Table of Contents
Tutorial to aid adding a new e2program to the e2projectmanager.py
This tutorial covers the necessary steps to incorporate a e2program into the projectmanager.
Modifications to the e2program itself
Canonical e2programs must maintain the following standards 1. Options are handled via EMArgumentParser, which is a subclass of Python's argparse module (version 2.7 and higher). For more information on argparse, see the python documentation. http://docs.python.org/dev/library/argparse.html 2. Arguments are handled via EMArgumentParser. 3. A line usage = “”“blah, blah, blah…”“” must be present to give help info on the e2program 4. A line progname = os.path.basename(sys.argv[0]) must be present
To illustrate what an e2program should look like, here is an example program:
#!highlight python
#!/usr/bin/env python
#
# GPL licensing info goes here
#
from EMAN2 import *
def main():
progname = os.path.basename(sys.argv[0])
usage = """prog arg1, arg2, [options]
This is an example program """
parser = EMArgumentParser(usage=usage,version=EMANVERSION)
parser.add_argument("--option1",type=str,help="This is the first option",default="myvalue")
parser.add_argument("--option2",type=int,help="This is the second option",default=1)
parser.add_argument("--option3",type=float,help="This is the third option",default=3.14)
parser.add_argument("--option4",action="store_true",help="This is the fourth option",default=False)
(options, args) = parser.parse_args()
print "Arguments are", args
print "Options are", options
if %%__%%name%%__%% == %%__%%main%%__%%:
main()
To enable this program to be integrated into the GUI the following item must be implemented: 5. For each argument you must add the method: parser.add_pos_argument() 6. To add dividing lines with help info into the GUI, add the method: parser.add_header() 7. The option PPID must be added to enable cross platform PPID support 8. To all parser 'add' methods the following keyword arguments must be added 9. guitype=“”, this specifies what type of widget we want to use for this GUI 10. row=“”, this specifies what row the widget should appear in 11. col=“”, this specifies what column the widget should appear in 12. rowspan=“”, this specifies how many rows the widget should span 13. colspan=“”, this specifies how many columns the widget should span 14. browser=“”, if the widget represents and option that refers to a file, this keyword argument lists a filebrowser to use.
To illustrate how to integrate the above example e2program int the GUI, the following example is given:
#!highlight python
#!/usr/bin/env python
#
# GPL licensing info goes here
#
from EMAN2 import *
def main():
progname = os.path.basename(sys.argv[0])
usage = """prog arg1, arg2, [options]
This is an example program """
parser = EMArgumentParser(usage=usage,version=EMANVERSION)
#For the add_pos_Argument() and add_header() methods, you must add the name="" keyword argument. For the add_argument() method, the 'name' is taken from the --option argument
parser.add_pos_argument(name="argument1",help="First argument, this will be a file", default="", guitype='filetype', browser="EMBrowserWidget(withmodal=True,multiselect=True)", row=0, col=0,rowspan=1,colspan=2)
parser.add_header(name="header1", help="Use the header to display useful info in the GUI", title="### Actual info goes here ###", row=1, col=0,rowspan=1,colspan=2)
parser.add_argument("--option1",type=str,help="This is the first option",default="myvalue",guitype='strbox', row=2,col=0,rowspan=1,colspan=1)
parser.add_argument("--option2",type=int,help="This is the second option",default=1,guitype='intbox',row=2,col=1,rowspan=1,colspan=1)
parser.add_argument("--option3",type=float,help="This is the third option",default=3.14,guitype='floatbox',row=3,col=0,rowspan=1,colspan=1)
parser.add_argument("--option4",action="store_true",help="This is the fourth option",default=False,guitype='boolbox',row=3,col=1,rowspan=1,colspan=1)
# This is needed by all e2programs that run on the GUI
parser.add_argument("--ppid",type=int,help="Set the PID of the parent process, used for cross platform PPID",default=-1)
(options, args) = parser.parse_args()
print "Arguments are", args
print "Options are", options
if %%__%%name%%__%% == %%__%%main%%__%%:
main()
Modification of the workflow JSON file
If your program is for single particle applications, modify the spr.json file found in /libEM/pmconfig. If your program is for tomographic applications, modify tomo.json file.
For example the spr.json will look something like this.
#!highlight python
{
"ICON": "ctf",
"TABLE": "EMCTFcorrectedParticlesTable(withmodal=False,multiselect=True)",
"NAME": "CTF",
"CHILDREN": [
{
"ICON": "ctf",
"PROGRAM": "e2ctf.py",
"MODE": "autofit",
"WIKIPAGE": "http://blake.bcm.tmc.edu/emanwiki/EMAN2/Programs/e2ctf",
"NAME": "Automated Fitting -e2ctf",
"NOTELEVEL": "1",
"CHILDREN": []
},
{
"ICON": "ctf",
"PROGRAM": "e2ctf.py",
"MODE": "tuning",
"WIKIPAGE": "http://blake.bcm.tmc.edu/emanwiki/EMAN2/Programs/e2ctf",
"NAME": "Interactive Tuning -e2ctf",
"CHILDREN": []
},
{
"ICON": "ctf",
"PROGRAM": "e2ctf.py",
"MODE": "genoutp",
"WIKIPAGE": "http://blake.bcm.tmc.edu/emanwiki/EMAN2/Programs/e2ctf",
"NAME": "Generate Output - e2ctf",
"NOTELEVEL": "1",
"CHILDREN": []
},
{
"ICON": "ctf",
"PROGRAM": "e2ctf.py",
"MODE": "gensf",
"WIKIPAGE": "http://blake.bcm.tmc.edu/emanwiki/EMAN2/Programs/e2ctf",
"NAME": "Generate Structure Factor - e2ctf",
"NOTELEVEL": "1",
"CHILDREN": []
}
]
},
Adding your new e2program is quite straight forward. To the JSON file just add(as a child in a CHILDREN list), in the appropriate location:
#!highlight python
{
"ICON": "single boxes",
"PROGRAM": "e2myprogram.py",
"NAME": "Do some stuff - e2myprogram",
"CHILDREN": []
}
There are multiple other options, such as Wizard, Expert, etc. For a list and explanation see: Programs/e2projectmanager