Expedition 330 Technical Reports
LOUISVILLE SEAMOUNT TRAIL

LO–ALO Handover notes

Bill Mills, Cheih Peng & Heather Barnes
The following technical reports, cover both Expeditions 335 and the 335T.
Expedition 335 is the forth expedition to site U1256D (Superfast) in an attempt to deepen the hole into the cumulate gabbros section and beyond. Unfortunately, the majority of the drilling effort was spent stabilizing the hole, removing cuttings and retrieving parts of a failed bit. Only a few meters of core were recovered including large amounts of cuttings and numerous large boulders. The hole was logged and left in a clean, stable condition.
Expedition 335T was the transit from Balboa, Panama to Curcao (via the Panama Canal) where the ship will remain for approximately 3 month during an operational stand down period. The 335 science party and along with some technical staff, disembarked at Balboa, Panama. There we took on 4 guests, that included Dr. Chester Raymo (professor and science writer), his daughter Dr. Maureen Raymo (Paleoclimatologist, and past Co-chief Scientist), Wendy Jacob (freelance artist), and Amy Mayer (freelance reporter). They interviewed staff, wrote daily blogs (http://blog.sciencemusings.com/2011/06/aboard-jr.html) and gave evening talks.
The transit thru the canal was shared with IODP at College Station along with friends and family of the crew via web cameras along the canal route.
Operations Summary
On the 13^th of April 2011, the technical staff from Expedition 334 crossed-over with oncoming technicians and then began routine logistic activities. The following day the scientist transferred from their hotel in San Jose to the vessel. The last line was released on 17 April at 04:20, and the vessel began transit to Site U1256. The expedition ended in Balboa, Panama on 3 June 2011. Throughout the expedition seafloor magnetic and bathymetry data was collected routinely on all transits. There were no seismic surveys or VSP operations.
After spending 2 days at anchorage taking on fuel, the JR began its transit of the Panama Canal at 07:45, 6 June and cleared the Colon breakwater at 16:15 on the same day. At 0945, 9 June the JR tied up at the Steiger Wharf 2, Caracas Bay, Curacao. On 10 June, Expedition 335 samples and data were offloaded and supplies for tie-up projects brought onboard.

SPECIAL PROJECTS

• New coffee counter top installed.
• The entire Science Pallet storage area was stripped down and rebuilt during the expedition. Improvements include:
  • Gas bottles moved to the starboard side and now have full open access so that staff can be safely connected bottles to the manifold systems.
  • Cage area expanded to hold all paper towel, Kimwipes, Kimtowels, cardboard boxes (except Core boxes), snap-cap vials, dividers.
  • Wax core box storage expanded
  • Safety barrier installed around the watertight doors to heavy tools
  • Material bins installed for wood, aluminum and steel supplies.
  • N2 booster and bottle fill station installed (waiting on N2 bottles to complete N2 tank farm)
  • Over head loft storage provide for curation supplies
  • Decks re-painted.

• Chemistry lab re-organization project:
  • General clean up of the gas distribution systems.
  • Shelving upgraded and expanded.
  • Additional counter tops installed.
  • New glass ware storage cabinets installed.
  • Electrical services relocated and upgraded.

• Treadmill was not working when we came onboard. The motor has died and we didn't have any spares to repair the motor. A new motor was installed in Curacao. A second treadmill is being purchased.

• Movie Room: It was to our surprised that the projection system in the movie room is gone, and replaced by a 60" TV. Several staff members expressed disappointment in the fact that none of the staff in this crew were aware of this change and the effect of watching a movie in a "theater" environment is missing. Both the TV and projector have pros. If we could set up both in the movie room that would satisfy all involved.

LOGISTICS

In addition to our standard freight the following were returned to CS:

• LN2 dewars, 7 ea, leaving 4 onboard
• Pallet jacks, old blue one and red one with scale
• DOE van (all 3 -86 freezers remain onboard)
• Lab waste from BRAD van.

The Upper 'tween Store Room (UTS) underwent a detailed physical count and items were re-organized to utilize the space more efficiently. Most items remained where they were previously except the oils and grease which were moved to the UTSHOP. The large amount of tubing was decreased by half - those that we no longer use are being sent back to College Station. UTSHOP nuts/bolts/washers were ordered to top up quantities.

AREA-BY-AREA SUMMARY

Bridge Deck

Planning Office: New coffee counter top installed

Core Deck

Catwalk: No issues
Core Entry:
Laser Engraver: TransOcean unable to determine the issues with lab exhaust system and have ok'd installation of the in line booster to exhaust laser cabinet. Work on the system should be completed and the laser engraving system available to the North Pond expedition.
Physical Properties Lab
NGR: Hydraulic lifts installed on doors covering electronics
SHMSL: Installed the Minolta's dark trap replacing the PVC tube. No significant change was noted in the output but the bore hole is larger and is more tolerant of position errors.
Pycnometer: New control board was installed. Pyncometer's internal wiring was complete rewired.
Thermcon: Half-space probes failed. This is a continuing problem that needs to be addressed with the supplier.
Splitting Room
Leaking drain line in overhead repaired
Core Description
DESClogik: Significant improvements were made this trip.
Tables: Large monitor's removed at science party request.
SHIL: The new Whole Round Imaging Adaptor was installed and tested.
Magnetics Lab
CryoMag: IRM is still a problem in samples demagnetized in high fields. Discrete sample data scatter determined to be the result of the sample's small geometry and the SRM's large measurement volume.
Thermal Demag: As reported on X330: Insulation is failing and heating elements are exposed. The whole unit needs to be replaced.
AGICO Spinner: Rotator shaft jamming in bent alignment tube.
Paleo Lab: Saw minimum use, no problems to report.
Close-Up Photography: No other problems reported.
PICAT: Saw extensive use without issues.
Microscope Labs: Emile Meylan spent several days during port call assessing the status of our microscope systems. The microscopes were cleaned, aligned and configured.

Fo'c'sle Deck

Hazmat Response Locker: No problems to report.
Publications: The new version of Strater was installed; working well with no issues.
Chemistry Lab:
General: The new 240V transformer was installed for the furnace and the CHNS.
Coulometer: No issues
CHNS: Supplied with 240V now
GC-PFT: Was not used this leg.
ICP: No issues to report. ICP data reduction program was updated.
Carver Presses: Still leaking oil, no action taken.
GC3: Gas leak was repaired by installing the correct gas fittings.
XRD Lab: Just was cleaned of the sample rotation bearings.
Thin Section: No issues to report.
Sample Prep Lab: No issues to report.
Microbiology Van: Was not used.
Underway Lab and Fantail: Bathy 2010 PC was upgraded to Win7

UPPER TWEEN and Hold Decks

Logistics Stores: No problems to report.
Shop: No problems to report.
Pallet Storage and Staging: See special projects
Core Storage: No problems to report.

LOWER TWEEN DECK

Data Center, User Room and Offices: No problems to report. Floors still need refinishing
IT Services
Satellite: VSAT satellite services presented multiple challenges maintaining an online status. The main cause was failure of both dome's SSPA (Solid State Power Amplifier) amplifiers and the requisite tuning of equipment parameters to stabilize the equipment.
Developers: Kept very busy, refer to their report.
Gym: Numerous floor cracks have appeared and need to be repaired during the transit or tie-up. New tread mill motor was installed in Curacao.
Lounge and Movie Room: Our video server has died and will be returned to shore for repair.

ALL OTHER AREAS

Elevator: No problems to report.
Cross Training:

• Heather Barnes, Chieh Peng, David Fackler and Sandy Dillard as well as Chad Broyles received training on the thin section imager
• Heather Barnes and Chieh Peng was crossed trained on microscope adjustment and objective and eye piece exchange.
• Chieh Peng and Tim Fulton both completed cross training in this lab.
• Erik Moortgat was trained on various instruments in the Chemistry lab
• Yulia Vasilyeva trained on Physical Properties systems
• Heather Barnes and Chieh Peng trained on DescLogik

Core Description

Thomas Gorgas

INTRODUCTION

EXP335 was a very unique and great opportunity to further develop and modify the software application DESClogik. Indeed, the expedition started already in College Station with a 2-day long workshop, with various scientists and IODP staff warming up to the task of describing rock material from Site 1256D. During this workshop, the group of EXP335-participating scientists and IODP Staff developed basic concepts, and identified variables and parameters how to describe the expected (gabbroic and other) core material, and to eventually transcribe those (values/parameters) into "DESClogik Templates".
On board of the JR, this process of "thinking it through from the very beginning" continued for several days; the result of this exercise were very detailed XLS spreadsheets, created and endorsed by the entire science party and EPM Dr. Peter Blum. The actual transcription of those XLS spreadsheets into DESClogik was then the logical next/last step in this entire process – a first remarkable "Breakthrough Point" in the process of developing a successful workflow with DESClogik on a daily base.
Using the application throughout EXP335 further highlighted (again!) how impertinently important the currently ongoing "DESClogik Enhancement Project" indeed is.
The following goals were set prior to EXP335:
Fine-tune the DL process to create templates and apply them properly throughout the expedition; one key point has become to develop the template draft in the XLS domain and then utilize the "BULK ENTRY" function to transform this draft into the DL Domain.
Empower the scientists to the point of autonomy using the application so well that the DL Tech indeed has more liberties to help with other important tasks in the Core Lab (i.e., core flow and core processing; supporting the physical property (PP) lab and supervising new PP Tech team members; supporting other/additional projects around the laboratory and ship environment, like remodeling the "Upper Tween Storage Room").
In short: Mentoring & supporting our scientists by providing an optimized and superior science service during each and every expedition.

EXP335 Core Description Summary:

Due to the inherent difficulties to drill through very hard rock material (as it is the case at Site 1256D), EXP335 was not blessed with a very high rate of core recovery; however, instead of retrieving regular core material, a good number of large rock pieces were retrieved in so-called "Junk Baskets", which provided a great opportunity to study the great variety of the ocean crust architecture at Site 1256D. The following tables summarize information about material as it was retrieved and described for both EXP335(312)UI1256D (from the previous EXP312) and (now) EXP335-U1256D (note: tables include data from Physical Property and Imaging measurements as they are intrinsically connected with macro and microscopic core descriptions entered into DESClogik):

Recommended DESCLogik Workflow Procedures for EXP335:

The following working steps were applied throughout EXP335, which allowed an overall smooth operation and utilization of DESClogik (see also the attached WORD-doc alongside with this report:
"335_DESClogik_GoodWorkingHabits_20110607" - Production Version.V12):

• Enter data initially into XLS spreadsheets, which resemble EXCACTLY the structure of the DESClogik template. That is the key for a reproducible workflow model.
• Make sure that ALL HIDDEN columns are moved to the RIGHT-HAND SIDE of the DESClogik template (to avoid unwarranted "copy & paste" effects later on – albeit fixed with the new & "face-lifted" DESClogik application).
• Make sure that ALL HIDDEN columns are deleted within the XLS-backup file, which had been derived from EXPORT-DATA within the DESClogik (DL) domain.
• CANCEL all (unwarranted) rows in the DESClogik template prior to uploading any warranted data (to avoid double-entries in the DL Template).
• When downloading data, always use "Filter Downloaded Results by: TEMPLATE" (i.e., CLICK the corresponding button to be active) in order to avoid unwarranted "Cross-Talk" from one template containing columns of similar/same definition into another template.
• Delete the SAMPLE 2 (Selection) window in order to "copy & paste" pertinent depth information into the DESClogik template column. SAMPLE 2 has been taken out of the regular "Production Version" of DESClogik, but still is available as a "Hidden Column". In any case: Pay attention to it as it can pop back into the "game" when using an older template (created prior to EXP335).

EXP335 Achievements:

To get this straight and put it upfront: What we were able to accomplish during EXP335 would have never been able without the stellar support from the LO/ALO Office on board the JR, and by all others who supported our efforts on a daily base. This is important to always keep in mind – as the sacrifice of those involved & exposed to the effects of this development process has been substantial at times.
However, EXP335 provided THE golden opportunity to develop and improve the entire DESClogik application package due to the above, plus the lucky fact that the actual recovery rates were dismally low (which was not entirely unexpected, based on previous drilling experiences from EXP321).
This "restructuring" process entailed everything 1) from the pre-cruise preparations (during a workshop in College Station 3 weeks prior to sailing), 2) to establishing a new work flow based on EXCEL spreadsheets as fundament for our DL templates, and 3) implementing a whole serious of new features and "de-bugging" the code as it has been used (almost unchanged) since EXP320.
This process included the two main programmers of the DL Application (Chris Bennight and Tim Blaisdell), two ALPHA TESTERS on board of the JR (Peter Blum, EPM of EXP335 & Thomas Gorgas as DL Tech), two ALPHA Testers onshore (Zenon Mateo and Maggie Hastedt), and a number of BETA TESTERS onshore (publication specialists and staff scientists alike).
The workflow for this improvement process was normally to 1) identify the "Requirements", 2) translate those into "Specifications", 3) develop a written "Test Protocol", 4) test the "Improvements" (by both ALPHA & BETA testers), and 5) "Rework issues" as they re-occur throughout the programming effort.
By doing so, we took one big-leap-forward to achieve one of our main goals, i.e., to reduce the work load on and/or enhancing the amount of contributions to affiliated working groups and segments of the core lab operation (incl. Physical Properties, Core Handling & Processing, Applications Developer/Data Manager, Publications Specialist, etc.)
So, in sum: With the team effort put into this project and its all-encompassing support, plus the special circumstances encountered during EXP335, we could focus almost entirely on the "DESClogik Enhancement Project" (monitor currently ongoing project at: https://sites.google.com/site/enhancedesclogikapplication/alpha-testing ).
Some of the soon-to-be-permanently installed 20+ improvements & accomplishments during EXP335 have been:
Defining & establishing new parameters and definitions for dynamic columns (to produce a "higher-definition" for describing core material).
Testing new DL Template TAB's and workflow from EXCEL-to-DESCLogik (and reverse).
For example: Parameter & qualifier lists as they are used within the DESClogik (DL) domain leads to the development of an "EXCEL Master Spreadsheet" (See: graphic depcition above). Both (DL & EXCEL domains) are equally important for this "Work Flow Model". The "EXCEL Master Spreadsheet" and DL Template MUST be a 1:1 duplicate in order to allow a quick & accurate transcription from EXCEL-to-DESClogik (which is one of the main programming achievements from this EXP335). It is important to develop & update the EXCEL spreadsheets in alignment with the METHODS SECTION of corresponding working groups to optimize the accuracy of the digital core description.

A very simple "improvement" since EXP330 (see: TECH REOPRT EXP330) has been the establishment of a "Daily Suggestion Tracking Sheet". It has been an effective tool to compile & modify existing DL templates; annotations by the scientists on this official "logging sheet" help to quickly address immediate needs of the science customer during their shift. This method also provides an easy way to implement rapid updates of the current DL template, going through the aforementioned "Work Flow" process of updating both column and value list content (first in the "EXCEL Master Spreadsheet" and then transcribe this content into the DL template).

Summary:

A total of 20+ new features were tested and implemented during EXP335 (with 20+ more pending thereafter) – a process that will continue beyond this expedition. Improvements include a number of "feedback windows" to inform the USER what to expect, do next, and so forth. Some examples of these features are shown below:
"Warning/Feedback Message" to save and/or upload your data into LIMS before you close your DL template.
"Marquee Style Feedback Window" during "Uploading Process":





Uploading of several tabs simultaneously after copy and paste of a large data sheet into DL templates (HUGE improvement compared to previous DL Versions):









Another new feature that provides an additonal "safety net" : a new AUTOSAVE function, which allows the user to collect & enter data into DL in the background; according to a preset temporal pattern, a time-snapshot is created as a backup. The ADMIN USER only has permission to load data directly from this "autosaved file" into the DL template (which distinguishes this new feature from the old "Workspace Feature").
One of the best developments from EXP335 has been the possibility to create a DL Template from a MASTER EXCEL Spreadsheet: an IMPORT function in DL allows generating any kind of template to any degree of complexity within miutes:

This new tool has been applied successfully for the first time during EXP335 on a "Testing Base Only", and – in conjunction with a modified working flow as described above – is THE ultimate digital "weapon" to create DL Templates, and to respond and adjust to the individual needs of the core-describing scientist and the highly complex task of describing rocks and sediments; it thereby allows to follow the paradigm of implementing a global data base.



What else in the future can we do to make it better from here on?
Further future improvements in the entire workflow process can come from the following:

• Paying attention to simple, but important details prior to the actual data collection and logging with DESClogik – for example, by providing ONE name for a specific template and then stick to it. Additional changes & modifications on a DL template throughout the expedition complicate the tracking of entered data prior & post-template modifications. The simple solution to this "issue" is to stick to one name of the DL template, and then log all data into this template under the same name. We experienced complications around this issue several times throughout EXP330 and also EXP335; we plan to improve on this simple detail-matter in the future.
• The workflow briefly described in this EXP335 report (i.e., creating EXCEL-based "Master Sheets" and subsequent transcription of their content into the DL domai, vice versus) also prescribes the possibility of a digital VCD (as part of LIMS PEAK). This allows scientists to enjoy both benefits: the visual display of a growing data set while collecting and modifying their observations within the EXCEL domain, and then ultimately uploading the final version of the data in one "Big Gulp" to LIMS via DESClogik.
• This workflow strategy essentially boils down to a flexible hybrid model of using both EXCEL and DESClogik in concert; describers can utlize the data base-related tools (DESClogik and LIMS Report/Web Tabular) while also working at ease with tools they are very familiar with (e.g., EXCEL). At the moment this appears to be the most appealing compromise for everyone as long as the up/download routines are working properly within the DESClogik domain (which they are doing now according to our tests).
• Additional recomended steps to further improve the performance in the Core Description Lab and the usage of DESClogik:
• 24/7 coverage of the Core Description Lab Environment with two technical staff members so that DL-related issues can be addressed effectively & immediately.
• Either Chris Bennight or Tim Blaisdell as developers sail on each EXP (unless more programmers are getting up to speed where they can effectively maintain and modify the software).

Acknowledgement:
We want to thank ALL technical staff, scientists and also management for their involvement, kind support and endurance to "suffer" through this important and necessary process to develop and continuously improve DESClogik as a viable and essential tool for IODP's Scientific Ocean Drilling mission.

Physical Properties

Yulia Vasilyeva

Summary

• Most of instruments, except fast track (STMSL), performed satisfactory.
• Logging tracks (WRMST, NGR, SHMSL, SHIL) saw minimal use due the lack of cores during this expedition.
• In Gantry, Pycnometer and Thermocon areas scientists were running more extensive study of samples on purpose to get a better statistic for the method optimization.
• Detailed analysis of the thermo conductivity and p-way velocity had been run on samples from Exp.312 and 335.

Analysis Summary

Problems

• Operation on logging tracks with hard rock cores, often represented by discrete chain of small rocks, had shown a necessity of further software or hardware adjustments for discrete cores (see details in the instrument sections).
• New half-space probe for Thermocon has failed after few weeks of effective performance. The failure has happen mostly due corrosion in the needle-wires area, which is located sill in plastic, but within less than1 mm from the surface.
• Upgrades
• In the Pycnometer system the electronic interface was successfully replaced with better version. The SHIL system was also successfully accomplished with additional 360^o rotation image track adjustment and related to that software.

Shipment to the shore

The following equipment will be shipped at the Curacao port call for the maintenance, repair, upgrade and training at IODP shore lab:

• Pycnometer (body, cables, el. interface, computer)
• Mettler -Toledo balances
• P-wave velocity gantry (controller, PWL actuator with LDVT, caliper, power supplies, Ultrasonic AMP, ERS coax LEADS, 200 LVDT)
• Exlar actuator TLM 20
• ER8 NI Relay box
• WRMST and STMST GRA detector and source mounts
• PWL actuator with LDVT (part of WRMST)
• 200 MS/s digitizer with LDVT (P-wave gantry)
• Laser distance measurement equipment – Acity, AR 1000
• Acuity AR200-50 (laser source)
• 200M/S Digitizer, type PCI-5124
• JAI Line Scan Camera CV-L107CL
• Niton XL3 hand held XRF analyzer and accessories
• Thermocon half-space probe H11015
• P-wave velocity Al, Cu and Acrylic standards

Personnel

Through infrequent analytical workflow, the technical personnel had a sufficient time for detail related, training and organizing activities.

SYSTEM STATUS

STMSL

• For hard rock expedition there were no needs for the fast track operation, therefore in the beginning of expedition it came disassembled and partly relocated on purpose to make additional space for external experiment (Anelastic strain recovery - ASR), conducted by scientists party. At the end of expedition STMSL was assembled back.

• The new version of software was installed on STMST during the transit to Curacao by D. Fackler and currently it's on testing and further development stage.

WRMST

• Whole–round track had been in use for the first few weeks and had not shown any significant problem with its performance.
• After first initial calibration, scientists had seen relatively high (~5%) error for quality control sample (water-core), but after following calibration, the error reading for QC core went to range of 2%.
• The system is scheduled for some minor hardware and software upgrades. The new version of software was installed on WRMST during the transit to Curacao by D. Fackler and currently it's on testing and further development stage.

NGR

• NGR logger was showing a proper functioning during this expedition, and had not shown problem with detectors, track or LIMS downloading software.
• It was noticed again that additional software development for features like K, Th and U concentration data calculation would be highly desirable for commendable LIMS output.
• Also in regard of data correction for discrete and hard rock cores, it seems to be very helpful to implement in NGR system additional software and hardware tools like application of GRA data in NGR data correction file and utilization ether of high quality laser scanning track or its reading from SHMISL data.
• Some minor arrangement had been done for NGR operation: 1) the interface board for the NGR track system was mounted with screws by ETs on the front side of electronic rack, because with previous arrangement the board kept falling from sticky pads; 2) star-up UG was written for training activities.

SHIL

Section Half Imaging Logger had shown a satisfactory performance.
New features:

• Bill Crawford had installed 360^o image rotation track unit of original design and related software. His new project had passed successfully the testing and following analysis, showing no problem.
• In addition Bill Crawford made a wire adjustment for the label plate in front of scanner, which helped to avoid difficulties of label reading, that happed many times before.
• Tim Blaisdell had improved a printer program for obtained images. He enriched the operator choices with one column printing option (read details in the SHIL documentation or in appendix of that report). Before the operator could print profile only in two columns, which was not handy for the series of short hard rock cores. Instructions are provided in the SHIL documents.

SHMLS

Section Half Multi Sensor Logger was used successfully during this expedition. However, in the beginning of operation there were noticed a systematic failure of software to generate a proper file name, when a scanning operation was done. The troubleshooting analysis had linked to utilization of "Skip position" option from acquisition file menu. Apparently only when this feature had been applied in acquisition, the file name corruption would follow the analysis. Otherwise data file was coming normally. That issue was reported to Bill Mill, and he had fixed the software error. Details The following operation had shown a smooth work flow both with "skip position" and without "skip position" application.

GANTRY

At Gantry system only discrete analysis features were employed during this expedition. It was noticed that lubricating/cleaning procedure of metal X-axis of caliper transducers system is very desirable before every expedition, and should be added to monthly maintenance list for the Gantry.
Series of calibration on different standards Acrylic, copper and Al had been run on purpose of observation of system reading stability. In general scientists have expressed a positive impression from instrument design and operation. However sometimes they observe a certain degree of inconsistency in their data reading. Initially it was only sample reading inconsistency (error ~5%), but during following experiment shifted reading of standards, were observed. It was hard to estimate the degree of shift due absence of certified standards.
In this regard for the future operation, it would be necessary to ether obtain some type of certification for existing Acrylic, Cu and Al standards, or buy additional standards with verified p-way velocity.
Scientists had been trying to root down the source of inconsistency with p-wave reading. According to their estimation, measurement of saturated sample cubes in water bath is giving most stable reading. Dry or wet cubes in the air are giving more inconsistency in p-wave data reading. Also it was noticed that most of inconsistency in data reading would be more related to the time variation. Scientists observe a system delay time shift, which probably caused a data reading shift as well, when they had been using a water bath for sample measurement.
All these study results and consideration had been reported to Trevor Cobine, who is currently working on software and possible hardware upgrades for the Gantry system.
At the end of expedition the Gantry system will be shipped back to shore for scheduled upgrade work there.

PYCNOMETER

The installation of new electronic interface (see the picture) at the beginning of expedition, performed by Mike Merling, and following programming adjustment, performed by Erik Moortgate, went excellently.

The major changes had been described by Mike Merling as a following:
"The Pycnometer interface boards mounted on the bottom of each cell were replaced with an integrated Electronics Interface Board mounted external to the cell enclosure.
This arrangement made the electronics accessible for faultfinding and eliminated the potential risk of flooding by temperature stabilizing water.
Additional features included: Separate screened wiring for signal currents from transducers and the switching currents to the solenoids. 
Current pulses to solenoids are timed to the optimal 30mS, regardless of the input trigger signal duration.
A reset circuit will inhibit random switching of solenoids when board is powered up.
Labview hardware and interface electronics are electrically isolated by optocouplers.
LED's indicate presence of trigger and solenoid pulses as diagnostic help.
A complete set of spares and technical manual was handed to ET's"
Detailed description of new interface can be found in the "Pycnometer Electronic Interface Technical Manual" that stores in PP-2G drawer (all drawer in Physical Properties area were numbered and labeled on purpose of easier inventory counting).
Erik Moortgate in his report described that he "configured the Volume Control application to incorporate the changes." Erik also wrote:
"Programmatically, the digital output remained the same as original design, but for the pressure transducers (analog inputs), a few edits were required. Since the original install, a couple of the connectors had to be switched.
The range of transducers was pointed out to be 30 psi, instead of 20 psi, so I therefore changed the code to multiply each voltage reading by 6, instead of prior division by 0.2.
Also, Mike had successfully configured the cell RTDs. I could now use those analog voltages to translate into individual cell temperature. Most of the code in the program was already developed, just had to be touched up. Using a table, provided by Mike, of voltages/temperatures measured, and using a linear interpolation, the following relationships are used:
Cell 1: temperature = 120.00 voltage -434.3
Cell 2: temperature = 109.09 voltage -392.6
Cell 3: temperature = 109.09 voltage -392.6
Cell 4: temperature = 109.09 voltage -392.6
Cell 5: temperature = 92.308 voltage -442.0
Cell 6: temperature = 109.09 voltage -391.5
The input terminal configuration (AI Voltage) are configured as Referenced Single Ended (RSE).
Each cell now has their individual temperature recorded in the LIMS, instead of a parameter that was manually entered by the user from a visual inspection of the water bath."
Eric had installed two additional shelves above the pycnometer. The water bath was moved to one of the shelf, and tubing was shortened. The water was cleaned from mold using 10% bleach solution. The tap water in the tubing was replaced with 50/50 solution of propylene glycol and DI water.
Pycnometer cell had been calibrated surpassingly several times. After that a few samples from expedition 312 and 335 had been successfully analyzed by scientists.
The Mettler Toledo Balance system, Pycnometer and Download software had not shown any trouble.
However, in the beginning there were a few time consuming problems with correction of different type of operator error, because software design is done in the manner of intolerance of any operator mistake (and for one sample we may have up to four operators for each step – logging properly sample, weighing dry mass, weighing wet mass and measuring volume operations).
In this regard it would be very helpful to implement the Mad Max software written by Tim Blaisdell for the pycnometer system to accommodate more efficient operation in the future. MadMax software would allow operator to verify the typing data before they will be entering into database, which will help to avoid frustration, and save programmers time.

THERMOCON

At the hard rock expedition scientists were working with
half-space probes only. The Thermo-conductivity unit had been working very well with a new probe for a few weeks. Graham Baines had conducted a detailed study on different type of contact surface lubricant (DI water, sea water, thermo-joint compound), and different type of probe alignment from the edge of the section half piece. Detailed results of his study can be seen in the expedition physical properties group report. These data perhaps further study to obtain a robust statistic about half-space probe application choices.

After few weeks of intensive usage mainly in the sea water bath (core section was mounted on Al rack and tightened with probe by Velcro belt – see the picture), the probe started to show an electronic corrosion signs: software had been failing sometime to finish the successfully hardware check -up procedure, indicating probe sensor connection problem. Later most of analysis had been failing (regardless, if hardware check was a positive - no error message for the probe sensor connection), because the drift temperature had failed to stabilized to the appropriate values.
Additional evidence of that failure was found in ".dwl" files, program had generated, that showed wrong water bath temperature reading.









Examination of the probe had shown a corrosion spot.
The picture of corroded spot and problem description was sent to TAS and Lab working groups on purpose to obtain the following plan of probe corrosion.
Also alternative design for custom probe from TeKa was suggested by PP and ET group (see the picture below):

Presumably that design will protect better electrical contacts from surrounding micro-cracks, which may provide some moisture access to this area, leading to fast corrosion.
The decision about Thermocon half-space probes repair is left to TAS management.

SECIAL PROJECTS

• The design of vacuum system in Paleo lab for saturating rock samples (Thermocon and MAD analysis) was revised. ETs had replaced tubing onto clear one with sicker wall and better grip, which helped to eliminate most of the leakage in the system. Through clear walls the moisture condensation drops were observed. According to the vacuum pump manual – no moisture should go to the pump, therefore a "filter" flask with dryerite inside was installed between desiccator and pump inlet. Transparent walls of glass flask help to observe dryerite color and change it to dry, as soon as used one will turn to pink. With constantly working pump a lot of moisture may go off the water containers, so dryerite consumption is expected to be high. Therefore it was decided to keep pump most of the saturation time off. Ti should be enough to let pump work for 10 min, create a vacuum of -100 , and switch it off.
• On purpose to increase the capacity of saturating system, a second desiccators was added. We need to order T connector * P/N* to keep both chamber operation independent.
• Niton XL3 hand held XRF analyzer reading stand had been installed in the corner between NGR and splitting room. That type of setting helps to ensure the safe XRF gun operation, preventing the operator from accidental exposure to operating X-ray source.
• He tank was installed by the splitting room door on side of NGR to provide the XRF gun with the He flow.
• All storage drawers within Physical Properties lab had been labeled with PP-N numeration on purpose to facilitate the inventory records.

P-mag Laboratory

Trevor Cobine

Overview

This was a low recovery expedition with no oriented core pieces. A small number of oriented samples were cut from Exp 312 core and measured. The equipment saw little use. The Scientists performed several test to determine the characteristics of the SRM and JR6a Spinner magnetometer. They quantified the problem of weak discrete samples and data scatter which is very useful for defining a possible measuring limit of the SRM. See Initial Reports, also Issues:

Issues:

• SRM: Testing showed the usual IRM in some samples demagnetized in high fields (40mT to 80mT).
• AGICO JR6a spinner Magnetometer. The auto sample holder rotator shaft was jamming. This was also observed on Exp330. The small brass actuator shaft is bent and binding on its tube. When it won't retract fully it can destroy sample holders. Magnetometer is to be used in the manual mode until we get a replacement shaft and tube.
• SRM, Discrete samples: As discrete samples are demagnetized and their intensities decrease the data scatters progressively. The central tendency of multiple readings (24 positions) is still correct but single readings are not reliable. Believed to be caused by the small sample's geometry and the very large measuring volume of the SRM. This was apparent on Expedition 330 with Jeff Gees personal standards which are of low intensity. We now have an understanding of this issue and it appears to be a limitation of the large bore magnetometer.

Changes:

• The SRM-Crest amplifier had the cooling fan replaced. New fan is 230v and powered from the crest amplifier, replacing an externally powered 110v fan, ensuring the amplifier doesn't operate without sufficient cooling, although it is thermally protected.

Returned to Shore:

• 2G/Applied Physics Degauss Controller & Grey Capacitor box for modification –part of solution by Applied Physics for the IRM problem.
• CTI 8200 Cryo compressor for refurbishment.
• Obsolete spare power supply for the old D-Tech 2000 controller.

Engineering / Downhole Lab

Mike Meiring

DHML

Windows7 change-over

The DHML PC was converted to Win7 OS.
Wintemp, TPfit and Hyperterminal applications were loaded and found to run without a problem. A Win7 version of Wintemp is available and will be purchased and shipped.
The USB to serial box used for communication with SET/SETP has a compatibility issue with Win7. Until this issue is resolved the straight connection (purple cable) must be used for communication.

WSTP

Prepared WSTP for deployment by replacing O-rings and pressure testing sampling plumbing to 5000psi. Found a leak on outlet of hi-pressure valve and repaired. The sampling plumbing, including the overflow chamber, was rinsed with 1 N HC1 and then with 18.2 mOhm milliQ water as per scientist instruction. The WSTP was not deployed. Drained the water from the sampling tubing, removed electronics and batteries and prepared and crated tool for shipping to CS.

SET/SETP

Removed batteries from SETP tools.
Dismantled SETP S/N2 and crated for return to CS.

APCT3 Temperature tools

Tool S/N 1858005 does not have a cal file and must not be deployed.
Dean Ferrell looking into it.

MicroSmart pressure transducers:

4 x pressure gauges were returned to CS for calibration

Spares in stock:

2 x WSTP/DSS 12V Batteries
7 x CDAQ Batteries
7 x APCT3 Batteries

RIG INSTRUMENTATION SYSTEM

MCS configured the Driller in drill shack to auto log-on on start-up. This will eliminate the need for a Rigwatch keyboard in the drill shack.
Kraketoa crashed. The DHML PC was configured as Master and Rigwatch service restored.
The draw works encoder was reset after line slip and cut.
Converted all Jobs folders to ASCII and saved at T:\ data1
Updated RIS User manual with help from Karen Graber on shore.
ET, Etienne Claassen received training on the Rigwatch system, theory and practice.

Windows7 change-over

When the Rigwatch8 application was first loaded on a box with Windows7 OS it could not read the software key. The problem was traced to the 1-wire software that natively installs with Rigwatch. It was not compatible with Win7. Our MCS team was pointed to new software by Dallas Semiconductor and was successful in running Rigwatch on both Win7 and 2008 server. The driller and DHML machines were then changed to Win7 OS. Rigwatch8 is currently running as a system on Win7. The remainder of the Rigwatch "remotes" will be changed-over to Win7 during transit to Curacao.
Startech serial port extender devices provide communication to the Veeder Root depth counters, Tracer pump and XBob video overlay. These devices are not compatible with Windows 2008 server (Win7). A Win7 compatible version was purchased by IT (PG) and will be tested on shore before being shipped out for installation.

Instrumented Loadpins

Replaced the 12V battery which was down to 6V.
Replace both PORT and STBD transmitters with modified units now running off of the system (only) 12V battery.
With load step changes of ~200klbs, the PORT loadpin showed no correlation and the STBD loadpin showed little correlation.
Both loadpins S/N 10204 and S/N 10205 are unserviceable..
Static measurement on spare loadpins S/N 0005937 and S/N 0005938 indicated outputs of 3.7m A and 3.84m A respectively. History suggests a reliability issue. It is speculated that the strain gauges detach from loadpins. Both spare loadpins were crated to be returned to CS for repair/calibration.
Loadpins currently in service will be replaced with standard loadpins and returned to CS.
Loadpins are calibrated for 0 – 500klb with output of 4-20mA
Omega wireless daq has a resolution of 8u A. This equates to 250lb/pin. The two pins share the hookload thus Instrumented Hookload resolution = 500lbs

To do

Replace the current 12v battery with a Li-Ion battery of 14.8V/20Ah.. The battery incorporates internal low voltage cut-off and auto charge regulation.
A 5W solar panel mounted on the S/S box should provide sufficient charge to keep the battery topped up. One of the spare transmitters can be temporarily connected to monitor battery voltage to confirm endurance. This arrangement should reduce maintenance considerably.

XBob Video Overlay System for Coreline depth indication

Intermittent operation of the core line depth video overlay indication was traced to a faulty network switch. The switch was part of the original Rigwatch installation by Canrig and was mounted inside the Data-box in the Sub-Sea shop. Non related is the Win7 incompatibility of the Startech device which forms part of the XBob system. This is now a known issue and will be resolved soon.

Pycnometer installation:

The new Pycnometer Electronics Interface board was installed commissioned and it was confirmed serviceable. A technical manual was printed and handed over to Physical properties tech and copies e-mailed to ET's. Complete set of spares were handed over to ET's.

ET Report

Jurie Kotze: Etienne Claassen

Core lab

• All six pygnometer cells were stripped out and all the old electronic cards were removed and wired from scratch to incorporate the new control board which was installed against the bulkhead above the pygnometer housing. Some changes were made to improve the water flow through it. The instrument was officially handed over after a commissioning run on all the cells with the firmware sorted out as well. It's a superb instrument now!
• A small change was made to the DIS- track non-reflective spot for zero light calibration, an absorber box with a black offset mirror was fitted in place of the screw-on cap with light absorbent material fitted inside. a Small fraction of environmental lighting still enters between the pickup face and the track calibration surface, it's not too bad and could be adjusted out if the instrument is available to play with in port/transit.
• The AGICO magnetometer got a bit of damage after the brass push-rod locking pin got caught up against the sample holder cage while it was spinning. The rod has a slight bend in it at the moment. Not sure what happened there but it will need a new push rod, we think that a general service checkup might be best at this stage as we will have a bit of time during tie-up. It has shown some signs that it might need some proper service by the manufacturer; it has been working for quite some time and might be due for deep clean and service. It is still in service as the sample direction can be changed manually and it seems like it might be a quicker way to get around, the automated procedure is pretty slow.( seems like some scientists prefer to do it manually !)

Chem lab

• The last spares that was ordered for the 4, 2 deg C lab incubator arrived and the unit was repaired and tested and in good working order again. A spare set of overhauling components and control card was put together and handed to the Chem techs for future use if needed. It will be stored in the chem lab.
• The Muffler oven was fitted with the newly ordered 5 KVA step-up transformer to get the Furnace to reach its maximum temperature of 1150 deg. C. The furnace could only make it to 980 with the ships 208V mains, the installed transformer steps the supply up from 208 to 230 V as specified by the manufacturer.
• A new digital thermometer plus two "Type-K" thermocouple probes arrived and given to the chem techs as well for use with the muffler furnace.
• New racks was built with t slots and two new cabinet was built for glass wear, table tops was made from maple wood for glass wear cabinets and for islands in lab frames was made for islands from t slot. An 6 feet by 3 feet shelf was built above the instruments, and wood shelving was made to fit in the aluminum frame.

Down hole lab

• Mike Meiring sailed this expedition and he ran the DHML and will present it with his tech report.
• Etienne went through some extensive Rigwatch (and related instrument) training with Mike Meiring.

Paleo lab

The old Welch vacuum pump was replaced by a newer spare that we had, the old one needed oil changes very often with most of the internal shafts, bushes and seals being so worn that moisture easily came through to the oil sump and it has reached its end of useful life, it might still be possible to overhaul but its became so noisy due to excessive wear that it became a source of irritation by running so loud, we will send it back to C/S as surplus. It's not worth the cost for a recondition.

Pallet store

The Nitrogen booster pump was installed in the pallet store with the gas bottles and tested but it had a fine crack on the inlet manifold segment on the pump, it was swopped around with a second spare one but it could not reach the expected pressure. It was overhauled and is working fine. The gas sensor probes was installed and wired to the signal conditioning card that links it to the ships communication network. A set of spares was ordered as stock item for future maintenance. The booster pump with the leak was repaired and put back in the store as spare.
All steel structure in stores was removed, an all-new box aria lockable store room was built in old gas bottle aria, new place was built for gas bottles and platform was erected above gas racks

Store roOms

The RIGID orbital sander's speed control board packed up and it was wired to run at full speed for the moment and a new speed control card assembly was ordered. The images of the stripped tool were placed on the ET drive on the server for the "repairman", whoever will be receiving the spares. The speed control knob and drawing is in the video tester's drawer in the ET shop.

Gym

Tried mill motor was removed, motor bushes was found to be worn down and damage the commentator, electrical shop try to repair the commentator but could not repair it this time

General

V-SAT

• The aft V-sat power amp failed during the expedition and the forward dish was in service due to the failure. The forward dish had a problem with the satellite being behind the radar mast and caused some ship DP difficulties as the ship had to be positioned at an angle against the oncoming water current which in turn had some increasing power demand from the generators to keep it at that angle. The aft equipment was moved piece by piece to the forward dish and tested to make sure that the aft feed horn did not have a reflection problem. After we were sure that it was okay we moved the forward power amp into the aft dish and had it back on air relieving the ship's DP issue.
• The second amp failed a week or so later as well with a similar burn on the output circuit and I have concerns that the feed horn might have a bit of a mismatch but that is only suspicion till we measure it , it could have been a coincidence but will be good if Rignet can sweep it with a Spectrum analyzer to establish its health. Both amps could be fixed as the burning problem occurred on the PC board tracks and not failed components. Our Spectrum analyzer cannot reach the Freq. span that it's operating at so we could not sweep it ourselves. Our analyzer can reach 3 Ghz and the V-sat operates close to 6 Ghz. It will be good if Rignet can give the system a thorough inspection.

Liquid Nitrogen generator

• The LN2 generator had some strange symptoms that did not make sense, after some hunting around we found that the ship's chilled water to the unit was at 18deg C instead of not more than 8 deg's. After that was sorted out by the ship engineers it came back to normal. It might be something to take note of and always push a thermometer through the pipe insulating foam onto the pipe to check on the water temp before starting a major investigation, it will in most cases be the problem if all else seems in good order.

CURATORIAL REPORT

Chad Broyles

Summary

Samples – A total of 761 samples were taken for Expedition 335. This total includes samples taken for Leg 312 which is designated as 335(312), and Expedition 335. For 335(312), 14 shipboard samples were taken, and 170 personal samples. For Expedition 335, 101 shipboard samples were taken, and 476 personal samples.

Shipments

Core – There were 4 cores received on Expedition 335. 10 boxes of Leg 312 cores were sent from the GCR to the JR. 12 boxes (Archive & Working) are being shipped to the GCR. These boxes contain all Leg 312 cores sent to the ship, and the core material received on Exp. 335.
U-Line Red Boxes-6 U-line red boxes and 6 P-Boxes are being shipped to the GCR. These contain the remaining junk basket material, residues, and shipboard thin sections obtained on Exp. 335.
Residues – The residue distribution is as follows:
Residue Destination
335(312) MADC (PP)all to Morris
335 MADC (PP) 1 to Morris, rest to GCR
335 TSB Anma, Dick, Endo, Godard,
Koepke, Lissenberg, Miyashita, Payot, Python, rest to GCR
335 ICP Godard, Harris, Miyashita
Thin Sections – Sandy prepared a total of 41 thin sections. A complete list is also available from LIMS Web Tabular Reports by searching Exp. 335, with a Test List qualifier of TS. An excel spread sheet of this inventory is also being sent to the USIO Curator and GCR Superintendent.

Curation Activities

Processing of 312 1256D Cores

89 sections of working and archive half cores from Leg 312 were sent to the JR for processing. Exp. 335 is a continuation of Leg 312 in the same hole (U1256D). The archive half sections were re-described by the Exp. 335 science party using the new shipboard systems. The following working and archive half cores were sent to the ship from the GCR: 312 1256D 201G-234R.

Sampling of 312 1256D Cores

The working halves were available for shipboard and personal sampling. These sections became very important as very little core material was recovered on Exp. 335. Since Leg 312, working halves had been sampled heavily. Exp. 335 scientists formed a number of groups to combine their efforts, and preserve core material based on the co-chiefs request.

335 Hard Rock Core Processing

Cores were processed in a similar manner to Exp. 324, 327, and 330 with the following exceptions:
Core liners were not used while drilling. When the core came up on the rig floor, the curator and other technicians waited with pre-split core liners at the end of the catwalk. Once the core barrel was lowered horizontally, each rock piece was removed from the core barrel one by one, and placed in the split liner. Before each piece was removed, the curator marked the bottom of all oriented pieces. The core catcher was added to the bottom section. If possible, enough space was left in the bottom most section and the core catcher added to the very bottom of the entire core. If there was not enough room for the core catcher in the last section, it was placed in a separate liner.
360 Degree Core Imaging- Once all the proper curated information was entered and uploaded, two scientists, along with the Curator/ALO worked together to obtain a 360 degree image of the core. It was important to ensure pieces were not flipped over, or put in the wrong place in the section. This was done carefully as the whole round core pieces were not labeled. The only people that touched the core at this time were the scientists dedicated to this procedure, and/or the curator/ALO.
However, very little core was received on Expedition 335.

Junk Baskets (and associated samples)

Several junk baskets were acquired as a result of drilling problems experienced on Exp. 335. Junk basket material consisted of broken pieces of hard rock that had fallen down the hole, ground up rock material (sand to gravel sized), large to extra large boulders of volcanic rock, cement, and sometimes pieces of the drilling bit. Junk basket rock and mineral material was entered into the database as a sample from the hole (U1256D). The interval was entered based on the depths the materials were retrieved from. This was acquired via Co-chiefs from the Operations Superintendent. Any additional important information was placed in the Comment field of Sample Master. All junk basket material was washed, sieved, dried, sorted, labeled, and bagged.

Entering Junk Basket Material into the database (Sample Master & LIMS)

There was a very large amount of junk basket material received on this expedition, and very little core material. Therefore scientists were much more interested in this than they would be on a routine hard rock cruise. We had to devise an organized system to catalogue this material. The co-chiefs and staff scientist decided it was best to first catalogue by the run number of the bit as defined by operations. The next level of information was the type of tool (i.e. junk basket) used to retrieve rock material. A wide variety of different junk baskets were used. Examples include: the External Junk Basket (EXJB), the Reverse Circulation Junk Basket (RCJB), Bit Sub Junk Basket (BSJB), and Flow Through Junk Basket (FTJB). These were the primary tools used to collect this material. Rock material was also extracted from the Drill Collar above the junk basket (DC) and the Fishing Magnet (FM). The next level of definition was labeling actual rock material. We received very large pieces of rock (boulder sized) from the RCJB. The scientists then picked rocks they were interested in, and we labeled them with an alphabetical system A-J. The next level of definition was the type of sample taken (e.g. TSB). Every sample was entered individually into the Name field of Sample Master. This was the only option as samples were taken off of the Hole. Sample Master does not allow you to take subsamples of samples taken from the Hole since Core, Section, and Section Half information is missing. The following table is an example of how this system was implemented:

Run02-EXJB & Run 06-EXJB
Run02 and Run06 acquired rock material from 0 to 923 mbsf. These runs consisted of ground up gravel sized volcanic rock material.
Run10 (DC, EXJB, FM)
Run 10 retrieved rock material from 0 to 1434 mbsf. When the junk basket arrived on deck both it and the pipe above it were stuffed with ground up rock material. Subsequently three separate batches of junk basket material were received. Run10-DC mainly consisted of fine grained ground up volcanic rock. Run10-EXJB was a mixture of rock and cement. The cement was a result of drilling techniques implemented earlier in the expedition. A small amount of mud was also retrieved. A mixture of rock and metal was received from the Fishing Magnet. In all cases the rocks were rinsed with water as they were coated in mud and grease from drilling. The finer grained material was washed and sieved. The sieved portions were dried and separated.
Run11 (DC, EXJB)
Junk basket material came from 1353 to 1520 mbsf, and yielded pieces of deeper crustal material. The size of rock material ranged from sand sized particles to large pieces. A decent amount of metal shavings were filtered out of the rock material by the technical and me. The scientists chose 6 large pieces for close ups and thin sections. Again these samples were taken as 'children' of hole U1256D. The bulk of the material was logged as cuttings (Type=CUTS). The Test, "SCRAPE" was assigned so the close up application would recognize the samples. The 6 Thin Section Billets (TSB) were logged as separate samples. Since there were no piece numbers assigned to pieces, we labeled the 6 chosen pieces J-1 to J-6. This was to ensure the close up images and thin sections could be matched by the scientists.
Run 12 (DC, EXJB, RCJB)
A very large amount of fine grained rock material was received from the DC. The EXJB consisted of fine grained to large size pieces of rock. The depth range of the EXJB was 1328 to 1518 mbsf. The Reverse Circulation Junk Basket (RCJB) ranged from large pieces of rock to extra large sized boulders from a depth of 1516 to 1518 mbsf. The large sized boulders, and significant pieces picked by the scientists were labeled Rocks A-Y. An example of an entry in the 'Name' field is: Run12-RCJB-RockA. Close up images were taken for the large boulders. The extra large boulders were sliced, described, and subsequently sampled for shipboard analysis.
Run 13 (DC, EXJB, RCJB)
The RCJB yielded two large sized boulders from depths of 270 to 1518m. The EXJB and DC yielded fine grained sand to pieces of rock from the same depths.
Runs 14, 15, 17, 18 19, 20, 21, 22
The last eight runs used the same aforementioned junk baskets in various configurations. In general, material from the DC consisted of fine grained sand. EXJBs and BSJBs recovered material ranging from sand sized grains to larger pieces of rock. The RCJB and FTJB yielded large to extra large sized boulders. In all cases the scientists classified different rock types and did structural descriptions on the larger boulders. Naming nomenclature and sampling was the same as previous runs.

Daily Shipboard Sampling

Every day at noon the scientists, co-chiefs, and I would gather around the sampling table to discuss shipboard sampling. Prior to this larger rock pieces were cut to reveal features such as veins, and magmatic fabrics. Samples consisted of thin section billets (TSB), ICP, and PP/PMAG. The scientists then marked their samples with a red china wax pencil, and filled out appropriate TSB forms. Once all shipboard samples had been marked, myself and the technicians on hand, would enter and cut all samples. ICP samples were then delivered to the XRD technician. Thin section billets were placed in a labeled box, in the core lab. The thin section technician would pick these up when he came on shift.

Thin Section Imaging

On Expedition 335, I learned how to image Thin Sections with the Thin Section Imaging System. After entering the thin sections into the database I took cross polarized and single polarized images of all thin sections and uploaded the images into LIMS.

Sample Party

A sample party was implemented in the last week of the cruise after we received the final core.
To begin with, a sample party was carried out for the 312 core material sent to the ship.
After this was completed, all Exp. 335 core, and junk basket material was laid out for scientists to pick their samples. A lot of the junk basket material consisted of pebbles in plastic bags. For these samples, scientists placed their stickers directly on the bags. They then picked a subset of what they wanted, separated it in a smaller bag with proper identifying information, and put it back into the larger bag. The larger boulders were laid out on trays. The scientists interested in sampling these rocks placed their stickers on the trays. Once scientists picked all of their samples, the Sampling Allocation Committee (SAC) went though and approved/disapproved all samples. During this time, scientists interested in the large boulders, explained what they required. At this time, conflicts were sorted out and compromises made. Once samples had been approved, requesting scientists filled out request forms for all samples picked. The first samples to be cut were PMAG cubes for the magnetic fabrics team led by Tony Morris. The remaining samples were cut afterwards according to the requestors instructions.

Action Items

Thin Sections

A few thin sections made on Exp. 335 have been requested for borrowing. A complete list of thin section borrow requests is being sent to the USIO Curator and GCR Superintendent

Problems Encountered

This expedition proved difficult in that we received very little core material. However we did receive a large volume of junk basket material. The Sample Master program is designed to handle the traditional core and section system that is typically received on IODP expeditions. In turn we used the 'Name' and 'Comment' field to describe the material that was received.

Computer Software and Hardware

Sample Master-Sample master was updated to a new version on Exp. 335. This version corrected bugs such as 'Edit' issues in Piece entry. For example, piece edits were not carrying down to the section half level when auto-split. However, major bugs still exist in the 'Edit' function of the program. The program would not allow me to edit the 'Name' field, or 'Sample Request Number field'. I worked with the programmers to document these issues. Tim Blaisedale was very responsive and helpful with correcting problems. We brainstormed several new ideas that I think will benefit the software including a sort function. The latest version of Sample Master is 2.2.0.13.
Piece length-At the co-chiefs request, procedures and the Sample Master program were modified to take into account actual piece length. On past Phase II expeditions, bin lengths for individual pieces in a section were recorded. The program automatically equated bin length with actual piece length and assigned this quantity to a column Piece length. Sometimes these two quantities (bin length and piece length) are not the same. To take this discrepancy into account an extra column was added to the Piece entry tab in Sample Master. Bin lengths are still recorded, and Bin Length is calculated. This length has a column heading, 'Bin Length'. Individual intact whole round pieces are also measured. This is recorded in the Piece length column of the Piece tab in Sample Master. Half pieces (W and A) are not given a value as they can differ. If scientists find discrepancies once the piece is split, it is their responsibility to record this information. They then can pass this data on to the curator for entry into the sampling program.

Special Projects

Installation of keyboard and monitor mounting arm at sample station-The Sampling Station keyboard and monitor were cramped into a corner, and not accessible. At the beginning of Exp. 335 I installed a mounting arm for the monitor and keyboard. It is now more accessible, and comfortable to enter data at this station.
Curator folder backup-During Exp. 335, I backed up all important curator files saved on the JR servers onto my 1 TB external hard drive. This is to ensure curation does not lose valuable information. It is also to ensure that we have a copy of this data on shore.
Curatorial Cookbook Update-I began to update the Curatorial Cookbook on this expedition. This will take quite some time as many procedures have changed. Also the Core Lab has completely changed, with the addition of many new instruments. We also have a completely new database (LIMS), and a new suite of software.

IMAGING LAB

William Crawford

SPECIAL PROJECTS

Line Scan Camera Whole Round Imaging Adaptor. The modification to the Line scan imaging system was installed. Testing of the system to confirm viability of the concept was done. Two routes were taken as to the actual stitching of the system. Douglas Wilson, sailing as a Geophysicist and former Co-Chief took the lead writing a program using tiffs and pixel counts to blend the images.Other methods using Photoshop and Panorama Maker were also used and the images compared. Unfortunately the lack of samples harvested in core form was not enough to test the system thoroughly.
The line scan camera can be changed back to split half and vice versa in a matter of minutes. I rack was built behind the scanner across from the pycnometers to store and secure the two adaptors.
An extruded core tray was added to the front of the scanner to hold the samples prior to loading. This was done in anticipation of a possible workflow arrangement; however the lack of core did not allow a testing of different workflow arrangements.

Alignment, Color and Density Calibrations

Core recovery was minimal due to the nature of the Expedition. The samples that were harvested we imaged on the Close-up station rather than the line scan camera.
During the period of time of anticipation of coring, the line scan camera bar code arrangement was modified.
The reflective nature of a curved surface, coupled with the type of illumination of the current bar scan arrangement successful reading of the bar code label on the bottom of the core liner has been problematic and led to delays and frustration with operators. This has led to the operators using and scanning the end caps for the input of data. This system has problems also. One of which was the sighting of the bar scan gun to the bar scan label. To lesson this problem, I fabricated a End-cap holder that places the cap accurately and the bar code is scanned without delay. This modification sits above the keyboard conveniently.
The Line scan camera system was checked for dynamic range and calibrated for color. It is my understanding (2011-06-07) the computer systems were modified or replaced at the end of the expedition and I do not know the status of the system as this time.

MICROSCOPES

Configuration and alignment. During the course of this task, one of the 40X objectives were found to have plier tool teeth marks on the lower barrel indicating someone not trained had changed out or attempted to change the microscope configuration. During his stay I ask Emile to identify the 160mm Gray Standard Microscope equipment for possible return to shore. We aligned and cleaned the best 160mm scope to remain on the ship for back up or special needs. Emile discovered the two new specimen holders would not fit the stages. He made measurements in order to machine adaptors for them. He provided drawings, which will be sent to shore.
I selected a collection of objectives to remain on the ship for that scope and the one in the Thin Section Lab. The remainder of the 160 equipment was packed for return to shore.
Heather Barnes and Chieh Peng was crossed trained on microscope adjustment and objective and eye piece exchange.

Overall Microscope Assessment. Other than configuring the microscopes for specific needs in the first few weeks after departure, the microscopes required little attention other than cleaning and minor adjustments.
The scientist were pleased with the performance of the microscopes and the ease of gathering the micrographs with the appropriate metadata was observed with 2102 micrograph images loaded to the data base despite the recovery performance of the Expedition.
David Fackler instructed me on how to edit the config files for each microscope station to reflect the configure of the microscope as being used.

Close-Up Photography

The close up capture station worked well and was in effect substituted for the line scan camera to capture an archive record. The samples were photographed as needed whether that was multi-sided non-split, split, split or polished or wet or dry. 166 close-ups were taken and added to the database.
There were some issues with the labeling system as a non-standard label was required which cause overlap and wrapping problems. David Fackler provided solutions and this should not occur on legs with out Junk basket sample retrieval.

Video and still efforts

My video efforts concentrated on video capture and editing. 96 gb of AVCHD digital footage was taken of ship activity as well as the cannel crossing. It was requested a video be made of the rig floor activities and I produced an assemble edit for the Transocean crew.
Assemble edits of the Expedition was created but not rendered. The assemble edit of the canal crossing is in progress.
At this time 697gb of "RAW" and processed video has been used. This is beyond the capacity of the hard drive provided on the video-editing computer. I shuffled files around and made room on a 2 tb drive and used the E-Sata docking system to augment the system. It was found to be fast enough to edit directly from the external hard drive. This will become my operations standard.
73gb of raw still images were taken for PR and request.
Sarah Saunders with Ocean Leadership participated in the Expedition as the Education Officer and we worked together on several projects requiring images.
The Hasselblad cameras returned from repair and were put in to operation.
One Canon flash extension cable was found to be cracked and was repaired by the ETs.
The Epson Printer functioned with no problems and turning the printer off during long idle times seems to be the cure for nozzle clogging.

Petrographic image capture and archiving tool (picat)

The Petrographic Image Capture and Archiving Tool was use extensively with 88 thin section images added to the data base. Heather Barnes, Chieh Peng, David Fackler and Sandy Dillard as well as Chad Broyles received training on the thin section imager. Two of the larger 2x3 thin sections were produced and through the use of the diffuser the machine was easily adaptable to image those as well.

Other projects.

I have created a workflow document for still images and for other aspects of the Imaging specialist task.
Considerable time and effort went into organizing and maintaining the various digital assets.

Vit recordings

As a part of normal workflow, it was established the Imaging Specialist be brought in as part of the VIT archiving system. In the process of this work flow model, the file is duplicated and another copy is given to Engineering. In doing so a collection of the re-entries are archived on the hard drive.
I was asked by one of the Co-Chiefs if he could copy those files to a hard drive and of course I agreed. I was then approached by the Expedition Project Manager and was requested to edit those files to show only the point of re-entry. This requires the files to go through 2 different conversions before entering the editor. Total time to convert edit and produce the files was approximately 30 hours. This can be done and we have the ability and equipment to do so on board. I believe it should be discussed at a management level whether this should become a part of our normal requirements. Have we evolved beyond a need for a DVD format? During the time of the programs consideration of replacing the VIT Camera system, this may be a point to be included.

Publications Specialist Technical Report

Tim Fulton

Summary

Overall expedition 335 was very light due to drilling problems encountered with the hole. No issues with equipment and software have occurred to date. Strater 2 was installed on Exp. 334 and after 2 days of working with it I was comfortable. It worked well with no crashes. During this cruise the Mac's and PC had Adobe CS5 installed with no issues. Exactly 38 visual core descriptions for Hole U1256D, 335(312) - 34 and 335 - 4 were created, proofed and corrected during the expedition.

Equipment and software performance summary

The new version of Strater was installed to the publication office PC during the last expedition. The upgrade seems to work well with no issues to report.

Database, entries and data upload or download related

No issues to report in regards to database uploads or downloads. It took some time to identify the columns to plot, however, once done it seemed fairly routine. It was largely a trial and error process working with Lims2Excel, however, with patience the process seemed smooth.

Volume material

Due to the drilling issues encountered the volume material did was not received till a couple of days before the end of the expedition. With there only being one site this did not seem unusual, however, it did make for a somewhat frantic finish.

General duties performed

• Provided administrative, graphics and publication support throughout the expedition.
• Distributed and completed necessary expedition paperwork. To include; wireless device, communication policy, photo release, manuscript and photo copyright forms.
• Collaborated with the staff scientist to create server directories for the scientists, as well as creating the Publication directory for transfer of volume material to shore.
• Communicated with shore based IODP travel administrator to verify hotel arrangements for end of expedition.
• Worked with science party and Desclogik administrator to create accurate graphic data reports and specific figure requests as well as troubleshoot any issues as they arose.
• Provided support for visual core descriptions, methods figure and core recovery summary figures.
• Collected, organized and tracked final volume material submitted for the expedition.
• Modified initial shore-created Strater templates and Methods figure during the start of the expedition to display specific plots requested by science party. Continue to update Methods figure as needed for the expedition.
• Assisted and coordinated social events, including; birthdays, expedition t-shirt design contest and other special occasions.
• Trained in the thin section lab.
• Helped with the redesign and construction on the Uppertween storage area.

Additional duties

• Communicated with shore staff regularly to provide updates and seek expertise.
• Restocked Publication supply cabinet as needed, and provided science party with supplies per request.
• Downloaded corrections for Exp 327 VCD's and applied the corrections from the postcruise meeting.
• Printed and collated expedition paperwork for next expedition.

Suggestions

More training with Lims2Excel and Desclogic would be a benefit. On Exp. 335 I had time to do a trial and error method of creating the XML for the database download for the VCD's. With more familiarity it would require less experimentation in getting the proper columns to export.

Chemistry Lab Technicians Report

Mike Bertoli, Chris Bennight (ICP-OES) and Erik Moortgat

Overview

Expedition 335 was a hard-rock leg with a very low number of chemistry samples, primarily due to the condition of U1256 since the last expedition to utilize it. This allowed for several projects/remodeling, including

• a complete overhaul of the UT gas system (N₂, He, and Ar)
• installing new shelving above the Cahn balance and above the coulometer/CHNS bench, new benches near the SRA, DA, and GC3, and new cabinets under each porthole (when materials are available)
• remodeling the GC3/NGA/IC/DA bench (removing one cabinet, installing new shelving, rerouting ducts, gas and electrical lines, drilling new countertop holes, and rearranging the instruments)
• installing and mounting new gas lines all over the lab
• documentation (revision of CHNS, GC2 manuals)
• general lab inventory (updates to the inventory sheets, including some locations, duplicate part numbers, and misleading nomenclature
• repair of GC3 after X334

Issue Summary

Included below are outstanding issues that the laboratory officer or others may need to be aware of.

• Carver Presses – this issue was raised several expeditions ago and is listed in the X330 tech report; to date, these fittings are still faulty.
• Rechargeable gas canisters – these were ordered and sent to the ship, but do not seem to have arrived.

Parts on Order

• New "clickers" for the chlorinity titrator.

Instrument Status

Cahn Balance

• The Cahn 29 performed without error during this expedition.

Mettler-Toledo Dual Balances

• The Mettler-Toledo balances were not used during X335.

Coulometer

• The coulometer was not used during X335.

CHNS

• The CHNS was used this expedition to analyze carbon and hydrogen content of eleven samples. No issues with the instrument were encountered; 80mM L-Cys solution was used as the calibration standard (aliquots of 5, 10, 20, 30, 40, 50, and 60µL) and we ran both JP-1 and BAS140 rock standards as drift standards. In total, we ran and analyzed 182 samples (including blanks and standards).

We also heated the powdered samples in an oven at 110oC for 12h (to drive off any moisture, thereby reducing the hydrogen peak); it worked. This will be incorporated into the revised CHNS User Guide.
It should be noted that the hydrogen and sulfur peaks have massive overlap (see the chromatogram below); if we intend to analyze hydrogen we should consider some sort of sulfur trap (so long as this doesn't degrade the sample gas' other components), or a different separation column, or a dual-reactor column setup, something to better separate the two peaks. We accommodated the huge hydrogen peaks by increasing the runtime to 20min (from 10min) and by running blanks between every sample, eliminating carryover as best we could.
Figure 1. Chromatogram of BAS140, depicting co-elution of the hydrogen and sulfur peaks.

SR Analyzer

• The SRA was not used during X335.

Water System

• No issues to report; we replaced the larger NANOpure DIamond cartridge pack, which improved the water from 18.0MΩ to 18.2MΩ.

Dionex IC

• The IC was not used during X335.

DA

• The DA was not used during X335.

GC3

• The GC3 was not used during X335. GC3 went down during X334, and was repaired during X335. The inside of the rotor was gouged, and one of the connection nuts inside the oven was improperly used (didn't fit the threading), resulting in a gas leak. This problem became apparent due to action taken during X334, when all threaded connections were loosened, then tightened.

NGA

• The NGA was not used during X335.

GC-MSD

• The GC-MSD was not used during X335.

Alkalinity

• The Alkalinity device was not used during X335. In response to complaints made following X334, we tested the manual-dose "clicker" on our newest-model alkalinity titrator(s); they didn't work. New clickers should be on their way (note: the clickers are for chlorinity titration, not alkalinity titration).

GC-PFT (GC2)

• The GC2 was not used during X335. Additionally, this manual is in the process of being developed/updated.

ICP-OES

• 14 Samples were analyzed on the ICP-AES this expedition (three samples had two beads).  Initial runs demonstrated an abnormally large standard deviation on replicate measurements.   The successive runs each exhibited a decrease in response.   It was postulated that a gradient forming in the sample matrix was responsible for this phenomenon.  The samples were re-run, and this time a 20 minute sonication step was added prior to analysis.  This brought down the standard deviation to within acceptable limits (RSD < 0.5%).
• New versions of each of the rock standards were created and uploaded to the LIMS.  These versions represented the ignited powder and had their constituent masses normalized to 100%.  These standards were designated by appending a "_I" to the end of the standard name. 
• Additional features were added to the ICP data reduction program:
  • A new worksheet page showing the standard deviation and relative standard deviation for each measurement was added.
  • A summary section for each line showing the highest and lowest calibrated standards for each line as well as the standard deviation, 3 sigma, and 10 sigma values of the acid blank.
• The blank sample itself was split into two types:
• Acid Blank – this is treated as the instrument background for calculating LOD/LOQ values.
• Bead Blank – this is the method blank and what is used to correct other measurements.

Carver Presses

• From the X330 tech report: "The presses were all leaking/broken in various ways at the beginning of the expedition. This was a known problem and was communicated at cross-over. New fittings (many of which were cracked) are ordered and should be installed during the upcoming transit."
• These issues are still unresolved; the left-most automated Carver press leaks from a cracked valve, and the middle automated Carver press leaks from an improper seal around its casing/housing. These issues must be addressed during the Curacao tie-up, or else they will be down for the upcoming microbiology cruise X336.

DIC/DOC

• This instrument was not used this expedition.

Miscellaneous

General Lab

• The UT gas systems were completely remodeled to better utilize space; the Ar bottles are easier to access, and we now have a permanent location for He (no more lugging bottles in the elevator). We will however keep a location for He in the lab, just in case. O₂ bottles will still be carted to the lab.
• The new shelving above the Cahn balance and above the CHNS better accommodates binders, computer towers, and will offer a place to put the desiccator chambers so that they aren't free to move about. The remodeling of the GC3/NGA/IC/DA bench improves the gas lines, electrical lines, and general storage in the area. We've also incorporated the IC and DA into one computer.

XRD Lab

Heather Barnes

Summary:

Exp 335 was a very low recovery expedition. No major issues, all equipment in good working order.
Sanmple Summary:
Total XRD Sample: 4
Total ICP Sample: 11

Equipment Performance Summary

The ICP sample preparation equipment ran without any issues. The Pt Crucibles are in good condition. We ran LOI's on 5 g of material to decrease the relative error.
The XRay Diffractometer had a lot of corrosion/rust on the sample rotation bearings. The corrosion was found when I went to remove the anti air scatter before running a QAQC verification. The corrosion is most likely due to a wet sample being scanned. For future reference all samples must be completely dry before running.
In the process of cleaning this rust from the spinner we moved the goniometer's theta drive by mistake. This flagged an alarm in the D4 Tools software. Error: A hard limit switch on the theta drive had been hit. I emailed Dan Grey at Bruker for advice and he said the machine will produce that error if the theta drive has been moved, even if it does not touch the hard limit switch. For equipment protection, if the theta drive is moved, even by the slightest, the software will flag a hard limit switch error. To remedy/override this error you must remove the Goniometer's banana clips (red and black on the right hand side of the goniometer) and adjust the drives in the D4Tools. Emails relevant to this are copied below.
Below: Emails between Bruker and Heather. Please note that the emails are in reverse order. The last email is actually the beginning of the error discussion.
Sent: Thursday, April 21, 2011 3:49 PMTo: Gray, DanielCc: David Houpt; Brad JulsonSubject: RE: Verification QAQC question
Hi Dan,
 
Everything looks good with the  Instrument verification. You are right the anti air scatter was causing the low intensities.
see attached Verification sheet.
 
thanks for your help,
Heather
 
>>> "Gray, Daniel" <Daniel.Gray@bruker-axs.com> 4/21/2011 2:11 PM >>>
<span style="color: #1f497d">Me again....</span>
<span style="color: #1f497d">Sorry, right after I sent the last email I remembered what else I wanted to say.  The lift has a solenoid break on it.  As soon as power is applied to the motor, power also energizes the break solenoid, which disengaged the break.  The break is normally on with power removed (D4 off).  This keeps the lift from crashing down.  This is the only drive in the D4 that has such a thing.</span>
<span style="color: #1f497d">In the cleaning, Theta probably got moved slightly, or possibly 2Theta.  When you turned it back on, the system registered this as a collision.  It is not serious, but you just have to know to remove those plugs, re-initialize, and put the plugs back to fix it.</span>
<span style="color: #1f497d">When Theta is moved down (negative) the stage will physically be moving clockwise, 2Theta is the same.</span>
<span style="color: #1f497d">Good luck.</span>
<span style="color: #1f497d">Dan Gray</span>
<span style="color: #1f497d">1.800.234.X-Ray (9729)</span>
<span style="color: #0000ff">www.brukersupport.com</span>
<span style="color: #1f497d">Hello Heather,</span>
<span style="color: #1f497d">               The first thing I would like to see is a sts file from D4Tools, please.</span>
<span style="color: #1f497d">               From your explanation, I am guessing that you are getting the error that does not say that whether it is the upper or lower limit, it just simply says that a drive is at a limit switch.  It this is the case, you need to go into the Goniometer compartment.  On the right side of the Goniometer (looking at it from the front), there will be 2 pair of one red and one black banana plugs and cables.  One set goes to the Vantec1 beam stop, the other goes around to the back of the Goniometer.  Remove the set that goes to the back of the Goniometer, close up the D4, and try to find reference and initialize the drives.  When all the drives are initialized, put the banana plugs back into the Goniometer.</span>
<span style="color: #1f497d">Regards,</span>
<span style="color: #1f497d">Dan Gray</span>
<span style="color: #1f497d">1.800.234.X-Ray (9729)</span>
<span style="color: #0000ff">www.brukersupport.com</span>
From: JR Heather Barnes [mailto:jr_barnes@ship.iodp.tamu.edu] Sent: Wednesday, April 20, 2011 5:12 PM To: Gray, Daniel Subject: RE: Verification QAQC question
Hi Dan,
 
thanks,
After cleaning the spinner and the little switch above the spinner, I decided I should make sure none of the drives were moved or hit during the cleaning before I started up the QAQC.
In doing so I have created a larger problem.
The theta drive will not move at all, computer is indicating I have hit the hard limit.
The theta drive was the only drive not sure where it was.
The sample lift is below the swing (I am able to move the swing) but cannot get the sample lift to lift out via computer command, nor can we move it manually with equipment off.
We do not want to force anything obviously, but I thought the sample lift should be able to move up and down easliy like all the other drives when power is off (assuming nothing is in the way).
 
What are your thoughts? How do we proceed to get things moving.
We are off the coast of Costa Rica.
 
thanks Dan,
Heather

From: JR Heather Barnes [mailto:jr_barnes@ship.iodp.tamu.edu] Sent: Wednesday, April 20, 2011 11:49 PM To: Gray, Daniel Subject: RE: Verification QAQC question
Hi again Dan,
 
The anti air screen was down quite far, so that is probably what caused the poor values on the upper angles. I will run the QAQC once I get the sample handler errors sorted.
 
As you got in my previous email I now have a collision issue. A hard limit switch for the theta and 2theta drives are hit (this is what D4 tools is telling me see attached screen shots in the word file).
With theta is down counterclockwise or clockwise?
 
I cannot proceed with the sample handler adjustment because I am unable to move the sample lift to a safe position.
 
May be easier if I call you tomorrow afternoon? I can send pictures or skype with laptop.
 
talk to you tomorrow,
Heather
 

>>> "Gray, Daniel" <Daniel.Gray@bruker-axs.com> 4/20/2011 7:53 PM >>>
<span style="color: #1f497d">Hi Heather,</span>
<span style="color: #1f497d">               That isn't good. </span>
<span style="color: #1f497d">               What is the temperature of the water cooling the D4, and what is the room temperature?</span>
<span style="color: #1f497d">               I am about 80% certain that this is from the Air scatter screen.  All the peaks below 70 degrees are virtually identical.  The further above 70 degrees the worse the problem gets.  This is solely indictable of the Air Scatter Screen.   I will not rule out anything else, including the rust and corrosion, but I doubt it.</span>
<span style="color: #1f497d">Dan Gray</span>
<span style="color: #1f497d">1.800.234.X-Ray (9729)</span>
<span style="color: #0000ff">www.brukersupport.com</span>
From: JR Heather Barnes [mailto:jr_barnes@ship.iodp.tamu.edu] Sent: Wednesday, April 20, 2011 1:36 PM To: Gray, Daniel Subject: RE: Verification QAQC question
Hello Dan,
 
I just opened the front and there is some corrosion and rust on the bearings for the rotation cup along with the limit switch for the sample lift.
The ET onboard is going to clean it up.
I suspect a wet sample was placed in the machine and caused this corrosion.
Do you think this is causing some of the problems?
 
thanks,
Heather
 
>>> "Gray, Daniel" <Daniel.Gray@bruker-axs.com> 4/20/2011 1:49 PM >>>
<span style="color: #1f497d">Hi Heather,</span>
<span style="color: #1f497d">               Please send me the actual .raw files for the data you sent me.</span>
<span style="color: #1f497d">Regards,</span>
<span style="color: #1f497d">Dan Gray</span>
<span style="color: #1f497d">1.800.234.X-Ray (9729)</span>
<span style="color: #0000ff">www.brukersupport.com</span>
From: JR Heather Barnes [mailto:jr_barnes@ship.iodp.tamu.edu] Sent: Tuesday, April 19, 2011 10:45 PM To: Gray, Daniel Subject: Verification QAQC question
Hello Dan,
 
If you get a chance, could you have a look at the attached excel file QAQC_19_04_2011.xls
It is the alignment verification I completed today. (This is the first verification since December see attached QAQC_8_12_2010. December's intensities were good).
 
Why are these values off?
Is this normal drift?
Should I try and remedy the issue?
 
many thanks,
Heather
 
 

THIN SECTION

Edgar (Sandy) Dillard

Summary

This wasn't a busy leg in this lab but we did have 41 thin sections made. Two of these were oversized. In addition, training of the ALO and a few other techs was started. Chieh P. and Tim F. both completed cross training in this lab. We also polished up to 600 grit sandpaper several slabs for the petrologist of the junk basket materials that were brought up.

Projects

An additional LED light strip was made and silconed to the front cup of the petrothin as the lighting in that part of the lab is insufficient. I would suggest that the original strip be moved from under the arm of the petrothin to the window inside to back illuminate the sample and the well. Another shelf was also installed into the lab and it did help greatly. Suggest one or two additional shelves that would go both below and above the window in the lab. This would make for a lot more space and getting small items off the counter.
Lastly, I looked into the problem that Gus had with the LP50 flatness monitor. Emails were sent to Logitech UK and they responded as below:

[McAneny, Jim]

Anyway, to use the auto-lap to get a comparative reading (but not exactly the same as the dial gauge due to a different diameter, a calibrated probe and running on a layer of abrasive):
1. Run system checks to 'home' the arm pillars
2. Use the 'setting tool' placed in the centre recess of the plate to position the roller arms by sitting test block in each arm in turn and sliding the outer diameter against the setting tool before tightening the lever.
3. Set the monitor on the master reference flat (with loading weight fitted) and use the monitor set up screen to press 'auto-zero'. This will remove any error offset in the monitor in the same way as you manually zero the dial gauge on the reference flat.
4. Place the monitor in the rear left smaller roller arm. with the load weight on top and the test block in the front right.
5. Use 9um or 15um particle size abrasive at 10-15% powder/water mix and 1-2 drips per second.
6. Run the system for 20mins at 70rpm and check the reading from the monitor as it runs. Initially the reading will change quickly and settle down after a few minutes.
7. As soon as the speed is started the monitor signal will be averaged for 30 seconds and then if the value is not withinh the target value (zero) then the arms will move in or out to the preset positions to change the plate shape towards the target. For example if the target is zero and the plate shape reading says 5um convex, the arms will move in to a position where the test block outer diameter is almost in line over the outer diameter of the plate and the main load of the test block has moved in to wear the centre area faster. If the plate shape is 5um concave then the arms will move outwards until the test block outer diameter is almost in line with the centre recess rim and the load of the test block will wear more or the outer area of the plate track.
8. If this is happening it may take another 4-5hours for the plate to be brought to zero as the cast iron slowly changes shape at ~1um/hour.
But for further clarification, you run the monitor, test block and the jig at the same time? Monitor in back left, test block in front right and jig where? or are you only running the monitor and the test block or the monitor and the jig?

[McAneny, Jim]

You should run the monitor and the jig when processing and the sections should wear the plate. If the material is soft the shape should hold steady, if hard the monitor will move the arms more often to keep correcting the plate shape around the target value. It can also be run with the test block but it will wear out faster if you use the test block all the time.
2] In normal operation, are the front right and back left the normal positions to run the jig and monitor respectively?

[McAneny, Jim]

Yes, the monitor is only for the rear left and the jig can run in any of the other three. Whichever is easiest to handle. I usually put the test block in the front left and if running one jig I use the front right.

I did find that this indeed did help me and moved the small arm into the stated position and this seemed to work better. In addition, that regularly checking the flatness monitor on the master flat seemed to be key to keeping the plate flat.

Problems

• I did have some more problems with the pumps in the middle of the leg and surmised that they had not been serviced recently so I did minor service on them along with an oil change and it did help immensely.
• I also had some problem with the set up to put vacuum on the billets so I ran another tube to the VS2 to over the hot plates and thus could do the impregnation etc. right by the bonding jig.
• Lastly I had problem with the glass trap on the VS2 so looked into getting new parts for it. Below is the response that I got from Jim.

[McAneny, Jim] 2GLS-001 is the glass trap number, 2PNR-093 is the plastic drip tray and VS21-0001 is the side clip.

Shipments

The following items came into the lab Filter elements, more slide boxes, micrometers, caps (in cabinet for Gus), alumina powder, Igneous Book, and ethane diol.

FANTAIL

William Mills
The magnetometer was ran routinely without problems. VSP was cancelled due to lack of hole suitable for this type of logging. Ship's crew is currently planning on painting the deck in Curacao.

Underway Geophysics LAB

Erik Moortgat

Data Summary

Expedition 335 consisted of three transits (∑ ≈ 1969nm) and one site.
Transits: Puntarenas, CR to U1256 (L1T ≈ 465nm)
U1256 to Panama Anchorage (L2T ≈ 750nm)
Panama Anchorage to Curacao(L3T = 754nm)
Site: U1256D
Site fix was not required.
Event data points were gathered every sixty seconds when underway and every five minutes when on-site. Even though a site fix was not performed, site data was collected.
During L2T, magnetics data was collected only from U1256 to approximately N6 55 & W82 05 because of the approach to fishing grounds.

Equipment Performance Summary

WinFrog
WinFrog1 was used entirely for primary navigation acquisition. There were no problems encountered. WinFrog2 was available as a backup.
Gyro
NMEA GYRO #3 from DP was the gyro used for the duration of the Expedition.
Trimble/Ashtech GPS
The aft Trimble GPS was the primary GPS used for the duration of the Expedition. No problems were encountered. The Ashtech GPS unit was available as a backup.
Bathy 2010
The PC was updated (while on site) to Windows7. So far the PC can function 'normally' without 100% hardware interrupts when the serial cables are plugged in and the Bathy software not running. It was a challenge finding Win7 drivers for the dual PCI 4-port serial cards but Grant (MCS) found a driver for a chipset that matched our hardware.
GPS from WinFrog:COM7
Depth to WinFrog: COM10
After L2T was started (12kHz mode) and running for about five hours, it was noticed that the SEG file was no longer being updated. Recording was stopped and re-started. Initial collection was called L2T_1 and after the restart, L2T_2. However, shortly after restart, the SEG file once again stopped being recorded. Both SEG files will be recreated from the ODEC files. This has once again occurred on L3T. SyQwest will be contacted.
SeaSpy/SeaLINK
The towfish was successfully deployed on L1T & L2T. The towfish was not deployed on L3T.
We once again (two consecutive days) encountered the midnight (GMT) GPS Append error while running SeaLINK. This only occurred during L1T.
GPS Error = 6
SeaLINK v.7.9.7(Note: we are running v.8.00047)
Marine Magnetics was informed. They mentioned that in a couple of months they will be releasing a 'new' version of SeaLINK named "BOB". I asked them to keep us informed. It will be free of charge.
VSP
The planned VSP was not performed. The lab was ready to prep the G-GUN cluster/deployment hardware.
Misc
A little bit of our propylene glycol solution was given to the Physical Properties Tech for use in the water bath for the pycnometer. This item might be considered for addition to the inventory.

Items arrived in port

100' braided line, 2 each
bearing swivel, 1 each

Requisition made

New set (16 sheet) of general bathymetric charts of the oceans (GEBCO). This is a repeat request from a couple of Expeditions ago because no action was taken prior.

Data backups

Data files for the Expedition were copied to:
\\JR1\Vol1\data1\1.5 Ops Navigation
\\JR1\Vol1\data1\1.6 Ops Bathymetry - PDR pulse depth recorder
\\JR1\Vol1\data1\1.7 Ops Magnetics

IT System Manager's Report

Grant Banta and Mike Hodge 

Summary

During Expedition 335 the IT infrastructure performed as intended with minimal adverse impact to operations. Some resources such as GroupWise Web Access and file access would stop occasionally and would require restarting the service. The Cumulus service on Etna continues to consume disk space at the rate of about 6% per day until disk full alarm threshold is reached. A restart of the service frees disk space, frequency is about 10 days. We had some hardware failure in our servers but this caused no interruptions to service.
VSAT satellite services presented multiple challenges maintaining an online status. The main cause was failure of both dome's SSPA (Solid State Power Amplifier) amplifiers and the requisite tuning of equipment parameters to stabilize the equipment.

Servers (Microsoft):

• Incremental backups continue to hang. A ticket has been opened with the vendor and continual efforts have been made to resolve the matter. This is still an ongoing concern.
• We were able to get the RigWatch Instrumentation software working on the Windows 7 platform.
• The server running the RigWatch software was upgraded to Windows 2008 server.

Servers (Novell):

• On multiple occasions file access on the servers would hang or be very slow coping. The immediate fix was to migrate the volume mount from one node to another node. The problem appears to be with the TomCat/Java applications trying up the CPU to where no other resources could be used.
• Implemented SAMBA for our science party to use during this expedition. It showed to be more reliable than AFP. This will provide file access services for our scientists without requiring them to install a client on their computers. Although one of our nodes is not able to run this protocol at this time. A service ticket has been opened to resolve this issue.
• Set GroupWise email size limits to 5MB out and 10MB in for all users.

Servers (Solaris):

• Added a new DCHP pool for VLAN 51 (Video Conferencing).
• Shipboard Cumulus installation encountering a condition that consumes disk space and does not release this disk space until reset. Shore version of Cumulus not experiencing this symptom. The cycle appears every 10 days in which Cumulus has to be reset to free disk space.

EVA4000 Storage:

• During portcall MGE UPS troubleshooting encountered EVA fan failure. Replacement unit ordered and will be shipped to Curacao portcall for installation.

Network:

• Setup a new VLAN 51 for Video Conference access only. Requires a unique password that can be changed each expedition.
• The Engineer and Developer worked many hours on trying to resolve an issue with the overlay software. It would crash from time to time. We assisted and found that they encountered a malfunctioning switch in Subsea shop. Replaced unit and all has worked fine since.
• Renamed all of the WAP ports to identify which WAP was connected to each switch port. This will facilitate finding a user on our wireless network.
• Upgraded NetSight to version 4.0.1.34.

Printers:

• Found a problem with a printer driver for our 4350 printers on Windows 7 32bit. Had to update the driver.
• Found that shore was running iPrint v05.40.00 and we were on v05.32.0. We applied the latest version v05.60.00.

PC/Workstations:

• Started effort to convert Rigwatch workstations to Windows 7. Following stations done; PC51591, 51564, PC51641, PC51561 and 51555. The remainder to be done by portcall or during tie-up period.
• Upgraded all general workstation PCs with the following software;
  • NAC agent v1.5.4.0
  • Microsoft Office2010
  • Microsoft Visio 2010
  • Firefox v4.0
  • Java JRE 6u25
  • Adobe Flash v10.2.159.1
  • Intel Raid Storage Manager v10.1.0.1008
  • McAfee VirusScan Enterprise 8.7i patch 5
  • Adobe CS5 (Photoshop and Illustrator)
  • HP BIOS v2.07
  • nVidia video driver v270.71 per specific OS installed
  • Applied all critical updates and security patches
• Attempted to upgrade HP nw8240 and nw8420 laptops to Windows 7. Not able to do because drivers not available. Kept one HP nw8240 as a spare for WinFrog video display laptop and shipped to shore two other units for surplus.
• Upgraded the Bathy system in Underway to Win7 32bit install.
• Installed quad-port serial card in PMag PC51557 for connecting DTech, Agico JR-6A and FlexIT instruments.
• Upgraded Augmentix and Dell 630 laptops to Windows 7 32bit OS.
• Upgraded HP 8400 (SHIL) PC to Windows 7 32bit OS.
• Swapped IOCOM Dell Precision 450 PC with HP xw4400 PC and migrated IOCOM software to Windows 7 OS. Reconnected USB camera to HP PC and made operational for camera control. Two concerns with that system.
  • Video cable is tight. If that box moves it could damage something.
  • Same with the video port 4 connection, not much room for that system to move around.

Apple Mac Workstations:

• Upgraded all OSX systems with following software;
  • Microsoft Office 2011
  • Adobe CS5 (Photoshop and Illustrator)
  • Firefox v4.0
  • Adobe Flash v10.2.159.1
  • NAC agent v1.5.4.0

Satellite/Internet/Phones:

• Encountered multiple problems with VSAT system all expedition;
• April 19th Aft dome dropped offline. No error indicators all appeared to be functioning correctly. After much troubleshooting, swapped out the SSPA from the Bow dome and installed in the aft dome. This fixed the aft dome and made operational. This also highlighted the fact that the SSPA in the aft dome had failed. The reason for moving the SSPA to the aft dome was due to DP operators were encountering challenges trying to maintain a heading for continual reception by the Bow dome.
• Transocean ET technician was able to effect repairs on the failed SSPA and placed unit back into operation in the Bow dome.
• May 4th blew a fuse in aft dome Codan 5582B power supply. Replaced fuse.
• Also on May 4th discovered threshold set too narrow causing domes to switch back and forth. Adjusted to new AGC values stopped switching back and forth. May have been reason a fuse was blown in the Codan power supply.
• May 21st encounter satellite outage of unknown reason. All indicators appeared normal and operational. Physical inspection of the aft dome indicated that the SSPA had failed, fan blowing on unit, cool to the touch. Removal and inspection revealed same failure as previous SSPA failure. Implemented repairs and returned unit to operational status. Repaired Bow dome SSPA maintained our connection while implementing repairs for the failed aft dome SSPA.
• May 22nd contacted RigNet Houston and discussed attenuation levels set in VSAT network locker and aft dome. Under RigNet engineer's consultation reduced power transmission from Modem in VSAT locker and increased SSPA power in aft dome. End results were a more balanced work load between VSAT locker and aft dome. Modem was not over driving SSPA and SSPA did not have to over attenuate transmission power. Specifics are:
  • RigNet follow-up: After consultation with level 2 engineers, it was noted that the modem in the VSAT locker TX power was at -4dB which was over-driving the SSPAs, following changes implemented;
  • Both domes,
  • Aft dome - lowered Codan Transceiver from -17dB to -12dB
  • Bow dome - lowered Codan Transceiver from -14dB to -12dB
  • Both Aft & Bow modems TX power changed from -4dB to -9dB
  • All is more balanced now as per RigNet engineers, optimum would be modem and Transceivers match power levels, equipment variances prevent 1 to 1 setting.
• May 29th encounter satellite outage of unknown reason. Aft dome failed satellite communications, Bow dome at the time was experiencing obstruction. All indicators appeared normal and operational, suspected another aft dome SSPA failure. Several hours later reexamined equipment and found operational.
• June 6th encounter satellite outage again. In cooperation with Transocean ET Technician, through inspection revealed connector problem with main TX cable to pedestal mount in aft dome. Connector pin was making intermittent connection within the connector. Disassembly and repair of the connector remedied problem. Suspect unexplained outage on May 29th related to this problem.

Other Equipment:

• MGE UPS encountered another communications failure on Expedition 334. Attempted repairs during Expedition 335 portcall but Transocean electrician unable to identify correct equipment failure. Because of beginning expedition postpone further troubleshooting until end of expedition.
• Observed during a routine power generator test that the RASP panel located in the MCS office did not activate, another symptom of the MGE 50KVA UPS communications failure.

Special Projects:

• Conducted NSF Presidential Awards for Excellence in Mathematics and Science Teaching Recognition Program – PAEMST video conference session. Was considered very successful by all parties involved.
• Installed IOCOM IGMeeting on Panasonic Toughbook for PAEMST event. Teacher onboard held a walk about with this laptop before conference room Q&A session.

Equipment Repairs:

• PC50303 retrieved from Chemlab for shipment to shore as surplus.
• Send LT51626 to shore with potential memory / mother board problems and bad battery.
• HP called about a hard drive failure in server Spur. Replaced drive with one of our spares and shipped failed unit back to shore for exchange.
• Replaced power supply from slot 2 on Mauna-Loa – HP Proliant GL380 G5 server tag 90614 – S/N: USE712N0ZX. Shipped to shore for replacement.
• Two HP laptops shipped to shore for surplus.
• Two VBricks shipped to shore for repairs, no more VBrick decoders available on board for spares.
• HP xw4100 shipped to shore for surplus, from Underway lab.
• Replaced HP server power supply shipped to shore for return to vendor, failed on Exp334, replacement arrived to Exp335 portcall.

DEVELOPER'S Report

Tim Blaisdale and David Fackler (Trevor Cobine, Chris Bennight and Wm. Mills,)

[x334 off-going] Dwight Hornbacher, Algie Morgan

Overview

This document highlights changes in laboratory data acquisition and collection systems, and changes in the development work environment. Notable issues and changes are presented in-line. Issues not addressed and features requested are collated in Addendum C: Issues and Features. Bracketed attributions are provided to aid in routing questions that do and will arise—abuse for glory or blame as your psyche requires.

Curation and Core Handling

SampleMaster. Production remains at release 2.1.1.6. Alpha release is 2.2.0.13 and remains under review and test at the Core Entry workstation. Noted changes for the Alpha:

• Piece length (vs. bin length) handling.
• Added an additional Pump for the drillers. "1/2" means both pumps are being used.
• Removed inefficient depth compute call (25 second response-request round trip time).

Alpha version available here:
http://web/tasapps/samplemaster/alpha
Notable revisions in progress, demoed, but not deployed:

• Improvements to sample hierarchy browser usage and efficiency (derives from related work in DescLogik) [Blaisdell].

• Sortable columns (also derives from related DescLogik work) [Blaisdell].

Curation. Numerous samples are attached to the hole without reference to intervening cores or sections. A naming convention was developed for sample material derived from junk-baskets and hole remediation efforts. The resultant naming and labeling conventions led to numerous unplanned-for effects in multiple laboratory systems. Much re-work to accommodate and keep the joint running. See Addendum C for specifics.
Laser Engraver. Not used this period.

Geophysics

Whole core systems

Whole-round logger (WRMSL) and Special task logger (STMSL). New software is deployed in code. All sensors, both tracks, tested fully operational and functional with new code [before tie-up teardown and packing of PWL, GRA components]. Upgraded workstations to Win 7 x32 [Cobine, Fackler].
Natural gamma (NGR). This system remains on Windows XP. Application launch speed improved from 30-45 seconds to 3-6 seconds. Root cause was OS calls to check certificates for signed code. Disabled the certificate lookup mechanism to achieve the speedup [Fackler].

Split core systems

Line-scan imager (IL). Now supports section-half split surface and whole round surface scanning.

• Limits of travel extended (range 172 cm) so that full coverage could be obtained for the whole round surface tray vs. the section half tray [Fackler, Crawford].

• Modifications to enable tray interchangeability [Crawford].

• The label scanner has been removed from underneath the track body and mounted underneath the imaging monitor. Workflow scans an end-cap from the section half D-tube [Crawford].

• Code revised to tag the output images and raw files appropriately [Cobine].

• Updated the PRINTME scripts to provide additional user print layouts [Blaisdell].

In the source code repository, this project is now referenced as IL (image logger)—formerly was referenced as SHIL:

• https://build/svn/jr/LabVIEW/il/trunk https://build/svn/jr/LabVIEW/il/release/jr-2.1.0.0
• Former SHIL-only code snapshot and tagged as release 1.7.
• WRIL (whole-round image logger) code snapshot and tagged as release 2.1.0.0.

Toward answering these questions:

1. Is the image logger faster with current National Instruments vision drivers installed?

Testing…

1. Can the system be run on Windows 7 x32?

Yes. Only previous sticking point was the Microscan barcode image—they have Windows 7 x32 and x64 bit drivers. All other components have been running under Windows 7 on shore for some time [Fackler].
the spare imaging host station has been converted to a Windows 7 x32 box with release 2.1 of the image logger code. PENDING: swap in and test before departure from Curacao.
Sonic velocity (GANTRY). No changes to this production system. Significant development effort applied toward the replacement of this system. Available for demo, only on development workstations [Cobine].
Reflectance and susceptibility (SHMSL). System has been updated to support a touch screen. Fix reported motion control issues and generation of zero-length data files under some circumstances. Revisions to parsing of section labels due first encounter with revised labeling standards (e.g. "335" vs "335(312)", "U1256" vs "1256"). For a brief moment in time the skip-list functionality was failing also, repaired [Mills].
Penetration strength. Java application for entering penetrometer data into LIMS. New code committed in port call [Hornbacher].

Discrete sample systems

Thermal conductivity (TCON). No changes for this period.
Moisture and density (MAD). New electronics deployed and debugged with existing production software. [Meiring, Moortgat]. Measurement Studio will suffice for re-working pycnometer interface and communications. Entire system is packed to go home.
MadMax. Migrated to Visual Studio 2010, .NET 4.0. Explored wrappering National Instruments hardware from C# and Measurement Studio rather than via LabVIEW [Fackler].

Paleomagnetics

Point susceptibility. Not used this period. [Applied some expeditions as a stand-alone quality check.]
Agico JR-6A. Used. Data is stored as part of the expedition initial reports. No integrated data upload is provided [at present] for this system. A new version of the control software was downloaded from the vendor. Participants decided they preferred the existing version. Update stored on the Desktop and here \\jr1\vol1\tas\dml\software\labsystems\Remasoft. [Banta, Fackler]
Kappa Bridge KLY-4S. Used. Data is stored as part of the expedition initial reports. No integrated data upload is provided [at present] for this system.
GPS sighting. Not used this period.
Superconducting magnetometer (SRM section). Not used this period.
Superconducting magnetometer (SRM discrete). Any sample may be scanned. Program filters the label ID to ensure that valid raw data file names are generated [Cobine].
Fluxgate Field Survey. A proof-of-concept tool was put together toward conducting a magnetometer field survey [Cobine].

Underway

Navigation, bathymetry feed. The server on which this data feed runs was updated to Windows 2008 x32. Software was re-installed from http://web/tasapps/navigation. Configuration files were updated for the new OS environment [Fackler].
Magnetometer. Not used this period.
JR NAV. Version 335 of JRNav was deployed on the transit from Balboa to Curaco. Changesfrom version 330 include:

• TCP/IP buffer is cleanly handled now, no backing up and crashing. The TCP/IP connection to Winfrog is open, a clean data string is collected and the connection closed clearing the buffer. This is repeated after a user set delayed.
• Way point names are displayed in Google Earth.
• Corrected a problem with shared "styles". Styles are only shared within a KML "document" object. Any geometry object (ie. points, lines, polygons, etc) can only access the styles within the same document container; otherwise they default to GE style..
• Estimates of distance and time to final destination are improved. Distance is now calculated from the current ships position to the next way plus the sum of distances between the remaining waypoints. No corner cutting! Time is still base on current speed therefore subject to error.
• JRNav now tracks the waypoints and determines if they have been crossed or not. This is still experimental but appears to work correctly in situations tested so far.
• Eliminated the overlay box in Google Earth. A LabView front panel displays the navigation data information. Therefore both JRNav and GE must be run on the same computer.
• PDR depth is now captured and displayed.
• Previous data loads faster when restarting JRNav than before.
• Used VNCTight so that web browsers can display Navigation data along with VBrick.

JNav is a beta application and not ready for real world use. First user friendly version is planned for the North Pond expedition. [Mills].

Geochemistry

Alkalinity. No change for this period.
ChemWorklistGenerator. Fix last row failure to export. Project preening. Tool used for sample and run management at CHNS [Bennight].
Coulometer. No change for this period.
ICPAnalyzer. Improvements to error reporting. Bug fixes. Production release at > 1.0.3.0 [Bennight].
X-ray fluorescence. Hardware was setup on yet another workstation. Verified to work under Windows 7 x32, and run this way for the duration of the expedition. System underwent additional review and use by the science party, specifically reported by Parijat Roy. No further automation has been applied to this data. The content is placed in spreadsheets and published as part of the expedition initial reports.

Geology

DESCLogik

Dedicated project effort headed by Blum. Much improved and changed. Database modifications (schema DESCINFO2) were applied to support the on-going development and testing efforts. Production DescLogik is at release 3.23.0.12. On-going alpha releases are at 3.23.3.52+ [Bennight, Blaisdell]. Alpha releases no longer carry Oracle client components. Retrieval and insertion of data is now handled entirely via web-services. For finer-grained detail on changes, see DESCLogik project reports.
For a breakdown of production descriptive content captured this expedition, see Addendum A: DESCLogik Data Dashboard.

Barrel sheet production (VCD)

L2E (Lims2Excel). No changes this period.
Strater. No changes this period

Closeup, Microphoto, Thinsection Capture

Closeups. Production release still at 1.0.8.0. Alpha release at 1.0.9.5: Revised the label generation capability to accommodate changes in sample naming. Revised the Sample Browser dialog to accommodate search for samples attached to the hole. Alpha release available from http://web/tasapps/imagecapture/alpha [Fackler].

RADVAN

Cahn Balance. The communications electronics intermittently fails on this device: may take seconds, may take hours, may take days. Requires electronics remediation if this device is to continue to be used. The laptop on which the balance software is installed was upgraded to Windows 7 x32. Appropriate drivers were installed for the USB-to-Serial converter interface to the Cahn. The setup is available via remote desktop to avoid trips into the RadVan [Fackler].

Operations

Core/VIT winch counter video overlay. Failure of overlay transmission isolated: to a failed Startech and failing or underpowered hub [OEM]. Spare Startech device put in place. New hub put in place. Latest deployed revision of overlay transmitter software (Xbob) hardcoded for serial ports currently in use [Blaisdell]. Improved documentation of system configuration; much isolation testing [Meiring, Banta, Fackler]. New Startech devices placed on order; to be purchased with software that will function correctly under Windows 7 and Windows 2008.
RigWatch. Master server upgraded to Windows 2008 x32. Slave systems all upgraded to Window 7 x32.

Other

Reporting Systems

WebTabular reports. No change this period. See Addendum C: Issues and Features for specifics.
LIMS Reports. Deployed at release 2.4.6. These reports are no longer listed as "BETA" on the link index page. Incorporates the Piece Log report defined for use in the shipboard environment [Blaisdell].
LimsPeak. Production at release 1.7.4. Image and image caching issues were being encountered frequently. Applied a random number to the end of every image request to bypass local browser document caching [Bennight].
Gas bottle monitoring. Revised to reflect new pallet stores (upper tween) gas bottle layouts. Reduced number of web-service calls. [Bennight] Consists of: an OEM component to read gas monitor devices; an IODP .NET component to scrape the OEM component for data and load it into LIMS (https://build/svn/jr/NET/GasMonitorUploader/trunk); and a Silverlight-based component providing report and alert services (https://build/svn/jr/Silverlight/GasStatus/trunk).

Web Services

IODPUtils. Numerous feature additions. Most related to implementation of DescLogik features [Bennight, Blaisdell].
.NET web-services wrapper (Lims.dll). Removed all LabWare SOAP-based services. Numerous changes supporting DescLogik: most notably move of DescLogik I/O completely to web-services [Bennight, Blaisdell].
Resteasy-asman Added file rename service. Used to support renaming of a closeup, thin section, and microscope images with poorly generated filenames due (trickle-down effects of lacking core and section ancestry for many samples) [Bennight].
resteasy-desclogik-services Deployed at release 1.2. Direct Oracle access now fully replaced by web-services for DescLogik releases 3.23.3.46 and above. Uses ojdbc6.jar; specifically required for improvements to CLOB support [Bennight].
resteasy-image-tiling Enable generation of image tiles for material having hole as the ancestor, but not core or section [Bennight].
resteasy-lims-webservices Deployed at release 4.4.3. Revised to support: piece length logging; specification of formatted_entry as distinct from entry field inputs [Bennight, Blaisdell].
resteasy-monitor Web-service supporting I/O of gas bottle monitoring data [Bennight].
resteasy-reports Deployed shipboard to mirror shore LIMS Reports deployments. Additions to support shipboard piece log report [Blaisdell].
WTR Variant of web-tabular reports with cleaner UI [Morgan].

Laboratory System Services

MegaUploadaTron. Production release at version 2.0.6.9. Alpha release at 2.0.7.2. Alpha release supports cataloging of whole round image surfaces to sections, rather than section half samples as for LSIMG [Bennight].
Zebra Printers. Label format changes to accommodate larger number of characters in the label ID. Revised barcode matrix size. Revised wrap points in several cases [Fackler, Blaisdell].

Miscellaneous

Alt-M Master. Extended to take any keystroke sentence. Applied as an automated testing tool for Radvan Cahn balance troubleshooting and for video overlay transmitter troubleshooting [Fackler].Typical usage: setup keystroke sentence to query a device via a terminal emulator, repeat that sentence until failure condition occurs. Monitor traffic up to the failure point with PortMon [Sysinternals].
Depth Updates. No change this period [shipboard environment only].
Database Overview. No change this period [shipboard environment only].
Filename Fixer. Utility for the MCS to search for special characters that prevent file access and media backups in our cross-platform environment. Re-write of java command-line utility as a .NET ClickOnce application. Available here: http://web/tasapps/filenamefixer. Code at https://build/svn/jr/NET/FileNameFixer/trunk [Blaisdell].
Janus2Lims. Updated for Visual Studio 2010 and .NET 4.0. Got just enough working to save time migrating U1256 material from expedition 312. Revisions committed to trunk, no new formal release or deployment [Fackler].

Developer Resources

Desktops

Desktop box. Updated to JDK 1.6.0_25. Installed National Instruments driver update Feb. 2011. Installed National Instruments Measurement Studio 2010 product. NcFTP updated to 3.2.5. Adobe Reader to version 10.0.1. TortoiseSVN to version 1.6.16. Installed OpenOffice 3.3.1. Uninstalled Ankh replaced with RocketSVNvs 1.0.1 Visual Studio Subversion client. Updated Fiddler2Beta to 2.3.3.5. Netbeans updated to 7.0. Updated all Sysinternal utilities [Process Explorer, etc.]. Broadcom network drivers updated to release 14.6.1.0. Nvidia video drivers updated to release 270.61. MATLAB installed [MCS]. Oracle 10.2.0.1.0 client with Enterprise Manager installed. Release 11.2.0.2.0 of Oracle data access components installed, including Visual Studio plugins for Oracle. NuGet maven-like package manager installed as Visual Studio plugin. Removed XP mode virtual machine due to space limitations on the current hard drive. Installed Microsoft Office 2010 applications [MCS]. Updated to GalilTools 1.5.0.398. FireFox updated to 4.0.1. Installed VNC viewer for accessing development Macintosh.
Macintosh. MATLAB installed [MCS].
Environment. Installed 2^nd HP LP3065 large monitor at Macintosh workstation. Keyboard switch re-configured to support the Macintosh and laptop docking station.

Servers

Load balancing. Load balancing is implemented for these additional services: resteasy-desclogik-services, resteasy-printer, resteasy-monitor, resteasy-drillreport, resteasy-MAD, resteasy-reqmgmt, WTR.
BUILD box. Java updated to 1.6.0_25. National Instruments driver updates Feb. 2011 installed. Installed National Instruments Measurement Studio 2010 product. Revised maven repository content to reside in "c:\srv\maven2\usio.jr" with a junction from "c:\develop\.m2\repository". NcFTP updated to 3.2.5. Password Safe updated to 3.25.1. TortoiseSVN updated to 1.6.16. Netbeans updated to 7.0. Ankh svn for Visual Studio replaced by RocketSVNvs 1.0.1. FireFox updated to 4.0.1. BeyondCompare updated to 3.2.4.13298 and license applied. ImageMagick updated to 6.6.9-4-Q8. Adobe Reader X updates applied. Rsync server updated to 4.1.0. Release 11.2.0.2.0 of Oracle data access components installed, including Visual Studio plugins for Oracle. NuGet maven-like package manager installed as Visual Studio plugin.
Digital master library. This local cache of instrument host and development system drivers and control software now has a permanent home:
JR\\jr1\vol1\tas\dml HQ\\odpads\tas\dml
Test servers. None available at this time.
Testing practice. Ararat and web:8080 were made available throughout the expedition for development test code under the respective Tomcat application servers.
Krakatoa. Has been upgraded to Windows 2008 x32. Backups of the shipboard BUILD box are no longer pulled to here. This server is dedicated for RigWatch Master usage and supports the Navigation data feed.

Data Statistics

See Addendum D: Sample, Test, Result Statistical Methods for the respective query methods (#).

Data Acquired

Breakdowns of samples analyzed, tests conducted, results collected: organized by analytical tests. See Addendum B: Data Acquired Method for query method.

Addendum A: DESCLogik Data Dashboard

Observed column indicates number of result records present for that tab and template. Does not reflect actual rows you will see in DESCLogik—better used as a gross indication of presence/absence of data. Status (S) column separates notes and separates canceled (X) content from "live" (E) production content.

Method. Query used to extract the above content.
set timing on linesize 160 pagesize 50000
column "User" format a10
column "Exp" format a8
column "Hole" format a6
column "Stat" format 999999
column "S" format a1
column "Template'n'Tab" format a70
select
count(distinct r.test_number) "Stat"
, s.x_expedition "Exp"
, s.x_site||s.x_hole "Hole"
, r.entered_by "User"
, r.status "S"
, regexp_substr(r.entry,'^[|]') ||': ' ||regexp_substr(r.entry,'[^|]$') "Template'n'Tab"
from
sample s inner join result r on s.sample_number = r.sample_number
where 1=1
and s.sample_number in (select sample_number from sample where x_expedition in ('335', '335(312) '))
and r.analysis='DESC' and r.name='templateID' and r.entry like '335%'
group by s.x_expedition, s.x_site, s.x_hole, r.entered_by, r.status
, regexp_substr(r.entry,'^[|]') ||': ' ||regexp_substr(r.entry,'[^|]$')
order by 2, 3, 5, 6, 4;

Addendum B: Data Acquired

Sample Column Query

select analysis, count(distinct sample_number) from test where sample_number in (select sample_number from sample where x_expedition in ('335', '335(312)') and instr('ICPAR', status) > 0) and instr('ICPAR', status) > 0 group by analysis order by analysis;

Test Column Query

select analysis, count from test where sample_number in (select sample_number from sample where x_expedition in ('335', '335(312)') and instr('ICPAR', status) > 0) and instr('ICPAR', status) > 0 group by analysis order by analysis;

Result Column Query

select analysis, count from result where sample_number in (select sample_number from sample where x_expedition in ('335', '335(312)') and instr('ICPAR', status) > 0) and instr('EMAR', status) > 0 group by analysis order by analysis;

Addendum C: Issues and Features

Items in green have been addressed. Others are outstanding. To be forwarded to the appropriate Lab Working Groups. Bracket indicators "[x###]" identify carry-overs from previous expeditions and reports.

Section Half Imager

BUG [x334] Imager will randomly drop line scans in interval between 100 and 120.
FEATURE [x334] Recovering from image scan errors [wrong name assigned] is difficult: name embedded in the full and consumer image must be fixed, relational data and metadata in LIMS must be fixed, file names on the ASMAN catalog must also be fixed. Would like a tool to automate the process. The image may be re-scanned only in some circumstances—on a sediment expedition color alteration in air is often rapid—in those cases it is desirable to preserve the first scan.

SRM Section

FEATURE [x330] Desirable to have a "skip list" for hard rock expeditions. Reduces post-data-upload processing. Increases up-front run setup. Skip list used to skip measurements at piece edges, rubble bins, rollers, and material known to produce undesirable results.

MegaUploadaTron

BUG [x330] When the application is first started and "Set Upload Directory" is used to set a new watch directory, the application must be fully shut-down and restarted before it will populate the upload list with files in the selected directory.
BUG [x330] Identical to the above, but for the 'Set Log Directory".
FEATURE Application does not allow specification of the "Archive" directory. Is presently hard-coded relative to the selected input directory (aka watched dropbox). Would be useful to give the technicians that flexibility.
FEATURE Display the watched and managed directories on the front panel status bar.
BUG [x334, x335] If an external process has a lock on a file, the uploader can move it, but leaves a zero-length file in the watched directory. The desire is to prevent the zero-length file [detect lock conditions before moving] or delete the file after moving [still detect lock conditions, but clean up in safe-to-move cases where a target file of the same name but possibly different timestamp exists that is non-zero in content]. Report occurrences of the lock condition to the central logging facility.
BUG When a raw file is generated that lacks a sample identifier, MUT goes through the motions of uploading it, then gives an error. That error is not meaningful to an end-user. Change it.

SampleMaster

BUG [x334, x335] Occasionally when printing labels from the View tab the application will crash and must be restarted. Afterwards reprinting the labels print successfully. Precise reproducibility case not yet identified.
BUG SampleMaster does not clear orange background after samples are uploaded successfully. Orange background can only be cleared by restarting SampleMaster or selecting the affected rows and using "Delete entire row..." feature.
BUG [x330, x334, x335] When autoprint on upload is enabled, program often fails to print the first label. Occurs during section and sample-table entry. Fault is known to be in SampleMaster [tracing HTTP traffic indicates label is already missing in the stream submitted to the printer services]. Issue in SampleMaster is related to keeping track of how many valid rows of data are in the spreadsheet. An off-by-one problem of some sort: zero-indexed vs. 1-indexed spreadsheet rows; possible failure in updating row-count when deleting row(s) or clearing the form.
BUG Use of the right-click "Delete entire row..." feature is frequently associated with the above two errors.
BUG When the legacy flag is set on samples, SampleMaster acts as if it is uploading the samples, then fails without a meaningful message. The legacy flag is used to intentionally prevent data edits on selected material. SampleMaster should display a message to this effect to the end-user.
BUG Entering pieces. As piece lengths are spaced out, the red validation highlighting comes on for the bottom interval of about half of the records. Appears that an incorrect validation rule is being applied. Results in having to click twice to force an upload.
FEATURE Piece length defaults to bin length if piece length not specified. Test what happens if no bin length is specified. First release 2.2.0.12 [Blaisdell].
BUG Copy down does not honor above row setting of Y/N for auto-splitting.
BUG Auto-splitting Y/N is not honored. Always splits. Technically is a function of the logSample web-service.
BUG Hierarchy search now shows part of a horizontal scrollbar that has not been displayed previously.
BUG Edit mode: tabs lack drop-down lists like the data entry tabs carry for Test lists and Tool types. Driller see similar for Flapper selection on Cores. [Curator, Drillers].
BUG Edit mode tabs: cut and paste not available in this mode.
BUG Editing pieces does not properly update the x_sect_offset field.
BUG SampleMaster no meaningful message returned when samples will not upload: when legacy field set.
FEATURE SampleMaster Enable hierarchy browser to display other samples--stick to hierarchy rather than type. Partition routine types (HOLE, CORE, SECT, HALF) to top of list, but still show others (based on ancestry) below the canonical ancestors.
FEATURE Default sort order makes it difficult to find samples. Useful to be able to apply other sorting criteria based on user column selections [Broyles x335]. Protype implemented [Blaisdell].
BUG Possible code regression over earlier builds. "Slow" to upload samples compared to 2.1.1.6 release. Watching traffic in HTTP proxy/debug tool (Fiddler) shows that:

• Given a list of samples edited, ALL get uploaded, even if only one field changed. Very inefficient.
• Recalculation of depths occurs at the end, but is presently occurring for the Hole instead of a list of specific samples where offset, curated length, or advancement changed.

Logic needs to tighten up in SampleMaster to improve:

• Inserts, update handling for dirty records
• Efficient application of depth recomputation

Temporarily removed automatic depth recomputation step [Blaisdell]. Stop-gap ony.
BUG SampleMaster depends on parsing of Label_id field to assign hole, core, section, section half parentage. Not very robust given sample with ancestry outside the traditional core, section hierarchy. Also is tied to underlying resteasy-lims-webservices...getLimsData call bugs.
BUG Overloaded UI. When browsing for samples to edit, should only show edit, view tabs that have samples to look at. If tab is empty, hide it. Conversely show it again when mode or content changes.
BUG Sample cataloged against immediate ancestor hole, cannot subsequently be edited because label ID parsing in SampleMaster is incorrect for these sample leading to inability to identify actual sample parentage [Broyles x335].
BUG Piece entry. Cells turn red inappropriately--e.g. when bin bottom is beyond length of material? Correct the validation behavior. [Peng x335].
FEATURE File upload for LOI spreadsheets.
FEATURE File upload for XRF spreadsheets and files. Processing is not yet routine.
FEATURE File upload for Kappa Bridge data.
FEATURE File upload for JR-6A spinner files.
FEATURE Replace independent downhole tools data parser and file loaders (SET, SETP, APCT3, WSTP) with dedicated module within MUT framework.
FEATURE Replace independent core orientation tool (FlexIT) data loader with dedicated module within the MUT framework.
FEATURE Replace navigation bathymetry magnetometer data feed with direct MUT upload of selected NMEA content from the local WinFrog *.RAW files. Greatly simplifies the tool chain. Reduces technician workload at end of expedition (as files will be cataloged to ASMAN as uploaded. Improves technician control of system as loader module is then contained on WinFrog system (one less password and server system to navigate).
FEATURE Incorporate Thermcon uploader process into the MUT framework.

Reporting

BUG WebTabular [reported by Steve Midgley on 8 April 2011, as this report was being created] not reporting RCB hole on the "Drilling Summary (Core Tech Sheet" report. Also, after RCB hole information is entered in SampleMaster the "master" totals at the end of the report no longer display.
FEATURE Analysis and components lists indexed on the Apache web-server (linked via the Web Tabular Science Data report page) are static and tend to be out of date. Would be useful to automate refresh of these reference pages via an Oracle job or an operating system cron job.

Web-tabular

BUG Return of standards data is inconsistent or fails outright. Selecting exp=QAQC, analysis=GRA, QAQC=true returns no data. Exp=QAQC, analysis=PYC, QAQC=true returns lots of data. Why? Info: Fiddler shows web-service error. Debugging.
BUG WTR Return of standards data is inconsistent or fails outright. PWAVE_C QAQC results will not display. Web services appears to be generating an exception. Trace and fix. Info: variant of GRA item first logged.
BUG Precise behavior of QAQC and QAQC reporting is not clear from the report. Examine in code and add definitions to the display. Info: QAQC queries by group_name. Expedition querying is orthogonal to this so returns nothing.
BUG Specifying filter by selected user name returns results regardless of those names. Not used or not applied against the appropriate columns?
FEATURE Image report: (1) single report for all possible kinds of images; (2) use the thumbnails where we have them so people can see the content with the data record. [Crawford]. The distinction between "thin section image" vs "micrograph of a thin section" vs "closeup of a thin section" is non-sensical hair-splitting from the reporting and data retrieval stand-point. "I took a picture. Where is it?" Searching one place is easier than searching 3 or more. [Same issue applies to LIMS Reports imaging queries.] Alternatives in the form of Pivot reports prototyped [Bennight].

Moisture and Density

Pycnometer and Balance
FEATURE Pycnometer—sort sample list in container number order; currently the order is completely random.
BUG Pycnometer: Sample-list is not honoring "canceled" results, if there are canceled results the container-number/text-id will show up in the sample list multiple times.
BUG [x330] Duplicate MAD_MASS analyses are being generated: same sample_number, same test_number, different result_numbers. Been happening for 3 expeditions now. Balance change? Log test change? Unknown. Checking. Should use existing test record created by SampleMaster at sample cataloging time. We are obtaining duplicate container entries and mass_dry entries on MAD_MASS records: one comes from SampleMaster, the other from? Balance or web-service or invocation combo.
FEATURE [x334] MAD analyzer: it would be nice to have a software tool that allows users to scan LIMS and detect common problems in the MAD_MASS, PYC, and MAD analyses. On expeditions with heavy MAD analysis such a tool could be used to proactively find and correct problems.
Pycnometer Diagnostics
FEATURE remove settings panel--not needed for diagnostics control.
FEATURE cell buttons should only set context, not trigger action.
FEATURE operator should have full control of the cell inputs and outputs to test behavior of electronics connected to PCI 6224 A/D I/O card.
MadMax
FEATURE Subsume above considerations into line-items for MadMax.

Resteasy Error Reporting

BUG Occurrences of phoning home to millstone.iodp.tamu.edu have been observed. Clean up configuration to use production services in local environment.

Janus2Lims

FEATURE Enable Janus2Lims to selectively migrate sample categories, e.g. only thinsections, only headspace.
BUG crashes when run on x64 (laptop). Due to Oracle dependency management. If Oracle installed locally, assembly search path and load order precedences can result in the wrong version of Oracle being invoked, instead of the copy deployed with Janus2Lims.
BUG does not cause depths to compute (verify)
BUG generates its own legacy style depth scale (12761)
BUG swaps curated and liner length (variance between historical sediment vs. hard rock field usage?)
BUG should use curated length (x_length) to compute x_offset, not liner lengths (x_orig_len)
FEATURE Support import of specific sample types. E.g. Thin Sections only.

SHMSL

BUG [x335] Point susceptibility control data check file is not referenced properly in the MSPOINT raw data file. File placed on disk under the "control data" heading rather than "calibration data" heading. Content is presently not loaded or available in LIMS.
BUG [x335] Skip list does not work on SHMSL. Using skip list results in a file being saved with XXXX in the name. Or no file at all. Fixed[Mills].

Build Box

FEATURE Centralize maven repository support. Recommend the tool Nexus over previously examined tool Archiva.
FEATURE Centralize .NET assembly, external OEM, DLL support. Recommend the tool NuGet. Already in use for DescLogik.
FEATURE Chat server for the development group. If it catches on, expect it will replace JR_Programmers email group.

Video Overlay Trans(X)mitter (aka Xbob)

FEATURE Remove email notification. Sufficient to print a meaningful message to the video overlay display.
FEATURE Revise the serial communication to auto-recover from serial link failure. No operator intervention should be required to re-establish communication unless total failure of a component occurs.

Database

FEATURE Tagging tests by project. Web-service revisions: (1) populate changed_by field appropriately from submitted user/pass; (2) add support and default behavior for x_project in sample and test.
FEATURE Automated synchronization for DESCINFO schema configurations. Thoughts towards LIMS configurations too. Asynchronicity required. Robustness in the face of unreliable connectivity absolutely required. Paves the way for real-time trickling of sample, test, result. Functionality provided by Oracle archive logging and the Oracle streams package. See Oracle whitepaper "Asynchronous Change Data Capture Cookbook".

Web Services

FEATURE Load balancing Provide Lims.NET support for base path in load balance servers--e.g. web.ship.iodp.tamu.edu:80/ws should get carried through by SampleMaster and DESCLogik when invoking a connection via load balancing.
BUG Resteasy-lims-webservices getLimsData will not return selected fields: e.g. x_hole, x_core, x_core_type, x_section, x_sect_half. Service was written before these fields were added as a convenience. The convenience applied is sample parent lookup; attribution of offset relative to section half for many types of samples.
BUG Image tiling services. Does not generate tiles if the core or section is null. Yet another casualty of hanging junk baskets off of holes. Fixed [Bennight].

[Advanced] Bulk Printer

BUG Fails to substitute many fields in the sample labels generated: x_core_type, x_core. Leads to labels printing with the ugly substitution variables on them.
FEATURE Can print anything by typing into Exp, Site, Hole, Core field; but populating Sample Identity field results in substitution variables being displayed on the label rather than the provided text.
BUG Printing 1 or 2 replicates of a label works. But 6 replicates fails silently. Why?

LIMS Reports

FEATURE Replace "Download file?" with radio-button set: Display below (default) | Display in new tab | Download file.
FEATURE Revise layout to make more efficient use of screen real-estate. Combine Select Report Tree and Select Sample Range. Make Select Report Tree scrollable and when selection made fill in selection in slide-box header. Select Sample Range should never fully obscure Selected report. Remove "Select Depth Scale". Move "Advanced Filter Options" where "Select Sample Range" used to be. Default display it. The "About this Report", "Example Report" and actual content then all move to the far left and pull up in visibility. Report title line and header should display filter parameters applied for report verification.

Image Capture (Closeup, Thin Section, Micrographs)

FEATURE Extend the sample lookup capability. Need to be able to search by sample type. Used test-list in this case to tag a junk basket sample. Release 1.0.9.5 added sample type search capability [Fackler, Bennight].
BUG Label IDs are mangled with different business logic than in SampleMaster or other label printing programs, leading to filenames that do not closely resemble sample label content.
BUG Long labels do not wrap appropriately. Different wrapping behavior required for material with only hole ancestry vs. core and section ancestry included. Adapt the business logic for x335 corner cases.
FEATURE Chnge default directory where captured images are dropped. Keep ending up in TEMP directory rather than archiving in the configured image directory or preferrably defacto default "c:\data" directory.. Revise defaults so this occurs under c:\Data like other stations.
FEATURE Add better support for John Beck workflow, where images are treated as external selections (Import) rather than acquired and placed direct from TWAIN acquisition.
BUG Atalasoft TWAIN driver receives errors when communicating with the Spot acquisition driver under Windows 7 x32. Communication in progress with vendor. Need to complete debug cycle with vendor programming staff.

Thermcon Loader

BUG Opening access yaps about security issues when attempting to convert old access files generated by the thermcon software.
BUG Interface not providing enough guidance about what it is doing. Have encountered cases of sample directory three levels deep where placement of data for a different sample was at each level.

TPFIT Data Loader

FEATURE Fold into MUT data load framework.
FEATURE Add support to load the WTF file if present.
FEATURE All files of the same base name should be moved to the archive directory together. Several files are left hanging.
FEATURE Enable operator to identify which tool was used if not clear from data file name: SET, SETP, APCT3, and one other one.
BUG Verify. Are we loading temperature data as at the bottom of the previous [specified] core? Is the supplied drillers depth for the measurement being converted to CSF-A?

WRMSL & STMSL

[With respect to subversion codebase https://build/svn/jr/LabVIEW/msl/trunk which is applied to both systems.]
BUG End-of-travel switch has no effect when triggered. Works find on STMSL.
BUG Running a sample followed by running a standard-as-part-of-the-sequence results in motion but no measurement for the standard or remaining portion of the previous sample.
FEATURE Revise the PWL Get data from array class to conduct a check for driver errors as the other equivalent methods do. Improves robustness in case of errors at the sensor driver level.
FEATURE When a Bartington driver serial read error occurs, it can result in a zero measurement. Revise to return NaN for this no (failed) observation case.
BUG End-of-travel switch is only checked once. If the dialog is Ok'd without actually releasing the switch (clearing material), the program goes into error handling and shuts down.
BUG Check for laser obstruction during "Find Laser" operation only checks once. If the operator clears the dialog box without clearing the obstruction, the puck racks out at the forward limit.
FEATURE Improve user experience for configuration file management from within the code.
FEATURE Ability to skip measuring over a list of intervals or an entire range is still desirable.
FEATURE Clarify the function of the pusher vs. material under study. Improve the interface wording to reflect this distinction.

Addendum D: Sample, Test, ResultStatistical Methods

Sample Method Reference

1. select count "Routine Samples" from sample;
2. select count "Exp Samples" from sample where x_expedition in ('335', '335(312)') and standard='F' and instr('ICPAR', status) > 0;
3. select count "Std Ref Materials" from sample where x_expedition='QAQC' and standard='T' and instr('ICPAR', status) > 0 and sample_name not like 'CONT%';
4. select count "Exp Canceled Samples" from sample where x_expedition in ('335', '335(312)') and standard='F' and instr('X', status) > 0;
5. select count "Samples Filfilling Requests" from sample where x_expedition in ('335', '335(312)') and (x_req_code is not null or x_requestor is not null) and instr('ICPA', status) > 0;
6. select count "Routine Shipboard Samples" from sample where x_expedition in ('335', '335(312)') and (x_req_code is null and x_requestor is null) and instr('ICPA', status) > 0;
7. select sample_type, count from sample where x_expedition in ('335', '335(312)') and instr('ICPA', status) > 0 and sample_type in ('HOLE', 'CORE', 'SECT', 'SHLF', 'PC', 'TS', 'SS') group by sample_type;

Test Method Reference

1. select count "Total Tests" from test;
2. select count "Exp Tests Conducted" from test where sample_number in (select sample_number from sample where x_expedition in ('335', '335(312)') and instr('ICPAR', status) > 0) and instr('ICPAR', status) > 0;
3. select count "Exp Tests Canceled" from test where sample_number in (select sample_number from sample where x_expedition in ('335', '335(312)') and instr('ICPAR', status) > 0) and instr('X', status) > 0;
4. select count "Ext QAQC" from test where sample_number in (select sample_number from sample where standard='T' and instr('ICPAR', status) > 0) and instr('ICPAR', status) > 0 and date_received > to_date('2011-04-13 00:00:00', 'yyyy-mm-dd hh24:mi:ss') and date_received < to_date('2011-06-08 23:59:59', 'yyyy-mm-dd hh24:mi:ss');

Result Method Reference

1. select count "Total Results" from result;
2. select count "Exp Results" from result where sample_number in (select sample_number from sample where x_expedition in ('335', '335(312)') and instr('ICPAR', status) > 0) and instr('EMAR', status) > 0;
3. select count "Exp Results Cancled" from result where sample_number in (select sample_number from sample where x_expedition in ('335', '335(312)') and instr('ICPAR', status) > 0) and instr('X', status) > 0;
4. select count "QAQC Results" from result where sample_number in (select sample_number from sample where standard='T' and instr('ICPAR', status) > 0) and instr('EMAR', status) > 0 and entered_on > to_date('2011-04-13 00:00:00', 'yyyy-mm-dd hh24:mi:ss') and entered_on < to_date('2011-06-08 23:59:59', 'yyyy-mm-dd hh24:mi:ss');