Combining numpy arrays inside a loop

Question

I am using a for loop to open 12 files in a directory, each representing a month in the year, with shapes as shown:

(31, 180, 140)
(28, 180, 140)
(31, 180, 140)
(30, 180, 140)
(31, 180, 140)
(30, 180, 140)
(31, 180, 140)
(31, 180, 140)
(30, 180, 140)
(31, 180, 140)
(30, 180, 140)
(31, 180, 140)

I was trying to use append to combine these files into one list, as shown:

directory = r"C:\Users\matth\Downloads\TRMM_3B42RT"
for root, dirs, filenames in os.walk(directory):
    precip_subsetland2010 = []
    for f in filenames:
        if f.startswith("3B42RT_Daily.2010"):
            log = open(os.path.join(root, f), 'r')
            datapath2 = (("C:\\Users\\matth\\Downloads\\TRMM_3B42RT\\") + f)
            f = Dataset(datapath2)

            latbounds = [ -45 , -10 ]
            lonbounds = [ 105, 150 ] 
            lats = f.variables['lat'][:] 
            lons = f.variables['lon'][:]

            # latitude lower and upper index
            latli = np.argmin( np.abs( lats - latbounds[0] ) )
            latui = np.argmin( np.abs( lats - latbounds[1] ) ) 

            # longitude lower and upper index
            lonli = np.argmin( np.abs( lons - lonbounds[0] ) )
            lonui = np.argmin( np.abs( lons - lonbounds[1] ) )

            precip_subset = f.variables['precipitation'][ : , lonli:lonui , latli:latui ]
            precip_subsetland2010.append(precip_subset)
            precipsubsetland2010 = np.asarray(precip_subsetland2010)
            print(precipsubsetland2010.shape)

However, I get an output as shown:

OUTPUT:

(1, 31, 180, 140)
(2,)
(3,)
(4,)
(5,)
(6,)
(7,)
(8,)
(9,)
(10,)
(11,)
(12,)

I would ultimately like to add the data to a list, then convert into an array with a shape of (365, 180, 140). How can I achieve this? Is this the correct application of append?

Does precip_subset have the shapes you mentioned? Print its shape out. — cs95
– cs95, Commented Aug 6, 2017 at 22:26
@cᴏʟᴅsᴘᴇᴇᴅ: The list of shapes I printed at the beginning are the shapes of precip_subset of the 12 files. — user8365869
– user8365869, Commented Aug 6, 2017 at 22:34

cs95 · Accepted Answer · 2017-08-06 22:37:01Z

2

Inside the loop, just append precip_subset to your list:

precip_subsetland2010.append(precip_subset)

Outside the loop, call np.vstack, to vertically stack your data.

output = np.vstack(precip_subsetland2010)

Printing output.shape should give you something like (X, 180, 140) (X being the sum of all rows of the constituent arrays).

answered Aug 6, 2017 at 22:37

cs95

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