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市区町村のNDVI

livebooks/tellus/city_ndvi.livemd

Ryo Wakabayashi

@RyoWakabayashi

elixir-learning

More notebooks

市区町村のNDVI

Mix.install(
  [
    {:nx, "~> 0.6"},
    {:evision, "~> 0.1.33"},
    {:exla, "~> 0.6"},
    {:geo, "~> 3.5"},
    {:jason, "~> 1.4"},
    {:kino, "~> 0.12"},
    {:kino_maplibre, "~> 0.1"},
    {:kino_vega_lite, "~> 0.1"}
  ],
  config: [
    nx: [
      default_backend: EXLA.Backend
    ]
  ]
)

データの指定

提供：だいち(ALOS)　AVNIR-2　データ(JAXA)

だいち(ALOS) AVNIR-2 の仕様はこちら

https://www.eorc.jaxa.jp/ALOS/jp/alos/sensor/avnir2_j.htm

scene_id_list = [
  "202ce08d-ba4b-4ffe-8165-109fd3a8b917",
  "34d8dc6f-fdd1-4542-a038-c1235a5a97fa",
  "12ad308b-6ce1-40ec-9ebf-f0215c30500e",
  "e2e85b2e-a208-4a65-87fd-b92721b037a8",
  "208a3618-7700-421b-bf05-fd59551cc1aa",
  "d5ce7320-5b25-4ced-bda5-0e25a9d75940",
  "9d14706f-cee7-4eb4-9151-2558609c3de0",
  "3f4555ac-eaf3-4066-a1ba-20bb1ec1c0b3"
]

ヘッダーファイルの読込

ヘッダーファイルの仕様はこちら

defmodule Coordinate do
  defstruct latitude: 0.0, longitude: 0.0
end

defmodule BandInfo do
  defstruct gain: 0.0, offset: 0.0
end

defmodule Affine do
  defstruct a: 0.0, b: 0.0, c: 0.0, d: 0.0
end

defmodule Conversion do
  defstruct x: 0.0, y: 0.0
end

defmodule HeaderInfo do
  defstruct blue_band: %BandInfo{},
            green_band: %BandInfo{},
            red_band: %BandInfo{},
            nir_band: %BandInfo{},
            center: %Coordinate{},
            left_top: %Coordinate{},
            right_top: %Coordinate{},
            left_bottom: %Coordinate{},
            right_bottom: %Coordinate{},
            affine: %Affine{},
            conversion: %Conversion{},
            degree: 0.0,
            map_degree: 0.0,
            datetime: nil,
            product_id: ""

  def get_string(info, start, value) do
    info
    |> String.slice(start, value)
    |> String.trim()
  end

  def get_value(info, start, value) do
    info
    |> get_string(start, value)
    |> String.to_float()
  end

  def read(hdr_file_path) do
    info = File.read!(hdr_file_path)

    %HeaderInfo{
      # 青色光バンド
      blue_band: %BandInfo{
        gain: get_value(info, 1721, 8),
        offset: get_value(info, 1729, 8)
      },
      # 緑色光バンド
      green_band: %BandInfo{
        gain: get_value(info, 1737, 8),
        offset: get_value(info, 1745, 8)
      },
      # 赤色光バンド
      red_band: %BandInfo{
        gain: get_value(info, 1752, 8),
        offset: get_value(info, 1760, 8)
      },
      # 近赤外線バンド
      nir_band: %BandInfo{
        gain: get_value(info, 1768, 8),
        offset: get_value(info, 1776, 8)
      },
      # 画像中央
      center: %Coordinate{
        latitude: get_value(info, 248, 16),
        longitude: get_value(info, 264, 16)
      },
      # 画像左上
      left_top: %Coordinate{
        latitude: get_value(info, 376, 16),
        longitude: get_value(info, 392, 16)
      },
      # 画像右上
      right_top: %Coordinate{
        latitude: get_value(info, 408, 16),
        longitude: get_value(info, 424, 16)
      },
      # 画像左下
      left_bottom: %Coordinate{
        latitude: get_value(info, 440, 16),
        longitude: get_value(info, 456, 16)
      },
      # 画像右下
      right_bottom: %Coordinate{
        latitude: get_value(info, 472, 16),
        longitude: get_value(info, 488, 16)
      },
      affine: %Affine{
        a: get_value(info, 1224, 16),
        b: get_value(info, 1240, 16),
        c: get_value(info, 1256, 16),
        d: get_value(info, 1272, 16)
      },
      conversion: %Conversion{
        x: get_value(info, 1208, 8),
        y: get_value(info, 1216, 8)
      },
      degree: get_value(info, 760, 16),
      map_degree: get_value(info, 921, 16),
      datetime:
        info
        |> get_string(192, 24)
        |> then(fn str ->
          String.slice(str, 0, 4) <>
            "-" <>
            String.slice(str, 4, 2) <>
            "-" <>
            String.slice(str, 6, 2) <>
            "T" <>
            String.slice(str, 8, 2) <>
            ":" <>
            String.slice(str, 10, 2) <>
            ":" <> String.slice(str, 12, 2)
        end)
        |> NaiveDateTime.from_iso8601!(),
      product_id: get_string(info, 128, 16)
    }
  end
end

NDVIの算出

defmodule NDVI do
  def read_header(file_path_list) do
    file_path_list
    |> Enum.find(fn file -> Path.extname(file) == ".txt" end)
    |> HeaderInfo.read()
  end

  def get_band_tensor(file_path_list, prefix) do
    file_path_list
    |> Enum.find(fn file ->
      file
      |> Path.basename()
      |> String.starts_with?(prefix)
    end)
    |> Evision.imread(flags: Evision.Constant.cv_IMREAD_GRAYSCALE())
    |> Evision.Mat.to_nx(EXLA.Backend)
  end

  def calc(file_path_list) do
    header_info = read_header(file_path_list)

    red_tensor =
      file_path_list
      |> get_band_tensor("IMG-03")
      |> Nx.multiply(header_info.red_band.gain)
      |> Nx.add(header_info.red_band.offset)

    nir_tensor =
      file_path_list
      |> get_band_tensor("IMG-04")
      |> Nx.multiply(header_info.nir_band.gain)
      |> Nx.add(header_info.nir_band.offset)

    ndvi_tensor =
      Nx.select(
        Nx.multiply(
          Nx.not_equal(red_tensor, 0),
          Nx.not_equal(nir_tensor, 0)
        ),
        Nx.divide(
          Nx.subtract(nir_tensor, red_tensor),
          Nx.add(nir_tensor, red_tensor)
        ),
        0
      )

    {header_info, ndvi_tensor}
  end
end

ndvi_list =
  scene_id_list
  |> Enum.map(fn scene_id ->
    "/tmp/#{scene_id}"
    |> File.ls!()
    |> Enum.map(fn filename -> Path.join(["/tmp", scene_id, filename]) end)
    |> NDVI.calc()
  end)

{header_info, ndvi_tensor} = Enum.at(ndvi_list, 0)

ndvi_map =
  ndvi_tensor
  |> Nx.multiply(128)
  |> Nx.add(128)
  |> Nx.as_type(:u8)
  |> Evision.Mat.from_nx_2d()
  |> Evision.applyColorMap(Evision.Constant.cv_COLORMAP_WINTER())

Evision.resize(ndvi_map, {640, 640})

center = {header_info.center.longitude, header_info.center.latitude}

coordinates = [
  [header_info.left_top.longitude, header_info.left_top.latitude],
  [header_info.right_top.longitude, header_info.right_top.latitude],
  [header_info.right_bottom.longitude, header_info.right_bottom.latitude],
  [header_info.left_bottom.longitude, header_info.left_bottom.latitude]
]

# 地図にプロットするために BASE64 エンコードする
get_data_url = fn mat ->
  Evision.imencode(".png", mat)
  |> Base.encode64()
  |> then(&amp;"data:image/png;base64,#{&amp;1}")
end

img_url =
  ndvi_map
  |> Evision.resize({4960, 4960})
  |> get_data_url.()

MapLibre.new(center: center, zoom: 8, style: :terrain)
|> MapLibre.add_source("image", type: :image, url: img_url, coordinates: coordinates)
|> MapLibre.add_layer(id: "overlay", source: "image", type: :raster)

市区町村のポリゴンデータを用意する

青森県の行政区域データを /tmp/GML にダウンロードしておく

出典: 「国土数値情報（行政区域データ）」（国土交通省）（https://nlftp.mlit.go.jp/ksj/gml/datalist/KsjTmplt-N03-v3_1.html）を加工して作成

gml_dir = "/tmp/GML"

geojson_file =
  gml_dir
  # ファイル一覧取得
  |> File.ls!()
  # `.geojson` で終わるもののうち先頭を取得
  |> Enum.find(&amp;String.ends_with?(&amp;1, ".geojson"))

geojson_data =
  [gml_dir, geojson_file]
  |> Path.join()
  |> File.read!()
  |> Jason.decode!()
  |> Geo.JSON.decode!()

行政コード = 02361 (藤崎町)のデータを取得する

city_geojson = %Geo.GeometryCollection{
  geometries: Enum.filter(geojson_data.geometries, &amp;(&amp;1.properties["N03_007"] == "02361"))
}

city_map =
  MapLibre.new(center: {140.5, 40.68}, zoom: 11, style: :terrain)
  |> MapLibre.add_geo_source("city_geojson", city_geojson)
  |> MapLibre.add_layer(
    id: "city_geojson",
    source: "city_geojson",
    type: :fill,
    paint: [fill_color: "#00ff00", fill_opacity: 0.5]
  )

NDVI画像の回転

{ndvi_height, ndvi_width, 3} = Evision.Mat.shape(ndvi_map)

header_info.degree

wrap_rotate = fn mat, degree ->
  # 元の大きさ
  {src_height, src_width, 3} = mat.shape

  # 四隅がはみ出ることを考慮しない回転のアフィン変換
  affine =
    {src_width / 2, src_height / 2}
    |> Evision.getRotationMatrix2D(degree, 1)
    |> Evision.Mat.to_nx(EXLA.Backend)

  # 回転後に四隅を画像内に含むためのサイズを計算
  cos = Nx.abs(affine[[0, 0]])
  sin = Nx.abs(affine[[0, 1]])

  dst_width =
    Nx.add(Nx.multiply(src_height, sin), Nx.multiply(src_width, cos))
    |> Nx.to_number()
    |> trunc()

  dst_height =
    Nx.add(Nx.multiply(src_height, cos), Nx.multiply(src_width, sin))
    |> Nx.to_number()
    |> trunc()

  # (変換後サイズ - 変更前サイズ) / 2 の分だけずらして画像の中心を回転の中心に合わせる
  bias =
    Nx.tensor([
      [0, 0, (dst_width - src_width) / 2],
      [0, 0, (dst_height - src_height) / 2]
    ])

  # 四隅を画像内に含めるアフィン変換
  new_affine = Nx.add(affine, bias)

  Evision.warpAffine(mat, new_affine, {dst_width, dst_height})
end

rotated_map = wrap_rotate.(ndvi_map, -header_info.degree)

Evision.resize(rotated_map, {640, 640})

上辺と下辺の差を計算する

diff_longitude =
  header_info.left_top.longitude - header_info.right_top.longitude -
    (header_info.left_bottom.longitude - header_info.right_bottom.longitude)

1ピクセルあたりの緯度経度を計算する

ndvi_longitudes = [
  header_info.left_top.longitude,
  header_info.right_top.longitude,
  header_info.left_bottom.longitude,
  header_info.right_bottom.longitude
]

ndvi_latitudes = [
  header_info.left_top.latitude,
  header_info.right_top.latitude,
  header_info.left_bottom.latitude,
  header_info.right_bottom.latitude
]

ndvi_min_longitude = Enum.min(ndvi_longitudes)
ndvi_max_longitude = Enum.max(ndvi_longitudes)
ndvi_min_latitude = Enum.min(ndvi_latitudes)
ndvi_max_latitude = Enum.max(ndvi_latitudes)

{ndvi_min_longitude, ndvi_max_longitude, ndvi_min_latitude, ndvi_max_latitude}

{ndvi_height, ndvi_width, 3} = Evision.Mat.shape(rotated_map)

pix_per_longitude = ndvi_width / (ndvi_max_longitude - ndvi_min_longitude)
pix_per_latitude = ndvi_height / (ndvi_max_latitude - ndvi_min_latitude)

{pix_per_longitude, pix_per_latitude}

横方向への補正値を計算する

diff_x = trunc(diff_longitude / 2 * pix_per_longitude)

補正値の分だけ水平移動する

affine =
  [
    [1, 0, diff_x],
    [0, 1, 0]
  ]
  |> Nx.tensor()
  |> Nx.as_type(:f32)

corrected_map = Evision.warpAffine(rotated_map, affine, {ndvi_width, ndvi_height})

Evision.resize(corrected_map, {640, 640})

マスク画像による切り抜き

# 緯度経度の最大最小を求める
city_coordinates =
  city_geojson.geometries
  |> Enum.map(&amp; &amp;1.coordinates)
  |> List.flatten()

city_longitudes = Enum.map(city_coordinates, &amp;elem(&amp;1, 0))
city_latitudes = Enum.map(city_coordinates, &amp;elem(&amp;1, 1))

city_min_longitude = Enum.min(city_longitudes)
city_max_longitude = Enum.max(city_longitudes)
city_min_latitude = Enum.min(city_latitudes)
city_max_latitude = Enum.max(city_latitudes)

{city_min_longitude, city_max_longitude, city_min_latitude, city_max_latitude}

# 最大最小の差からマスク画像の大きさを求める
city_width = trunc((city_max_longitude - city_min_longitude) * pix_per_longitude)
city_height = trunc((city_max_latitude - city_min_latitude) * pix_per_latitude)

{city_width, city_height}

# 緯度経度の最小から最大をピクセル数の0から幅・高さにスケールする
normalized_points =
  city_geojson.geometries
  |> Enum.map(&amp; &amp;1.coordinates)
  |> Enum.map(fn coordinate ->
    coordinate
    |> Enum.at(0)
    |> Enum.map(fn {x, y} ->
      [
        trunc((x - city_min_longitude) * pix_per_longitude),
        # 縦方向は緯度が北緯の場合逆転するため、高さから引く
        trunc(city_height - (y - city_min_latitude) * pix_per_latitude)
      ]
    end)
    |> Nx.tensor(type: :s32)
  end)

# 空画像を用意する
empty_mat =
  [0, 0, 0, 255]
  |> Nx.tensor(type: :u8)
  |> Nx.tile([city_height, city_width, 1])
  |> Evision.Mat.from_nx_2d()

Evision.resize(empty_mat, {640, 640})

# ポリゴンを透明色で塗りつぶす
mask_mat = Evision.fillPoly(empty_mat, normalized_points, {0, 0, 0, 0})

Evision.resize(mask_mat, {640, 640})

地図へのプロット

city_center = {
  (city_min_longitude + city_max_longitude) / 2,
  (city_min_latitude + city_max_latitude) / 2
}

city_bbox_coordinates = [
  [city_min_longitude, city_max_latitude],
  [city_max_longitude, city_max_latitude],
  [city_max_longitude, city_min_latitude],
  [city_min_longitude, city_min_latitude]
]

image_url =
  mask_mat
  |> Evision.resize({trunc(city_height / 4), trunc(city_width / 4)})
  |> get_data_url.()

MapLibre.new(center: city_center, zoom: 11, style: :terrain)
|> MapLibre.add_source("city_mask",
  type: :image,
  url: image_url,
  coordinates: city_bbox_coordinates
)
|> MapLibre.add_layer(id: "overlay", source: "city_mask", type: :raster)

NDVI を行政区域で切り抜く

# 緯度経度を元に NDVI 画像内の行政区域の位置を計算する
city_left_top_x = trunc((city_min_longitude - ndvi_min_longitude) * pix_per_longitude)
city_left_top_y = trunc((ndvi_max_latitude - city_max_latitude) * pix_per_latitude)

{city_left_top_x, city_left_top_y}

city_ndvi_bbox_map =
  corrected_map
  |> Evision.Mat.to_nx(EXLA.Backend)
  |> then(
    &amp; &amp;1[
      [
        city_left_top_y..(city_left_top_y + city_height - 1),
        city_left_top_x..(city_left_top_x + city_width - 1)
      ]
    ]
  )
  |> Evision.Mat.from_nx_2d()

mask_mat
|> Evision.Mat.to_nx(EXLA.Backend)
|> Nx.slice_along_axis(3, 1, axis: 2)
|> Nx.tile([3])
|> Nx.select(0, Evision.Mat.to_nx(city_ndvi_bbox_map, EXLA.Backend))
|> Nx.as_type(:u8)
|> Evision.Mat.from_nx_2d()

時系列による推移

defmodule CityNDVI do
  def get_lat_lon(header_info) do
    ndvi_longitudes = [
      header_info.left_top.longitude,
      header_info.right_top.longitude,
      header_info.left_bottom.longitude,
      header_info.right_bottom.longitude
    ]

    ndvi_latitudes = [
      header_info.left_top.latitude,
      header_info.right_top.latitude,
      header_info.left_bottom.latitude,
      header_info.right_bottom.latitude
    ]

    ndvi_min_longitude = Enum.min(ndvi_longitudes)
    ndvi_max_longitude = Enum.max(ndvi_longitudes)
    ndvi_min_latitude = Enum.min(ndvi_latitudes)
    ndvi_max_latitude = Enum.max(ndvi_latitudes)

    {ndvi_min_longitude, ndvi_max_longitude, ndvi_min_latitude, ndvi_max_latitude}
  end

  def wrap_rotate(tensor, degree) do
    {src_height, src_width} = Nx.shape(tensor)

    affine =
      {src_width / 2, src_height / 2}
      |> Evision.getRotationMatrix2D(degree, 1)
      |> Evision.Mat.to_nx(EXLA.Backend)

    cos = Nx.abs(affine[[0, 0]])
    sin = Nx.abs(affine[[0, 1]])

    dst_width =
      Nx.add(Nx.multiply(src_height, sin), Nx.multiply(src_width, cos))
      |> Nx.to_number()
      |> trunc()

    dst_height =
      Nx.add(Nx.multiply(src_height, cos), Nx.multiply(src_width, sin))
      |> Nx.to_number()
      |> trunc()

    bias =
      Nx.tensor([
        [0, 0, (dst_width - src_width) / 2],
        [0, 0, (dst_height - src_height) / 2]
      ])

    new_affine = Nx.add(affine, bias)

    Evision.warpAffine(tensor, new_affine, {dst_width, dst_height})
  end

  def correct(ndvi_tensor, header_info, ndvi_lat_lon) do
    {ndvi_min_longitude, ndvi_max_longitude, _, _} = ndvi_lat_lon

    rotated_mat = wrap_rotate(ndvi_tensor, -header_info.degree)

    diff_longitude =
      header_info.left_top.longitude - header_info.right_top.longitude -
        (header_info.left_bottom.longitude - header_info.right_bottom.longitude)

    {ndvi_height, ndvi_width} = rotated_mat.shape

    pix_per_longitude = ndvi_width / (ndvi_max_longitude - ndvi_min_longitude)

    diff_x = trunc(diff_longitude / 2 * pix_per_longitude)

    affine =
      [
        [1, 0, diff_x],
        [0, 1, 0]
      ]
      |> Nx.tensor()
      |> Nx.as_type(:f32)

    Evision.warpAffine(rotated_mat, affine, {ndvi_width, ndvi_height})
  end

  def get_city_bbox(corrected_mat, mask_mat, city_geojson, ndvi_lat_lon) do
    {ndvi_min_longitude, ndvi_max_longitude, ndvi_min_latitude, ndvi_max_latitude} = ndvi_lat_lon

    city_coordinates =
      city_geojson.geometries
      |> Enum.map(&amp; &amp;1.coordinates)
      |> List.flatten()

    city_longitudes = Enum.map(city_coordinates, &amp;elem(&amp;1, 0))
    city_latitudes = Enum.map(city_coordinates, &amp;elem(&amp;1, 1))

    city_min_longitude = Enum.min(city_longitudes)
    city_max_latitude = Enum.max(city_latitudes)

    {ndvi_height, ndvi_width} = corrected_mat.shape

    pix_per_longitude = ndvi_width / (ndvi_max_longitude - ndvi_min_longitude)
    pix_per_latitude = ndvi_height / (ndvi_max_latitude - ndvi_min_latitude)

    {city_height, city_width, 4} = mask_mat.shape

    city_left_top_x = trunc((city_min_longitude - ndvi_min_longitude) * pix_per_longitude)
    city_left_top_y = trunc((ndvi_max_latitude - city_max_latitude) * pix_per_latitude)

    corrected_mat
    |> Evision.Mat.to_nx(EXLA.Backend)
    |> then(
      &amp; &amp;1[
        [
          city_left_top_y..(city_left_top_y + city_height - 1),
          city_left_top_x..(city_left_top_x + city_width - 1)
        ]
      ]
    )
  end

  def crop(city_bbox, mask_mat) do
    mask_mat
    |> Evision.Mat.to_nx(EXLA.Backend)
    |> Nx.slice_along_axis(3, 1, axis: 2)
    |> Nx.select(0, city_bbox)
  end

  def get_city_ndvi(ndvi_tensor, header_info, mask_mat, city_geojson) do
    ndvi_lat_lon = get_lat_lon(header_info)

    corrected_mat = correct(ndvi_tensor, header_info, ndvi_lat_lon)

    city_bbox = get_city_bbox(corrected_mat, mask_mat, city_geojson, ndvi_lat_lon)

    city_mean_ndvi =
      mask_mat
      |> Evision.Mat.to_nx(EXLA.Backend)
      |> Nx.slice_along_axis(3, 1, axis: 2)
      |> Nx.squeeze()
      # マスク内だけで平均する
      |> Nx.select(0, 1)
      |> then(&amp;Nx.weighted_mean(city_bbox, &amp;1))
      |> Nx.to_number()

    city_ndvi_map =
      city_bbox
      |> Nx.multiply(128)
      |> Nx.add(128)
      |> Nx.as_type(:u8)
      |> Evision.applyColorMap(Evision.Constant.cv_COLORMAP_WINTER())
      |> Evision.Mat.to_nx(EXLA.Backend)

    croped_city_ndvi_map =
      mask_mat
      |> Evision.Mat.to_nx(EXLA.Backend)
      |> Nx.slice_along_axis(3, 1, axis: 2)
      |> Nx.tile([3])
      |> Nx.select(0, city_ndvi_map)
      |> Nx.as_type(:u8)

    {city_mean_ndvi, croped_city_ndvi_map}
  end
end

city_ndvi_list =
  ndvi_list
  |> Enum.map(fn {header_info, ndvi_tensor} ->
    # 観測日をタブにする
    date =
      header_info.datetime
      |> NaiveDateTime.to_iso8601()
      |> String.slice(0..9)

    IO.inspect(date)

    {city_ndvi, city_ndvi_map} =
      CityNDVI.get_city_ndvi(ndvi_tensor, header_info, mask_mat, city_geojson)

    {date, city_ndvi, city_ndvi_map}
  end)

city_ndvi_list
|> Enum.map(fn {date, _, city_ndvi_map} ->
  {date, city_ndvi_map |> Nx.reverse(axes: [2]) |> Kino.Image.new()}
end)
|> Kino.Layout.tabs()

plot_data =
  city_ndvi_list
  |> Enum.map(fn {date, city_mean_ndvi, _} ->
    %{
      date: date,
      ndvi: city_mean_ndvi
    }
  end)

VegaLite.new(width: 700)
|> VegaLite.data_from_values(plot_data)
|> VegaLite.mark(:bar)
|> VegaLite.encode_field(:x, "date", type: :temporal)
|> VegaLite.encode_field(:y, "ndvi", type: :quantitative)

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