예제 #1
0
def STEP7_calc_centrality():
    """ Analyze network centrality using Circuitscape
        given Linkage Mapper outputs

    """
    try:
        lu.dashline(0)
        gprint('Running script ' + _SCRIPT_NAME)

        arcpy.env.workspace = cfg.SCRATCHDIR

        # Check for valid LCP shapefile
        prevLcpShapefile = lu.get_lcp_shapefile(None, thisStep=7)
        if not arcpy.Exists(prevLcpShapefile):
            msg = ('Cannot find an LCP shapefile from step 5.  Please '
                   'rerun that step and any previous ones if necessary.')
            lu.raise_error(msg)

        # Remove lcp shapefile from this step if run previously
        lcpShapefile = path.join(cfg.DATAPASSDIR, "lcpLines_s7.shp")
        lu.delete_data(lcpShapefile)

        invalidFNs = ['fid', 'id', 'oid', 'shape']
        if cfg.COREFN.lower() in invalidFNs:
            #if cfg.COREFN == 'FID' or cfg.COREFN == 'ID':
            lu.dashline(1)
            msg = ('ERROR: Core area field names ID, FID, SHAPE, and OID are'
                   ' reserved for ArcGIS. \nPlease choose another field- must'
                   ' be a positive integer.')
            lu.raise_error(msg)

        lu.dashline(1)
        gprint('Mapping centrality of network cores and links'
               '\nusing Circuitscape....')
        lu.dashline(0)

        # set the analysis extent and cell size to that of the resistance
        # surface
        coreCopy = path.join(cfg.SCRATCHDIR, 'cores.shp')
        arcpy.CopyFeatures_management(cfg.COREFC, coreCopy)
        if not arcpy.ListFields(coreCopy, "CF_Central"):
            arcpy.AddField_management(coreCopy, "CF_Central", "DOUBLE")

        inLinkTableFile = lu.get_prev_step_link_table(step=7)
        linkTable = lu.load_link_table(inLinkTableFile)
        numLinks = linkTable.shape[0]
        numCorridorLinks = lu.report_links(linkTable)
        if numCorridorLinks == 0:
            lu.dashline(1)
            msg = ('\nThere are no linkages. Bailing.')
            lu.raise_error(msg)

        if linkTable.shape[1] < 16:  # If linktable has no entries from prior
            # centrality or pinchpint analyses
            extraCols = npy.zeros((numLinks, 6), dtype=npy.float64)
            linkTable = linkTable[:, 0:10]
            linkTable = npy.append(linkTable, extraCols, axis=1)
            linkTable[:, cfg.LTB_LCPLEN] = -1
            linkTable[:, cfg.LTB_CWDEUCR] = -1
            linkTable[:, cfg.LTB_CWDPATHR] = -1
            linkTable[:, cfg.LTB_EFFRESIST] = -1
            linkTable[:, cfg.LTB_CWDTORR] = -1
            del extraCols

        linkTable[:, cfg.LTB_CURRENT] = -1

        coresToProcess = npy.unique(linkTable[:,
                                              cfg.LTB_CORE1:cfg.LTB_CORE2 + 1])
        maxCoreNum = max(coresToProcess)
        del coresToProcess

        lu.dashline(0)

        coreList = linkTable[:, cfg.LTB_CORE1:cfg.LTB_CORE2 + 1]
        coreList = npy.sort(coreList)

        # set up directory for centrality
        INCENTRALITYDIR = cfg.CENTRALITYBASEDIR
        OUTCENTRALITYDIR = path.join(cfg.CENTRALITYBASEDIR,
                                     cfg.CIRCUITOUTPUTDIR_NM)
        CONFIGDIR = path.join(INCENTRALITYDIR, cfg.CIRCUITCONFIGDIR_NM)

        # Set Circuitscape options and write config file
        options = lu.set_cs_options()
        options['data_type'] = 'network'
        options['habitat_file'] = path.join(INCENTRALITYDIR,
                                            'Circuitscape_graph.txt')
        # Setting point file equal to graph to do all pairs in Circuitscape
        options['point_file'] = path.join(INCENTRALITYDIR,
                                          'Circuitscape_graph.txt')
        outputFN = 'Circuitscape_network.out'
        options['output_file'] = path.join(OUTCENTRALITYDIR, outputFN)
        configFN = 'Circuitscape_network.ini'
        outConfigFile = path.join(CONFIGDIR, configFN)
        lu.write_cs_cfg_file(outConfigFile, options)

        delRows = npy.asarray(npy.where(linkTable[:, cfg.LTB_LINKTYPE] < 1))
        delRowsVector = npy.zeros((delRows.shape[1]), dtype="int32")
        delRowsVector[:] = delRows[0, :]
        LT = lu.delete_row(linkTable, delRowsVector)
        del delRows
        del delRowsVector
        graphList = npy.zeros((LT.shape[0], 3), dtype=npy.float64)
        graphList[:, 0] = LT[:, cfg.LTB_CORE1]
        graphList[:, 1] = LT[:, cfg.LTB_CORE2]
        graphList[:, 2] = LT[:, cfg.LTB_CWDIST]

        write_graph(options['habitat_file'], graphList)
        gprint('\nCalculating current flow centrality using Circuitscape...')

        memFlag = lu.call_circuitscape(cfg.CSPATH, outConfigFile)

        outputFN = 'Circuitscape_network_branch_currents_cum.txt'
        currentList = path.join(OUTCENTRALITYDIR, outputFN)

        if not arcpy.Exists(currentList):
            write_graph(options['habitat_file'], graphList)
            gprint('\nCalculating current flow centrality using Circuitscape '
                   '(2nd try)...')
            memFlag = lu.call_circuitscape(cfg.CSPATH, outConfigFile)
            if not arcpy.Exists(currentList):
                lu.dashline(1)
                msg = ('ERROR: No Circuitscape output found.\n'
                       'It looks like Circuitscape failed.')
                arcpy.AddError(msg)
                lu.write_log(msg)
                exit(1)

        currents = load_graph(currentList,
                              graphType='graph/network',
                              datatype=npy.float64)

        numLinks = currents.shape[0]
        for x in range(0, numLinks):
            corex = currents[x, 0]
            corey = currents[x, 1]

            #linkId = LT[x,cfg.LTB_LINKID]
            row = lu.get_links_from_core_pairs(linkTable, corex, corey)
            #row = lu.get_linktable_row(linkId, linkTable)
            linkTable[row, cfg.LTB_CURRENT] = currents[x, 2]

        coreCurrentFN = 'Circuitscape_network_node_currents_cum.txt'
        nodeCurrentList = path.join(OUTCENTRALITYDIR, coreCurrentFN)
        nodeCurrents = load_graph(nodeCurrentList,
                                  graphType='graph/network',
                                  datatype=npy.float64)

        numNodeCurrents = nodeCurrents.shape[0]
        rows = arcpy.UpdateCursor(coreCopy)
        row = rows.newRow()
        for row in rows:
            coreID = row.getValue(cfg.COREFN)
            for i in range(0, numNodeCurrents):
                if coreID == nodeCurrents[i, 0]:
                    row.setValue("CF_Central", nodeCurrents[i, 1])
                    break
            rows.updateRow(row)
            #row = rows.newRow()
        del row, rows
        gprint('Done with centrality calculations.')

        finalLinkTable = lu.update_lcp_shapefile(linkTable,
                                                 lastStep=5,
                                                 thisStep=7)
        linkTableFile = path.join(cfg.DATAPASSDIR, "linkTable_s5_plus.csv")
        lu.write_link_table(finalLinkTable, linkTableFile, inLinkTableFile)
        linkTableFinalFile = path.join(cfg.OUTPUTDIR,
                                       cfg.PREFIX + "_linkTable_s5_plus.csv")
        lu.write_link_table(finalLinkTable, linkTableFinalFile,
                            inLinkTableFile)
        gprint('Copy of final linkTable written to ' + linkTableFinalFile)

        finalCoreFile = path.join(cfg.CORECENTRALITYGDB, cfg.PREFIX + '_Cores')
        #copy core area map to gdb.
        if not arcpy.Exists(cfg.CORECENTRALITYGDB):
            arcpy.CreateFileGDB_management(
                cfg.OUTPUTDIR, path.basename(cfg.CORECENTRALITYGDB))
        arcpy.CopyFeatures_management(coreCopy, finalCoreFile)

        gprint('Creating shapefiles with linework for links.')
        lu.write_link_maps(linkTableFinalFile, step=7)

        # Copy final link maps to gdb and clean up.
        lu.copy_final_link_maps(step=7)

    # Return GEOPROCESSING specific errors
    except arcpy.ExecuteError:
        lu.dashline(1)
        gprint('****Failed in step 7. Details follow.****')
        lu.exit_with_geoproc_error(_SCRIPT_NAME)

    # Return any PYTHON or system specific errors
    except Exception:
        lu.dashline(1)
        gprint('****Failed in step 7. Details follow.****')
        lu.exit_with_python_error(_SCRIPT_NAME)

    return
예제 #2
0
def STEP3_calc_cwds():
    """Calculates cost-weighted distances from each core area.
    Uses bounding circles around source and target cores to limit
    extent of cwd calculations and speed computation.

    """
    try:
        lu.dashline(1)
        gprint('Running script ' + _SCRIPT_NAME)
        lu.dashline(0)

        # Super secret setting to re-start failed run.  Enter 'RESTART' as the
        # Name of the pairwise distance table in step 2, and uncheck step 2.
        # We can eventually place this in a .ini file.
        rerun = False
        if cfg.S2EUCDISTFILE != None:
            if cfg.S2EUCDISTFILE.lower() == "restart":
                rerun = True

        # if cfg.TMAXCWDIST is None:
           	# gprint('NOT using a maximum cost-weighted distance.')
        # else:
            # gprint('Max cost-weighted distance for CWD calcs set '
                              # 'to ' + str(cfg.TMAXCWDIST) + '\n')

                              
        if (cfg.BUFFERDIST) is not None:
            gprint('Bounding circles plus a buffer of ' +
                              str(float(cfg.BUFFERDIST)) + ' map units will '
                              'be used \n to limit extent of cost distance '
                              'calculations.')
        elif cfg.TOOL <> cfg.TOOL_CC:
            gprint('NOT using bounding circles in cost distance '
                              'calculations.')

        # set the analysis extent and cell size
        # So we don't extract rasters that go beyond extent of original raster
        if arcpy:
            arcpy.env.cellSize = cfg.RESRAST
            arcpy.env.extent="MINOF"
        else:
            gp.cellSize = gp.Describe(cfg.RESRAST).MeanCellHeight
            gp.Extent = "MINOF"
        gp.mask = cfg.RESRAST
        if arcpy:
            arcpy.env.overwriteOutput = True
            arcpy.env.workspace = cfg.SCRATCHDIR
            arcpy.env.scratchWorkspace = cfg.ARCSCRATCHDIR
        else:
            gp.OverwriteOutput = True
            gp.workspace = cfg.SCRATCHDIR
            gp.scratchWorkspace = cfg.ARCSCRATCHDIR

        # Load linkTable (created in previous script)
        linkTableFile = lu.get_prev_step_link_table(step=3)
        linkTable = lu.load_link_table(linkTableFile)
        lu.report_links(linkTable)

        # Identify cores to map from LinkTable
        coresToMap = npy.unique(linkTable[:, cfg.LTB_CORE1:cfg.LTB_CORE2 + 1])
        numCoresToMap = len(coresToMap)

        if numCoresToMap < 3:
            # No need to check for intermediate cores, because there aren't any
            cfg.S3DROPLCCSic = False
        else:
            cfg.S3DROPLCCSic = cfg.S3DROPLCCS
        gprint('\nNumber of core areas to connect: ' +
                          str(numCoresToMap))

        if rerun:
            # If picking up a failed run, make sure needed files are there
            lu.dashline(1)
            gprint ('\n****** RESTART MODE ENABLED ******\n')
            gprint ('**** NOTE: This mode picks up step 3 where a\n'
                    'previous run left off due to a crash or user\n'
                    'abort.  It assumes you are using the same input\n'
                    'data used in the terminated run.\n\n')
            lu.warn('IMPORTANT: Your LCP and stick feature classes\n'
                    'will LOSE LCPs that were already created, but\n'
                    'your final raster corridor map should be complete.\n')
                    
            lu.dashline(0)
            lu.snooze(10)
            savedLinkTableFile = path.join(cfg.DATAPASSDIR,
                                           "temp_linkTable_s3_partial.csv")
            coreListFile = path.join(cfg.DATAPASSDIR, "temp_cores_to_map.csv")

            if not path.exists(savedLinkTableFile) or not path.exists(
                                                          coreListFile):

                gprint('No partial results file found from previous '
                       'stopped run. Starting run from beginning.\n')
                lu.dashline(0)
                rerun = False

        # If picking up a failed run, use old folders
        if not rerun:
            startIndex = 0
            if cfg.TOOL <> cfg.TOOL_CC:
                lu.make_cwd_paths(max(coresToMap)) # Set up cwd directories

        # make a feature layer for input cores to select from
        gp.MakeFeatureLayer(cfg.COREFC, cfg.FCORES)

        # Drop links that are too long
        gprint('\nChecking for corridors that are too long to map.')
        DISABLE_LEAST_COST_NO_VAL = False
        linkTable,numDroppedLinks = lu.drop_links(linkTable, cfg.MAXEUCDIST, 0,
                                                  cfg.MAXCOSTDIST, 0,
                                                  DISABLE_LEAST_COST_NO_VAL)
        # ------------------------------------------------------------------
        # Bounding boxes
        if (cfg.BUFFERDIST) is not None:
            # create bounding boxes around cores
            start_time = time.clock()
            # lu.dashline(1)
            gprint('Calculating bounding boxes for core areas.')
            extentBoxList = npy.zeros((0,5), dtype='float32')
            for x in range(len(coresToMap)):
                core = coresToMap[x]
                boxCoords = lu.get_extent_box_coords(core)
                extentBoxList = npy.append(extentBoxList, boxCoords, axis=0)
            gprint('\nDone calculating bounding boxes.')
            start_time = lu.elapsed_time(start_time)
            # lu.dashline()

        # Bounding circle code
        if cfg.BUFFERDIST is not None:
            # Make a set of circles encompassing core areas we'll be connecting
            start_time = time.clock()
            gprint('Calculating bounding circles around potential'
                          ' corridors.')

            # x y corex corey radius- stores data for bounding circle centroids
            boundingCirclePointArray  = npy.zeros((0,5), dtype='float32')

            circleList = npy.zeros((0,3), dtype='int32')

            numLinks = linkTable.shape[0]
            for x in range(0, numLinks):
                if ((linkTable[x,cfg.LTB_LINKTYPE] == cfg.LT_CORR) or
                    (linkTable[x,cfg.LTB_LINKTYPE] == cfg.LT_KEEP)):
                    # if it's a valid corridor link
                    linkId = int(linkTable[x,cfg.LTB_LINKID])
                    # fixme- this code is clumsy- can trim down
                    cores = npy.zeros((1,3), dtype='int32')
                    cores[0,:] = npy.sort([0, linkTable[x,cfg.LTB_CORE1],
                                      linkTable[x,cfg.LTB_CORE2]])
                    corex = cores[0,1]
                    corey = cores[0,2]
                    cores[0,0] = linkId

                    ###################
                    foundFlag = False
                    for y in range(0,len(circleList)):  # clumsy
                        if (circleList[y,1] == corex and
                            circleList[y,2] == corey):
                            foundFlag = True
                    if not foundFlag:
                        circlePointData = (
                            lu.get_bounding_circle_data(extentBoxList,
                            corex, corey, cfg.BUFFERDIST))
                        boundingCirclePointArray = (
                            npy.append(boundingCirclePointArray,
                            circlePointData, axis=0))
                        # keep track of which cores we draw bounding circles
                        # around
                        circleList = npy.append(circleList, cores, axis=0)

            gprint('\nCreating bounding circles using buffer '
                              'analysis.')

            dir, BNDCIRCENS = path.split(cfg.BNDCIRCENS)
            lu.make_points(cfg.SCRATCHDIR, boundingCirclePointArray,
                           BNDCIRCENS)
            lu.delete_data(cfg.BNDCIRS)
            gp.buffer_analysis(cfg.BNDCIRCENS, cfg.BNDCIRS, "radius")
            gp.deletefield (cfg.BNDCIRS, "BUFF_DIST")

            gprint('Successfully created bounding circles around '
                              'potential corridors using \na buffer of ' +
                              str(float(cfg.BUFFERDIST)) + ' map units.')
            start_time = lu.elapsed_time(start_time)

            gprint('Reducing global processing area using bounding '
                              'circle plus buffer of ' +
                              str(float(cfg.BUFFERDIST)) + ' map units.\n')


            extentBoxList = npy.zeros((0,5),dtype='float32')
            boxCoords = lu.get_extent_box_coords()
            extentBoxList = npy.append(extentBoxList,boxCoords,axis=0)
            extentBoxList[0,0] = 0

            boundingCirclePointArray  = npy.zeros((0,5),dtype='float32')
            circlePointData=lu.get_bounding_circle_data(extentBoxList, 0,
                                                        0, cfg.BUFFERDIST)

            dir, BNDCIRCEN = path.split(cfg.BNDCIRCEN)
            lu.make_points(cfg.SCRATCHDIR, circlePointData, BNDCIRCEN)
            lu.delete_data(cfg.BNDCIR)
            gp.buffer_analysis(cfg.BNDCIRCEN, cfg.BNDCIR, "radius")

            gprint('Extracting raster....')
            cfg.BOUNDRESIS = cfg.BOUNDRESIS + tif
            lu.delete_data(cfg.BOUNDRESIS)
            count = 0
            statement = (
                'gp.ExtractByMask_sa(cfg.RESRAST, cfg.BNDCIR, cfg.BOUNDRESIS)')
            while True:
                try:
                    exec statement
                    randomerror()
                except:
                    count,tryAgain = lu.retry_arc_error(count,statement)
                    if not tryAgain: exec statement
                else: break
            gprint('\nReduced resistance raster extracted using '
                              'bounding circle.')

        else: #if not using bounding circles, just go with resistance raster.
            cfg.BOUNDRESIS = cfg.RESRAST

        # ---------------------------------------------------------------------
        # Rasterize core areas to speed cost distance calcs
        # lu.dashline(1)
        gprint("Creating core area raster.")

        gp.SelectLayerByAttribute(cfg.FCORES, "CLEAR_SELECTION")

        if arcpy:
            arcpy.env.cellSize = cfg.BOUNDRESIS
            arcpy.env.extent = cfg.BOUNDRESIS
        else:
            gp.cellSize = gp.Describe(cfg.BOUNDRESIS).MeanCellHeight
            gp.extent = gp.Describe(cfg.BOUNDRESIS).extent

        if rerun:
            # saved linktable replaces the one now in memory
            linkTable = lu.load_link_table(savedLinkTableFile)
            coresToMapSaved = npy.loadtxt(coreListFile, dtype='Float64',
                                          comments='#', delimiter=',')
            startIndex = coresToMapSaved[0] # Index of core where we left off
            del coresToMapSaved
            gprint ('\n****** Re-starting run at core area number '
                    + str(int(coresToMap[startIndex]))+ ' ******\n')
            lu.dashline(0)

        if arcpy:
            arcpy.env.extent = "MINOF"
        else:
            gp.extent = "MINOF"

        #----------------------------------------------------------------------
        # Loop through cores, do cwd calcs for each
        if cfg.TOOL == cfg.TOOL_CC:
            gprint("\nMapping least-cost paths.\n")
        else:
            gprint("\nStarting cost distance calculations.\n")
        lcpLoop = 0
        failures = 0
        x = startIndex
        endIndex = len(coresToMap)
        linkTableMod = linkTable.copy()
        while x < endIndex:
            startTime1 = time.clock()
            # Modification of linkTable in function was causing problems. so
            # make a copy:
            linkTablePassed = linkTableMod.copy()

            (linkTableReturned, failures, lcpLoop) = do_cwd_calcs(x,
                        linkTablePassed, coresToMap, lcpLoop, failures)
            if failures == 0:
                # If iteration was successful, continue with next core
                linkTableMod = linkTableReturned
                sourceCore = int(coresToMap[x])
                gprint('Done with all calculations for core ID #' +
                        str(sourceCore) + '. ' + str(int(x + 1)) + ' of ' +
                        str(endIndex) + ' cores have been processed.')
                start_time = lu.elapsed_time(startTime1)

                outlinkTableFile = path.join(cfg.DATAPASSDIR,
                                             "temp_linkTable_s3_partial.csv")
                lu.write_link_table(linkTableMod, outlinkTableFile)
                # Increment  loop counter
                x = x + 1
            else:
                # If iteration failed, try again after a wait period
                delay_restart(failures)
        #----------------------------------------------------------------------

        linkTable = linkTableMod

        # reinstate temporarily disabled links
        rows = npy.where(linkTable[:,cfg.LTB_LINKTYPE] > 1000)
        linkTable[rows,cfg.LTB_LINKTYPE] = (linkTable[rows,cfg.LTB_LINKTYPE] -
                                            1000)

        # Drop links that are too long
        DISABLE_LEAST_COST_NO_VAL = True
        linkTable,numDroppedLinks = lu.drop_links(linkTable, cfg.MAXEUCDIST,
                                               cfg.MINEUCDIST, cfg.MAXCOSTDIST,
                                               cfg.MINCOSTDIST,
                                               DISABLE_LEAST_COST_NO_VAL)

        # Write link table file
        outlinkTableFile = lu.get_this_step_link_table(step=3)
        gprint('Updating ' + outlinkTableFile)
        lu.write_link_table(linkTable, outlinkTableFile)
        linkTableLogFile = path.join(cfg.LOGDIR, "linkTable_s3.csv")
        lu.write_link_table(linkTable, linkTableLogFile)

        start_time = time.clock()
        gprint('Creating shapefiles with linework for links...')
        try:
            lu.write_link_maps(outlinkTableFile, step=3)
        except:
            lu.write_link_maps(outlinkTableFile, step=3)
        start_time = lu.elapsed_time(start_time)

        gprint('\nIndividual cost-weighted distance layers written '
                          'to "cwd" directory. \n')
        gprint(outlinkTableFile +
                '\n updated with cost-weighted distances between core areas.')

        #Clean up temporary files for restart code
        tempFile = path.join(cfg.DATAPASSDIR, "temp_cores_to_map.csv")
        lu.delete_file(tempFile)
        tempFile = path.join(cfg.DATAPASSDIR, "temp_linkTable_s3_partial.csv")
        lu.delete_file(tempFile)

        # Check if climate tool is calling linkage mapper
        if cfg.TOOL == cfg.TOOL_CC:
            coreList = npy.unique(linkTable[:, cfg.LTB_CORE1:cfg.LTB_CORE2 + 1])
            for core in coreList:
                cwdRaster = lu.get_cwd_path(int(core))
                back_rast = cwdRaster.replace("cwd_", "back_")        
                lu.delete_data(back_rast)
        

    # Return GEOPROCESSING specific errors
    except arcgisscripting.ExecuteError:
        lu.dashline(1)
        gprint('****Failed in step 3. Details follow.****')
        lu.exit_with_geoproc_error(_SCRIPT_NAME)

    # Return any PYTHON or system specific errors
    except:
        lu.dashline(1)
        gprint('****Failed in step 3. Details follow.****')
        lu.exit_with_python_error(_SCRIPT_NAME)

    return
예제 #3
0
def calc_lccs(normalize):
    try:
        if normalize:
            mosaicBaseName = "_corridors"
            writeTruncRaster = cfg.WRITETRUNCRASTER
            outputGDB = cfg.OUTPUTGDB
            SAVENORMLCCS = cfg.SAVENORMLCCS
        else:
            mosaicBaseName = "_NON_NORMALIZED_corridors"
            SAVENORMLCCS = False
            outputGDB = cfg.EXTRAGDB
            writeTruncRaster = False

        lu.dashline(1)
        gprint('Running script ' + _SCRIPT_NAME)
        linkTableFile = lu.get_prev_step_link_table(step=5)
        arcpy.env.workspace = cfg.SCRATCHDIR
        arcpy.env.scratchWorkspace = cfg.ARCSCRATCHDIR
        arcpy.env.compression = "NONE"

        if cfg.MAXEUCDIST is not None:
            gprint('Max Euclidean distance between cores')
            gprint('for linkage mapping set to ' +
                              str(cfg.MAXEUCDIST))

        if cfg.MAXCOSTDIST is not None:
            gprint('Max cost-weighted distance between cores')
            gprint('for linkage mapping set to ' +
                              str(cfg.MAXCOSTDIST))


        # set the analysis extent and cell size to that of the resistance
        # surface
        arcpy.env.extent = cfg.RESRAST
        arcpy.env.cellSize = arcpy.Describe(cfg.RESRAST).MeanCellHeight
        arcpy.env.snapRaster = cfg.RESRAST
        arcpy.env.mask = cfg.RESRAST

        linkTable = lu.load_link_table(linkTableFile)
        numLinks = linkTable.shape[0]
        numCorridorLinks = lu.report_links(linkTable)
        if numCorridorLinks == 0:
            lu.dashline(1)
            msg =('\nThere are no corridors to map. Bailing.')
            lu.raise_error(msg)


        if not cfg.STEP3 and not cfg.STEP4:
            # re-check for links that are too long or in case script run out of
            # sequence with more stringent settings
            gprint('Double-checking for corridors that are too long to map.')
            DISABLE_LEAST_COST_NO_VAL = True
            linkTable,numDroppedLinks = lu.drop_links(
                linkTable, cfg.MAXEUCDIST, cfg.MINEUCDIST, cfg.MAXCOSTDIST,
                cfg.MINCOSTDIST, DISABLE_LEAST_COST_NO_VAL)

        # Added to try to speed up:
        arcpy.env.pyramid = "NONE"
        arcpy.env.rasterStatistics = "NONE"

        # set up directories for normalized lcc and mosaic grids
        dirCount = 0
        gprint("Creating output folder: " + cfg.LCCBASEDIR)
        lu.delete_dir(cfg.LCCBASEDIR)
        arcpy.CreateFolder_management(path.dirname(cfg.LCCBASEDIR),
                                       path.basename(cfg.LCCBASEDIR))
        arcpy.CreateFolder_management(cfg.LCCBASEDIR, cfg.LCCNLCDIR_NM)
        clccdir = path.join(cfg.LCCBASEDIR, cfg.LCCNLCDIR_NM)
        gprint("")
        if normalize:
            gprint('Normalized least-cost corridors will be written '
                          'to ' + clccdir + '\n')
        PREFIX = cfg.PREFIX

        # Add CWD layers for core area pairs to produce NORMALIZED LCC layers
        numGridsWritten = 0
        coreList = linkTable[:,cfg.LTB_CORE1:cfg.LTB_CORE2+1]
        coreList = npy.sort(coreList)

        x = 0
        linkCount = 0
        endIndex = numLinks
        while x < endIndex:
            if (linkTable[x, cfg.LTB_LINKTYPE] < 1): # If not a valid link
                x = x + 1
                continue

            linkCount = linkCount + 1
            start_time = time.clock()

            linkId = str(int(linkTable[x, cfg.LTB_LINKID]))

            # source and target cores
            corex=int(coreList[x,0])
            corey=int(coreList[x,1])

            # Get cwd rasters for source and target cores
            cwdRaster1 = lu.get_cwd_path(corex)
            cwdRaster2 = lu.get_cwd_path(corey)

            if not arcpy.Exists(cwdRaster1):
                msg =('\nError: cannot find cwd raster:\n' + cwdRaster1)
            if not arcpy.Exists(cwdRaster2):
                msg =('\nError: cannot find cwd raster:\n' + cwdRaster2)
                lu.raise_error(msg)


            lccNormRaster = path.join(clccdir, str(corex) + "_" +
                                      str(corey))# + ".tif")
            arcpy.env.extent = "MINOF"

            link = lu.get_links_from_core_pairs(linkTable, corex, corey)

            offset = 10000

            # Normalized lcc rasters are created by adding cwd rasters and
            # subtracting the least cost distance between them.
            lcDist = (float(linkTable[link,cfg.LTB_CWDIST]) - offset)

            if normalize:
                statement = ('outras = arcpy.sa.Raster(cwdRaster1) '
                             '+ arcpy.sa.Raster(cwdRaster2) - lcDist; '
                             'outras.save(lccNormRaster)')
            else:
                statement = ('outras = arcpy.sa.Raster(cwdRaster1) '
                             '+ arcpy.sa.Raster(cwdRaster2); '
                             'outras.save(lccNormRaster)')

            count = 0
            while True:
                try:
                    exec(statement)
                except Exception:
                    count,tryAgain = lu.retry_arc_error(count,statement)
                    if not tryAgain:
                        exec(statement)
                else: break

            if normalize:
                try:
                    minObject = arcpy.GetRasterProperties_management(lccNormRaster, "MINIMUM")
                    rasterMin = float(str(minObject.getOutput(0)))
                except Exception:
                    lu.warn('\n------------------------------------------------')
                    lu.warn('WARNING: Raster minimum check failed in step 5. \n'
                        'This may mean the output rasters are corrupted. Please \n'
                        'be sure to check for valid rasters in '+ outputGDB)
                    rasterMin = 0
                tolerance = (float(arcpy.env.cellSize) * -10)
                if rasterMin < tolerance:
                    lu.dashline(1)
                    msg = ('WARNING: Minimum value of a corridor #' + str(x+1)
                           + ' is much less than zero ('+str(rasterMin)+').'
                           '\nThis could mean that BOUNDING CIRCLE BUFFER DISTANCES '
                           'were too small and a corridor passed outside of a '
                           'bounding circle, or that a corridor passed outside of the '
                           'resistance map. \n')
                    lu.warn(msg)

            arcpy.env.extent = cfg.RESRAST

            mosaicDir = path.join(cfg.LCCBASEDIR,'mos'+str(x+1))
            lu.create_dir(mosaicDir)
            mosFN = 'mos'#.tif' change and move
            mosaicRaster = path.join(mosaicDir,mosFN)

            if numGridsWritten == 0 and dirCount == 0:
                #If this is the first grid then copy rather than mosaic
                arcpy.CopyRaster_management(lccNormRaster, mosaicRaster)
            else:
                statement = (
                    'arcpy.MosaicToNewRaster_management('
                    'input_rasters=";".join([lccNormRaster, '
                    'lastMosaicRaster]), output_location=mosaicDir, '
                    'raster_dataset_name_with_extension=mosFN, '
                    'pixel_type="32_BIT_FLOAT", cellsize=arcpy.env.cellSize, '
                    'number_of_bands="1", mosaic_method="MINIMUM")')

                count = 0
                while True:
                    try:
                        lu.write_log('Executing mosaic for link #'+str(linkId))
                        exec(statement)
                        lu.write_log('Done with mosaic.')
                    except Exception:
                        count,tryAgain = lu.retry_arc_error(count,statement)
                        lu.delete_data(mosaicRaster)
                        lu.delete_dir(mosaicDir)
                        # Try a new directory
                        mosaicDir = path.join(cfg.LCCBASEDIR,'mos'+str(x+1)+ '_' + str(count))
                        lu.create_dir(mosaicDir)
                        mosaicRaster = path.join(mosaicDir,mosFN)
                        if not tryAgain:
                            exec(statement)
                    else: break
            endTime = time.clock()
            processTime = round((endTime - start_time), 2)

            if normalize == True:
                printText = "Normalized and mosaicked "
            else:
                printText = "Mosaicked NON-normalized "
            gprint(printText + "corridor for link ID #" + str(linkId) +
                    " connecting core areas " + str(corex) +
                    " and " + str(corey)+ " in " +
                    str(processTime) + " seconds. " + str(int(linkCount)) +
                    " out of " + str(int(numCorridorLinks)) + " links have been "
                    "processed.")

            # temporarily disable links in linktable - don't want to mosaic
            # them twice
            for y in range (x+1,numLinks):
                corex1 = int(coreList[y,0])
                corey1 = int(coreList[y,1])
                if corex1 == corex and corey1 == corey:
                    linkTable[y,cfg.LTB_LINKTYPE] = (
                        linkTable[y,cfg.LTB_LINKTYPE] + 1000)
                elif corex1==corey and corey1==corex:
                    linkTable[y,cfg.LTB_LINKTYPE] = (
                            linkTable[y,cfg.LTB_LINKTYPE] + 1000)

            numGridsWritten = numGridsWritten + 1
            if not SAVENORMLCCS:
                lu.delete_data(lccNormRaster)
                lu.delete_dir(clccdir)
                lu.create_dir(clccdir)
            else:
                if numGridsWritten == 100:
                    # We only write up to 100 grids to any one folder
                    # because otherwise Arc slows to a crawl
                    dirCount = dirCount + 1
                    numGridsWritten = 0
                    clccdir = path.join(cfg.LCCBASEDIR,
                                        cfg.LCCNLCDIR_NM + str(dirCount))
                    gprint("Creating output folder: " + clccdir)
                    arcpy.CreateFolder_management(cfg.LCCBASEDIR,
                                               path.basename(clccdir))

            if numGridsWritten > 1 or dirCount > 0:
                lu.delete_data(lastMosaicRaster)
                lu.delete_dir(path.dirname(lastMosaicRaster))

            lastMosaicRaster = mosaicRaster
            x = x + 1

        #rows that were temporarily disabled
        rows = npy.where(linkTable[:,cfg.LTB_LINKTYPE]>1000)
        linkTable[rows,cfg.LTB_LINKTYPE] = (
            linkTable[rows,cfg.LTB_LINKTYPE] - 1000)
        # ---------------------------------------------------------------------

        # Create output geodatabase
        if not arcpy.Exists(outputGDB):
            arcpy.CreateFileGDB_management(cfg.OUTPUTDIR, path.basename(outputGDB))

        arcpy.env.workspace = outputGDB

        arcpy.env.pyramid = "NONE"
        arcpy.env.rasterStatistics = "NONE"

        # ---------------------------------------------------------------------
        # convert mosaic raster to integer
        intRaster = path.join(outputGDB,PREFIX + mosaicBaseName)
        statement = ('outras = arcpy.sa.Int(arcpy.sa.Raster(mosaicRaster) '
                     '- offset + 0.5); '
                     'outras.save(intRaster)')
        count = 0
        while True:
            try:
                exec(statement)
            except Exception:
                count,tryAgain = lu.retry_arc_error(count,statement)
                if not tryAgain: exec(statement)
            else: break
        # ---------------------------------------------------------------------


        if writeTruncRaster:
            # -----------------------------------------------------------------
            # Set anything beyond cfg.CWDTHRESH to NODATA.
            truncRaster = (outputGDB + '\\' + PREFIX + mosaicBaseName +
                           '_truncated_at_' + lu.cwd_cutoff_str(cfg.CWDTHRESH))

            statement = ('outRas = arcpy.sa.Raster(intRaster)'
                         '* (arcpy.sa.Con(arcpy.sa.Raster(intRaster) '
                         '<= cfg.CWDTHRESH, 1)); '
                         'outRas.save(truncRaster)')

            count = 0
            while True:
                try:
                    exec(statement)
                except Exception:
                    count,tryAgain = lu.retry_arc_error(count,statement)
                    if not tryAgain: exec(statement)
                else: break
        # ---------------------------------------------------------------------
        # Check for unreasonably low minimum NLCC values
        try:
            mosaicGrid = path.join(cfg.LCCBASEDIR,'mos')
            # Copy to grid to test
            arcpy.CopyRaster_management(mosaicRaster, mosaicGrid)
            minObject = arcpy.GetRasterProperties_management(mosaicGrid, "MINIMUM")
            rasterMin = float(str(minObject.getOutput(0)))
        except Exception:
            lu.warn('\n------------------------------------------------')
            lu.warn('WARNING: Raster minimum check failed in step 5. \n'
                'This may mean the output rasters are corrupted. Please \n'
                'be sure to check for valid rasters in '+ outputGDB)
            rasterMin = 0
        tolerance = (float(arcpy.env.cellSize) * -10)
        if rasterMin < tolerance:
            lu.dashline(1)
            msg = ('WARNING: Minimum value of mosaicked corridor map is '
                   'much less than zero ('+str(rasterMin)+').'
                   '\nThis could mean that BOUNDING CIRCLE BUFFER DISTANCES '
                   'were too small and a corridor passed outside of a '
                   'bounding circle, or that a corridor passed outside of the '
                   'resistance map. \n')
            lu.warn(msg)


        gprint('\nWriting final LCP maps...')
        if cfg.STEP4:
            finalLinkTable = lu.update_lcp_shapefile(linkTable, lastStep=4,
                                                     thisStep=5)
        elif cfg.STEP3:
            finalLinkTable = lu.update_lcp_shapefile(linkTable, lastStep=3,
                                                     thisStep=5)
        else:
            # Don't know if step 4 was run, since this is started at step 5.
            # Use presence of previous linktable files to figure this out.
            # Linktable name includes step number.
            prevLinkTableFile = lu.get_prev_step_link_table(step=5)
            prevStepInd = len(prevLinkTableFile) - 5
            lastStep = prevLinkTableFile[prevStepInd]

            finalLinkTable = lu.update_lcp_shapefile(linkTable, lastStep,
                                                     thisStep=5)

        outlinkTableFile = lu.get_this_step_link_table(step=5)
        gprint('Updating ' + outlinkTableFile)
        lu.write_link_table(linkTable, outlinkTableFile)

        linkTableLogFile = path.join(cfg.LOGDIR, "linkTable_s5.csv")
        lu.write_link_table(linkTable, linkTableLogFile)

        linkTableFinalFile = path.join(cfg.OUTPUTDIR, PREFIX +
                                       "_linkTable_s5.csv")
        lu.write_link_table(finalLinkTable, linkTableFinalFile)
        gprint('Copy of final linkTable written to '+
                          linkTableFinalFile)

        gprint('Creating shapefiles with linework for links.')
        try:
            lu.write_link_maps(outlinkTableFile, step=5)
        except Exception:
            lu.write_link_maps(outlinkTableFile, step=5)

        # Create final linkmap files in output directory, and remove files from
        # scratch.
        lu.copy_final_link_maps(step=5)

        if not SAVENORMLCCS:
            lu.delete_dir(cfg.LCCBASEDIR)

        # Build statistics for corridor rasters
        arcpy.AddMessage('\nBuilding output statistics and pyramids '
                          'for corridor raster')
        lu.build_stats(intRaster)

        if writeTruncRaster:
            arcpy.AddMessage('Building output statistics '
                              'for truncated corridor raster')
            lu.build_stats(truncRaster)

        save_parameters()
        if cfg.OUTPUTFORMODELBUILDER:
            arcpy.CopyFeatures_management(cfg.COREFC, cfg.OUTPUTFORMODELBUILDER)

    # Return GEOPROCESSING specific errors
    except arcpy.ExecuteError:
        lu.dashline(1)
        gprint('****Failed in step 5. Details follow.****')
        lu.exit_with_geoproc_error(_SCRIPT_NAME)

    # Return any PYTHON or system specific errors
    except Exception:
        lu.dashline(1)
        gprint('****Failed in step 5. Details follow.****')
        lu.exit_with_python_error(_SCRIPT_NAME)

    return
예제 #4
0
def STEP6_calc_barriers():
    """Detects influential barriers given CWD calculations from
       s3_calcCwds.py.

    """

    try:
        arcpy.CheckOutExtension("spatial")
        lu.dashline(0)
        gprint('Running script ' + _SCRIPT_NAME)

        if cfg.BARRIER_CWD_THRESH is not None:
            lu.dashline(1)
            gprint('Invoking CWD Threshold of ' + str(cfg.BARRIER_CWD_THRESH) +
                   ' map units.')

        if cfg.SUM_BARRIERS:
            sumSuffix = '_Sum'
            cfg.BARRIERBASEDIR = cfg.BARRIERBASEDIR + sumSuffix
            baseName, extension = path.splitext(cfg.BARRIERGDB)
            cfg.BARRIERGDB = baseName + sumSuffix + extension

            gprint('\nBarrier scores will be SUMMED across core pairs.')
        else:
            sumSuffix = ''

        # Delete contents of final ouptut geodatabase
        # lu.clean_out_workspace(cfg.BARRIERGDB) #xxx try not doing this to allow multiple radii to be analyzed in separate runs
        if not arcpy.Exists(cfg.BARRIERGDB):
            # Create output geodatabase
            arcpy.CreateFileGDB_management(cfg.OUTPUTDIR,
                                           path.basename(cfg.BARRIERGDB))

        startRadius = int(cfg.STARTRADIUS)
        endRadius = int(cfg.ENDRADIUS)
        radiusStep = int(cfg.RADIUSSTEP)
        if radiusStep == 0:
            endRadius = startRadius  # Calculate at just one radius value
            radiusStep = 1
        linkTableFile = lu.get_prev_step_link_table(step=6)
        arcpy.env.workspace = cfg.SCRATCHDIR
        arcpy.env.scratchWorkspace = cfg.ARCSCRATCHDIR
        arcpy.RefreshCatalog(cfg.PROJECTDIR)
        PREFIX = path.basename(cfg.PROJECTDIR)
        # For speed:
        arcpy.env.pyramid = "NONE"
        arcpy.env.rasterStatistics = "NONE"

        # set the analysis extent and cell size to that of the resistance
        # surface
        arcpy.OverWriteOutput = True
        arcpy.env.extent = cfg.RESRAST
        arcpy.env.cellSize = cfg.RESRAST
        arcpy.env.snapRaster = cfg.RESRAST
        spatialref = arcpy.Describe(cfg.RESRAST).spatialReference
        mapUnits = (str(spatialref.linearUnitName)).lower()
        if len(mapUnits) > 1 and mapUnits[-1] != 's':
            mapUnits = mapUnits + 's'

        if float(arcpy.env.cellSize) > startRadius or startRadius > endRadius:
            msg = ('Error: minimum detection radius must be greater than '
                   'cell size (' + str(arcpy.env.cellSize) +
                   ') \nand less than or equal to maximum detection radius.')
            lu.raise_error(msg)

        linkTable = lu.load_link_table(linkTableFile)
        numLinks = linkTable.shape[0]
        numCorridorLinks = lu.report_links(linkTable)
        if numCorridorLinks == 0:
            lu.dashline(1)
            msg = ('\nThere are no linkages. Bailing.')
            lu.raise_error(msg)

        # set up directories for barrier and barrier mosaic grids
        dirCount = 0
        gprint("Creating intermediate output folder: " + cfg.BARRIERBASEDIR)
        lu.delete_dir(cfg.BARRIERBASEDIR)
        lu.create_dir(cfg.BARRIERBASEDIR)
        arcpy.CreateFolder_management(cfg.BARRIERBASEDIR, cfg.BARRIERDIR_NM)
        cbarrierdir = path.join(cfg.BARRIERBASEDIR, cfg.BARRIERDIR_NM)

        coresToProcess = npy.unique(linkTable[:,
                                              cfg.LTB_CORE1:cfg.LTB_CORE2 + 1])
        maxCoreNum = max(coresToProcess)

        # Set up focal directories.
        # To keep there from being > 100 grids in any one directory,
        # outputs are written to:
        # barrier\focalX_ for cores 1-99 at radius X
        # barrier\focalX_1 for cores 100-199
        # etc.
        lu.dashline(0)

        for radius in range(startRadius, endRadius + 1, radiusStep):
            core1path = lu.get_focal_path(1, radius)
            path1, dir1 = path.split(core1path)
            path2, dir2 = path.split(path1)
            arcpy.CreateFolder_management(path.dirname(path2),
                                          path.basename(path2))
            arcpy.CreateFolder_management(path.dirname(path1),
                                          path.basename(path1))

            if maxCoreNum > 99:
                gprint('Creating subdirectories for ' + str(radius) + ' ' +
                       str(mapUnits) + ' radius analysis scale.')
                maxDirCount = int(maxCoreNum / 100)
                focalDirBaseName = dir2

                cp100 = (coresToProcess.astype('int32')) / 100
                ind = npy.where(cp100 > 0)
                dirNums = npy.unique(cp100[ind])
                for dirNum in dirNums:
                    focalDir = focalDirBaseName + str(dirNum)
                    gprint('...' + focalDir)
                    arcpy.CreateFolder_management(path2, focalDir)

        # Create resistance raster with filled-in Nodata values for later use
        arcpy.env.extent = cfg.RESRAST
        resistFillRaster = path.join(cfg.SCRATCHDIR, "resist_fill")
        output = arcpy.sa.Con(IsNull(cfg.RESRAST), 1000000000,
                              Raster(cfg.RESRAST) - 1)
        output.save(resistFillRaster)

        coreList = linkTable[:, cfg.LTB_CORE1:cfg.LTB_CORE2 + 1]
        coreList = npy.sort(coreList)

        # Loop through each search radius to calculate barriers in each link
        import time
        radId = 0  #keep track of number of radii processed- used for temp dir naming
        for radius in range(startRadius, endRadius + 1, radiusStep):
            radId = radId + 1
            linkTableTemp = linkTable.copy()

            @retry(10)
            #can't pass vars in and modify them.
            def doRadiusLoop():
                linkTable = linkTableTemp.copy()
                startTime = time.clock()
                randomerror()
                linkLoop = 0
                pctDone = 0
                gprint('\nMapping barriers at a radius of ' + str(radius) +
                       ' ' + str(mapUnits))
                if cfg.SUM_BARRIERS:
                    gprint('using SUM method')
                else:
                    gprint('using MAXIMUM method')
                if numCorridorLinks > 1:
                    gprint('0 percent done')
                lastMosaicRaster = None
                lastMosaicRasterPct = None
                for x in range(0, numLinks):
                    pctDone = lu.report_pct_done(linkLoop, numCorridorLinks,
                                                 pctDone)
                    linkId = str(int(linkTable[x, cfg.LTB_LINKID]))
                    if ((linkTable[x, cfg.LTB_LINKTYPE] > 0)
                            and (linkTable[x, cfg.LTB_LINKTYPE] < 1000)):
                        linkLoop = linkLoop + 1
                        # source and target cores
                        corex = int(coreList[x, 0])
                        corey = int(coreList[x, 1])

                        # Get cwd rasters for source and target cores
                        cwdRaster1 = lu.get_cwd_path(corex)
                        cwdRaster2 = lu.get_cwd_path(corey)

                        # Mask out areas above CWD threshold
                        cwdTemp1 = None
                        cwdTemp2 = None
                        if cfg.BARRIER_CWD_THRESH is not None:
                            if x == 1:
                                lu.dashline(1)
                                gprint('  Using CWD threshold of ' +
                                       str(cfg.BARRIER_CWD_THRESH) +
                                       ' map units.')
                            arcpy.env.extent = cfg.RESRAST
                            arcpy.env.cellSize = cfg.RESRAST
                            arcpy.env.snapRaster = cfg.RESRAST
                            cwdTemp1 = path.join(cfg.SCRATCHDIR,
                                                 "tmp" + str(corex))
                            outCon = arcpy.sa.Con(
                                cwdRaster1 < float(cfg.BARRIER_CWD_THRESH),
                                cwdRaster1)
                            outCon.save(cwdTemp1)
                            cwdRaster1 = cwdTemp1
                            cwdTemp2 = path.join(cfg.SCRATCHDIR,
                                                 "tmp" + str(corey))
                            outCon = arcpy.sa.Con(
                                cwdRaster2 < float(cfg.BARRIER_CWD_THRESH),
                                cwdRaster2)
                            outCon.save(cwdTemp2)
                            cwdRaster2 = cwdTemp2

                        focalRaster1 = lu.get_focal_path(corex, radius)
                        focalRaster2 = lu.get_focal_path(corey, radius)

                        link = lu.get_links_from_core_pairs(
                            linkTable, corex, corey)
                        lcDist = float(linkTable[link, cfg.LTB_CWDIST])

                        # Detect barriers at radius using neighborhood stats
                        # Create the Neighborhood Object
                        innerRadius = radius - 1
                        outerRadius = radius

                        dia = 2 * radius
                        InNeighborhood = ("ANNULUS " + str(innerRadius) + " " +
                                          str(outerRadius) + " MAP")

                        @retry(10)
                        def execFocal():
                            randomerror()
                            # Execute FocalStatistics
                            if not path.exists(focalRaster1):
                                arcpy.env.extent = cwdRaster1
                                outFocalStats = arcpy.sa.FocalStatistics(
                                    cwdRaster1, InNeighborhood, "MINIMUM",
                                    "DATA")
                                if setCoresToNull:
                                    outFocalStats2 = arcpy.sa.Con(
                                        outFocalStats > 0, outFocalStats
                                    )  # Set areas overlapping cores to NoData xxx
                                    outFocalStats2.save(focalRaster1)  #xxx
                                else:
                                    outFocalStats.save(focalRaster1)  #xxx
                                arcpy.env.extent = cfg.RESRAST

                            if not path.exists(focalRaster2):
                                arcpy.env.extent = cwdRaster2
                                outFocalStats = arcpy.sa.FocalStatistics(
                                    cwdRaster2, InNeighborhood, "MINIMUM",
                                    "DATA")
                                if setCoresToNull:
                                    outFocalStats2 = arcpy.sa.Con(
                                        outFocalStats > 0, outFocalStats
                                    )  # Set areas overlapping cores to NoData xxx
                                    outFocalStats2.save(focalRaster2)  #xxx
                                else:
                                    outFocalStats.save(focalRaster2)  #xxx

                                arcpy.env.extent = cfg.RESRAST

                        execFocal()

                        lu.delete_data(cwdTemp1)
                        lu.delete_data(cwdTemp2)

                        barrierRaster = path.join(
                            cbarrierdir, "b" + str(radius) + "_" + str(corex) +
                            "_" + str(corey) + '.tif')

                        if cfg.SUM_BARRIERS:  # Need to set nulls to 0, also
                            # create trim rasters as we go

                            outRas = ((lcDist - Raster(focalRaster1) -
                                       Raster(focalRaster2) - dia) / dia)
                            outCon = arcpy.sa.Con(IsNull(outRas), 0, outRas)
                            outCon2 = arcpy.sa.Con(outCon < 0, 0, outCon)
                            outCon2.save(barrierRaster)

                            # Execute FocalStatistics to fill out search radii
                            InNeighborhood = "CIRCLE " + str(
                                outerRadius) + " MAP"
                            fillRaster = path.join(
                                cbarrierdir, "b" + str(radius) + "_" +
                                str(corex) + "_" + str(corey) + "_fill.tif")
                            outFocalStats = arcpy.sa.FocalStatistics(
                                barrierRaster, InNeighborhood, "MAXIMUM",
                                "DATA")
                            outFocalStats.save(fillRaster)

                            if cfg.WRITE_TRIM_RASTERS:
                                trmRaster = path.join(
                                    cbarrierdir,
                                    "b" + str(radius) + "_" + str(corex) +
                                    "_" + str(corey) + "_trim.tif")
                                rasterList = [fillRaster, resistFillRaster]
                                outCellStatistics = arcpy.sa.CellStatistics(
                                    rasterList, "MINIMUM")
                                outCellStatistics.save(trmRaster)

                        else:
                            #Calculate potential benefit per map unit restored
                            @retry(10)
                            def calcBen():
                                randomerror()
                                outRas = ((lcDist - Raster(focalRaster1) -
                                           Raster(focalRaster2) - dia) / dia)
                                outRas.save(barrierRaster)

                            calcBen()

                        if cfg.WRITE_PCT_RASTERS:
                            #Calculate PERCENT potential benefit per unit restored
                            barrierRasterPct = path.join(
                                cbarrierdir, "b" + str(radius) + "_" +
                                str(corex) + "_" + str(corey) + '_pct.tif')

                            @retry(10)
                            def calcBenPct():
                                randomerror()
                                outras = (100 *
                                          (Raster(barrierRaster) / lcDist))
                                outras.save(barrierRasterPct)

                            calcBenPct()

                        # Mosaic barrier results across core area pairs
                        mosaicDir = path.join(
                            cfg.SCRATCHDIR,
                            'mos' + str(radId) + '_' + str(x + 1))
                        lu.create_dir(mosaicDir)

                        mosFN = 'mos_temp'
                        tempMosaicRaster = path.join(mosaicDir, mosFN)
                        tempMosaicRasterTrim = path.join(
                            mosaicDir, 'mos_temp_trm')
                        arcpy.env.workspace = mosaicDir
                        if linkLoop == 1:
                            #If this is the first grid then copy rather than mosaic
                            arcpy.CopyRaster_management(
                                barrierRaster, tempMosaicRaster)
                            if cfg.SUM_BARRIERS and cfg.WRITE_TRIM_RASTERS:
                                arcpy.CopyRaster_management(
                                    trmRaster, tempMosaicRasterTrim)

                        else:
                            if cfg.SUM_BARRIERS:
                                outCon = arcpy.sa.Con(
                                    Raster(barrierRaster) < 0,
                                    lastMosaicRaster,
                                    Raster(barrierRaster) +
                                    Raster(lastMosaicRaster))
                                outCon.save(tempMosaicRaster)
                                if cfg.WRITE_TRIM_RASTERS:
                                    outCon = arcpy.sa.Con(
                                        Raster(trmRaster) < 0,
                                        lastMosaicRasterTrim,
                                        Raster(trmRaster) +
                                        Raster(lastMosaicRasterTrim))
                                    outCon.save(tempMosaicRasterTrim)

                            else:
                                rasterString = ('"' + barrierRaster + ";" +
                                                lastMosaicRaster + '"')

                                @retry(10)
                                def mosaicToNew():
                                    randomerror()
                                    arcpy.MosaicToNewRaster_management(
                                        rasterString, mosaicDir, mosFN, "",
                                        "32_BIT_FLOAT", arcpy.env.cellSize,
                                        "1", "MAXIMUM", "MATCH")

                                mosaicToNew()
                                # gprint(str(corex)+'0'+str(corey))

                        if linkLoop > 1:  #Clean up from previous loop
                            lu.delete_data(lastMosaicRaster)
                            lastMosaicDir = path.dirname(lastMosaicRaster)
                            lu.clean_out_workspace(lastMosaicDir)
                            lu.delete_dir(lastMosaicDir)

                        lastMosaicRaster = tempMosaicRaster
                        if cfg.WRITE_TRIM_RASTERS:
                            lastMosaicRasterTrim = tempMosaicRasterTrim
                        if cfg.WRITE_PCT_RASTERS:
                            mosPctFN = 'mos_temp_pct'
                            mosaicDirPct = path.join(
                                cfg.SCRATCHDIR,
                                'mosP' + str(radId) + '_' + str(x + 1))
                            lu.create_dir(mosaicDirPct)
                            tempMosaicRasterPct = path.join(
                                mosaicDirPct, mosPctFN)
                            if linkLoop == 1:
                                # If this is the first grid then copy
                                # rather than mosaic
                                if cfg.SUM_BARRIERS:
                                    outCon = arcpy.sa.Con(
                                        Raster(barrierRasterPct) < 0, 0,
                                        arcpy.sa.Con(IsNull(barrierRasterPct),
                                                     0, barrierRasterPct))
                                    outCon.save(tempMosaicRasterPct)
                                else:
                                    arcpy.CopyRaster_management(
                                        barrierRasterPct, tempMosaicRasterPct)

                            else:
                                if cfg.SUM_BARRIERS:

                                    @retry(10)
                                    def sumBarriers():
                                        randomerror()
                                        outCon = arcpy.sa.Con(
                                            Raster(barrierRasterPct) < 0,
                                            lastMosaicRasterPct,
                                            Raster(barrierRasterPct) +
                                            Raster(lastMosaicRasterPct))
                                        outCon.save(tempMosaicRasterPct)

                                    sumBarriers()
                                else:
                                    rasterString = ('"' + barrierRasterPct +
                                                    ";" + lastMosaicRasterPct +
                                                    '"')

                                    @retry(10)
                                    def maxBarriers():
                                        randomerror()
                                        arcpy.MosaicToNewRaster_management(
                                            rasterString, mosaicDirPct,
                                            mosPctFN, "", "32_BIT_FLOAT",
                                            arcpy.env.cellSize, "1", "MAXIMUM",
                                            "MATCH")

                                    maxBarriers()

                            if linkLoop > 1:  #Clean up from previous loop
                                lu.delete_data(lastMosaicRasterPct)
                                lastMosaicDirPct = path.dirname(
                                    lastMosaicRasterPct)
                                lu.clean_out_workspace(lastMosaicDirPct)
                                lu.delete_dir(lastMosaicDirPct)

                            # lu.delete_data(lastMosaicRasterPct)
                            lastMosaicRasterPct = tempMosaicRasterPct

                        if not cfg.SAVEBARRIERRASTERS:
                            lu.delete_data(barrierRaster)
                            if cfg.WRITE_PCT_RASTERS:
                                lu.delete_data(barrierRasterPct)
                            if cfg.WRITE_TRIM_RASTERS:
                                lu.delete_data(trmRaster)

                        # Temporarily disable links in linktable -
                        # don't want to mosaic them twice
                        for y in range(x + 1, numLinks):
                            corex1 = int(coreList[y, 0])
                            corey1 = int(coreList[y, 1])
                            if corex1 == corex and corey1 == corey:
                                linkTable[y, cfg.LTB_LINKTYPE] = (
                                    linkTable[y, cfg.LTB_LINKTYPE] + 1000)
                            elif corex1 == corey and corey1 == corex:
                                linkTable[y, cfg.LTB_LINKTYPE] = (
                                    linkTable[y, cfg.LTB_LINKTYPE] + 1000)

                if numCorridorLinks > 1 and pctDone < 100:
                    gprint('100 percent done')
                gprint('Summarizing barrier data for search radius.')
                #rows that were temporarily disabled
                rows = npy.where(linkTable[:, cfg.LTB_LINKTYPE] > 1000)
                linkTable[rows, cfg.LTB_LINKTYPE] = (
                    linkTable[rows, cfg.LTB_LINKTYPE] - 1000)

                # -----------------------------------------------------------------

                # Set negative values to null or zero and write geodatabase.
                mosaicFN = (PREFIX + "_BarrierCenters" + sumSuffix + "_Rad" +
                            str(radius))
                mosaicRaster = path.join(cfg.BARRIERGDB, mosaicFN)
                arcpy.env.extent = cfg.RESRAST

                # if setCoresToNull:
                # outCon = arcpy.sa.Con(Raster(tempMosaicRaster) < 0, 0,
                # tempMosaicRaster) #xxx
                # outCon.save(mosaicRaster) #xxx
                # else:
                outSetNull = arcpy.sa.SetNull(tempMosaicRaster,
                                              tempMosaicRaster,
                                              "VALUE < 0")  #xxx orig
                outSetNull.save(mosaicRaster)

                lu.delete_data(tempMosaicRaster)

                if cfg.SUM_BARRIERS and cfg.WRITE_TRIM_RASTERS:
                    mosaicFN = (PREFIX + "_BarrierCircles_RBMin" + sumSuffix +
                                "_Rad" + str(radius))
                    mosaicRasterTrim = path.join(cfg.BARRIERGDB, mosaicFN)
                    arcpy.CopyRaster_management(tempMosaicRasterTrim,
                                                mosaicRasterTrim)
                    lu.delete_data(tempMosaicRaster)

                if cfg.WRITE_PCT_RASTERS:
                    # Do same for percent raster
                    mosaicPctFN = (PREFIX + "_BarrierCenters_Pct" + sumSuffix +
                                   "_Rad" + str(radius))
                    arcpy.env.extent = cfg.RESRAST
                    outSetNull = arcpy.sa.SetNull(tempMosaicRasterPct,
                                                  tempMosaicRasterPct,
                                                  "VALUE < 0")
                    mosaicRasterPct = path.join(cfg.BARRIERGDB, mosaicPctFN)
                    outSetNull.save(mosaicRasterPct)
                    lu.delete_data(tempMosaicRasterPct)

                # 'Grow out' maximum restoration gain to
                # neighborhood size for display
                InNeighborhood = "CIRCLE " + str(outerRadius) + " MAP"
                # Execute FocalStatistics
                fillRasterFN = "barriers_fill" + str(outerRadius) + tif
                fillRaster = path.join(cfg.BARRIERBASEDIR, fillRasterFN)
                outFocalStats = arcpy.sa.FocalStatistics(
                    mosaicRaster, InNeighborhood, "MAXIMUM", "DATA")
                outFocalStats.save(fillRaster)

                if cfg.WRITE_PCT_RASTERS:
                    # Do same for percent raster
                    fillRasterPctFN = "barriers_fill_pct" + str(
                        outerRadius) + tif
                    fillRasterPct = path.join(cfg.BARRIERBASEDIR,
                                              fillRasterPctFN)
                    outFocalStats = arcpy.sa.FocalStatistics(
                        mosaicRasterPct, InNeighborhood, "MAXIMUM", "DATA")
                    outFocalStats.save(fillRasterPct)

                #Place copies of filled rasters in output geodatabase
                arcpy.env.workspace = cfg.BARRIERGDB
                fillRasterFN = (PREFIX + "_BarrrierCircles" + sumSuffix +
                                "_Rad" + str(outerRadius))
                arcpy.CopyRaster_management(fillRaster, fillRasterFN)
                if cfg.WRITE_PCT_RASTERS:
                    fillRasterPctFN = (PREFIX + "_BarrrierCircles_Pct" +
                                       sumSuffix + "_Rad" + str(outerRadius))
                    arcpy.CopyRaster_management(fillRasterPct, fillRasterPctFN)

                if not cfg.SUM_BARRIERS and cfg.WRITE_TRIM_RASTERS:
                    # Create pared-down version of filled raster- remove pixels
                    # that don't need restoring by allowing a pixel to only
                    # contribute its resistance value to restoration gain
                    outRasterFN = "barriers_trm" + str(outerRadius) + tif
                    outRaster = path.join(cfg.BARRIERBASEDIR, outRasterFN)
                    rasterList = [fillRaster, resistFillRaster]
                    outCellStatistics = arcpy.sa.CellStatistics(
                        rasterList, "MINIMUM")
                    outCellStatistics.save(outRaster)

                    #SECOND ROUND TO CLIP BY DATA VALUES IN BARRIER RASTER
                    outRaster2FN = ("barriers_trm" + sumSuffix +
                                    str(outerRadius) + "_2" + tif)
                    outRaster2 = path.join(cfg.BARRIERBASEDIR, outRaster2FN)
                    output = arcpy.sa.Con(IsNull(fillRaster), fillRaster,
                                          outRaster)
                    output.save(outRaster2)
                    outRasterFN = (PREFIX + "_BarrierCircles_RBMin" +
                                   sumSuffix + "_Rad" + str(outerRadius))

                    outRasterPath = path.join(cfg.BARRIERGDB, outRasterFN)
                    arcpy.CopyRaster_management(outRaster2, outRasterFN)
                randomerror()
                startTime = lu.elapsed_time(startTime)

            # Call the above function
            doRadiusLoop()

        # Combine rasters across radii
        gprint('\nCreating summary rasters...')
        if startRadius != endRadius:
            radiiSuffix = ('_Rad' + str(int(startRadius)) + 'To' +
                           str(int(endRadius)) + 'Step' + str(int(radiusStep)))
            mosaicFN = "bar_radii"
            mosaicPctFN = "bar_radii_pct"
            arcpy.env.workspace = cfg.BARRIERBASEDIR
            for radius in range(startRadius, endRadius + 1, radiusStep):
                #Fixme: run speed test with gdb mosaicking above and here
                radiusFN = (PREFIX + "_BarrierCenters" + sumSuffix + "_Rad" +
                            str(radius))
                radiusRaster = path.join(cfg.BARRIERGDB, radiusFN)

                if radius == startRadius:
                    #If this is the first grid then copy rather than mosaic
                    arcpy.CopyRaster_management(radiusRaster, mosaicFN)
                else:
                    mosaicRaster = path.join(cfg.BARRIERBASEDIR, mosaicFN)
                    arcpy.Mosaic_management(radiusRaster, mosaicRaster,
                                            "MAXIMUM", "MATCH")

                if cfg.WRITE_PCT_RASTERS:
                    radiusPctFN = (PREFIX + "_BarrierCenters_Pct" + sumSuffix +
                                   "_Rad" + str(radius))
                    radiusRasterPct = path.join(cfg.BARRIERGDB, radiusPctFN)

                    if radius == startRadius:
                        #If this is the first grid then copy rather than mosaic
                        arcpy.CopyRaster_management(radiusRasterPct,
                                                    mosaicPctFN)
                    else:
                        mosaicRasterPct = path.join(cfg.BARRIERBASEDIR,
                                                    mosaicPctFN)
                        arcpy.Mosaic_management(radiusRasterPct,
                                                mosaicRasterPct, "MAXIMUM",
                                                "MATCH")

            # Copy results to output geodatabase
            arcpy.env.workspace = cfg.BARRIERGDB
            mosaicFN = PREFIX + "_BarrierCenters" + sumSuffix + radiiSuffix
            arcpy.CopyRaster_management(mosaicRaster, mosaicFN)

            if cfg.WRITE_PCT_RASTERS:
                mosaicPctFN = (PREFIX + "_BarrierCenters_Pct" + sumSuffix +
                               radiiSuffix)
                arcpy.CopyRaster_management(mosaicRasterPct, mosaicPctFN)

            #GROWN OUT rasters
            fillMosaicFN = "barriers_radii_fill" + tif
            fillMosaicPctFN = "barriers_radii_fill_pct" + tif
            fillMosaicRaster = path.join(cfg.BARRIERBASEDIR, fillMosaicFN)
            fillMosaicRasterPct = path.join(cfg.BARRIERBASEDIR,
                                            fillMosaicPctFN)

            arcpy.env.workspace = cfg.BARRIERBASEDIR
            for radius in range(startRadius, endRadius + 1, radiusStep):
                radiusFN = "barriers_fill" + str(radius) + tif
                #fixme- do this when only a single radius too
                radiusRaster = path.join(cfg.BARRIERBASEDIR, radiusFN)
                if radius == startRadius:
                    #If this is the first grid then copy rather than mosaic
                    arcpy.CopyRaster_management(radiusRaster, fillMosaicFN)
                else:
                    arcpy.Mosaic_management(radiusRaster, fillMosaicRaster,
                                            "MAXIMUM", "MATCH")

                if cfg.WRITE_PCT_RASTERS:
                    radiusPctFN = "barriers_fill_pct" + str(radius) + tif
                    #fixme- do this when only a single radius too
                    radiusRasterPct = path.join(cfg.BARRIERBASEDIR,
                                                radiusPctFN)
                    if radius == startRadius:
                        #If this is the first grid then copy rather than mosaic
                        arcpy.CopyRaster_management(radiusRasterPct,
                                                    fillMosaicPctFN)
                    else:
                        arcpy.Mosaic_management(radiusRasterPct,
                                                fillMosaicRasterPct, "MAXIMUM",
                                                "MATCH")

            # Copy result to output geodatabase
            arcpy.env.workspace = cfg.BARRIERGDB
            fillMosaicFN = PREFIX + "_BarrierCircles" + sumSuffix + radiiSuffix
            arcpy.CopyRaster_management(fillMosaicRaster, fillMosaicFN)
            if cfg.WRITE_PCT_RASTERS:
                fillMosaicPctFN = (PREFIX + "_BarrierCircles_Pct" + sumSuffix +
                                   radiiSuffix)
                arcpy.CopyRaster_management(fillMosaicRasterPct,
                                            fillMosaicPctFN)


#            if not cfg.SUM_BARRIERS:
#GROWN OUT AND TRIMMED rasters (Can't do percent)
            if cfg.WRITE_TRIM_RASTERS:
                trimMosaicFN = "bar_radii_trm"
                arcpy.env.workspace = cfg.BARRIERBASEDIR
                trimMosaicRaster = path.join(cfg.BARRIERBASEDIR, trimMosaicFN)
                for radius in range(startRadius, endRadius + 1, radiusStep):
                    radiusFN = (PREFIX + "_BarrierCircles_RBMin" + sumSuffix +
                                "_Rad" + str(radius))
                    #fixme- do this when only a single radius too
                    radiusRaster = path.join(cfg.BARRIERGDB, radiusFN)

                    if radius == startRadius:
                        #If this is the first grid then copy rather than mosaic
                        arcpy.CopyRaster_management(radiusRaster, trimMosaicFN)
                    else:
                        arcpy.Mosaic_management(radiusRaster, trimMosaicRaster,
                                                "MAXIMUM", "MATCH")
                # Copy result to output geodatabase
                arcpy.env.workspace = cfg.BARRIERGDB
                trimMosaicFN = (PREFIX + "_BarrierCircles_RBMin" + sumSuffix +
                                radiiSuffix)
                arcpy.CopyRaster_management(trimMosaicRaster, trimMosaicFN)

        if not cfg.SAVE_RADIUS_RASTERS:
            arcpy.env.workspace = cfg.BARRIERGDB
            rasters = arcpy.ListRasters()
            for raster in rasters:
                if 'rad' in raster.lower() and not 'step' in raster.lower():
                    lu.delete_data(raster)

        arcpy.env.workspace = cfg.BARRIERGDB
        rasters = arcpy.ListRasters()
        for raster in rasters:
            gprint('\nBuilding output statistics and pyramids\n'
                   'for raster ' + raster)
            lu.build_stats(raster)

        #Clean up temporary files and directories
        if not cfg.SAVEBARRIERRASTERS:
            lu.delete_dir(cbarrierdir)
            lu.delete_dir(cfg.BARRIERBASEDIR)

        if not cfg.SAVEFOCALRASTERS:
            for radius in range(startRadius, endRadius + 1, radiusStep):
                core1path = lu.get_focal_path(1, radius)
                path1, dir1 = path.split(core1path)
                path2, dir2 = path.split(path1)
                lu.delete_dir(path2)

    # Return GEOPROCESSING specific errors
    except arcpy.ExecuteError:
        lu.dashline(1)
        gprint('****Failed in step 6. Details follow.****')
        lu.exit_with_geoproc_error(_SCRIPT_NAME)

    # Return any PYTHON or system specific errors
    except:
        lu.dashline(1)
        gprint('****Failed in step 6. Details follow.****')
        lu.exit_with_python_error(_SCRIPT_NAME)

    return
예제 #5
0
def STEP8_calc_pinchpoints():
    """ Maps pinch points in Linkage Mapper corridors using Circuitscape
        given CWD calculations from s3_calcCwds.py.

    """
    try:
        lu.dashline(0)
        gprint('Running script ' + _SCRIPT_NAME)
        
        restartFlag = False
        if cfg.CWDCUTOFF < 0:
            cfg.CWDCUTOFF = cfg.CWDCUTOFF * -1
            restartFlag = True # Restart code in progress
        
        CSPATH = lu.get_cs_path()                
        outputGDB = path.join(cfg.OUTPUTDIR, path.basename(cfg.PINCHGDB))
        
        arcpy.OverWriteOutput = True
        arcpy.env.workspace = cfg.SCRATCHDIR
        arcpy.env.scratchWorkspace = cfg.ARCSCRATCHDIR
        arcpy.env.pyramid = "NONE"
        arcpy.env.rasterstatistics = "NONE"

        # set the analysis extent and cell size to that of the resistance
        # surface
        arcpy.env.extent = cfg.RESRAST
        arcpy.env.cellSize = cfg.RESRAST
        arcpy.snapraster = cfg.RESRAST

        resRaster = cfg.RESRAST
        arcpy.env.extent = "MINOF"

        
        minObject = arcpy.GetRasterProperties_management(resRaster, "MINIMUM") 
        rasterMin = float(str(minObject.getOutput(0)))
        if rasterMin <= 0:
            msg = ('Error: resistance raster cannot have 0 or negative values.')
            lu.raise_error(msg)
                
        if cfg.DO_ADJACENTPAIRS:
            prevLcpShapefile = lu.get_lcp_shapefile(None, thisStep = 8)
            if not arcpy.Exists(prevLcpShapefile):
                msg = ('Cannot find an LCP shapefile from step 5.  Please '
                        'rerun that step and any previous ones if necessary.')
                lu.raise_error(msg)

            # Remove lcp shapefile
            lcpShapefile = path.join(cfg.DATAPASSDIR, "lcpLines_s8.shp")
            lu.delete_data(lcpShapefile)

        inLinkTableFile = lu.get_prev_step_link_table(step=8)
        linkTable = lu.load_link_table(inLinkTableFile)
        numLinks = linkTable.shape[0]
        numCorridorLinks = lu.report_links(linkTable)
        if numCorridorLinks == 0:
            lu.dashline(1)
            msg =('\nThere are no linkages. Bailing.')
            lu.raise_error(msg)

        if linkTable.shape[1] < 16: # If linktable has no entries from prior
                                    # centrality or pinchpint analyses
            extraCols = npy.zeros((numLinks, 6), dtype="float64")
            linkTable = linkTable[:,0:10]
            linkTable = npy.append(linkTable, extraCols, axis=1)
            linkTable[:, cfg.LTB_LCPLEN] = -1
            linkTable[:, cfg.LTB_CWDEUCR] = -1
            linkTable[:, cfg.LTB_CWDPATHR] = -1
            linkTable[:, cfg.LTB_EFFRESIST] = -1
            linkTable[:, cfg.LTB_CWDTORR] = -1
            linkTable[:, cfg.LTB_CURRENT] = -1
            del extraCols

        # set up directories for circuit and circuit mosaic grids
        # Create output geodatabase
        if not arcpy.Exists(cfg.PINCHGDB):
            arcpy.CreateFileGDB_management(cfg.OUTPUTDIR,
                                            path.basename(cfg.PINCHGDB))

        mosaicRaster = path.join(cfg.CIRCUITBASEDIR, "current_mos" + tif)
        coresToProcess = npy.unique(
                                linkTable[:, cfg.LTB_CORE1:cfg.LTB_CORE2 + 1])
        maxCoreNum = max(coresToProcess)
        del coresToProcess

        lu.dashline(0)
        coreList = linkTable[:,cfg.LTB_CORE1:cfg.LTB_CORE2+1]
        coreList = npy.sort(coreList)
        #gprint('There are ' + str(len(npy.unique(coreList))) ' core areas.')

        INCIRCUITDIR = cfg.CIRCUITBASEDIR
        OUTCIRCUITDIR = path.join(cfg.CIRCUITBASEDIR,
                                  cfg.CIRCUITOUTPUTDIR_NM)
        CONFIGDIR = path.join(INCIRCUITDIR, cfg.CIRCUITCONFIGDIR_NM)

        # Cutoff value text to append to filenames
        cutoffText = str(cfg.CWDCUTOFF)
        if cutoffText[-6:] == '000000':
            cutoffText = cutoffText[0:-6]+'m' 
        elif cutoffText[-3:] == '000':
            cutoffText = cutoffText[0:-3]+'k' 

        if cfg.SQUARERESISTANCES:
            # Square resistance values
            squaredRaster = path.join(cfg.SCRATCHDIR,'res_sqr')
            arcpy.env.workspace = cfg.SCRATCHDIR
            arcpy.env.scratchWorkspace = cfg.ARCSCRATCHDIR
            outRas = Raster(resRaster) * Raster(resRaster)
            outRas.save(squaredRaster)
            resRaster = squaredRaster

        if cfg.DO_ADJACENTPAIRS:
            linkLoop = 0
            lu.dashline(1)
            gprint('Mapping pinch points in individual corridors \n'
                    'using Circuitscape.')
            lu.dashline(1)
            gprint('If you try to cancel your run and the Arc dialog hangs, ')
            gprint('you can kill Circuitscape by opening Windows Task Manager')
            gprint('and ending the cs_run.exe process.')                    
            lu.dashline(2)

            for x in range(0,numLinks):            
                linkId = str(int(linkTable[x,cfg.LTB_LINKID]))
                if not (linkTable[x,cfg.LTB_LINKTYPE] > 0):
                    continue
                linkLoop = linkLoop + 1
                linkDir = path.join(cfg.SCRATCHDIR, 'link' + linkId)
                if restartFlag == True and path.exists(linkDir):
                    gprint('continuing')
                    continue
                restartFlag = False
                lu.create_dir(linkDir)
                start_time1 = time.clock()

                # source and target cores
                corex=int(coreList[x,0])
                corey=int(coreList[x,1])

                # Get cwd rasters for source and target cores
                cwdRaster1 = lu.get_cwd_path(corex)
                cwdRaster2 = lu.get_cwd_path(corey)

                lccNormRaster = path.join(linkDir, 'lcc_norm')
                arcpy.env.extent = "MINOF"

                link = lu.get_links_from_core_pairs(linkTable, corex,
                                                    corey)
                lcDist = float(linkTable[link,cfg.LTB_CWDIST])

                # Normalized lcc rasters are created by adding cwd rasters
                # and subtracting the least cost distance between them.
                outRas = Raster(cwdRaster1) + Raster(cwdRaster2) - lcDist
                outRas.save(lccNormRaster)

                #create raster mask
                resMaskRaster = path.join(linkDir, 'res_mask'+tif)

                #create raster mask
                outCon = arcpy.sa.Con(Raster(lccNormRaster) <= cfg.CWDCUTOFF, 1)
                outCon.save(resMaskRaster)

                # Convert to poly.  Use as mask to clip resistance raster.
                resMaskPoly = path.join(linkDir,
                                        'res_mask_poly.shp')
                arcpy.RasterToPolygon_conversion(resMaskRaster, resMaskPoly,
                                              "NO_SIMPLIFY")
                arcpy.env.extent = resMaskPoly

                # Includes 0 values in some cases with CP LI model if tif
                # so using ESRI Grid format
                resClipRasterMasked = path.join(linkDir,
                                                'res_clip_m') 
                # Extract masked resistance raster.  
                # Needs to be float to get export to npy to work.
                outRas = arcpy.sa.ExtractByMask(resRaster, resMaskPoly) + 0.0 
                outRas.save(resClipRasterMasked)
               
                resNpyFN = 'resistances_link_' + linkId + '.npy'
                resNpyFile = path.join(INCIRCUITDIR, resNpyFN)
                numElements, numResistanceNodes = export_ras_to_npy(resClipRasterMasked,
                                                          resNpyFile)
                
                totMem, availMem = lu.get_mem()
                # gprint('Total memory: str(totMem))
                if numResistanceNodes / availMem > 2000000:
                    lu.dashline(1)
                    gwarn('Warning:')
                    gwarn('Circuitscape can only solve 2-3 million nodes')
                    gwarn('per gigabyte of available RAM. \nTotal physical RAM'
                            ' on your machine is ~' + str(totMem) 
                            + ' GB. \nAvailable memory is ~'+ str(availMem) 
                            + ' GB. \nYour resistance raster has '
                            + str(numResistanceNodes) + ' nodes.')                                                          
                    lu.dashline(2)
                corePairRaster = path.join(linkDir, 'core_pairs'+tif)
                arcpy.env.extent = resClipRasterMasked

                # Next result needs to be floating pt for numpy export
                outCon = arcpy.sa.Con(Raster(cwdRaster1) == 0, corex,
                            arcpy.sa.Con(Raster(cwdRaster2) == 0, corey + 0.0))
                outCon.save(corePairRaster)

                coreNpyFN = 'cores_link_' + linkId + '.npy'
                coreNpyFile = path.join(INCIRCUITDIR, coreNpyFN)
                numElements, numNodes = export_ras_to_npy(corePairRaster,
                                                          coreNpyFile)

                arcpy.env.extent = "MINOF"

                # Set circuitscape options and call
                options = lu.setCircuitscapeOptions()
                if cfg.WRITE_VOLT_MAPS == True:
                    options['write_volt_maps']=True
                options['habitat_file'] = resNpyFile
                
                # if int(linkId) > 2:
                    # options['habitat_file'] = 'c:\\test.dummy'
                                
                options['point_file'] = coreNpyFile
                options['set_focal_node_currents_to_zero']=True
                outputFN = 'Circuitscape_link' + linkId + '.out'
                options['output_file'] = path.join(OUTCIRCUITDIR, outputFN)
                if numElements > 250000:
                    options['print_timings']=True
                configFN = 'pinchpoint_config' + linkId + '.ini'

                outConfigFile = path.join(CONFIGDIR, configFN)
                lu.writeCircuitscapeConfigFile(outConfigFile, options)                    
                gprint('Processing link ID #' + str(linkId) + '. Resistance map'
                        ' has ' + str(int(numResistanceNodes)) + ' nodes.') 

                memFlag = call_circuitscape(CSPATH, outConfigFile)
                      
                currentFN = ('Circuitscape_link' + linkId 
                            + '_cum_curmap.npy')
                currentMap = path.join(OUTCIRCUITDIR, currentFN)
                
                if not arcpy.Exists(currentMap):
                    print_failure(numResistanceNodes, memFlag, 10)
                    numElements, numNodes = export_ras_to_npy(
                                                resClipRasterMasked,resNpyFile)
                    memFlag = call_circuitscape(CSPATH, outConfigFile)

                    currentFN = ('Circuitscape_link' + linkId 
                                + '_cum_curmap.npy')
                    currentMap = path.join(OUTCIRCUITDIR, currentFN)
                
                if not arcpy.Exists(currentMap):                
                    msg = ('\nCircuitscape failed. See error information above.')
                    arcpy.AddError(msg)
                    lu.write_log(msg)
                    exit(1)

                # Either set core areas to nodata in current map or
                # divide each by its radius
                currentRaster = path.join(linkDir, "current" + tif)
                import_npy_to_ras(currentMap,corePairRaster,currentRaster)
                
                if cfg.WRITE_VOLT_MAPS == True:
                    voltFN = ('Circuitscape_link' + linkId + '_voltmap_'
                           + str(corex) + '_'+str(corey) + '.npy')
                    voltMap = path.join(OUTCIRCUITDIR, voltFN)
                    voltRaster = path.join(outputGDB,
                             cfg.PREFIX + "_voltMap_"+ str(corex) + '_'+str(corey))                
                    import_npy_to_ras(voltMap,corePairRaster,voltRaster)
                    gprint('Building output statistics and pyramids '
                                   'for voltage raster\n')
                    lu.build_stats(voltRaster) 
                    
                arcpy.env.extent = currentRaster

                if SETCORESTONULL:
                    # Set core areas to NoData in current map for color ramping
                    currentRaster2 = currentRaster + '2' + tif
                    outCon = arcpy.sa.Con(arcpy.sa.IsNull(Raster
                                      (corePairRaster)), Raster(currentRaster))
                    outCon.save(currentRaster2)
                    currentRaster = currentRaster2
                arcpy.env.extent = "MAXOF"
                if linkLoop == 1:
                    lu.delete_data(mosaicRaster)
                    @retry(10)
                    def copyRas2():
                        arcpy.CopyRaster_management(currentRaster,
                                                    mosaicRaster)
                    copyRas2()
                else:
                    @retry(10)
                    def mosaicRas():                
                        arcpy.Mosaic_management(currentRaster,
                                         mosaicRaster, "MAXIMUM", "MATCH")
                    mosaicRas()
                    
                resistancesFN = ('Circuitscape_link' + linkId
                            + '_resistances_3columns.out')

                resistancesFile = path.join(OUTCIRCUITDIR,resistancesFN)
                resistances = npy.loadtxt(resistancesFile,
                                          dtype = 'Float64', comments='#')

                resistance = float(str(arcpy.env.cellSize)) * resistances[2]
                linkTable[link,cfg.LTB_EFFRESIST] = resistance

                # Ratio
                if not cfg.SQUARERESISTANCES:
                    linkTable[link,cfg.LTB_CWDTORR] = (linkTable[link,
                           cfg.LTB_CWDIST] / linkTable[link,cfg.LTB_EFFRESIST])
                # Clean up
                if cfg.SAVE_TEMP_CIRCUIT_FILES == False:
                    lu.delete_file(coreNpyFile)
                    coreNpyBase, extension = path.splitext(coreNpyFile)
                    lu.delete_data(coreNpyBase + '.hdr')                    
                    lu.delete_file(resNpyFile)
                    resNpyBase, extension = path.splitext(resNpyFile)
                    lu.delete_data(resNpyBase + '.hdr')                    
                    lu.delete_file(currentMap)
                    curMapBase, extension = path.splitext(currentMap)
                    lu.delete_data(curMapBase + '.hdr')
                    lu.delete_data(currentRaster) 
                    lu.clean_out_workspace(linkDir)
                    lu.delete_dir(linkDir) 
                gprint('Finished with link ID #' + str(linkId) + '. ' + 
                        str(linkLoop) + ' out of ' + str(numCorridorLinks) + 
                        ' links have been processed.')
                start_time1 = lu.elapsed_time(start_time1)
                
            outputRaster = path.join(outputGDB, cfg.PREFIX + 
                                     "_current_adjacentPairs_" + cutoffText)
            lu.delete_data(outputRaster)
            
            @retry(10)
            def copyRas():
                arcpy.CopyRaster_management(mosaicRaster, outputRaster)
            copyRas()

            gprint('Building output statistics and pyramids '
                                  'for corridor pinch point raster\n')
            lu.build_stats(outputRaster)
            
            finalLinkTable = lu.update_lcp_shapefile(linkTable, lastStep=5,
                                                      thisStep=8)

            linkTableFile = path.join(cfg.DATAPASSDIR, "linkTable_s5_plus.csv")
            lu.write_link_table(finalLinkTable, linkTableFile, inLinkTableFile)
            linkTableFinalFile = path.join(cfg.OUTPUTDIR, cfg.PREFIX + 
                                           "_linkTable_s5_plus.csv")
            lu.write_link_table(finalLinkTable,
                                linkTableFinalFile, inLinkTableFile)
            gprint('Copy of linkTable written to '+
                              linkTableFinalFile)
            #fixme: update sticks?

            gprint('Creating shapefiles with linework for links.')
            lu.write_link_maps(linkTableFinalFile, step=8)

            # Copy final link maps to gdb.
            lu.copy_final_link_maps(step=8)

            lu.delete_data(mosaicRaster)

        if not cfg.DO_ALLPAIRS:
            # Clean up temporary files
            if not cfg.SAVECURRENTMAPS:
                lu.delete_dir(OUTCIRCUITDIR)
            return

        lu.dashline(1)
        gprint('Mapping global pinch points among all\n'
                'core area pairs using Circuitscape.')                   
                
        if cfg.ALL_PAIR_SCENARIO=='pairwise':
            gprint('Circuitscape will be run in PAIRWISE mode.')
                        
        else:
            gprint('Circuitscape will be run in ALL-TO-ONE mode.')     
        arcpy.env.workspace = cfg.SCRATCHDIR
        arcpy.env.scratchWorkspace = cfg.ARCSCRATCHDIR
        arcpy.env.extent = cfg.RESRAST
        arcpy.env.cellSize = cfg.RESRAST

        S8CORE_RAS = "s8core_ras"
        s8CoreRasPath = path.join(cfg.SCRATCHDIR,S8CORE_RAS)

        arcpy.FeatureToRaster_conversion(cfg.COREFC, cfg.COREFN,
                                         s8CoreRasPath, arcpy.env.cellSize)
        binaryCoreRaster = path.join(cfg.SCRATCHDIR,"core_ras_bin")

        # The following commands cause file lock problems on save.  using gp
        # instead.
        # outCon = arcpy.sa.Con(S8CORE_RAS, 1, "#", "VALUE > 0")
        # outCon.save(binaryCoreRaster)
        # gp.Con_sa(s8CoreRasPath, 1, binaryCoreRaster, "#", "VALUE > 0")
        outCon = arcpy.sa.Con(Raster(s8CoreRasPath) > 0, 1)
        outCon.save(binaryCoreRaster)
        s5corridorRas = path.join(cfg.OUTPUTGDB,cfg.PREFIX + "_corridors")
        
        if not arcpy.Exists(s5corridorRas):
            s5corridorRas = path.join(cfg.OUTPUTGDB,cfg.PREFIX + 
                                      "_lcc_mosaic_int")

        outCon = arcpy.sa.Con(Raster(s5corridorRas) <= cfg.CWDCUTOFF, Raster(
                              resRaster), arcpy.sa.Con(Raster(
                              binaryCoreRaster) > 0, Raster(resRaster)))

        resRasClipPath = path.join(cfg.SCRATCHDIR,'res_ras_clip')
        outCon.save(resRasClipPath)

        arcpy.env.cellSize = resRasClipPath
        arcpy.env.extent = resRasClipPath
        s8CoreRasClipped = s8CoreRasPath + '_c'

        # Produce core raster with same extent as clipped resistance raster
        # added to ensure correct data type- nodata values were positive for 
        # cores otherwise
        outCon = arcpy.sa.Con(arcpy.sa.IsNull(Raster(s8CoreRasPath)), 
                              -9999, Raster(s8CoreRasPath))  
        outCon.save(s8CoreRasClipped)

        resNpyFN = 'resistances.npy'
        resNpyFile = path.join(INCIRCUITDIR, resNpyFN)
        numElements, numResistanceNodes = export_ras_to_npy(resRasClipPath,resNpyFile)

        totMem, availMem = lu.get_mem()
        # gprint('Total memory: str(totMem))
        if numResistanceNodes / availMem > 2000000:
            lu.dashline(1)
            gwarn('Warning:')
            gwarn('Circuitscape can only solve 2-3 million nodes')
            gwarn('per gigabyte of available RAM. \nTotal physical RAM '
                    'on your machine is ~' + str(totMem)
                    + ' GB. \nAvailable memory is ~'+ str(availMem)
                    + ' GB. \nYour resistance raster has '
                    + str(numResistanceNodes) + ' nodes.')   
            lu.dashline(0)

        coreNpyFN = 'cores.npy'
        coreNpyFile = path.join(INCIRCUITDIR, coreNpyFN)
        numElements, numNodes = export_ras_to_npy(s8CoreRasClipped,coreNpyFile)

        arcpy.env.extent = "MINOF"

        options = lu.setCircuitscapeOptions()
        options['scenario']=cfg.ALL_PAIR_SCENARIO
        options['habitat_file'] = resNpyFile
        options['point_file'] = coreNpyFile
        options['set_focal_node_currents_to_zero']=True
        outputFN = 'Circuitscape.out'
        options['output_file'] = path.join(OUTCIRCUITDIR, outputFN)
        options['print_timings']=True
        configFN = 'pinchpoint_allpair_config.ini'
        outConfigFile = path.join(CONFIGDIR, configFN)
        lu.writeCircuitscapeConfigFile(outConfigFile, options)
        gprint('\nResistance map has ' + str(int(numResistanceNodes)) + ' nodes.') 
        lu.dashline(1)
        gprint('If you try to cancel your run and the Arc dialog hangs, ')
        gprint('you can kill Circuitscape by opening Windows Task Manager')
        gprint('and ending the cs_run.exe process.')             
        lu.dashline(0)
        
        call_circuitscape(CSPATH, outConfigFile)
        # test = subprocess.call([CSPATH, outConfigFile],
                               # creationflags = subprocess.CREATE_NEW_CONSOLE)

        if options['scenario']=='pairwise':
            rasterSuffix =  "_current_allPairs_" + cutoffText
                        
        else:
            rasterSuffix =  "_current_allToOne_" + cutoffText

        currentFN = 'Circuitscape_cum_curmap.npy'
        currentMap = path.join(OUTCIRCUITDIR, currentFN)
        outputRaster = path.join(outputGDB, cfg.PREFIX + rasterSuffix)
        currentRaster = path.join(cfg.SCRATCHDIR, "current")

        try:
            import_npy_to_ras(currentMap,resRasClipPath,outputRaster)
        except:
            lu.dashline(1)
            msg = ('ERROR: Circuitscape failed. \n'
                  'Note: Circuitscape can only solve 2-3 million nodes'
                  '\nper gigabyte of available RAM. The resistance '
                  '\nraster for the last corridor had '
                  + str(numResistanceNodes) + ' nodes.\n\nResistance '
                  'raster values that vary by >6 orders of \nmagnitude'
                  ' can also cause failures, as can a mismatch in '
                  '\ncore area and resistance raster extents.')
            arcpy.AddError(msg)
            lu.write_log(msg)
            exit(1)

        #set core areas to nodata 
        if SETCORESTONULL:                  
            # Set core areas to NoData in current map for color ramping
            outputRasterND = outputRaster + '_noDataCores' 
            outCon = arcpy.sa.SetNull(Raster(s8CoreRasClipped) > 0, 
                                      Raster(outputRaster))   
            outCon.save(outputRasterND)                

        gprint('\nBuilding output statistics and pyramids ' 
                'for centrality raster.')        
        lu.build_stats(outputRaster)
        lu.build_stats(outputRasterND)

        # Clean up temporary files
        if not cfg.SAVECURRENTMAPS:
            lu.delete_dir(OUTCIRCUITDIR)

    # Return GEOPROCESSING specific errors
    except arcpy.ExecuteError:
        lu.dashline(1)
        gprint('****Failed in step 8. Details follow.****')
        lu.exit_with_geoproc_error(_SCRIPT_NAME)

    # Return any PYTHON or system specific errors
    except:
        lu.dashline(1)
        gprint('****Failed in step 8. Details follow.****')
        lu.exit_with_python_error(_SCRIPT_NAME)
예제 #6
0
def STEP8_calc_pinchpoints():
    """ Maps pinch points in Linkage Mapper corridors using Circuitscape
        given CWD calculations from s3_calcCwds.py.

    """
    try:
        lu.dashline(0)
        gprint('Running script ' + _SCRIPT_NAME)

        restartFlag = False
        if cfg.CWDCUTOFF < 0:
            cfg.CWDCUTOFF = cfg.CWDCUTOFF * -1
            restartFlag = True  # Restart code in progress

        CSPATH = lu.get_cs_path()
        outputGDB = path.join(cfg.OUTPUTDIR, path.basename(cfg.PINCHGDB))

        arcpy.OverWriteOutput = True
        arcpy.env.workspace = cfg.SCRATCHDIR
        arcpy.env.scratchWorkspace = cfg.ARCSCRATCHDIR
        arcpy.env.pyramid = "NONE"
        arcpy.env.rasterstatistics = "NONE"

        # set the analysis extent and cell size to that of the resistance
        # surface
        arcpy.env.extent = cfg.RESRAST
        arcpy.env.cellSize = cfg.RESRAST
        arcpy.snapraster = cfg.RESRAST

        resRaster = cfg.RESRAST
        arcpy.env.extent = "MINOF"

        minObject = arcpy.GetRasterProperties_management(resRaster, "MINIMUM")
        rasterMin = float(str(minObject.getOutput(0)))
        if rasterMin <= 0:
            msg = (
                'Error: resistance raster cannot have 0 or negative values.')
            lu.raise_error(msg)

        if cfg.DO_ADJACENTPAIRS:
            prevLcpShapefile = lu.get_lcp_shapefile(None, thisStep=8)
            if not arcpy.Exists(prevLcpShapefile):
                msg = ('Cannot find an LCP shapefile from step 5.  Please '
                       'rerun that step and any previous ones if necessary.')
                lu.raise_error(msg)

            # Remove lcp shapefile
            lcpShapefile = path.join(cfg.DATAPASSDIR, "lcpLines_s8.shp")
            lu.delete_data(lcpShapefile)

        inLinkTableFile = lu.get_prev_step_link_table(step=8)
        linkTable = lu.load_link_table(inLinkTableFile)
        numLinks = linkTable.shape[0]
        numCorridorLinks = lu.report_links(linkTable)
        if numCorridorLinks == 0:
            lu.dashline(1)
            msg = ('\nThere are no linkages. Bailing.')
            lu.raise_error(msg)

        if linkTable.shape[1] < 16:  # If linktable has no entries from prior
            # centrality or pinchpint analyses
            extraCols = npy.zeros((numLinks, 6), dtype="float64")
            linkTable = linkTable[:, 0:10]
            linkTable = npy.append(linkTable, extraCols, axis=1)
            linkTable[:, cfg.LTB_LCPLEN] = -1
            linkTable[:, cfg.LTB_CWDEUCR] = -1
            linkTable[:, cfg.LTB_CWDPATHR] = -1
            linkTable[:, cfg.LTB_EFFRESIST] = -1
            linkTable[:, cfg.LTB_CWDTORR] = -1
            linkTable[:, cfg.LTB_CURRENT] = -1
            del extraCols

        # set up directories for circuit and circuit mosaic grids
        # Create output geodatabase
        if not arcpy.Exists(cfg.PINCHGDB):
            arcpy.CreateFileGDB_management(cfg.OUTPUTDIR,
                                           path.basename(cfg.PINCHGDB))

        mosaicRaster = path.join(cfg.CIRCUITBASEDIR, "current_mos" + tif)
        coresToProcess = npy.unique(linkTable[:,
                                              cfg.LTB_CORE1:cfg.LTB_CORE2 + 1])
        maxCoreNum = max(coresToProcess)
        del coresToProcess

        lu.dashline(0)
        coreList = linkTable[:, cfg.LTB_CORE1:cfg.LTB_CORE2 + 1]
        coreList = npy.sort(coreList)
        #gprint('There are ' + str(len(npy.unique(coreList))) ' core areas.')

        INCIRCUITDIR = cfg.CIRCUITBASEDIR
        OUTCIRCUITDIR = path.join(cfg.CIRCUITBASEDIR, cfg.CIRCUITOUTPUTDIR_NM)
        CONFIGDIR = path.join(INCIRCUITDIR, cfg.CIRCUITCONFIGDIR_NM)

        # Cutoff value text to append to filenames
        cutoffText = str(cfg.CWDCUTOFF)
        if cutoffText[-6:] == '000000':
            cutoffText = cutoffText[0:-6] + 'm'
        elif cutoffText[-3:] == '000':
            cutoffText = cutoffText[0:-3] + 'k'

        if cfg.SQUARERESISTANCES:
            # Square resistance values
            squaredRaster = path.join(cfg.SCRATCHDIR, 'res_sqr')
            arcpy.env.workspace = cfg.SCRATCHDIR
            arcpy.env.scratchWorkspace = cfg.ARCSCRATCHDIR
            outRas = Raster(resRaster) * Raster(resRaster)
            outRas.save(squaredRaster)
            resRaster = squaredRaster

        if cfg.DO_ADJACENTPAIRS:
            linkLoop = 0
            lu.dashline(1)
            gprint('Mapping pinch points in individual corridors \n'
                   'using Circuitscape.')
            lu.dashline(1)
            gprint('If you try to cancel your run and the Arc dialog hangs, ')
            gprint('you can kill Circuitscape by opening Windows Task Manager')
            gprint('and ending the cs_run.exe process.')
            lu.dashline(2)

            for x in range(0, numLinks):
                linkId = str(int(linkTable[x, cfg.LTB_LINKID]))
                if not (linkTable[x, cfg.LTB_LINKTYPE] > 0):
                    continue
                linkLoop = linkLoop + 1
                linkDir = path.join(cfg.SCRATCHDIR, 'link' + linkId)
                if restartFlag == True and path.exists(linkDir):
                    gprint('continuing')
                    continue
                restartFlag = False
                lu.create_dir(linkDir)
                start_time1 = time.clock()

                # source and target cores
                corex = int(coreList[x, 0])
                corey = int(coreList[x, 1])

                # Get cwd rasters for source and target cores
                cwdRaster1 = lu.get_cwd_path(corex)
                cwdRaster2 = lu.get_cwd_path(corey)

                lccNormRaster = path.join(linkDir, 'lcc_norm')
                arcpy.env.extent = "MINOF"

                link = lu.get_links_from_core_pairs(linkTable, corex, corey)
                lcDist = float(linkTable[link, cfg.LTB_CWDIST])

                # Normalized lcc rasters are created by adding cwd rasters
                # and subtracting the least cost distance between them.
                outRas = Raster(cwdRaster1) + Raster(cwdRaster2) - lcDist
                outRas.save(lccNormRaster)

                #create raster mask
                resMaskRaster = path.join(linkDir, 'res_mask' + tif)

                #create raster mask
                outCon = arcpy.sa.Con(
                    Raster(lccNormRaster) <= cfg.CWDCUTOFF, 1)
                outCon.save(resMaskRaster)

                # Convert to poly.  Use as mask to clip resistance raster.
                resMaskPoly = path.join(linkDir, 'res_mask_poly.shp')
                arcpy.RasterToPolygon_conversion(resMaskRaster, resMaskPoly,
                                                 "NO_SIMPLIFY")
                arcpy.env.extent = resMaskPoly

                # Includes 0 values in some cases with CP LI model if tif
                # so using ESRI Grid format
                resClipRasterMasked = path.join(linkDir, 'res_clip_m')
                # Extract masked resistance raster.
                # Needs to be float to get export to npy to work.
                outRas = arcpy.sa.ExtractByMask(resRaster, resMaskPoly) + 0.0
                outRas.save(resClipRasterMasked)

                resNpyFN = 'resistances_link_' + linkId + '.npy'
                resNpyFile = path.join(INCIRCUITDIR, resNpyFN)
                numElements, numResistanceNodes = export_ras_to_npy(
                    resClipRasterMasked, resNpyFile)

                totMem, availMem = lu.get_mem()
                # gprint('Total memory: str(totMem))
                if numResistanceNodes / availMem > 2000000:
                    lu.dashline(1)
                    lu.warn('Warning:')
                    lu.warn('Circuitscape can only solve 2-3 million nodes')
                    lu.warn(
                        'per gigabyte of available RAM. \nTotal physical RAM'
                        ' on your machine is ~' + str(totMem) +
                        ' GB. \nAvailable memory is ~' + str(availMem) +
                        ' GB. \nYour resistance raster has ' +
                        str(numResistanceNodes) + ' nodes.')
                    lu.dashline(2)
                corePairRaster = path.join(linkDir, 'core_pairs' + tif)
                arcpy.env.extent = resClipRasterMasked

                # Next result needs to be floating pt for numpy export
                outCon = arcpy.sa.Con(
                    Raster(cwdRaster1) == 0, corex,
                    arcpy.sa.Con(Raster(cwdRaster2) == 0, corey + 0.0))
                outCon.save(corePairRaster)

                coreNpyFN = 'cores_link_' + linkId + '.npy'
                coreNpyFile = path.join(INCIRCUITDIR, coreNpyFN)
                numElements, numNodes = export_ras_to_npy(
                    corePairRaster, coreNpyFile)

                arcpy.env.extent = "MINOF"

                # Set circuitscape options and call
                options = lu.setCircuitscapeOptions()
                if cfg.WRITE_VOLT_MAPS == True:
                    options['write_volt_maps'] = True
                options['habitat_file'] = resNpyFile

                # if int(linkId) > 2:
                # options['habitat_file'] = 'c:\\test.dummy'

                options['point_file'] = coreNpyFile
                options['set_focal_node_currents_to_zero'] = True
                outputFN = 'Circuitscape_link' + linkId + '.out'
                options['output_file'] = path.join(OUTCIRCUITDIR, outputFN)
                if numElements > 250000:
                    options['print_timings'] = True
                configFN = 'pinchpoint_config' + linkId + '.ini'

                outConfigFile = path.join(CONFIGDIR, configFN)
                lu.writeCircuitscapeConfigFile(outConfigFile, options)
                gprint('Processing link ID #' + str(linkId) +
                       '. Resistance map'
                       ' has ' + str(int(numResistanceNodes)) + ' nodes.')

                memFlag = call_circuitscape(CSPATH, outConfigFile)

                currentFN = ('Circuitscape_link' + linkId + '_cum_curmap.npy')
                currentMap = path.join(OUTCIRCUITDIR, currentFN)

                if not arcpy.Exists(currentMap):
                    print_failure(numResistanceNodes, memFlag, 10)
                    numElements, numNodes = export_ras_to_npy(
                        resClipRasterMasked, resNpyFile)
                    memFlag = call_circuitscape(CSPATH, outConfigFile)

                    currentFN = ('Circuitscape_link' + linkId +
                                 '_cum_curmap.npy')
                    currentMap = path.join(OUTCIRCUITDIR, currentFN)

                if not arcpy.Exists(currentMap):
                    msg = (
                        '\nCircuitscape failed. See error information above.')
                    arcpy.AddError(msg)
                    lu.write_log(msg)
                    exit(1)

                # Either set core areas to nodata in current map or
                # divide each by its radius
                currentRaster = path.join(linkDir, "current" + tif)
                import_npy_to_ras(currentMap, corePairRaster, currentRaster)

                if cfg.WRITE_VOLT_MAPS == True:
                    voltFN = ('Circuitscape_link' + linkId + '_voltmap_' +
                              str(corex) + '_' + str(corey) + '.npy')
                    voltMap = path.join(OUTCIRCUITDIR, voltFN)
                    voltRaster = path.join(
                        outputGDB, cfg.PREFIX + "_voltMap_" + str(corex) +
                        '_' + str(corey))
                    import_npy_to_ras(voltMap, corePairRaster, voltRaster)
                    gprint('Building output statistics and pyramids '
                           'for voltage raster\n')
                    lu.build_stats(voltRaster)

                arcpy.env.extent = currentRaster

                if SETCORESTONULL:
                    # Set core areas to NoData in current map for color ramping
                    currentRaster2 = currentRaster + '2' + tif
                    outCon = arcpy.sa.Con(
                        arcpy.sa.IsNull(Raster(corePairRaster)),
                        Raster(currentRaster))
                    outCon.save(currentRaster2)
                    currentRaster = currentRaster2
                arcpy.env.extent = "MAXOF"
                if linkLoop == 1:
                    lu.delete_data(mosaicRaster)

                    @retry(10)
                    def copyRas2():
                        arcpy.CopyRaster_management(currentRaster,
                                                    mosaicRaster)

                    copyRas2()
                else:

                    @retry(10)
                    def mosaicRas():
                        arcpy.Mosaic_management(currentRaster, mosaicRaster,
                                                "MAXIMUM", "MATCH")

                    mosaicRas()

                resistancesFN = ('Circuitscape_link' + linkId +
                                 '_resistances_3columns.out')

                resistancesFile = path.join(OUTCIRCUITDIR, resistancesFN)
                resistances = npy.loadtxt(resistancesFile,
                                          dtype='Float64',
                                          comments='#')

                resistance = float(str(arcpy.env.cellSize)) * resistances[2]
                linkTable[link, cfg.LTB_EFFRESIST] = resistance

                # Ratio
                if not cfg.SQUARERESISTANCES:
                    linkTable[link, cfg.LTB_CWDTORR] = (
                        linkTable[link, cfg.LTB_CWDIST] /
                        linkTable[link, cfg.LTB_EFFRESIST])
                # Clean up
                if cfg.SAVE_TEMP_CIRCUIT_FILES == False:
                    lu.delete_file(coreNpyFile)
                    coreNpyBase, extension = path.splitext(coreNpyFile)
                    lu.delete_data(coreNpyBase + '.hdr')
                    lu.delete_file(resNpyFile)
                    resNpyBase, extension = path.splitext(resNpyFile)
                    lu.delete_data(resNpyBase + '.hdr')
                    lu.delete_file(currentMap)
                    curMapBase, extension = path.splitext(currentMap)
                    lu.delete_data(curMapBase + '.hdr')
                    lu.delete_data(currentRaster)
                    lu.clean_out_workspace(linkDir)
                    lu.delete_dir(linkDir)
                gprint('Finished with link ID #' + str(linkId) + '. ' +
                       str(linkLoop) + ' out of ' + str(numCorridorLinks) +
                       ' links have been processed.')
                start_time1 = lu.elapsed_time(start_time1)

            outputRaster = path.join(
                outputGDB, cfg.PREFIX + "_current_adjacentPairs_" + cutoffText)
            lu.delete_data(outputRaster)

            @retry(10)
            def copyRas():
                arcpy.CopyRaster_management(mosaicRaster, outputRaster)

            copyRas()

            gprint('Building output statistics and pyramids '
                   'for corridor pinch point raster\n')
            lu.build_stats(outputRaster)

            finalLinkTable = lu.update_lcp_shapefile(linkTable,
                                                     lastStep=5,
                                                     thisStep=8)

            linkTableFile = path.join(cfg.DATAPASSDIR, "linkTable_s5_plus.csv")
            lu.write_link_table(finalLinkTable, linkTableFile, inLinkTableFile)
            linkTableFinalFile = path.join(
                cfg.OUTPUTDIR, cfg.PREFIX + "_linkTable_s5_plus.csv")
            lu.write_link_table(finalLinkTable, linkTableFinalFile,
                                inLinkTableFile)
            gprint('Copy of linkTable written to ' + linkTableFinalFile)
            #fixme: update sticks?

            gprint('Creating shapefiles with linework for links.')
            lu.write_link_maps(linkTableFinalFile, step=8)

            # Copy final link maps to gdb.
            lu.copy_final_link_maps(step=8)

            lu.delete_data(mosaicRaster)

        if not cfg.DO_ALLPAIRS:
            # Clean up temporary files
            if not cfg.SAVECURRENTMAPS:
                lu.delete_dir(OUTCIRCUITDIR)
            return

        lu.dashline(1)
        gprint('Mapping global pinch points among all\n'
               'core area pairs using Circuitscape.')

        if cfg.ALL_PAIR_SCENARIO == 'pairwise':
            gprint('Circuitscape will be run in PAIRWISE mode.')

        else:
            gprint('Circuitscape will be run in ALL-TO-ONE mode.')
        arcpy.env.workspace = cfg.SCRATCHDIR
        arcpy.env.scratchWorkspace = cfg.ARCSCRATCHDIR
        arcpy.env.extent = cfg.RESRAST
        arcpy.env.cellSize = cfg.RESRAST

        S8CORE_RAS = "s8core_ras"
        s8CoreRasPath = path.join(cfg.SCRATCHDIR, S8CORE_RAS)

        arcpy.FeatureToRaster_conversion(cfg.COREFC, cfg.COREFN, s8CoreRasPath,
                                         arcpy.env.cellSize)
        binaryCoreRaster = path.join(cfg.SCRATCHDIR, "core_ras_bin")

        # The following commands cause file lock problems on save.  using gp
        # instead.
        # outCon = arcpy.sa.Con(S8CORE_RAS, 1, "#", "VALUE > 0")
        # outCon.save(binaryCoreRaster)
        # gp.Con_sa(s8CoreRasPath, 1, binaryCoreRaster, "#", "VALUE > 0")
        outCon = arcpy.sa.Con(Raster(s8CoreRasPath) > 0, 1)
        outCon.save(binaryCoreRaster)
        s5corridorRas = path.join(cfg.OUTPUTGDB, cfg.PREFIX + "_corridors")

        if not arcpy.Exists(s5corridorRas):
            s5corridorRas = path.join(cfg.OUTPUTGDB,
                                      cfg.PREFIX + "_lcc_mosaic_int")

        outCon = arcpy.sa.Con(
            Raster(s5corridorRas) <= cfg.CWDCUTOFF, Raster(resRaster),
            arcpy.sa.Con(Raster(binaryCoreRaster) > 0, Raster(resRaster)))

        resRasClipPath = path.join(cfg.SCRATCHDIR, 'res_ras_clip')
        outCon.save(resRasClipPath)

        arcpy.env.cellSize = resRasClipPath
        arcpy.env.extent = resRasClipPath
        s8CoreRasClipped = s8CoreRasPath + '_c'

        # Produce core raster with same extent as clipped resistance raster
        # added to ensure correct data type- nodata values were positive for
        # cores otherwise
        outCon = arcpy.sa.Con(arcpy.sa.IsNull(Raster(s8CoreRasPath)), -9999,
                              Raster(s8CoreRasPath))
        outCon.save(s8CoreRasClipped)

        resNpyFN = 'resistances.npy'
        resNpyFile = path.join(INCIRCUITDIR, resNpyFN)
        numElements, numResistanceNodes = export_ras_to_npy(
            resRasClipPath, resNpyFile)

        totMem, availMem = lu.get_mem()
        # gprint('Total memory: str(totMem))
        if numResistanceNodes / availMem > 2000000:
            lu.dashline(1)
            lu.warn('Warning:')
            lu.warn('Circuitscape can only solve 2-3 million nodes')
            lu.warn('per gigabyte of available RAM. \nTotal physical RAM '
                    'on your machine is ~' + str(totMem) +
                    ' GB. \nAvailable memory is ~' + str(availMem) +
                    ' GB. \nYour resistance raster has ' +
                    str(numResistanceNodes) + ' nodes.')
            lu.dashline(0)

        coreNpyFN = 'cores.npy'
        coreNpyFile = path.join(INCIRCUITDIR, coreNpyFN)
        numElements, numNodes = export_ras_to_npy(s8CoreRasClipped,
                                                  coreNpyFile)

        arcpy.env.extent = "MINOF"

        options = lu.setCircuitscapeOptions()
        options['scenario'] = cfg.ALL_PAIR_SCENARIO
        options['habitat_file'] = resNpyFile
        options['point_file'] = coreNpyFile
        options['set_focal_node_currents_to_zero'] = True
        outputFN = 'Circuitscape.out'
        options['output_file'] = path.join(OUTCIRCUITDIR, outputFN)
        options['print_timings'] = True
        configFN = 'pinchpoint_allpair_config.ini'
        outConfigFile = path.join(CONFIGDIR, configFN)
        lu.writeCircuitscapeConfigFile(outConfigFile, options)
        gprint('\nResistance map has ' + str(int(numResistanceNodes)) +
               ' nodes.')
        lu.dashline(1)
        gprint('If you try to cancel your run and the Arc dialog hangs, ')
        gprint('you can kill Circuitscape by opening Windows Task Manager')
        gprint('and ending the cs_run.exe process.')
        lu.dashline(0)

        call_circuitscape(CSPATH, outConfigFile)
        # test = subprocess.call([CSPATH, outConfigFile],
        # creationflags = subprocess.CREATE_NEW_CONSOLE)

        if options['scenario'] == 'pairwise':
            rasterSuffix = "_current_allPairs_" + cutoffText

        else:
            rasterSuffix = "_current_allToOne_" + cutoffText

        currentFN = 'Circuitscape_cum_curmap.npy'
        currentMap = path.join(OUTCIRCUITDIR, currentFN)
        outputRaster = path.join(outputGDB, cfg.PREFIX + rasterSuffix)
        currentRaster = path.join(cfg.SCRATCHDIR, "current")

        try:
            import_npy_to_ras(currentMap, resRasClipPath, outputRaster)
        except:
            lu.dashline(1)
            msg = ('ERROR: Circuitscape failed. \n'
                   'Note: Circuitscape can only solve 2-3 million nodes'
                   '\nper gigabyte of available RAM. The resistance '
                   '\nraster for the last corridor had ' +
                   str(numResistanceNodes) + ' nodes.\n\nResistance '
                   'raster values that vary by >6 orders of \nmagnitude'
                   ' can also cause failures, as can a mismatch in '
                   '\ncore area and resistance raster extents.')
            arcpy.AddError(msg)
            lu.write_log(msg)
            exit(1)

        #set core areas to nodata
        if SETCORESTONULL:
            # Set core areas to NoData in current map for color ramping
            outputRasterND = outputRaster + '_noDataCores'
            outCon = arcpy.sa.SetNull(
                Raster(s8CoreRasClipped) > 0, Raster(outputRaster))
            outCon.save(outputRasterND)

        gprint('\nBuilding output statistics and pyramids '
               'for centrality raster.')
        lu.build_stats(outputRaster)
        lu.build_stats(outputRasterND)

        # Clean up temporary files
        if not cfg.SAVECURRENTMAPS:
            lu.delete_dir(OUTCIRCUITDIR)

    # Return GEOPROCESSING specific errors
    except arcpy.ExecuteError:
        lu.dashline(1)
        gprint('****Failed in step 8. Details follow.****')
        lu.exit_with_geoproc_error(_SCRIPT_NAME)

    # Return any PYTHON or system specific errors
    except:
        lu.dashline(1)
        gprint('****Failed in step 8. Details follow.****')
        lu.exit_with_python_error(_SCRIPT_NAME)
예제 #7
0
def STEP6_calc_barriers():
    """Detects influential barriers given CWD calculations from
       s3_calcCwds.py.

    """
    
    try:
        arcpy.CheckOutExtension("spatial")
        lu.dashline(0)
        gprint('Running script ' + _SCRIPT_NAME)
        
        if cfg.BARRIER_CWD_THRESH is not None:
            lu.dashline(1)
            gprint('Invoking CWD Threshold of ' + str(cfg.BARRIER_CWD_THRESH) + ' map units.')
        
        if cfg.SUM_BARRIERS:
            sumSuffix = '_Sum'
            cfg.BARRIERBASEDIR = cfg.BARRIERBASEDIR + sumSuffix
            baseName, extension = path.splitext(cfg.BARRIERGDB)
            cfg.BARRIERGDB = baseName + sumSuffix + extension

            gprint('\nBarrier scores will be SUMMED across core pairs.')
        else:
            sumSuffix = ''

        # Delete contents of final ouptut geodatabase           
        # lu.clean_out_workspace(cfg.BARRIERGDB) #xxx try not doing this to allow multiple radii to be analyzed in separate runs
        if not arcpy.Exists(cfg.BARRIERGDB):
            # Create output geodatabase
            arcpy.CreateFileGDB_management(cfg.OUTPUTDIR,
                                           path.basename(cfg.BARRIERGDB))             
                                           
        startRadius = int(cfg.STARTRADIUS)
        endRadius = int(cfg.ENDRADIUS)
        radiusStep = int(cfg.RADIUSSTEP)
        if radiusStep == 0:
            endRadius = startRadius # Calculate at just one radius value
            radiusStep = 1
        linkTableFile = lu.get_prev_step_link_table(step=6)
        arcpy.env.workspace = cfg.SCRATCHDIR
        arcpy.env.scratchWorkspace = cfg.ARCSCRATCHDIR
        arcpy.RefreshCatalog(cfg.PROJECTDIR)
        PREFIX = path.basename(cfg.PROJECTDIR)
        # For speed:
        arcpy.env.pyramid = "NONE"
        arcpy.env.rasterStatistics = "NONE"

        # set the analysis extent and cell size to that of the resistance
        # surface
        arcpy.OverWriteOutput = True
        arcpy.env.extent = cfg.RESRAST
        arcpy.env.cellSize = cfg.RESRAST
        arcpy.env.snapRaster = cfg.RESRAST
        spatialref = arcpy.Describe(cfg.RESRAST).spatialReference                
        mapUnits = (str(spatialref.linearUnitName)).lower()
        if len(mapUnits) > 1 and mapUnits[-1] != 's':
            mapUnits = mapUnits + 's'

        if float(arcpy.env.cellSize) > startRadius or startRadius > endRadius:
            msg = ('Error: minimum detection radius must be greater than '
                    'cell size (' + str(arcpy.env.cellSize) +
                    ') \nand less than or equal to maximum detection radius.')
            lu.raise_error(msg)

        linkTable = lu.load_link_table(linkTableFile)
        numLinks = linkTable.shape[0]
        numCorridorLinks = lu.report_links(linkTable)
        if numCorridorLinks == 0:
            lu.dashline(1)
            msg =('\nThere are no linkages. Bailing.')
            lu.raise_error(msg)
        
        # set up directories for barrier and barrier mosaic grids
        dirCount = 0
        gprint("Creating intermediate output folder: " + cfg.BARRIERBASEDIR)
        lu.delete_dir(cfg.BARRIERBASEDIR)
        lu.create_dir(cfg.BARRIERBASEDIR)
        arcpy.CreateFolder_management(cfg.BARRIERBASEDIR, cfg.BARRIERDIR_NM)
        cbarrierdir = path.join(cfg.BARRIERBASEDIR, cfg.BARRIERDIR_NM)

        coresToProcess = npy.unique(linkTable
                                    [:, cfg.LTB_CORE1:cfg.LTB_CORE2 + 1])
        maxCoreNum = max(coresToProcess)

        # Set up focal directories.
        # To keep there from being > 100 grids in any one directory,
        # outputs are written to:
        # barrier\focalX_ for cores 1-99 at radius X
        # barrier\focalX_1 for cores 100-199
        # etc.
        lu.dashline(0)

        for radius in range(startRadius, endRadius + 1, radiusStep):
            core1path = lu.get_focal_path(1,radius)
            path1, dir1 = path.split(core1path)
            path2, dir2 = path.split(path1)
            arcpy.CreateFolder_management(path.dirname(path2),
                                          path.basename(path2))
            arcpy.CreateFolder_management(path.dirname(path1),
                                         path.basename(path1))

            if maxCoreNum > 99:
                gprint('Creating subdirectories for ' + str(radius) + ' ' + 
                       str(mapUnits) + ' radius analysis scale.')
                maxDirCount = int(maxCoreNum/100)
                focalDirBaseName = dir2

                cp100 = (coresToProcess.astype('int32'))/100
                ind = npy.where(cp100 > 0)
                dirNums = npy.unique(cp100[ind])
                for dirNum in dirNums:
                    focalDir = focalDirBaseName + str(dirNum)
                    gprint('...' + focalDir)
                    arcpy.CreateFolder_management(path2, focalDir)                        
        
        # Create resistance raster with filled-in Nodata values for later use
        arcpy.env.extent = cfg.RESRAST
        resistFillRaster = path.join(cfg.SCRATCHDIR, "resist_fill")
        output = arcpy.sa.Con(IsNull(cfg.RESRAST), 1000000000, 
                              Raster(cfg.RESRAST) - 1)
        output.save(resistFillRaster)

        coreList = linkTable[:,cfg.LTB_CORE1:cfg.LTB_CORE2+1]
        coreList = npy.sort(coreList)

        # Loop through each search radius to calculate barriers in each link
        import time
        radId = 0 #keep track of number of radii processed- used for temp dir naming
        for radius in range (startRadius, endRadius + 1, radiusStep):
            radId = radId + 1
            linkTableTemp = linkTable.copy()
            @retry(10)
            #can't pass vars in and modify them. 
            def doRadiusLoop():
                linkTable = linkTableTemp.copy()
                startTime = time.clock()
                randomerror()
                linkLoop = 0
                pctDone = 0
                gprint('\nMapping barriers at a radius of ' + str(radius) +
                       ' ' + str(mapUnits))             
                if cfg.SUM_BARRIERS:  
                    gprint('using SUM method')
                else:
                    gprint('using MAXIMUM method')                   
                if numCorridorLinks > 1:
                    gprint('0 percent done')
                lastMosaicRaster = None
                lastMosaicRasterPct = None
                for x in range(0,numLinks):
                    pctDone = lu.report_pct_done(linkLoop, numCorridorLinks,
                                                pctDone)
                    linkId = str(int(linkTable[x,cfg.LTB_LINKID]))
                    if ((linkTable[x,cfg.LTB_LINKTYPE] > 0) and
                       (linkTable[x,cfg.LTB_LINKTYPE] < 1000)):
                        linkLoop = linkLoop + 1
                        # source and target cores
                        corex=int(coreList[x,0])
                        corey=int(coreList[x,1])

                        # Get cwd rasters for source and target cores
                        cwdRaster1 = lu.get_cwd_path(corex)
                        cwdRaster2 = lu.get_cwd_path(corey)
                        
                        # Mask out areas above CWD threshold
                        cwdTemp1 = None
                        cwdTemp2 = None
                        if cfg.BARRIER_CWD_THRESH is not None:
                            if x == 1:
                                lu.dashline(1)
                                gprint('  Using CWD threshold of ' + str(cfg.BARRIER_CWD_THRESH) + ' map units.')
                            arcpy.env.extent = cfg.RESRAST
                            arcpy.env.cellSize = cfg.RESRAST
                            arcpy.env.snapRaster = cfg.RESRAST
                            cwdTemp1 = path.join(cfg.SCRATCHDIR, "tmp"+str(corex))
                            outCon = arcpy.sa.Con(cwdRaster1 < float(cfg.BARRIER_CWD_THRESH),cwdRaster1)
                            outCon.save(cwdTemp1)
                            cwdRaster1 = cwdTemp1
                            cwdTemp2 = path.join(cfg.SCRATCHDIR, "tmp"+str(corey))
                            outCon = arcpy.sa.Con(cwdRaster2 < float(cfg.BARRIER_CWD_THRESH),cwdRaster2)
                            outCon.save(cwdTemp2)
                            cwdRaster2 = cwdTemp2                        
                        
                        focalRaster1 = lu.get_focal_path(corex,radius)
                        focalRaster2 = lu.get_focal_path(corey,radius)
                                                                     
                        link = lu.get_links_from_core_pairs(linkTable,
                                                            corex, corey)
                        lcDist = float(linkTable[link,cfg.LTB_CWDIST])
                        
                        # Detect barriers at radius using neighborhood stats
                        # Create the Neighborhood Object
                        innerRadius = radius - 1
                        outerRadius = radius

                        dia = 2 * radius
                        InNeighborhood = ("ANNULUS " + str(innerRadius) + " " +
                                         str(outerRadius) + " MAP")

                        @retry(10)
                        def execFocal():
                            randomerror()
                            # Execute FocalStatistics
                            if not path.exists(focalRaster1):
                                arcpy.env.extent = cwdRaster1
                                outFocalStats = arcpy.sa.FocalStatistics(cwdRaster1,
                                                    InNeighborhood, "MINIMUM","DATA")
                                if setCoresToNull:                    
                                    outFocalStats2 = arcpy.sa.Con(outFocalStats > 0, outFocalStats) # Set areas overlapping cores to NoData xxx
                                    outFocalStats2.save(focalRaster1) #xxx
                                else:
                                    outFocalStats.save(focalRaster1) #xxx
                                arcpy.env.extent = cfg.RESRAST

                            if not path.exists(focalRaster2):
                                arcpy.env.extent = cwdRaster2
                                outFocalStats = arcpy.sa.FocalStatistics(cwdRaster2,
                                                InNeighborhood, "MINIMUM","DATA")
                                if setCoresToNull:                    
                                    outFocalStats2 = arcpy.sa.Con(outFocalStats > 0, outFocalStats) # Set areas overlapping cores to NoData xxx
                                    outFocalStats2.save(focalRaster2)#xxx
                                else:
                                    outFocalStats.save(focalRaster2) #xxx

                                arcpy.env.extent = cfg.RESRAST
                        execFocal()
                                                
                        lu.delete_data(cwdTemp1)
                        lu.delete_data(cwdTemp2)
                        
                        barrierRaster = path.join(cbarrierdir, "b" + str(radius)
                              + "_" + str(corex) + "_" +
                              str(corey)+'.tif') 
                             
                        if cfg.SUM_BARRIERS: # Need to set nulls to 0, also 
                                             # create trim rasters as we go

                            outRas = ((lcDist - Raster(focalRaster1) - 
                                      Raster(focalRaster2) - dia) / dia)
                            outCon = arcpy.sa.Con(IsNull(outRas),0,outRas)
                            outCon2 = arcpy.sa.Con(outCon<0,0,outCon)                            
                            outCon2.save(barrierRaster)
                            
                            # Execute FocalStatistics to fill out search radii                            
                            InNeighborhood = "CIRCLE " + str(outerRadius) + " MAP"
                            fillRaster = path.join(cbarrierdir, "b" + str(radius)
                            + "_" + str(corex) + "_" + str(corey) +"_fill.tif")
                            outFocalStats = arcpy.sa.FocalStatistics(barrierRaster,
                                                  InNeighborhood, "MAXIMUM","DATA")
                            outFocalStats.save(fillRaster)                            

                            if cfg.WRITE_TRIM_RASTERS:                            
                                trmRaster = path.join(cbarrierdir, "b" + 
                                                      str(radius)
                                + "_" + str(corex) + "_" + str(corey) +"_trim.tif")
                                rasterList = [fillRaster, resistFillRaster]
                                outCellStatistics = arcpy.sa.CellStatistics(
                                                            rasterList, "MINIMUM")
                                outCellStatistics.save(trmRaster)
                               
                        else:
                            #Calculate potential benefit per map unit restored
                            @retry(10)
                            def calcBen():
                                randomerror()
                                outRas = ((lcDist - Raster(focalRaster1)
                                      - Raster(focalRaster2) - dia) / dia)
                                outRas.save(barrierRaster)
                            calcBen()

                        if cfg.WRITE_PCT_RASTERS:
                            #Calculate PERCENT potential benefit per unit restored                        
                            barrierRasterPct = path.join(cbarrierdir, "b" + 
                                                    str(radius)
                                                    + "_" + str(corex) + "_" +
                                                    str(corey)+'_pct.tif') 
                            @retry(10)
                            def calcBenPct():                            
                                randomerror()
                                outras = (100 * (Raster(barrierRaster) / lcDist))
                                outras.save(barrierRasterPct)
                            calcBenPct()
                            
                        # Mosaic barrier results across core area pairs                    
                        mosaicDir = path.join(cfg.SCRATCHDIR,'mos'+str(radId)+'_'+str(x+1)) 
                        lu.create_dir(mosaicDir)
                        
                        mosFN = 'mos_temp'
                        tempMosaicRaster = path.join(mosaicDir,mosFN)
                        tempMosaicRasterTrim = path.join(mosaicDir,'mos_temp_trm')
                        arcpy.env.workspace = mosaicDir            
                        if linkLoop == 1:
                            #If this is the first grid then copy rather than mosaic
                            arcpy.CopyRaster_management(barrierRaster, 
                                                            tempMosaicRaster)
                            if cfg.SUM_BARRIERS and cfg.WRITE_TRIM_RASTERS:
                                arcpy.CopyRaster_management(trmRaster, 
                                                            tempMosaicRasterTrim)                       
                            
                        else:                    
                            if cfg.SUM_BARRIERS:
                                outCon = arcpy.sa.Con(Raster (barrierRaster) < 0, lastMosaicRaster, 
                                        Raster(barrierRaster) + Raster(lastMosaicRaster))
                                outCon.save(tempMosaicRaster)                      
                                if cfg.WRITE_TRIM_RASTERS:
                                    outCon = arcpy.sa.Con(Raster
                                    (trmRaster) < 0, lastMosaicRasterTrim, 
                                    Raster(trmRaster) + Raster(
                                    lastMosaicRasterTrim))
                                    outCon.save(tempMosaicRasterTrim) 
                                
                            else:
                                rasterString = ('"'+barrierRaster+";" + 
                                                lastMosaicRaster+'"')
                                @retry(10)
                                def mosaicToNew():
                                    randomerror()
                                    arcpy.MosaicToNewRaster_management(
                                        rasterString,mosaicDir,mosFN, "", 
                                        "32_BIT_FLOAT", arcpy.env.cellSize, "1", 
                                        "MAXIMUM", "MATCH")
                                mosaicToNew()
                                # gprint(str(corex)+'0'+str(corey))
                                
                                
                        if linkLoop>1: #Clean up from previous loop
                            lu.delete_data(lastMosaicRaster)
                            lastMosaicDir =path.dirname(lastMosaicRaster) 
                            lu.clean_out_workspace(lastMosaicDir)
                            lu.delete_dir(lastMosaicDir)
                            
                        lastMosaicRaster = tempMosaicRaster
                        if cfg.WRITE_TRIM_RASTERS:
                            lastMosaicRasterTrim = tempMosaicRasterTrim             
                        if cfg.WRITE_PCT_RASTERS:
                            mosPctFN = 'mos_temp_pct'
                            mosaicDirPct = path.join(cfg.SCRATCHDIR,'mosP'+str(radId)+'_'+str(x+1)) 
                            lu.create_dir(mosaicDirPct)                            
                            tempMosaicRasterPct = path.join(mosaicDirPct,mosPctFN)
                            if linkLoop == 1:
                                # If this is the first grid then copy 
                                # rather than mosaic
                                if cfg.SUM_BARRIERS:
                                    outCon = arcpy.sa.Con(Raster(barrierRasterPct) 
                                        < 0, 0, arcpy.sa.Con(IsNull(
                                        barrierRasterPct), 0, barrierRasterPct)) 
                                    outCon.save(tempMosaicRasterPct)
                                else:
                                    arcpy.CopyRaster_management(barrierRasterPct, 
                                                             tempMosaicRasterPct)
                                                
                            else:                
                                if cfg.SUM_BARRIERS:
                                    @retry(10)
                                    def sumBarriers():
                                        randomerror()
                                        outCon = arcpy.sa.Con(Raster(barrierRasterPct) < 0, 
                                            lastMosaicRasterPct, Raster(barrierRasterPct) + Raster(
                                            lastMosaicRasterPct))
                                        outCon.save(tempMosaicRasterPct)
                                    sumBarriers()
                                else:
                                    rasterString = ('"' + barrierRasterPct + ";" + 
                                                    lastMosaicRasterPct + '"')
                                    @retry(10)
                                    def maxBarriers():
                                        randomerror()
                                        arcpy.MosaicToNewRaster_management(
                                            rasterString,mosaicDirPct,mosPctFN, "", 
                                            "32_BIT_FLOAT", arcpy.env.cellSize, "1", 
                                            "MAXIMUM", "MATCH")
                                    maxBarriers()
                                    
                            if linkLoop>1: #Clean up from previous loop
                                lu.delete_data(lastMosaicRasterPct)
                                lastMosaicDirPct =path.dirname(lastMosaicRasterPct) 
                                lu.clean_out_workspace(lastMosaicDirPct)
                                lu.delete_dir(lastMosaicDirPct)
                            
                            # lu.delete_data(lastMosaicRasterPct)
                            lastMosaicRasterPct = tempMosaicRasterPct                    
                        
                        if not cfg.SAVEBARRIERRASTERS:
                            lu.delete_data(barrierRaster)
                            if cfg.WRITE_PCT_RASTERS:
                                lu.delete_data(barrierRasterPct)
                            if cfg.WRITE_TRIM_RASTERS:                                                    
                                lu.delete_data(trmRaster)                            
                            
                            
                        # Temporarily disable links in linktable -
                        # don't want to mosaic them twice
                        for y in range (x+1,numLinks):
                            corex1 = int(coreList[y,0])
                            corey1 = int(coreList[y,1])
                            if corex1 == corex and corey1 == corey:
                                linkTable[y,cfg.LTB_LINKTYPE] = (
                                    linkTable[y,cfg.LTB_LINKTYPE] + 1000)
                            elif corex1==corey and corey1==corex:
                                linkTable[y,cfg.LTB_LINKTYPE] = (
                                    linkTable[y,cfg.LTB_LINKTYPE] + 1000)               

                if numCorridorLinks > 1 and pctDone < 100:
                    gprint('100 percent done')
                gprint('Summarizing barrier data for search radius.')
                #rows that were temporarily disabled
                rows = npy.where(linkTable[:,cfg.LTB_LINKTYPE]>1000)
                linkTable[rows,cfg.LTB_LINKTYPE] = (
                    linkTable[rows,cfg.LTB_LINKTYPE] - 1000)

                # -----------------------------------------------------------------
                
                # Set negative values to null or zero and write geodatabase. 
                mosaicFN = (PREFIX + "_BarrierCenters" + sumSuffix + "_Rad" + 
                           str(radius))
                mosaicRaster = path.join(cfg.BARRIERGDB, mosaicFN) 
                arcpy.env.extent = cfg.RESRAST
                
                # if setCoresToNull:                
                    # outCon = arcpy.sa.Con(Raster(tempMosaicRaster) < 0, 0, 
                                   # tempMosaicRaster) #xxx
                    # outCon.save(mosaicRaster) #xxx                            
                # else:
                outSetNull = arcpy.sa.SetNull(tempMosaicRaster, tempMosaicRaster,
                                              "VALUE < 0") #xxx orig
                outSetNull.save(mosaicRaster)
                
                lu.delete_data(tempMosaicRaster)
                
                if cfg.SUM_BARRIERS and cfg.WRITE_TRIM_RASTERS:
                    mosaicFN = (PREFIX + "_BarrierCircles_RBMin" + sumSuffix + 
                                "_Rad" + str(radius))
                    mosaicRasterTrim = path.join(cfg.BARRIERGDB, mosaicFN)
                    arcpy.CopyRaster_management(tempMosaicRasterTrim, 
                                                            mosaicRasterTrim)
                    lu.delete_data(tempMosaicRaster)
                            
                if cfg.WRITE_PCT_RASTERS:                        
                    # Do same for percent raster
                    mosaicPctFN = (PREFIX + "_BarrierCenters_Pct" + sumSuffix + 
                                   "_Rad" + str(radius))
                    arcpy.env.extent = cfg.RESRAST
                    outSetNull = arcpy.sa.SetNull(tempMosaicRasterPct, 
                                                  tempMosaicRasterPct, "VALUE < 0")
                    mosaicRasterPct = path.join(cfg.BARRIERGDB, mosaicPctFN)
                    outSetNull.save(mosaicRasterPct)
                    lu.delete_data(tempMosaicRasterPct)
                           
                
                # 'Grow out' maximum restoration gain to
                # neighborhood size for display
                InNeighborhood = "CIRCLE " + str(outerRadius) + " MAP"
                # Execute FocalStatistics
                fillRasterFN = "barriers_fill" + str(outerRadius) + tif
                fillRaster = path.join(cfg.BARRIERBASEDIR, fillRasterFN)
                outFocalStats = arcpy.sa.FocalStatistics(mosaicRaster,
                                                InNeighborhood, "MAXIMUM","DATA")
                outFocalStats.save(fillRaster)

                if cfg.WRITE_PCT_RASTERS:
                    # Do same for percent raster
                    fillRasterPctFN = "barriers_fill_pct" + str(outerRadius) + tif
                    fillRasterPct = path.join(cfg.BARRIERBASEDIR, fillRasterPctFN)
                    outFocalStats = arcpy.sa.FocalStatistics(mosaicRasterPct,
                                                InNeighborhood, "MAXIMUM","DATA")
                    outFocalStats.save(fillRasterPct)
                

                #Place copies of filled rasters in output geodatabase
                arcpy.env.workspace = cfg.BARRIERGDB
                fillRasterFN = (PREFIX + "_BarrrierCircles" + sumSuffix + "_Rad" + 
                                str(outerRadius))
                arcpy.CopyRaster_management(fillRaster, fillRasterFN) 
                if cfg.WRITE_PCT_RASTERS:
                    fillRasterPctFN = (PREFIX + "_BarrrierCircles_Pct" + sumSuffix + 
                                      "_Rad" + str(outerRadius))
                    arcpy.CopyRaster_management(fillRasterPct, fillRasterPctFN) 

                if not cfg.SUM_BARRIERS and cfg.WRITE_TRIM_RASTERS:
                    # Create pared-down version of filled raster- remove pixels 
                    # that don't need restoring by allowing a pixel to only 
                    # contribute its resistance value to restoration gain
                    outRasterFN = "barriers_trm" + str(outerRadius) + tif
                    outRaster = path.join(cfg.BARRIERBASEDIR,outRasterFN)
                    rasterList = [fillRaster, resistFillRaster]
                    outCellStatistics = arcpy.sa.CellStatistics(rasterList, 
                                                                "MINIMUM")
                    outCellStatistics.save(outRaster)

                    #SECOND ROUND TO CLIP BY DATA VALUES IN BARRIER RASTER
                    outRaster2FN = ("barriers_trm"  + sumSuffix + str(outerRadius) 
                                   + "_2" + tif)
                    outRaster2 = path.join(cfg.BARRIERBASEDIR,outRaster2FN)
                    output = arcpy.sa.Con(IsNull(fillRaster),fillRaster,outRaster)
                    output.save(outRaster2)
                    outRasterFN = (PREFIX + "_BarrierCircles_RBMin"  + sumSuffix + 
                                  "_Rad" + str(outerRadius))

                    outRasterPath= path.join(cfg.BARRIERGDB, outRasterFN)
                    arcpy.CopyRaster_management(outRaster2, outRasterFN)
                randomerror()
                startTime=lu.elapsed_time(startTime)
            
            # Call the above function
            doRadiusLoop()
        
        # Combine rasters across radii
        gprint('\nCreating summary rasters...')
        if startRadius != endRadius:
            radiiSuffix = ('_Rad' + str(int(startRadius)) + 'To' + str(int(
                            endRadius)) + 'Step' + str(int(radiusStep)))
            mosaicFN = "bar_radii" 
            mosaicPctFN = "bar_radii_pct" 
            arcpy.env.workspace = cfg.BARRIERBASEDIR
            for radius in range (startRadius, endRadius + 1, radiusStep):
                #Fixme: run speed test with gdb mosaicking above and here
                radiusFN = (PREFIX + "_BarrierCenters" + sumSuffix + "_Rad" 
                           + str(radius))
                radiusRaster = path.join(cfg.BARRIERGDB, radiusFN)

                if radius == startRadius:
                #If this is the first grid then copy rather than mosaic
                    arcpy.CopyRaster_management(radiusRaster, mosaicFN)
                else:
                    mosaicRaster = path.join(cfg.BARRIERBASEDIR,mosaicFN)
                    arcpy.Mosaic_management(radiusRaster, mosaicRaster,
                                         "MAXIMUM", "MATCH")
            
                if cfg.WRITE_PCT_RASTERS:                         
                    radiusPctFN = (PREFIX + "_BarrierCenters_Pct" + sumSuffix + 
                                   "_Rad" + str(radius))
                    radiusRasterPct = path.join(cfg.BARRIERGDB, radiusPctFN)

                    if radius == startRadius:
                    #If this is the first grid then copy rather than mosaic
                        arcpy.CopyRaster_management(radiusRasterPct, 
                                                    mosaicPctFN)
                    else:
                        mosaicRasterPct = path.join(cfg.BARRIERBASEDIR,
                                                    mosaicPctFN)
                        arcpy.Mosaic_management(radiusRasterPct, 
                                                mosaicRasterPct,
                                                "MAXIMUM", "MATCH")
                                         
            # Copy results to output geodatabase
            arcpy.env.workspace = cfg.BARRIERGDB
            mosaicFN = PREFIX + "_BarrierCenters" + sumSuffix + radiiSuffix
            arcpy.CopyRaster_management(mosaicRaster, mosaicFN)

            if cfg.WRITE_PCT_RASTERS:            
                mosaicPctFN = (PREFIX + "_BarrierCenters_Pct" + sumSuffix + 
                              radiiSuffix)
                arcpy.CopyRaster_management(mosaicRasterPct, mosaicPctFN)
                      
            
            #GROWN OUT rasters
            fillMosaicFN = "barriers_radii_fill" + tif
            fillMosaicPctFN = "barriers_radii_fill_pct" + tif
            fillMosaicRaster = path.join(cfg.BARRIERBASEDIR,fillMosaicFN)
            fillMosaicRasterPct = path.join(cfg.BARRIERBASEDIR,fillMosaicPctFN)
            
            arcpy.env.workspace = cfg.BARRIERBASEDIR
            for radius in range (startRadius, endRadius + 1, radiusStep):
                radiusFN = "barriers_fill" + str(radius) + tif
                #fixme- do this when only a single radius too
                radiusRaster = path.join(cfg.BARRIERBASEDIR, radiusFN)
                if radius == startRadius:
                #If this is the first grid then copy rather than mosaic
                    arcpy.CopyRaster_management(radiusRaster, fillMosaicFN)
                else:
                    arcpy.Mosaic_management(radiusRaster, fillMosaicRaster,
                                         "MAXIMUM", "MATCH")
                                         
                if cfg.WRITE_PCT_RASTERS:
                    radiusPctFN = "barriers_fill_pct" + str(radius) + tif
                    #fixme- do this when only a single radius too
                    radiusRasterPct = path.join(cfg.BARRIERBASEDIR, 
                                                radiusPctFN)
                    if radius == startRadius:
                    #If this is the first grid then copy rather than mosaic
                        arcpy.CopyRaster_management(radiusRasterPct, 
                                                    fillMosaicPctFN)
                    else:
                        arcpy.Mosaic_management(radiusRasterPct, 
                                                fillMosaicRasterPct,
                                                "MAXIMUM", "MATCH")
                                         
            # Copy result to output geodatabase
            arcpy.env.workspace = cfg.BARRIERGDB
            fillMosaicFN = PREFIX + "_BarrierCircles" + sumSuffix + radiiSuffix
            arcpy.CopyRaster_management(fillMosaicRaster, fillMosaicFN)
            if cfg.WRITE_PCT_RASTERS:
                fillMosaicPctFN = (PREFIX + "_BarrierCircles_Pct" + sumSuffix 
                                  + radiiSuffix)
                arcpy.CopyRaster_management(fillMosaicRasterPct, 
                                            fillMosaicPctFN)
            
#            if not cfg.SUM_BARRIERS:
                #GROWN OUT AND TRIMMED rasters (Can't do percent)
            if cfg.WRITE_TRIM_RASTERS:
                trimMosaicFN = "bar_radii_trm"
                arcpy.env.workspace = cfg.BARRIERBASEDIR
                trimMosaicRaster = path.join(cfg.BARRIERBASEDIR,trimMosaicFN)
                for radius in range (startRadius, endRadius + 1, radiusStep):
                    radiusFN = (PREFIX + "_BarrierCircles_RBMin" + sumSuffix  
                            + "_Rad" + str(radius))
                    #fixme- do this when only a single radius too
                    radiusRaster = path.join(cfg.BARRIERGDB, radiusFN)

                    if radius == startRadius:
                    #If this is the first grid then copy rather than mosaic
                        arcpy.CopyRaster_management(radiusRaster, trimMosaicFN)
                    else:
                        arcpy.Mosaic_management(radiusRaster, trimMosaicRaster,
                                             "MAXIMUM", "MATCH")
                # Copy result to output geodatabase
                arcpy.env.workspace = cfg.BARRIERGDB
                trimMosaicFN = (PREFIX + "_BarrierCircles_RBMin" + sumSuffix 
                                + radiiSuffix)
                arcpy.CopyRaster_management(trimMosaicRaster, trimMosaicFN)
        
        if not cfg.SAVE_RADIUS_RASTERS:
            arcpy.env.workspace = cfg.BARRIERGDB
            rasters = arcpy.ListRasters()
            for raster in rasters:
                if 'rad' in raster.lower() and not 'step' in raster.lower():
                    lu.delete_data(raster)
                
                
                
        arcpy.env.workspace = cfg.BARRIERGDB
        rasters = arcpy.ListRasters()
        for raster in rasters:
            gprint('\nBuilding output statistics and pyramids\n'
                        'for raster ' + raster)
            lu.build_stats(raster)

        #Clean up temporary files and directories
        if not cfg.SAVEBARRIERRASTERS:
            lu.delete_dir(cbarrierdir)
            lu.delete_dir(cfg.BARRIERBASEDIR)

        if not cfg.SAVEFOCALRASTERS:
            for radius in range(startRadius, endRadius + 1, radiusStep):
                core1path = lu.get_focal_path(1,radius)
                path1, dir1 = path.split(core1path)
                path2, dir2 = path.split(path1)
                lu.delete_dir(path2)

    # Return GEOPROCESSING specific errors
    except arcpy.ExecuteError:
        lu.dashline(1)
        gprint('****Failed in step 6. Details follow.****')
        lu.exit_with_geoproc_error(_SCRIPT_NAME)

    # Return any PYTHON or system specific errors
    except:
        lu.dashline(1)
        gprint('****Failed in step 6. Details follow.****')
        lu.exit_with_python_error(_SCRIPT_NAME)

    return
예제 #8
0
def STEP3_calc_cwds():
    """Calculates cost-weighted distances from each core area.
    Uses bounding circles around source and target cores to limit
    extent of cwd calculations and speed computation.

    """
    try:
        lu.dashline(1)
        gprint('Running script ' + _SCRIPT_NAME)
        lu.dashline(0)

        # Super secret setting to re-start failed run.  Enter 'RESTART' as the
        # Name of the pairwise distance table in step 2, and uncheck step 2.
        # We can eventually place this in a .ini file.
        rerun = False
        if cfg.S2EUCDISTFILE != None:
            if cfg.S2EUCDISTFILE.lower() == "restart":
                rerun = True

        # if cfg.TMAXCWDIST is None:
           	# gprint('NOT using a maximum cost-weighted distance.')
        # else:
            # gprint('Max cost-weighted distance for CWD calcs set '
                              # 'to ' + str(cfg.TMAXCWDIST) + '\n')

                              
        if (cfg.BUFFERDIST) is not None:
            gprint('Bounding circles plus a buffer of ' +
                              str(float(cfg.BUFFERDIST)) + ' map units will '
                              'be used \n to limit extent of cost distance '
                              'calculations.')
        elif cfg.TOOL <> cfg.TOOL_CC:
            gprint('NOT using bounding circles in cost distance '
                              'calculations.')

        # set the analysis extent and cell size
        # So we don't extract rasters that go beyond extent of original raster
        if arcpy:
            arcpy.env.cellSize = cfg.RESRAST
            arcpy.env.extent="MINOF"
        else:
            gp.cellSize = gp.Describe(cfg.RESRAST).MeanCellHeight
            gp.Extent = "MINOF"
        gp.mask = cfg.RESRAST
        if arcpy:
            arcpy.env.overwriteOutput = True
            arcpy.env.workspace = cfg.SCRATCHDIR
            arcpy.env.scratchWorkspace = cfg.ARCSCRATCHDIR
        else:
            gp.OverwriteOutput = True
            gp.workspace = cfg.SCRATCHDIR
            gp.scratchWorkspace = cfg.ARCSCRATCHDIR

        # Load linkTable (created in previous script)
        linkTableFile = lu.get_prev_step_link_table(step=3)
        linkTable = lu.load_link_table(linkTableFile)
        lu.report_links(linkTable)

        # Identify cores to map from LinkTable
        coresToMap = npy.unique(linkTable[:, cfg.LTB_CORE1:cfg.LTB_CORE2 + 1])
        numCoresToMap = len(coresToMap)

        if numCoresToMap < 3:
            # No need to check for intermediate cores, because there aren't any
            cfg.S3DROPLCCSic = False
        else:
            cfg.S3DROPLCCSic = cfg.S3DROPLCCS
        gprint('\nNumber of core areas to connect: ' +
                          str(numCoresToMap))

        if rerun:
            # If picking up a failed run, make sure needed files are there
            lu.dashline(1)
            gprint ('\n****** RESTART MODE ENABLED ******\n')
            gprint ('**** NOTE: This mode picks up step 3 where a\n'
                    'previous run left off due to a crash or user\n'
                    'abort.  It assumes you are using the same input\n'
                    'data used in the terminated run.****\n')
            lu.dashline(0)
            lu.snooze(10)
            savedLinkTableFile = path.join(cfg.DATAPASSDIR,
                                           "temp_linkTable_s3_partial.csv")
            coreListFile = path.join(cfg.DATAPASSDIR, "temp_cores_to_map.csv")

            if not path.exists(savedLinkTableFile) or not path.exists(
                                                          coreListFile):

                gprint('No partial results file found from previous '
                       'stopped run. Starting run from beginning.\n')
                lu.dashline(0)
                rerun = False

        # If picking up a failed run, use old folders
        if not rerun:
            startIndex = 0
            if cfg.TOOL <> cfg.TOOL_CC:
                lu.make_cwd_paths(max(coresToMap)) # Set up cwd directories

        # make a feature layer for input cores to select from
        gp.MakeFeatureLayer(cfg.COREFC, cfg.FCORES)

        # Drop links that are too long
        gprint('\nChecking for corridors that are too long to map.')
        DISABLE_LEAST_COST_NO_VAL = False
        linkTable,numDroppedLinks = lu.drop_links(linkTable, cfg.MAXEUCDIST, 0,
                                                  cfg.MAXCOSTDIST, 0,
                                                  DISABLE_LEAST_COST_NO_VAL)
        # ------------------------------------------------------------------
        # Bounding boxes
        if (cfg.BUFFERDIST) is not None:
            # create bounding boxes around cores
            start_time = time.clock()
            # lu.dashline(1)
            gprint('Calculating bounding boxes for core areas.')
            extentBoxList = npy.zeros((0,5), dtype='float32')
            for x in range(len(coresToMap)):
                core = coresToMap[x]
                boxCoords = lu.get_extent_box_coords(core)
                extentBoxList = npy.append(extentBoxList, boxCoords, axis=0)
            gprint('\nDone calculating bounding boxes.')
            start_time = lu.elapsed_time(start_time)
            # lu.dashline()

        # Bounding circle code
        if cfg.BUFFERDIST is not None:
            # Make a set of circles encompassing core areas we'll be connecting
            start_time = time.clock()
            gprint('Calculating bounding circles around potential'
                          ' corridors.')

            # x y corex corey radius- stores data for bounding circle centroids
            boundingCirclePointArray  = npy.zeros((0,5), dtype='float32')

            circleList = npy.zeros((0,3), dtype='int32')

            numLinks = linkTable.shape[0]
            for x in range(0, numLinks):
                if ((linkTable[x,cfg.LTB_LINKTYPE] == cfg.LT_CORR) or
                    (linkTable[x,cfg.LTB_LINKTYPE] == cfg.LT_KEEP)):
                    # if it's a valid corridor link
                    linkId = int(linkTable[x,cfg.LTB_LINKID])
                    # fixme- this code is clumsy- can trim down
                    cores = npy.zeros((1,3), dtype='int32')
                    cores[0,:] = npy.sort([0, linkTable[x,cfg.LTB_CORE1],
                                      linkTable[x,cfg.LTB_CORE2]])
                    corex = cores[0,1]
                    corey = cores[0,2]
                    cores[0,0] = linkId

                    ###################
                    foundFlag = False
                    for y in range(0,len(circleList)):  # clumsy
                        if (circleList[y,1] == corex and
                            circleList[y,2] == corey):
                            foundFlag = True
                    if not foundFlag:
                        circlePointData = (
                            lu.get_bounding_circle_data(extentBoxList,
                            corex, corey, cfg.BUFFERDIST))
                        boundingCirclePointArray = (
                            npy.append(boundingCirclePointArray,
                            circlePointData, axis=0))
                        # keep track of which cores we draw bounding circles
                        # around
                        circleList = npy.append(circleList, cores, axis=0)

            gprint('\nCreating bounding circles using buffer '
                              'analysis.')

            dir, BNDCIRCENS = path.split(cfg.BNDCIRCENS)
            lu.make_points(cfg.SCRATCHDIR, boundingCirclePointArray,
                           BNDCIRCENS)
            lu.delete_data(cfg.BNDCIRS)
            gp.buffer_analysis(cfg.BNDCIRCENS, cfg.BNDCIRS, "radius")
            gp.deletefield (cfg.BNDCIRS, "BUFF_DIST")

            gprint('Successfully created bounding circles around '
                              'potential corridors using \na buffer of ' +
                              str(float(cfg.BUFFERDIST)) + ' map units.')
            start_time = lu.elapsed_time(start_time)

            gprint('Reducing global processing area using bounding '
                              'circle plus buffer of ' +
                              str(float(cfg.BUFFERDIST)) + ' map units.\n')


            extentBoxList = npy.zeros((0,5),dtype='float32')
            boxCoords = lu.get_extent_box_coords()
            extentBoxList = npy.append(extentBoxList,boxCoords,axis=0)
            extentBoxList[0,0] = 0

            boundingCirclePointArray  = npy.zeros((0,5),dtype='float32')
            circlePointData=lu.get_bounding_circle_data(extentBoxList, 0,
                                                        0, cfg.BUFFERDIST)

            dir, BNDCIRCEN = path.split(cfg.BNDCIRCEN)
            lu.make_points(cfg.SCRATCHDIR, circlePointData, BNDCIRCEN)
            lu.delete_data(cfg.BNDCIR)
            gp.buffer_analysis(cfg.BNDCIRCEN, cfg.BNDCIR, "radius")

            gprint('Extracting raster....')
            cfg.BOUNDRESIS = cfg.BOUNDRESIS + tif
            lu.delete_data(cfg.BOUNDRESIS)
            count = 0
            statement = (
                'gp.ExtractByMask_sa(cfg.RESRAST, cfg.BNDCIR, cfg.BOUNDRESIS)')
            while True:
                try:
                    exec statement
                    randomerror()
                except:
                    count,tryAgain = lu.retry_arc_error(count,statement)
                    if not tryAgain: exec statement
                else: break
            gprint('\nReduced resistance raster extracted using '
                              'bounding circle.')

        else: #if not using bounding circles, just go with resistance raster.
            cfg.BOUNDRESIS = cfg.RESRAST

        # ---------------------------------------------------------------------
        # Rasterize core areas to speed cost distance calcs
        # lu.dashline(1)
        gprint("Creating core area raster.")

        gp.SelectLayerByAttribute(cfg.FCORES, "CLEAR_SELECTION")

        if arcpy:
            arcpy.env.cellSize = cfg.BOUNDRESIS
            arcpy.env.extent = cfg.BOUNDRESIS
        else:
            gp.cellSize = gp.Describe(cfg.BOUNDRESIS).MeanCellHeight
            gp.extent = gp.Describe(cfg.BOUNDRESIS).extent

        if rerun:
            # saved linktable replaces the one now in memory
            linkTable = lu.load_link_table(savedLinkTableFile)
            coresToMapSaved = npy.loadtxt(coreListFile, dtype='Float64',
                                          comments='#', delimiter=',')
            startIndex = coresToMapSaved[0] # Index of core where we left off
            del coresToMapSaved
            gprint ('\n****** Re-starting run at core area number '
                    + str(int(coresToMap[startIndex]))+ ' ******\n')
            lu.dashline(0)

        if arcpy:
            arcpy.env.extent = "MINOF"
        else:
            gp.extent = "MINOF"

        #----------------------------------------------------------------------
        # Loop through cores, do cwd calcs for each
        if cfg.TOOL == cfg.TOOL_CC:
            gprint("\nMapping least-cost paths.\n")
        else:
            gprint("\nStarting cost distance calculations.\n")
        lcpLoop = 0
        failures = 0
        x = startIndex
        endIndex = len(coresToMap)
        linkTableMod = linkTable.copy()
        while x < endIndex:
            startTime1 = time.clock()
            # Modification of linkTable in function was causing problems. so
            # make a copy:
            linkTablePassed = linkTableMod.copy()

            (linkTableReturned, failures, lcpLoop) = do_cwd_calcs(x,
                        linkTablePassed, coresToMap, lcpLoop, failures)
            if failures == 0:
                # If iteration was successful, continue with next core
                linkTableMod = linkTableReturned
                sourceCore = int(coresToMap[x])
                gprint('Done with all calculations for core ID #' +
                        str(sourceCore) + '. ' + str(int(x + 1)) + ' of ' +
                        str(endIndex) + ' cores have been processed.')
                start_time = lu.elapsed_time(startTime1)

                outlinkTableFile = path.join(cfg.DATAPASSDIR,
                                             "temp_linkTable_s3_partial.csv")
                lu.write_link_table(linkTableMod, outlinkTableFile)
                # Increment  loop counter
                x = x + 1
            else:
                # If iteration failed, try again after a wait period
                delay_restart(failures)
        #----------------------------------------------------------------------

        linkTable = linkTableMod

        # reinstate temporarily disabled links
        rows = npy.where(linkTable[:,cfg.LTB_LINKTYPE] > 1000)
        linkTable[rows,cfg.LTB_LINKTYPE] = (linkTable[rows,cfg.LTB_LINKTYPE] -
                                            1000)

        # Drop links that are too long
        DISABLE_LEAST_COST_NO_VAL = True
        linkTable,numDroppedLinks = lu.drop_links(linkTable, cfg.MAXEUCDIST,
                                               cfg.MINEUCDIST, cfg.MAXCOSTDIST,
                                               cfg.MINCOSTDIST,
                                               DISABLE_LEAST_COST_NO_VAL)

        # Write link table file
        outlinkTableFile = lu.get_this_step_link_table(step=3)
        gprint('Updating ' + outlinkTableFile)
        lu.write_link_table(linkTable, outlinkTableFile)
        linkTableLogFile = path.join(cfg.LOGDIR, "linkTable_s3.csv")
        lu.write_link_table(linkTable, linkTableLogFile)

        start_time = time.clock()
        gprint('Creating shapefiles with linework for links...')
        try:
            lu.write_link_maps(outlinkTableFile, step=3)
        except:
            lu.write_link_maps(outlinkTableFile, step=3)
        start_time = lu.elapsed_time(start_time)

        gprint('\nIndividual cost-weighted distance layers written '
                          'to "cwd" directory. \n')
        gprint(outlinkTableFile +
                '\n updated with cost-weighted distances between core areas.')

        #Clean up temporary files for restart code
        tempFile = path.join(cfg.DATAPASSDIR, "temp_cores_to_map.csv")
        lu.delete_file(tempFile)
        tempFile = path.join(cfg.DATAPASSDIR, "temp_linkTable_s3_partial.csv")
        lu.delete_file(tempFile)

        # Check if climate tool is calling linkage mapper
        if cfg.TOOL == cfg.TOOL_CC:
            coreList = npy.unique(linkTable[:, cfg.LTB_CORE1:cfg.LTB_CORE2 + 1])
            for core in coreList:
                cwdRaster = lu.get_cwd_path(int(core))
                back_rast = cwdRaster.replace("cwd_", "back_")        
                lu.delete_data(back_rast)
        

    # Return GEOPROCESSING specific errors
    except arcgisscripting.ExecuteError:
        lu.dashline(1)
        gprint('****Failed in step 3. Details follow.****')
        lu.exit_with_geoproc_error(_SCRIPT_NAME)

    # Return any PYTHON or system specific errors
    except:
        lu.dashline(1)
        gprint('****Failed in step 3. Details follow.****')
        lu.exit_with_python_error(_SCRIPT_NAME)

    return
예제 #9
0
def calc_lccs(normalize):
    try:  
        if normalize:
            mosaicBaseName = "_corridors"
            writeTruncRaster = cfg.WRITETRUNCRASTER
            outputGDB = cfg.OUTPUTGDB
            if cfg.CALCNONNORMLCCS:
                SAVENORMLCCS = False
            else:
                SAVENORMLCCS = cfg.SAVENORMLCCS
        else:
            mosaicBaseName = "_NON_NORMALIZED_corridors"
            SAVENORMLCCS = False
            outputGDB = cfg.EXTRAGDB
            writeTruncRaster = False

        lu.dashline(1)
        gprint('Running script ' + _SCRIPT_NAME)
        linkTableFile = lu.get_prev_step_link_table(step=5)
        if cfg.useArcpy:
            arcpy.env.workspace = cfg.SCRATCHDIR
            arcpy.env.scratchWorkspace = cfg.ARCSCRATCHDIR
            arcpy.env.overwriteOutput = True  
            arcpy.env.compression = "NONE"
        else:        
            gp.workspace = cfg.SCRATCHDIR
            gp.scratchWorkspace = cfg.ARCSCRATCHDIR
            gp.OverwriteOutput = True            

        if cfg.MAXEUCDIST is not None:
            gprint('Max Euclidean distance between cores')
            gprint('for linkage mapping set to ' +
                              str(cfg.MAXEUCDIST))

        if cfg.MAXCOSTDIST is not None:
            gprint('Max cost-weighted distance between cores')
            gprint('for linkage mapping set to ' +
                              str(cfg.MAXCOSTDIST))


        # set the analysis extent and cell size to that of the resistance
        # surface
        if cfg.useArcpy:
            arcpy.env.Extent = cfg.RESRAST
            arcpy.env.cellSize = cfg.RESRAST
            arcpy.env.snapRaster = cfg.RESRAST
            arcpy.env.mask = cfg.RESRAST
        else:
            gp.Extent = (gp.Describe(cfg.RESRAST)).Extent 
            gp.cellSize = gp.Describe(cfg.RESRAST).MeanCellHeight
            gp.mask = cfg.RESRAST
            gp.snapraster = cfg.RESRAST

        linkTable = lu.load_link_table(linkTableFile)
        numLinks = linkTable.shape[0]
        numCorridorLinks = lu.report_links(linkTable)
        if numCorridorLinks == 0:
            lu.dashline(1)
            msg =('\nThere are no corridors to map. Bailing.')
            lu.raise_error(msg)


        if not cfg.STEP3 and not cfg.STEP4:
            # re-check for links that are too long or in case script run out of
            # sequence with more stringent settings
            gprint('Double-checking for corridors that are too long to map.')
            DISABLE_LEAST_COST_NO_VAL = True
            linkTable,numDroppedLinks = lu.drop_links(
                linkTable, cfg.MAXEUCDIST, cfg.MINEUCDIST, cfg.MAXCOSTDIST,
                cfg.MINCOSTDIST, DISABLE_LEAST_COST_NO_VAL)

        # Added to try to speed up:
        gp.pyramid = "NONE"
        gp.rasterstatistics = "NONE"

        # set up directories for normalized lcc and mosaic grids
        dirCount = 0
        gprint("Creating output folder: " + cfg.LCCBASEDIR)
        lu.delete_dir(cfg.LCCBASEDIR)
        gp.CreateFolder_management(path.dirname(cfg.LCCBASEDIR),
                                       path.basename(cfg.LCCBASEDIR))
        gp.CreateFolder_management(cfg.LCCBASEDIR, cfg.LCCNLCDIR_NM)
        clccdir = path.join(cfg.LCCBASEDIR, cfg.LCCNLCDIR_NM)
        # mosaicGDB = path.join(cfg.LCCBASEDIR, "mosaic.gdb")
        # gp.createfilegdb(cfg.LCCBASEDIR, "mosaic.gdb")
        #mosaicRaster = mosaicGDB + '\\' + "nlcc_mos" # Full path
        gprint("")
        if normalize:
            gprint('Normalized least-cost corridors will be written '
                          'to ' + clccdir + '\n')
        PREFIX = cfg.PREFIX

        # Add CWD layers for core area pairs to produce NORMALIZED LCC layers
        numGridsWritten = 0
        coreList = linkTable[:,cfg.LTB_CORE1:cfg.LTB_CORE2+1]
        coreList = npy.sort(coreList)

        x = 0
        linkCount = 0
        endIndex = numLinks
        while x < endIndex:
            if (linkTable[x, cfg.LTB_LINKTYPE] < 1): # If not a valid link
                x = x + 1
                continue
                
            linkCount = linkCount + 1
            start_time = time.clock() 
            
            linkId = str(int(linkTable[x, cfg.LTB_LINKID]))

            # source and target cores
            corex=int(coreList[x,0])
            corey=int(coreList[x,1])

            # Get cwd rasters for source and target cores
            cwdRaster1 = lu.get_cwd_path(corex)
            cwdRaster2 = lu.get_cwd_path(corey)

            if not gp.Exists(cwdRaster1):
                msg =('\nError: cannot find cwd raster:\n' + cwdRaster1) 
            if not gp.Exists(cwdRaster2):
                msg =('\nError: cannot find cwd raster:\n' + cwdRaster2) 
                lu.raise_error(msg)

            
            lccNormRaster = path.join(clccdir, str(corex) + "_" +
                                      str(corey))# + ".tif")
            if cfg.useArcpy: 
                arcpy.env.Extent = "MINOF"
            else:
                gp.Extent = "MINOF"

            # FIXME: need to check for this?:
            # if exists already, don't re-create
            #if not gp.Exists(lccRaster):

            link = lu.get_links_from_core_pairs(linkTable, corex, corey)

            offset = 10000 

            # Normalized lcc rasters are created by adding cwd rasters and
            # subtracting the least cost distance between them.
            count = 0
            if arcpyAvailable:
                cfg.useArcpy = True # Fixes Canran Liu's bug with lcDist
            if cfg.useArcpy:
                
                lcDist = (float(linkTable[link,cfg.LTB_CWDIST]) - offset) 
                
                if normalize:
                    statement = ('outras = Raster(cwdRaster1) + Raster('
                        'cwdRaster2) - lcDist; outras.save(lccNormRaster)') 
                                                
                else:
                    statement = ('outras =Raster(cwdRaster1) + Raster('
                                'cwdRaster2); outras.save(lccNormRaster)')
            else:
                if normalize:
                    lcDist = str(linkTable[link,cfg.LTB_CWDIST] - offset)  
                    expression = (cwdRaster1 + " + " + cwdRaster2 + " - " 
                                  + lcDist)
                else:
                    expression = (cwdRaster1 + " + " + cwdRaster2) 
                statement = ('gp.SingleOutputMapAlgebra_sa(expression, '
                     'lccNormRaster)')
            count = 0
            while True:
                try: 
                    exec statement                    
                    randomerror()
                except:
                    count,tryAgain = lu.retry_arc_error(count,statement)
                    if not tryAgain:    
                        exec statement
                else: break
            cfg.useArcpy = False # End fix for Conran Liu's bug with lcDist
            
            if normalize and cfg.useArcpy: 
                try: 
                    minObject = gp.GetRasterProperties(lccNormRaster, "MINIMUM") 
                    rasterMin = float(str(minObject.getoutput(0)))
                except:
                    gp.AddWarning('\n------------------------------------------------')
                    gp.AddWarning('WARNING: Raster minimum check failed in step 5. \n'
                        'This may mean the output rasters are corrupted. Please \n'
                        'be sure to check for valid rasters in '+ outputGDB)
                    rasterMin = 0
                tolerance = (float(gp.cellSize) * -10) + offset
                if rasterMin < tolerance:
                    lu.dashline(1)
                    msg = ('WARNING: Minimum value of a corridor #' + str(x+1) 
                           + ' is much less than zero ('+str(rasterMin)+').'
                           '\nThis could mean that BOUNDING CIRCLE BUFFER DISTANCES '
                           'were too small and a corridor passed outside of a '
                           'bounding circle, or that a corridor passed outside of the '
                           'resistance map. \n')
                    gp.AddWarning(msg)

            
            if cfg.useArcpy: 
                arcpy.env.Extent = cfg.RESRAST
            else:
                gp.Extent = (gp.Describe(cfg.RESRAST)).Extent

            mosaicDir = path.join(cfg.LCCBASEDIR,'mos'+str(x+1))  
            lu.create_dir(mosaicDir) 
            mosFN = 'mos'#.tif' change and move
            mosaicRaster = path.join(mosaicDir,mosFN) 
                       
            if numGridsWritten == 0 and dirCount == 0:
                #If this is the first grid then copy rather than mosaic
                arcObj.CopyRaster_management(lccNormRaster, mosaicRaster) 
            else:
                
                rasterString = '"'+lccNormRaster+";"+lastMosaicRaster+'"'
                statement = ('arcObj.MosaicToNewRaster_management('
                            'rasterString,mosaicDir,mosFN, "", '
                            '"32_BIT_FLOAT", gp.cellSize, "1", "MINIMUM", '
                            '"MATCH")') 
                # statement = ('arcpy.Mosaic_management(lccNormRaster, '
                                 # 'mosaicRaster, "MINIMUM", "MATCH")') 
                
                count = 0
                while True:
                    try:
                        lu.write_log('Executing mosaic for link #'+str(linkId))
                        exec statement
                        lu.write_log('Done with mosaic.')
                        randomerror()
                    except:
                        count,tryAgain = lu.retry_arc_error(count,statement)
                        lu.delete_data(mosaicRaster)
                        lu.delete_dir(mosaicDir)
                        # Try a new directory
                        mosaicDir = path.join(cfg.LCCBASEDIR,'mos'+str(x+1)+ '_' + str(count))
                        lu.create_dir(mosaicDir)
                        mosaicRaster = path.join(mosaicDir,mosFN)                        
                        if not tryAgain:    
                            exec statement
                    else: break
            endTime = time.clock()
            processTime = round((endTime - start_time), 2)

            if normalize == True:
                printText = "Normalized and mosaicked "
            else:
                printText = "Mosaicked NON-normalized "
            gprint(printText + "corridor for link ID #" + str(linkId) +
                    " connecting core areas " + str(corex) +
                    " and " + str(corey)+ " in " +
                    str(processTime) + " seconds. " + str(int(linkCount)) +
                    " out of " + str(int(numCorridorLinks)) + " links have been "
                    "processed.")

            # temporarily disable links in linktable - don't want to mosaic
            # them twice
            for y in range (x+1,numLinks):
                corex1 = int(coreList[y,0])
                corey1 = int(coreList[y,1])
                if corex1 == corex and corey1 == corey:
                    linkTable[y,cfg.LTB_LINKTYPE] = (
                        linkTable[y,cfg.LTB_LINKTYPE] + 1000)
                elif corex1==corey and corey1==corex:
                    linkTable[y,cfg.LTB_LINKTYPE] = (
                            linkTable[y,cfg.LTB_LINKTYPE] + 1000)

            numGridsWritten = numGridsWritten + 1
            if not SAVENORMLCCS:
                lu.delete_data(lccNormRaster)
                lu.delete_dir(clccdir)
                lu.create_dir(clccdir)  
            else:
                if numGridsWritten == 100:
                    # We only write up to 100 grids to any one folder
                    # because otherwise Arc slows to a crawl
                    dirCount = dirCount + 1
                    numGridsWritten = 0
                    clccdir = path.join(cfg.LCCBASEDIR,
                                        cfg.LCCNLCDIR_NM + str(dirCount))
                    gprint("Creating output folder: " + clccdir)
                    gp.CreateFolder_management(cfg.LCCBASEDIR,
                                               path.basename(clccdir))

            if numGridsWritten > 1 or dirCount > 0:                                       
                lu.delete_data(lastMosaicRaster)
                lu.delete_dir(path.dirname(lastMosaicRaster))

            lastMosaicRaster = mosaicRaster
            x = x + 1
            
        #rows that were temporarily disabled
        rows = npy.where(linkTable[:,cfg.LTB_LINKTYPE]>1000)
        linkTable[rows,cfg.LTB_LINKTYPE] = (
            linkTable[rows,cfg.LTB_LINKTYPE] - 1000)
        # ---------------------------------------------------------------------

        # Create output geodatabase
        if not gp.exists(outputGDB):
            gp.createfilegdb(cfg.OUTPUTDIR, path.basename(outputGDB))

        if cfg.useArcpy:
            arcpy.env.workspace = outputGDB
        else:        
            gp.workspace = outputGDB

        gp.pyramid = "NONE"
        gp.rasterstatistics = "NONE"

        
        # Copy mosaic raster to output geodatabase
        saveFloatRaster = False
        if saveFloatRaster == True:
            floatRaster = outputGDB + '\\' + PREFIX + mosaicBaseName + '_flt' # Full path 
            statement = 'arcObj.CopyRaster_management(mosaicRaster, floatRaster)'
            try:
                exec statement
            except:
                pass
                

        # ---------------------------------------------------------------------
        # convert mosaic raster to integer
        intRaster = path.join(outputGDB,PREFIX + mosaicBaseName)
        if cfg.useArcpy:
            statement = ('outras = Int(Raster(mosaicRaster) - offset + 0.5); ' 
                        'outras.save(intRaster)')
        else:
            expression = "int(" + mosaicRaster + " - " + str(offset) + " + 0.5)"
            statement = 'gp.SingleOutputMapAlgebra_sa(expression, intRaster)'
        count = 0
        while True:
            try: 
                exec statement
                randomerror()
            except:
                count,tryAgain = lu.retry_arc_error(count,statement)
                if not tryAgain: exec statement
            else: break
        # ---------------------------------------------------------------------       
        

        if writeTruncRaster:
            # -----------------------------------------------------------------
            # Set anything beyond cfg.CWDTHRESH to NODATA.
            if arcpyAvailable:
                cfg.useArcpy = True # For Alissa Pump's error with 10.1
            cutoffText = str(cfg.CWDTHRESH)
            if cutoffText[-6:] == '000000':
                cutoffText = cutoffText[0:-6]+'m' 
            elif cutoffText[-3:] == '000':
                cutoffText = cutoffText[0:-3]+'k' 
            
            truncRaster = (outputGDB + '\\' + PREFIX + mosaicBaseName + 
                           '_truncated_at_' + cutoffText)

            count = 0
            if cfg.useArcpy:
                statement = ('outRas = Raster(intRaster) * '
                            '(Con(Raster(intRaster) <= cfg.CWDTHRESH,1)); '
                            'outRas.save(truncRaster)')
            else:
                expression = ("(" + intRaster + " * (con(" + intRaster + "<= " 
                              + str(cfg.CWDTHRESH) + ",1)))")
                statement = ('gp.SingleOutputMapAlgebra_sa(expression, '
                                                          'truncRaster)')
            count = 0
            while True:
                try: 
                    exec statement
                    randomerror()
                except:
                    count,tryAgain = lu.retry_arc_error(count,statement)
                    if not tryAgain: exec statement
                else: break
            cfg.useArcpy = False # End fix for Alissa Pump's error with 10.1                
        # ---------------------------------------------------------------------
        # Check for unreasonably low minimum NLCC values    
        try:
            mosaicGrid = path.join(cfg.LCCBASEDIR,'mos') 
            # Copy to grid to test
            arcObj.CopyRaster_management(mosaicRaster, mosaicGrid)
            minObject = gp.GetRasterProperties(mosaicGrid, "MINIMUM") 
            rasterMin = float(str(minObject.getoutput(0)))
        except:
            gp.AddWarning('\n------------------------------------------------')
            gp.AddWarning('WARNING: Raster minimum check failed in step 5. \n'
                'This may mean the output rasters are corrupted. Please \n'
                'be sure to check for valid rasters in '+ outputGDB)
            rasterMin = 0
        tolerance = (float(gp.cellSize) * -10)
           
        if rasterMin < tolerance:
            lu.dashline(1)
            msg = ('WARNING: Minimum value of mosaicked corridor map is ' 
                   'much less than zero ('+str(rasterMin)+').'
                   '\nThis could mean that BOUNDING CIRCLE BUFFER DISTANCES '
                   'were too small and a corridor passed outside of a '
                   'bounding circle, or that a corridor passed outside of the '
                   'resistance map. \n')
            gp.AddWarning(msg) 
                            

        gprint('\nWriting final LCP maps...')
        if cfg.STEP4:
            finalLinkTable = lu.update_lcp_shapefile(linkTable, lastStep=4,
                                                     thisStep=5)
        elif cfg.STEP3:
            finalLinkTable = lu.update_lcp_shapefile(linkTable, lastStep=3,
                                                     thisStep=5)
        else:
            # Don't know if step 4 was run, since this is started at step 5.
            # Use presence of previous linktable files to figure this out.
            # Linktable name includes step number.
            prevLinkTableFile = lu.get_prev_step_link_table(step=5)
            prevStepInd = len(prevLinkTableFile) - 5
            lastStep = prevLinkTableFile[prevStepInd]

            finalLinkTable = lu.update_lcp_shapefile(linkTable, lastStep,
                                                     thisStep=5)

        outlinkTableFile = lu.get_this_step_link_table(step=5)
        gprint('Updating ' + outlinkTableFile)
        lu.write_link_table(linkTable, outlinkTableFile)

        linkTableLogFile = path.join(cfg.LOGDIR, "linkTable_s5.csv")
        lu.write_link_table(linkTable, linkTableLogFile)

        linkTableFinalFile = path.join(cfg.OUTPUTDIR, PREFIX +
                                       "_linkTable_s5.csv")
        lu.write_link_table(finalLinkTable, linkTableFinalFile)
        gprint('Copy of final linkTable written to '+
                          linkTableFinalFile)

        gprint('Creating shapefiles with linework for links.')
        try:
            lu.write_link_maps(outlinkTableFile, step=5)
        except:
            lu.write_link_maps(outlinkTableFile, step=5)

        # Create final linkmap files in output directory, and remove files from
        # scratch.
        lu.copy_final_link_maps(step=5)

        if not SAVENORMLCCS:
            lu.delete_dir(cfg.LCCBASEDIR)

        # Build statistics for corridor rasters
        gp.addmessage('\nBuilding output statistics and pyramids '
                          'for corridor raster')
        lu.build_stats(intRaster)

        if writeTruncRaster:
            gp.addmessage('Building output statistics '
                              'for truncated corridor raster')
            lu.build_stats(truncRaster)

    # Return GEOPROCESSING specific errors
    except arcgisscripting.ExecuteError:
        lu.dashline(1)
        gprint('****Failed in step 5. Details follow.****')
        lu.exit_with_geoproc_error(_SCRIPT_NAME)

    # Return any PYTHON or system specific errors
    except:
        lu.dashline(1)
        gprint('****Failed in step 5. Details follow.****')
        lu.exit_with_python_error(_SCRIPT_NAME)

    return
예제 #10
0
def STEP4_refine_network():
    """Allows user to only connect each core area to its N
    nearest neighbors, then connect any disjunct clusters ('constellations')
    of core areas to their nearest neighboring cluster

    """
    try:

        lu.dashline(1)
        gprint('Running script ' + _SCRIPT_NAME)
        cfg.gp.Workspace = cfg.OUTPUTDIR

        linkTableFile = lu.get_prev_step_link_table(step=4)

        linkTable = lu.load_link_table(linkTableFile)
        numLinks = linkTable.shape[0]
        lu.report_links(linkTable)

        if not cfg.STEP3:
            # re-check for links that are too long in case script run out of
            # sequence with more stringent settings
            gprint('Double-checking for corridors that are too long'
                              ' or too short to map.')
            DISABLE_LEAST_COST_NO_VAL = True
            linkTable,numDroppedLinks = lu.drop_links(
                linkTable, cfg.MAXEUCDIST, 0, cfg.MAXCOSTDIST, 0,
                DISABLE_LEAST_COST_NO_VAL)

        rows, cols = npy.where(
                     linkTable[:,cfg.LTB_LINKTYPE:cfg.LTB_LINKTYPE + 1] > 0)
        # == cfg.LT_CORR
            # or
            # linkTable[:,cfg.LTB_LINKTYPE:cfg.LTB_LINKTYPE + 1] == cfg.LT_KEEP)
        corridorLinks = linkTable[rows,:]
        coresToProcess = npy.unique(
            corridorLinks[:, cfg.LTB_CORE1:cfg.LTB_CORE2 + 1])

        if cfg.S4DISTTYPE_EU:
            distCol = cfg.LTB_EUCDIST
        else:
            distCol = cfg.LTB_CWDIST

        # Flag links that do not connect any core areas to their nearest
        # N neighbors. (N = cfg.S4MAXNN)
        lu.dashline(1)
        gprint('Connecting each core area to its nearest ' +
                          str(cfg.S4MAXNN) + ' nearest neighbors.')

        # Code written assuming NO duplicate core pairs
        for core in coresToProcess:
            rows,cols = npy.where(
                corridorLinks[:,cfg.LTB_CORE1:cfg.LTB_CORE2+1] == core)
            distsFromCore = corridorLinks[rows,:]

            # Sort by distance from target core
            ind = npy.argsort(distsFromCore[:,distCol])
            distsFromCore = distsFromCore[ind]

            # Set N nearest neighbor connections to Nearest Neighbor (NNCT)
            maxRange = min(len(rows), cfg.S4MAXNN)
            for link in range (0, maxRange):
                linkId = distsFromCore[link, cfg.LTB_LINKID]
                # assumes linktable sequentially numbered with no gaps
                linkTable[linkId - 1, cfg.LTB_LINKTYPE] = cfg.LT_NNCT

        # Connect constellations (aka compoments or clusters)
        # Fixme: needs testing.  Move to function.
        if cfg.S4CONNECT:
            lu.dashline(1)
            gprint('Connecting constellations')

            # linkTableComp has 4 extra cols to track COMPONENTS
            numLinks = linkTable.shape[0]
            # g1' g2' THEN c1 c2
            compCols = npy.zeros((numLinks, 4), dtype="int32")
            linkTableComp = npy.append(linkTable, compCols, axis=1)
            del compCols

            # renumber cores to save memory for this next step.  Place in
            # columns 10 and 11
            for coreInd in range(0, len(coresToProcess)):
                # here, cols are 0 for cfg.LTB_CORE1 and 1 for cfg.LTB_CORE2
                rows, cols = npy.where(
                    linkTableComp[:,cfg.LTB_CORE1:cfg.LTB_CORE2+1] ==
                    coresToProcess[coreInd])
                # want results in cols 10 and 11- These are NEW core numbers
                # (0 - numcores)
                linkTableComp[rows, cols + 10] = coreInd

            rows, cols = npy.where(
                linkTableComp[:, cfg.LTB_LINKTYPE:cfg.LTB_LINKTYPE + 1] ==
                cfg.LT_NNCT)
            # The new, improved corridorLinks- only NN links
            corridorLinksComp = linkTableComp[rows, :]
            # These are NEW core numbers (range from 0 to numcores)
            coresToProcess = npy.unique(linkTableComp[:, 10:12])

            #Create graph describing connected cores.
            Graph = npy.zeros((len(coresToProcess), len(coresToProcess)),
                          dtype="int32")
            rows = corridorLinksComp[:,10].astype('int32')
            cols = corridorLinksComp[:,11].astype('int32')
            vals = npy.where(corridorLinksComp[:,cfg.LTB_LINKTYPE] ==
                         cfg.LT_NNCT, cfg.LT_CORR, 0)

            Graph[rows,cols] = vals
            Graph = Graph + Graph.T

            # Use graph to identify components (disconnected sub-groups) in
            # core area network
            components = lu.components_no_sparse(Graph)

            for coreInd in range(0,len(coresToProcess)):
                # In resulting cols, cols are 0 for LTB_CORE1 and 1 for
                # LTB_CORE2
                rows, cols = (npy.where(linkTableComp[:,10:12] ==
                              coresToProcess[coreInd]))
                # want results in cols 12 and 13  Note: we've replaced new core
                # numbers with COMPONENT numbers.
                linkTableComp[rows,cols+12] = components[coreInd]
            # Additional column indexes for linkTableComp
            component1Col = 12
            component2Col = 13
            linkTableComp[:,cfg.LTB_CLUST1] = linkTableComp[:,component1Col]
            linkTableComp[:,cfg.LTB_CLUST2] = linkTableComp[:,component2Col]

            # Sort by distance
            ind = npy.argsort(linkTableComp[:,distCol])
            linkTableComp = linkTableComp[ind]

            # Connect constellations via shortest inter-constellation links,
            # until all constellations connected.
            for row in range(0,numLinks):
                if ((linkTableComp[row,distCol] > 0) and
                    ((linkTableComp[row,cfg.LTB_LINKTYPE] == cfg.LT_CORR) or
                    (linkTableComp[row,cfg.LTB_LINKTYPE] == cfg.LT_KEEP)) and
                    (linkTableComp[row,component1Col] !=
                     linkTableComp[row,component2Col])):
                    # Make this an inter-component link
                    linkTableComp[row,cfg.LTB_LINKTYPE] = cfg.LT_CLU
                    newComp = min(linkTableComp
                                  [row,component1Col:component2Col + 1])
                    oldComp = max(linkTableComp
                                  [row,component1Col:component2Col + 1])
                    # cols are 0 and 1
                    rows, cols = npy.where(linkTableComp
                                       [:,component1Col:component2Col + 1]
                                       == oldComp)
                    # want results in cols 12 and 13
                    linkTableComp[rows,cols + 12] = newComp

            # Remove extra columns from link table
            linkTable = lu.delete_col(linkTableComp,[10, 11, 12, 13])

            # Re-sort link table by link ID
            ind = npy.argsort(linkTable[:,cfg.LTB_LINKID])
            linkTable = linkTable[ind]

        # At end, any non-constellation links that are not NN's get dropped
        # (too long to be in cfg.S4MAXNN, not a component link)
        rows = npy.where(linkTable[:,cfg.LTB_LINKTYPE] == cfg.LT_CORR)
        linkTable[rows,cfg.LTB_LINKTYPE] = cfg.LT_CPLK

        # set NNCT links to NN corridor links (NNC), get rid
        # of extra columns, re-sort linktable
        rows = npy.where(linkTable[:,cfg.LTB_LINKTYPE] == cfg.LT_NNCT)
        linkTable[rows,cfg.LTB_LINKTYPE] = cfg.LT_NNC

        # Write linkTable to disk
        outlinkTableFile = lu.get_this_step_link_table(step=4)
        # lu.dashline(1)
        gprint('\nWriting ' + outlinkTableFile)
        lu.write_link_table(linkTable, outlinkTableFile)
        linkTableLogFile = path.join(cfg.LOGDIR, "linkTable_s4.csv")
        lu.write_link_table(linkTable, linkTableLogFile)

        start_time = time.clock()
        lu.update_lcp_shapefile(linkTable, lastStep=3, thisStep=4)
        start_time = lu.elapsed_time(start_time)

        # lu.dashline()
        gprint('Creating shapefiles with linework for links.')
        try:
            lu.write_link_maps(outlinkTableFile, step=4)
        except:
            lu.write_link_maps(outlinkTableFile, step=4)

    # Return GEOPROCESSING specific errors
    except arcgisscripting.ExecuteError:
        gprint('****Failed in step 4. Details follow.****')
        lu.exit_with_geoproc_error(_SCRIPT_NAME)

    # Return any PYTHON or system specific errors
    except:
        gprint('****Failed in step 4. Details follow.****')
        lu.exit_with_python_error(_SCRIPT_NAME)

    return
예제 #11
0
def STEP4_refine_network():
    """Allows user to only connect each core area to its N
    nearest neighbors, then connect any disjunct clusters ('constellations')
    of core areas to their nearest neighboring cluster

    """
    try:

        lu.dashline(1)
        gprint('Running script ' + _SCRIPT_NAME)
        cfg.gp.Workspace = cfg.OUTPUTDIR

        linkTableFile = lu.get_prev_step_link_table(step=4)

        linkTable = lu.load_link_table(linkTableFile)
        numLinks = linkTable.shape[0]
        lu.report_links(linkTable)

        if not cfg.STEP3:
            # re-check for links that are too long in case script run out of
            # sequence with more stringent settings
            gprint('Double-checking for corridors that are too long'
                   ' or too short to map.')
            DISABLE_LEAST_COST_NO_VAL = True
            linkTable, numDroppedLinks = lu.drop_links(
                linkTable, cfg.MAXEUCDIST, 0, cfg.MAXCOSTDIST, 0,
                DISABLE_LEAST_COST_NO_VAL)

        rows, cols = npy.where(
            linkTable[:, cfg.LTB_LINKTYPE:cfg.LTB_LINKTYPE + 1] > 0)
        # == cfg.LT_CORR
        # or
        # linkTable[:,cfg.LTB_LINKTYPE:cfg.LTB_LINKTYPE + 1] == cfg.LT_KEEP)
        corridorLinks = linkTable[rows, :]
        coresToProcess = npy.unique(
            corridorLinks[:, cfg.LTB_CORE1:cfg.LTB_CORE2 + 1])

        if cfg.S4DISTTYPE_EU:
            distCol = cfg.LTB_EUCDIST
        else:
            distCol = cfg.LTB_CWDIST

        # Flag links that do not connect any core areas to their nearest
        # N neighbors. (N = cfg.S4MAXNN)
        lu.dashline(1)
        # optionally ignore max nearest neighbor setting
        if cfg.IGNORES4MAXNN:
            gprint('Connecting each core area to all its neighbors.')
        else:
            gprint('Connecting each core area to its nearest ' +
                   str(cfg.S4MAXNN) + ' nearest neighbors.')

        # Code written assuming NO duplicate core pairs
        for core in coresToProcess:
            rows, cols = npy.where(corridorLinks[:,
                                                 cfg.LTB_CORE1:cfg.LTB_CORE2 +
                                                 1] == core)
            distsFromCore = corridorLinks[rows, :]

            # Sort by distance from target core
            ind = npy.argsort(distsFromCore[:, distCol])
            distsFromCore = distsFromCore[ind]

            # Set N nearest neighbor connections to Nearest Neighbor (NNCT)
            # optionally ignore max nearest neighbor setting
            if cfg.IGNORES4MAXNN:
                maxRange = len(rows)
            else:
                maxRange = min(len(rows), cfg.S4MAXNN)
            for link in range(0, maxRange):
                linkId = distsFromCore[link, cfg.LTB_LINKID]
                # assumes linktable sequentially numbered with no gaps
                linkTable[linkId - 1, cfg.LTB_LINKTYPE] = cfg.LT_NNCT

        # Connect constellations (aka components or clusters)
        # Fixme: needs testing.  Move to function.
        if cfg.S4CONNECT:
            lu.dashline(1)
            gprint('Connecting constellations')

            # linkTableComp has 4 extra cols to track COMPONENTS
            numLinks = linkTable.shape[0]
            # g1' g2' THEN c1 c2
            compCols = npy.zeros((numLinks, 4), dtype="int32")
            linkTableComp = npy.append(linkTable, compCols, axis=1)
            del compCols

            # renumber cores to save memory for this next step.  Place in
            # columns 10 and 11
            for coreInd in range(0, len(coresToProcess)):
                # here, cols are 0 for cfg.LTB_CORE1 and 1 for cfg.LTB_CORE2
                rows, cols = npy.where(
                    linkTableComp[:, cfg.LTB_CORE1:cfg.LTB_CORE2 +
                                  1] == coresToProcess[coreInd])
                # want results in cols 10 and 11- These are NEW core numbers
                # (0 - numcores)
                linkTableComp[rows, cols + 10] = coreInd

            rows, cols = npy.where(
                linkTableComp[:, cfg.LTB_LINKTYPE:cfg.LTB_LINKTYPE +
                              1] == cfg.LT_NNCT)
            # The new, improved corridorLinks- only NN links
            corridorLinksComp = linkTableComp[rows, :]
            # These are NEW core numbers (range from 0 to numcores)
            coresToProcess = npy.unique(linkTableComp[:, 10:12])

            #Create graph describing connected cores.
            Graph = npy.zeros((len(coresToProcess), len(coresToProcess)),
                              dtype="int32")
            rows = corridorLinksComp[:, 10].astype('int32')
            cols = corridorLinksComp[:, 11].astype('int32')
            vals = npy.where(
                corridorLinksComp[:, cfg.LTB_LINKTYPE] == cfg.LT_NNCT,
                cfg.LT_CORR, 0)

            Graph[rows, cols] = vals
            Graph = Graph + Graph.T

            # Use graph to identify components (disconnected sub-groups) in
            # core area network
            components = lu.components_no_sparse(Graph)

            for coreInd in range(0, len(coresToProcess)):
                # In resulting cols, cols are 0 for LTB_CORE1 and 1 for
                # LTB_CORE2
                rows, cols = (npy.where(
                    linkTableComp[:, 10:12] == coresToProcess[coreInd]))
                # want results in cols 12 and 13  Note: we've replaced new core
                # numbers with COMPONENT numbers.
                linkTableComp[rows, cols + 12] = components[coreInd]
            # Additional column indexes for linkTableComp
            component1Col = 12
            component2Col = 13
            linkTableComp[:, cfg.LTB_CLUST1] = linkTableComp[:, component1Col]
            linkTableComp[:, cfg.LTB_CLUST2] = linkTableComp[:, component2Col]

            # Sort by distance
            ind = npy.argsort(linkTableComp[:, distCol])
            linkTableComp = linkTableComp[ind]

            # Connect constellations via shortest inter-constellation links,
            # until all constellations connected.
            for row in range(0, numLinks):
                if ((linkTableComp[row, distCol] > 0) and
                    ((linkTableComp[row, cfg.LTB_LINKTYPE] == cfg.LT_CORR) or
                     (linkTableComp[row, cfg.LTB_LINKTYPE] == cfg.LT_KEEP))
                        and (linkTableComp[row, component1Col] !=
                             linkTableComp[row, component2Col])):
                    # Make this an inter-component link
                    linkTableComp[row, cfg.LTB_LINKTYPE] = cfg.LT_CLU
                    newComp = min(
                        linkTableComp[row, component1Col:component2Col + 1])
                    oldComp = max(
                        linkTableComp[row, component1Col:component2Col + 1])
                    # cols are 0 and 1
                    rows, cols = npy.where(
                        linkTableComp[:, component1Col:component2Col +
                                      1] == oldComp)
                    # want results in cols 12 and 13
                    linkTableComp[rows, cols + 12] = newComp

            # Remove extra columns from link table
            linkTable = lu.delete_col(linkTableComp, [10, 11, 12, 13])

            # Re-sort link table by link ID
            ind = npy.argsort(linkTable[:, cfg.LTB_LINKID])
            linkTable = linkTable[ind]

        # At end, any non-constellation links that are not NN's get dropped
        # (too long to be in cfg.S4MAXNN, not a component link)
        rows = npy.where(linkTable[:, cfg.LTB_LINKTYPE] == cfg.LT_CORR)
        linkTable[rows, cfg.LTB_LINKTYPE] = cfg.LT_CPLK

        # set NNCT links to NN corridor links (NNC), get rid
        # of extra columns, re-sort linktable
        rows = npy.where(linkTable[:, cfg.LTB_LINKTYPE] == cfg.LT_NNCT)
        linkTable[rows, cfg.LTB_LINKTYPE] = cfg.LT_NNC

        # Write linkTable to disk
        outlinkTableFile = lu.get_this_step_link_table(step=4)
        # lu.dashline(1)
        gprint('\nWriting ' + outlinkTableFile)
        lu.write_link_table(linkTable, outlinkTableFile)
        linkTableLogFile = path.join(cfg.LOGDIR, "linkTable_s4.csv")
        lu.write_link_table(linkTable, linkTableLogFile)

        start_time = time.clock()
        lu.update_lcp_shapefile(linkTable, lastStep=3, thisStep=4)
        start_time = lu.elapsed_time(start_time)

        # lu.dashline()
        gprint('Creating shapefiles with linework for links.')
        try:
            lu.write_link_maps(outlinkTableFile, step=4)
        except:
            lu.write_link_maps(outlinkTableFile, step=4)

    # Return GEOPROCESSING specific errors
    except arcgisscripting.ExecuteError:
        gprint('****Failed in step 4. Details follow.****')
        lu.exit_with_geoproc_error(_SCRIPT_NAME)

    # Return any PYTHON or system specific errors
    except:
        gprint('****Failed in step 4. Details follow.****')
        lu.exit_with_python_error(_SCRIPT_NAME)

    return
예제 #12
0
def STEP7_calc_centrality():
    """ Analyze network centrality using Circuitscape
        given Linkage Mapper outputs

    """
    try:
        lu.dashline(0)
        gprint('Running script ' + _SCRIPT_NAME)

        arcpy.env.workspace = cfg.SCRATCHDIR

        # Check for valid LCP shapefile
        prevLcpShapefile = lu.get_lcp_shapefile(None, thisStep = 7)
        if not arcpy.Exists(prevLcpShapefile):
            msg = ('Cannot find an LCP shapefile from step 5.  Please '
                    'rerun that step and any previous ones if necessary.')
            lu.raise_error(msg)

        # Remove lcp shapefile from this step if run previously
        lcpShapefile = path.join(cfg.DATAPASSDIR, "lcpLines_s7.shp")
        lu.delete_data(lcpShapefile)

        csPath = lu.get_cs_path()

        invalidFNs = ['fid','id','oid','shape']
        if cfg.COREFN.lower() in invalidFNs:
        #if cfg.COREFN == 'FID' or cfg.COREFN == 'ID':
            lu.dashline(1)
            msg = ('ERROR: Core area field names ID, FID, SHAPE, and OID are'
                    ' reserved for ArcGIS. \nPlease choose another field- must'
                    ' be a positive integer.')
            lu.raise_error(msg)

        lu.dashline(1)
        gprint('Mapping centrality of network cores and links'
                '\nusing Circuitscape....')
        lu.dashline(0)

        # set the analysis extent and cell size to that of the resistance
        # surface
        coreCopy =  path.join(cfg.SCRATCHDIR, 'cores.shp')

        arcpy.CopyFeatures_management(cfg.COREFC, coreCopy)
        arcpy.AddField_management(coreCopy, "CF_Central", "DOUBLE", "10", "2")

        inLinkTableFile = lu.get_prev_step_link_table(step=7)
        linkTable = lu.load_link_table(inLinkTableFile)
        numLinks = linkTable.shape[0]
        numCorridorLinks = lu.report_links(linkTable)
        if numCorridorLinks == 0:
            lu.dashline(1)
            msg =('\nThere are no linkages. Bailing.')
            lu.raise_error(msg)

        if linkTable.shape[1] < 16: # If linktable has no entries from prior
                                    # centrality or pinchpint analyses
            extraCols = npy.zeros((numLinks, 6), dtype="float64")
            linkTable = linkTable[:,0:10]
            linkTable = npy.append(linkTable, extraCols, axis=1)
            linkTable[:, cfg.LTB_LCPLEN] = -1
            linkTable[:, cfg.LTB_CWDEUCR] = -1
            linkTable[:, cfg.LTB_CWDPATHR] = -1
            linkTable[:, cfg.LTB_EFFRESIST] = -1
            linkTable[:, cfg.LTB_CWDTORR] = -1
            del extraCols

        linkTable[:, cfg.LTB_CURRENT] = -1

        coresToProcess = npy.unique(linkTable[:, cfg.LTB_CORE1:cfg.LTB_CORE2 + 1])
        maxCoreNum = max(coresToProcess)
        del coresToProcess

        lu.dashline(0)

        coreList = linkTable[:,cfg.LTB_CORE1:cfg.LTB_CORE2+1]
        coreList = npy.sort(coreList)
        #gprint('There are ' + str(len(npy.unique(coreList))) ' core areas.')

        # set up directory for centrality
        INCENTRALITYDIR = cfg.CENTRALITYBASEDIR
        OUTCENTRALITYDIR = path.join(cfg.CENTRALITYBASEDIR,
                                     cfg.CIRCUITOUTPUTDIR_NM)
        CONFIGDIR = path.join(INCENTRALITYDIR, cfg.CIRCUITCONFIGDIR_NM)

        # Set Circuitscape options and write config file
        options = lu.setCircuitscapeOptions()
        options['data_type']='network'
        options['habitat_file'] = path.join(INCENTRALITYDIR,
                                            'Circuitscape_graph.txt')
        # Setting point file equal to graph to do all pairs in Circuitscape
        options['point_file'] = path.join(INCENTRALITYDIR,
                                          'Circuitscape_graph.txt')
        outputFN = 'Circuitscape_network.out'
        options['output_file'] = path.join(OUTCENTRALITYDIR, outputFN)
        configFN = 'Circuitscape_network.ini'
        outConfigFile = path.join(CONFIGDIR, configFN)
        lu.writeCircuitscapeConfigFile(outConfigFile, options)

        delRows = npy.asarray(npy.where(linkTable[:,cfg.LTB_LINKTYPE] < 1))
        delRowsVector = npy.zeros((delRows.shape[1]), dtype="int32")
        delRowsVector[:] = delRows[0, :]
        LT = lu.delete_row(linkTable, delRowsVector)
        del delRows
        del delRowsVector
        graphList = npy.zeros((LT.shape[0],3), dtype="float64")
        graphList[:,0] = LT[:,cfg.LTB_CORE1]
        graphList[:,1] = LT[:,cfg.LTB_CORE2]
        graphList[:,2] = LT[:,cfg.LTB_CWDIST]

        write_graph(options['habitat_file'] ,graphList)
        gprint('\nCalculating current flow centrality using Circuitscape...')
        #subprocess.call([csPath, outConfigFile], shell=True)   
        
        memFlag = call_circuitscape(csPath, outConfigFile)        
        
        outputFN = 'Circuitscape_network_branch_currents_cum.txt'
        currentList = path.join(OUTCENTRALITYDIR, outputFN)

        if not arcpy.Exists(currentList):
            write_graph(options['habitat_file'] ,graphList)
            gprint('\nCalculating current flow centrality using Circuitscape '
                   '(2nd try)...')
            # subprocess.call([csPath, outConfigFile], shell=True)  
            memFlag = call_circuitscape(csPath, outConfigFile)                    
            if not arcpy.Exists(currentList):
                lu.dashline(1)
                msg = ('ERROR: No Circuitscape output found.\n'
                       'It looks like Circuitscape failed.')
                arcpy.AddError(msg)
                lu.write_log(msg)
                exit(1)

                
        currents = load_graph(currentList,graphType='graph/network',
                              datatype='float64')

        numLinks = currents.shape[0]
        for x in range(0,numLinks):
            corex = currents[x,0]
            corey = currents[x,1]

            #linkId = LT[x,cfg.LTB_LINKID]
            row = lu.get_links_from_core_pairs(linkTable, corex, corey)
            #row = lu.get_linktable_row(linkId, linkTable)
            linkTable[row,cfg.LTB_CURRENT] = currents[x,2]

        coreCurrentFN = 'Circuitscape_network_node_currents_cum.txt'
        nodeCurrentList = path.join(OUTCENTRALITYDIR, coreCurrentFN)
        nodeCurrents = load_graph(nodeCurrentList,graphType='graph/network',
                              datatype='float64')

        numNodeCurrents = nodeCurrents.shape[0]
        rows = arcpy.UpdateCursor(coreCopy)
        row = rows.newRow()
        for row in rows:
            coreID = row.getValue(cfg.COREFN)
            for i in range (0, numNodeCurrents):
                if coreID == nodeCurrents[i,0]:
                    row.setValue("CF_Central", nodeCurrents[i,1])
                    break
            rows.updateRow(row)
            #row = rows.newRow()
        del row, rows
        gprint('Done with centrality calculations.')

        finalLinkTable = lu.update_lcp_shapefile(linkTable, lastStep=5,
                                                  thisStep=7)
        linkTableFile = path.join(cfg.DATAPASSDIR, "linkTable_s5_plus.csv")
        lu.write_link_table(finalLinkTable, linkTableFile, inLinkTableFile)
        linkTableFinalFile = path.join(cfg.OUTPUTDIR,
                                       cfg.PREFIX + "_linkTable_s5_plus.csv")
        lu.write_link_table(finalLinkTable,
                            linkTableFinalFile, inLinkTableFile)
        gprint('Copy of final linkTable written to '+
                          linkTableFinalFile)

        finalCoreFile = path.join(cfg.CORECENTRALITYGDB,
                                     cfg.PREFIX + '_Cores')
        #copy core area map to gdb.
        if not arcpy.Exists(cfg.CORECENTRALITYGDB):
            arcpy.CreateFileGDB_management(cfg.OUTPUTDIR,
                             path.basename(cfg.CORECENTRALITYGDB))
        arcpy.CopyFeatures_management(coreCopy, finalCoreFile)

        gprint('Creating shapefiles with linework for links.')
        lu.write_link_maps(linkTableFinalFile, step=7)

        # Copy final link maps to gdb and clean up.
        lu.copy_final_link_maps(step=7)

    # Return GEOPROCESSING specific errors
    except arcpy.ExecuteError:
        lu.dashline(1)
        gprint('****Failed in step 7. Details follow.****')
        lu.exit_with_geoproc_error(_SCRIPT_NAME)

    # Return any PYTHON or system specific errors
    except:
        lu.dashline(1)
        gprint('****Failed in step 7. Details follow.****')
        lu.exit_with_python_error(_SCRIPT_NAME)

    return
예제 #13
0
def calc_lccs(normalize):
    try:
        if normalize:
            mosaicBaseName = "_corridors"
            writeTruncRaster = cfg.WRITETRUNCRASTER
            outputGDB = cfg.OUTPUTGDB
            if cfg.CALCNONNORMLCCS:
                SAVENORMLCCS = False
            else:
                SAVENORMLCCS = cfg.SAVENORMLCCS
        else:
            mosaicBaseName = "_NON_NORMALIZED_corridors"
            SAVENORMLCCS = False
            outputGDB = cfg.EXTRAGDB
            writeTruncRaster = False

        lu.dashline(1)
        gprint('Running script ' + _SCRIPT_NAME)
        linkTableFile = lu.get_prev_step_link_table(step=5)
        if cfg.useArcpy:
            arcpy.env.workspace = cfg.SCRATCHDIR
            arcpy.env.scratchWorkspace = cfg.ARCSCRATCHDIR
            arcpy.env.overwriteOutput = True
            arcpy.env.compression = "NONE"
        else:
            gp.workspace = cfg.SCRATCHDIR
            gp.scratchWorkspace = cfg.ARCSCRATCHDIR
            gp.OverwriteOutput = True

        if cfg.MAXEUCDIST is not None:
            gprint('Max Euclidean distance between cores')
            gprint('for linkage mapping set to ' + str(cfg.MAXEUCDIST))

        if cfg.MAXCOSTDIST is not None:
            gprint('Max cost-weighted distance between cores')
            gprint('for linkage mapping set to ' + str(cfg.MAXCOSTDIST))

        # set the analysis extent and cell size to that of the resistance
        # surface
        if cfg.useArcpy:
            arcpy.env.Extent = cfg.RESRAST
            arcpy.env.cellSize = cfg.RESRAST
            arcpy.env.snapRaster = cfg.RESRAST
            arcpy.env.mask = cfg.RESRAST
        else:
            gp.Extent = (gp.Describe(cfg.RESRAST)).Extent
            gp.cellSize = gp.Describe(cfg.RESRAST).MeanCellHeight
            gp.mask = cfg.RESRAST
            gp.snapraster = cfg.RESRAST

        linkTable = lu.load_link_table(linkTableFile)
        numLinks = linkTable.shape[0]
        numCorridorLinks = lu.report_links(linkTable)
        if numCorridorLinks == 0:
            lu.dashline(1)
            msg = ('\nThere are no corridors to map. Bailing.')
            lu.raise_error(msg)

        if not cfg.STEP3 and not cfg.STEP4:
            # re-check for links that are too long or in case script run out of
            # sequence with more stringent settings
            gprint('Double-checking for corridors that are too long to map.')
            DISABLE_LEAST_COST_NO_VAL = True
            linkTable, numDroppedLinks = lu.drop_links(
                linkTable, cfg.MAXEUCDIST, cfg.MINEUCDIST, cfg.MAXCOSTDIST,
                cfg.MINCOSTDIST, DISABLE_LEAST_COST_NO_VAL)

        # Added to try to speed up:
        gp.pyramid = "NONE"
        gp.rasterstatistics = "NONE"

        # set up directories for normalized lcc and mosaic grids
        dirCount = 0
        gprint("Creating output folder: " + cfg.LCCBASEDIR)
        lu.delete_dir(cfg.LCCBASEDIR)
        gp.CreateFolder_management(path.dirname(cfg.LCCBASEDIR),
                                   path.basename(cfg.LCCBASEDIR))
        gp.CreateFolder_management(cfg.LCCBASEDIR, cfg.LCCNLCDIR_NM)
        clccdir = path.join(cfg.LCCBASEDIR, cfg.LCCNLCDIR_NM)
        # mosaicGDB = path.join(cfg.LCCBASEDIR, "mosaic.gdb")
        # gp.createfilegdb(cfg.LCCBASEDIR, "mosaic.gdb")
        #mosaicRaster = mosaicGDB + '\\' + "nlcc_mos" # Full path
        gprint("")
        if normalize:
            gprint('Normalized least-cost corridors will be written '
                   'to ' + clccdir + '\n')
        PREFIX = cfg.PREFIX

        # Add CWD layers for core area pairs to produce NORMALIZED LCC layers
        numGridsWritten = 0
        coreList = linkTable[:, cfg.LTB_CORE1:cfg.LTB_CORE2 + 1]
        coreList = npy.sort(coreList)

        x = 0
        linkCount = 0
        endIndex = numLinks
        while x < endIndex:
            if (linkTable[x, cfg.LTB_LINKTYPE] < 1):  # If not a valid link
                x = x + 1
                continue

            linkCount = linkCount + 1
            start_time = time.clock()

            linkId = str(int(linkTable[x, cfg.LTB_LINKID]))

            # source and target cores
            corex = int(coreList[x, 0])
            corey = int(coreList[x, 1])

            # Get cwd rasters for source and target cores
            cwdRaster1 = lu.get_cwd_path(corex)
            cwdRaster2 = lu.get_cwd_path(corey)

            if not gp.Exists(cwdRaster1):
                msg = ('\nError: cannot find cwd raster:\n' + cwdRaster1)
            if not gp.Exists(cwdRaster2):
                msg = ('\nError: cannot find cwd raster:\n' + cwdRaster2)
                lu.raise_error(msg)

            lccNormRaster = path.join(clccdir,
                                      str(corex) + "_" +
                                      str(corey))  # + ".tif")
            if cfg.useArcpy:
                arcpy.env.Extent = "MINOF"
            else:
                gp.Extent = "MINOF"

            # FIXME: need to check for this?:
            # if exists already, don't re-create
            #if not gp.Exists(lccRaster):

            link = lu.get_links_from_core_pairs(linkTable, corex, corey)

            offset = 10000

            # Normalized lcc rasters are created by adding cwd rasters and
            # subtracting the least cost distance between them.
            count = 0
            if arcpyAvailable:
                cfg.useArcpy = True  # Fixes Canran Liu's bug with lcDist
            if cfg.useArcpy:

                lcDist = (float(linkTable[link, cfg.LTB_CWDIST]) - offset)

                if normalize:
                    statement = (
                        'outras = Raster(cwdRaster1) + Raster('
                        'cwdRaster2) - lcDist; outras.save(lccNormRaster)')

                else:
                    statement = ('outras =Raster(cwdRaster1) + Raster('
                                 'cwdRaster2); outras.save(lccNormRaster)')
            else:
                if normalize:
                    lcDist = str(linkTable[link, cfg.LTB_CWDIST] - offset)
                    expression = (cwdRaster1 + " + " + cwdRaster2 + " - " +
                                  lcDist)
                else:
                    expression = (cwdRaster1 + " + " + cwdRaster2)
                statement = ('gp.SingleOutputMapAlgebra_sa(expression, '
                             'lccNormRaster)')
            count = 0
            while True:
                try:
                    exec statement
                    randomerror()
                except:
                    count, tryAgain = lu.retry_arc_error(count, statement)
                    if not tryAgain:
                        exec statement
                else:
                    break
            cfg.useArcpy = False  # End fix for Conran Liu's bug with lcDist

            if normalize and cfg.useArcpy:
                try:
                    minObject = gp.GetRasterProperties(lccNormRaster,
                                                       "MINIMUM")
                    rasterMin = float(str(minObject.getoutput(0)))
                except:
                    gp.AddWarning(
                        '\n------------------------------------------------')
                    gp.AddWarning(
                        'WARNING: Raster minimum check failed in step 5. \n'
                        'This may mean the output rasters are corrupted. Please \n'
                        'be sure to check for valid rasters in ' + outputGDB)
                    rasterMin = 0
                tolerance = (float(gp.cellSize) * -10) + offset
                if rasterMin < tolerance:
                    lu.dashline(1)
                    msg = (
                        'WARNING: Minimum value of a corridor #' + str(x + 1) +
                        ' is much less than zero (' + str(rasterMin) + ').'
                        '\nThis could mean that BOUNDING CIRCLE BUFFER DISTANCES '
                        'were too small and a corridor passed outside of a '
                        'bounding circle, or that a corridor passed outside of the '
                        'resistance map. \n')
                    gp.AddWarning(msg)

            if cfg.useArcpy:
                arcpy.env.Extent = cfg.RESRAST
            else:
                gp.Extent = (gp.Describe(cfg.RESRAST)).Extent

            mosaicDir = path.join(cfg.LCCBASEDIR, 'mos' + str(x + 1))
            lu.create_dir(mosaicDir)
            mosFN = 'mos'  #.tif' change and move
            mosaicRaster = path.join(mosaicDir, mosFN)

            if numGridsWritten == 0 and dirCount == 0:
                #If this is the first grid then copy rather than mosaic
                arcObj.CopyRaster_management(lccNormRaster, mosaicRaster)
            else:

                rasterString = '"' + lccNormRaster + ";" + lastMosaicRaster + '"'
                statement = ('arcObj.MosaicToNewRaster_management('
                             'rasterString,mosaicDir,mosFN, "", '
                             '"32_BIT_FLOAT", gp.cellSize, "1", "MINIMUM", '
                             '"MATCH")')
                # statement = ('arcpy.Mosaic_management(lccNormRaster, '
                # 'mosaicRaster, "MINIMUM", "MATCH")')

                count = 0
                while True:
                    try:
                        lu.write_log('Executing mosaic for link #' +
                                     str(linkId))
                        exec statement
                        lu.write_log('Done with mosaic.')
                        randomerror()
                    except:
                        count, tryAgain = lu.retry_arc_error(count, statement)
                        lu.delete_data(mosaicRaster)
                        lu.delete_dir(mosaicDir)
                        # Try a new directory
                        mosaicDir = path.join(
                            cfg.LCCBASEDIR,
                            'mos' + str(x + 1) + '_' + str(count))
                        lu.create_dir(mosaicDir)
                        mosaicRaster = path.join(mosaicDir, mosFN)
                        if not tryAgain:
                            exec statement
                    else:
                        break
            endTime = time.clock()
            processTime = round((endTime - start_time), 2)

            if normalize == True:
                printText = "Normalized and mosaicked "
            else:
                printText = "Mosaicked NON-normalized "
            gprint(printText + "corridor for link ID #" + str(linkId) +
                   " connecting core areas " + str(corex) + " and " +
                   str(corey) + " in " + str(processTime) + " seconds. " +
                   str(int(linkCount)) + " out of " +
                   str(int(numCorridorLinks)) + " links have been "
                   "processed.")

            # temporarily disable links in linktable - don't want to mosaic
            # them twice
            for y in range(x + 1, numLinks):
                corex1 = int(coreList[y, 0])
                corey1 = int(coreList[y, 1])
                if corex1 == corex and corey1 == corey:
                    linkTable[y, cfg.LTB_LINKTYPE] = (
                        linkTable[y, cfg.LTB_LINKTYPE] + 1000)
                elif corex1 == corey and corey1 == corex:
                    linkTable[y, cfg.LTB_LINKTYPE] = (
                        linkTable[y, cfg.LTB_LINKTYPE] + 1000)

            numGridsWritten = numGridsWritten + 1
            if not SAVENORMLCCS:
                lu.delete_data(lccNormRaster)
                lu.delete_dir(clccdir)
                lu.create_dir(clccdir)
            else:
                if numGridsWritten == 100:
                    # We only write up to 100 grids to any one folder
                    # because otherwise Arc slows to a crawl
                    dirCount = dirCount + 1
                    numGridsWritten = 0
                    clccdir = path.join(cfg.LCCBASEDIR,
                                        cfg.LCCNLCDIR_NM + str(dirCount))
                    gprint("Creating output folder: " + clccdir)
                    gp.CreateFolder_management(cfg.LCCBASEDIR,
                                               path.basename(clccdir))

            if numGridsWritten > 1 or dirCount > 0:
                lu.delete_data(lastMosaicRaster)
                lu.delete_dir(path.dirname(lastMosaicRaster))

            lastMosaicRaster = mosaicRaster
            x = x + 1

        #rows that were temporarily disabled
        rows = npy.where(linkTable[:, cfg.LTB_LINKTYPE] > 1000)
        linkTable[rows,
                  cfg.LTB_LINKTYPE] = (linkTable[rows, cfg.LTB_LINKTYPE] -
                                       1000)
        # ---------------------------------------------------------------------

        # Create output geodatabase
        if not gp.exists(outputGDB):
            gp.createfilegdb(cfg.OUTPUTDIR, path.basename(outputGDB))

        if cfg.useArcpy:
            arcpy.env.workspace = outputGDB
        else:
            gp.workspace = outputGDB

        gp.pyramid = "NONE"
        gp.rasterstatistics = "NONE"

        # Copy mosaic raster to output geodatabase
        saveFloatRaster = False
        if saveFloatRaster == True:
            floatRaster = outputGDB + '\\' + PREFIX + mosaicBaseName + '_flt'  # Full path
            statement = 'arcObj.CopyRaster_management(mosaicRaster, floatRaster)'
            try:
                exec statement
            except:
                pass

        # ---------------------------------------------------------------------
        # convert mosaic raster to integer
        intRaster = path.join(outputGDB, PREFIX + mosaicBaseName)
        if cfg.useArcpy:
            statement = ('outras = Int(Raster(mosaicRaster) - offset + 0.5); '
                         'outras.save(intRaster)')
        else:
            expression = "int(" + mosaicRaster + " - " + str(
                offset) + " + 0.5)"
            statement = 'gp.SingleOutputMapAlgebra_sa(expression, intRaster)'
        count = 0
        while True:
            try:
                exec statement
                randomerror()
            except:
                count, tryAgain = lu.retry_arc_error(count, statement)
                if not tryAgain: exec statement
            else: break
        # ---------------------------------------------------------------------

        if writeTruncRaster:
            # -----------------------------------------------------------------
            # Set anything beyond cfg.CWDTHRESH to NODATA.
            if arcpyAvailable:
                cfg.useArcpy = True  # For Alissa Pump's error with 10.1
            cutoffText = str(cfg.CWDTHRESH)
            if cutoffText[-6:] == '000000':
                cutoffText = cutoffText[0:-6] + 'm'
            elif cutoffText[-3:] == '000':
                cutoffText = cutoffText[0:-3] + 'k'

            truncRaster = (outputGDB + '\\' + PREFIX + mosaicBaseName +
                           '_truncated_at_' + cutoffText)

            count = 0
            if cfg.useArcpy:
                statement = ('outRas = Raster(intRaster) * '
                             '(Con(Raster(intRaster) <= cfg.CWDTHRESH,1)); '
                             'outRas.save(truncRaster)')
            else:
                expression = ("(" + intRaster + " * (con(" + intRaster +
                              "<= " + str(cfg.CWDTHRESH) + ",1)))")
                statement = ('gp.SingleOutputMapAlgebra_sa(expression, '
                             'truncRaster)')
            count = 0
            while True:
                try:
                    exec statement
                    randomerror()
                except:
                    count, tryAgain = lu.retry_arc_error(count, statement)
                    if not tryAgain: exec statement
                else: break
            cfg.useArcpy = False  # End fix for Alissa Pump's error with 10.1
        # ---------------------------------------------------------------------
        # Check for unreasonably low minimum NLCC values
        try:
            mosaicGrid = path.join(cfg.LCCBASEDIR, 'mos')
            # Copy to grid to test
            arcObj.CopyRaster_management(mosaicRaster, mosaicGrid)
            minObject = gp.GetRasterProperties(mosaicGrid, "MINIMUM")
            rasterMin = float(str(minObject.getoutput(0)))
        except:
            gp.AddWarning('\n------------------------------------------------')
            gp.AddWarning(
                'WARNING: Raster minimum check failed in step 5. \n'
                'This may mean the output rasters are corrupted. Please \n'
                'be sure to check for valid rasters in ' + outputGDB)
            rasterMin = 0
        tolerance = (float(gp.cellSize) * -10)

        if rasterMin < tolerance:
            lu.dashline(1)
            msg = ('WARNING: Minimum value of mosaicked corridor map is '
                   'much less than zero (' + str(rasterMin) + ').'
                   '\nThis could mean that BOUNDING CIRCLE BUFFER DISTANCES '
                   'were too small and a corridor passed outside of a '
                   'bounding circle, or that a corridor passed outside of the '
                   'resistance map. \n')
            gp.AddWarning(msg)

        gprint('\nWriting final LCP maps...')
        if cfg.STEP4:
            finalLinkTable = lu.update_lcp_shapefile(linkTable,
                                                     lastStep=4,
                                                     thisStep=5)
        elif cfg.STEP3:
            finalLinkTable = lu.update_lcp_shapefile(linkTable,
                                                     lastStep=3,
                                                     thisStep=5)
        else:
            # Don't know if step 4 was run, since this is started at step 5.
            # Use presence of previous linktable files to figure this out.
            # Linktable name includes step number.
            prevLinkTableFile = lu.get_prev_step_link_table(step=5)
            prevStepInd = len(prevLinkTableFile) - 5
            lastStep = prevLinkTableFile[prevStepInd]

            finalLinkTable = lu.update_lcp_shapefile(linkTable,
                                                     lastStep,
                                                     thisStep=5)

        outlinkTableFile = lu.get_this_step_link_table(step=5)
        gprint('Updating ' + outlinkTableFile)
        lu.write_link_table(linkTable, outlinkTableFile)

        linkTableLogFile = path.join(cfg.LOGDIR, "linkTable_s5.csv")
        lu.write_link_table(linkTable, linkTableLogFile)

        linkTableFinalFile = path.join(cfg.OUTPUTDIR,
                                       PREFIX + "_linkTable_s5.csv")
        lu.write_link_table(finalLinkTable, linkTableFinalFile)
        gprint('Copy of final linkTable written to ' + linkTableFinalFile)

        gprint('Creating shapefiles with linework for links.')
        try:
            lu.write_link_maps(outlinkTableFile, step=5)
        except:
            lu.write_link_maps(outlinkTableFile, step=5)

        # Create final linkmap files in output directory, and remove files from
        # scratch.
        lu.copy_final_link_maps(step=5)

        if not SAVENORMLCCS:
            lu.delete_dir(cfg.LCCBASEDIR)

        # Build statistics for corridor rasters
        gp.addmessage('\nBuilding output statistics and pyramids '
                      'for corridor raster')
        lu.build_stats(intRaster)

        if writeTruncRaster:
            gp.addmessage('Building output statistics '
                          'for truncated corridor raster')
            lu.build_stats(truncRaster)

    # Return GEOPROCESSING specific errors
    except arcgisscripting.ExecuteError:
        lu.dashline(1)
        gprint('****Failed in step 5. Details follow.****')
        lu.exit_with_geoproc_error(_SCRIPT_NAME)

    # Return any PYTHON or system specific errors
    except:
        lu.dashline(1)
        gprint('****Failed in step 5. Details follow.****')
        lu.exit_with_python_error(_SCRIPT_NAME)

    return
예제 #14
0
def step6_calc_barriers():
    """Detect influential barriers given CWD calculations from Step 3."""
    try:
        arcpy.CheckOutExtension("spatial")
        lu.dashline(0)
        gprint('Running script ' + _SCRIPT_NAME)

        if cfg.BARRIER_CWD_THRESH is not None:
            lu.dashline(1)
            gprint('Invoking CWD Threshold of ' + str(cfg.BARRIER_CWD_THRESH)
                   + ' map units.')

        if cfg.SUM_BARRIERS:
            sum_suffix = '_Sum'
            cfg.BARRIERBASEDIR = cfg.BARRIERBASEDIR + sum_suffix
            base_name, extension = path.splitext(cfg.BARRIERGDB)
            cfg.BARRIERGDB = base_name + sum_suffix + extension

            gprint('\nBarrier scores will be SUMMED across core pairs.')
        else:
            sum_suffix = ''

        if not arcpy.Exists(cfg.BARRIERGDB):
            # Create output geodatabase
            arcpy.CreateFileGDB_management(cfg.OUTPUTDIR,
                                           path.basename(cfg.BARRIERGDB))

        start_radius = int(cfg.STARTRADIUS)
        end_radius = int(cfg.ENDRADIUS)
        radius_step = int(cfg.RADIUSSTEP)
        if radius_step == 0:
            end_radius = start_radius  # Calculate at just one radius value
            radius_step = 1

        link_table_file = lu.get_prev_step_link_table(step=6)
        arcpy.env.workspace = cfg.SCRATCHDIR
        arcpy.env.scratchWorkspace = cfg.ARCSCRATCHDIR
        prefix = path.basename(cfg.PROJECTDIR)
        # For speed:
        arcpy.env.pyramid = "NONE"
        arcpy.env.rasterStatistics = "NONE"

        # set the analysis extent and cell size to that of the resistance
        # surface
        arcpy.env.extent = cfg.RESRAST
        arcpy.env.cellSize = arcpy.Describe(cfg.RESRAST).MeanCellHeight
        arcpy.env.snapRaster = cfg.RESRAST
        spatialref = arcpy.Describe(cfg.RESRAST).spatialReference
        map_units = (str(spatialref.linearUnitName)).lower()
        if len(map_units) > 1 and map_units[-1] != 's':
            map_units = map_units + 's'

        if (float(arcpy.env.cellSize) > start_radius
                or start_radius > end_radius):
            msg = ('Error: minimum detection radius must be greater than '
                   'cell size (' + arcpy.env.cellSize +
                   ') \nand less than or equal to maximum detection radius.')
            lu.raise_error(msg)

        link_table = lu.load_link_table(link_table_file)
        num_links = link_table.shape[0]
        num_corridor_links = lu.report_links(link_table)
        if num_corridor_links == 0:
            lu.dashline(1)
            msg = '\nThere are no linkages. Bailing.'
            lu.raise_error(msg)

        # set up directories for barrier and barrier mosaic grids
        gprint("Creating intermediate output folder: " + cfg.BARRIERBASEDIR)
        lu.delete_dir(cfg.BARRIERBASEDIR)
        lu.create_dir(cfg.BARRIERBASEDIR)
        arcpy.CreateFolder_management(cfg.BARRIERBASEDIR, cfg.BARRIERDIR_NM)
        cbarrierdir = path.join(cfg.BARRIERBASEDIR, cfg.BARRIERDIR_NM)

        cores_to_process = npy.unique(
            link_table[:, cfg.LTB_CORE1:cfg.LTB_CORE2 + 1])
        max_core_num = max(cores_to_process)

        # Set up focal directories.
        # To keep there from being > 100 grids in any one directory,
        # outputs are written to:
        # barrier\focalX_ for cores 1-99 at radius X
        # barrier\focalX_1 for cores 100-199
        # etc.
        lu.dashline(0)

        for radius in range(start_radius, end_radius + 1, radius_step):
            core1path = lu.get_focal_path(1, radius)
            path1 = path.split(core1path)[0]
            path2, dir2 = path.split(path1)
            arcpy.CreateFolder_management(path.dirname(path2),
                                          path.basename(path2))
            arcpy.CreateFolder_management(path.dirname(path1),
                                          path.basename(path1))

            if max_core_num > 99:
                gprint('Creating subdirectories for ' + str(radius) + ' ' +
                       str(map_units) + ' radius analysis scale.')
                focal_dir_base_name = dir2

                cp100 = cores_to_process.astype('int32') // 100
                ind = npy.where(cp100 > 0)
                dir_nums = npy.unique(cp100[ind])
                for dir_num in dir_nums:
                    focal_dir = focal_dir_base_name + str(dir_num)
                    gprint('...' + focal_dir)
                    arcpy.CreateFolder_management(path2, focal_dir)

        # Create resistance raster with filled-in Nodata values for later use
        arcpy.env.extent = cfg.RESRAST
        resist_fill_ras = path.join(cfg.SCRATCHDIR, "resist_fill")
        output = arcpy.sa.Con(arcpy.sa.IsNull(cfg.RESRAST), 1000000000,
                              arcpy.sa.Raster(cfg.RESRAST) - 1)
        output.save(resist_fill_ras)

        core_list = link_table[:, cfg.LTB_CORE1:cfg.LTB_CORE2 + 1]
        core_list = npy.sort(core_list)

        # Loop through each search radius to calculate barriers in each link
        rad_id = 0  # Keep track of no of radii processed - used for temp dir
        for radius in range(start_radius, end_radius + 1, radius_step):
            rad_id = rad_id + 1
            link_table_tmp = link_table.copy()

            @Retry(10)
            # Can't pass vars in and modify them.
            def do_radius_loop():
                """Do radius loop."""
                link_table = link_table_tmp.copy()
                start_time = time.clock()
                link_loop = 0
                pct_done = 0
                gprint('\nMapping barriers at a radius of ' + str(radius) +
                       ' ' + str(map_units))
                if cfg.SUM_BARRIERS:
                    gprint('using SUM method')
                else:
                    gprint('using MAXIMUM method')
                if num_corridor_links > 1:
                    gprint('0 percent done')
                last_mosaic_ras = None
                last_mosaic_ras_pct = None
                for x in range(0, num_links):
                    pct_done = lu.report_pct_done(
                        link_loop, num_corridor_links, pct_done)
                    if ((link_table[x, cfg.LTB_LINKTYPE] > 0) and
                            (link_table[x, cfg.LTB_LINKTYPE] < 1000)):
                        link_loop = link_loop + 1
                        # source and target cores
                        corex = int(core_list[x, 0])
                        corey = int(core_list[x, 1])

                        # Get cwd rasters for source and target cores
                        cwd_ras1 = lu.get_cwd_path(corex)
                        cwd_ras2 = lu.get_cwd_path(corey)

                        # Mask out areas above CWD threshold
                        cwd_tmp1 = None
                        cwd_tmp2 = None
                        if cfg.BARRIER_CWD_THRESH is not None:
                            if x == 1:
                                lu.dashline(1)
                                gprint('  Using CWD threshold of '
                                       + str(cfg.BARRIER_CWD_THRESH)
                                       + ' map units.')
                            arcpy.env.extent = cfg.RESRAST
                            arcpy.env.cellSize = cfg.RESRAST
                            arcpy.env.snapRaster = cfg.RESRAST
                            cwd_tmp1 = path.join(cfg.SCRATCHDIR,
                                                 "tmp" + str(corex))
                            out_con = arcpy.sa.Con(
                                cwd_ras1 < float(cfg.BARRIER_CWD_THRESH),
                                cwd_ras1)
                            out_con.save(cwd_tmp1)
                            cwd_ras1 = cwd_tmp1
                            cwd_tmp2 = path.join(cfg.SCRATCHDIR,
                                                 "tmp" + str(corey))
                            out_con = arcpy.sa.Con(
                                cwd_ras2 < float(cfg.BARRIER_CWD_THRESH),
                                cwd_ras2)
                            out_con.save(cwd_tmp2)
                            cwd_ras2 = cwd_tmp2

                        focal_ras1 = lu.get_focal_path(corex, radius)
                        focal_ras2 = lu.get_focal_path(corey, radius)

                        link = lu.get_links_from_core_pairs(link_table,
                                                            corex, corey)
                        lc_dist = float(link_table[link, cfg.LTB_CWDIST])

                        # Detect barriers at radius using neighborhood stats
                        # Create the Neighborhood Object
                        inner_radius = radius - 1
                        outer_radius = radius

                        dia = 2 * radius
                        in_neighborhood = ("ANNULUS " + str(inner_radius)
                                           + " " + str(outer_radius) + " MAP")

                        @Retry(10)
                        def exec_focal():
                            """Execute focal statistics."""
                            if not path.exists(focal_ras1):
                                arcpy.env.extent = cwd_ras1
                                out_focal_stats = arcpy.sa.FocalStatistics(
                                    cwd_ras1, in_neighborhood,
                                    "MINIMUM", "DATA")
                                if SET_CORES_TO_NULL:
                                    # Set areas overlapping cores to NoData xxx
                                    out_focal_stats2 = arcpy.sa.Con(
                                        out_focal_stats > 0, out_focal_stats)
                                    out_focal_stats2.save(focal_ras1)
                                else:
                                    out_focal_stats.save(focal_ras1)
                                arcpy.env.extent = cfg.RESRAST

                            if not path.exists(focal_ras2):
                                arcpy.env.extent = cwd_ras2
                                out_focal_stats = arcpy.sa.FocalStatistics(
                                    cwd_ras2, in_neighborhood,
                                    "MINIMUM", "DATA")
                                if SET_CORES_TO_NULL:
                                    # Set areas overlapping cores to NoData xxx
                                    out_focal_stats2 = arcpy.sa.Con(
                                        out_focal_stats > 0, out_focal_stats)
                                    out_focal_stats2.save(focal_ras2)
                                else:
                                    out_focal_stats.save(focal_ras2)
                                arcpy.env.extent = cfg.RESRAST
                        exec_focal()

                        lu.delete_data(cwd_tmp1)
                        lu.delete_data(cwd_tmp2)

                        barrier_ras = path.join(
                            cbarrierdir, "b" + str(radius) + "_" + str(corex)
                            + "_" + str(corey)+'.tif')

                        # Need to set nulls to 0,
                        # also create trim rasters as we go
                        if cfg.SUM_BARRIERS:
                            out_ras = ((lc_dist - arcpy.sa.Raster(focal_ras1) -
                                        arcpy.sa.Raster(focal_ras2) - dia)
                                       / dia)
                            out_con = arcpy.sa.Con(arcpy.sa.IsNull(out_ras),
                                                   0, out_ras)
                            out_con2 = arcpy.sa.Con(out_con < 0, 0, out_con)
                            out_con2.save(barrier_ras)

                            # Execute FocalStatistics to fill out search radii
                            in_neighborhood = ("CIRCLE " + str(outer_radius)
                                               + " MAP")
                            fill_ras = path.join(
                                cbarrierdir, "b" + str(radius) + "_"
                                + str(corex) + "_" + str(corey) + "_fill.tif")
                            out_focal_stats = arcpy.sa.FocalStatistics(
                                barrier_ras, in_neighborhood,
                                "MAXIMUM", "DATA")
                            out_focal_stats.save(fill_ras)

                            if cfg.WRITE_TRIM_RASTERS:
                                trm_ras = path.join(
                                    cbarrierdir, "b" + str(radius) + "_"
                                    + str(corex) + "_" + str(corey)
                                    + "_trim.tif")
                                ras_list = [fill_ras, resist_fill_ras]
                                out_cell_statistics = arcpy.sa.CellStatistics(
                                    ras_list, "MINIMUM")
                                out_cell_statistics.save(trm_ras)

                        else:

                            @Retry(10)
                            def clac_ben():
                                """Calculate potential benefit.

                                Calculate potential benefit per map unit
                                restored.
                                """
                                out_ras = (
                                    (lc_dist - arcpy.sa.Raster(focal_ras1)
                                     - arcpy.sa.Raster(focal_ras2) - dia)
                                    / dia)
                                out_ras.save(barrier_ras)
                            clac_ben()

                        if cfg.WRITE_PCT_RASTERS:
                            # Calculate % potential benefit per unit restored
                            barrier_ras_pct = path.join(
                                cbarrierdir, "b" + str(radius) + "_"
                                + str(corex) + "_" + str(corey)
                                + '_pct.tif')

                            @Retry(10)
                            def calc_ben_pct():
                                """Calc benefit percentage."""
                                outras = (100 * (arcpy.sa.Raster(barrier_ras)
                                                 / lc_dist))
                                outras.save(barrier_ras_pct)
                            calc_ben_pct()

                        # Mosaic barrier results across core area pairs
                        mosaic_dir = path.join(cfg.SCRATCHDIR, 'mos'
                                               + str(rad_id) + '_'
                                               + str(x + 1))
                        lu.create_dir(mosaic_dir)

                        mos_fn = 'mos_temp'
                        tmp_mosaic_ras = path.join(mosaic_dir, mos_fn)
                        tmp_mosaic_ras_trim = path.join(mosaic_dir,
                                                        'mos_temp_trm')
                        arcpy.env.workspace = mosaic_dir
                        if link_loop == 1:
                            last_mosaic_ras_trim = None
                            # For first grid copy rather than mosaic
                            arcpy.CopyRaster_management(barrier_ras,
                                                        tmp_mosaic_ras)
                            if cfg.SUM_BARRIERS and cfg.WRITE_TRIM_RASTERS:
                                arcpy.CopyRaster_management(
                                    trm_ras, tmp_mosaic_ras_trim)
                        else:
                            if cfg.SUM_BARRIERS:
                                out_con = arcpy.sa.Con(
                                    arcpy.sa.Raster(barrier_ras) < 0,
                                    last_mosaic_ras,
                                    arcpy.sa.Raster(barrier_ras)
                                    + arcpy.sa.Raster(last_mosaic_ras))
                                out_con.save(tmp_mosaic_ras)
                                if cfg.WRITE_TRIM_RASTERS:
                                    out_con = arcpy.sa.Con(
                                        arcpy.sa.Raster(trm_ras) < 0,
                                        last_mosaic_ras_trim,
                                        arcpy.sa.Raster(trm_ras)
                                        + arcpy.sa.Raster(last_mosaic_ras_trim)
                                        )
                                    out_con.save(tmp_mosaic_ras_trim)

                            else:
                                in_rasters = (";".join([barrier_ras,
                                                        last_mosaic_ras]))

                                @Retry(10)
                                def mosaic_to_new():
                                    """Mosaic to new raster."""
                                    arcpy.MosaicToNewRaster_management(
                                        input_rasters=in_rasters,
                                        output_location=mosaic_dir,
                                        raster_dataset_name_with_extension\
                                        =mos_fn,
                                        pixel_type="32_BIT_FLOAT",
                                        cellsize=arcpy.env.cellSize,
                                        number_of_bands="1",
                                        mosaic_method="MAXIMUM")
                                mosaic_to_new()

                        if link_loop > 1:  # Clean up from previous loop
                            lu.delete_data(last_mosaic_ras)
                            last_mosaic_dir = path.dirname(last_mosaic_ras)
                            lu.clean_out_workspace(last_mosaic_dir)
                            lu.delete_dir(last_mosaic_dir)

                        last_mosaic_ras = tmp_mosaic_ras
                        if cfg.WRITE_TRIM_RASTERS:
                            last_mosaic_ras_trim = tmp_mosaic_ras_trim
                        if cfg.WRITE_PCT_RASTERS:
                            mos_pct_fn = 'mos_temp_pct'
                            mosaic_dir_pct = path.join(cfg.SCRATCHDIR, 'mosP'
                                                       + str(rad_id) + '_'
                                                       + str(x+1))
                            lu.create_dir(mosaic_dir_pct)
                            tmp_mosaic_ras_pct = path.join(mosaic_dir_pct,
                                                           mos_pct_fn)
                            if link_loop == 1:
                                # If this is the first grid then copy
                                # rather than mosaic
                                if cfg.SUM_BARRIERS:
                                    out_con = arcpy.sa.Con(
                                        arcpy.sa.Raster(barrier_ras_pct)
                                        < 0, 0,
                                        arcpy.sa.Con(arcpy.sa.IsNull
                                                     (barrier_ras_pct),
                                                     0, barrier_ras_pct))
                                    out_con.save(tmp_mosaic_ras_pct)
                                else:
                                    arcpy.CopyRaster_management(
                                        barrier_ras_pct, tmp_mosaic_ras_pct)

                            else:
                                if cfg.SUM_BARRIERS:

                                    @Retry(10)
                                    def sum_barriers():
                                        """Sum barriers."""
                                        out_con = arcpy.sa.Con(
                                            arcpy.sa.Raster(barrier_ras_pct)
                                            < 0,
                                            last_mosaic_ras_pct,
                                            arcpy.sa.Raster(barrier_ras_pct)
                                            + arcpy.sa.Raster(
                                                last_mosaic_ras_pct))
                                        out_con.save(tmp_mosaic_ras_pct)
                                    sum_barriers()
                                else:
                                    in_rasters = (";".join([barrier_ras_pct,
                                                  last_mosaic_ras_pct]))

                                    @Retry(10)
                                    def max_barriers():
                                        """Get max barriers."""
                                        arcpy.MosaicToNewRaster_management(
                                            input_rasters=in_rasters,
                                            output_location=mosaic_dir_pct,
                                            raster_dataset_name_with_extension
                                            =mos_pct_fn,
                                            pixel_type="32_BIT_FLOAT",
                                            cellsize=arcpy.env.cellSize,
                                            number_of_bands="1",
                                            mosaic_method="MAXIMUM")
                                    max_barriers()

                            if link_loop > 1:  # Clean up from previous loop
                                lu.delete_data(last_mosaic_ras_pct)
                                last_mosaic_dir_pct = path.dirname(
                                    last_mosaic_ras_pct)
                                lu.clean_out_workspace(last_mosaic_dir_pct)
                                lu.delete_dir(last_mosaic_dir_pct)

                            last_mosaic_ras_pct = tmp_mosaic_ras_pct

                        if not cfg.SAVEBARRIERRASTERS:
                            lu.delete_data(barrier_ras)
                            if cfg.WRITE_PCT_RASTERS:
                                lu.delete_data(barrier_ras_pct)
                            if cfg.WRITE_TRIM_RASTERS:
                                lu.delete_data(trm_ras)

                        # Temporarily disable links in linktable -
                        # don't want to mosaic them twice
                        for y in range(x + 1, num_links):
                            corex1 = int(core_list[y, 0])
                            corey1 = int(core_list[y, 1])
                            if corex1 == corex and corey1 == corey:
                                link_table[y, cfg.LTB_LINKTYPE] = (
                                    link_table[y, cfg.LTB_LINKTYPE] + 1000)
                            elif corex1 == corey and corey1 == corex:
                                link_table[y, cfg.LTB_LINKTYPE] = (
                                    link_table[y, cfg.LTB_LINKTYPE] + 1000)

                if num_corridor_links > 1 and pct_done < 100:
                    gprint('100 percent done')
                gprint('Summarizing barrier data for search radius.')
                # Rows that were temporarily disabled
                rows = npy.where(link_table[:, cfg.LTB_LINKTYPE] > 1000)
                link_table[rows, cfg.LTB_LINKTYPE] = (
                    link_table[rows, cfg.LTB_LINKTYPE] - 1000)
                # -----------------------------------------------------------------
                # Set negative values to null or zero and write geodatabase.
                mosaic_fn = (prefix + "_BarrierCenters" + sum_suffix + "_Rad" +
                             str(radius))
                mosaic_ras = path.join(cfg.BARRIERGDB, mosaic_fn)
                arcpy.env.extent = cfg.RESRAST

                out_set_null = arcpy.sa.SetNull(tmp_mosaic_ras,
                                                tmp_mosaic_ras,
                                                "VALUE < 0")  # xxx orig
                out_set_null.save(mosaic_ras)

                lu.delete_data(tmp_mosaic_ras)

                if cfg.SUM_BARRIERS and cfg.WRITE_TRIM_RASTERS:
                    mosaic_fn = (prefix + "_BarrierCircles_RBMin" + sum_suffix
                                 + "_Rad" + str(radius))
                    mosaic_ras_trim = path.join(cfg.BARRIERGDB, mosaic_fn)
                    arcpy.CopyRaster_management(tmp_mosaic_ras_trim,
                                                mosaic_ras_trim)
                    lu.delete_data(tmp_mosaic_ras)

                if cfg.WRITE_PCT_RASTERS:
                    # Do same for percent raster
                    mosaic_pct_fn = (prefix + "_BarrierCenters_Pct"
                                     + sum_suffix + "_Rad" + str(radius))
                    arcpy.env.extent = cfg.RESRAST
                    out_set_null = arcpy.sa.SetNull(tmp_mosaic_ras_pct,
                                                    tmp_mosaic_ras_pct,
                                                    "VALUE < 0")
                    mosaic_ras_pct = path.join(cfg.BARRIERGDB, mosaic_pct_fn)
                    out_set_null.save(mosaic_ras_pct)
                    lu.delete_data(tmp_mosaic_ras_pct)

                # 'Grow out' maximum restoration gain to
                # neighborhood size for display
                in_neighborhood = "CIRCLE " + str(outer_radius) + " MAP"
                # Execute FocalStatistics
                fill_ras_fn = "barriers_fill" + str(outer_radius) + TIF
                fill_ras = path.join(cfg.BARRIERBASEDIR, fill_ras_fn)
                out_focal_stats = arcpy.sa.FocalStatistics(
                    mosaic_ras, in_neighborhood, "MAXIMUM", "DATA")
                out_focal_stats.save(fill_ras)

                if cfg.WRITE_PCT_RASTERS:
                    # Do same for percent raster
                    fill_ras_pct_fn = (
                        "barriers_fill_pct" + str(outer_radius) + TIF)
                    fill_ras_pct = path.join(cfg.BARRIERBASEDIR,
                                             fill_ras_pct_fn)
                    out_focal_stats = arcpy.sa.FocalStatistics(
                        mosaic_ras_pct, in_neighborhood, "MAXIMUM", "DATA")
                    out_focal_stats.save(fill_ras_pct)

                # Place copies of filled rasters in output geodatabase
                arcpy.env.workspace = cfg.BARRIERGDB
                fill_ras_fn = (prefix + "_BarrrierCircles" + sum_suffix
                               + "_Rad" + str(outer_radius))
                arcpy.CopyRaster_management(fill_ras, fill_ras_fn)
                if cfg.WRITE_PCT_RASTERS:
                    fill_ras_pct_fn = (prefix + "_BarrrierCircles_Pct"
                                       + sum_suffix + "_Rad"
                                       + str(outer_radius))
                    arcpy.CopyRaster_management(fill_ras_pct,
                                                fill_ras_pct_fn)

                if not cfg.SUM_BARRIERS and cfg.WRITE_TRIM_RASTERS:
                    # Create pared-down version of filled raster- remove pixels
                    # that don't need restoring by allowing a pixel to only
                    # contribute its resistance value to restoration gain
                    out_ras_fn = "barriers_trm" + str(outer_radius) + TIF
                    out_ras = path.join(cfg.BARRIERBASEDIR, out_ras_fn)
                    ras_list = [fill_ras, resist_fill_ras]
                    out_cell_statistics = arcpy.sa.CellStatistics(ras_list,
                                                                  "MINIMUM")
                    out_cell_statistics.save(out_ras)

                    # SECOND ROUND TO CLIP BY DATA VALUES IN BARRIER RASTER
                    out_ras_2fn = ("barriers_trm" + sum_suffix
                                   + str(outer_radius) + "_2" + TIF)
                    out_ras2 = path.join(cfg.BARRIERBASEDIR, out_ras_2fn)
                    output = arcpy.sa.Con(arcpy.sa.IsNull(fill_ras),
                                          fill_ras, out_ras)
                    output.save(out_ras2)
                    out_ras_fn = (prefix + "_BarrierCircles_RBMin"
                                  + sum_suffix + "_Rad"
                                  + str(outer_radius))
                    arcpy.CopyRaster_management(out_ras2, out_ras_fn)
                start_time = lu.elapsed_time(start_time)

            # Call the above function
            do_radius_loop()

        # Combine rasters across radii
        gprint('\nCreating summary rasters...')
        if start_radius != end_radius:
            radii_suffix = ('_Rad' + str(int(start_radius)) + 'To'
                            + str(int(end_radius)) + 'Step'
                            + str(int(radius_step)))
            mosaic_fn = "bar_radii"
            mosaic_pct_fn = "bar_radii_pct"
            arcpy.env.workspace = cfg.BARRIERBASEDIR
            for radius in range(start_radius, end_radius + 1, radius_step):
                # Fixme: run speed test with gdb mosaicking above and here
                radius_fn = (prefix + "_BarrierCenters" + sum_suffix + "_Rad"
                             + str(radius))
                radius_ras = path.join(cfg.BARRIERGDB, radius_fn)

                if radius == start_radius:
                    # If this is the first grid then copy rather than mosaic
                    arcpy.CopyRaster_management(radius_ras, mosaic_fn)
                else:
                    mosaic_ras = path.join(cfg.BARRIERBASEDIR, mosaic_fn)
                    arcpy.Mosaic_management(radius_ras, mosaic_ras,
                                            "MAXIMUM", "MATCH")

                if cfg.WRITE_PCT_RASTERS:
                    radius_pct_fn = (prefix + "_BarrierCenters_Pct"
                                     + sum_suffix + "_Rad" + str(radius))
                    radius_ras_pct = path.join(cfg.BARRIERGDB, radius_pct_fn)

                    if radius == start_radius:
                        # If this is the first grid then copy rather than
                        # mosaic
                        arcpy.CopyRaster_management(radius_ras_pct,
                                                    mosaic_pct_fn)
                    else:
                        mosaic_ras_pct = path.join(cfg.BARRIERBASEDIR,
                                                   mosaic_pct_fn)
                        arcpy.Mosaic_management(radius_ras_pct,
                                                mosaic_ras_pct,
                                                "MAXIMUM", "MATCH")

            # Copy results to output geodatabase
            arcpy.env.workspace = cfg.BARRIERGDB
            mosaic_fn = prefix + "_BarrierCenters" + sum_suffix + radii_suffix
            arcpy.CopyRaster_management(mosaic_ras, mosaic_fn)

            if cfg.WRITE_PCT_RASTERS:
                mosaic_pct_fn = (prefix + "_BarrierCenters_Pct" + sum_suffix +
                                 radii_suffix)
                arcpy.CopyRaster_management(mosaic_ras_pct, mosaic_pct_fn)

            # GROWN OUT rasters
            fill_mosaic_fn = "barriers_radii_fill" + TIF
            fill_mosaic_pct_fn = "barriers_radii_fill_pct" + TIF
            fill_mosaic_ras = path.join(cfg.BARRIERBASEDIR, fill_mosaic_fn)
            trim_mosaic_ras_pct = path.join(cfg.BARRIERBASEDIR,
                                            fill_mosaic_pct_fn)

            arcpy.env.workspace = cfg.BARRIERBASEDIR
            for radius in range(start_radius, end_radius + 1, radius_step):
                radius_fn = "barriers_fill" + str(radius) + TIF
                # fixme- do this when only a single radius too
                radius_ras = path.join(cfg.BARRIERBASEDIR, radius_fn)
                if radius == start_radius:
                    # If this is the first grid then copy rather than mosaic
                    arcpy.CopyRaster_management(radius_ras, fill_mosaic_fn)
                else:
                    arcpy.Mosaic_management(radius_ras, fill_mosaic_ras,
                                            "MAXIMUM", "MATCH")

                if cfg.WRITE_PCT_RASTERS:
                    radius_pct_fn = "barriers_fill_pct" + str(radius) + TIF
                    # fixme- do this when only a single radius too
                    radius_ras_pct = path.join(cfg.BARRIERBASEDIR,
                                               radius_pct_fn)
                    if radius == start_radius:
                        # For first grid copy rather than mosaic
                        arcpy.CopyRaster_management(radius_ras_pct,
                                                    fill_mosaic_pct_fn)
                    else:
                        arcpy.Mosaic_management(radius_ras_pct,
                                                trim_mosaic_ras_pct,
                                                "MAXIMUM", "MATCH")

            # Copy result to output geodatabase
            arcpy.env.workspace = cfg.BARRIERGDB
            fill_mosaic_fn = (prefix + "_BarrierCircles" + sum_suffix
                              + radii_suffix)
            arcpy.CopyRaster_management(fill_mosaic_ras, fill_mosaic_fn)
            if cfg.WRITE_PCT_RASTERS:
                fill_mosaic_pct_fn = (prefix + "_BarrierCircles_Pct"
                                      + sum_suffix + radii_suffix)
                arcpy.CopyRaster_management(trim_mosaic_ras_pct,
                                            fill_mosaic_pct_fn)

            # GROWN OUT AND TRIMMED rasters (Can't do percent)
            if cfg.WRITE_TRIM_RASTERS:
                trim_mosaic_fn = "bar_radii_trm"
                arcpy.env.workspace = cfg.BARRIERBASEDIR
                trim_mosaic_ras = path.join(cfg.BARRIERBASEDIR, trim_mosaic_fn)
                for radius in range(start_radius, end_radius + 1, radius_step):
                    radius_fn = (prefix + "_BarrierCircles_RBMin" + sum_suffix
                                 + "_Rad" + str(radius))
                    # fixme- do this when only a single radius too
                    radius_ras = path.join(cfg.BARRIERGDB, radius_fn)

                    if radius == start_radius:
                        # For first grid copy rather than mosaic
                        arcpy.CopyRaster_management(radius_ras, trim_mosaic_fn)
                    else:
                        arcpy.Mosaic_management(radius_ras, trim_mosaic_ras,
                                                "MAXIMUM", "MATCH")
                # Copy result to output geodatabase
                arcpy.env.workspace = cfg.BARRIERGDB
                trim_mosaic_fn = (prefix + "_BarrierCircles_RBMin" + sum_suffix
                                  + radii_suffix)
                arcpy.CopyRaster_management(trim_mosaic_ras, trim_mosaic_fn)

        if not cfg.SAVE_RADIUS_RASTERS:
            arcpy.env.workspace = cfg.BARRIERGDB
            rasters = arcpy.ListRasters()
            for raster in rasters:
                if 'rad' in raster.lower() and 'step' not in raster.lower():
                    lu.delete_data(raster)

        arcpy.env.workspace = cfg.BARRIERGDB
        rasters = arcpy.ListRasters()
        for raster in rasters:
            gprint('\nBuilding output statistics and pyramids\n'
                   'for raster ' + raster)
            lu.build_stats(raster)

        # Clean up temporary files and directories
        if not cfg.SAVEBARRIERRASTERS:
            lu.delete_dir(cbarrierdir)
            lu.delete_dir(cfg.BARRIERBASEDIR)

        if not cfg.SAVEFOCALRASTERS:
            for radius in range(start_radius, end_radius + 1, radius_step):
                core1path = lu.get_focal_path(1, radius)
                path1 = path.split(core1path)[0]
                path2 = path.split(path1)[0]
                lu.delete_dir(path2)

    # Return GEOPROCESSING specific errors
    except arcpy.ExecuteError:
        lu.dashline(1)
        gprint('****Failed in step 6. Details follow.****')
        lu.exit_with_geoproc_error(_SCRIPT_NAME)

    # Return any PYTHON or system specific errors
    except Exception:
        lu.dashline(1)
        gprint('****Failed in step 6. Details follow.****')
        lu.exit_with_python_error(_SCRIPT_NAME)

    return