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Merge pull request #88 from petebankhead/for-v0.5.0
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Updates for v0.5.0
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@petebankhead
petebankhead committed Nov 10, 2023
2 parents fe0873e + 8ca7bf0 commit 1f3ca47
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4 changes: 4 additions & 0 deletions _static/css/custom.css
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Expand Up @@ -13,3 +13,7 @@ p.caption {
.inline-icon {
width: 1.5em;
}

.tool-icon {
width: 3em;
}
124 changes: 70 additions & 54 deletions conf.py
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Expand Up @@ -101,88 +101,104 @@

html_favicon = 'docs/images/QuPath.ico'

release = '0.4.4'
version = '0.4'
release = '0.5.0'
version = '0.5'

# myst_heading_anchors = 2

myst_substitutions = {

"rectangle": '<img src="../images/icons/Rectangle.png" />',
"icon_rectangle": '<img src="../images/icons/Rectangle.png" class="inline-icon" />',
"rectangle": '<img src="../images/icons/RECTANGLE_TOOL.png" />',
"icon_rectangle": '<img src="../images/icons/RECTANGLE_TOOL.png" class="inline-icon" />',
"tool_rectangle": '<img src="../images/icons/RECTANGLE_TOOL.png" class="tool-icon" />',

"ellipse": '<img src="../images/icons/Ellipse.png" />',
"icon_ellipse": '<img src="../images/icons/Ellipse.png" class="inline-icon" />',
"ellipse": '<img src="../images/icons/ELLIPSE_TOOL.png" />',
"icon_ellipse": '<img src="../images/icons/ELLIPSE_TOOL.png" class="inline-icon" />',
"tool_ellipse": '<img src="../images/icons/ELLIPSE_TOOL.png" class="tool-icon" />',

"line": '<img src="../images/icons/Line.png" />',
"icon_line": '<img src="../images/icons/Line.png" class="inline-icon" />',
"line": '<img src="../images/icons/LINE_TOOL.png" />',
"icon_line": '<img src="../images/icons/LINE_TOOL.png" class="inline-icon" />',
"tool_line": '<img src="../images/icons/LINE_TOOL.png" class="tool-icon" />',

"polygon": '<img src="../images/icons/Polygon.png" />',
"icon_polygon": '<img src="../images/icons/Polygon.png" class="inline-icon" />',
"polygon": '<img src="../images/icons/POLYGON_TOOL.png" />',
"icon_polygon": '<img src="../images/icons/POLYGON_TOOL.png" class="inline-icon" />',
"tool_polygon": '<img src="../images/icons/POLYGON_TOOL.png" class="tool-icon" />',

"brush": '<img src="../images/icons/Brush.png" />',
"icon_brush": '<img src="../images/icons/Brush.png" class="inline-icon" />',
"polyline": '<img src="../images/icons/POLYLINE_TOOL.png" />',
"icon_polyline": '<img src="../images/icons/POLYLINE_TOOL.png" class="inline-icon" />',
"tool_polyline": '<img src="../images/icons/POLYLINE_TOOL.png" class="tool-icon" />',

"wand": '<img src="../images/icons/Wand.png" />',
"icon_wand": '<img src="../images/icons/Wand.png" class="inline-icon" />',
"brush": '<img src="../images/icons/BRUSH_TOOL.png" />',
"icon_brush": '<img src="../images/icons/BRUSH_TOOL.png" class="inline-icon" />',
"tool_brush": '<img src="../images/icons/BRUSH_TOOL.png" class="tool-icon" />',

"points": '<img src="../images/icons/Points.png" />',
"icon_points": '<img src="../images/icons/Points.png" class="inline-icon" />',
"wand": '<img src="../images/icons/WAND_TOOL.png" />',
"icon_wand": '<img src="../images/icons/WAND_TOOL.png" class="inline-icon" />',
"tool_wand": '<img src="../images/icons/WAND_TOOL.png" class="tool-icon" />',

"move": '<img src="../images/icons/Move.png" />',
"icon_move": '<img src="../images/icons/Move.png" class="inline-icon" />',
"points": '<img src="../images/icons/POINTS_TOOL.png" />',
"icon_points": '<img src="../images/icons/POINTS_TOOL.png" class="inline-icon" />',
"tool_points": '<img src="../images/icons/POINTS_TOOL.png" class="tool-icon" />',

"grid": '<img src="../images/icons/Grid.png" />',
"icon_grid": '<img src="../images/icons/Grid.png" class="inline-icon" />',
"move": '<img src="../images/icons/MOVE_TOOL.png" />',
"icon_move": '<img src="../images/icons/MOVE_TOOL.png" class="inline-icon" />',
"tool_move": '<img src="../images/icons/MOVE_TOOL.png" class="tool-icon" />',

"measure": '<img src="../images/icons/Measure.png" />',
"icon_measure": '<img src="../images/icons/Measure.png" class="inline-icon" />',
"selection_mode": '<img src="../images/icons/SELECTION_MODE.png" />',
"icon_selection_mode": '<img src="../images/icons/SELECTION_MODE.png" class="inline-icon" />',
"tool_selection_mode": '<img src="../images/icons/SELECTION_MODE.png" class="tool-icon" />',

"table": '<img src="../images/icons/Table.png" />',
"icon_table": '<img src="../images/icons/Table.png" class="inline-icon" />',
"help": '<img src="../images/icons/HELP.png" />',
"icon_help": '<img src="../images/icons/HELP.png" class="inline-icon" />',
"tool_help": '<img src="../images/icons/HELP.png" class="tool-icon" />',

"cog": '<img src="../images/icons/Cog.png" />',
"icon_cog": '<img src="../images/icons/Cog.png" class="inline-icon" />',
"log": '<img src="../images/icons/LOG_VIEWER.png" />',
"icon_log": '<img src="../images/icons/LOG_VIEWER.png" class="inline-icon" />',
"tool_log": '<img src="../images/icons/LOG_VIEWER.png" class="tool-icon" />',

"annotations": '<img src="../images/icons/Annotations.png" />',
"icon_annotations": '<img src="../images/icons/Annotations.png" class="inline-icon" />',
"grid": '<img src="../images/icons/GRID.png" />',
"icon_grid": '<img src="../images/icons/GRID.png" class="inline-icon" />',

"detections": '<img src="../images/icons/Detections.png" />',
"icon_detections": '<img src="../images/icons/Detections.png" class="inline-icon" />',
"measure": '<img src="../images/icons/MEASURE.png" />',
"icon_measure": '<img src="../images/icons/MEASURE.png" class="inline-icon" />',

"annotations_fill": '<img src="../images/icons/Annotations_fill.png" />',
"icon_annotations_fill": '<img src="../images/icons/Annotations_fill.png" class="inline-icon" />',
"table": '<img src="../images/icons/TABLE.png" />',
"icon_table": '<img src="../images/icons/TABLE.png" class="inline-icon" />',

"detections_fill": '<img src="../images/icons/Detections_fill.png" />',
"icon_detections_fill": '<img src="../images/icons/Detections_fill.png" class="inline-icon" />',
"cog": '<img src="../images/icons/COG.png" />',
"icon_cog": '<img src="../images/icons/COG.png" class="inline-icon" />',

"annotations": '<img src="../images/icons/ANNOTATIONS.png" />',
"icon_annotations": '<img src="../images/icons/ANNOTATIONS.png" class="inline-icon" />',

"tma_grid": '<img src="../images/icons/TMA_grid.png" />',
"icon_tma_grid": '<img src="../images/icons/TMA_grid.png" class="inline-icon" />',
"detections": '<img src="../images/icons/DETECTIONS.png" />',
"icon_detections": '<img src="../images/icons/DETECTIONS.png" class="inline-icon" />',

"screenshot": '<img src="../images/icons/Screenshot.png" />',
"icon_screenshot": '<img src="../images/icons/Screenshot.png" class="inline-icon" />',
"annotations_fill": '<img src="../images/icons/ANNOTATIONS_FILL.png" />',
"icon_annotations_fill": '<img src="../images/icons/ANNOTATIONS_FILL.png" class="inline-icon" />',

"detections_fill": '<img src="../images/icons/DETECTIONS_FILL.png" />',
"icon_detections_fill": '<img src="../images/icons/Detections_fill.png" class="inline-icon" />',

"extract_image": '<img src="../images/icons/Extract_image.png" />',
"icon_extract_image": '<img src="../images/icons/Extract_image.png" class="inline-icon" />',
"tma_grid": '<img src="../images/icons/TMA_GRID.png" />',
"icon_tma_grid": '<img src="../images/icons/TMA_GRID.png" class="inline-icon" />',

"contrast": '<img src="../images/icons/Contrast.png" />',
"icon_contrast": '<img src="../images/icons/Contrast.png" class="inline-icon" />',
"screenshot": '<img src="../images/icons/SCREENSHOT.png" />',
"icon_screenshot": '<img src="../images/icons/SCREENSHOT.png" class="inline-icon" />',

"play": '<img src="../images/icons/Play.png" />',
"icon_play": '<img src="../images/icons/Play.png" class="inline-icon" />',
"extract_image": '<img src="../images/icons/EXTRACT_REGION.png" />',
"icon_extract_image": '<img src="../images/icons/EXTRACT_REGION.png" class="inline-icon" />',

"stop": '<img src="../images/icons/Stop.png" />',
"icon_stop": '<img src="../images/icons/Stop.png" class="inline-icon" />',
"contrast": '<img src="../images/icons/CONTRAST.png" />',
"icon_contrast": '<img src="../images/icons/CONTRAST.png" class="inline-icon" />',

"record": '<img src="../images/icons/Record.png" />',
"icon_record": '<img src="../images/icons/Record.png" class="inline-icon" />',
"play": '<img src="../images/icons/PLAYBACK_PLAY.png" />',
"icon_play": '<img src="../images/icons/PLAYBACK_PLAY.png" class="inline-icon" />',

# "polyline": '<img src="../images/icons/Polyline.png" />',
# "icon_polyline": '<img src="../images/icons/Polyline.png" class="inline-icon" />',
"stop": '<img src="../images/icons/TRACKING_STOP.png" />',
"icon_stop": '<img src="../images/icons/TRACKING_STOP.png" class="inline-icon" />',

# "record_start": '<img src="../images/icons/Start_recording.png" />',
# "icon_record_start": '<img src="../images/icons/Start_recording.png" class="inline-icon" />',
"record": '<img src="../images/icons/TRACKING_RECORD.png" />',
"icon_record": '<img src="../images/icons/TRACKING_RECORD.png" class="inline-icon" />',

# "record_stop": '<img src="../images/icons/Stop_recording.png" />',
# "icon_record_stop": '<img src="../images/icons/Stop_recording.png" class="inline-icon" />',
}
6 changes: 3 additions & 3 deletions docs/deep/djl.md
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Expand Up @@ -51,9 +51,9 @@ To use an NVIDIA GPU with either TensorFlow or Pytorch, you will need to have a

'Compatible' here depends upon some other versions.

QuPath v0.4.4 uses Deep Java Library 0.20.0, which by default uses
* [PyTorch 1.13.0](https://docs.djl.ai/engines/pytorch/pytorch-engine/index.html#supported-pytorch-versions), which requires [CUDA 11.6 or 11.7](https://pytorch.org/get-started/previous-versions/#v1130)
* [TensorFlow 2.7.4](https://github.com/deepjavalibrary/djl/releases/tag/v0.20.0), which requires [CUDA 11.2](https://www.tensorflow.org/install/source#gpu).
QuPath v0.5.0 uses Deep Java Library 0.24.0, which by default uses
* [PyTorch 2.0.1](https://docs.djl.ai/engines/pytorch/pytorch-engine/index.html#supported-pytorch-versions), which requires [CUDA 11.7 or 11.8](https://pytorch.org/get-started/previous-versions/#v201)
* [TensorFlow 2.10.1](https://github.com/deepjavalibrary/djl/releases/tag/v0.22.1), which requires [CUDA 11.2](https://www.tensorflow.org/install/source#gpu).

The fact that PyTorch and TensorFlow require different CUDA versions is... not helpful. So you may be able to get GPU support for only one.
:::
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4 changes: 1 addition & 3 deletions docs/deep/wsinfer.md
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Expand Up @@ -107,9 +107,7 @@ The options available will depend upon your computer's capabilities (at least as
* **GPU**: This should appear if you have an NVIDIA GPU, CUDA... and a little bit of luck.

If either MPS or GPU work for you, they should reduce the time required for inference by a *lot*.
However configuration for GPU can be tricky, as it will depend upon other hardware and software on your computer.

QuPath v0.4.x uses PyTorch 1.13.x by default, which is expected to work with CUDA 11.6 or 11.7.
However configuration for GPU can be tricky, as it will depend upon other hardware and software on your computer - CUDA in particular.
For more info, see [the Deep Java Library page](deep-java-library-gpu).

:::{admonition} PyTorch & CUDA versions
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