Versions Compared

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.
Comment: Added component table

...

  1. Start up the Capture One software
  2. Under the File menu open a session or create a new one.  This will set the file structure for the images.
  3. Take an image using the shutter button on the camera or use the Capture button in Capture One but make sure no body parts are in the way of the flashes.  The flashes should go off and the image will appear in Capture One.  If the image is out of focus or something needs adjusting, make the adjustments and take another image[j1] .
  4. Crop the image if necessary.
  5. Adjust the image using the Eye drop tool on the tool bar.
    1.  Right click the eye drop and select “Pick White Balance” then click on the medium gray card.
    2. Right click the eye drop and select “Pick Highlight Level” then click on the white card.
    3.  Right click the eye drop and select “Pick Shadow Level” then click on the dark gray card.
  6. Process the image by entering Ctrl-D on the keyboard or right click the image and select Process.  This will create the jpg and tiff images.
  7. Go to Image Capture to tag and upload the images to the database.

...

  1. Open the IODP Image Capture software and login using your LIMS username and password. In the settings menu, select the destination folder of the images taken by Capture One and select the Closeup Mode.


  2. Once you have logged in to the software you will notice a listing of images in the upper left corner.  These are the images which were just taken (the JPG files specifically).  Click on one of the images to select it for uploading.


  3. Next we need to associate this image with a sample, so click on the Browse button.
  4. After clicking browse select a site and hole to pick a sample from.  The sample type will be defaulted to Section half and a list of available thin sections will appear in the window on the right.   Click on the appropriate sample then swap back to the main window (you can close/minimize/ignore the sample browser window at your discretion.  If you close it then it will open back to the same location).
  5. Note that the sample textid field has been populated, and a new label has been generated in the top right.  This label indicates what the renamed filename will be, and is based on the sample selected.  If multiple pictures are taken the filename will be appended with _2, _3, _4 etc.  based on the number of previous images already taken *and processed*.   Fill out the rest of the values based on the conditions when you took the image.
  6. Add the comment and name of requestor from the close-up request sheet into the Comments field.
  7. When upload was clicked a window will pop up indicating the upload status.  When the upload process is finished another dialog will appear indicating that the process is complete.
  8. At this point the previously selected image will have been removed from the pending uploads list and will be loaded into LIMS. You can continue processing additional images.  Go to LORE reports and verify that the images are uploaded.
  9. The images themselves, after upload, are moved to the archive folder (at the same level as the capture folder). Under the archive folder there will be 3 subfolders:
    1. JPEG
    2. TIFF     (Tiff’s will not generally be created in the standard workflow)
    3. RAW
  10. These folders will contain a hierarchy in the form of \{Expedition}\{SiteHole}\filename.ext  of all the files.  (Essentially pictures will be organized by type, expedition, and sitehole when put in the archive folder.)  These pictures do not need to be backed up (as they are already in lims/asman) but can be taken by the photographers, etc. for alternate archiving if desired.
  11. Note that these images may be deleted at any time, without notice, by the technicians or other scientists.  They are always available via LIMS, and if you wish to save a local copy you may do so.

Shut Down the Instrument

LIMS Component Table

The following table contains all of the LIMS components for the entire CLOSEUP process.

ANALYSISTABLENAMEABOUT TEXT
CLOSEUPSAMPLEExpExp: expedition number
CLOSEUPSAMPLESiteSite: site number
CLOSEUPSAMPLEHoleHole: hole number
CLOSEUPSAMPLECoreCore: core number
CLOSEUPSAMPLETypeType: type indicates the coring tool used to recover the core (typical types are F, H, R, X).
CLOSEUPSAMPLESectSect: section number
CLOSEUPSAMPLEA/WA/W: archive (A) or working (W) section half.
CLOSEUPSAMPLEtext_idText_ID: automatically generated database identifier for a sample, also carried on the printed labels. This identifier is guaranteed to be unique across all samples.
CLOSEUPSAMPLEsample_numberSample Number: automatically generated database identifier for a sample. This is the primary key of the SAMPLE table.
CLOSEUPSAMPLElabel_idLabel identifier: automatically generated, human readable name for a sample that is printed on labels. This name is not guaranteed unique across all samples.
CLOSEUPSAMPLEsample_nameSample name: short name that may be specified for a sample. You can use an advanced filter to narrow your search by this parameter.
CLOSEUPSAMPLEx_sample_stateSample state: Single-character identifier always set to "W" for samples; standards can vary.
CLOSEUPSAMPLEx_projectProject: similar in scope to the expedition number, the difference being that the project is the current cruise, whereas expedition could refer to material/results obtained on previous cruises
CLOSEUPSAMPLEx_capt_locCaptured location: "captured location," this field is usually null and is unnecessary because any sample captured on the JR has a sample_number ending in 1, and GCR ending in 2
CLOSEUPSAMPLElocationLocation: location that sample was taken; this field is usually null and is unnecessary because any sample captured on the JR has a sample_number ending in 1, and GCR ending in 2
CLOSEUPSAMPLEx_sampling_toolSampling tool: sampling tool used to take the sample (e.g., syringe, spatula)
CLOSEUPSAMPLEchanged_byChanged by: username of account used to make a change to a sample record
CLOSEUPSAMPLEchanged_onChanged on: date/time stamp for change made to a sample record
CLOSEUPSAMPLEsample_typeSample type: type of sample from a predefined list (e.g., HOLE, CORE, LIQ)
CLOSEUPSAMPLEx_offsetOffset (m): top offset of sample from top of parent sample, expressed in meters.
CLOSEUPSAMPLEx_offset_cmOffset (cm): top offset of sample from top of parent sample, expressed in centimeters. This is a calculated field (offset, converted to cm)
CLOSEUPSAMPLEx_bottom_offset_cmBottom offset (cm): bottom offset of sample from top of parent sample, expressed in centimeters. This is a calculated field (offset + length, converted to cm)
CLOSEUPSAMPLEx_diameterDiameter (cm): diameter of sample, usually applied only to CORE, SECT, SHLF, and WRND samples; however this field is null on both Exp. 390 and 393, so it is no longer populated by Sample Master
CLOSEUPSAMPLEx_orig_lenOriginal length (m): field for the original length of a sample; not always (or reliably) populated
CLOSEUPSAMPLEx_lengthLength (m): field for the length of a sample [as entered upon creation]
CLOSEUPSAMPLEx_length_cmLength (cm): field for the length of a sample. This is a calculated field (length, converted to cm).
CLOSEUPSAMPLEstatusStatus: single-character code for the current status of a sample (e.g., active, canceled)
CLOSEUPSAMPLEold_statusOld status: single-character code for the previous status of a sample; used by the LIME program to restore a canceled sample
CLOSEUPSAMPLEoriginal_sampleOriginal sample: field tying a sample below the CORE level to its parent HOLE sample
CLOSEUPSAMPLEparent_sampleParent sample: the sample from which this sample was taken (e.g., for PWDR samples, this might be a SHLF or possibly another PWDR)
CLOSEUPSAMPLEstandardStandard: T/F field to differentiate between samples (standard=F) and QAQC standards (standard=T)
CLOSEUPSAMPLElogin_byLogin by: username of account used to create the sample (can be the LIMS itself [e.g., SHLFs created when a SECT is created])
CLOSEUPSAMPLElogin_dateLogin date: creation date of the sample
CLOSEUPSAMPLElegacyLegacy flag: T/F indicator for when a sample is from a previous expedition and is locked/uneditable on this expedition
CLOSEUPTESTtest changed_onTEST changed on: date/time stamp for a change to a test record.
CLOSEUPTESTtest statusTEST status: single-character code for the current status of a test (e.g., active, in process, canceled)
CLOSEUPTESTtest old_statusTEST old status: single-character code for the previous status of a test; used by the LIME program to restore a canceled test
CLOSEUPTESTtest test_numberTEST test number: automatically generated database identifier for a test record. This is the primary key of the TEST table.
CLOSEUPTESTtest date_receivedTEST date received: date/time stamp for the creation of the test record.
CLOSEUPTESTtest instrumentTEST instrument [instrument group]: field that describes the instrument group (most often this applies to loggers with multiple sensors); often obscure (e.g., user_input)
CLOSEUPTESTtest analysisTEST analysis: analysis code associated with this test (foreign key to the ANALYSIS table)
CLOSEUPTESTtest x_projectTEST project: similar in scope to the expedition number, the difference being that the project is the current cruise, whereas expedition could refer to material/results obtained on previous cruises
CLOSEUPTESTtest sample_numberTEST sample number: the sample_number of the sample to which this test record is attached; a foreign key to the SAMPLE table
CLOSEUPCALCULATEDTop depth CSF-A (m)Top depth CSF-A (m): position of observation expressed relative to the top of the hole.
CLOSEUPCALCULATEDBottom depth CSF-A (m)Bottom depth CSF-A (m): position of observation expressed relative to the top of the hole.
CLOSEUPCALCULATEDTop depth CSF-B (m)Top depth [other] (m): position of observation expressed relative to the top of the hole. The location is presented in a scale selected by the science party or the report user.
CLOSEUPCALCULATEDBottom depth CSF-B (m)Bottom depth [other] (m): position of observation expressed relative to the top of the hole. The location is presented in a scale selected by the science party or the report user.
CLOSEUPRESULTapertureRESULT aperture: aperture setting for the camera (e.g. F/22)
CLOSEUPRESULTbottom_offsetRESULT bottom offset (cm): bottom offset of the close-up request expressed in cm from top of section
CLOSEUPRESULTcameraRESULT camera: vendor and model of camera used for closeup photo
CLOSEUPRESULTdate_takenRESULT date taken: date/time stamp for when the image was captured
CLOSEUPRESULTfocal_lengthRESULT focal length (unit varies): focal length of lens (e.g., 50 mm); unit is expressed in the entry field
CLOSEUPRESULTisoRESULT iso number: ISO number of the light sensitivity of the camera
CLOSEUPRESULTjpeg_asman_idRESULT jpeg image ASMAN_ID: serial number of ASMAN record for the JPG/JPEG format image
CLOSEUPRESULTjpeg_filenameRESULT jpeg image filename: file name for the JPG/JPEG format image
CLOSEUPRESULTraw_asman_idRESULT raw image ASMAN_ID: serial number of ASMAN record for the raw camera format image
CLOSEUPRESULTraw_filenameRESULT raw image filename: file name for the raw camera format image
CLOSEUPRESULTshutter_speedRESULT shutter speed (s): shutter speed of the camera, usually expressed in a fraction of a second
CLOSEUPRESULTstateRESULT sample state: field to record sample state (e.g., wet or dry)
CLOSEUPRESULTtiff_asman_idRESULT tiff image ASMAN_ID: serial number of ASMAN record for the TIF/TIFF format image
CLOSEUPRESULTtiff_filenameRESULT tiff image filename: file name for the TIF/TIFF format image
CLOSEUPRESULTtop_offsetRESULT top_offset (cm): top offset of the close-up request expressed in cm from top of section
CLOSEUPSAMPLEsample descriptionSAMPLE comment: contents of the SAMPLE.description field, usually shown on reports as "Sample comments"
CLOSEUPTESTtest test_commentTEST comment: contents of the TEST.comment field, usually shown on reports as "Test comments"
CLOSEUPRESULTresult commentsRESULT comment: contents of a result parameter with name = "comment," usually shown on reports as "Result comments"