diff --git a/.gitignore b/.gitignore index 626ed41..6272d1a 100644 --- a/.gitignore +++ b/.gitignore @@ -176,4 +176,8 @@ venv/ .DS_Store # written by setuptools_scm -**/_version.py \ No newline at end of file +**/_version.py + +.quarto +_site +models \ No newline at end of file diff --git a/docs/_quarto.yml b/docs/_quarto.yml new file mode 100644 index 0000000..e1602fd --- /dev/null +++ b/docs/_quarto.yml @@ -0,0 +1,89 @@ +project: + type: website + +metadata-files: + - _sidebar.yml + +website: + page-navigation: true + navbar: + left: + - file: tutorials/ + text: Tutorials + - href: reference/ + text: Reference + +format: + html: + theme: cosmo + css: + - api/_styles-quartodoc.css + - styles.css + toc: true + +quartodoc: + # the name used to import the package you want to create reference docs for + package: napari_activelearning + + # write sidebar data to this file + sidebar: _sidebar.yml + + sections: + - title: Some functions + desc: Functions to inspect docstrings. + contents: + # the functions being documented in the package. + # you can refer to anything: class methods, modules, etc.. + - LayerChannel + - LayersGroup + - ImageGroup + - ImageGroupRoot + - ImageGroupEditor + - MaskGenerator + - ImageGroupsManager + - ImageGroupsManager.set_active_item + - ImageGroupsManager.get_active_item + - ImageGroupsManager.focus_active_item + - ImageGroupsManager.update_group + - ImageGroupsManager.create_group + - ImageGroupsManager.create_layers_group + - ImageGroupsManager.add_layers_to_group + - ImageGroupsManager.remove_layer + - ImageGroupsManager.remove_layers_group + - ImageGroupsManager.remove_group + - ImageGroupsManager.save_layers_group + - ImageGroupsManager.dump_dataset_specs + # - LabelItem + # - LabelGroup + # - LabelGroupRoot + # - LabelsManager + # - LabelsManager.add_labels + # - LabelsManager.remove_labels + # - LabelsManager.remove_labels_group + # - LabelsManager.navigate + # - LabelsManager.focus_region + # - LabelsManager.focus_and_edit_region + # - LabelsManager.edit_labels + # - LabelsManager.commit + - AcquisitionFunction + - compute_BALD + - compute_acquisition_superpixel + - compute_acquisition_fun + - compute_segmentation + - add_multiscale_output_layer + - DropoutEvalOverrider + - add_dropout + - SegmentationMethod + - SegmentationMethod._run_pred + - SegmentationMethod._run_eval + - SegmentationMethod.probs + - SegmentationMethod.segment + - FineTuningMethod + - FineTuningMethod._get_transform + - FineTuningMethod._fine_tune + - FineTuningMethod.fine_tune + - TunableMethod + - AcquisitionFunction + - AcquisitionFunction.compute_acquisition + - AcquisitionFunction.compute_acquisition_layers + - AcquisitionFunction.fine_tune \ No newline at end of file diff --git a/docs/_sidebar.yml b/docs/_sidebar.yml new file mode 100644 index 0000000..c639f24 --- /dev/null +++ b/docs/_sidebar.yml @@ -0,0 +1,49 @@ +website: + sidebar: + - contents: + - reference/index.qmd + - contents: + - reference/LayerChannel.qmd + - reference/LayersGroup.qmd + - reference/ImageGroup.qmd + - reference/ImageGroupRoot.qmd + - reference/ImageGroupEditor.qmd + - reference/MaskGenerator.qmd + - reference/ImageGroupsManager.qmd + - reference/ImageGroupsManager.set_active_item.qmd + - reference/ImageGroupsManager.get_active_item.qmd + - reference/ImageGroupsManager.focus_active_item.qmd + - reference/ImageGroupsManager.update_group.qmd + - reference/ImageGroupsManager.create_group.qmd + - reference/ImageGroupsManager.create_layers_group.qmd + - reference/ImageGroupsManager.add_layers_to_group.qmd + - reference/ImageGroupsManager.remove_layer.qmd + - reference/ImageGroupsManager.remove_layers_group.qmd + - reference/ImageGroupsManager.remove_group.qmd + - reference/ImageGroupsManager.save_layers_group.qmd + - reference/ImageGroupsManager.dump_dataset_specs.qmd + - reference/AcquisitionFunction.qmd + - reference/compute_BALD.qmd + - reference/compute_acquisition_superpixel.qmd + - reference/compute_acquisition_fun.qmd + - reference/compute_segmentation.qmd + - reference/add_multiscale_output_layer.qmd + - reference/DropoutEvalOverrider.qmd + - reference/add_dropout.qmd + - reference/SegmentationMethod.qmd + - reference/SegmentationMethod._run_pred.qmd + - reference/SegmentationMethod._run_eval.qmd + - reference/SegmentationMethod.probs.qmd + - reference/SegmentationMethod.segment.qmd + - reference/FineTuningMethod.qmd + - reference/FineTuningMethod._get_transform.qmd + - reference/FineTuningMethod._fine_tune.qmd + - reference/FineTuningMethod.fine_tune.qmd + - reference/TunableMethod.qmd + - reference/AcquisitionFunction.qmd + - reference/AcquisitionFunction.compute_acquisition.qmd + - reference/AcquisitionFunction.compute_acquisition_layers.qmd + - reference/AcquisitionFunction.fine_tune.qmd + section: Some functions + id: reference + - id: dummy-sidebar diff --git a/docs/about.qmd b/docs/about.qmd new file mode 100644 index 0000000..07c5e7f --- /dev/null +++ b/docs/about.qmd @@ -0,0 +1,5 @@ +--- +title: "About" +--- + +About this site diff --git a/docs/index.qmd b/docs/index.qmd new file mode 100644 index 0000000..f920537 --- /dev/null +++ b/docs/index.qmd @@ -0,0 +1,7 @@ +--- +title: "Active Learning plugin for Napari" +--- + +This is a Quarto website. + +To learn more about Quarto websites visit . diff --git a/docs/objects.json b/docs/objects.json new file mode 100644 index 0000000..35e7bb9 --- /dev/null +++ b/docs/objects.json @@ -0,0 +1 @@ +{"project": "napari_activelearning", "version": "0.0.9999", "count": 82, "items": [{"name": "napari_activelearning.LayerChannel", "domain": "py", "role": "class", "priority": "1", "uri": "reference/LayerChannel.html#napari_activelearning.LayerChannel", "dispname": "-"}, {"name": "napari_activelearning._layers.LayerChannel", "domain": "py", "role": "class", "priority": "1", "uri": "reference/LayerChannel.html#napari_activelearning.LayerChannel", "dispname": "napari_activelearning.LayerChannel"}, {"name": 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"reference/AcquisitionFunction.fine_tune.html#napari_activelearning.AcquisitionFunction.fine_tune", "dispname": "-"}, {"name": "napari_activelearning._acquisition.AcquisitionFunction.fine_tune", "domain": "py", "role": "function", "priority": "1", "uri": "reference/AcquisitionFunction.fine_tune.html#napari_activelearning.AcquisitionFunction.fine_tune", "dispname": "napari_activelearning.AcquisitionFunction.fine_tune"}]} \ No newline at end of file diff --git a/docs/reference/AcquisitionFunction.compute_acquisition.qmd b/docs/reference/AcquisitionFunction.compute_acquisition.qmd new file mode 100644 index 0000000..e8d1f64 --- /dev/null +++ b/docs/reference/AcquisitionFunction.compute_acquisition.qmd @@ -0,0 +1,12 @@ +# AcquisitionFunction.compute_acquisition { #napari_activelearning.AcquisitionFunction.compute_acquisition } + +```python +AcquisitionFunction.compute_acquisition( + dataset_metadata + acquisition_fun + segmentation_out + sampling_positions=None + segmentation_only=False +) +``` + diff --git a/docs/reference/AcquisitionFunction.compute_acquisition_layers.qmd b/docs/reference/AcquisitionFunction.compute_acquisition_layers.qmd new file mode 100644 index 0000000..59b54cd --- /dev/null +++ b/docs/reference/AcquisitionFunction.compute_acquisition_layers.qmd @@ -0,0 +1,10 @@ +# AcquisitionFunction.compute_acquisition_layers { #napari_activelearning.AcquisitionFunction.compute_acquisition_layers } + +```python +AcquisitionFunction.compute_acquisition_layers( + run_all=False + segmentation_group_name='segmentation' + segmentation_only=False +) +``` + diff --git a/docs/reference/AcquisitionFunction.fine_tune.qmd b/docs/reference/AcquisitionFunction.fine_tune.qmd new file mode 100644 index 0000000..7f1920f --- /dev/null +++ b/docs/reference/AcquisitionFunction.fine_tune.qmd @@ -0,0 +1,6 @@ +# AcquisitionFunction.fine_tune { #napari_activelearning.AcquisitionFunction.fine_tune } + +```python +AcquisitionFunction.fine_tune() +``` + diff --git a/docs/reference/AcquisitionFunction.qmd b/docs/reference/AcquisitionFunction.qmd new file mode 100644 index 0000000..52cedbd --- /dev/null +++ b/docs/reference/AcquisitionFunction.qmd @@ -0,0 +1,11 @@ +# AcquisitionFunction { #napari_activelearning.AcquisitionFunction } + +```python +AcquisitionFunction( + self + image_groups_manager + labels_manager + tunable_segmentation_method +) +``` + diff --git a/docs/reference/DropoutEvalOverrider.qmd b/docs/reference/DropoutEvalOverrider.qmd new file mode 100644 index 0000000..e6d4620 --- /dev/null +++ b/docs/reference/DropoutEvalOverrider.qmd @@ -0,0 +1,6 @@ +# DropoutEvalOverrider { #napari_activelearning.DropoutEvalOverrider } + +```python +DropoutEvalOverrider(self, dropout_module) +``` + diff --git a/docs/reference/FineTuningMethod._fine_tune.qmd b/docs/reference/FineTuningMethod._fine_tune.qmd new file mode 100644 index 0000000..ffdf68e --- /dev/null +++ b/docs/reference/FineTuningMethod._fine_tune.qmd @@ -0,0 +1,6 @@ +# FineTuningMethod._fine_tune { #napari_activelearning.FineTuningMethod._fine_tune } + +```python +FineTuningMethod._fine_tune(train_data, train_labels, test_data, test_labels) +``` + diff --git a/docs/reference/FineTuningMethod._get_transform.qmd b/docs/reference/FineTuningMethod._get_transform.qmd new file mode 100644 index 0000000..0e847c6 --- /dev/null +++ b/docs/reference/FineTuningMethod._get_transform.qmd @@ -0,0 +1,6 @@ +# FineTuningMethod._get_transform { #napari_activelearning.FineTuningMethod._get_transform } + +```python +FineTuningMethod._get_transform() +``` + diff --git a/docs/reference/FineTuningMethod.fine_tune.qmd b/docs/reference/FineTuningMethod.fine_tune.qmd new file mode 100644 index 0000000..90363bb --- /dev/null +++ b/docs/reference/FineTuningMethod.fine_tune.qmd @@ -0,0 +1,11 @@ +# FineTuningMethod.fine_tune { #napari_activelearning.FineTuningMethod.fine_tune } + +```python +FineTuningMethod.fine_tune( + dataset_metadata_list + train_data_proportion=0.8 + patch_sizes=256 + model_axes='YXC' +) +``` + diff --git a/docs/reference/FineTuningMethod.qmd b/docs/reference/FineTuningMethod.qmd new file mode 100644 index 0000000..bbfd28c --- /dev/null +++ b/docs/reference/FineTuningMethod.qmd @@ -0,0 +1,6 @@ +# FineTuningMethod { #napari_activelearning.FineTuningMethod } + +```python +FineTuningMethod(self) +``` + diff --git a/docs/reference/ImageGroup.qmd b/docs/reference/ImageGroup.qmd new file mode 100644 index 0000000..0ba86c1 --- /dev/null +++ b/docs/reference/ImageGroup.qmd @@ -0,0 +1,6 @@ +# ImageGroup { #napari_activelearning.ImageGroup } + +```python +ImageGroup(self, group_name=None, group_dir=None) +``` + diff --git a/docs/reference/ImageGroupEditor.qmd b/docs/reference/ImageGroupEditor.qmd new file mode 100644 index 0000000..2096cbf --- /dev/null +++ b/docs/reference/ImageGroupEditor.qmd @@ -0,0 +1,6 @@ +# ImageGroupEditor { #napari_activelearning.ImageGroupEditor } + +```python +ImageGroupEditor(self) +``` + diff --git a/docs/reference/ImageGroupRoot.qmd b/docs/reference/ImageGroupRoot.qmd new file mode 100644 index 0000000..b771a50 --- /dev/null +++ b/docs/reference/ImageGroupRoot.qmd @@ -0,0 +1,6 @@ +# ImageGroupRoot { #napari_activelearning.ImageGroupRoot } + +```python +ImageGroupRoot(self) +``` + diff --git a/docs/reference/ImageGroupsManager.add_layers_to_group.qmd b/docs/reference/ImageGroupsManager.add_layers_to_group.qmd new file mode 100644 index 0000000..50c6c96 --- /dev/null +++ b/docs/reference/ImageGroupsManager.add_layers_to_group.qmd @@ -0,0 +1,6 @@ +# ImageGroupsManager.add_layers_to_group { #napari_activelearning.ImageGroupsManager.add_layers_to_group } + +```python +ImageGroupsManager.add_layers_to_group() +``` + diff --git a/docs/reference/ImageGroupsManager.create_group.qmd b/docs/reference/ImageGroupsManager.create_group.qmd new file mode 100644 index 0000000..9d0d2a2 --- /dev/null +++ b/docs/reference/ImageGroupsManager.create_group.qmd @@ -0,0 +1,6 @@ +# ImageGroupsManager.create_group { #napari_activelearning.ImageGroupsManager.create_group } + +```python +ImageGroupsManager.create_group() +``` + diff --git a/docs/reference/ImageGroupsManager.create_layers_group.qmd b/docs/reference/ImageGroupsManager.create_layers_group.qmd new file mode 100644 index 0000000..d73d0e2 --- /dev/null +++ b/docs/reference/ImageGroupsManager.create_layers_group.qmd @@ -0,0 +1,6 @@ +# ImageGroupsManager.create_layers_group { #napari_activelearning.ImageGroupsManager.create_layers_group } + +```python +ImageGroupsManager.create_layers_group() +``` + diff --git a/docs/reference/ImageGroupsManager.dump_dataset_specs.qmd b/docs/reference/ImageGroupsManager.dump_dataset_specs.qmd new file mode 100644 index 0000000..e364564 --- /dev/null +++ b/docs/reference/ImageGroupsManager.dump_dataset_specs.qmd @@ -0,0 +1,6 @@ +# ImageGroupsManager.dump_dataset_specs { #napari_activelearning.ImageGroupsManager.dump_dataset_specs } + +```python +ImageGroupsManager.dump_dataset_specs() +``` + diff --git a/docs/reference/ImageGroupsManager.focus_active_item.qmd b/docs/reference/ImageGroupsManager.focus_active_item.qmd new file mode 100644 index 0000000..2cdb28a --- /dev/null +++ b/docs/reference/ImageGroupsManager.focus_active_item.qmd @@ -0,0 +1,6 @@ +# ImageGroupsManager.focus_active_item { #napari_activelearning.ImageGroupsManager.focus_active_item } + +```python +ImageGroupsManager.focus_active_item(item) +``` + diff --git a/docs/reference/ImageGroupsManager.get_active_item.qmd b/docs/reference/ImageGroupsManager.get_active_item.qmd new file mode 100644 index 0000000..052c48c --- /dev/null +++ b/docs/reference/ImageGroupsManager.get_active_item.qmd @@ -0,0 +1,6 @@ +# ImageGroupsManager.get_active_item { #napari_activelearning.ImageGroupsManager.get_active_item } + +```python +ImageGroupsManager.get_active_item() +``` + diff --git a/docs/reference/ImageGroupsManager.qmd b/docs/reference/ImageGroupsManager.qmd new file mode 100644 index 0000000..1ea7cfe --- /dev/null +++ b/docs/reference/ImageGroupsManager.qmd @@ -0,0 +1,6 @@ +# ImageGroupsManager { #napari_activelearning.ImageGroupsManager } + +```python +ImageGroupsManager(self, default_axis_labels='TZYX') +``` + diff --git a/docs/reference/ImageGroupsManager.remove_group.qmd b/docs/reference/ImageGroupsManager.remove_group.qmd new file mode 100644 index 0000000..f130886 --- /dev/null +++ b/docs/reference/ImageGroupsManager.remove_group.qmd @@ -0,0 +1,6 @@ +# ImageGroupsManager.remove_group { #napari_activelearning.ImageGroupsManager.remove_group } + +```python +ImageGroupsManager.remove_group() +``` + diff --git a/docs/reference/ImageGroupsManager.remove_layer.qmd b/docs/reference/ImageGroupsManager.remove_layer.qmd new file mode 100644 index 0000000..db807b0 --- /dev/null +++ b/docs/reference/ImageGroupsManager.remove_layer.qmd @@ -0,0 +1,6 @@ +# ImageGroupsManager.remove_layer { #napari_activelearning.ImageGroupsManager.remove_layer } + +```python +ImageGroupsManager.remove_layer() +``` + diff --git a/docs/reference/ImageGroupsManager.remove_layers_group.qmd b/docs/reference/ImageGroupsManager.remove_layers_group.qmd new file mode 100644 index 0000000..f3eb35d --- /dev/null +++ b/docs/reference/ImageGroupsManager.remove_layers_group.qmd @@ -0,0 +1,6 @@ +# ImageGroupsManager.remove_layers_group { #napari_activelearning.ImageGroupsManager.remove_layers_group } + +```python +ImageGroupsManager.remove_layers_group() +``` + diff --git a/docs/reference/ImageGroupsManager.save_layers_group.qmd b/docs/reference/ImageGroupsManager.save_layers_group.qmd new file mode 100644 index 0000000..0766c0e --- /dev/null +++ b/docs/reference/ImageGroupsManager.save_layers_group.qmd @@ -0,0 +1,6 @@ +# ImageGroupsManager.save_layers_group { #napari_activelearning.ImageGroupsManager.save_layers_group } + +```python +ImageGroupsManager.save_layers_group() +``` + diff --git a/docs/reference/ImageGroupsManager.set_active_item.qmd b/docs/reference/ImageGroupsManager.set_active_item.qmd new file mode 100644 index 0000000..7dc06a6 --- /dev/null +++ b/docs/reference/ImageGroupsManager.set_active_item.qmd @@ -0,0 +1,6 @@ +# ImageGroupsManager.set_active_item { #napari_activelearning.ImageGroupsManager.set_active_item } + +```python +ImageGroupsManager.set_active_item(item=None) +``` + diff --git a/docs/reference/ImageGroupsManager.update_group.qmd b/docs/reference/ImageGroupsManager.update_group.qmd new file mode 100644 index 0000000..086fc19 --- /dev/null +++ b/docs/reference/ImageGroupsManager.update_group.qmd @@ -0,0 +1,6 @@ +# ImageGroupsManager.update_group { #napari_activelearning.ImageGroupsManager.update_group } + +```python +ImageGroupsManager.update_group() +``` + diff --git a/docs/reference/LabelsManager.qmd b/docs/reference/LabelsManager.qmd new file mode 100644 index 0000000..2061aba --- /dev/null +++ b/docs/reference/LabelsManager.qmd @@ -0,0 +1,6 @@ +# LabelsManager { #napari_activelearning.LabelsManager } + +```python +LabelsManager(self) +``` + diff --git a/docs/reference/LayerChannel.qmd b/docs/reference/LayerChannel.qmd new file mode 100644 index 0000000..d2a961f --- /dev/null +++ b/docs/reference/LayerChannel.qmd @@ -0,0 +1,6 @@ +# LayerChannel { #napari_activelearning.LayerChannel } + +```python +LayerChannel(self, layer, channel=0, source_axes='TZYX') +``` + diff --git a/docs/reference/LayersGroup.qmd b/docs/reference/LayersGroup.qmd new file mode 100644 index 0000000..8da7c3f --- /dev/null +++ b/docs/reference/LayersGroup.qmd @@ -0,0 +1,12 @@ +# LayersGroup { #napari_activelearning.LayersGroup } + +```python +LayersGroup( + self + layers_group_name + source_axes=None + use_as_input_image=False + use_as_sampling_mask=False +) +``` + diff --git a/docs/reference/MaskGenerator.qmd b/docs/reference/MaskGenerator.qmd new file mode 100644 index 0000000..cf496e3 --- /dev/null +++ b/docs/reference/MaskGenerator.qmd @@ -0,0 +1,6 @@ +# MaskGenerator { #napari_activelearning.MaskGenerator } + +```python +MaskGenerator(self) +``` + diff --git a/docs/reference/SegmentationMethod._run_eval.qmd b/docs/reference/SegmentationMethod._run_eval.qmd new file mode 100644 index 0000000..35b7415 --- /dev/null +++ b/docs/reference/SegmentationMethod._run_eval.qmd @@ -0,0 +1,6 @@ +# SegmentationMethod._run_eval { #napari_activelearning.SegmentationMethod._run_eval } + +```python +SegmentationMethod._run_eval(img, *args, **kwargs) +``` + diff --git a/docs/reference/SegmentationMethod._run_pred.qmd b/docs/reference/SegmentationMethod._run_pred.qmd new file mode 100644 index 0000000..1c5b499 --- /dev/null +++ b/docs/reference/SegmentationMethod._run_pred.qmd @@ -0,0 +1,6 @@ +# SegmentationMethod._run_pred { #napari_activelearning.SegmentationMethod._run_pred } + +```python +SegmentationMethod._run_pred(img, *args, **kwargs) +``` + diff --git a/docs/reference/SegmentationMethod.probs.qmd b/docs/reference/SegmentationMethod.probs.qmd new file mode 100644 index 0000000..4250849 --- /dev/null +++ b/docs/reference/SegmentationMethod.probs.qmd @@ -0,0 +1,6 @@ +# SegmentationMethod.probs { #napari_activelearning.SegmentationMethod.probs } + +```python +SegmentationMethod.probs(img, *args, **kwargs) +``` + diff --git a/docs/reference/SegmentationMethod.qmd b/docs/reference/SegmentationMethod.qmd new file mode 100644 index 0000000..46e2111 --- /dev/null +++ b/docs/reference/SegmentationMethod.qmd @@ -0,0 +1,6 @@ +# SegmentationMethod { #napari_activelearning.SegmentationMethod } + +```python +SegmentationMethod(self) +``` + diff --git a/docs/reference/SegmentationMethod.segment.qmd b/docs/reference/SegmentationMethod.segment.qmd new file mode 100644 index 0000000..8f3c7cc --- /dev/null +++ b/docs/reference/SegmentationMethod.segment.qmd @@ -0,0 +1,6 @@ +# SegmentationMethod.segment { #napari_activelearning.SegmentationMethod.segment } + +```python +SegmentationMethod.segment(img, *args, **kwargs) +``` + diff --git a/docs/reference/TunableMethod.qmd b/docs/reference/TunableMethod.qmd new file mode 100644 index 0000000..1081f82 --- /dev/null +++ b/docs/reference/TunableMethod.qmd @@ -0,0 +1,6 @@ +# TunableMethod { #napari_activelearning.TunableMethod } + +```python +TunableMethod(self) +``` + diff --git a/docs/reference/add_dropout.qmd b/docs/reference/add_dropout.qmd new file mode 100644 index 0000000..92be702 --- /dev/null +++ b/docs/reference/add_dropout.qmd @@ -0,0 +1,6 @@ +# add_dropout { #napari_activelearning.add_dropout } + +```python +add_dropout(net, p=0.05) +``` + diff --git a/docs/reference/add_multiscale_output_layer.qmd b/docs/reference/add_multiscale_output_layer.qmd new file mode 100644 index 0000000..b72ac82 --- /dev/null +++ b/docs/reference/add_multiscale_output_layer.qmd @@ -0,0 +1,20 @@ +# add_multiscale_output_layer { #napari_activelearning.add_multiscale_output_layer } + +```python +add_multiscale_output_layer( + root + axes + scale + data_group + group_name + layers_group_name + image_group + reference_source_axes + reference_scale + output_filename=None + contrast_limits=None + colormap=None + add_func=napari.Viewer.add_image +) +``` + diff --git a/docs/reference/compute_BALD.qmd b/docs/reference/compute_BALD.qmd new file mode 100644 index 0000000..b87f129 --- /dev/null +++ b/docs/reference/compute_BALD.qmd @@ -0,0 +1,6 @@ +# compute_BALD { #napari_activelearning.compute_BALD } + +```python +compute_BALD(probs) +``` + diff --git a/docs/reference/compute_acquisition_fun.qmd b/docs/reference/compute_acquisition_fun.qmd new file mode 100644 index 0000000..f46cfa6 --- /dev/null +++ b/docs/reference/compute_acquisition_fun.qmd @@ -0,0 +1,11 @@ +# compute_acquisition_fun { #napari_activelearning.compute_acquisition_fun } + +```python +compute_acquisition_fun( + tunable_segmentation_method + img + img_sp + MC_repetitions +) +``` + diff --git a/docs/reference/compute_acquisition_superpixel.qmd b/docs/reference/compute_acquisition_superpixel.qmd new file mode 100644 index 0000000..82d97cb --- /dev/null +++ b/docs/reference/compute_acquisition_superpixel.qmd @@ -0,0 +1,6 @@ +# compute_acquisition_superpixel { #napari_activelearning.compute_acquisition_superpixel } + +```python +compute_acquisition_superpixel(probs, super_pixel_labels) +``` + diff --git a/docs/reference/compute_segmentation.qmd b/docs/reference/compute_segmentation.qmd new file mode 100644 index 0000000..3271b96 --- /dev/null +++ b/docs/reference/compute_segmentation.qmd @@ -0,0 +1,6 @@ +# compute_segmentation { #napari_activelearning.compute_segmentation } + +```python +compute_segmentation(tunable_segmentation_method, img, labels_offset=0) +``` + diff --git a/docs/reference/index.qmd b/docs/reference/index.qmd new file mode 100644 index 0000000..0ded7e7 --- /dev/null +++ b/docs/reference/index.qmd @@ -0,0 +1,49 @@ +# Function reference {.doc .doc-index} + +## Some functions + +Functions to inspect docstrings. + +| | | +| --- | --- | +| [LayerChannel](LayerChannel.qmd#napari_activelearning.LayerChannel) | | +| [LayersGroup](LayersGroup.qmd#napari_activelearning.LayersGroup) | | +| [ImageGroup](ImageGroup.qmd#napari_activelearning.ImageGroup) | | +| [ImageGroupRoot](ImageGroupRoot.qmd#napari_activelearning.ImageGroupRoot) | | +| [ImageGroupEditor](ImageGroupEditor.qmd#napari_activelearning.ImageGroupEditor) | | +| [MaskGenerator](MaskGenerator.qmd#napari_activelearning.MaskGenerator) | | +| [ImageGroupsManager](ImageGroupsManager.qmd#napari_activelearning.ImageGroupsManager) | | +| [ImageGroupsManager.set_active_item](ImageGroupsManager.set_active_item.qmd#napari_activelearning.ImageGroupsManager.set_active_item) | | +| [ImageGroupsManager.get_active_item](ImageGroupsManager.get_active_item.qmd#napari_activelearning.ImageGroupsManager.get_active_item) | | +| [ImageGroupsManager.focus_active_item](ImageGroupsManager.focus_active_item.qmd#napari_activelearning.ImageGroupsManager.focus_active_item) | | +| [ImageGroupsManager.update_group](ImageGroupsManager.update_group.qmd#napari_activelearning.ImageGroupsManager.update_group) | | +| [ImageGroupsManager.create_group](ImageGroupsManager.create_group.qmd#napari_activelearning.ImageGroupsManager.create_group) | | +| [ImageGroupsManager.create_layers_group](ImageGroupsManager.create_layers_group.qmd#napari_activelearning.ImageGroupsManager.create_layers_group) | | +| [ImageGroupsManager.add_layers_to_group](ImageGroupsManager.add_layers_to_group.qmd#napari_activelearning.ImageGroupsManager.add_layers_to_group) | | +| [ImageGroupsManager.remove_layer](ImageGroupsManager.remove_layer.qmd#napari_activelearning.ImageGroupsManager.remove_layer) | | +| [ImageGroupsManager.remove_layers_group](ImageGroupsManager.remove_layers_group.qmd#napari_activelearning.ImageGroupsManager.remove_layers_group) | | +| [ImageGroupsManager.remove_group](ImageGroupsManager.remove_group.qmd#napari_activelearning.ImageGroupsManager.remove_group) | | +| [ImageGroupsManager.save_layers_group](ImageGroupsManager.save_layers_group.qmd#napari_activelearning.ImageGroupsManager.save_layers_group) | | +| [ImageGroupsManager.dump_dataset_specs](ImageGroupsManager.dump_dataset_specs.qmd#napari_activelearning.ImageGroupsManager.dump_dataset_specs) | | +| [AcquisitionFunction](AcquisitionFunction.qmd#napari_activelearning.AcquisitionFunction) | | +| [compute_BALD](compute_BALD.qmd#napari_activelearning.compute_BALD) | | +| [compute_acquisition_superpixel](compute_acquisition_superpixel.qmd#napari_activelearning.compute_acquisition_superpixel) | | +| [compute_acquisition_fun](compute_acquisition_fun.qmd#napari_activelearning.compute_acquisition_fun) | | +| [compute_segmentation](compute_segmentation.qmd#napari_activelearning.compute_segmentation) | | +| [add_multiscale_output_layer](add_multiscale_output_layer.qmd#napari_activelearning.add_multiscale_output_layer) | | +| [DropoutEvalOverrider](DropoutEvalOverrider.qmd#napari_activelearning.DropoutEvalOverrider) | | +| [add_dropout](add_dropout.qmd#napari_activelearning.add_dropout) | | +| [SegmentationMethod](SegmentationMethod.qmd#napari_activelearning.SegmentationMethod) | | +| [SegmentationMethod._run_pred](SegmentationMethod._run_pred.qmd#napari_activelearning.SegmentationMethod._run_pred) | | +| [SegmentationMethod._run_eval](SegmentationMethod._run_eval.qmd#napari_activelearning.SegmentationMethod._run_eval) | | +| [SegmentationMethod.probs](SegmentationMethod.probs.qmd#napari_activelearning.SegmentationMethod.probs) | | +| [SegmentationMethod.segment](SegmentationMethod.segment.qmd#napari_activelearning.SegmentationMethod.segment) | | +| [FineTuningMethod](FineTuningMethod.qmd#napari_activelearning.FineTuningMethod) | | +| [FineTuningMethod._get_transform](FineTuningMethod._get_transform.qmd#napari_activelearning.FineTuningMethod._get_transform) | | +| [FineTuningMethod._fine_tune](FineTuningMethod._fine_tune.qmd#napari_activelearning.FineTuningMethod._fine_tune) | | +| [FineTuningMethod.fine_tune](FineTuningMethod.fine_tune.qmd#napari_activelearning.FineTuningMethod.fine_tune) | | +| [TunableMethod](TunableMethod.qmd#napari_activelearning.TunableMethod) | | +| [AcquisitionFunction](AcquisitionFunction.qmd#napari_activelearning.AcquisitionFunction) | | +| [AcquisitionFunction.compute_acquisition](AcquisitionFunction.compute_acquisition.qmd#napari_activelearning.AcquisitionFunction.compute_acquisition) | | +| [AcquisitionFunction.compute_acquisition_layers](AcquisitionFunction.compute_acquisition_layers.qmd#napari_activelearning.AcquisitionFunction.compute_acquisition_layers) | | +| [AcquisitionFunction.fine_tune](AcquisitionFunction.fine_tune.qmd#napari_activelearning.AcquisitionFunction.fine_tune) | | \ No newline at end of file diff --git a/docs/styles.css b/docs/styles.css new file mode 100644 index 0000000..2ddf50c --- /dev/null +++ b/docs/styles.css @@ -0,0 +1 @@ +/* css styles */ diff --git a/docs/tutorials/cellpose_tutorial.qmd b/docs/tutorials/cellpose_tutorial.qmd new file mode 100644 index 0000000..4a4d7bd --- /dev/null +++ b/docs/tutorials/cellpose_tutorial.qmd @@ -0,0 +1,20 @@ +--- +title: "Tutorial: How to fine tune a Cellpose model" +author: Fernando Cervantes (fernando.cervantes@jax.org) +format: + revealjs: + code-fold: false + progress: true + controls: true + fontsize: 22pt + + ipynb: + roc: true + +execute: + echo: + true + +jupyter: python3 +--- +