From 41bcff803cad08696dab8688a38d92ee8cc6fc1e Mon Sep 17 00:00:00 2001 From: Alan O'Callaghan Date: Thu, 12 Feb 2026 12:37:01 +0000 Subject: [PATCH] Move to reduce build warnings Ignore common venv directories Add file prefixes to autolabels to reduce duplicate labels (two pairs remain that cannot be solved without dirty tricks) Reduce prominence of v0.2.0 object hierarchy update --- conf.py | 6 ++++-- docs/concepts/object_hierarchy.md | 9 ++------- docs/deep/stardist.md | 2 +- docs/deep/wsinfer.md | 2 +- docs/intro/installation.md | 8 ++++---- docs/reference/building.md | 4 ++-- docs/reference/faqs.md | 6 +++--- docs/reference/tips_and_tricks.md | 9 --------- docs/tutorials/density_maps.md | 4 ++-- docs/tutorials/separating_stains.md | 4 ++-- index.md | 2 +- 11 files changed, 22 insertions(+), 34 deletions(-) delete mode 100644 docs/reference/tips_and_tricks.md diff --git a/conf.py b/conf.py index 4bf2174..e022890 100644 --- a/conf.py +++ b/conf.py @@ -40,7 +40,7 @@ # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. # This pattern also affects html_static_path and html_extra_path. -exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] +exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', "env", ".env", ".venv", "README.md"] # -- Options for HTML output ------------------------------------------------- @@ -93,12 +93,14 @@ "tasklist", ] +autosectionlabel_prefix_document = True +autosectionlabel_maxdepth = 3 highlight_language = 'groovy' html_logo = 'docs/images/qupath_128.png' -html_favicon = 'docs/images/QuPath.ico' +html_favicon = 'docs/images/qupath.ico' # Variables for current QuPath version release = '0.6.0' diff --git a/docs/concepts/object_hierarchy.md b/docs/concepts/object_hierarchy.md index 839e5cc..c045683 100644 --- a/docs/concepts/object_hierarchy.md +++ b/docs/concepts/object_hierarchy.md @@ -2,11 +2,6 @@ {doc}`Objects ` in QuPath need to be stored somewhere - and that place is the *object hierarchy*. -:::{important} -The hierarchy behavior has changed in v0.2.0!
-If you are familiar with the old behavior, be sure to read {ref}`Differences from QuPath v0.1.2`. -::: - The name comes from the fact that the objects are all stored in a hierarchical, tree-like structure. This is achieved by each object having having a reference to: @@ -128,8 +123,8 @@ This is crucial because the `PathObjectHierarchy` class uses spatial caching and In QuPath v0.1.2, the hierarchy was resolved automatically (without asking) and this was *essential* to make sense of the measurements. -The behavior of the object hierarchy has changed in QuPath v0.2.0, with the aim of making the software faster, more powerful, and more intuitive. -In v0.2.0 the details of the hierarchy can very often be ignored, and exists only to support sophisticated workflows where it might be needed. +The behavior of the object hierarchy changed in QuPath v0.2.0, with the aim of making the software faster, more powerful, and more intuitive. +In v0.2.0 and onwards, the details of the hierarchy can very often be ignored, and exists only to support sophisticated workflows where it might be needed. [This blog post](https://petebankhead.github.io/qupath/2019/11/17/changing-the-hierarchy.html) describes the reasons why it changed. To read about the earlier behavior see [Object hierarchies](https://github.com/qupath/qupath/wiki/Object-hierarchies) on the old wiki. diff --git a/docs/deep/stardist.md b/docs/deep/stardist.md index f5b56d3..5fa269d 100644 --- a/docs/deep/stardist.md +++ b/docs/deep/stardist.md @@ -403,7 +403,7 @@ def stardist = StarDist2D.builder(pathModel) Furthermore, we can use preprocessing to convert images to become more compatible with pretrained StarDist models. For example, `dsb2018_heavy_augment.pb` works very well for fluorescence microscopy images, but only supports a single input channel. -However, by applying {ref}`color deconvolution` as preprocessing we can convert a 3-channel brightfield image to a single-channel image that *looks* much more like a fluorescence image. +However, by applying {ref}`color deconvolution` as preprocessing we can convert a 3-channel brightfield image to a single-channel image that *looks* much more like a fluorescence image. If needed, we can add extra things like filters to reduce noise as well. ```groovy diff --git a/docs/deep/wsinfer.md b/docs/deep/wsinfer.md index be14b9b..64b6f32 100644 --- a/docs/deep/wsinfer.md +++ b/docs/deep/wsinfer.md @@ -153,7 +153,7 @@ wsinfer The QuPath WSInfer extension is scriptable, which makes it much easier to apply across multiple images. -When a model is run, the command parameters are stored in the [workflow](workflows) so that a [script can be generated automatically](workflows-to-scripts). +When a model is run, the command parameters are stored in the [workflow](docs/scripting/workflows:Workflows) so that a [script can be generated automatically](docs/scripting/workflows_to_scripts:Workflows to scripts). An example script would be diff --git a/docs/intro/installation.md b/docs/intro/installation.md index 8b03e35..1b4e0d4 100644 --- a/docs/intro/installation.md +++ b/docs/intro/installation.md @@ -23,7 +23,7 @@ QuPath requires 64-bit Windows. Running QuPath on 32-bit Windows is not supported. ::: -#### Installing the Windows .msi package +### Installing the Windows .msi package Double-click to launch the installer. Windows tries to protect you from software it does not know, so you'll probably see a scary-looking warning whenever the QuPath installer is first run: @@ -57,7 +57,7 @@ If the QuPath installer does not start at all, you may not have administrator pr Try downloading the `.zip` file instead, which should not need such privileges. ::: -#### Installing the Windows .zip package +### Installing the Windows .zip package Right-click on the .zip file and choose to extract all the contents. This should give you a normal folder containing QuPath's files. @@ -70,7 +70,7 @@ The first time you try this, you might see similar warning dialogs to those show On Windows, you can either run `QuPath.exe` or `QuPath (console).exe`. The difference is that `QuPath (console).exe` will also open a small window that contains QuPath's log messages. -The console can be useful for debugging problems, or when using the {ref}`Command line`. +The console can be useful for debugging problems, or when using the {ref}`docs/advanced/command_line:Command line`. ::: :::{admonition} QuPath won't launch! @@ -170,4 +170,4 @@ QuPath for Linux was compiled on Ubuntu - with best efforts made to include all ## Running from source -If all else fails, you can try [](building) - which should work on Windows, macOS and Linux. \ No newline at end of file +If all else fails, you can try [](building) - which should work on Windows, macOS and Linux. diff --git a/docs/reference/building.md b/docs/reference/building.md index 16da98e..8f352d7 100644 --- a/docs/reference/building.md +++ b/docs/reference/building.md @@ -65,7 +65,7 @@ Example of command line build success **That's it!** You can find QuPath inside the `./build/dist/` subdirectory. -If it *didn't* go so well, check out [](#Troubleshooting). +If it *didn't* go so well, check out {ref}`docs/reference/building:Troubleshooting`. :::{admonition} Which Java version do I need? :class: tip @@ -181,7 +181,7 @@ Check out the docs associated with the specific version if this is the case. (building-qupath-fiji)= ## Building with Fiji By default, QuPath embeds a version of [ImageJ](https://imagej.net/software/imagej/). -This allows you to [send image regions to ImageJ, and even use custom ImageJ plugins](ImageJ). +This allows you to [send image regions to ImageJ, and even use custom ImageJ plugins](docs/advanced/imagej:ImageJ). [Fiji](https://fiji.sc) is a special distribution of ImageJ that contains a *lot* of custom plugins, and many extra features and other changes. diff --git a/docs/reference/faqs.md b/docs/reference/faqs.md index d231f76..8ba2708 100644 --- a/docs/reference/faqs.md +++ b/docs/reference/faqs.md @@ -131,7 +131,7 @@ It is designed so that other machine learning libraries could potentially be use ### Why do I see a warning when I try to install QuPath? -See {ref}`Installation`. +See {ref}`docs/intro/installation:Installation`. (set-max-memory)= @@ -185,11 +185,11 @@ See {doc}`../intro/formats` for details about which formats are supported, and t ### {menuselection}`File --> Open URI...` doesn't work for me! {menuselection}`File --> Open URI...` requires a compatible extension needs to read images hosted remotely. -See {ref}`Open URI` for more details. +See {ref}`docs/intro/formats:Open URI` for more details. ### Why does my image open but look weird? -See {ref}`Why can't QuPath open my image?` +See {ref}`docs/reference/faqs:Why can't QuPath open my image?` ### Is it possible to view slide labels? diff --git a/docs/reference/tips_and_tricks.md b/docs/reference/tips_and_tricks.md deleted file mode 100644 index 1cd465e..0000000 --- a/docs/reference/tips_and_tricks.md +++ /dev/null @@ -1,9 +0,0 @@ -(tips-and-tricks)= -# Tips and Tricks - -This page is dedicated to sharing shortcuts that can help you work more efficiently with QuPath. -Check back often for new tips and tricks! - -If you draw an annotation you don't like and its selected, you can simply press the {kbd}`Backspace` or {kbd}`Delete` key to remove the currently selected objects. - -Most sub-windows can be quickly closed from the keyboard with {kbd}`Ctrl`/{kbd}`Cmd` + {kbd}`W` or {kbd}`Esc`. \ No newline at end of file diff --git a/docs/tutorials/density_maps.md b/docs/tutorials/density_maps.md index bb8ca55..26dcc85 100644 --- a/docs/tutorials/density_maps.md +++ b/docs/tutorials/density_maps.md @@ -20,7 +20,7 @@ In some cases, density maps can even be a replacement for {doc}`pixel_classifica :::{warning} Like most commands in QuPath, Density Maps are currently calculated only in 2D. -And, like many other commands, you should create Density Maps within a {ref}`project ` if you want to reuse them later. +And, like many other commands, you should create Density Maps within a {ref}`project ` if you want to reuse them later. ::: ## Getting started with density maps @@ -61,7 +61,7 @@ Hovering your mouse over any option should provide some help text. The {guilabel}`Object type` and {guilabel}`Main class` define which objects will contribute to the density map in some way. -Left to the defaults, the density map will make use of all detection objects (which {ref}`includes cells `) regardless of their classification. +Left to the defaults, the density map will make use of all detection objects (which {ref}`includes cells `) regardless of their classification. If I choose the {guilabel}`Main class` to be **Tumor**, then the density map will *only* include detections that are classified as **Tumor**. diff --git a/docs/tutorials/separating_stains.md b/docs/tutorials/separating_stains.md index b71122d..09230c9 100644 --- a/docs/tutorials/separating_stains.md +++ b/docs/tutorials/separating_stains.md @@ -16,7 +16,7 @@ QuPath supports images of different kinds. Some commands will work on almost any kind of image without complaint, while some need to know a bit more about the image. -This information can be provided by {ref}`setting the image type `. +This information can be provided by {ref}`setting the image type `. Typically the type will be either *Brightfield* or *Fluorescence*. @@ -118,7 +118,7 @@ The stain vectors are key to color deconvolution. They ought to give a normalized representation of the color of each 'pure' stain in the image, without regard for staining intensity. A similar color vector characterizing the background encodes what 'no stain' looks like, and also plays an important role in the calculations. -When {ref}`setting the image type ` to *Brightfield (H&E)*, *Brightfield (H-DAB)* or *Brightfield (Other)*, QuPath will set default stain vectors to characterize hematoxylin, eosin or DAB. +When {ref}`setting the image type ` to *Brightfield (H&E)*, *Brightfield (H-DAB)* or *Brightfield (Other)*, QuPath will set default stain vectors to characterize hematoxylin, eosin or DAB. However, you may see better results with some commands (e.g. *Cell detection*) by setting the stain and background vectors explicitly to better match the actual staining in the image. This requires two steps: diff --git a/index.md b/index.md index c5343e5..5fdccf7 100644 --- a/index.md +++ b/index.md @@ -13,7 +13,7 @@ To read up on the latest changes, check out the [release notes](https://github.c ## Quick links Can't install QuPath? -: Check out {ref}`installation` for instructions & solutions to common problems +: Check out {ref}`docs/intro/installation:installation` for instructions & solutions to common problems Images won't open? : See {ref}`supported-image-formats` to find out which formats *should* work - and ways to increase this.