t.rast.gapfill.py 8.28 KB
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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
############################################################################
#
# MODULE:       t.rast.gapfill
# AUTHOR(S):    Soeren Gebbert
#
# PURPOSE:      Replace gaps in a space time raster dataset with interpolated raster maps.
# COPYRIGHT:    (C) 2012-2017 by the GRASS Development Team
#
#  This program is free software; you can redistribute it and/or modify
#  it under the terms of the GNU General Public License as published by
#  the Free Software Foundation; either version 2 of the License, or
#  (at your option) any later version.
#
#  This program is distributed in the hope that it will be useful,
#  but WITHOUT ANY WARRANTY; without even the implied warranty of
#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#  GNU General Public License for more details.
#
#############################################################################

#%module
#% description: Replaces gaps in a space time raster dataset with interpolated raster maps.
#% keyword: temporal
#% keyword: interpolation
#% keyword: raster
#% keyword: time
#% keyword: no-data filling
#%end

#%option G_OPT_STRDS_INPUT
#%end

#%option G_OPT_T_WHERE
#%end

#%option
#% key: basename
#% type: string
#% label: Basename of the new generated output maps
#% description: A numerical suffix separated by an underscore will be attached to create a unique identifier
#% required: yes
#% multiple: no
#% gisprompt:
#%end

#%option
#% key: suffix
#% type: string
#% description: Suffix to add at basename: set 'gran' for granularity, 'time' for the full time format, 'num' for numerical suffix with a specific number of digits (default %05)
#% answer: gran
#% required: no
#% multiple: no
#%end

#%option
#% key: nprocs
#% type: integer
#% description: Number of interpolation processes to run in parallel
#% required: no
#% multiple: no
#% answer: 1
#%end

#%flag
#% key: t
#% description: Assign the space time raster dataset start and end time to the output map
#%end

import sys
import copy
from multiprocessing import Process
import grass.script as grass
from grass.exceptions import FatalError

############################################################################


def main():
    # lazy imports
    import grass.temporal as tgis
    import grass.pygrass.modules as pymod

    # Get the options
    input = options["input"]
    base = options["basename"]
    where = options["where"]
    nprocs = options["nprocs"]
    tsuffix = options["suffix"]

    mapset = grass.gisenv()["MAPSET"]

    # Make sure the temporal database exists
    tgis.init()

    # We need a database interface
    dbif = tgis.SQLDatabaseInterfaceConnection()
    dbif.connect()

    sp = tgis.open_old_stds(input, "strds")

    maps = sp.get_registered_maps_as_objects_with_gaps(where, dbif)

    num = len(maps)

    # Configure the r.to.vect module
    gapfill_module = pymod.Module("r.series.interp",
                             overwrite=grass.overwrite(), quiet=True, run_=False,
                             finish_=False,)

    process_queue = pymod.ParallelModuleQueue(int(nprocs))

    gap_list = []
    overwrite_flags = {}

    # Identify all gaps and create new names
    count = 0
    for _map in maps:
        if _map.get_id() is None:
            count += 1
            if sp.get_temporal_type() == 'absolute' and tsuffix in ['gran', 'time']:
                _id = "{ba}@{ma}".format(ba=base, ma=mapset)
            else:
                map_name = tgis.create_numeric_suffix(base, num + count, tsuffix)
                _id = "{name}@{ma}".format(name=map_name, ma=mapset)
            _map.set_id(_id)

            gap_list.append(_map)

    if len(gap_list) == 0:
        grass.message(_("No gaps found"))
        return

    # Build the temporal topology
    tb = tgis.SpatioTemporalTopologyBuilder()
    tb.build(maps)

    # Do some checks before computation
    for _map in gap_list:
        if not _map.get_precedes() or not _map.get_follows():
            grass.fatal(_("Unable to determine successor "
                          "and predecessor of a gap."))

        if len(_map.get_precedes()) > 1:
            grass.warning(_("More than one successor of the gap found. "
                            "Using the first found."))

        if len(_map.get_follows()) > 1:
            grass.warning(_("More than one predecessor of the gap found. "
                            "Using the first found."))

    # Interpolate the maps using parallel processing
    result_list = []

    for _map in gap_list:
        predecessor = _map.get_follows()[0]
        successor = _map.get_precedes()[0]

        gran = sp.get_granularity()
        tmpval,  start = predecessor.get_temporal_extent_as_tuple()
        end,  tmpval = successor.get_temporal_extent_as_tuple()
        
        # Now resample the gap
        map_matrix = tgis.AbstractSpaceTimeDataset.resample_maplist_by_granularity((_map, ),start, end,  gran)
        
        map_names = []
        map_positions = []
        
        increment = 1.0/ (len(map_matrix) + 1.0)
        position = increment
        count = 0
        for intp_list in map_matrix:
            new_map = intp_list[0]
            count += 1
            if sp.get_temporal_type() == 'absolute' and tsuffix == 'gran':
                suffix = tgis.create_suffix_from_datetime(new_map.temporal_extent.get_start_time(),
                                                          sp.get_granularity())
                new_id = "{ba}_{su}@{ma}".format(ba=new_map.get_name(),
                                                 su=suffix, ma=mapset)
            elif sp.get_temporal_type() == 'absolute' and tsuffix == 'time':
                suffix = tgis.create_time_suffix(new_map)
                new_id = "{ba}_{su}@{ma}".format(ba=new_map.get_name(),
                                                 su=suffix, ma=mapset)
            else:
                map_name = tgis.create_numeric_suffix(new_map.get_name(),
                                                      count, tsuffix)
                new_id = "{name}@{ma}".format(name=map_name, ma=mapset)

            new_map.set_id(new_id)
            
            overwrite_flags[new_id] = False
            if new_map.map_exists() or new_map.is_in_db(dbif):
                if not grass.overwrite():
                        grass.fatal(_("Map with name <%s> already exists. "
                                      "Please use another base name." % (_id)))
                else:
                    if new_map.is_in_db(dbif):
                        overwrite_flags[new_id] = True

            map_names.append(new_map.get_name())
            map_positions.append(position)
            position += increment
            
            result_list.append(new_map)

        mod = copy.deepcopy(gapfill_module)
        mod(input=(predecessor.get_map_id(), successor.get_map_id()),
                datapos=(0, 1), output=map_names,  samplingpos=map_positions)
        sys.stderr.write(mod.get_bash() + "\n")
        process_queue.put(mod)

    # Wait for unfinished processes
    process_queue.wait()

    # Insert new interpolated maps in temporal database and dataset
    for _map in result_list:
        id = _map.get_id()
        if overwrite_flags[id] == True:
            if _map.is_time_absolute():
                start, end = _map.get_absolute_time()
                if _map.is_in_db():
                    _map.delete(dbif)
                _map = sp.get_new_map_instance(id)
                _map.set_absolute_time(start, end)
            else:
                start, end, unit = _map.get_relative_time()
                if _map.is_in_db():
                    _map.delete(dbif)
                _map = sp.get_new_map_instance(id)
                _map.set_relative_time(start, end, unit)
        _map.load()
        _map.insert(dbif)
        sp.register_map(_map, dbif)

    sp.update_from_registered_maps(dbif)
    sp.update_command_string(dbif=dbif)
    dbif.close()

###############################################################################


def run_interp(inputs, dpos, output, outpos):
    """Helper function to run r.series.interp in parallel"""
    return grass.run_command("r.series.interp", input=inputs, datapos=dpos,
                             output=output, samplingpos=outpos,
                             overwrite=grass.overwrite(), quiet=True)

if __name__ == "__main__":
    options, flags = grass.parser()
    main()