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.. _ahelp_afni_python_wrapper.py:
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afni_python_wrapper.py
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afni_python_wrapper.py: use to call afnipy functions from the shell
By default, this loads module afni_util, and attempts use functions from it.
To use a function from a different module, apply -module.
MODULE will subsequently to the imported module.
options:
-help : show this help
-module MODULE : specify the python module to import
By default, functions to process are imported from afni_util. To
import a different module, apply this option.
Example:
afni_python_wrapper.py -module afni_base ...
-module_dir : show the elements returned by dir()
This option is useful to get a list of all module functions.
Examples:
afni_python_wrapper.py -module_dir
afni_python_wrapper.py -module afni_base -module_dir
-eval STRING : evaluate STRING in context of MODULE
(i.e. STRING can be function calls or other)
This option is used to simply execute the code in STRING.
Examples for eval:
afni_python_wrapper.py -eval "show_process_stack()"
afni_python_wrapper.py -eval "show_process_stack(verb=2)"
afni_python_wrapper.py -eval "show_process_stack(pid=1000)"
# write a command in pretty format
cat INPUT | afni_python_wrapper.py -eval 'wrap_file_text()'
# display out.ss_review.FT.txt as a json dictionary
afni_python_wrapper.py -eval \
'write_data_as_json(read_text_dictionary( \
"out.ss_review.FT.txt")[1])'
afni_python_wrapper.py -eval \
'write_data_as_json(read_text_dictionary( \
"out.ss_review.FT.txt", compact=1)[1])'
afni_python_wrapper.py -module module_test_lib \
-eval 'test_import("afnipy.afni_util", verb=4)'
-exec STRING : execute STRING in context of MODULE
This option is used to simply execute the code in STRING.
Examples for exec:
afni_python_wrapper.py -exec "y = 3+4 ; print y"
afni_python_wrapper.py -exec "import PyQt4"
afni_python_wrapper.py -exec "show_process_stack()"
-funchelp FUNC : print the help for module function FUNC
Print the FUNC.__doc__ text, if any.
Example:
afni_python_wrapper.py -funchelp wrap_file_text
-print STRING : print the result of executing STRING
Akin to -eval, but print the results of evaluating STRING.
Examples for print:
afni_python_wrapper.py \
-print "get_last_history_ver_pack('DSET+tlrc')"
afni_python_wrapper.py \
-print "get_last_history_version('DSET+tlrc')"
afni_python_wrapper.py -print 'gaussian_at_fwhm(3,5)'
afni_python_wrapper.py -print 'gaussian_at_hwhm_frac.__doc__'
-lprint STRING : line print: print result list, one element per line
The 'l' stands for 'line' (or 'list'). This is akin to -print,
but prints a list with one element per line.
Examples for lprint:
# show alt+z slice timing for 20 slices and TR=2s
afni_python_wrapper.py \
-lprint "slice_pattern_to_timing('alt+z', 20, 2)"
-listfunc [SUB_OPTS] FUNC LIST ... : execute FUNC(LIST)
With this option, LIST is a list of values to be passed to FUNC().
Note that LIST can be simply '-' or 'stdin', in which case the
list values are read from stdin.
This is similar to eval, but instead of requiring:
-eval "FUNC([v1,v2,v3,...])"
the list values can be left as trailing arguments:
-listfunc FUNC v1 v2 v3 ...
(where LIST = v1 v2 v3 ...).
SUB_OPTS sub-options:
-float : convert the list to floats before passing to FUNC()
-print : print the result
-join : print the results join()'d together
-joinc : print the results join()'d together with commas
-joinn : print the results join()'d together with newlines
Examples for listfunc:
afni_python_wrapper.py -listfunc min_mean_max_stdev 1 2 3 4 5
afni_python_wrapper.py -listfunc -print min_mean_max_stdev 1 2 3 4 5
afni_python_wrapper.py -listfunc -join min_mean_max_stdev 1 2 3 4 5
afni_python_wrapper.py -listfunc -join -float demean 1 2 3 4 5
afni_python_wrapper.py -listfunc -join shuffle \
`count_afni -digits 4 1 124`
count -digits 4 1 124 | afni_python_wrapper.py -listfunc \
-join shuffle -
afni_python_wrapper.py -listfunc glob2stdout 'EPI_run1/8*'
afni_python_wrapper.py -listfunc -joinc list_minus_glob_form *HEAD
afni_python_wrapper.py -listfunc -join -float linear_fit \
2 3 5 4 8 5 8 9
Also, if LIST contains -list2, then 2 lists can be input to do
something like:
-eval "FUNC([v1,v2,v3], [v4,v5,v6])"
Examples with -list2:
afni_python_wrapper.py -listfunc -print -float ttest 1 2 3 4 5 \
-list2 2 2 4 6 8
afni_python_wrapper.py -listfunc -print -float ttest_paired \
1 2 3 4 5 -list2 2 4 5 6 8
afni_python_wrapper.py -listfunc -join -float linear_fit \
`cat y.1D` -list2 `cat x.1D`
afni_python_wrapper.py -listfunc -join list_intersect \
`cat fileA` -list2 `cat fileB` \
| tr ' ' '\n'
# same, but use -joinn instead of tr, for newline separation
afni_python_wrapper.py -listfunc -joinn list_intersect \
`cat fileA` -list2 `cat fileB`
afni_python_wrapper.py -listfunc -joinn list_diff \
`cat fileA` -list2 `cat fileB`
Author: R Reynolds Feb, 2020 (moved from afni_util.py)