Add VISTA2D dependencies (#1745)

* update the dependencies part Signed-off-by: binliu <[email protected]> * remove opencv package Signed-off-by: binliu <[email protected]> * remove redundant dependencies Signed-off-by: binliu <[email protected]> --------- Signed-off-by: binliu <[email protected]> Co-authored-by: tangy5 <[email protected]>
Project-MONAI · Sep 27, 2024 · b85d6b1 · b85d6b1
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diff --git a/sample-apps/vista2d/README.md b/sample-apps/vista2d/README.md
@@ -56,11 +56,35 @@ Segmentation Masks
 # skip this if you have already downloaded the app or using github repository (dev mode)
 monailabel apps --download --name vista2d --output apps
 
+# install the dependencies
+pip install -r ./apps/vista2d/requirements.txt
+
 # Start server with vista2d model
 monailabel start_server --app apps/vista2d --studies datasets --conf models vista2d --conf preload true --conf skip_trainers true
 ```
 
+**Important Note**
+
+If your environment already contains OpenCV, installing `cellpose` may lead to conflicts and produce errors such as:
+
+```
+AttributeError: partially initialized module 'cv2' has no attribute 'dnn' (most likely due to a circular import)
+```
+
+when executing. To resolve this issue, please uninstall OpenCV and then re-install `cellpose` with a command like:
+
+```Bash
+pip uninstall -y opencv && rm /usr/local/lib/python3.x/dist-packages/cv2
+```
+
+Alternatively, you can use the following command to install `cellpose` without its dependencies:
+
+```
+pip install --no-deps cellpose
+```
+
 **Specify bundle version** (Optional)
+
 Above command will download the latest bundles from Model-Zoo by default. If a specific or older bundle version is used, users can add version `_v` followed by the bundle name. Example:
 
 ```bash

diff --git a/sample-apps/vista2d/requirements.txt b/sample-apps/vista2d/requirements.txt
@@ -1,10 +1,14 @@
 # Copyright (c) MONAI Consortium
-# Licensed under the Apache License, Version 2.0 (the "License");
+# Licensed under the Apache License Version 2.0 (the License);
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
 #     http://www.apache.org/licenses/LICENSE-2.0
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# Unless required by applicable law or agreed to in writing software
+# distributed under the License is distributed on an AS IS BASIS
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
+cellpose==3.0.8
+natsort==8.4.0
+roifile==2024.5.24
+fastremap==1.15.0