Changes between Version 1 and Version 2 of Procedures/AZEagleHawkProcessing
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- Jul 4, 2011, 10:31:32 AM (13 years ago)
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Procedures/AZEagleHawkProcessing
v1 v2 1 Once the data have been unpacked and the nav data have been processed, the Eagle/Hawk data need to be run through the AZ Systems processing chain (primarily azspec, azimport, aznav and azgcorr). 2 Creating the Config file ¶ 1 = Eagle/Hawk Processing = 2 3 Once the [wiki:Procedures/NewDataArrival data have been unpacked] and the [wiki:Procedures/ProcessingChainInstructions/NavigationProcessing nav data have been processed], the Eagle/Hawk data need to be run through the [wiki:Processing/Flow AZ Systems processing chain] (primarily azspec, azimport, aznav and azgcorr). 4 5 == Creating the Config file == 3 6 4 7 generate_runscripts.py is the script used to create the config file, which is in turn used to process the eagle and hawk lines. Before beginning, make sure the raw files are present as well as a processed navigation (sbet) file in applanix/proc and a suitable dem (see below). You may also need to create a text version of the logsheet. … … 6 9 Run with -h flag to get full usage help. An example command is below: 7 10 8 generate_runscripts.py -s s -n 5 -j 196 -y 2010 -l admin/196-10_Eufar10-03.txt Beware that the method is not robust and may fill in the wrong data details, especially for the per-line information. For unknown variables (global or flight line specific) a "?" will be inserted in the config file and should be replaced by hand. 11 generate_runscripts.py -s s -n 5 -j 196 -y 2010 -l admin/196-10_Eufar10-03.txt 12 13 Beware that the method is not robust and may fill in the wrong data details, especially for the per-line information. 14 For unknown variables (global or flight line specific) a "?" will be inserted in the config file and should be replaced by hand. 9 15 10 If no log sheet is available, one can use the keywords on the command line to specify the global variables, using "" if requires a space within the name: 16 If no log sheet is available, one can use the keywords on the command line to specify the global variables, using "" if requires a space within the name: 11 17 12 generate_runscripts.py -s s -n 4 --JDAY=200 --YEAR=2009 --PI="P.I. Name" --SITE="Over There" --PROJCODE=EX01_99 18 generate_runscripts.py -s s -n 4 --JDAY=200 --YEAR=2009 --PI="P.I. Name" --SITE="Over There" --PROJCODE=EX01_99 13 19 14 Adding keywords to the command line and using a logsheet results in the command line keywords taking precedent over the logsheet keyword. For a full list of keywords and their default values run: generate_runscripts.py -h. 20 Adding keywords to the command line and using a logsheet results in the command line keywords taking precedent over the logsheet keyword. 21 For a full list of keywords and their default values run: generate_runscripts.py -h. 15 22 16 23 To use the logsheet just for the global variables you can add to command line --NOPERLINELOG. This will then use the logsheet for global variables, but not for per flight line values. For the per flight line values it will use liblogwriter.py and the raw eagle/hawk header and sbet files to extract average values for the speed/altitude/direction. But using this method will not name the scripts by flight line order on the logsheet, but by the filename of the raw data. Use the --NOPERLINELOG parameter if you wish to manually add the per line data to the config file. 17 24 18 Use the --EXCLUDE="n1 n2 n3 ... -1 m1 m2 m3... -1" parameter if you want to exclude line numbers from the config file. In this case -n linesNo, linesNo can be the number of lines with the previously specified ones excluded. 19 Processing the Lines ¶ 20 Easy Way ¶ 25 Use the --EXCLUDE="n1 n2 n3 ... -1 m1 m2 m3... -1" parameter if you want to exclude line numbers from the config file. 26 In this case -n linesNo, linesNo can be the number of lines with the previously specified ones excluded. 27 28 == Processing the Lines == 29 30 === Easy Way === 21 31 22 32 You should now have in the root of the project directory a .cfg file named with the year and julian day of the project. In order to run the project on the gridengine with default settings, run: 23 33 24 specim_qsub.py <cfg_file> 34 `specim_qsub.py <cfg_file>` 25 35 26 36 By default this will do timing runs for each line on the gridengine using SCT offsets between -0.1 and 0.1. … … 28 38 If you have any problems, check the files created in logs. E.g. 29 39 30 EUFAR10-03_2010-196_eagle_-2.o293411 EUFAR10-03_2010-196_eagle_-2.e293411 40 EUFAR10-03_2010-196_eagle_-2.o293411 41 EUFAR10-03_2010-196_eagle_-2.e293411 31 42 32 43 The first one is an output file (hence the 'o') and the second is the error file ('e'). The last part of the name is the grid node job number. 33 44 34 Check these for errors (look for stars). Check the errors against the example errorsbelow.45 Check these for errors (look for stars). Check the errors against the [#Problems example errors] below. 35 46 36 47 Now you need to find and record the correct SCT value for each flightline. Look for wobbles in straight lines and try to correct them. Once you have a value for each flightline, enter this for the start and end sct variables in the config file for each flightline. Run once more and the script will no longer delete the lev1s. These are the final product to go in the delivery. 37 48 38 49 Check against OS vectors if this is a UK project. 39 Old-fashioned way ¶ 50 51 === Old-fashioned way === 40 52 41 53 If you're unlucky and the automated script fails for some reason, you may need to do at least some of the processing the old-fashioned way. 42 54 43 44 2. Ensure that directories called "logs", "dem", "lev1" and "lev3" have been created.45 3. If there isn't one already, create a "calibration" symlink to the calibration data: ln -s ~arsf/calibration/<year> calibration.46 4. Create a DEM for the project. If it's in the UK you can use Nextmap data (try running nextmapdem.sh in the project directory to do it automatically, otherwise see the wiki page). If it's non-UK, you'll need to use LiDAR data (you may wish to use this anyway if it's available - see here on how to do this using a script), or failing that SRTM 90m data. Copy it into the dem directory.47 5. Create a symlink to the SBET file if there isn't one already.48 1. cd applanix49 2. ln -s Proc/sbet_01.out apa<year><jday>.sbet50 3. cd ..51 6. Copy the sample config file from ~arsf/sample_scripts/<year> to the project directory - you need specim_qsub.py, process_specim_line.py and template_specim_config.cfg.52 7. Comparing the .cfg file with the logsheet, replace the entries that need to be replaced as appropriate. You should be able to see which bits these are in the sample scripts because they'll have keywords instead of values. You will need to create one cfg file section flightline per sensor.53 54 * Note that times must be of the form HH:MM:SS (must use : as a separator)55 8. Run the processing scripts. You can either do this via the gridengine (recommended) by running specim_qsub.py, or you can do it on your machine one line at a time on your machine by running process_specim_line.py with appropriate arguments for each line/sensor combination from the root of the project directory. If you do the latter you should pipe the output to tee to ensure a log file is generated: rune/e12301.sh 2>&1 | tee rune/e12301.log.56 9. Check each set of flightlines to work out which has the best timing offset (ie has the straightest roads, etc). Make a note of the timing offset values in the ticket57 10. Check against OS vectors55 1. cd to the project directory. 56 1. Ensure that directories called "logs", "dem", "lev1" and "lev3" have been created. 57 1. If there isn't one already, create a "calibration" symlink to the calibration data: `ln -s ~arsf/calibration/<year> calibration`. 58 1. Create a DEM for the project. If it's in the UK you can use [wiki:Processing/NextMapDEMs Nextmap data] (try running `nextmapdem.sh` in the project directory to do it automatically, otherwise see the [wiki:Processing/NextMapDEMs wiki page]). If it's non-UK, you'll need to use [wiki:Help/LeicaLidarDems LiDAR data] (you may wish to use this anyway if it's available - see [wiki:Processing/CreateTifs here] on how to do this using a script), or failing that [wiki:Processing/SRTMDEMs SRTM 90m data]. Copy it into the dem directory. 59 1. Create a symlink to the SBET file if there isn't one already. 60 1. `cd applanix` 61 1. `ln -s Proc/sbet_01.out apa<year><jday>.sbet` 62 1. `cd ..` 63 1. Copy the sample config file from ~arsf/sample_scripts/<year> to the project directory - you need specim_qsub.py, process_specim_line.py and template_specim_config.cfg. 64 1. Comparing the .cfg file with the logsheet, replace the entries that need to be replaced as appropriate. You should be able to see which bits these are in the sample scripts because they'll have keywords instead of values. You will need to create one cfg file section flightline per sensor. 65 * Note that dates must be of the form DD/MM/YY or DD/MM/YYYY (must use / as a separator) 66 * Note that times must be of the form HH:MM:SS (must use : as a separator) 67 1. Run the processing scripts. You can either do this via the gridengine (recommended) by running specim_qsub.py, or you can do it on your machine one line at a time on your machine by running process_specim_line.py with appropriate arguments for each line/sensor combination from the root of the project directory. If you do the latter you should pipe the output to tee to ensure a log file is generated: `rune/e12301.sh 2>&1 | tee rune/e12301.log`. 68 1. Check each set of flightlines to work out which has the best timing offset (ie has the straightest roads, etc). Make a note of the timing offset values in the ticket 69 1. Check against OS vectors 58 70 59 dem? 71 '''dem?''' 60 72 61 To return sensible results you will need a dem. One should have already been completed in the unpacking stage. If not, it will need to be created. If the project is in the UK you can use Nextmap data (try running nextmapdem.sh in the project directory to do it automatically, otherwise see the wiki page). If it's non-UK, you'll need to use LiDAR data (you may wish to use this anyway if it's available - see here on how to do this using a script), or failing that SRTM 90m data. Copy it into the dem directory. Once you've done this include the DEM file in the config file by entering "dem=<dem_file_name>" under the DEFAULT section. 62 Problems ¶ 73 To return sensible results you will need a dem. One should have already been completed in the unpacking stage. If not, it will need to be created. If the project is in the UK you can use [wiki:Processing/NextMapDEMs Nextmap data] (try running `nextmapdem.sh` in the project directory to do it automatically, otherwise see the [wiki:Processing/NextMapDEMs wiki page]). If it's non-UK, you'll need to use [wiki:Help/LeicaLidarDems LiDAR data] (you may wish to use this anyway if it's available - see [wiki:Processing/CreateTifs here] on how to do this using a script), or failing that [wiki:Processing/SRTMDEMs SRTM 90m data]. Copy it into the dem directory. Once you've done this include the DEM file in the config file by entering "dem=<dem_file_name>" under the DEFAULT section. 63 74 64 Sync 75 == Problems == 76 77 ---- 78 79 '''Sync''' 65 80 66 81 If you get something in the log file like: 67 82 68 ** End of POSATT file with NO Specim sync found 69 ** no sync within 5.00 secs of raw file header time: 49915.6683 ** End of POSATT file with NO Specim sync found[[BR]] 84 ** no sync within 5.00 secs of raw file header time: 49915.66 70 85 71 then there is no sync info in the nav file for that line and and the range of possible sct values will increase (up to a few seconds). You will need to include 'has_sync = false' in the config file line entry and input a wider range of scts, e.g. 86 then there is no sync info in the nav file for that line and and the range of possible sct values will increase (up to a few seconds). You will need to include 'has_sync = false' in the config file line entry and input a wider range of scts, e.g. 72 87 73 [hawk_-11] 74 ... 75 ... 76 ... 77 has_sync = false 78 sctend = -1 79 sctincrement = -0.1 80 sctstart = 1 88 [hawk_-11] [[BR]] 89 ...[[BR]] 90 ...[[BR]] 91 ...[[BR]] 92 has_sync = false[[BR]] 93 sctend = -1[[BR]] 94 sctincrement = -0.1[[BR]] 95 sctstart = 1[[BR]] 81 96 82 [hawk_-12] 97 [hawk_-12][[BR]] 83 98 ... 84 99 85 A less likely reason for the above output is that the raw header file in question contains invalid GPS times (either start time or end time) and therefore also results in not lying within the times of the .nav file. If both GPS Starting Position and GPS Start Time are missing (accordingly for End Position/End Time) then the best guess is to replace the invalid time/position with the raw header file from the other sensor (eagle/hawk), making sure that it is the correct corresponding flightline. If only one of the two are missing, time or position, then the navigation files should be used to find the missing data, this is easier done when the position is missing (open .gpb file from applanix/extract) but still possible when the time is missing (.gpb again, but will have to track position). 100 A less likely reason for the above output is that the raw header file in question contains invalid GPS times (either start time or end time) 101 and therefore also results in not lying within the times of the .nav file. If both GPS Starting Position and GPS Start Time are missing (accordingly for End Position/End Time) 102 then the best guess is to replace the invalid time/position with the raw header file from the other sensor (eagle/hawk), making sure that it is the correct corresponding flightline. If only one of the two are missing, time or position, then the navigation files should be used to find the missing data, this is easier done when the position 103 is missing (open .gpb file from applanix/extract) but still possible when the time is missing (.gpb again, but will have to track position). 86 104 87 Turns 105 ----------------------------------------------- 106 107 '''Turns''' 88 108 89 109 If you get something in the log file like: 90 110 91 ** flight line may have a turn in it ** 92 ** heading spread over approximately: 120 degs **111 ** flight line may have a turn in it **[[BR]] 112 ** heading spread over approximately: 120 degs ** 93 113 94 114 ** run terminated due to turn ** … … 96 116 then there is a bend in the line that is too sharp. You need to add a -bend flag to the azcorr arguments for the line entry in the config file, e.g. 97 117 98 [eagle_-7] 99 ... 100 ... 101 ... 118 [eagle_-7][[BR]] 119 ...[[BR]] 120 ...[[BR]] 121 ...[[BR]] 102 122 azgcorr_args_extra = -bend 103 123 104 [eagle_-8] 124 [eagle_-8][[BR]] 105 125 ... 106 126 107 127 Once processed, it is best to exclude the lines which are causing the problems by including a -l flag in azspec followed by the line numbers delineating the part of the line you want to keep, then reprocessing. E.g. if the bend is at the start of the line: 108 128 109 [eagle_-7] 110 ... 111 ... 112 ... 113 azgcorr_args_extra = -bend 129 130 [eagle_-7][[BR]] 131 ...[[BR]] 132 ...[[BR]] 133 ...[[BR]] 134 azgcorr_args_extra = -bend[[BR]] 114 135 azspec_args_extra = -l 50 2000 115 136 116 137 will exclude the first 50 lines. Make sure the second value takes into account dark frames: the number of lines given in the header file will include dark frames and if you want to process to the end of the line you should therefore specify the line number before the figure given in 'autodarkstartline' (also in the header file). 117 138 118 For anything else, check: Common or known problems. This is now a bit out-of-date - if your solution isn't on there then please add it once you find what it is. 119 Finished? ¶ 139 -------------------------------------------------- 120 140 121 Once you're satisfied with the processed data, you need to create a delivery directory for it. 141 For anything else, check: [wiki:Processing/KnownProblems Common or known problems]. This is now a bit out-of-date - if your solution isn't on there then please add it once you find what it is. 142 143 --------- 144 145 == Finished? == 146 147 Once you're satisfied with the processed data, you need to [wiki:Procedures/DeliveryCreation create a delivery directory] for it.