Feature Request - Output required arguments and optional parameters
Thanks for your suggestion.
I believe this is the complete list of command-line switches that ctffind will accept. All are optional. Do you have any parameter specifically you are thinking about when you say this isn't a complete list?
Most parameters are given to ctffind after the program has launched, via the standard input (or via a network socket if controlled by cisTEM). I don't have any plans to add another interface to the program, though this would be feasible given the structure of the code, with user interaction separated from the meat of the program.
Hope this helps clarify the situation,
Alexis
Hi Chris,
Typically, a script to run ctffind would look something like this (*):
/path/to/ctffind <\<\eof
$input_image_file
$output_diag_image
$pixel_size
$acceleration_voltage
$spherical_aberration
$amplitude_contrast
$spectrum_dim
$min_res
$max_res
$min_def
$max_def
$step_def
no
no
yes
$expected_astig
yes
$min_phase_shift
$max_phase_shift
$step_phase_shift
no
eofHi Chris,
Typically, a shell script to run ctffind would look something like this:
/path/to/ctffind <\<\eof
$input_image_file
$output_diag_image
$pixel_size
$acceleration_voltage
$spherical_aberration
$amplitude_contrast
$spectrum_dim
$min_res
$max_res
$min_def
$max_def
$step_def
no
no
yes
$expected_astig
yes
$min_phase_shift
$max_phase_shift
$step_phase_shift
no
eof
Note that depending on the user's answers, the interaction changes and more or less questions may be asked. For the meaning of individual questions and the expected answers, please consult with your users or refer to the ctffind4 paper. You will have to define different interactions depending on
- whether the users are giving images or movies as input
- whether they want to restrain astigmatism
- whether they want to search of additional phase shift
- whether they want to set expert options
You should be able to ask one of your more experienced users for what settings they normally use.
In terms of exit codes, I can't completely guarantee that a return of 0 always means everything worked correctly, but I'm pretty sure it does. Users are expected to pay attention to the output.
You may want to consult existing wrappers around ctffind4, e.g. scipion, appion, or focus.
Hope this helps,
Alexis
Note that depending on the user's answers, the interaction changes and more or less questions may be asked. For the meaning of individual questions and the expected answers, please consult with your users or refer to the ctffind4 paper. You will have to define different interactions depending on
- whether the users are giving images or movies as input
- whether they want to restrain astigmatism
- whether they want to search of additional phase shift
- whether they want to set expert options
You should be able to ask one of your more experienced users for what settings they normally use.
In terms of exit codes, I can't completely guarantee that a return of 0 always means everything worked correctly, but I'm pretty sure it does. Users are expected to pay attention to the output.
You may want to consult existing wrappers around ctffind4, e.g. scipion, appion, or focus.
Hope this helps,
Alexis
(*) This forum attempts to interpret "less than" glyphs as html, so I had to put backslashes in front of them, but obviously you'd ignore those
Hi Alexis,
Thank you very much for the information.