Adding new/updated cellcanvas_generate-pixel-embedding_0.1.8

cellcanvas · Aug 13, 2024 · 1255220 · 1255220
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Showing 4 changed files with 16 additions and 11 deletions.
diff --git a/album_catalog_index.db b/album_catalog_index.db
diff --git a/solutions/cellcanvas/generate-pixel-embedding/CHANGELOG.md b/solutions/cellcanvas/generate-pixel-embedding/CHANGELOG.md
@@ -4,6 +4,9 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.1.8] - 2024-08-13
+
+
 ## [0.1.7] - 2024-08-11
 Remove defaults
 

diff --git a/solutions/cellcanvas/generate-pixel-embedding/solution.py b/solutions/cellcanvas/generate-pixel-embedding/solution.py
@@ -8,12 +8,12 @@
   - nvidia
   - conda-forge
 dependencies:
-  - python=3.10
-  - cudatoolkit=11.8
+  - python=3.9
+  - cudatoolkit
   - pytorch
   - torchvision
   - torchaudio
-  - pytorch-cuda=11.8
+  - pytorch-cuda
   - numpy
   - pip
   - pytorch-lightning
@@ -22,7 +22,7 @@
   - zarr
   - pip:
     - git+https://github.com/morphometrics/morphospaces.git
-    - git+https://github.com/uermel/copick.git
+    - copick==0.5.5
 """
 
 MODEL_URL = "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/model_swinvit.pt"
@@ -56,12 +56,14 @@ def run():
     import numpy as np
     from monai.inferers import sliding_window_inference
     from copick.impl.filesystem import CopickRootFSSpec
-    from copick.models import TCopickFeatures
+   # from copick.models import TCopickFeatures
     from morphospaces.networks.swin_unetr import PixelEmbeddingSwinUNETR
     from numcodecs import Blosc
     from torch.cuda.amp import autocast
     import sys
+    import torch
 
+    print(f'Cuda is available {torch.cuda.is_available()}')
     # Dummy classes for Qt components
     class DummyQtComponent:
         def __init__(self, *args, **kwargs):
@@ -121,7 +123,7 @@ class DummyQtWidgetsModule:
 
     print(f"Determined embedding dimension: {embedding_dim}")
 
-    copick_features: TCopickFeatures = tomogram.new_features(embedding_name)
+    copick_features = tomogram.new_features(embedding_name)
     out_array = zarr.open_array(store=copick_features.zarr(),
                                 compressor=Blosc(cname='zstd', clevel=3, shuffle=2),
                                 dtype='float32',
@@ -173,7 +175,7 @@ def sliding_window_processor(image, roi_size, overlap, device):
 setup(
     group="cellcanvas",
     name="generate-pixel-embedding",
-    version="0.1.7",
+    version="0.1.8",
     title="Predict Tomogram Embeddings with SwinUNETR using Copick API",
     description="Apply a SwinUNETR model to a tomogram fetched using the Copick API to produce embeddings, and save them in a Zarr.",
     solution_creators=["Kyle Harrington"],
@@ -192,4 +194,4 @@ def sliding_window_processor(image, roi_size, overlap, device):
     dependencies={
         "environment_file": env_file
     },
-)
+)
diff --git a/solutions/cellcanvas/generate-pixel-embedding/solution.yml b/solutions/cellcanvas/generate-pixel-embedding/solution.yml
@@ -24,7 +24,7 @@ args:
   name: embedding_name
   required: true
   type: string
-changelog: Remove defaults
+changelog: null
 description: Apply a SwinUNETR model to a tomogram fetched using the Copick API to
   produce embeddings, and save them in a Zarr.
 group: cellcanvas
@@ -37,6 +37,6 @@ tags:
 - deep learning
 - cryoet
 - tomogram
-timestamp: '2024-08-11T10:17:32.207012'
+timestamp: '2024-08-13T15:10:07.510854'
 title: Predict Tomogram Embeddings with SwinUNETR using Copick API
-version: 0.1.7
+version: 0.1.8