rebase from yunjunz repo

.gitignore

@@ -5,3 +5,6 @@
 *.nc4
 *checkpoint.ipynb
 
+examples/TestECMWF.py
+examples/multilook_geometry.ipynb
+*.BK

README.md

@@ -18,8 +18,8 @@ export PYTHONPATH=${PYAPS_HOME}:${PYTHONPATH}
 Installing Python dependencies
 
 ```
-mdkir PyAPS; cd PyAPS
-git clone https://github.com/AngeliqueBenoit/pyaps3.git
+mkdir PyAPS; cd PyAPS
+git clone https://github.com/yunjunz/pyaps3.git
 
 wget https://github.com/ecmwf/cdsapi/archive/v0.1.4.tar.gz -O cdsapi-0.1.4.tar.gz
 tar -xvf cdsapi-0.1.4.tar.gz; cd cdsapi-0.1.4
@@ -29,16 +29,18 @@ python setup.py install
 
 ## Account setup for global atmospheric models
 ### [ERA-5](https://retostauffer.org/code/Download-ERA5/)
-ERA-5 data set is redistributed over the Copernicus Climate Data Store (CDS), [create a new account](https://cds.climate.copernicus.eu/user/register) on the CDS website if you don't own a user account yet. On the profile, you will find your user id (**UID**) and your personal **API Key**.
-
-For batch script data downloads you’ll have to create a local ASCII file with your user information (UID, API key) which is used by the python package (cdsapi). To do so (linux) simply create a file called .cdsapirc in your home directory and add the following two lines:
+ERA-5 data set is redistributed over the Copernicus Climate Data Store (CDS), [create a new account](https://cds.climate.copernicus.eu/user/register) on the CDS website if you don't own a user account yet. On the profile, you will find your user id (**UID**) and your personal **API Key**. Add the key to the `model.cfg` file as below:
 
 ```
-url: https://cds.climate.copernicus.eu/api/v2
-key: 1234:abcdefghij-134-abcdefgadf-82391b9d3f
+#####key for ECMWF in Climate Data Store Application Program Interface
+#Get it from https://retostauffer.org/code/Download-ERA5/
+[CDS]
+key = 12345:abcdefghij-134-abcdefgadf-82391b9d3f
 ```
 
-where 1234 is your personal user ID (UID), the part behind the colon your personal API key. Line one simply contains the URL to the web API. More details can be found [here](https://cds.climate.copernicus.eu/api-how-to).
+where 12345 is your personal user ID (UID), the part behind the colon your personal API key. More details on CDSAPI can be found [here](https://cds.climate.copernicus.eu/api-how-to).
+
+Run `examples/TestECMWF.ipynb` in Jupyter Notebook in your local machine to check if everything works.
 
 ## Citing this work
 The metholody and validation of DelayPackage can be found in:

__init__.py

@@ -7,11 +7,11 @@
 	Details of the python module can be obtained `here. <http://code.google.com/p/pyaps>`_
 '''
 
-__all__ = ['geocoord','rdrcoord','autoget','pyapsobj']
+__all__ = ['geocoord','rdrcoord','autoget','objects']
 
 #from .geocoord import PyAPS_geo
 #from .rdrcoord import PyAPS_rdr
-from .pyapsobj import PyAPS
+from .objects import PyAPS
 from .autoget import *
 
 

autoget.py

@@ -40,7 +40,7 @@ def ECMWFdload(bdate,hr,filedir,model='ERA5',datatype='fc',humidity='Q',snwe=Non
     # Initialize
 
     # Check data
-    assert model in ('ERA5', 'ERAINT', 'HRES'), 'Unknown model for ECMWF'
+    assert model in ('ERA5', 'ERAINT', 'HRES'), 'Unknown model for ECMWF: {}'.format(model)
 
     # Infos for downloading
     if model in 'ERAINT':
@@ -61,7 +61,7 @@ def ECMWFdload(bdate,hr,filedir,model='ERA5',datatype='fc',humidity='Q',snwe=Non
         else:
             humidparam = 133
     elif humidity in 'R':
-        if model in 'era5':
+        if model in 'ERA5':
             humidparam = 'relative_humidity'
         else:
             humidparam = 157
@@ -77,6 +77,8 @@ def ECMWFdload(bdate,hr,filedir,model='ERA5',datatype='fc',humidity='Q',snwe=Non
     if not flist:
         flist = []
         for k in range(len(bdate)):
+            day = bdate[k]
+
             if model == 'ERA5':
                 fname = os.path.join(filedir, 'ERA-5_{}_{}.grb'.format(day, hr))
             elif model == 'ERAINT':
@@ -129,7 +131,7 @@ def ECMWFdload(bdate,hr,filedir,model='ERA5',datatype='fc',humidity='Q',snwe=Non
                 print(indict)
 
                 # Make the request
-                c.retrieve('reanalysis-{}-pressure-levels'.format(model),indict,target=fname)
+                c.retrieve('reanalysis-{}-pressure-levels'.format(model.lower()),indict,target=fname)
 
         #-------------------------------------------
         # CASE 2: request for WEB API client (old ECMWF platform, deprecated, for ERA-Int and HRES)

era.py

@@ -91,8 +91,7 @@ def get_era(fname,minlat,maxlat,minlon,maxlon,cdic, humidity='Q',verbose=False):
     grb=grbs.read(1)[0]
     lats,lons = grb.latlons()
     g = cdic['g']    
-    mask = (lats > minlat) & (lats < maxlat) \
-    & (lons > minlon) & (lons < maxlon)
+    mask = (lats > minlat) & (lats < maxlat) & (lons > minlon) & (lons < maxlon)
     [ii,jj] = np.where(mask == True)
     del mask
     latlist = lats[ii,jj]
@@ -170,7 +169,7 @@ def get_ecmwf(model,fname,minlat,maxlat,minlon,maxlon,cdic, humidity='Q',verbose
     assert model in ('ERA5', 'ERAINT','HRES'), 'Model not recognized.'
     if verbose:
         print('PROGRESS: READING GRIB FILE')
-    if model in 'hres':
+    if model in 'HRES':
         if verbose:
             print('INFO: USING PRESSURE LEVELS OF HRES DATA')
         lvls = np.array([1, 2, 3, 5, 7, 10, 20, 30, 50, 70, 100, 150, 
@@ -191,7 +190,9 @@ def get_ecmwf(model,fname,minlat,maxlat,minlon,maxlon,cdic, humidity='Q',verbose
     grbs.seek(gphind[0])
     grb = grbs.read(1)[0]
     lats,lons = grb.latlons()
-    g = cdic['g']    
+    if model == 'ERA5':
+        lons[lons < 0.] += 360.
+    g = cdic['g']
 
     mask = ((lats > minlat) & (lats < maxlat)) & ((lons > minlon) & (lons < maxlon))
     #extrqct indices 

examples/TestPyAPS.py

@@ -1,3 +1,4 @@
+#!/usr/bin/env python
 import pyaps3 as pa
 import numpy as np
 import matplotlib.pyplot as plt

model.cfg.template → model.cfg

@@ -2,7 +2,7 @@
 #####key for ECMWF in Climate Data Store Application Program Interface
 #Get it from https://retostauffer.org/code/Download-ERA5/
 [CDS]
-key = 
+key = your-uid:your-api-key
 
 #The key to the new server for ECMWF
 ##Get it from https://software.ecmwf.int/wiki/display/WEBAPI/Accessing+ECMWF+data+servers+in+batch 
@@ -28,4 +28,3 @@ key =
 [MERRA]
 user = the-user-name-used-as-login@earthdata.nasa.gov
 password = the-password-used-as-login@earthdata.nasa.gov
-