Example BX610: perform model fitting using method=‘amoeba’ for the Band 4 Cycle 5 DataSet¶
import sys
import glob
import os
import io
import logging
from pprint import pprint
print(sys.version)
import socket
if 'hypersion' or 'mini' in socket.gethostname() :
os.chdir('/Users/Rui/Documents/Workspace/projects/GMaKE/examples/output/')
print(socket.gethostname())
print(os.getcwd())
import gmake
print(gmake.__version__)
print(gmake.__email__)
print(gmake.__demo__)
inpfile=gmake.__demo__+'/../examples/inpfile/bx610_b4c5_uv_ab.inp'
logfile=''
#gmake.logger_config()
#gmake.logger_status()
#import pprint
#pprint.pprint(logging.Logger.manager.loggerDict)
gmake.logger_config()
inp_dct=gmake.read_inp(inpfile)
inp_dct=gmake.inp_validate(inp_dct)
outdir=inp_dct['general']['outdir']
gmake.logger_config(logfile=outdir+'/gmake.log',loglevel='DEBUG',logfilelevel='DEBUG')
gmake.logger_status()
%reload_ext line_profiler
%reload_ext memory_profiler
3.7.5 (default, Oct 19 2019, 11:15:26)
[Clang 11.0.0 (clang-1100.0.33.8)]
hyperion
/Volumes/S1/projects/GMaKE/examples/output
0.2.dev1
rx.astro@gmail.com
/Users/Rui/Documents/Workspace/projects/GMaKE/gmake
<Logger gmake (DEBUG)>
[<FileHandler /Volumes/S1/projects/GMaKE/examples/output/bx610_b4c5_uv_ab/gmake.log (DEBUG)>, <StreamHandler stderr (DEBUG)>]
#%time dat_dct=gmake.read_data(inp_dct,fill_mask=True,fill_error=True)
#%prun dat_dct=gmake.read_data(inp_dct,fill_mask=True,fill_error=True)
#%lprun -f gmake.read_data dat_dct=gmake.read_data(inp_dct,fill_mask=True,fill_error=True)
#del dat_dct
#%memit dat_dct=gmake.read_data(inp_dct)
#%mprun -f gmake.read_data dat_dct=gmake.read_data(inp_dct)
dat_dct=gmake.read_data(inp_dct)
read data (may take some time..)
Read: ../data/bx610/alma/2017.1.01045.S/bb1.ms.pt2
data@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt2 complex64 (275794, 128) 269 MiB
uvw@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt2 float32 (275794, 3) 3 MiB
weight@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt2 float32 (275794,) 1 MiB
>>percentiles (0,16,50,84,100)%: [ 39.59812164 185.1169751 253.05403137 324.3769751 594.16479492]
chanfreq@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt2 (128,) 143301022036.5513 Hz 143797143423.9031 Hz
chanwidth@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt2 (128,) -3906467.6169 Hz -3906467.6169 Hz
phasecenter@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt2 23h46m09.438s 12d49m19.25s
Read: ../data/bx610/alma/2017.1.01045.S/bb3.ms.pt2
data@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt2 complex64 (276124, 179) 377 MiB
uvw@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt2 float32 (276124, 3) 3 MiB
weight@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt2 float32 (276124,) 1 MiB
>>percentiles (0,16,50,84,100)%: [ 36.37529755 156.95782593 215.15796661 281.27739258 531.50854492]
chanfreq@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt2 (179,) 153003656218.1177 Hz 153699007453.9771 Hz
chanwidth@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt2 (179,) 3906467.6172 Hz 3906467.6172 Hz
phasecenter@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt2 23h46m09.438s 12d49m19.25s
Read: ../data/bx610/alma/2017.1.01045.S/bb1.ms.pt1
data@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt1 complex64 (275794, 1) 2 MiB
uvw@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt1 float32 (275794, 3) 3 MiB
weight@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt1 float32 (275794,) 1 MiB
>>percentiles (0,16,50,84,100)%: [ 6731.69726562 31469.71625 43019.20117188 55143.775
101009.09375 ]
chanfreq@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt1 (1,) 142967019055.3026 Hz 142967019055.3026 Hz
chanwidth@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt1 (1,) -664099494.8804 Hz -664099494.8804 Hz
phasecenter@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt1 23h46m09.438s 12d49m19.25s
Read: ../data/bx610/alma/2017.1.01045.S/bb1.ms.pt3
data@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt3 complex64 (275794, 1) 2 MiB
uvw@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt3 float32 (275794, 3) 3 MiB
weight@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt3 float32 (275794,) 1 MiB
>>percentiles (0,16,50,84,100)%: [ 7088.08105469 33135.7590625 45296.69335938 58063.151875
106356.640625 ]
chanfreq@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt3 (1,) 144148725509.4280 Hz 144148725509.4280 Hz
chanwidth@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt3 (1,) -699257703.4329 Hz -699257703.4329 Hz
phasecenter@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt3 23h46m09.438s 12d49m19.25s
Read: ../data/bx610/alma/2017.1.01045.S/bb2.ms.mfs
data@../data/bx610/alma/2017.1.01045.S/bb2.ms.mfs complex64 (276124, 1) 2 MiB
uvw@../data/bx610/alma/2017.1.01045.S/bb2.ms.mfs float32 (276124, 3) 3 MiB
weight@../data/bx610/alma/2017.1.01045.S/bb2.ms.mfs float32 (276124,) 1 MiB
>>percentiles (0,16,50,84,100)%: [ 10749.33203125 71887.625625 100576.19921875 129892.62875
242941.46875 ]
chanfreq@../data/bx610/alma/2017.1.01045.S/bb2.ms.mfs (1,) 141738204024.6475 Hz 141738204024.6475 Hz
chanwidth@../data/bx610/alma/2017.1.01045.S/bb2.ms.mfs (1,) -1863385053.3984 Hz -1863385053.3984 Hz
phasecenter@../data/bx610/alma/2017.1.01045.S/bb2.ms.mfs 23h46m09.438s 12d49m19.25s
Read: ../data/bx610/alma/2017.1.01045.S/bb3.ms.pt1
data@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt1 complex64 (276124, 1) 2 MiB
uvw@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt1 float32 (276124, 3) 3 MiB
weight@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt1 float32 (276124,) 1 MiB
>>percentiles (0,16,50,84,100)%: [ 3019.16308594 13027.213125 17858.26757812 23346.20828125
44115.19140625]
chanfreq@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt1 (1,) 152839584578.1958 Hz 152839584578.1958 Hz
chanwidth@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt1 (1,) 324236812.2266 Hz 324236812.2266 Hz
phasecenter@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt1 23h46m09.438s 12d49m19.25s
Read: ../data/bx610/alma/2017.1.01045.S/bb3.ms.pt3
data@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt3 complex64 (276124, 1) 2 MiB
uvw@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt3 float32 (276124, 3) 3 MiB
weight@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt3 float32 (276124,) 1 MiB
>>percentiles (0,16,50,84,100)%: [ 7820.72753906 33745.1590625 46259.30664062 60475.089375
114274.328125 ]
chanfreq@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt3 (1,) 154120905956.6333 Hz 154120905956.6333 Hz
chanwidth@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt3 (1,) 839890537.6953 Hz 839890537.6953 Hz
phasecenter@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt3 23h46m09.438s 12d49m19.25s
Read: ../data/bx610/alma/2017.1.01045.S/bb4.ms.mfs
data@../data/bx610/alma/2017.1.01045.S/bb4.ms.mfs complex64 (276124, 1) 2 MiB
uvw@../data/bx610/alma/2017.1.01045.S/bb4.ms.mfs float32 (276124, 3) 3 MiB
weight@../data/bx610/alma/2017.1.01045.S/bb4.ms.mfs float32 (276124,) 1 MiB
>>percentiles (0,16,50,84,100)%: [ 10978.32617188 60905.94515625 85937.25 113244.640625
218176.15625 ]
chanfreq@../data/bx610/alma/2017.1.01045.S/bb4.ms.mfs (1,) 155441364443.2279 Hz 155441364443.2279 Hz
chanwidth@../data/bx610/alma/2017.1.01045.S/bb4.ms.mfs (1,) 1863385053.3984 Hz 1863385053.3984 Hz
phasecenter@../data/bx610/alma/2017.1.01045.S/bb4.ms.mfs 23h46m09.438s 12d49m19.25s
--------------------------------------------------------------------------------
--- dat_dct size 692.76 Mibyte ---
--- took 14.62557 seconds ---
#
#mod_dct=gmake.inp2mod(inp_dct)
#gmake.pprint(mod_dct)
#gmake.model_vrot(mod_dct)
#gmake.pprint(mod_dct)
#gmake.model_vrot_plot(mod_dct['co76'])
inp_dct=gmake.read_inp(inpfile)
inp_dct=gmake.inp_validate(inp_dct)
mod_dct=gmake.inp2mod(inp_dct)
gmake.model_vrot(mod_dct)
#mod_dct['co76']
%mprun -f gmake.model_eval.model_lnlike2 fit_dct=gmake.fit_setup(inp_dct,dat_dct,save_model=False,initial_model=False)
#fit_dct=gmake.fit_setup(inp_dct,dat_dct,initial_model=True,save_model=False)
#%mprun -f gmake.fit_iterate gmake.fit_iterate(fit_dct,inp_dct,dat_dct)
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
optimizer: amoeba
optimizing parameters:
----------------------------------------------------------------------------------------------------
index name unit start lo_limit up_limit scale
0 vsys@basics km / s 100.00 ( 0.00 , 220.00 ) 120.00
1 disk_sd@diskdyn solMass / pc2 3000.00 ( 100.00 , 50000.00 ) 47000.00
2 disk_rs@diskdyn kpc 2.00 ( 0.20 , 10.00 ) 8.00
3 vdis@basics km / s 50.00 ( 0.00 , 200.00 ) 150.00
4 pa@basics deg -52.40 ( -132.40 , 27.60 ) 80.00
5 inc@basics deg 44.06 ( 5.00 , 85.00 ) 40.94
6 xypos.ra@basics deg 356.5393258 ( 356.5390481 , 356.5396036 ) 0.0002778
7 xypos.dec@basics deg 12.8220182 ( 12.8217404 , 12.8222960 ) 0.0002778
8 lineflux@co43 Jy km / s 1.00 ( 0.10 , 200.00 ) 199.00
9 sbser[0]@co43 arcsec 0.22 ( 0.01 , 2.00 ) 1.78
10 lineflux@ci10 Jy km / s 0.50 ( 0.10 , 200.00 ) 199.50
11 sbser[0]@ci10 arcsec 0.19 ( 0.01 , 2.00 ) 1.81
12 contflux@cont Jy 0.00 ( 0.00 , 0.01 ) 0.01
13 sbser[0]@cont arcsec 0.15 ( 0.01 , 2.00 ) 1.85
14 alpha@cont 3.72 ( 3.00 , 4.50 ) 0.78
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
ndim: 15
outdir: bx610_b4c5_uv_ab
--- save to: bx610_b4c5_uv_ab/fit.h5
#%mprun -f gmake.model_eval.model_lnprob lnl,lnprob,chisq,ndata,npar=gmake.model_lnprob(fit_dct['p_start'],fit_dct,inp_dct,dat_dct,savemodel=None)
#%timeit lnl,lnprob,chisq,ndata,npar=gmake.model_lnprob(fit_dct['p_start'],fit_dct,inp_dct,dat_dct,savemodel=None)
#%timeit lnl,lnprob,chisq,ndata,npar=gmake.model_lnprob2(fit_dct['p_start'],fit_dct,inp_dct,dat_dct,savemodel=None)
#%lprun -f gmake.model_func.model_uvchi2 lnl,lnprob,chisq,ndata,npar=gmake.model_lnprob2(fit_dct['p_start'],fit_dct,inp_dct,dat_dct,savemodel=None)
%mprun -f gmake.model_func.model_uvchi2 lnl,lnprob,chisq,ndata,npar=gmake.model_lnprob2(fit_dct['p_start'],fit_dct,inp_dct,dat_dct,savemodel=None)
Filename: /Users/Rui/Documents/Workspace/projects/GMaKE/gmake/model_func.py
Line # Mem usage Increment Line Contents
================================================
783 3115.3 MiB 2523.8 MiB def model_uvchi2(xymod3d,xymod2d,xyheader,
784 uvdata,uvw,phasecenter,uvweight,
785 average=True,verbose=True):
786 """
787 simulate the observation in the UV-domain
788 The input reference 2D / 3D model (e.g. continuume+line) is expected in units of Jy/pix
789
790 uvw shape: nrecord x 3
791 uvmodel shape: nrecord x nchan (less likely: nrecord x nchan x ncorr)
792 xymodel shape: nstokes x nchan x ny x nx
793
794 note1:
795 Because sampleImaging() can be only applied to single-wavelength dataset, we have to loop over
796 all channels for multi-frequency dataset (e.g. spectral cubes). This loop operations is typically
797 the bottle-neck. To reduce the number of operation, we can only do uvsampling for frequency-plane
798 with varying morphology and process frequency-inpdent emission using one operation:
799 the minimal number of operations required is:
800 nplane(with varying morphology) + 1 x sampleImage()
801 we already trim any else overhead (e.g. creating new array) and reach close to this limit.
802
803 note2:
804 when <uvmodel> is provided as input, a new model will be added into the array without additional memory usage
805 the return variable is just a reference of mutable <uvmodel>
806
807 """
808
809 #print('3d:',xymod3d is not None)
810 #print('2d:',xymod2d is not None)
811
812 3115.3 MiB 0.0 MiB cell=np.sqrt(abs(xyheader['CDELT1']*xyheader['CDELT2']))
813 3115.3 MiB 0.0 MiB nchan=xyheader['NAXIS3']
814 3115.3 MiB 0.0 MiB nrecord=(uvw.shape)[0]
815
816 # + zeros_like vs. zeros()
817 # the memory of an array created by zeros() can allocated on-the-fly
818 # the creation will appear to be faster but the looping+plan initialization may be slightly slower (or comparable?)
819 # + set order='F' as we want to have quick access to each column:
820 # i.a. first dimension is consequential in memory
821 # this will improve on the performance of picking uvdata from each channel
822 # we force order='F', so the first dimension is continiuous and we can quicky fetch each channel
823 # as the information in a single channel is saved in a block
824
825
826 3115.3 MiB 0.0 MiB if verbose==True:
827 start_time = time.time()
828 print('nchan,nrecord:',nchan,nrecord)
829
830 # assume that CRPIX1/CRPIX2 is at model image "center" floor(naxis/2);
831 # which is true for the mock-up/reference model image xyheader
832 # more information on the pixel index /ra-dec mapping, see:
833 # https://mtazzari.github.io/galario/tech-specs.html
834 3115.3 MiB 0.0 MiB dRA=np.deg2rad(+(xyheader['CRVAL1']-phasecenter[0].to_value(u.deg)))
835 3115.3 MiB 0.0 MiB dDec=np.deg2rad(+(xyheader['CRVAL2']-phasecenter[1].to_value(u.deg)))
836
837 3115.3 MiB 0.0 MiB cc=0
838 3115.3 MiB 0.0 MiB chi2=0
839
840 3115.3 MiB 0.0 MiB if xymod2d is not None:
841 3115.3 MiB 0.0 MiB i0=int(nchan/2.0)
842 3115.3 MiB 0.0 MiB xymodelsum=xymod2d.sum(axis=(0,2,3))
843 3115.3 MiB 0.0 MiB xymodel_zscale=xymodelsum/xymodelsum[i0]
844 3115.3 MiB 0.0 MiB wv=const.c/(xyheader['CDELT3']*i0+xyheader['CRVAL3'])
845 3115.3 MiB 0.0 MiB cc+=1
846 #ss=time.time()
847 3115.3 MiB 0.0 MiB uvmod2d=sampleImage((xymod2d[0,i0,:,:]),
848 3115.3 MiB 0.0 MiB (np.deg2rad(cell)).astype(np.float32),
849 3115.3 MiB 0.0 MiB (uvw[:,0]/wv),
850 3115.3 MiB 0.0 MiB (uvw[:,1]/wv),
851 3115.3 MiB 0.0 MiB dRA=dRA.astype(np.float32),dDec=dDec.astype(np.float32),
852 3115.3 MiB 0.2 MiB PA=0.0,check=False,origin='lower')
853
854 3115.3 MiB 0.0 MiB if xymod3d is not None:
855 3115.3 MiB 0.0 MiB for i in range(nchan):
856 3115.3 MiB 0.0 MiB if ne.evaluate("sum(a)",local_dict={'a':xymod3d[0,i,:,:]})==0.0:
857 3115.3 MiB 0.0 MiB delta_uv=ne.evaluate('a2*a3-b',
858 3115.3 MiB 0.0 MiB local_dict={'a2':uvmod2d,
859 3115.3 MiB 0.0 MiB 'a3':xymodel_zscale[i],
860 3115.3 MiB 4.2 MiB 'b':uvdata[:,i]})
861 3115.3 MiB 0.0 MiB chi2+=ne.evaluate('sum( ( (a.real)**2+(a.imag)**2 ) *c)',
862 3115.3 MiB 0.0 MiB local_dict={'a':delta_uv,
863 3115.3 MiB 0.0 MiB 'c':uvweight})
864 #chi2+=ne.evaluate('sum( abs(a)**2*c)',
865 # local_dict={'a':delta_uv,
866 # 'c':uvweight})
867 else:
868 3115.3 MiB 0.0 MiB wv=const.c/(xyheader['CDELT3']*i+xyheader['CRVAL3'])
869 3115.3 MiB 0.0 MiB cc+=1
870 #uvmod3d=sampleImage((xymod3d[0,i,:,:]),
871 # (np.deg2rad(cell)).astype(np.float32),
872 # (uvw[:,0]/wv),
873 # (uvw[:,1]/wv),
874 # dRA=dRA.astype(np.float32),dDec=dDec.astype(np.float32),
875 # PA=0.,check=False,origin='lower')
876 #uvmodel=uvmod3d+uvmod2d*xymodel_zscale[i]
877 3115.3 MiB 0.0 MiB delta_uv=ne.evaluate('a2*a3+a1-b',
878 3115.3 MiB 0.0 MiB local_dict={'a1':sampleImage((xymod3d[0,i,:,:]),
879 3115.3 MiB 0.0 MiB (np.deg2rad(cell)).astype(np.float32),
880 3115.3 MiB 0.0 MiB (uvw[:,0]/wv),
881 3115.3 MiB 0.0 MiB (uvw[:,1]/wv),
882 3115.3 MiB 0.0 MiB dRA=dRA.astype(np.float32),dDec=dDec.astype(np.float32),
883 3115.3 MiB 2.1 MiB PA=0.,check=False,origin='lower'),
884 3115.3 MiB 0.0 MiB 'a2':uvmod2d,
885 3115.3 MiB 0.0 MiB 'a3':xymodel_zscale[i],
886 3115.3 MiB 4.3 MiB 'b':uvdata[:,i]})
887 3115.3 MiB 0.0 MiB chi2+=ne.evaluate('sum( ( (a.real)**2+(a.imag)**2 ) *c)',
888 3115.3 MiB 0.0 MiB local_dict={'a':delta_uv,
889 3115.3 MiB 0.0 MiB 'c':uvweight})
890 #chi2+=ne.evaluate('sum( abs(a)**2*c)',
891 # local_dict={'a':delta_uv,
892 # 'c':uvweight})
893
894
895 3115.3 MiB 0.0 MiB return chi2
#
#mod_dct=gmake.inp2mod(inp_dct)
#gmake.pprint(mod_dct)
#gmake.model_vrot(mod_dct)
#gmake.pprint(mod_dct)
#gmake.model_vrot_plot(mod_dct['co76'])
import gmake
inp_dct=gmake.read_inp(inpfile)
inp_dct=gmake.inp_validate(inp_dct)
mod_dct=gmake.inp2mod(inp_dct)
gmake.model_vrot(mod_dct)
#mod_dct['co76']
%mprun -f gmake.model_eval.model_lnprob fit_dct=gmake.fit_setup(inp_dct,dat_dct)
#fit_dct=gmake.fit_setup(inp_dct,dat_dct,initial_model=True,save_model=False)
#%mprun -f gmake.fit_iterate gmake.fit_iterate(fit_dct,inp_dct,dat_dct)
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
optimizer: amoeba
optimizing parameters:
----------------------------------------------------------------------------------------------------
index name unit start lo_limit up_limit scale
0 vsys@basics km / s 100.00 ( 0.00 , 220.00 ) 120.00
1 disk_sd@diskdyn solMass / pc2 3000.00 ( 100.00 , 50000.00 ) 47000.00
2 disk_rs@diskdyn kpc 2.00 ( 0.20 , 10.00 ) 8.00
3 vdis@basics km / s 50.00 ( 0.00 , 200.00 ) 150.00
4 pa@basics deg -52.40 ( -132.40 , 27.60 ) 80.00
5 inc@basics deg 44.06 ( 5.00 , 85.00 ) 40.94
6 xypos.ra@basics deg 356.5393258 ( 356.5390481 , 356.5396036 ) 0.0002778
7 xypos.dec@basics deg 12.8220182 ( 12.8217404 , 12.8222960 ) 0.0002778
8 lineflux@co43 Jy km / s 1.00 ( 0.10 , 200.00 ) 199.00
9 sbser[0]@co43 arcsec 0.22 ( 0.01 , 2.00 ) 1.78
10 lineflux@ci10 Jy km / s 0.50 ( 0.10 , 200.00 ) 199.50
11 sbser[0]@ci10 arcsec 0.19 ( 0.01 , 2.00 ) 1.81
12 contflux@cont Jy 0.00 ( 0.00 , 0.01 ) 0.01
13 sbser[0]@cont arcsec 0.15 ( 0.01 , 2.00 ) 1.85
14 alpha@cont 3.72 ( 3.00 , 4.50 ) 0.78
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
ndim: 15
outdir: bx610_b4c5_uv_ab
one trial : 4.98618 seconds
ndata->0.0
chisq->149336333.31762546
--- save to: bx610_b4c5_uv_ab/fit.h5
Filename: /Users/Rui/Documents/Workspace/projects/GMaKE/gmake/model_eval.py
Line # Mem usage Increment Line Contents
================================================
348 4518.4 MiB 4518.4 MiB def model_lnprob(theta,fit_dct,inp_dct,dat_dct,
349 savemodel=None,decomp=False,nsamps=1e5,
350 packblobs=False,
351 verbose=False):
352 """
353 this is the evaluating function for emcee
354 packblobs=True:
355 lnl,blobs
356 packblobs=False:
357 lnl,lnp,chisq,ndata,npar
358 """
359
360 4518.4 MiB 0.0 MiB if verbose==True:
361 start_time = time.time()
362
363 4518.4 MiB 0.0 MiB lp = model_lnprior(theta,fit_dct)
364
365 4518.4 MiB 0.0 MiB if not np.isfinite(lp):
366 blobs={'lnprob':-np.inf,'chisq':+np.inf,'ndata':0.0,'npar':len(theta)}
367 if packblobs==True:
368 return -np.inf,blobs
369 else:
370 return -np.inf,-np.inf,+np.inf,0.0,len(theta)
371
372
373
374 4518.4 MiB 0.0 MiB lnl,blobs=model_lnlike2(theta,fit_dct,inp_dct,dat_dct,
375 4518.4 MiB 0.0 MiB savemodel=savemodel,decomp=decomp,nsamps=nsamps,
376 4518.4 MiB 0.0 MiB verbose=verbose)
377
378 4518.4 MiB 0.0 MiB if verbose==True:
379 print("try ->",theta)
380 print("---{0:^10} : {1:<8.5f} seconds ---".format('lnprob',time.time()-start_time))
381
382 # np.array: to creat a zero-d object array
383 4518.4 MiB 0.0 MiB if packblobs==True:
384 return lp+lnl,blobs
385 else:
386 4518.4 MiB 0.0 MiB return lp+lnl,blobs['lnprob'],blobs['chisq'],blobs['ndata'],blobs['npar']
#%mprun -f gmake.model_eval.model_lnprob lnl,lnprob,chisq,ndata,npar=gmake.model_lnprob(fit_dct['p_start'],fit_dct,inp_dct,dat_dct,savemodel=None)
%timeit lnl,lnprob,chisq,ndata,npar=gmake.model_lnprob(fit_dct['p_start'],fit_dct,inp_dct,dat_dct,savemodel=None)
3.96 s ± 65.6 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)
#from hickle import SerializedWarning
%matplotlib inline
#%matplotlib notebook
gmake.fit_analyze(inpfile,export=True)
#print(fit_dct['p_scale'])
--- save to: bx610_b4c5_uv_ab/fit.h5
Check optimized parameters:
0 vsys@basics = 104.63 <- 100.00 ( 0.00 , 220.00 )
1 disk_sd@diskdyn = 3194.29 <- 3000.00 ( 100.00 , 50000.00 )
2 disk_rs@diskdyn = 2.78 <- 2.00 ( 0.20 , 10.00 )
3 vdis@basics = 50.43 <- 50.00 ( 0.00 , 200.00 )
4 pa@basics = -54.23 <- -52.40 ( -132.40 , 27.60 )
5 inc@basics = 46.25 <- 44.06 ( 5.00 , 85.00 )
6 xypos.ra@basics = 356.5393221 <- 356.5393258 ( 356.5390481 , 356.5396036 )
7 xypos.dec@basics = 12.8220133 <- 12.8220182 ( 12.8217404 , 12.8222960 )
8 lineflux@co43 = 1.08 <- 1.00 ( 0.10 , 200.00 )
9 sbser[0]@co43 = 0.21 <- 0.22 ( 0.01 , 2.00 )
10 lineflux@ci10 = 0.49 <- 0.50 ( 0.10 , 200.00 )
11 sbser[0]@ci10 = 0.27 <- 0.19 ( 0.01 , 2.00 )
12 contflux@cont = 0.00 <- 0.00 ( 0.00 , 0.01 )
13 sbser[0]@cont = 0.18 <- 0.15 ( 0.01 , 2.00 )
14 alpha@cont = 3.79 <- 3.72 ( 3.00 , 4.50 )
analyzing outfolder:bx610_b4c5_uv_ab
plotting...bx610_b4c5_uv_ab/iteration.pdf
data@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt2 125111663.73342288 35301632
data@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt2 168486213.07584742 49426196
data@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt1 1118139.3760106005 275794
data@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt3 1161359.330965863 275794
data@../data/bx610/alma/2017.1.01045.S/bb2.ms.mfs 1157667.521734547 276124
data@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt1 1205064.410572111 276124
data@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt3 1156301.2026866334 276124
data@../data/bx610/alma/2017.1.01045.S/bb4.ms.mfs 1160934.690953595 276124
export the model set: bx610_b4c5_uv_ab/model_0 (may take some time..)
-->data_b4c5_bb1.ms.pt2
imod2d@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt2
write reference model image:
imod2d@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt2 to bx610_b4c5_uv_ab/model_0/imod2d_b4c5_bb1.ms.pt2.fits
imod3d@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt2
write reference model image:
imod3d@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt2 to bx610_b4c5_uv_ab/model_0/imod3d_b4c5_bb1.ms.pt2.fits
pbeam@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt2
write reference model image:
pbeam@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt2 to bx610_b4c5_uv_ab/model_0/pbeam_b4c5_bb1.ms.pt2.fits
write reference model profile:
imod3d_prof@co43@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt2 to bx610_b4c5_uv_ab/model_0/imodrp_co43_b4c5_bb1.ms.pt2.fits
copy ms container:
../data/bx610/alma/2017.1.01045.S/bb1.ms.pt2 to bx610_b4c5_uv_ab/model_0/model_b4c5_bb1.ms.pt2
write ms column:
uvmodel@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt2 to data@bx610_b4c5_uv_ab/model_0/model_b4c5_bb1.ms.pt2
create symlink:
/Users/Rui/Documents/Workspace/projects/GMaKE/examples/data/bx610/alma/2017.1.01045.S/bb1.ms.pt2 to bx610_b4c5_uv_ab/model_0/data_b4c5_bb1.ms.pt2
-->data_b4c5_bb3.ms.pt2
imod2d@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt2
write reference model image:
imod2d@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt2 to bx610_b4c5_uv_ab/model_0/imod2d_b4c5_bb3.ms.pt2.fits
imod3d@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt2
write reference model image:
imod3d@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt2 to bx610_b4c5_uv_ab/model_0/imod3d_b4c5_bb3.ms.pt2.fits
pbeam@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt2
write reference model image:
pbeam@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt2 to bx610_b4c5_uv_ab/model_0/pbeam_b4c5_bb3.ms.pt2.fits
write reference model profile:
imod3d_prof@ci10@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt2 to bx610_b4c5_uv_ab/model_0/imodrp_ci10_b4c5_bb3.ms.pt2.fits
copy ms container:
../data/bx610/alma/2017.1.01045.S/bb3.ms.pt2 to bx610_b4c5_uv_ab/model_0/model_b4c5_bb3.ms.pt2
write ms column:
uvmodel@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt2 to data@bx610_b4c5_uv_ab/model_0/model_b4c5_bb3.ms.pt2
create symlink:
/Users/Rui/Documents/Workspace/projects/GMaKE/examples/data/bx610/alma/2017.1.01045.S/bb3.ms.pt2 to bx610_b4c5_uv_ab/model_0/data_b4c5_bb3.ms.pt2
-->data_b4c5_bb1.ms.pt1
imod2d@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt1
write reference model image:
imod2d@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt1 to bx610_b4c5_uv_ab/model_0/imod2d_b4c5_bb1.ms.pt1.fits
imod3d@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt1
write reference model image:
imod3d@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt1 to bx610_b4c5_uv_ab/model_0/imod3d_b4c5_bb1.ms.pt1.fits
pbeam@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt1
write reference model image:
pbeam@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt1 to bx610_b4c5_uv_ab/model_0/pbeam_b4c5_bb1.ms.pt1.fits
copy ms container:
../data/bx610/alma/2017.1.01045.S/bb1.ms.pt1 to bx610_b4c5_uv_ab/model_0/model_b4c5_bb1.ms.pt1
write ms column:
uvmodel@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt1 to data@bx610_b4c5_uv_ab/model_0/model_b4c5_bb1.ms.pt1
create symlink:
/Users/Rui/Documents/Workspace/projects/GMaKE/examples/data/bx610/alma/2017.1.01045.S/bb1.ms.pt1 to bx610_b4c5_uv_ab/model_0/data_b4c5_bb1.ms.pt1
-->data_b4c5_bb1.ms.pt3
imod2d@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt3
write reference model image:
imod2d@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt3 to bx610_b4c5_uv_ab/model_0/imod2d_b4c5_bb1.ms.pt3.fits
imod3d@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt3
write reference model image:
imod3d@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt3 to bx610_b4c5_uv_ab/model_0/imod3d_b4c5_bb1.ms.pt3.fits
pbeam@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt3
write reference model image:
pbeam@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt3 to bx610_b4c5_uv_ab/model_0/pbeam_b4c5_bb1.ms.pt3.fits
copy ms container:
../data/bx610/alma/2017.1.01045.S/bb1.ms.pt3 to bx610_b4c5_uv_ab/model_0/model_b4c5_bb1.ms.pt3
write ms column:
uvmodel@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt3 to data@bx610_b4c5_uv_ab/model_0/model_b4c5_bb1.ms.pt3
create symlink:
/Users/Rui/Documents/Workspace/projects/GMaKE/examples/data/bx610/alma/2017.1.01045.S/bb1.ms.pt3 to bx610_b4c5_uv_ab/model_0/data_b4c5_bb1.ms.pt3
-->data_b4c5_bb2.ms.mfs
imod2d@../data/bx610/alma/2017.1.01045.S/bb2.ms.mfs
write reference model image:
imod2d@../data/bx610/alma/2017.1.01045.S/bb2.ms.mfs to bx610_b4c5_uv_ab/model_0/imod2d_b4c5_bb2.ms.mfs.fits
imod3d@../data/bx610/alma/2017.1.01045.S/bb2.ms.mfs
write reference model image:
imod3d@../data/bx610/alma/2017.1.01045.S/bb2.ms.mfs to bx610_b4c5_uv_ab/model_0/imod3d_b4c5_bb2.ms.mfs.fits
pbeam@../data/bx610/alma/2017.1.01045.S/bb2.ms.mfs
write reference model image:
pbeam@../data/bx610/alma/2017.1.01045.S/bb2.ms.mfs to bx610_b4c5_uv_ab/model_0/pbeam_b4c5_bb2.ms.mfs.fits
copy ms container:
../data/bx610/alma/2017.1.01045.S/bb2.ms.mfs to bx610_b4c5_uv_ab/model_0/model_b4c5_bb2.ms.mfs
write ms column:
uvmodel@../data/bx610/alma/2017.1.01045.S/bb2.ms.mfs to data@bx610_b4c5_uv_ab/model_0/model_b4c5_bb2.ms.mfs
create symlink:
/Users/Rui/Documents/Workspace/projects/GMaKE/examples/data/bx610/alma/2017.1.01045.S/bb2.ms.mfs to bx610_b4c5_uv_ab/model_0/data_b4c5_bb2.ms.mfs
-->data_b4c5_bb3.ms.pt1
imod2d@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt1
write reference model image:
imod2d@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt1 to bx610_b4c5_uv_ab/model_0/imod2d_b4c5_bb3.ms.pt1.fits
imod3d@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt1
write reference model image:
imod3d@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt1 to bx610_b4c5_uv_ab/model_0/imod3d_b4c5_bb3.ms.pt1.fits
pbeam@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt1
write reference model image:
pbeam@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt1 to bx610_b4c5_uv_ab/model_0/pbeam_b4c5_bb3.ms.pt1.fits
copy ms container:
../data/bx610/alma/2017.1.01045.S/bb3.ms.pt1 to bx610_b4c5_uv_ab/model_0/model_b4c5_bb3.ms.pt1
write ms column:
uvmodel@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt1 to data@bx610_b4c5_uv_ab/model_0/model_b4c5_bb3.ms.pt1
create symlink:
/Users/Rui/Documents/Workspace/projects/GMaKE/examples/data/bx610/alma/2017.1.01045.S/bb3.ms.pt1 to bx610_b4c5_uv_ab/model_0/data_b4c5_bb3.ms.pt1
-->data_b4c5_bb3.ms.pt3
imod2d@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt3
write reference model image:
imod2d@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt3 to bx610_b4c5_uv_ab/model_0/imod2d_b4c5_bb3.ms.pt3.fits
imod3d@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt3
write reference model image:
imod3d@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt3 to bx610_b4c5_uv_ab/model_0/imod3d_b4c5_bb3.ms.pt3.fits
pbeam@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt3
write reference model image:
pbeam@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt3 to bx610_b4c5_uv_ab/model_0/pbeam_b4c5_bb3.ms.pt3.fits
copy ms container:
../data/bx610/alma/2017.1.01045.S/bb3.ms.pt3 to bx610_b4c5_uv_ab/model_0/model_b4c5_bb3.ms.pt3
write ms column:
uvmodel@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt3 to data@bx610_b4c5_uv_ab/model_0/model_b4c5_bb3.ms.pt3
create symlink:
/Users/Rui/Documents/Workspace/projects/GMaKE/examples/data/bx610/alma/2017.1.01045.S/bb3.ms.pt3 to bx610_b4c5_uv_ab/model_0/data_b4c5_bb3.ms.pt3
-->data_b4c5_bb4.ms.mfs
imod2d@../data/bx610/alma/2017.1.01045.S/bb4.ms.mfs
write reference model image:
imod2d@../data/bx610/alma/2017.1.01045.S/bb4.ms.mfs to bx610_b4c5_uv_ab/model_0/imod2d_b4c5_bb4.ms.mfs.fits
imod3d@../data/bx610/alma/2017.1.01045.S/bb4.ms.mfs
write reference model image:
imod3d@../data/bx610/alma/2017.1.01045.S/bb4.ms.mfs to bx610_b4c5_uv_ab/model_0/imod3d_b4c5_bb4.ms.mfs.fits
pbeam@../data/bx610/alma/2017.1.01045.S/bb4.ms.mfs
write reference model image:
pbeam@../data/bx610/alma/2017.1.01045.S/bb4.ms.mfs to bx610_b4c5_uv_ab/model_0/pbeam_b4c5_bb4.ms.mfs.fits
copy ms container:
../data/bx610/alma/2017.1.01045.S/bb4.ms.mfs to bx610_b4c5_uv_ab/model_0/model_b4c5_bb4.ms.mfs
write ms column:
uvmodel@../data/bx610/alma/2017.1.01045.S/bb4.ms.mfs to data@bx610_b4c5_uv_ab/model_0/model_b4c5_bb4.ms.mfs
create symlink:
/Users/Rui/Documents/Workspace/projects/GMaKE/examples/data/bx610/alma/2017.1.01045.S/bb4.ms.mfs to bx610_b4c5_uv_ab/model_0/data_b4c5_bb4.ms.mfs
--------------------------------------------------------------------------------
--- took 29.00081 seconds ---
--- save to: bx610_b4c5_uv_ab/model_0/models.h5
save the model input parameter: bx610_b4c5_uv_ab/model_0/model.inp
model_0:
{'chisq': 300557343.3421936,
'lnprob': 8519061.630641665,
'ndata': 86383912.0,
'npar': 15}
data@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt2 125111592.61012563 35301632
data@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt2 168486258.64972007 49426196
data@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt1 1118138.674951935 275794
data@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt3 1161366.5592344531 275794
data@../data/bx610/alma/2017.1.01045.S/bb2.ms.mfs 1157663.9855508006 276124
data@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt1 1205062.388948932 276124
data@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt3 1156303.2738797683 276124
data@../data/bx610/alma/2017.1.01045.S/bb4.ms.mfs 1160942.1459157672 276124
export the model set: bx610_b4c5_uv_ab/model_1 (may take some time..)
-->data_b4c5_bb1.ms.pt2
imod2d@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt2
write reference model image:
imod2d@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt2 to bx610_b4c5_uv_ab/model_1/imod2d_b4c5_bb1.ms.pt2.fits
imod3d@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt2
write reference model image:
imod3d@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt2 to bx610_b4c5_uv_ab/model_1/imod3d_b4c5_bb1.ms.pt2.fits
pbeam@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt2
write reference model image:
pbeam@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt2 to bx610_b4c5_uv_ab/model_1/pbeam_b4c5_bb1.ms.pt2.fits
write reference model profile:
imod3d_prof@co43@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt2 to bx610_b4c5_uv_ab/model_1/imodrp_co43_b4c5_bb1.ms.pt2.fits
copy ms container:
../data/bx610/alma/2017.1.01045.S/bb1.ms.pt2 to bx610_b4c5_uv_ab/model_1/model_b4c5_bb1.ms.pt2
write ms column:
uvmodel@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt2 to data@bx610_b4c5_uv_ab/model_1/model_b4c5_bb1.ms.pt2
create symlink:
/Users/Rui/Documents/Workspace/projects/GMaKE/examples/data/bx610/alma/2017.1.01045.S/bb1.ms.pt2 to bx610_b4c5_uv_ab/model_1/data_b4c5_bb1.ms.pt2
-->data_b4c5_bb3.ms.pt2
imod2d@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt2
write reference model image:
imod2d@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt2 to bx610_b4c5_uv_ab/model_1/imod2d_b4c5_bb3.ms.pt2.fits
imod3d@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt2
write reference model image:
imod3d@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt2 to bx610_b4c5_uv_ab/model_1/imod3d_b4c5_bb3.ms.pt2.fits
pbeam@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt2
write reference model image:
pbeam@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt2 to bx610_b4c5_uv_ab/model_1/pbeam_b4c5_bb3.ms.pt2.fits
write reference model profile:
imod3d_prof@ci10@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt2 to bx610_b4c5_uv_ab/model_1/imodrp_ci10_b4c5_bb3.ms.pt2.fits
copy ms container:
../data/bx610/alma/2017.1.01045.S/bb3.ms.pt2 to bx610_b4c5_uv_ab/model_1/model_b4c5_bb3.ms.pt2
write ms column:
uvmodel@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt2 to data@bx610_b4c5_uv_ab/model_1/model_b4c5_bb3.ms.pt2
create symlink:
/Users/Rui/Documents/Workspace/projects/GMaKE/examples/data/bx610/alma/2017.1.01045.S/bb3.ms.pt2 to bx610_b4c5_uv_ab/model_1/data_b4c5_bb3.ms.pt2
-->data_b4c5_bb1.ms.pt1
imod2d@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt1
write reference model image:
imod2d@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt1 to bx610_b4c5_uv_ab/model_1/imod2d_b4c5_bb1.ms.pt1.fits
imod3d@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt1
write reference model image:
imod3d@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt1 to bx610_b4c5_uv_ab/model_1/imod3d_b4c5_bb1.ms.pt1.fits
pbeam@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt1
write reference model image:
pbeam@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt1 to bx610_b4c5_uv_ab/model_1/pbeam_b4c5_bb1.ms.pt1.fits
copy ms container:
../data/bx610/alma/2017.1.01045.S/bb1.ms.pt1 to bx610_b4c5_uv_ab/model_1/model_b4c5_bb1.ms.pt1
write ms column:
uvmodel@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt1 to data@bx610_b4c5_uv_ab/model_1/model_b4c5_bb1.ms.pt1
create symlink:
/Users/Rui/Documents/Workspace/projects/GMaKE/examples/data/bx610/alma/2017.1.01045.S/bb1.ms.pt1 to bx610_b4c5_uv_ab/model_1/data_b4c5_bb1.ms.pt1
-->data_b4c5_bb1.ms.pt3
imod2d@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt3
write reference model image:
imod2d@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt3 to bx610_b4c5_uv_ab/model_1/imod2d_b4c5_bb1.ms.pt3.fits
imod3d@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt3
write reference model image:
imod3d@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt3 to bx610_b4c5_uv_ab/model_1/imod3d_b4c5_bb1.ms.pt3.fits
pbeam@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt3
write reference model image:
pbeam@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt3 to bx610_b4c5_uv_ab/model_1/pbeam_b4c5_bb1.ms.pt3.fits
copy ms container:
../data/bx610/alma/2017.1.01045.S/bb1.ms.pt3 to bx610_b4c5_uv_ab/model_1/model_b4c5_bb1.ms.pt3
write ms column:
uvmodel@../data/bx610/alma/2017.1.01045.S/bb1.ms.pt3 to data@bx610_b4c5_uv_ab/model_1/model_b4c5_bb1.ms.pt3
create symlink:
/Users/Rui/Documents/Workspace/projects/GMaKE/examples/data/bx610/alma/2017.1.01045.S/bb1.ms.pt3 to bx610_b4c5_uv_ab/model_1/data_b4c5_bb1.ms.pt3
-->data_b4c5_bb2.ms.mfs
imod2d@../data/bx610/alma/2017.1.01045.S/bb2.ms.mfs
write reference model image:
imod2d@../data/bx610/alma/2017.1.01045.S/bb2.ms.mfs to bx610_b4c5_uv_ab/model_1/imod2d_b4c5_bb2.ms.mfs.fits
imod3d@../data/bx610/alma/2017.1.01045.S/bb2.ms.mfs
write reference model image:
imod3d@../data/bx610/alma/2017.1.01045.S/bb2.ms.mfs to bx610_b4c5_uv_ab/model_1/imod3d_b4c5_bb2.ms.mfs.fits
pbeam@../data/bx610/alma/2017.1.01045.S/bb2.ms.mfs
write reference model image:
pbeam@../data/bx610/alma/2017.1.01045.S/bb2.ms.mfs to bx610_b4c5_uv_ab/model_1/pbeam_b4c5_bb2.ms.mfs.fits
copy ms container:
../data/bx610/alma/2017.1.01045.S/bb2.ms.mfs to bx610_b4c5_uv_ab/model_1/model_b4c5_bb2.ms.mfs
write ms column:
uvmodel@../data/bx610/alma/2017.1.01045.S/bb2.ms.mfs to data@bx610_b4c5_uv_ab/model_1/model_b4c5_bb2.ms.mfs
create symlink:
/Users/Rui/Documents/Workspace/projects/GMaKE/examples/data/bx610/alma/2017.1.01045.S/bb2.ms.mfs to bx610_b4c5_uv_ab/model_1/data_b4c5_bb2.ms.mfs
-->data_b4c5_bb3.ms.pt1
imod2d@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt1
write reference model image:
imod2d@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt1 to bx610_b4c5_uv_ab/model_1/imod2d_b4c5_bb3.ms.pt1.fits
imod3d@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt1
write reference model image:
imod3d@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt1 to bx610_b4c5_uv_ab/model_1/imod3d_b4c5_bb3.ms.pt1.fits
pbeam@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt1
write reference model image:
pbeam@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt1 to bx610_b4c5_uv_ab/model_1/pbeam_b4c5_bb3.ms.pt1.fits
copy ms container:
../data/bx610/alma/2017.1.01045.S/bb3.ms.pt1 to bx610_b4c5_uv_ab/model_1/model_b4c5_bb3.ms.pt1
write ms column:
uvmodel@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt1 to data@bx610_b4c5_uv_ab/model_1/model_b4c5_bb3.ms.pt1
create symlink:
/Users/Rui/Documents/Workspace/projects/GMaKE/examples/data/bx610/alma/2017.1.01045.S/bb3.ms.pt1 to bx610_b4c5_uv_ab/model_1/data_b4c5_bb3.ms.pt1
-->data_b4c5_bb3.ms.pt3
imod2d@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt3
write reference model image:
imod2d@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt3 to bx610_b4c5_uv_ab/model_1/imod2d_b4c5_bb3.ms.pt3.fits
imod3d@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt3
write reference model image:
imod3d@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt3 to bx610_b4c5_uv_ab/model_1/imod3d_b4c5_bb3.ms.pt3.fits
pbeam@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt3
write reference model image:
pbeam@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt3 to bx610_b4c5_uv_ab/model_1/pbeam_b4c5_bb3.ms.pt3.fits
copy ms container:
../data/bx610/alma/2017.1.01045.S/bb3.ms.pt3 to bx610_b4c5_uv_ab/model_1/model_b4c5_bb3.ms.pt3
write ms column:
uvmodel@../data/bx610/alma/2017.1.01045.S/bb3.ms.pt3 to data@bx610_b4c5_uv_ab/model_1/model_b4c5_bb3.ms.pt3
create symlink:
/Users/Rui/Documents/Workspace/projects/GMaKE/examples/data/bx610/alma/2017.1.01045.S/bb3.ms.pt3 to bx610_b4c5_uv_ab/model_1/data_b4c5_bb3.ms.pt3
-->data_b4c5_bb4.ms.mfs
imod2d@../data/bx610/alma/2017.1.01045.S/bb4.ms.mfs
write reference model image:
imod2d@../data/bx610/alma/2017.1.01045.S/bb4.ms.mfs to bx610_b4c5_uv_ab/model_1/imod2d_b4c5_bb4.ms.mfs.fits
imod3d@../data/bx610/alma/2017.1.01045.S/bb4.ms.mfs
write reference model image:
imod3d@../data/bx610/alma/2017.1.01045.S/bb4.ms.mfs to bx610_b4c5_uv_ab/model_1/imod3d_b4c5_bb4.ms.mfs.fits
pbeam@../data/bx610/alma/2017.1.01045.S/bb4.ms.mfs
write reference model image:
pbeam@../data/bx610/alma/2017.1.01045.S/bb4.ms.mfs to bx610_b4c5_uv_ab/model_1/pbeam_b4c5_bb4.ms.mfs.fits
copy ms container:
../data/bx610/alma/2017.1.01045.S/bb4.ms.mfs to bx610_b4c5_uv_ab/model_1/model_b4c5_bb4.ms.mfs
write ms column:
uvmodel@../data/bx610/alma/2017.1.01045.S/bb4.ms.mfs to data@bx610_b4c5_uv_ab/model_1/model_b4c5_bb4.ms.mfs
create symlink:
/Users/Rui/Documents/Workspace/projects/GMaKE/examples/data/bx610/alma/2017.1.01045.S/bb4.ms.mfs to bx610_b4c5_uv_ab/model_1/data_b4c5_bb4.ms.mfs
--------------------------------------------------------------------------------
--- took 30.39432 seconds ---
--- save to: bx610_b4c5_uv_ab/model_1/models.h5
save the model input parameter: bx610_b4c5_uv_ab/model_1/model.inp
model_1:
{'chisq': 300557328.28832734,
'lnprob': 8519069.157574806,
'ndata': 86383912.0,
'npar': 15}
<Figure size 432x288 with 0 Axes>
models=gmake.hdf2dct(inp_dct['general']['outdir']+'/model_1/models.h5')
#gmake.pprint(models['mod_dct']['co43'])
gmake.model_vrot_plot(models['mod_dct']['co43'])
<Figure size 432x288 with 0 Axes>
from galario.single import sampleImage
from galario.single import chi2Image
import numexpr as ne
import numpy as np
def method_sampleImage(dat_dct):
xymodel=np.ones((512,512),dtype=np.float32)
data=dat_dct['data@../data/bx610/alma/2017.1.01045.S/bb2.ms.mfs']
uvw=dat_dct['uvw@../data/bx610/alma/2017.1.01045.S/bb2.ms.mfs']
weight=dat_dct['weight@../data/bx610/alma/2017.1.01045.S/bb2.ms.mfs']
wv=np.mean(dat_dct['chanfreq@../data/bx610/alma/2017.1.01045.S/bb4.ms.mfs'])
uvmodel=sampleImage(xymodel,np.deg2rad(0.007/60./60.).astype(np.float32),
(uvw[:,0]/wv),(uvw[:,1]/wv),
dRA=0,dDec=0,PA=0.,check=False,origin='lower')
#print(uvmodel[:,np.newaxis].shape)
#print(data.shape)
#print(weight[:,np.newaxis].shape)
chi2=ne.evaluate('sum(((a.real-b.real)**2.0+(a.imag-b.imag)**2)*c)',
local_dict={'a':data,
'b':uvmodel[:,np.newaxis],
'c':weight[:,np.newaxis]})
return chi2
def method_chi2Image(dat_dct):
xymodel=np.ones((512,512),dtype=np.float32,order='')
data=dat_dct['data@../data/bx610/alma/2017.1.01045.S/bb2.ms.mfs']
real=np.ascontiguousarray(data[:,0].real)
imag=np.ascontiguousarray(data[:,0].imag)
uvw=dat_dct['uvw@../data/bx610/alma/2017.1.01045.S/bb2.ms.mfs']
weight=dat_dct['weight@../data/bx610/alma/2017.1.01045.S/bb2.ms.mfs']
wv=np.mean(dat_dct['chanfreq@../data/bx610/alma/2017.1.01045.S/bb4.ms.mfs'])
chi2=chi2Image(xymodel,np.deg2rad(0.007/60./60.).astype(np.float32),
uvw[:,0]/wv,uvw[:,1]/wv,
real,imag,weight,
dRA=0,dDec=0,PA=0.,check=False,origin='lower')
return chi2
#%lprun -f method_sampleImage chi2=method_sampleImage(dat_dct)
#print(chi2)
%timeit chi2=method_sampleImage(dat_dct)
print(chi2)
#%lprun -f method_chi2Image chi2=method_chi2Image(dat_dct)
#print(chi2)
#%timeit chi2=method_chi2Image(dat_dct)
#print(chi2)
9.41 ms ± 376 µs per loop (mean ± std. dev. of 7 runs, 100 loops each)
1.926698859779456e+21