Microscope camera kiosk
Touchscreen kiosk for the Raspberry Pi HQ camera (IMX477) used as a microscope: live preview from boot, raw frame recording, full-resolution stills, and automatic capture-SSD mounting. - app.py: GTK3 fullscreen UI over cage — preview, REC/STOP, PHOTO, 90-degree rotate button, tap-to-open exposure/gain/settings sliders, and an "SSD NOT MOUNTED" badge - camera.py: picamera2 wrapper with separate video (ISP preview + packed 12-bit raw) and still (4056x3040) configurations - recorder.py: writer thread turning the raw stream into one Bayer frame per file plus index.jsonl/session.json, with dropped/missed accounting - photos.py: still capture to DNG + JPEG, and a background worker that renders a viewable 16-bit sRGB TIFF from the 12-bit Bayer frame - storage.py: SSD mount state and the date/time/format session layout - tools/unpack_raw.py: desktop-side unpacker/demosaicer - system/ + install.sh: systemd units, udev rule, mount helper, sudoers Note: raw frames are written byte-for-byte as the sensor produced them, so they stay decodeable regardless of how the stills pipeline evolves.
This commit is contained in:
Microscope Camera
365
tools/unpack_raw.py
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365
tools/unpack_raw.py
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#!/usr/bin/env python3
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"""Unpack the microscope camera's raw frames on a desktop machine.
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Recording writes MIPI-packed 12-bit Bayer frames (``SBGGR12_CSI2P`` style: two
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pixels in three bytes) straight off the sensor. This tool turns them into files
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you can actually look at:
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unpack_raw.py frame_000001.raw -> frame_000001.npy (uint16)
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unpack_raw.py --png frame_000001.raw -> frame_000001.png (quick look)
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unpack_raw.py --tiff16 frame_000001.raw -> frame_000001.tiff (16-bit mono)
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unpack_raw.py --debayer --rgb16 frame_000001.raw-> frame_000001_rgb.tiff (16-bit RGB)
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unpack_raw.py /mnt/microscope/2026-10-30/21-33-05 (whole session)
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unpack_raw.py --info /mnt/microscope/2026-10-30/21-33-05
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Geometry (width, height, stride, Bayer pattern) is picked up automatically from
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the session's ``session.json``; if that is missing the tool falls back to the
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file size and the command line defaults.
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"""
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import argparse
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import json
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import os
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import sys
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import numpy as np
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PATTERNS = {
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# pattern -> (row parity, col parity) of the red sample in the 2x2 tile
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"RGGB": (0, 0),
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"BGGR": (1, 1),
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"GRBG": (0, 1),
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"GBRG": (1, 0),
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}
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def pattern_from_format(fmt):
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text = (fmt or "SRGGB12").upper()
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if text.startswith("S"):
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text = text[1:]
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head = text[:4]
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return head if head in PATTERNS else "RGGB"
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def unpack_mipi12(packed, width, height, stride):
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"""Unpack MIPI CSI-2 RAW12 (3 bytes -> 2 pixels).
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Byte order matters: byte0 holds the low 8 bits of pixel 0, byte1 holds the
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high 4 bits of pixel 0 in its HIGH nibble and the high 4 bits of pixel 1 in
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its LOW nibble. Treating byte1's low nibble as pixel 0's high bits (and
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its high nibble as pixel 1's) transposes the 12-bit words within each pair,
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which scrambles the Bayer mosaic and produces colour-fringed output.
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"""
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rows = packed[: stride * height].reshape(height, stride)
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useful = rows[:, : (width * 3) // 2]
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triplets = useful.reshape(height, width // 2, 3).astype(np.uint16)
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b0 = triplets[:, :, 0]
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b1 = triplets[:, :, 1]
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b2 = triplets[:, :, 2]
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even = (b0 << 4) | (b1 >> 4)
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odd = ((b1 & 0x0F) << 8) | b2
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out = np.empty((height, width), dtype=np.uint16)
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out[:, 0::2] = even
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out[:, 1::2] = odd
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return out
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def demosaic(raw, pattern="RGGB"):
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rp, cp = PATTERNS.get(pattern, (0, 0))
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h, w = raw.shape
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tiles = raw.reshape(h // 2, 2, w // 2, 2).transpose(0, 2, 1, 3)
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red = tiles[..., rp, cp].astype(np.uint32)
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blue = tiles[..., 1 - rp, 1 - cp].astype(np.uint32)
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green_r = tiles[..., rp, 1 - cp]
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green_b = tiles[..., 1 - rp, cp]
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def upsample(plane):
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p = np.pad(plane, 1, mode="edge")
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center = p[1:-1, 1:-1]
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left, right = p[1:-1, :-2], p[1:-1, 2:]
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up, down = p[:-2, 1:-1], p[2:, 1:-1]
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col_n = right if cp == 0 else left
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row_n = down if rp == 0 else up
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corner = p[2:, 2:] if (cp == 0 and rp == 0) else \
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p[2:, :-2] if (cp == 0 and rp == 1) else \
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p[:-2, 2:] if (cp == 1 and rp == 0) else p[:-2, :-2]
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full = np.empty((h, w), dtype=np.uint16)
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full[rp::2, cp::2] = center
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full[rp::2, (1 - cp)::2] = (center + col_n) // 2
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full[(1 - rp)::2, cp::2] = (center + row_n) // 2
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full[(1 - rp)::2, (1 - cp)::2] = (center + col_n + row_n + corner) // 4
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return full
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red_full, blue_full = upsample(red), upsample(blue)
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g1 = np.pad(green_r.astype(np.uint32), 1, mode="edge")
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g2 = np.pad(green_b.astype(np.uint32), 1, mode="edge")
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green_full = np.empty((h, w), dtype=np.uint16)
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green_full[rp::2, (1 - cp)::2] = green_r
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green_full[(1 - rp)::2, cp::2] = green_b
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green_full[rp::2, cp::2] = (g1[1:-1, 1:-1] + g1[1:-1, :-2]) // 2
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green_full[(1 - rp)::2, (1 - cp)::2] = (g2[1:-1, 1:-1] + g2[1:-1, 2:]) // 2
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rgb = np.empty((h, w, 3), dtype=np.uint16)
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rgb[..., 1] = green_full
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return rgb, red_full, blue_full
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def apply_rotation(image, rotation):
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"""Rotate an array clockwise by 0/90/180/270 degrees."""
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rotation = int(rotation or 0) % 360
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if rotation == 0:
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return image
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if rotation == 90:
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return np.ascontiguousarray(np.rot90(image, k=3))
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if rotation == 180:
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return np.ascontiguousarray(np.rot90(image, k=2))
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if rotation == 270:
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return np.ascontiguousarray(np.rot90(image, k=1))
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return image
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_PATTERN_TILE = {
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"RGGB": (("R", "G"), ("G", "B")),
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"BGGR": (("B", "G"), ("G", "R")),
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"GRBG": (("G", "R"), ("B", "G")),
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"GBRG": (("G", "B"), ("R", "G")),
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}
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def rotate_pattern(pattern, rotation):
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"""CFA pattern after rotating the Bayer plane clockwise.
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Rotating a mosaic without moving its pattern would put red samples where
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blue belong, so a rotated .npy/.tiff must record the rotated pattern.
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"""
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steps = (int(rotation or 0) % 360) // 90
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if not steps:
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return pattern
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tile = [list(row) for row in _PATTERN_TILE.get(pattern, _PATTERN_TILE["RGGB"])]
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for _ in range(steps):
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tile = [[tile[1][0], tile[0][0]], [tile[1][1], tile[0][1]]] # 90 deg clockwise
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text = "".join(tile[0] + tile[1])
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for name, known in _PATTERN_TILE.items():
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if "".join(known[0] + known[1]) == text:
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return name
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return pattern
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def find_session(path):
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"""Walk up from *path* looking for session.json / photo.json."""
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current = os.path.abspath(path if os.path.isdir(path) else os.path.dirname(path))
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for _ in range(4):
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for name in ("session.json", "photo.json"):
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candidate = os.path.join(current, name)
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if os.path.isfile(candidate):
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return current, candidate
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parent = os.path.dirname(current)
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if parent == current:
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break
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current = parent
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return None, None
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def geometry_for(path, args):
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width, height, stride, pattern = args.width, args.height, args.stride, args.pattern
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session_dir, meta_file = find_session(path)
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meta = {}
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if meta_file:
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try:
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with open(meta_file, "r", encoding="utf-8") as handle:
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meta = json.load(handle)
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except (OSError, ValueError):
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meta = {}
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raw = meta.get("raw") or {}
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if raw:
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width = width or raw.get("width")
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height = height or raw.get("height")
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stride = stride or raw.get("stride")
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pattern = args.pattern or pattern_from_format(raw.get("format"))
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path_size = os.path.getsize(path)
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height = height or 1520
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if not width:
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# packed 12-bit: bytes per row = width * 3/2
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if stride:
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width = int(stride * 2 / 3)
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else:
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width = 2028
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if not stride:
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stride = path_size // height
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expected = width * height if args.unpacked else stride * height
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if path_size < expected:
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raise SystemExit(
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"%s is %d bytes but %dx%d needs %d — pass --width/--height/--stride"
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% (os.path.basename(path), path_size, width, height, expected)
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)
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rotation = args.rotate if args.rotate is not None else int(meta.get("rotation") or 0)
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return width, height, stride, pattern, session_dir, meta, rotation
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def contrast_stretch(image):
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lo, hi = np.percentile(image, (0.5, 99.5))
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if hi <= lo:
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hi = lo + 1
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scaled = np.clip((image.astype(np.float32) - lo) * (255.0 / (hi - lo)), 0, 255)
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return scaled.astype(np.uint8)
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def srgb_encode(rgb16):
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"""Linear 16-bit RGB -> display-ready 8-bit sRGB.
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Without this the frame looks flat and washed out, because linear sensor data
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held in a 16-bit container has all its mid-tones crammed into the dark end.
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"""
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x = np.clip(rgb16.astype(np.float32) / 65535.0, 0.0, 1.0)
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x = np.where(x <= 0.0031308, x * 12.92,
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1.055 * np.power(x, 1.0 / 2.4) - 0.055)
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return np.clip(x * 255.0 + 0.5, 0, 255).astype(np.uint8)
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def white_balance(rgb, red_full, blue_full, gains):
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"""Apply camera white balance. Only called when --white-balance is given:
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gains above 1.0 clip at 65535, which loses highlight data."""
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if not gains:
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gains = (1.0, 1.0)
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out = rgb
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out[..., 0] = np.clip(red_full.astype(np.float32) * float(gains[0]), 0, 65535).astype(np.uint16)
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out[..., 2] = np.clip(blue_full.astype(np.float32) * float(gains[1]), 0, 65535).astype(np.uint16)
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return out
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def process(path, args):
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width, height, stride, pattern, session_dir, meta, rotation = geometry_for(path, args)
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stem = os.path.splitext(os.path.basename(path))[0]
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outdir = args.outdir or os.path.dirname(os.path.abspath(path))
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os.makedirs(outdir, exist_ok=True)
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payload = np.fromfile(path, dtype=np.uint8)
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if args.unpacked:
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image = payload[: width * height * 2].view(np.uint16).reshape(height, width)
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else:
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image = unpack_mipi12(payload, width, height, stride)
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print("%-28s %dx%d %s stride=%d rotation=%d° max=%d mean=%.1f"
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% (os.path.basename(path), width, height, pattern, stride, rotation,
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int(image.max()), float(image.mean())))
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# The session's rotation is the operator's display orientation, so honour it
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# in everything this tool writes. Bayer exports are rotated *with* their CFA
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# pattern; the RGB path is demosaiced first and then turned, which is
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# equivalent and avoids re-deriving the pattern.
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bayer = apply_rotation(image, rotation)
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bayer_pattern = rotate_pattern(pattern, rotation)
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made = []
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if args.npy or not (args.png or args.tiff16 or args.rgb16):
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out = os.path.join(outdir, stem + ".npy")
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np.save(out, bayer)
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made.append(out)
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if args.png:
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from PIL import Image
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out = os.path.join(outdir, stem + ".png")
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Image.fromarray(contrast_stretch(bayer)).save(out)
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made.append(out)
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if args.tiff16:
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import tifffile
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out = os.path.join(outdir, stem + ".tiff")
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tifffile.imwrite(out, bayer,
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description="16-bit unpacked Bayer %s (rotated %d deg clockwise)"
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% (bayer_pattern, rotation))
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made.append(out)
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if args.rgb16:
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import tifffile
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gains = meta.get("awb")
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# Demosaic in sensor orientation, fill all three channels, then rotate:
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# rotating an RGB triple is equivalent to rotating the mosaic and
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# re-deriving its CFA pattern, without the pattern bookkeeping.
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rgb, red_full, blue_full = demosaic(image, pattern)
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rgb[..., 0] = np.clip(red_full.astype(np.float32) * 16.0, 0, 65535).astype(np.uint16)
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rgb[..., 2] = np.clip(blue_full.astype(np.float32) * 16.0, 0, 65535).astype(np.uint16)
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rgb[..., 1] = np.clip(rgb[..., 1].astype(np.float32) * 16.0, 0, 65535).astype(np.uint16)
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del red_full, blue_full, image
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if rotation:
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rgb = apply_rotation(rgb, rotation)
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applied = False
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if args.white_balance:
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rgb = white_balance(rgb, rgb[..., 0], rgb[..., 2], gains)
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applied = True
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out = os.path.join(outdir, stem + "_rgb.tiff")
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tifffile.imwrite(out, rgb, photometric="rgb",
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description="linear 16-bit RGB, %s, rotation=%d deg clockwise, "
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"white_balance_applied=%s camera_white_balance=%s"
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% (pattern, rotation, applied, gains))
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made.append(out)
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for item in made:
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print(" -> %s (%.1f MB)" % (item, os.path.getsize(item) / 1e6))
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return made
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def show_info(target):
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session_dir, meta_file = find_session(target)
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if not meta_file:
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raise SystemExit("no session.json/photo.json found near %s" % target)
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with open(meta_file, "r", encoding="utf-8") as handle:
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meta = json.load(handle)
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print(json.dumps(meta, indent=2))
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def collect_inputs(paths, recursive):
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files = []
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for path in paths:
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if os.path.isdir(path):
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raw_dir = os.path.join(path, "raw")
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scan = raw_dir if os.path.isdir(raw_dir) else path
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for name in sorted(os.listdir(scan)):
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if name.endswith(".raw"):
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files.append(os.path.join(scan, name))
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else:
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files.append(path)
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return files
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def main():
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parser = argparse.ArgumentParser(description=__doc__,
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formatter_class=argparse.RawDescriptionHelpFormatter)
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parser.add_argument("paths", nargs="+", help="raw files, session dirs, or date dirs")
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parser.add_argument("--outdir", help="where to write results (default: next to input)")
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parser.add_argument("--npy", action="store_true", help="write 16-bit .npy (default)")
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parser.add_argument("--png", action="store_true", help="write 8-bit contrast-stretched PNG")
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parser.add_argument("--tiff16", action="store_true", help="write 16-bit Bayer TIFF")
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parser.add_argument("--rgb16", action="store_true", help="write 16-bit RGB TIFF (demosaiced)")
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parser.add_argument("--debayer", action="store_true", help="alias for --rgb16")
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parser.add_argument("--rotate", type=int, choices=(0, 90, 180, 270),
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help="override the session's display rotation (degrees clockwise)")
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parser.add_argument("--no-rotate", dest="rotate", action="store_const", const=0,
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help="ignore the rotation recorded in the session metadata")
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parser.add_argument("--white-balance", action="store_true",
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help="apply the camera's colour gains to the RGB output "
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"(clips highlights; off by default, gains are recorded anyway)")
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parser.add_argument("--info", action="store_true", help="print session metadata and exit")
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parser.add_argument("--pattern", choices=sorted(PATTERNS), help="Bayer pattern override")
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parser.add_argument("--width", type=int, help="frame width override")
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parser.add_argument("--height", type=int, help="frame height override")
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parser.add_argument("--stride", type=int, help="row stride in bytes override")
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parser.add_argument("--unpacked", action="store_true",
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help="input is already unpacked 16-bit little-endian")
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args = parser.parse_args()
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if args.debayer:
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args.rgb16 = True
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if args.info:
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for path in args.paths:
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show_info(path)
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return 0
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files = collect_inputs(args.paths, recursive=True)
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if not files:
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raise SystemExit("no .raw files found")
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total = 0
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for path in files:
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total += len(process(path, args))
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print("done: %d file(s) from %d input(s)" % (total, len(files)))
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return 0
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if __name__ == "__main__":
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sys.exit(main())
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