Merge pull request #20 from bioimage-io/add-logo

Display BioImageIO logo and refactoring example plugin

MANIFEST.in

@@ -1,6 +1,7 @@
 include LICENSE
 include README.md
 include napari_bioimageio/VERSION
+include napari_bioimageio/bioimage-io-logo-white.png
 exclude requirements*.txt
 exclude .*
 exclude pylintrc

README.md

@@ -1,6 +1,10 @@
-# napari-bioimage-io
+# napari-bioimageio
 
-napari plugin for managing AI models in the BioImage Model Zoo.
+napari plugin for managing AI models in the [BioImage Model Zoo](https://bioimage.io).
+
+> **WARNING**: This is an alpha release. The API may change in future versions, and please feel free to create issues to report bugs or provide feedbacks.
+
+![](assets/screenshot-model-manager-1.png)
 
 ## Installation
 
@@ -15,7 +19,6 @@ pip install napari-bioimageio
 This library is meant for helping developers to ease the handling of models in napari.
 
 We provide a set of API functions for managing and selecting models.
-
 ### `show_model_manager()`
 Show the model manager with a model list pulled from the BioImage Model Zoo, the user can explore all the available models, download or remove models.
 
@@ -43,6 +46,7 @@ if model_info:
         pipeline, input_image, padding=padding
     )
 ```
+Note: To run the models, you need to setup the conda environment properly according to the [installation guide of bioimageio.core](https://github.com/bioimage-io/core-bioimage-io-python#installation).
 
 For more examples, see [this example notebook](https://github.com/bioimage-io/core-bioimage-io-python/blob/main/example/bioimageio-core-usage.ipynb) for `bioimageio.core`.
 

examples/bioimageio-hpa/README.md → examples/hpa-single-cell/README.md

@@ -6,6 +6,6 @@ This plugin demonstrate how to use the bioimageio model manager to fetch and run
 ## Installation
 
 ```
-cd examples/bioimageio-hpa
+cd examples/hpa-single-cell
 pip install .
 ```

examples/hpa-single-cell/hpa_single_cell/__init__.py

@@ -0,0 +1,5 @@
+from ._bhpa import QTHPASingleCell
+
+__all__ = [
+    "QTHPASingleCell",
+]

examples/bioimageio-hpa/bioimageio_hpa/_bhpa.py → examples/hpa-single-cell/hpa_single_cell/_bhpa.py

@@ -83,7 +83,7 @@
 custom_style = get_stylesheet("dark")
 
 
-class QtBioImageIOHPA(QDialog):
+class QTHPASingleCell(QDialog):
     def __init__(self, viewer: "napari.viewer.Viewer"):
         super().__init__()
         self._viewer = viewer

examples/hpa-single-cell/hpa_single_cell/napari.yaml

@@ -0,0 +1,12 @@
+name: hpa-single-cell
+display_name: HPA Single Cell
+
+contributions:
+  commands:
+  - id: hpa-single-cell.QTHPASingleCell
+    python_name: hpa_single_cell._bhpa:QTHPASingleCell
+    title: HPA Single Cell
+
+  widgets:
+  - command: hpa-single-cell.QTHPASingleCell
+    display_name: HPA Single Cell

examples/bioimageio-hpa/setup.cfg → examples/hpa-single-cell/setup.cfg

@@ -1,5 +1,5 @@
 [metadata]
-name = bioimageio_hpa
+name = hpa_single_cell
 version = 0.0.1
 classifiers =
     Framework :: napari
@@ -18,7 +18,7 @@ include_package_data = True
 
 [options.entry_points]
 napari.manifest =
-    bioimageio-hpa = bioimageio_hpa:napari.yaml
+    hpa-single-cell = hpa_single_cell:napari.yaml
 
 [options.package_data]
-bioimageio_hpa = napari.yaml
+hpa_single_cell = napari.yaml

napari_bioimageio/VERSION

@@ -1 +1 @@
-0.1.2
+0.1.3

napari_bioimageio/_bmm.py

@@ -429,11 +429,23 @@ def inspect_popup(self):
             d.exec_()
 
     def setup_ui(self):
-        self.resize(1080, 525)
+        self.resize(1080, 825)
 
         vlay_1 = QVBoxLayout(self)
 
         folderBox = QHBoxLayout()
+        logo_file = os.path.join(
+            os.path.dirname(__file__), "bioimage-io-logo-white.png"
+        )
+        # TODO: Deal with light theme
+        logo_label = QLabel(f'<img src="{logo_file}">')
+        folderBox.addWidget(logo_label)
+        folderBox.addSpacing(10)
+        folderBox.addStretch()
+        vlay_1.addLayout(folderBox)
+
+        folderBox = QHBoxLayout()
+
         modfol_label = QLabel("Models folder:")
         self.modfol_value = QLabel(self.models_folder)
         modfol_folder_btn = QPushButton("Change")
@@ -450,6 +462,7 @@ def setup_ui(self):
         mov.setScaledSize(QSize(18, 18))
         self.working_indicator.setMovie(mov)
         mov.start()
+
         folderBox.addWidget(modfol_label)
         folderBox.addSpacing(10)
         folderBox.addWidget(self.modfol_value)
@@ -481,12 +494,13 @@ def setup_ui(self):
         downloaded = QWidget(self.v_splitter)
         lay = QVBoxLayout(downloaded)
         lay.setContentsMargins(0, 2, 0, 2)
-        self.downloaded_label = QLabel("downloaded models:")
+        self.downloaded_label = QLabel("Downloaded models:")
         mid_layout = QHBoxLayout()
         mid_layout.addWidget(self.downloaded_label)
         mid_layout.addStretch()
         lay.addLayout(mid_layout)
         self.downloaded_list = QtModelList(downloaded, self, self.select_mode)
+        self.downloaded_list.setFixedHeight(250)
         lay.addWidget(self.downloaded_list)
 
         available = QWidget(self.v_splitter)
@@ -498,6 +512,7 @@ def setup_ui(self):
         mid_layout.addStretch()
         lay.addLayout(mid_layout)
         self.available_list = QtModelList(available, self, False)
+        self.available_list.setFixedHeight(250)
         lay.addWidget(self.available_list)
 
         self.v_splitter.setStretchFactor(1, 2)

setup.cfg

@@ -1,6 +1,8 @@
 [metadata]
 name = napari_bioimageio
 version = file: napari_bioimageio/VERSION
+long_description = file: README.md
+long_description_content_type = text/markdown; charset=UTF-8; variant=GFM
 classifiers =
     Framework :: napari
     Programming Language :: Python