GitLab 14.5 is now available. 🚀 Learn what's new.

Commit 08d028fc authored by Timm Schoening's avatar Timm Schoening
Browse files
parent a1d3ae9a
Creative Commons Attribution-NonCommercial 4.0 International Public License
By exercising the Licensed Rights (defined below), You accept and agree to be bound by the terms and conditions of this Creative Commons Attribution-NonCommercial 4.0 International Public License ("Public License"). To the extent this Public License may be interpreted as a contract, You are granted the Licensed Rights in consideration of Your acceptance of these terms and conditions, and the Licensor grants You such rights in consideration of benefits the Licensor receives from making the Licensed Material available under these terms and conditions.
Section 1 – Definitions.
Adapted Material means material subject to Copyright and Similar Rights that is derived from or based upon the Licensed Material and in which the Licensed Material is translated, altered, arranged, transformed, or otherwise modified in a manner requiring permission under the Copyright and Similar Rights held by the Licensor. For purposes of this Public License, where the Licensed Material is a musical work, performance, or sound recording, Adapted Material is always produced where the Licensed Material is synched in timed relation with a moving image.
Adapter's License means the license You apply to Your Copyright and Similar Rights in Your contributions to Adapted Material in accordance with the terms and conditions of this Public License.
Copyright and Similar Rights means copyright and/or similar rights closely related to copyright including, without limitation, performance, broadcast, sound recording, and Sui Generis Database Rights, without regard to how the rights are labeled or categorized. For purposes of this Public License, the rights specified in Section 2(b)(1)-(2) are not Copyright and Similar Rights.
Effective Technological Measures means those measures that, in the absence of proper authority, may not be circumvented under laws fulfilling obligations under Article 11 of the WIPO Copyright Treaty adopted on December 20, 1996, and/or similar international agreements.
Exceptions and Limitations means fair use, fair dealing, and/or any other exception or limitation to Copyright and Similar Rights that applies to Your use of the Licensed Material.
Licensed Material means the artistic or literary work, database, or other material to which the Licensor applied this Public License.
Licensed Rights means the rights granted to You subject to the terms and conditions of this Public License, which are limited to all Copyright and Similar Rights that apply to Your use of the Licensed Material and that the Licensor has authority to license.
Licensor means the individual(s) or entity(ies) granting rights under this Public License.
NonCommercial means not primarily intended for or directed towards commercial advantage or monetary compensation. For purposes of this Public License, the exchange of the Licensed Material for other material subject to Copyright and Similar Rights by digital file-sharing or similar means is NonCommercial provided there is no payment of monetary compensation in connection with the exchange.
Share means to provide material to the public by any means or process that requires permission under the Licensed Rights, such as reproduction, public display, public performance, distribution, dissemination, communication, or importation, and to make material available to the public including in ways that members of the public may access the material from a place and at a time individually chosen by them.
Sui Generis Database Rights means rights other than copyright resulting from Directive 96/9/EC of the European Parliament and of the Council of 11 March 1996 on the legal protection of databases, as amended and/or succeeded, as well as other essentially equivalent rights anywhere in the world.
You means the individual or entity exercising the Licensed Rights under this Public License. Your has a corresponding meaning.
Section 2 – Scope.
License grant.
Subject to the terms and conditions of this Public License, the Licensor hereby grants You a worldwide, royalty-free, non-sublicensable, non-exclusive, irrevocable license to exercise the Licensed Rights in the Licensed Material to:
reproduce and Share the Licensed Material, in whole or in part, for NonCommercial purposes only; and
produce, reproduce, and Share Adapted Material for NonCommercial purposes only.
Exceptions and Limitations. For the avoidance of doubt, where Exceptions and Limitations apply to Your use, this Public License does not apply, and You do not need to comply with its terms and conditions.
Term. The term of this Public License is specified in Section 6(a).
Media and formats; technical modifications allowed. The Licensor authorizes You to exercise the Licensed Rights in all media and formats whether now known or hereafter created, and to make technical modifications necessary to do so. The Licensor waives and/or agrees not to assert any right or authority to forbid You from making technical modifications necessary to exercise the Licensed Rights, including technical modifications necessary to circumvent Effective Technological Measures. For purposes of this Public License, simply making modifications authorized by this Section 2(a)(4) never produces Adapted Material.
Downstream recipients.
Offer from the Licensor – Licensed Material. Every recipient of the Licensed Material automatically receives an offer from the Licensor to exercise the Licensed Rights under the terms and conditions of this Public License.
No downstream restrictions. You may not offer or impose any additional or different terms or conditions on, or apply any Effective Technological Measures to, the Licensed Material if doing so restricts exercise of the Licensed Rights by any recipient of the Licensed Material.
No endorsement. Nothing in this Public License constitutes or may be construed as permission to assert or imply that You are, or that Your use of the Licensed Material is, connected with, or sponsored, endorsed, or granted official status by, the Licensor or others designated to receive attribution as provided in Section 3(a)(1)(A)(i).
Other rights.
Moral rights, such as the right of integrity, are not licensed under this Public License, nor are publicity, privacy, and/or other similar personality rights; however, to the extent possible, the Licensor waives and/or agrees not to assert any such rights held by the Licensor to the limited extent necessary to allow You to exercise the Licensed Rights, but not otherwise.
Patent and trademark rights are not licensed under this Public License.
To the extent possible, the Licensor waives any right to collect royalties from You for the exercise of the Licensed Rights, whether directly or through a collecting society under any voluntary or waivable statutory or compulsory licensing scheme. In all other cases the Licensor expressly reserves any right to collect such royalties, including when the Licensed Material is used other than for NonCommercial purposes.
Section 3 – License Conditions.
Your exercise of the Licensed Rights is expressly made subject to the following conditions.
Attribution.
If You Share the Licensed Material (including in modified form), You must:
retain the following if it is supplied by the Licensor with the Licensed Material:
identification of the creator(s) of the Licensed Material and any others designated to receive attribution, in any reasonable manner requested by the Licensor (including by pseudonym if designated);
a copyright notice;
a notice that refers to this Public License;
a notice that refers to the disclaimer of warranties;
a URI or hyperlink to the Licensed Material to the extent reasonably practicable;
indicate if You modified the Licensed Material and retain an indication of any previous modifications; and
indicate the Licensed Material is licensed under this Public License, and include the text of, or the URI or hyperlink to, this Public License.
You may satisfy the conditions in Section 3(a)(1) in any reasonable manner based on the medium, means, and context in which You Share the Licensed Material. For example, it may be reasonable to satisfy the conditions by providing a URI or hyperlink to a resource that includes the required information.
If requested by the Licensor, You must remove any of the information required by Section 3(a)(1)(A) to the extent reasonably practicable.
If You Share Adapted Material You produce, the Adapter's License You apply must not prevent recipients of the Adapted Material from complying with this Public License.
Section 4 – Sui Generis Database Rights.
Where the Licensed Rights include Sui Generis Database Rights that apply to Your use of the Licensed Material:
for the avoidance of doubt, Section 2(a)(1) grants You the right to extract, reuse, reproduce, and Share all or a substantial portion of the contents of the database for NonCommercial purposes only;
if You include all or a substantial portion of the database contents in a database in which You have Sui Generis Database Rights, then the database in which You have Sui Generis Database Rights (but not its individual contents) is Adapted Material; and
You must comply with the conditions in Section 3(a) if You Share all or a substantial portion of the contents of the database.
For the avoidance of doubt, this Section 4 supplements and does not replace Your obligations under this Public License where the Licensed Rights include other Copyright and Similar Rights.
Section 5 – Disclaimer of Warranties and Limitation of Liability.
Unless otherwise separately undertaken by the Licensor, to the extent possible, the Licensor offers the Licensed Material as-is and as-available, and makes no representations or warranties of any kind concerning the Licensed Material, whether express, implied, statutory, or other. This includes, without limitation, warranties of title, merchantability, fitness for a particular purpose, non-infringement, absence of latent or other defects, accuracy, or the presence or absence of errors, whether or not known or discoverable. Where disclaimers of warranties are not allowed in full or in part, this disclaimer may not apply to You.
To the extent possible, in no event will the Licensor be liable to You on any legal theory (including, without limitation, negligence) or otherwise for any direct, special, indirect, incidental, consequential, punitive, exemplary, or other losses, costs, expenses, or damages arising out of this Public License or use of the Licensed Material, even if the Licensor has been advised of the possibility of such losses, costs, expenses, or damages. Where a limitation of liability is not allowed in full or in part, this limitation may not apply to You.
The disclaimer of warranties and limitation of liability provided above shall be interpreted in a manner that, to the extent possible, most closely approximates an absolute disclaimer and waiver of all liability.
Section 6 – Term and Termination.
This Public License applies for the term of the Copyright and Similar Rights licensed here. However, if You fail to comply with this Public License, then Your rights under this Public License terminate automatically.
Where Your right to use the Licensed Material has terminated under Section 6(a), it reinstates:
automatically as of the date the violation is cured, provided it is cured within 30 days of Your discovery of the violation; or
upon express reinstatement by the Licensor.
For the avoidance of doubt, this Section 6(b) does not affect any right the Licensor may have to seek remedies for Your violations of this Public License.
For the avoidance of doubt, the Licensor may also offer the Licensed Material under separate terms or conditions or stop distributing the Licensed Material at any time; however, doing so will not terminate this Public License.
Sections 1, 5, 6, 7, and 8 survive termination of this Public License.
Section 7 – Other Terms and Conditions.
The Licensor shall not be bound by any additional or different terms or conditions communicated by You unless expressly agreed.
Any arrangements, understandings, or agreements regarding the Licensed Material not stated herein are separate from and independent of the terms and conditions of this Public License.
Section 8 – Interpretation.
For the avoidance of doubt, this Public License does not, and shall not be interpreted to, reduce, limit, restrict, or impose conditions on any use of the Licensed Material that could lawfully be made without permission under this Public License.
To the extent possible, if any provision of this Public License is deemed unenforceable, it shall be automatically reformed to the minimum extent necessary to make it enforceable. If the provision cannot be reformed, it shall be severed from this Public License without affecting the enforceability of the remaining terms and conditions.
No term or condition of this Public License will be waived and no failure to comply consented to unless expressly agreed to by the Licensor.
Nothing in this Public License constitutes or may be interpreted as a limitation upon, or waiver of, any privileges and immunities that apply to the Licensor or You, including from the legal processes of any jurisdiction or authority.
> **Preamble:** We strive to make marine image data [FAIR](https://gitlab.hzdr.de/datahub/marehub/ag-videosimages/metadata-profiles-fdos/-/blob/master/FAIR-marine-images.md). We maintain [data profiles](https://gitlab.hzdr.de/datahub/marehub/ag-videosimages/metadata-profiles-fdos) to establish a common language of marine imagery, we develop - here in this repository - best-practice [operating procedures](https://gitlab.hzdr.de/datahub/marehub/ag-videosimages/standard-operating-procedures) for handling marine images and we develop [software tools](https://gitlab.hzdr.de/datahub/marehub/ag-videosimages/software/mar-iqt) to apply the vocabulary and procedures to marine imagery.
## Preface
Publishing marine image data in a FAIR and open way requires data curation for both image data and image metadata. These quality control steps need to follow common standard operating procedures (SOPs) to facilitate joint data interpretation. This repository mainly collects SOPs for the QA/QC steps between acquisition and publication. It also contains some example SOPs on image acquisition for the interested user. It does not yet provide operational steps for the publication phase (e.g. physical file transfer to Pangaea). The SOPs vary in granularity and not all may be applicable to your usecase.
To make full use of the [MarIQT software tools](https://gitlab.hzdr.de/datahub/marehub/ag-videosimages/software/mar-iqt) that implement some of the SOPs functionalities, you need to follow the guidelines on [file formats](https://gitlab.hzdr.de/datahub/marehub/ag-videosimages/standard-operating-procedures/-/blob/master/file-formats.md), adhere to the [folder structure](https://gitlab.hzdr.de/datahub/marehub/ag-videosimages/standard-operating-procedures/-/blob/master/folder-structure.md) and the [provenance documentation](https://gitlab.hzdr.de/datahub/marehub/ag-videosimages/standard-operating-procedures/-/blob/master/provenance-documentation.md) (which is done for you automatically while using MarIQT).
# Standard operating procedures (SOPs)
This section is your starting point for exploring the MareHub AG V/I SOP documents. This readme provides some background and context information on how visualizations of the SOPs are structured and how the data workflow is explained. It is like an SOP for SOPs. You can find the existing marine imaging SOPs [here](https://gitlab.hzdr.de/datahub/marehub/ag-videosimages/standard-operating-procedures/-/tree/master/SOPs).
### General workflows
![MareHub AG Videos/Images SOP documentation: general workflow](https://gitlab.hzdr.de/datahub/marehub/ag-videosimages/standard-operating-procedures/-/raw/master/SOPs/graphics/AGVI_SOP-documentation-1-workflow.jpeg "MareHub AG Videos/Images SOP documentation: general workflow")
SOPs generally describe how processes create or modify entities which are managed in infrastructure.
### A project's data workflow
![MareHub AG Videos/Images SOP documentation: project workflow](https://gitlab.hzdr.de/datahub/marehub/ag-videosimages/standard-operating-procedures/-/raw/master/SOPs/graphics/AGVI_SOP-documentation-2-project.jpeg "MareHub AG Videos/Images SOP documentation: project workflow")
In terms of research data, this is expressed by a data creation process that produces a data set entity which is managed in a data repository.
### Actors in a workflow
![MareHub AG Videos/Images SOP documentation: project workflow with actors](https://gitlab.hzdr.de/datahub/marehub/ag-videosimages/standard-operating-procedures/-/raw/master/SOPs/graphics/AGVI_SOP-documentation-3-project-actors.jpeg "MareHub AG Videos/Images SOP documentation: project workflow with actors")
Processes are conducted by an actor - in this case researchers - and similarly infrastructure is operated by actors - in this case a research data management (RDM) team. Infrastructure is further characterized by whether it is publicly accessible and whether it is machine-accessible. Accessibility by humans is always expected.
### Documentation entities
![MareHub AG Videos/Images SOP documentation: project workflow with documentation](https://gitlab.hzdr.de/datahub/marehub/ag-videosimages/standard-operating-procedures/-/raw/master/SOPs/graphics/AGVI_SOP-documentation-4-project-documentation.jpeg "MareHub AG Videos/Images SOP documentation: project workflow with documentation")
Processes and entities can be accompanied by one or many documentation entities. These can take various forms, depending on use cases, SOPs, software tools used, etc. These documentation entities may be seen by some as just another data entity (_"one wo:mans data is another wo:mans metadata"_), we like to keep it separate. The format of the documentation entities (file format, information content, etc.) is defined by one or several actors. In case the file format is machine-readable, the documentation entity will be marked as such. Like data entities, documentation entities cannot be the end of a workflow. They needs to be further processed or be placed into an infrastructure. This infrastructure might also be access-restricted.
### Status information
![MareHub AG Videos/Images SOP documentation: project workflow with status information](https://gitlab.hzdr.de/datahub/marehub/ag-videosimages/standard-operating-procedures/-/raw/master/SOPs/graphics/AGVI_SOP-documentation-5-project-status.jpeg "MareHub AG Videos/Images SOP documentation: project workflow with status information")
Of course, all SOPs should represent the best-case scenario and of course all their components should be in place and work as described. But as the marine imaging community is still developing their best-practices, some of the elements of SOPs are still under development. In that case, this is color-coded in the workflow figures: either there is no solution for the entire concept (of a process, entity, infrastructure or documentation) or there is one but it is not commonly supported, operated, executed or maintained.
# Cheatsheet of the graphical elements
![MareHub AG Videos/Images SOP documentation: cheatsheet of the graphical elements](https://gitlab.hzdr.de/datahub/marehub/ag-videosimages/standard-operating-procedures/-/raw/master/SOPs/graphics/MareHubSOP_graphics_cheatsheet.png "MareHub AG Videos/Images SOP documentation: cheatsheet of the graphical elements")
# This repository is outdated!
Please find the iFDO and SOP documentation pages here: https://datahub.pages.hzdr.de/marehub/ag-videosimages/fair-marine-images/sops/SOP_image-curation/ which are built from here: https://gitlab.hzdr.de/datahub/marehub/ag-videosimages/fair-marine-images
\ No newline at end of file
# High-level SOP on the general image curation workflow
## The overall image curation workflow from the project planning phase until the data publication in the open repositories
### Image data management - all
for one single deployment - a close-up of the project management workflow
![Image curation SOP introduction figure 1 by the MareHub AG Videos/Images](https://gitlab.hzdr.de/datahub/marehub/ag-videosimages/standard-operating-procedures/-/raw/master/SOPs/graphics/AGVI_SOP-documentation-image-workflow-1.jpeg "Image curation SOP introduction figure 1 by the MareHub AG Videos/Images")
For image data, the general project data management workflow consists of several high-level processes, data entities and those are managed in multiple infrastructures.
### Image data manangement - data creation
for one single deployment - a close-up of the project management workflow
![Image curation SOP introduction figure 2 by the MareHub AG Videos/Images](https://gitlab.hzdr.de/datahub/marehub/ag-videosimages/standard-operating-procedures/-/raw/master/SOPs/graphics/AGVI_SOP-documentation-image-workflow-2-creation.jpeg "Image curation SOP introduction figure 2 by the MareHub AG Videos/Images")
It is important to note here, that the data creation part of the general workflow includes the curation processes both for the navigation data as well as the image data.
### Image data manangement - data sets
for one single deployment - a close-up of the project management workflow
![Image curation SOP introduction figure 3 by the MareHub AG Videos/Images](https://gitlab.hzdr.de/datahub/marehub/ag-videosimages/standard-operating-procedures/-/raw/master/SOPs/graphics/AGVI_SOP-documentation-image-workflow-3-data.jpeg "Image curation SOP introduction figure 3 by the MareHub AG Videos/Images")
The central data entities are the curated (i.e. quality-controlled and processed) navigation data and the curated (i.e. quality-controlled and processed) image data.
### Image data manangement - data repositories
for one single deployment - a close-up of the project management workflow
![Image curation SOP introduction figure 4 by the MareHub AG Videos/Images](https://gitlab.hzdr.de/datahub/marehub/ag-videosimages/standard-operating-procedures/-/raw/master/SOPs/graphics/AGVI_SOP-documentation-image-workflow-4-repositories.jpeg "Image curation SOP introduction figure 4 by the MareHub AG Videos/Images")
Sharing and/or publication of the data entities of the image curation workflow is facilitated in different infrastructures. The Elements media asset management system is contains the work repository of the imagery. Other platforms - more suited for collaborative data exchange - e.g. OSIS (attention: other HGF centers might put their own data repository here!) or a geoserver.
The following section zooms in even further into the process and looks at specific aspects of the image curation workflow in more detail and with documentation entities.
## Details of the image curation process as close-ups of the overall image curation workflow
### Project curation (step 1/5)
for one single deployment - a close-up of the image data management workflow
![Image curation SOP project curation by the MareHub AG Videos/Images](https://gitlab.hzdr.de/datahub/marehub/ag-videosimages/standard-operating-procedures/-/raw/master/SOPs/graphics/AGVI_SOP-documentation-image-workflow-details-2-project-curation-status.jpeg "Image curation SOP project curation by the MareHub AG Videos/Images")
**Project curation** starts before a project has been applied for!
1. In order to establish the FAIR data creation of any project, a [data management plan]() (DMP) needs to be developed by the researchers and the RDM. This DMP needs to reside in a shared infrastructure (e.g. a cloud folder) which is maintained by the RDM team.
2. Equipment that creates image data (or navigation data) needs to be well-defined, ideally in central or shared infrastructure. At GEOMAR this is done in the _Marine Facilities Planning_ (MFP) tool. Equipment information from this source needs to be regurlarly synchronized with other such repositories like AWI sensors, the DSHIP devices, the OSIS devices etc. Synchronization is facilitated at GEOMAR bya Git repository bundling all information from the various sources. This is a background activity conducted by the RDM team and not directly related to the project data management.
3. Setting up a shared working space between researchers and the RDM for a specific project. This can come in the form of a Git repository for a project (or cruise). This repository is semi-automatically filled by information available in the DMP and the equipment Git. In the shared project space, one essential documentation entity is a machine-readable file containing a multitude of overarching project information: the project curation setting *.yaml file.
### Camera deployment (step 2/5)
for one single deployment - a close-up of the image data management workflow
![Image curation SOP camera deployment by the MareHub AG Videos/Images](https://gitlab.hzdr.de/datahub/marehub/ag-videosimages/standard-operating-procedures/-/raw/master/SOPs/graphics/AGVI_SOP-documentation-image-workflow-details-3-camera-deployment.jpeg "Image curation SOP camera deployment by the MareHub AG Videos/Images")
Deploying the cameras and acquiring imagery is the sole responsibility of the researchers. Information on these processes needs to become available to the RDM and/or publicly. SOPs on deploying cameras and acquiring imagery need to be created by the researchers and can be placed in a central infromation hub for others to benefit from this knowledge: the SOP cloud. While the SOP cloud contains general SOPs, which can be seen as SOP templates, an equipment deployment requires creating instances of these SOPs which are then populated with information on conducting the SOP for this specific project or deployment. These instances need to be accessible by the researchers and the RDM and contribute required information to subsequent processing steps and documentation entitites. One key entity is the deployment protocol (some see this as the instance of the deployment SOP) for which currently no infrastructure solution exists at GEOMAR. The deployment SOP instances also feed information into the DMP, underlining its existence as a living document.
### Navigation data curation (step 3/5)
for one single deployment - a close-up of the image data management workflow
![Image curation SOP navigation curation by the MareHub AG Videos/Images](https://gitlab.hzdr.de/datahub/marehub/ag-videosimages/standard-operating-procedures/-/raw/master/SOPs/graphics/AGVI_SOP-documentation-image-workflow-details-4-navigation-curation.jpeg "Image curation SOP navigation curation by the MareHub AG Videos/Images")
Processing the navigation data should be done according to an SOP for this task. The processing itself can be done with python code provided by the MareHub AG. This processing requires input from the action log.
Outputs of the navigation data processing are data files (*.txt and *.geojson) for the data infrastructures and a file documenting the provenance of the processing steps. This provenance file needs to be publicly available to make the navigation data FAIR. Again, the processing has an effect on the DMP which needs to be updated accordingly.
### Image data curation (step 4/5)
for one single deployment - a close-up of the image data management workflow
![Image curation SOP image curation 1 by the MareHub AG Videos/Images](https://gitlab.hzdr.de/datahub/marehub/ag-videosimages/standard-operating-procedures/-/raw/master/SOPs/graphics/AGVI_SOP-documentation-image-workflow-details-5-image-curation.jpeg "Image curation SOP image curation 1 by the MareHub AG Videos/Images")
Curation of the image data is split in two parts here. The goal of the process is to create an iFDO (image FAIR digital objects) and pFDO (proxy FAIR digital object) of the image data set. The two key components for that are i) making sure that the image acquisition time is correct (to link the image data with other and meta data) and ii) to assign a unique id (UUID4 - random) to each image. Once the acquisition time has been checked and a UUID incorporated into the image header the files can be renamed on disk, resulting in the curated image data set.
### Image data curation (step 5/5)
for one single deployment - a close-up of the image data management workflow
![Image curation SOP image curation 2 by the MareHub AG Videos/Images](https://gitlab.hzdr.de/datahub/marehub/ag-videosimages/standard-operating-procedures/-/raw/master/SOPs/graphics/AGVI_SOP-documentation-image-workflow-details-6-image-curation.png "Image curation SOP image curation 2 by the MareHub AG Videos/Images")
Once the curated image data is ready, two additional processes can create the remaining required information for the iFDO and pFDO: i) scale determination provides the resolution of the images (i.e. the size of one pixel in SI units) and ii) file hashing provides a value to check the file integrity later on. All the data and process documentation entities can now be bundled into the iFDO and pFDO. During this process provenance information on the processing itself is recorded and published alongside the image metadata. iFDOs enable FAIRness of images and have a use of their own (thus should be shared through OSIS) as well as facilitate using the image data (thus should be shared through Elements).
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment