0].set_xlabel('time(hr)')
+            ax[0].set_ylabel('rad/s')
+            ax[0].grid(True)
+
+            ax[1].plot(data[:, 0]/3600, data[:, 4+i])
+            ax[1].set_xlabel('time(hr)')
+            ax[1].set_ylabel('m/s^2')
+            ax[1].grid(True)
+        fig.tight_layout()
+        plt.show(block=False)
+        plt.pause(.5)
+
+    def save_to_mat(self, acc_data):
+
+        acc_data_dict = {"fs_hz": self.avg_fs,
+                         "duration_hr": self.duration_in_hr,
+                         "offset_hr": self.offset_in_hr,
+                         "timestamp": acc_data[:, 0],
+                         "gyro_x": acc_data[:, 1],
+                         "gyro_y": acc_data[:, 2],
+                         "gyro_z": acc_data[:, 3],
+                         "accel_x": acc_data[:, 4],
+                         "accel_y": acc_data[:, 5],
+                         "accel_z": acc_data[:, 6],
+                         "temperature": acc_data[:, 7]}
+
+        savemat(os.path.join(self.config.output_directory_path,
+                self.config.output_file_name + '.mat'), acc_data_dict)
+
+
+# data = np.load(
+#     r'E:\Windows\Documents\Northeastern\NEUFRL\IMU_Paper_Part_2\dataset-calib-imu-static2.npy', mmap_mode='r')
+
+
+def check_config(config):
+    try:
+        assert(os.path.exists(config.input_file_path)
+               ), 'Invalid path for input npy file'
+        _, _, ext = file_path_parts(config.input_file_path)
+        assert(ext == ".npy"), 'Invalid extention for input file'
+        if config.output_directory_path == None and config.output_file_name == None:
+            config.output_directory_path, config.output_file_name, _ = file_path_parts(
+                config.input_file_path)
+
+        elif config.output_directory_path == None:
+            config.output_directory_path, _, _ = file_path_parts(
+                config.input_file_path)
+
+        elif config.output_file_name == None:
+            config.output_file_name, _, _ = file_path_parts(
+                config.input_file_path)
+
+        if (not os.path.exists(config.output_directory_path)):
+            os.path.mkdir(config.output_directory_path)
+    except AssertionError as msg:
+        print(msg)
+        sys.exit()
+
+
+def file_path_parts(full_file_path):
+    output_dir, file = os.path.split(full_file_path)
+    filename, ext = os.path.splitext(file)
+    return output_dir, filename, ext
+
+    # ax[1:0].plot(data[:, 0], data[:, 7])
+
+
+if __name__ == '__main__':
+    argument_parser = argparse.ArgumentParser(
+        prog="numpy 2 mat inputs", usage="converts .npy file to .mat")
+    argument_parser.add_argument(
+        '-i', '--input_file_path', type=str, required=True, help='Input numpy file path', default='./dataset-calib-imu-static2.npy')
+    argument_parser.add_argument(
+        '-o', '--output_file_name', type=str, help='Output mat file path')
+    argument_parser.add_argument(
+        '-d', '--output_directory_path', type=str, help='Output mat file directory')
+    argument_parser.add_argument(
+        '--offset', type=int, help='offset of samples', default=1)
+    argument_parser.add_argument(
+        '--duration', type=int, help="Duration of samples extracted", default=7)
+    config = argument_parser.parse_args()
+    check_config(config)
+    print(vars(config))
+    print("----------------")
+    stationary_acclerometer_data = np.load(
+        config.input_file_path, mmap_mode='r')
+
+    # Slice data
+    tum_npy2mat = TUM_npy2mat(config)
+    sliced_data = tum_npy2mat.slice_accelerometer_data(
+        stationary_acclerometer_data, config.offset, config.duration)
+
+    tum_npy2mat.save_to_mat(sliced_data)
+    tum_npy2mat.visualize_accelerometer_data(
+        sliced_data)
+    plt.show(block=True)

python/numpy_2_mat.py

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+addpath( genpath('config_files'),...
+        genpath('fcns'),...
+        genpath('scripts'));