def test_rename_inplace(self):
stack = Raster(self.predictors)
band3_stats = stack.lsat7_2000_30.mean()
# rename band 3
stack.rename(names={"lsat7_2000_30": "new_name"}, in_place=True)
# check that renaming occurred in Raster
self.assertEqual(stack.names[2], "new_name")
self.assertNotIn("lsat7_2000_30", stack.names)
# check that Raster layer properties also renamed
self.assertIn("new_name", dir(stack))
self.assertNotIn("lsat7_2000_30", dir(stack))
# check that internal name of RasterLayer was also renamed
self.assertEqual(stack.iloc[2].names[0], "new_name")
# check that the RasterLayer attached to the new name is the same
self.assertEqual(stack["new_name"].mean(), band3_stats)
self.assertEqual(stack["new_name"].mean(), band3_stats)
self.assertEqual(stack.new_name.mean(), band3_stats)
self.assertEqual(stack.iloc[2].mean(), band3_stats)
# check that a new Raster object derived from the renamed data
# have the right names
new_raster = Raster(src=stack.iloc[2])
self.assertIn("new_name", new_raster.names)
def test_rename_with_copy(self):
stack = Raster(self.predictors)
names = list(stack.names)
band3_stats = stack.lsat7_2000_30.mean()
# rename band 3
result = stack.rename(names={"lsat7_2000_30": "new_name"},
in_place=False)
# check that original is untouched
self.assertEqual(list(stack.names), names)
# check that renaming occurred in Raster
self.assertEqual(list(result.names)[2], "new_name")
self.assertNotIn("lsat7_2000_30", result.names)
# check that Raster layer properties also renamed
self.assertIn("new_name", dir(result))
self.assertNotIn("lsat7_2000_30", dir(result))
# check that internal name of RasterLayer was also renamed
self.assertEqual(result.iloc[2].name, "new_name")
# check that the RasterLayer attached to the new name is the same
self.assertEqual(result["new_name"].mean(), band3_stats)
self.assertEqual(result["new_name"].mean(), band3_stats)
self.assertEqual(result.new_name.mean(), band3_stats)
self.assertEqual(result.iloc[2].mean(), band3_stats)
# check that a new Raster object derived from the renamed data
# have the right names
new_raster = Raster(src=result.iloc[2])
self.assertIn("new_name", new_raster.names)
def test_indexing(self):
stack = Raster(self.predictors + [self.multiband])
# replace band 1 with band 7
band7_mean = stack.loc['lsat7_2000_70'].read(masked=True).mean()
stack.iloc[0] = Raster(self.band7).iloc[0]
self.assertEqual(stack.iloc[0].read(masked=True).mean(), band7_mean)
self.assertEqual(stack.loc['lsat7_2000_10'].read(masked=True).mean(),
band7_mean)
self.assertEqual(stack['lsat7_2000_10'].read(masked=True).mean(),
band7_mean)
self.assertEqual(
stack.lsat7_2000_10.read(masked=True).mean(), band7_mean)
# append another Raster containing a single layer
stack.append(Raster(self.band7))
self.assertEqual(stack.names[5], 'lsat7_2000_70_1')
self.assertEqual(stack.names[-1], 'lsat7_2000_70_2')
self.assertEqual(
stack.lsat7_2000_70_1.read(masked=True).mean(),
stack.lsat7_2000_70_2.read(masked=True).mean(), band7_mean)
# append a multiband raster
stack.append(Raster(self.multiband))
self.assertEqual(stack.names[6], 'landsat_multiband_1_1')
self.assertEqual(stack.names[12], 'landsat_multiband_1_2')
# rename layers
band3_mean = stack.lsat7_2000_30.read(masked=True).mean()
stack.rename({'lsat7_2000_30': 'new_name'})
self.assertEqual(stack['new_name'].read(masked=True).mean(),
band3_mean)
self.assertEqual(stack.new_name.read(masked=True).mean(), band3_mean)
self.assertEqual(stack.loc['new_name'].read(masked=True).mean(),
band3_mean)
self.assertEqual(stack.iloc[-1].read(masked=True).mean(), band3_mean)
# Drop a layer
stack.names
stack.drop(labels='lsat7_2000_50')
self.assertNotIn('lsat7_2000_50', stack.names)
def test_subseting(self):
stack = Raster(self.predictors + [nc.multiband])
# RasterLayer indexing which returns a RasterLayer
self.assertIsInstance(stack.iloc[0], RasterLayer)
self.assertIsInstance(stack.loc['lsat7_2000_10'], RasterLayer)
self.assertIsInstance(stack.lsat7_2000_10, RasterLayer)
self.assertListEqual(
stack.iloc[0:3],
stack.loc[['lsat7_2000_10', 'lsat7_2000_20', 'lsat7_2000_30']])
# RasterStack subsetting
subset_raster = stack[['lsat7_2000_10', 'lsat7_2000_70']]
self.assertListEqual(subset_raster.names, ['lsat7_2000_10', 'lsat7_2000_70'])
self.assertEqual(subset_raster.lsat7_2000_10.read(masked=True).mean(), 80.56715262406088)
self.assertEqual(subset_raster.lsat7_2000_70.read(masked=True).mean(), 59.17773813401238)
# subsetting after name change
stack.rename({'lsat7_2000_10': 'testme'})
expected_names = [
'testme',
'lsat7_2000_20',
'lsat7_2000_30',
'lsat7_2000_40',
'lsat7_2000_50',
'lsat7_2000_70',
'landsat_multiband_1',
'landsat_multiband_2',
'landsat_multiband_3',
'landsat_multiband_4',
'landsat_multiband_5'
]
self.assertListEqual(stack.names, expected_names)
self.assertListEqual(stack.iloc[0].names, ['testme'])
self.assertListEqual(
stack[['testme', 'lsat7_2000_20']].names,
['testme', 'lsat7_2000_20'])
# check that RasterLayer internal name is carried over to new Raster
self.assertListEqual(Raster(stack.iloc[0]).names, ['testme'])
def rename_in_memory(self):
# Create a fake 3-band image for testing
arr = np.random.rand(3, 64, 64)
file = NamedTemporaryFile(prefix="test", suffix=".tif").name
with rasterio.open(file, "w", width=64, height=64, count=3, dtype=np.float32) as dst:
dst.write(arr)
r = Raster(file)
in_memory = r.aggregate((32, 32), in_memory=True)
renamed = r.rename(dict(zip(in_memory.names, ["Red", "Green", "Blue"])))
self.assertListEqual(list(renamed.names), ["Red", "Green", "Blue"])
def rename_multiband(self):
# Create a fake 3-band image for testing
arr = np.random.rand(3, 64, 64)
file = NamedTemporaryFile(prefix="test", suffix=".tif").name
layer_name = os.path.basename(file).split(".")[0]
layer_names = ["_".join([layer_name, str(i)]) for i in [1, 2 ,3]]
with rasterio.open(file, "w", width=64, height=64, count=3, dtype=np.float32) as dst:
dst.write(arr)
r = Raster(file)
self.assertListEqual(list(r.names), layer_names)
renamed = r.rename(dict(zip(r.names, ["Red", "Green", "Blue"])))
self.assertListEqual(list(renamed.names), ["Red", "Green", "Blue"])
# RasterLayer indexing which returns a RasterLayer
stack.iloc[0] # index
stack.iloc[0:3] # slice
stack.loc['lsat7_2000_10'] # key
stack.loc[('lsat7_2000_10', 'lsat7_2000_20')] # list or tuple of keys
stack.lsat7_2000_10 # attribute
# RasterStack subsetting
subset_raster = stack[['lsat7_2000_10', 'lsat7_2000_70']]
subset_raster.names
subset_raster.lsat7_2000_10
print(subset_raster.lsat7_2000_10.read(masked=True).mean())
print(subset_raster.lsat7_2000_70.read(masked=True).mean())
# subsetting after name change
stack.rename({'lsat7_2000_10': 'testme'})
stack.names
stack.iloc[-1].names
stack[['testme', 'lsat7_2000_20']].names
Raster(layers=stack.iloc[-1]).names
# Replace a layer
print(stack.iloc[0].read(masked=True).mean())
stack.iloc[0] = Raster(nc.band7).iloc[0]
print(stack.iloc[0].read(masked=True).mean())
print(stack.loc['testme'].read(masked=True).mean())
print(stack['testme'].read(masked=True).mean())
print(stack.testme.read(masked=True).mean())
# Add a layer
new_raster = stack.append(Raster(nc.band7))
def nre_fun(x, y):
nre = (x - y) / (x + y)
return nre
##############################################################################
# RASTER
##############################################################################
raw_fp = "C:/Users/linds/NOAA/shapefile_training/data_raw/" # file path to raw data folder
raster_fp = raw_fp + 'white_small_sub.tif' # combine with tif file
stack = Raster(raster_fp)
stack.names
stack.rename({'white_small_sub_1': 'coastal'})
stack.rename({'white_small_sub_2': 'blue'})
stack.rename({'white_small_sub_3': 'green'})
stack.rename({'white_small_sub_4': 'yellow'})
stack.rename({'white_small_sub_5': 'red'})
stack.rename({'white_small_sub_6': 'rededge'})
stack.rename({'white_small_sub_7': 'NIR1'})
stack.rename({'white_small_sub_8': 'NIR2'})
# Check the dimensions and bands
print(stack.shape) # dimensions
print(stack.count) # bands
##############################################################################
# SHAPEFILE
##############################################################################
class TestInit(TestCase):
def setUp(self) -> None:
# inputs
self.predictors = [nc.band1, nc.band2, nc.band3, nc.band4, nc.band5,
nc.band7]
# test results
self.stack = None
def tearDown(self) -> None:
self.stack.close()
def test_initiation_files(self):
# test init from list of file paths
self.stack = Raster(self.predictors)
self.assertIsInstance(self.stack, Raster)
self.assertEqual(self.stack.count, 6)
def test_initiation_file(self):
# test init from single file path
self.stack = Raster(nc.band1)
self.assertIsInstance(self.stack, Raster)
self.assertEqual(self.stack.count, 1)
def test_initiation_datasetreader(self):
# test init from single rasterio.io.datasetreader
with rasterio.open(nc.band1) as src:
self.stack = Raster(src)
self.assertIsInstance(self.stack, Raster)
self.assertEqual(self.stack.count, 1)
def test_initiation_list_datasetreader(self):
# test init from list of rasterio.io.datasetreader objects
srcs = []
for f in self.predictors:
srcs.append(rasterio.open(f))
self.stack = Raster(srcs)
self.assertIsInstance(self.stack, Raster)
self.assertEqual(self.stack.count, 6)
def test_initiation_band(self):
# test init from single rasterio.band object
with rasterio.open(nc.band1) as src:
band = rasterio.band(src, 1)
self.stack = Raster(band)
self.assertIsInstance(self.stack, Raster)
self.assertEqual(self.stack.count, 1)
def test_initiation_list_bands(self):
# test init from list of rasterio.band objects
bands = []
for f in self.predictors:
src = rasterio.open(f)
bands.append(rasterio.band(src, 1))
self.stack = Raster(bands)
self.assertIsInstance(self.stack, Raster)
self.assertEqual(self.stack.count, 6)
def test_initiation_rasterlayer(self):
# test init from a single RasterLayer object
with rasterio.open(nc.band1) as src:
band = rasterio.band(src, 1)
layer = RasterLayer(band)
self.stack = Raster(layer)
self.assertIsInstance(self.stack, Raster)
self.assertEqual(self.stack.count, 1)
def test_initiation_list_rasterlayer(self):
# test init from a list of RasterLayer objects
layers = []
for f in self.predictors:
src = rasterio.open(f)
band = rasterio.band(src, 1)
layers.append(RasterLayer(band))
self.stack = Raster(layers)
self.assertIsInstance(self.stack, Raster)
self.assertEqual(self.stack.count, 6)
def test_initiation_array(self):
# check initiation of single-band raster from file
arr = np.zeros((100, 100))
self.stack = Raster(arr)
# check output is written to tempfile
self.assertTrue(os.path.exists(self.stack.iloc[0].file))
# check some operations on the created raster
layer_name = list(self.stack.names)[0]
self.stack = self.stack.rename({layer_name: 'new_layer'})
self.assertEqual(list(self.stack.names)[0], 'new_layer')
# check initiation from array in memory
arr = np.zeros((100, 100))
self.stack = Raster(arr, in_memory=True)
layer_name = list(self.stack.names)[0]
self.stack = self.stack.rename({layer_name: 'new_layer'})
self.assertEqual(list(self.stack.names)[0], 'new_layer')
aoi_file = os.path.join(path_shapes, 'aoi.geojson') # Formato geográfico
manzana_file = os.path.join(path_shapes, 'manzana.geojson') # Formato geográfico
img_name = img_train.split('_')[0]
# Cargar la imagen como un objeto Raster Dataframe y el shape de aoi como Geodaataframe
stack = Raster(img_file)
training = gpd.read_file(aoi_file)
manzana = gpd.read_file(manzana_file)
bandsio = ['B2', 'B3', 'B4', 'B5', 'B6', 'B7', 'B8', 'B8A', 'B11', 'B12']
bandsio_names = ['B2 (Blue)', 'B3 (Green)', 'B4 (Red)', 'B5 (Veg. red edge)',
'B6 (Veg. red edge)', 'B7 (Veg. red edge)', 'B8 (NIR)',
'B8A (Narrow NIR)', 'B11 (SWIR)', 'B12 (SWIR)']
# Mapea los nombres de bandas de entrada
[stack.rename({name: bandsio[idx]}, in_place=True) for idx, name in enumerate(stack.names)]
extent = es.rio.plot.plotting_extent(stack)
# %% [markdown]
# ## Se define la selección de bandas de entrenamineto y salida para todo el proceso
# %%
bandsout = ['B2', 'B3', 'B4', 'B5', 'B6', 'B7', 'B8', 'B8A', 'B11', 'B12']
bandsout_names = ['B2 (Blue)', 'B3 (Green)', 'B4 (Red)', 'B5 (Veg. red edge)',
'B6 (Veg. red edge)', 'B7 (Veg. red edge)', 'B8 (NIR)',
'B8A (Narrow NIR)', 'B11 (SWIR)', 'B12 (SWIR)']
# %% [markdown]
"""
## Anáisis exploratorio de datos
Despliegue de imágenes y análisis exploratorio