Get labware names, files, xyz coordinates from deck layout file

bowlineknot · April 6, 2023, 9:15pm

Hello,

I am working on parsing the xyz coordinates and labware names from the deck layout file, and I was able to have a script get that into a results file. I’m having trouble figuring out if I could get the labware file name/location information via running the Venus method and generating a results file. Is there a way to do this? The purpose of this project is to keep track of the xyz coordinates in our methods across instruments.

rickwierenga · April 6, 2023, 10:23pm

Maybe the PyLabRobot implementation is helpful:

github.com

PyLabRobot/pylabrobot/blob/main/pylabrobot/resources/hamilton/hamilton_decks.py#L164


      
            for og_resource in self.children:
              og_x = cast(Coordinate, og_resource.location).x
              og_y = cast(Coordinate, og_resource.location).y
          
              # A resource is not allowed to overlap with another resource. Resources overlap when a
              # corner of one resource is inside the boundaries of another resource.
              if any([
                og_x <= resource_location.x < og_x + og_resource.get_absolute_size_x(),
                og_x < resource_location.x + resource.get_absolute_size_x() \
                  < og_x + og_resource.get_absolute_size_x()
                ]) and any(
                  [
                    og_y <= resource_location.y < og_y + og_resource.get_absolute_size_y(),
                    og_y < resource_location.y + resource.get_absolute_size_y() \
                      < og_y + og_resource.get_absolute_size_y()
                  ]
                ):
                raise ValueError(f"Location {resource_location} is already occupied by resource "
                                  f"'{og_resource.name}'.")
          
          return super().assign_child_resource(resource, location=resource_location, reassign=reassign)

bowlineknot · April 7, 2023, 12:17am

Thanks! I’ll take a look.

NickHealy_Hamilton · April 7, 2023, 1:30pm

@bowlineknot - Yes, you can parse out labware definition files as well as deck coordinates from deck layouts using VENUS commands. Linked below are a couple posts that provide more context:

Retrieving deck coordinates via labware ID:
https://forums.pylabrobot.org/t/extracting-labware-coordinates-on-from-the-deck-layout/1098

Retrieving labware definition file path via labware ID:
https://forums.pylabrobot.org/t/library-downloads-requests/40/79?u=nickhealy_hamilton

By whatever programmatic preference, you would compile the labware IDs of the deck positions you are interested in, and use the above tools to retrieve the relevant data which could then be written to a file.

-Nick

bowlineknot · April 7, 2023, 5:57pm

Thanks Nick! That was very helpful. Is there a easy way to retrieve the position of the labware within the carrier?
I’m looking at using this

or this

and this together.

DanHartman_Hamilton · April 7, 2023, 6:17pm

@bowlineknot can you confirm what you mean by “position of the labware within the carrier”?

If you’re referring to the carrier (template) Site ID, then the Labware Access library @NickHealy_Hamilton linked is your best bet. It contains the following command, which will perform exactly that:

I suggest downloading, installing, and taking a look through. The Labware Access library does a good job of simplifying a lot of the processes from the HSLDevLib, and is a great tool when doing any sort of Deck Layout modification or information gathering at run time.

Thank you,
Dan

bowlineknot · April 7, 2023, 6:25pm

Thanks Dan for the suggestion! What I mean by the position of the labware within the carrier is: i.e. the position of a rack of tips (labware) on a tip carrier is returned by the script to be Position 1 of 5 Pos Tip Carrier 1. Hope that makes sense, I think we are on the same page.

I haven’t used the Labware Access library much compared to the DevLib. Hamilton Venus has a lot of libraries!
Once again thanks for pointing me in the right direction!

bowlineknot · April 10, 2023, 6:02pm

Thanks for the help everyone! @DanHartman_Hamilton @NickHealy_Hamilton @rickwierenga Some late in the evening scripting got me this. (a sample)

Gareth · May 9, 2024, 3:20pm

Sorry for bumping an old thread, but what’s the best way to get a list of labware IDs and sequence IDs? Most of the functions in HSLDev, HSLLabwrAccess, LPQ need either one of them…

If the answer is to use GetLabwareIDsAndTemplateSiteIDsForTemplateID and then GetDefaultSequenceForLabwareID, then how do you get a list of template IDs…

NickHealy_Hamilton · May 9, 2024, 3:34pm

Hi Gareth,

Is your intent to collect all template IDs from a deck? Or simply to identify the parent template ID for a rack that is bound to one of it’s sites?

Thanks.

-Nick

Gareth · May 9, 2024, 3:54pm

I’m essentially wanting to replicate what bowlineknot did. I’ve got all the labware given an array of template ids, and I can get sequences given the labware, but at the moment the array of template ids is hard-coded…

NickHealy_Hamilton · May 9, 2024, 4:21pm

Is your array of template IDs supposed to represent all the templates used for the deck layout?

I am unclear if the request is to get the coordinates of all racks in the layout, or a specified subset.

Thanks.

-Nick

Gareth · May 9, 2024, 4:27pm

The aim is to get an array of labware IDs for all labware in the deck layout.

This works, but I’d like the arrLabwareIds to be dynamic (or use another way of getting all labware ids):

I’d also like to get an array of all sequences in a deck layout (not just default sequences).

AlvaroCuevas_Hamilton · May 9, 2024, 7:05pm

Hi Gareth, Give this one a try: GetLabIDsAndSeqNames_Library_and_Demo.zip :: Hamilton

It´s an .smt with one function that will return all labware IDs and Sequence Names.

Then you can use HSLDev > DevGetSequence to get a copy of the deck sequence from a given name.

Gareth · May 10, 2024, 9:18am

Thank you Alvaro! Really appreciate it.

The HSL is interesting to me. Is there any documentation about the IEditDeckLayout5 and HXPARAMSLib.HxPars objects? It seems the HxPars is a dict-like object?

AlvaroCuevas_Hamilton · May 10, 2024, 1:18pm

Unfortunately there´s no external documentation available. The HxPars is a propietary type of dictionary used in the VENUS code base and it´s not a friendly format.

We have other custom libraries that offer dictionary functions:

Install this ASW Standard v16.zip :: Hamilton
Then install HSLExtensionsSetupv110.zip :: Hamilton

#2 provides an extended framework (\Library\HSLExtensions) including a Dictionary library, and uses libraries installed by #1 (\Library\ASWStandard)

Gareth · May 13, 2024, 8:32am

Ah ok, that’s a shame.

I knew about the dictionary libraries - but am interested in the objects like you used to get more information about the method/deck!