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Nithyanandan Thyagarajan
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Add scripts/replicate_sim.py to repo
From 8696533 (master): ===================== (*) Add prisim/examples/simparms/replicatesim.yaml to repo (*) Add scripts/replicate_sim.py to repo In prisim/interferometry.py, (*) Add input datakeys in __init__() member function of class InterferometerData. Update member function docstring accordingly (*) In __init__() member function of class InterferometerData, only set arrays for specified keys in input datakeys (*) In member function write_uvfits() of class InterferometerArray, add key 'datapool' to write only specified portions of the simulated data to UVFITS file. Update member function docstring accordingly. (*) In member function write_uvfits() of class InterferometerArray, write only specified portions of the simulated data to UVFITS file. In scripts/run_prisim.py, (*) Pass datapool info in uvfits_parms before calling write_uvfits() member function of class InterferometerArray
1 parent 8696533 commit 1dd0c3b

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Lines changed: 346 additions & 46 deletions

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‎.gitignore‎

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/prisim/*.pyc
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/prisim/*.tar.gz
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/prisim/interferometry.py.rej
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/prisim/examples/simparms/replicatesim.yaml~

‎changelog.txt‎

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From 8696533 (master):
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=====================
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(*) Add prisim/examples/simparms/replicatesim.yaml to repo
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(*) Add scripts/replicate_sim.py to repo
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In prisim/interferometry.py,
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(*) Add input datakeys in __init__() member function of class
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InterferometerData. Update member function docstring accordingly
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(*) In __init__() member function of class InterferometerData, only
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set arrays for specified keys in input datakeys
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(*) In member function write_uvfits() of class InterferometerArray,
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add key 'datapool' to write only specified portions of the simulated
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data to UVFITS file. Update member function docstring accordingly.
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(*) In member function write_uvfits() of class InterferometerArray,
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write only specified portions of the simulated data to UVFITS file.
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In scripts/run_prisim.py,
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(*) Pass datapool info in uvfits_parms before calling write_uvfits()
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member function of class InterferometerArray
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From 31aeae9 (fov):
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==================
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‎prisim/examples/simparms/replicatesim.yaml‎

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##### IMPORTANT INFORMATION #####
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##### DO NOT MODIFY THIS FILE #####
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##### MAKE A COPY OF THIS FILE AND CUSTOMIZE #####
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########## Directory Structure information #########
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dirstruct :
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# Directory information
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indir : '/path/to/simulation/directory/'
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# Directory containing simulations
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infile : null
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# Filename (without extension) of
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# the simulation in indir. If set
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# to null, only noise will be
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# realized multiple time as requested
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# with no sky signal
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infmt : 'hdf5'
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# Simulation formats. Accepted values
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# are 'hdf5' (default) and 'uvfits'
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outdir : '/path/to/output/'
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# Path to output
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outfile : 'simvis'
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# Outfile prefix. The files will be
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# appended with a number corresponding
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# to the realization and an extension
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# given by outfmt
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outfmt : 'npz'
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# Output format. Accepted values are
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# 'npz' (default) and 'uvfits'.
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# 'npz' will only work if infmt is
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# set to 'hdf5', otherwise will
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# automatically change to 'uvfits'
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######## Telescope information #########
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telescope :
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A_eff : 154
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# Effective area of antenna element
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# in m^2
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eff_Q : 0.89
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# Interferometer efficiency. Value
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# must lie in [0,1]. Default=0.89
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Trx : 50.0
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# Receiver temperature (in K)
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Tant_freqref : 150000000.0
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# Reference frequency (in Hz) for
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# antenna temperature
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Tant_spindex : -2.55
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# Spectral index for antenna
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# temperature
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Tant_ref : 200.0
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# Antenna temperature at reference
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# frequency
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# Tsys = Trx + Tant * (f/f0)^alpha
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Tsys : null
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# System temperature (in K)
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######### Replicate information ############
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replicate :
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# Replication parameters
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n_avg : 1
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# Number of averages in determining
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# final noise RMS that is to be made
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# multiple realizations of. Default=1
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# The original noise RMS will be
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# reduced by a factor sqrt(n_avg)
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n_realize : 1
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# Number of random realizations of
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# noise. Must be greater than 0.
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# Default=1
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seed : 100
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# Use a fixed seed for reproducibility
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# else set it to null and a random
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# seed will be used
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########## Diagnosis parameters ###########
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diagnosis :
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wait_after_run : true
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# If true, keep python shell open
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# after completing the run using
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# set_trace() of python debugger.
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# If false, close python shell
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# and return to command prompt
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# after successful completion

‎prisim/interferometry.py‎

Lines changed: 87 additions & 45 deletions
Original file line numberDiff line numberDiff line change
@@ -8647,46 +8647,57 @@ def write_uvfits(self, outfile, uvfits_parms=None, overwrite=False,
86478647

86488648
Keyword Input(s):
86498649

8650-
uvfits_parms [dictionary] specifies basic parameters required for
8651-
saving in UVFITS format. If set to None (default), the
8652-
data will not be saved in UVFITS format. To save in UVFITS
8653-
format, the following keys and values are required:
8654-
'ref_point' [dictionary] Contains information about the
8655-
reference position to which projected
8656-
baselines and rotated visibilities are to
8657-
be computed. Default=None (no additional
8658-
phasing will be performed). It must be
8659-
contain the following keys with the
8660-
following values:
8661-
'coords' [string] Refers to the
8662-
coordinate system in which value
8663-
in key 'location' is specified
8664-
in. Accepted values are 'radec',
8665-
'hadec', 'altaz' and 'dircos'
8666-
'location' [numpy array] Must be a Mx2 (if
8667-
value in key 'coords' is set to
8668-
'radec', 'hadec', 'altaz' or
8669-
'dircos') or Mx3 (if value in
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key 'coords' is set to
8671-
'dircos'). M can be 1 or equal
8672-
to number of timestamps. If M=1,
8673-
the same reference point in the
8674-
same coordinate system will be
8675-
repeated for all tiemstamps. If
8676-
value under key 'coords' is set
8677-
to 'radec', 'hadec' or 'altaz',
8678-
the value under this key
8679-
'location' must be in units of
8680-
degrees.
8681-
'method' [string] specifies method to be used in
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saving in UVFITS format. Accepted values are
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'uvdata', 'uvfits' or None (default). If set
8684-
to 'uvdata', the UVFITS writer in uvdata
8685-
module is used. If set to 'uvfits', the
8686-
in-house UVFITS writer is used. If set to
8687-
None, first uvdata module will be attempted
8688-
but if it fails then the in-house UVFITS
8689-
writer will be tried.
8650+
uvfits_parms
8651+
[dictionary] specifies basic parameters required for
8652+
saving in UVFITS format. If set to None (default), the
8653+
data will not be saved in UVFITS format. To save in UVFITS
8654+
format, the following keys and values are required:
8655+
'ref_point' [dictionary] Contains information about the
8656+
reference position to which projected
8657+
baselines and rotated visibilities are to
8658+
be computed. Default=None (no additional
8659+
phasing will be performed). It must be
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contain the following keys with the
8661+
following values:
8662+
'coords' [string] Refers to the
8663+
coordinate system in which value
8664+
in key 'location' is specified
8665+
in. Accepted values are 'radec',
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'hadec', 'altaz' and 'dircos'
8667+
'location' [numpy array] Must be a Mx2 (if
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value in key 'coords' is set to
8669+
'radec', 'hadec', 'altaz' or
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'dircos') or Mx3 (if value in
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key 'coords' is set to
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'dircos'). M can be 1 or equal
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to number of timestamps. If M=1,
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the same reference point in the
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same coordinate system will be
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repeated for all tiemstamps. If
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value under key 'coords' is set
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to 'radec', 'hadec' or 'altaz',
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the value under this key
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'location' must be in units of
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degrees.
8682+
'method' [string] specifies method to be used in
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saving in UVFITS format. Accepted values are
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'uvdata', 'uvfits' or None (default). If set
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to 'uvdata', the UVFITS writer in uvdata
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module is used. If set to 'uvfits', the
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in-house UVFITS writer is used. If set to
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None, first uvdata module will be attempted
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but if it fails then the in-house UVFITS
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writer will be tried.
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8692+
'datapool' [NoneType or list] Indicates which portion
8693+
of the data is to be written to the UVFITS
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file. If set to None (default), all of
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skyvis_freq, vis_freq, and vis_noise_freq
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attributes will be written. Otherwise,
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accepted values are a list of strings that
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can include 'noiseless' (skyvis_freq
8699+
attribute), 'noisy' (vis_freq attribute),
8700+
and 'noise' (vis_nosie_freq attribute).
86908701

86918702
overwrite [boolean] True indicates overwrite even if a file already
86928703
exists. Default = False (does not overwrite). Beware this
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87068717
uvfits_parms['ref_point'] = None
87078718
if 'method' not in uvfits_parms:
87088719
uvfits_parms['method'] = None
8709-
dataobj = InterferometerData(self, ref_point=uvfits_parms['ref_point'])
8720+
if 'datapool' not in uvfits_parms:
8721+
uvfits_parms['datapool'] = ['noiseless', 'noisy', 'noise']
8722+
if uvfits_parms['datapool'] is None:
8723+
uvfits_parms['datapool'] = ['noiseless', 'noisy', 'noise']
8724+
if not isinstance(uvfits_parms['datapool'], list):
8725+
raise TypeError('Key datapool in input uvfits_parms must be a list')
8726+
else:
8727+
datapool_list = [dpool.lower() for dpool in uvfits_parms['datapool'] if (isinstance(dpool, str) and dpool.lower() in ['noiseless', 'noise', 'noisy'])]
8728+
if len(datapool_list) == 0:
8729+
raise ValueError('No valid datapool string found in input uvfits_parms')
8730+
uvfits_parms['datapool'] = datapool_list
8731+
8732+
dataobj = InterferometerData(self, ref_point=uvfits_parms['ref_point'], datakeys=uvfits_parms['datapool'])
87108733
for datakey in dataobj.infodict['data_array']:
8711-
dataobj.write(outfile+'-{0}.uvfits'.format(datakey), datatype=datakey, fmt='UVFITS', uvfits_method=uvfits_parms['method'], overwrite=overwrite)
8734+
if dataobj.infodict['data_array'][datakey] is not None:
8735+
dataobj.write(outfile+'-{0}.uvfits'.format(datakey), datatype=datakey, fmt='UVFITS', uvfits_method=uvfits_parms['method'], overwrite=overwrite)
87128736

87138737
#################################################################################
87148738

@@ -9006,7 +9030,7 @@ class InterferometerData(object):
90069030
----------------------------------------------------------------------------
90079031
"""
90089032

9009-
def __init__(self, prisim_object, ref_point=None):
9033+
def __init__(self, prisim_object, ref_point=None, datakeys=None):
90109034

90119035
"""
90129036
------------------------------------------------------------------------
@@ -9041,6 +9065,14 @@ class InterferometerArray used to initialize an
90419065
is set to 'radec', 'hadec' or 'altaz', the
90429066
value under this key 'location' must be in
90439067
units of degrees.
9068+
9069+
datakeys [NoneType or list] Indicates which portion of the data
9070+
is to be written to the UVFITS file. If set to None
9071+
(default), all of skyvis_freq, vis_freq, and
9072+
vis_noise_freq attributes will be written. Otherwise,
9073+
accepted values are a list of strings that can include
9074+
'noiseless' (skyvis_freq attribute), 'noisy' (vis_freq
9075+
attribute), and 'noise' (vis_nosie_freq attribute).
90449076
------------------------------------------------------------------------
90459077
"""
90469078

@@ -9052,8 +9084,18 @@ class InterferometerArray used to initialize an
90529084
prisim_object.rotate_visibilities(ref_point)
90539085
if not isinstance(prisim_object, InterferometerArray):
90549086
raise TypeError('Inout prisim_object must be an instance of class InterferometerArray')
9055-
datatypes = ['noiseless', 'noisy', 'noise']
9056-
visibilities = {key: None for key in datatypes}
9087+
if datakeys is None:
9088+
datakeys = ['noiseless', 'noisy', 'noise']
9089+
if not isinstance(datakeys, list):
9090+
raise TypeError('Input datakeys must be a list')
9091+
else:
9092+
datapool_list = [dpool.lower() for dpool in datakeys if (isinstance(dpool, str) and dpool.lower() in ['noiseless', 'noise', 'noisy'])]
9093+
if len(datapool_list) == 0:
9094+
raise ValueError('No valid datapool string found in input uvfits_parms')
9095+
datakeys = datapool_list
9096+
9097+
# datatypes = ['noiseless', 'noisy', 'noise']
9098+
visibilities = {key: None for key in datakeys}
90579099
for key in visibilities:
90589100
# Conjugate visibilities for compatibility with UVFITS and CASA imager
90599101
if key == 'noiseless':

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