Cleanup and restructuring of scripts. Implement simulate / image / reduce scripts.

(Pure Python, no CASA dependencies.)

Author: timstaley

setup.py

@@ -14,6 +14,21 @@
     'scipy',
 ]
 
+
+entry_points=('''
+        [console_scripts]
+        fastimg_casa_ms_to_npz=fastimgproto.scripts.casa.ms_to_npz:cli
+        fastimg_casa_compare_imagers=fastimgproto.scripts.casa.compare_imagers:cli
+        fastimg_casa_simulate_vis=fastimgproto.scripts.casa.simulate_vis:cli
+        fastimg_extract_lsm=fastimgproto.scripts.extract_lsm:cli
+        fastimg_image=fastimgproto.scripts.image:cli
+        fastimg_make_config=fastimgproto.scripts.config:make_config
+        fastimg_reduce=fastimgproto.scripts.reduce:cli
+        fastimg_simulate_data=fastimgproto.scripts.simulate_data:cli
+        fastimg_sourcefind=fastimgproto.scripts.sourcefind:cli
+        ''')
+
+
 setup(
     name="fastimgproto",
     version=versioneer.get_version(),
@@ -26,15 +41,5 @@
     author_email="github@timstaley.co.uk",
     # url="https://github.com/",
     install_requires=install_requires,
-    entry_points='''
-        [console_scripts]
-        fastimg_casavis_to_npz=fastimgproto.scripts.casavis_to_npz:cli
-        fastimg_compare_imagers=fastimgproto.scripts.compare_imagers:cli
-        fastimg_extract_lsm=fastimgproto.scripts.extract_lsm:cli
-        fastimg_simpipe=fastimgproto.scripts.simpipe:cli
-        fastimg_simple_imager=fastimgproto.scripts.simple_imager:cli
-        fastimg_simulate_vis_with_casa=fastimgproto.scripts.simulate_vis_with_casa:cli
-        fastimg_simulate_vis=fastimgproto.scripts.simulate_vis:cli
-        fastimg_sourcefind=fastimgproto.scripts.sourcefind:cli
-        ''',
+    entry_points=entry_points,
 )

src/fastimgproto/fixtures/data/simple_vis.npz

@@ -0,0 +1,34 @@
+import json
+
+import click
+
+from collections import OrderedDict
+
+
+class ConfigKeys:
+    """
+    Define the string literals to be used as keys in the JSON config file.
+    """
+    image_size_pix = 'image_size_pix'
+    cell_size_arcsec = 'cell_size_arcsec'
+    sourcefind_detection = 'sourcefind_detection'
+    sourcefind_analysis = 'sourcefind_analysis'
+
+
+default_config_path = 'fastimg_config.json'
+
+
+@click.command()
+@click.argument('config_path', type=click.File(mode='wb'),
+                default=default_config_path)
+def make_config(config_path):
+    """
+    Write out a json file with default fastimg config settings.
+    """
+    default_config = OrderedDict((
+        (ConfigKeys.image_size_pix, 1024),
+        (ConfigKeys.cell_size_arcsec, 1),
+        (ConfigKeys.sourcefind_detection, 50),
+        (ConfigKeys.sourcefind_analysis, 50),
+    ))
+    json.dump(default_config, config_path, indent=2)

src/fastimgproto/scripts/casa/__init__.py

@@ -1,47 +1,26 @@
 #!/usr/bin/env python
 from __future__ import print_function
-import click
+
+import json
 import logging
 import sys
-import json
+
 import astropy.units as u
+import click
 import numpy as np
+
 import fastimgproto.imager as imager
 from fastimgproto.gridder.conv_funcs import GaussianSinc
+from .config import ConfigKeys, default_config_path
 
 
-class ConfigKeys:
-    """
-    Define the string literals to be used as keys in the JSON config file.
-    """
-    image_size_pix = 'image_size_pix'
-    cell_size_arcsec = 'cell_size_arcsec'
-
-def write_config(ctx, param, value):
-    """
-    Used as a Click 'eager callback', to write out a template config-JSON-File.
-    """
-    if not value or ctx.resilient_parsing:
-        return
-    default_config = {
-        ConfigKeys.image_size_pix: 1024,
-        ConfigKeys.cell_size_arcsec: 3,
-    }
-    config_file_path = 'image_config.json'
-    click.echo("Writing config JSON to '{}'".format(config_file_path))
-    with open(config_file_path, 'w') as f:
-        json.dump(default_config,f)
-    ctx.exit()
-
 @click.command()
-@click.option('--makeconfig', is_flag=True, callback=write_config,
-              expose_value=False, is_eager=True,
-              help="Write out config-JSON file and quit")
-@click.argument('config_json', type=click.File(mode='r'))
+@click.option(
+    '-c', '--config_json', type=click.File(mode='r'), default=default_config_path,
+    help="Path to config file. Default:'{}' ".format(default_config_path))
 @click.argument('in_vis', type=click.File(mode='rb'))
 @click.argument('out_img', type=click.File(mode='wb'))
 def cli(config_json, in_vis, out_img):
-    logging.basicConfig(level=logging.DEBUG)
     """
     Load uvw / vis data from npz, produce a dirty image , save in npz format.
 
@@ -50,6 +29,7 @@ def cli(config_json, in_vis, out_img):
     Outputs an npz file containing dirty image and synthesized beam
     (keys 'image', 'beam').
     """
+    logging.basicConfig(level=logging.DEBUG)
     config = json.load(config_json)
     cell_size = config[ConfigKeys.cell_size_arcsec] * u.arcsec
     image_size = config[ConfigKeys.image_size_pix] * u.pix
@@ -62,10 +42,11 @@ def cli(config_json, in_vis, out_img):
     kernel_support = 3
     kernel_func = GaussianSinc(trunc=kernel_support)
     image, beam = imager.image_visibilities(vis, uvw_lambda,
-                              image_size=image_size, cell_size=cell_size,
-                              kernel_func=kernel_func,
-                              kernel_support=kernel_support,
-                              kernel_oversampling=None)
+                                            image_size=image_size,
+                                            cell_size=cell_size,
+                                            kernel_func=kernel_func,
+                                            kernel_support=kernel_support,
+                                            kernel_oversampling=None)
 
     np.savez(out_img, image=image, beam=beam)
     sys.exit(0)

src/fastimgproto/scripts/compare_imagers.py src/fastimgproto/scripts/casa/compare_imagers.py

@@ -0,0 +1,92 @@
+"""
+Simulated pipeline run
+"""
+from __future__ import print_function
+
+import json
+
+import astropy.units as u
+import click
+import numpy as np
+
+import fastimgproto.imager as imager
+from fastimgproto.gridder.conv_funcs import GaussianSinc
+from fastimgproto.sourcefind.image import SourceFindImage
+from .config import (default_config_path, ConfigKeys)
+
+
+# @click.argument(
+#     'output_img', type=click.File(mode='wb'))
+@click.command(context_settings=dict(max_content_width=120))
+@click.option(
+    '-c', '--config_json', type=click.File(mode='r'),
+    default=default_config_path,
+    help="Path to config file. Default: '{}' ".format(default_config_path))
+@click.argument('input_npz', type=click.File(mode='rb'))
+def cli(config_json, input_npz, ):
+    """
+    Load simulated data from INPUT_NPZ, and search for transients as follows:
+
+    \b
+     * Apply difference imaging (subtract model visibilities from data, apply
+       synthesis-imaging).
+     * Run sourcefinding on the resulting diff-image.
+    """
+
+    npz_content = np.load(input_npz)
+    uvw_lambda = npz_content['uvw_lambda']
+    model_vis = npz_content['model']
+    data_vis = npz_content['vis']
+
+    config = json.load(config_json)
+    cell_size = config[ConfigKeys.cell_size_arcsec] * u.arcsec
+    image_size = config[ConfigKeys.image_size_pix] * u.pix
+    detection_n_sigma = config[ConfigKeys.sourcefind_detection]
+    analysis_n_sigma = config[ConfigKeys.sourcefind_analysis]
+
+    sfimage = main(
+        uvw_lambda=uvw_lambda,
+        model_vis=model_vis,
+        data_vis=data_vis,
+        image_size=image_size,
+        cell_size=cell_size,
+        detection_n_sigma=detection_n_sigma,
+        analysis_n_sigma=analysis_n_sigma,
+    )
+
+    print("Found residual sources")
+    for found_src in sfimage.islands:
+        print(found_src)
+
+
+def main(uvw_lambda,
+         model_vis,
+         data_vis,
+         image_size,
+         cell_size,
+         detection_n_sigma,
+         analysis_n_sigma,
+         ):
+    """
+    Represents the difference-image + detect stages of the FastImaging pipeline.
+    """
+
+    # Subtract model-generated visibilities from incoming data
+    residual_vis = data_vis - model_vis
+
+    # Kernel generation - might configure this via config-file in future.
+    kernel_support = 3
+    kernel_func = GaussianSinc(trunc=kernel_support)
+    image, beam = imager.image_visibilities(residual_vis, uvw_lambda,
+                                            image_size=image_size,
+                                            cell_size=cell_size,
+                                            kernel_func=kernel_func,
+                                            kernel_support=kernel_support,
+                                            kernel_oversampling=None)
+
+    sfimage = SourceFindImage(data=np.real(image),
+                              detection_n_sigma=detection_n_sigma,
+                              analysis_n_sigma=analysis_n_sigma,
+                              )
+
+    return sfimage