def gen_img_samples(src, chunk_size, *band_order):
"""
Args:
src: input image (rasterio object)
chunk_size: image tile size
*band_order: ignore
Returns: generator object
"""
subdiv = 2.0
step = int(chunk_size / subdiv)
for row in range(0, src.height, step):
for column in range(0, src.width, step):
window = Window.from_slices(slice(row, row + chunk_size),
slice(column, column + chunk_size))
if band_order:
window_array = reshape_as_image(
src.read(band_order[0], window=window))
else:
window_array = reshape_as_image(src.read(window=window))
if window_array.shape[0] < chunk_size or window_array.shape[
1] < chunk_size:
window_array = _pad_diff(window_array, window_array.shape[0],
window_array.shape[1], chunk_size)
window_array = _pad(window_array, chunk_size)
yield window_array, row, column
def dtc_pred_stack(model,stack2pred_img,outfile=None):
"""
Function to classfy raster stack image
"""
if type(stack2pred_img)==str:
with rio.open(stack2pred_img) as src:
img = src.read()
profile = src.profile
reshaped_img = reshape_as_image(img)
raster_pred = model.predict(reshaped_img.reshape(-1,len(img)))
class_prediction = raster_pred.reshape(reshaped_img[:, :, 0].shape)
class_prediction = class_prediction + 1
profile.update({'nodata': 0,'dtype': rio.uint8,'count':1})
with rio.open(outfile, 'w', **profile) as dst:
dst.write(class_prediction.astype(rio.uint8), 1)
elif type(stack2pred_img)==np.ndarray:
stack2pred_img[np.isnan(stack2pred_img)]=0
reshaped_img = reshape_as_image(stack2pred_img)
raster_pred = model.predict(reshaped_img.reshape(-1,len(stack2pred_img)))
class_prediction = raster_pred.reshape(reshaped_img[:, :, 0].shape)
class_prediction = class_prediction + 1
return class_prediction.astype(rio.uint8)
def divide_into_pieces(self, filename, image_path, data_path):
os.makedirs(f'{data_path}/images', exist_ok=True)
os.makedirs(f'{data_path}/geojson_polygons', exist_ok=True)
full_mask = imageio.imread(f'{data_path}/full_mask.png')
with rasterio.open(image_path) as src, open(
f'{data_path}/image_pieces.csv', 'w') as csvFile:
writer = csv.writer(csvFile)
writer.writerow([
'original_image', 'piece_image', 'piece_geojson', 'start_x',
'start_y', 'width', 'height'
])
for j in tqdm(range(0, src.height // self.height)):
for i in range(0, src.width // self.width):
raster_window = src.read(
window=Window(i * self.width, j *
self.height, self.width, self.height))
image_array = reshape_as_image(raster_window)[:, :, :3]
is_mask = full_mask[j * self.height:j * self.height +
self.height,
i * self.width:i * self.width +
self.width].sum() > 0
if image_non_zero(image_array) and is_mask:
image_format = 'tiff'
piece_name = f'{filename}_{j}_{i}.{image_format}'
poly = Polygon([
src.xy(j * self.height, i * self.width),
src.xy(j * self.height, (i + 1) * self.width),
src.xy((j + 1) * self.height,
(i + 1) * self.width),
src.xy((j + 1) * self.height, i * self.width),
src.xy(j * self.height, i * self.width)
])
gs = GeoSeries([poly])
gs.crs = src.crs
piece_geojson_name = f'{filename}_{j}_{i}.geojson'
gs.to_file(
f'{data_path}/geojson_polygons/{piece_geojson_name}',
driver='GeoJSON')
image_array = reshape_as_image(raster_window)
meta = src.meta
meta['height'] = image_array.shape[0]
meta['width'] = image_array.shape[1]
with rasterio.open(f'{data_path}/images/{piece_name}',
'w', **meta) as dst:
for ix in range(image_array.shape[2]):
dst.write(image_array[:, :, ix], ix + 1)
writer.writerow([
filename, piece_name, piece_geojson_name,
i * self.width, j * self.height, self.width,
self.height
])
def divide_into_pieces(image_path, save_path, width, height):
if not os.path.exists(save_path):
os.makedirs(save_path, exist_ok=True)
print('Data directory created.')
os.makedirs(f'{save_path}/images', exist_ok=True)
os.makedirs(f'{save_path}/geojson_polygons', exist_ok=True)
with rasterio.open(image_path) as src, open(
f'{save_path}/image_pieces.csv', 'w') as csvFile:
writer = csv.writer(csvFile)
writer.writerow([
'original_image', 'piece_image', 'piece_geojson', 'start_x',
'start_y', 'width', 'height'
])
for j in tqdm(range(0, src.height // height)):
for i in range(0, src.width // width):
raster_window = src.read(window=Window(i * width, j *
height, width, height))
image_array = reshape_as_image(raster_window)[:, :, :3]
if np.count_nonzero(image_array) > image_array.size * 0.9:
filename_w_ext = os.path.basename(image_path)
filename, _ = os.path.splitext(filename_w_ext)
image_format = 'tiff'
piece_name = f'{filename}_{j}_{i}.{image_format}'
poly = Polygon([
src.xy(j * height, i * width),
src.xy(j * height, (i + 1) * width),
src.xy((j + 1) * height, (i + 1) * width),
src.xy((j + 1) * height, i * width),
src.xy(j * height, i * width)
])
gs = GeoSeries([poly])
gs.crs = src.crs
piece_geojson_name = f'{filename}_{j}_{i}.geojson'
gs.to_file(
f'{save_path}/geojson_polygons/{piece_geojson_name}',
driver='GeoJSON')
image_array = reshape_as_image(raster_window)
meta = src.meta
meta['height'] = image_array.shape[0]
meta['width'] = image_array.shape[1]
with rasterio.open(f'{save_path}/images/{piece_name}', 'w',
**meta) as dst:
for ix in range(image_array.shape[2]):
dst.write(image_array[:, :, ix], ix + 1)
dst.close()
writer.writerow([
filename_w_ext, piece_name, piece_geojson_name,
i * width, j * height, width, height
])
csvFile.close()
def predict_raster(img_current,
img_previous,
channels,
network,
model_weights_path,
input_size=56,
neighbours=3):
logging.info(f'network:{network}')
logging.info(f'model_weights_path: {model_weights_path}')
logging.info(f'channels: {channels}')
logging.info(f'neighbours: {neighbours}')
model, device = load_model(network, model_weights_path, channels,
neighbours)
with rasterio.open(img_current) as source_current, \
rasterio.open(img_previous) as source_previous:
meta = source_current.meta
meta['count'] = 1
clearcut_mask = np.zeros((source_current.height, source_current.width))
for i in tqdm(range(source_current.width // input_size)):
for j in range(source_current.height // input_size):
bottom_row = j * input_size
upper_row = (j + 1) * input_size
left_column = i * input_size
right_column = (i + 1) * input_size
corners = [
source_current.xy(bottom_row, left_column),
source_current.xy(bottom_row, right_column),
source_current.xy(upper_row, right_column),
source_current.xy(upper_row, left_column),
source_current.xy(bottom_row, left_column)
]
window = Window(bottom_row, left_column, input_size,
input_size)
image_current = reshape_as_image(
source_current.read(window=window))
image_previous = reshape_as_image(
source_previous.read(window=window))
difference_image = diff(image_current, image_previous)
image_tensor = transforms.ToTensor()(difference_image.astype(
np.uint8)).to(device, dtype=torch.float)
predicted = predict(image_tensor, model, channels, neighbours,
input_size, device)
predicted = mask_postprocess(predicted)
clearcut_mask[left_column:right_column,
bottom_row:upper_row] += predicted
meta['dtype'] = 'float32'
return clearcut_mask.astype(np.float32), meta
def _parse_bytes_gdal_numpyfunc(img_bytes_np, tgt_bytes_np):
with MemoryFile(img_bytes_np) as memfile:
with memfile.open() as src:
img_arr = src.read()
with MemoryFile(tgt_bytes_np) as memfile:
with memfile.open() as src:
target_arr = src.read()
return (reshape_as_image(img_arr).astype(np.float32),
reshape_as_image(target_arr).astype(np.float32))
def show_rgb_with_mask(rgb, mask, alpha=0.5, figsize=(20, 20), title=""):
"""
Show the rgb image overlayed with the mask image with the given alpha value applied
to the mask image
Args:
- rgb (str/Path or np.array):
- if str or Path, it's a path to the rgb file
- if np.array, it's a 1, 3 or 4D numpy.array with (h,w,d,a) dimensions
- mask (str/Path or np.array):
- if str or Path, it's a path to the mask file to overlay on top of the rgb
- if np.array, uint8 type numpy array of the same size of `rgb_arr`
- the image array must be 2 or 3 dimensional. If 3dim, one of the axis will be
assumed to be 1 and flattened out
- alpha (float, [0,1])
- figsize (tuple)
Returns:
- f, ax containing the rgb_arr overlayed by the mask image
"""
f, ax = plt.subplots(figsize=figsize)
# Set axis title
ax_title = "RGB w/ road buffer mask"
if len(title) > 0:
ax_title += ": " + title
ax.set_title(ax_title)
# Read the images if the paths are the input args
if not isinstance(rgb, (str, Path)):
raise TypeError('First input should be a string or path object')
if not isinstance(mask, (str, Path)):
raise TypeError('Second input should be a string or path object')
with rio.open(str(rgb), 'r') as ds:
rgb = reshape_as_image(ds.read())
with rio.open(str(mask), 'r') as ds:
mask = reshape_as_image(ds.read())
if not isinstance(rgb, np.ndarray):
raise TypeError('rgb must be an np array at this point')
if not isinstance(mask, np.ndarray):
raise TypeError('mask must be an np array at this point')
# Show rgb and mask overlay
ax.imshow(rgb)
# remove an empty dimension if mask np.array is 3dimensional
# np.squeeze() is inplace
ax.imshow(np.squeeze(mask), alpha=alpha)
return f, ax
def data_as_image(self) -> numpy.ndarray:
"""Return the data array reshaped into an image processing/visualization software friendly order.
(bands, rows, columns) -> (rows, columns, bands).
"""
return reshape_as_image(self.data)
def clip_advanced(in_raster, in_polygon, cliptype, clipped_raster=""):
"""
Args:
in_raster: raster to be clipped
in_polygon: as
cliptype : either 'bbox', 'shp', 'geojson'
clipped_raster: raster to be saved if not it will .....
"""
with rio.open(in_raster) as src:
out_meta = src.meta
# get clip shape from polygon shape
if cliptype == "shp":
with fiona.open(in_polygon, "r") as polygon:
shapes = [feature["geometry"] for feature in polygon]
# get clip shape from bounding box
elif cliptype == "bbox":
# convert it to a polygon bbox
bbox_pol = box(in_polygon[0], in_polygon[1], in_polygon[2],
in_polygon[3])
# use geopandas to transform the bounding box into a json polygon
geo = gpd.GeoDataFrame({'geometry': bbox_pol},
index=[0],
crs=src.crs)
# convert it to a json polygon
shapes = [json.loads(geo.to_json())['features'][0]['geometry']]
# or getting directly a geojson string (as above)
elif cliptype == "geojson":
shapes = in_polygon
else:
None
# print error
# clipping of raster
out_image, out_transform = mask.mask(src, shapes, crop=True)
# if clipped raster, we save the data to a tif (otherwise just return out_image)
if clipped_raster:
out_meta.update({
"driver": "GTiff",
"height": out_image.shape[1],
"width": out_image.shape[2],
"transform": out_transform
})
with rio.open(clipped_raster, "w", **out_meta) as dst:
dst.write(out_image)
else:
None
return reshape_as_image(out_image)
def read(in_raster, pixelextent=None):
"""Read a raster.
Args:
filename: File to read
pixelextent: (xoff, yoff, nx, ny)
Returns:
numpy array of shape (bands, ny, nx)
"""
# open in_raster image
with rio.open(in_raster) as src:
# if pixel extent is provided, get raster data only for pixels
if pixelextent:
# if a rio.Windows.Window is provided
if type(pixelextent) == rio.windows.Window:
array = src.read(window=pixelextent)
# if a list provided
else:
array = src.read(window=rio.windows.Window(*pixelextent))
else:
array = src.read()
# reshape to (rows, columns, bands) from (bands, rows, columns)
return reshape_as_image(array)
def compute_pca_score(file,
band_order,
bands,
nr_components,
subset_name=None):
expvar_data = {}
#read all bands (except B9 and B1 = 60m) and metadata
with rio.open(file) as src:
img = src.read(band_order)
profile = src.profile.copy()
arr = reshape_as_image(img).reshape(-1, len(img))
PC = PCA(n_components=nr_components, random_state=42).fit(arr)
eigenvectors_df = pd.DataFrame(
PC.components_,
columns=bands,
index=[f'PC{str(i)}' for i in range(1, nr_components + 1)])
eigenvectors_df = round(eigenvectors_df, 3)
expvar_data['variance'] = PC.explained_variance_ratio_
if subset_name != None:
eigenvectors_df['subset'] = subset_name
pc_nr = [f'PC{str(i)}' for i in range(1, nr_components + 1)]
expvar_df = pd.DataFrame(expvar_data, index=pc_nr).round(4)
score = pd.concat([eigenvectors_df, expvar_df], axis=1)
return (score)
def stack_to_disk(rfiles, new_rname, new_rmeta, outdir, mask=None):
"""
Stack several rasters layer on a single raster and
save it to disk
*********
params:
rfiles -> list of raster path to be stacked
new_rname -> name of the final stack
new_rmeta -> metadata of the final raster
outdir -> output directory
mask -> 3D boolean masked array
"""
assert (new_rmeta['driver'] == 'GTiff'),\
"Please use GTiff driver to write to disk. \
Passed {} instead." .format(new_rmeta['driver'])
name = new_rname + '.tif'
new_rpath = os.path.join(outdir, name)
with rasterio.open(new_rpath, 'w', **new_rmeta) as dst:
for _id, fl in enumerate(rfiles, start=1):
with rasterio.open(fl) as src1:
np_arr = reshape_as_image(src1.read())
if mask is not None:
np_arr = mask_and_fill(np_arr, mask)
dst.write_band(_id, np_arr[:, :,
0].astype(new_rmeta['dtype']))
return new_rpath
def extract_images(urls, to_folder, test_data=False):
fpath_tiff = urls[0]
fpath_geojson = urls[1]
print("Reading in: {} tif image".format(fpath_tiff.split("/")[-2]))
with rasterio.open(fpath_tiff) as tiff:
df_roof_geometries = gpd.read_file(fpath_geojson)
tiff_crs = tiff.crs.data
df_roof_geometries['projected_geometry'] = (
df_roof_geometries['geometry'].to_crs(tiff_crs)
)
roof_geometries = ""
if not test_data:
roof_geometries = (
df_roof_geometries[['id', 'roof_material', 'projected_geometry']].values
)
else:
roof_geometries = (
df_roof_geometries[['id', 'projected_geometry']].values
)
numof_data = len(roof_geometries)
for i, roof in enumerate(roof_geometries):
print("Generating {} -> {} / {}".format(fpath_tiff.split("/")[-2], i+1, numof_data))
if not test_data:
roof_id, roof_material, projected_geometry = roof
target_path = os.path.join(to_folder, roof_material, str(roof_id)+'-'+roof_material+'.png')
else:
roof_id, projected_geometry = roof
target_path = os.path.join(to_folder, str(roof_id)+'.png')
img = mask(tiff, [projected_geometry], crop=True)[0]
cv2.imwrite(target_path, reshape_as_image(img))
def divide_into_pieces(image_path, save_path, pieces_file, width, height):
if not os.path.exists(save_path):
os.makedirs(save_path, exist_ok=True)
print('Data directory created.')
with rasterio.open(image_path) as src, open(pieces_file, 'w') as csvFile:
writer = csv.writer(csvFile)
writer.writerow([
'original_image', 'piece_image', 'piece_geojson', 'start_x',
'start_y', 'width', 'height'
])
for j in tqdm(range(0, src.height // height)):
for i in range(0, src.width // width):
raster_window = src.read(window=Window(i * width, j *
height, width, height))
image_array = reshape_as_image(raster_window)[:, :, [3, 0, 1]]
if np.count_nonzero(image_array) > image_array.size * 0.9:
filename_w_ext = os.path.basename(image_path)
filename, _ = os.path.splitext(filename_w_ext)
image_format = 'png'
piece_name = f'{filename}_nrg_{j}_{i}.{image_format}'
imageio.imwrite(f'{save_path}/{piece_name}', image_array)
writer.writerow([
filename_w_ext, piece_name, 'piece_geojson_name',
i * width, j * height, width, height
])
csvFile.close()
def predict_arr(patch, classifier):
"""
Use a classifier to predict on an array
params:
----------
patch : nd numpy array
classifier: optimized classifier
return:
2D numpy array of int with
the same size as the window
"""
patch = reshape_as_image(patch)
np.nan_to_num(patch, copy=False, nan=0.0, posinf=0, neginf=0)
# Generate a prediction array
# new rows: rows * cols
# new cols: bands
class_prediction = classifier.predict(patch.reshape(-1, patch.shape[2]))
# Reshape our classification map back into a 2D matrix so we can visualize it
class_prediction = class_prediction.reshape(patch[:, :, 0].shape)
return class_prediction
def split_cloud(self, cloud_path, save_cloud_path, image_pieces_path):
pieces_info = pd.read_csv(image_pieces_path,
dtype={
'start_x': np.int64,
'start_y': np.int64,
'width': np.int64,
'height': np.int64
})
with rasterio.open(cloud_path) as cld:
clouds = reshape_as_image(cld.read())
clouds = cv2.resize(clouds, (self.image_width, self.image_height),
interpolation=cv2.INTER_CUBIC)
# to [-1; 1]
clouds = np.clip(clouds, 0, 100)
clouds = (clouds / 100 * 2 - 1)
clouds = img_as_ubyte(clouds)
for i in range(pieces_info.shape[0]):
piece = pieces_info.loc[i]
piece_cloud = clouds[piece['start_y']:piece['start_y'] +
piece['height'],
piece['start_x']:piece['start_x'] +
piece['width']]
filename_cloud = '{}/{}.png'.format(
save_cloud_path,
re.split(r'[/.]', piece['piece_image'])[-2])
imageio.imwrite(filename_cloud, piece_cloud)
def visualize_image(img,
title: str = '',
filename: str = None,
rgb: Tuple[int, int, int] = (0, 1, 2),
figsplt: FigSplt = None,
stretch: bool = True,
show: bool = False,
as_image: bool = False):
"""Visualize the satellite image data."""
assert len(rgb) == 3, 'Exactly three bands should be passed as rgb'
assert img.dtype in (
np.uint8, np.float32,
np.float64), 'RGB images can be only certain types in matplotlib'
if as_image:
img = reshape_as_image(img)
if stretch:
img = hist_stretch_image(img)
else:
img = hist_stretch_image(img, clip_extremes=0)
fig, splt = get_fig_splt(figsplt)
splt.set_title(title)
splt.imshow(img)
if filename:
fig.savefig(filename)
if show:
plt.show()
return splt
def classify(self):
def calculate_chunks(width, height, tiles):
pixels = width * height
max_pixels = pixels / tiles
chunk_size = int(math.floor(math.sqrt(max_pixels)))
ncols = int(math.ceil(width / chunk_size))
nrows = int(math.ceil(height / chunk_size))
chunk_windows = []
for col in range(ncols):
col_offset = col * chunk_size
w = min(chunk_size, width - col_offset)
for row in range(nrows):
row_offset = row * chunk_size
h = min(chunk_size, height - row_offset)
chunk_windows.append(
((row, col), Window(col_offset, row_offset, w, h)))
return chunk_windows
with rasterio.open(self.rlayer.dataProvider().dataSourceUri()) as src:
width = src.width
height = src.height
bands = src.count
meta = src.meta
dtype = src.dtypes
self.signals.status.emit(strftime("%Y-%m-%d %H:%M:%S", gmtime()),
"Predicting image values ... ")
chunk_blocks = calculate_chunks(width, height, self.tiles)
meta.update({"count": 1, "dtype": dtype[0]})
with rasterio.open(self.outlayer, "w", **meta) as dst:
counter = 1
for idx, window in chunk_blocks:
self.signals.status.emit(
strftime("%Y-%m-%d %H:%M:%S",
gmtime()), "Processing Block: " +
str(counter) + " of " + str(len(chunk_blocks)))
img = src.read(window=window)
dtype = rasterio.dtypes.get_minimum_dtype(img)
reshaped_img = reshape_as_image(img)
rows, cols, bands_n = reshaped_img.shape
class_prediction = self.classifier.predict(
reshaped_img.reshape(-1, bands))
classification = np.zeros((rows, cols, 1)).astype(dtype)
classification[:, :, 0] = class_prediction.reshape(
reshaped_img[:, :, 1].shape).astype(dtype)
final = reshape_as_raster(classification)
dst.write(final, window=window)
counter += 1
seconds_elapsed = time() - self.starttime
self.signals.status.emit(
strftime("%Y-%m-%d %H:%M:%S", gmtime()),
"Execution completed in " +
str(np.around(seconds_elapsed, decimals=2)) + " seconds",
)
return self.outlayer
def reader_nm():
method = request.method
INPUT = os.path.join(BASE_PATH, 'u.0p25.grib')
if method == 'GET':
if not request.args or 'dataName' not in request.args:
abort(400)
else:
INPUT = os.path.join(BASE_PATH, request.args['dataName']
or 'u.0p25.grib')
elif method == 'POST':
if not request.json or 'dataName' not in request.json:
abort(400)
else:
INPUT = os.path.join(BASE_PATH, request.args['dataName']
or 'u.0p25.grib')
grib_header = {}
bands = import_data(INPUT)
grib_header["umin"] = bands[0, :, :].min()
grib_header["umax"] = bands[0, :, :].max()
grib_header["vmin"] = bands[1, :, :].min()
grib_header["vmax"] = bands[1, :, :].max()
bands = prepare_array(bands)
image = reshape_as_image(bands)
write_image(os.path.join(BASE_PATH, 'i.png'), image)
return jsonify({'code': 200, 'msg': 'success', 'data': grib_header})
def read_geotiff(geotiff_path):
"""Read geotiff, return reshaped image and metadata."""
with rasterio.open(geotiff_path, 'r') as src:
img = src.read()
img_meta = src.meta
return reshape_as_image(img), img_meta
def load_data(stand_path, chip_size=None, offsets=None):
"""Loads NAIP, LANDSAT, and stand delineation data"""
dirname, cell_id, state_name, year, agency = parse_stand_path(stand_path)
naip_path = get_naip_path(dirname, cell_id, state_name, year)
landsat_path = get_landsat_path(dirname, cell_id, state_name, year)
with rasterio.open(naip_path) as src:
profile = src.profile
height, width = src.shape
if chip_size is not None:
if offsets is not None:
row_off, col_off = offsets
else:
row_off = np.random.randint(0, height - chip_size)
col_off = np.random.randint(0, width - chip_size)
window = windows.Window(col_off, row_off, chip_size, chip_size)
else:
window = None
naip = reshape_as_image(src.read(window=window))
if window is not None:
trf = src.window_transform(window)
bbox = src.window_bounds(window)
else:
trf = src.transform
bbox = src.bounds
with rasterio.open(landsat_path) as src:
if chip_size is not None:
window = windows.from_bounds(*bbox,
transform=src.transform,
height=chip_size,
width=chip_size)
else:
window = windows.from_bounds(*bbox,
transform=src.transform,
height=height,
width=width)
landsat = ((reshape_as_image(
np.stack([src.read(band + 1, window=window)
for band in range(4)])) / 3000).clip(0, 1) * 255).astype(
np.uint8)
stands = gpd.read_file(stand_path)
stands = gpd.clip(stands, box(*bbox))
return naip, landsat, profile, trf, stands
def matplot_image(ax, image):
# based on rasterio.plot, but accepts in-memory images
rgb = extract_rgb(image)
rgb = reshape_as_image(rgb)
# https://stackoverflow.com/questions/24739769/matplotlib-imshow-plots-different-if-using-colormap-or-rgb-array
lo, hi = np.min(rgb), np.max(rgb)
rgb = ((rgb - lo) / (hi - lo)) ** (1 / 2.2)
ax.imshow(rgb)
def show_img(fpath, n):
with rasterio.open(fpath) as src:
arr = src.read([3, 2, 1], masked=True)
print(type(arr))
print(arr.shape)
if arr.dtype == 'uint16':
arr = (255 * (arr / np.max(arr))).astype(np.uint8)
pyplot.figure(n)
return pyplot.imshow(reshape_as_image(arr))
def array_to_img(arr, tileformat='png', mask=None, color_map=None):
"""Convert an array to an base64 encoded img
Attributes
----------
arr : numpy ndarray
Image array to encode.
tileformat : str (default: png)
Image format to return (Accepted: "jpg" or "png")
Mask: numpy ndarray
Mask
color_map: numpy array
ColorMap array (see: utils.get_colormap)
Returns
-------
out : str
base64 encoded PNG or JPEG image.
"""
if tileformat not in ['png', 'jpg']:
raise InvalidFormat('Invalid {} extension'.format(tileformat))
if arr.dtype != np.uint8:
logger.error('Data casted to UINT8')
arr = arr.astype(np.uint8)
if len(arr.shape) >= 3:
arr = reshape_as_image(arr)
arr = arr.squeeze()
if len(arr.shape) != 2 and color_map:
raise InvalidFormat('Cannot apply colormap on a multiband image')
if len(arr.shape) == 2:
mode = 'L'
else:
mode = 'RGB'
img = Image.fromarray(arr, mode=mode)
if color_map:
img.putpalette(color_map)
sio = BytesIO()
if tileformat == 'jpg':
tileformat = 'jpeg'
params = {'subsampling': 0, 'quality': 100}
else:
if mask is not None:
mask_img = Image.fromarray(mask.astype(np.uint8))
img.putalpha(mask_img)
params = {'compress_level': 0}
img.save(sio, tileformat, **params)
sio.seek(0)
return base64.b64encode(sio.getvalue()).decode()
def read_image_around_latlon(self, img: str, lat: float, lon: float,
size: float):
t = rasterio.open(self.path / img)
window = self.window_around_latlon(t, lat, lon, size)
# TODO downsample image if the zoom level is too low / the image too large
tw = reshape_as_image(t.read(window=window, boundless=True))
return tw, window, t
def clip_image(img_fp):
with rasterio.open(img_fp) as src:
img = src.read()[:, 400:1500, 1500:3000]
# Take our full image and reshape into long 2d array (nrow * ncol, nband) for classification
reshaped_img = reshape_as_image(img)
return img, reshaped_img
def update(self, step, T, E, acceptance, improvement):
"""Print progress."""
if acceptance is None:
acceptance = 0
if improvement is None:
improvement = 0
if step > 0:
elapsed = time.time() - self.start
remain = (self.steps - step) * (elapsed / step)
# print('Time {} ({} Remaing)'.format(time_string(elapsed), time_string(remain)))
else:
elapsed = 0
remain = 0
curr = self.cmd(self.state)
curr_score = float(E)
best = self.cmd(self.best_state)
best_score = self.best_energy
report = progress_report(
curr,
best,
curr_score,
best_score,
step,
self.steps,
acceptance * 100,
improvement * 100,
time_string(elapsed),
time_string(remain),
)
print(report)
if fig:
imgs[1].set_data(
reshape_as_image(self.apply_color(self.src.copy(), self.state))
)
imgs[2].set_data(
reshape_as_image(self.apply_color(self.src.copy(), self.best_state))
)
if txt:
txt.set_text(report)
fig.canvas.draw()
def __normalize_rgb(self, tile):
tile = tile[[3, 2, 1], :, :].astype(np.float64)
max_val = 4000
min_val = 0
# Enforce maximum and minimum values
tile[tile[:, :, :] > max_val] = max_val
tile[tile[:, :, :] < min_val] = min_val
for b in range(tile.shape[0]):
tile[b, :, :] = tile[b, :, :] * 1 / (max_val - min_val)
tile_reshaped = reshape_as_image(tile)
return tile_reshaped
def gen_img_samples(rst_pth, tile_size, dist_samples, *band_order):
with rasterio.open(rst_pth) as src:
for row in range(0, src.height, dist_samples):
for column in range(0, src.width, dist_samples):
window = Window.from_slices(slice(row, row + tile_size),
slice(column, column + tile_size))
if band_order:
window_array = reshape_as_image(
src.read(band_order[0], window=window))
else:
window_array = reshape_as_image(src.read(window=window))
if window_array.shape[0] < tile_size or window_array.shape[
1] < tile_size:
padding = pad_diff(window_array.shape[0],
window_array.shape[1], tile_size,
tile_size)
window_array = pad(window_array, padding, fill=np.nan)
yield window_array
def load_image_rasterio(img_path, parse_dltile_filename=True, decode=True):
"""Process a single image file, for any GDAL-compatible image type
Parameters:
img_path: the path to the GDAL-compatible raster image
parse_dltile_filename: if True then the image filename will be assumed to be a DLTile key
with ':' replaced by '#'. This DLTile key will be returned as tile_key. If False then
tile_key will consist of '|'.join([filename, str(image_geotransform), str(img_crs)])
decode: if True then the image data will be read and returned as an array. If False then the
raw file bytes will be returned.
Returns:
5-tuple of (image_data, height, width, bands, tile_key)
Where image_data and tile_key depend on chosen parameters as above.
"""
# we use rasterio to parse the actual image data into an array
# so that we can handle multi bands, different filetypes, dtypes
# But we still use tf api to handle the actual file reading as it is
# so much faster.
img_arr = None
with tf.io.gfile.GFile(img_path, 'rb') as f:
image_data = f.read()
with MemoryFile(image_data) as memfile:
with memfile.open() as src:
if decode:
img_arr = src.read()
gt_str = str(src.get_transform())
crs_str = str(src.read_crs())
height = src.height
width = src.width
bands = src.count
# as opposed to:
#with rasterio.open(img_path) as src:
# img_arr = src.read() # reads all bands to 3d array bands,rows,cols
# gt_str = str(src.get_transform())
# crs_str = str(src.read_crs())
if parse_dltile_filename:
tile_key = '.'.join(os.path.basename(img_path).split(os.extsep)[:-1]).replace('#',':')
else:
if not (gt_str is None or crs_str is None):
tile_key = '|'.join((os.path.basename(img_path),
gt_str, crs_str))
else:
tile_key = os.path.basename(img_path)
if decode:
img_arr = reshape_as_image(img_arr) # converts dim order to rows,cols,bands
# just in case we later extend to read a window/part of the dataset, put this trap
# in to make sure we don't trip over returning the wrong shape
assert (height,width,bands)==img_arr.shape
return img_arr, height, width, bands, tile_key
else:
return image_data, height, width, bands, tile_key
def test_plotting_extent():
from rasterio.plot import reshape_as_image
expected = (101985.0, 339315.0, 2611485.0, 2826915.0)
with rasterio.open('tests/data/RGB.byte.tif') as src:
assert plotting_extent(src) == expected
assert plotting_extent(
reshape_as_image(src.read()), transform=src.affine) == expected
assert plotting_extent(
src.read(1), transform=src.transform) == expected
# array requires a transform
with pytest.raises(ValueError):
plotting_extent(src.read(1))
def test_reshape():
with rasterio.open('tests/data/RGB.byte.tif') as src:
im_data = plot.reshape_as_image(src.read())
assert im_data.shape == (718, 791, 3)
def test_roundtrip_reshape():
with rasterio.open('tests/data/RGB.byte.tif') as src:
data = src.read()
im_data = plot.reshape_as_image(data)
assert np.array_equal(data, rasterio.plot.reshape_as_raster(im_data))