Merge pull request #432 from SpheMakh/montage_mosaic

Montage mosaic

Author: SpheMakh

stimela/cargo/cab/montage_mosaic/Dockerfile

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+FROM stimela/montage:1.1.3
+MAINTAINER <sphemakh@gmail.com>
+ADD src /scratch/code
+ENV LOGFILE ${OUTPUT}/logfile.txt
+CMD /scratch/code/run.sh

stimela/cargo/cab/montage_mosaic/parameters.json

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+{
+    "task": "montage_mosaic", 
+    "base": "stimela/montage", 
+    "tag": "1.1.3", 
+    "description": "A package that allows continuum (2D) images and spectral (3D) images to be mosaicked together, using montage commands.", 
+    "prefix": "--", 
+    "binary": "montage-mosaic", 
+    "msdir": false, 
+    "parameters": [
+        {
+            "info": "State 'continuum' or 'spectral' as the type of mosaic to be made.", 
+            "name": "mosaic-type", 
+            "default": null, 
+            "dtype": "str", 
+            "required": true
+        }, 
+        {
+            "info": "Include this argument if you wish to use montage for regridding the images and beams (if they have not already been created).", 
+            "name": "domontage", 
+            "default": null, 
+            "dtype": "bool", 
+            "required": false 
+        }, 
+        {
+            "info": "The cutoff in the primary beam to use (assuming a Gaussian at the moment). E.g. The default of 0.1 means going down to the 10 percent level for each pointing.", 
+            "name": "cutoff",
+            "default": 0.1, 
+            "dtype": "float",
+            "required": false 
+        }, 
+        {
+            "info": "The prefix to be used for output files.", 
+            "name": "name",  
+            "default": "mymosaic", 
+            "dtype": "str", 
+            "required": false
+        },  
+        {
+            "info": "The filenames of each target/pointing image to be mosaicked. A suffix of 'image.fits' is expected, and this is replaced by 'pb.fits' in order to locate the corresponding beams (which are also required as input).", 
+            "name": "target-images", 
+            "io": "input", 
+            "default": null, 
+            "dtype": "list:file", 
+            "required": true
+        }
+    ]
+}

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

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+import os
+import sys
+
+sys.path.append('/scratch/stimela')
+import utils
+
+
+CONFIG = os.environ["CONFIG"]
+INPUT = os.environ["INPUT"]
+MSDIR = os.environ["MSDIR"]
+OUTPUT = os.environ["OUTPUT"]
+
+cab = utils.readJson(CONFIG)
+args = []
+targets = None
+for param in cab['parameters']:
+    name = param['name']
+    value = param['value']
+
+    if value is None:
+        continue
+    elif value is False:
+        continue
+    elif value is True:
+        value = ''
+    elif name == 'target-images':
+        targets = value
+        continue
+
+    args += ['{0}{1} {2}'.format(cab['prefix'], name, value)]
+
+indir = os.path.dirname(targets[0])
+target_names = map(os.path.basename, targets)
+target_images = "--target-images " + " --target-images ".join(target_names)
+
+args += ["--input {0:s} {1:s} --output {2:s}".format(indir, target_images,
+    OUTPUT)]
+
+if target_images:
+    utils.xrun(cab['binary'], args)
+else:
+    raise RuntimeError('Filenames of the images to be mosaicked have not been specified.')

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

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