Merge branch 'main' into tutorial_2023

README.md

@@ -4,9 +4,8 @@ CAP is a set of Python 3 libraries and command-line executables that streamline
 
 Please check the [tutorial/](./tutorial/) directory for:
 
-* detailed installation instructions for Linux, MacOS, Windows
-* a lecture presenting the functionalities of the CAP
-* a set of practice exercises to get familiar with CAP
+* Detailed installation instructions for Linux, MacOS, Windows [Step-by-Step Installation](./tutorial/CAP_Install.md)
+* A lecture presenting the functionalities of the CAP [Introduction to CAP and Documentation of its Functions](./tutorial/CAP_lecture.md)
+* Two sets of practice exercises to get familiar with CAP for the [NASA Ames MGCM](./tutorial/CAP_Exercises.md) and the [Legacy GCM outputs](./tutorial/CAP_Exercises_2021.md)
 
-
-The tutorial uses outputs from GCM simulations extensively documented in [Haberle et al. 2019](https://www.sciencedirect.com/science/article/pii/S0019103518305761)
+The tutorial uses outputs from MGCM simulations extensively documented in [Haberle et al. 2019](https://www.sciencedirect.com/science/article/pii/S0019103518305761) and available for download on the [MCMC Data Portal](https://data.nas.nasa.gov/mcmc/index.html)

README.rst

@@ -0,0 +1,14 @@
+MarsPlot
+============
+
+Welcome to the Mars Climate Modeling Center (MCMC) **Community Analysis Pipeline (CAP)**.
+
+**CAP** is a set of Python3 libraries and command-line executables that streamline downloading, processing, and plotting output from the NASA Ames Mars Global Climate Models: the NASA Ames Legacy Mars GCM and the NASA Ames Mars GCM.
+
+Please see  directory for:
+
+* Installation instructions for Linux, MacOS, and Windows
+* Documentation for CAP functions
+* A set of exercises to get familiar with CAP
+
+MGCM output is extensively documented in `Haberle et al. 2019 <https://www.sciencedirect.com/science/article/pii/S0019103518305761>`_.

amescap/Ncdf_wrapper.py

@@ -782,5 +782,5 @@ def _linInterpLs(self,Ls,stride=16):
         Lsdi=np.append(Lsdi,2*Lsdi[-1]-Lsdi[-2])
 
         for i in range(len(Ls)//stride):
-            Ls_out[i*stride:(i+1)*stride]=np.arange(0,stride)/np.float(stride)*(Lsdi[i+1]-Lsdi[i])+Lsdi[i]
+            Ls_out[i*stride:(i+1)*stride]=np.arange(0,stride)/np.float32(stride)*(Lsdi[i+1]-Lsdi[i])+Lsdi[i]
         return Ls_out

amescap/Script_utils.py

@@ -10,12 +10,26 @@
 
 
 # The functions below allow to print in different color
-def prRed(skk): print("\033[91m{}\033[00m".format(skk))
-def prGreen(skk): print("\033[92m{}\033[00m".format(skk))
-def prCyan(skk): print("\033[96m{}\033[00m".format(skk))
-def prYellow(skk): print("\033[93m{}\033[00m".format(skk))
-def prPurple(skk): print("\033[95m{}\033[00m".format(skk))
-def prLightPurple(skk): print("\033[94m{}\033[00m".format(skk))
+def prRed(input_txt):
+    print(f"\033[91m{input_txt}\033[00m")
+def prGreen(input_txt):
+    print(f"\033[92m{input_txt}\033[00m")
+def prCyan(input_txt):
+    print(f"\033[96m{input_txt}\033[00m")
+def prYellow(input_txt):
+    print(f"\033[93m{input_txt}\033[00m")
+def prPurple(input_txt):
+    print(f"\033[95m{input_txt}\033[00m")
+def prLightPurple(input_txt):
+    print(f"\033[94m{input_txt}\033[00m")
+
+Cyan = "\033[96m"
+Blue = "\033[94m"
+Yellow = "\033[93m"
+NoColor = "\033[00m"
+Red = "\033[91m"
+Green = "\033[92m"
+Purple = "\033[95m"
 
 def MY_func(Ls_cont):
     '''
@@ -51,10 +65,10 @@ def print_fileContent(fileNcdf):
         None (print in the terminal)
     '''
     #Define Colors for printing
-    def Green(skk): return"\033[92m{}\033[00m".format(skk)
-    def Cyan(skk): return "\033[96m{}\033[00m".format(skk)
-    def Yellow(skk):return"\033[93m{}\033[00m".format(skk)
-    def Purple(skk):return"\033[95m{}\033[00m".format(skk)
+    def Green(input_txt): return"\033[92m{}\033[00m".format(input_txt)
+    def Cyan(input_txt): return "\033[96m{}\033[00m".format(input_txt)
+    def Yellow(input_txt):return"\033[93m{}\033[00m".format(input_txt)
+    def Purple(input_txt):return"\033[95m{}\033[00m".format(input_txt)
     if not os.path.isfile(fileNcdf):
         print(fileNcdf+' not found')
     else:
@@ -104,8 +118,8 @@ def print_varContent(fileNcdf,list_varfull,print_stat=False):
         None (print in the terminal)
     '''
     #Define Colors for printing
-    def Cyan(skk): return "\033[96m{}\033[00m".format(skk)
-    def Red(skk):  return "\033[91m{}\033[00m".format(skk)
+    def Cyan(input_txt): return "\033[96m{}\033[00m".format(input_txt)
+    def Red(input_txt):  return "\033[91m{}\033[00m".format(input_txt)
     if not os.path.isfile(fileNcdf):
         print(fileNcdf+' not found')
     else:
@@ -259,7 +273,7 @@ def FV3_file_type(fNcdf):
         fNcdf: an (open) Netcdf file object
     Return:
        f_type (string): 'fixed', 'contineous', or 'diurn'
-       interp_type (string): 'pfull','pstd','zstd','zagl','zgrid'
+       interp_type (string): 'pfull','pstd','zstd','zagl'
     '''
     #Get the full path from the file
     fullpath=get_Ncdf_path(fNcdf)
@@ -289,7 +303,6 @@ def FV3_file_type(fNcdf):
     if 'pstd'  in dims: interp_type='pstd'
     if 'zstd'  in dims: interp_type='zstd'
     if 'zagl'  in dims: interp_type='zagl'
-    if 'zgrid' in dims: interp_type='zgrid'
     return f_type,interp_type
 
 def alt_FV3path(fullpaths,alt,test_exist=True):
@@ -539,7 +552,7 @@ def section_content_amescap_profile(section_ID):
     '''
     Execude code section in /home/user/.amescap_profile
     Args:
-        section_ID: string defining the section to loa, e.g 'Pressure definitions for pstd'
+        section_ID: string defining the section to load, e.g 'Pressure definitions for pstd'
     Returns
         return line in that section as python code
     '''
@@ -567,7 +580,7 @@ def section_content_amescap_profile(section_ID):
     except FileNotFoundError:
         prRed("Error: %s config file not found "%(input_file))
         prYellow("To use this feature, create a hidden config file from the template in your home directory with:")
-        prCyan("    cp amesCAP/mars_templates/amescap_profile  ~/.amescap_profile")
+        prCyan("    cp AmesCAP/mars_templates/amescap_profile  ~/.amescap_profile")
         exit()
     except Exception as exception: #Return the error
         prRed('Error')

amescap/Spectral_utils.py

@@ -71,7 +71,7 @@ def diurn_extract(VAR,N,tod,lon):
 
     #Reshape input variable VAR as a 2D array (tod,Nelements) for generalization
 
-    Ndim= np.int(np.prod(dimsIN[1:]))   #Ndim is the product of all dimensions but the time of day axis, e.g. time x lat x lon
+    Ndim= int(np.prod(dimsIN[1:]))   #Ndim is the product of all dimensions but the time of day axis, e.g. time x lat x lon
     dimsFLAT=np.append([nsteps],[Ndim])  # Shape of flattened array
     dimsOUT_flat=np.append([N],[Ndim])   # Shape of flattened array
     VAR= VAR.reshape(dimsFLAT)     #Flatten array to  (tod,Nelements)
@@ -191,7 +191,7 @@ def space_time(lon,timex, varIN,kmx,tmx):
     lon_id= dims[0]    # lon
     time_id= dims[-1]  # time
     dim_sup_id=dims[1:-1] #additional dimensions stacked in the middle
-    jd= np.int(np.prod( dim_sup_id))     #jd is the total number of dimensions in the middle is varIN>3D
+    jd= int(np.prod( dim_sup_id))     #jd is the total number of dimensions in the middle is varIN>3D
 
     varIN= np.reshape(varIN, (lon_id, jd, time_id) )   #flatten the middle dimensions if any
 

bin/MarsCalendar.py

@@ -0,0 +1,65 @@
+#!/usr/bin/env python
+from amescap.FV3_utils import sol2ls,ls2sol
+from amescap.Script_utils import prYellow,prRed
+import argparse #parsing arguments
+import numpy as np
+
+
+parser = argparse.ArgumentParser(description='Gives the solar longitude from a SOL or a SOL array (start stop, step), adapted from areols.py',
+                                formatter_class=argparse.RawTextHelpFormatter)
+
+parser.add_argument('sol', nargs='+',type=float,
+                             help='''Input is sol number, return solar longitude \n'''
+                                  '''Usage: ./MarsCalendar.py 750. \n'''
+                                  '''       ./MarsCalendar.py start stop step''')
+
+parser.add_argument('-ls','--ls', action='store_true',
+                    help="""Reverse operation. Inpout is Ls, output is sol \n"""
+                    """> Usage: ./MarsCalendar.py start stop step' -ls \n"""
+                    """ \n""")
+
+
+parser.add_argument('-my', nargs='+',type=float,default=0.,
+                             help=''' Mars Year For ls>sol add 668 if my=1,1336 if my=2 etc.. \n'''
+                                  '''Usage: ./MarsCalendar.py  350 -ls -my 2 \n''')
+
+parser.add_argument('-cum', action='store_true',
+                             help='''For sol>ls return ls as cummulative 0>360>720... instead of [0-360] \n'''
+                                  '''Usage: ./MarsCalendar.py  670 -cum \n''')
+
+
+if __name__ == '__main__':
+
+
+    #Load in Mars YEAR (if any, default is zero) and cummulative Ls
+    my=np.asarray(parser.parse_args().my).astype(float)
+    cum=False
+    if parser.parse_args().cum:cum=True
+
+    data_input=np.asarray(parser.parse_args().sol).astype(float)
+
+    if len(data_input)==1:
+        in_array=data_input
+    elif len(data_input)==3:
+        in_array=np.arange(data_input[0],data_input[1],data_input[2]) #start stop step
+    else:
+        prRed('Wrong number of arguments: enter [sol/ls] or [start stop step]')
+        exit()
+
+    #Requesting ls instead
+    if parser.parse_args().ls:
+        txt_multi='   Ls    |    Sol    '
+        result=ls2sol(in_array)
+    else:
+        txt_multi='    SOL    |    Ls    '
+        result=sol2ls(in_array,cummulative=cum)
+
+    #Is scalar, turn as float
+    if len(np.atleast_1d(result))==1:result=[result]
+    #Display data
+    print(txt_multi)
+    print('-----------------------')
+    for i in range(0,len(in_array)):
+        print(' %7.2f   |    %7.3f  '%(in_array[i],result[i]+my*668.))
+
+