Merge pull request #596 from Mulan-94/update_ragavi

Update ragavi parameter files
ratt-ru · May 6, 2020 · 4b8b25e · 4b8b25e
2 parents 19d0f4e + e9c0292
commit 4b8b25e
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Showing 6 changed files with 41 additions and 22 deletions.
diff --git a/stimela/cargo/base/ragavi/Dockerfile b/stimela/cargo/base/ragavi/Dockerfile
@@ -1,10 +1,7 @@
 FROM stimela/meqtrees:1.2.0
 RUN docker-apt-install curl
-RUN curl -sL https://deb.nodesource.com/setup_8.x | bash -
+RUN curl -sL https://deb.nodesource.com/setup_10.x | bash -
 RUN docker-apt-install nodejs python3-pip
-RUN add-apt-repository ppa:git-core/ppa
 RUN apt-get update
-RUN apt-get install -y git
 RUN pip3 install -U pip setuptools
-RUN pip3 install ragavi
-RUN pip3 install git+git://github.com/ska-sa/xova.git@master
+RUN pip3 install ragavi
diff --git a/stimela/cargo/cab/ragavi/Dockerfile b/stimela/cargo/cab/ragavi/Dockerfile
@@ -1,4 +1,4 @@
-FROM stimela/ragavi:1.2.6
+FROM stimela/ragavi:1.4.4
 MAINTAINER <[email protected]>
 ADD src /scratch/code
 ENV LOGFILE ${OUTPUT}/logfile.txt

diff --git a/stimela/cargo/cab/ragavi/parameters.json b/stimela/cargo/cab/ragavi/parameters.json
@@ -1,7 +1,7 @@
 {
     "task": "ragavi",
     "base": "stimela/ragavi",
-    "tag": "1.2.6",
+    "tag": "1.4.4",
     "description": "Radio Astronomy Gain and Visibility Inspector",
     "prefix": "--",
     "binary": "ragavi-gains",
@@ -73,7 +73,7 @@
             "name": "field"
         },
         {
-            "info": "Output HTML file name",
+            "info": "Output HTML file name (without .html suffix)",
             "dtype": "str",
             "required": false,
             "name": "htmlname",

diff --git a/stimela/cargo/cab/ragavi_vis/Dockerfile b/stimela/cargo/cab/ragavi_vis/Dockerfile
@@ -1,4 +1,4 @@
-FROM stimela/ragavi:1.2.6
+FROM stimela/ragavi:1.4.4
 MAINTAINER <[email protected]>
 ADD src /scratch/code
 ENV LOGFILE ${OUTPUT}/logfile.txt

diff --git a/stimela/cargo/cab/ragavi_vis/parameters.json b/stimela/cargo/cab/ragavi_vis/parameters.json
@@ -1,7 +1,7 @@
 {
     "task": "ragavi",
     "base": "stimela/ragavi",
-    "tag": "1.2.6",
+    "tag": "1.4.4",
     "description": "Radio Astronomy Gain and Visibility Inspector",
     "prefix": "--",
     "binary": "ragavi-vis",
@@ -25,17 +25,16 @@
             "choices": [
                 "antenna1", 
                 "antenna2", 
-                "baseline",
+                "amplitude",
                 "channel",
-                "corr", 
-                "field", 
                 "frequency",
+                "imaginary",
                 "phase",
                 "real",
                 "scan", 
                 "time",
                 "uvdist",
-                "uvwave"
+                "uvwave",
                 ]
         },
         {
@@ -48,7 +47,7 @@
                 "amplitude", 
                 "imaginary", 
                 "phase",
-                "real"
+                "real",
                 ]
         },
         {
@@ -72,6 +71,13 @@
             "name": "cbin",
             "default": null
         },
+        {
+            "info": "Select baselines where ANTENNA1 corresponds to the supplied antenna(s)",
+            "dtype": "str",
+            "required": false,
+            "name": "ant",
+            "default": null
+        },
         {
             "info": "Channels to select. Defaults to all.",
             "dtype": "str",
@@ -109,6 +115,13 @@
                 "spw"
                 ]
         },
+        {
+            "info": "Number columns in grid if iteration is active",
+            "dtype": "int",
+            "required": false,
+            "name": "cols",
+            "default": 5
+        },
         {
             "info": "Correlation index or subset to plot. Can be specified using normal python slicing syntax. Defaults to all.",
             "dtype": "str",
@@ -138,7 +151,7 @@
             "default": null
         },
         {
-            "info": "Output HTML file name",
+            "info": "Output HTML file name (without .html suffix)",
             "dtype": "str",
             "required": false,
             "name": "htmlname",
@@ -152,6 +165,7 @@
             "name": "iter-axis",
             "default": null,
             "choices": [
+                "antenna",
                 "antenna1", 
                 "antenna2", 
                 "baseline",

diff --git a/stimela/main.py b/stimela/main.py
@@ -21,7 +21,9 @@
 
 loglevels = "info debug error"
 
+
 class MultilineFormatter(argparse.HelpFormatter):
+
     def _fill_text(self, text, width, indent):
         text = self._whitespace_matcher.sub(' ', text).strip()
         paragraphs = text.split('|n ')
@@ -32,11 +34,12 @@ def _fill_text(self, text, width, indent):
             multiline_text = multiline_text + formatted_paragraph
         return multiline_text
 
+
 def build(argv):
     for i, arg in enumerate(argv):
         if (arg[0] == '-') and arg[1].isdigit():
             argv = ' ' + arg
-    
+
     parser = ArgumentParser(description='Build executor (a.k.a cab) images')
     parser.add_argument("-b", "--base", action="store_true",
                         help="Build base images")
@@ -335,9 +338,11 @@ def pull(argv):
     args.image = images_ or args.image
     if args.image:
         for image in args.image:
-            simage = image.replace("/", "_")
-            simage = simage.replace(":", "_") + singularity.suffix
             if args.singularity:
+                simage = image.replace("/", "_")
+                if not hasattr(singularity, "suffix"):
+                    raise SystemExit("Cannot find singularity on this system")
+                simage = simage.replace(":", "_") + singularity.suffix
                 singularity.pull(
                     image, simage, directory=pull_folder, force=args.force)
             elif args.docker:
@@ -361,6 +366,8 @@ def pull(argv):
         for image in base:
             if args.singularity:
                 simage = image.replace("/", "_")
+                if not hasattr(singularity, "suffix"):
+                    raise SystemExit("Cannot find singularity on this system")
                 simage = simage.replace(":", "_") + singularity.suffix
                 singularity.pull(
                     image, simage, directory=pull_folder, force=args.force)
@@ -549,7 +556,8 @@ def clean(argv):
                 status = "no there"
 
             if status == 'running':
-                # Kill the container instead of stopping it, so that effect can be felt py parent process
+                # Kill the container instead of stopping it, so that effect can
+                # be felt py parent process
                 utils.xrun('docker', ['kill', container])
                 cont.remove()
             elif status in ['exited', 'dead']:
@@ -595,8 +603,8 @@ def main(argv):
             command = cmd
 
             index = argv.index(cmd)
-            options = argv[index+1:]
-            argv = argv[:index+1]
+            options = argv[index + 1:]
+            argv = argv[:index + 1]
 
     args = parser.parse_args(argv)