| 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: |
| 17 | | |
| 18 | | generate_runscripts.py -s s -n 4 --JDAY=200 --YEAR=2009 --PI="P.I. Name" --SITE="Over There" --PROJCODE=EX01_99 |
| 19 | | |
| 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. |
| 22 | | |
| 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. |
| 24 | | |
| 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 === |
| 31 | | |
| 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: |
| 33 | | |
| 34 | | `specim_qsub.py <cfg_file>` |
| 35 | | |
| 36 | | By default this will do timing runs for each line on the gridengine using SCT offsets between -0.1 and 0.1. |
| 37 | | |
| 38 | | If you have any problems, check the files created in logs. E.g. |
| 39 | | |
| 40 | | EUFAR10-03_2010-196_eagle_-2.o293411 |
| 41 | | EUFAR10-03_2010-196_eagle_-2.e293411 |
| 42 | | |
| 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. |
| 44 | | |
| 45 | | Check these for errors (look for stars). Check the errors against the [#Problems example errors] below. |
| 46 | | |
| 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. |
| 48 | | |
| 49 | | Check against OS vectors if this is a UK project. |
| 50 | | |
| 51 | | === Old-fashioned way === |
| 52 | | |
| 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. |
| 54 | | |
| 55 | | 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 |
| 70 | | |
| 71 | | '''dem?''' |
| 72 | | |
| 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. |
| 74 | | |
| 75 | | == Problems == |
| 76 | | |
| 77 | | ---- |
| 78 | | |
| 79 | | '''Sync''' |
| 80 | | |
| 81 | | If you get something in the log file like: |
| 82 | | |
| 83 | | ** End of POSATT file with NO Specim sync found[[BR]] |
| 84 | | ** no sync within 5.00 secs of raw file header time: 49915.66 |
| 85 | | |
| 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. |
| 87 | | |
| 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]] |
| 96 | | |
| 97 | | [hawk_-12][[BR]] |
| 98 | | ... |
| 99 | | |
| 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). |
| 104 | | |
| 105 | | ----------------------------------------------- |
| 106 | | |
| 107 | | '''Turns''' |
| 108 | | |
| 109 | | If you get something in the log file like: |
| 110 | | |
| 111 | | ** flight line may have a turn in it **[[BR]] |
| 112 | | ** heading spread over approximately: 120 degs ** |
| 113 | | |
| 114 | | ** run terminated due to turn ** |
| 115 | | |
| 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. |
| 117 | | |
| 118 | | [eagle_-7][[BR]] |
| 119 | | ...[[BR]] |
| 120 | | ...[[BR]] |
| 121 | | ...[[BR]] |
| 122 | | azgcorr_args_extra = -bend |
| 123 | | |
| 124 | | [eagle_-8][[BR]] |
| 125 | | ... |
| 126 | | |
| 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: |
| | 14 | * project_code |
| | 15 | * dem and dem_origin |
| | 16 | * transform_projection is correct for the data |
| 147 | | Once you're satisfied with the processed data, you need to [wiki:Procedures/DeliveryCreation create a delivery directory] for it. |
| | 33 | Hawk : -0.345 0.29 0.35 |
| | 34 | |
| | 35 | === Making a Delivery === |
| | 36 | |
| | 37 | Use the make_hyper_delivery.py script to make the delivery directory. Run it from within the main project directory. By default it runs in dry run mode. |
| | 38 | |
| | 39 | Use --final if happy with what it says it will do. Use -m <config> to generate screenshots and mosaics |
| | 40 | |
| | 41 | To make the readme file use the script: create_latex_hyperspectral_apl_readme.py |
| | 42 | |
| | 43 | === Individual processing stages: === |
| | 44 | |
| | 45 | ==== Stage 1: Radiometric Calibration ==== |
| | 46 | The software that performs this is called aplcal. It uses the cal files to calibrate the raw data to level 1b. It strips off the FODIS region (also calibrated to level 1b), "flips" the data such that: |
| | 47 | * eagle runs low->high wavelengths |
| | 48 | * hawk mirrored so that it is comparable to eagle (i.e. things on the left of the aircraft are on the left of the data file) |
| | 49 | It also applies smear correction to the eagle data. Rather than mask out bad pixels it creates a separate mask file that contains flags for the following: |
| | 50 | * overflows |
| | 51 | * underflows |
| | 52 | * smear affected |
| | 53 | * bad ccd pixel |
| | 54 | * dropped scans |
| | 55 | Example command to calibrate a file: |
| | 56 | `aplcal -input VNIR11092-1.raw -output e09201b.bil -calfile calibration/2011/eagle/SN001 ` |
| | 57 | Example command to calibrate first 2501 lines of file: |
| | 58 | `aplcal -input VNIR11092-1.raw -output e09201b.bil -calfile calibration/2011/eagle/SN001 -lines 0 2500` |
| | 59 | |
| | 60 | ==== Stage 2: Navigation syncing ==== |
| | 61 | This is performed using the aplnav software. It can use navigation data either from an SBET or specim nav file, depending on whether you want to use post-processed or real-time data. |
| | 62 | It is possible to add a timing offset to shift the navgation data w.r.t the scan lines, or to shift the position w.r.t to attitude. It would be rare to require the latter as this suggests a problem with the SBET file. |
| | 63 | |
| | 64 | Lever arms and boresight values are entered here to offset the position and attitude to the eagle/hawk sensor view direction. It is possible to smooth the data (using a triangle filter) and interpolate the scan time data using either linear or spline methods. |
| | 65 | BIL files containing quality flags for the navigation data are output also. |
| | 66 | |
| | 67 | '''IMPORTANT NOTE:''' |
| | 68 | |
| | 69 | * Lever arms are entered as X Y Z in the aircraft coordinates (X +ve forward, Y +ve to starboard, Z +ve down). This is different to using aznav, which used X +ve forward, Y +ve port, Z +ve up. |
| | 70 | * Specim have previously said that there is a -0.055 second offset to apply to the sync message. Rather than hard code this into aplnav, you should add it onto the scantimeoffset parameter. This is automatically done using the processing scripts by the sct_global_offset parameter. |
| | 71 | |
| | 72 | Example command to sync post-processed navigation data: |
| | 73 | `aplnav -nav VNIR092-11-1.nav -sbet sbet_2011092.out -lev1 e092011b.bil -interp Spline -leverarm 0.559 0.015 1.543 -boresight -0.28 0.16 0.38 -scantimeoffset 0.045 -output e092011b_p_sct0.1_nav_post_processed.bil -qualityfile e092011b_nav_post_processed_quality.bil` |
| | 74 | |
| | 75 | ==== Stage 3: Geocorrection ==== |
| | 76 | The first step of geocorrection is to generate the IGM file using aplcorr. This takes an optional 1-band BIL / BSQ DEM (in WGS-84 Lat/Lon) and the instrument FOV vector file. |
| | 77 | |
| | 78 | Example command: |
| | 79 | `aplcorr -lev1file e092011b.bil -vvfile eagle_fov_fullccd_vectors.bil -navfile e092011b_p_sct0.1_nav_post_processed.bil -dem ASTER_resampled_0.1667_arcsec.dem -igmfile e092013b_p_sct0.1.igm` |
| | 80 | |
| | 81 | The second step of geocorrection is to re-project the IGM file into the chosen map projection, using apltran. |
| | 82 | |
| | 83 | Example commands: |
| | 84 | `apltran -inproj latlong WGS84 -igm e092013b_p_sct0.1.igm -outproj utm_wgs84N 31 -output e092013b_p_sct0.1_utm31n.igm` |
| | 85 | |
| | 86 | `apltran -inproj latlong WGS84 -igm e092013b_p_sct0.1.igm -outproj osng /users/rsg/arsf/dems/ostn02/OSTN02_NTv2.gsb -output e092013b_p_sct0.1_utm31n.igm` |
| | 87 | |
| | 88 | The third step is then to map it. |
| | 89 | |
| | 90 | Example commands: |
| | 91 | `aplmap -igm e092013b_p_sct0.1_utm31n.igm -lev1 e092011b.bil -mapname e092013b_utm31.mapped -bandlist 30 15 7` |
| | 92 | |
| | 93 | `aplmap -igm e092013b_p_sct0.1_utm31n.igm -lev1 e092011b.bil -mapname e092013b_utm31.mapped -bandlist 30 15 7` -pixelsize 2 2 |
| | 94 | |
| | 95 | `aplmap -igm e092013b_p_sct0.1_utm31n.igm -lev1 e092011b.bil -mapname e092013b_utm31.mapped -bandlist 30 15 7` -oversample 3 3 |