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SpheMakhSpheMakh
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Merge pull request #477 from shilparanchod/shadems
add shadems
2 parents 12a80ae + 9c45fe0 commit 0c08169

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‎stimela/cargo/base/shadems/Dockerfile‎

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FROM stimela/meqtrees:1.2.3
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RUN pip install git+https://github.com/IanHeywood/shadeMS

‎stimela/cargo/cab/shadems/Dockerfile‎

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FROM stimela/shadems:1.2.3
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MAINTAINER <sphemakh@gmial.com>
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ADD src /scratch/code
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ENV LOGFILE ${OUTPUT}/logfile.txt
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CMD /scratch/code/run.sh

‎stimela/cargo/cab/shadems/parameters.json‎

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{
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"task": "shadems",
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"base": "stimela/shadems",
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"tag": "1.2.3",
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"description": "Rapid Measurement Set plotting with xarray-ms and datashader.",
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"prefix": "--",
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"binary": "shadems",
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"msdir": true,
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"parameters": [
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{
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"info": "Measurement set",
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"name": "ms",
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"io": "msfile",
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"default": null,
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"dtype": "file",
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"required": true
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},
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{
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"info": "X axis: [t]ime (default), [f]requency, [c]hannels, [u], [uv]distance, [r]eal, [a]mplitude",
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"dtype": "str",
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"default": "t",
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"name": "xaxis",
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"choices": ["t","f","c","u","uv","r","a"]
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},
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{
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"info": "Y axis: [a]mplitude (default), [p]hase, [r]eal, [i]maginary, [v]",
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"dtype": "str",
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"default": "a",
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"name": "yaxis",
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"choices": ["a","p","r","i","v"]
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},
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{
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"info": "Measurement Set column to plot (default = DATA)",
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"dtype": "str",
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"default": "DATA",
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"name": "col"
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},
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{
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"info": "Field ID(s) to plot (comma separated list, default = all)",
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"dtype": "list:str",
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"default": "all",
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"name": "field"
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},
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{
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"info": "Spectral windows (DDIDs) to plot (comma separated list, default = all)",
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"dtype": "str",
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"default": "all",
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"name": "spws"
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},
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{
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"info": "Correlation index to plot (default = 0)",
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"dtype": "int",
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"default": 0,
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"name": "corr"
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},
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{
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"info": "Plot flagged data (default = False)",
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"dtype": "bool",
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"default": false,
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"name": "noflags"
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},
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{
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"info": "Do not show conjugate points in u,v plots (default = plot conjugates)",
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"dtype": "bool",
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"default": false,
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"name": "noconj"
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},
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{
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"info": "Minimum x-axis value (default = data min)",
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"dtype": "str",
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"default": null,
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"name": "xmin"
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},
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{
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"info": "Maximum x-axis value (default = data max)",
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"dtype": "str",
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"default": null,
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"name": "xmax"
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},
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{
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"info": "Minimum y-axis value (default = data min)",
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"dtype": "str",
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"default": null,
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"name": "ymin"
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},
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{
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"info": "Maximum y-axis value (default = data ymax)",
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"dtype": "str",
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"default": null,
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"name": "ymax"
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},
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{
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"info": "Canvas x-size in pixels (default = 1280)",
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"dtype": "int",
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"default": 1280,
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"name": "xcanvas"
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},
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{
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"info": "Canvas y-size in pixels (default = 800)",
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"dtype": "int",
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"default": 800,
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"name": "ycanvas"
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},
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{
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"info": "Pixel scale normalization: eq_hist (default), cbrt, log, linear",
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"dtype": "str",
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"default": "eq_hist",
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"name": "norm"
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},
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{
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"info": "Colorcet map to use (default = bkr)",
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"dtype": "str",
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"default": "bkr",
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"name": "cmap"
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},
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{
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"info": "RGB hex code for background colour (default = FFFFFF)",
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"dtype": "str",
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"default": "FFFFFF",
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"name": "bgcol"
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},
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{
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"info": "Font size for all text elements (default = 20)",
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"dtype": "float",
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"default": 20,
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"name": "fontsize"
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},
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{
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"info": "PNG name (default = something verbose)",
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"dtype": "str",
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"io": "output",
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"default": null,
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"name": "png"
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},
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{
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"info": "Add timestamp to default PNG name",
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"dtype": "bool",
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"default": false,
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"name": "stamp"
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}
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]
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}

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

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import os
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import sys
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sys.path.append('/scratch/stimela')
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utils = __import__('utils')
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CONFIG = os.environ["CONFIG"]
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INPUT = os.environ["INPUT"]
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MSDIR = os.environ["MSDIR"]
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cab = utils.readJson(CONFIG)
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args = []
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for param in cab['parameters']:
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name = param['name']
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value = param['value']
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if value is None:
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continue
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elif value is False:
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continue
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if isinstance(value, list):
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val = map(str, value)
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args += ['{0}{1} {2}'.format(cab['prefix'], name, " ".join(val))]
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continue
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args += ['{0}{1} {2}'.format(cab['prefix'], name, value)]
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utils.xrun(cab['binary'], args)

‎stimela/cargo/cab/shadems/src/run.sh‎

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#!/usr/bin/env bash
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python /scratch/code/run.py 2>&1 | tee -a $LOGFILE
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(exit ${PIPESTATUS[0]})

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