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View Code? Open in Web Editor NEWPython API for low-level analysis of NR data: Psi4, strain, modeling, lal+pycbc interface when appropriate
License: MIT License
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Label swap issue for edge cases (and possible phase-shift need for BAM)
nrutils_dev/nrutils/handlers/bam.py
Line 650 in 7301aa1
I'm not sure how nrutils handles the q1a08 cases internally where the BAM data is already swapped, but I could see an issue here with the dynamics if this isn't taken into account later.
Inconsistent Spin in dynamics
nrutils_dev/nrutils/core/nrsc.py
Line 5008 in 7301aa1
Potential inconsistency in calculating J using the orbital angular momentum and spin information at different times. I couldn't see the spin data being updated in the attributes of the gwylm object prior to J being computed here with the new values of L.
Top level import Error
A basic import of the nrutils module fails to import the internal packages defined in the init.py
For example:
[jclark@taranis] $ python -c "import nrutils"
The highest level init for nrutils is located at: /home/jclark/.local/lib/python2.7/site-packages/nrutils-1.0-py2.7.egg/nrutils/__init__.pyc
>> Initiating nrutils ...
>> Sub-Packages to be imported:
->
->
->
->
>> Please note style conventions:
* lower case function/method/variable names
* no underscore in names unless there are repeated letters, or counfounded syllables
* information is implicitely in time domain unless explicitely stated.
* frequency domain information will start with "fd".
nrutils:
.:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/home/jclark/.local/lib/python2.7/site-packages/nrutils-1.0-py2.7.egg/nrutils/__init__.py", line 83, in <module>
exec r'import %s' % p
File "<string>", line 1
import
^
SyntaxError: invalid syntaxI think I found a error in the meta data of one of the BAM runs
I think this particular case has some bug with it's metadata or something. When I try to get the an instance of gwylm of this particular case I get a strange error.
case10=scsearch(keyword='/Users/sebastian/phd/mounts/hogshead_mount/NR_data/ReducedData-hogshead/dirac-nr-followup/q1.2_dcp2dphi1/')
gw_case10 = gwylm( scentry_obj = case10, lm=[2,2], dt=0.4, verbose=False )
traceback below.
any ideas?
(gwylm)>> Found clean (=False) keyword.
(gwylm)>> Found dt (=0.4) keyword.
(gwylm)>> Found lm (=[2, 2]) keyword.
(gwylm)>> Found load (=True) keyword.
(gwylm)>> Found scentry_obj (=<nrutils.core.nrsc.scentry instance at 0x108a54758>) keyword.
(gwylm)>> Found verbose (=False) keyword.
(**) Waveform not uniform in time-step. Interpolation will be applied.
(**) Warning: No dt given to gwf(). We will assume that the input waveform array is in geometric units, and that dt = 0.294408 will more than suffice.
---------------------------------------------------------------------------
IndexError Traceback (most recent call last)
<ipython-input-162-862f5ec8352a> in <module>()
----> 1 gw_case10 = gwylm( scentry_obj = case10, lm=[2,2], dt=0.4, verbose=False )
/Users/sebastian/projects/phenEOB/env/lib/python2.7/site-packages/nrutils-1.0-py2.7.egg/nrutils/core/nrsc.pyc in __init__(this, scentry_obj, lm, lmax, dt, load, clean, extraction_parameter, verbose)
1285
1286 # Load the waveform data
-> 1287 if load==True: this.__load__(lmax=lmax,lm=lm)
1288
1289 # Characterize the waveform's start and store related information to this.starting
/Users/sebastian/projects/phenEOB/env/lib/python2.7/site-packages/nrutils-1.0-py2.7.egg/nrutils/core/nrsc.pyc in __load__(this, lmax, lm, extraction_parameter, dt, verbose)
1362 else: # Else, if lm is a single mode index
1363 #
-> 1364 this.load(lm=lm,extraction_parameter=extraction_parameter,dt=dt)
1365
1366 # load the waveform data
/Users/sebastian/projects/phenEOB/env/lib/python2.7/site-packages/nrutils-1.0-py2.7.egg/nrutils/core/nrsc.pyc in load(this, lm, file_location, dt, extraction_parameter, output, verbose)
1441 extraction_parameter=extraction_parameter,
1442 dt=dt,
-> 1443 kind='psi4')
1444
1445 # ---------------------------------------------------- #
/Users/sebastian/projects/phenEOB/env/lib/python2.7/site-packages/nrutils-1.0-py2.7.egg/nrutils/core/nrsc.pyc in __init__(this, wfarr, dt, ref_scentry, l, m, extraction_parameter, kind, friend, verbose)
739 # use the raw waveform data to define all fields
740 this.wfarr = wfarr
--> 741 this.setfields(wfarr=wfarr,dt=dt)
742
743 # If desired, Copy fields from related gwf object.
/Users/sebastian/projects/phenEOB/env/lib/python2.7/site-packages/nrutils-1.0-py2.7.egg/nrutils/core/nrsc.pyc in setfields(this, wfarr, dt)
846
847 phi_ = unwrap( angle( this.y ) ) # Phase: NOTE, here we make the phase constant where the amplitude is zero
--> 848 k = find( (this.amp > 0) * (this.amp<max(this.amp)) )[0]
849 phi_[0:k] = phi_[k]
850 this.phi = phi_
IndexError: index 0 is out of bounds for axis 0 with size 0
Reconciling master with branch named "before the rain"
SXS server update
SXS have changed the format used to save their hdf5 files on their main server. The sxsdltool will need to be updated. (note to self)
confing ini files 'catalog_dir' needs to end in slash
In catalogue ini files the filed ' catalog_dir ' is a path such as
catalog_dir = /Users/sebastian/phd/mounts/hogshead_mount/NR_data/ReducedData-hogshead/dirac-nr-followup/
If if doesn't end in a slash then I think you get an error.
Just a not here for me to fix it later
sxs.template broken
ValueError: (!!) Error -- config file at /Users/sebastian/work/git/nrutils_dev/nrutils/config/sxs.ini does NOT contain required field is_rscaled
in minion.template
it has
is_rscaled=0
What should it be for sxs?
issue with importing /data
----> 2 import nrutils as nr
3 from matplotlib import rc
4 rc('font',**{'family':'sans-serif','sans-serif':['Helvetica']})
5 rc('text', usetex=True)
/usr/local/lib/python2.7/site-packages/nrutils/init.py in ()
91 for p in internal_packages:
92 if verbose: print ' .%s: ' % p
---> 93 exec r'import %s' % p
94 # exec 'from %s import *' % p
95
in ()
/usr/local/lib/python2.7/site-packages/nrutils/data/init.py in ()
59 if len(internal_packages) == 0:
60 msg = '(!!) Unable to automatically find internal packages. Please report this bug to the developers. (https://github.com/llondon6/nrutils_dev/tree/master/nrutils)'
---> 61 raise ValueError(msg)
62
63 # Store package settings (useful directories etc) to a settings field
ValueError: (!!) Unable to automatically find internal packages. Please report this bug to the developers. (https://github.com/llondon6/nrutils_dev/tree/master/nrutils)
Unable to import after nrutils install with pip
This appears to happen after a fresh pip install:
In [1]: import nrutils
>> Initiating nrutils.
>> Please note style conventions:
* lower case function/method/variable names
* no underscore in names unless there are repeated letters, or counfounded syllables
* information is implicitely in time domain unless explicitely stated.
* frequency domain information will start with "fd".
nrutils:
.:
File "<string>", line 1
import
^
SyntaxError: invalid syntaxI'm working on it.
I would like to be able to specify which SXS waveform to use based on their Lev number
nrutils_dev package not working with ipython notebooks
Hey guys,
I'm trying to use nrutils_dev with ipython notebooks.
Just try the following commands in an ipython notebook
from nrutils.core.nrsc import *
A = scsearch(keyword="base",unique=True,verbose=True)
y = gwylm( scentry_obj = A[0], lm=[2,2], dt=0.4, verbose=True )
I get the following output :(
(gwylm)>> Found clean (=False) keyword.
(gwylm)>> Found dt (=0.4) keyword.
(gwylm)>> Found lm (=[2, 2]) keyword.
(gwylm)>> Found load (=True) keyword.
(gwylm)>> Found scentry_obj (=<nrutils.core.nrsc.scentry instance at 0x10d0781b8>) keyword.
(gwylm)>> Found verbose (=True) keyword.
(load)>> Loading: psi3col.r5.l5.l2.m2.gz
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
<ipython-input-15-9453ca2f6cbe> in <module>()
1 # Convert a single simulation into a waveform object with desired multipoles
----> 2 y = gwylm( scentry_obj = A[0], lm=[2,2], dt=0.4, verbose=True )
/Users/sebastian/git/nrutils_dev/nrutils/core/nrsc.pyc in __init__(this, scentry_obj, lm, lmax, extraction_parameter, dt, load, clean, verbose)
1278
1279 # Load the waveform data
-> 1280 if load==True: this.__load__(lmax=lmax,lm=lm)
1281
1282 # Characterize the waveform's start and store related information to this.starting
/Users/sebastian/git/nrutils_dev/nrutils/core/nrsc.pyc in __load__(this, lmax, lm)
1349 else: # Else, if lm is a single mode index
1350 #
-> 1351 this.load(lm=lm)
1352
1353 # load the waveform data
/Users/sebastian/git/nrutils_dev/nrutils/core/nrsc.pyc in load(this, lm, file_location, dt, output)
1420 # Enforce internal sign convention for Psi4 multipoles
1421 msk_ = y_.amp > 0.01*max(y_.amp)
-> 1422 external_sign_convention = mode( sign( y_.dphi[msk_] ) ).mode[0]
1423 if M_RELATIVE_SIGN_CONVENTION != external_sign_convention:
1424 wfarr[:,2] = -wfarr[:,2]
AttributeError: 'tuple' object has no attribute 'mode'
scbuild failing for me - any ideas?
I'm just trying to get my setup ready to do some work on the train tomorrow. I am up to date with the current master but when I try to build a catalogue it fails :(
(overwatch) SebastiansMBP2:nrutils_dev sebastian$ ipython
Python 2.7.6 (default, Sep 9 2014, 15:04:36)
Type "copyright", "credits" or "license" for more information.
IPython 5.1.0 -- An enhanced Interactive Python.
? -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help -> Python's own help system.
object? -> Details about 'object', use 'object??' for extra details.
In [1]: from nrutils.core.nrsc import *
The highest level init for nrutils is located at: /Users/sebastian/git/nrutils_dev/nrutils/__init__.pyc
>> Initiating nrutils ...
>> Sub-Packages to be imported:
-> core
-> manipulate
-> tools
>> Please note style conventions:
* lower case function/method/variable names
* no underscore in names unless there are repeated letters, or counfounded syllables
* information is implicitely in time domain unless explicitely stated.
* frequency domain information will start with "fd".
nrutils:
.core:
.basics*
.basics
.nrsc
.manipulate:
.bundlers
.tools:
.unit:
.conversion
In [2]: scbuild()
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
<ipython-input-2-10b07758f881> in <module>()
----> 1 scbuild()
/Users/sebastian/git/nrutils_dev/nrutils/core/nrsc.pyc in scbuild(save)
307
308 # Create config objects from list of config files
--> 309 configs = [ scconfig( config_path ) for config_path in cpath_list ]
310
311 # For earch config
/Users/sebastian/git/nrutils_dev/nrutils/core/nrsc.pyc in __init__(this, config_file_location)
27 # call wrapper for constructor
28 this.config_file_location = config_file_location
---> 29 this.reconfig()
30
31 # The actual constructor: this will be called within utility functions so that scentry objects are configured with local settings.
/Users/sebastian/git/nrutils_dev/nrutils/core/nrsc.pyc in reconfig(this)
41
42 # validate the information learned from the configuration file against minimal standards
---> 43 this.valid = this.validate()
44
45 # In some cases, it is useful to have this function return this
/Users/sebastian/git/nrutils_dev/nrutils/core/nrsc.pyc in validate(this)
108 if 'dir' in attr:
109 if this.__dict__[attr][-1] != '/':
--> 110 this.__dict__[attr][-1] += '/'
111 # Make sure that user symbols (~) are expanded
112 for attr in this.__dict__:
TypeError: 'str' object does not support item assignment
calculation of location of max amp via argmax needs to be improved
For some of the higher modes the current method of shifting the time series by the peak amplitude doesn't work and is indeed wrong I think when dealing with multiple modes.
Currently in the gwf class the time domain data is shifted by the location of the peak amplitude to line it up at zero.
This doesn't work when the junk radiation is larger that the peak at merger and I think this is actually the wrong way to treat this problem. The time delay between the peaks of different modes should be preserved and so we should shift them by the time-shift applied to the 22 mode.
We will have to think how to incorporate this in... maybe when multiple modes are requested they are shifted with respect to the 22 mode....
I think lvcnr5_to_gwylm needs to have M_RELATIVE_SIGN_CONVENTION implemented
The function to load lvcnr into nrutils seems to be lacking the M_RELATIVE_SIGN_CONVENTION check
https://github.com/llondon6/nrutils_dev/blob/master/nrutils/core/nrsc.py#L4105
NameError: global name 'upbow' is not defined
I pulled the latest code. I'm running on minion so I'm using the database files and config files that come with master.
from nrutils import scsearch,gwylm
A = scsearch(precessing=True,q=[3,6],verbose=True)
y = gwylm( scentry_obj = A[2], lm=([2,2],[2,1],[2,-2],[2,-1]), verbose=True )
And I get the following error
In [8]: y = gwylm( scentry_obj = A[2], lm=([2,2],[2,1],[2,-2],[2,-1]), verbose=True )
(gwylm)>> Found dt (=0.15) keyword.
(gwylm)>> Found lm (=([2, 2], [2, 1], [2, -2], [2, -1])) keyword.
(gwylm)>> Found scentry_obj (=<nrutils.core.nrsc.scentry instance at 0x77007a0>) keyword.
(gwylm)>> Found verbose (=True) keyword.
(gwylm)>> The (extraction_parameter,level) is (75.0,None), which differs from the config values of (75,0). You have either manually input the non-config values, or the handler has set them by looking at the contents of the simulation directory.
(__make_lmlist__)>> The following spherical multipoles will be loaded:[(2, 2), (2, 1), (2, -2), (2, -1)]
(load)>> Loading: Ylm_WEYLSCAL4::Psi4r_l2_m2_r75.00.asc
(load)>> Imposing a default padding of 3 to the data.
(pad_wfarr)>> The shape was (7660, 3). Now the shape is (7663, 3).
(load)>> Loading: Ylm_WEYLSCAL4::Psi4r_l2_m1_r75.00.asc
(load)>> Imposing a default padding of 3 to the data.
(pad_wfarr)>> The shape was (7660, 3). Now the shape is (7663, 3).
(load)>> Loading: Ylm_WEYLSCAL4::Psi4r_l2_m-2_r75.00.asc
(load)>> Imposing a default padding of 3 to the data.
(pad_wfarr)>> The shape was (7660, 3). Now the shape is (7663, 3).
(load)>> Loading: Ylm_WEYLSCAL4::Psi4r_l2_m-1_r75.00.asc
(load)>> Imposing a default padding of 3 to the data.
(pad_wfarr)>> The shape was (7660, 3). Now the shape is (7663, 3).
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-8-9aee6411efe5> in <module>()
----> 1 y = gwylm( scentry_obj = A[2], lm=([2,2],[2,1],[2,-2],[2,-1]), verbose=True )
/mnt/hogshead/home/spx8sk/git/nrutils_dev/nrutils/core/nrsc.py in __init__(this, scentry_obj, lm, lmax, dt, load, clean, extraction_parameter, level, w22, lowpass, calcstrain, calcnews, enforce_polarization_convention, fftfactor, pad, verbose)
2164 if scentry_obj.config:
2165 # Only do this if the scentry object has config information; otheriwse, it was probably created outside of scbuild and will probably break code
-> 2166 this.characterize_start_end()
2167
2168 # If w22 is input, then use the input value for strain calculation. Otherwise, use the algorithmic estimate.
/mnt/hogshead/home/spx8sk/git/nrutils_dev/nrutils/core/nrsc.py in characterize_start_end(this)
2792 # Characterize the END of the waveform (post-ringdown) #
2793 #%%&%%&%%&%%&%%&%%&%%&%%&%%&%%&%%&%%&%%&%%&%%&%%&%%&%%&%%&%%&#
-> 2794 this.postringdown = gwfcharend( y22 )
2795 # After endindex, the data is dominated by noise
2796 this.endindex = this.postringdown.right_index
/mnt/hogshead/home/spx8sk/git/nrutils_dev/nrutils/core/nrsc.py in __init__(this, ylm)
3910 this.__characterize_amplitude__(ylm)
3911 # Use frequency
-> 3912 this.__characterize_frequency__(ylm)
3913 # Characterize the end of the waveform using values of the amplitude
3914 def __characterize_amplitude__(this,ylm):
/mnt/hogshead/home/spx8sk/git/nrutils_dev/nrutils/core/nrsc.py in __characterize_frequency__(this, ylm)
3944 B = ylm.t > ylm.t[ ylm.k_amp_max ]
3945 #
-> 3946 a = upbow(ylm.dphi[B])
3947 knots,rl = romline(ylm.t[B],a,5)
3948 #
NameError: global name 'upbow' is not defined
sad
Add tortoise coordinate functionality
nrutils_dev/nrutils/core/nrsc.py
Line 4985 in 7301aa1
The mapping between the source dynamics time and the waveform time is fixed to be a shift by the extraction radius. I would like to add functionality to choose between either extraction radius or the tortoise coordinate, something like:
MADM = this.raw_metadata.initial_ADM_energy
extraction_radius = this.extraction_radius + 2.0 * MADM * np.log(this.extraction_radius / (2.0 * MADM) - 1.0)
This could be implemented with the addition of a flag in load_dynamics:
load_dynamics(this,waveform_times=None,verbose=False,output=False,tortoise=False)
Things to Do
- Command line tool for user configuration
---> seed ini files with desired information
---> rename template ini files
---> ask if user wishes to download the SXS catalog; if so, warn of space requirements and ask which multipoles are desired
---> command line tool for catalog building? - Ensure that all gwylm objects are in the same frame:
---> Add a stand alone function that rotates a gwylm object from one frame into another in the time domain
---> Add formatting method to gwylm to put it in the J or L frame when w = w0
---> Add formatting method to convert static frame gwylm to dynamic frame gwylm (i.e. corotating frame transformation) - Create feature-alignment modules for GW-ML tools:
---> generalized inner-product definition (e.g. frequency whitening or generalized kernel)
---> time and phase alignment via optimal inner-product
---> time and phase alignment via reference time or reference frequency
Broken silures catalog with no L and no valid relaxed data
@llondon6 With the current silures catalog there are no L attributes because I believe it was built before cd13318#diff-5c8bebdb8173e0ca200215a18c36663d. This is now an issue because external_sign_convention has now been forced to None in d9c5d15#diff-30ce82bdc95d9bf98cc05c25af6268c5R2409
nrutils_dev/nrutils/core/nrsc.py
Line 2409 in d9c5d15
which triggers d9c5d15#diff-30ce82bdc95d9bf98cc05c25af6268c5R2622
nrutils_dev/nrutils/core/nrsc.py
Lines 2622 to 2630 in d9c5d15
which has no path that is free of L.
On attempting to rebuild the silures catalog you get failures because of there are no afterjunk attributes in many the silures data directories (for example BAM/q8EqualSpin/q8am085v6D10_96c025 has after-junkradiation-spin1x = ie nothing) which triggers cd13318#diff-5c8bebdb8173e0ca200215a18c36663dR179
nrutils_dev/nrutils/handlers/bam.py
Lines 179 to 192 in cd13318
which subsequently causes cd13318#diff-5c8bebdb8173e0ca200215a18c36663dR205 to fail because of a call norm(None).
nrutils_dev/nrutils/handlers/bam.py
Line 205 in cd13318
I will work on a patch for this, but reporting if you get round to this before me, or actually there is something I have done wrong that you can see. Thanks 😊
First Issue! - core_example.py import fail
Cyberface has tried to run core_example.py on his mac and as encountered an error
Sebastians-MacBook-Pro-2:examples sebastian$ python core_example.py
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/font_manager.py:273: UserWarning: Matplotlib is building the font cache using fc-list. This may take a moment.
warnings.warn('Matplotlib is building the font cache using fc-list. This may take a moment.')
>> Initiating nrutils.
>> Please note style conventions:
* lower case function/method/variable names
* no underscore in names unless there are repeated letters
* information is implicitely in time domain unless explicitely stated.
* frequency domain information will start with "fd".
nrutils:
.:
Traceback (most recent call last):
File "core_example.py", line 11, in <module>
from nrutils.core.nrsc import *
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nrutils/__init__.py", line 68, in <module>
exec 'import %s' % p
File "<string>", line 1
import
^
SyntaxError: invalid syntax
Name ideas
Did we miss a trick calling it something like
pyNR or NRpy
it doesn't really sound catchy tbh :)
but we could pronounce it pyNER or NERpi haha.
Don't get me wrong, nrutils is good too!
nrutils(3) raises ImportError with latest positive
Installing the latest version of positive alongside the nrutils3 branch of this project results in an ImportError:
File "/opt/hostedtoolcache/Python/3.7.12/x64/lib/python3.7/site-packages/pwca/__init__.py", line 12, in <module>
from . import core
File "/opt/hostedtoolcache/Python/3.7.12/x64/lib/python3.7/site-packages/pwca/core.py", line 20, in <module>
pwca_catalog = pickle.load( open( pwca_catalog_path, "rb" ) )
File "/opt/hostedtoolcache/Python/3.7.12/x64/lib/python3.7/site-packages/nrutils/__init__.py", line 105, in <module>
exec( r'import nrutils.%s' % p)
File "<string>", line 1, in <module>
File "/opt/hostedtoolcache/Python/3.7.12/x64/lib/python3.7/site-packages/nrutils/manipulate/__init__.py", line 12, in <module>
exec( 'from nrutils.manipulate.%s import *' % module)
File "<string>", line 1, in <module>
File "/opt/hostedtoolcache/Python/3.7.12/x64/lib/python3.7/site-packages/nrutils/manipulate/rotate.py", line 4, in <module>
from positive.maths import wdelement,wdmatrix
ImportError: cannot import name 'wdelement' from 'positive.maths' (/opt/hostedtoolcache/Python/3.7.12/x64/lib/python3.7/site-packages/positive/maths.py)Build log: https://github.com/cardiffgravity/PhenomDCP/runs/4507939776?check_suite_focus=true
Case troubles: angry tortoises
I am creating this issue to catalog a case trouble that I've seen with gwylm's load_dynamics.
The code state of interest is after the recent merge request with tortoise_coordinate and dynamics loading fixes: 97615f7
Note that this code state may be needed to access BAM NR data after their move to the super-computing wales facilities:
1b12671
I have started a branch that includes the fixes to access BAM from super-computing wales, but does not includes changes related to tortoise_coordinate and dynamics loading:
https://github.com/llondon6/nrutils_dev/tree/before_the_rain
I am preparing a notebook to demonstrate the case issue.
Import nrutils on Master broken for me
any ideas?
In [1]: import nrutils
The highest level init for nrutils is located at: /Users/sebastian/work/git/nrutils_dev/nrutils/__init__.pyc
>> Initiating nrutils ...
>> Sub-Packages to be imported:
-> core
-> generate
-> manipulate
-> tools
>> Please note style conventions:
* lower case function/method/variable names
* no underscore in names unless there are repeated letters, or counfounded syllables
* information is implicitely in time domain unless explicitely stated.
* frequency domain information will start with "fd".
nrutils:
.core:
.basics*
.basics
.nrsc
.generate:
.basics*
.basics
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
<ipython-input-1-a28e3810b6c4> in <module>()
----> 1 import nrutils
/Users/sebastian/work/git/nrutils_dev/nrutils/__init__.py in <module>()
86 for p in internal_packages:
87 if verbose: print ' .%s: ' % p
---> 88 exec r'import %s' % p
89 # exec 'from %s import *' % p
90
<string> in <module>()
/Users/sebastian/work/git/nrutils_dev/nrutils/generate/__init__.py in <module>()
20 for module in modules:
21 if verbose: print ' .%s' % module
---> 22 exec 'import %s' % module
<string> in <module>()
ImportError: No module named basics
what does is_extrapolated = 1 do
What does it mean for each code?
for example in silures.ini this is set to 1.
but for my BAM ini file I have this to 0.
what does it do?
virtual environments, paths.ini and scbuild
Seb, Ed, would either of you mind adding a description of "pip install -e ..." to the readme?
Python 3 compatibility
@llondon6 what's the state of Python 3 compatibility for this repo? I'm happy to help but see that there's already a python3_compatibility branch and don't want to repeat what you've already done.
error when building catalog with latest versions
/mnt/hogshead/home/spx8sk/git/nrutils_dev/nrutils/core/nrsc.pyc in scbuild(keyword, save)
456 wave_train = ''#'~~~~<vvvvvvvvvvvvvWw>~~~~'
457 hline = wave_train*3
--> 458 msg = '\n\n#%s#\n%s with \"%s\". The related log file is at \"%s\".\n#%s#'%(hline,hlblack('Done'),green(config.catalog_dir),green(logfstr),hline)
459 alert(msg,'scbuild')
460
NameError: global name 'hlblack' is not defined
scbuild failing for one case
I'm trying to build a new database and it seems to be failing for this particular case :/
## The following is invalid: /Users/sebastian/phd/mounts/raid_mount/data/ReducedData/q3_a-0.5_a0.75_64_128/psi4modes.bbh
## The following is invalid: /Users/sebastian/phd/mounts/raid_mount/data/ReducedData/q3_a-0.5_a0.75_64_128/q3_a-0.5_a0.75_64_128.raw.bbh
## Working: /Users/sebastian/phd/mounts/raid_mount/data/ReducedData/q3_a-0.5_a0.75_64_128/q3_a-0.5_a0.75_64_128.bbh
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-6-10b07758f881> in <module>()
----> 1 scbuild()
/Users/sebastian/projects/phenEOB/env/lib/python2.7/site-packages/nrutils-1.0-py2.7.egg/nrutils/core/nrsc.pyc in scbuild(save)
323 for mdfile in mdfile_list:
324 # Create tempoary scentry object
--> 325 entry = scentry(config,mdfile)
326 # If the obj is valid, add it to the catalog list, else ignore
327 if entry.is_valid :
/Users/sebastian/projects/phenEOB/env/lib/python2.7/site-packages/nrutils-1.0-py2.7.egg/nrutils/core/nrsc.pyc in __init__(this, config_obj, metadata_file_location)
143
144 #
--> 145 this.label = sclabel( this )
146 else:
147 print '## The following is '+red('invalid')+': %s' % cyan(metadata_file_location)
/Users/sebastian/projects/phenEOB/env/lib/python2.7/site-packages/nrutils-1.0-py2.7.egg/nrutils/core/nrsc.pyc in sclabel(entry, use_q)
699 label = sclabel_many( entry = entry, use_q = use_q )
700 elif isinstance( entry, scentry ):
--> 701 label,_ = sclabel_single( entry = entry, use_q = use_q )
702 else:
703 msg = 'input must be list scentry objects, or single scentry'
/Users/sebastian/projects/phenEOB/env/lib/python2.7/site-packages/nrutils-1.0-py2.7.egg/nrutils/core/nrsc.pyc in sclabel_single(entry, use_q)
672
673 # Run is spin aligned if net spin is parallel to net L
--> 674 if allclose( dot(e.S1,L) , norm(e.S1)*norm(L) , atol=tol ) and allclose( dot(e.S2,L) , norm(e.S2)*norm(L) , atol=tol ) and (not 'ns' in tag):
675 tag.append('sa')
676
ValueError: shapes (3,0) and (3,) not aligned: 0 (dim 1) != 3 (dim 0)
BAM extraction parameter needed as variable
I loaded a bam waveform using my bam.ini file and
I noticed a small problem. The "l" with is something to do with
the extraction level or the resolution at which the data
was extracted was hard coded to 5 as below but for this
particular data set only l=6 was available.
So I had to change my bam.ini file first as below and then it worked.
So I think we should add this as an option for the bam waveforms or something.
; data_file_name_format = Psi4ModeDecomp/psi3col.r%i.l5.l%i.m%i.gz
data_file_name_format = Psi4ModeDecomp/psi3col.r%i.l6.l%i.m%i.gz
data_file_param_order = extraction_parameter, l, m
i.e., we add another variable to data_file_param_order = extraction_parameter, l, m
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