if not out_dir.exists():
os.makedirs(out_dir)
start = time()
huc2s = sorted(
pd.read_feather(
data_dir / "boundaries/huc4.feather", columns=["HUC2"]
).HUC2.unique()
)
### Merge NHD lines and areas that represent dams and dam-related features
print("Reading NHD points, lines, and areas, and merging...")
nhd_pts = read_feathers(
[raw_dir / huc2 / "nhd_points.feather" for huc2 in huc2s],
geo=True,
new_fields={"HUC2": huc2s},
)
nhd_pts = nhd_pts.loc[nhd_pts.FType.isin([343])].copy()
# write original points for SARP
write_dataframe(nhd_pts, out_dir / "nhd_dam_pts_nhdpoint.fgb")
nhd_pts["source"] = "NHDPoint"
# create circular buffers to merge with others
nhd_pts["geometry"] = pg.buffer(nhd_pts.geometry.values.data, 5)
nhd_lines = read_feathers(
[raw_dir / huc2 / "nhd_lines.feather" for huc2 in huc2s],
# "14",
# "15",
# "16",
# "17",
# "21",
# ]
start = time()
### Aggregate barriers
kinds = ["waterfall", "dam", "small_barrier"]
kind_ids = [WATERFALLS_ID, DAMS_ID, SB_ID]
barriers = read_feathers(
[barriers_dir / f"{kind}s.feather" for kind in kinds],
geo=True,
new_fields={"kind": kinds},
)
for kind, init_id in zip(kinds, kind_ids):
ix = barriers.kind == kind
barriers.loc[ix, "barrierID"] = barriers.loc[ix].id + init_id
barriers.barrierID = barriers.barrierID.astype("uint64")
barriers.to_feather(out_dir / "all_barriers.feather")
if DEBUG:
write_dataframe(barriers, out_dir / "all_barriers.fgb")
### Cut flowlines in each HUC2
for huc2 in huc2s:
dups.loc[ix, "dup_tolerance"] = DUPLICATE_TOLERANCE["likely duplicate"]
export_duplicate_areas(dups, qa_dir / "dams_duplicate_areas.fgb")
### Join to line atts
flowlines = (
read_feathers(
[
nhd_dir / "clean" / huc2 / "flowlines.feather"
for huc2 in df.HUC2.unique()
if huc2
],
columns=[
"lineID",
"NHDPlusID",
"GNIS_Name",
"sizeclass",
"StreamOrde",
"FCode",
"loop",
],
)
.rename(columns={"StreamOrde": "StreamOrder"})
.set_index("lineID")
)
df = df.join(flowlines, on="lineID")
df.StreamOrder = df.StreamOrder.fillna(-1).astype("int8")
# Add name from snapped flowline if not already present
)
.set_index("NHDPlusID")
.rename(columns={"nat_floodplain_km2": "natfldkm2", "floodplain_km2": "fldkm2"})
)
floodplains["natfldpln"] = (100 * floodplains.natfldkm2 / floodplains.fldkm2).astype(
"float32"
)
# HUC2s that specifically overlap SECAS states (SARP states + WV)
for group in huc2_groups:
segments = (
read_feathers(
[src_dir / "clean" / huc2 / "network_segments.feather" for huc2 in group],
columns=["lineID", barrier_type],
)
.rename(columns={barrier_type: "networkID"})
.set_index("lineID")
)
stats = (
read_feathers(
[
src_dir / "clean" / huc2 / f"{barrier_type}_network_stats.feather"
for huc2 in group
],
columns=[
"networkID",
"total_miles",
"perennial_miles",
"intermittent_miles",
# "12",
# "13",
# "14",
# "15",
# "16",
# "17",
# "21",
# ]
print("Finding connected HUC2s")
joins = read_feathers(
[src_dir / huc2 / "flowline_joins.feather" for huc2 in huc2s],
columns=[
"upstream",
"downstream",
"type",
"marine",
"upstream_id",
"downstream_id",
],
new_fields={"HUC2": huc2s},
)
groups, joins = connect_huc2s(joins)
print(f"Found {len(groups)} HUC2 groups in {time() - start:,.2f}s")
# persist table of connected HUC2s
connected_huc2s = pd.DataFrame({"HUC2": groups}).explode(column="HUC2")
connected_huc2s["group"] = connected_huc2s.index.astype("uint8")
connected_huc2s.reset_index(drop=True).to_feather(
data_dir / "networks/connected_huc2s.feather")
start = time()
huc2_df = pd.read_feather(data_dir / "boundaries/huc2.feather",
columns=["HUC2"])
huc2s = huc2_df.HUC2.sort_values().values
drains = (read_feathers(
[
data_dir / "nhd/clean/" / huc2 / "waterbody_drain_points.feather"
for huc2 in huc2s
],
new_fields={
"HUC2": huc2s
},
geo=True,
).drop(columns=["snap_to_junction", "snap_dist"]).rename(
columns={
"MaxElevSmo": "maxelev",
"MinElevSmo": "minelev",
"Slope": "slope",
"StreamOrde": "fsorder",
"km2": "wb_km2",
"flowlineLength": "flength",
}).set_index("drainID"))
drains["intermittent"] = drains.lineFCode.isin([46003, 46007])
merged = None
for huc2 in huc2s:
huc2_start = time()
print(f"Extracting dams from waterbodies in {huc2}")
def get_network_results(df, network_type, barrier_type=None, rank=True):
"""Read network results, calculate derived metric classes, and calculate
tiers.
Only barriers that are not unranked (invasive spp barriers) have tiers calculated.
Parameters
----------
df : DataFrame
barriers data; must contain State and unranked
network_type : {"dams", "small_barriers"}
network scenario
barrier_type : {"dams", "small_barriers", "waterfalls"}, optional (default: None)
if present, used to filter barrier kind from network results
rank : bool, optional (default: True)
if True, results will include tiers for the Southeast and state level
Returns
-------
DataFrame
Contains network metrics and tiers
"""
barrier_type = barrier_type or network_type
huc2s = [huc2 for huc2 in df.HUC2.unique() if huc2]
networks = (
read_feathers(
[
Path("data/networks/clean") / huc2 / f"{network_type}_network.feather"
for huc2 in huc2s
],
columns=NETWORK_COLUMNS,
)
.rename(columns=NETWORK_COLUMN_NAMES)
.set_index("id")
)
# FIXME: temporary fix
networks.PercentPerennialUnaltered = networks.PercentPerennialUnaltered.fillna(0)
# select barrier type
networks = networks.loc[networks.kind == barrier_type[:-1]].drop(columns=["kind"])
# Convert dtypes to allow missing data when joined to barriers later
# NOTE: upNetID or downNetID may be 0 if there aren't networks on that side, but
# we set to int dtype instead of uint to allow -1 for missing data later
for col in ["upNetID", "downNetID"]:
networks[col] = networks[col].astype("int")
for col in ["NumBarriersDownstream"]:
networks[col] = networks[col].astype("int16")
for column in ("Landcover", "SizeClasses", "FlowsToOcean"):
networks[column] = networks[column].astype("int8")
# sanity check to make sure no duplicate networks
if networks.groupby(level=0).size().max() > 1:
raise Exception(
f"ERROR: multiple networks found for some {barrier_type} networks"
)
networks = networks.join(df[df.columns.intersection(["unranked", "State"])])
# update data types and calculate total fields
# calculate size classes GAINED instead of total
# doesn't apply to those that don't have upstream networks
networks.loc[networks.SizeClasses > 0, "SizeClasses"] -= 1
# Calculate miles GAINED if barrier is removed
# this is the lesser of the upstream or free downstream lengths.
# Non-free miles downstream (downstream waterbodies) are omitted from this analysis.
networks["GainMiles"] = networks[["TotalUpstreamMiles", "FreeDownstreamMiles"]].min(
axis=1
)
networks["PerennialGainMiles"] = networks[
["PerennialUpstreamMiles", "FreePerennialDownstreamMiles"]
].min(axis=1)
# TotalNetworkMiles is sum of upstream and free downstream miles
networks["TotalNetworkMiles"] = networks[
["TotalUpstreamMiles", "FreeDownstreamMiles"]
].sum(axis=1)
networks["TotalPerennialNetworkMiles"] = networks[
["PerennialUpstreamMiles", "FreePerennialDownstreamMiles"]
].sum(axis=1)
# Round floating point columns to 3 decimals
for column in [c for c in networks.columns if c.endswith("Miles")]:
networks[column] = networks[column].round(3).fillna(-1).astype("float32")
# Calculate network metric classes
networks["GainMilesClass"] = classify_gainmiles(networks.GainMiles)
networks["PerennialGainMilesClass"] = classify_gainmiles(
networks.PerennialGainMiles
)
if not rank:
return networks.drop(columns=["unranked", "State"], errors="ignore")
# only calculate ranks / tiers for ranked barriers
# (exclude unranked invasive spp. barriers)
to_rank = networks.loc[~networks.unranked]
### Calculate regional tiers for SARP (Southeast) region
# NOTE: this is limited to SARP region; other regions are not ranked at regional level
# TODO: consider deprecating this
ix = to_rank.State.isin(SARP_STATE_NAMES)
sarp_tiers = calculate_tiers(to_rank.loc[ix])
sarp_tiers = sarp_tiers.rename(
columns={col: f"SE_{col}" for col in sarp_tiers.columns}
)
### Calculate state tiers for each of total and perennial
state_tiers = None
for state in to_rank.State.unique():
state_tiers = append(
state_tiers,
calculate_tiers(to_rank.loc[to_rank.State == state]).reset_index(),
)
state_tiers = state_tiers.set_index("id").rename(
columns={col: f"State_{col}" for col in state_tiers.columns}
)
networks = networks.join(sarp_tiers).join(state_tiers)
for col in [col for col in networks.columns if col.endswith("_tier")]:
networks[col] = networks[col].fillna(-1).astype("int8")
return networks.drop(columns=["unranked", "State"])
if not out_dir.exists():
os.makedirs(out_dir)
barrier_type = "small_barriers"
ext = "fgb"
# groups_df = pd.read_feather(src_dir / "connected_huc2s.feather")
# for group in groups_df.groupby("group").HUC2.apply(set).values:
for group in [{"02"}]:
segments = (read_feathers(
[
src_dir / "clean" / huc2 / "network_segments.feather"
for huc2 in group
],
columns=["lineID", barrier_type],
).rename(columns={
barrier_type: "networkID"
}).set_index("lineID"))
# FIXME: remove, debug only
s = segments.groupby(level=0).size()
print("dups", s[s > 1])
stats = read_feathers([
src_dir / "clean" / huc2 / f"{barrier_type}_network_stats.feather"
for huc2 in group
]).set_index("networkID")
# use smaller data types for smaller output files
start = time()
groups_df = pd.read_feather(src_dir / "connected_huc2s.feather")
region_tiles = []
for group in groups_df.groupby("group").HUC2.apply(set).values:
group = sorted(group)
print(f"\n\n===========================\nProcessing group {group}")
segments = read_feathers(
[
src_dir / "clean" / huc2 / "network_segments.feather"
for huc2 in group
],
columns=[
"lineID",
"dams",
"small_barriers",
],
).set_index("lineID")
# create output files by HUC2 based on where the segments occur
for huc2 in group:
print(f"----------------------\nProcessing {huc2}")
huc2_start = time()
huc2_mbtiles_filename = intermediate_dir / f"region{huc2}_networks.mbtiles"
region_tiles.append(huc2_mbtiles_filename)
data_dir = Path("data")
out_dir = Path("/tmp/sarp")
if not out_dir.exists():
os.makedirs(out_dir)
huc4_df = pd.read_feather(
data_dir / "boundaries/huc4.feather",
columns=["HUC2"],
)
huc2s = huc4_df.HUC2.unique()
df = read_feathers(
[
data_dir / "nhd/raw" / huc2 / "nhd_altered_rivers.feather"
for huc2 in huc2s
],
geo=True,
new_fields={"HUC2": huc2s},
)
write_dataframe(df, out_dir / "nhd_altered_rivers.shp")
df = read_feathers(
[data_dir / "nwi/raw" / huc2 / "altered_rivers.feather" for huc2 in huc2s],
geo=True,
new_fields={"HUC2": huc2s},
)
write_dataframe(df, out_dir / "nwi_altered_rivers.shp")