xarray

.codeclimate.yml

@@ -0,0 +1,2 @@
+languages:
+  python: true

.travis.yml

@@ -1,38 +1,26 @@
-language: generic
+language: python
+fast_finish: true
 
-os:
-  - linux
-  - osx
+python:
+  - 3.6
+
+os: linux
 
-env: 
-  - TRAVIS_PYTHON_VERSION=3.6
+group: edge
 
 notifications:
   email: false
 
 git:
   depth: 3
 
-before_install:
-    - if [[ $TRAVIS_OS_NAME == osx ]]; then
-        wget https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O miniconda.sh;
-      else
-        wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
-      fi
-
-    - 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 update -q conda
-    - conda create -n test python=$TRAVIS_PYTHON_VERSION
-    - source activate test
-    - pip -q install coveralls
+before_install:
+  - pip -q install coveralls
 
-install:
-    - python setup.py develop
+install: pip install -e .
 
 script: coverage run tests/test.py -v
 
 after_success: coveralls
+

PlotDASC.py

@@ -29,6 +29,6 @@ def plotdasc(img,wavelength,odir,cadence,rows,cols):
 
 
 
-    img,times,waz,wel,wlla,wwl = readallDasc(p.indir,p.azfn,p.elfn,p.wavelength,p.minmax,p.tlim)
+    img = readallDasc(p.indir,p.azfn,p.elfn,p.wavelength,p.minmax,p.tlim)
 
-    plotdasc(img,wwl,p.odir,p.cadence,None,None)
+    plotdasc(img,p.odir,p.cadence,None,None)

README.rst

@@ -3,11 +3,16 @@
 
 .. image:: http://img.shields.io/badge/powered%20by-AstroPy-orange.svg?style=flat
     :target: http://www.astropy.org/
+
 .. image:: https://travis-ci.org/scivision/dascutils.svg?branch=master
     :target: https://travis-ci.org/scivision/dascutils
 
 .. image:: https://coveralls.io/repos/github/scivision/dascutils/badge.svg?branch=master 
-    :target: https://coveralls.io/github/scivision/dascutils?branch=master    
+    :target: https://coveralls.io/github/scivision/dascutils?branch=master  
+
+.. image:: https://api.codeclimate.com/v1/badges/36b08deedc7d2bf750c8/maintainability
+   :target: https://codeclimate.com/github/scivision/dascutils/maintainability
+   :alt: Maintainability  
 
 ============
 DASC utils
@@ -26,14 +31,15 @@ Install
 =======
 ::
 
-	python setup.py develop
+	pip install -e .
 	
 Download raw DASC files by time
 ===========================
 Example download October 7, 2015 from 8:23 to 8:54 UTC::
 
     ./DownloadDASC.py 2015-10-07T08:23Z 2015-10-07T08:54Z 
     
+    
 -o  download directory
 -c  clobber existing files
 -s  three-letter site acronym PKR for poker flat etc.

dascutils/readDASCfits.py

@@ -4,40 +4,50 @@
 Run standalone from PlayDASC.py
 """
 from pathlib import Path
+from dateutil.parser import parse
+import xarray
+import logging
 from warnings import filterwarnings # corrupt FITS files let off a flood of AstroPy warnings
 from astropy.io.fits.verify import VerifyWarning
-import logging
 from astropy.io import fits
 import numpy as np
-from dateutil.parser import parse
 #
 from . import totimestamp
 #
 from sciencedates import forceutc
 
 
-def readallDasc(indir,azfn,elfn,wl,minmax,tlim=None):
+def readallDasc(indir:Path, azfn:Path, elfn:Path, wl, minmax, tlim=None) -> xarray.DataArray:
     """
     returns Dasc images in list by wavelength, then by time
     """
-
-    img = []; times = []; wlused=[]
+    imgs=[]
     for w in wl:
         try:
             data,azel,sensorloc,time  = readCalFITS(indir,azfn,elfn,w,minmax,tlim)
-            img.append(data['image'])
-            times.append(time)
-            wlused.append(w)
+
+            img = xarray.DataArray(data['image'],
+                                   coords={'time':time[:,0],
+                                    'x':range(data['image'][0].shape[-1]),
+                                    'y':range(data['image'][0].shape[-2]),
+                                    },
+                                   dims=['time','y','x'])
+
+            imgs.append(img)
         except FileNotFoundError:
             pass
-#%% histogram
+
+# %% histogram
     try:
         az = azel[0]
         el = azel[1]
     except Exception: #azel data wasn't loaded
         az=el=None
+# %% prepare metadata
+    imgs[0].attrs={'sensorloc':sensorloc,'az':az,'el':el}
+
+    return imgs
 
-    return img,times,az,el,sensorloc,wlused
 
 def readCalFITS(indir,azfn,elfn,wl,minmax,tlim=None):
     indir = Path(indir).expanduser()
@@ -47,8 +57,10 @@ def readCalFITS(indir,azfn,elfn,wl,minmax,tlim=None):
     #flist = []
     #for w in wl:
     flist = sorted(indir.glob("PKR_DASC_0{}_*.FITS".format(wl)))
+
     return readDASC(flist,azfn,elfn,minmax,tlim)
 
+
 def readDASC(flist,azfn=None,elfn=None,minmax=None,treq=None):
     """
     reads FITS images and spatial az/el calibration for allsky camera
@@ -59,7 +71,8 @@ def readDASC(flist,azfn=None,elfn=None,minmax=None,treq=None):
     if not flist:
         raise FileNotFoundError('no files of this wavelength')
 
-    flist = np.atleast_1d(flist)
+    if isinstance(flist,(str,Path)):
+        flist = [flist]
 
     treq = totimestamp(treq)
 #%% read one file mode
@@ -99,7 +112,7 @@ def readDASC(flist,azfn=None,elfn=None,minmax=None,treq=None):
 #%% preallocate, assuming all images the same size
     for f in flist: #find the first "good" file
         try:
-            with fits.open(str(f),mode='readonly') as h:
+            with fits.open(f, mode='readonly') as h:
                 img = h[0].data
                 sensorloc={'lat':h[0].header['GLAT'],
                            'lon':h[0].header['GLON'],
@@ -116,7 +129,7 @@ def readDASC(flist,azfn=None,elfn=None,minmax=None,treq=None):
 #%% iterate over image files
     for i,fn in enumerate(flist):
         try:
-            with fits.open(str(fn),mode='readonly') as h:
+            with fits.open(fn, mode='readonly') as h:
                 expstart = forceutc(parse(h[0].header['OBSDATE'] + ' ' + h[0].header['OBSSTART'])).timestamp()
 
                 times[i,:] = [expstart,expstart + h[0].header['EXPTIME']] #EXPTIME is in seconds

pyproject.toml

@@ -0,0 +1,5 @@
+[build-system]
+requires = ["setuptools", "wheel",
+'python-dateutil','pytz','numpy','astropy','sciencedates',
+'scipy','matplotlib','seaborn',
+ "nose"] 

setup.py

@@ -1,31 +1,25 @@
 #!/usr/bin/env python
-req = ['nose','python-dateutil','pytz','numpy','astropy','scipy','matplotlib']
-pipreq = ['sciencedates']
-
-import pip
-try:
-    import conda.cli
-    conda.cli.main('install',*req)
-except Exception as e:
-    pip.main(['install'] + req)
-pip.main(['install'] + pipreq)
+req = ['nose','python-dateutil','pytz','numpy','astropy','sciencedates']
 # %%
-from setuptools import setup
+from setuptools import setup, find_packages
 
 setup(name='dascutils',
-      packages=['dascutils'],
+      packages=find_packages(),
       author='Michael Hirsch, Ph.D.',
       url='https://github.com/scivision/dascutils',
       description='Utilities for UAF Digital All-Sky Camera: reading and plotting',
-      version = '0.5',
-      classifiers=[      'Intended Audience :: Science/Research',
+      version = '0.5.0',
+      classifiers=[
+      'Intended Audience :: Science/Research',
       'Development Status :: 4 - Beta',
       'License :: OSI Approved :: MIT License',
       'Topic :: Scientific/Engineering :: Atmospheric Science',
-      'Programming Language :: Python :: 3.6',
+      'Programming Language :: Python :: 3',
       ],
-      extras_requires={'themisasi':['themisasi']},
-      install_requires=req+pipreq,
+      extras_require={'io':['themisasi'],
+                      'plot':['scipy','matplotlib'],},
+      install_requires=req,
+      python_requires='>=3.6',
 	  )
 
 

tests/test.py

@@ -1,4 +1,14 @@
 #!/usr/bin/env python
-
+from pathlib import Path
+import numpy.testing as npt
+#
 from dascutils.readDASCfits import readallDasc
+#
+fn = 'tests/PKR_DASC_0428_20151007_082305.930.FITS'
+rdir = Path(__file__).parents[0]
+
+def test_readdasc():
+    imgs = readallDasc(rdir,None,None,[428],None)
 
+if __name__ == '__main__':
+    npt.run_module_suite()