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Merge pull request #1675 from danielpeter/devel
adds possibility to read external source time function files in binary format
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...lications/meshfem3D_examples/regular_element_mesh/create_external_source_time_function.py
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,233 @@ | ||
| #!/usr/bin/env python | ||
| # | ||
| # creates an external source time function file | ||
| # | ||
| # example: | ||
| # ./create_external_source_time_function.py OUTPUT_FILES/plot_source_time_function.txt | ||
| # | ||
| # requires access to: DATA/Par_file | ||
| # | ||
| import sys | ||
| import os | ||
| import array | ||
|
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| import numpy as np | ||
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| def write_ascii_file(filename,data): | ||
| """ | ||
| writes data array to ascii file | ||
| """ | ||
| with open(filename, mode='w') as f: | ||
| # user output | ||
| print(" filename: ",filename) | ||
| print(" number of points in array = ",len(data)) | ||
|
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| # comment lines | ||
| f.write("# Source time function\n") | ||
| f.write("# number of time steps: {}\n".format(len(data))) | ||
| # data values | ||
| f.write("# STF values\n") | ||
| for i in range(len(data)): | ||
| val = data[i] | ||
| f.write("{}\n".format(val)) | ||
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| print(" file written") | ||
| print("") | ||
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| def write_binary_file(filename,data): | ||
| """ | ||
| writes data array to binary file | ||
| """ | ||
| # float 'f' by default (otherwise 'd' for double precision) | ||
| custom_type = 'f' | ||
|
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| with open(filename, mode='wb') as f: | ||
| # gets array length in bytes | ||
| # marker | ||
| binlength = array.array('i') | ||
| num_points = data.size | ||
| if custom_type == 'f': | ||
| # float (4 bytes) for single precision | ||
| binlength.fromlist([num_points * 4]) | ||
| else: | ||
| # double precision | ||
| binlength.fromlist([num_points * 8]) | ||
|
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| # user output | ||
| print(" filename: ",filename) | ||
| print(" array length = ",binlength," Bytes") | ||
| print(" number of points in array = ",num_points) | ||
|
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| # writes array data | ||
| binvalues = array.array(custom_type) | ||
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| data = np.reshape(data, (num_points), order='F') # fortran-like index ordering | ||
| #print("debug: data ",data.tolist()) | ||
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| binvalues.fromlist(data.tolist()) #.tolist()) | ||
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| # fortran binary file: file starts with array-size again | ||
| binlength.tofile(f) | ||
| # data | ||
| binvalues.tofile(f) | ||
| # fortran binary file: file ends with array-size again | ||
| binlength.tofile(f) | ||
|
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| print(" file written") | ||
| print("") | ||
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| def create_external_source_time_function(input_file,use_ascii=True): | ||
| """ | ||
| creates an external STF file in DATA/ | ||
| """ | ||
|
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| print("") | ||
| print("creating external source time function file: DATA/stf.dat") | ||
| print(" input file : ",input_file) | ||
| print("") | ||
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| if len(input_file) == 0: usage() | ||
|
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| # checks if file exists | ||
| if not os.path.isfile(input_file): | ||
| print("Please check if file exists: ",input_file) | ||
| sys.exit(1) | ||
|
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| # reads in input file | ||
| with open(input_file, 'r') as f: | ||
| content = f.readlines() | ||
|
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| # checks number of lines | ||
| if len(content) == 0: | ||
| print("File is empty, please check input file") | ||
| sys.exit(1) | ||
|
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| # get data entries | ||
| stf_data = np.array([]) | ||
| for line in content: | ||
| # count valid data lines | ||
| if "#" in line or "!" in line: | ||
| # comment line | ||
| continue | ||
| else: | ||
| # assumes this is a data line | ||
| # cleans line from whitespace and extra characters | ||
| line = line.strip() | ||
| # check for empty line | ||
| if len(line) == 0: continue | ||
|
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| # reads in value(s) | ||
| numbers = line.split() | ||
|
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| if len(numbers) == 0: | ||
| # nothing to read | ||
| continue | ||
| if len(numbers) == 1: | ||
| # single data entry per line | ||
| val = float(numbers[0]) | ||
| elif len(numbers) == 2: | ||
| # line contains two numbers (like plot_source_time_function.txt) | ||
| # we'll take the second | ||
| val = float(numbers[1]) | ||
| else: | ||
| # line contains multiple numbers | ||
| # we'll take the last | ||
| val = float(numbers[-1]) | ||
|
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| # store data value | ||
| stf_data = np.append(stf_data,val) | ||
|
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| print("number of STF time steps found: ",len(stf_data)) | ||
| print("") | ||
|
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| # checks with Par_file setting | ||
| filename = "DATA/Par_file" | ||
| with open(filename,'r') as f: | ||
| content_par = f.readlines() | ||
|
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| NSTEP = None | ||
| for line in content_par: | ||
| # skip comments | ||
| if "#" in line or "!" in line: continue | ||
|
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| # search for NSTEP | ||
| if "NSTEP" in line and "=" in line: | ||
| NSTEP = int(line.split('=')[1]) | ||
|
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| print("Par_file:") | ||
| print(" simulation NSTEP = ",NSTEP) | ||
| print("") | ||
|
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| # checks | ||
| if NSTEP is None: | ||
| print("Couldn't find NSTEP in DATA/Par_file") | ||
| sys.exit(1) | ||
|
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| # checks lengths | ||
| # must have at least NSTEP data entries in input file | ||
| if NSTEP > len(stf_data): | ||
| print("Error: simulation length NSTEP = {} is longer than the available STF data {}".format(NSTEP,len(stf_data))) | ||
| print(" Please use another input file...") | ||
| sys.exit(1) | ||
|
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| # warning if data length is too long | ||
| if NSTEP < len(stf_data): | ||
| print("WARNING: simulation length NSTEP == {} is shorter than the available STF data {}".format(NSTEP,len(stf_data))) | ||
| print(" Only the first {} data entries will be written to the output STF file, all the others will be ignored".format(NSTEP)) | ||
| print("") | ||
|
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| # cuts STF data to simulation length | ||
| stf_data = stf_data[0:NSTEP] | ||
|
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| # stats | ||
| stf_min = stf_data.min() | ||
| stf_max = stf_data.max() | ||
| print("stats:") | ||
| print(" source time function values: min/max = {} / {}".format(stf_min,stf_max)) | ||
| print("") | ||
|
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| # output STF file | ||
| if use_ascii: | ||
| filename = "DATA/stf.dat" | ||
| print("writing ascii output:") | ||
| write_ascii_file(filename,stf_data) | ||
| else: | ||
| filename ="DATA/stf.dat.bin" | ||
| print("writing binary output:") | ||
| write_binary_file(filename,stf_data) | ||
|
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| print("written external source time function to: ",filename) | ||
| print("") | ||
| print("all done") | ||
| print("") | ||
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| def usage(): | ||
| print("usage: ./create_external_source_time_function.py input_file [--ascii or --binary]") | ||
| print(" with") | ||
| print(" input_file - ascii file with trace, e.g., OUTPUT_FILES/plot_source_time_function.txt") | ||
| print(" --ascii - (optional) writes out STF as ascii file (default)") | ||
| print(" --binary - (optional) writes out STF as binary file") | ||
| sys.exit(1) | ||
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| if __name__ == '__main__': | ||
| # init | ||
| input_file = "" | ||
| use_ascii = True | ||
| # reads arguments | ||
| #print("\nnumber of arguments: " + str(len(sys.argv))) | ||
| if len(sys.argv) < 1: usage() | ||
|
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| input_file = sys.argv[1] | ||
| if len(sys.argv) == 3: | ||
| if sys.argv[2] == "--ascii": | ||
| use_ascii = True | ||
| elif sys.argv[2] == "--binary": | ||
| use_ascii = False | ||
|
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| # main routine | ||
| create_external_source_time_function(input_file,use_ascii) |
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