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PLR Plate Quadrant Definition Standardization (#410)
Co-authored-by: Rick Wierenga <rick_wierenga@icloud.com>
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‎.gitignore‎

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*.log
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build/lib
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myenv
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myenv
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env/*

‎docs/conf.py‎

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html_extra_path = ["resources/library/img"]
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html_theme_options = {
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"show_nav_level": 4,
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"use_edit_page_button": True,
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"navbar_start": ["navbar-logo"],
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"navbar_center": ["navbar-nav"],

‎docs/resources/carrier/carrier.rst‎

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Carrier
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================
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A **carrier** is a component of the deck layout that holds labware such as plates, tip racks, tubes, or troughs/reservoirs. Carriers serve as modular, standardized platforms that allow for flexible deck configurations, ensuring that labware is positioned accurately.
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Each carrier type is optimized for specific resource types (like plates, tip racks, etc.), allowing for efficient sample handling and workflow customization.
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The :class:`~pylabrobot.resources.carrier.Carrier` class provides a base structure from which specialized carrier types inherit, ensuring modularity and flexibility in system configurations.
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-----
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Subclasses of `Carrier`
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-----------------------
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.. toctree::
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:maxdepth: 4
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plate-carrier/plate_carriers
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mfx-carrier/mfx_carriers
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-----
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Carrier Types
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-------------
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- **Plate Carriers**: These carriers hold standard microplates and deep-well plates, ensuring proper alignment for automated pipetting and handling.
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- **MFX Carriers**: A specific type of carrier designed for flexible reconfiguration of that carrier layout by removably screwing "MFX Modules" onto the MFX Carrier of choice.

docs/resources/mfx.ipynb renamed to docs/resources/carrier/mfx-carrier/mfx_carriers.ipynb

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docs/resources/plate_carriers.ipynb renamed to docs/resources/carrier/plate-carrier/plate_carriers.ipynb

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‎docs/resources/index.md‎

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# Resource Library
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The PLR Resource Library (PLR-RL) is the world's biggest and most accurate centralized collection of labware. If you cannot find something, please contribute what you are looking for!
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The PyLabRobot Resource Library (PLR-RL) is PyLabRobot's open-source, crowd-sourced collection of labware.
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Laboratories across the world use an almost infinite number of different resources/labware.
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We believe the way to most efficient capture the largest portion of this resource superset is via crowd-sourcing, and peer-reviewing new entries.
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If you cannot find something, please contribute what you are looking for!
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----
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```{toctree}
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:maxdepth: 1
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introduction
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custom-resources
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plr-rl-naming-conventions
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```
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----
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## `Resource` subclasses
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In PLR every physical object is a subclass of the `Resource` superclass (except for `Tip`).
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Each subclass adds unique methods or attributes to represent its unique physical specifications and behavior.
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Some standard `Resource` subclasses in the inheritance tree are:
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```
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Resource
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├── Carrier
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│ ├── TipCarrier
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│ ├── PlateCarrier
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│ ├── MFXCarrier
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│ ├── ShakerCarrier
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│ └── TubeCarrier
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├── Container
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│ ├── Well
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│ ├── PetriDish
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│ ├── Tube
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│ └── Trough
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├── ItemizedResource
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│ ├── Plate
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│ ├── TipRack
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│ └── TubeRack
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├── Lid
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└── PlateAdapter
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```
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See more detailed documentatino below (WIP).
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PLR's `Resource` subclasses in the inheritance tree are:
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<style>
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.tree {
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border: 3px solid black; /* Thick border around the entire table */
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border-collapse: collapse; /* Ensures borders don’t double */
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background-color: #FAF3DD; /* Light background */
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margin-left: 5px; /* A bit of left margin */
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}
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.tree td {
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font-family: "Fira Code", monospace; /* Code-like font */
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font-size: 15px; /* Matches code cell output */
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font-weight: bold; /* Make all text bold */
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line-height: 1.2; /* Slightly tighten vertical spacing */
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padding: 0 10px; /* Padding around each line */
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border: none; /* Remove inner borders */
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white-space: pre; /* Preserve spacing exactly */
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}
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</style>
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<table class="tree">
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<tr><td><a href="introduction.html">Resource</a></td></tr>
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<!-- Carrier subtree -->
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<tr><td>├── <a href="carrier/carrier.html">Carrier</a></td></tr>
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<tr><td>│ ├── <a href="carrier/plate-carrier/plate_carriers.html">PlateCarrier</a></td></tr>
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<tr><td>│ ├── TipCarrier</td></tr>
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<tr><td>│ ├── <a href="carrier/mfx-carrier/mfx_carriers.html">MFXCarrier</a></td></tr>
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<tr><td>│ ├── TroughCarrier</td></tr>
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<tr><td>│ └── TubeCarrier</td></tr>
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<!-- Container subtree -->
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<tr><td>├── Container</td></tr>
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<tr><td>│ ├── Well</td></tr>
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<tr><td>│ ├── PetriDish</td></tr>
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<tr><td>│ ├── Tube</td></tr>
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<tr><td>│ └── Trough</td></tr>
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<!-- ItemizedResource subtree -->
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<tr><td>├── <a href="itemized-resource/itemized-resource.html">ItemizedResource</a></td></tr>
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<tr><td>│ ├── <a href="itemized-resource/plate/plate.html">Plate</a></td></tr>
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<tr><td>│ ├── TipRack</td></tr>
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<tr><td>│ └── TubeRack</td></tr>
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<!-- ResourceHolder subtree -->
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<tr><td>├── ResourceHolder</td></tr>
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<tr><td>│ └── PlateHolder</td></tr>
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<!-- Others -->
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<tr><td>├── Lid</td></tr>
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<tr><td>├── PlateAdapter</td></tr>
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<tr><td>└── ResourceStack</td></tr>
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</table>
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----
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```{toctree}
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:caption: Resource subclasses
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:maxdepth: 3
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:caption: Resource subclass explanations
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:hidden:
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carrier/carrier
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containers
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itemized_resource
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plates
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plate_carriers
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mfx
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itemized-resource/itemized-resource
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```
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## Library
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### Plate Naming Standard
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PLR is not actively enforcing a specific plate naming standard but recommends the following:
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![PLR_plate_naming_standards](img/PLR_plate_naming_standards.png)
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This standard is similar to the [Opentrons API labware naming standard](https://ecatalog.corning.com/life-sciences/b2b/UK/en/Microplates/Assay-Microplates/96-Well-Microplates/Costar%C2%AE-Multiple-Well-Cell-Culture-Plates/p/3516) but 1) further sub-categorizes "wellplates" to facilitate communication with day-to-day users, and 2) adds information about the well-bottom geometry.
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```{toctree}
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:caption: Library
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‎docs/resources/itemized-resource/itemized-resource.rst‎

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ItemizedResource
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================
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Resources that contain items in a grid are subclasses of :class:`pylabrobot.resources.itemized_resource.ItemizedResource`. This class provides convenient methods for accessing the child-resources, such as by integer or SBS "A1" style-notation, as well as for traversing items in an ``ItemizedResource``. Examples of subclasses of ``ItemizedResource`` are :class:`pylabrobot.resources.plate.Plate` and :class:`pylabrobot.resources.tip_rack.TipRack`.
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To instantiate an ``ItemizedResource``, it is convenient to use the ``pylabrobot.resources.utils.create_equally_spaced_2d`` method to quickly initialize a grid of child-resources in a grid. Here's an example of a simple ``ItemizedResource``:
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.. code-block:: python
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from pylabrobot.resources import ItemizedResource
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from pylabrobot.resources.utils import create_equally_spaced_2d
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from pylabrobot.resources.well import Well, WellBottomType
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plate = ItemizedResource(
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name="plate",
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size_x=127,
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size_y=86,
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size_z=10,
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items=create_equally_spaced_2d(
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Well, # the class of the items
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num_items_x=12,
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num_items_y=8,
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dx=12, # distance between the left items and the left border in the x-axis
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dy=12, # distance between the bottom items and the front border in the y-axis
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dz=0, # distance between the items and the bottom border in the z-axis
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item_dx=9, # distance between the items in the x-axis
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item_dy=9, # distance between the items in the y-axis
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bottom_type=WellBottomType.FLAT, # a custom keyword argument passed to the Well initializer
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)
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)
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Subclasseses of :class:`ItemizedResource`
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------------------------------------------
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.. toctree::
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:maxdepth: 1
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plate/plate

‎docs/resources/itemized-resource/plate/definition-plate.md‎

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# Tutorial: Plate Definition
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work in progress
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Aim: give a complete Notebook people can download an directly use to sequentially measure `dz` and `material_z_thickness` of a new `Plate` definition they want to generate.
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## YouTube tutorial
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<iframe width="720" height="405" src="https://www.youtube.com/embed/ViHgIhU476Q" title="YouTube video player" frameborder="0" allow="autoplay; encrypted-media; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>

‎docs/resources/itemized-resource/plate/img/250304_explainer_fill_order.jpg‎

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‎docs/resources/itemized-resource/plate/img/250304_explainer_quadrant_identifiers.jpg‎

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