add tools which could help with pre-processing of the data collected …

…over USB serial

Arduino_BHY2/examples/SyncAndCollectIMUData/tools/README.md

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+# process_nicla_bhy2_log_base64.py
+This script is used to convert the log encoded in base64 to ascii
+## Usage
+```
+./process_nicla_bhy2_log_base64.py [log_file_name]
+```
+## Example
+./process_nicla_bhy2_log_base64.py log_nicla_bhy2.txt
+
+
+# check_for_data_loss.sh
+This script is used to check for any potential data loss during the transfer,
+and it reports some errors if it does find any data loss
+
+## Usage
+```
+./check_for_data_loss.sh [OPTION] [log_file_name]
+```
+
+## Example
+- Example 1
+    ```
+    ./check_for_data_loss.sh -b ./minicom.log
+    ```
+    The above command check for the data loss using the log "./minicom.log" which is base on base64 encoding
+- Example 2
+    ```
+    ./check_for_data_loss.sh -a ./minicom.log
+    ```
+    The above command check for the data loss using the log "./minicom.log" which is base on ascii encoding
+

Arduino_BHY2/examples/SyncAndCollectIMUData/tools/check_for_data_loss.py

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+#!/usr/bin/env python
+# this script resamples the data from the log to 1/60hz
+
+import sys
+import time
+import datetime
+import pandas as pd
+import math
+
+
+#DEBUG  = True
+DEBUG  = False
+SEP_COLUMN = ','
+
+LINE_TO_SKIP = 500
+
+DOWNSAMPLE_FACTOR=1
+
+def PDBG(*args):
+    if DEBUG:
+        print("DEBUG:", *args, file=sys.stderr)
+
+
+PDBG('Number of arguments:', len(sys.argv))
+
+if (len(sys.argv) < 2):
+    raise BaseException("missing argument")
+
+filename_in  = sys.argv[1]
+file_out = None
+
+if (len(sys.argv) > 2):
+    filename_out = sys.argv[2]
+    file_out = open(filename_out, 'w')
+    sys.stdout = file_out
+
+
+line_cnt = 1    #first row is the header
+df_in = pd.read_csv(filename_in, sep=SEP_COLUMN)
+
+seq_last = None
+
+
+for index, row in df_in.iterrows():
+    line_cnt += 1
+    if (line_cnt <= LINE_TO_SKIP):
+        continue
+
+    seq = row['seq']
+    if (seq_last is not None):
+        try:
+            delta = seq - seq_last
+            if (seq < seq_last):
+                delta += 10
+            if (delta != 1):
+                if (line_cnt < len(df_in.index)):
+                    print("error: line: ", line_cnt, " has data missing, delta:", delta, "seq:", seq)
+                else:
+                   PDBG("last line: ignored")
+            seq_last = seq
+        except:
+            if (line_cnt < len(df_in.index)):
+                print("error: line: ", line_cnt, " has data missing")
+            else:
+                PDBG("last line: ignored")
+            pass
+    else:
+        PDBG("first row")
+        seq_last = seq
+
+
+if file_out is not None:
+    file_out.close()

Arduino_BHY2/examples/SyncAndCollectIMUData/tools/check_for_data_loss.sh

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+#!/bin/sh
+
+
+log_encoding_is_base64=false
+
+if [ ":""$1" = ":-b" ] ; then
+    log_encoding_is_base64=true
+    echo "log is using base64 encoding"
+elif [ ":""$1" = ":-a" ] ; then
+    log_encoding_is_base64=false
+    echo "log is using ascii encoding"
+else
+    echo "usage: ./check_for_data_loss.sh [OPTION] [log_filename] [info_included_in_data]"
+    echo "\t[OPTION]:"
+    echo "\t\t" "-a"
+    echo "\t\t" "\t:log use ascii encoding"
+    echo "\t\t" "-b"
+    echo "\t\t" "\t:log use base64 encoding"
+    echo "\t[info_included_in_data]:"
+    echo "\t\t" '"accel" or "accel+meta"'
+    echo "\t\t" '"gyro" or "gyro+meta"'
+    echo "\t\t" '"accel+gyro" or "accel+gyro+meta"'
+
+
+    echo "\texample: ./check_for_data_loss.sh -b minicom.cap accel+gyro+meta"
+    return
+fi
+
+if [ ":""$2" = ":" ] ; then
+    log_file="./minicom.cap"
+else
+    log_file="$2"
+fi
+
+if [ ":""$3" = ":" ] ; then
+    info_included_in_data="accel+gyro+meta"
+else
+    info_included_in_data="$3"
+fi
+
+
+tmp_file="./tmp.csv"
+log_file_cp="${log_file}.cp"
+log_file_in="${log_file_cp}.tmp"
+
+echo "log_file:$log_file"
+
+
+if [ $log_encoding_is_base64 = true ] ; then
+    cp $log_file $log_file_cp
+    ./process_nicla_bhy2_log_base64.py $log_file_cp $info_included_in_data > $log_file_in
+else
+    cp $log_file $log_file_in
+fi
+
+echo "log_id,seq,ax,ay,az,gx,gy,gz" > $tmp_file
+
+sed 's/.*\([a-zA-Z]\)\([0-9]\)/\1,\2/g' $log_file_in >> $tmp_file
+./check_for_data_loss.py $tmp_file
+
+rm -f $tmp_file
+rm  -f $log_file_cp
+rm  -f $log_file_in

Arduino_BHY2/examples/SyncAndCollectIMUData/tools/process_nicla_bhy2_log_base64.py

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+#!/usr/bin/env python
+import math
+import base64
+import struct
+import sys
+
+#configurations
+#DEBUG = True
+DEBUG = False
+lines_to_ignore = 500
+
+# the following should be set according to the fimrware settings on the Nicla Senes ME firmware/sketch
+data_include_acc = False
+data_include_gyr = False
+data_include_meta_info = False
+
+
+if (len(sys.argv) > 1):
+    log_file_name = sys.argv[1]
+else:
+    log_file_name = 'log_nicla_bhy2.txt'
+
+if (len(sys.argv) > 2):
+    info_included_in_data = sys.argv[2]
+    if "accel" in info_included_in_data:
+        data_include_acc = True
+        if DEBUG:
+            print("accel data included")
+    if "gyro" in info_included_in_data:
+        data_include_gyr = True
+        if DEBUG:
+            print("gyro data included")
+    if "meta" in info_included_in_data:
+        data_include_meta_info= True
+        if DEBUG:
+            print("meta data included")
+
+#working variables
+file_log = open(log_file_name, 'r')
+lines = file_log.readlines()
+
+lineCnt = 0
+record_len = 0
+record_len_before_encoding = 0
+
+if data_include_meta_info:
+    record_len_before_encoding += 2
+
+if data_include_acc:
+    record_len_before_encoding += 6
+
+if data_include_gyr:
+    record_len_before_encoding += 6
+
+
+record_len = int(math.ceil(record_len_before_encoding / 3)) * 4
+if DEBUG:
+    print("record_len:", record_len)
+
+
+DEBUG  = False
+# Strips the newline character
+for line in lines:
+    lineCnt += 1
+
+    if (lineCnt <= lines_to_ignore):
+        continue
+
+    line = line.strip()
+    len_line = len(line)
+
+    if (len_line < record_len) or (line[len_line - 1] != '='):
+        if (lineCnt < len(lines)):
+            print("line:", lineCnt, " skipped")
+        else:
+            if DEBUG:
+                print("last line:", lineCnt, " skipped")
+        continue
+
+    line = line[-record_len:]
+    try:
+        data_imu = base64.b64decode(line)
+        if DEBUG:
+            print(data_imu)
+            print(len(data_imu))
+
+        try:
+            if (data_include_acc and data_include_gyr):
+                (log_id, seq, ax,ay,az,gx,gy,gz) = struct.unpack("<cBhhhhhh", data_imu)
+                log_id = log_id.decode('ascii')
+                print(log_id.strip(), ",", seq, ",", ax, ",", ay, ",", az, ",",  gx,",", gy, ",", gz, sep='')
+            else:
+                (log_id,seq, x,y,z) = struct.unpack("<cBhhh", data_imu)
+                log_id = log_id.decode('ascii')
+                print(log_id, ",", seq, ",",  x,",", y, ",", z, sep='')
+        except struct.error:
+            print("error: line:", lineCnt, " unpack")
+
+    except base64.binascii.Error:
+        print("error: line:", lineCnt, " incomplete data")
+        pass
+