jaimemarijke · November 16, 2018 01:47
diff --git a/PiCamera prototyping (raspi).ipynb b/PiCamera prototyping (raspi).ipynb
 {
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [],
   "source": [
    "from fractions import Fraction\n",
    "import time\n",
    "\n",
    "import picamera\n",
    "import picamera.array\n",
    "import numpy as np\n",
    "import tifffile"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "def print_camera_settings(camera, context_msg='', requested_shutter_speed=None):\n",
    "    print('\\n----')\n",
    "    print(context_msg)\n",
    "    print('----')\n",
    "    print('sensor_mode:', camera.sensor_mode)\n",
    "    print('Requested shutter speed:', requested_shutter_speed)\n",
    "    print('shutter_speed:', camera.shutter_speed)\n",
    "    print('exposure_speed:', camera.exposure_speed) # Docs: \"returns the shutter speed currently being used by the camera.\"\n",
    "    print('iso:', camera.iso)\n",
    "    print('framerate:', camera.framerate)\n",
    "    print('analog_gain:', camera.analog_gain)\n",
    "    print('digital_gain:', camera.digital_gain)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Bit Depths\n",
    "Our images are captured with 10-bits, but we want to save them in image formats with larger bit depths. By applying a scaling factor, we can make our saved images look roughly the correct brightness\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 45,
   "metadata": {},
   "outputs": [],
   "source": [
    "CAPTURED_IMAGE_BIT_DEPTH = 2 ** 10\n",
    "IMAGE_FORMAT_BIT_DEPTH = 2 ** 16\n",
    "BIT_DEPTH_SCALE_FACTOR = int(IMAGE_FORMAT_BIT_DEPTH / CAPTURED_IMAGE_BIT_DEPTH)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Use PiBayerArray to save directly to TIFF\n",
    "This example shows how to capture directly to a numpy array using the PiBayerArray stream.\n",
    "\n",
    "The downside is that (as far as I can tell) this means that EXIF data doesn't get recorded anywere"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 46,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "----\n",
      "Camera settings after capture\n",
      "----\n",
      "sensor_mode: 0\n",
      "Requested shutter speed: 500000\n",
      "shutter_speed: 499982\n",
      "exposure_speed: 499982\n",
      "iso: 400\n",
      "framerate: 1\n",
      "analog_gain: 1311/256\n",
      "digital_gain: 1/64\n",
      "\n",
      "Done!\n"
     ]
    }
   ],
   "source": [
    "def picamera_capture_to_bayer_stream_to_tiff(iso=100, shutter_speed=int(0.01 * 1000 * 1000), compression_level=1):\n",
    "    filename_root = f'picamera_ss{shutter_speed}_iso{iso}_compress{compression_level}'\n",
    "    tiff_filename = f'{filename_root}.tiff'\n",
    "    \n",
    "    with picamera.PiCamera(framerate=1) as camera:      \n",
    "        camera.awb_mode = 'off'\n",
    "        # I think this would use Pagnutti's numbers\n",
    "        # camera.awb_gains = (1.307,1.615) \n",
    "\n",
    "        camera.iso = iso\n",
    "        camera.shutter_speed = shutter_speed\n",
    "\n",
    "        with picamera.array.PiBayerArray(camera) as stream:\n",
    "            camera.capture(stream, 'jpeg', bayer=True) # To get bayer data, the image must be captured to the 'jpeg' format\n",
    "\n",
    "            print_camera_settings(camera, 'Camera settings after capture', shutter_speed)\n",
    "\n",
    "            tifffile.imsave(tiff_filename, stream.array.astype(np.uint16) * BIT_DEPTH_SCALE_FACTOR, compress=compression_level)\n",
    "\n",
    "            camera.framerate = 1  # Hack to make camera close properly (https://github.com/waveform80/picamera/issues/528)\n",
    "    \n",
    "    print('\\nDone!')\n",
    "    \n",
    "picamera_capture_to_bayer_stream_to_tiff(iso=400, shutter_speed=int(0.5 * 1000 * 1000))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Save as JPEG+RAW, use PiBayerArray to extract RAW\n",
    "This example shows how to capture to a JPEG+RAW file (just like raspistill!), then crack that file back open and extract the raw using PiBayerArray. (Based on this random person's gist I found)\n",
    "\n",
    "The advantage to this approach is that the EXIF data gets saved in the .jpeg, and then we can (theoretically)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [],
   "source": [
    "import PIL.Image\n",
    "import PIL.ExifTags\n",
    "\n",
    "def _read_exif_tags(image_path):\n",
    "    '''\n",
    "    Uses (an \"experimental\" private function from) PIL to read EXIF tags from an image file.\n",
    "    Returns a dictionary of tag names to values\n",
    "    '''\n",
    "    PIL_image = PIL.Image.open(image_path)\n",
    "    EXIF_CODES_TO_NAMES = PIL.ExifTags.TAGS\n",
    "    # _getexif() returns a dictionary of {tag code: tag value}. Use PIL.ExifTags.TAGS dictionary of {tag code: tag name}\n",
    "    # to construct a more digestible dictionary of {tag name: tag value}\n",
    "    tags = {\n",
    "        EXIF_CODES_TO_NAMES[tag_code]: tag_value\n",
    "        for tag_code, tag_value in PIL_image._getexif().items()\n",
    "        if tag_code in EXIF_CODES_TO_NAMES\n",
    "    }\n",
    "    return tags"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "----\n",
      "Camera settings after capture\n",
      "----\n",
      "sensor_mode: 0\n",
      "Requested shutter speed: 10000\n",
      "shutter_speed: 9991\n",
      "exposure_speed: 9991\n",
      "iso: 100\n",
      "framerate: 1\n",
      "analog_gain: 331/128\n",
      "digital_gain: 105/128\n",
      "----\n",
      "EXIF data:\n",
      "----\n",
      "ImageWidth: 720\n",
      "ImageLength: 480\n",
      "ResolutionUnit: 2\n",
      "ExifOffset: 192\n",
      "Make: RaspberryPi\n",
      "Model: RP_imx219\n",
      "DateTime: 2018:11:15 17:38:41\n",
      "YCbCrPositioning: 1\n",
      "XResolution: (72, 1)\n",
      "YResolution: (72, 1)\n",
      "ExifVersion: b'0220'\n",
      "ComponentsConfiguration: b'\\x01\\x02\\x03\\x00'\n",
      "ShutterSpeedValue: (6645155, 1000000)\n",
      "DateTimeOriginal: 2018:11:15 17:38:41\n",
      "DateTimeDigitized: 2018:11:15 17:38:41\n",
      "ApertureValue: (20000, 10000)\n",
      "BrightnessValue: (8, 100)\n",
      "MaxApertureValue: (20000, 10000)\n",
      "MeteringMode: 2\n",
      "Flash: 0\n",
      "FocalLength: (30390, 10000)\n",
      "ColorSpace: 1\n",
      "ExifImageWidth: 720\n",
      "ExifInteroperabilityOffset: 906\n",
      "ExifImageHeight: 480\n",
      "ExposureTime: (9991, 1000000)\n",
      "FNumber: (20000, 10000)\n",
      "ExposureProgram: 3\n",
      "ISOSpeedRatings: 100\n",
      "ExposureMode: 0\n",
      "FlashPixVersion: b'0100'\n",
      "WhiteBalance: 0\n",
      "MakerNote: b'ev=-1 mlux=-1 exp=9991 ag=469 focus=255 gain_r=0.000 gain_b=0.000 greenness=0 ccm=6022,-2314,394,-936,4728,310,300,-4324,8126,0,0,0 md=0 tg=2454 7480 oth=0 0 b=0 f=2454 7480 fi=0 ISP Build Date: Jun  7 2018, 15:36:07 VC_BUILD_ID_VERSION: 4800f08a139d6ca1c5ecbee345ea6682e2160881 (clean) VC_BUILD_ID_USER: dc4 VC_BUILD_ID_BRANCH: master '\n"
     ]
    }
   ],
   "source": [
    "# Cadged from https://gist.github.com/rwb27/c2ea3afb204a634f9f21a99bd8dd1541\n",
    "def _extract_raw_from_jpeg(jpeg_filename):\n",
    "    ''' Make a fake camera and use it to set up the PiBayerArray stream, \n",
    "        then write the jpeg contents to it to get it to extract the raw bayer data\n",
    "    '''\n",
    "    class DummyCam(object):\n",
    "        full_resolution = (3280,2464)\n",
    "        resolution = full_resolution\n",
    "        revision = 'IMX219'\n",
    "        sensor_mode = 0\n",
    "    \n",
    "    with open(jpeg_filename, mode=\"rb\") as file:\n",
    "        jpeg_data = file.read()\n",
    "\n",
    "    cam = DummyCam()\n",
    "    bayer_array = picamera.array.PiBayerArray(cam)\n",
    "    bayer_array.write(jpeg_data)\n",
    "    bayer_array.flush()\n",
    "    \n",
    "    return bayer_array.array\n",
    "\n",
    "def picamera_capture_as_jpeg_extract_to_tiff(iso=100, shutter_speed=int(0.01 * 1000 * 1000), compress_level=1):\n",
    "    filename_root = f'picamera_ss{shutter_speed}_iso{iso}_compress{compress_level}'\n",
    "    jpeg_filename = f'{filename_root}.jpeg'\n",
    "    tiff_filename = f'{filename_root}.tiff'\n",
    "    \n",
    "    # 1. First take an image and save it as a JPEG+RAW\n",
    "    with picamera.PiCamera(framerate=1) as camera:      \n",
    "        camera.awb_mode = 'off'\n",
    "        # I think this would use Pagnutti's numbers\n",
    "        # camera.awb_gains = (1.307,1.615) \n",
    "\n",
    "        camera.iso = iso\n",
    "        camera.shutter_speed = shutter_speed\n",
    "\n",
    "        camera.capture(jpeg_filename, bayer=True)\n",
    "        \n",
    "        print_camera_settings(camera, 'Camera settings after capture', shutter_speed)\n",
    "        \n",
    "        camera.framerate = 1  # Hack to make camera close properly (https://github.com/waveform80/picamera/issues/528)\n",
    "    \n",
    "    # 2. Then crack open that JPEG, and read out the RAW and EXIF data, save to TIFF\n",
    "    raw_image = _extract_raw_from_jpeg(jpeg_filename)\n",
    "    exif = _read_exif_tags(jpeg_filename)\n",
    "    \n",
    "    tifffile.imsave(tiff_filename, raw_image.astype(np.uint16) * BIT_DEPTH_SCALE_FACTOR, compress=compress_level)\n",
    "    \n",
    "    # Unfortunately... I haven't found a way to write EXIF data to TIFF!\n",
    "    print('----\\nEXIF data:\\n----')\n",
    "    for tag, value in exif.items():\n",
    "        print(f'{tag}: {value}')\n",
    "\n",
    "picamera_capture_as_jpeg_extract_to_tiff()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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 }
	{
	"cells": [
	{
	"cell_type": "code",
	"execution_count": 18,
	"metadata": {},
	"outputs": [],
	"source": [
	"from fractions import Fraction\n",
	"import time\n",
	"\n",
	"import picamera\n",
	"import picamera.array\n",
	"import numpy as np\n",
	"import tifffile"
	]
	},
	{
	"cell_type": "code",
	"execution_count": null,
	"metadata": {},
	"outputs": [],
	"source": [
	"def print_camera_settings(camera, context_msg='', requested_shutter_speed=None):\n",
	" print('\\n----')\n",
	" print(context_msg)\n",
	" print('----')\n",
	" print('sensor_mode:', camera.sensor_mode)\n",
	" print('Requested shutter speed:', requested_shutter_speed)\n",
	" print('shutter_speed:', camera.shutter_speed)\n",
	" print('exposure_speed:', camera.exposure_speed) # Docs: \"returns the shutter speed currently being used by the camera.\"\n",
	" print('iso:', camera.iso)\n",
	" print('framerate:', camera.framerate)\n",
	" print('analog_gain:', camera.analog_gain)\n",
	" print('digital_gain:', camera.digital_gain)"
	]
	},
	{
	"cell_type": "markdown",
	"metadata": {},
	"source": [
	"# Bit Depths\n",
	"Our images are captured with 10-bits, but we want to save them in image formats with larger bit depths. By applying a scaling factor, we can make our saved images look roughly the correct brightness\n"
	]
	},
	{
	"cell_type": "code",
	"execution_count": 45,
	"metadata": {},
	"outputs": [],
	"source": [
	"CAPTURED_IMAGE_BIT_DEPTH = 2 ** 10\n",
	"IMAGE_FORMAT_BIT_DEPTH = 2 ** 16\n",
	"BIT_DEPTH_SCALE_FACTOR = int(IMAGE_FORMAT_BIT_DEPTH / CAPTURED_IMAGE_BIT_DEPTH)"
	]
	},
	{
	"cell_type": "markdown",
	"metadata": {},
	"source": [
	"# Use PiBayerArray to save directly to TIFF\n",
	"This example shows how to capture directly to a numpy array using the PiBayerArray stream.\n",
	"\n",
	"The downside is that (as far as I can tell) this means that EXIF data doesn't get recorded anywere"
	]
	},
	{
	"cell_type": "code",
	"execution_count": 46,
	"metadata": {},
	"outputs": [
	{
	"name": "stdout",
	"output_type": "stream",
	"text": [
	"\n",
	"----\n",
	"Camera settings after capture\n",
	"----\n",
	"sensor_mode: 0\n",
	"Requested shutter speed: 500000\n",
	"shutter_speed: 499982\n",
	"exposure_speed: 499982\n",
	"iso: 400\n",
	"framerate: 1\n",
	"analog_gain: 1311/256\n",
	"digital_gain: 1/64\n",
	"\n",
	"Done!\n"
	]
	}
	],
	"source": [
	"def picamera_capture_to_bayer_stream_to_tiff(iso=100, shutter_speed=int(0.01 * 1000 * 1000), compression_level=1):\n",
	" filename_root = f'picamera_ss{shutter_speed}_iso{iso}_compress{compression_level}'\n",
	" tiff_filename = f'{filename_root}.tiff'\n",
	" \n",
	" with picamera.PiCamera(framerate=1) as camera: \n",
	" camera.awb_mode = 'off'\n",
	" # I think this would use Pagnutti's numbers\n",
	" # camera.awb_gains = (1.307,1.615) \n",
	"\n",
	" camera.iso = iso\n",
	" camera.shutter_speed = shutter_speed\n",
	"\n",
	" with picamera.array.PiBayerArray(camera) as stream:\n",
	" camera.capture(stream, 'jpeg', bayer=True) # To get bayer data, the image must be captured to the 'jpeg' format\n",
	"\n",
	" print_camera_settings(camera, 'Camera settings after capture', shutter_speed)\n",
	"\n",
	" tifffile.imsave(tiff_filename, stream.array.astype(np.uint16) * BIT_DEPTH_SCALE_FACTOR, compress=compression_level)\n",
	"\n",
	" camera.framerate = 1 # Hack to make camera close properly (https://github.com/waveform80/picamera/issues/528)\n",
	" \n",
	" print('\\nDone!')\n",
	" \n",
	"picamera_capture_to_bayer_stream_to_tiff(iso=400, shutter_speed=int(0.5 * 1000 * 1000))"
	]
	},
	{
	"cell_type": "markdown",
	"metadata": {},
	"source": [
	"# Save as JPEG+RAW, use PiBayerArray to extract RAW\n",
	"This example shows how to capture to a JPEG+RAW file (just like raspistill!), then crack that file back open and extract the raw using PiBayerArray. (Based on this random person's gist I found)\n",
	"\n",
	"The advantage to this approach is that the EXIF data gets saved in the .jpeg, and then we can (theoretically)"
	]
	},
	{
	"cell_type": "code",
	"execution_count": 23,
	"metadata": {},
	"outputs": [],
	"source": [
	"import PIL.Image\n",
	"import PIL.ExifTags\n",
	"\n",
	"def _read_exif_tags(image_path):\n",
	" '''\n",
	" Uses (an \"experimental\" private function from) PIL to read EXIF tags from an image file.\n",
	" Returns a dictionary of tag names to values\n",
	" '''\n",
	" PIL_image = PIL.Image.open(image_path)\n",
	" EXIF_CODES_TO_NAMES = PIL.ExifTags.TAGS\n",
	" # _getexif() returns a dictionary of {tag code: tag value}. Use PIL.ExifTags.TAGS dictionary of {tag code: tag name}\n",
	" # to construct a more digestible dictionary of {tag name: tag value}\n",
	" tags = {\n",
	" EXIF_CODES_TO_NAMES[tag_code]: tag_value\n",
	" for tag_code, tag_value in PIL_image._getexif().items()\n",
	" if tag_code in EXIF_CODES_TO_NAMES\n",
	" }\n",
	" return tags"
	]
	},
	{
	"cell_type": "code",
	"execution_count": 32,
	"metadata": {},
	"outputs": [
	{
	"name": "stdout",
	"output_type": "stream",
	"text": [
	"\n",
	"----\n",
	"Camera settings after capture\n",
	"----\n",
	"sensor_mode: 0\n",
	"Requested shutter speed: 10000\n",
	"shutter_speed: 9991\n",
	"exposure_speed: 9991\n",
	"iso: 100\n",
	"framerate: 1\n",
	"analog_gain: 331/128\n",
	"digital_gain: 105/128\n",
	"----\n",
	"EXIF data:\n",
	"----\n",
	"ImageWidth: 720\n",
	"ImageLength: 480\n",
	"ResolutionUnit: 2\n",
	"ExifOffset: 192\n",
	"Make: RaspberryPi\n",
	"Model: RP_imx219\n",
	"DateTime: 2018:11:15 17:38:41\n",
	"YCbCrPositioning: 1\n",
	"XResolution: (72, 1)\n",
	"YResolution: (72, 1)\n",
	"ExifVersion: b'0220'\n",
	"ComponentsConfiguration: b'\\x01\\x02\\x03\\x00'\n",
	"ShutterSpeedValue: (6645155, 1000000)\n",
	"DateTimeOriginal: 2018:11:15 17:38:41\n",
	"DateTimeDigitized: 2018:11:15 17:38:41\n",
	"ApertureValue: (20000, 10000)\n",
	"BrightnessValue: (8, 100)\n",
	"MaxApertureValue: (20000, 10000)\n",
	"MeteringMode: 2\n",
	"Flash: 0\n",
	"FocalLength: (30390, 10000)\n",
	"ColorSpace: 1\n",
	"ExifImageWidth: 720\n",
	"ExifInteroperabilityOffset: 906\n",
	"ExifImageHeight: 480\n",
	"ExposureTime: (9991, 1000000)\n",
	"FNumber: (20000, 10000)\n",
	"ExposureProgram: 3\n",
	"ISOSpeedRatings: 100\n",
	"ExposureMode: 0\n",
	"FlashPixVersion: b'0100'\n",
	"WhiteBalance: 0\n",
	"MakerNote: b'ev=-1 mlux=-1 exp=9991 ag=469 focus=255 gain_r=0.000 gain_b=0.000 greenness=0 ccm=6022,-2314,394,-936,4728,310,300,-4324,8126,0,0,0 md=0 tg=2454 7480 oth=0 0 b=0 f=2454 7480 fi=0 ISP Build Date: Jun 7 2018, 15:36:07 VC_BUILD_ID_VERSION: 4800f08a139d6ca1c5ecbee345ea6682e2160881 (clean) VC_BUILD_ID_USER: dc4 VC_BUILD_ID_BRANCH: master '\n"
	]
	}
	],
	"source": [
	"# Cadged from https://gist.github.com/rwb27/c2ea3afb204a634f9f21a99bd8dd1541\n",
	"def _extract_raw_from_jpeg(jpeg_filename):\n",
	" ''' Make a fake camera and use it to set up the PiBayerArray stream, \n",
	" then write the jpeg contents to it to get it to extract the raw bayer data\n",
	" '''\n",
	" class DummyCam(object):\n",
	" full_resolution = (3280,2464)\n",
	" resolution = full_resolution\n",
	" revision = 'IMX219'\n",
	" sensor_mode = 0\n",
	" \n",
	" with open(jpeg_filename, mode=\"rb\") as file:\n",
	" jpeg_data = file.read()\n",
	"\n",
	" cam = DummyCam()\n",
	" bayer_array = picamera.array.PiBayerArray(cam)\n",
	" bayer_array.write(jpeg_data)\n",
	" bayer_array.flush()\n",
	" \n",
	" return bayer_array.array\n",
	"\n",
	"def picamera_capture_as_jpeg_extract_to_tiff(iso=100, shutter_speed=int(0.01 * 1000 * 1000), compress_level=1):\n",
	" filename_root = f'picamera_ss{shutter_speed}_iso{iso}_compress{compress_level}'\n",
	" jpeg_filename = f'{filename_root}.jpeg'\n",
	" tiff_filename = f'{filename_root}.tiff'\n",
	" \n",
	" # 1. First take an image and save it as a JPEG+RAW\n",
	" with picamera.PiCamera(framerate=1) as camera: \n",
	" camera.awb_mode = 'off'\n",
	" # I think this would use Pagnutti's numbers\n",
	" # camera.awb_gains = (1.307,1.615) \n",
	"\n",
	" camera.iso = iso\n",
	" camera.shutter_speed = shutter_speed\n",
	"\n",
	" camera.capture(jpeg_filename, bayer=True)\n",
	" \n",
	" print_camera_settings(camera, 'Camera settings after capture', shutter_speed)\n",
	" \n",
	" camera.framerate = 1 # Hack to make camera close properly (https://github.com/waveform80/picamera/issues/528)\n",
	" \n",
	" # 2. Then crack open that JPEG, and read out the RAW and EXIF data, save to TIFF\n",
	" raw_image = _extract_raw_from_jpeg(jpeg_filename)\n",
	" exif = _read_exif_tags(jpeg_filename)\n",
	" \n",
	" tifffile.imsave(tiff_filename, raw_image.astype(np.uint16) * BIT_DEPTH_SCALE_FACTOR, compress=compress_level)\n",
	" \n",
	" # Unfortunately... I haven't found a way to write EXIF data to TIFF!\n",
	" print('----\\nEXIF data:\\n----')\n",
	" for tag, value in exif.items():\n",
	" print(f'{tag}: {value}')\n",
	"\n",
	"picamera_capture_as_jpeg_extract_to_tiff()"
	]
	},
	{
	"cell_type": "code",
	"execution_count": null,
	"metadata": {},
	"outputs": [],
	"source": []
	}
	],
	"metadata": {
	"kernelspec": {
	"display_name": "Python 3",
	"language": "python",
	"name": "python3"
	},
	"language_info": {
	"codemirror_mode": {
	"name": "ipython",
	"version": 3
	},
	"file_extension": ".py",
	"mimetype": "text/x-python",
	"name": "python",
	"nbconvert_exporter": "python",
	"pygments_lexer": "ipython3",
	"version": "3.6.5"
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