diff --git a/docs/source/calibrator.rst b/docs/source/calibrator.rst
index 05be6471ac60fbfec1a6db3dbdb1b294b9f76a1d..a97b18d77a39399d33c64488a2254c983ef25737 100644
--- a/docs/source/calibrator.rst
+++ b/docs/source/calibrator.rst
@@ -39,7 +39,7 @@ The workflow ``prep`` consists of:
- determining suitable calibrator skymodel (steps ``find_skymodel_cal``, ``make_sourcedb``)
- checking for nearby A-Team sources (step ``check_Ateam_separation``)
- creating a model of A-Team sources to be subtracted (step ``make_sourcedb_ateam``)
- - basic flagging and averaging (subworkflow ``ndppp_prep_cal``)
+ - basic flagging and averaging (subworkflow ``dp3_prep_cal``)
- edges of the band (``flagedge``) -- only used if ``raw_data : true``
- statistical flagging (``aoflag``) -- only used in ``raw_data : true``
- baseline flagging (``flagbaseline``)
@@ -276,7 +276,7 @@ A comprehensive explanation of the baseline selection syntax can be found `here`
**Parameters for pipeline performance**
-- ``max_dppp_threads``: number of threads per process for DP3 (default: 10)
+- ``max_dp3_threads``: number of threads per process for DP3 (default: 10)
- ``memoryperc``: maximum of memory used for aoflagger in raw_flagging mode in percent (default: 20)
- ``aoflag_reorder``: make aoflagger reorder the measurement set before running the detection. This prevents that aoflagger will use its memory reading mode, which is faster but uses more memory (see the `AOFlagger manual`_`)
@@ -294,6 +294,6 @@ A comprehensive explanation of the baseline selection syntax can be found `here`
- ``avg_freqresolution`` : final frequency resolution of the data after averaging (default: 48.82kHz, which translates to 4 channels per subband)
- ``bandpass_freqresolution``: frequency resolution of the bandpass solution table (default: 195.3125kHz, which translates to 1 channel per subband)
-.. _here: https://www.astron.nl/lofarwiki/doku.php?id=public:user_software:documentation:ndppp#description_of_baseline_selection_parameters
+.. _here: https://dp3.readthedocs.io/en/latest/steps/Description%20of%20baseline%20selection%20parameters.html
.. _AOFlagger: https://gitlab.com/aroffringa/aoflagger.git
.. _AOFlagger manual: https://aoflagger.readthedocs.io/en/latest/using_aoflagger.html
\ No newline at end of file
diff --git a/docs/source/changelog.rst b/docs/source/changelog.rst
index 6d6da40bede33e258daa5851e328be5b810e6340..ce3d5a9b7b88fd83d396f7b8731f85a63cd164bd 100644
--- a/docs/source/changelog.rst
+++ b/docs/source/changelog.rst
@@ -36,7 +36,7 @@ Version 2.0
* applying Ionospheric RM corrections
* grouping of subbands by actual frequency
- * speed and disk usage improvements by optimized usage of NDPPP
+ * speed and disk usage improvements by optimized usage of DP3
* (optional) wide-band cleaning in Initial-Subtract
* more diagnostic plots
* documentation moved to GitHib wiki: https://github.com/lofar-astron/prefactor/wiki
diff --git a/docs/source/parset.rst b/docs/source/parset.rst
index 25684225cde07bb8d8a7dc2236ff76afeaecf293..75712bf64f487e76cb7d1bebe1345bb4409d4d63 100644
--- a/docs/source/parset.rst
+++ b/docs/source/parset.rst
@@ -19,16 +19,16 @@ A minimum input file may look like this::
{
"msin": [
- {"class": "Directory", "path": "3C286/L228161_SB000_uv.dppp.MS"},
- {"class": "Directory", "path": "3C286/L228161_SB001_uv.dppp.MS"},
- {"class": "Directory", "path": "3C286/L228161_SB002_uv.dppp.MS"},
- {"class": "Directory", "path": "3C286/L228161_SB003_uv.dppp.MS"},
- {"class": "Directory", "path": "3C286/L228161_SB004_uv.dppp.MS"},
- {"class": "Directory", "path": "3C286/L228161_SB005_uv.dppp.MS"},
- {"class": "Directory", "path": "3C286/L228161_SB006_uv.dppp.MS"},
- {"class": "Directory", "path": "3C286/L228161_SB007_uv.dppp.MS"},
- {"class": "Directory", "path": "3C286/L228161_SB008_uv.dppp.MS"},
- {"class": "Directory", "path": "3C286/L228161_SB009_uv.dppp.MS"}
+ {"class": "Directory", "path": "3C286/L228161_SB000_uv.MS"},
+ {"class": "Directory", "path": "3C286/L228161_SB001_uv.MS"},
+ {"class": "Directory", "path": "3C286/L228161_SB002_uv.MS"},
+ {"class": "Directory", "path": "3C286/L228161_SB003_uv.MS"},
+ {"class": "Directory", "path": "3C286/L228161_SB004_uv.MS"},
+ {"class": "Directory", "path": "3C286/L228161_SB005_uv.MS"},
+ {"class": "Directory", "path": "3C286/L228161_SB006_uv.MS"},
+ {"class": "Directory", "path": "3C286/L228161_SB007_uv.MS"},
+ {"class": "Directory", "path": "3C286/L228161_SB008_uv.MS"},
+ {"class": "Directory", "path": "3C286/L228161_SB009_uv.MS"}
],
}
@@ -36,16 +36,16 @@ There are more parameters you may want to adjust that can be added to this input
{
"msin": [
- {"class": "Directory", "path": "3C286/L228161_SB000_uv.dppp.MS"},
- {"class": "Directory", "path": "3C286/L228161_SB001_uv.dppp.MS"},
- {"class": "Directory", "path": "3C286/L228161_SB002_uv.dppp.MS"},
- {"class": "Directory", "path": "3C286/L228161_SB003_uv.dppp.MS"},
- {"class": "Directory", "path": "3C286/L228161_SB004_uv.dppp.MS"},
- {"class": "Directory", "path": "3C286/L228161_SB005_uv.dppp.MS"},
- {"class": "Directory", "path": "3C286/L228161_SB006_uv.dppp.MS"},
- {"class": "Directory", "path": "3C286/L228161_SB007_uv.dppp.MS"},
- {"class": "Directory", "path": "3C286/L228161_SB008_uv.dppp.MS"},
- {"class": "Directory", "path": "3C286/L228161_SB009_uv.dppp.MS"}
+ {"class": "Directory", "path": "3C286/L228161_SB000_uv.MS"},
+ {"class": "Directory", "path": "3C286/L228161_SB001_uv.MS"},
+ {"class": "Directory", "path": "3C286/L228161_SB002_uv.MS"},
+ {"class": "Directory", "path": "3C286/L228161_SB003_uv.MS"},
+ {"class": "Directory", "path": "3C286/L228161_SB004_uv.MS"},
+ {"class": "Directory", "path": "3C286/L228161_SB005_uv.MS"},
+ {"class": "Directory", "path": "3C286/L228161_SB006_uv.MS"},
+ {"class": "Directory", "path": "3C286/L228161_SB007_uv.MS"},
+ {"class": "Directory", "path": "3C286/L228161_SB008_uv.MS"},
+ {"class": "Directory", "path": "3C286/L228161_SB009_uv.MS"}
],
"refant": "CS00.*",
"flag_baselines": [],
@@ -72,7 +72,7 @@ There are more parameters you may want to adjust that can be added to this input
"ion_3rd": false,
"clock_smooth": true,
"tables2export": "clock",
- "max_dppp_threads": 10,
+ "max_dp3_threads": 10,
"memoryperc": 20,
"min_separation": 30,
"max_separation_arcmin": 1.0,
@@ -90,16 +90,16 @@ If you just want to alter one of the defaults it is sufficient to override it by
{
"msin": [
- {"class": "Directory", "path": "3C286/L228161_SB000_uv.dppp.MS"},
- {"class": "Directory", "path": "3C286/L228161_SB001_uv.dppp.MS"},
- {"class": "Directory", "path": "3C286/L228161_SB002_uv.dppp.MS"},
- {"class": "Directory", "path": "3C286/L228161_SB003_uv.dppp.MS"},
- {"class": "Directory", "path": "3C286/L228161_SB004_uv.dppp.MS"},
- {"class": "Directory", "path": "3C286/L228161_SB005_uv.dppp.MS"},
- {"class": "Directory", "path": "3C286/L228161_SB006_uv.dppp.MS"},
- {"class": "Directory", "path": "3C286/L228161_SB007_uv.dppp.MS"},
- {"class": "Directory", "path": "3C286/L228161_SB008_uv.dppp.MS"},
- {"class": "Directory", "path": "3C286/L228161_SB009_uv.dppp.MS"}
+ {"class": "Directory", "path": "3C286/L228161_SB000_uv.MS"},
+ {"class": "Directory", "path": "3C286/L228161_SB001_uv.MS"},
+ {"class": "Directory", "path": "3C286/L228161_SB002_uv.MS"},
+ {"class": "Directory", "path": "3C286/L228161_SB003_uv.MS"},
+ {"class": "Directory", "path": "3C286/L228161_SB004_uv.MS"},
+ {"class": "Directory", "path": "3C286/L228161_SB005_uv.MS"},
+ {"class": "Directory", "path": "3C286/L228161_SB006_uv.MS"},
+ {"class": "Directory", "path": "3C286/L228161_SB007_uv.MS"},
+ {"class": "Directory", "path": "3C286/L228161_SB008_uv.MS"},
+ {"class": "Directory", "path": "3C286/L228161_SB009_uv.MS"}
],
"demix": true,
}
@@ -108,16 +108,16 @@ If you run the target pipeline you also need to provide the calibrator solution
{
"msin": [
- {"class": "Directory", "path": "?????/L228163_SB000_uv.dppp.MS"},
- {"class": "Directory", "path": "?????/L228163_SB001_uv.dppp.MS"},
- {"class": "Directory", "path": "?????/L228163_SB002_uv.dppp.MS"},
- {"class": "Directory", "path": "?????/L228163_SB003_uv.dppp.MS"},
- {"class": "Directory", "path": "?????/L228163_SB004_uv.dppp.MS"},
- {"class": "Directory", "path": "?????/L228163_SB005_uv.dppp.MS"},
- {"class": "Directory", "path": "?????/L228163_SB006_uv.dppp.MS"},
- {"class": "Directory", "path": "?????/L228163_SB007_uv.dppp.MS"},
- {"class": "Directory", "path": "?????/L228163_SB008_uv.dppp.MS"},
- {"class": "Directory", "path": "?????/L228163_SB009_uv.dppp.MS"}
+ {"class": "Directory", "path": "?????/L228163_SB000_uv.MS"},
+ {"class": "Directory", "path": "?????/L228163_SB001_uv.MS"},
+ {"class": "Directory", "path": "?????/L228163_SB002_uv.MS"},
+ {"class": "Directory", "path": "?????/L228163_SB003_uv.MS"},
+ {"class": "Directory", "path": "?????/L228163_SB004_uv.MS"},
+ {"class": "Directory", "path": "?????/L228163_SB005_uv.MS"},
+ {"class": "Directory", "path": "?????/L228163_SB006_uv.MS"},
+ {"class": "Directory", "path": "?????/L228163_SB007_uv.MS"},
+ {"class": "Directory", "path": "?????/L228163_SB008_uv.MS"},
+ {"class": "Directory", "path": "?????/L228163_SB009_uv.MS"}
],
"cal_solutions": {"class": "File", "path": "cal_solutions.h5"}
}
diff --git a/docs/source/target.rst b/docs/source/target.rst
index 12435a8ccea3bf8de80f7862734c756fe67607f8..d51637e63c2adef2bfd4e515d24f094e81262f11 100644
--- a/docs/source/target.rst
+++ b/docs/source/target.rst
@@ -42,7 +42,7 @@ The workflow ``prep`` consists of:
.. image:: RMextract.png
- - basic flagging, applying solutions, and averaging (subworkflow ``ndppp_prep_target``)
+ - basic flagging, applying solutions, and averaging (subworkflow ``dp3_prep_target``)
- edges of the band (``flagedge``) -- only used if ``raw_data : true``
- statistical flagging (``aoflag``) -- only used in ``raw_data : true``
- baseline flagging (``flagbaseline``)
@@ -302,9 +302,9 @@ A comprehensive explanation of the baseline selection syntax can be found `here`
**Parameters for pipeline performance**
-- ``max_dppp_threads``: number of threads per process for DP3 (default: 10)
+- ``max_dp3_threads``: number of threads per process for DP3 (default: 10)
- ``memoryperc``: maximum of memory used for aoflagger in raw_flagging mode in percent (default: 20)
-- ``aoflag_reorder``: make aoflagger reorder the measurement set before running the detection. This prevents that aoflagger will use its memory reading mode, which is faster but uses more memory (see the `AOFlagger manual`_`)
+- ``aoflag_reorder``: make aoflagger reorder the measurement set before running the detection. This prevents that aoflagger will use its memory reading mode, which is faster but uses more memory (see the `AOFlagger manual`_)
*Skymodel directory*
@@ -342,8 +342,8 @@ If your **LBA** data has **not** been demixed before you may still want to keep
.. _RMextract: https://github.com/lofar-astron/RMextract/
.. _factor: https://github.com/lofar-astron/factor/
.. _killMS: https://github.com/saopicc/killMS/
-.. _TGSS ADR: https://http://tgssadr.strw.leidenuniv.nl/
+.. _TGSS ADR: https://tgssadr.strw.leidenuniv.nl/
.. _Dysco: https://github.com/aroffringa/dysco/
.. _AOFlagger: https://gitlab.com/aroffringa/aoflagger.git
-.. _here: https://www.astron.nl/lofarwiki/doku.php?id=public:user_software:documentation:ndppp#description_of_baseline_selection_parameters
-.. _AOFlagger manual: https://aoflagger.readthedocs.io/en/latest/using_aoflagger.html
\ No newline at end of file
+.. _here: https://dp3.readthedocs.io/en/latest/steps/Description%20of%20baseline%20selection%20parameters.html
+.. _AOFlagger manual: https://aoflagger.readthedocs.io/en/latest/using_aoflagger.html
diff --git a/scripts/sort_times_into_freqGroups.py b/scripts/sort_times_into_freqGroups.py
index 4c401ff53cda51f6eb542bf22c9249aa4d971b51..829792b4342d7ab18f09dd1835603392487fde37 100755
--- a/scripts/sort_times_into_freqGroups.py
+++ b/scripts/sort_times_into_freqGroups.py
@@ -59,7 +59,7 @@ def input2int(invar):
########################################################################
-def main(MSfile, numSB=10, NDPPPfill=True, stepname=None, mergeLastGroup=False, truncateLastSBs=True, firstSB=None):
+def main(MSfile, numSB=10, DP3fill=True, stepname=None, mergeLastGroup=False, truncateLastSBs=True, firstSB=None):
"""
Check a list of MS files for missing frequencies
@@ -71,13 +71,13 @@ def main(MSfile, numSB=10, NDPPPfill=True, stepname=None, mergeLastGroup=False,
How many files should go into one frequency group. Values <= 0 mean put
all files of the same time-step into one group.
default = -1
- NDPPPfill : bool, optional
- Add dummy file-names for missing frequencies, so that NDPPP can
+ DP3fill : bool, optional
+ Add dummy file-names for missing frequencies, so that DP3 can
fill the data with flagged dummy data.
default = True
target_path : str, optional
Change the path of the "groups" files to this. (I.e. write output files
- into this directory with the subsequent NDPPP call.)
+ into this directory with the subsequent DP3 call.)
default = keep path of input files
stepname : str, optional
Add this step-name into the file-names of the output files.
@@ -90,7 +90,7 @@ def main(MSfile, numSB=10, NDPPPfill=True, stepname=None, mergeLastGroup=False,
mergeLastGroup = False, truncateLastSBs = True:
ignore last files, that don't make for a full group (not all files are used).
mergeLastGroup = False, truncateLastSBs = False:
- keep inclomplete last group, or - with NDPPPfill=True - fill
+ keep inclomplete last group, or - with DP3fill=True - fill
last group with dummies.
firstSB : int, optional
If set, then reference the grouping of files to this station-subband. As if a file
@@ -104,7 +104,7 @@ def main(MSfile, numSB=10, NDPPPfill=True, stepname=None, mergeLastGroup=False,
"""
- NDPPPfill = input2bool(NDPPPfill)
+ DP3fill = input2bool(DP3fill)
mergeLastGroup = input2bool(mergeLastGroup)
truncateLastSBs = input2bool(truncateLastSBs)
firstSB = input2int(firstSB)
@@ -197,15 +197,15 @@ def main(MSfile, numSB=10, NDPPPfill=True, stepname=None, mergeLastGroup=False,
# this is the case for concatenating all subbands
groupBW = maxfreq-minfreq
truncateLastSBs = input2bool(False)
- NDPPPfill = input2bool(True)
+ DP3fill = input2bool(True)
freqborders = np.arange(minfreq,maxfreq,groupBW)
if mergeLastGroup:
freqborders[-1] = maxfreq
elif truncateLastSBs:
pass #nothing to do! # left to make the logic more clear!
- elif not truncateLastSBs and NDPPPfill:
+ elif not truncateLastSBs and DP3fill:
freqborders = np.append(freqborders,(freqborders[-1]+groupBW))
- elif not truncateLastSBs and not NDPPPfill:
+ elif not truncateLastSBs and not DP3fill:
freqborders = np.append(freqborders,maxfreq)
freqborders = freqborders[freqborders>(np.min(freqliste)-groupBW)]
@@ -233,7 +233,7 @@ def main(MSfile, numSB=10, NDPPPfill=True, stepname=None, mergeLastGroup=False,
else:
(freq,fname) = (1e12,'This_shouldn\'t_show_up')
skip_this = False
- elif NDPPPfill:
+ elif DP3fill:
files.append('dummy.ms')
if not skip_this:
freqID = int((freqborders[groupIdx]+freqborders[groupIdx+1])/2e6)
@@ -265,8 +265,8 @@ if __name__ == '__main__':
help='One (or more MSs) for which you want to get the antenna list.')
parser.add_argument('--numbands', type=int, default=10,
help='Number of how many files should be grouped together in frequency. (default=10)')
- parser.add_argument('--NDPPPfill', type=bool, default=True,
- help='Add dummy file-names for missing frequencies, so that NDPPP can fill the data with flagged dummy data.')
+ parser.add_argument('--DP3fill', type=bool, default=True,
+ help='Add dummy file-names for missing frequencies, so that DP3 can fill the data with flagged dummy data.')
parser.add_argument('--stepname', type=str, default=None,
help='Add this step-name into the file-names of the output files.')
parser.add_argument('--mergeLastGroup', type=bool, default=False,
@@ -289,4 +289,4 @@ if __name__ == '__main__':
logging.root.addHandler(log)
# first argument: pattern for measurement-sets
- main(args.MSfiles, numSB=args.numbands, NDPPPfill=args.NDPPPfill, stepname=args.stepname, mergeLastGroup=args.mergeLastGroup, truncateLastSBs=args.truncateLastSBs, firstSB=args.firstSB)
+ main(args.MSfiles, numSB=args.numbands, DP3fill=args.DP3fill, stepname=args.stepname, mergeLastGroup=args.mergeLastGroup, truncateLastSBs=args.truncateLastSBs, firstSB=args.firstSB)
diff --git a/skymodels/3C295-sweijen.skymodel b/skymodels/3C295-sweijen.skymodel
index 08177ff6e80d912c21a3c9c51adeb902ef53171e..77ea67fe0e5a792d70d0543e6ad1e7fd3b97b484 100644
--- a/skymodels/3C295-sweijen.skymodel
+++ b/skymodels/3C295-sweijen.skymodel
@@ -2,7 +2,7 @@
# This model of 3C 295 was created by Frits Sweijen.
# A pointed 8 hour synthesis observation was taken early 2019 (surveys setup in terms of subbands) and all available international (DE, FR, IE, UK, PL, SE) stations were present.
-# Selfcal was done using the full bandwidth from about 121 MHz up to 168 MHz, using DPPP and WSClean.
+# Selfcal was done using the full bandwidth from about 121 MHz up to 168 MHz, using DP3 and WSClean.
# WSClean's -spectral-correction option was used to try and keep the model at least somewhat near the Scaife&Heald scale, but no guarantees are given.
# The bandpasses are not perfect yet, but are a lot better compared to the current two-component model.
# If you want to share this model, please ask me first as it is planned to be used in a publication at some point.
diff --git a/steps/LoSoTo.Flag.cwl b/steps/LoSoTo.Flag.cwl
index 0437853669e605a4af64289e3631e3915153c682..988d55a4515263ae7eadbbee06cc1022a63bbc2e 100644
--- a/steps/LoSoTo.Flag.cwl
+++ b/steps/LoSoTo.Flag.cwl
@@ -82,7 +82,7 @@ inputs:
- id: preflagzeros
type: boolean?
doc:
- Flag zeros/ones (bad solutions in BBS/DPPP).
+ Flag zeros/ones (bad solutions in BBS/DP3).
They should be flagged at import time. By default False.
- id: mode
type: string?
diff --git a/steps/dppp_make_parset_cal.cwl b/steps/dp3_make_parset_cal.cwl
similarity index 98%
rename from steps/dppp_make_parset_cal.cwl
rename to steps/dp3_make_parset_cal.cwl
index a5d394199280e016c82c07b7ad2e172a60c84767..4b5ad37c828d9ae53f98381e9cc99f5f60dab82e 100755
--- a/steps/dppp_make_parset_cal.cwl
+++ b/steps/dp3_make_parset_cal.cwl
@@ -60,7 +60,7 @@ outputs:
- id: output
type: File
outputBinding:
- glob: DPPP.parset
+ glob: DP3.parset
baseCommand:
- cp
arguments:
@@ -71,7 +71,7 @@ arguments:
- prefix: ''
shellQuote: false
position: 0
- valueFrom: DPPP.parset
+ valueFrom: DP3.parset
requirements:
- class: InlineJavascriptRequirement
- class: ShellCommandRequirement
diff --git a/steps/dppp_make_parset_target.cwl b/steps/dp3_make_parset_target.cwl
similarity index 99%
rename from steps/dppp_make_parset_target.cwl
rename to steps/dp3_make_parset_target.cwl
index 040c695a818c7a99b2ac34452fa50f5c6d03b736..6d9d93fbff7c1fe738d7f798715e41bb35077e7d 100755
--- a/steps/dppp_make_parset_target.cwl
+++ b/steps/dp3_make_parset_target.cwl
@@ -78,7 +78,7 @@ outputs:
- id: output
type: File
outputBinding:
- glob: DPPP.parset
+ glob: DP3.parset
baseCommand:
- cp
arguments:
@@ -89,7 +89,7 @@ arguments:
- prefix: ''
shellQuote: false
position: 0
- valueFrom: DPPP.parset
+ valueFrom: DP3.parset
requirements:
- class: InlineJavascriptRequirement
- class: ShellCommandRequirement
diff --git a/steps/dppp_prep_cal.cwl b/steps/dp3_prep_cal.cwl
similarity index 97%
rename from steps/dppp_prep_cal.cwl
rename to steps/dp3_prep_cal.cwl
index d574db8d6fdafa02ec5673904acc862af15b1563..dd39c7bb5513fc31ccdeb2cf74f0a9da74281681 100755
--- a/steps/dppp_prep_cal.cwl
+++ b/steps/dp3_prep_cal.cwl
@@ -1,6 +1,6 @@
class: CommandLineTool
cwlVersion: v1.2
-id: dppp
+id: dp3
baseCommand:
- DP3
inputs:
@@ -107,12 +107,12 @@ outputs:
- id: logfile
type: File[]
outputBinding:
- glob: 'DPPP*.log'
+ glob: 'DP3*.log'
hints:
- class: DockerRequirement
dockerPull: astronrd/linc
-stdout: DPPP.log
-stderr: DPPP_err.log
+stdout: DP3.log
+stderr: DP3_err.log
requirements:
- class: InlineJavascriptRequirement
- class: ResourceRequirement
diff --git a/steps/dppp_prep_target.cwl b/steps/dp3_prep_target.cwl
similarity index 98%
rename from steps/dppp_prep_target.cwl
rename to steps/dp3_prep_target.cwl
index 27db45a7dafae6db7184b7c31c5f8698eb2ca75c..567b1106e6b21ec785d29e958c113a90b2dc76c7 100755
--- a/steps/dppp_prep_target.cwl
+++ b/steps/dp3_prep_target.cwl
@@ -1,6 +1,6 @@
class: CommandLineTool
cwlVersion: v1.2
-id: dppp
+id: dp3
baseCommand:
- DP3
inputs:
@@ -163,12 +163,12 @@ outputs:
- id: logfile
type: File[]
outputBinding:
- glob: 'DPPP*.log'
+ glob: 'DP3*.log'
hints:
- class: DockerRequirement
dockerPull: astronrd/linc
-stdout: DPPP.log
-stderr: DPPP_err.log
+stdout: DP3.log
+stderr: DP3_err.log
requirements:
- class: InlineJavascriptRequirement
- class: ResourceRequirement
diff --git a/steps/dpppconcat.cwl b/steps/dp3concat.cwl
similarity index 99%
rename from steps/dpppconcat.cwl
rename to steps/dp3concat.cwl
index 08e3d3f7ba9ac89e2d0b9cdceaba7cdc783dff2b..d66d27f0de49e1c0d0b2251b3b4641ca51fe96fe 100644
--- a/steps/dpppconcat.cwl
+++ b/steps/dp3concat.cwl
@@ -1,6 +1,6 @@
class: CommandLineTool
cwlVersion: v1.2
-id: dpppconcat
+id: dp3concat
baseCommand:
- DP3
inputs:
diff --git a/steps/sort_times_into_freqGroups.cwl b/steps/sort_times_into_freqGroups.cwl
index 94f4a21a3755985a0c48d860b2630adb3fb56df3..a9b2eb530835e9a3e2bcfda08b580e61c787d675 100644
--- a/steps/sort_times_into_freqGroups.cwl
+++ b/steps/sort_times_into_freqGroups.cwl
@@ -14,10 +14,10 @@ inputs:
type: int?
default: 10
doc: Number of how many files should be grouped together in frequency.
- - id: NDPPPfill
+ - id: DP3fill
type: boolean?
default: True
- doc: Add dummy file-names for missing frequencies, so that NDPPP can fill the data with flagged dummy data.
+ doc: Add dummy file-names for missing frequencies, so that DP3 can fill the data with flagged dummy data.
- id: stepname
type: string?
default: '.ms'
@@ -29,11 +29,11 @@ inputs:
- id: mergeLastGroup
type: boolean?
default: False
- doc: Add dummy file-names for missing frequencies, so that NDPPP can fill the data with flagged dummy data.
+ doc: Add dummy file-names for missing frequencies, so that DP3 can fill the data with flagged dummy data.
- id: truncateLastSBs
type: boolean?
default: True
- doc: Add dummy file-names for missing frequencies, so that NDPPP can fill the data with flagged dummy data.
+ doc: Add dummy file-names for missing frequencies, so that DP3 can fill the data with flagged dummy data.
requirements:
- class: InlineJavascriptRequirement
- class: InitialWorkDirRequirement
@@ -49,12 +49,12 @@ requirements:
numbands = inputs['numbands']
stepname = inputs['stepname']
- NDPPPfill = inputs['NDPPPfill']
+ DP3fill = inputs['DP3fill']
mergeLastGroup = inputs['mergeLastGroup']
truncateLastSBs = inputs['truncateLastSBs']
firstSB = inputs['firstSB']
- output = sort_times_into_freqGroups(mss, numbands, NDPPPfill, stepname, mergeLastGroup, truncateLastSBs, firstSB)
+ output = sort_times_into_freqGroups(mss, numbands, DP3fill, stepname, mergeLastGroup, truncateLastSBs, firstSB)
filenames = output['filenames']
groupnames = output['groupnames']
diff --git a/workflows/HBA_calibrator.cwl b/workflows/HBA_calibrator.cwl
index fe9c79980f30d9ee62106a684ec4d8a38f9f1d91..6ac44938f53f8d104d22726e43cb2e665be1be0f 100644
--- a/workflows/HBA_calibrator.cwl
+++ b/workflows/HBA_calibrator.cwl
@@ -86,7 +86,7 @@ inputs:
- id: tables2export
type: string?
default: clock
- - id: max_dppp_threads
+ - id: max_dp3_threads
type: int?
default: 10
- id: memoryperc
@@ -197,8 +197,8 @@ steps:
source: clock_smooth
- id: tables2export
source: tables2export
- - id: max_dppp_threads
- source: max_dppp_threads
+ - id: max_dp3_threads
+ source: max_dp3_threads
- id: memoryperc
source: memoryperc
- id: min_separation
diff --git a/workflows/HBA_target.cwl b/workflows/HBA_target.cwl
index ba9d64d7a6540992ef556b64ec020a84a6fbd4c5..3c439b169d1b044f52ce4983a0bec5379cd9eb09 100644
--- a/workflows/HBA_target.cwl
+++ b/workflows/HBA_target.cwl
@@ -74,7 +74,7 @@ inputs:
- id: updateweights
type: boolean?
default: true
- - id: max_dppp_threads
+ - id: max_dp3_threads
type: int?
default: 10
- id: memoryperc
@@ -221,8 +221,8 @@ steps:
source: demix
- id: updateweights
source: updateweights
- - id: max_dppp_threads
- source: max_dppp_threads
+ - id: max_dp3_threads
+ source: max_dp3_threads
- id: memoryperc
source: memoryperc
- id: min_separation
diff --git a/workflows/LBA_calibrator.cwl b/workflows/LBA_calibrator.cwl
index 1341938ffadbfdfb378f7cfbc4075d95de04561c..ba0bfd5fec9b01bdc33881c584dc65dfd062e996 100644
--- a/workflows/LBA_calibrator.cwl
+++ b/workflows/LBA_calibrator.cwl
@@ -86,7 +86,7 @@ inputs:
- id: tables2export
type: string?
default: phaseOrig
- - id: max_dppp_threads
+ - id: max_dp3_threads
type: int?
default: 10
- id: memoryperc
@@ -195,8 +195,8 @@ steps:
source: clock_smooth
- id: tables2export
source: tables2export
- - id: max_dppp_threads
- source: max_dppp_threads
+ - id: max_dp3_threads
+ source: max_dp3_threads
- id: memoryperc
source: memoryperc
- id: min_separation
diff --git a/workflows/linc_calibrator.cwl b/workflows/linc_calibrator.cwl
index f6ec7a22c2aee8bd09e8ee8b4edf0be066eb9531..6ca990f207c59e88040bc853b1f45af5d923fd04 100644
--- a/workflows/linc_calibrator.cwl
+++ b/workflows/linc_calibrator.cwl
@@ -85,7 +85,7 @@ inputs:
- id: tables2export
type: string?
default: clock
- - id: max_dppp_threads
+ - id: max_dp3_threads
type: int?
default: 10
- id: memoryperc
@@ -178,8 +178,8 @@ steps:
source: flagunconverged
- id: demix
source: demix
- - id: max_dppp_threads
- source: max_dppp_threads
+ - id: max_dp3_threads
+ source: max_dp3_threads
- id: memoryperc
source: memoryperc
- id: flag_baselines
diff --git a/workflows/linc_calibrator/ndppp_prep_cal.cwl b/workflows/linc_calibrator/dp3_prep_cal.cwl
similarity index 93%
rename from workflows/linc_calibrator/ndppp_prep_cal.cwl
rename to workflows/linc_calibrator/dp3_prep_cal.cwl
index 88992a6b0ee24f0553f7ddb8e801027a662b908f..4d95fec0d4354ab9677294a68c99a1265089237a 100644
--- a/workflows/linc_calibrator/ndppp_prep_cal.cwl
+++ b/workflows/linc_calibrator/dp3_prep_cal.cwl
@@ -1,7 +1,7 @@
class: Workflow
cwlVersion: v1.2
-id: ndppp_prep_cal
-label: ndppp_prep_cal
+id: dp3_prep_cal
+label: dp3_prep_cal
inputs:
- id: baselines_to_flag
type: string[]?
@@ -67,7 +67,7 @@ outputs:
type: Directory
- id: logfile
outputSource:
- - concat_logfiles_dppp/output
+ - concat_logfiles_dp3/output
type: File
- id: flagged_fraction_dict
outputSource:
@@ -114,7 +114,7 @@ steps:
source: lbfgs_robustdof
out:
- id: output
- run: ../../steps/dppp_make_parset_cal.cwl
+ run: ../../steps/dp3_make_parset_cal.cwl
label: make_parset
- id: dp3_execute
in:
@@ -143,19 +143,19 @@ steps:
- id: msout
- id: flagged_fraction_dict
- id: logfile
- run: ../../steps/dppp_prep_cal.cwl
+ run: ../../steps/dp3_prep_cal.cwl
label: DP3.Execute
- - id: concat_logfiles_dppp
+ - id: concat_logfiles_dp3
in:
- id: file_list
source:
- dp3_execute/logfile
- id: file_prefix
- default: dppp
+ default: dp3
out:
- id: output
run: ../../steps/concatenate_files.cwl
- label: concat_logfiles_dppp
+ label: concat_logfiles_dp3
requirements:
- class: SubworkflowFeatureRequirement
- class: StepInputExpressionRequirement
diff --git a/workflows/linc_calibrator/prep.cwl b/workflows/linc_calibrator/prep.cwl
index a709288e795edb6cc6a923a11a625009ae351552..0e1fbb0942d0370e6b81d42d65c62af00351807c 100644
--- a/workflows/linc_calibrator/prep.cwl
+++ b/workflows/linc_calibrator/prep.cwl
@@ -19,7 +19,7 @@ inputs:
default: false
- id: demix
type: boolean?
- - id: max_dppp_threads
+ - id: max_dp3_threads
type: int?
default: 10
- id: memoryperc
@@ -111,7 +111,7 @@ outputs:
type: string[]
- id: flagged_fraction_dict
outputSource:
- - ndppp_prep_cal/flagged_fraction_dict
+ - dp3_prep_cal/flagged_fraction_dict
type: string[]
- id: logfiles
outputSource:
@@ -136,7 +136,7 @@ steps:
- id: output
run: ../../steps/selectfirstdirectory.cwl
label: select_only_first
- - id: ndppp_prep_cal
+ - id: dp3_prep_cal
in:
- id: baselines_to_flag
default: []
@@ -180,7 +180,7 @@ steps:
source: find_skymodel_cal/model_name
- id: ntimechunk
default: 10
- source: max_dppp_threads
+ source: max_dp3_threads
- id: subtract_sources
source: check_demix/out_demix_sources
- id: lbfgs_historysize
@@ -191,8 +191,8 @@ steps:
- id: msout
- id: flagged_fraction_dict
- id: logfile
- run: ./ndppp_prep_cal.cwl
- label: ndppp_prep_cal
+ run: ./dp3_prep_cal.cwl
+ label: dp3_prep_cal
scatter:
- msin
- id: predict_calibrate
@@ -224,7 +224,7 @@ steps:
in:
- id: msin
linkMerge: merge_flattened
- source: ndppp_prep_cal/msout
+ source: dp3_prep_cal/msout
- id: verbose
default: true
- id: concatenate-frequency
@@ -300,9 +300,9 @@ steps:
- id: file_list
linkMerge: merge_flattened
source:
- - ndppp_prep_cal/logfile
+ - dp3_prep_cal/logfile
- id: file_prefix
- default: ndppp_prep_cal
+ default: dp3_prep_cal
out:
- id: output
run: ../../steps/concatenate_files.cwl
diff --git a/workflows/linc_target.cwl b/workflows/linc_target.cwl
index c1f5d5b8b7bbc5afb90a5626f39acae21f51b733..46cef17ba633ee645282614a69c46de0f52e9491 100644
--- a/workflows/linc_target.cwl
+++ b/workflows/linc_target.cwl
@@ -74,7 +74,7 @@ inputs:
- id: updateweights
type: boolean?
default: true
- - id: max_dppp_threads
+ - id: max_dp3_threads
type: int?
default: 10
- id: memoryperc
@@ -229,8 +229,8 @@ steps:
source: apply_beam
- id: updateweights
source: updateweights
- - id: max_dppp_threads
- source: max_dppp_threads
+ - id: max_dp3_threads
+ source: max_dp3_threads
- id: memoryperc
source: memoryperc
- id: min_separation
diff --git a/workflows/linc_target/concat.cwl b/workflows/linc_target/concat.cwl
index bbae3ea8a0f4ec1827782c0a06d4791f2b630050..1ae800b7ae1c1f6def03b0f92d58654748bc3ea2 100644
--- a/workflows/linc_target/concat.cwl
+++ b/workflows/linc_target/concat.cwl
@@ -21,15 +21,15 @@ inputs:
outputs:
- id: flagged_fraction_dict
outputSource:
- - dpppconcat/flagged_fraction_dict
+ - dp3concat/flagged_fraction_dict
type: string
- id: msout
outputSource:
- - dpppconcat/msout
+ - dp3concat/msout
type: Directory
- - id: dpppconcat.log
+ - id: dp3concat.log
outputSource:
- - concat_logfiles_dpppconcat/output
+ - concat_logfiles_dp3concat/output
type: File
steps:
- id: filter_ms_group
@@ -46,7 +46,7 @@ steps:
- id: selected_ms
run: ../../steps/filter_ms_group.cwl
label: filter_ms_group
- - id: dpppconcat
+ - id: dp3concat
in:
- id: msin
source:
@@ -81,18 +81,18 @@ steps:
- id: msout
- id: flagged_fraction_dict
- id: logfile
- run: ../../steps/dpppconcat.cwl
- label: dpppconcat
- - id: concat_logfiles_dpppconcat
+ run: ../../steps/dp3concat.cwl
+ label: dp3concat
+ - id: concat_logfiles_dp3concat
in:
- id: file_list
source:
- - dpppconcat/logfile
+ - dp3concat/logfile
- id: file_prefix
- default: dpppconcat
+ default: dp3concat
out:
- id: output
run: ../../steps/concatenate_files.cwl
- label: concat_logfiles_dpppconcat
+ label: concat_logfiles_dp3concat
requirements: []
diff --git a/workflows/linc_target/ndppp_prep_targ.cwl b/workflows/linc_target/dp3_prep_targ.cwl
similarity index 96%
rename from workflows/linc_target/ndppp_prep_targ.cwl
rename to workflows/linc_target/dp3_prep_targ.cwl
index 46168a249cbe76807fe7746d2b05ecf689c959b3..f56a63edde2ec9a174c76c93ae09c81251832804 100644
--- a/workflows/linc_target/ndppp_prep_targ.cwl
+++ b/workflows/linc_target/dp3_prep_targ.cwl
@@ -1,7 +1,7 @@
class: Workflow
cwlVersion: v1.2
-id: ndppp_prep_targ
-label: ndppp_prep_targ
+id: dp3_prep_targ
+label: dp3_prep_targ
inputs:
- id: baselines_to_flag
type: string[]?
@@ -101,7 +101,7 @@ outputs:
type: string
- id: prep_logfile
outputSource:
- - concat_logfiles_dppp/output
+ - concat_logfiles_dp3/output
type: File
- id: predict_logfile
outputSource:
@@ -177,19 +177,19 @@ steps:
source: lbfgs_robustdof
out:
- id: output
- run: ../../steps/dppp_make_parset_target.cwl
+ run: ../../steps/dp3_make_parset_target.cwl
label: make_parset
- - id: concat_logfiles_dppp
+ - id: concat_logfiles_dp3
in:
- id: file_list
source:
- dp3_execute/logfile
- id: file_prefix
- default: dppp
+ default: dp3
out:
- id: output
run: ../../steps/concatenate_files.cwl
- label: concat_logfiles_dppp
+ label: concat_logfiles_dp3
- id: concat_logfiles_predict
in:
- id: file_list
@@ -250,7 +250,7 @@ steps:
- id: flagged_fraction_dict_initial
- id: flagged_fraction_dict_prep
- id: logfile
- run: ../../steps/dppp_prep_target.cwl
+ run: ../../steps/dp3_prep_target.cwl
label: DP3.Execute
- id: predict
in:
diff --git a/workflows/linc_target/gsmcal.cwl b/workflows/linc_target/gsmcal.cwl
index f3b6b3474dcf3af54fdbaddb82f3cc35632ee901..5c66cd5f3871de87ded976778097cb341b3db968 100644
--- a/workflows/linc_target/gsmcal.cwl
+++ b/workflows/linc_target/gsmcal.cwl
@@ -83,7 +83,7 @@ outputs:
- concat_logfiles_RefAnt/output
- sort_times_into_freqGroups/logfile
- concat_logfiles_calib/output
- - concat_logfiles_dpppconcat/output
+ - concat_logfiles_dp3concat/output
- concat_logfiles_blsmooth/output
- concat_logfiles_unflagged/output
- aoflag/logfile
@@ -153,10 +153,10 @@ steps:
- msin
- id: numbands
source: num_SBs_per_group
- - id: NDPPPfill
+ - id: DP3fill
default: true
- id: stepname
- default: .dpppconcat
+ default: .dp3concat
- id: firstSB
source: reference_stationSB
- id: truncateLastSBs
@@ -168,17 +168,17 @@ steps:
- id: logfile
run: ../../steps/sort_times_into_freqGroups.cwl
label: sorttimesintofreqGroups
- - id: concat_logfiles_dpppconcat
+ - id: concat_logfiles_dp3concat
in:
- id: file_list
source:
- - concat/dpppconcat.log
+ - concat/dp3concat.log
- id: file_prefix
- default: dpppconcat
+ default: dp3concat
out:
- id: output
run: ../../steps/concatenate_files.cwl
- label: concat_logfiles_dpppconcat
+ label: concat_logfiles_dp3concat
- id: concat_logfiles_blsmooth
in:
- id: file_list
@@ -273,7 +273,7 @@ steps:
out:
- id: msout
- id: flagged_fraction_dict
- - id: dpppconcat.log
+ - id: dp3concat.log
run: ./concat.cwl
label: concat
scatter:
diff --git a/workflows/linc_target/prep.cwl b/workflows/linc_target/prep.cwl
index 19de109e6491e8dd9219d17cf5fb5b3071dbc1d9..6d7c9da0122c1dd78b2072d1bc71420b0b8e32e5 100644
--- a/workflows/linc_target/prep.cwl
+++ b/workflows/linc_target/prep.cwl
@@ -62,7 +62,7 @@ inputs:
- id: updateweights
type: boolean?
default: true
- - id: max_dppp_threads
+ - id: max_dp3_threads
type: int?
default: 10
- id: memoryperc
@@ -142,7 +142,7 @@ outputs:
pickValue: all_non_null
- id: msout
outputSource:
- - dppp_prep_target/msout
+ - dp3_prep_target/msout
type: Directory[]
- id: check_Ateam_separation.json
outputSource:
@@ -212,7 +212,7 @@ steps:
in:
- id: flagged_fraction_dict
source:
- - dppp_prep_target/initial_flags_out
+ - dp3_prep_target/initial_flags_out
- id: filter_station
default: ''
- id: state
@@ -226,7 +226,7 @@ steps:
in:
- id: flagged_fraction_dict
source:
- - dppp_prep_target/prep_flags_out
+ - dp3_prep_target/prep_flags_out
- id: filter_station
default: ''
- id: state
@@ -331,7 +331,7 @@ steps:
- id: parset
run: ../../steps/LoSoTo.Plot.cwl
label: losoto_plot_RM
- - id: dppp_prep_target
+ - id: dp3_prep_target
in:
- id: baselines_to_flag
source:
@@ -363,7 +363,7 @@ steps:
- id: process_baselines_target
source: process_baselines_target
- id: ntimechunk
- source: max_dppp_threads
+ source: max_dp3_threads
- id: subtract_sources
source: check_demix/out_demix_sources
- id: parmdb
@@ -400,8 +400,8 @@ steps:
- id: clipper_logfile
- id: msout
- id: clipper_output
- run: ./ndppp_prep_targ.cwl
- label: ndppp_prep_target
+ run: ./dp3_prep_targ.cwl
+ label: dp3_prep_target
scatter:
- msin
- id: plot_Ateamclipper
@@ -420,7 +420,7 @@ steps:
- id: file_list
linkMerge: merge_flattened
source:
- - dppp_prep_target/clipper_output
+ - dp3_prep_target/clipper_output
- id: file_prefix
default: Ateamclipper
- id: file_suffix
@@ -437,9 +437,9 @@ steps:
- id: file_list
linkMerge: merge_flattened
source:
- - dppp_prep_target/prep_logfile
+ - dp3_prep_target/prep_logfile
- id: file_prefix
- default: ndppp_prep_targ
+ default: dp3_prep_targ
out:
- id: output
run: ../../steps/concatenate_files.cwl
@@ -449,7 +449,7 @@ steps:
- id: file_list
linkMerge: merge_flattened
source:
- - dppp_prep_target/predict_logfile
+ - dp3_prep_target/predict_logfile
- id: file_prefix
default: predict_targ
- id: execute
@@ -464,7 +464,7 @@ steps:
- id: file_list
linkMerge: merge_flattened
source:
- - dppp_prep_target/clipper_logfile
+ - dp3_prep_target/clipper_logfile
pickValue: all_non_null
- id: file_prefix
default: Ateamclipper