276 lines
8.3 KiB
Python
276 lines
8.3 KiB
Python
class DnsCase:
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data_start = (4+8*6+4) + (4+8*3+4) + 3 * (4+8*2+4) + 4
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def __init__ (self, case_root, case_name=None):
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import os
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import re
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# Case name
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if case_name is None:
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self.name = os.path.basename(case_root)
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else:
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self.name = case_name
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# Case root directory path
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self.case_root = os.path.abspath(case_root)
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# List of data files. fort.xxxx[x*]
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# matches fort.? files with more than 4 digits
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p = re.compile("fort[.][0-9]{4,}")
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self.data_files = (sorted(filter(p.match, os.listdir(case_root))))
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# Read meta data from the first data file
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# t0, it0, data array shape
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info = self.read_info(os.path.join(case_root, self.data_files[0]))
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self.t0 = info["time"]
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self.it0 = info["itime"]
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self.shape = (info["nx"], info["ny"], info["nz"])
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# Read meta data from the first data file
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info = self.read_info(os.path.join(case_root, self.data_files[-1]))
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self.t1 = info["time"]
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self.it1 = info["itime"]
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self.time = None
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self.itime = None
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self.st = None
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def setup_files (self, dst):
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import os, shutil
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# Make symbolic links to data files
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for datafile in self.data_files:
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os.symlink(
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os.path.join(self.case_root, datafile),
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os.path.join(dst, datafile)
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)
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# Copy Input Parameterfiles
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try:
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shutil.copy(
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os.path.join(self.case_root, "00_lessmag.in"),
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dst
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)
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except IOError as e:
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print(e)
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def read_all_info (self):
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"""
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Loop over all data files to gather all info
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"""
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import os
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if self.time is None:
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self.time = []
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self.itime = []
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self.st = []
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for filename in self.data_files:
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filepath = os.path.join(self.case_root, filename)
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info = self.read_info(filepath)
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self.time.append(info["time"])
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self.itime.append(info["itime"])
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self.st.append(info["u0"])
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def read_info (self, fname):
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'''
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Read Info from a Single DNS Data File
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'''
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import struct
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info_dict = {}
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with open(fname, 'rb') as f1 :
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f1.seek(0)
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raw_info = f1.read(4+8*6+4)[4:-4]
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info_dict['time'] = struct.unpack('d', raw_info[ 0: 8])[0] # fdmtime, double
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info_dict['nx'] = struct.unpack('q', raw_info[ 8:16])[0] # nx, integer
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info_dict['ny'] = struct.unpack('q', raw_info[16:24])[0] # ny, integer
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info_dict['nz'] = struct.unpack('q', raw_info[24:32])[0] # nz integer
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# oldsumc, double
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# time_int, double
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raw_info = f1.read(4+8*3+4)[4:-4]
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info_dict['itime'] = struct.unpack('q', raw_info[ 0: 8])[0] # fdmcyc, integer
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info_dict['dt'] = struct.unpack('d', raw_info[ 8:16])[0] # DT, double
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info_dict['u0'] = struct.unpack('d', raw_info[16:24])[0] # dummyu_, double
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raw_info = f1.read(4+8*2+4)[4:-4]
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# dt_fdmsave, double
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# dt_fdm_fullsave, double
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raw_info = f1.read(4+8*2+4)[4:-4]
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# t_fdmsave, double
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# t_fullsave, double
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raw_info = f1.read(4+8*2+4)[4:-4]
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# in_yr, double
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# out_yr, double
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return info_dict
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def read_data (self, fname):
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'''
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Read Single DNS Data File
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'''
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import numpy as np
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offset_data = self.data_start
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info_dict = self.read_info(fname)
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t = info_dict['time']
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nx = info_dict['nx']
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ny = info_dict['ny']
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nz = info_dict['nz']
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with open(fname, 'rb') as f1 :
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f1.seek(offset_data)
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count = nx*ny*nz
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V = np.fromfile(f1, dtype=np.double, count=(3*count)).reshape((3,nz,ny,nx))
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s = np.fromfile(f1, dtype=np.double, count=(2*count)).reshape((2,nz,ny,nx))
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return t, (nx, ny, nz), V, s
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def read_single_field (self, fname, ifield):
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'''
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Read Single DNS Data File
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'''
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import numpy as np
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offset_data = self.data_start
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info_dict = self.read_info(fname)
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t = info_dict['time']
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nx = info_dict['nx']
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ny = info_dict['ny']
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nz = info_dict['nz']
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with open(fname, 'rb') as f1 :
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count = nx*ny*nz
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f1.seek(offset_data + count * 8 * ifield)
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V = np.fromfile(f1, dtype=np.double, count=count).reshape((nz,ny,nx))
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return t, V
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def case_library ():
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'''
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Return DNS case object library
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'''
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import os
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cases = '''
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IC1 /home1/dhkim/4pi_IC1/4pi_IC1_01_kfmax10_lt58
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IC2 /home1/dhkim/Backup_jinyeong/DNS/run/4pi_IC2/4pi_IC2_01_kfmax19_lt60
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IC3 /home1/dhkim/Backup_jinyeong/DNS/run/4pi_IC3/4pi_IC3_03_kfmax19_lt61_smallDt
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IC4 /home1/dhkim/4pi_IC4/moved/4pi-IC4-additional_new
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IC8 /home1/dhkim/Backup_jinyeong/DNS/run/4pi_IC8/4pi-IC8-02
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IC10 /home1/dhkim/4pi_IC10/4pi_IC10_06_kfmax_22
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IC11 /home1/dhkim/4pi_IC11
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IC12 /home1/dhkim/Backup_jinyeong/DNS/run/4pi_IC12
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IC13 /home1/dhkim/Backup_jinyeong/DNS/run/4pi_IC13/4pi_IC13_lt60'''.split()
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cic_case_dict = dict(zip(cases[0::2], cases[1::2]))
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database_root = '/home1/ignis/ignis/'
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names = 'VIC1 VIC2 VIC4 VIC10 VIC13 '.split()
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cases = 'ic1-5dm ic2-5dm ic4-5dm ic10-5dm ic13-5dm'.split()
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for case_name, case_dir in zip(names, cases):
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case_root = os.path.join(database_root, case_dir)
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cic_case_dict[case_name] = case_root
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case_dict = dict([ (case_name, DnsCase(cic_case_dict[case_name], case_name=case_name))
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for case_name in cic_case_dict
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])
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return case_dict
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if __name__ == "__main__":
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import os, sys, argparse
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cases = '''
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IC1 /home1/dhkim/4pi_IC1/4pi_IC1_01_kfmax10_lt58
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IC2 /home1/dhkim/Backup_jinyeong/DNS/run/4pi_IC2/4pi_IC2_01_kfmax19_lt60
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IC3 /home1/dhkim/Backup_jinyeong/DNS/run/4pi_IC3/4pi_IC3_03_kfmax19_lt61_smallDt
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IC4 /home1/dhkim/4pi_IC4/moved/4pi-IC4-additional_new
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IC8 /home1/dhkim/Backup_jinyeong/DNS/run/4pi_IC8/4pi-IC8-02
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IC10 /home1/dhkim/4pi_IC10/4pi_IC10_06_kfmax_22
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IC11 /home1/dhkim/4pi_IC11
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IC12 /home1/dhkim/Backup_jinyeong/DNS/run/4pi_IC12
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IC13 /home1/dhkim/Backup_jinyeong/DNS/run/4pi_IC13/4pi_IC13_lt60'''.split()
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cic_case_dict = dict(zip(cases[0::2], cases[1::2]))
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database_root = '/home1/ignis/ignis/'
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names = 'VIC1 VIC2 VIC4 VIC10 VIC13 '.split()
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cases = 'ic1-5dm ic2-5dm ic4-5dm ic10-5dm ic13-5dm'.split()
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for case_name, case_dir in zip(names, cases):
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case_root = os.path.join(database_root, case_dir)
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cic_case_dict[case_name] = case_root
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# Commandline argument parser
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parser = argparse.ArgumentParser()
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parser.add_argument("-l", "--list", help="list all cases", action='store_true')
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parser.add_argument("-c", "--create", help="create a case or all cases")
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args = parser.parse_args()
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params = vars(args)
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# List all cases
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if params["list"]:
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for case_name in sorted(cic_case_dict):
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print(case_name, cic_case_dict[case_name])
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sys.exit(0)
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# Create case directories
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create_case = params["create"]
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if create_case:
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if create_case == "all":
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print ("Creating All DNS Cases for Post-processing")
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for case_name in sorted(cic_case_dict):
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print ("Creating DNS Case {} for Post-processing".format(case_name))
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os.mkdir(case_name)
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# Create DNS Case Object
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case_obj = DnsCase(cic_case_dict[case_name], case_name=case_name)
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case_obj.setup_files(case_name)
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else:
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if create_case in cic_case_dict:
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print ("Creating DNS Case {} for Post-processing".format(create_case))
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os.mkdir(create_case)
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# Create DNS Case Object
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case_obj = DnsCase(cic_case_dict[create_case], case_name=create_case)
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case_obj.setup_files(create_case)
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else:
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print ("Can't find DNS Case {}".format(create_case))
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