def _calc(undercutVals, visitTopoVals):
"""
Calculate undercut metrics
:param undercutVals: dictionary of undercut API data
:param visitTopoVals: dictionary of visit topo metrics
:return: metrics dictionary
"""
# initialize all metrics as zero
dMetrics = {
'Length' : 0.0,
'LengthPercent' : 0.0,
'Area' : 0.0,
'AreaPerecent' : 0.0
}
if len(undercutVals) > 0:
# Calculate the total undercut length and area
for undercut in undercutVals:
dMetrics['Length'] += undercut['EstimatedLength']
try:
dMetrics['Area'] += undercut['EstimatedLength'] * (undercut['Width25Percent'] + undercut['Width50Percent'] + undercut['Width75Percent']) / 3.0
except TypeError, e:
raise DataException("Undercut: Unhandled 'None' values during length calculation")
# Calculate the percent length and area of the site that is undercut
if visitTopoVals['Lgth_Wet'] is None:
raise DataException("Lgth_Wet cannot be null")
if visitTopoVals['Area_Wet'] is None:
raise DataException("Area_Wet cannot be null")
dMetrics['LengthPercent'] = dMetrics['Length'] / (visitTopoVals['Lgth_Wet'] * 100 / 2)
dMetrics['AreaPerecent'] = dMetrics['Area'] / (visitTopoVals['Area_Wet'] + dMetrics['Area']) * 100
def _CenterlineSummaryMetrics(self, dMetrics):
"""
:param dMetrics:
:return:
"""
lMainParts = [x for x in dMetrics.itervalues() if x['Type'] == 'Main']
lSideParts = [x for x in dMetrics.itervalues() if x['Type'] != 'Main']
if len(lMainParts) < 1:
raise DataException("Zero number of mainstem channel parts.")
self.metrics['ChannelCount'] = len([x for x in dMetrics.itervalues()])
self.metrics['MainstemCount']= len(lMainParts)
self.metrics['SideChannelCount'] = len(lSideParts)
self.metrics['MainstemLength'] = sum([fLen['Length'] for fLen in lMainParts])
# Let's avoid some divisions by zero
self.metrics['MainstemSinuosity'] = self.metrics['MainstemLength'] / sum([fLen['StraightLength'] for fLen in lMainParts])
self.metrics['SideChannelLength'] = sum([fLen['Length'] for fLen in lSideParts])
self.metrics['TotalChannelLength'] = self.metrics['MainstemLength'] + self.metrics['SideChannelLength']
if self.metrics['ChannelCount'] > 0:
self.metrics['AverageSideChannelLength'] = self.metrics['TotalChannelLength'] / self.metrics['ChannelCount']
if self.metrics['MainstemLength'] > 0:
self.metrics['Braidedness'] = (self.metrics['MainstemLength'] + self.metrics['SideChannelLength']) / self.metrics['MainstemLength']
if len(dMetrics) > 1:
self.metrics['ChannelType'] = 'complex'
else:
self.metrics['ChannelType'] = 'simple'
def calc(self, a, b, c):
self.metrics['a'] = a
self.metrics['b'] = b
self.metrics['c'] = c
if a <= 0 or b <= 0 or c <= 0:
raise DataException(
"I AM AN EXCEPTION. LOOK AT ME AND DESPAIR")
def _CenterlinePartMetrics(self, centerline):
"""
Centerline Part Metrics
:param centerline:
:return:
"""
self.log.info("Loading centerline shapefile: {}".format(centerline))
clShp = Shapefile(centerline)
clList = clShp.featuresToShapely()
dMetrics = {}
lineIndex = 1
for aLine in clList:
if type(aLine['geometry']) is MultiLineString:
raise DataException('Multipart features in centerline')
curvedLength = aLine['geometry'].length
firstPoint = Point(aLine['geometry'].coords[0])
lastPoint = Point(aLine['geometry'].coords[-1])
straightLength = firstPoint.distance(lastPoint)
if straightLength == 0:
raise DataException("Zero length centerline feature encountered")
if 'Channel' not in aLine['fields']:
raise DataException("Centerline 'Channel' field missing")
if aLine['fields']['Channel'] is None:
raise DataException("Centerline 'Channel' field contains no data")
dMetrics[lineIndex] = {}
dMetrics[lineIndex]['Type'] = aLine['fields']['Channel']
dMetrics[lineIndex]['Length'] = curvedLength
dMetrics[lineIndex]['Sinuosity'] = curvedLength / straightLength
dMetrics[lineIndex]['StraightLength'] = straightLength
lineIndex += 1
return dMetrics
def visitFishCountMetrics(visitMetrics, visitobj):
snorkelFish = visitobj['snorkelFish']
snorkelFishBinned = visitobj['snorkelFishBinned']
snorkelFishSteelheadBinned = visitobj['snorkelFishSteelheadBinned']
for mItem in metricMapping:
try:
visitFishCountMetricsForSpecies(visitMetrics, snorkelFish,
snorkelFishBinned,
snorkelFishSteelheadBinned,
mItem[0], mItem[1])
except AttributeError, e:
raise DataException(
"visitFishCountMetricsForSpecies: Missing attribute for item: {}, {}"
.format(str(mItem[0]), str(mItem[1])))
def tier1FishCountMetrics(tier1Metrics, visitobj):
channelUnits = visitobj['channelUnits']
snorkelFish = visitobj['snorkelFish']
snorkelFishBinned = visitobj['snorkelFishBinned']
snorkelFishSteelheadBinned = visitobj['snorkelFishSteelheadBinned']
for mItem in metricMapping:
try:
tier1FishCountMetricsForSpecies(tier1Metrics, channelUnits,
snorkelFish, snorkelFishBinned,
snorkelFishSteelheadBinned,
mItem[0], mItem[1])
except AttributeError, e:
raise DataException(
"tier1FishCountMetrics: Missing attribute for item: {}, {}".
format(str(mItem[0]), str(mItem[1])))
def interpolatePointsAlongLine(line, fStationInterval):
"""
Given a cross section (Linestring) and a spacing point return regularly spaced points
along that line
:param line:
:param fStationInterval:
:return:
"""
try:
points = [
line.interpolate(currDist)
for currDist in np.arange(0, line.length, fStationInterval)
]
except TypeError, e:
raise DataException(
"Error interpolating thalweg in channel unit. Only linear types support this operation. Type of 'line' is '{}'"
.format(line.type))
def dryWidth(xs, rivershapeWithDonuts):
"""
:param xs: shapely cross section object
:param rivershapeWithDonuts: Polygon with non-qualifying donuts retained
:return:
"""
# Get all intersects of this crosssection with the rivershape
log = Logger("dryWidth")
try:
intersects = xs.intersection(rivershapeWithDonuts.buffer(0)) #KMW: buffer(0) clears up invalid geoms
except TopologicalError as e:
log.error(e.message)
raise DataException("Could not perform intersection on `rivershapeWithDonuts`. Look for small, invalid islands as a possible cause.")
# The intersect may be one object (LineString) or many. We have to handle both cases
if intersects.type == "LineString":
intersects = MultiLineString([intersects])
elif intersects.type == "Point":
return 0
return sum([intersect.length for intersect in intersects])
def calc(self, apiData):
"""
Calculate large wood metrics
:param apiData: dictionary of API data. Key is API call name. Value is API data
:return: metrics dictionary
"""
self.log.info("Running Large Wood Metrics")
# Retrieve the site wetted length from the latest topo metrics
metricInstance = latestMetricInstance(apiData['TopoVisitMetrics'])
if metricInstance is None:
raise MissingException('Missing topo visit metric instance')
siteWettedLength = metricInstance['Lgth_Wet']
if apiData['VisitDetails']['sampleYear'] < 2014:
woodData = [
val['value'] for val in apiData['LargeWoodyDebris']['values']
]
# Only 2011 and 2012 have separate wood jam data
jamData = None
if 'WoodyDebrisJam' in apiData:
jamData = [
val['value'] for val in apiData['WoodyDebrisJam']['values']
]
metrics = LargeWoodMetrics._calcFrequency2011to2013(
woodData, jamData, siteWettedLength)
else:
if 'LargeWoodyPiece' not in apiData:
raise DataException("LargeWoodyPiece needed and not found.")
woodData = [
val['value'] for val in apiData['LargeWoodyPiece']['values']
]
metrics = LargeWoodMetrics._calcFrequency2014On(
woodData, siteWettedLength)
self.metrics = {'VisitMetrics': {'Frequency': metrics}}
def hydro_gis_export(hydro_project_xml, topo_project_xml, outfolder):
"""
:param jsonFilePath:
:param outputFolder:
:param bVerbose:
:return:
"""
#gdal.UseExceptions()
log = Logger("Hydro GIS Export")
# 1 todo Read project.rs.xml
rs_hydro = Project(hydro_project_xml)
rs_topo = TopoProject(topo_project_xml)
hydro_results_folder = os.path.dirname(hydro_project_xml)
if not rs_hydro.ProjectMetadata.has_key("Visit"):
raise MissingException("Cannot Find Visit ID")
visit_id = rs_hydro.ProjectMetadata['Visit']
dem = gdal.Open(rs_topo.getpath("DEM"))
dem_srs = dem.GetProjection()
dem_x_size = dem.RasterXSize
dem_y_size = dem.RasterYSize
dem_band = dem.GetRasterBand(1)
dem_ndv = dem_band.GetNoDataValue()
dem_geotransfrom = dem.GetGeoTransform()
# 3 Get data columns in csv file
csvfile = os.path.join(hydro_results_folder, "dem_grid_results.csv")
csvfile_clean = os.path.join(hydro_results_folder, "dem_grid_results_clean_header.csv")
if not os.path.isfile(csvfile):
raise MissingException("Required file {} does not exist.".format(csvfile))
with open(csvfile, "rb") as f_in, open(csvfile_clean, "wb") as f_out:
reader = csv.reader(f_in)
# writer = csv.writer(f_out)
cols = [col for col in reader.next() if col not in ["Y", "X"]]#[col.replace(".", "_") for col in reader.next() if col not in ["Y", "X"]]
log.info("Loaded fields from csv file.")
# writer.writerow(['X', 'Y'] + cols)
# for row in reader:
# writer.writerow(row)
# log.info("Saved csv file with sanitized headers.")
# Write VRT file
vrt = os.path.join(hydro_results_folder, '{}.vrt'.format("dem_grid_results"))
with open(vrt, 'wt') as f:
f.write('<OGRVRTDataSource>\n')
f.write('\t<OGRVRTLayer name="{}">\n'.format("dem_grid_results"))
f.write('\t\t<SrcDataSource>{}</SrcDataSource>\n'.format(csvfile))
f.write('\t\t<SrcLayer>{}</SrcLayer>\n'.format("dem_grid_results"))
f.write('\t\t<GeometryType>wkbPoint25D</GeometryType>\n')
f.write('\t\t<LayerSRS>{}</LayerSRS>\n'.format(dem_srs))
f.write('\t\t<GeometryField encoding="PointFromColumns" x="X" y="Y" />\n')
for field in cols:
f.write('\t\t<Field name="{}" type="Real" subtype="Float32" />\n'.format(field))
f.write('\t</OGRVRTLayer>\n')
f.write('</OGRVRTDataSource>\n')
log.info("Generated vrt file {}".format(vrt))
# Open csv as OGR
ogr_vrt = ogr.Open(vrt, 1)
if ogr_vrt is None:
raise DataException("unable to open {}".format(vrt))
layer = ogr_vrt.GetLayer()
# 4 Generate geotiff for each column in the CSV file
driver = gdal.GetDriverByName("GTiff")
for col in cols:
out_tif = os.path.join(outfolder, '{}.tif'.format(col))
out_raster = driver.Create(out_tif, dem_x_size, dem_y_size, 1, gdalconst.GDT_Float32)
out_raster.SetGeoTransform(dem_geotransfrom)
out_raster.SetProjection(dem_srs)
band = out_raster.GetRasterBand(1)
band.SetNoDataValue(dem_ndv)
band.FlushCache()
gdal.RasterizeLayer(out_raster, [1], layer, options=["ATTRIBUTE={}".format(col)])
band.GetStatistics(0, 1)
band.FlushCache()
out_raster.FlushCache()
log.info("Generated {} for attribute {}".format(out_tif, col))
if col == "Depth":
raw = numpy.array(band.ReadAsArray())
masked = numpy.ma.masked_array(raw, raw == dem_ndv)
bool_raster = numpy.array(masked, "bool")
numpy.greater(masked, 0, bool_raster)
raster_mem = gdal.GetDriverByName("GTIFF").Create(os.path.join(outfolder, "Temp.tif"), dem_x_size, dem_y_size, 1, gdalconst.GDT_Int16)
raster_mem.SetGeoTransform(dem_geotransfrom)
raster_mem.SetProjection(dem_srs)
band_mem = raster_mem.GetRasterBand(1)
band_mem.WriteArray(bool_raster, 0, 0)
band_mem.SetNoDataValue(dem_ndv)
band_mem.FlushCache()
temp = ogr.GetDriverByName("ESRI Shapefile").CreateDataSource(os.path.join(outfolder, "TempExtent.shp"))
temp_layer = temp.CreateLayer("RawExtent", osr.SpatialReference(wkt=dem_srs), ogr.wkbPolygon)
temp_layer.CreateField(ogr.FieldDefn("Value", ogr.OFTInteger))
temp_layer.CreateField(ogr.FieldDefn("Area", ogr.OFTReal))
gdal.Polygonize(band_mem, None, temp_layer, 0)
del raster_mem
#
# for feature in temp_layer:
# feature.SetField("Area", feature.GetGeometryRef().GetArea())
# temp_layer.SetFeature(feature)
# Stage Extent
# temp_layer.SetAttributeFilter("Value=1")
# shp_extent = os.path.join(outfolder, "StageExtent.shp")
# driver_extent = ogr.GetDriverByName("ESRI Shapefile").CreateDataSource(shp_extent)
# driver_extent.CopyLayer(temp_layer, "StageExtent")
# driver_extent = None
# ogr_extent = ogr.Open(shp_extent, 1)
# layer_extent = ogr_extent.GetLayer("StageExtent")
# field_extent = ogr.FieldDefn("ExtentType", ogr.OFTString)
# layer_extent.CreateField(field_extent)
# area_current = 0.0
# fid_current = None
# for feature in layer_extent:
# area_feat = feature.GetGeometryRef().GetArea()
# if area_feat > area_current:
# area_current = area_feat
# fid_current = feature.GetFID()
#
# edit_feat = layer_extent.GetFeature(fid_current)
# edit_feat.SetField("ExtentType", "Channel")
# layer_extent.SetFeature(edit_feat)
#
# layer_extent.DeleteField(layer_extent.FindFieldIndex("Value", True))
# #ogr_extent.Destroy()
# log.info("Generated Stage Extent Shapefile {}".format(shp_extent))
#
# # Stage Islands
# import time
# time.sleep(5)
# temp_layer.ResetReading()
# temp_layer.SetAttributeFilter("Value=0")
# shp_islands = os.path.join(outfolder, "StageIslands.shp")
# driver_islands = ogr.GetDriverByName("ESRI Shapefile").CreateDataSource(shp_islands)
# driver_islands.CopyLayer(temp_layer, "StageIslands")
# driver_islands = None
# ogr_islands = ogr.Open(shp_islands, 1)
# layer_islands = ogr_islands.GetLayer("StageIslands")
#
# field_qual = ogr.FieldDefn("Qualifying", ogr.OFTInteger)
# field_qual.SetDefault("0")
# field_valid = ogr.FieldDefn("IsValid", ogr.OFTInteger)
# field_valid.SetDefault("0")
# layer_islands.CreateField(field_qual)
# layer_islands.CreateField(field_valid)
# layer_islands.SyncToDisk()
#
# area_current = 0.0
# fid_current = None
# for feature in layer_islands:
# if feature is not None:
# g = feature.GetGeometryRef()
# area_feat = g.GetArea()
# # todo identify qualifying islands here?
# if area_feat > area_current:
# area_current = area_feat
# fid_current = feature.GetFID()
#
# #feat_del = layer_islands.GetFeature(fid_current)
# layer_islands.DeleteFeature(fid_current)
#
# layer_islands.DeleteField(layer_islands.FindFieldIndex("Value", True))
# ogr_islands = None
# ogr_extent = None
# log.info("Generated Stage Islands Shapefile {}".format(shp_islands))
temp = None
del out_raster
shp_hydroresults = os.path.join(outfolder, "HydroResults.shp")
ogr.GetDriverByName("ESRI Shapefile").CopyDataSource(ogr_vrt, shp_hydroresults)
#out_shp = ogr.GetDriverByName("ESRI Shapefile").CreateDataSource()
# ogr_shp = ogr.Open(shp_hydroresults, 1)
# lyr = ogr_shp.GetLayer()
# lyr_defn = lyr.GetLayerDefn()
# for i in range(lyr_defn.GetFieldCount()):
# fielddefn = lyr_defn.GetFieldDefn(i)
# fielddefn.SetName(fielddefn.GetName().replace(".","_"))
# lyr.AlterFieldDefn(i, fielddefn, ogr.ALTER_NAME_FLAG)
#
# new_field = ogr.FieldDefn('V_Bearing', ogr.OFTReal)
# lyr.CreateField(new_field)
# # Calculate Velocity Bearing
# for feat in lyr:
# vel_x = feat.GetField("X_Velocity")
# vel_y = feat.GetField("Y_Velocity")
# dir = 90 - math.degrees(math.atan2(float(vel_y), float(vel_x)))
# bearing = 360 + dir if dir < 0 else dir
# feat.SetField('V_Bearing', float(bearing))
# lyr.SetFeature(feat)
log.info("Generated Hydro Results Shapefile {}".format(shp_hydroresults))
ogr_vrt = None
ogr_shp = None
return 0
def generate_substrate_raster(topo_project_folder,
out_path,
di_values,
dict_ocular_values,
out_channel_value=4000.0):
"""Generate Substrate Raster from Channel units and ocular substrate estimates for each di value provided
:param str topo_project_folder: folder source of the topo project
:param str out_path: path for outputs
:param list di_values: list of int percentile values for roughness calculation
:param dict dict_ocular_values: dictionary of ocular estimates of grain size values
:param float out_channel_value: roughness value to use for out of channel areas, default = 4000
:return: 0 for success
"""
# Load Topo Project
log = Logger("SubstrateRaster")
log.info("topo_project_folder: {}".format(str(topo_project_folder)))
log.info("outputPath: {}".format(str(out_path)))
log.info("D Values: {}".format(str(di_values)))
project = topoproject.TopoProject(topo_project_folder)
topo_rs_project = riverscapes.Project(
os.path.join(topo_project_folder, "project.rs.xml"))
log.info("Topo project loaded")
# Initialize Riverscapes Project
rsproject = riverscapes.Project()
rsproject.create("Substrate", "Substrate", __version__)
for tagname, tags in {
"Site": ["Site", "SiteName"],
"Visit": ["Visit", "VisitID"],
"Year": ["Year", "FieldSeason"],
"Watershed": ["Watershed", "Watershed"]
}.iteritems():
if tags[0] in topo_rs_project.ProjectMetadata or tags[
1] in topo_rs_project.ProjectMetadata:
rsproject.addProjectMetadata(
tagname, topo_rs_project.ProjectMetadata[tags[0]]
if tags[0] in topo_rs_project.ProjectMetadata else
topo_rs_project.ProjectMetadata[tags[1]])
else:
raise DataException("Missing project metadata")
# 1. Do some math on the dictionary of substrate values for each di
dict_di_roughness_values = {}
list_keep_units = []
for di in di_values:
dict_units = dict_ocular_by_unit(dict_ocular_values)
dict_roughness_values = {}
for unitid, dict_unit in dict_units.iteritems():
if all(dict_unit[key] is not None for key in [
"Bedrock", "Boulders", "Cobbles", "CourseGravel",
"FineGravel", "Fines", "Sand"
]):
dict_roughness_values[int(unitid)] = calculate_grain_size(
dict_unit, di)
if unitid not in list_keep_units:
list_keep_units.append(unitid)
else:
log.warning(
"Missing Channel Unit Substrate Values for Unit {}.".
format(str(unitid)))
dict_roughness_values[0] = float(
out_channel_value) # Out of Channel "UnitNumber" == 0
dict_di_roughness_values[di] = pandas.DataFrame(
list(dict_roughness_values.iteritems()),
index=dict_roughness_values.keys(),
columns=["UnitNumber", "Roughness"])
log.info("Calculated Roughness Values for D{}".format(str(di)))
# 2. Spread the channel Unit areas
gdf_expanded_channel_units = expand_polygons(
project.getpath("ChannelUnits"),
project.getpath("BankfullExtent"),
keep_units=list_keep_units)
log.info("Channel Units expanded to Bankfull Area")
# 3. Add DEM area
gdf_demextent = geopandas.GeoDataFrame.from_features(
geopandas.GeoSeries(get_data_polygon(project.getpath("DEM"))))
if not all(gdf_demextent.geometry.is_valid):
gdf_demextent.geometry = gdf_demextent.geometry.buffer(0)
log.info("Fix invalid geoms for DEM Extent")
gdf_demextent["UnitNumber"] = 0
gdf_in_channel_union = geopandas.GeoDataFrame.from_features(
geopandas.GeoSeries(gdf_expanded_channel_units.unary_union.buffer(0)))
gdf_out_of_channel = geopandas.overlay(gdf_demextent, gdf_in_channel_union,
"difference")
gdf_full_polygons = gdf_expanded_channel_units.append(gdf_out_of_channel)
log.info("Out of Channel Area generated")
for di, df_roughness_values in dict_di_roughness_values.iteritems():
# 4 Add dict to channel units
gdf_full_polygons_merged = gdf_full_polygons.merge(df_roughness_values,
on="UnitNumber")
gdf_final_polys = gdf_full_polygons_merged.rename(
columns={"Roughness_y": "Roughness"})
gdf_final_polys.drop([
col for col in gdf_final_polys.columns
if col not in ["UnitNumber", "Roughness", 'geometry']
],
axis=1,
inplace=True)
log.info("Roughness Values added to Channel Units for D{}".format(
str(di)))
# 5. Rasterize Polygons
raster_substrate = path.join(out_path,
"substrate_D{}.tif".format(str(di)))
shp_substrate = path.join(out_path,
"substrate_D{}.shp".format(str(di)))
gdf_final_polys.to_file(shp_substrate)
log.info("Saved Substrate Shapefile: {}".format(shp_substrate))
rasterize_polygons(shp_substrate, project.getpath("DEM"),
raster_substrate, "Roughness")
log.info("Created Substrate Raster: {}".format(raster_substrate))
# Add Realization to Riverscapes
realization = riverscapes.Realization("Substrate")
realization.name = "Substrate_D{}".format(str(di))
realization.productVersion = __version__
ds_shapefile = riverscapes.Dataset().create(
"Substrate_Shapefile", "substrate_D{}.shp".format(str(di)))
ds_raster = riverscapes.Dataset().create(
"Substrate_Raster", "substrate_D{}.tif".format(str(di)))
ds_shapefile.metadata["D_Value"] = str(di)
ds_raster.metadata["D_Value"] = str(di)
ds_shapefile.id = "substrate_shapefile_d{}".format(str(di))
ds_raster.id = "substrate_shapefile_d{}".format(str(di))
realization.outputs[ds_shapefile.name] = ds_shapefile
realization.outputs[ds_raster.name] = ds_raster
rsproject.addRealization(realization)
# Write Riverscapes Project.
rsprojectxml = os.path.join(out_path, "project.rs.xml")
rsproject.writeProjectXML(rsprojectxml)
log.info("Riverscapes Project file saved: {}".format(rsprojectxml))
return 0
def calc(self, shpCUPath, shpThalweg, rasDepth, visitMetrics, dUnits,
unitDefs):
if not os.path.isfile(shpCUPath):
raise MissingException("Channel units file not found")
if not os.path.isfile(shpThalweg):
raise MissingException("Thalweg shape file not found")
if not os.path.isfile(rasDepth):
raise MissingException("Depth raster file not found")
siteLength = visitMetrics['Wetted']['Centerline']['MainstemLength']
if siteLength is None:
raise DataException("No valid site length found in visit metrics")
# Give us a fresh template with 0's in the value positions
self.metrics = self._templateMaker(0, unitDefs)
dResultsChannelSummary = self.metrics['ResultsChannelSummary']
dResultsTier1 = self.metrics['ResultsTier1']
dResultsTier2 = self.metrics['ResultsTier2']
resultsCU = self.metrics['resultsCU']
#Load the Thalweg feature
thalweg = Shapefile(shpThalweg).featuresToShapely()
thalwegLine = thalweg[0]['geometry']
# Load the depth raster
depthRaster = Raster(rasDepth)
# Load the channel unit polygons and calculate the total area
# The channel units should be clipped to the wetted extent and so this
# can be used as the site area wetted
shpCU = Shapefile(shpCUPath)
arrCU = depthRaster.rasterMaskLayer(shpCUPath, "UnitNumber")
feats = shpCU.featuresToShapely()
for aFeat in feats:
dResultsChannelSummary['Main']['Area'] += aFeat['geometry'].area
# Loop over each channel unit and calculate topometrics
for aFeat in feats:
nCUNumber = int(aFeat['fields']['UnitNumber'])
if nCUNumber not in dUnits:
self.log.error(
"Channel Unit: '{0}' not present in the aux data.".format(
nCUNumber))
# Keep it general for the exception so we can aggregate them
raise DataException(
"The Channel Unit ShapeFile contains a unit number that is not present in the aux data."
)
tier1Name = dUnits[nCUNumber][0]
tier2Name = dUnits[nCUNumber][1]
nSegment = dUnits[nCUNumber][2]
#print "Channel Unit Number {0}, Segment {1}, Tier 1 - {2}, Tier 2 - {3}".format(nCUNumber, nSegment, tier1Name, tier2Name)
unitMetrics = {}
resultsCU.append(unitMetrics)
unitMetrics['ChannelUnitNumber'] = nCUNumber
unitMetrics['Area'] = aFeat['geometry'].area
unitMetrics['Tier1'] = tier1Name
unitMetrics['Tier2'] = tier2Name
unitMetrics['Length'] = None
unitMetrics['ResidualDepth'] = None
unitMetrics['DepthAtThalwegExit'] = None
unitMetrics['ThalwegIntersect'] = 0
# Get the depth raster for this unit as variable so we can check
# whether it is entirely masked below.
depArr = depthRaster.array[arrCU == nCUNumber]
if depArr.count() == 0:
unitMetrics['MaxDepth'] = 0
unitMetrics['Volume'] = 0
else:
unitMetrics['MaxDepth'] = np.max(depArr)
unitMetrics['Volume'] = np.sum(depthRaster.array[
arrCU == nCUNumber]) * (depthRaster.cellWidth**2)
if nSegment != 1:
dSideChannelSummary = dResultsChannelSummary[
'SideChannelSummary']
dMain = dResultsChannelSummary['Main']
# Side channel summary captures both small and large side channels
dSideChannelSummary['Area'] += aFeat['geometry'].area
dSideChannelSummary['Count'] += 1
dSideChannelSummary['Percent'] = 100 * dSideChannelSummary[
'Area'] / dMain['Area']
dSideChannelSummary['Volume'] += unitMetrics['Volume']
if 'side' in tier1Name.lower():
dSmallSideChannel = dResultsChannelSummary[
'SmallSideChannel']
dSmallSideChannel['Area'] += aFeat['geometry'].area
dSmallSideChannel['Count'] += 1
dSmallSideChannel['Percent'] = 100 * dSmallSideChannel[
'Area'] / dMain['Area']
dSmallSideChannel['Volume'] += unitMetrics['Volume']
else:
dLargeSideChannel = dResultsChannelSummary[
'LargeSideChannel']
dLargeSideChannel['Area'] += aFeat['geometry'].area
dLargeSideChannel['Count'] += 1
dLargeSideChannel['Percent'] = 100 * dLargeSideChannel[
'Area'] / dMain['Area']
dLargeSideChannel['Volume'] += unitMetrics['Volume']
if tier1Name is None:
raise DataException("tier1Name cannot be 'None'")
if 'side' in tier1Name.lower():
dResultsChannelSummary['ChannelUnitBreakdown'][
'SmallSideChannel'] += 1
else:
dResultsChannelSummary['ChannelUnitBreakdown']['Other'] += 1
if (thalwegLine.intersects(aFeat['geometry'])):
cuThalwegLine = thalwegLine.intersection(aFeat['geometry'])
exitPoint = None
if cuThalwegLine.type == 'LineString':
exitPoint = cuThalwegLine.coords[0]
else:
exitPoint = cuThalwegLine[0].coords[0]
# Retrieve a list of points along the Thalweg in the channel unit
thalwegPoints = ChannelUnitMetrics.interpolatePointsAlongLine(
cuThalwegLine, 0.13)
thalwegDepths = ChannelUnitMetrics.lookupRasterValuesAtPoints(
thalwegPoints, depthRaster)
unitMetrics['MaxDepth'] = np.nanmax(thalwegDepths['values'])
unitMetrics['DepthAtThalwegExit'] = depthRaster.getPixelVal(
exitPoint)
unitMetrics['ResidualDepth'] = unitMetrics[
'MaxDepth'] - unitMetrics['DepthAtThalwegExit']
unitMetrics['Length'] = cuThalwegLine.length
unitMetrics['ThalwegIntersect'] = 1
# Tier 1 and tier 2 topometrics. Note that metric dictionary keys are used for XML tags & require cleaning
tier1NameClean = getCleanTierName(tier1Name)
self._calcTierLevelMetrics(dResultsTier1[tier1NameClean],
tier1Name, unitMetrics, siteLength,
dResultsChannelSummary['Main']['Area'])
tier2NameClean = getCleanTierName(tier2Name)
self._calcTierLevelMetrics(dResultsTier2[tier2NameClean],
tier2Name, unitMetrics, siteLength,
dResultsChannelSummary['Main']['Area'])
# Calculate the average of the channel unit max depths for each tier 1 and tier 2 type
for tierKey, tierMetrics in {
'Tier1': dResultsTier1,
'Tier2': dResultsTier2
}.iteritems():
for tierName, metricDict in tierMetrics.iteritems():
maxDepthList = [
aResult['MaxDepth'] for aResult in resultsCU
if getCleanTierName(aResult[tierKey]) == tierName
]
if len(maxDepthList) > 0:
metricDict['AvgMaxDepth'] = np.average(maxDepthList)
# Convert the sum of residual depth and depth at thalweg exist
# to average residual depth for each tier 1 and tier 2 type
for tierMetricDict in [dResultsTier1, dResultsTier2]:
for tierName, tierMetrics in tierMetricDict.iteritems():
# channel unit types that don't occur should retain the value None for Residual Depth and Depth at Thalweg exit
if tierMetrics['Count'] > 0 and tierMetrics[
'ThalwegIntersectCount'] > 0:
for metricName in ['ResidualDepth', 'DepthAtThalwegExit']:
if tierMetrics[metricName] is not None and tierMetrics[
metricName] != 0:
tierMetrics[metricName] = tierMetrics[
metricName] / tierMetrics[
'ThalwegIntersectCount']
else:
tierMetrics[metricName] = 0
def getCleanTierName(sTierName):
try:
return sTierName.replace(' ', '').replace('/', '').replace('-', '')
except Exception, e:
raise DataException(
"Invalid or null tiername passed to 'getCleanTierName()'")
def getfield(feat, listfields):
for field in listfields:
if field in feat['fields']:
return field
raise DataException('Could not find field {} in shapefile'.format(str(listfields)))
def export_cad_files(project_xml, out_path):
"""exports dxf files containing tin components of topo tin and Topographic Survey Points, Lines and Survey Extent"""
log = Logger("CADExport")
# Load Topo project
log.info("Load Topo project")
project = topoproject.TopoProject(project_xml)
# TIN stuff
log.info("Beginning TIN Work")
tin = TIN(project.getpath("TopoTin"))
dict_tinlayers = {}
dict_tinlayers["tin_points"] = {"layer_type":"POINT", "Features":[feat for feat in tin.nodes.values()]}
dict_tinlayers["tin_lines"] = {"layer_type":"POLYLINE", "Features":[feat['geometry'] for feat in tin.breaklines.values()]}#, "linetype_field":"LineType"}
dict_tinlayers["tin_area"] = {"layer_type":"POLYGON", "Features":[feat for feat in tin.hull_polygons.values()]}
out_tin_dxf = export_as_dxf(dict_tinlayers, os.path.join(out_path, "TopoTin.dxf"))
# Topo Stuff
log.info("Beginning Topo Work")
shpTopo = Shapefile(project.getpath("Topo_Points"))
shpEOW = Shapefile(project.getpath("EdgeofWater_Points"))
shpCP = Shapefile(project.getpath("Control_Points"))
shpBL = Shapefile(project.getpath("Breaklines")) if project.layer_exists("Breaklines") else None
shpExtent = Shapefile(project.getpath("Survey_Extent"))
dict_topolayers = {}
dict_topolayers["Topo_Points"] = {"layer_type":"POINT", "Features":[feat['geometry'] for feat in shpTopo.featuresToShapely()]}
dict_topolayers["EdgeofWater_Points"] = {"layer_type":"POINT", "Features":[feat['geometry'] for feat in shpEOW.featuresToShapely()]}
dict_topolayers["Control_Points"] = {"layer_type":"POINT", "Features":[feat['geometry'] for feat in shpCP.featuresToShapely()]}
dict_topolayers["Breaklines"] = {"layer_type":"POLYLINE", "Features":[feat['geometry'] for feat in shpBL.featuresToShapely()]} if shpBL else None
dict_topolayers["Survey_Extent"] = {"layer_type":"POLYGON", "Features":[feat['geometry'] for feat in shpExtent.featuresToShapely()]}
out_topo_dxf = export_as_dxf(dict_topolayers, os.path.join(out_path, "SurveyTopography.dxf"))
out_topo_csv = exportAsCSV(shpTopo.featuresToShapely() + shpEOW.featuresToShapely(), os.path.join(out_path, "SurveyTopographyPoints.csv"))
out_control_csv = exportAsCSV(shpCP.featuresToShapely(), os.path.join(out_path, "ControlNetworkPoints.csv"))
topo_rs_project = riverscapes.Project(project_xml)
out_project = riverscapes.Project()
out_project.create("CHaMP_Survey_CAD_Export", "CAD_Export", __version__)
out_project.addProjectMetadata("Watershed", topo_rs_project.ProjectMetadata["Watershed"])
# find previous meta tags
for tagname, tags in {"Site": ["Site", "SiteName"], "Visit": ["Visit", "VisitID"], "Year": ["Year", "FieldSeason"], "Watershed": ["Watershed", "Watershed"]}.iteritems():
if tags[0] in topo_rs_project.ProjectMetadata or tags[1] in topo_rs_project.ProjectMetadata:
out_project.addProjectMetadata(tagname, topo_rs_project.ProjectMetadata[tags[0]] if tags[0] in topo_rs_project.ProjectMetadata else topo_rs_project.ProjectMetadata[tags[1]])
else:
raise DataException("Missing project metadata")
out_realization = riverscapes.Realization("CAD_Export")
out_realization.name = "CHaMP Survey CAD Export"
out_realization.productVersion = out_project.projectVersion
ds = []
ds.append(out_project.addInputDataset("TopoTin", "tin", None, None, "TIN", project.get_guid("TopoTin")))
ds.append(out_project.addInputDataset("Topo_Points", "topo_points", None, guid=project.get_guid("Topo_Points")))
ds.append(out_project.addInputDataset("EdgeofWater_Points", "eow_points", None, guid=project.get_guid("EdgeofWater_Points")))
ds.append(out_project.addInputDataset("Control_Points", "control_ponts", None, guid=project.get_guid("Control_Points")))
if shpBL:
ds.append(out_project.addInputDataset("Breaklines", "breaklines", None, guid=project.get_guid("Breaklines")))
ds.append(out_project.addInputDataset("Survey_Extent", "survey_extent", None, guid=project.get_guid("Survey_Extent")))
for inputds in ds:
out_realization.inputs[inputds.name] = inputds.id
ds_tin_dxf = riverscapes.Dataset()
ds_tin_dxf.create("TIN_DXF", "TopoTin.dxf")
ds_tin_dxf.id = 'tin_dxf'
ds_topo_dxf = riverscapes.Dataset()
ds_topo_dxf.create("Topo_DXF", "SurveyTopography.dxf")
ds_topo_dxf.id = 'topo_dxf'
ds_topo_csv = riverscapes.Dataset()
ds_topo_csv.create("Topo_CSV", "SurveyTopographyPoints.csv", "CSV")
ds_topo_csv.id = 'topo_csv'
ds_con_csv = riverscapes.Dataset()
ds_con_csv.create("Control_CSV", "ControlNetworkPoints.csv", "CSV")
ds_con_csv.id = 'control_csv'
out_realization.outputs.update({"TIN_DXF": ds_tin_dxf,
"Topo_DXF": ds_topo_dxf,
"Topo_CSV": ds_topo_csv,
"Control_CSV": ds_con_csv})
out_project.addRealization(out_realization)
out_project.writeProjectXML(os.path.join(out_path, "project.rs.xml"))
return 0
def calc(self, sThalwegshp, sDepthRaster, sWaterSurfaceRaster, fDist,
visitMetrics):
if not path.isfile(sThalwegshp):
raise MissingException("Thalweg shapefile missing")
if not path.isfile(sDepthRaster):
raise MissingException("Depth raster missing")
if not path.isfile(sWaterSurfaceRaster):
raise MissingException("Surface raster missing")
wettedMainstemLength = visitMetrics['Wetted']['Centerline'][
'MainstemLength']
if wettedMainstemLength is None:
raise MissingException(
"No wetted mainstem length found in visit metrics")
sfile = Shapefile(sThalwegshp).featuresToShapely()
if len(sfile) < 1:
raise DataException("Thalweg shapefile has no features")
thalweg = sfile[0]['geometry']
depthRaster = Raster(sDepthRaster)
waterSurfaceRaster = Raster(sWaterSurfaceRaster)
samplepts = ThalwegMetrics.interpolateRasterAlongLine(thalweg, fDist)
results = ThalwegMetrics.lookupRasterValues(samplepts,
depthRaster)['values']
# Get the elevation at the first (downstream) point on the Thalweg
dsElev = waterSurfaceRaster.getPixelVal(thalweg.coords[0])
usElev = waterSurfaceRaster.getPixelVal(thalweg.coords[-1])
if (np.isnan(dsElev)):
raise DataException(
'nodata detected in the raster for downstream point on the thalweg'
)
elif np.isnan(usElev):
raise DataException(
'nodata detected in the raster for upstream point on the thalweg'
)
waterSurfaceGradientRatio = (usElev - dsElev) / thalweg.length
waterSurfaceGradientPC = waterSurfaceGradientRatio * 100.0
# Thalweg straight length and sinuosity
firstPoint = Point(thalweg.coords[0])
lastPoint = Point(thalweg.coords[-1])
straightLength = firstPoint.distance(lastPoint)
sinuosity = thalweg.length / straightLength
self.metrics = {
'Min': np.nanmin(results),
'Max': np.nanmax(results),
'Mean': np.mean(results),
'StDev': np.std(results),
'Count': np.count_nonzero(results),
'Length': thalweg.length,
'WSGradientRatio': waterSurfaceGradientRatio,
'WSGradientPC': waterSurfaceGradientPC,
'Sinuosity': sinuosity,
'CV': 0.0,
'ThalwegToCenterlineRatio': thalweg.length / wettedMainstemLength
#, 'Values': results.data
}
if self.metrics['StDev'] != 0 and self.metrics['Mean'] != 0:
self.metrics['CV'] = self.metrics['StDev'] / self.metrics['Mean']
def calc(self, crosssections, waterExtent, demPath, stationInterval):
# Save space by only loading the desired fields from the ShapeFile.
# We also need the 'Channel' and 'IsValid' fields if they exist.
desiredFields = CrossSectionMetrics.dMetricTypes.keys()
desiredFields.append('IsValid')
# Open the cross section ShapeFile & build a list of all features with a dictionary of the desired fields
clShp = Shapefile(crosssections)
lChannels = ['Main']
if not clShp.loaded:
return
if "Channel" in clShp.fields:
desiredFields.append('Channel')
lChannels.append('Side')
# Older Cross Section Layers don't have the width and depth fields calculated.
# So if all the necessary metric fields are present then continue to load
# ShapeFile features. Otherwise we need to calculate the topometrics from scratch
bMetricCalculationNeeded = False
for aMetric in desiredFields:
if not aMetric in clShp.fields:
bMetricCalculationNeeded = True
break
allFeatures = []
if bMetricCalculationNeeded:
# Retrieve the water extent polygon exterior
rivershp = Shapefile(waterExtent)
polyRiverShapeFeats = rivershp.featuresToShapely()
# Try and find a channel shape. Thers's a lot of variance here.
if len(polyRiverShapeFeats) == 0 or 'geometry' not in polyRiverShapeFeats[0]:
raise DataException("No features in crosssection shape file")
# If there's only one shape then just use it
elif len(polyRiverShapeFeats) == 1:
polyRiverShape = polyRiverShapeFeats[0]['geometry']
# If there's more than one shape then see if
else:
channelShapes = [feat['geometry'] for feat in polyRiverShapeFeats if feat['fields']['ExtentType'] == 'Channel']
if len(channelShapes) == 0:
raise DataException("No features in crosssection shape file")
polyRiverShape = channelShapes[0]
# Calculate the topometrics from scratch for a single cross section
shpXS = Shapefile(crosssections)
demRaster = Raster(demPath)
if shpXS.loaded:
for aFeat in shpXS.featuresToShapely():
# Calculate the topometrics for this cross section. They will be stored on the aFeat dict under key 'topometrics'
calcXSMetrics(aFeat, polyRiverShape , demRaster, stationInterval)
# Build the all features dictionary that would be expect had the topometrics already
# existed in the XS shapefile and simply got loaded. This is a combination of the new topometrics
# and also the existing fields on the XS ShapeFile.
singleXSMetrics = copy.deepcopy(aFeat['topometrics'])
singleXSMetrics.update(aFeat['fields'])
allFeatures.append(singleXSMetrics)
# Destroying the raster object appears to prevent warning messages on Windows
demRaster = None
else:
allFeatures = clShp.attributesToList(desiredFields)
# For simple ShapeFiles, make every feature part of the main channel, and
# set every feature as valid. This helps keep code below generic
for x in allFeatures:
if 'Channel' not in x:
x['Channel'] = 'Main'
if 'IsValid' not in x:
x['IsValid'] = 1
for channelName in lChannels:
# Filter the list of features to just those in this channel
# PGB - 24 Apr 2017 - observed NULL values in 'Channel' ShapeFile field in Harold results.
# Cast field contents to string to avoid crash here.
channelFeatures = [x for x in allFeatures if str(x['Channel']).lower() == channelName.lower()]
# Filter the list of features to just those that the crew considered valid
validFeatures = [x for x in channelFeatures if x['IsValid'] <> 0]
# Filter the features to just those with a length that is within 4 standard deviations of mean wetted width
channelStatistics = getStatistics(channelFeatures, 'WetWidth')
autoFeatures = None
if channelStatistics['StdDev'] is not None:
wetWidthThreshold = channelStatistics['StdDev'] * 4
autoFeatures = [x for x in channelFeatures if abs(x['WetWidth'] - channelStatistics['Mean']) < wetWidthThreshold]
# Loop over each desired metric and calculate the statistics for each filtering type
for metricName, bestFiltering in CrossSectionMetrics.dMetricTypes.iteritems():
populateChannelStatistics(self.metrics[channelName], 'None', metricName, channelFeatures)
populateChannelStatistics(self.metrics[channelName], 'Crew', metricName, validFeatures)
if channelStatistics['StdDev'] is not None:
populateChannelStatistics(self.metrics[channelName], 'Auto', metricName, autoFeatures)
self.metrics[channelName]['Best'] = self.metrics[channelName][bestFiltering]
# The topometrics for the whole channel are always the results for 'Main'.
# For complex ShapeFiles this will be just the results for the main channel.
# For simple, single threaded, ShapeFiles this will all cross sections.
self.metrics['Channel'] = self.metrics['Main']
