def main(): """ NAME cart_dir.py DESCRIPTION converts cartesian coordinates to geomagnetic elements INPUT (COMMAND LINE ENTRY) x1 x2 x3 if only two columns, assumes magnitude of unity OUTPUT declination inclination magnitude SYNTAX cart_dir.py [command line options] [< filename] OPTIONS -h prints help message and quits -i for interactive data entry -f FILE to specify input filename -F OFILE to specify output filename (also prints to screen) """ ofile="" if '-h' in sys.argv: print main.__doc__ sys.exit() if '-F' in sys.argv: ind=sys.argv.index('-F') ofile=sys.argv[ind+1] outfile=open(ofile,'w') if '-i' in sys.argv: cont=1 while cont==1: cart=[] try: ans=raw_input('X: [ctrl-D to quit] ') cart.append(float(ans)) ans=raw_input('Y: ') cart.append(float(ans)) ans=raw_input('Z: ') cart.append(float(ans)) except: print "\n Good-bye \n" sys.exit() dir= pmag.cart2dir(cart) # send dir to dir2cart and spit out result print '%7.1f %7.1f %10.3e'%(dir[0],dir[1],dir[2]) elif '-f' in sys.argv: ind=sys.argv.index('-f') file=sys.argv[ind+1] input=numpy.loadtxt(file) # read from a file else: input = numpy.loadtxt(sys.stdin,dtype=numpy.float) # read from standard input dir=pmag.cart2dir(input) for line in dir: print '%7.1f %7.1f %10.3e'%(line[0],line[1],line[2]) if ofile!="": outstring='%7.1f %7.1f %10.8e\n' %(line[0],line[1],line[2]) outfile.write(outstring)
def spitout(line): cart=[] # initialize list for dec,inc,intensity dat=line.split() # split the data on a space into columns for element in dat: # step through dec,inc, int cart.append(float(element)) # append floating point variable to "cart" dir= pmag.cart2dir(cart) # send cart to cart2dir print '%7.1f %7.1f %10.3e'%(dir[0],dir[1],dir[2]) return dir
def Rotate_zijderveld(Zdata, rot_declination): if len(Zdata) == 0: return ([]) CART_rot = [] for i in range(0, len(Zdata)): DIR = cart2dir(Zdata[i]) DIR[0] = (DIR[0] - rot_declination) % 360. CART_rot.append(array(dir2cart(DIR))) CART_rot = array(CART_rot) return (CART_rot)
def Rotate_zijderveld(Zdata,rot_declination): if len(Zdata)==0: return([]) CART_rot=[] for i in range(0,len(Zdata)): DIR=cart2dir(Zdata[i]) DIR[0]=(DIR[0]-rot_declination)%360. CART_rot.append(array(dir2cart(DIR))) CART_rot=array(CART_rot) return(CART_rot)
def plotELL(pars,col,lower,plot): #Modified from PmagPy (Tauxe et al., 2016) """ function to calculate points on an ellipse about Pdec,Pdip with angle beta,gamma """ #pylab.figure(num=fignum) Pdec,Pinc,beta,Bdec,Binc,gamma,Gdec,Ginc=pars[0],pars[1],pars[2],pars[3],pars[4],pars[5],pars[6],pars[7] if beta > 90. or gamma>90: beta=180.-beta gamma=180.-beta Pdec=Pdec-180. Pinc=-Pinc beta,gamma=beta*rad,gamma*rad # convert to radians X_ell,Y_ell,X_up,Y_up,PTS=[],[],[],[],[] nums=201 xnum=float(nums-1.)/2. # set up t matrix t=[[0,0,0],[0,0,0],[0,0,0]] X=pmag.dir2cart((Pdec,Pinc,1.0)) # convert to cartesian coordintes if lower==1 and X[2]<0: for i in range(3): X[i]=-X[i] # set up rotation matrix t t[0][2]=X[0] t[1][2]=X[1] t[2][2]=X[2] X=pmag.dir2cart((Bdec,Binc,1.0)) if lower==1 and X[2]<0: for i in range(3): X[i]=-X[i] t[0][0]=X[0] t[1][0]=X[1] t[2][0]=X[2] X=pmag.dir2cart((Gdec,Ginc,1.0)) if lower==1 and X[2]<0: for i in range(3): X[i]=-X[i] t[0][1]=X[0] t[1][1]=X[1] t[2][1]=X[2] # set up v matrix v=[0,0,0] for i in range(nums): # incremental point along ellipse psi=float(i)*np.pi/xnum v[0]=np.sin(beta)*np.cos(psi) v[1]=np.sin(gamma)*np.sin(psi) v[2]=np.sqrt(1.-v[0]**2 - v[1]**2) elli=[0,0,0] # calculate points on the ellipse for j in range(3): for k in range(3): elli[j]=elli[j] + t[j][k]*v[k] # cartesian coordinate j of ellipse PTS.append(pmag.cart2dir(elli)) R=np.sqrt( 1.-abs(elli[2]))/(np.sqrt(elli[0]**2+elli[1]**2)) # put on an equal area projection if elli[2]<0: # for i in range(3): elli[i]=-elli[i] X_up.append(elli[1]*R) Y_up.append(elli[0]*R) else: X_ell.append(elli[1]*R) Y_ell.append(elli[0]*R) if plot==1: if X_ell!=[]:plt.plot(X_ell,Y_ell,col,linewidth=2,zorder=5)#pylab.plot(X_ell,Y_ell,col,zorder=3) if X_up!=[]:plt.plot(X_up,Y_up,col,linewidth=2,zorder=5)#pylab.plot(X_up,Y_up,'g-',zorder=3) #pylab.draw() else: return PTS
def main(): """ NAME LIVMW_magic.py DESCRIPTION converts Liverpool microwave format files to magic_measurements format files SYNTAX LIVMW_magic.py [command line options] OPTIONS -h: prints the help message and quits. -f FILE: specify liverpool format input file, required -usr USER: identify user, default is "" -ins INST: identify instrument, e.g., LIV-TRISTAN, LIV-OLD14GHZ, default is "" -loc LOCNAME : specify location/study name, required -F FILE: specify output file, default is magic_measurements.txt -Fsa FILE: specify er_samples formatted file for appending, default is new er_samples.txt -spc NUM : specify number of characters to designate a specimen, default = 1 -sit Site_name : specify site name for this specimen -unc measurement units are uncalibrated (default is uAm^2) -B PHI THETA: dc lab field phi, theta, default is 0, 90 -ncn NCON: specify naming convention - required if -sit not specified Sample naming convention: do not use if -sit option used! [1] XXXXY: where XXXX is an arbitrary length site designation and Y is the single character sample designation. e.g., TG001a is the first sample from site TG001. [default] [2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length) [3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length) [4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX [5] site name same as sample [6] site is entered under a separate column [7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY NB: all others you will have to customize your self or e-mail [email protected] for help. """ # initialize some stuff version_num = pmag.get_version() noave = 0 methcode, instcode = "", "" phi, theta, peakfield, labfield = 0, 0, 0, 0 pMRM, MD, samp_con, Z, site = 0, 0, "6", "", "" er_location_name = "" citation = "This study" args = sys.argv methcode = "LP-NO" # NRM specnum, measnum = 1, 1 powt_max = 0 ErSamps, Samps = [], [] # # get command line arguments # dirpath = "." meas_file, samp_file = dirpath + "/magic_measurements.txt", dirpath + "/er_samples.txt" user = "" unc = 0 if "-WD" in args: ind = args.index("-WD") dirpath = args[ind + 1] if "-h" in args: print main.__doc__ sys.exit() if "-usr" in args: ind = args.index("-usr") user = args[ind + 1] if "-ins" in args: ind = args.index("-ins") instcode = args[ind + 1] if "-F" in args: ind = args.index("-F") meas_file = dirpath + "/" + args[ind + 1] if "-Fsa" in args: ind = args.index("-Fsa") samp_file = args[ind + 1] samp_file = dirpath + "/" + samp_file try: open(samp_file, "rU") ErSamps, file_type = pmag.magic_read(samp_file) print "sample information will be appended to new er_samples.txt file" except: print "er_samples.txt file does not exist" print "sample information will be stored in new er_samples.txt file" if "-f" in args: ind = args.index("-f") magfile = args[ind + 1] magfile = dirpath + "/" + magfile try: input = open(magfile, "rU") except: print "bad mag file name" sys.exit() else: print "mag_file field is required option" print main.__doc__ sys.exit() if "-B" in args: ind = args.index("-B") phi = args[ind + 1] theta = args[ind + 2] else: phi, theta = "0.", "90." if "-spc" in args: ind = args.index("-spc") specnum = int(args[ind + 1]) if specnum != 0: specnum = -specnum if "-loc" in args: ind = args.index("-loc") er_location_name = args[ind + 1] if "-unc" in args: unc = 1 if "-sit" in args: ind = args.index("-sit") site = args[ind + 1] if "-ncn" in args: ind = args.index("-ncn") samp_con = sys.argv[ind + 1] if "4" in samp_con: if "-" not in samp_con: print "option [4] must be in form 4-Z where Z is an integer" sys.exit() else: Z = samp_con.split("-")[1] samp_con = "4" if "7" in samp_con: if "-" not in samp_con: print "option [7] must be in form 7-Z where Z is an integer" sys.exit() else: Z = samp_con.split("-")[1] samp_con = "7" if samp_con == "6" and site == "": print "you must either specify a naming convention, or a site name" print main.__doc__ sys.exit() MagRecs = [] if len(ErSamps) > 1: for samp in ErSamps: if samp["er_sample_name"] not in Samps: Samps.append(samp["er_sample_name"]) Data = input.readlines() if 1: # never mind for line in Data: if len(line) > 1: rec = line.split(",") MagRec = {} MagRec["er_citation_names"] = "This study" MagRec["er_location_name"] = er_location_name MagRec["magic_software_packages"] = version_num MagRec["treatment_temp"] = "%8.3e" % (273) # room temp in kelvin MagRec["measurement_temp"] = "%8.3e" % (273) # room temp in kelvin MagRec["treatment_ac_field"] = "0" MagRec["treatment_dc_field"] = "0" MagRec["treatment_dc_field_phi"] = "" MagRec["treatment_dc_field_theta"] = "" MagRec["treatment_mw_integral"] = "" meas_type = "LT-NO" MagRec["er_specimen_name"] = rec[0][1:-1] MagRec["er_location_name"] = er_location_name if specnum != 0: MagRec["er_sample_name"] = rec[0][1:-1][:specnum] else: MagRec["er_sample_name"] = rec[0][1:-1] if site == "": site = pmag.parse_site(MagRec["er_sample_name"], samp_con, Z) MagRec["er_site_name"] = site MagRec["treatment_mw_power"] = rec[2] MagRec["treatment_mw_time"] = rec[3] powt = int(float(MagRec["treatment_mw_power"]) * (float(MagRec["treatment_mw_time"]))) MagRec["treatment_mw_energy"] = "%7.1f" % (powt) if powt > powt_max: powt_max = powt treat = rec[1].strip('"').upper() if treat == "Z": # in zero field meas_type = "LT-M-Z" # as opposed to LT-MV-Z if powt < powt_max: meas_type = "LT-PMRM-Z" elif treat == "A": # in zero field meas_type = "LT-M-I" # as opposed to LT-MV-I labfield = float(rec[10]) * 1e-6 # assuming uT, convert to T MagRec["treatment_dc_field"] = "%8.3e" % (labfield) # labfield in tesla (convert from microT) MagRec["treatment_dc_field_phi"] = phi # labfield phi MagRec["treatment_dc_field_theta"] = theta # labfield theta if powt < powt_max: meas_type = "LT-PMRM-I" if len(rec) > 10: MagRec["treatment_mw_integral"] = rec[10] if unc == 0: MagRec["measurement_magn_moment"] = "%10.3e" % (float(rec[4]) * 1e-6) # moment in Am^2 (from uAm^2) if unc == 1: MagRec["measurement_magnitude"] = rec[4] # uncalibrated moment cart = [] cart.append(float(rec[7])) cart.append(float(rec[8])) cart.append(float(rec[9])) dir = pmag.cart2dir(cart) MagRec["measurement_dec"] = "%9.3f" % (dir[0]) MagRec["measurement_inc"] = "%9.3f" % (dir[1]) MagRec["magic_instrument_codes"] = instcode MagRec["magic_method_codes"] = meas_type MagRec["measurement_flag"] = "g" MagRec["measurement_standard"] = "u" MagRec["measurement_number"] = "%i" % (measnum) MagRec["magic_experiment_name"] = MagRec["er_specimen_name"] + ":" + methcode measnum += 1 MagRecs.append(MagRec) if MagRec["er_sample_name"] not in Samps: # add this puppy to the list in er_samples.txt Samps.append(MagRec["er_sample_name"]) ErSamp = {} ErSamp["er_sample_name"] = Samps[-1] ErSamp["er_location_name"] = MagRec["er_location_name"] ErSamp["er_site_name"] = site ErSamp["er_citation_names"] = "This study" gdec = float(rec[5]) ginc = float(rec[6]) az, pl = pmag.get_azpl(dir[0], dir[1], gdec, ginc) ErSamp["sample_azimuth"] = "%7.1f" % az ErSamp["sample_dip"] = "%7.1f" % pl ErSamps.append(ErSamp) MagOuts = pmag.mw_measurements_methods(MagRecs) pmag.magic_write(meas_file, MagOuts, "magic_measurements") print "measurements put in ", meas_file pmag.magic_write(samp_file, ErSamps, "er_samples") print "sample names put in ", samp_file
def main(command_line=True, **kwargs): """ NAME IODP_jr6_magic.py DESCRIPTION converts shipboard .jr6 format files to magic_measurements format files SYNTAX IODP_jr6_magic.py [command line options] OPTIONS -h: prints the help message and quits. -f FILE: specify input file, or -F FILE: specify output file, default is magic_measurements.txt -fsa FILE: specify er_samples.txt file for sample name lookup , default is 'er_samples.txt' -loc HOLE : specify hole name (U1456A) -A: don't average replicate measurements INPUT JR6 .jr6 format file """ def fix_separation(filename, new_filename): old_file = open(filename, 'rU') data = old_file.readlines() new_data = [] for line in data: new_line = line.replace('-', ' -') new_line = new_line.replace(' ', ' ') new_data.append(new_line) new_file = open(new_filename, 'w') for s in new_data: new_file.write(s) old_file.close() new_file.close() return new_filename def old_fix_separation(filename, new_filename): old_file = open(filename, 'rU') data = old_file.readlines() new_data = [] for line in data: new_line = [] for i in line.split(): if '-' in i[1:]: lead_char = '-' if i[0] == '-' else '' if lead_char: v = i[1:].split('-') else: v = i.split('-') new_line.append(lead_char + v[0]) new_line.append('-' + v[1]) else: new_line.append(i) new_line = (' '.join(new_line)) + '\n' new_data.append(new_line) new_file = open(new_filename, 'w') for s in new_data: new_file.write(s) new_file.close() old_file.close() return new_filename # initialize some stuff noave=0 volume=2.5**3 #default volume is a 2.5cm cube inst="" samp_con,Z='5',"" missing=1 demag="N" er_location_name="unknown" citation='This study' args=sys.argv meth_code="LP-NO" version_num=pmag.get_version() dir_path='.' MagRecs=[] samp_file = 'er_samples.txt' meas_file = 'magic_measurements.txt' mag_file = '' # # get command line arguments # if command_line: if '-WD' in sys.argv: ind = sys.argv.index('-WD') dir_path=sys.argv[ind+1] if '-ID' in sys.argv: ind = sys.argv.index('-ID') input_dir_path = sys.argv[ind+1] else: input_dir_path = dir_path output_dir_path = dir_path if "-h" in args: print main.__doc__ return False if '-F' in args: ind=args.index("-F") meas_file = args[ind+1] if '-fsa' in args: ind = args.index("-fsa") samp_file = args[ind+1] if samp_file[0]!='/': samp_file = os.path.join(input_dir_path, samp_file) try: open(samp_file,'rU') ErSamps,file_type=pmag.magic_read(samp_file) except: print samp_file,' not found: ' print ' download csv file and import to MagIC with IODP_samples_magic.py' if '-f' in args: ind = args.index("-f") mag_file= args[ind+1] if "-loc" in args: ind=args.index("-loc") er_location_name=args[ind+1] if "-A" in args: noave=1 if not command_line: dir_path = kwargs.get('dir_path', '.') input_dir_path = kwargs.get('input_dir_path', dir_path) output_dir_path = dir_path meas_file = kwargs.get('meas_file', 'magic_measurements.txt') mag_file = kwargs.get('mag_file', '') samp_file = kwargs.get('samp_file', 'er_samples.txt') specnum = kwargs.get('specnum', 1) samp_con = kwargs.get('samp_con', '1') if len(str(samp_con)) > 1: samp_con, Z = samp_con.split('-') else: Z = '' er_location_name = kwargs.get('er_location_name', '') noave = kwargs.get('noave', 0) # default (0) means DO average meth_code = kwargs.get('meth_code', "LP-NO") # format variables meth_code=meth_code+":FS-C-DRILL-IODP:SP-SS-C:SO-V" meth_code=meth_code.strip(":") if mag_file: mag_file = os.path.join(input_dir_path, mag_file) samp_file = os.path.join(input_dir_path, samp_file) meas_file = os.path.join(output_dir_path, meas_file) # validate variables if not mag_file: print "You must provide an IODP_jr6 format file" return False, "You must provide an IODP_jr6 format file" if not os.path.exists(mag_file): print 'The input file you provided: {} does not exist.\nMake sure you have specified the correct filename AND correct input directory name.'.format(os.path.join(input_dir_path, mag_file)) return False, 'The input file you provided: {} does not exist.\nMake sure you have specified the correct filename AND correct input directory name.'.format(magfile) if not os.path.exists(samp_file): print 'samp_file', samp_file print "Your input directory:\n{}\nmust contain an er_samples.txt file, or you must explicitly provide one".format(input_dir_path) return False, "Your input directory:\n{}\nmust contain an er_samples.txt file, or you must explicitly provide one".format(input_dir_path) # parse data temp = os.path.join(output_dir_path, 'temp.txt') fix_separation(mag_file, temp) #os.rename('temp.txt', mag_file) #data = open(mag_file, 'rU').readlines() data=pd.read_csv(temp, delim_whitespace=True,header=None) os.remove(temp) samples,filetype = pmag.magic_read(samp_file) data.columns=['specname','step','negz','y','x','expon','sample_azimuth','sample_dip','sample_bed_dip_direction','sample_bed_dip','bed_dip_dir2','bed_dip2','param1','param2','param3','param4','measurement_csd'] cart=np.array([data['x'],data['y'],-data['negz']]).transpose() dir= pmag.cart2dir(cart).transpose() data['measurement_dec']=dir[0] data['measurement_inc']=dir[1] data['measurement_magn_volume']=dir[2]*(10.0**data['expon']) # A/m - data in A/m data['measurement_flag']='g' data['measurement_standard']='u' data['measurement_number']='1' data['measurement_temp']='273' data['er_location_name']=er_location_name for rowNum, row in data.iterrows(): MagRec={} spec_text_id=row['specname'].split('_')[1] SampRecs=pmag.get_dictitem(samples,'er_sample_alternatives',spec_text_id,'has') # retrieve sample record for this specimen if len(SampRecs)>0: # found one MagRec['er_specimen_name']=SampRecs[0]['er_sample_name'] MagRec['er_sample_name']=MagRec['er_specimen_name'] MagRec['er_site_name']=MagRec['er_specimen_name'] MagRec["er_citation_names"]="This study" MagRec['er_location_name']=er_location_name MagRec['magic_software_packages']=version_num MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin MagRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin MagRec["measurement_flag"]='g' MagRec["measurement_standard"]='u' MagRec["measurement_number"]='1' MagRec["treatment_ac_field"]='0' volume=float(SampRecs[0]['sample_volume']) moment=row['measurement_magn_volume'] * volume MagRec["measurement_magn_moment"]=str(moment) MagRec["measurement_magn_volume"]=str(row['measurement_magn_volume']) MagRec["measurement_dec"]='%7.1f'%(row['measurement_dec']) MagRec["measurement_inc"]='%7.1f'%(row['measurement_inc']) if row['step'] == 'NRM': meas_type="LT-NO" elif row['step'][0:2] == 'AD': meas_type="LT-AF-Z" treat=float(row['step'][2:]) MagRec["treatment_ac_field"]='%8.3e' %(treat*1e-3) # convert from mT to tesla elif row['step'][0] == 'TD': meas_type="LT-T-Z" treat=float(row['step'][2:]) MagRec["treatment_temp"]='%8.3e' % (treat+273.) # temp in kelvin elif row['step'][0:3]=='ARM': # meas_type="LT-AF-I" treat=float(row['step'][3:]) MagRec["treatment_ac_field"]='%8.3e' %(treat*1e-3) # convert from mT to tesla MagRec["treatment_dc_field"]='%8.3e' %(50e-6) # assume 50uT DC field MagRec["measurement_description"]='Assumed DC field - actual unknown' elif row['step'][0:3]=='IRM': # meas_type="LT-IRM" treat=float(row['step'][3:]) MagRec["treatment_dc_field"]='%8.3e' %(treat*1e-3) # convert from mT to tesla else: print 'unknown treatment type for ',row return False, 'unknown treatment type for ',row MagRec['magic_method_codes']=meas_type MagRecs.append(MagRec.copy()) else: print 'sample name not found: ',row['specname'] MagOuts=pmag.measurements_methods(MagRecs,noave) file_created, error_message = pmag.magic_write(meas_file,MagOuts,'magic_measurements') if file_created: return True, meas_file else: return False, 'Results not written to file'
def main(command_line=True, **kwargs): """ NAME BGC_magic.py DESCRIPTION converts Berkeley Geochronology Center (BGC) format files to magic_measurements format files SYNTAX BGC_magic.py [command line options] OPTIONS -h: prints the help message and quits. -f FILE: specify input file, or -F FILE: specify output file, default is magic_measurements.txt -Fsa: specify er_samples format file for appending, default is new er_samples.txt (Not working yet) -loc LOCNAME : specify location/study name -site SITENAME : specify site name -A: don't average replicate measurements -mcd [SO-MAG,SO-SUN,SO-SIGHT...] supply how these samples were oriented -v NUM : specify the volume in cc of the sample, default 2.5^3cc. Will use vol in data file if volume!=0 in file. INPUT BGC paleomag format file """ # initialize some stuff noave = 0 volume = 0.025 ** 3 # default volume is a 2.5cm cube # inst="" # samp_con,Z='1',"" # missing=1 # demag="N" er_location_name = "unknown" er_site_name = "unknown" # citation='This study' args = sys.argv meth_code = "LP-NO" # specnum=1 version_num = pmag.get_version() mag_file = "" dir_path = "." MagRecs = [] SampOuts = [] samp_file = "er_samples.txt" meas_file = "magic_measurements.txt" meth_code = "" # # get command line arguments # if command_line: if "-WD" in sys.argv: ind = sys.argv.index("-WD") dir_path = sys.argv[ind + 1] if "-ID" in sys.argv: ind = sys.argv.index("-ID") input_dir_path = sys.argv[ind + 1] else: input_dir_path = dir_path output_dir_path = dir_path if "-h" in args: print main.__doc__ return False if "-F" in args: ind = args.index("-F") meas_file = args[ind + 1] if "-Fsa" in args: ind = args.index("-Fsa") samp_file = args[ind + 1] # try: # open(samp_file,'rU') # ErSamps,file_type=pmag.magic_read(samp_file) # print 'sample information will be appended to ', samp_file # except: # print samp_file,' not found: sample information will be stored in new er_samples.txt file' # samp_file = output_dir_path+'/er_samples.txt' if "-f" in args: ind = args.index("-f") mag_file = args[ind + 1] if "-loc" in args: ind = args.index("-loc") er_location_name = args[ind + 1] if "-site" in args: ind = args.index("-site") er_site_name = args[ind + 1] if "-A" in args: noave = 1 if "-mcd" in args: ind = args.index("-mcd") meth_code = args[ind + 1] # samp_con='5' if "-v" in args: ind = args.index("-v") volume = float(args[ind + 1]) * 1e-6 # enter volume in cc, convert to m^3 if not command_line: dir_path = kwargs.get("dir_path", ".") input_dir_path = kwargs.get("input_dir_path", dir_path) output_dir_path = dir_path meas_file = kwargs.get("meas_file", "magic_measurements.txt") mag_file = kwargs.get("mag_file") samp_file = kwargs.get("samp_file", "er_samples.txt") er_location_name = kwargs.get("er_location_name", "") er_site_name = kwargs.get("er_site_name", "") noave = kwargs.get("noave", 0) # default (0) means DO average meth_code = kwargs.get("meth_code", "LP-NO") volume = float(kwargs.get("volume", 0)) if not volume: volume = 0.025 ** 3 # default volume is a 2.5 cm cube, translated to meters cubed else: # convert cm^3 to m^3 volume *= 1e-6 # format variables if not mag_file: return False, "You must provide a BCG format file" mag_file = os.path.join(input_dir_path, mag_file) meas_file = os.path.join(output_dir_path, meas_file) samp_file = os.path.join(output_dir_path, samp_file) ErSampRec = {} # parse data # Open up the BGC file and read the header information print "mag_file in BGC_magic", mag_file pre_data = open(mag_file, "rU") line = pre_data.readline() line_items = line.split(" ") sample_name = line_items[2] sample_name = sample_name.replace("\n", "") line = pre_data.readline() line = pre_data.readline() line_items = line.split("\t") sample_azimuth = float(line_items[1]) sample_dip = 90.0 - float(line_items[2]) sample_bed_dip = line_items[3] sample_bed_azimuth = line_items[4] sample_lon = line_items[5] sample_lat = line_items[6] tmp_volume = line_items[7] if tmp_volume != 0.0: volume = float(tmp_volume) * 1e-6 pre_data.close() data = pd.read_csv(mag_file, sep="\t", header=3, index_col=False) # print "\ndata\n", data cart = np.array([data["X"], data["Y"], data["Z"]]).transpose() direction = pmag.cart2dir(cart).transpose() data["measurement_dec"] = direction[0] data["measurement_inc"] = direction[1] data["measurement_magn_moment"] = direction[2] * 1000 * volume # the data are in EMU - this converts to Am^2 data["measurement_magn_volume"] = direction[2] * 1000 # EMU - data converted to A/m # DGEOs, IGEOs = [], [] # print "len(data)=",len(data) # for ind in range(len(data)): # dgeo,igeo=pmag.dogeo(data.ix[ind]['measurement_dec'],data.ix[ind]['measurement_inc'],90-sample_azimuth,sample_dip) # DGEOs.append(dgeo) # IGEOs.append(igeo) # data['specimen_dec']=DGEOs # data['specimen_inc']=IGEOs # data['specimen_tilt']='1' # print "data specimn_dec=",DGEOs # print "data specimn_inc=",IGEOs # Configure the er_sample table ErSampRec["er_sample_name"] = sample_name ErSampRec["sample_azimuth"] = sample_azimuth ErSampRec["sample_dip"] = sample_dip ErSampRec["sample_bed_dip_direction"] = sample_bed_azimuth ErSampRec["sample_bed_dip"] = sample_bed_dip ErSampRec["sample_lat"] = sample_lat ErSampRec["sample_lon"] = sample_lon ErSampRec["magic_method_codes"] = meth_code ErSampRec["er_location_name"] = er_location_name ErSampRec["er_site_name"] = er_site_name ErSampRec["er_citation_names"] = "This study" SampOuts.append(ErSampRec.copy()) # Configure the magic_measurements table for rowNum, row in data.iterrows(): MagRec = {} MagRec["measurement_description"] = "Date: " + str(row["Date"]) + " Time: " + str(row["Time"]) MagRec["er_citation_names"] = "This study" MagRec["er_location_name"] = er_location_name MagRec["er_site_name"] = er_site_name MagRec["er_sample_name"] = sample_name MagRec["magic_software_packages"] = version_num MagRec["treatment_temp"] = "%8.3e" % (273) # room temp in kelvin MagRec["measurement_temp"] = "%8.3e" % (273) # room temp in kelvin MagRec["measurement_flag"] = "g" MagRec["measurement_standard"] = "u" MagRec["measurement_number"] = "1" MagRec["er_specimen_name"] = sample_name MagRec["treatment_ac_field"] = "0" if row["DM Val"] == "0": meas_type = "LT-NO" elif int(row["DM Type"]) > 0.0: meas_type = "LT-AF-Z" treat = float(row["DM Val"]) MagRec["treatment_ac_field"] = "%8.3e" % (treat * 1e-3) # convert from mT to tesla elif int(row["DM Type"]) == -1: meas_type = "LT-T-Z" treat = float(row["DM Val"]) MagRec["treatment_temp"] = "%8.3e" % (treat + 273.0) # temp in kelvin else: print "measurement type unknown:", row["DM Type"], " in row ", rowNum MagRec["measurement_magn_moment"] = str(row["measurement_magn_moment"]) MagRec["measurement_magn_volume"] = str(row["measurement_magn_volume"]) MagRec["measurement_dec"] = str(row["measurement_dec"]) MagRec["measurement_inc"] = str(row["measurement_inc"]) MagRec["magic_method_codes"] = meas_type MagRec["measurement_csd"] = "0.0" # added due to magic.write error MagRec["measurement_positions"] = "1" # added due to magic.write error MagRecs.append(MagRec.copy()) pmag.magic_write(samp_file, SampOuts, "er_samples") print "sample orientations put in ", samp_file MagOuts = pmag.measurements_methods(MagRecs, noave) pmag.magic_write(meas_file, MagOuts, "magic_measurements") print "results put in ", meas_file print "exit!" return True, meas_file
def main(): """ NAME UR_jr6_magic.py DESCRIPTION converts University of Rome JR6 format files to magic_measurements format files SYNTAX UR_jr6_magic.py [command line options] OPTIONS -h: prints the help message and quits. -F FILE: specify output measurements file, default is magic_measurements.txt -Fsa FILE: specify output er_samples.txt file for appending, default is er_samples.txt -dc B PHI THETA: dc lab field (in micro tesla) and phi,theta, default is none NB: use PHI, THETA = -1 -1 to signal that it changes, i.e. in anisotropy experiment -ac B : peak AF field (in mT) for ARM acquisition, default is none -A : don't average replicate measurements -spc NUM : specify number of characters to designate a specimen, default = 0 -loc LOCNAME : specify location/study name, must have either LOCNAME or SAMPFILE or be a synthetic -mcd: specify sampling method codes as a colon delimited string: [default is: FS-FD:SO-POM:SO-SUN] FS-FD field sampling done with a drill FS-H field sampling done with hand samples FS-LOC-GPS field location done with GPS FS-LOC-MAP field location done with map SO-POM a Pomeroy orientation device was used SO-SUN orientations are from a sun compass SO-MAG orientations are from a magnetic compass SO-MAG-CMD orientations declination corrected magnetic compass -ncn NCON: specify naming convention: default is #1 below Sample naming convention: [1] XXXXY: where XXXX is an arbitrary length site designation and Y is the single character sample designation. e.g., TG001a is the first sample from site TG001. [default] [2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length) [3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length) [4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX [5] site name same as sample [6] site is entered under a separate column [7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY NB: all others you will have to customize your self or e-mail [email protected] for help. [8] synthetic - has no site name [9] ODP naming convention INPUT Put data from separate experiments (all AF, thermal, thellier, trm aquisition, Shaw, etc.) in separate directory """ # # version_num=pmag.get_version() er_location_name="" ErSpecs,ErSamps,ErSites,ErLocs,ErCits=[],[],[],[],[] MagRecs=[] citation="This study" dir_path,demag='.','NRM' args=sys.argv noave=0 specnum=0 sampmeths='FS-FD:SO-POM:SO-SUN' samp_con,Z="4","2" if '-WD' in args: ind=args.index("-WD") dir_path=args[ind+1] meas_file=dir_path+'/'+'magic_measurements.txt' samp_file=dir_path+'/'+'er_samples.txt' if "-h" in args: print main.__doc__ sys.exit() if "-A" in args: noave=1 if '-F' in args: ind=args.index("-F") meas_file=dir_path+'/'+args[ind+1] if '-Fsa' in args: ind=args.index("-Fsa") samp_file=dir_path+'/'+args[ind+1] ErSamps,file_type=pmag.magic_read(samp_file) if "-ncn" in args: ind=args.index("-ncn") samp_con=sys.argv[ind+1] if "4" in samp_con: if "-" not in samp_con: print "option [4] must be in form 4-Z where Z is an integer" sys.exit() else: Z=samp_con.split("-")[1] samp_con="4" if "7" in samp_con: if "-" not in samp_con: print "option [4] must be in form 7-Z where Z is an integer" sys.exit() else: Z=samp_con.split("-")[1] samp_con="4" if "-mcd" in args: ind=args.index("-mcd") sampmeths=(sys.argv[ind+1]) if "-loc" in args: ind=args.index("-loc") er_location_name=args[ind+1] if "-spc" in args: ind=args.index("-spc") specnum=int(args[ind+1]) if specnum!=0:specnum=-specnum if '-LP' in args: ind=args.index("-LP") codelist=args[ind+1] codes=codelist.split(':') if "AF" in codes: demag='AF' if'-dc' not in args: methcode="LT-AF-Z" if'-dc' in args: methcode="LT-AF-I" if "T" in codes: demag="T" if '-dc' not in args: methcode="LT-T-Z" if '-dc' in args: methcode="LT-T-I" if "I" in codes: methcode="LP-IRM" if "S" in codes: demag="S" methcode="LP-PI-TRM:LP-PI-ALT-AFARM" trm_labfield=labfield ans=raw_input("DC lab field for ARM step: [50uT] ") if ans=="": arm_labfield=50e-6 else: arm_labfield=float(ans)*1e-6 ans=raw_input("temperature for total trm step: [600 C] ") if ans=="": trm_peakT=600+273 # convert to kelvin else: trm_peakT=float(ans)+273 # convert to kelvin if "G" in codes: methcode="LT-AF-G" if "D" in codes: methcode="LT-AF-D" if "TRM" in codes: demag="T" trm=1 if demag=="T" and "ANI" in codes: methcode="LP-AN-TRM" if demag=="AF" and "ANI" in codes: methcode="LP-AN-ARM" if labfield==0: labfield=50e-6 if peakfield==0: peakfield=.180 filelist=os.listdir(dir_path) # read in list of files to import samples=[] MagRecs,SampRecs=[],[] for samp in ErSamps: if samp['er_sample_name'] not in samples: samples.append(samp['er_sample_name']) SampRecs.append(samp) for file in filelist: # parse each file parts=file.split('.') if parts[1].upper()=='JR6': print 'processing: ',file treatment_type,treatment_value,user="","","" inst="UR-JR6" input=open(dir_path+'/'+file,'rU').readlines() for line in input: newline=line.replace('-',' -') rec=newline.split() MagRec,SampRec={},{} specimen=rec[0] if specnum!=0: SampRec['er_sample_name']=specimen[:specnum] else: SampRec['er_sample_name']=specimen er_site_name=pmag.parse_site(SampRec['er_sample_name'],samp_con,Z) SampRec['er_site_name']=er_site_name SampRec['er_location_name']=er_location_name for key in SampRec.keys():MagRec[key]=SampRec[key] SampRec['sample_azimuth']=rec[7] SampRec['sample_dip']='-'+rec[8] SampRec['sample_bed_dip_direction']=rec[9] SampRec['sample_bed_dip']=rec[10] SampRec['magic_method_codes']=sampmeths MagRec['er_specimen_name']=specimen MagRec['er_analyst_mail_names']=user MagRec['magic_software_packages']=version_num MagRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin MagRec["treatment_ac_field"]='0' MagRec["treatment_dc_field"]='0' MagRec["treatment_dc_field_phi"]='0' MagRec["treatment_dc_field_theta"]='0' MagRec["measurement_flag"]='g' # assume all data are "good" MagRec["measurement_standard"]='u' # assume all data are "good" MagRec["measurement_csd"]='' # set csd to blank MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin MagRec['magic_method_codes']='LT-NO' if rec[2]=='C': temp=float(rec[1])+273. if temp>298: MagRec["treatment_temp"]='%8.3e' % (temp) # room temp in kelvin MagRec['magic_method_codes']='LT-T-Z' else: # measurement is in oe AC=float(rec[1])*1e-4 # convert to tesla if AC!=0.: MagRec["treatment_ac_field"]='%8.3e' %(AC) MagRec['magic_method_codes']='LT-AF-Z' vol=10.8*1e-6 # standard Roma lab volume MagRec['magic_instrument_codes']=inst MagRec['measurement_number']='1' mexp=10**(float(rec[6])) x,y,z=mexp*float(rec[3]),mexp*float(rec[4]),mexp*float(rec[5]) Cart=[x,y,z] Dir=pmag.cart2dir(Cart) MagRec['measurement_dec']='%7.1f'%(Dir[0]) MagRec['measurement_inc']='%7.1f'%(Dir[1]) MagRec['measurement_magn_volume']='%8.3e'%(Dir[2]) MagRec['measurement_magn_moment']='%8.3e'%(Dir[2]*vol) MagRec['measurement_description']='converted A/m to Am^2 using volume of '+str(vol)+' m^3' MagRecs.append(MagRec) if MagRec['er_sample_name'] not in samples: samples.append(MagRec['er_sample_name']) SampRecs.append(SampRec) if len(SampRecs)>0: SampOut,keys=pmag.fillkeys(SampRecs) pmag.magic_write(samp_file,SampOut,'er_samples') print 'samples stored in ',samp_file Fixed=pmag.measurements_methods(MagRecs,noave) pmag.magic_write(meas_file,Fixed,'magic_measurements') print 'data stored in ',meas_file
def average_duplicates(duplicates): ''' avarage replicate measurements. ''' carts_s,carts_g,carts_t=[],[],[] for rec in duplicates: moment=float(rec['moment']) if 'dec_s' in rec.keys() and 'inc_s' in rec.keys(): if rec['dec_s']!="" and rec['inc_s']!="": dec_s=float(rec['dec_s']) inc_s=float(rec['inc_s']) cart_s=pmag.dir2cart([dec_s,inc_s,moment]) carts_s.append(cart_s) if 'dec_g' in rec.keys() and 'inc_g' in rec.keys(): if rec['dec_g']!="" and rec['inc_g']!="": dec_g=float(rec['dec_g']) inc_g=float(rec['inc_g']) cart_g=pmag.dir2cart([dec_g,inc_g,moment]) carts_g.append(cart_g) if 'dec_t' in rec.keys() and 'inc_t' in rec.keys(): if rec['dec_t']!="" and rec['inc_t']!="": dec_t=float(rec['dec_t']) inc_t=float(rec['inc_t']) cart_t=pmag.dir2cart([dec_t,inc_t,moment]) carts_t.append(cart_t) if len(carts_s)>0: carts=scipy.array(carts_s) x_mean=scipy.mean(carts[:,0]) y_mean=scipy.mean(carts[:,1]) z_mean=scipy.mean(carts[:,2]) mean_dir=pmag.cart2dir([x_mean,y_mean,z_mean]) mean_dec_s="%.2f"%mean_dir[0] mean_inc_s="%.2f"%mean_dir[1] mean_moment="%10.3e"%mean_dir[2] else: mean_dec_s,mean_inc_s="","" if len(carts_g)>0: carts=scipy.array(carts_g) x_mean=scipy.mean(carts[:,0]) y_mean=scipy.mean(carts[:,1]) z_mean=scipy.mean(carts[:,2]) mean_dir=pmag.cart2dir([x_mean,y_mean,z_mean]) mean_dec_g="%.2f"%mean_dir[0] mean_inc_g="%.2f"%mean_dir[1] mean_moment="%10.3e"%mean_dir[2] else: mean_dec_g,mean_inc_g="","" if len(carts_t)>0: carts=scipy.array(carts_t) x_mean=scipy.mean(carts[:,0]) y_mean=scipy.mean(carts[:,1]) z_mean=scipy.mean(carts[:,2]) mean_dir=pmag.cart2dir([x_mean,y_mean,z_mean]) mean_dec_t="%.2f"%mean_dir[0] mean_inc_t="%.2f"%mean_dir[1] mean_moment="%10.3e"%mean_dir[2] else: mean_dec_t,mean_inc_t="","" meanrec={} for key in duplicates[0].keys(): if key in ['dec_s','inc_s','dec_g','inc_g','dec_t','inc_t','moment']: continue else: meanrec[key]=duplicates[0][key] meanrec['dec_s']=mean_dec_s meanrec['dec_g']=mean_dec_g meanrec['dec_t']=mean_dec_t meanrec['inc_s']=mean_inc_s meanrec['inc_g']=mean_inc_g meanrec['inc_t']=mean_inc_t meanrec['moment']=mean_moment return meanrec
def main(command_line=True, **kwargs): """ NAME IODP_jr6_magic.py DESCRIPTION converts shipboard .jr6 format files to magic_measurements format files SYNTAX IODP_jr6_magic.py [command line options] OPTIONS -h: prints the help message and quits. -f FILE: specify input file, or -F FILE: specify output file, default is magic_measurements.txt -fsa FILE: specify er_samples.txt file for sample name lookup , default is 'er_samples.txt' -loc HOLE : specify hole name (U1456A) -A: don't average replicate measurements INPUT JR6 .jr6 format file """ def fix_separation(filename, new_filename): old_file = open(filename, "rU") data = old_file.readlines() new_data = [] for line in data: new_line = line.replace("-", " -") new_line = new_line.replace(" ", " ") new_data.append(new_line) new_file = open(new_filename, "w") for s in new_data: new_file.write(s) old_file.close() new_file.close() return new_filename def old_fix_separation(filename, new_filename): old_file = open(filename, "rU") data = old_file.readlines() new_data = [] for line in data: new_line = [] for i in line.split(): if "-" in i[1:]: lead_char = "-" if i[0] == "-" else "" if lead_char: v = i[1:].split("-") else: v = i.split("-") new_line.append(lead_char + v[0]) new_line.append("-" + v[1]) else: new_line.append(i) new_line = (" ".join(new_line)) + "\n" new_data.append(new_line) new_file = open(new_filename, "w") for s in new_data: new_file.write(s) new_file.close() old_file.close() return new_filename # initialize some stuff noave = 0 volume = 2.5 ** 3 # default volume is a 2.5cm cube inst = "" samp_con, Z = "5", "" missing = 1 demag = "N" er_location_name = "unknown" citation = "This study" args = sys.argv meth_code = "LP-NO" version_num = pmag.get_version() dir_path = "." MagRecs = [] samp_file = "er_samples.txt" meas_file = "magic_measurements.txt" mag_file = "" # # get command line arguments # if command_line: if "-WD" in sys.argv: ind = sys.argv.index("-WD") dir_path = sys.argv[ind + 1] if "-ID" in sys.argv: ind = sys.argv.index("-ID") input_dir_path = sys.argv[ind + 1] else: input_dir_path = dir_path output_dir_path = dir_path if "-h" in args: print main.__doc__ return False if "-F" in args: ind = args.index("-F") meas_file = args[ind + 1] if "-fsa" in args: ind = args.index("-fsa") samp_file = args[ind + 1] if samp_file[0] != "/": samp_file = os.path.join(input_dir_path, samp_file) try: open(samp_file, "rU") ErSamps, file_type = pmag.magic_read(samp_file) except: print samp_file, " not found: " print " download csv file and import to MagIC with IODP_samples_magic.py" if "-f" in args: ind = args.index("-f") mag_file = args[ind + 1] if "-loc" in args: ind = args.index("-loc") er_location_name = args[ind + 1] if "-A" in args: noave = 1 if not command_line: dir_path = kwargs.get("dir_path", ".") input_dir_path = kwargs.get("input_dir_path", dir_path) output_dir_path = dir_path meas_file = kwargs.get("meas_file", "magic_measurements.txt") mag_file = kwargs.get("mag_file", "") samp_file = kwargs.get("samp_file", "er_samples.txt") specnum = kwargs.get("specnum", 1) samp_con = kwargs.get("samp_con", "1") if len(str(samp_con)) > 1: samp_con, Z = samp_con.split("-") else: Z = "" er_location_name = kwargs.get("er_location_name", "") noave = kwargs.get("noave", 0) # default (0) means DO average meth_code = kwargs.get("meth_code", "LP-NO") # format variables meth_code = meth_code + ":FS-C-DRILL-IODP:SP-SS-C:SO-V" meth_code = meth_code.strip(":") if mag_file: mag_file = os.path.join(input_dir_path, mag_file) samp_file = os.path.join(input_dir_path, samp_file) meas_file = os.path.join(output_dir_path, meas_file) # validate variables if not mag_file: print "You must provide an IODP_jr6 format file" return False, "You must provide an IODP_jr6 format file" if not os.path.exists(mag_file): print "The input file you provided: {} does not exist.\nMake sure you have specified the correct filename AND correct input directory name.".format( mag_file ) return ( False, "The input file you provided: {} does not exist.\nMake sure you have specified the correct filename AND correct input directory name.".format( mag_file ), ) if not os.path.exists(samp_file): print "Your input directory:\n{}\nmust contain an er_samples.txt file, or you must explicitly provide one".format( input_dir_path ) return ( False, "Your input directory:\n{}\nmust contain an er_samples.txt file, or you must explicitly provide one".format( input_dir_path ), ) # parse data temp = os.path.join(output_dir_path, "temp.txt") fix_separation(mag_file, temp) samples, filetype = pmag.magic_read(samp_file) lines = open(temp, "rU").readlines() os.remove(temp) for line in lines: MagRec = {} line = line.split() spec_text_id = line[0].split("_")[1] SampRecs = pmag.get_dictitem(samples, "er_sample_alternatives", spec_text_id, "has") if len(SampRecs) > 0: # found one MagRec["er_specimen_name"] = SampRecs[0]["er_sample_name"] MagRec["er_sample_name"] = MagRec["er_specimen_name"] MagRec["er_site_name"] = MagRec["er_specimen_name"] MagRec["er_citation_names"] = "This study" MagRec["er_location_name"] = er_location_name MagRec["magic_software_packages"] = version_num MagRec["treatment_temp"] = "%8.3e" % (273) # room temp in kelvin MagRec["measurement_temp"] = "%8.3e" % (273) # room temp in kelvin MagRec["measurement_flag"] = "g" MagRec["measurement_standard"] = "u" MagRec["measurement_number"] = "1" MagRec["treatment_ac_field"] = "0" volume = float(SampRecs[0]["sample_volume"]) x = float(line[4]) y = float(line[3]) negz = float(line[2]) cart = np.array([x, y, -negz]).transpose() direction = pmag.cart2dir(cart).transpose() expon = float(line[5]) magn_volume = direction[2] * (10.0 ** expon) moment = magn_volume * volume MagRec["measurement_magn_moment"] = str(moment) MagRec["measurement_magn_volume"] = str(magn_volume) # str(direction[2] * (10.0 ** expon)) MagRec["measurement_dec"] = "%7.1f" % (direction[0]) MagRec["measurement_inc"] = "%7.1f" % (direction[1]) step = line[1] if step == "NRM": meas_type = "LT-NO" elif step[0:2] == "AD": meas_type = "LT-AF-Z" treat = float(step[2:]) MagRec["treatment_ac_field"] = "%8.3e" % (treat * 1e-3) # convert from mT to tesla elif step[0:2] == "TD": meas_type = "LT-T-Z" treat = float(step[2:]) MagRec["treatment_temp"] = "%8.3e" % (treat + 273.0) # temp in kelvin elif step[0:3] == "ARM": # meas_type = "LT-AF-I" treat = float(row["step"][3:]) MagRec["treatment_ac_field"] = "%8.3e" % (treat * 1e-3) # convert from mT to tesla MagRec["treatment_dc_field"] = "%8.3e" % (50e-6) # assume 50uT DC field MagRec["measurement_description"] = "Assumed DC field - actual unknown" elif step[0:3] == "IRM": # meas_type = "LT-IRM" treat = float(step[3:]) MagRec["treatment_dc_field"] = "%8.3e" % (treat * 1e-3) # convert from mT to tesla else: print "unknown treatment type for ", row return False, "unknown treatment type for ", row MagRec["magic_method_codes"] = meas_type MagRecs.append(MagRec.copy()) else: print "sample name not found: ", row["specname"] MagOuts = pmag.measurements_methods(MagRecs, noave) file_created, error_message = pmag.magic_write(meas_file, MagOuts, "magic_measurements") if file_created: return True, meas_file else: return False, "Results not written to file"
def main(): """ NAME IPG_magic.py DESCRIPTION converts PMD (IPG - PaleoMac) format files to magic_measurements format files SYNTAX IPG_magic.py [command line options] OPTIONS -h: prints the help message and quits. -usr USER: identify user, default is "" -f FILE: specify input file, or -F FILE: specify output file, default is magic_measurements.txt -Fsa: specify er_samples format file for appending, default is new er_samples.txt -spc NUM : specify number of characters to designate a specimen, default = 1 -loc LOCNAME : specify location/study name -A: don't average replicate measurements -ncn NCON: specify naming convention Sample naming convention: [1] XXXXY: where XXXX is an arbitrary length site designation and Y is the single character sample designation. e.g., TG001a is the first sample from site TG001. [default] [2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length) [3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length) [4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX [5] site name same as sample [6] site is entered under a separate column [7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY NB: all others you will have to customize your self or e-mail [email protected] for help. INPUT IPG-PMD format files """ # initialize some stuff noave = 0 methcode, inst = "", "" samp_con, Z = "1", "" missing = 1 demag = "N" er_location_name = "unknown" citation = "This study" args = sys.argv methcode = "LP-NO" specnum = -1 MagRecs = [] version_num = pmag.get_version() Samps = [] # keeps track of sample orientations DIspec = [] MagFiles = [] # # get command line arguments # user = "" mag_file = "" dir_path = "." ErSamps = [] SampOuts = [] if "-WD" in sys.argv: ind = sys.argv.index("-WD") dir_path = sys.argv[ind + 1] samp_file = dir_path + "/er_samples.txt" meas_file = dir_path + "/magic_measurements.txt" if "-h" in args: print main.__doc__ sys.exit() if "-usr" in args: ind = args.index("-usr") user = args[ind + 1] if "-F" in args: ind = args.index("-F") meas_file = dir_path + "/" + args[ind + 1] if "-Fsa" in args: ind = args.index("-Fsa") samp_file = dir_path + "/" + args[ind + 1] try: open(samp_file, "rU") ErSamps, file_type = pmag.magic_read(samp_file) print "sample information will be appended to ", samp_file except: print samp_file, " not found: sample information will be stored in new er_samples.txt file" samp_file = dir_path + "/er_samples.txt" if "-f" in args: ind = args.index("-f") mag_file = dir_path + "/" + args[ind + 1] if "-spc" in args: ind = args.index("-spc") specnum = int(args[ind + 1]) if specnum != 0: specnum = -specnum if "-ncn" in args: ind = args.index("-ncn") samp_con = sys.argv[ind + 1] if "4" in samp_con: if "-" not in samp_con: print "option [4] must be in form 4-Z where Z is an integer" sys.exit() else: Z = samp_con.split("-")[1] samp_con = "4" if "7" in samp_con: if "-" not in samp_con: print "option [7] must be in form 7-Z where Z is an integer" sys.exit() else: Z = samp_con.split("-")[1] samp_con = "7" if "-loc" in args: ind = args.index("-loc") er_location_name = args[ind + 1] if "-A" in args: noave = 1 data = open(mag_file, "rU").readlines() # read in data from file for line in data: rec = line.split() if "E-" not in rec[1] and "E+" not in rec[1]: # new specimen er_specimen_name = rec[0] ErSampRec, ErSiteRec = {}, {} # make a sample record if specnum != 0: er_sample_name = rec[0][:specnum] else: er_sample_name = rec[0] if len(ErSamps) > 0: # need to copy existing for samp in ErSamps: if samp["er_sample_name"] == er_sample_name: ErSampRec = samp # we'll ammend this one else: SampOuts.append(samp) # keep all the others if int(samp_con) < 6: er_site_name = pmag.parse_site(er_sample_name, samp_con, Z) else: if "er_site_name" in ErSampRec.keys(): er_site_name = ErSampREc["er_site_name"] if "er_location_name" in ErSampRec.keys(): er_location_name = ErSampREc["er_location_name"] ErSampRec["er_sample_name"] = er_sample_name ErSampRec["sample_azimuth"] = rec[1] dip = -float(rec[2]) ErSampRec["sample_dip"] = "%7.1f" % (dip) ErSampRec["sample_bed_dip_direction"] = "%7.1f" % (float(rec[3]) + 90.0) ErSampRec["sample_bed_dip"] = rec[4] if "er_location_name" not in ErSampRec.keys(): ErSampRec["er_location_name"] = er_location_name if "er_site_name" not in ErSampRec.keys(): ErSampRec["er_site_name"] = er_site_name if "er_citation_names" not in ErSampRec.keys(): ErSampRec["er_citation_names"] = "This study" if "magic_method_codes" not in ErSampRec.keys(): ErSampRec["magic_method_codes"] = "SO-NO" SampOuts.append(ErSampRec) elif rec[0][0] == "N" or rec[0][0] == "T" or rec[0][0] == "M": if len(rec) > 1: # skip blank lines at bottom MagRec = {} # MagRec['measurement_date']=measdate MagRec["er_citation_names"] = "This study" MagRec["er_location_name"] = er_location_name MagRec["er_site_name"] = er_site_name MagRec["er_sample_name"] = er_sample_name MagRec["magic_software_packages"] = version_num MagRec["treatment_temp"] = "%8.3e" % (273) # room temp in kelvin MagRec["measurement_temp"] = "%8.3e" % (273) # room temp in kelvin MagRec["measurement_flag"] = "g" MagRec["measurement_standard"] = "u" MagRec["measurement_number"] = "1" MagRec["er_specimen_name"] = er_specimen_name if rec[0] == "NRM": meas_type = "LT-NO" elif rec[0][0] == "M": meas_type = "LT-AF-Z" elif rec[0][0] == "T": meas_type = "LT-T-Z" else: print "measurement type unknown" sys.exit() X = [float(rec[1]), float(rec[2]), float(rec[3])] Vec = pmag.cart2dir(X) MagRec["measurement_magn_moment"] = "%10.3e" % (Vec[2]) # Am^2 # MagRec["measurement_magn_volume"]=rec[4] # A/m MagRec["measurement_dec"] = "%7.1f" % (Vec[0]) MagRec["measurement_inc"] = "%7.1f" % (Vec[1]) MagRec["treatment_ac_field"] = "0" if meas_type != "LT-NO": treat = float(rec[0][1:]) else: treat = 0 if meas_type == "LT-AF-Z": MagRec["treatment_ac_field"] = "%8.3e" % (treat * 1e-3) # convert from mT to tesla elif meas_type == "LT-T-Z": MagRec["treatment_temp"] = "%8.3e" % (treat + 273.0) # temp in kelvin MagRec["magic_method_codes"] = meas_type MagRecs.append(MagRec) MagOuts = pmag.measurements_methods(MagRecs, noave) pmag.magic_write(meas_file, MagOuts, "magic_measurements") print "results put in ", meas_file pmag.magic_write(samp_file, SampOuts, "er_samples") print "sample orientations put in ", samp_file
def main(): """ NAME orientation_magic.py DESCRIPTION takes tab delimited field notebook information and converts to MagIC formatted tables SYNTAX orientation_magic.py [command line options] OPTIONS -f FILE: specify input file, default is: orient.txt -Fsa FILE: specify output file, default is: er_samples.txt -Fsi FILE: specify output site location file, default is: er_sites.txt -app append/update these data in existing er_samples.txt, er_sites.txt files -ocn OCON: specify orientation convention, default is #1 below -dcn DCON [DEC]: specify declination convention, default is #1 below if DCON = 2, you must supply the declination correction -BCN don't correct bedding_dip_dir for magnetic declination -already corrected -ncn NCON: specify naming convention: default is #1 below -a: averages all bedding poles and uses average for all samples: default is NO -gmt HRS: specify hours to subtract from local time to get GMT: default is 0 -mcd: specify sampling method codes as a colon delimited string: [default is: FS-FD:SO-POM] FS-FD field sampling done with a drill FS-H field sampling done with hand samples FS-LOC-GPS field location done with GPS FS-LOC-MAP field location done with map SO-POM a Pomeroy orientation device was used SO-ASC an ASC orientation device was used INPUT FORMAT Input files must be tab delimited and have in the first line: tab location_name Note: The "location_name" will facilitate searching in the MagIC database. Data from different "locations" should be put in separate files. The definition of a "location" is rather loose. Also this is the word 'tab' not a tab, which will be indicated by '\t'. The second line has the names of the columns (tab delimited), e.g.: site_name sample_name mag_azimuth field_dip date lat long sample_lithology sample_type sample_class shadow_angle hhmm stratigraphic_height bedding_dip_direction bedding_dip GPS_baseline image_name image_look image_photographer participants method_codes site_description sample_description GPS_Az, sample_igsn, sample_texture, sample_cooling_rate, cooling_rate_corr, cooling_rate_mcd Notes: 1) column order doesn't matter but the NAMES do. 2) sample_name, sample_lithology, sample_type, sample_class, lat and long are required. all others are optional. 3) If subsequent data are the same (e.g., date, bedding orientation, participants, stratigraphic_height), you can leave the field blank and the program will fill in the last recorded information. BUT if you really want a blank stratigraphic_height, enter a '-1'. These will not be inherited and must be specified for each entry: image_name, look, photographer or method_codes 4) hhmm must be in the format: hh:mm and the hh must be in 24 hour time. date must be mm/dd/yy (years < 50 will be converted to 20yy and >50 will be assumed 19yy) 5) image_name, image_look and image_photographer are colon delimited lists of file name (e.g., IMG_001.jpg) image look direction and the name of the photographer respectively. If all images had same look and photographer, just enter info once. The images will be assigned to the site for which they were taken - not at the sample level. 6) participants: Names of who helped take the samples. These must be a colon delimited list. 7) method_codes: Special method codes on a sample level, e.g., SO-GT5 which means the orientation is has an uncertainty of >5 degrees for example if it broke off before orienting.... 8) GPS_Az is the place to put directly determined GPS Azimuths, using, e.g., points along the drill direction. 9) sample_cooling_rate is the cooling rate in K per Ma 10) int_corr_cooling_rate 11) cooling_rate_mcd: data adjustment method code for cooling rate correction; DA-CR-EG is educated guess; DA-CR-PS is percent estimated from pilot samples; DA-CR-TRM is comparison between 2 TRMs acquired with slow and rapid cooling rates. is the percent cooling rate factor to apply to specimens from this sample, DA-CR-XX is the method code Orientation convention: Samples are oriented in the field with a "field arrow" and measured in the laboratory with a "lab arrow". The lab arrow is the positive X direction of the right handed coordinate system of the specimen measurements. The lab and field arrows may not be the same. In the MagIC database, we require the orientation (azimuth and plunge) of the X direction of the measurements (lab arrow). Here are some popular conventions that convert the field arrow azimuth (mag_azimuth in the orient.txt file) and dip (field_dip in orient.txt) to the azimuth and plunge of the laboratory arrow (sample_azimuth and sample_dip in er_samples.txt). The two angles, mag_azimuth and field_dip are explained below. [1] Standard Pomeroy convention of azimuth and hade (degrees from vertical down) of the drill direction (field arrow). lab arrow azimuth= sample_azimuth = mag_azimuth; lab arrow dip = sample_dip =-field_dip. i.e. the lab arrow dip is minus the hade. [2] Field arrow is the strike of the plane orthogonal to the drill direction, Field dip is the hade of the drill direction. Lab arrow azimuth = mag_azimuth-90 Lab arrow dip = -field_dip [3] Lab arrow is the same as the drill direction; hade was measured in the field. Lab arrow azimuth = mag_azimuth; Lab arrow dip = 90-field_dip [4] lab azimuth and dip are same as mag_azimuth, field_dip : use this for unoriented samples too [5] Same as AZDIP convention explained below - azimuth and inclination of the drill direction are mag_azimuth and field_dip; lab arrow is as in [1] above. lab azimuth is same as mag_azimuth,lab arrow dip=field_dip-90 [6] Lab arrow azimuth = mag_azimuth-90; Lab arrow dip = 90-field_dip [7] all others you will have to either customize your self or e-mail [email protected] for help. Magnetic declination convention: [1] Use the IGRF value at the lat/long and date supplied [default] [2] Will supply declination correction [3] mag_az is already corrected in file [4] Correct mag_az but not bedding_dip_dir Sample naming convention: [1] XXXXY: where XXXX is an arbitrary length site designation and Y is the single character sample designation. e.g., TG001a is the first sample from site TG001. [default] [2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length) [3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length) [4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX [5] site name = sample name [6] site name entered in site_name column in the orient.txt format input file [7-Z] [XXX]YYY: XXX is site designation with Z characters from samples XXXYYY NB: all others you will have to either customize your self or e-mail [email protected] for help. OUTPUT output saved in er_samples.txt and er_sites.txt - will overwrite any existing files """ # # initialize variables # stratpos="" args=sys.argv date,lat,lon="","","" # date of sampling, latitude (pos North), longitude (pos East) bed_dip,bed_dip_dir="","" participantlist="" Lats,Lons=[],[] # list of latitudes and longitudes SampOuts,SiteOuts,ImageOuts=[],[],[] # lists of Sample records and Site records samplelist,sitelist,imagelist=[],[],[] samp_con,Z,average_bedding,DecCorr="1",1,"0",0. newbaseline,newbeddir,newbeddip="","","" meths='' delta_u="0" sclass,lithology,type="","","" newclass,newlith,newtype='','','' user="" BPs=[]# bedding pole declinations, bedding pole inclinations # # dir_path,AddTo='.',0 if "-WD" in args: ind=args.index("-WD") dir_path=sys.argv[ind+1] orient_file,samp_file,or_con,corr = dir_path+"/orient.txt",dir_path+"/er_samples.txt","1","1" site_file=dir_path+"/er_sites.txt" image_file=dir_path+"/er_images.txt" SampRecs,SiteRecs,ImageRecs=[],[],[] if "-h" in args: print main.__doc__ sys.exit() if "-f" in args: ind=args.index("-f") orient_file=dir_path+'/'+sys.argv[ind+1] if "-Fsa" in args: ind=args.index("-Fsa") samp_file=dir_path+'/'+sys.argv[ind+1] if "-Fsi" in args: ind=args.index("-Fsi") site_file=dir_path+'/'+sys.argv[ind+1] if '-app' in args: AddTo=1 try: SampRecs,file_type=pmag.magic_read(samp_file) print 'sample data to be appended to: ', samp_file except: print 'problem with existing file: ',samp_file, ' will create new.' try: SiteRecs,file_type=pmag.magic_read(site_file) print 'site data to be appended to: ',site_file except: print 'problem with existing file: ',site_file,' will create new.' try: ImageRecs,file_type=pmag.magic_read(image_file) print 'image data to be appended to: ',image_file except: print 'problem with existing file: ',image_file,' will create new.' if "-ocn" in args: ind=args.index("-ocn") or_con=sys.argv[ind+1] if "-dcn" in args: ind=args.index("-dcn") corr=sys.argv[ind+1] if corr=="2": DecCorr=float(sys.argv[ind+2]) elif corr=="3": DecCorr=0. if '-BCN' in args: BedCorr=0 else: BedCorr=1 if "-ncn" in args: ind=args.index("-ncn") samp_con=sys.argv[ind+1] if "4" in samp_con: if "-" not in samp_con: print "option [4] must be in form 4-Z where Z is an integer" sys.exit() else: Z=samp_con.split("-")[1] samp_con="4" if "7" in samp_con: if "-" not in samp_con: print "option [7] must be in form 7-Z where Z is an integer" sys.exit() else: Z=samp_con.split("-")[1] samp_con="7" if "-gmt" in args: ind=args.index("-gmt") delta_u=(sys.argv[ind+1]) if "-mcd" in args: ind=args.index("-mcd") meths=(sys.argv[ind+1]) if "-a" in args: average_bedding="1" # # read in file to convert # OrData,location_name=pmag.magic_read(orient_file) # # step through the data sample by sample # for OrRec in OrData: if 'mag_azimuth' not in OrRec.keys():OrRec['mag_azimuth']="" if 'field_dip' not in OrRec.keys():OrRec['field_dip']="" if OrRec['mag_azimuth']==" ":OrRec["mag_azimuth"]="" if OrRec['field_dip']==" ":OrRec["field_dip"]="" if 'sample_description' in OrRec.keys(): sample_description=OrRec['sample_description'] else: sample_description="" if 'sample_igsn' in OrRec.keys(): sample_igsn=OrRec['sample_igsn'] else: sample_igsn="" if 'sample_texture' in OrRec.keys(): sample_texture=OrRec['sample_texture'] else: sample_texture="" if 'sample_cooling_rate' in OrRec.keys(): sample_cooling_rate=OrRec['sample_cooling_rate'] else: sample_cooling_rate="" if 'cooling_rate_corr' in OrRec.keys(): cooling_rate_corr=OrRec['cooling_rate_corr'] if 'cooling_rate_mcd' in OrRec.keys(): cooling_rate_mcd=OrRec['cooling_rate_mcd'] else: cooling_rate_mcd='DA-CR' else: cooling_rate_corr="" cooling_rate_mcd="" sample_orientation_flag='g' if 'sample_orientation_flag' in OrRec.keys(): if OrRec['sample_orientation_flag']=='b' or OrRec["mag_azimuth"]=="": sample_orientation_flag='b' methcodes=meths # initialize method codes if meths!='': if 'method_codes' in OrRec.keys() and OrRec['method_codes'].strip()!="":methcodes=methcodes+":"+OrRec['method_codes'] # add notes else: if 'method_codes' in OrRec.keys() and OrRec['method_codes'].strip()!="":methcodes=OrRec['method_codes'] # add notes codes=methcodes.replace(" ","").split(":") MagRec={} MagRec["er_location_name"]=location_name MagRec["er_citation_names"]="This study" MagRec['sample_orientation_flag']=sample_orientation_flag MagRec['sample_igsn']=sample_igsn MagRec['sample_texture']=sample_texture MagRec['sample_cooling_rate']=sample_cooling_rate MagRec['cooling_rate_corr']=cooling_rate_corr MagRec['cooling_rate_mcd']=cooling_rate_mcd # # parse information common to all orientation methods # MagRec["er_sample_name"]=OrRec["sample_name"] if "IGSN" in OrRec.keys(): MagRec["sample_igsn"]=OrRec["IGSN"] else: MagRec["sample_igsn"]="" MagRec["sample_height"],MagRec["sample_bed_dip_direction"],MagRec["sample_bed_dip"]="","","" if "er_sample_alternatives" in OrRec.keys():MagRec["er_sample_alternatives"]=OrRec["sample_alternatives"] sample=OrRec["sample_name"] if OrRec['mag_azimuth']=="" and OrRec['field_dip']!="": OrRec['mag_azimuth']='999' if OrRec["mag_azimuth"]!="": labaz,labdip=pmag.orient(float(OrRec["mag_azimuth"]),float(OrRec["field_dip"]),or_con) if labaz<0:labaz+=360. else: labaz,labdip="","" if OrRec['mag_azimuth']=='999':labaz="" if "GPS_baseline" in OrRec.keys() and OrRec['GPS_baseline']!="":newbaseline=OrRec["GPS_baseline"] if newbaseline!="":baseline=float(newbaseline) if 'participants' in OrRec.keys() and OrRec['participants']!="" and OrRec['participants']!=participantlist: participantlist=OrRec['participants'] MagRec['er_scientist_mail_names']=participantlist newlat=OrRec["lat"] if newlat!="":lat=float(newlat) if lat=="": print "No latitude specified for ! ",sample sys.exit() MagRec["sample_lat"]='%11.5f'%(lat) newlon=OrRec["long"] if newlon!="":lon=float(newlon) if lon=="": print "No longitude specified for ! ",sample sys.exit() MagRec["sample_lon"]='%11.5f'%(lon) if 'bedding_dip_direction' in OrRec.keys(): newbeddir=OrRec["bedding_dip_direction"] if newbeddir!="":bed_dip_dir=OrRec['bedding_dip_direction'] if 'bedding_dip' in OrRec.keys(): newbeddip=OrRec["bedding_dip"] if newbeddip!="":bed_dip=OrRec['bedding_dip'] MagRec["sample_bed_dip"]=bed_dip MagRec["sample_bed_dip_direction"]=bed_dip_dir if "sample_class" in OrRec.keys():newclass=OrRec["sample_class"] if newclass!="":sclass=newclass if sclass=="": sclass="Not Specified" MagRec["sample_class"]=sclass if "sample_lithology" in OrRec.keys():newlith=OrRec["sample_lithology"] if newlith!="":lithology=newlith if lithology=="": lithology="Not Specified" MagRec["sample_lithology"]=lithology if "sample_type" in OrRec.keys():newtype=OrRec["sample_type"] if newtype!="":type=newtype if type=="": type="Not Specified" MagRec["sample_type"]=type if labdip!="": MagRec["sample_dip"]='%7.1f'%labdip else: MagRec["sample_dip"]="" if "date" in OrRec.keys(): newdate=OrRec["date"] if newdate!="":date=newdate mmddyy=date.split('/') yy=int(mmddyy[2]) if yy>50: yy=1900+yy else: yy=2000+yy decimal_year=yy+float(mmddyy[0])/12 sample_date='%i:%s:%s'%(yy,mmddyy[0],mmddyy[1]) MagRec["sample_date"]=sample_date if labaz!="": MagRec["sample_azimuth"]='%7.1f'%(labaz) else: MagRec["sample_azimuth"]="" if "stratigraphic_height" in OrRec.keys(): if OrRec["stratigraphic_height"]!="": MagRec["sample_height"]=OrRec["stratigraphic_height"] stratpos=OrRec["stratigraphic_height"] elif OrRec["stratigraphic_height"]=='-1': MagRec["sample_height"]="" # make empty else: MagRec["sample_height"]=stratpos # keep last record if blank # if corr=="1" and MagRec['sample_azimuth']!="": # get magnetic declination (corrected with igrf value) x,y,z,f=pmag.doigrf(lon,lat,0,decimal_year) Dir=pmag.cart2dir( (x,y,z)) DecCorr=Dir[0] if "bedding_dip" in OrRec.keys(): if OrRec["bedding_dip"]!="": MagRec["sample_bed_dip"]=OrRec["bedding_dip"] bed_dip=OrRec["bedding_dip"] else: MagRec["sample_bed_dip"]=bed_dip else: MagRec["sample_bed_dip"]='0' if "bedding_dip_direction" in OrRec.keys(): if OrRec["bedding_dip_direction"]!="" and BedCorr==1: dd=float(OrRec["bedding_dip_direction"])+DecCorr if dd>360.:dd=dd-360. MagRec["sample_bed_dip_direction"]='%7.1f'%(dd) dip_dir=MagRec["sample_bed_dip_direction"] else: MagRec["sample_bed_dip_direction"]=OrRec['bedding_dip_direction'] else: MagRec["sample_bed_dip_direction"]='0' if average_bedding!="0": BPs.append([float(MagRec["sample_bed_dip_direction"]),float(MagRec["sample_bed_dip"])-90.,1.]) if MagRec['sample_azimuth']=="" and MagRec['sample_dip']=="": MagRec["sample_declination_correction"]='' methcodes=methcodes+':SO-NO' MagRec["magic_method_codes"]=methcodes MagRec['sample_description']=sample_description # # work on the site stuff too if 'site_name' in OrRec.keys(): site=OrRec['site_name'] else: site=pmag.parse_site(OrRec["sample_name"],samp_con,Z) # parse out the site name MagRec["er_site_name"]=site site_description="" # overwrite any prior description if 'site_description' in OrRec.keys() and OrRec['site_description']!="": site_description=OrRec['site_description'].replace(",",";") if "image_name" in OrRec.keys(): images=OrRec["image_name"].split(":") if "image_look" in OrRec.keys(): looks=OrRec['image_look'].split(":") else: looks=[] if "image_photographer" in OrRec.keys(): photographers=OrRec['image_photographer'].split(":") else: photographers=[] for image in images: if image !="" and image not in imagelist: imagelist.append(image) ImageRec={} ImageRec['er_image_name']=image ImageRec['image_type']="outcrop" ImageRec['image_date']=sample_date ImageRec['er_citation_names']="This study" ImageRec['er_location_name']=location_name ImageRec['er_site_name']=MagRec['er_site_name'] k=images.index(image) if len(looks)>k: ImageRec['er_image_description']="Look direction: "+looks[k] elif len(looks)>=1: ImageRec['er_image_description']="Look direction: "+looks[-1] else: ImageRec['er_image_description']="Look direction: unknown" if len(photographers)>k: ImageRec['er_photographer_mail_names']=photographers[k] elif len(photographers)>=1: ImageRec['er_photographer_mail_names']=photographers[-1] else: ImageRec['er_photographer_mail_names']="unknown" ImageOuts.append(ImageRec) if site not in sitelist: sitelist.append(site) # collect unique site names SiteRec={} SiteRec["er_site_name"]=site SiteRec["site_definition"]="s" SiteRec["er_location_name"]=location_name SiteRec["er_citation_names"]="This study" SiteRec["site_lat"]=MagRec["sample_lat"] SiteRec["site_lon"]=MagRec["sample_lon"] SiteRec["site_height"]=MagRec["sample_height"] SiteRec["site_class"]=MagRec["sample_class"] SiteRec["site_lithology"]=MagRec["sample_lithology"] SiteRec["site_type"]=MagRec["sample_type"] SiteRec["site_description"]=site_description SiteOuts.append(SiteRec) if sample not in samplelist: samplelist.append(sample) if MagRec['sample_azimuth']!="": # assume magnetic compass only MagRec['magic_method_codes']=MagRec['magic_method_codes']+':SO-MAG' MagRec['magic_method_codes']=MagRec['magic_method_codes'].strip(":") SampOuts.append(MagRec) if MagRec['sample_azimuth']!="" and corr!='3': az=labaz+DecCorr if az>360.:az=az-360. CMDRec={} for key in MagRec.keys(): CMDRec[key]=MagRec[key] # make a copy of MagRec CMDRec["sample_azimuth"]='%7.1f'%(az) CMDRec["magic_method_codes"]=methcodes+':SO-CMD-NORTH' CMDRec["magic_method_codes"]=CMDRec['magic_method_codes'].strip(':') CMDRec["sample_declination_correction"]='%7.1f'%(DecCorr) if corr=='1': CMDRec['sample_description']=sample_description+':Declination correction calculated from IGRF' else: CMDRec['sample_description']=sample_description+':Declination correction supplied by user' CMDRec["sample_description"]=CMDRec['sample_description'].strip(':') SampOuts.append(CMDRec) if "mag_az_bs" in OrRec.keys() and OrRec["mag_az_bs"] !="" and OrRec["mag_az_bs"]!=" ": SRec={} for key in MagRec.keys(): SRec[key]=MagRec[key] # make a copy of MagRec labaz=float(OrRec["mag_az_bs"]) az=labaz+DecCorr if az>360.:az=az-360. SRec["sample_azimuth"]='%7.1f'%(az) SRec["sample_declination_correction"]='%7.1f'%(DecCorr) SRec["magic_method_codes"]=methcodes+':SO-SIGHT-BACK:SO-CMD-NORTH' SampOuts.append(SRec) # # check for suncompass data # if "shadow_angle" in OrRec.keys() and OrRec["shadow_angle"]!="": # there are sun compass data if delta_u=="": delta_u=raw_input("Enter hours to SUBTRACT from time for GMT: [0] ") if delta_u=="":delta_u="0" SunRec,sundata={},{} shad_az=float(OrRec["shadow_angle"]) sundata["date"]='%i:%s:%s:%s'%(yy,mmddyy[0],mmddyy[1],OrRec["hhmm"]) # if eval(delta_u)<0: # MagRec["sample_time_zone"]='GMT'+delta_u+' hours' # else: # MagRec["sample_time_zone"]='GMT+'+delta_u+' hours' sundata["delta_u"]=delta_u sundata["lon"]='%7.1f'%(lon) sundata["lat"]='%7.1f'%(lat) sundata["shadow_angle"]=OrRec["shadow_angle"] sundec=pmag.dosundec(sundata) for key in MagRec.keys(): SunRec[key]=MagRec[key] # make a copy of MagRec SunRec["sample_azimuth"]='%7.1f'%(sundec) SunRec["sample_declination_correction"]='' SunRec["magic_method_codes"]=methcodes+':SO-SUN' SunRec["magic_method_codes"]=SunRec['magic_method_codes'].strip(':') SampOuts.append(SunRec) # # check for differential GPS data # if "prism_angle" in OrRec.keys() and OrRec["prism_angle"]!="": # there are diff GPS data GPSRec={} for key in MagRec.keys(): GPSRec[key]=MagRec[key] # make a copy of MagRec prism_angle=float(OrRec["prism_angle"]) laser_angle=float(OrRec["laser_angle"]) if OrRec["GPS_baseline"]!="": baseline=float(OrRec["GPS_baseline"]) # new baseline gps_dec=baseline+laser_angle+prism_angle-90. while gps_dec>360.: gps_dec=gps_dec-360. while gps_dec<0: gps_dec=gps_dec+360. for key in MagRec.keys(): GPSRec[key]=MagRec[key] # make a copy of MagRec GPSRec["sample_azimuth"]='%7.1f'%(gps_dec) GPSRec["sample_declination_correction"]='' GPSRec["magic_method_codes"]=methcodes+':SO-GPS-DIFF' SampOuts.append(GPSRec) if "GPS_Az" in OrRec.keys() and OrRec["GPS_Az"]!="": # there are differential GPS Azimuth data GPSRec={} for key in MagRec.keys(): GPSRec[key]=MagRec[key] # make a copy of MagRec GPSRec["sample_azimuth"]='%7.1f'%(float(OrRec["GPS_Az"])) GPSRec["sample_declination_correction"]='' GPSRec["magic_method_codes"]=methcodes+':SO-GPS-DIFF' SampOuts.append(GPSRec) if average_bedding!="0": fpars=pmag.fisher_mean(BPs) print 'over-writing all bedding with average ' Samps=[] for rec in SampOuts: if average_bedding!="0": rec['sample_bed_dip_direction']='%7.1f'%(fpars['dec']) rec['sample_bed_dip']='%7.1f'%(fpars['inc']+90.) Samps.append(rec) else: Samps.append(rec) for rec in SampRecs: if rec['er_sample_name'] not in samplelist: # overwrite prior for this sample Samps.append(rec) for rec in SiteRecs: if rec['er_site_name'] not in sitelist: # overwrite prior for this sample SiteOuts.append(rec) for rec in ImageRecs: if rec['er_image_name'] not in imagelist: # overwrite prior for this sample ImageOuts.append(rec) print 'saving data...' SampsOut,keys=pmag.fillkeys(Samps) Sites,keys=pmag.fillkeys(SiteOuts) pmag.magic_write(samp_file,SampsOut,"er_samples") pmag.magic_write(site_file,Sites,"er_sites") print "Data saved in ", samp_file,' and ',site_file if len(ImageOuts)>0: Images,keys=pmag.fillkeys(ImageOuts) pmag.magic_write(image_file,Images,"er_images") print "Image info saved in ",image_file
def main(command_line=True, **kwargs): """ NAME PMD_magic.py DESCRIPTION converts PMD (Enkin) format files to magic_measurements format files SYNTAX PMD_magic.py [command line options] OPTIONS -h: prints the help message and quits. -f FILE: specify input file, or -F FILE: specify output file, default is magic_measurements.txt -Fsa: specify er_samples format file for appending, default is new er_samples.txt -spc NUM : specify number of characters to designate a specimen, default = 1 -loc LOCNAME : specify location/study name -A: don't average replicate measurements -ncn NCON: specify naming convention -mcd [SO-MAG,SO-SUN,SO-SIGHT...] supply how these samples were oriented Sample naming convention: [1] XXXXY: where XXXX is an arbitrary length site designation and Y is the single character sample designation. e.g., TG001a is the first sample from site TG001. [default] [2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length) [3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length) [4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX [5] site name same as sample [6] site is entered under a separate column [7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY NB: all others you will have to customize your self or e-mail [email protected] for help. INPUT PMD format files """ # initialize some stuff noave=0 inst="" samp_con,Z='1',"" missing=1 demag="N" er_location_name="unknown" citation='This study' args=sys.argv meth_code="LP-NO" specnum=-1 MagRecs=[] version_num=pmag.get_version() Samps=[] # keeps track of sample orientations DIspec=[] MagFiles=[] user="" mag_file="" dir_path='.' ErSamps=[] SampOuts=[] samp_file = 'er_samples.txt' meas_file = 'magic_measurements.txt' # # get command line arguments # if command_line: if '-WD' in sys.argv: ind = sys.argv.index('-WD') dir_path=sys.argv[ind+1] if '-ID' in sys.argv: ind = sys.argv.index('-ID') input_dir_path = sys.argv[ind+1] else: input_dir_path = dir_path output_dir_path = dir_path if "-h" in args: print main.__doc__ return False if '-F' in args: ind=args.index("-F") meas_file = args[ind+1] if '-Fsa' in args: ind = args.index("-Fsa") samp_file = args[ind+1] #try: # open(samp_file,'rU') # ErSamps,file_type=pmag.magic_read(samp_file) # print 'sample information will be appended to ', samp_file #except: # print samp_file,' not found: sample information will be stored in new er_samples.txt file' # samp_file = output_dir_path+'/er_samples.txt' if '-f' in args: ind = args.index("-f") mag_file= args[ind+1] if "-spc" in args: ind = args.index("-spc") specnum = int(args[ind+1]) if "-ncn" in args: ind=args.index("-ncn") samp_con=sys.argv[ind+1] if "-loc" in args: ind=args.index("-loc") er_location_name=args[ind+1] if "-A" in args: noave=1 if "-mcd" in args: ind=args.index("-mcd") meth_code=args[ind+1] if not command_line: dir_path = kwargs.get('dir_path', '.') input_dir_path = kwargs.get('input_dir_path', dir_path) output_dir_path = dir_path meas_file = kwargs.get('meas_file', 'magic_measurements.txt') mag_file = kwargs.get('mag_file') samp_file = kwargs.get('samp_file', 'er_samples.txt') specnum = kwargs.get('specnum', 0) samp_con = kwargs.get('samp_con', '1') er_location_name = kwargs.get('er_location_name', '') noave = kwargs.get('noave', 0) # default (0) means DO average meth_code = kwargs.get('meth_code', "LP-NO") print samp_con # format variables mag_file = input_dir_path+"/" + mag_file meas_file = output_dir_path+"/" + meas_file samp_file = output_dir_path+"/" + samp_file if specnum!=0:specnum=-specnum if "4" in samp_con: if "-" not in samp_con: print "naming convention option [4] must be in form 4-Z where Z is an integer" return False, "naming convention option [4] must be in form 4-Z where Z is an integer" else: Z=samp_con.split("-")[1] samp_con="4" if "7" in samp_con: if "-" not in samp_con: print "option [7] must be in form 7-Z where Z is an integer" return False, "naming convention option [7] must be in form 7-Z where Z is an integer" else: Z=samp_con.split("-")[1] samp_con="7" # parse data data=open(mag_file,'rU').readlines() # read in data from file comment=data[0] line=data[1].strip() line=line.replace("=","= ") # make finding orientations easier rec=line.split() # read in sample orientation, etc. er_specimen_name=rec[0] ErSampRec,ErSiteRec={},{} # make a sample record if specnum!=0: er_sample_name=rec[0][:specnum] else: er_sample_name=rec[0] if len(ErSamps)>0: # need to copy existing for samp in ErSamps: if samp['er_sample_name']==er_sample_name: ErSampRec=samp # we'll ammend this one else: SampOuts.append(samp) # keep all the others if int(samp_con)<6: er_site_name=pmag.parse_site(er_sample_name,samp_con,Z) else: if 'er_site_name' in ErSampRec.keys():er_site_name=ErSampREc['er_site_name'] if 'er_location_name' in ErSampRec.keys():er_location_name=ErSampREc['er_location_name'] az_ind=rec.index('a=')+1 ErSampRec['er_sample_name']=er_sample_name ErSampRec['er_sample_description']=comment ErSampRec['sample_azimuth']=rec[az_ind] dip_ind=rec.index('b=')+1 dip=-float(rec[dip_ind]) ErSampRec['sample_dip']='%7.1f'%(dip) strike_ind=rec.index('s=')+1 ErSampRec['sample_bed_dip_direction']='%7.1f'%(float(rec[strike_ind])+90.) bd_ind=rec.index('d=')+1 ErSampRec['sample_bed_dip']=rec[bd_ind] v_ind=rec.index('v=')+1 vol=rec[v_ind][:-3] date=rec[-2] time=rec[-1] ErSampRec['magic_method_codes']=meth_code if 'er_location_name' not in ErSampRec.keys():ErSampRec['er_location_name']=er_location_name if 'er_site_name' not in ErSampRec.keys():ErSampRec['er_site_name']=er_site_name if 'er_citation_names' not in ErSampRec.keys():ErSampRec['er_citation_names']='This study' if 'magic_method_codes' not in ErSampRec.keys():ErSampRec['magic_method_codes']='SO-NO' SampOuts.append(ErSampRec) for k in range(3,len(data)): # read in data line=data[k] rec=line.split() if len(rec)>1: # skip blank lines at bottom MagRec={} MagRec['measurement_description']='Date: '+date+' '+time MagRec["er_citation_names"]="This study" MagRec['er_location_name']=er_location_name MagRec['er_site_name']=er_site_name MagRec['er_sample_name']=er_sample_name MagRec['magic_software_packages']=version_num MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin MagRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin MagRec["measurement_flag"]='g' MagRec["measurement_standard"]='u' MagRec["measurement_number"]='1' MagRec["er_specimen_name"]=er_specimen_name if rec[0]=='NRM': meas_type="LT-NO" elif rec[0][0]=='M' or rec[0][0]=='H': meas_type="LT-AF-Z" elif rec[0][0]=='T': meas_type="LT-T-Z" else: print "measurement type unknown" return False, "measurement type unknown" X=[float(rec[1]),float(rec[2]),float(rec[3])] Vec=pmag.cart2dir(X) MagRec["measurement_magn_moment"]='%10.3e'% (Vec[2]) # Am^2 MagRec["measurement_magn_volume"]=rec[4] # A/m MagRec["measurement_dec"]='%7.1f'%(Vec[0]) MagRec["measurement_inc"]='%7.1f'%(Vec[1]) MagRec["treatment_ac_field"]='0' if meas_type!='LT-NO': treat=float(rec[0][1:]) else: treat=0 if meas_type=="LT-AF-Z": MagRec["treatment_ac_field"]='%8.3e' %(treat*1e-3) # convert from mT to tesla elif meas_type=="LT-T-Z": MagRec["treatment_temp"]='%8.3e' % (treat+273.) # temp in kelvin MagRec['magic_method_codes']=meas_type MagRecs.append(MagRec) MagOuts=pmag.measurements_methods(MagRecs,noave) pmag.magic_write(meas_file,MagOuts,'magic_measurements') print "results put in ",meas_file pmag.magic_write(samp_file,SampOuts,'er_samples') print "sample orientations put in ",samp_file return True, meas_file
def main(): """ NAME UU_magic.py DESCRIPTION takes Fort Hoofddijk (University of Utrecht) format magnetometer files and converts them to magic_measurements and er_samples.txt SYNTAX UU_magic.py [command line options] OPTIONS -f FILE: specify input file -fpos FILE: specify stratigraphic position file (.saf format) -F FILE: specify magic_measurements output file, default is: magic_measurements.txt -Fsa FILE: specify output file, default is: er_samples.txt -ncn NCON: specify naming convention: default is #1 below -ocn OCON: specify orientation convention, default is #1 below -mcd: specify sampling method codes as a colon delimited string: [default is: FS-FD:SO-POM] FS-FD field sampling done with a drill FS-H field sampling done with hand samples FS-LOC-GPS field location done with GPS FS-LOC-MAP field location done with map SO-POM a Pomeroy orientation device was used SO-ASC an ASC orientation device was used SO-MAG orientation with magnetic compass SO-SUN orientation with sun compass -loc: location name, default="unknown" -spc NUM : specify number of characters to designate a specimen, default = 0 -ins INST : specify instsrument name INPUT FORMAT Input files must be colon delimited: "file_name", "instrument" "specimen name","",az,pl,vol(cc),strike,dip treatment,X,Y,Z,CSD,"yy-mm-dd","hh:mm" Orientation convention: [1] Lab arrow azimuth= mag_azimuth; Lab arrow dip=-dip i.e., dip is degrees from vertical down - the hade [default] [2] Lab arrow azimuth = mag_azimuth-90; Lab arrow dip = -dip i.e., mag_azimuth is strike and dip is hade [3] Lab arrow azimuth = mag_azimuth; Lab arrow dip = dip-90 e.g. dip is degrees from horizontal of drill direction [4] Lab arrow azimuth = mag_azimuth; Lab arrow dip = dip [5] Lab arrow azimuth = mag_azimuth; Lab arrow dip = 90-dip [6] all others you will have to either customize your self or e-mail [email protected] for help. Magnetic declination convention: Az is already corrected in file Sample naming convention: [1] XXXXY: where XXXX is an arbitrary length site designation and Y is the single character sample designation. e.g., TG001a is the first sample from site TG001. [default] [2] XXXX-YY: YY sample from site XXXX (XXX, YY of arbitary length) [3] XXXX.YY: YY sample from site XXXX (XXX, YY of arbitary length) [4-Z] XXXX[YYY]: YYY is sample designation with Z characters from site XXX [5] site name same as sample [6] site is entered under a separate column [7-Z] [XXXX]YYY: XXXX is site designation with Z characters with sample name XXXXYYYY NB: all others you will have to customize your self or e-mail [email protected] for help. OUTPUT output saved in magic_measurements.txt & er_samples.txt formatted files will overwrite any existing files """ # # initialize variables # uu_file,samp_file,or_con,corr,meas_file = "","er_samples.txt","1","1","magic_measurements.txt" pos_file="" specnum=-1 args=sys.argv bed_dip,bed_dip_dir="","" samp_con,Z,average_bedding="1",1,"0" meths='FS-FD:SO-POM' sclass,lithology,type="","","" user,inst="","" or_con='1' corr=="3" DecCorr=0. location_name="unknown" # # dir_path='.' if '-WD' in args: ind=args.index("-WD") dir_path=sys.argv[ind+1] if "-h" in args: print main.__doc__ sys.exit() if "-f" in args: ind=args.index("-f") uu_file=sys.argv[ind+1] d=uu_file.split('.') if d[1].upper()=="AF":demag="AF" if d[1].upper()=="TH":demag="T" if "-fpos" in args: ind=args.index("-fpos") pos_file=sys.argv[ind+1] if "-F" in args: ind=args.index("-F") meas_file=sys.argv[ind+1] if "-Fsa" in args: ind=args.index("-Fsa") samp_file=sys.argv[ind+1] if "-ocn" in args: ind=args.index("-ocn") or_con=sys.argv[ind+1] if "-ncn" in args: ind=args.index("-ncn") samp_con=sys.argv[ind+1] if "4" in samp_con: if "-" not in samp_con: print "option [4] must be in form 4-Z where Z is an integer" sys.exit() else: Z=samp_con.split("-")[1] samp_con="4" if "7" in samp_con: if "-" not in samp_con: print "option [7] must be in form 7-Z where Z is an integer" sys.exit() else: Z=samp_con.split("-")[1] samp_con="7" if "-mcd" in args: ind=args.index("-mcd") meths=(sys.argv[ind+1]) if "-loc" in args: ind=args.index("-loc") location_name=(sys.argv[ind+1]) if "-spc" in args: ind=args.index("-spc") specnum=-int(args[ind+1]) if specnum!=0:specnum=-specnum if "-ins" in args: ind=args.index("-ins") inst=args[ind+1] # # uu_file=dir_path+'/'+uu_file samp_file=dir_path+'/'+samp_file meas_file=dir_path+'/'+meas_file if pos_file!="":pos_file=dir_path+'/'+pos_file samplist=[] try: SampOut,file_type=pmag.magic_read(samp_file) for rec in SampOut: if rec['er_sample_name'] not in samplist: samplist.append(rec['er_sample_name']) except: SampOut=[] PosData=[] if pos_file != "": p=open(pos_file,'rU') PosIn=p.readlines() p.close() for line in PosIn: srec=line.split()[0].split(',') Prec={'er_site_name':srec[0],'sample_height':srec[1]} PosData.append(Prec) infile=open(uu_file,'rU') Data=infile.readlines() infile.close() MagRecs=[] header=Data[0].split(',') if inst=="":inst=header[1].strip('"') if inst=='2G DC': inst=="FH-2GDC" # Dc Squid machine at Fort Hoofddijk else: inst="" newsamp=1 for k in range(1,len(Data)-1): # step through file, skipping header and "END" statement line=Data[k].split('\n')[0] rec=line.split(',') if newsamp==1 and rec[0].lower()!='end': newsamp=0 specname=rec[0].strip('"') # take off quotation marks if specnum!=0: sample=specname[:specnum] else: sample=specname site=pmag.parse_site(sample,samp_con,Z) # parse out the site name SampRec={} SampRec["er_sample_name"]=sample SampRec["er_location_name"]=location_name SampRec["er_citation_names"]="This study" labaz,labdip=pmag.orient(float(rec[2]),float(rec[3]),or_con) bed_dip=float(rec[6]) if bed_dip!=0: bed_dip_dir=float(rec[5])+90. # assume dip to right of strike if bed_dip_dir>=360:bed_dip_dir=bed_dip_dir-360. else: bed_dip_dir=float(rec[5]) # parse information common to all orientation methods # SampRec["sample_bed_dip"]='%7.1f'%(bed_dip) SampRec["sample_bed_dip_direction"]='%7.1f'%(bed_dip_dir) SampRec["sample_dip"]='%7.1f'%(labdip) SampRec["sample_azimuth"]='%7.1f'%(labaz) vol=float(rec[4])*1e-6 SampRec["sample_volume"]='%10.3e'%(vol) # convert cc into m^3 SampRec["sample_class"]=sclass SampRec["sample_lithology"]=lithology SampRec["sample_type"]=type SampRec["magic_method_codes"]=meths SampRec["er_site_name"]=site # # find position data # if PosData!=[]: for srec in PosData: if srec['er_site_name']==site: SampRec['sample_height']=srec['sample_height'] break if sample not in samplist: samplist.append(sample) SampOut.append(SampRec) elif rec[0]=='9999': # end of this specimen k=k+1 # move on newsamp=1 elif rec[0].lower()!='end' and rec[0]!="": # got some data line=Data[k].split('\n')[0] rec=line.split(',') MagRec={} MagRec["treatment_temp"]='%8.3e' % (273) # room temp in kelvin MagRec["measurement_temp"]='%8.3e' % (273) # room temp in kelvin MagRec["treatment_ac_field"]='0' MagRec["treatment_dc_field"]='0' MagRec["treatment_dc_field_phi"]='0' MagRec["treatment_dc_field_theta"]='0' meas_type="LT-NO" MagRec["measurement_flag"]='g' MagRec["measurement_standard"]='u' MagRec["measurement_number"]='1' MagRec["er_specimen_name"]=specname MagRec["er_sample_name"]=sample MagRec["er_site_name"]=site MagRec["er_location_name"]=location_name MagRec["measurement_csd"]=rec[4] cart=[] cart.append(-float(rec[2])) # appending x,y,z from data record cart.append(float(rec[3])) cart.append(-float(rec[1])) Dir=pmag.cart2dir(cart) MagRec["measurement_magn_volume"]='%10.3e'% (float(Dir[2])*1e-6) # moment in A/m (from 10^-6 A/m) MagRec["measurement_magn_moment"]='%10.3e'% (float(Dir[2])*vol*1e-6) # moment in Am^2 MagRec["measurement_dec"]='%7.1f'%(Dir[0]) MagRec["measurement_inc"]='%7.1f'%(Dir[1]) MagRec["magic_instrument_codes"]=inst MagRec["er_analyst_mail_names"]="" MagRec["er_citation_names"]="This study" MagRec["magic_method_codes"]=meas_type if demag=="AF": MagRec["treatment_ac_field"]='%8.3e' %(float(rec[0])*1e-3) # peak field in tesla meas_type="LT-AF-Z" MagRec["treatment_dc_field"]='0' elif demag=="T": MagRec["treatment_temp"]='%8.3e' % (float(rec[0])+273.) # temp in kelvin meas_type="LT-T-Z" MagRec['magic_method_codes']=meas_type # date=rec[5].strip('"').split('-') # time=rec[6].strip('"') # if int(date[0])<50: # assume this century # yyyy='20'+date[0] # else: # yyyy='19'+date[0] # assume last century # dstring=yyyy+':'+date[1]+':'+date[2]+":"+time # MagRec['measurement_date']=dstring MagRecs.append(MagRec) MagOuts=pmag.measurements_methods(MagRecs,0) pmag.magic_write(meas_file,MagOuts,'magic_measurements') print "Measurements put in ",meas_file pmag.magic_write(samp_file,SampOut,"er_samples") print "Sample orientation info saved in ", samp_file print "Good bye"
def main(): """ NAME ani_depthplot.py DESCRIPTION plots tau, V3_inc, P and chi versus core_depth SYNTAX ani_depthplot.py [command line optins] OPTIONS -h prints help message and quits -f FILE: specify input rmag_anisotropy format file from magic -fb FILE: specify input magic_measurements format file from magic -fsa FILE: specify input er_samples format file from magic -fa FILE: specify input er_ages format file from magic -d min max [in m] depth range to plot -ds [mcd,mbsf], specify depth scale, default is mbsf -sav save plot without review -fmt specfiy format for figures - default is svg DEFAULTS: Anisotropy file: rmag_anisotropy.txt Bulk susceptibility file: magic_measurements.txt Samples file: er_samples.txt """ fmt='.svg' dir_path="./" pcol=3 verbose=pmagplotlib.verbose plots=0 age_file="" if '-WD' in sys.argv: ind=sys.argv.index('-WD') dir_path=sys.argv[ind+1] ani_file=dir_path+'/rmag_anisotropy.txt' meas_file=dir_path+'/magic_measurements.txt' samp_file=dir_path+'/er_samples.txt' if '-h' in sys.argv: print main.__doc__ sys.exit() if '-f' in sys.argv: ind=sys.argv.index('-f') ani_file=dir_path+'/'+sys.argv[ind+1] if '-fb' in sys.argv: ind=sys.argv.index('-fb') meas_file=dir_path+'/'+sys.argv[ind+1] if '-fsa' in sys.argv: ind=sys.argv.index('-fsa') samp_file=dir_path+'/'+sys.argv[ind+1] if '-fa' in sys.argv: print main.__doc__ print 'only -fsa OR -fa - not both' sys.exit() elif '-fa' in sys.argv: ind=sys.argv.index('-fa') age_file=dir_path+"/"+sys.argv[ind+1] if '-fmt' in sys.argv: ind=sys.argv.index('-fmt') fmt='.'+sys.argv[ind+1] dmin,dmax=-1,-1 if '-d' in sys.argv: ind=sys.argv.index('-d') dmin=float(sys.argv[ind+1]) dmax=float(sys.argv[ind+2]) if '-ds' in sys.argv and 'mcd' in sys.argv: # sets depth scale to meters composite depth (as opposed to meters below sea floor) depth_scale='sample_composite_depth' elif age_file=="": depth_scale='sample_core_depth' else: depth_scale='age' if '-sav' in sys.argv: plots=1 verbose=0 # # get data read in isbulk=0 # tests if there are bulk susceptibility measurements AniData,file_type=pmag.magic_read(ani_file) # read in tensor elements if age_file=="": Samps,file_type=pmag.magic_read(samp_file) # read in sample depth info from er_sample.txt format file else: Samps,file_type=pmag.magic_read(age_file) # read in sample age info from er_ages.txt format file age_unit=Samps[0]['age_unit'] for s in Samps:s['er_sample_name']=s['er_sample_name'].upper() # change to upper case for every sample name Meas,file_type=pmag.magic_read(meas_file) if file_type=='magic_measurements':isbulk=1 Data=[] Bulks=[] BulkDepths=[] for rec in AniData: samprecs=pmag.get_dictitem(Samps,'er_sample_name',rec['er_sample_name'].upper(),'T') # look for depth record for this sample sampdepths=pmag.get_dictitem(samprecs,depth_scale,'','F') # see if there are non-blank depth data if dmax!=-1: sampdepths=pmag.get_dictitem(sampdepths,depth_scale,dmax,'max') # fishes out records within depth bounds sampdepths=pmag.get_dictitem(sampdepths,depth_scale,dmin,'min') if len(sampdepths)>0: # if there are any.... rec['core_depth'] = sampdepths[0][depth_scale] # set the core depth of this record Data.append(rec) # fish out data with core_depth if isbulk: # if there are bulk data chis=pmag.get_dictitem(Meas,'er_specimen_name',rec['er_specimen_name'],'T') chis=pmag.get_dictitem(chis,'measurement_chi_volume','','F') # get the non-zero values for this specimen if len(chis)>0: # if there are any.... Bulks.append(1e6*float(chis[0]['measurement_chi_volume'])) # put in microSI BulkDepths.append(float(sampdepths[0][depth_scale])) if len(Bulks)>0: # set min and max bulk values bmin=min(Bulks) bmax=max(Bulks) xlab="Depth (m)" if len(Data)>0: location=Data[0]['er_location_name'] else: print 'no data to plot' sys.exit() # collect the data for plotting tau and V3_inc Depths,Tau1,Tau2,Tau3,V3Incs,P=[],[],[],[],[],[] Axs=[] # collect the plot ids if len(Bulks)>0: pcol+=1 s1=pmag.get_dictkey(Data,'anisotropy_s1','f') # get all the s1 values from Data as floats s2=pmag.get_dictkey(Data,'anisotropy_s2','f') s3=pmag.get_dictkey(Data,'anisotropy_s3','f') s4=pmag.get_dictkey(Data,'anisotropy_s4','f') s5=pmag.get_dictkey(Data,'anisotropy_s5','f') s6=pmag.get_dictkey(Data,'anisotropy_s6','f') Depths=pmag.get_dictkey(Data,'core_depth','f') Ss=numpy.array([s1,s4,s5,s4,s2,s6,s5,s6,s3]).transpose() # make an array Ts=numpy.reshape(Ss,(len(Ss),3,-1)) # and re-shape to be n-length array of 3x3 sub-arrays for k in range(len(Depths)): tau,Evecs= pmag.tauV(Ts[k]) # get the sorted eigenvalues and eigenvectors v3=pmag.cart2dir(Evecs[2])[1] # convert to inclination of the minimum eigenvector V3Incs.append(v3) Tau1.append(tau[0]) Tau2.append(tau[1]) Tau3.append(tau[2]) P.append(tau[0]/tau[2]) if len(Depths)>0: if dmax==-1: dmax=max(Depths) dmin=min(Depths) tau_max=max(Tau1) tau_min=min(Tau3) P_max=max(P) P_min=min(P) #dmax=dmax+.05*dmax #dmin=dmin-.05*dmax pylab.figure(1,figsize=(10,8)) # make the figure version_num=pmag.get_version() pylab.figtext(.02,.01,version_num) # attach the pmagpy version number ax=pylab.subplot(1,pcol,1) # make the first column Axs.append(ax) ax.plot(Tau1,Depths,'rs') ax.plot(Tau2,Depths,'b^') ax.plot(Tau3,Depths,'ko') ax.axis([tau_min,tau_max,dmax,dmin]) ax.set_xlabel('Eigenvalues') if depth_scale=='sample_core_depth': ax.set_ylabel('Depth (mbsf)') elif depth_scale=='age': ax.set_ylabel('Age ('+age_unit+')') else: ax.set_ylabel('Depth (mcd)') ax2=pylab.subplot(1,pcol,2) # make the second column ax2.plot(P,Depths,'rs') ax2.axis([P_min,P_max,dmax,dmin]) ax2.set_xlabel('P') ax2.set_title(location) Axs.append(ax2) ax3=pylab.subplot(1,pcol,3) Axs.append(ax3) ax3.plot(V3Incs,Depths,'ko') ax3.axis([0,90,dmax,dmin]) ax3.set_xlabel('V3 Inclination') if pcol==4: ax4=pylab.subplot(1,pcol,4) Axs.append(ax4) ax4.plot(Bulks,BulkDepths,'bo') ax4.axis([bmin-1,bmax+1,dmax,dmin]) ax4.set_xlabel('Bulk Susc. (uSI)') for x in Axs:pmagplotlib.delticks(x) # this makes the x-tick labels more reasonable - they were overcrowded using the defaults figname=location+'_ani-depthplot'+fmt if verbose: pylab.draw() ans=raw_input("S[a]ve plot? Return to quit ") if ans=='a': pylab.savefig(figname) print 'Plot saved as ',figname elif plots: pylab.savefig(figname) print 'Plot saved as ',figname sys.exit() else: print "No data points met your criteria - try again"
def plotELL(pars,col,lower,plot): """ function to calculate points on an ellipse about Pdec,Pdip with angle beta,gamma """ rad=np.pi/180. Pdec,Pinc,beta,Bdec,Binc,gamma,Gdec,Ginc=pars[0],pars[1],pars[2],pars[3],pars[4],pars[5],pars[6],pars[7] if beta > 90. or gamma>90: beta=180.-beta gamma=180.-beta Pdec=Pdec-180. Pinc=-Pinc beta,gamma=beta*rad,gamma*rad # convert to radians X_ell,Y_ell,X_up,Y_up,PTS=[],[],[],[],[] nums=201 xnum=float(nums-1.)/2. # set up t matrix t=[[0,0,0],[0,0,0],[0,0,0]] X=pmag.dir2cart((Pdec,Pinc,1.0)) # convert to cartesian coordintes if lower==1 and X[2]<0: for i in range(3): X[i]=-X[i] # set up rotation matrix t t[0][2]=X[0] t[1][2]=X[1] t[2][2]=X[2] X=pmag.dir2cart((Bdec,Binc,1.0)) if lower==1 and X[2]<0: for i in range(3): X[i]=-X[i] t[0][0]=X[0] t[1][0]=X[1] t[2][0]=X[2] X=pmag.dir2cart((Gdec,Ginc,1.0)) if lower==1 and X[2]<0: for i in range(3): X[i]=-X[i] t[0][1]=X[0] t[1][1]=X[1] t[2][1]=X[2] # set up v matrix v=[0,0,0] for i in range(nums): # incremental point along ellipse psi=float(i)*np.pi/xnum v[0]=np.sin(beta)*np.cos(psi) v[1]=np.sin(gamma)*np.sin(psi) v[2]=np.sqrt(1.-v[0]**2 - v[1]**2) elli=[0,0,0] # calculate points on the ellipse for j in range(3): for k in range(3): elli[j]=elli[j] + t[j][k]*v[k] # cartesian coordinate j of ellipse PTS.append(pmag.cart2dir(elli)) R=np.sqrt( 1.-abs(elli[2]))/(np.sqrt(elli[0]**2+elli[1]**2)) # put on an equal area projection if elli[2]<0: # for i in range(3): elli[i]=-elli[i] X_up.append(elli[1]*R) Y_up.append(elli[0]*R) # Adding None values stops plotting of an additional straight line # between the points where the ellipse crosses the edge of the stereonet X_ell.append(None) Y_ell.append(None) else: X_ell.append(elli[1]*R) Y_ell.append(elli[0]*R) if plot==1: if X_ell!=[]:plt.plot(X_ell,Y_ell,color=col, linewidth=2, zorder=6) if X_up!=[]:plt.plot(X_up,Y_up,color=col,linewidth=2,linestyle=':') else: return PTS
def dokent(data, NN): #From PmagPy (Tauxe et al., 2016) """ gets Kent parameters for data ([D,I],N) """ X, kpars = [], {} N = len(data) if N < 2: return kpars # # get fisher mean and convert to co-inclination (theta)/dec (phi) in radians # fpars = pmag.fisher_mean(data) pbar = fpars["dec"] * np.pi / 180. tbar = (90. - fpars["inc"]) * np.pi / 180. # # initialize matrices # H = [[0., 0., 0.], [0., 0., 0.], [0., 0., 0.]] w = [[0., 0., 0.], [0., 0., 0.], [0., 0., 0.]] b = [[0., 0., 0.], [0., 0., 0.], [0., 0., 0.]] gam = [[0., 0., 0.], [0., 0., 0.], [0., 0., 0.]] xg = [] # # set up rotation matrix H # H = [[ np.cos(tbar) * np.cos(pbar), -np.sin(pbar), np.sin(tbar) * np.cos(pbar) ], [ np.cos(tbar) * np.sin(pbar), np.cos(pbar), np.sin(pbar) * np.sin(tbar) ], [-np.sin(tbar), 0., np.cos(tbar)]] # # get cartesian coordinates of data # for rec in data: X.append(pmag.dir2cart([rec[0], rec[1], 1.])) # # put in T matrix # T = pmag.Tmatrix(X) for i in range(3): for j in range(3): T[i][j] = old_div(T[i][j], float(NN)) # # compute B=H'TH # for i in range(3): for j in range(3): for k in range(3): w[i][j] += T[i][k] * H[k][j] for i in range(3): for j in range(3): for k in range(3): b[i][j] += H[k][i] * w[k][j] # # choose a rotation w about North pole to diagonalize upper part of B # psi = 0.5 * np.arctan(2. * b[0][1] / (b[0][0] - b[1][1])) w = [[np.cos(psi), -np.sin(psi), 0], [np.sin(psi), np.cos(psi), 0], [0., 0., 1.]] for i in range(3): for j in range(3): gamtmp = 0. for k in range(3): gamtmp += H[i][k] * w[k][j] gam[i][j] = gamtmp for i in range(N): xg.append([0., 0., 0.]) for k in range(3): xgtmp = 0. for j in range(3): xgtmp += gam[j][k] * X[i][j] xg[i][k] = xgtmp # compute asymptotic ellipse parameters # xmu, sigma1, sigma2 = 0., 0., 0. for i in range(N): xmu += xg[i][2] sigma1 = sigma1 + xg[i][0]**2 sigma2 = sigma2 + xg[i][1]**2 xmu = old_div(xmu, float(N)) sigma1 = old_div(sigma1, float(N)) sigma2 = old_div(sigma2, float(N)) g = -2.0 * np.log(0.05) / (float(NN) * xmu**2) if np.sqrt(sigma1 * g) < 1: eta = np.arcsin(np.sqrt(sigma1 * g)) if np.sqrt(sigma2 * g) < 1: zeta = np.arcsin(np.sqrt(sigma2 * g)) if np.sqrt(sigma1 * g) >= 1.: eta = old_div(np.pi, 2.) if np.sqrt(sigma2 * g) >= 1.: zeta = old_div(np.pi, 2.) # # convert Kent parameters to directions,angles # kpars["dec"] = fpars["dec"] kpars["inc"] = fpars["inc"] kpars["n"] = NN ZDir = pmag.cart2dir([gam[0][1], gam[1][1], gam[2][1]]) EDir = pmag.cart2dir([gam[0][0], gam[1][0], gam[2][0]]) kpars["Zdec"] = ZDir[0] kpars["Zinc"] = ZDir[1] kpars["Edec"] = EDir[0] kpars["Einc"] = EDir[1] if kpars["Zinc"] < 0: kpars["Zinc"] = -kpars["Zinc"] kpars["Zdec"] = (kpars["Zdec"] + 180.) % 360. if kpars["Einc"] < 0: kpars["Einc"] = -kpars["Einc"] kpars["Edec"] = (kpars["Edec"] + 180.) % 360. kpars["Zeta"] = zeta * 180. / np.pi kpars["Eta"] = eta * 180. / np.pi return kpars
def main(): """ NAME igrf.py DESCRIPTION This program calculates igrf field values using the routine of Malin and Barraclough (1981) based on d/igrfs from 1900 to 2010. between 1900 and 1000BCE, it uses CALS3K.4 or ARCH3K.1 Prior to 1000BCE, it uses CALS10k-4b Calculates reference field vector at specified location and time. SYNTAX igrf.py [-h] [-i] -f FILE [< filename] OPTIONS: -h prints help message and quits -i for interactive data entry -f FILE specify file name with input data -F FILE specify output file name -ages MIN MAX INCR: specify age minimum in years (+/- AD), maximum and increment, default is line by line -loc LAT LON; specify location, default is line by line -alt ALT; specify altitude in km, default is sealevel (0) -plt; make a plot of the time series -fmt [pdf,jpg,eps,svg] specify format for output figure (default is svg) -mod [arch3k,cals3k] specify model for 3ka to 1900 AD, default is cals3k.4b INPUT FORMAT interactive entry: date: decimal year alt: altitude in km lat: positive north lon: positive east for file entry: space delimited string: date alt lat long OUTPUT FORMAT Declination Inclination Intensity (nT) date alt lat long """ plt,fmt=0,'svg' if '-fmt' in sys.argv: ind=sys.argv.index('-fmt') fmt=sys.argv[ind+1] if len(sys.argv)!=0 and '-h' in sys.argv: print main.__doc__ sys.exit() if '-mod' in sys.argv: ind=sys.argv.index('-mod') mod3k=sys.argv[ind+1] else: mod3k='' if '-f' in sys.argv: ind=sys.argv.index('-f') file=sys.argv[ind+1] input=numpy.loadtxt(file) elif '-i' in sys.argv: while 1: try: line=[] line.append(float(raw_input("Decimal year: <cntrl-D to quit> "))) alt=raw_input("Elevation in km [0] ") if alt=="":alt="0" line.append(float(alt)) line.append(float(raw_input("Latitude (positive north) "))) line.append(float(raw_input("Longitude (positive east) "))) if mod3k=='': x,y,z,f=pmag.doigrf(line[3]%360.,line[2],line[1],line[0]) else: x,y,z,f=pmag.doigrf(line[3]%360.,line[2],line[1],line[0],mod3k=mod3k) Dir=pmag.cart2dir((x,y,z)) print '%7.1f %7.1f %8.0f'%(Dir[0],Dir[1],f) except EOFError: print "\n Good-bye\n" sys.exit() elif '-ages' in sys.argv: ind=sys.argv.index('-ages') agemin=float(sys.argv[ind+1]) agemax=float(sys.argv[ind+2]) ageincr=float(sys.argv[ind+3]) if '-loc' in sys.argv: ind=sys.argv.index('-loc') lat=float(sys.argv[ind+1]) lon=float(sys.argv[ind+2]) else: print "must specify lat/lon if using age range option" sys.exit() if '-alt' in sys.argv: ind=sys.argv.index('-alt') alt=float(sys.argv[ind+1]) else: alt=0 ages=numpy.arange(agemin,agemax,ageincr) lats=numpy.ones(len(ages))*lat lons=numpy.ones(len(ages))*lon alts=numpy.ones(len(ages))*alt input=numpy.array([ages,alts,lats,lons]).transpose() else: input=numpy.loadtxt(sys.stdin,dtype=numpy.float) if '-F' in sys.argv: ind=sys.argv.index('-F') outfile=sys.argv[ind+1] out=open(outfile,'w') else:outfile="" if '-plt' in sys.argv: plt=1 import matplotlib matplotlib.use("TkAgg") import pylab pylab.ion() Ages,Decs,Incs,Ints,VADMs=[],[],[],[],[] for line in input: if mod3k=='': x,y,z,f=pmag.doigrf(line[3]%360.,line[2],line[1],line[0]) else: x,y,z,f=pmag.doigrf(line[3]%360.,line[2],line[1],line[0],mod3k=mod3k) Dir=pmag.cart2dir((x,y,z)) if outfile!="": out.write('%7.1f %7.1f %8.0f %7.1f %7.1f %7.1f %7.1f\n'%(Dir[0],Dir[1],f,line[0],line[1],line[2],line[3])) elif plt: Ages.append(line[0]) if Dir[0]>180: Dir[0]=Dir[0]-360.0 Decs.append(Dir[0]) Incs.append(Dir[1]) Ints.append(f*1e-3) VADMs.append(pmag.b_vdm(f*1e-9,line[2])*1e-21) else: print '%7.1f %7.1f %8.0f %7.1f %7.1f %7.1f %7.1f'%(Dir[0],Dir[1],f,line[0],line[1],line[2],line[3]) if plt: fig=pylab.figure(num=1,figsize=(7,9)) fig.add_subplot(411) pylab.plot(Ages,Decs) pylab.ylabel('Declination ($^{\circ}$)') fig.add_subplot(412) pylab.plot(Ages,Incs) pylab.ylabel('Inclination ($^{\circ}$)') fig.add_subplot(413) pylab.plot(Ages,Ints) pylab.ylabel('Intensity ($\mu$T)') fig.add_subplot(414) pylab.plot(Ages,VADMs) pylab.ylabel('VADMs (ZAm$^2$)') pylab.xlabel('Ages') pylab.draw() ans=raw_input("S[a]ve to save figure, <Return> to quit ") if ans=='a': pylab.savefig('igrf.'+fmt) print 'Figure saved as: ','igrf.'+fmt sys.exit()
def plotELL(pars, col, lower, plot): """ function to calculate points on an ellipse about Pdec,Pdip with angle beta,gamma """ rad = np.pi / 180. Pdec, Pinc, beta, Bdec, Binc, gamma, Gdec, Ginc = pars[0], pars[1], pars[ 2], pars[3], pars[4], pars[5], pars[6], pars[7] if beta > 90. or gamma > 90: beta = 180. - beta gamma = 180. - beta Pdec = Pdec - 180. Pinc = -Pinc beta, gamma = beta * rad, gamma * rad # convert to radians X_ell, Y_ell, X_up, Y_up, PTS = [], [], [], [], [] nums = 201 xnum = float(nums - 1.) / 2. # set up t matrix t = [[0, 0, 0], [0, 0, 0], [0, 0, 0]] X = pmag.dir2cart((Pdec, Pinc, 1.0)) # convert to cartesian coordintes if lower == 1 and X[2] < 0: for i in range(3): X[i] = -X[i] # set up rotation matrix t t[0][2] = X[0] t[1][2] = X[1] t[2][2] = X[2] X = pmag.dir2cart((Bdec, Binc, 1.0)) if lower == 1 and X[2] < 0: for i in range(3): X[i] = -X[i] t[0][0] = X[0] t[1][0] = X[1] t[2][0] = X[2] X = pmag.dir2cart((Gdec, Ginc, 1.0)) if lower == 1 and X[2] < 0: for i in range(3): X[i] = -X[i] t[0][1] = X[0] t[1][1] = X[1] t[2][1] = X[2] # set up v matrix v = [0, 0, 0] for i in range(nums): # incremental point along ellipse psi = float(i) * np.pi / xnum v[0] = np.sin(beta) * np.cos(psi) v[1] = np.sin(gamma) * np.sin(psi) v[2] = np.sqrt(1. - v[0]**2 - v[1]**2) elli = [0, 0, 0] # calculate points on the ellipse for j in range(3): for k in range(3): elli[j] = elli[j] + t[j][k] * v[ k] # cartesian coordinate j of ellipse PTS.append(pmag.cart2dir(elli)) R = np.sqrt(1. - abs(elli[2])) / (np.sqrt(elli[0]**2 + elli[1]**2) ) # put on an equal area projection if elli[2] < 0: # for i in range(3): elli[i]=-elli[i] X_up.append(elli[1] * R) Y_up.append(elli[0] * R) # Adding None values stops plotting of an additional straight line # between the points where the ellipse crosses the edge of the stereonet X_ell.append(None) Y_ell.append(None) else: X_ell.append(elli[1] * R) Y_ell.append(elli[0] * R) if plot == 1: if X_ell != []: plt.plot(X_ell, Y_ell, color=col, linewidth=2, zorder=6) if X_up != []: plt.plot(X_up, Y_up, color=col, linewidth=2, linestyle=':') else: return PTS
def calculate_aniso_parameters(B,K): aniso_parameters={} S_bs=dot(B,K) # normalize by trace trace=S_bs[0]+S_bs[1]+S_bs[2] S_bs=S_bs/trace s1,s2,s3,s4,s5,s6=S_bs[0],S_bs[1],S_bs[2],S_bs[3],S_bs[4],S_bs[5] s_matrix=[[s1,s4,s6],[s4,s2,s5],[s6,s5,s3]] # calculate eigen vector, t,evectors=eig(s_matrix) # sort vectors t=list(t) t1=max(t) ix_1=t.index(t1) t3=min(t) ix_3=t.index(t3) for tt in range(3): if t[tt]!=t1 and t[tt]!=t3: t2=t[tt] ix_2=t.index(t2) v1=[evectors[0][ix_1],evectors[1][ix_1],evectors[2][ix_1]] v2=[evectors[0][ix_2],evectors[1][ix_2],evectors[2][ix_2]] v3=[evectors[0][ix_3],evectors[1][ix_3],evectors[2][ix_3]] DIR_v1=pmag.cart2dir(v1) DIR_v2=pmag.cart2dir(v2) DIR_v3=pmag.cart2dir(v3) aniso_parameters['anisotropy_s1']="%f"%s1 aniso_parameters['anisotropy_s2']="%f"%s2 aniso_parameters['anisotropy_s3']="%f"%s3 aniso_parameters['anisotropy_s4']="%f"%s4 aniso_parameters['anisotropy_s5']="%f"%s5 aniso_parameters['anisotropy_s6']="%f"%s6 aniso_parameters['anisotropy_degree']="%f"%(t1/t3) aniso_parameters['anisotropy_t1']="%f"%t1 aniso_parameters['anisotropy_t2']="%f"%t2 aniso_parameters['anisotropy_t3']="%f"%t3 aniso_parameters['anisotropy_v1_dec']="%.1f"%DIR_v1[0] aniso_parameters['anisotropy_v1_inc']="%.1f"%DIR_v1[1] aniso_parameters['anisotropy_v2_dec']="%.1f"%DIR_v2[0] aniso_parameters['anisotropy_v2_inc']="%.1f"%DIR_v2[1] aniso_parameters['anisotropy_v3_dec']="%.1f"%DIR_v3[0] aniso_parameters['anisotropy_v3_inc']="%.1f"%DIR_v3[1] # modified from pmagpy: if len(K)/3==9 or len(K)/3==6 or len(K)/3==15: n_pos=len(K)/3 tmpH = Matrices[n_pos]['tmpH'] a=s_matrix S=0. comp=zeros((n_pos*3),'f') for i in range(n_pos): for j in range(3): index=i*3+j compare=a[j][0]*tmpH[i][0]+a[j][1]*tmpH[i][1]+a[j][2]*tmpH[i][2] comp[index]=compare for i in range(n_pos*3): d=K[i]/trace - comp[i] # del values S+=d*d nf=float(n_pos*3-6) # number of degrees of freedom if S >0: sigma=math.sqrt(S/nf) hpars=pmag.dohext(nf,sigma,[s1,s2,s3,s4,s5,s6]) aniso_parameters['anisotropy_sigma']="%f"%sigma aniso_parameters['anisotropy_ftest']="%f"%hpars["F"] aniso_parameters['anisotropy_ftest12']="%f"%hpars["F12"] aniso_parameters['anisotropy_ftest23']="%f"%hpars["F23"] aniso_parameters['result_description']="Critical F: %s"%(hpars['F_crit']) aniso_parameters['anisotropy_F_crit']="%f"%float(hpars['F_crit']) aniso_parameters['anisotropy_n']=n_pos return(aniso_parameters)