Merge pull request #20 from TheJacksonLaboratory/dev

Changing tensorstore to zarr for creating layers
TheJacksonLaboratory · Nov 13, 2024 · a2e6b98 · a2e6b98
2 parents 3567d8e + 74bdb6c
commit a2e6b98
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diff --git a/.gitignore b/.gitignore
@@ -176,4 +176,8 @@ venv/
 .DS_Store
 
 # written by setuptools_scm
-**/_version.py
+**/_version.py
+
+.quarto
+_site
+models
diff --git a/docs/.gitignore b/docs/.gitignore
@@ -0,0 +1 @@
+/.quarto/
diff --git a/docs/_quarto.yml 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
diff --git a/docs/_sidebar.yml 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
@@ -0,0 +1,5 @@
+---
+title: "About"
+---
+
+About this site
diff --git a/docs/index.qmd 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 <https://quarto.org/docs/websites>.
diff --git a/docs/objects.json b/docs/objects.json
diff --git a/docs/reference/AcquisitionFunction.compute_acquisition.qmd 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -0,0 +1,6 @@
+# FineTuningMethod { #napari_activelearning.FineTuningMethod }
+
+```python
+FineTuningMethod(self)
+```
+
diff --git a/docs/reference/ImageGroup.qmd 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
@@ -0,0 +1,6 @@
+# ImageGroupEditor { #napari_activelearning.ImageGroupEditor }
+
+```python
+ImageGroupEditor(self)
+```
+
diff --git a/docs/reference/ImageGroupRoot.qmd 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -0,0 +1,6 @@
+# LabelsManager { #napari_activelearning.LabelsManager }
+
+```python
+LabelsManager(self)
+```
+
diff --git a/docs/reference/LayerChannel.qmd 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
@@ -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
@@ -0,0 +1,6 @@
+# MaskGenerator { #napari_activelearning.MaskGenerator }
+
+```python
+MaskGenerator(self)
+```
+