Hello Paquo team,

First, thank you very much for your work on this piece of software!

When I use add_image with a new project, and the image is located on a Windows share, I am getting java.lang.IllegalArgumentException: java.lang.IllegalArgumentException: URI has an authority component. This is the case when the file name is of any of the following forms:

• //example/path/to subdirectory/image.png
• M:/path/to subdirectory/image.png (i.e., using a network drive mapping instead)
• file:/M:/path/to subdirectory/image.png

(If I use file:///example/path/to subdirectory/image.png), I get a different error, FileNotFoundError: image_provider can't provide URI for requested image_id.

To confirm, is this expected? Should I be using a different approach to adding images on a network share?

I am using Paquo v0.4.0 with QuPath v0.2.3, Python v3.8.12, and Windows 10.

with QuPathProject('//example/path/to project directory', mode="a") as project:  # This works.
    tile = project.add_image(
                '//example/path/to subdirectory/image.png',  # This raises the above error.
                image_type=QuPathImageType.BRIGHTFIELD_H_E,
            )

The full traceback:

Exception                                 Traceback (most recent call last)
~\Miniconda3\envs\example\lib\site-packages\_jpype.cp38-win_amd64.pyd in qupath.lib.images.servers.ImageServerProvider.getPreferredUriImageSupport()

~\Miniconda3\envs\example\lib\site-packages\_jpype.cp38-win_amd64.pyd in qupath.lib.images.servers.ImageServerProvider.getServerBuilders()

~\Miniconda3\envs\example\lib\site-packages\_jpype.cp38-win_amd64.pyd in java.io.File.<init>()

Exception: Java Exception

The above exception was the direct cause of the following exception:

java.lang.IllegalArgumentException        Traceback (most recent call last)
l:\home\path\to\qupath.py in <module>
----> 175 tile = project.add_image(
      176     '//example/path/to subdirectory/image.png',
      177     # image_type=QuPathImageType.BRIGHTFIELD_H_E,
      178 )
      179 

~\Miniconda3\envs\example\lib\contextlib.py in inner(*args, **kwds)
     73         def inner(*args, **kwds):
     74             with self._recreate_cm():
---> 75                 return func(*args, **kwds)
     76         return inner
     77 

~\Miniconda3\envs\example\lib\site-packages\paquo\projects.py in add_image(self, image_id, image_type, allow_duplicates)
    302         # first get a server builder
    303         try:
--> 304             support = ImageServerProvider.getPreferredUriImageSupport(
    305                 BufferedImage,
    306                 String(str(img_uri))

java.lang.IllegalArgumentException: java.lang.IllegalArgumentException: URI has an authority component

I would be grateful for any advice. Thank you again!

Hello, I am struggeling with the proper installation of Paquo, Following error is always shown as soon as I import paquo to a python script:

A fatal error has been detected by the Java Runtime Environment:

EXCEPTION_ACCESS_VIOLATION (0xc0000005) at pc=0x0000000000000000, pid=5276, tid=11108

JRE version: (16.0.2+7) (build ) Java VM: OpenJDK 64-Bit Server VM (16.0.2+7, mixed mode, tiered, compressed oops, compressed class ptrs, g1 gc, windows-amd64) Problematic frame: C 0x0000000000000000

No core dump will be written. Minidumps are not enabled by default on client versions of Windows

This is my current operating system:

• Intel(R) Core(TM) i5-9400 CPU @ 2.90GHz, 6 cores, 15G, Windows 10 , 64 bit Build 17763 (10.0.17763.2300)
• Python 3.8.12

I installed Paquo using pip install paquo and placed the ".paquo.toml" file including the path to my QuPath directory in one directory which was listed as possible locations.

Does one know how to debug my installation? Thanks, Hannes

Hello, when I try to access an image I get an GLib error that crashes the program.

qp = paquo.projects.QuPathProject("./qp/project.qpproj")
img = qp.images[0]

This produces the output: (process:14712): GLib-GObject-CRITICAL **: 11:20:36.970: _g_enum_types_init: assertion 'initialized == FALSE' failed (process:14712): GLib-GObject-CRITICAL **: 11:20:36.970: _g_object_type_init: assertion 'initialized == FALSE' failed

I am running Linux. I was unable to fix this so far. Does someone have an idea what could cause this?

This requires both:

• [x] ~verbatim display~
• [x] ~converting into polygons~

We're using Tiles (PathDetectionObjects) to display heatmaps for now. See https://forum.image.sc/t/best-way-to-display-additional-information-as-overlay/40901/6 for more information

Issue

Some image files like .czi files and .vsi files hold multiple scenes. For .czi files this can be multiple regions imaged on a slide, while for .vsi files this can be an overview image (scene 1) + the full pyramidal image (scene 2). When images are added to a project with the QuPath GUI with add images, all scenes are loaded. But when loaded through Paquo with qp.add_image(), only the first scene is loaded.

Expected behaviour

qp.add_image() loads all scenes from an image file, or at least gives the option to specifiy which scene is loaded

Context

This was mentioned on https://forum.image.sc/t/paquo-read-write-qupath-projects-from-python/41892/29?u=merrick but I don't think raised as a github issue so I raise it here myself

This can wait until just before we have the first paquo release.

We could generate docs via sphinx or something else. Is there any strong preference?

And should these be hosted on gh-pages or readthedocs or ...?

Draft of pull request related to #78.

Some time ago I implemented the possibility to remove an image from a QuPath project, although now I noticed that it is no longer working properly. In any case, maybe you can provide some feedback so I can figure out what I am doing wrong.

Points for review:

• Calling project.java_object.removeImage(image_entry_to_be_removed.java_object, True) used to do the job, but now when I call that method the image is not deleted correctly. Instead, if I open the project in QuPath after "deleting" an image, I see that its thumbnail is gone (see attached screenshot), and when I click on it QuPath asks me to set the image type (as if the image was never opened before).

• Currently, the new project.remove_image method takes an image path as input and checks if it is indeed part of the project. Not sure if it makes more sense to pass the entry_id of the image to be deleted instead. If we pass the path, then we should also handle possible duplicates in the project (currently only the first instance with a given path is removed)

Really cool project!

I had a quick question that I suspect you know the answer to.

If I know exactly the detection I want to access, is there a way to get to it?

>>> type(qpitem.hierarchy.detections)
paquo.hierarchy._PathObjectSetProxy


>>>qpitem.hierarchy.detections
QuPathPathDetectionObjectSet(n=40865)

>>>qpitem.hierarchy.detections[1]
---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-58-ee8b4cffc9d4> in <module>
----> 1 qpitem.hierarchy.detections[1]

TypeError: '_PathObjectSetProxy' object is not subscriptable

I'm thinking about the case of where I know which subset of 1,000 detections i want inside of a list of 40,000

I could instantiate the entire list, or use something like this: https://stackoverflow.com/questions/2300756/get-the-nth-item-of-a-generator-in-python

But was wondering if there was something more elegant you were thinking?

Thanks

we need to decide what's nicest for the user.

Best would probably be to auto discover in the default installation paths for qupath, and then verify if the qupath version is compatible.

override could be done via envvar and/or provide some pre java import interface to set the path: (possible way this could be implemented --- it's not yet)

import paquo
paquo.cue_qupath_path("~/my_custom_qupath_installation")  # :P

from paquo.projects import QuPathProject
...

We want to be internally consistent in paquo so that it's immediately clear which parts access the java world and which parts are native to the python world.

Toplevel options are all combinations of prefixing or not prefixing Java classes and Python classes.

Examples could be:

• Java classes get prefixed with "J", python wrapper classes get the original name (java: JPathClass and py: PathClass)
• Java classes keep their names, python wrapper classes get a prefix (java: PathClass and py: QuPathPathClass)
• both get prefixed (java: JPathClass, py: QuPathPathClass)

Note: maybe "Paquo" might be a prefix for python classes that keeps better readability (PaquoPathClass vs QuPathPathClass)

I have no strong opinion. As long as we stay consistent. 😃

I do not know how well this would work with setuptools_scm, but should we try to sync with the qupath version we are targeting? e.g. since now we are developing against 0.2.1, should we have our version be 0.2.1-something as well?

Hi, I would like to know if there is a way I can use Paquo to add annotations as children of other annotations as described here: https://qupath.readthedocs.io/en/stable/docs/concepts/object_hierarchy.html

The documentation does a good job of explaining how to add annotations as children of the image root (all having the same level in the hierarchy). It would be great to have a way to add annotations while specifying the parent that they belong to, as seen in the image below:

Hi,

Really excellent work with this, just a quick question. Is there an easy way to get the file path of the QuPath Program directory that is being used in the paquo environment??

Hope this makes sense, Many thanks

I am trying to use paquo on a linux cluster. I login to a node with 200GB of memory.

Once on the node I use tmux to open two terminals on the same node. In one of the terminals I activate a conda environment and open up a python window and run

import os
os.getpid()

I then go to my other window and run

top -p <my_pid>

which, as I understand it, allows me to see how much memory I am using. At this point it shows 134060 under VIRT.

In the python window I then run

from paquo.projects import QuPathProject

and then it shows 102.7g under VIRT. As I understand it, this means the QuPathProject object is currently using 102.7GB of memory. This is then giving me errors further down in my pipeline where I try and do much smaller operations but I don't have any memory left.

Here is my conda environment environment(1).txt

See this post on image.sc

We could expose this functionality for the PathObjectHierarchy. We already support to_geojson and to_ome_xml. Could maybe offer to_image or to_segmentation_mask.

Hi paquo team. I wondered whether it would be useful to extend paquo's functionality by, e.g. option to create .jpeg/.png tiles from slides. This summer, I finished one medical image segmentation/classification deep learning project, so I could implement such functionality in the fork.

I would use OpenSlide, though, which creates an additional dependency.

Are you interested?