Rename csv_to_shp to csv_to_geojson

develop
Chris Leaman 6 years ago
parent 3f2cfa50aa
commit e50fadb35c

@ -0,0 +1,298 @@
"""
Converts .csv files to .shape files
"""
import os
import numpy.ma as ma
import click
import fiona
import numpy as np
import pandas as pd
from fiona.crs import from_epsg
from shapely.geometry import Point, mapping, LineString
from collections import OrderedDict
from utils import crossings, convert_coord_systems
from logs import setup_logging
logger = setup_logging()
def lat_lon_from_profile_x_coord(center_lat_lon, orientation, center_profile_x, x_coord):
"""
Returns the lat/lon of a point on a profile with the given x_coord
:param center_lat_lon: Shapely point of lat/lon of profile center
:param orientation: Orientation of the profile (positive east, counterclockwise)
:param center_profile_x: x value of the center of the profile
:param x_coord: X coordinate of the point to get a lat lon from
:return:
"""
center_xy = convert_coord_systems(center_lat_lon)
center_x, center_y = center_xy.xy
point_x = center_x + (center_profile_x - x_coord) * np.cos(np.deg2rad(orientation))
point_y = center_y + (center_profile_x - x_coord) * np.sin(np.deg2rad(orientation))
point_xy = Point(point_x, point_y)
point_lat_lon = convert_coord_systems(point_xy, in_coord_system="EPSG:28356", out_coord_system="EPSG:4326")
return point_lat_lon
@click.command()
@click.option("--sites-csv", required=True, help=".csv file to convert")
@click.option("--profile-csv", required=True, help=".csv file to convert")
@click.option("--impacts-csv", required=True, help=".csv file to convert")
@click.option("--output-geojson", required=True, help="where to store .geojson file")
def R_high_to_geojson(sites_csv, profiles_csv, impacts_csv, output_geojson):
"""
Converts impact R_high into a lat/lon geojson that we can plot in QGIS
:param sites_csv:
:param profiles_csv:
:param impacts_csv:
:param output_geojson:
:return:
"""
sites_csv = "./data/interim/sites.csv"
profiles_csv = "./data/interim/profiles.csv"
impacts_csv = "./data/interim/impacts_forecasted_mean_slope_sto06.csv"
output_geojson = "./data/interim/R_high_forecasted_mean_slope_sto06.geojson"
df_sites = pd.read_csv(sites_csv, index_col=[0])
df_profiles = pd.read_csv(profiles_csv, index_col=[0, 1, 2])
df_impacts = pd.read_csv(impacts_csv, index_col=[0])
# Create geojson file
schema = {
"geometry": "Point",
"properties": OrderedDict([("beach", "str"), ("site_id", "str"), ("elevation", "float")]),
}
with fiona.open(output_geojson, "w", driver="GeoJSON", crs=from_epsg(4326), schema=schema) as output:
for index, row in df_impacts.iterrows():
site_id = index
beach = index[:-4]
# Find lat/lon of R_high position
R_high_z = row["R_high"]
# Get poststorm profile (or should this be prestorm?)
df_profile = df_profiles.query('site_id=="{}" & profile_type=="prestorm"'.format(index))
int_x = crossings(df_profile.index.get_level_values("x").tolist(), df_profile.z.tolist(), R_high_z)
# Take most landward interesection. Continue to next site if there is no intersection
try:
int_x = max(int_x)
except:
continue
# Get lat/lon on intercept position
site = df_sites.loc[site_id]
point_lat_lon = lat_lon_from_profile_x_coord(
center_lat_lon=Point(site["lon"], site["lat"]),
orientation=site["orientation"],
center_profile_x=site["profile_x_lat_lon"],
x_coord=int_x,
)
prop = OrderedDict([("beach", beach), ("site_id", site_id), ("elevation", R_high_z)])
output.write({"geometry": mapping(point_lat_lon), "properties": prop})
@click.command()
@click.option("--sites-csv", required=True, help=".csv file to convert")
@click.option("--profile-features-csv", required=True, help=".csv file to convert")
@click.option("--output-geojson", required=True, help="where to store .geojson file")
def profile_features_to_geojson(sites_csv, profile_features_csv, output_geojson):
"""
Converts profile_features containing dune toes and crest locations to a geojson we can load into QGIS
:param sites_csv:
:param profiles_csv:
:param profile_features_csv:
:param output_geojson:
:return:
"""
logger.info("Creating profile features geojson")
# Read files from interim folder
df_sites = pd.read_csv(sites_csv, index_col=[0])
df_profile_features = pd.read_csv(profile_features_csv, index_col=[0])
# Create geojson file
schema = {
"geometry": "Point",
"properties": OrderedDict(
[
("beach", "str"),
("site_id", "str"),
(
"point_type",
"str",
), # prestorm_dune_toe, prestorm_dune_crest, poststorm_dune_toe, poststorm_dune_crest
("profile_type", "str"),
("elevation", "float"),
]
),
}
with fiona.open(output_geojson, "w", driver="GeoJSON", crs=from_epsg(4326), schema=schema) as output:
for index, row in df_profile_features.iterrows():
beach = index[:-4]
site_id = index
profile_type = row["profile_type"]
for point_type in ["crest", "toe"]:
# point_type='crest'
elevation = row["dune_{}_z".format(point_type)]
x = row["dune_{}_x".format(point_type)]
if np.isnan(x):
continue
# Geojsons need to use 'null' instead of 'nan'
if np.isnan(elevation):
elevation = None
# Convert x position to lat/lon
site = df_sites.loc[site_id]
point_lat_lon = lat_lon_from_profile_x_coord(
center_lat_lon=Point(site["lon"], site["lat"]),
orientation=site["orientation"],
center_profile_x=site["profile_x_lat_lon"],
x_coord=x,
)
prop = OrderedDict(
[
("beach", beach),
("site_id", site_id),
("point_type", point_type),
("profile_type", profile_type),
("elevation", elevation),
]
)
output.write({"geometry": mapping(point_lat_lon), "properties": prop})
@click.command()
@click.option("--input-csv", required=True, help=".csv file to convert")
@click.option("--output-geojson", required=True, help="where to store .geojson file")
def sites_csv_to_geojson(input_csv, output_geojson):
"""
Converts our dataframe of sites to .geojson to load in QGis. Sites are loaded as linestrings of the profile
cross-sections
:param input_csv:
:param output_geojson:
:return:
"""
logger.info("Converting %s to %s", input_csv, output_geojson)
df_sites = pd.read_csv(input_csv, index_col=[0])
logger.info(os.environ.get("GDAL_DATA", None))
schema = {"geometry": "LineString", "properties": OrderedDict([("beach", "str"), ("site_id", "str")])}
with fiona.open(output_geojson, "w", driver="GeoJSON", crs=from_epsg(4326), schema=schema) as output:
for index, row in df_sites.iterrows():
center_lat_lon = Point(row["lon"], row["lat"])
# Work out where landward profile limit is
land_lat_lon = lat_lon_from_profile_x_coord(
center_lat_lon=center_lat_lon,
orientation=row["orientation"],
center_profile_x=row["profile_x_lat_lon"],
x_coord=0,
)
# Work out where seaward profile limit is
sea_lat_lon = lat_lon_from_profile_x_coord(
center_lat_lon=center_lat_lon,
orientation=row["orientation"],
center_profile_x=row["profile_x_lat_lon"],
x_coord=2 * row["profile_x_lat_lon"],
)
line_string = LineString([land_lat_lon, center_lat_lon, sea_lat_lon])
prop = OrderedDict([("beach", row["beach"]), ("site_id", index)])
output.write({"geometry": mapping(line_string), "properties": prop})
logger.info("Done!")
@click.command()
@click.option("--sites-csv", required=True, help="sites.csv file to convert")
@click.option("--observed-impacts-csv", required=True, help="impacts-observed.csv file to convert")
@click.option("--forecast-impacts-csv", required=True, help="impacts-forecast.csv file to convert")
@click.option("--output-geojson", required=True, help="where to store .geojson file")
def impacts_to_geojson(sites_csv, observed_impacts_csv, forecast_impacts_csv, output_geojson):
"""
Converts impacts observed and forecasted to a geojson for visualization in QGIS
:param sites_csv:
:param observed_impacts_csv:
:param forecast_impacts_csv:
:param output_geojson:
:return:
"""
# Get information from .csv and read into pandas dataframe
df_sites = pd.read_csv(sites_csv, index_col=[0])
df_observed = pd.read_csv(observed_impacts_csv, index_col=[0])
df_forecast = pd.read_csv(forecast_impacts_csv, index_col=[0]).rename({"storm_regime": "forecast_storm_regime"})
# Rename columns, so we can distinguish between forecast and observed
df_observed = df_observed.rename(columns={"storm_regime": "observed_storm_regime"})
df_forecast = df_forecast.rename(columns={"storm_regime": "forecast_storm_regime"})
# Concat into one big dataframe
df = pd.concat([df_sites, df_observed, df_forecast], sort=True, axis=1)
# Make new column for accuracy of forecast. Use underpredict/correct/overpredict classes
df.loc[df.observed_storm_regime == df.forecast_storm_regime, "forecast_accuray"] = "correct"
# Observed/Forecasted/Class for each combination
classes = [
("swash", "collision", "overpredict"),
("swash", "swash", "correct"),
("swash", "overwash", "overpredict"),
("collision", "swash", "underpredict"),
("collision", "collision", "correct"),
("collision", "overwash", "overpredict"),
("overwash", "swash", "underpredict"),
("overwash", "collision", "underpredict"),
("overwash", "overwash", "correct"),
]
for c in classes:
df.loc[(df.observed_storm_regime == c[0]) & (df.forecast_storm_regime == c[1]), "forecast_accuracy"] = c[2]
schema = {
"geometry": "Point",
"properties": OrderedDict(
[
("beach", "str"),
("site_id", "str"),
("forecast_storm_regime", "str"),
("observed_storm_regime", "str"),
("forecast_accuracy", "str"),
]
),
}
with fiona.open(output_geojson, "w", driver="GeoJSON", crs=from_epsg(4326), schema=schema) as output:
for index, row in df.iterrows():
# Locate the marker at the seaward end of the profile to avoid cluttering the coastline.
# Work out where seaward profile limit is
sea_lat_lon = lat_lon_from_profile_x_coord(
center_lat_lon=Point(row["lon"], row["lat"]),
orientation=row["orientation"],
center_profile_x=row["profile_x_lat_lon"],
x_coord=2 * row["profile_x_lat_lon"],
)
prop = OrderedDict(
[
("beach", row["beach"]),
("site_id", index),
("forecast_storm_regime", row["forecast_storm_regime"]),
("observed_storm_regime", row["observed_storm_regime"]),
("forecast_accuracy", row["forecast_accuracy"]),
]
)
output.write({"geometry": mapping(sea_lat_lon), "properties": prop})
logger.info("Done!")

@ -1,333 +0,0 @@
"""
Converts .csv files to .shape files
"""
import os
import numpy.ma as ma
import click
import fiona
import numpy as np
import pandas as pd
from fiona.crs import from_epsg
from shapely.geometry import Point, mapping, LineString
from collections import OrderedDict
from data.parse_shp import convert_coord_systems
from utils import setup_logging
logger = setup_logging()
def R_high_to_geojson(sites_csv, profiles_csv, impacts_csv, output_geojson):
sites_csv = './data/interim/sites.csv'
profiles_csv = './data/interim/profiles.csv'
impacts_csv = './data/interim/impacts_forecasted_mean_slope_sto06.csv'
output_geojson = './data/interim/R_high_forecasted_mean_slope_sto06.geojson'
df_sites = pd.read_csv(sites_csv, index_col=[0])
df_profiles = pd.read_csv(profiles_csv, index_col=[0,1,2])
df_impacts = pd.read_csv(impacts_csv, index_col=[0])
# Create geojson file
schema = {
'geometry': 'Point',
'properties': OrderedDict([
('beach', 'str'),
('site_id', 'str'),
('elevation', 'float'),
])
}
with fiona.open(output_geojson, 'w', driver='GeoJSON', crs=from_epsg(4326), schema=schema) as output:
for index, row in df_impacts.iterrows():
site_id = index
beach = index[:-4]
# Find lat/lon of R_high position
R_high_z = row['R_high']
# Get poststorm profile (or should this be prestorm?)
df_profile = df_profiles.query('site_id=="{}" & profile_type=="prestorm"'.format(index))
int_x = crossings(df_profile.index.get_level_values('x').tolist(),
df_profile.z.tolist(),
R_high_z)
# Take most landward interesection. Continue to next site if there is no intersection
try:
int_x = max(int_x)
except:
continue
# Get lat/lon on intercept position
site = df_sites.loc[site_id]
center_profile_x = site["profile_x_lat_lon"]
orientation = site["orientation"]
center_lat_lon = Point(site['lon'], site['lat']) # Get lat/lon of center of profile
center_xy = convert_coord_systems(center_lat_lon)
center_x, center_y = center_xy.xy
# Calculate xy position of point and convert to lat/lon
point_x = center_x + (center_profile_x - int_x) * np.cos(np.deg2rad(orientation))
point_y = center_y + (center_profile_x - int_x) * np.sin(np.deg2rad(orientation))
point_xy = Point(point_x, point_y)
point_lat_lon = convert_coord_systems(point_xy,
in_coord_system="EPSG:28356",
out_coord_system="EPSG:4326")
prop = OrderedDict([
('beach', beach),
('site_id', site_id),
('elevation', R_high_z),
])
output.write({"geometry": mapping(point_lat_lon), "properties": prop})
def crossings(profile_x, profile_z, constant_z):
"""
Finds the x coordinate of a z elevation for a beach profile. Much faster than using shapely to calculate
intersections since we are only interested in intersections of a constant value. Will return multiple
intersections if found. Used in calculating beach slope.
Adapted from https://stackoverflow.com/a/34745789
:param profile_x: List of x coordinates for the beach profile section
:param profile_z: List of z coordinates for the beach profile section
:param constant_z: Float of the elevation to find corresponding x coordinates
:return: List of x coordinates which correspond to the constant_z
"""
# Remove nans to suppress warning messages
valid = ~ma.masked_invalid(profile_z).mask
profile_z = np.array(profile_z)[valid]
profile_x = np.array(profile_x)[valid]
# Normalize the 'signal' to zero.
# Use np.subtract rather than a list comprehension for performance reasons
z = np.subtract(profile_z, constant_z)
# Find all indices right before any crossing.
# TODO Sometimes this can give a runtime warning https://stackoverflow.com/a/36489085
indicies = np.where(z[:-1] * z[1:] < 0)[0]
# Use linear interpolation to find intersample crossings.
return [profile_x[i] - (profile_x[i] - profile_x[i + 1]) / (z[i] - z[i + 1]) * (z[i]) for i in indicies]
@click.command()
@click.option("--sites-csv", required=True, help=".csv file to convert")
@click.option("--profile-features-csv", required=True, help=".csv file to convert")
@click.option("--output-geojson", required=True, help="where to store .geojson file")
def profile_features_to_geojson(sites_csv, profile_features_csv, output_geojson):
"""
Converts profile_features containing dune toes and crest locations to a geojson we can load into QGIS
:param sites_csv:
:param profiles_csv:
:param profile_features_csv:
:param output_geojson:
:return:
"""
logger.info("Creating profile features geojson")
# Read files from interim folder
df_sites = pd.read_csv(sites_csv, index_col=[0])
df_profile_features = pd.read_csv(profile_features_csv, index_col=[0])
# Create geojson file
schema = {
'geometry': 'Point',
'properties': OrderedDict([
('beach', 'str'),
('site_id', 'str'),
('point_type', 'str'), # prestorm_dune_toe, prestorm_dune_crest, poststorm_dune_toe, poststorm_dune_crest
('profile_type', 'str'),
('elevation', 'float'),
])
}
with fiona.open(output_geojson, 'w', driver='GeoJSON', crs=from_epsg(4326), schema=schema) as output:
for index, row in df_profile_features.iterrows():
beach = index[:-4]
site_id = index
profile_type = row['profile_type']
for point_type in ['crest', 'toe']:
# point_type='crest'
elevation = row['dune_{}_z'.format(point_type)]
x = row['dune_{}_x'.format(point_type)]
if np.isnan(x):
continue
# Geojsons need to use 'null' instead of 'nan'
if np.isnan(elevation):
elevation = None
# Convert x position to lat/lon
site = df_sites.loc[site_id]
center_profile_x = site["profile_x_lat_lon"]
orientation = site["orientation"]
center_lat_lon = Point(site['lon'], site['lat']) # Get lat/lon of center of profile
center_xy = convert_coord_systems(center_lat_lon)
center_x, center_y = center_xy.xy
# Calculate xy position of point and convert to lat/lon
point_x = center_x + (center_profile_x - x) * np.cos(np.deg2rad(orientation))
point_y = center_y + (center_profile_x - x) * np.sin(np.deg2rad(orientation))
point_xy = Point(point_x, point_y)
point_lat_lon = convert_coord_systems(point_xy,
in_coord_system="EPSG:28356",
out_coord_system="EPSG:4326")
prop = OrderedDict([
('beach', beach),
('site_id',site_id),
('point_type', point_type),
('profile_type', profile_type),
('elevation', elevation),
])
output.write({"geometry": mapping(point_lat_lon), "properties": prop})
@click.command()
@click.option("--input-csv", required=True, help=".csv file to convert")
@click.option("--output-geojson", required=True, help="where to store .geojson file")
def sites_csv_to_geojson(input_csv, output_geojson):
"""
Converts our dataframe of sites to .geojson to load in QGis. Sites are loaded as linestrings of the profile
cross-sections
:param input_csv:
:param output_geojson:
:return:
"""
logger.info("Converting %s to %s", input_csv, output_geojson)
df_sites = pd.read_csv(input_csv, index_col=[0])
logger.info(os.environ.get("GDAL_DATA", None))
schema = {
'geometry': 'LineString',
'properties': OrderedDict([
('beach','str'),
('site_id', 'str'),
])
}
with fiona.open(output_geojson, 'w', driver='GeoJSON', crs=from_epsg(4326), schema=schema) as output:
for index, row in df_sites.iterrows():
# Work out where center of profile is
orientation = row["orientation"]
center_profile_x = row["profile_x_lat_lon"]
center_lon = row["lon"]
center_lat = row["lat"]
center_lat_lon = Point(center_lon, center_lat)
center_xy = convert_coord_systems(center_lat_lon)
center_x, center_y = center_xy.xy
# Work out where landward profile limit is
land_x = center_x + center_profile_x * np.cos(np.deg2rad(orientation))
land_y = center_y + center_profile_x * np.sin(np.deg2rad(orientation))
land_xy = Point(land_x, land_y)
land_lat_lon = convert_coord_systems(land_xy, in_coord_system="EPSG:28356",
out_coord_system="EPSG:4326")
# Work out where seaward profile limit is
sea_x = center_x - center_profile_x * np.cos(np.deg2rad(orientation))
sea_y = center_y - center_profile_x * np.sin(np.deg2rad(orientation))
sea_xy = Point(sea_x, sea_y)
sea_lat_lon = convert_coord_systems(sea_xy, in_coord_system="EPSG:28356", out_coord_system="EPSG:4326")
line_string = LineString([land_lat_lon, center_lat_lon, sea_lat_lon])
prop = OrderedDict([("beach", row["beach"]),
("site_id", index)])
output.write({"geometry": mapping(line_string), "properties": prop})
logger.info("Done!")
@click.command()
@click.option("--sites-csv", required=True, help="sites.csv file to convert")
@click.option("--observed-impacts-csv", required=True, help="impacts-observed.csv file to convert")
@click.option("--forecast-impacts-csv", required=True, help="impacts-forecast.csv file to convert")
@click.option("--output-geojson", required=True, help="where to store .geojson file")
def impacts_to_geojson(sites_csv, observed_impacts_csv, forecast_impacts_csv, output_geojson):
"""
Converts impacts observed and forecasted to a geojson for visualization in QGIS
:param sites_csv:
:param observed_impacts_csv:
:param forecast_impacts_csv:
:param output_geojson:
:return:
"""
# Get information from .csv and read into pandas dataframe
df_sites = pd.read_csv(sites_csv, index_col=[0])
df_observed = pd.read_csv(observed_impacts_csv, index_col=[0])
df_forecast = pd.read_csv(forecast_impacts_csv, index_col=[0]).rename({'storm_regime': 'forecast_storm_regime'})
# Rename columns, so we can distinguish between forecast and observed
df_observed = df_observed.rename(columns={'storm_regime': 'observed_storm_regime'})
df_forecast = df_forecast.rename(columns={'storm_regime': 'forecast_storm_regime'})
# Concat into one big dataframe
df = pd.concat([df_sites, df_observed, df_forecast], sort=True,axis=1)
# Make new column for accuracy of forecast. Use underpredict/correct/overpredict classes
df.loc[df.observed_storm_regime == df.forecast_storm_regime, 'forecast_accuray'] = 'correct'
# Observed/Forecasted/Class for each combination
classes = [('swash', 'collision', 'overpredict'),
('swash', 'swash', 'correct'),
('swash', 'overwash', 'overpredict'),
('collision', 'swash', 'underpredict'),
('collision', 'collision', 'correct'),
('collision', 'overwash', 'overpredict'),
('overwash', 'swash', 'underpredict'),
('overwash', 'collision', 'underpredict'),
('overwash', 'overwash', 'correct')]
for c in classes:
df.loc[(df.observed_storm_regime == c[0])&(df.forecast_storm_regime == c[1]), 'forecast_accuracy'] = c[2]
schema = {
'geometry': 'Point',
'properties': OrderedDict([
('beach','str'),
('site_id', 'str'),
('forecast_storm_regime', 'str'),
('observed_storm_regime', 'str',),
('forecast_accuracy', 'str')
])
}
# TODO Impact marker location should be at the seaward end of the profile
with fiona.open(output_geojson, 'w', driver='GeoJSON', crs=from_epsg(4326), schema=schema) as output:
for index, row in df.iterrows():
# Locate the marker at the seaward end of the profile to avoid cluttering the coastline.
# Work out where seaward profile limit is
orientation = row["orientation"]
center_profile_x = row["profile_x_lat_lon"]
center_lon = row["lon"]
center_lat = row["lat"]
center_lat_lon = Point(center_lon, center_lat)
center_xy = convert_coord_systems(center_lat_lon)
center_x, center_y = center_xy.xy
sea_x = center_x - center_profile_x * np.cos(np.deg2rad(orientation))
sea_y = center_y - center_profile_x * np.sin(np.deg2rad(orientation))
sea_xy = Point(sea_x, sea_y)
sea_lat_lon = convert_coord_systems(sea_xy, in_coord_system="EPSG:28356", out_coord_system="EPSG:4326")
prop = OrderedDict([
('beach',row["beach"]),
('site_id', index),
('forecast_storm_regime', row["forecast_storm_regime"]),
('observed_storm_regime', row["observed_storm_regime"],),
('forecast_accuracy', row["forecast_accuracy"])
])
output.write({"geometry": mapping(sea_lat_lon), "properties": prop})
logger.info("Done!")
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