To Be or Not to Be

I have seen the rise of the ultimate mega. And I have heard about its potential. And like what Lincoln Stephens wrote in 1919, he exclaimed:

I have seen the future, and it works!

Mirroring to Stephens’ awe at the Bolshevik, I do, and yes I do at the current mega today.

And what is the purpose if the mega can do things much better.
What is the purpose if all of your questions can be answered.
And what if, what if, if everything at the start is wrong, and the mega is the only solution.

And in my final process of finishing the 3d scanner, I realized that I cannot push forward without the mega. Yet, the mega can move forward without me.

Microstepping

Behind

Well, ignore all the words I just said couple weeks ago. Github have been a pandora box in my current position. And I feel that I can manipulate my access easily.

I think I found a parallel connection between my relationship with Github and the public relationship with the stock markets. It goes red when after you bought it, it goes green after you sold it.

Micro-stepping

Referring back to this document:

A4988_DMOS

CNC Shield

These two documents showed that microstepping is simply adding jumpers:

I have converted the official documents into a chart for reference:

A4988 Stepper Driver configuration

M0 M1 M2 Microstep Resolution
Low Low Low Full step
High Low Low Half step
Low High Low Quarter step
High High Low Eighth step
High High High Sixteenth step

So I have tested both Quarter Step and Sixteenth Step and trust me, once you get the smooth operation it is as if the song Smooth Operator from Carlos Sainz.

Just as a fun clip:

So how to use microstepping:

Microstepping increases resolution not precision –– unknown author named Pigtt

Formulas

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```M = microstep factor``` 

```k = microstep index``` (integer)

I LOVE LATEX

$$
\text{Total\_Steps} = S \times M
$$

$$
\Delta\theta = \frac{360}{S \times M}
$$

$$
\theta(k) = \frac{360k}{S \times M}
$$



So for example is M = 4 or ```Quarter Step```

```arduino
N = 200 × 4 = 800
Δθ = 360 / 800 = 0.45°
θ(k) = 0.45k

If M = 16 or Sixteenth Step

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N = 200 × 16 = 3200
Δθ = 360 / 3200 = 0.1125°
θ(k) = 0.1125k

HankShakes:

What are handshakes?

What are tokens?

What are Private Keys and public keys?

Essentially: it is a method of identification.

For the arduino code to communicate with python, it needs a hand shake.

My python plot code needs to see a green-light signal to began, or else it will not be on the same panel with the code and thus it fails.

Some basic token demonstrations:

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void setup() {
  Serial.begin(115200);
  while (!Serial);          // INFINITE LOOP wait for USB
  Serial.println("READY");  // say ready
}

void loop() {
  if (Serial.readStringUntil('\n') == "GO") {
    Serial.println("OK");   // confirm
    while (1);              // stop
  }
}

Python receiving handshake and giving back a kiss.

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import serial
import time

ser = serial.Serial("/dev/cu.usbmodem1301", 115200, timeout=2)
time.sleep(2)

# wait for READY
while ser.readline().decode().strip() != "READY":
    pass

# send GO
ser.write(b"GO\n")

# read response
print(ser.readline().decode().strip())

On the Arduino side, Serial.begin(115200) starts the USB serial connection at the same port speed 115200 that math Python’s.

WARING: If not you will receive ````???```.

(!Serial)``` forces the Arduino to wait until the computer actually opens the USB connection, which prevents the first message from being lost during reset.
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```Serial.println("READY")``` is sent once to clearly tell Python “HELLO there. I have EARS. I am not daydreaming” 

Inside ```loop(), Serial.readStringUntil('\n')``` waits until Python sends a full line ending in a newline, which guarantees Arduino reads a complete command. 

```"GO"``` ensures Arduino only proceeds when it receives the exact expected signal.

When ```"GO"``` is received, ```Serial.println("OK") ``` responds, and ```while (1)``` stops the program so this exchange happens only once. 



Videos (Very Long):
<iframe width="560" height="315" src="https://www.youtube.com/embed/CITZIv3SmvU?si=IDvPfL7c0gn9T1A_" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>

#### My mistake of over-relying on ```WebbGPT```.

When you add too much handshakes and maybe, maybe deleted your own handshake.

I am not going to paste an entire chunk of code. But I am going to show you the specific bugs that I've encounter:

```py
ser = serial.Serial(port, baudrate, timeout=2)
time.sleep(2)  # Give Arduino time to reset
ser.reset_input_buffer()
...
print("Waiting for 'start' signal...")

What I did is that I open serial which resets arduino.
Then I wait 2 seconds while Arduino boots and prints ready

However, the code reset_input_buffer delete everything Arduino just sent, including ready.

WHAT AM I DOING

Solution:

A simply solution would be re-ordering the code, so that it clears the trash first:

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ser = serial.Serial(port, baudrate, timeout=2)

ser.reset_input_buffer()  
time.sleep(2)

Even better, we can actually wait for ready

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print("Waiting for 'ready'...")
while True:
    line = ser.readline().decode("utf-8", errors="ignore").strip()
    if not line:
        continue
    print("RX:", line)
    if "ready" in line.lower():
        break

print("Sending 'go'...")
ser.write(b"go\n")
ser.flush()

print("Waiting for 'start'...")
while True:
    line = ser.readline().decode("utf-8", errors="ignore").strip()
    if not line:
        continue
    print("RX:", line)
    if "start" in line.lower():
        break

Code simply for reference:

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#include <math.h>
#include <Arduino.h>

// ---------------- Pins ----------------
const int X_STEP = 2, X_DIR = 5;
const int Y_STEP = 3, Y_DIR = 6;
const int ENABLE_PIN = 8;
const int SENSOR_PIN = A2;

// --------- Motion / scan settings -----
const int STEP_DELAY_US    = 300;
const int SAMPLE_PAUSE_US  = 2000;

const long  STEPS_PER_REV  = 3200;   // 200 * 16 microsteps
const float X_SWEEP_DEG    = 90.0;
const float X_SAMPLE_DEG   = 1.0;    // desired angle spacing
const float Y_STEP_DEG     = 1.0;
const float Y_MAX_DEG      = 90.0;

// --------- Sensor calibration ----------
const float VCC_VOLTS = 5.0;
const float D_MIN_MM  = 20.0, D_MAX_MM = 800.0;

// V(L) = A - B ln(L)  =>  L = exp((A - V)/B)
float voltsToDistMM(float v) {
  const float A = 10.02f;
  const float B =  1.40f;

  if (v < 0.01f) v = 0.01f;
  if (v > VCC_VOLTS) v = VCC_VOLTS;

  float d = expf((A - v) / B);
  if (d < D_MIN_MM) d = D_MIN_MM;
  if (d > D_MAX_MM) d = D_MAX_MM;
  return d;
}

// --------------- Helpers --------------
inline long stepsForDeg(float deg) {
  return lroundf(deg * (float)STEPS_PER_REV / 360.0f);
}

inline void stepOnce(int stepPin) {
  digitalWrite(stepPin, HIGH);
  delayMicroseconds(STEP_DELAY_US);
  digitalWrite(stepPin, LOW);
  delayMicroseconds(STEP_DELAY_US);
}

void stepN(int stepPin, long n) {
  for (long i = 0; i < n; i++) stepOnce(stepPin);
}

int readAdcAvg4() {
  uint32_t sum = 0;
  for (int i = 0; i < 4; i++) sum += analogRead(SENSOR_PIN);
  return (sum + 2) / 4;
}

float readDistanceMM() {
  int adc = readAdcAvg4();
  float v = (adc * VCC_VOLTS) / 1023.0f;
  return voltsToDistMM(v);
}

// Wait for a full line "go"
bool waitForGo(unsigned long timeout_ms) {
  unsigned long t0 = millis();
  while (millis() - t0 < timeout_ms) {
    if (Serial.available()) {
      String s = Serial.readStringUntil('\n');
      s.trim();
      s.toLowerCase();
      if (s == "go") return true;
    }
    delay(5);
  }
  return false;
}

void setup() {
  Serial.begin(115200);

  pinMode(X_STEP, OUTPUT); pinMode(X_DIR, OUTPUT);
  pinMode(Y_STEP, OUTPUT); pinMode(Y_DIR, OUTPUT);
  pinMode(ENABLE_PIN, OUTPUT);
  pinMode(SENSOR_PIN, INPUT);

  // Motors disabled until Python says go
  digitalWrite(ENABLE_PIN, HIGH);

  Serial.println("ready");
  Serial.flush();

  if (!waitForGo(30000)) {
    Serial.println("ERROR: timeout waiting for go");
    while (true) delay(1000);
  }

  digitalWrite(ENABLE_PIN, LOW);  // enable motors
  delay(50);

  Serial.println("start");
  Serial.flush();
}

void loop() {
  // ---- Define consistent X sampling in integer counts ----
  // Example: 90 deg sweep at 1 deg spacing => 91 samples (0..90 inclusive)
  const int xSamples = (int)lroundf(X_SWEEP_DEG / X_SAMPLE_DEG) + 1;
  const long xSweepSteps = stepsForDeg(X_SWEEP_DEG);

  // steps between samples (integer). This makes motion consistent.
  // Any remainder is handled by snapping the last sample with a correction step.
  const long xStepPerSample = max(1L, xSweepSteps / (xSamples - 1));
  const long xTotalPlannedSteps = xStepPerSample * (xSamples - 1);
  const long xRemainderSteps = xSweepSteps - xTotalPlannedSteps; // can be >= 0

  long yPosSteps = 0;
  bool forward = true;

  for (float yDeg = 0.0; yDeg <= Y_MAX_DEG + 0.0001f; yDeg += Y_STEP_DEG) {
    // ---- Move Y to target ----
    long yTarget = stepsForDeg(yDeg);
    long yDelta  = yTarget - yPosSteps;

    digitalWrite(Y_DIR, (yDelta >= 0) ? LOW : HIGH);
    stepN(Y_STEP, labs(yDelta));
    yPosSteps = yTarget;

    // ---- Set X direction for snaking ----
    digitalWrite(X_DIR, forward ? HIGH : LOW);

    // ---- Scan one row ----
    for (int i = 0; i < xSamples; i++) {
      float xDeg = forward ? (i * X_SAMPLE_DEG) : (X_SWEEP_DEG - i * X_SAMPLE_DEG);
      float dist = readDistanceMM();

      // CSV: x,y,dist
      Serial.print(xDeg, 2);
      Serial.print(",");
      Serial.print(yDeg, 2);
      Serial.print(",");
      Serial.println(dist, 1);

      // move to next sample (except after last)
      if (i < xSamples - 1) {
        stepN(X_STEP, xStepPerSample);
        // apply the remainder only once at the very end of the sweep
        if (i == xSamples - 2 && xRemainderSteps > 0) {
          stepN(X_STEP, xRemainderSteps);
        }
      }

      delayMicroseconds(SAMPLE_PAUSE_US);
    }

    forward = !forward;
  }

  Serial.println("done");
  Serial.flush();

  digitalWrite(ENABLE_PIN, HIGH); // disable motors
  while (true) delay(1000);
}

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import time
import serial
from math import sin, cos, radians
import matplotlib.pyplot as plt

PORT = "/dev/cu.usbmodem1301"
BAUD = 115200

SENSOR_OFFSET_MM = 60.0
PAN_OFFSET_DEG = 90.0

READY_TIMEOUT_S = 10
START_TIMEOUT_S = 10
SCAN_TIMEOUT_S = 300
PLOT_EVERY_N = 200


def wait_for(ser, token, timeout_s, echo=True):
    t0 = time.time()
    while time.time() - t0 < timeout_s:
        line = ser.readline().decode("utf-8", errors="ignore").strip()
        if not line:
            continue
        if echo:
            print("RX:", line)
        if token in line.lower():
            return True
    return False


def parse_csv3(line):
    parts = line.split(",")
    if len(parts) != 3:
        return None
    try:
        return float(parts[0]), float(parts[1]), float(parts[2])
    except ValueError:
        return None


def to_xyz(x_deg_raw, y_deg_raw, dist_raw_mm):
    r = dist_raw_mm + SENSOR_OFFSET_MM
    pan = radians(x_deg_raw - PAN_OFFSET_DEG)
    tilt = radians(y_deg_raw)

    z = r * sin(tilt)
    plane = r * cos(tilt)
    x = plane * cos(pan)
    y = plane * sin(pan)
    return x, y, z


# ---- connect ----
ser = serial.Serial(PORT, BAUD, timeout=1)

# Immediately clear junk that existed BEFORE the reset (safe)
ser.reset_input_buffer()

# Opening the port resets many Arduino boards; give it a moment to boot
time.sleep(1.5)

print("Waiting for 'ready'...")
if not wait_for(ser, "ready", READY_TIMEOUT_S, echo=True):
    print("Did not see 'ready'. Sending 'go' anyway (failsafe).")

print("TX: go")
ser.write(b"go\n")
ser.flush()

print("Waiting for 'start' (optional)...")
wait_for(ser, "start", START_TIMEOUT_S, echo=True)

# ---- plot setup ----
xs, ys, zs = [], [], []
plt.ion()
fig = plt.figure()
ax = fig.add_subplot(111, projection="3d")

print("Receiving data...")
t0 = time.time()
n = 0

try:
    while True:
        if time.time() - t0 > SCAN_TIMEOUT_S:
            print("Safety timeout stopping.")
            break

        line = ser.readline().decode("utf-8", errors="ignore").strip()
        if not line:
            continue

        low = line.lower()
        if "done" in low:
            print("Scan complete!")
            break
        if low.startswith("#") or "error" in low or "ready" in low or "start" in low:
            continue

        parsed = parse_csv3(line)
        if not parsed:
            continue

        x_deg, y_deg, dist = parsed
        x, y, z = to_xyz(x_deg, y_deg, dist)
        xs.append(x)
        ys.append(y)
        zs.append(z)
        n += 1

        if n % 50 == 0:
            print(f"{n} pts | x={x_deg:.1f} y={y_deg:.1f} d={dist:.1f} -> z={z:.1f}")

        if n % PLOT_EVERY_N == 0:
            ax.cla()
            ax.scatter(xs, ys, zs, s=1)
            plt.draw()
            plt.pause(0.001)

except KeyboardInterrupt:
    print("Stopped by user.")
finally:
    ser.close()
    plt.ioff()
    plt.show()

Super duper GPT version

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import time
import serial
import numpy as np
from math import sin, cos, radians
import matplotlib.pyplot as plt
from collections import deque

PORT = "/dev/cu.usbmodem1301"
BAUD = 115200

SENSOR_OFFSET_MM = 60.0
PAN_OFFSET_DEG = 90.0

READY_TIMEOUT_S = 10
START_TIMEOUT_S = 10
SCAN_TIMEOUT_S = 300

# ---- must match Arduino ----
X_SWEEP_DEG = 90.0
X_SAMPLE_DEG = 1.0
Y_MAX_DEG = 90.0
Y_STEP_DEG = 1.0

# ---- basic sanity (still helpful) ----
DIST_MIN_MM = 30.0
DIST_MAX_MM = 800.0

# ---- “keep only the real surface” knobs ----
# 1) Local consistency: keep points whose distance agrees with neighbors
NEIGHBOR_WIN = 1                 # 1 => 3x3 neighborhood
NEIGHBOR_ABS_MM = 35.0           # allow +/- mm difference vs neighbors
NEIGHBOR_REL = 0.06              # allow +/- % of distance (helps at far range)
MIN_GOOD_NEIGHBORS = 2           # must have at least this many agreeing neighbors

# 2) Connected component: keep only the largest connected region
CONNECT_8 = True                 # True => 8-connectivity (recommended)
MIN_COMPONENT_SIZE = 300         # safety: ignore tiny blobs as “noise”

# 3) Final downsample for elegance (optional)
KEEP_EVERY_N = 1                 # 1=keep all, 2=keep half, 3=keep one-third, etc.


def wait_for_token(ser, token: str, timeout_s: float, echo=True):
    token = token.lower()
    t0 = time.time()
    while time.time() - t0 < timeout_s:
        line = ser.readline().decode("utf-8", errors="ignore").strip()
        if not line:
            continue
        low = line.lower()
        if echo:
            print("RX:", line)
        if token in low:
            return True
        if low.startswith("error"):
            return False
    return False


def parse_csv3(line: str):
    parts = line.split(",")
    if len(parts) != 3:
        return None
    try:
        return float(parts[0]), float(parts[1]), float(parts[2])
    except ValueError:
        return None


def to_xyz(x_deg_raw, y_deg_raw, dist_raw_mm):
    r = dist_raw_mm + SENSOR_OFFSET_MM
    pan = radians(x_deg_raw - PAN_OFFSET_DEG)
    tilt = radians(y_deg_raw)

    z = r * sin(tilt)
    plane = r * cos(tilt)
    x = plane * cos(pan)
    y = plane * sin(pan)
    return x, y, z


def build_grid_axes():
    x_vals = np.round(np.arange(0.0, X_SWEEP_DEG + 1e-6, X_SAMPLE_DEG), 2)
    y_vals = np.round(np.arange(0.0, Y_MAX_DEG + 1e-6, Y_STEP_DEG), 2)
    return x_vals, y_vals


def neighbor_consistency_mask(dist_grid):
    """
    Keep a point if it agrees with enough neighbors in a window.
    Agreement threshold is max(NEIGHBOR_ABS_MM, NEIGHBOR_REL * dist).
    """
    H, W = dist_grid.shape
    valid = ~np.isnan(dist_grid)
    keep = np.zeros((H, W), dtype=bool)

    for r in range(H):
        r0 = max(0, r - NEIGHBOR_WIN)
        r1 = min(H, r + NEIGHBOR_WIN + 1)
        for c in range(W):
            if not valid[r, c]:
                continue

            c0 = max(0, c - NEIGHBOR_WIN)
            c1 = min(W, c + NEIGHBOR_WIN + 1)

            center = dist_grid[r, c]
            window = dist_grid[r0:r1, c0:c1].reshape(-1)
            window = window[~np.isnan(window)]

            if window.size <= 1:
                continue

            thr = max(NEIGHBOR_ABS_MM, NEIGHBOR_REL * center)
            # count neighbors (excluding itself) that are close in distance
            close = np.sum(np.abs(window - center) <= thr) - 1
            if close >= MIN_GOOD_NEIGHBORS:
                keep[r, c] = True

    return keep


def largest_connected_component(mask):
    """
    Return a mask containing only the largest connected component of True cells.
    """
    H, W = mask.shape
    visited = np.zeros_like(mask, dtype=bool)

    if CONNECT_8:
        neighbors = [(-1, -1), (-1, 0), (-1, 1),
                     ( 0, -1),          ( 0, 1),
                     ( 1, -1), ( 1, 0), ( 1, 1)]
    else:
        neighbors = [(-1, 0), (1, 0), (0, -1), (0, 1)]

    best_cells = None
    best_size = 0

    for r in range(H):
        for c in range(W):
            if not mask[r, c] or visited[r, c]:
                continue

            q = deque([(r, c)])
            visited[r, c] = True
            cells = [(r, c)]

            while q:
                rr, cc = q.popleft()
                for dr, dc in neighbors:
                    nr, nc = rr + dr, cc + dc
                    if 0 <= nr < H and 0 <= nc < W and mask[nr, nc] and not visited[nr, nc]:
                        visited[nr, nc] = True
                        q.append((nr, nc))
                        cells.append((nr, nc))

            size = len(cells)
            if size > best_size:
                best_size = size
                best_cells = cells

    out = np.zeros_like(mask, dtype=bool)
    if best_cells is not None and best_size >= MIN_COMPONENT_SIZE:
        for r, c in best_cells:
            out[r, c] = True

    return out, best_size


def set_equalish_3d(ax, X, Y, Z):
    if len(X) < 10:
        return
    x_min, x_max = float(np.min(X)), float(np.max(X))
    y_min, y_max = float(np.min(Y)), float(np.max(Y))
    z_min, z_max = float(np.min(Z)), float(np.max(Z))

    cx = 0.5 * (x_min + x_max)
    cy = 0.5 * (y_min + y_max)
    cz = 0.5 * (z_min + z_max)

    span = max(x_max - x_min, y_max - y_min, z_max - z_min)
    if span <= 1e-6:
        return
    half = 0.5 * span
    ax.set_xlim(cx - half, cx + half)
    ax.set_ylim(cy - half, cy + half)
    ax.set_zlim(cz - half, cz + half)


# ------------------- READ SCAN INTO GRID -------------------
x_vals, y_vals = build_grid_axes()
nx, ny = len(x_vals), len(y_vals)

dist_grid = np.full((ny, nx), np.nan, dtype=np.float32)
x_to_i = {float(x): i for i, x in enumerate(x_vals)}
y_to_j = {float(y): j for j, y in enumerate(y_vals)}

ser = serial.Serial(PORT, BAUD, timeout=1)
ser.reset_input_buffer()
time.sleep(1.5)

print("Waiting for 'ready'...")
wait_for_token(ser, "ready", READY_TIMEOUT_S, echo=True)

print("TX: go")
ser.write(b"go\n")
ser.flush()

print("Waiting for 'start'...")
wait_for_token(ser, "start", START_TIMEOUT_S, echo=True)

print("Receiving data into range image...")
t0 = time.time()
n_recv = 0
n_store = 0

try:
    while True:
        if time.time() - t0 > SCAN_TIMEOUT_S:
            print("Safety timeout stopping.")
            break

        line = ser.readline().decode("utf-8", errors="ignore").strip()
        if not line:
            continue

        low = line.lower()
        if "done" in low:
            print("Scan complete!")
            break
        if low.startswith("error"):
            print("Arduino error:", line)
            break
        if low in ("ready", "start"):
            continue

        parsed = parse_csv3(line)
        if not parsed:
            continue

        x_deg, y_deg, dist = parsed
        n_recv += 1

        if dist < DIST_MIN_MM or dist > DIST_MAX_MM:
            continue

        # quantize to grid (handles float formatting tiny errors)
        xq = float(np.round(x_deg / X_SAMPLE_DEG) * X_SAMPLE_DEG)
        yq = float(np.round(y_deg / Y_STEP_DEG) * Y_STEP_DEG)
        xq = float(np.round(xq, 2))
        yq = float(np.round(yq, 2))

        if xq in x_to_i and yq in y_to_j:
            dist_grid[y_to_j[yq], x_to_i[xq]] = dist
            n_store += 1

        if n_recv % 3000 == 0:
            print(f"recv={n_recv} stored={n_store}")

finally:
    ser.close()

raw_valid = np.count_nonzero(~np.isnan(dist_grid))
print(f"Raw valid grid points: {raw_valid}")

# ------------------- FILTER: KEEP ONLY REAL SECTION -------------------
print("Filtering: neighbor consistency...")
mask_consistent = neighbor_consistency_mask(dist_grid)
print(f"Consistent points: {np.count_nonzero(mask_consistent)}")

print("Filtering: largest connected component...")
mask_lcc, lcc_size = largest_connected_component(mask_consistent)
print(f"Largest component size: {lcc_size}")

# If LCC is too small, fall back to consistent mask (still better than raw)
final_mask = mask_lcc if lcc_size >= MIN_COMPONENT_SIZE else mask_consistent

# ------------------- CONVERT TO XYZ -------------------
ys_idx, xs_idx = np.where(final_mask)
if KEEP_EVERY_N > 1:
    sel = np.arange(len(xs_idx)) % KEEP_EVERY_N == 0
    ys_idx, xs_idx = ys_idx[sel], xs_idx[sel]

Xlist, Ylist, Zlist = [], [], []
for j, i in zip(ys_idx, xs_idx):
    x_deg = float(x_vals[i])
    y_deg = float(y_vals[j])
    d = float(dist_grid[j, i])
    x, y, z = to_xyz(x_deg, y_deg, d)
    Xlist.append(x); Ylist.append(y); Zlist.append(z)

X = np.array(Xlist, dtype=np.float32)
Y = np.array(Ylist, dtype=np.float32)
Z = np.array(Zlist, dtype=np.float32)

print(f"Final plotted points: {len(X)}")

# ------------------- ELEGANT PLOT -------------------
plt.figure()
ax = plt.axes(projection="3d")
sc = ax.scatter(X, Y, Z, s=3, c=Z, cmap="viridis", alpha=0.9)

ax.set_xlabel("X (mm)")
ax.set_ylabel("Y (mm)")
ax.set_zlabel("Z (mm)")
ax.set_title("Scanned Object Section (denoised + largest region)")

set_equalish_3d(ax, X, Y, Z)
plt.colorbar(sc, ax=ax, shrink=0.6, label="Z (mm)")
plt.show()

Joke

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I have a gift for you.
What is the best language in the world.

A) Java
B) Python
C) C++
D) ALL of the ABOUVE

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