Wiki » History » Version 1
Goret, Gael, 30/01/2015 09:07 AM
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| 3 | 1 | Goret, Gael | [1.1] How to Start-up the 3DRSR execution : 3DRSR_config |
| 4 | 1 | Goret, Gael | |
| 5 | 1 | Goret, Gael | The configuration program for 3DRSR is made of two consecutive procedures : firstly an initial auto-assignment of the parameters from configuration file(s) inputted, then, a manual definition of all the parameters that has not been defined automatically. |
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| 7 | 1 | Goret, Gael | 3DRSR_config is launched in this way: |
| 8 | 1 | Goret, Gael | |
| 9 | 1 | Goret, Gael | >>> python 3DRSR_config.py Xcalibur_parameter_file.par [Inhouse_config_file.cfg] |
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| 11 | 1 | Goret, Gael | * Inhouse_config_file.cfg being optional |
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| 13 | 1 | Goret, Gael | Inhouse_config_file.cfg format (without the “---” lignes): |
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| 15 | 1 | Goret, Gael | -------------------------------------------------------------------------------- |
| 16 | 1 | Goret, Gael | # gfs1_2 - file name template |
| 17 | 1 | Goret, Gael | |
| 18 | 1 | Goret, Gael | # 1800 - number of input files |
| 19 | 1 | Goret, Gael | |
| 20 | 1 | Goret, Gael | # 1 - starting from number |
| 21 | 1 | Goret, Gael | |
| 22 | 1 | Goret, Gael | # 2463 - Size-Fastest-Dimension |
| 23 | 1 | Goret, Gael | |
| 24 | 1 | Goret, Gael | # 2527 - Size-Second-Dimension |
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| 26 | 1 | Goret, Gael | # 0 - starting angle |
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| 28 | 1 | Goret, Gael | # 0.1 - oscillation size in degrees |
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| 30 | 1 | Goret, Gael | # 1 - apply symmetry (0/1) |
| 31 | 1 | Goret, Gael | |
| 32 | 1 | Goret, Gael | # 53.898 - 1st tilt of U matrix |
| 33 | 1 | Goret, Gael | |
| 34 | 1 | Goret, Gael | # 29.653 - 2nd tilt of U matrix |
| 35 | 1 | Goret, Gael | |
| 36 | 1 | Goret, Gael | # 54.696 - 3rd tilt of U matrix |
| 37 | 1 | Goret, Gael | -------------------------------------------------------------------------------- |
| 38 | 1 | Goret, Gael | |
| 39 | 1 | Goret, Gael | The configuration procedure start by assigning the parameter values available in the Xcalibur parameter file and (if present) in the inhouse configuration file. |
| 40 | 1 | Goret, Gael | Then the program display a summary of the parameters associated with their values or “None” if the program has failed to initialize one parameter. |
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| 42 | 1 | Goret, Gael | Then the program inspect the configuration object and ask the user to set manually the value of each parameter with an undefined value. |
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| 44 | 1 | Goret, Gael | At the end of the manual setting procedure, the program display again the list of parameter values, and write an ASCII file, named 3DRSR.conf containing all the information on parameters. |
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| 46 | 1 | Goret, Gael | This file can be edited by any text editor in order to modify the configuration before setting the file as input of 3DRSR. |
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| 48 | 1 | Goret, Gael | [1.2] 3DRSR : 3D Reciprocal Space Reconstruction |
| 49 | 1 | Goret, Gael | |
| 50 | 1 | Goret, Gael | Once you have obtained a 3DRSR.conf file [see 1.1], you can start 3DRSR using the following syntax : |
| 51 | 1 | Goret, Gael | |
| 52 | 1 | Goret, Gael | >>> python 3DRSR.py 3DRSR.conf Filter_file images-file(s) |
| 53 | 1 | Goret, Gael | |
| 54 | 1 | Goret, Gael | e.g. : python 3DRSR.py conf/3DRSR.conf mask6M ~/data/GFS/images/* |
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| 56 | 1 | Goret, Gael | where, |
| 57 | 1 | Goret, Gael | |
| 58 | 1 | Goret, Gael | “conf/3DRSR.conf” is the path to the configuration file, |
| 59 | 1 | Goret, Gael | |
| 60 | 1 | Goret, Gael | “mask6M” is the path to the filtering mask (in the example located in the current dir), |
| 61 | 1 | Goret, Gael | |
| 62 | 1 | Goret, Gael | “and ~/data/GFS/images/*” is a list of X-ray detector images (given to the program by the command shell via the keyword *) |
| 63 | 1 | Goret, Gael | |
| 64 | 1 | Goret, Gael | The Input file formats handled are the following : |
| 65 | 1 | Goret, Gael | =================== |
| 66 | 1 | Goret, Gael | * Bruker |
| 67 | 1 | Goret, Gael | o brukerimage |
| 68 | 1 | Goret, Gael | o bruker100image |
| 69 | 1 | Goret, Gael | o kcdimage: Nonius KappaCCD diffractometer |
| 70 | 1 | Goret, Gael | * Mar Research |
| 71 | 1 | Goret, Gael | o marccd (fileformat derived from Tiff) |
| 72 | 1 | Goret, Gael | o mar345 imaging plate with PCK compression |
| 73 | 1 | Goret, Gael | * Dectris |
| 74 | 1 | Goret, Gael | o cbfimage (implements a fast byte offset decompression scheme in python/cython) |
| 75 | 1 | Goret, Gael | o pilatusimage (fileformat derived from Tiff) |
| 76 | 1 | Goret, Gael | * ESRF |
| 77 | 1 | Goret, Gael | o edfimage: The ESRF data Format |
| 78 | 1 | Goret, Gael | o xsdimage: XML serialized image from EDNA |
| 79 | 1 | Goret, Gael | o fit2dmaskimage: Fit2d Mask format |
| 80 | 1 | Goret, Gael | o fit2dspreadsheetimage: Fit2d ascii tables (spread-sheet) |
| 81 | 1 | Goret, Gael | * ADSC |
| 82 | 1 | Goret, Gael | o adscimage |
| 83 | 1 | Goret, Gael | * GE detector at APS |
| 84 | 1 | Goret, Gael | o GEimage |
| 85 | 1 | Goret, Gael | * PNM |
| 86 | 1 | Goret, Gael | o pnmimage |
| 87 | 1 | Goret, Gael | * Tiff |
| 88 | 1 | Goret, Gael | o tifimage |
| 89 | 1 | Goret, Gael | * D3M |
| 90 | 1 | Goret, Gael | o d3mimage |
| 91 | 1 | Goret, Gael | * Hamamatsu |
| 92 | 1 | Goret, Gael | o HiPiCimage |
| 93 | 1 | Goret, Gael | * Oxford Diffraction Sapphire 3 |
| 94 | 1 | Goret, Gael | o OXDimage |
| 95 | 1 | Goret, Gael | * Nonius |
| 96 | 1 | Goret, Gael | o KappaCCD |
| 97 | 1 | Goret, Gael | * Raw Binary without compression |
| 98 | 1 | Goret, Gael | =================== |
| 99 | 1 | Goret, Gael | |
| 100 | 1 | Goret, Gael | Once 3DRSR is launched with the proper attributes, the logo is displayed, and the first question appears : |
| 101 | 1 | Goret, Gael | |
| 102 | 1 | Goret, Gael | !! |