2010 Appion Developer Workshop » History » Version 6
Neil Voss, 06/08/2010 10:15 AM
1 | 1 | Neil Voss | h1. 2010 Appion Developer Workshop |
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3 | h2. Setting up a development enviroment |
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5 | h4. Subversion |
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6 | |||
7 | <pre> |
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8 | svn checkout http://emg.nysbc.org/svn/myami/trunk/ myami/ |
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9 | </pre> |
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10 | |||
11 | h4. Sinedon.cfg |
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13 | At AMI, you do not normally need a sinedon.cfg file, but if you have your own testing environment you will need one. |
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15 | h4. Web page |
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17 | At AMI, put myamiweb into your ami_html directory and it will be available on both cronus3 and fly as http://cronus3.scripps.edu/~username/myamiweb/ |
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19 | You will need to run Eric's web setup wizard to get it working: http://cronus3.scripps.edu/~username/myamiweb/setup/ |
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23 | ______ |
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24 | |||
25 | h2. Add a new option to a program |
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27 | * Problem statement: Add student's T distribution to maxlike alignment, see #552 |
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28 | * Goal: allow user to use the @-student@ option for maxlike alignment using a radio button |
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29 | * Steps to implement: |
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30 | *# add feature to python code |
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31 | *## add command line input |
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32 | *## check flag to add to xmipp program |
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33 | *## insert value into database |
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34 | *# add feature to web page |
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35 | *## add radio button to web page |
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36 | *## add help message |
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37 | *## receive variable from $_POST |
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38 | *## check if value is valid |
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39 | *## add flag to command line |
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41 | 2 | Neil Voss | h2. Add an output directory to hierarchical classification |
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43 | 2 | Neil Voss | * You cannot change the directory if the filesystem is full. |
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45 | ______ |
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46 | |||
47 | h2. Organization of the Python programs |
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48 | |||
49 | We have two major folders in the appion folder: |
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51 | * appionlib: contains libraries, a collection of common functions that are needed by more than one python program, e.g., ssnrResolution, averageStack, and lowPassFilter. |
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52 | * bin: contains the programs that take command line input, e.g., makestack2.py, templateCorrelator.py, maxlikeAlignment.py |
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53 | |||
54 | Other useful directories: |
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56 | * pyami: a collection of common functions to both appion and leginon, save MRC file, save SPIDER file, etc. |
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58 | 6 | Neil Voss | h2. Most important python files: |
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60 | 6 | Neil Voss | h3. Database mapping file |
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62 | 1 | Neil Voss | * source:trunk/appion/appionlib/appiondata.py: describes how the database is put together, if you need to add a new column go here |
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64 | 3 | Neil Voss | .bq see also source:trunk/leginon/leginondata.py and source:trunk/leginon/projectdata.py |
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66 | 6 | Neil Voss | h3. Appion Script hierarchy |
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68 | 6 | Neil Voss | h4. basicScript |
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70 | 1 | Neil Voss | * source:trunk/appion/appionlib/basicScript.py |
71 | 5 | Neil Voss | * contains all the base functions: @setupParserOptions@, @checkConflicts@, @start@ |
72 | * used only for basic scripts outside of the pipeline, e.g., _source:trunk/appion/bin/makeSnapshots.py_, _source:trunk/appion/bin/ApDogPicker.py_ |
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73 | 1 | Neil Voss | * write a log file |
74 | 5 | Neil Voss | * running statistics |
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76 | 6 | Neil Voss | h4. appionScript |
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78 | * source:trunk/appion/appionlib/appionScript.py |
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79 | * Most common function class used 68 programs in appion, e.g., _source:trunk/appion/bin/uploadStack.py_, _source:trunk/appion/bin/subStack.py_, and _source:trunk/appion/bin/maxlikeAlignment.py_ |
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80 | * based on basicScript, but |
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81 | ** adds database connection to log information about run |
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82 | ** adds default commandline options, such as --runname, --commit, -- |
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85 | 3 | Neil Voss | *** source:trunk/appion/appionlib/appionLoop2.py |
86 | **** source:trunk/appion/appionlib/filterLoop.py |
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87 | ***** source:trunk/appion/appionlib/particleLoop2.py |
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88 | 1 | Neil Voss | ______ |
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90 | h2. Organization of the PHP programs |
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94 | ______ |
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96 | h2. Create a program from scratch |
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98 | * Problem statement: I have program X that I want to put into the pipeline: |
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99 | ** EMAN 2d alignment, "refine2d.py":http://blake.bcm.tmc.edu/eman/eman1/progs/refine2d.py.html or "classalign2":http://blake.bcm.tmc.edu/eman/eman1/progs/classalign2.html |
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100 | ** Bsoft program, nothing really any good |
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103 | ______ |
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105 | h2. Create a program, database structure, and report pages from scratch (if time) |
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107 | * 3D MSA? |