Merge pull request #65 from Athanaseus/region_stats

Region stats

.github/workflows/test_installation.yml

@@ -9,35 +9,55 @@ on:
  pull_request:
  branches: [ master ]
 
+env:
+ POETRY_VERSION: 1.4.0
+
 jobs:
- build:
+ test:
  runs-on: ${{ matrix.os }}
  strategy:
+ fail-fast: false
  matrix:
  os: [ ubuntu-20.04, ubuntu-22.04 ]
- python-version: [3.8, 3.9]
-
+ python-version: ["3.8", "3.9", "3.10"]
  steps:
- - uses: actions/checkout@v3
- - name: Set up Python ${{ matrix.python-version }}
- uses: actions/setup-python@v1
- with:
- python-version: ${{ matrix.python-version }}
- - name: Install dependencies
- run: |
- python -m pip install --upgrade pip
- pip install --upgrade setuptools wheel
- pip install flake8 pytest
- pip install .
- - name: Lint with flake8
- run: |
- # stop the build if there are Python syntax errors or undefined names
- flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
- # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
- flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
- - name: Test with pytest
- run: |
- pytest -s -vvv
- - name: Test command
- run: |
- aimfast -h
+ - name: Set up Python ${{ matrix.python-version }}
+ uses: actions/setup-python@v4
+ with:
+ python-version: ${{ matrix.python-version }}
+
+ - name: Cache Installations
+ id: cache-installs
+ uses: actions/cache@v3
+ with:
+ path: ~/.local
+ key: install-${{ env.INSTALL_CACHE_HASH }}-3
+
+ - name: Install Poetry
+ if: steps.cache-installs.outputs.cache-hit != 'true'
+ run: |
+ curl -sSL https://install.python-poetry.org | python3 - --version ${{ env.POETRY_VERSION }}
+
+ - name: Test poetry
+ run: poetry --version
+
+ - name: Checkout source
+ uses: actions/checkout@v2
+ with:
+ fetch-depth: 1
+
+ - name: Install aimfast
+ run: poetry install --extras "source_finders" --with tests
+
+ - name: Lint with flake8
+ run: |
+ # stop the build if there are Python syntax errors or undefined names
+ poetry run flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+ # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+ poetry run flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+
+ - name: Test command
+ run: poetry run aimfast -h
+
+ - name: Run testsuite
+ run: poetry run py.test -vvv aimfast/

aimfast/aimfast.py

@@ -10,6 +10,7 @@
 import tempfile
 import numpy as np
 
+from regions import Regions
 from functools import partial
 from collections import OrderedDict
 
@@ -527,6 +528,43 @@ def image_stats(image_data, test_normality=None, data_range=None):
  return img_stats
 
 
+def fix_wcs_fits(wcs, dropaxis=2):
+ """This removes the degenerated dimensions in APLpy 2.X...
+ The input must be the object returned by aplpy.FITSFigure().
+ `dropaxis` is the index where to start dropping the axis (by default it assumes the 3rd,4th place).
+ """
+ temp_wcs = wcs.dropaxis(dropaxis)
+ temp_wcs = temp_wcs.dropaxis(dropaxis)
+ return temp_wcs
+
+
+def get_region_stats(fitsname, regions_file):
+ """Extract flux densities measurements within the provided region"""
+ regions_stats = dict()
+ LOGGER.info(f'Reading region file: {regions_file}')
+ regions_list = Regions.read(regions_file, format='ds9')
+ LOGGER.info(f'Number of regions: {len(regions_list)}')
+ image = fitsio.open(fitsname)
+ image_data = image[0].data
+ fitsinfo = fitsInfo(fitsname)
+ wcs = fitsinfo['wcs']
+ beam = fitsinfo['b_size']
+ dra = fitsinfo['dra']
+ beam_area = (beam[0]*beam[1])/(dra*dra)
+ for i, input_region in enumerate(regions_list):
+ if hasattr(input_region, 'to_pixel'):
+ input_region = input_region.to_pixel(fix_wcs_fits(wcs))
+ mask = input_region.to_mask().to_image(image_data.shape[-2:])
+ data = mask * image_data[0][0]
+ #nndata=nndata[~np.isnan(data)]
+ nndata = np.flip(data, axis=0)
+ nndata = nndata[~np.isnan(nndata)]
+ nndata = nndata[nndata != -0.0]
+ stats = image_stats(nndata)
+ regions_stats[f'region-{i}'] = stats
+ return regions_stats
+
+
 def normality_testing(data, test_normality='normaltest', data_range=None):
  """Performs a normality test on the image data.
 
@@ -2955,6 +2993,8 @@ def get_argparser():
  help='Name of the mask image fits file')
  argument('-fdr', '--fidelity-results', dest='json',
  help='aimfast fidelity results file (JSON format)')
+ argument('-reg', '--input-regions', dest='reg',
+ help='Region file with regions to generate stats)')
  # Source finding
  argument('-c', '--config', dest='config',
  help='Config file to run source finder of choice (YAML format)')
@@ -3178,7 +3218,7 @@ def main():
  'DR_global_rms' : DR['global_rms'],
  'DR_local_rms' : DR['local_rms']}})
  output_dict[residual_label] = stats
- elif args.residual:
+ elif args.residual and not args.reg:
  if args.residual not in output_dict.keys():
  if args.test_normality in ['shapiro', 'normaltest']:
  stats = residual_image_stats(args.residual,
@@ -3426,6 +3466,10 @@ def main():
  LOGGER.error(f"{R}Provide Centre coordinates in pixels "
  f"and size of subimage(s).{W}")
 
+ if args.reg:
+ centre_coords = []
+ stats = get_region_stats(args.residual, args.reg)
+ output_dict[residual_label] = stats
 
  if output_dict:
  if args.outfile:

aimfast/bin/aimfast → aimfast/main.py

@@ -1,5 +1,4 @@
-#!/usr/bin/env python3
-
 from aimfast.aimfast import main
 
-main()
+def driver():
+ main()