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Merge pull request #21 from simontorres/suggested_changes
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Requested changes
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Simon Torres authored Jul 17, 2019
2 parents 610e985 + ce15f01 commit 9b0b57b
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39 changes: 17 additions & 22 deletions .travis.yml
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@@ -1,29 +1,24 @@
language: python
python:
- '3.6'

- '3.6'
branches:
only:
- master

- master
install:
- sudo apt-get update
- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;


- bash miniconda.sh -b -p $HOME/miniconda
- export PATH="$HOME/miniconda/bin:$PATH"
- hash -r
- conda config --set always_yes yes --set changeps1 no
- conda env create -q python=$TRAVIS_PYTHON_VERSION -f environment.yml
- source activate goodman_focus


- python setup.py test
- python setup.py install

- sudo apt-get update
- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
- bash miniconda.sh -b -p $HOME/miniconda
- export PATH="$HOME/miniconda/bin:$PATH"
- hash -r
- conda config --set always_yes yes --set changeps1 no
- conda env create -q python=$TRAVIS_PYTHON_VERSION -f environment.yml
- source activate goodman_focus
- python setup.py test
- python setup.py install
script:
- coverage run --branch --source= setup.py test

- coverage run --branch --source= setup.py test
after_success:
- coveralls
- coveralls
notifications:
slack:
secure: nJCEgN2ou41cgpRZ89GVBkNbKsxaMaIYVClJcOoU/hTFI3/XLLxsWSe1x+Shp6relrdS/P+T1gwSwvGqKrZWBZ/TDRSAwCyLxZ4l49sfNV7JoHmEgyg4qulXKkPwLpCK7R3PJwE0MAIaZAaklNcxTKV63KjjAXiFuyF3ldK2sjQMwjUeqlomRG+3EZQJUxkQTKAnrupq5gPO+iZlI2jevTYm1qwmT6KhUeg0wQMT49PkA1AZbDK9ch2NysIYAQgEW6nyot7k30rytU3rFetCcrmuzuT7i33LCsjQd/ltyOnnqujVMNE5nFRJLA0k16IV6zZbpIIKhfUb2k3ObtJW8A2lhULF+s4N8ayPl5hZJPZ6c9riLDm96iqLIfi79s09UL3Ws4vN3oTWOgbd/28fNgwl4yqZecuYFT9EUPidTkgYg2P1Pi0r0InsAP+KbELTeQoN+XltBS0sJnoCKkIK/fe1ZZHVXEVkUMt5AqPcv6+UMSS49OjU0+bIkqXlqamlFHWIstcWPVdshNHu9aWqxMtWrYQdhkZDjBbfM9BG9Bv0K8zfNi5n4UyJslmUY6vZl7x+gx5xU7tgZYVmZSckBu1n14PZC8lGQHuuuP4poLlQ954Q+TB7Jwv177apR20Vx6DKw/od7i6Zy2MwxbUhFtn8V7oa8wLSQYInnUXlL4I=
3 changes: 3 additions & 0 deletions CHANGES.rst
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Expand Up @@ -3,6 +3,9 @@

- Created dedicated documentation for rtd
- Fixed bug where return was missing
- GoodmanFocus need to be instantiated only once [#19]
- Argument --file-pattern is now actually used in file selection [#18]
- Eliminated some warnings

0.2.0
=====
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173 changes: 120 additions & 53 deletions goodman_focus/goodman_focus.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@
import re
import sys

from astropy.io import fits
from astropy.stats import sigma_clip
from astropy.modeling import models, fitting, Model
from ccdproc import CCDData
Expand Down Expand Up @@ -112,7 +113,7 @@ def get_peaks(ccd, file_name='', plots=False):
raw_profile = np.median(ccd.data[low_limit:high_limit, :], axis=0)
x_axis = np.array(range(len(raw_profile)))

clipped_profile = sigma_clip(raw_profile, sigma=1, iters=5)
clipped_profile = sigma_clip(raw_profile, sigma=1, maxiters=5)

_mean = np.mean(clipped_profile)

Expand All @@ -122,7 +123,7 @@ def get_peaks(ccd, file_name='', plots=False):
background_model = models.Linear1D(slope=0,
intercept=np.mean(clipped_profile))

fitter = fitting.SimplexLSQFitter()
fitter = fitting.LinearLSQFitter()

fitted_background = fitter(background_model,
clipped_x_axis,
Expand Down Expand Up @@ -227,7 +228,7 @@ def get_fwhm(peaks, values, x_axis, profile, model):
else:
log.info("Applying sigma clipping to collected FWHM values."
" SIGMA: 3, ITERATIONS: 1")
clipped_fwhm = sigma_clip(all_fwhm, sigma=3, iters=1)
clipped_fwhm = sigma_clip(all_fwhm, sigma=3, maxiters=1)

if np.ma.is_masked(clipped_fwhm):
cleaned_fwhm = clipped_fwhm[~clipped_fwhm.mask]
Expand Down Expand Up @@ -319,59 +320,80 @@ def __init__(self,
self.log.critical("No such directory")
sys.exit(0)

_ifc = ImageFileCollection(self.full_path, keywords=self.keywords)

self.ifc = _ifc.summary.to_pandas()
self.log.debug("Found {} FITS files".format(self.ifc.shape[0]))
self.ifc = self.ifc[(self.ifc['OBSTYPE'] == self.obstype)]
if self.ifc.shape[0] != 0:
self.log.debug("Found {} FITS files with OBSTYPE = FOCUS".format(
self.ifc.shape[0]))

self.focus_groups = []
configs = self.ifc.groupby(['CAM_TARG',
'GRT_TARG',
'FILTER',
'FILTER2',
'GRATING',
'SLIT',
'WAVMODE',
'RDNOISE',
'GAIN',
'ROI']).size().reset_index().rename(
columns={0: 'count'})
# print(configs.to_string())
for i in configs.index:
focus_group = self.ifc[((self.ifc['CAM_TARG'] == configs.iloc[i]['CAM_TARG']) &
(self.ifc['GRT_TARG'] == configs.iloc[i]['GRT_TARG']) &
(self.ifc['FILTER'] == configs.iloc[i]['FILTER']) &
(self.ifc['FILTER2'] == configs.iloc[i]['FILTER2']) &
(self.ifc['GRATING'] == configs.iloc[i]['GRATING']) &
(self.ifc['SLIT'] == configs.iloc[i]['SLIT']) &
(self.ifc['WAVMODE'] == configs.iloc[i]['WAVMODE']) &
(self.ifc['RDNOISE'] == configs.iloc[i]['RDNOISE']) &
(self.ifc['GAIN'] == configs.iloc[i]['GAIN']) &
(self.ifc['ROI'] == configs.iloc[i]['ROI']))]
self.focus_groups.append(focus_group)
def __call__(self, files=None):
if files is None:

_ifc = ImageFileCollection(location=self.full_path,
keywords=self.keywords,
glob_include=self.file_pattern)

self.ifc = _ifc.summary.to_pandas()
self.log.debug("Found {} FITS files".format(self.ifc.shape[0]))
self.ifc = self.ifc[(self.ifc['OBSTYPE'] == self.obstype)]
if self.ifc.shape[0] != 0:
self.log.debug("Found {} FITS files with OBSTYPE = FOCUS".format(
self.ifc.shape[0]))

self.focus_groups = []
configs = self.ifc.groupby(['CAM_TARG',
'GRT_TARG',
'FILTER',
'FILTER2',
'GRATING',
'SLIT',
'WAVMODE',
'RDNOISE',
'GAIN',
'ROI']).size().reset_index().rename(
columns={0: 'count'})
# print(configs.to_string())
for i in configs.index:
focus_group = self.ifc[
((self.ifc['CAM_TARG'] == configs.iloc[i]['CAM_TARG']) &
(self.ifc['GRT_TARG'] == configs.iloc[i]['GRT_TARG']) &
(self.ifc['FILTER'] == configs.iloc[i]['FILTER']) &
(self.ifc['FILTER2'] == configs.iloc[i]['FILTER2']) &
(self.ifc['GRATING'] == configs.iloc[i]['GRATING']) &
(self.ifc['SLIT'] == configs.iloc[i]['SLIT']) &
(self.ifc['WAVMODE'] == configs.iloc[i]['WAVMODE']) &
(self.ifc['RDNOISE'] == configs.iloc[i]['RDNOISE']) &
(self.ifc['GAIN'] == configs.iloc[i]['GAIN']) &
(self.ifc['ROI'] == configs.iloc[i]['ROI']))]
self.focus_groups.append(focus_group)
else:
self.log.critical('Focus files must have OBSTYPE keyword equal to '
'"FOCUS", none found.')
self.log.info('Please use "--obstype" to change the value though '
'it is not recommended to use neither "OBJECT" nor '
'"FLAT" because it may contaminate the sample with '
'non focus images.')
sys.exit(0)
else:
self.log.critical('Focus files must have OBSTYPE keyword equal to '
'"FOCUS", none found.')
self.log.info('Please use "--obstype" to change the value though '
'it is not recommended to use neither "OBJECT" nor '
'"FLAT" because it may contaminate the sample with '
'non focus images.')
sys.exit(0)
if isinstance(files, list):
full_path_content = os.listdir(self.full_path)

@property
def fwhm(self):
return self._fwhm
if not all([_file in full_path_content for _file in files]):
files_dont_exist = [_file for _file in files if _file not in full_path_content]
for _file in files_dont_exist:
self.log.critical("File {} does not exist in {}"
"".format(_file, self.full_path))
sys.exit(0)
else:
data = {'file': files}

for key in ['INSTCONF', 'FILTER', 'FILTER2', 'WAVMODE']:
key_data = [fits.getval(os.path.join(self.full_path,
_file), key) for _file in files]

data[key] = key_data

self.focus_groups = [pandas.DataFrame(data)]

else:
self.log.critical('"files" argument must be a list')
sys.exit(0)

@fwhm.setter
def fwhm(self, value):
if value is not None:
self._fwhm = value

def __call__(self, *args, **kwargs):
results = {}
for focus_group in self.focus_groups:
mode_name = self._get_mode_name(focus_group)
Expand Down Expand Up @@ -399,6 +421,15 @@ def __call__(self, *args, **kwargs):

return results

@property
def fwhm(self):
return self._fwhm

@fwhm.setter
def fwhm(self, value):
if value is not None:
self._fwhm = value

def _fit(self, df):
focus = df['focus'].tolist()
fwhm = df['fwhm'].tolist()
Expand Down Expand Up @@ -504,7 +535,43 @@ def run_goodman_focus(args=None): # pragma: no cover
features_model=args.features_model,
plot_results=args.plot_results,
debug=args.debug)
goodman_focus()
result = goodman_focus()
log.info("Summary")
for key in result.keys():
log.info("Mode: {} Best Focus: {}".format(key, result[key]))


# def run_goodman_focus_list(args=None): # pragma: no cover
# """Entrypoint
#
# Args:
# args (list): (optional) a list of arguments and respective values.
#
# """
# args = get_args(arguments=args)
# goodman_focus = GoodmanFocus(data_path=args.data_path,
# file_pattern=args.file_pattern,
# obstype=args.obstype,
# features_model=args.features_model,
# plot_results=args.plot_results,
# debug=args.debug)
#
# file_list = ['0016_foc_400m2.fits',
# '0018_foc_400m2.fits',
# '0020_foc_400m2.fits',
# '0022_foc_400m2.fits',
# '0024_foc_400m2.fits',
# '0026_foc_400m2.fits',
# '0028_foc_400m2.fits',
# '0017_foc_400m2.fits',
# '0019_foc_400m2.fits',
# '0021_foc_400m2.fits',
# '0023_foc_400m2.fits',
# '0025_foc_400m2.fits',
# '0027_foc_400m2.fits']
#
# result = goodman_focus(files=file_list)
# print(result)


if __name__ == '__main__': # pragma: no cover
Expand Down
17 changes: 16 additions & 1 deletion goodman_focus/tests/test_goodman_focus.py
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Original file line number Diff line number Diff line change
Expand Up @@ -130,6 +130,7 @@ def setUp(self):
ccd = CCDData(data=np.ones((100, 1000)),
meta=fits.Header(),
unit='adu')
ccd.header['instconf'] = 'Red'
ccd.header['obstype'] = 'FOCUS'
ccd.header['cam_foc'] = self.focus_values[i]
ccd.header['cam_targ'] = 0
Expand Down Expand Up @@ -190,6 +191,19 @@ def test__call__Moffat1D(self):
self.goodman_focus()
self.assertIsNotNone(self.goodman_focus.fwhm)

def test__call__with_list(self):
self.assertIsNone(self.goodman_focus.fwhm)
result = self.goodman_focus(files=self.file_list)
self.assertIsNotNone(self.goodman_focus.fwhm)

def test__call__list_file_no_exist(self):
file_list = ["no_file_{}.fits".format(i) for i in range(10, 20)]
self.assertRaises(SystemExit, self.goodman_focus, file_list)

def test__call__not_a_list(self):
_string = 'not a list'
self.assertRaises(SystemExit, self.goodman_focus, _string)

def tearDown(self):
for _file in self.file_list:
os.unlink(_file)
Expand Down Expand Up @@ -269,7 +283,8 @@ def test_directory_not_empty_and_no_matching_files(self):

def test_no_focus_files(self):
path_no_focus_files = os.path.join(os.getcwd(), 'test_dir_no_focus')
self.assertRaises(SystemExit, GoodmanFocus, path_no_focus_files)
goodman_focus = GoodmanFocus(data_path=path_no_focus_files)
self.assertRaises(SystemExit, goodman_focus)

def tearDown(self):

Expand Down

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