How to iterate over column names with PyTable? - python-3.x

Question

I have a large matrix (15000 rows x 2500 columns) stored using PyTables and getting see how to iterate over the columns of a row. In the documentation I only see how to access each row by name manually.
I have columns like:
ID
X20160730_Day10_123a_2
X20160730_Day10_123b_1
X20160730_Day10_123b_2
The ID column value is a string like '10692.RFX7' but all other cell values are floats. This selection works and I can iterate the rows of results but I cannot see how to iterate over the columns and check their values:
from tables import *
import numpy
def main():
h5file = open_file('carlo_seth.h5', mode='r', title='Three-file test')
table = h5file.root.expression.readout
condition = '(ID == b"10692.RFX7")'
for row in table.where(condition):
print(row['ID'].decode())
for col in row.fetch_all_fields():
print("{0}\t{1}".format(col, row[col]))
h5file.close()
if __name__ == '__main__':
main()
If I just iterate with "for col in row" nothing happens. As the code is above, I get a stack:
10692.RFX7
Traceback (most recent call last):
File "tables/tableextension.pyx", line 1497, in tables.tableextension.Row.__getitem__ (tables/tableextension.c:17226)
KeyError: b'10692.RFX7'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "tables/tableextension.pyx", line 126, in tables.tableextension.get_nested_field_cache (tables/tableextension.c:2532)
KeyError: b'10692.RFX7'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "./read_carlo_pytable.py", line 31, in <module>
main()
File "./read_carlo_pytable.py", line 25, in main
print("{0}\t{1}".format(col, row[col]))
File "tables/tableextension.pyx", line 1501, in tables.tableextension.Row.__getitem__ (tables/tableextension.c:17286)
File "tables/tableextension.pyx", line 133, in tables.tableextension.get_nested_field_cache (tables/tableextension.c:2651)
File "tables/utilsextension.pyx", line 927, in tables.utilsextension.get_nested_field (tables/utilsextension.c:8707)
AttributeError: 'numpy.bytes_' object has no attribute 'encode'
Closing remaining open files:carlo_seth.h5...done

Answer 1

You can access a column value by name in each row:
for row in table:
print(row["10692.RFX7"])
Iterate over all columns:
names = table.coldescrs.keys()
for row in table:
for name in names:
print(name, row[name])