open_apqc.py

usage: open_apqc.py [-infiles INFILES [INFILES …]] [-jump_to JUMP_TO]

[-disp_jump_ids] [-new_tabs_only] [-new_windows_only] [-pause_time PAUSE_TIME] [-open_pages_off] [-portnum PORTNUM] [-port_nsearch PORT_NSEARCH] [-host HOST] [-nv_dir NV_DIR] [-verb VERB] [-ver] [-help] [-hview]

Overview

This program is used to open one or more of afni_proc.py's quality
control (APQC) HTML files.

It is designed to allow saving QC ratings and notes as the files are
browsed, as well as the execution of 'interactive QC' scripts, by
using a local server.  **This functionality requires Python's Flask
and Flask-CORS modules to both be installed.**  You can still run this
script without those modules and view the QC images, but the fancy
buttons will not work.  It is highly recommended to install those
modules before using this program, to greatly improve your QC
experience.

Options

options:
  -infiles INFILES [INFILES ...]
                        path to one or more APQC index.html files
  -jump_to JUMP_TO      when opening the APQC HTML, jump to the provided QC
                        block or sub-block name (e.g., "ve2a", "qsumm", etc.)
  -disp_jump_ids        display list of IDs within first index.html file that
                        can be jumped to with the "-jump_to .." option (must
                        be used with "-infiles ..")
  -new_tabs_only        open each page in new tab (def: open first page in a
                        new window, then any more in new tabs)
  -new_windows_only     open each page in a new window (def: open first page
                        in a new window, then any more in new tabs)
  -pause_time PAUSE_TIME
                        total time (s) to pause to let pages load (def: 2.0)
  -open_pages_off       (not typically needed) turn off default behavior to
                        open pages in a browswer (def: open in new
                        window[+tabs])
  -portnum PORTNUM      (not typically needed) specify port number to first
                        try to open (def: 5000)
  -port_nsearch PORT_NSEARCH
                        (not typically needed) specify how many port numbers
                        to search through (def: 500)
  -host HOST            (not typically needed) specify hostname (def:
                        127.0.0.1)
  -nv_dir NV_DIR        (not typically needed) path to directory containing
                        "niivue_afni.umd.js" (def: use the location of "afni"
                        program)
  -verb VERB            verbosity level (def: 1)
  -ver                  display version
  -help                 display help in terminal
  -hview                display help in a text editor

Notes on usage

While running/viewing the HTMLs:
  When the server is running, the terminal must be left open so the
  server can keep running (a lot like using a Jupyter-Notebook).

When finished:
  When you are doing viewing the APQC HTMLs, you can close all of
  them, and type 'Ctrl+c' in the terminal (to cancel/exit the server).

Notes on dependencies

To get the most information (and fun!) when using the program, the
following Python modules should be installed, to enable a local server
to be up and running:
     flask (ver >= 2.1.2)
     flask_cors (ver >= 3.0.10)
These could/should be installed with a package manager, Conda, etc.

Examples

  1) Open many APQC HTML pages for several subjects, with the server
     on so QC ratings/comments will be saved:

     open_apqc.py  -infiles  data_21_ap/sub*/*results/QC_*/index.html

  2) The same as #1, but have each page jump to the 'vstat' block of
     the HTML:

     open_apqc.py                                                 \
         -infiles  data_21_ap/sub*/*results/QC_*/index.html       \
         -jump_to  vstat

  3) The same as #2, but open all pages in new tabs of the existing
     browser window (instead of starting new window):

     open_apqc.py                                                 \
         -infiles  data_21_ap/sub*/*results/QC_*/index.html       \
         -jump_to  vstat                                          \
         -new_tabs_only

written by: T Hanayik (Oxford Uni, UK)
            PA Taylor (SSCC, NIMH, NIH, USA)