def parse_extent(extent, src_ds_list=None, t_srs=None):
"""Parse arbitrary input extent
Parameters
----------
extent : str or gdal.Dataset or filename or list of float
Arbitrary input extent
src_ds_list : list of gdal.Dataset objects, optional
Needed if specifying 'first', 'last', 'intersection', or 'union'
t_srs : osr.SpatialReference() object, optional
Projection for res calculations
Returns
-------
extent : list of float
Output extent [xmin, ymin, xmax, ymax]
None if source extent should be preserved
"""
#Default to using first t_srs for extent calculations
if t_srs is not None:
t_srs = parse_srs(t_srs, src_ds_list)
#Valid strings
extent_str_list = ['first', 'last', 'intersection', 'union']
if extent in extent_str_list and src_ds_list is not None:
if len(src_ds_list) == 1 and (extent == 'intersection'
or extent == 'union'):
extent = None
elif extent == 'first':
extent = geolib.ds_geom_extent(src_ds_list[0], t_srs=t_srs)
#extent = geolib.ds_extent(src_ds_list[0], t_srs=t_srs)
elif extent == 'last':
extent = geolib.ds_geom_extent(src_ds_list[-1], t_srs=t_srs)
#extent = geolib.ds_extent(src_ds_list[-1], t_srs=t_srs)
elif extent == 'intersection':
#By default, compute_intersection takes ref_srs from ref_ds
extent = geolib.ds_geom_intersection_extent(src_ds_list,
t_srs=t_srs)
if len(src_ds_list) > 1 and extent is None:
sys.exit("Input images do not intersect")
elif extent == 'union':
#Need to clean up union t_srs handling
extent = geolib.ds_geom_union_extent(src_ds_list, t_srs=t_srs)
elif extent == 'source':
extent = None
elif isinstance(extent, gdal.Dataset):
extent = geolib.ds_geom_extent(extent, t_srs=t_srs)
elif isinstance(extent, str) and os.path.exists(extent):
extent = geolib.ds_geom_extent(gdal.Open(extent), t_srs=t_srs)
elif isinstance(extent, (list, tuple, np.ndarray)):
extent = list(extent)
else:
extent = [float(i) for i in extent.split(' ')]
return extent
def shp_overlay(ax, ds, shp_fn, gt=None, color='darkgreen'):
from osgeo import ogr
from pygeotools.lib import geolib
#ogr2ogr -f "ESRI Shapefile" output.shp input.shp -clipsrc xmin ymin xmax ymax
shp_ds = ogr.Open(shp_fn)
lyr = shp_ds.GetLayer()
lyr_srs = lyr.GetSpatialRef()
lyr.ResetReading()
nfeat = lyr.GetFeatureCount()
#Note: this is inefficient for large numbers of features
#Should produce collections of points or lines, then have single plot call
for n, feat in enumerate(lyr):
geom = feat.GetGeometryRef()
geom_type = geom.GetGeometryType()
#Points
if geom_type == 1:
mX, mY, z = geom.GetPoint()
attr = {'marker':'o', 'markersize':5, 'linestyle':'None'}
#Line
elif geom_type == 2:
l, mX, mY = geolib.line2pts(geom)
z = 0
#attr = {'marker':None, 'linestyle':'-', 'linewidth':0.5, 'alpha':0.8}
attr = {'marker':None, 'linestyle':'-', 'linewidth':1.0, 'alpha':0.8}
#attr = {'marker':'.', 'markersize':0.5, 'linestyle':'None'}
#Polygon, placeholder
#Note: this should be done with the matplotlib patch functionality
#http://matplotlib.org/users/path_tutorial.html
elif geom_type == 3:
print("Polygon support not yet implemented")
#ogr2ogr -nlt LINESTRING out.shp in.shp
l, mX, mY = geolib.line2pts(geom)
z = 0
attr = {'marker':None, 'linestyle':'-', 'facecolor':'w'}
ds_srs = geolib.get_ds_srs(ds)
if gt is None:
gt = ds.GetGeoTransform()
if not lyr_srs.IsSame(ds_srs):
mX, mY, z = geolib.cT_helper(mX, mY, z, lyr_srs, ds_srs)
#ds_extent = geolib.ds_extent(ds)
ds_extent = geolib.ds_geom_extent(ds)
mX = np.ma.array(mX)
mY = np.ma.array(mY)
mX[mX < ds_extent[0]] = np.ma.masked
mX[mX > ds_extent[2]] = np.ma.masked
mY[mY < ds_extent[1]] = np.ma.masked
mY[mY > ds_extent[3]] = np.ma.masked
mask = np.ma.getmaskarray(mY) | np.ma.getmaskarray(mX)
mX = mX[~mask]
mY = mY[~mask]
if mX.count() > 0:
ax.set_autoscale_on(False)
if geom_type == 1:
pX, pY = geolib.mapToPixel(np.array(mX), np.array(mY), gt)
ax.plot(pX, pY, color=color, **attr)
else:
l = np.ma.array(l)
l = l[~mask]
lmed = np.ma.median(np.diff(l))
lbreaks = (np.diff(l) > lmed*2).nonzero()[0]
if lbreaks.size:
a = 0
lbreaks = list(lbreaks)
lbreaks.append(l.size)
for b in lbreaks:
mmX = mX[a:b+1]
mmY = mY[a:b+1]
a = b+1
#import ipdb; ipdb.set_trace()
#pX, pY = geolib.mapToPixel(np.array(mX), np.array(mY), gt)
pX, pY = geolib.mapToPixel(mmX, mmY, gt)
print(n, np.diff(pX).max(), np.diff(pY).max())
#ax.plot(pX, pY, color='LimeGreen', **attr)
#ax.plot(pX, pY, color='LimeGreen', alpha=0.5, **attr)
#ax.plot(pX, pY, color='w', alpha=0.5, **attr)
ax.plot(pX, pY, color=color, **attr)
else:
pX, pY = geolib.mapToPixel(np.array(mX), np.array(mY), gt)
ax.plot(pX, pY, color=color, **attr)
def warp(src_ds, res=None, extent=None, t_srs=None, r='cubic', driver=mem_drv, dst_fn=None, dst_ndv=None, verbose=True):
"""Warp an input dataset with predetermined arguments specifying output res/extent/srs
This is the function that actually calls gdal.ReprojectImage
Parameters
----------
src_ds : gdal.Dataset object
Dataset to be warped
res : float
Desired output resolution
extent : list of float
Desired output extent in t_srs coordinate system
t_srs : osr.SpatialReference()
Desired output spatial reference
r : str
Desired resampling algorithm
driver : GDAL Driver to use for warp
Either MEM or GTiff
dst_fn : str
Output filename (for disk warp)
dst_ndv : float
Desired output NoData Value
Returns
-------
dst_ds : gdal.Dataset object
Warped dataset (either in memory or on disk)
"""
src_srs = geolib.get_ds_srs(src_ds)
if t_srs is None:
t_srs = geolib.get_ds_srs(src_ds)
src_gt = src_ds.GetGeoTransform()
#Note: get_res returns [x_res, y_res]
#Could just use gt here and average x_res and y_res
src_res = geolib.get_res(src_ds, t_srs=t_srs, square=True)[0]
if res is None:
res = src_res
if extent is None:
extent = geolib.ds_geom_extent(src_ds, t_srs=t_srs)
#Note: GDAL Lanczos creates block artifacts
#Wait for gdalwarp to support gaussian resampling
#Want to use Lanczos for downsampling
#if src_res < res:
# gra = gdal.GRA_Lanczos
#See http://blog.codinghorror.com/better-image-resizing/
# Suggests cubic for downsampling, bilinear for upsampling
# gra = gdal.GRA_Cubic
#Cubic for upsampling
#elif src_res >= res:
# gra = gdal.GRA_Bilinear
gra = parse_rs_alg(r)
#At this point, the resolution and extent values must be float
#Extent must be list
res = float(res)
extent = [float(i) for i in extent]
#Might want to move this to memwarp_multi, keep memwarp basic w/ gdal.GRA types
#Create progress function
prog_func = None
if verbose:
prog_func = gdal.TermProgress
if dst_fn is None:
#This is a dummy fn if only in mem, but can be accessed later via GetFileList()
#Actually, no, doesn't look like the filename survivies
dst_fn = ''
#Compute output image dimensions
dst_nl = int(round((extent[3] - extent[1])/res))
dst_ns = int(round((extent[2] - extent[0])/res))
#dst_nl = int(math.ceil((extent[3] - extent[1])/res))
#dst_ns = int(math.ceil((extent[2] - extent[0])/res))
#dst_nl = int(math.floor((extent[3] - extent[1])/res))
#dst_ns = int(math.floor((extent[2] - extent[0])/res))
if verbose:
print('nl: %i ns: %i res: %0.3f' % (dst_nl, dst_ns, res))
#Create output dataset
src_b = src_ds.GetRasterBand(1)
src_dt = src_b.DataType
src_nl = src_ds.RasterYSize
src_ns = src_ds.RasterXSize
dst_ds = driver.Create(dst_fn, dst_ns, dst_nl, src_ds.RasterCount, src_dt)
dst_ds.SetProjection(t_srs.ExportToWkt())
#Might be an issue to use src_gt rotation terms here with arbitrary extent/res
dst_gt = [extent[0], res, src_gt[2], extent[3], src_gt[4], -res]
dst_ds.SetGeoTransform(dst_gt)
#This will smooth the input before downsampling to prevent aliasing, fill gaps
#Pretty inefficent, as we need to create another intermediate dataset
gauss = False
for n in range(1, src_ds.RasterCount+1):
if dst_ndv is None:
src_b = src_ds.GetRasterBand(n)
src_ndv = iolib.get_ndv_b(src_b)
dst_ndv = src_ndv
b = dst_ds.GetRasterBand(n)
b.SetNoDataValue(dst_ndv)
b.Fill(dst_ndv)
if gauss:
from pygeotools.lib import filtlib
#src_a = src_b.GetVirtualMemArray()
#Compute resampling ratio to determine filter window size
res_ratio = float(res)/src_res
if verbose:
print("Resampling factor: %0.3f" % res_ratio)
#Might be more efficient to do iterative gauss filter with size 3, rather than larger windows
f_size = math.floor(res_ratio/2.)*2+1
#This is conservative to avoid filling holes with noise
#f_size = math.floor(res_ratio/2.)*2-1
if f_size <= 1:
continue
if verbose:
print("Smoothing window size: %i" % f_size)
#Create temp dataset to store filtered array - avoid overwriting original
temp_ds = driver.Create('', src_ns, src_nl, src_ds.RasterCount, src_dt)
temp_ds.SetProjection(src_srs.ExportToWkt())
temp_ds.SetGeoTransform(src_gt)
temp_b = temp_ds.GetRasterBand(n)
temp_b.SetNoDataValue(dst_ndv)
temp_b.Fill(dst_ndv)
src_a = iolib.b_getma(src_b)
src_a = filtlib.gauss_fltr_astropy(src_a, size=f_size)
#Want to run with maskfill, so only fills gaps, without expanding isolated points
temp_b.WriteArray(src_a)
src_ds = temp_ds
#In theory, NN should be fine since we already smoothed. In practice, cubic still provides slightly better results
#gra = gdal.GRA_NearestNeighbour
"""
if not verbose:
#Suppress GDAL progress bar
orig_stdout = sys.stdout
sys.stdout = open(os.devnull, 'w')
"""
#Note: default maxerror=0.0, second 0.0 argument
gdal.ReprojectImage(src_ds, dst_ds, src_srs.ExportToWkt(), t_srs.ExportToWkt(), gra, 0.0, 0.0, prog_func)
"""
if not verbose:
sys.stdout.close()
sys.stdout = orig_stdout
"""
#Note: this is now done in diskwarp
#Write out to disk
#if driver != mem_drv:
# dst_ds.FlushCache()
#Return GDAL dataset object in memory
return dst_ds