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InOutput.py
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InOutput.py
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"""
InOutput.py
For documentation see the major file PyCigale.py
This file contains the file-in/output functions for the PyCigale package
"""
from PyGalKin import *
## SHORTCUTS
tab='\t'
nl='\n'
bs='\\'
sp=' '
null='\0'
def dump(data,filename):
file=open(filename,'w')
pickle.dump(data,file)
file.close()
def load(filename):
file=open(filename,'r')
data=pickle.load(file)
file.close()
return data
def fromPAR(p={},filename='par'):
""" reading my own parameter file with relevant parameters """
p['parname']=filename
for line in open(filename):
line=line.split()
if line[0] == 'cen': p['cen'] = int(line[1]),int(line[2])
elif line[0] == 'relsize': p['relsize']=int(line[1])
elif line[0] == 'pa': p['pa']=float(line[1])
elif line[0] == 'dyncen': p['dyncen']= int(line[1]),int(line[2])
elif line[0] == 'monocuts': p['monocuts']= int(line[1]),int(line[2])
elif line[0] == 'contcuts': p['contcuts']= int(line[1]),int(line[2])
elif line[0] == 'velcuts': p['velcuts']= int(line[1]),int(line[2])
elif line[0] == 'sigcuts': p['sigcuts']= int(line[1]),int(line[2])
elif line[0] == 'minmask': p['minmask']=float(line[1])
elif line[0] == 'incl': p['incl']=float(line[1])
elif line[0] == 'wedge': p['wedge']=float(line[1])
elif line[0] == 'gid': p['gid']= int(line[1])
elif line[0] == 'coor': p['coor'] = float(line[1]),float(line[2])
return p
def toPAR(inarr,filename=None):
""" writing my own parameter file with relevant parameters """
if filename == None:
if inarr.parname == None:
print "I know no filename"
return 1
else:
filename=inarr.parname
file=open(filename,'w')
file.write('cen'+sp+str(inarr.p['cen'][0])+sp+str(inarr.p['cen'][1])+nl)
file.write('relsize'+sp+str(inarr.p['relsize'])+nl)
file.write('pa'+sp+str(inarr.p['pa'])+nl)
file.write('dyncen'+sp+str(inarr.p['dyncen'][0])+sp+str(inarr.p['dyncen'][1])+nl)
file.write('monocuts'+sp+str(inarr.p['monocuts'][0])+sp+str(inarr.p['monocuts'][1])+nl)
file.write('contcuts'+sp+str(inarr.p['contcuts'][0])+sp+str(inarr.p['contcuts'][1])+nl)
file.write('velcuts'+sp+str(inarr.p['velcuts'][0])+sp+str(inarr.p['velcuts'][1])+nl)
file.write('minmask'+sp+str(inarr.p['minmask'])+nl)
file.close()
def fromAD(filename, readparams=True):
"""
reading files from adhoc file format, setting the parameters right. returns adhoc-class
"""
tmpF=N.fromfile(filename,dtype='Float32')
tmpI=N.fromfile(filename,dtype='Int32')
ndim=tmpI[-64]
nx=tmpI[-61]
ny=tmpI[-60]
nz=tmpI[-59]
if ndim == 2:
shape=(nx,ny)
data = N.fromfile(filename,dtype='Float32',count=nx*ny).reshape(shape)
data = data[::-1,:]
elif ndim ==3:
shape=(nx,ny,nz)
data = N.fromfile(filename,dtype='Float32',count=nx*ny*nz).reshape(shape)
data = data[::-1,:,:]
else:
pass
data=data.swapaxes(0,1) # to be make origin at lower right
# setting some parameters
p={}
p['cen']=nx/2,ny/2
p['imagename']=filename
# setting the Adhoc-parameters
p['echelle']=float(tmpF[-58])
p['xl1']=float(tmpF[-54])
p['xil']=float(tmpF[-53])
p['vr0']=float(tmpF[-52])
p['p']=float(tmpF[-50])
p['xlp']=float(tmpF[-49])
p['xlneb']=float(tmpF[-48])
p['v1']=float(tmpF[-47])
p['interfr_kms']=float(tmpF[-46])
if (readparams==True):
fromADP(p,'par.adp')
fromPAR(p,'par')
#data.getsaltzer()
data=N.ascontiguousarray(data)
return C.adhoc(data,p=p)
def toAD(input,filename=None):
""" writes ADHOC files. for file format see: adw_what.htm
by default uses original filename
"""
inarr=input.copy()
if filename == None:
if inarr.p['imagename'] == None:
print "I know no filename"
return 1
else:
filename=inarr.p['imagename']
file=open(filename,'w')
inarr=inarr.swapaxes(0,1) # flipping axes again to be consistent with ADHOC
inarr=inarr[::-1,:,:]
inarr.astype('Float32').tofile(file) # the data
N.array([inarr.ndim()],'Int32').tofile(file) # number of dimensios
N.array([0],'Int32').tofile(file) # id1 what is this?
N.array([0],'Int32').tofile(file) # id2
N.array([inarr.nx()],'Int32').tofile(file) # x-dim
N.array([inarr.ny()],'Int32').tofile(file) # y-dim
N.array([inarr.nz()],'Int32').tofile(file) # z-dim
N.array([inarr.p['echelle']],'Float32').tofile(file) # pixel scale
N.array([0],'Int32').tofile(file) # ix0
N.array([0],'Int32').tofile(file) # iy0
N.array([1],'Float32').tofile(file) # zoom
if inarr.ndim() == 2:
print "Writing 2D file"
N.array([0],'Int32').tofile(file)
N.array([0],'Float32').tofile(file)
N.array([1],'Float32').tofile(file)
N.array([256],'Int32').tofile(file)
N.array([1],'Int32').tofile(file)
N.arange(17,dtype='Int32').tofile(file) # unsused 68 bytes
elif inarr.ndim() == 3:
print "Writing 3D file"
N.array([inarr.p['xl1']],'Float32').tofile(file)
N.array([inarr.p['xil']],'Float32').tofile(file)
N.array([inarr.p['vr0']],'Float32').tofile(file)
N.array([0],'Float32').tofile(file) # velocity correction
N.array([inarr.p['p']],'Float32').tofile(file)
N.array([inarr.p['xlp']],'Float32').tofile(file)
N.array([inarr.p['xlneb']],'Float32').tofile(file)
N.array([inarr.p['v1']],'Float32').tofile(file)
N.array([inarr.p['interfr_kms']],'Float32').tofile(file)
N.arange(13,dtype='Int32').tofile(file) # unsused 52 bytes
else:
pass
N.arange(32,dtype='Int32').tofile(file) # the 128 byte of comment
file.close()
def fromADP(p,filename):
""" read an ADP file into an ADP class
"""
p['paraname']=filename
for line in open(filename).readlines():
line=line.split()
if line.__len__() <= 1: p['objname']=line[0]
elif line[1] == 'lx': p['lx']=int(line[0])
elif line[1] == 'ly': p['ly']=int(line[0])
elif line[1] == 'lz': p['lz']=int(line[0])
elif line[1] == 'ix0': p['ix0']=int(line[0])
elif line[1] == 'iy0': p['iy0']=int(line[0])
elif line[1] == 'iz0': p['iz0']=int(line[0])
elif line[1] == 'modefp': p['modefp']=int(line[0])
elif line[1] == 'p': p['p']=int(line[0])
elif line[1] == 'xlp': p['xlp']=float(line[0])
elif line[1] == 'xleta': p['xleta']=float(line[0])
elif line[1] == 'xlbeta': p['xlbeta']=float(line[0])
elif line[1] == 'xlneb': p['xlneb']=float(line[0])
elif line[1] == 'xlbneb': p['xlbneb']=float(line[0])
elif line[1] == 'xil': p['xil']=float(line[0])
elif line[1] == 'xl1': p['xl1']=float(line[0])
elif line[1] == 'vr0': p['vr0']=float(line[0])
elif line[1] == 'corrv': p['corrv']=float(line[0])
elif line[1] == 'echelle': p['echelle']=float(line[0])
elif line[1] == 'xc': p['xc']=float(line[0])
elif line[1] == 'yc': p['yc']=float(line[0])
elif line[1] == 'ellipt': p['ellipt']=float(line[0])
elif line[1] == 'mode_c': p['mode_c']=int(line[0])
elif line[1] == 'mode_e': p['mode_e']=int(line[0])
elif line[1] == 'min_a': p['min_a']=float(line[0])
elif line[1] == 'max_a': p['max_a']=float(line[0])
elif line[1] == 'min_r': p['min_r']=float(line[0])
elif line[1] == 'max_r': p['max_r']=float(line[0])
else: pass
def toADP(inADP,filename=None):
""" write adp-class to adp-file
uses original filename bu default
"""
if filename == None:
if inADP.p['paraname'] == None:
print "I know no filename"
return 1
else:
filename=inADP.p['paraname']
file=open(filename,'w')
file.write(inADP.p['objname'] +nl)
file.write(tab + str(inADP.p['lx']) + tab + 'lx' + tab + 'dimension X' +nl)
file.write(tab + str(inADP.p['ly']) + tab + 'ly' + tab + 'dimension Y' +nl)
file.write(tab + str(inADP.p['lz']) + tab + 'lz' + tab + 'dimension Z' +nl)
file.write(tab + str(inADP.p['ix0']) + tab + 'ix0' + tab + 'corner X' +nl)
file.write(tab + str(inADP.p['iy0']) + tab + 'iy0' + tab + 'corner Y' +nl)
file.write(tab + str(inADP.p['iz0']) + tab + 'iz0' + tab + 'corner Z' +nl)
file.write(tab + str(inADP.p['modefp']) + tab + 'modefp' + tab + '1=PF,2=tabectro' +nl)
file.write(tab + str(inADP.p['p']) + tab + 'p' + tab + 'PF interference order' +nl)
file.write(tab + str(inADP.p['xlp']) + tab + 'xlp' + tab + 'lmd reference p' +nl)
file.write(tab + str(inADP.p['xleta']) + tab + 'xleta' + tab + 'lmd calibration line' +nl)
file.write(tab + str(inADP.p['xlbeta']) + tab + 'xlbeta' + tab + 'lmd calibration scan' +nl)
file.write(tab + str(inADP.p['xlneb']) + tab + 'xlneb' + tab + 'lmd zero object' +nl)
file.write(tab + str(inADP.p['xlbneb']) + tab + 'xlbneb' + tab + 'lmd object scan' +nl)
file.write(tab + str(inADP.p['xil']) + tab + 'xil' + tab + 'tabectral length/interfringe in Angstroems' +nl)
file.write(tab + str(inADP.p['xl1']) + tab + 'xl1' + tab + 'lmd channel 1' +nl)
file.write(tab + str(inADP.p['vr0']) + tab + 'vr0' + tab + 'mean RV of the object in km/s' +nl)
file.write(tab + str(inADP.p['corrv']) + tab + 'corrv' + tab + 'heliocentric correction to add to measures in km/s' +nl)
file.write(tab + str(inADP.p['echelle']) + tab + 'echelle' + tab + 'scale ("/pix)' +nl)
file.write(tab + str(inADP.p['xc']) + tab + 'xc' + tab + 'center rings X' +nl)
file.write(tab + str(inADP.p['yc']) + tab + 'yc' + tab + 'center rings Y' +nl)
file.write(tab + str(inADP.p['ellipt']) + tab + 'ellipt' + tab + 'X/Y pixel ratio' +nl)
file.write(tab + str(inADP.p['mode_c']) + tab + 'mode_c' + tab + 'mode center/ellips of rings (0=normal; 1=enforced)' +nl)
file.write(tab + str(inADP.p['mode_e']) + tab + 'mode_e' + tab + 'force ellips to 1 if CCD (0=normal; 1=enforced)' +nl)
file.write(tab + str(inADP.p['min_a']) + tab + 'min_a' + tab + 'min angle for phase' +nl)
file.write(tab + str(inADP.p['max_a']) + tab + 'max_a' + tab + 'max angle for phase' +nl)
file.write(tab + str(inADP.p['min_r']) + tab + 'min_r' + tab + 'min radius for phase' +nl)
file.write(tab + str(inADP.p['max_r']) + tab + 'max_r' + tab + 'max radius for phase' +nl)
file.write(""" 0 alpha hours
0 alpha minutes
0.0000000 alpha seconds
0 delta degrees
0 delta minutes
0.0000000 alpha seconds
0.0000000 reference year
0.0000000 time minutes
0 time hours
0 time day
0 time month
0 time year
0 dummy
0 dummy
0 dummy
0 dummy
0 dummy
0.0000000 dummy
0.0000000 dummy
0.0000000 dummy
0.0000000 dummy
0.0000000 dummy
0 numcom last command number executed
""")
file.close()
def read_fits (file):
"""
gives back the data from a fits file
"""
ima1=pyfits.open(file)
ima=ima1[0]
im=ima.data
return im
def write_fits (data, name):
"""
writes a matrix into a fits file
no special headers so far
"""
fitsfile=pyfits.HDUList()
primary=pyfits.PrimaryHDU()
primary.data=data
fitsfile.append(primary)
fitsfile.writeto(name)
def read_model(filename):
"""Reads filename.model and returns a model_list that can be used with
functions in ModelVF.
Usage: model_list = read_model(filename)
"""
pars={}
models=[]
file=open(filename + '.model','r')
# Read parameters and models
for line in file:
line=line.split()
if len(line) == 0: pass
elif line[0]=='model_sys': models += [str(line[1])]
elif line[0]=='model_rot': models += [str(line[1])]
elif line[0]=='model_exp': models += [str(line[1])]
elif line[0]=='dim': pars['dim']=int(line[1])
elif line[0]=='a_scale': pars['a_scale']=[float(line[1]),int(line[2])]
elif line[0]=='v_system': pars['v_system']=[float(line[1]),int(line[2])]
elif line[0]=='inclination': pars['inclination']=[float(line[1]),int(line[2])]
elif line[0]=='pa': pars['pa']=[float(line[1]),int(line[2])]
elif line[0]=='v_expansion': pars['v_expansion']=[float(line[1]),int(line[2])]
elif line[0]=='v_max': pars['v_max']=[float(line[1]),int(line[2])]
elif line[0]=='exp_max': pars['exp_max']=[float(line[1]),int(line[2])]
elif line[0]=='r_max': pars['r_max']=[float(line[1]),int(line[2])]
elif line[0]=='x0': pars['centr_offset_x']=[float(line[1]),int(line[2])]
elif line[0]=='y0': pars['centr_offset_y']=[float(line[1]),int(line[2])]
file.close()
# Create the model_list
model_list = []
for i in range(len(models)):
model_list += [[models[i], pars]]
return model_list
def write_model(filename, model_list):
"""Writes the model_list to filename.model in the .model-format. Note: Only
one model of each type (system, rotation and expansion) is supported.
Warning! If the file exists it will be overwritten!
Usage: write_model(filename, model_list)
"""
# Open the file for writing
file=open(filename + '.model', 'w')
# Write the models in the list
for i in range(len(model_list)):
if (model_list[i][0] == 'system'): file.write('model_sys'+tab+model_list[i][0]+nl)
elif (model_list[i][0] == 'expansion'): file.write('model_exp'+tab+model_list[i][0]+nl)
elif (model_list[i][0] == 'linear'): file.write('model_rot'+tab+model_list[i][0]+nl)
elif (model_list[i][0] == 'disk'): file.write('model_rot'+tab+model_list[i][0]+nl)
elif (model_list[i][0] == 'kepler'): file.write('model_rot'+tab+model_list[i][0]+nl)
elif (model_list[i][0] == 'pure_kepler'): file.write('model_rot'+tab+model_list[i][0]+nl)
elif (model_list[i][0] == 'expansion'): file.write('model_rot'+tab+model_list[i][0]+nl)
# Write the model-parameters
file.write(nl)
file.write('dim'+tab+tab+tab+str(model_list[0][1]['dim'])+nl)
file.write('v_system'+tab+str(model_list[0][1]['v_system'][0])+tab+tab+str(model_list[0][1]['v_system'][1])+nl)
file.write('a_scale'+tab+tab+str(model_list[0][1]['a_scale'][0])+tab+tab+str(model_list[0][1]['a_scale'][1])+nl)
file.write('inclination'+tab+str(model_list[0][1]['inclination'][0])+tab+tab+str(model_list[0][1]['inclination'][1])+nl)
file.write('pa'+tab+tab+tab+str(model_list[0][1]['pa'][0])+tab+tab+str(model_list[0][1]['pa'][1])+nl)
file.write('v_expansion'+tab+str(model_list[0][1]['v_expansion'][0])+tab+tab+str(model_list[0][1]['v_expansion'][1])+nl)
file.write('v_max'+tab+tab+str(model_list[0][1]['v_max'][0])+tab+tab+str(model_list[0][1]['v_max'][1])+nl)
file.write('exp_max'+tab+tab+str(model_list[0][1]['exp_max'][0])+tab+tab+str(model_list[0][1]['exp_max'][1])+nl)
file.write('r_max'+tab+tab+str(model_list[0][1]['r_max'][0])+tab+tab+str(model_list[0][1]['r_max'][1])+nl)
file.write('x0'+tab+tab+tab+str(model_list[0][1]['centr_offset_x'][0])+tab+tab+str(model_list[0][1]['centr_offset_x'][1])+nl)
file.write('y0'+tab+tab+tab+str(model_list[0][1]['centr_offset_y'][0])+tab+tab+str(model_list[0][1]['centr_offset_y'][1])+nl)
file.close()
def read_slit (filename):
"""Read slit parameters from a filename.slit. Returns a dictionary with the
parameters.
Usage: pars = read_slit(filename)
"""
pars={}
file=open(filename + '.slit','r')
for line in file:
line=line.split()
if len(line) == 0: pass
elif line[0]=='slitwidth': pars['slitwidth']=float(line[1])
elif line[0]=='angle': pars['angle']=float(line[1])
elif line[0]=='offset': pars['offset']=N.array([float(line[1]), float(line[2])])
elif line[0] == 'slit_angle_dep': pars['slit_angle_dep']=int(line[1])
file.close()
return pars
def write_rc (filename,position, velocity, error):
"""Writes an rc output-file (from RCslit or gauss_slit).
Usage: write_rc(filename, pos, vel, err)
pos, vel and err are arrays with the positions, velocities and errors.
"""
outfile=open(filename + '.rc','w')
for i in range(len(position)):
outfile.write('%g %g %g \n' % (position[i], velocity[i],error[i]))
outfile.close()
#### NOT WORKING RIGHT NOW! LEGACY!!!
def ADTtoADP(outname,objname,ADT):
""" make a parameter file, using values from an ADT file
NOT WORKING RIGHT NOW! LEGACY!!!
"""
outfile=open(outname,'w')
adt=open(ADT+'.ADT','r')
outfile.write(objname+nl)
adt.readline()
if adt.readline().split()[1] != ADT: print "observation numer mismatch"
adt.readline()
if adt.readline().split()[2] != objname: print "object name mismatch"
pf=adt.readline().split()[3]
filter=adt.readline().split()[2]
adt.readline()
tmp=adt.readline().split()
nx,ny=int(tmp[5]),int(tmp[6])
nz=int(adt.readline().split()[4])
adt.readline()
exppchan=float(adt.readline().split()[5])
scanlamb=float(adt.readline().split()[2])
queen=float(adt.readline().split()[2])
## extracting the number of cycles
tmp=adt.readlines()
tmp.reverse()
for i in range(5):
if ' cy=' in tmp[i]:
numbercycles=int(tmp[i].split()[5].split('=')[1])
break
# GETTING INFO FROM .ADT FILE FINISHED
adt.close()
print pf,filter,nx,ny,nz,exppchan,scanlamb,queen
outfile.write(tab+str(nx)+tab+'lx'+tab+'dimension X'+nl)
outfile.write(tab+str(ny)+tab+'lx'+tab+'dimension X'+nl)
outfile.write(tab+str(nz)+tab+'lx'+tab+'dimension X'+nl)
outfile.write(tab+"""1 ix0 corner X
1 iy0 corner Y
1 iz0 corner Z
1 modefp 1=PF,2=spectro""" + nl)
if pf == 'OM798': outfile.write(tab+'793'+tab+'p'+tab+'PF interference order'+nl)
elif pf == 'OM1938': outfile.write(tab+'1983'+tab+'p'+tab+'PF interference order'+nl)
else: outfile.write(tab+'0'+tab+'p'+tab+'PF interference order'+nl)
outfile.write(tab+"""6562.7797852 xlp lmd reference p
6598.9531250 xleta lmd calibration line
6598.9531250 xlbeta lmd calibration scan
6562.7797852 xlneb lmd zero object"""+nl)
outfile.write(tab+str(scanlamb)+tab+'xlbneb'+tab+'lmd object scan')
bulk="""
8.3223772 xil spectral length/interfringe in Angstroems
6583.0000000 xl1 lmd channel 1
1099.0000000 vr0 mean RV of the object in km/s
0.0000000 corrv heliocentric correction to add to measures in km/s
0.4170000 echelle scale (\"/pix)
256.0000 xc center rings X
256.0000 yc center rings Y
1.0000000 ellipt X/Y pixel ratio
0 mode_c mode center/ellips of rings (0=normal; 1=enforced)
1 mode_e force ellips to 1 if CCD (0=normal; 1=enforced)
0.0000 min_a min angle for phase
360.0000 max_a max angle for phase
0.0000 min_r min radius for phase
99999.0000 max_r max radius for phase
0 alpha hours
0 alpha minutes
0.0000000 alpha seconds
0 delta degrees
0 delta minutes
0.0000000 alpha seconds
0.0000000 reference year
0.0000000 time minutes
0 time hours
0 time day
0 time month
0 time year
0 dummy
0 dummy
0 dummy
0 dummy
0 dummy
0.0000000 dummy
0.0000000 dummy
0.0000000 dummy
0.0000000 dummy
0.0000000 dummy
0 numcom last command number executed
"""
outfile.write(bulk)
outfile.close()
return numbercycles