Merge branch 'master' into wsclean_update

Author: Athanaseus

stimela/cargo/base/cubical/Dockerfile

@@ -1,7 +1,8 @@
-FROM stimela/ddfacet:1.7.1
+FROM quay.io/stimela/ddfacet:1.7.1
 RUN apt install -y \
     casacore-data
 RUN . /opt/venv/bin/activate && \
-    python -m pip install 'cubical[lsm-support,degridder-support]==1.6.1' 'scabha==0.3.2'
+    #python -m pip install 'cubical[lsm-support,degridder-support]==1.6.3' 'scabha==0.3.2'
+    python -m pip install git+https://github.com/ratt-ru/CubiCal.git scabha==0.3.2
 RUN DDF.py --help
 RUN gocubical --help

stimela/cargo/cab/casa_bandpass/src/run.py

@@ -20,16 +20,25 @@
 field_ids = numpy.unique(tab.getcol("FIELD_ID"))
 tab.close()
 
-tab = table(gtab+"::FIELD")
-field_names = tab.getcol("NAME")
-tab.close()
-
 field_in = parameters_dict["field"].split(",")
-
 try:
-    ids = list(map(int, field_in))
-except ValueError:
-    ids = list(map(lambda a: field_names.index(a), field_in))
+    tab = table(gtab+"::FIELD")
+    field_names = tab.getcol("NAME")
+    tab.close()
+except RuntimeError:
+    # possible new table format
+    # sadly Field name and Source name columns are empty
+    # will need to figure this out, but ignoring the tests for now
+    tab = table(gtab)
+    field_names = numpy.unique(tab.getcol("FIELD_NAME"))
+    tab.close()
+    pass
+
+if field_names:
+    try:
+        ids = list(map(int, field_in))
+    except ValueError:
+        ids = list(map(lambda a: field_names.index(a), field_in))
+    if not set(ids).issubset(field_ids):
+        raise RuntimeError(f"Some field(s) do not have solutions after the calibration. Please refer to CASA {config.binary} logfile for further details")
 
-if not set(ids).issubset(field_ids):
-    raise RuntimeError(f"Some field(s) do not have solutions after the calibration. Please refer to CASA {config.binary} logfile for further details")

stimela/cargo/cab/cubical/parameters.json

@@ -1,10 +1,10 @@
 {
     "task": "cubical", 
     "base": "stimela/cubical", 
-    "tag": ["1.5.8", "1.7.1", "1.7.2"], 
+    "tag": ["1.5.8", "1.7.1", "1.7.2", "1.7.8-dev"],
     "description": "CubiCal is a suite of fast radio interferometric calibration routines exploiting complex optimisation.", 
     "prefix": "--",
-    "version":["1.5.8", "1.5.11", "1.6.1"],
+    "version":["1.5.8", "1.5.11", "1.6.1", "1.6.3"],
     "binary": "gocubical",
     "junk":["cubical.last", "montblanc.log"],
     "msdir": true, 
@@ -514,11 +514,18 @@
             "info": "Generate summary plots.", 
             "dtype": "bool", 
             "name": "out-plots"
-        },                                                                              {
+        },
+        {
             "info": " If direction-dependent gains are in use and correction is being done, selects direction to correct in. If -1, corrects only for the last direction-independent term. Set to 0 to avoid. ", 
             "dtype": "int", 
             "name": "out-correct-dir"
-        }, 
+        },
+        {
+            "info": "Explicitly enables or disables derotation of output visibilities. Default (None) is to use the –model-pa-rotate and –model-feed-rotate settings", 
+            "dtype": "bool",
+            "name": "out-derotate",
+            "default": null
+        },
         {
             "info": "Number of processes", 
             "dtype": "int", 

stimela/cargo/cab/cubical/src/DefaultParset.cfg

@@ -46,6 +46,10 @@ beam-pattern	= None		    # Apply beams if specified eg. 'beam_$(corr)_$(reim).fi
                                   'beam_$(CORR)_$(REIM).fits'
 beam-l-axis		= None
 beam-m-axis		= None
+pa-rotate       = None         # Apply parallactic angle rotation to model visibilities.
+feed-rotate     = None         # Apply a feed angle rotation to the model visibilities
+null-v          = 0            # Rotate model Stokes V to zero. Special mode for some types of polcal. #options:None|0|1|-1
+                                  Use 1 if the PZD is expected to be from -90 to 90deg, or -1 if >90deg or <-90deg
 
 [montblanc]
 _Help           = Montblanc simulation options 
@@ -231,6 +235,7 @@ subtract-dirs   = :                 # Which model directions to subtract, if gen
 plots           = 1                 # Generate summary plots. Use 'show' to show summary plots interactively.
 casa-gaintables = 1                 # Export gaintables to CASA caltable format. Tables are exported to same
                                     directory as set for cubical databases. #type:bool
+derotate        = None              # Explicitly enables or disables derotation of output visibilities
 
 [log]
 _Help = Options related to logging

stimela/singularity.py

@@ -120,7 +120,7 @@ def run(self, *args, output_wrangler=None):
         self.status = "running"
         self._print("Starting container [{0:s}]. Timeout set to {1:d}. The container ID is printed below.".format(
             self.name, self.time_out))
-        utils.xrun(f"cd {self.execdir} && singularity run --workdir {self.execdir} --containall",
+        utils.xrun(f"cd {self.execdir} && singularity run --userns --workdir {self.execdir} --containall",
 		    list(args) + [volumes, self.image, self.RUNSCRIPT],
                     log=self.logger, timeout=self.time_out, output_wrangler=output_wrangler,
                     env=self._env, logfile=self.logfile)