def getFileType(filename): """ Determine whether input file is a shapefile or a grid (ESRI or GMT). Args: filename (str): Path to candidate filename. Returns: str: 'shapefile', 'grid', or 'unknown'. """ # TODO MOVE TO MAPIO. if os.path.isdir(filename): return 'dir' ftype = GMTGrid.getFileType(filename) if ftype != 'unknown': return 'gmt' # Skip over ESRI header files if filename.endswith('.hdr'): return 'unknown' try: GDALGrid.getFileGeoDict(filename) return 'esri' except: pass return 'unknown'
def sampleGridFile(gridfile, xypoints, method='nearest'): """Sample grid file (ESRI or GMT format) at each of a set of XY (decimal degrees) points. :param gridfile: Name of ESRI or GMT grid format file from which to sample values. :param xypoints: 2D numpy array of XY points, decimal degrees. :param method: Interpolation method, either 'nearest' or 'linear'. :returns: 1D numpy array of grid values at each of input XY points. """ xmin = np.min(xypoints[:, 0]) xmax = np.max(xypoints[:, 0]) ymin = np.min(xypoints[:, 1]) ymax = np.max(xypoints[:, 1]) gridtype = None try: fdict = GMTGrid.getFileGeoDict(gridfile) gridtype = 'gmt' except Exception as error: try: fdict = GDALGrid.getFileGeoDict(gridfile) gridtype = 'esri' except: pass if gridtype is None: raise Exception( 'File "%s" does not appear to be either a GMT grid or an ESRI grid.' % gridfile) xmin = xmin - fdict.dx * 3 xmax = xmax + fdict.dx * 3 ymin = ymin - fdict.dy * 3 ymax = ymax + fdict.dy * 3 #bounds = (xmin, xmax, ymin, ymax) if gridtype == 'gmt': fgeodict = GMTGrid.getFileGeoDict(gridfile) else: fgeodict = GDALGrid.getFileGeoDict(gridfile) dx, dy = (fgeodict.dx, fgeodict.dy) sdict = GeoDict.createDictFromBox(xmin, xmax, ymin, ymax, dx, dy) if gridtype == 'gmt': grid = GMTGrid.load(gridfile, samplegeodict=sdict, resample=False, method=method, doPadding=True) else: grid = GDALGrid.load(gridfile, samplegeodict=sdict, resample=False, method=method, doPadding=True) return sampleFromGrid(grid, xypoints)
def getFileType(filename): if os.path.isdir(filename): return 'dir' ftype = GMTGrid.getFileType(filename) if ftype != 'unknown': return 'gmt' #skip over ESRI header files if filename.endswith('.hdr'): return 'unknown' try: GDALGrid.getFileGeoDict(filename) return 'esri' except: pass return 'unknown'
def getFileType(filename): """ Determine whether input file is a shapefile or a grid (ESRI or GMT). :param filename: String path to candidate filename. :returns: String, one of 'shapefile','grid','unknown'. """ fname, fext = os.path.splitext(filename) dbf = fname + '.dbf' ftype = 'unknown' if os.path.isfile(dbf): ftype = 'shapefile' else: try: fdict = GMTGrid.getFileGeoDict(filename) ftype = 'grid' except Exception as error: try: fdict = GDALGrid.getFileGeoDict(filename) ftype = 'grid' except: pass return ftype
def sampleGridFile(gridfile,xypoints,method='nearest'): """ Sample grid file (ESRI or GMT format) at each of a set of XY (decimal degrees) points. :param gridfile: Name of ESRI or GMT grid format file from which to sample values. :param xypoints: 2D numpy array of XY points, decimal degrees. :param method: Interpolation method, either 'nearest' or 'linear'. :returns: 1D numpy array of grid values at each of input XY points. """ xmin = np.min(xypoints[:,0]) xmax = np.max(xypoints[:,0]) ymin = np.min(xypoints[:,1]) ymax = np.max(xypoints[:,1]) gridtype = None try: fdict = GMTGrid.getFileGeoDict(gridfile) gridtype = 'gmt' except Exception,error: try: fdict = GDALGrid.getFileGeoDict(gridfile) gridtype = 'esri' except: pass
def warp(infile, outfile, s_srs, t_srs, method='bilinear', fmt='EHdr'): """ Calls gdalwarp to reproject a raster USAGE s_srs, t_srs = warp(infile, outfile, s_srs, t_srs, method='bilinear', fmt='EHdr') :param infile: Single input file :param outfile: Single output file with extension :param s_srs: Projection of input file (EPSG or PROJ.4 string), if None, uses transverse mercator :param t_srs: Projection of output file (EPSG or PROJ.4 string), if None, uses transverse mercator :param method: method to use in warping, from gdalwarp's options, 'bilinear', 'nearest' etc., bilinear should be used for slopes to avoid weird artifacts :param fmt: Format of output, 'EHdr' or 'GMT' :returns: s_srs: s_srs that was used t_srs: t_srs that was used """ if s_srs is None or t_srs is None: temp, first_column_duplicated = GDALGrid.getFileGeoDict(infile) clat = temp.ymin + (temp.ymax - temp.ymin) / 2.0 clon = temp.xmin + (temp.xmax - temp.xmin) / 2.0 if s_srs is None: s_srs = '"+proj=tmerc +lat_0=%s +lon_0=%s +x_0=0 +y_0=0 +units=m +no_defs"' % ( clat, clon) elif t_srs is None: t_srs = '"+proj=tmerc +lat_0=%s +lon_0=%s +x_0=0 +y_0=0 +units=m +no_defs"' % ( clat, clon) build = 'gdalwarp -overwrite -s_srs %s -t_srs %s -r %s -of %s %s %s' % ( s_srs, t_srs, method, fmt, infile, outfile) #run code os.system(build) return s_srs, t_srs
def warp(infile, outfile, s_srs, t_srs, method='bilinear', fmt='EHdr'): """ Call gdalwarp to reproject a raster USAGE s_srs, t_srs = warp(infile, outfile, s_srs, t_srs, method='bilinear', fmt='EHdr') :param infile: Single input file :param outfile: Single output file with extension :param s_srs: Projection of input file (EPSG or PROJ.4 string), if None, uses transverse mercator :param t_srs: Projection of output file (EPSG or PROJ.4 string), if None, uses transverse mercator :param method: method to use in warping, from gdalwarp's options, 'bilinear', 'nearest' etc., bilinear should be used for slopes to avoid weird artifacts :param fmt: Format of output, 'EHdr' or 'GMT' :returns s_srs: s_srs that was used :returns t_srs: t_srs that was used """ if s_srs is None or t_srs is None: temp = GDALGrid.getFileGeoDict(infile) clat = temp.ymin + (temp.ymax-temp.ymin)/2.0 clon = temp.xmin + (temp.xmax-temp.xmin)/2.0 if s_srs is None: s_srs = '"+proj=tmerc +lat_0=%s +lon_0=%s +x_0=0 +y_0=0 +units=m +no_defs"' % (clat, clon) elif t_srs is None: t_srs = '"+proj=tmerc +lat_0=%s +lon_0=%s +x_0=0 +y_0=0 +units=m +no_defs"' % (clat, clon) build = 'gdalwarp -overwrite -s_srs %s -t_srs %s -r %s -of %s %s %s' % (s_srs, t_srs, method, fmt, infile, outfile) #run code os.system(build) return s_srs, t_srs
def getFileType(filename): """ Determine whether input file is a shapefile or a grid (ESRI or GMT). :param filename: String path to candidate filename. :returns: String, one of 'shapefile','grid','unknown'. """ fname, fext = os.path.splitext(filename) dbf = fname + '.dbf' ftype = 'unknown' if os.path.isfile(dbf): ftype = 'shapefile' else: try: fdict = GMTGrid.getFileGeoDict(filename) ftype = 'grid' except Exception as error: try: fdict = GDALGrid.getFileGeoDict(filename) ftype = 'grid' except: pass return ftype
def sampleGridFile(gridfile,xypoints,method='nearest'): """ Sample grid file (ESRI or GMT format) at each of a set of XY (decimal degrees) points. :param gridfile: Name of ESRI or GMT grid format file from which to sample values. :param xypoints: 2D numpy array of XY points, decimal degrees. :param method: Interpolation method, either 'nearest' or 'linear'. :returns: 1D numpy array of grid values at each of input XY points. """ if not len(xypoints): return np.array([]) xmin = np.min(xypoints[:,0]) xmax = np.max(xypoints[:,0]) ymin = np.min(xypoints[:,1]) ymax = np.max(xypoints[:,1]) gridtype = None try: fdict,tmp = GMTGrid.getFileGeoDict(gridfile) gridtype = 'gmt' except Exception as error: try: fdict,tmp = GDALGrid.getFileGeoDict(gridfile) gridtype = 'esri' except: pass if gridtype is None: raise Exception('File "%s" does not appear to be either a GMT grid or an ESRI grid.' % gridfile) xmin = xmin - fdict.dx*3 xmax = xmax + fdict.dx*3 ymin = ymin - fdict.dy*3 ymax = ymax + fdict.dy*3 bounds = (xmin,xmax,ymin,ymax) if gridtype == 'gmt': fgeodict,tmp = GMTGrid.getFileGeoDict(gridfile) else: fgeodict,tmp = GDALGrid.getFileGeoDict(gridfile) dx,dy = (fgeodict.dx,fgeodict.dy) sdict = GeoDict.createDictFromBox(xmin,xmax,ymin,ymax,dx,dy) if gridtype == 'gmt': grid = GMTGrid.load(gridfile,samplegeodict=sdict,resample=True,method=method,doPadding=True) else: grid = GDALGrid.load(gridfile,samplegeodict=sdict,resample=True,method=method,doPadding=True) return sampleFromGrid(grid,xypoints)
def _getFileGeoDict(fname): geodict = None try: geodict = GMTGrid.getFileGeoDict(fname) except Exception as msg1: try: geodict = GDALGrid.getFileGeoDict(fname) except Exception as msg2: msg = 'File geodict failure with %s - error messages: "%s"\n "%s"' % (fname,str(msg1),str(msg2)) raise ShakeMapException(msg) return geodict
def _getFileGeoDict(fname): geodict = None try: geodict = GMTGrid.getFileGeoDict(fname) except Exception as msg1: try: geodict = GDALGrid.getFileGeoDict(fname) except Exception as msg2: msg = 'File geodict failure with %s - error messages: "%s"\n "%s"' % ( fname, str(msg1), str(msg2)) raise ShakeMapException(msg) return geodict
def getGridType(gridfile): gridtype = None try: fdict = GMTGrid.getFileGeoDict(gridfile) gridtype = 'gmt' except Exception as error: try: fdict = GDALGrid.getFileGeoDict(gridfile) gridtype = 'esri' except: pass return gridtype
def get_file_type(file): """Internal method to figure out which file type (GMT or GDAL) the population/country code grid files are. """ if GMTGrid.getFileType(file) == 'unknown': try: gdict = GDALGrid.getFileGeoDict(file) return GDALGrid except: pass else: return GMTGrid return None
def getFileType(filename): """Determine whether input file is a shapefile or a grid (ESRI or GMT). EVENTUALLY WILL BE MOVED TO MAPIO :param filename: String path to candidate filename. :returns: String, one of 'shapefile','grid','unknown'. """ if os.path.isdir(filename): return 'dir' ftype = GMTGrid.getFileType(filename) if ftype != 'unknown': return 'gmt' #skip over ESRI header files if filename.endswith('.hdr'): return 'unknown' try: GDALGrid.getFileGeoDict(filename) return 'esri' except: pass return 'unknown'
def getFileType(filename): """Determine whether input file is a shapefile or a grid (ESRI or GMT). EVENTUALLY WILL BE MOVED TO MAPIO :param filename: String path to candidate filename. :returns: String, one of 'shapefile','grid','unknown'. """ if os.path.isdir(filename): return 'dir' ftype = GMTGrid.getFileType(filename) if ftype != 'unknown': return 'gmt' #skip over ESRI header files if filename.endswith('.hdr'): return 'unknown' try: GDALGrid.getFileGeoDict(filename) return 'esri' except: pass return 'unknown'
def godt2008(shakefile, config, uncertfile=None, saveinputs=False, displmodel=None, bounds=None, slopediv=100., codiv=10., numstd=None, trimfile=None): """ This function runs the Godt and others (2008) global method for a given ShakeMap. The Factor of Safety is calculated using infinite slope analysis assumuing dry conditions. The method uses threshold newmark displacement and estimates areal coverage by doing the calculations for each slope quantile. Args: shakefile (str): Path to shakemap xml file. config (ConfigObj): ConfigObj of config file containing inputs required for running the model uncertfile (str): Path to shakemap uncertainty xml file (optional). saveinputs (bool): Whether or not to return the model input layers, False (default) returns only the model output (one layer). displmodel (str): Newmark displacement regression model to use * ``'J_PGA'`` (default) -- PGA-based model, equation 6 from Jibson (2007). * ``'J_PGA_M'`` -- PGA and M-based model, equation 7 from Jibson (2007). * ``'RS_PGA_M'`` -- PGA and M-based model from from Rathje and Saygili (2009). * ``'RS_PGA_PGV'`` -- PGA and PGV-based model, equation 6 from Saygili and Rathje (2008). bounds (dict): Optional dictionary with keys 'xmin', 'xmax', 'ymin', 'ymax' that defines a subset of the shakemap area to compute. slopediv (float): Divide slope by this number to get slope in degrees (Verdin datasets need to be divided by 100). codiv (float): Divide cohesion input layer by this number (For Godt method, need to divide by 10 because that is how it was calibrated). numstd (float): Number of (+/-) standard deviations to use if uncertainty is computed (uncertfile must be supplied). trimfile (str): shapefile of earth's land masses to trim offshore areas of model Returns: dict: Dictionary containing output and input layers (if saveinputs=True): .. code-block:: python { 'grid': mapio grid2D object, 'label': 'label for colorbar and top line of subtitle', 'type': 'output or input to model', 'description': {'name': 'short reference of model', 'longref': 'full model reference', 'units': 'units of output', 'shakemap': 'information about shakemap used', 'event_id': 'shakemap event id', 'parameters': 'dictionary of model parameters used' } } Raises: NameError: when unable to parse the config correctly (probably a formatting issue in the configfile) or when unable to find the shakefile (Shakemap filepath) -- these cause program to end. """ # TODO: # - Add 'all' -- averages Dn from all four equations, add term to # convert PGA and PGV to Ia and use other equations, add Ambraseys and # Menu (1988) option. # Empty refs slopesref = 'unknown' slopelref = 'unknown' cohesionlref = 'unknown' cohesionsref = 'unknown' frictionsref = 'unknown' frictionlref = 'unknown' modellref = 'unknown' modelsref = 'unknown' # See if trimfile exists if trimfile is not None: if not os.path.exists(trimfile): print('trimfile defined does not exist: %s\n' 'Ocean will not be trimmed' % trimfile) trimfile = None if os.path.splitext(trimfile)[1] != '.shp': print('trimfile must be a shapefile, ocean will not be trimmed') trimfile = None # Parse config try: # May want to add error handling so if refs aren't given, just # includes unknown slopefilepath = config['godt_2008']['layers']['slope']['filepath'] slopeunits = config['godt_2008']['layers']['slope']['units'] cohesionfile = config['godt_2008']['layers']['cohesion']['file'] cohesionunits = config['godt_2008']['layers']['cohesion']['units'] frictionfile = config['godt_2008']['layers']['friction']['file'] frictionunits = config['godt_2008']['layers']['friction']['units'] thick = float(config['godt_2008']['parameters']['thick']) uwt = float(config['godt_2008']['parameters']['uwt']) nodata_cohesion = \ float(config['godt_2008']['parameters']['nodata_cohesion']) nodata_friction = \ float(config['godt_2008']['parameters']['nodata_friction']) dnthresh = float(config['godt_2008']['parameters']['dnthresh']) fsthresh = float(config['godt_2008']['parameters']['fsthresh']) acthresh = float(config['godt_2008']['parameters']['acthresh']) try: slopemin = float(config['godt_2008']['parameters']['slopemin']) except: slopemin = 0.01 print('No slopemin found in config file, using 0.01 deg ' 'for slope minimum') except Exception as e: raise NameError('Could not parse configfile, %s' % e) if displmodel is None: try: displmodel = config['godt_2008']['parameters']['displmodel'] except: print('No regression model specified, using default of J_PGA_M') displmodel = 'J_PGA_M' # TO DO: ADD ERROR CATCHING ON UNITS, MAKE SURE THEY ARE WHAT THEY SHOULD # BE FOR THIS MODEL try: # Try to fetch source information from config modelsref = config['godt_2008']['shortref'] modellref = config['godt_2008']['longref'] slopesref = config['godt_2008']['layers']['slope']['shortref'] slopelref = config['godt_2008']['layers']['slope']['longref'] cohesionsref = config['godt_2008']['layers']['cohesion']['shortref'] cohesionlref = config['godt_2008']['layers']['cohesion']['longref'] frictionsref = config['godt_2008']['layers']['friction']['shortref'] frictionlref = config['godt_2008']['layers']['friction']['longref'] except: print('Was not able to retrieve all references from config file. ' 'Continuing') # Figure out how/if need to cut anything geodict = ShakeGrid.getFileGeoDict(shakefile) # , adjust='res') if bounds is not None: # Make sure bounds are within ShakeMap Grid if geodict.xmin < geodict.xmax: # only if signs are not opposite if (geodict.xmin > bounds['xmin'] or geodict.xmax < bounds['xmax'] or geodict.ymin > bounds['ymin'] or geodict.ymax < bounds['ymax']): print('Specified bounds are outside shakemap area, using ' 'ShakeMap bounds instead.') bounds = None if bounds is not None: tempgdict = GeoDict.createDictFromBox(bounds['xmin'], bounds['xmax'], bounds['ymin'], bounds['ymax'], geodict.dx, geodict.dy, inside=False) # If Shakemap geodict crosses 180/-180 line, fix geodict so things don't break if geodict.xmin > geodict.xmax: if tempgdict.xmin < 0: geodict._xmin -= 360. else: geodict._xmax += 360. geodict = geodict.getBoundsWithin(tempgdict) basegeodict, firstcol = GDALGrid.getFileGeoDict( os.path.join(slopefilepath, 'slope_min.bil')) if basegeodict == geodict: sampledict = geodict else: sampledict = basegeodict.getBoundsWithin(geodict) # Do we need to subdivide baselayer? if 'divfactor' in config['godt_2008'].keys(): divfactor = float(config['godt_2008']['divfactor']) if divfactor != 1.: # adjust sampledict so everything will be resampled (cut one cell # of each edge so will be inside bounds) newxmin = sampledict.xmin - sampledict.dx/2. + \ sampledict.dx/(2.*divfactor) + sampledict.dx newymin = sampledict.ymin - sampledict.dy/2. + \ sampledict.dy/(2.*divfactor) + sampledict.dy newxmax = sampledict.xmax + sampledict.dx/2. - \ sampledict.dx/(2.*divfactor) - sampledict.dx newymax = sampledict.ymax + sampledict.dy/2. - \ sampledict.dy/(2.*divfactor) - sampledict.dy newdx = sampledict.dx / divfactor newdy = sampledict.dy / divfactor sampledict = GeoDict.createDictFromBox(newxmin, newxmax, newymin, newymax, newdx, newdy, inside=True) tmpdir = tempfile.mkdtemp() # Load in ShakeMap and get new geodictionary temp = ShakeGrid.load(shakefile) # , adjust='res') junkfile = os.path.join(tmpdir, 'temp.bil') GDALGrid.copyFromGrid(temp.getLayer('pga')).save(junkfile) pga = quickcut(junkfile, sampledict, precise=True, method='bilinear') os.remove(junkfile) GDALGrid.copyFromGrid(temp.getLayer('pgv')).save(junkfile) pgv = quickcut(junkfile, sampledict, precise=True, method='bilinear') os.remove(junkfile) # Update geodictionary sampledict = pga.getGeoDict() t2 = temp.getEventDict() M = t2['magnitude'] event_id = t2['event_id'] shakedict = temp.getShakeDict() del (temp) # read in uncertainty if present if uncertfile is not None: try: temp = ShakeGrid.load(uncertfile) # , adjust='res') GDALGrid.copyFromGrid(temp.getLayer('stdpga')).save(junkfile) uncertpga = quickcut(junkfile, sampledict, precise=True, method='bilinear', override=True) os.remove(junkfile) GDALGrid.copyFromGrid(temp.getLayer('stdpgv')).save(junkfile) uncertpgv = quickcut(junkfile, sampledict, precise=True, method='bilinear', override=True) os.remove(junkfile) except: print('Could not read uncertainty file, ignoring uncertainties') uncertfile = None if numstd is None: numstd = 1. # Read in all the slope files, divide all by 100 to get to slope in # degrees (because input files are multiplied by 100.) slopes = [] quantiles = [ 'slope_min.bil', 'slope10.bil', 'slope30.bil', 'slope50.bil', 'slope70.bil', 'slope90.bil', 'slope_max.bil' ] for quant in quantiles: tmpslp = quickcut(os.path.join(slopefilepath, quant), sampledict) tgd = tmpslp.getGeoDict() if tgd != sampledict: raise Exception('Input layers are not aligned to same geodict') else: slopes.append(tmpslp.getData() / slopediv) slopestack = np.dstack(slopes) # Change any zero slopes to a very small number to avoid dividing by # zero later slopestack[slopestack == 0] = 1e-8 # Read in the cohesion and friction files and duplicate layers so they # are same shape as slope structure tempco = quickcut(cohesionfile, sampledict, method='near') tempco = tempco.getData()[:, :, np.newaxis] / codiv cohesion = np.repeat(tempco, 7, axis=2) cohesion[cohesion == -999.9] = nodata_cohesion cohesion = np.nan_to_num(cohesion) cohesion[cohesion == 0] = nodata_cohesion tempfric = quickcut(frictionfile, sampledict, method='near') tempfric = tempfric.getData().astype(float)[:, :, np.newaxis] friction = np.repeat(tempfric, 7, axis=2) friction[friction == -9999] = nodata_friction friction = np.nan_to_num(friction) friction[friction == 0] = nodata_friction # Do the calculations using Jibson (2007) PGA only model for Dn FS = (cohesion / (uwt * thick * np.sin(slopestack * (np.pi / 180.))) + np.tan(friction * (np.pi / 180.)) / np.tan(slopestack * (np.pi / 180.))) FS[FS < fsthresh] = fsthresh # Compute critical acceleration, in g # This gives ac in g, equations that multiply by g give ac in m/s2 Ac = (FS - 1) * np.sin(slopestack * (np.pi / 180.)).astype(float) Ac[Ac < acthresh] = acthresh # Get PGA in g (PGA is %g in ShakeMap, convert to g) PGA = np.repeat(pga.getData()[:, :, np.newaxis] / 100., 7, axis=2).astype(float) if 'PGV' in displmodel: # Load in PGV also, in cm/sec PGV = np.repeat(pgv.getData()[:, :, np.newaxis], 7, axis=2).astype(float) else: PGV = None if uncertfile is not None: stdpga = np.repeat(uncertpga.getData()[:, :, np.newaxis], 7, axis=2).astype(float) stdpgv = np.repeat(uncertpgv.getData()[:, :, np.newaxis], 7, axis=2).astype(float) # estimate PGA +- 1std PGAmin = np.exp(np.log(PGA * 100) - numstd * stdpga) / 100 PGAmax = np.exp(np.log(PGA * 100) + numstd * stdpga) / 100 if 'PGV' in displmodel: PGVmin = np.exp(np.log(PGV) - numstd * stdpgv) PGVmax = np.exp(np.log(PGV) + numstd * stdpgv) else: PGVmin = None PGVmax = None # Ignore errors so still runs when Ac > PGA, just leaves nan instead # of crashing. np.seterr(invalid='ignore') Dn, logDnstd, logtype = NMdisp(Ac, PGA, model=displmodel, M=M, PGV=PGV) if uncertfile is not None: Dnmin, logDnstdmin, logtype = NMdisp(Ac, PGAmin, model=displmodel, M=M, PGV=PGVmin) Dnmax, logDnstdmax, logtype = NMdisp(Ac, PGAmax, model=displmodel, M=M, PGV=PGVmax) PROB = Dn.copy() PROB[PROB < dnthresh] = 0. PROB[PROB >= dnthresh] = 1. PROB = np.sum(PROB, axis=2) if uncertfile is not None: PROBmin = Dnmin.copy() PROBmin[PROBmin <= dnthresh] = 0. PROBmin[PROBmin > dnthresh] = 1. PROBmin = np.sum(PROBmin, axis=2) PROBmax = Dnmax.copy() PROBmax[PROBmax <= dnthresh] = 0. PROBmax[PROBmax > dnthresh] = 1. PROBmax = np.sum(PROBmax, axis=2) PROB[PROB == 1.] = 0.01 PROB[PROB == 2.] = 0.10 PROB[PROB == 3.] = 0.30 PROB[PROB == 4.] = 0.50 PROB[PROB == 5.] = 0.70 PROB[PROB == 6.] = 0.90 PROB[PROB == 7.] = 0.99 if uncertfile is not None: PROBmin[PROBmin == 1.] = 0.01 PROBmin[PROBmin == 2.] = 0.10 PROBmin[PROBmin == 3.] = 0.30 PROBmin[PROBmin == 4.] = 0.50 PROBmin[PROBmin == 5.] = 0.70 PROBmin[PROBmin == 6.] = 0.90 PROBmin[PROBmin == 7.] = 0.99 PROBmax[PROBmax == 1.] = 0.01 PROBmax[PROBmax == 2.] = 0.10 PROBmax[PROBmax == 3.] = 0.30 PROBmax[PROBmax == 4.] = 0.50 PROBmax[PROBmax == 5.] = 0.70 PROBmax[PROBmax == 6.] = 0.90 PROBmax[PROBmax == 7.] = 0.99 if slopemin is not None: PROB[slopestack[:, :, 6] <= slopemin] = 0. # uncert too if uncertfile is not None: PROBmin[slopestack[:, :, 6] <= slopemin] = 0. PROBmax[slopestack[:, :, 6] <= slopemin] = 0. # Turn output and inputs into into grids and put in mapLayers dictionary maplayers = collections.OrderedDict() shakedetail = '%s_ver%s' % (shakedict['shakemap_id'], shakedict['shakemap_version']) description = { 'name': modelsref, 'longref': modellref, 'units': 'Proportion of Area Affected', 'shakemap': shakedetail, 'event_id': event_id, 'parameters': { 'displmodel': displmodel, 'thickness_m': thick, 'unitwt_kNm3': uwt, 'dnthresh_cm': dnthresh, 'acthresh_g': acthresh, 'fsthresh': fsthresh, 'modeltype': 'Landslide' } } PROBgrid = GDALGrid(PROB, sampledict) if trimfile is not None: PROBgrid = trim_ocean(PROBgrid, trimfile) maplayers['model'] = { 'grid': PROBgrid, 'label': 'Landslide - Proportion of Area Affected', 'type': 'output', 'description': description } if uncertfile is not None: PROBmingrid = GDALGrid(PROBmin, sampledict) PROBmaxgrid = GDALGrid(PROBmax, sampledict) if trimfile is not None: PROBmingrid = trim_ocean(PROBmingrid, trimfile) PROBmaxgrid = trim_ocean(PROBmaxgrid, trimfile) maplayers['modelmin'] = { 'grid': PROBmingrid, 'label': 'Landslide Probability-%1.2fstd' % numstd, 'type': 'output', 'description': description } maplayers['modelmax'] = { 'grid': PROBmaxgrid, 'label': 'Landslide Probability+%1.2fstd' % numstd, 'type': 'output', 'description': description } if saveinputs is True: maplayers['pga'] = { 'grid': GDALGrid(PGA[:, :, 0], sampledict), 'label': 'PGA (g)', 'type': 'input', 'description': { 'units': 'g', 'shakemap': shakedetail } } if 'PGV' in displmodel: maplayers['pgv'] = { 'grid': GDALGrid(PGV[:, :, 0], sampledict), 'label': 'PGV (cm/s)', 'type': 'input', 'description': { 'units': 'cm/s', 'shakemap': shakedetail } } maplayers['minFS'] = { 'grid': GDALGrid(np.min(FS, axis=2), sampledict), 'label': 'Min Factor of Safety', 'type': 'input', 'description': { 'units': 'unitless' } } maplayers['max slope'] = { 'grid': GDALGrid(slopestack[:, :, -1], sampledict), 'label': r'Maximum slope ($^\circ$)', 'type': 'input', 'description': { 'units': 'degrees', 'name': slopesref, 'longref': slopelref } } maplayers['cohesion'] = { 'grid': GDALGrid(cohesion[:, :, 0], sampledict), 'label': 'Cohesion (kPa)', 'type': 'input', 'description': { 'units': 'kPa (adjusted)', 'name': cohesionsref, 'longref': cohesionlref } } maplayers['friction angle'] = { 'grid': GDALGrid(friction[:, :, 0], sampledict), 'label': r'Friction angle ($^\circ$)', 'type': 'input', 'description': { 'units': 'degrees', 'name': frictionsref, 'longref': frictionlref } } if uncertfile is not None: maplayers['pgamin'] = { 'grid': GDALGrid(PGAmin[:, :, 0], sampledict), 'label': 'PGA - %1.2fstd (g)' % numstd, 'type': 'input', 'description': { 'units': 'g', 'shakemap': shakedetail } } maplayers['pgamax'] = { 'grid': GDALGrid(PGAmax[:, :, 0], sampledict), 'label': 'PGA + %1.2fstd (g)' % numstd, 'type': 'input', 'description': { 'units': 'g', 'shakemap': shakedetail } } if 'PGV' in displmodel: if uncertfile is not None: maplayers['pgvmin'] = { 'grid': GDALGrid(PGVmin[:, :, 0], sampledict), 'label': 'PGV - %1.2fstd (cm/s)' % numstd, 'type': 'input', 'description': { 'units': 'cm/s', 'shakemap': shakedetail } } maplayers['pgvmax'] = { 'grid': GDALGrid(PGVmax[:, :, 0], sampledict), 'label': 'PGV + %1.2fstd (cm/s)' % numstd, 'type': 'input', 'description': { 'units': 'cm/s', 'shakemap': shakedetail } } shutil.rmtree(tmpdir) return maplayers
try: fdict = GDALGrid.getFileGeoDict(gridfile) gridtype = 'esri' except: pass if gridtype is None: raise Exception('File "%s" does not appear to be either a GMT grid or an ESRI grid.' % gridfile) xmin = xmin - fdict.dx*3 xmax = xmax + fdict.dx*3 ymin = ymin - fdict.dy*3 ymax = ymax + fdict.dy*3 bounds = (xmin,xmax,ymin,ymax) if gridtype == 'gmt': fgeodict = GMTGrid.getFileGeoDict(gridfile) else: fgeodict = GDALGrid.getFileGeoDict(gridfile) dx,dy = (fgeodict.dx,fgeodict.dy) sdict = GeoDict.createDictFromBox(xmin,xmax,ymin,ymax,dx,dy) if gridtype == 'gmt': grid = GMTGrid.load(gridfile,samplegeodict=sdict,resample=False,method=method,doPadding=True) else: grid = GDALGrid.load(gridfile,samplegeodict=sdict,resample=False,method=method,doPadding=True) return sampleFromGrid(grid,xypoints) def sampleFromGrid(grid,xypoints,method='nearest'): """ Sample 2D grid object at each of a set of XY (decimal degrees) points. :param grid: Grid2D object at which to sample data. :param xypoints:
def __init__(self, config, shakefile, model, uncertfile=None): """Set up the logistic model :param config: configobj (config .ini file read in using configobj) defining the model and its inputs :type config: dictionary :param shakefile: Full file path to shakemap.xml file for the event of interest :type shakefile: string :param model: Name of model defined in config that should be run for the event of interest :type model: string :param uncertfile: :type uncertfile: """ if model not in getLogisticModelNames(config): raise Exception('Could not find a model called "%s" in config %s.' % (model, config)) #do everything here short of calculations - parse config, assemble eqn strings, load data. self.model = model cmodel = config['logistic_models'][model] self.modeltype = cmodel['gfetype'] self.coeffs = validateCoefficients(cmodel) self.layers = validateLayers(cmodel) # key = layer name, value = file name self.terms, timeField = validateTerms(cmodel, self.coeffs, self.layers) self.interpolations = validateInterpolations(cmodel, self.layers) self.units = validateUnits(cmodel, self.layers) self.gmused = [value for term, value in cmodel['terms'].items() if 'pga' in value.lower() or 'pgv' in value.lower() or 'mmi' in value.lower()] self.modelrefs, self.longrefs, self.shortrefs = validateRefs(cmodel) if 'baselayer' not in cmodel: raise Exception('You must specify a base layer file in config.') if cmodel['baselayer'] not in list(self.layers.keys()): raise Exception('You must specify a base layer corresponding to one of the files in the layer section.') #get the geodict for the shakemap geodict = ShakeGrid.getFileGeoDict(shakefile, adjust='res') griddict, eventdict, specdict, fields, uncertainties = getHeaderData(shakefile) #YEAR = eventdict['event_timestamp'].year MONTH = MONTHS[(eventdict['event_timestamp'].month)-1] #DAY = eventdict['event_timestamp'].day #HOUR = eventdict['event_timestamp'].hour #now find the layer that is our base layer and get the largest bounds we can guarantee not to exceed shakemap bounds basefile = self.layers[cmodel['baselayer']] ftype = getFileType(basefile) if ftype == 'esri': basegeodict, firstcol = GDALGrid.getFileGeoDict(basefile) sampledict = basegeodict.getBoundsWithin(geodict) elif ftype == 'gmt': basegeodict, firstcol = GMTGrid.getFileGeoDict(basefile) sampledict = basegeodict.getBoundsWithin(geodict) else: raise Exception('All predictor variable grids must be a valid GMT or ESRI file type') #now load the shakemap, resampling and padding if necessary self.shakemap = ShakeGrid.load(shakefile, samplegeodict=sampledict, resample=True, doPadding=True, adjust='res') # take uncertainties into account if uncertfile is not None: try: self.uncert = ShakeGrid.load(uncertfile, samplegeodict=sampledict, resample=True, doPadding=True, adjust='res') except: print('Could not read uncertainty file, ignoring uncertainties') self.uncert = None else: self.uncert = None #load the predictor layers into a dictionary self.layerdict = {} # key = layer name, value = grid object for layername, layerfile in self.layers.items(): if isinstance(layerfile, list): for lfile in layerfile: if timeField == 'MONTH': if lfile.find(MONTH) > -1: layerfile = lfile ftype = getFileType(layerfile) interp = self.interpolations[layername] if ftype == 'gmt': lyr = GMTGrid.load(layerfile, sampledict, resample=True, method=interp, doPadding=True) elif ftype == 'esri': lyr = GDALGrid.load(layerfile, sampledict, resample=True, method=interp, doPadding=True) else: msg = 'Layer %s (file %s) does not appear to be a valid GMT or ESRI file.' % (layername, layerfile) raise Exception(msg) self.layerdict[layername] = lyr else: #first, figure out what kind of file we have (or is it a directory?) ftype = getFileType(layerfile) interp = self.interpolations[layername] if ftype == 'gmt': lyr = GMTGrid.load(layerfile, sampledict, resample=True, method=interp, doPadding=True) elif ftype == 'esri': lyr = GDALGrid.load(layerfile, sampledict, resample=True, method=interp, doPadding=True) else: msg = 'Layer %s (file %s) does not appear to be a valid GMT or ESRI file.' % (layername, layerfile) raise Exception(msg) self.layerdict[layername] = lyr shapes = {} for layername, layer in self.layerdict.items(): shapes[layername] = layer.getData().shape self.nuggets = [str(self.coeffs['b0'])] ckeys = list(self.terms.keys()) ckeys.sort() for key in ckeys: term = self.terms[key] coeff = self.coeffs[key] self.nuggets.append('(%g * %s)' % (coeff, term)) self.equation = ' + '.join(self.nuggets) if self.uncert is not None: self.nugmin = copy.copy(self.nuggets) self.nugmax = copy.copy(self.nuggets) # Find the term with the shakemap input and replace for these nuggets for k, nug in enumerate(self.nuggets): if "self.shakemap.getLayer('pga').getData()" in nug: self.nugmin[k] = self.nugmin[k].replace("self.shakemap.getLayer('pga').getData()", "(np.exp(np.log(self.shakemap.getLayer('pga').getData()) - self.uncert.getLayer('stdpga').getData()))") self.nugmax[k] = self.nugmax[k].replace("self.shakemap.getLayer('pga').getData()", "(np.exp(np.log(self.shakemap.getLayer('pga').getData()) + self.uncert.getLayer('stdpga').getData()))") elif "self.layerdict['pgv'].getData()" in nug: self.nugmin[k] = self.nugmin[k].replace("self.shakemap.getLayer('pgv').getData()", "(np.exp(np.log(self.shakemap.getLayer('pgv').getData()) - self.uncert.getLayer('stdpgv').getData()))") self.nugmax[k] = self.nugmax[k].replace("self.shakemap.getLayer('pgv').getData()", "(np.exp(np.log(self.shakemap.getLayer('pgv').getData()) + self.uncert.getLayer('stdpgv').getData()))") elif "self.layerdict['mmi'].getData()" in nug: self.nugmin[k] = self.nugmin[k].replace("self.shakemap.getLayer('mmi').getData()", "(np.exp(np.log(self.shakemap.getLayer('mmi').getData()) - self.uncert.getLayer('stdmmi').getData()))") self.nugmax[k] = self.nugmax[k].replace("self.shakemap.getLayer('mmi').getData()", "(np.exp(np.log(self.shakemap.getLayer('mmi').getData()) + self.uncert.getLayer('stdmmi').getData()))") self.equationmin = ' + '.join(self.nugmin) self.equationmax = ' + '.join(self.nugmax) else: self.equationmin = None self.equationmax = None self.geodict = self.shakemap.getGeoDict() try: self.slopemin = float(config['logistic_models'][model]['slopemin']) self.slopemax = float(config['logistic_models'][model]['slopemax']) except: print('could not find slopemin and/or slopemax in config, no limits will be applied') self.slopemin = 0. self.slopemax = 90.
def __init__(self,config,shakefile,model): if model not in getLogisticModelNames(config): raise Exception('Could not find a model called "%s" in config %s.' % (model,config)) #do everything here short of calculations - parse config, assemble eqn strings, load data. self.model = model cmodel = config['logistic_models'][model] self.coeffs = validateCoefficients(cmodel) self.layers = validateLayers(cmodel)#key = layer name, value = file name self.terms,timeField = validateTerms(cmodel,self.coeffs,self.layers) self.interpolations = validateInterpolations(cmodel,self.layers) self.units = validateUnits(cmodel,self.layers) if 'baselayer' not in cmodel: raise Exception('You must specify a base layer file in config.') if cmodel['baselayer'] not in list(self.layers.keys()): raise Exception('You must specify a base layer corresponding to one of the files in the layer section.') #get the geodict for the shakemap geodict = ShakeGrid.getFileGeoDict(shakefile,adjust='res') griddict,eventdict,specdict,fields,uncertainties = getHeaderData(shakefile) YEAR = eventdict['event_timestamp'].year MONTH = MONTHS[(eventdict['event_timestamp'].month)-1] DAY = eventdict['event_timestamp'].day HOUR = eventdict['event_timestamp'].hour #now find the layer that is our base layer and get the largest bounds we can guaranteed not to exceed shakemap bounds basefile = self.layers[cmodel['baselayer']] ftype = getFileType(basefile) if ftype == 'esri': basegeodict = GDALGrid.getFileGeoDict(basefile) sampledict = basegeodict.getBoundsWithin(geodict) elif ftype == 'gmt': basegeodict = GMTGrid.getFileGeoDict(basefile) sampledict = basegeodict.getBoundsWithin(geodict) else: raise Exception('All predictor variable grids must be a valid GMT or ESRI file type') #now load the shakemap, resampling and padding if necessary self.shakemap = ShakeGrid.load(shakefile,samplegeodict=sampledict,resample=True,doPadding=True,adjust='res') #load the predictor layers into a dictionary self.layerdict = {} #key = layer name, value = grid object for layername,layerfile in self.layers.items(): if isinstance(layerfile,list): for lfile in layerfile: if timeField == 'MONTH': if lfile.find(MONTH) > -1: layerfile = lfile ftype = getFileType(layerfile) interp = self.interpolations[layername] if ftype == 'gmt': lyr = GMTGrid.load(layerfile,sampledict,resample=True,method=interp,doPadding=True) elif ftype == 'esri': lyr = GDALGrid.load(layerfile,sampledict,resample=True,method=interp,doPadding=True) else: msg = 'Layer %s (file %s) does not appear to be a valid GMT or ESRI file.' % (layername,layerfile) raise Exception(msg) self.layerdict[layername] = lyr else: #first, figure out what kind of file we have (or is it a directory?) ftype = getFileType(layerfile) interp = self.interpolations[layername] if ftype == 'gmt': lyr = GMTGrid.load(layerfile,sampledict,resample=True,method=interp,doPadding=True) elif ftype == 'esri': lyr = GDALGrid.load(layerfile,sampledict,resample=True,method=interp,doPadding=True) else: msg = 'Layer %s (file %s) does not appear to be a valid GMT or ESRI file.' % (layername,layerfile) raise Exception(msg) self.layerdict[layername] = lyr shapes = {} for layername,layer in self.layerdict.items(): shapes[layername] = layer.getData().shape x = 1 self.nuggets = [str(self.coeffs['b0'])] ckeys = list(self.terms.keys()) ckeys.sort() for key in ckeys: term = self.terms[key] coeff = self.coeffs[key] self.nuggets.append('(%g * %s)' % (coeff, term)) self.equation = ' + '.join(self.nuggets) self.geodict = self.shakemap.getGeoDict()
def classic(shakefile, config, uncertfile=None, saveinputs=False, regressionmodel='J_PGA', probtype='jibson2000', slopediv=1., codiv=1., bounds=None): """This function uses the Newmark method to estimate probability of failure at each grid cell. Factor of Safety and critcal accelerations are calculated following Jibson et al. (2000) and the Newmark displacement is estimated using PGA, PGV, and/or Magnitude (depending on equation used) from Shakemap with regression equations from Jibson (2007), Rathje and Saygili (2008) and Saygili and Rathje (2009) :param shakefile: URL or complete file path to the location of the Shakemap to use as input :type shakefile: string: :param config: Model configuration file object containing locations of input files and other input values config = ConfigObj(configfilepath) :type config: ConfigObj :param uncertfile: complete file path to the location of the uncertainty.xml for the shakefile, if this is not None, it will compute the model for +-std in addition to the best estimate :param saveinputs: Whether or not to return the model input layers, False (defeault) returns only the model output (one layer) :type saveinputs: boolean :param regressionmodel: Newmark displacement regression model to use 'J_PGA' (default) - PGA-based model from Jibson (2007) - equation 6 'J_PGA_M' - PGA and M-based model from Jibson (2007) - equation 7 'RS_PGA_M' - PGA and M-based model from from Rathje and Saygili (2009) 'RS_PGA_PGV' - PGA and PGV-based model from Saygili and Rathje (2008) - equation 6 :type regressionmodel: string :param probtype: Method used to estimate probability. Entering 'jibson2000' uses equation 5 from Jibson et al. (2000) to estimate probability from Newmark displacement. 'threshold' uses a specified threshold of Newmark displacement (defined in config file) and assumes anything greather than this threshold fails :type probtype: string :param slopediv: Divide slope by this number to get slope in degrees (Verdin datasets need to be divided by 100) :type slopediv: float :param codiv: Divide cohesion by this number to get reasonable numbers (For Godt method, need to divide by 10 because that is how it was calibrated, but values are reasonable without multiplying for regular analysis) :type codiv: float :returns maplayers: Dictionary containing output and input layers (if saveinputs=True) along with metadata formatted like maplayers['layer name']={'grid': mapio grid2D object, 'label': 'label for colorbar and top line of subtitle', 'type': 'output or input to model', 'description': 'detailed description of layer for subtitle, potentially including source information'} :type maplayers: OrderedDict :raises NameError: when unable to parse the config correctly (probably a formatting issue in the configfile) or when unable to find the shakefile (Shakemap URL or filepath) - these cause program to end :raises NameError: when probtype does not match a predifined probability type, will cause to default to 'jibson2000' """ # Empty refs slopesref = 'unknown' slopelref = 'unknown' cohesionlref = 'unknown' cohesionsref = 'unknown' frictionsref = 'unknown' frictionlref = 'unknown' modellref = 'unknown' modelsref = 'unknown' # Parse config - should make it so it uses defaults if any are missing... try: slopefile = config['mechanistic_models']['classic_newmark']['layers']['slope']['file'] slopeunits = config['mechanistic_models']['classic_newmark']['layers']['slope']['units'] cohesionfile = config['mechanistic_models']['classic_newmark']['layers']['cohesion']['file'] cohesionunits = config['mechanistic_models']['classic_newmark']['layers']['cohesion']['units'] frictionfile = config['mechanistic_models']['classic_newmark']['layers']['friction']['file'] frictionunits = config['mechanistic_models']['classic_newmark']['layers']['friction']['units'] thick = float(config['mechanistic_models']['classic_newmark']['parameters']['thick']) uwt = float(config['mechanistic_models']['classic_newmark']['parameters']['uwt']) nodata_cohesion = float(config['mechanistic_models']['classic_newmark']['parameters']['nodata_cohesion']) nodata_friction = float(config['mechanistic_models']['classic_newmark']['parameters']['nodata_friction']) try: dnthresh = float(config['mechanistic_models']['classic_newmark']['parameters']['dnthresh']) except: if probtype == 'threshold': dnthresh = 5. print('Unable to find dnthresh in config, using 5cm') else: dnthresh = None fsthresh = float(config['mechanistic_models']['classic_newmark']['parameters']['fsthresh']) acthresh = float(config['mechanistic_models']['classic_newmark']['parameters']['acthresh']) slopethresh = float(config['mechanistic_models']['classic_newmark']['parameters']['slopethresh']) try: m = float(config['mechanistic_models']['classic_newmark']['parameters']['m']) except: print('no constant saturated thickness specified, m=0 if no watertable file is found') m = 0. except Exception as e: raise NameError('Could not parse configfile, %s' % e) return try: # Try to fetch source information from config modelsref = config['mechanistic_models']['classic_newmark']['shortref'] modellref = config['mechanistic_models']['classic_newmark']['longref'] slopesref = config['mechanistic_models']['classic_newmark']['layers']['slope']['shortref'] slopelref = config['mechanistic_models']['classic_newmark']['layers']['slope']['longref'] cohesionsref = config['mechanistic_models']['classic_newmark']['layers']['cohesion']['shortref'] cohesionlref = config['mechanistic_models']['classic_newmark']['layers']['cohesion']['longref'] frictionsref = config['mechanistic_models']['classic_newmark']['layers']['friction']['shortref'] frictionlref = config['mechanistic_models']['classic_newmark']['layers']['friction']['longref'] except: print('Was not able to retrieve all references from config file. Continuing') # Cut and resample all files shkgdict = ShakeGrid.getFileGeoDict(shakefile, adjust='res') slpdict = GDALGrid.getFileGeoDict(slopefile) if bounds is not None: # Make sure bounds are within ShakeMap Grid if shkgdict.xmin > bounds['xmin'] or shkgdict.xmax < bounds['xmax'] or shkgdict.ymin > bounds['ymin'] or shkgdict.ymax < bounds['ymax']: print('Specified bounds are outside shakemap area, using ShakeMap bounds instead') bounds = None if bounds is not None: tempgdict = GeoDict({'xmin': bounds['xmin'], 'ymin': bounds['ymin'], 'xmax': bounds['xmax'], 'ymax': bounds['ymax'], 'dx': 100., 'dy': 100., 'nx': 100., 'ny': 100.}, adjust='res') gdict = slpdict.getBoundsWithin(tempgdict) else: # Get boundaries from shakemap if not specified shkgdict = ShakeGrid.getFileGeoDict(shakefile, adjust='res') slpdict = GDALGrid.getFileGeoDict(slopefile) gdict = slpdict.getBoundsWithin(shkgdict) # Load in slope file slopegrid = GDALGrid.load(slopefile, samplegeodict=gdict, resample=False) gdict = slopegrid.getGeoDict() # Get this again just in case it changed slope = slopegrid.getData().astype(float)/slopediv # Adjust slope to degrees, if needed # Change any zero slopes to a very small number to avoid dividing by zero later slope[slope == 0] = 1e-8 # Load in shakefile if not os.path.isfile(shakefile): if isURL(shakefile): shakefile = getGridURL(shakefile) # returns a file object else: raise NameError('Could not find "%s" as a file or a valid url' % (shakefile)) return # Load in shakemap, resample to slope file (this will be important when go to higher res) shakemap = ShakeGrid.load(shakefile, samplegeodict=gdict, resample=True, method='linear', adjust='res') M = shakemap.getEventDict()['magnitude'] # Read in uncertainty layer, if present if uncertfile is not None: try: uncert = ShakeGrid.load(uncertfile, samplegeodict=gdict, resample=True, method='linear', adjust='res') except: print('Could not read uncertainty file, ignoring uncertainties') uncertfile = None # Read in the cohesion and friction files, resampled to slope grid cohesion = GDALGrid.load(cohesionfile, samplegeodict=gdict, resample=True, method='nearest').getData().astype(float)/codiv cohesion[np.isnan(cohesion)] = nodata_cohesion friction = GDALGrid.load(frictionfile, samplegeodict=gdict, resample=True, method='nearest').getData().astype(float) friction[np.isnan(friction)] = nodata_friction # See if there is a water table depth file and read it in if there is try: waterfile = config['mechanistic_models']['classic_newmark']['layers']['watertable']['file'] watertable = GDALGrid.load(waterfile, samplegeodict=gdict, resample=True, method='linear').getData() # Needs to be in meters! uwtw = float(config['mechanistic_models']['classic_newmark']['parameters']['uwtw']) try: watersref = config['mechanistic_models']['classic_newmark']['layers']['watertable']['shortref'] waterlref = config['mechanistic_models']['classic_newmark']['layers']['watertable']['longref'] except: print('Was not able to retrieve water table references from config file. Continuing') except: print(('Water table file not specified or readable, assuming constant saturated thickness proportion of %0.1f' % m)) watertable = None try: uwtw = float(config['mechanistic_models']['classic_newmark']['parameters']['uwtw']) except: print('Could not read soil wet unit weight, using 18.8 kN/m3') uwtw = 18.8 # Factor of safety if watertable is not None: watertable[watertable > thick] = thick m = (thick - watertable)/thick FS = cohesion/(uwt*thick*np.sin(slope*(np.pi/180.))) + np.tan(friction*(np.pi/180.))/np.tan(slope*(np.pi/180.)) - (m*uwtw*np.tan(friction*(np.pi/180.)))/(uwt*np.tan(slope*(np.pi/180.))) FS[FS < fsthresh] = fsthresh # Compute critical acceleration, in g Ac = (FS-1.)*np.sin(slope*(np.pi/180.)) # This gives ac in g, equations that multiply by g give ac in m/s2 Ac[Ac < acthresh] = acthresh Ac[slope < slopethresh] = float('nan') # Get PGA in g (PGA is %g in ShakeMap, convert to g) PGA = shakemap.getLayer('pga').getData().astype(float)/100. PGV = shakemap.getLayer('pgv').getData().astype(float) if uncertfile is not None: stdpga = uncert.getLayer('stdpga') stdpgv = uncert.getLayer('stdpgv') # Estimate PGA +- 1std PGAmin = np.exp(np.log(PGA*100.) - stdpga.getData())/100. PGAmax = np.exp(np.log(PGA*100.) + stdpga.getData())/100. PGVmin = np.exp(np.log(PGV) - stdpgv.getData()) PGVmax = np.exp(np.log(PGV) + stdpgv.getData()) np.seterr(invalid='ignore') # Ignore errors so still runs when Ac > PGA, just leaves nan instead of crashing if regressionmodel is 'J_PGA': Dn = J_PGA(Ac, PGA) if uncertfile is not None: Dnmin = J_PGA(Ac, PGAmin) Dnmax = J_PGA(Ac, PGAmax) elif regressionmodel is 'J_PGA_M': Dn = J_PGA_M(Ac, PGA, M) if uncertfile is not None: Dnmin = J_PGA_M(Ac, PGAmin, M) Dnmax = J_PGA_M(Ac, PGAmax, M) elif regressionmodel is 'RS_PGA_M': Dn = RS_PGA_M(Ac, PGA, M) if uncertfile is not None: Dnmin = RS_PGA_M(Ac, PGAmin, M) Dnmax = RS_PGA_M(Ac, PGAmax, M) elif regressionmodel is 'RS_PGA_PGV': Dn = RS_PGA_PGV(Ac, PGA, PGV) if uncertfile is not None: Dnmin = RS_PGA_PGV(Ac, PGAmin, PGVmin) Dnmax = RS_PGA_PGV(Ac, PGAmax, PGVmax) else: print('Unrecognized regression model, aborting') return units = 'probability' label = 'Landslide Probability' if probtype.lower() in 'jibson2000': PROB = 0.335*(1-np.exp(-0.048*Dn**1.565)) dnthresh = None if uncertfile is not None: PROBmin = 0.335*(1-np.exp(-0.048*Dnmin**1.565)) PROBmax = 0.335*(1-np.exp(-0.048*Dnmax**1.565)) elif probtype.lower() in 'threshold': PROB = Dn.copy() PROB[PROB <= dnthresh] = 0 PROB[PROB > dnthresh] = 1 units = 'prediction' label = 'Predicted Landslides' if uncertfile is not None: PROBmin = Dnmin.copy() PROBmin[PROBmin <= dnthresh] = 0 PROBmin[PROBmin > dnthresh] = 1 PROBmax = Dnmax.copy() PROBmax[PROBmax <= dnthresh] = 0 PROBmax[PROBmax > dnthresh] = 1 else: raise NameError('invalid probtype, assuming jibson2000') PROB = 0.335*(1-np.exp(-0.048*Dn**1.565)) dnthresh = None if uncertfile is not None: PROBmin = 0.335*(1-np.exp(-0.048*Dnmin**1.565)) PROBmax = 0.335*(1-np.exp(-0.048*Dnmax**1.565)) # Turn output and inputs into into grids and put in mapLayers dictionary maplayers = collections.OrderedDict() temp = shakemap.getShakeDict() shakedetail = '%s_ver%s' % (temp['shakemap_id'], temp['shakemap_version']) if watertable is not None: des = 'variable' else: des = m description = {'name': modelsref, 'longref': modellref, 'units': units, 'shakemap': shakedetail, 'parameters': {'regressionmodel': regressionmodel, 'thickness_m': thick, 'unitwt_kNm3': uwt, 'dnthresh_cm': dnthresh, 'acthresh_g': acthresh, 'fsthresh': fsthresh, 'slopethresh': slopethresh, 'sat_proportion': des}} maplayers['model'] = {'grid': GDALGrid(PROB, gdict), 'label': label, 'type': 'output', 'description': description} if uncertfile is not None: maplayers['modelmin'] = {'grid': GDALGrid(PROBmin, gdict), 'label': label+' -1std', 'type': 'output', 'description': description} maplayers['modelmax'] = {'grid': GDALGrid(PROBmax, gdict), 'label': label+' +1std', 'type': 'output', 'description': description} if saveinputs is True: maplayers['pga'] = {'grid': GDALGrid(PGA, gdict), 'label': 'PGA (g)', 'type': 'input', 'description': {'units': 'g', 'shakemap': shakedetail}} maplayers['FS'] = {'grid': GDALGrid(FS, gdict), 'label': 'Factor of Safety', 'type': 'input', 'description': {'units': 'unitless'}} maplayers['Ac'] = {'grid': GDALGrid(Ac, gdict), 'label': 'Critical acceleration (g)', 'type': 'input'} maplayers['Dn'] = {'grid': GDALGrid(Dn, gdict), 'label': 'Newmark Displacement (cm)', 'type': 'input'} maplayers['slope'] = {'grid': GDALGrid(slope, gdict), 'label': 'Max slope ($^\circ$)', 'type': 'input', 'description': {'units': 'degrees', 'name': slopesref, 'longref': slopelref}} maplayers['cohesion'] = {'grid': GDALGrid(cohesion, gdict), 'label': 'Cohesion (kPa)', 'type': 'input', 'description': {'units': 'kPa (adjusted)', 'name': cohesionsref, 'longref': cohesionlref}} maplayers['friction angle'] = {'grid': GDALGrid(friction, gdict), 'label': 'Friction angle ($^\circ$)', 'type': 'input', 'description': {'units': 'degrees', 'name': frictionsref, 'longref': frictionlref}} if uncertfile is not None: maplayers['pgamin'] = {'grid': GDALGrid(PGAmin, gdict), 'label': 'PGA - 1std (g)', 'type': 'input', 'description': {'units': 'g', 'shakemap': shakedetail}} maplayers['pgamax'] = {'grid': GDALGrid(PGAmax, gdict), 'label': 'PGA + 1std (g)', 'type': 'input', 'description': {'units': 'g', 'shakemap': shakedetail}} if 'PGV' in regressionmodel: maplayers['pgv'] = {'grid': GDALGrid(PGV, gdict), 'label': 'PGV (cm/s)', 'type': 'input', 'description': {'units': 'cm/s', 'shakemap': shakedetail}} if uncertfile is not None: maplayers['pgvmin'] = {'grid': GDALGrid(PGVmin, gdict), 'label': 'PGV - 1std (cm/s)', 'type': 'input', 'description': {'units': 'cm/s', 'shakemap': shakedetail}} maplayers['pgvmax'] = {'grid': GDALGrid(PGVmax, gdict), 'label': 'PGV + 1std (cm/s)', 'type': 'input', 'description': {'units': 'cm/s', 'shakemap': shakedetail}} if watertable is not None: maplayers['sat thick prop'] = {'grid': GDALGrid(m, gdict), 'label': 'Saturated thickness proprtion [0,1]', 'type': 'input', 'description': {'units': 'meters', 'name': watersref, 'longref': waterlref}} return maplayers
def computePexp(grid, pop_file, shakefile=None, shakethreshtype='pga', shakethresh=0., probthresh=0., stdgrid2D=None, stdtype='full', maxP=1., sill1=None, range1=None): """ Get exposure-based statistics. Args: grid: Model grid. pop_file (str): Path to the landscan population grid. shakefile (str): Optional, path to shakemap file to use for ground motion threshold. shakethreshtype(str): Optional, Type of ground motion to use for shakethresh, 'pga', 'pgv', or 'mmi'. shakethresh: Float or list of shaking thresholds in %g for pga, cm/s for pgv, float for mmi. probthresh: Float, exclude any cells with probabilities less than or equal to this value stdgrid2D: grid2D object of model standard deviations (optional) stdtype (str): assumption of spatial correlation used to compute the stdev of the statistics, 'max', 'min', 'mean' of max and min, or 'full' (default) which estimates the range of correlation and accounts for covariance. Will return 'mean' if ridge and sill cannot be estimated. maxP (float): the maximum possible probability of the model sill1 (float): If known, the sill of the variogram of grid2D, will be estimated if None and stdtype='full' range1 (float): If known, the range of the variogram of grid2D, will be estimated if None and stdtype='full' Returns: dict: Dictionary with keys named exp_pop_# where # is the shakethresh and exp_std_# if stdgrid2D is supplied (stdev of exp_pop) and elim_#, the maximum exposure value possible with the applied thresholds and given maxP value p_exp_# beta distribution shape factor p (sometimes called alpha) q_exp_# beta distribution shape factor q (sometimes called beta) """ model = grid.getData().copy() mdict = grid.getGeoDict() # Figure out difference in resolution of popfile to shakefile ptemp, J = GDALGrid.getFileGeoDict(pop_file) factor = ptemp.dx/mdict.dx # Cut out area from population file popcut1 = quickcut(pop_file, mdict, precise=False, extrasamp=2., method='nearest') #tot1 = np.sum(popcut1.getData()) # Adjust for factor to prepare for upsampling to avoid creating new people popcut1.setData(popcut1.getData()/factor**2) # Upsample to mdict popcut = popcut1.interpolate2(mdict, method='nearest') popdat = popcut.getData() exp_pop = {} if shakefile is not None: if shakethresh < 0.: raise Exception('shaking threshold must be equal or greater ' 'than zero') # resample shakemap to grid2D temp = ShakeGrid.load(shakefile) shk = temp.getLayer(shakethreshtype) shk = shk.interpolate2(mdict) if shk.getGeoDict() != mdict: raise Exception('shakemap was not resampled to exactly the same ' 'geodict as the model') shkdat = shk.getData() model[shkdat < shakethresh] = float('nan') else: shakethresh = 0. shkdat = None mu = np.nansum(model[model >= probthresh] * popdat[model >= probthresh]) exp_pop['exp_pop_%1.2fg' % (shakethresh/100.,)] = mu #N = np.nansum([model >= probthresh]) #exp_pop['N_%1.2fg' % (shakethresh/100.,)] = N elim = np.nansum(popdat[model >= probthresh])*maxP exp_pop['elim_%1.2fg' % (shakethresh/100.,)] = elim if stdgrid2D is not None: std = stdgrid2D.getData().copy() if np.nanmax(std) > 0. and np.nanmax(model) >= probthresh: totalmin = np.sqrt(np.nansum((popdat[model >= probthresh]*std[model >= probthresh])**2.)) totalmax = np.nansum(std[model >= probthresh] * popdat[model >= probthresh]) if stdtype=='full': if sill1 is None or range1 is None: modelfresh = grid.getData().copy() range1, sill1 = semivario(modelfresh, probthresh, shakethresh=shakethresh, shakegrid=shkdat) if range1 is None: # Use mean exp_pop['exp_std_%1.2fg' % (shakethresh/100.,)] = (totalmax+totalmin)/2. else: # Zero out std at cells where the model probability was below # the threshold because we aren't including those cells in Hagg stdz = std.copy() stdz[model < probthresh] = 0. svar1 = svar(stdz, range1, sill1, scale=popdat) exp_pop['exp_std_%1.2fg' % (shakethresh/100.,)] = np.sqrt(svar1) #exp_pop['exp_range_%1.2fg' % (shakethresh/100.,)] = range1 #exp_pop['exp_sill_%1.2fg' % (shakethresh/100.,)] = sill1 elif stdtype == 'max': exp_pop['exp_std_%1.2fg' % (shakethresh/100.,)] = totalmax elif stdtype == 'min': exp_pop['exp_std_%1.2fg' % (shakethresh/100.,)] = totalmin else: exp_pop['exp_std_%1.2fg' % (shakethresh/100.,)] = (totalmax+totalmin)/2. # Beta distribution shape factors var = exp_pop['exp_std_%1.2fg' % (shakethresh/100.,)]**2. exp_pop['p_exp_%1.2fg' % (shakethresh/100.,)] = (mu/elim)*((elim*mu-mu**2)/var-1) exp_pop['q_exp_%1.2fg' % (shakethresh/100.,)] = (1-mu/elim)*((elim*mu-mu**2)/var-1) else: print('no std values above zero, filling with zeros') exp_pop['exp_std_%1.2fg' % (shakethresh/100.,)] = 0. exp_pop['p_exp_%1.2fg' % (shakethresh/100.,)] = 0. exp_pop['q_exp_%1.2fg' % (shakethresh/100.,)] = 0. else: exp_pop['exp_std_%1.2fg' % (shakethresh/100.,)] = 0. exp_pop['p_exp_%1.2fg' % (shakethresh/100.,)] = 0. exp_pop['q_exp_%1.2fg' % (shakethresh/100.,)] = 0. return exp_pop
def HAZUS(shakefile, config, uncertfile=None, saveinputs=False, modeltype='coverage', regressionmodel='J_PGA', probtype='jibson2000', bounds=None): """ Runs HAZUS landslide procedure (FEMA, 2003, Chapter 4) using susceptiblity categories from defined by HAZUS manual (I-X) :param shakefile: URL or complete file path to the location of the Shakemap to use as input :type shakefile: string: :param config: Model configuration file object containing locations of input files and other input values config = ConfigObj(configfilepath) :type config: ConfigObj :param saveinputs: Whether or not to return the model input layers, False (defeault) returns only the model output (one layer) :type saveinputs: boolean :param modeltype: 'coverage' if critical acceleration is exceeded by pga, this gives the estimated areal coverage of landsliding for that cell 'dn_hazus' - Outputs Newmark displacement using HAZUS methods without relating to probability of failure 'dn_prob' - Estimates Newmark displacement using HAZUS methods and relates to probability of failure using param probtype 'ac_classic_dn' - Uses the critical acceleration defined by HAZUS methodology and uses regression model defined by regressionmodel param to get Newmark displacement without relating to probability of failure 'ac_classic_prob' - Uses the critical acceleration defined by HAZUS methodology and uses regression model defined by regressionmodel param to get Newmark displacement and probability defined by probtype method :type modeltype: string :param regressionmodel: Newmark displacement regression model to use 'J_PGA' (default) - PGA-based model from Jibson (2007) - equation 6 'J_PGA_M' - PGA and M-based model from Jibson (2007) - equation 7 'RS_PGA_M' - PGA and M-based model from from Rathje and Saygili (2009) 'RS_PGA_PGV' - PGA and PGV-based model from Saygili and Rathje (2008) - equation 6 :type regressionmodel: string :param probtype: Method used to estimate probability. Entering 'jibson2000' uses equation 5 from Jibson et al. (2000) to estimate probability from Newmark displacement. 'threshold' uses a specified threshold of Newmark displacement (defined in config file) and assumes anything greather than this threshold fails :type probtype: string :param bounds: Boundaries to compute over if different from ShakeMap boundaries as dictionary with keys 'xmin', 'xmax', 'ymin', 'ymax' :returns maplayers: Dictionary containing output and input layers (if saveinputs=True) along with metadata formatted like maplayers['layer name']={'grid': mapio grid2D object, 'label': 'label for colorbar and top line of subtitle', 'type': 'output or input to model', 'description': 'detailed description of layer for subtitle, potentially including source information'} :type maplayers: OrderedDict """ # Empty refs suslref = 'unknown' sussref = 'unknown' modellref = 'unknown' modelsref = 'unknown' # Parse config and read in files sus = None susdat = None if uncertfile is not None: print('ground motion uncertainty option not implemented yet') # Read in susceptiblity file #try: susfile = config['mechanistic_models']['hazus']['layers']['susceptibility']['file'] shkgdict = ShakeGrid.getFileGeoDict(shakefile, adjust='res') susdict = GDALGrid.getFileGeoDict(susfile) if bounds is not None: # Make sure bounds are within ShakeMap Grid if shkgdict.xmin > bounds['xmin'] or shkgdict.xmax < bounds['xmax'] or shkgdict.ymin > bounds['ymin'] or shkgdict.ymax < bounds['ymax']: print('Specified bounds are outside shakemap area, using ShakeMap bounds instead') bounds = None if bounds is not None: tempgdict1 = GeoDict({'xmin': bounds['xmin'], 'ymin': bounds['ymin'], 'xmax': bounds['xmax'], 'ymax': bounds['ymax'], 'dx': 100., 'dy': 100., 'nx': 100., 'ny': 100.}, adjust='res') tempgdict = susdict.getBoundsWithin(tempgdict1) else: tempgdict = susdict.getBoundsWithin(shkgdict) sus = GDALGrid.load(susfile, samplegeodict=tempgdict, resample=False) gdict = sus.getGeoDict() susdat = sus.getData() #except Exception as e: # raise IOError('Unable to read in susceptibility category file specified in config, %s,' % e) # return try: # Try to fetch source information from config modelsref = config['mechanistic_models']['hazus']['shortref'] modellref = config['mechanistic_models']['hazus']['longref'] sussref = config['mechanistic_models']['hazus']['layers']['susceptibility']['shortref'] suslref = config['mechanistic_models']['hazus']['layers']['susceptibility']['longref'] except: print('Was not able to retrieve all references from config file. Continuing') try: dnthresh = float(config['mechanistic_models']['hazus']['values']['dnthresh']) except: if probtype == 'threshold': dnthresh = 5. print('Unable to find dnthresh in config, using 5cm') # Load in shakemap, resample to susceptibility file shakemap = ShakeGrid.load(shakefile, adjust='res') PGA = shakemap.getLayer('pga').subdivide(gdict).getData().astype(float)/100. # in units of g PGV = shakemap.getLayer('pgv').subdivide(gdict).getData().astype(float) # cm/sec M = shakemap.getEventDict()['magnitude'] # Get critical accelerations in g Ac = np.empty(np.shape(susdat)) Ac[(susdat < 1) & (susdat > 10)] = 9999. Ac[susdat == 1] = 0.6 Ac[susdat == 2] = 0.5 Ac[susdat == 3] = 0.4 Ac[susdat == 4] = 0.35 Ac[susdat == 5] = 0.3 Ac[susdat == 6] = 0.25 Ac[susdat == 7] = 0.2 Ac[susdat == 8] = 0.15 Ac[susdat == 9] = 0.1 Ac[susdat == 10] = 0.05 # can delete sus and susdat now, if don't need to output it, to free up memory if saveinputs is False: del susdat, sus if modeltype == 'coverage': areal = np.zeros(np.shape(PGA)) # This seems to be slow for large matrices areal[(PGA >= Ac) & (Ac == 0.6)] = 0.01 areal[(PGA >= Ac) & (Ac == 0.5)] = 0.02 areal[(PGA >= Ac) & (Ac == 0.4)] = 0.03 areal[(PGA >= Ac) & (Ac == 0.35)] = 0.05 areal[(PGA >= Ac) & (Ac == 0.3)] = 0.08 areal[(PGA >= Ac) & (Ac == 0.25)] = 0.1 areal[(PGA >= Ac) & (Ac == 0.2)] = 0.15 areal[(PGA >= Ac) & (Ac == 0.15)] = 0.2 areal[(PGA >= Ac) & (Ac == 0.1)] = 0.25 areal[(PGA >= Ac) & (Ac == 0.05)] = 0.3 # # But this way is even slower, takes 2x as long # numrows, numcols = np.shape(areal) # for j in np.arange(numrows): # for k in np.arange(numcols): # acval = Ac[j, k] # if PGA[j, k] >= acval: # if acval == 0.6: # areal[j, k] = 0.01 # elif acval == 0.5: # areal[j, k] = 0.02 # elif acval == 0.4: # areal[j, k] = 0.03 # elif acval == 0.35: # areal[j, k] = 0.05 # elif acval == 0.3: # areal[j, k] = 0.08 # elif acval == 0.25: # areal[j, k] = 0.1 # elif acval == 0.2: # areal[j, k] = 0.15 # elif acval == 0.15: # areal[j, k] = 0.2 # elif acval == 0.1: # areal[j, k] = 0.25 # elif acval == 0.05: # areal[j, k] = 0.3 elif modeltype == 'dn_hazus' or modeltype == 'dn_prob': ed_low, ed_high = est_disp(Ac, PGA) ed_mean = np.mean((np.dstack((ed_low, ed_high))), axis=2) # Get mean estimated displacements dn = ed_mean * numcycles(M) * PGA else: # Calculate newmark displacement using a regression model if regressionmodel is 'J_PGA': dn = J_PGA(Ac, PGA) elif regressionmodel is 'J_PGA_M': dn = J_PGA_M(Ac, PGA, M) elif regressionmodel is 'RS_PGA_M': dn = RS_PGA_M(Ac, PGA, M) elif regressionmodel is 'RS_PGA_PGV': dn = RS_PGA_PGV(Ac, PGA, PGV) else: print('Unrecognized model, using J_PGA\n') dn = J_PGA(Ac, PGA) # Calculate probability from dn, if necessary for selected model if modeltype == 'ac_classic_prob' or modeltype == 'dn_prob': if probtype.lower() in 'jibson2000': PROB = 0.335*(1-np.exp(-0.048*dn**1.565)) dnthresh = None elif probtype.lower() in 'threshold': PROB = dn.copy() PROB[PROB <= dnthresh] = 0 PROB[PROB > dnthresh] = 1 else: raise NameError('invalid probtype, assuming jibson2000') PROB = 0.335*(1-np.exp(-0.048*dn**1.565)) dnthresh = None # Turn output and inputs into into grids and put in maplayers dictionary maplayers = collections.OrderedDict() temp = shakemap.getShakeDict() shakedetail = '%s_ver%s' % (temp['shakemap_id'], temp['shakemap_version']) if modeltype == 'coverage': maplayers['model'] = {'grid': GDALGrid(areal, gdict), 'label': 'Areal coverage', 'type': 'output', 'description': {'name': modelsref, 'longref': modellref, 'units': 'coverage', 'shakemap': shakedetail, 'parameters': {'modeltype': modeltype}}} elif modeltype == 'dn_hazus': maplayers['model'] = {'grid': GDALGrid(dn, gdict), 'label': 'Dn (cm)', 'type': 'output', 'description': {'name': modelsref, 'longref': modellref, 'units': 'displacement', 'shakemap': shakedetail, 'parameters': {'regressionmodel': regressionmodel, 'modeltype': modeltype}}} elif modeltype == 'ac_classic_dn': maplayers['model'] = {'grid': GDALGrid(dn, gdict), 'label': 'Dn (cm)', 'type': 'output', 'description': {'name': modelsref, 'longref': modellref, 'units': 'displacement', 'shakemap': shakedetail, 'parameters': {'regressionmodel': regressionmodel, 'modeltype': modeltype}}} elif modeltype == 'dn_prob': maplayers['model'] = {'grid': GDALGrid(PROB, gdict), 'label': 'Landslide Probability', 'type': 'output', 'description': {'name': modelsref, 'longref': modellref, 'units': 'probability', 'shakemap': shakedetail, 'parameters': {'regressionmodel': regressionmodel, 'dnthresh_cm': dnthresh, 'modeltype': modeltype, 'probtype': probtype}}} elif modeltype == 'ac_classic_prob': maplayers['model'] = {'grid': GDALGrid(PROB, gdict), 'label': 'Landslide Probability', 'type': 'output', 'description': {'name': modelsref, 'longref': modellref, 'units': 'probability', 'shakemap': shakedetail, 'parameters': {'regressionmodel': regressionmodel, 'dnthresh_cm': dnthresh, 'modeltype': modeltype, 'probtype': probtype}}} if saveinputs is True: maplayers['suscat'] = {'grid': sus, 'label': 'Susceptibility Category', 'type': 'input', 'description': {'name': sussref, 'longref': suslref, 'units': 'Category'}} maplayers['Ac'] = {'grid': GDALGrid(Ac, gdict), 'label': 'Ac (g)', 'type': 'output', 'description': {'units': 'g', 'shakemap': shakedetail}} maplayers['pga'] = {'grid': GDALGrid(PGA, gdict), 'label': 'PGA (g)', 'type': 'input', 'description': {'units': 'g', 'shakemap': shakedetail}} if 'pgv' in regressionmodel.lower(): maplayers['pgv'] = {'grid': GDALGrid(PGV, gdict), 'label': 'PGV (cm/s)', 'type': 'input', 'description': {'units': 'cm/s', 'shakemap': shakedetail}} if 'dn' not in modeltype.lower() and modeltype != 'coverage': maplayers['dn'] = {'grid': GDALGrid(dn, gdict), 'label': 'Dn (cm)', 'type': 'output', 'description': {'units': 'displacement', 'shakemap': shakedetail, 'parameters': {'regressionmodel': regressionmodel, 'modeltype': modeltype}}} return maplayers
def kritikos_fuzzygamma(shakefile, config, bounds=None): """ Runs kritikos procedure with fuzzy gamma overlay method """ cmodel = config['statistical_models']['kritikos_2015'] gamma = cmodel['gamma_value'] ############ This section reads in items from the config file ## Read in layer files and get data layers = cmodel['layers'] try: # Slope slope_file = layers['slope'] # DFF dff_file = layers['dff'] # DFS dfs_file = layers['dfs'] # elev elev_file = layers['elev'] except: print('Unable to retrieve grid data.') try: div = cmodel['divisor'] # Load in divisors MMI_div = div['MMI'] slope_div = div['slope'] dff_div = div['dff'] dfs_div = div['dfs'] slope_pos_div = div['slope_pos'] except: print('Unable to retrieve divisors.') try: power = cmodel['power'] # Load in powers MMI_power = power['MMI'] slope_power = power['slope'] dff_power = power['dff'] dfs_power = power['dfs'] slope_pos_power = power['slope_pos'] except: print('Unable to retrieve powers.') # Cut and resample, create geodict try: bounds = None shkgdict = ShakeGrid.getFileGeoDict(shakefile, adjust='res') slopedict, duplicated = GDALGrid.getFileGeoDict(slope_file) if bounds is not None: # Make sure bounds are within ShakeMap Grid if shkgdict.xmin > bounds['xmin'] or shkgdict.xmax < bounds[ 'xmax'] or shkgdict.ymin > bounds[ 'ymin'] or shkgdict.ymax < bounds['ymax']: print( 'Specified bounds are outside shakemap area, using ShakeMap bounds instead' ) bounds = None if bounds is not None: tempgdict = GeoDict( { 'xmin': bounds['xmin'], 'ymin': bounds['ymin'], 'xmax': bounds['xmax'], 'ymax': bounds['ymax'], 'dx': 100., 'dy': 100., 'nx': 100., 'ny': 100. }, adjust='res') gdict = slpdict.getBoundsWithin(tempgdict) else: # Get boundaries from shakemap if not specified gdict = slopedict.getBoundsWithin(shkgdict) except: raise NameError('Unable to create base geodict.') # Load in data ############## Still need to make DFF and DFS layers try: # Load in slope data slopegrid = GDALGrid.load(slope_file, samplegeodict=gdict, resample=False) slope_data = slopegrid.getData().astype(float) # Load in MMI shakemap = ShakeGrid.load(shakefile, samplegeodict=gdict, resample=True, method='linear', adjust='res') MMI_data = shakemap.getLayer('mmi').getData().astype(float) # Load in Dff ############### STILL NEED THIS FILE dffgrid = GDALGrid.load(dff_file, samplegeodict=gdict, resample=False) dff_data = dffgrid.getData().astype(float) # Load in DFS ############### STILL NEED THIS FILE dfsgrid = GDALGrid.load(dfs_file, samplegeodict=gdict, resample=False) dfs_data = dfsgrid.getData().astype(float) # Load in elevation elev_grid = GDALGrid.load(elev_file, samplegeodict=gdict, resample=False) DEM = elev_grid.getData().astype(float) except: print('Data could not be retrieved.') # Read in classifications try: mmi_class = cmodel['classification']['MMI'] slope_class = cmodel['classification']['slope'] dff_class = cmodel['classification']['dff'] dfs_class = cmodel['classification']['dfs'] slope_pos_class = cmodel['classification']['slope_pos'] except: print('Could not recover classifications from config.') try: slope_pos_data = create_slopePos(slope_data, DEM, cmodel) except: print('Could not create slope position grid.') ####### Split classification strings into lists containing numbers and classify layers # MMI classifications try: mmi_classes = mmi_class.split(',') for i in mmi_classes: if i.find('-') != -1: j = i.split('-') if MMI_data in range(int(j[0]), int(j[1])): MMI_data = int(j[0]) else: MMI_data = int(i) except: print('Could not categorize MMI values') # Slope Classifications try: slope_classes = slope_class.split(',') k = 1 for i in mmi_classes: if i.find('-') != -1: j = i.split('-') if slope_data in range(int(j[0]), int(j[1])): slope_data = k k += 1 else: slope_data = 11 except: print('Could not recategorize Slope Values.') # DFF classifications try: dff_classes = dff_class.split(',') k = 1 for i in dff_classes: if i.find('-') != -1: j = i.split('-') if dff_data in range(int(j[0]), int(j[1])): dff_data = k k += 1 else: dff_data = 7 except: print('Could not recategorize DFF values.') # DFS classifications try: dfs_classes = dfs_class.split(',') k = 1 for i in dfs_classes: if i.find('-') != -1: j = i.split('-') if dfs_data in range(int(j[0]), int(j[1])): dfs_data = k k += 1 else: dfs_data = 6 except: print('Could not recategorize DFS values.') # Slope position classification try: slope_pos_classes = slope_pos_class.split(',') k = 1 for i in slope_poss_classes: if slope_pos_data == i: slope_pos_data = k k += 1 except: print('Could not recategorize slope position values.') ############## # This section runs all the calculations ############## # Run each layer through a membership function try: layers = [] # Calculate layers slope = 1 / (1 + np.exp(slope_data / slope_div, slope_power)) MMI = 1 / (1 + np.exp(MMI_data / MMI_div, MMI_power)) dff = 1 / (1 + np.exp(dff_data / dff_div, dff_power)) dfs = 1 / (1 + np.exp(dfs_data / dfs_div, dfs_power)) slope_pos = 1 / (1 + np.exp(slop_pos_data / slop_pos_div, slope_pos_power)) # Add to layers list (to be used in further calculations) layers.append(slope) layers.append(MMI) layers.append(dff) layers.append(dfs) layers.append(slope_pos) except: print('Layer calculations failed.') # Apply final calculations operator # From Kritikos paper equation 4 ############ Haven't run. try: a = np.prod(layers) b = np.prod(1 - layers) mu_x = np.power(a, 1 - gamma) * np.power(1 - b, gamma) except: print('Unable to calculate final product.')
def quickcut(filename, gdict, tempname=None, extrasamp=5., method='bilinear', precise=True, cleanup=True, verbose=False, override=False): """ Use gdal to trim a large global file down quickly so mapio can read it efficiently. (Cannot read Shakemap.xml files, must save as .bil filrst) Args: filename (str): File path to original input file (raster). gdict (geodict): Geodictionary to cut around and align with. tempname (str): File path to desired location of clipped part of filename. extrasamp (int): Number of extra cells to cut around each edge of geodict to have resampling buffer for future steps. method (str): If resampling is necessary, method to use. precise (bool): If true, will resample to the gdict as closely as possible, if False it will just roughly cut around the area of interest without changing resolution cleanup (bool): if True, delete tempname after reading it back in verbose (bool): if True, prints more details override (bool): if True, if filename extent is not fully contained by gdict, read in the entire file (only used for ShakeMaps) Returns: New grid2D layer Note: This function uses the subprocess approach because ``gdal.Translate`` doesn't hang on the command until the file is created which causes problems in the next steps. """ if gdict.xmax < gdict.xmin: raise Exception('quickcut: your geodict xmax is smaller than xmin') try: filegdict = GDALGrid.getFileGeoDict(filename) except: try: filegdict = GMTGrid.getFileGeoDict(filename) except: raise Exception('Cannot get geodict for %s' % filename) if tempname is None: tempdir = tempfile.mkdtemp() tempname = os.path.join(tempdir, 'junk.tif') deltemp = True else: tempdir = None deltemp = False # if os.path.exists(tempname): # os.remove(tempname) # print('Temporary file already there, removing file') filegdict = filegdict[0] # Get the right methods for mapio (method) and gdal (method2) if method == 'linear': method2 = 'bilinear' if method == 'nearest': method2 = 'near' if method == 'bilinear': method = 'linear' method2 = 'bilinear' if method == 'near': method = 'nearest' method2 = 'near' else: method2 = method if filegdict != gdict: # First cut without resampling tempgdict = GeoDict.createDictFromBox(gdict.xmin, gdict.xmax, gdict.ymin, gdict.ymax, filegdict.dx, filegdict.dy, inside=True) try: egdict = filegdict.getBoundsWithin(tempgdict) ulx = egdict.xmin - extrasamp * egdict.dx uly = egdict.ymax + extrasamp * egdict.dy lrx = egdict.xmax + (extrasamp + 1) * egdict.dx lry = egdict.ymin - (extrasamp + 1) * egdict.dy cmd = 'gdal_translate -a_srs EPSG:4326 -of GTiff -projwin %1.8f \ %1.8f %1.8f %1.8f -r %s %s %s' % (ulx, uly, lrx, lry, method2, filename, tempname) except Exception as e: if override: # When ShakeMap is being loaded, sometimes they won't align # right because it's already cut to the area, so just load # the whole file cmd = 'gdal_translate -a_srs EPSG:4326 -of GTiff -r %s %s %s' \ % (method2, filename, tempname) else: raise Exception('Failed to cut layer: %s' % e) rc, so, se = get_command_output(cmd) if not rc: raise Exception(se.decode()) else: if verbose: print(so.decode()) newgrid2d = GDALGrid.load(tempname) if precise: # Resample to exact geodictionary newgrid2d = newgrid2d.interpolate2(gdict, method=method) if cleanup: os.remove(tempname) if deltemp: shutil.rmtree(tempdir) else: ftype = GMTGrid.getFileType(filename) if ftype != 'unknown': newgrid2d = GMTGrid.load(filename) elif filename.endswith('.xml'): newgrid2d = ShakeGrid.load(filename) else: newgrid2d = GDALGrid.load(filename) return newgrid2d
def calculate(self): """Calculate the model :returns: a dictionary containing the model results and model inputs if saveinputs was set to True when class was set up, see <https://github.com/usgs/groundfailure#api-for-model-output> for a description of the structure of this output """ X = eval(self.equation) P = 1 / (1 + np.exp(-X)) if 'vs30max' in self.config[self.model].keys(): vs30 = self.layerdict['vs30'].getData() P[vs30 > float(self.config[self.model]['vs30max'])] = 0.0 if 'minpgv' in self.config[self.model].keys(): pgv = self.shakemap.getLayer('pgv').getData() P[pgv < float(self.config[self.model]['minpgv'])] = 0.0 if 'coverage' in self.config[self.model].keys(): eqn = self.config[self.model]['coverage']['eqn'] ind = copy.copy(P) P = eval(eqn) if self.uncert is not None: print(self.numstd) print(type(self.numstd)) Xmin = eval(self.equationmin) Xmax = eval(self.equationmax) Pmin = 1 / (1 + np.exp(-Xmin)) Pmax = 1 / (1 + np.exp(-Xmax)) if 'vs30max' in self.config[self.model].keys(): vs30 = self.layerdict['vs30'].getData() Pmin[vs30 > float(self.config[self.model]['vs30max'])] = 0.0 Pmax[vs30 > float(self.config[self.model]['vs30max'])] = 0.0 if 'minpgv' in self.config[self.model].keys(): pgv = self.shakemap.getLayer('pgv').getData() Pmin[pgv < float(self.config[self.model]['minpgv'])] = 0.0 Pmax[pgv < float(self.config[self.model]['minpgv'])] = 0.0 if 'coverage' in self.config[self.model].keys(): eqnmin = eqn.replace('P', 'Pmin') eqnmax = eqn.replace('P', 'Pmax') Pmin = eval(eqnmin) Pmax = eval(eqnmax) if self.slopefile is not None: ftype = getFileType(self.slopefile) sampledict = self.shakemap.getGeoDict() if ftype == 'gmt': if GMTGrid.getFileGeoDict(self.slopefile)[0] == sampledict: slope = GMTGrid.load( self.slopefile).getData() / self.slopediv else: slope = GMTGrid.load( self.slopefile, sampledict, resample=True, method='linear', doPadding=True).getData() / self.slopediv # Apply slope min/max limits print('applying slope thresholds') P[slope > self.slopemax] = 0. P[slope < self.slopemin] = 0. if self.uncert is not None: Pmin[slope > self.slopemax] = 0. Pmin[slope < self.slopemin] = 0. Pmax[slope > self.slopemax] = 0. Pmax[slope < self.slopemin] = 0. elif ftype == 'esri': if GDALGrid.getFileGeoDict(self.slopefile)[0] == sampledict: slope = GDALGrid.load( self.slopefile).getData() / self.slopediv else: slope = GDALGrid.load( self.slopefile, sampledict, resample=True, method='linear', doPadding=True).getData() / self.slopediv # Apply slope min/max limits print('applying slope thresholds') P[slope > self.slopemax] = 0. P[slope < self.slopemin] = 0. if self.uncert is not None: Pmin[slope > self.slopemax] = 0. Pmin[slope < self.slopemin] = 0. Pmax[slope > self.slopemax] = 0. Pmax[slope < self.slopemin] = 0. else: print( 'Slope file does not appear to be a valid GMT or ESRI file, not applying any slope thresholds.' % (self.slopefile)) else: print('No slope file provided, slope thresholds not applied') # Stuff into Grid2D object temp = self.shakemap.getShakeDict() shakedetail = '%s_ver%s' % (temp['shakemap_id'], temp['shakemap_version']) description = { 'name': self.modelrefs['shortref'], 'longref': self.modelrefs['longref'], 'units': 'probability', 'shakemap': shakedetail, 'parameters': { 'slopemin': self.slopemin, 'slopemax': self.slopemax } } Pgrid = Grid2D(P, self.geodict) rdict = collections.OrderedDict() rdict['model'] = { 'grid': Pgrid, 'label': ('%s Probability') % (self.modeltype.capitalize()), 'type': 'output', 'description': description } if self.uncert is not None: rdict['modelmin'] = { 'grid': Grid2D(Pmin, self.geodict), 'label': ('%s Probability (-%0.1f std ground motion)') % (self.modeltype.capitalize(), self.numstd), 'type': 'output', 'description': description } rdict['modelmax'] = { 'grid': Grid2D(Pmax, self.geodict), 'label': ('%s Probability (+%0.1f std ground motion)') % (self.modeltype.capitalize(), self.numstd), 'type': 'output', 'description': description } if self.saveinputs is True: for layername, layergrid in list(self.layerdict.items()): units = self.units[layername] if units is None: units = '' rdict[layername] = { 'grid': layergrid, 'label': '%s (%s)' % (layername, units), 'type': 'input', 'description': { 'units': units, 'shakemap': shakedetail } } for gmused in self.gmused: if 'pga' in gmused: units = '%g' getkey = 'pga' elif 'pgv' in gmused: units = 'cm/s' getkey = 'pgv' elif 'mmi' in gmused: units = 'intensity' getkey = 'mmi' else: continue # Layer is derived from several input layers, skip outputting this layer if getkey in rdict: continue layer = self.shakemap.getLayer(getkey) rdict[getkey] = { 'grid': layer, 'label': '%s (%s)' % (getkey.upper(), units), 'type': 'input', 'description': { 'units': units, 'shakemap': shakedetail } } if self.uncert is not None: layer1 = np.exp( np.log(layer.getData()) - self.uncert.getLayer('std' + getkey).getData()) rdict[getkey + 'modelmin'] = { 'grid': Grid2D(layer1, self.geodict), 'label': '%s - %0.1f std (%s)' % (getkey.upper(), self.numstd, units), 'type': 'input', 'description': { 'units': units, 'shakemap': shakedetail } } layer2 = np.exp( np.log(layer.getData()) + self.uncert.getLayer('std' + getkey).getData()) rdict[getkey + 'modelmax'] = { 'grid': Grid2D(layer2, self.geodict), 'label': '%s + %0.1f std (%s)' % (getkey.upper(), self.numstd, units), 'type': 'input', 'description': { 'units': units, 'shakemap': shakedetail } } return rdict
def check_input_extents(config, shakefile=None, bounds=None): """Make sure all input files exist and cover the extent desired Args: config: configObj of a single model shakefile: path to ShakeMap grid.xml file (used for bounds). If not provided, bounds must be provided bounds: dictionary of bounds with keys: 'xmin', 'xmax', 'ymin', 'ymax' Returns: tuple containing: notcovered: list of files that do not cover the entire area defined by bounds or shakefile newbounds: new dictionary of bounds of subarea of original bounds or shakefile extent that is covered by all input files """ if shakefile is None and bounds is None: raise Exception('Must define either a shakemap file or bounds') modelname = config.keys()[0] # Make dummy geodict to use if bounds is None: evdict = ShakeGrid.getFileGeoDict(shakefile) else: evdict = GeoDict.createDictFromBox( bounds['xmin'], bounds['xmax'], bounds['ymin'], bounds['ymax'], 0.00001, 0.00001, inside=False) # Check extents of all input layers notcovered = [] notcovgdicts = [] newbounds = None for item, value in config[modelname]['layers'].items(): if 'file' in value.keys(): filelook = value['file'] if getFileType(filelook) == 'gmt': tmpgd, _ = GMTGrid.getFileGeoDict(filelook) else: tmpgd, _ = GDALGrid.getFileGeoDict(filelook) # See if tempgd contains evdict contains = tmpgd.contains(evdict) if not contains: notcovered.append(filelook) notcovgdicts.append(tmpgd) # print(filelook) if len(notcovered) > 0: # Figure out what bounds COULD be run xmins = [gd.xmin for gd in notcovgdicts] xmaxs = [gd.xmax for gd in notcovgdicts] ymins = [gd.ymin for gd in notcovgdicts] ymaxs = [gd.ymax for gd in notcovgdicts] # Set in by a buffer of 0.05 degrees because mapio doesn't like # when bounds are exactly the same for getboundswithin newbounds = dict(xmin=evdict.xmin + 0.05, xmax=evdict.xmax - 0.05, ymin=evdict.ymin + 0.05, ymax=evdict.ymax - 0.05) # Which one is the problem? if evdict.xmin < np.max(xmins): newbounds['xmin'] = np.max(xmins) + 0.05 if evdict.xmax > np.min(xmaxs): newbounds['xmax'] = np.min(xmaxs) - 0.05 if evdict.ymin < np.max(ymins): newbounds['ymin'] = np.max(ymins) + 0.05 if evdict.ymax > np.min(ymaxs): newbounds['ymax'] = np.min(ymaxs) - 0.05 # See if this is a possible extent try: test = GeoDict.createDictFromBox( newbounds['xmin'], newbounds['xmax'], newbounds['ymin'], newbounds['ymax'], 0.00001, 0.00001, inside=False) except BaseException: print('Cannot make new bounds that will work') newbounds = None return notcovered, newbounds
def getFileGeoDict(filename,gridtype): if gridtype == 'gmt': fgeodict,tmp = GMTGrid.getFileGeoDict(filename) else: fgeodict,tmp = GDALGrid.getFileGeoDict(filename) return fgeodict
def __init__(self, shakefile, config, uncertfile=None, saveinputs=False, slopefile=None, bounds=None, slopemod=None, trimfile=None): """ Sets up the logistic model Args: shakefile (str): Path to shakemap grid.xml file for the event. config: configobj object defining the model and its inputs. Only one model should be described in each config file. uncertfile (str): Path to uncertainty.xml file. saveinputs (bool): Save input layers as Grid2D objects in addition to the model? If false (the default), it will just output the model. slopefile (str): Optional path to slopefile that will be resampled to the other input files for applying thresholds. OVERWRITES VALUE IN CONFIG. bounds (dict): Default of None uses ShakeMap boundaries, otherwise a dictionary of boundaries to cut to like .. code-block:: python bounds = { 'xmin': lonmin, 'xmax': lonmax, 'ymin': latmin, 'ymax': latmax } slopemod (str): How slope input should be modified to be in degrees: e.g., ``np.arctan(slope) * 180. / np.pi`` or ``slope/100.`` (note that this may be in the config file already). trimfile (str): shapefile of earth's landmasses to use to cut offshore areas. """ mnames = getLogisticModelNames(config) if len(mnames) == 0: raise Exception('No config file found or problem with config ' 'file format') if len(mnames) > 1: raise Exception('Config file contains more than one model which ' 'is no longer allowed, update your config file ' 'to the newer format') self.model = mnames[0] self.config = config cmodel = config[self.model] self.modeltype = cmodel['gfetype'] self.coeffs = validateCoefficients(cmodel) # key = layer name, value = file name self.layers = validateLayers(cmodel) self.terms, timeField = validateTerms(cmodel, self.coeffs, self.layers) self.interpolations = validateInterpolations(cmodel, self.layers) self.units = validateUnits(cmodel, self.layers) self.gmused = [ value for term, value in cmodel['terms'].items() if 'pga' in value.lower() or 'pgv' in value.lower() or 'mmi' in value.lower() ] self.modelrefs, self.longrefs, self.shortrefs = validateRefs(cmodel) #self.numstd = numstd self.clips = validateClips(cmodel, self.layers, self.gmused) self.notes = '' if cmodel['baselayer'] not in list(self.layers.keys()): raise Exception('You must specify a base layer corresponding to ' 'one of the files in the layer section.') self.saveinputs = saveinputs if slopefile is None: try: self.slopefile = cmodel['slopefile'] except: # print('Slopefile not specified in config, no slope ' # 'thresholds will be applied\n') self.slopefile = None else: self.slopefile = slopefile if slopemod is None: try: self.slopemod = cmodel['slopemod'] except: self.slopemod = None # See if trimfile exists if trimfile is not None: if not os.path.exists(trimfile): print('trimfile defined does not exist: %s\nOcean will not be ' 'trimmed' % trimfile) self.trimfile = None elif os.path.splitext(trimfile)[1] != '.shp': print('trimfile must be a shapefile, ocean will not be ' 'trimmed') self.trimfile = None else: self.trimfile = trimfile else: self.trimfile = None # Get month of event griddict, eventdict, specdict, fields, uncertainties = \ getHeaderData(shakefile) MONTH = MONTHS[(eventdict['event_timestamp'].month) - 1] # Figure out how/if need to cut anything geodict = ShakeGrid.getFileGeoDict(shakefile, adjust='res') if bounds is not None: # Make sure bounds are within ShakeMap Grid if geodict.xmin < geodict.xmax: # only if signs are not opposite if (geodict.xmin > bounds['xmin'] or geodict.xmax < bounds['xmax'] or geodict.ymin > bounds['ymin'] or geodict.ymax < bounds['ymax']): print('Specified bounds are outside shakemap area, using ' 'ShakeMap bounds instead.') bounds = None if bounds is not None: tempgdict = GeoDict.createDictFromBox(bounds['xmin'], bounds['xmax'], bounds['ymin'], bounds['ymax'], geodict.dx, geodict.dy, inside=False) # If Shakemap geodict crosses 180/-180 line, fix geodict so things don't break if geodict.xmin > geodict.xmax: if tempgdict.xmin < 0: geodict._xmin -= 360. else: geodict._xmax += 360. gdict = geodict.getBoundsWithin(tempgdict) else: gdict = geodict # Now find the layer that is our base layer and get the largest bounds # we can guarantee not to exceed shakemap bounds basefile = self.layers[cmodel['baselayer']] ftype = getFileType(basefile) if ftype == 'esri': basegeodict, firstcol = GDALGrid.getFileGeoDict(basefile) if basegeodict == gdict: sampledict = gdict else: sampledict = basegeodict.getBoundsWithin(gdict) elif ftype == 'gmt': basegeodict, firstcol = GMTGrid.getFileGeoDict(basefile) if basegeodict == gdict: sampledict = gdict else: sampledict = basegeodict.getBoundsWithin(gdict) else: raise Exception('All predictor variable grids must be a valid ' 'GMT or ESRI file type.') # Do we need to subdivide baselayer? if 'divfactor' in self.config[self.model].keys(): divfactor = float(self.config[self.model]['divfactor']) if divfactor != 1.: # adjust sampledict so everything will be resampled newxmin = sampledict.xmin - sampledict.dx / \ 2. + sampledict.dx/(2.*divfactor) newymin = sampledict.ymin - sampledict.dy / \ 2. + sampledict.dy/(2.*divfactor) newxmax = sampledict.xmax + sampledict.dx / \ 2. - sampledict.dx/(2.*divfactor) newymax = sampledict.ymax + sampledict.dy / \ 2. - sampledict.dy/(2.*divfactor) newdx = sampledict.dx / divfactor newdy = sampledict.dy / divfactor sampledict = GeoDict.createDictFromBox(newxmin, newxmax, newymin, newymax, newdx, newdy, inside=True) # Find slope thresholds, if applicable self.slopemin = 'none' self.slopemax = 'none' if self.slopefile is not None: try: self.slopemin = float(config[self.model]['slopemin']) self.slopemax = float(config[self.model]['slopemax']) except: print('Could not find slopemin and/or slopemax in config, ' 'limits. No slope thresholds will be applied.') self.slopemin = 'none' self.slopemax = 'none' # Make temporary directory for hdf5 pytables file storage self.tempdir = tempfile.mkdtemp() # now load the shakemap, resampling and padding if necessary temp = ShakeGrid.load(shakefile) # , adjust='res') self.shakedict = temp.getShakeDict() self.eventdict = temp.getEventDict() self.shakemap = {} # Read both PGA and PGV in, may need them for thresholds for gm in ['pga', 'pgv']: junkfile = os.path.join(self.tempdir, 'temp.bil') GDALGrid.copyFromGrid(temp.getLayer(gm)).save(junkfile) if gm in self.interpolations.keys(): intermeth = self.interpolations[gm] else: intermeth = 'bilinear' junkgrid = quickcut(junkfile, sampledict, precise=True, method=intermeth) if gm in self.clips: junkgrid.setData( np.clip(junkgrid.getData(), self.clips[gm][0], self.clips[gm][1])) self.shakemap[gm] = TempHdf( junkgrid, os.path.join(self.tempdir, '%s.hdf5' % gm)) os.remove(junkfile) del (temp) # get updated geodict sampledict = junkgrid.getGeoDict() # take uncertainties into account, if available if uncertfile is not None: self.uncert = {} try: # Only read in the ones that will be needed temp = ShakeGrid.load(uncertfile) already = [] for gm in self.gmused: if 'pgv' in gm: gmsimp = 'pgv' elif 'pga' in gm: gmsimp = 'pga' elif 'mmi' in gm: gmsimp = 'mmi' if gmsimp in already: continue junkfile = os.path.join(self.tempdir, 'temp.bil') GDALGrid.copyFromGrid(temp.getLayer('std%s' % gmsimp)).save(junkfile) if gmsimp in self.interpolations.keys(): intermeth = self.interpolations[gmsimp] else: intermeth = 'bilinear' junkgrid = quickcut(junkfile, sampledict, precise=True, method=intermeth) if gmsimp in self.clips: junkgrid.setData( np.clip(junkgrid.getData(), self.clips[gmsimp][0], self.clips[gmsimp][1])) self.uncert['std' + gmsimp] = TempHdf( junkgrid, os.path.join(self.tempdir, 'std%s.hdf5' % gmsimp)) already.append(gmsimp) os.remove(junkfile) del (temp) except: print('Could not read uncertainty file, ignoring ' 'uncertainties') self.uncert = None else: self.uncert = None # Load the predictor layers, save as hdf5 temporary files, put file # locations into a dictionary. # Will be replaced in the next section if a slopefile was defined self.nonzero = None # key = layer name, value = grid object self.layerdict = {} didslope = False for layername, layerfile in self.layers.items(): start = timer() if isinstance(layerfile, list): for lfile in layerfile: if timeField == 'MONTH': if lfile.find(MONTH) > -1: layerfile = lfile ftype = getFileType(layerfile) interp = self.interpolations[layername] temp = quickcut(layerfile, sampledict, precise=True, method=interp) if layername in self.clips: temp.setData( np.clip(temp.getData(), self.clips[layername][0], self.clips[layername][1])) self.layerdict[layername] = TempHdf( temp, os.path.join(self.tempdir, '%s.hdf5' % layername)) del (temp) else: interp = self.interpolations[layername] temp = quickcut(layerfile, sampledict, precise=True, method=interp) if layername in self.clips: temp.setData( np.clip(temp.getData(), self.clips[layername][0], self.clips[layername][1])) if layername == 'rock': # Convert unconsolidated sediments to a more reasonable coefficient sub1 = temp.getData() # Change to mixed sed rock coeff sub1[sub1 <= -3.21] = -1.36 temp.setData(sub1) self.notes += 'unconsolidated sediment coefficient changed\ to -1.36 (weaker) from -3.22 to better reflect that this \ unit is not actually strong\n' self.layerdict[layername] = TempHdf( temp, os.path.join(self.tempdir, '%s.hdf5' % layername)) td = temp.getGeoDict() if td != sampledict: raise Exception( 'Geodictionaries of resampled files do not match') if layerfile == self.slopefile: flag = 0 if self.slopemin == 'none' and self.slopemax == 'none': flag = 1 if self.slopemod is None: slope1 = temp.getData().astype(float) slope = 0 else: try: slope = temp.getData().astype(float) slope1 = eval(self.slopemod) except: print('slopemod provided not valid, continuing ' 'without slope thresholds.') flag = 1 if flag == 0: nonzero = np.array([(slope1 > self.slopemin) & (slope1 <= self.slopemax)]) self.nonzero = nonzero[0, :, :] del (slope1) del (slope) else: # Still remove areas where the slope equals exactly # 0.0 to remove offshore liq areas. nonzero = np.array([slope1 != 0.0]) self.nonzero = nonzero[0, :, :] del (slope1) didslope = True del (temp) print('Loading %s layer: %1.1f sec' % (layername, timer() - start)) if didslope is False and self.slopefile is not None: # Slope didn't get read in yet temp = quickcut(self.slopefile, sampledict, precise=True, method='bilinear') flag = 0 if self.slopemin == 'none' and self.slopemax == 'none': flag = 1 if self.slopemod is None: slope1 = temp.getData().astype(float) slope = 0 else: try: slope = temp.getData().astype(float) slope1 = eval(self.slopemod) except: print('slopemod provided not valid, continuing without ' 'slope thresholds') flag = 1 if flag == 0: nonzero = np.array([ (slope1 > self.slopemin) & (slope1 <= self.slopemax) ]) self.nonzero = nonzero[0, :, :] del (slope1) del (slope) else: # Still remove areas where the slope equals exactly # 0.0 to remove offshore liq areas. nonzero = np.array([slope1 != 0.0]) self.nonzero = nonzero[0, :, :] del (slope1) self.nuggets = [str(self.coeffs['b0'])] ckeys = list(self.terms.keys()) ckeys.sort() for key in ckeys: term = self.terms[key] coeff = self.coeffs[key] self.nuggets.append('(%g * %s)' % (coeff, term)) self.equation = ' + '.join(self.nuggets) self.geodict = sampledict
def __init__(self, shakefile, config, uncertfile=None, saveinputs=False, slopefile=None, slopediv=1., bounds=None, numstd=1): """Set up the logistic model # ADD BOUNDS TO THIS MODEL :param config: configobj (config .ini file read in using configobj) defining the model and its inputs. Only one model should be described in each config file. :type config: dictionary :param shakefile: Full file path to shakemap.xml file for the event of interest :type shakefile: string :param uncertfile: Full file path to xml file of shakemap uncertainties :type uncertfile: string :param saveinputs: if True, saves all the input layers as Grid2D objects in addition to the model if false, it will just output the model :type saveinputs: boolean :param slopefile: optional file path to slopefile that will be resampled to the other input files for applying thresholds OVERWRITES VALUE IN CONFIG :type slopefile: string :param slopediv: number to divide slope by to get to degrees (usually will be default of 1.) :type slopediv: float :param numstd: number of +/- standard deviations to use if uncertainty is computed (uncertfile is not None) """ mnames = getLogisticModelNames(config) if len(mnames) == 0: raise Exception( 'No config file found or problem with config file format') if len(mnames) > 1: raise Exception( 'Config file contains more than one model which is no longer allowed,\ update your config file to the newer format') self.model = mnames[0] self.config = config cmodel = config[self.model] self.modeltype = cmodel['gfetype'] self.coeffs = validateCoefficients(cmodel) self.layers = validateLayers( cmodel) # key = layer name, value = file name self.terms, timeField = validateTerms(cmodel, self.coeffs, self.layers) self.interpolations = validateInterpolations(cmodel, self.layers) self.units = validateUnits(cmodel, self.layers) self.gmused = [ value for term, value in cmodel['terms'].items() if 'pga' in value.lower() or 'pgv' in value.lower() or 'mmi' in value.lower() ] self.modelrefs, self.longrefs, self.shortrefs = validateRefs(cmodel) self.numstd = numstd if cmodel['baselayer'] not in list(self.layers.keys()): raise Exception( 'You must specify a base layer corresponding to one of the files in the layer section.' ) self.saveinputs = saveinputs if slopefile is None: try: self.slopefile = cmodel['slopefile'] except: print( 'Could not find slopefile term in config, no slope thresholds will be applied\n' ) self.slopefile = None else: self.slopefile = slopefile self.slopediv = slopediv #get the geodict for the shakemap geodict = ShakeGrid.getFileGeoDict(shakefile, adjust='res') griddict, eventdict, specdict, fields, uncertainties = getHeaderData( shakefile) #YEAR = eventdict['event_timestamp'].year MONTH = MONTHS[(eventdict['event_timestamp'].month) - 1] #DAY = eventdict['event_timestamp'].day #HOUR = eventdict['event_timestamp'].hour #now find the layer that is our base layer and get the largest bounds we can guarantee not to exceed shakemap bounds basefile = self.layers[cmodel['baselayer']] ftype = getFileType(basefile) if ftype == 'esri': basegeodict, firstcol = GDALGrid.getFileGeoDict(basefile) sampledict = basegeodict.getBoundsWithin(geodict) elif ftype == 'gmt': basegeodict, firstcol = GMTGrid.getFileGeoDict(basefile) sampledict = basegeodict.getBoundsWithin(geodict) else: raise Exception( 'All predictor variable grids must be a valid GMT or ESRI file type' ) #now load the shakemap, resampling and padding if necessary if ShakeGrid.getFileGeoDict(shakefile, adjust='res') == sampledict: self.shakemap = ShakeGrid.load(shakefile, adjust='res') flag = 1 else: self.shakemap = ShakeGrid.load(shakefile, samplegeodict=sampledict, resample=True, doPadding=True, adjust='res') flag = 0 # take uncertainties into account if uncertfile is not None: try: if flag == 1: self.uncert = ShakeGrid.load(uncertfile, adjust='res') else: self.uncert = ShakeGrid.load(uncertfile, samplegeodict=sampledict, resample=True, doPadding=True, adjust='res') except: print( 'Could not read uncertainty file, ignoring uncertainties') self.uncert = None else: self.uncert = None #load the predictor layers into a dictionary self.layerdict = {} # key = layer name, value = grid object for layername, layerfile in self.layers.items(): if isinstance(layerfile, list): for lfile in layerfile: if timeField == 'MONTH': if lfile.find(MONTH) > -1: layerfile = lfile ftype = getFileType(layerfile) interp = self.interpolations[layername] if ftype == 'gmt': if GMTGrid.getFileGeoDict( layerfile)[0] == sampledict: lyr = GMTGrid.load(layerfile) else: lyr = GMTGrid.load(layerfile, sampledict, resample=True, method=interp, doPadding=True) elif ftype == 'esri': if GDALGrid.getFileGeoDict( layerfile)[0] == sampledict: lyr = GDALGrid.load(layerfile) else: lyr = GDALGrid.load(layerfile, sampledict, resample=True, method=interp, doPadding=True) else: msg = 'Layer %s (file %s) does not appear to be a valid GMT or ESRI file.' % ( layername, layerfile) raise Exception(msg) self.layerdict[layername] = lyr else: #first, figure out what kind of file we have (or is it a directory?) ftype = getFileType(layerfile) interp = self.interpolations[layername] if ftype == 'gmt': if GMTGrid.getFileGeoDict(layerfile)[0] == sampledict: lyr = GMTGrid.load(layerfile) else: lyr = GMTGrid.load(layerfile, sampledict, resample=True, method=interp, doPadding=True) elif ftype == 'esri': if GDALGrid.getFileGeoDict(layerfile)[0] == sampledict: lyr = GDALGrid.load(layerfile) else: lyr = GDALGrid.load(layerfile, sampledict, resample=True, method=interp, doPadding=True) else: msg = 'Layer %s (file %s) does not appear to be a valid GMT or ESRI file.' % ( layername, layerfile) raise Exception(msg) self.layerdict[layername] = lyr shapes = {} for layername, layer in self.layerdict.items(): shapes[layername] = layer.getData().shape self.nuggets = [str(self.coeffs['b0'])] ckeys = list(self.terms.keys()) ckeys.sort() for key in ckeys: term = self.terms[key] coeff = self.coeffs[key] self.nuggets.append('(%g * %s)' % (coeff, term)) self.equation = ' + '.join(self.nuggets) if self.uncert is not None: self.nugmin = copy.copy(self.nuggets) self.nugmax = copy.copy(self.nuggets) # Find the term with the shakemap input and replace for these nuggets for k, nug in enumerate(self.nuggets): if "self.shakemap.getLayer('pga').getData()" in nug: self.nugmin[k] = self.nugmin[k].replace( "self.shakemap.getLayer('pga').getData()", "(np.exp(np.log(self.shakemap.getLayer('pga').getData())\ - self.numstd * self.uncert.getLayer('stdpga').getData()))" ) self.nugmax[k] = self.nugmax[k].replace( "self.shakemap.getLayer('pga').getData()", "(np.exp(np.log(self.shakemap.getLayer('pga').getData())\ + self.numstd * self.uncert.getLayer('stdpga').getData()))" ) elif "self.shakemap.getLayer('pgv').getData()" in nug: self.nugmin[k] = self.nugmin[k].replace( "self.shakemap.getLayer('pgv').getData()", "(np.exp(np.log(self.shakemap.getLayer('pgv').getData())\ - self.numstd * self.uncert.getLayer('stdpgv').getData()))" ) self.nugmax[k] = self.nugmax[k].replace( "self.shakemap.getLayer('pgv').getData()", "(np.exp(np.log(self.shakemap.getLayer('pgv').getData())\ + self.numstd * self.uncert.getLayer('stdpgv').getData()))" ) elif "self.shakemap.getLayer('mmi').getData()" in nug: self.nugmin[k] = self.nugmin[k].replace( "self.shakemap.getLayer('mmi').getData()", "(np.exp(np.log(self.shakemap.getLayer('mmi').getData())\ - self.numstd * self.uncert.getLayer('stdmmi').getData()))" ) self.nugmax[k] = self.nugmax[k].replace( "self.shakemap.getLayer('mmi').getData()", "(np.exp(np.log(self.shakemap.getLayer('mmi').getData())\ + self.numstd * self.uncert.getLayer('stdmmi').getData()))" ) self.equationmin = ' + '.join(self.nugmin) self.equationmax = ' + '.join(self.nugmax) else: self.equationmin = None self.equationmax = None self.geodict = self.shakemap.getGeoDict() try: self.slopemin = float(config[self.model]['slopemin']) self.slopemax = float(config[self.model]['slopemax']) except: print( 'could not find slopemin and/or slopemax in config, no limits will be applied' ) self.slopemin = 0. self.slopemax = 90.
def modelMap(grids, shakefile=None, suptitle=None, inventory_shapefile=None, plotorder=None, maskthreshes=None, colormaps=None, boundaries=None, zthresh=0, scaletype='continuous', lims=None, logscale=False, ALPHA=0.7, maproads=True, mapcities=True, isScenario=False, roadfolder=None, topofile=None, cityfile=None, oceanfile=None, roadcolor='#6E6E6E', watercolor='#B8EEFF', countrycolor='#177F10', outputdir=None, savepdf=True, savepng=True, showplots=False, roadref='unknown', cityref='unknown', oceanref='unknown', printparam=False, ds=True, dstype='mean', upsample=False): """ This function creates maps of mapio grid layers (e.g. liquefaction or landslide models with their input layers) All grids must use the same bounds TO DO change so that all input layers do not have to have the same bounds, test plotting multiple probability layers, and add option so that if PDF and PNG aren't output, opens plot on screen using plt.show() :param grids: Dictionary of N layers and metadata formatted like: maplayers['layer name']={ 'grid': mapio grid2D object, 'label': 'label for colorbar and top line of subtitle', 'type': 'output or input to model', 'description': 'detailed description of layer for subtitle'}. Layer names must be unique. :type name: Dictionary or Ordered dictionary - import collections; grids = collections.OrderedDict() :param shakefile: optional ShakeMap file (url or full file path) to extract information for labels and folder names :type shakefile: Shakemap Event Dictionary :param suptitle: This will be displayed at the top of the plots and in the figure names :type suptitle: string :param plotorder: List of keys describing the order to plot the grids, if None and grids is an ordered dictionary, it will use the order of the dictionary, otherwise it will choose order which may be somewhat random but it will always put a probability grid first :type plotorder: list :param maskthreshes: N x 1 array or list of lower thresholds for masking corresponding to order in plotorder or order of OrderedDict if plotorder is None. If grids is not an ordered dict and plotorder is not specified, this will not work right. If None (default), nothing will be masked :param colormaps: List of strings of matplotlib colormaps (e.g. cm.autumn_r) corresponding to plotorder or order of dictionary if plotorder is None. The list can contain both strings and None e.g. colormaps = ['cm.autumn', None, None, 'cm.jet'] and None's will default to default colormap :param boundaries: None to show entire study area, 'zoom' to zoom in on the area of action (only works if there is a probability layer) using zthresh as a threshold, or a dictionary defining lats and lons in the form of boundaries.xmin = minlon, boundaries.xmax = maxlon, boundaries.ymin = min lat, boundaries.ymax = max lat :param zthresh: threshold for computing zooming bounds, only used if boundaries = 'zoom' :type zthresh: float :param scaletype: Type of scale for plotting, 'continuous' or 'binned' - will be reflected in colorbar :type scaletype: string :param lims: None or Nx1 list of tuples or numpy arrays corresponding to plotorder defining the limits for saturating the colorbar (vmin, vmax) if scaletype is continuous or the bins to use (clev) if scaletype if binned. The list can contain tuples, arrays, and Nones, e.g. lims = [(0., 10.), None, (0.1, 1.5), np.linspace(0., 1.5, 15)]. When None is specified, the program will estimate the limits, when an array is specified but the scale type is continuous, vmin will be set to min(array) and vmax will be set to max(array) :param lims: None or Nx1 list of Trues and Falses corresponding to plotorder defining whether to use a linear or log scale (log10) for plotting the layer. This will be reflected in the labels :param ALPHA: Transparency for mapping, if there is a hillshade that will plot below each layer, it is recommended to set this to at least 0.7 :type ALPHA: float :param maproads: Whether to show roads or not, default True, but requires that roadfile is specified and valid to work :type maproads: boolean :param mapcities: Whether to show cities or not, default True, but requires that cityfile is specified and valid to work :type mapcities: boolean :param isScenario: Whether this is a scenario (True) or a real event (False) (default False) :type isScenario: boolean :param roadfolder: Full file path to folder containing road shapefiles :type roadfolder: string :param topofile: Full file path to topography grid (GDAL compatible) - this is only needed to make a hillshade if a premade hillshade is not specified :type topofile: string :param cityfile: Full file path to Pager file containing city & population information :type cityfile: string :param roadcolor: Color to use for roads, if plotted, default #6E6E6E :type roadcolor: Hex color or other matplotlib compatible way of defining color :param watercolor: Color to use for oceans, lakes, and rivers, default #B8EEFF :type watercolor: Hex color or other matplotlib compatible way of defining color :param countrycolor: Color for country borders, default #177F10 :type countrycolor: Hex color or other matplotlib compatible way of defining color :param outputdir: File path for outputting figures, if edict is defined, a subfolder based on the event id will be created in this folder. If None, will use current directory :param savepdf: True to save pdf figure, False to not :param savepng: True to save png figure, False to not :param ds: True to allow downsampling for display (necessary when arrays are quite large, False to not allow) :param dstype: What function to use in downsampling, options are 'min', 'max', 'median', or 'mean' :param upsample: True to upsample the layer to the DEM resolution for better looking hillshades :returns: * PDF and/or PNG of map * Downsampled and trimmed version of input grids. If no modification was needed for plotting, this will be identical to grids but without the metadata """ if suptitle is None: suptitle = ' ' plt.ioff() defaultcolormap = cm.jet if shakefile is not None: edict = ShakeGrid.load(shakefile, adjust='res').getEventDict() temp = ShakeGrid.load(shakefile, adjust='res').getShakeDict() edict['eventid'] = temp['shakemap_id'] edict['version'] = temp['shakemap_version'] else: edict = None # Get output file location if outputdir is None: print('No output location given, using current directory for outputs\n') outputdir = os.getcwd() if edict is not None: outfolder = os.path.join(outputdir, edict['event_id']) else: outfolder = outputdir if not os.path.isdir(outfolder): os.makedirs(outfolder) # Get plotting order, if not specified if plotorder is None: plotorder = list(grids.keys()) # Get boundaries to use for all plots cut = True if boundaries is None: cut = False keytemp = list(grids.keys()) boundaries = grids[keytemp[0]]['grid'].getGeoDict() elif boundaries == 'zoom': # Find probability layer (will just take the maximum bounds if there is # more than one) keytemp = list(grids.keys()) key1 = [key for key in keytemp if 'model' in key.lower()] if len(key1) == 0: print('Could not find model layer to use for zoom, using default boundaries') keytemp = list(grids.keys()) boundaries = grids[keytemp[0]]['grid'].getGeoDict() else: lonmax = -1.e10 lonmin = 1.e10 latmax = -1.e10 latmin = 1.e10 for key in key1: # get lat lons of areas affected and add, if no areas affected, # switch to shakemap boundaries temp = grids[key]['grid'] xmin, xmax, ymin, ymax = temp.getBounds() lons = np.linspace(xmin, xmax, temp.getGeoDict().nx) lats = np.linspace(ymax, ymin, temp.getGeoDict().ny) # backwards so it plots right row, col = np.where(temp.getData() > float(zthresh)) lonmin = lons[col].min() lonmax = lons[col].max() latmin = lats[row].min() latmax = lats[row].max() # llons, llats = np.meshgrid(lons, lats) # make meshgrid # llons1 = llons[temp.getData() > float(zthresh)] # llats1 = llats[temp.getData() > float(zthresh)] # if llons1.min() < lonmin: # lonmin = llons1.min() # if llons1.max() > lonmax: # lonmax = llons1.max() # if llats1.min() < latmin: # latmin = llats1.min() # if llats1.max() > latmax: # latmax = llats1.max() boundaries1 = {'dx': 100, 'dy': 100., 'nx': 100., 'ny': 100} # dummy fillers, only really care about bounds if xmin < lonmin-0.15*(lonmax-lonmin): boundaries1['xmin'] = lonmin-0.1*(lonmax-lonmin) else: boundaries1['xmin'] = xmin if xmax > lonmax+0.15*(lonmax-lonmin): boundaries1['xmax'] = lonmax+0.1*(lonmax-lonmin) else: boundaries1['xmax'] = xmax if ymin < latmin-0.15*(latmax-latmin): boundaries1['ymin'] = latmin-0.1*(latmax-latmin) else: boundaries1['ymin'] = ymin if ymax > latmax+0.15*(latmax-latmin): boundaries1['ymax'] = latmax+0.1*(latmax-latmin) else: boundaries1['ymax'] = ymax boundaries = GeoDict(boundaries1, adjust='res') else: # SEE IF BOUNDARIES ARE SAME AS BOUNDARIES OF LAYERS keytemp = list(grids.keys()) tempgdict = grids[keytemp[0]]['grid'].getGeoDict() if np.abs(tempgdict.xmin-boundaries['xmin']) < 0.05 and \ np.abs(tempgdict.ymin-boundaries['ymin']) < 0.05 and \ np.abs(tempgdict.xmax-boundaries['xmax']) < 0.05 and \ np.abs(tempgdict.ymax - boundaries['ymax']) < 0.05: print('Input boundaries are almost the same as specified boundaries, no cutting needed') boundaries = tempgdict cut = False else: try: if boundaries['xmin'] > boundaries['xmax'] or \ boundaries['ymin'] > boundaries['ymax']: print('Input boundaries are not usable, using default boundaries') keytemp = list(grids.keys()) boundaries = grids[keytemp[0]]['grid'].getGeoDict() cut = False else: # Build dummy GeoDict boundaries = GeoDict({'xmin': boundaries['xmin'], 'xmax': boundaries['xmax'], 'ymin': boundaries['ymin'], 'ymax': boundaries['ymax'], 'dx': 100., 'dy': 100., 'ny': 100., 'nx': 100.}, adjust='res') except: print('Input boundaries are not usable, using default boundaries') keytemp = list(grids.keys()) boundaries = grids[keytemp[0]]['grid'].getGeoDict() cut = False # Pull out bounds for various uses bxmin, bxmax, bymin, bymax = boundaries.xmin, boundaries.xmax, boundaries.ymin, boundaries.ymax # Determine if need a single panel or multi-panel plot and if multi-panel, # how many and how it will be arranged fig = plt.figure() numpanels = len(grids) if numpanels == 1: rowpan = 1 colpan = 1 # create the figure and axes instances. fig.set_figwidth(5) elif numpanels == 2 or numpanels == 4: rowpan = np.ceil(numpanels/2.) colpan = 2 fig.set_figwidth(13) else: rowpan = np.ceil(numpanels/3.) colpan = 3 fig.set_figwidth(15) if rowpan == 1: fig.set_figheight(rowpan*6.0) else: fig.set_figheight(rowpan*5.3) # Need to update naming to reflect the shakemap version once can get # getHeaderData to work, add edict['version'] back into title, maybe # shakemap id also? fontsizemain = 14. fontsizesub = 12. fontsizesmallest = 10. if rowpan == 1.: fontsizemain = 12. fontsizesub = 10. fontsizesmallest = 8. if edict is not None: if isScenario: title = edict['event_description'] else: timestr = edict['event_timestamp'].strftime('%b %d %Y') title = 'M%.1f %s v%i - %s' % (edict['magnitude'], timestr, edict['version'], edict['event_description']) plt.suptitle(title+'\n'+suptitle, fontsize=fontsizemain) else: plt.suptitle(suptitle, fontsize=fontsizemain) clear_color = [0, 0, 0, 0.0] # Cut all of them and release extra memory xbuff = (bxmax-bxmin)/10. ybuff = (bymax-bymin)/10. cutxmin = bxmin-xbuff cutymin = bymin-ybuff cutxmax = bxmax+xbuff cutymax = bymax+ybuff if cut is True: newgrids = collections.OrderedDict() for k, layer in enumerate(plotorder): templayer = grids[layer]['grid'] try: newgrids[layer] = {'grid': templayer.cut(cutxmin, cutxmax, cutymin, cutymax, align=True)} except Exception as e: print(('Cutting failed, %s, continuing with full layers' % e)) newgrids = grids continue del templayer gc.collect() else: newgrids = grids tempgdict = newgrids[list(grids.keys())[0]]['grid'].getGeoDict() # Upsample layers to same as topofile if desired for better looking hillshades if upsample is True and topofile is not None: try: topodict = GDALGrid.getFileGeoDict(topofile) if topodict.dx >= tempgdict.dx or topodict.dy >= tempgdict.dy: print('Upsampling not possible, resolution of results already smaller than DEM') pass else: tempgdict1 = GeoDict({'xmin': tempgdict.xmin-xbuff, 'ymin': tempgdict.ymin-ybuff, 'xmax': tempgdict.xmax+xbuff, 'ymax': tempgdict.ymax+ybuff, 'dx': topodict.dx, 'dy': topodict.dy, 'nx': topodict.nx, 'ny': topodict.ny}, adjust='res') tempgdict2 = tempgdict1.getBoundsWithin(tempgdict) for k, layer in enumerate(plotorder): newgrids[layer]['grid'] = newgrids[layer]['grid'].subdivide(tempgdict2) except: print('Upsampling failed, continuing') # Downsample all of them for plotting, if needed, and replace them in # grids (to save memory) tempgrid = newgrids[list(grids.keys())[0]]['grid'] xsize = tempgrid.getGeoDict().nx ysize = tempgrid.getGeoDict().ny inchesx, inchesy = fig.get_size_inches() divx = int(np.round(xsize/(500.*inchesx))) divy = int(np.round(ysize/(500.*inchesy))) xmin, xmax, ymin, ymax = tempgrid.getBounds() gdict = tempgrid.getGeoDict() # Will be replaced if downsampled del tempgrid gc.collect() if divx <= 1: divx = 1 if divy <= 1: divy = 1 if (divx > 1. or divy > 1.) and ds: if dstype == 'max': func = np.nanmax elif dstype == 'min': func = np.nanmin elif dstype == 'med': func = np.nanmedian else: func = np.nanmean for k, layer in enumerate(plotorder): layergrid = newgrids[layer]['grid'] dat = block_reduce(layergrid.getData().copy(), block_size=(divy, divx), cval=float('nan'), func=func) if k == 0: lons = block_reduce(np.linspace(xmin, xmax, layergrid.getGeoDict().nx), block_size=(divx,), func=np.mean, cval=float('nan')) if math.isnan(lons[-1]): lons[-1] = lons[-2] + (lons[1]-lons[0]) lats = block_reduce(np.linspace(ymax, ymin, layergrid.getGeoDict().ny), block_size=(divy,), func=np.mean, cval=float('nan')) if math.isnan(lats[-1]): lats[-1] = lats[-2] + (lats[1]-lats[0]) gdict = GeoDict({'xmin': lons.min(), 'xmax': lons.max(), 'ymin': lats.min(), 'ymax': lats.max(), 'dx': np.abs(lons[1]-lons[0]), 'dy': np.abs(lats[1]-lats[0]), 'nx': len(lons), 'ny': len(lats)}, adjust='res') newgrids[layer]['grid'] = Grid2D(dat, gdict) del layergrid, dat else: lons = np.linspace(xmin, xmax, xsize) lats = np.linspace(ymax, ymin, ysize) # backwards so it plots right side up #make meshgrid llons1, llats1 = np.meshgrid(lons, lats) # See if there is an oceanfile for masking bbox = PolygonSH(((cutxmin, cutymin), (cutxmin, cutymax), (cutxmax, cutymax), (cutxmax, cutymin))) if oceanfile is not None: try: f = fiona.open(oceanfile) oc = next(f) f.close shapes = shape(oc['geometry']) # make boundaries into a shape ocean = shapes.intersection(bbox) except: print('Not able to read specified ocean file, will use default ocean masking') oceanfile = None if inventory_shapefile is not None: try: f = fiona.open(inventory_shapefile) invshp = list(f.items(bbox=(bxmin, bymin, bxmax, bymax))) f.close() inventory = [shape(inv[1]['geometry']) for inv in invshp] except: print('unable to read inventory shapefile specified, will not plot inventory') inventory_shapefile = None # # Find cities that will be plotted if mapcities is True and cityfile is not None: try: mycity = BasemapCities.loadFromGeoNames(cityfile=cityfile) bcities = mycity.limitByBounds((bxmin, bxmax, bymin, bymax)) #bcities = bcities.limitByPopulation(40000) bcities = bcities.limitByGrid(nx=4, ny=4, cities_per_grid=2) except: print('Could not read in cityfile, not plotting cities') mapcities = False cityfile = None # Load in topofile if topofile is not None: try: topomap = GDALGrid.load(topofile, resample=True, method='linear', samplegeodict=gdict) except: topomap = GMTGrid.load(topofile, resample=True, method='linear', samplegeodict=gdict) topodata = topomap.getData().copy() # mask oceans if don't have ocean shapefile if oceanfile is None: topodata = maskoceans(llons1, llats1, topodata, resolution='h', grid=1.25, inlands=True) else: print('no hillshade is possible\n') topomap = None topodata = None # Load in roads, if needed if maproads is True and roadfolder is not None: try: roadslist = [] for folder in os.listdir(roadfolder): road1 = os.path.join(roadfolder, folder) shpfiles = glob.glob(os.path.join(road1, '*.shp')) if len(shpfiles): shpfile = shpfiles[0] f = fiona.open(shpfile) shapes = list(f.items(bbox=(bxmin, bymin, bxmax, bymax))) for shapeid, shapedict in shapes: roadslist.append(shapedict) f.close() except: print('Not able to plot roads') roadslist = None val = 1 for k, layer in enumerate(plotorder): layergrid = newgrids[layer]['grid'] if 'label' in list(grids[layer].keys()): label1 = grids[layer]['label'] else: label1 = layer try: sref = grids[layer]['description']['name'] except: sref = None ax = fig.add_subplot(rowpan, colpan, val) val += 1 clat = bymin + (bymax-bymin)/2.0 clon = bxmin + (bxmax-bxmin)/2.0 # setup of basemap ('lcc' = lambert conformal conic). # use major and minor sphere radii from WGS84 ellipsoid. m = Basemap(llcrnrlon=bxmin, llcrnrlat=bymin, urcrnrlon=bxmax, urcrnrlat=bymax, rsphere=(6378137.00, 6356752.3142), resolution='l', area_thresh=1000., projection='lcc', lat_1=clat, lon_0=clon, ax=ax) x1, y1 = m(llons1, llats1) # get projection coordinates axsize = ax.get_window_extent().transformed(fig.dpi_scale_trans.inverted()) if k == 0: wid, ht = axsize.width, axsize.height if colormaps is not None and \ len(colormaps) == len(newgrids) and \ colormaps[k] is not None: palette = colormaps[k] else: # Find preferred default color map for each type of layer if 'prob' in layer.lower() or 'pga' in layer.lower() or \ 'pgv' in layer.lower() or 'cohesion' in layer.lower() or \ 'friction' in layer.lower() or 'fs' in layer.lower(): palette = cm.jet elif 'slope' in layer.lower(): palette = cm.gnuplot2 elif 'precip' in layer.lower(): palette = cm2.s3pcpn else: palette = defaultcolormap if topodata is not None: if k == 0: ptopo = m.transform_scalar( np.flipud(topodata), lons+0.5*gdict.dx, lats[::-1]-0.5*gdict.dy, np.round(300.*wid), np.round(300.*ht), returnxy=False, checkbounds=False, order=1, masked=False) #use lightsource class to make our shaded topography ls = LightSource(azdeg=135, altdeg=45) ls1 = LightSource(azdeg=120, altdeg=45) ls2 = LightSource(azdeg=225, altdeg=45) intensity1 = ls1.hillshade(ptopo, fraction=0.25, vert_exag=1.) intensity2 = ls2.hillshade(ptopo, fraction=0.25, vert_exag=1.) intensity = intensity1*0.5 + intensity2*0.5 #hillshm_im = m.transform_scalar(np.flipud(hillshm), lons, lats[::-1], np.round(300.*wid), np.round(300.*ht), returnxy=False, checkbounds=False, order=0, masked=False) #m.imshow(hillshm_im, cmap='Greys', vmin=0., vmax=3., zorder=1, interpolation='none') # vmax = 3 to soften colors to light gray #m.pcolormesh(x1, y1, hillshm, cmap='Greys', linewidth=0., rasterized=True, vmin=0., vmax=3., edgecolors='none', zorder=1); # plt.draw() # Get the data dat = layergrid.getData().copy() # mask out anything below any specified thresholds # Might need to move this up to before downsampling...might give illusion of no hazard in places where there is some that just got averaged out if maskthreshes is not None and len(maskthreshes) == len(newgrids): if maskthreshes[k] is not None: dat[dat <= maskthreshes[k]] = float('NaN') dat = np.ma.array(dat, mask=np.isnan(dat)) if logscale is not False and len(logscale) == len(newgrids): if logscale[k] is True: dat = np.log10(dat) label1 = r'$log_{10}$(' + label1 + ')' if scaletype.lower() == 'binned': # Find order of range to know how to scale order = np.round(np.log(np.nanmax(dat) - np.nanmin(dat))) if order < 1.: scal = 10**-order else: scal = 1. if lims is None or len(lims) != len(newgrids): clev = (np.linspace(np.floor(scal*np.nanmin(dat)), np.ceil(scal*np.nanmax(dat)), 10))/scal else: if lims[k] is None: clev = (np.linspace(np.floor(scal*np.nanmin(dat)), np.ceil(scal*np.nanmax(dat)), 10))/scal else: clev = lims[k] # Adjust to colorbar levels dat[dat < clev[0]] = clev[0] for j, level in enumerate(clev[:-1]): dat[(dat >= clev[j]) & (dat < clev[j+1])] = clev[j] # So colorbar saturates at top dat[dat > clev[-1]] = clev[-1] #panelhandle = m.contourf(x1, y1, datm, clev, cmap=palette, linewidth=0., alpha=ALPHA, rasterized=True) vmin = clev[0] vmax = clev[-1] else: if lims is not None and len(lims) == len(newgrids): if lims[k] is None: vmin = np.nanmin(dat) vmax = np.nanmax(dat) else: vmin = lims[k][0] vmax = lims[k][-1] else: vmin = np.nanmin(dat) vmax = np.nanmax(dat) # Mask out cells overlying oceans or block with a shapefile if available if oceanfile is None: dat = maskoceans(llons1, llats1, dat, resolution='h', grid=1.25, inlands=True) else: #patches = [] if type(ocean) is PolygonSH: ocean = [ocean] for oc in ocean: patch = getProjectedPatch(oc, m, edgecolor="#006280", facecolor=watercolor, lw=0.5, zorder=4.) #x, y = m(oc.exterior.xy[0], oc.exterior.xy[1]) #xy = zip(x, y) #patch = Polygon(xy, facecolor=watercolor, edgecolor="#006280", lw=0.5, zorder=4.) ##patches.append(Polygon(xy, facecolor=watercolor, edgecolor=watercolor, zorder=500.)) ax.add_patch(patch) ##ax.add_collection(PatchCollection(patches)) if inventory_shapefile is not None: for in1 in inventory: if 'point' in str(type(in1)): x, y = in1.xy x = x[0] y = y[0] m.scatter(x, y, c='m', s=50, latlon=True, marker='^', zorder=100001) else: x, y = m(in1.exterior.xy[0], in1.exterior.xy[1]) xy = list(zip(x, y)) patch = Polygon(xy, facecolor='none', edgecolor='k', lw=0.5, zorder=10.) #patches.append(Polygon(xy, facecolor=watercolor, edgecolor=watercolor, zorder=500.)) ax.add_patch(patch) palette.set_bad(clear_color, alpha=0.0) # Plot it up dat_im = m.transform_scalar( np.flipud(dat), lons+0.5*gdict.dx, lats[::-1]-0.5*gdict.dy, np.round(300.*wid), np.round(300.*ht), returnxy=False, checkbounds=False, order=0, masked=True) if topodata is not None: # Drape over hillshade #turn data into an RGBA image cmap = palette #adjust data so scaled between vmin and vmax and between 0 and 1 dat1 = dat_im.copy() dat1[dat1 < vmin] = vmin dat1[dat1 > vmax] = vmax dat1 = (dat1 - vmin)/(vmax-vmin) rgba_img = cmap(dat1) maskvals = np.dstack((dat1.mask, dat1.mask, dat1.mask)) rgb = np.squeeze(rgba_img[:, :, 0:3]) rgb[maskvals] = 1. draped_hsv = ls.blend_hsv(rgb, np.expand_dims(intensity, 2)) m.imshow(draped_hsv, zorder=3., interpolation='none') # This is just a dummy layer that will be deleted to make the # colorbar look right panelhandle = m.imshow(dat_im, cmap=palette, zorder=0., vmin=vmin, vmax=vmax) else: panelhandle = m.imshow(dat_im, cmap=palette, zorder=3., vmin=vmin, vmax=vmax, interpolation='none') #panelhandle = m.pcolormesh(x1, y1, dat, linewidth=0., cmap=palette, vmin=vmin, vmax=vmax, alpha=ALPHA, rasterized=True, zorder=2.); #panelhandle.set_edgecolors('face') # add colorbar cbfmt = '%1.1f' if vmax is not None and vmin is not None: if (vmax - vmin) < 1.: cbfmt = '%1.2f' elif vmax > 5.: # (vmax - vmin) > len(clev): cbfmt = '%1.0f' #norm = mpl.colors.Normalize(vmin=vmin, vmax=vmax) if scaletype.lower() == 'binned': cbar = fig.colorbar(panelhandle, spacing='proportional', ticks=clev, boundaries=clev, fraction=0.036, pad=0.04, format=cbfmt, extend='both') #cbar1 = ColorbarBase(cbar.ax, cmap=palette, norm=norm, spacing='proportional', ticks=clev, boundaries=clev, fraction=0.036, pad=0.04, format=cbfmt, extend='both', extendfrac='auto') else: cbar = fig.colorbar(panelhandle, fraction=0.036, pad=0.04, extend='both', format=cbfmt) #cbar1 = ColorbarBase(cbar.ax, cmap=palette, norm=norm, fraction=0.036, pad=0.04, extend='both', extendfrac='auto', format=cbfmt) if topodata is not None: panelhandle.remove() cbar.set_label(label1, fontsize=10) cbar.ax.tick_params(labelsize=8) parallels = m.drawparallels(getMapLines(bymin, bymax, 3), labels=[1, 0, 0, 0], linewidth=0.5, labelstyle='+/-', fontsize=9, xoffset=-0.8, color='gray', zorder=100.) m.drawmeridians(getMapLines(bxmin, bxmax, 3), labels=[0, 0, 0, 1], linewidth=0.5, labelstyle='+/-', fontsize=9, color='gray', zorder=100.) for par in parallels: try: parallels[par][1][0].set_rotation(90) except: pass #draw roads on the map, if they were provided to us if maproads is True and roadslist is not None: try: for road in roadslist: try: xy = list(road['geometry']['coordinates']) roadx, roady = list(zip(*xy)) mapx, mapy = m(roadx, roady) m.plot(mapx, mapy, roadcolor, lw=0.5, zorder=9) except: continue except Exception as e: print(('Failed to plot roads, %s' % e)) #add city names to map if mapcities is True and cityfile is not None: try: fontname = 'Arial' fontsize = 8 if k == 0: # Only need to choose cities first time and then apply to rest fcities = bcities.limitByMapCollision( m, fontname=fontname, fontsize=fontsize) ctlats, ctlons, names = fcities.getCities() cxis, cyis = m(ctlons, ctlats) for ctlat, ctlon, cxi, cyi, name in zip(ctlats, ctlons, cxis, cyis, names): m.scatter(ctlon, ctlat, c='k', latlon=True, marker='.', zorder=100000) ax.text(cxi, cyi, name, fontname=fontname, fontsize=fontsize, zorder=100000) except Exception as e: print('Failed to plot cities, %s' % e) #draw star at epicenter plt.sca(ax) if edict is not None: elat, elon = edict['lat'], edict['lon'] ex, ey = m(elon, elat) plt.plot(ex, ey, '*', markeredgecolor='k', mfc='None', mew=1.0, ms=15, zorder=10000.) m.drawmapboundary(fill_color=watercolor) m.fillcontinents(color=clear_color, lake_color=watercolor) m.drawrivers(color=watercolor) ##m.drawcoastlines() #draw country boundaries m.drawcountries(color=countrycolor, linewidth=1.0) #add map scale m.drawmapscale((bxmax+bxmin)/2., (bymin+(bymax-bymin)/9.), clon, clat, np.round((((bxmax-bxmin)*111)/5)/10.)*10, barstyle='fancy', zorder=10) # Add border autoAxis = ax.axis() rec = Rectangle((autoAxis[0]-0.7, autoAxis[2]-0.2), (autoAxis[1]-autoAxis[0])+1, (autoAxis[3]-autoAxis[2])+0.4, fill=False, lw=1, zorder=1e8) rec = ax.add_patch(rec) rec.set_clip_on(False) plt.draw() if sref is not None: label2 = '%s\nsource: %s' % (label1, sref) # '%s\n' % label1 + r'{\fontsize{10pt}{3em}\selectfont{}%s}' % sref # else: label2 = label1 plt.title(label2, axes=ax, fontsize=fontsizesub) #draw scenario watermark, if scenario if isScenario: plt.sca(ax) cx, cy = m(clon, clat) plt.text(cx, cy, 'SCENARIO', rotation=45, alpha=0.10, size=72, ha='center', va='center', color='red') #if ds: # Could add this to print "downsampled" on map # plt.text() if k == 1 and rowpan == 1: # adjust single level plot axsize = ax.get_window_extent().transformed(fig.dpi_scale_trans.inverted()) ht2 = axsize.height fig.set_figheight(ht2*1.6) else: plt.tight_layout() # Make room for suptitle - tight layout doesn't account for it plt.subplots_adjust(top=0.92) if printparam is True: try: fig = plt.gcf() dictionary = grids['model']['description']['parameters'] paramstring = 'Model parameters: ' halfway = np.ceil(len(dictionary)/2.) for i, key in enumerate(dictionary): if i == halfway and colpan == 1: paramstring += '\n' paramstring += ('%s = %s; ' % (key, dictionary[key])) print(paramstring) fig.text(0.01, 0.015, paramstring, fontsize=fontsizesmallest) plt.draw() except: print('Could not display model parameters') if edict is not None: eventid = edict['eventid'] else: eventid = '' time1 = datetime.datetime.utcnow().strftime('%d%b%Y_%H%M') outfile = os.path.join(outfolder, '%s_%s_%s.pdf' % (eventid, suptitle, time1)) pngfile = os.path.join(outfolder, '%s_%s_%s.png' % (eventid, suptitle, time1)) if savepdf is True: print('Saving map output to %s' % outfile) plt.savefig(outfile, dpi=300) if savepng is True: print('Saving map output to %s' % pngfile) plt.savefig(pngfile) if showplots is True: plt.show() else: plt.close(fig) return newgrids
def kritikos_fuzzygamma(shakefile, config, bounds=None): """ Runs kritikos procedure with fuzzy gamma """ cmodel = config['statistic_models']['kritikos_2014'] gamma = cmodel['gamma_value'] ## Read in layer files and get data layers = cmodel['layers'] try: # Slope slope_file = layers['slope'] # DFF dff_file = layers['dff'] # DFS dfs_file = layers['dfs'] # Slope Position slope_pos_file = layers['slope_pos'] except: print('Unable to retrieve grid data.') try: div = cmodel['divisor'] # Load in divisors MMI_div = div['MMI'] slope_div = div['slope'] dff_div = div['dff'] dfs_div = div['dfs'] slope_pos_div = div['slope_pos'] except: print('Unable to retrieve divisors.') try: power = cmodel['power'] # Load in powers MMI_power = power['MMI'] slope_power = power['slope'] dff_power = power['dff'] dfs_power = power['dfs'] slope_pos_power = power['slope_pos'] except: print('Unable to retrieve powers.') # Cut and resample all files try: shkgdict = ShakeGrid.getFileGeoDict(shakefile, adjust='res') slopedict = GDALGrid.getFileGeoDict(slope_file) if bounds is not None: # Make sure bounds are within ShakeMap Grid if shkgdict.xmin > bounds['xmin'] or shkgdict.xmax < bounds['xmax'] or shkgdict.ymin > bounds['ymin'] or shkgdict.ymax < bounds['ymax']: print('Specified bounds are outside shakemap area, using ShakeMap bounds instead') bounds = None if bounds is not None: tempgdict = GeoDict({'xmin': bounds['xmin'], 'ymin': bounds['ymin'], 'xmax': bounds['xmax'], 'ymax': bounds['ymax'], 'dx': 100., 'dy': 100., 'nx': 100., 'ny': 100.}, adjust='res') gdict = slpdict.getBoundsWithin(tempgdict) else: # Get boundaries from shakemap if not specified shkgdict = ShakeGrid.getFileGeoDict(shakefile, adjust='res') slpdict = GDALGrid.getFileGeoDict(slopefile) gdict = slpdict.getBoundsWithin(shkgdict) except: print('Unable to create base geodict.') # Load in data try: # Load in slope data slopegrid = GDALGrid.load(slopefile, samplegeodict=gdict, resample=False) slope_data = slopefrid.getData().astype(float) # Load in MMI shakemap = ShakeGrid.load(shakefile, samplegeodict=gdict, resample=True, method='linear', adjust='res') MMI_data = shakemap.getLayer('MMI').getData().astype(float) # Load in Dff dffgrid = GDALGrid.load(slopefile, samplegeodict=gdict, resample=False) dff_data = dffgrid.getData().astype(float) # Load in DFS dfsgrid = GDALGrid.load(slopefile, samplegeodict=gdict, resample=False) dfs_data = dfsgrid.getData().astype(float) # Load in Slope Position slope_pos_grid = GDALGrid.load(slopefile, samplegeodict=gdict, resample=False) slope_pos_data = slop_pos_grid.getData().astype(float) except: print('Data could not be retrieved.') [[[classification]]] MMI = 5,6,7,8,9 slope = 0-4, 5-9, 10-14, 15-19, 20-24, 25-29, 30-34, 35-39, 40-44, 45-49, 50+ # Reclassify as 1,2,3,etc. dff = 0-4, 5-9, 10-19, 20-29, 30-39, 40-49, 50+ # Reclassify as 1,2,3,etc. dfs = 0-0.49, 0.5-0.99, 1.0-1.49, 1.5-1.99, 2.0-2.49, 2.5+ # Reclassify as 1,2,3,etc. slope_pos = 'Flat', 'Valley', 'Mid-Slope', 'Ridge' # Reclassify as 1,2,3,etc.