merge

.github/workflows/docker-image.yml

@@ -1,26 +1,26 @@
-name: Docker Image CI
+# name: Docker Image CI
 
-on:
-  push:
-    branches: [ "develop" ]
-  pull_request:
-    branches: [ "develop" ]
+# on:
+#   push:
+#     branches: [ "develop" ]
+#   pull_request:
+#     branches: [ "develop" ]
 
-jobs:
+# jobs:
 
-  build:
+#   build:
 
-    runs-on: ubuntu-latest
+#     runs-on: ubuntu-latest
 
-    steps:
-    - uses: actions/checkout@v3
-    - name: docker login
-      env:
-        DOCKER_USER: ${{secrets.DOCKER_USER}}
-        DOCKER_PASSWORD: ${{secrets.DOCKER_PASSWORD}}
-      run: |
-        docker login -u $DOCKER_USER -p $DOCKER_PASSWORD
-    - name: Build the Docker image
-      run: docker build . --file Dockerfile --tag neurodata/brainlit:latest
-    - name: Docker Push
-      run: docker push neurodata/brainlit
+#     steps:
+#     - uses: actions/checkout@v3
+#     - name: docker login
+#       env:
+#         DOCKER_USER: ${{secrets.DOCKER_USER}}
+#         DOCKER_PASSWORD: ${{secrets.DOCKER_PASSWORD}}
+#       run: |
+#         docker login -u $DOCKER_USER -p $DOCKER_PASSWORD
+#     - name: Build the Docker image
+#       run: docker build . --file Dockerfile --tag neurodata/brainlit:latest
+#     - name: Docker Push
+#       run: docker push neurodata/brainlit

README.md

@@ -2,7 +2,7 @@
 [![DOI](https://zenodo.org/badge/237507496.svg)](https://zenodo.org/badge/latestdoi/237507496)
 [![Python](https://img.shields.io/badge/python-3.7-blue.svg)]()
 ![Tests](https://img.shields.io/github/actions/workflow/status/neurodata/brainlit/python.yml)
-[![CircleCI](https://circleci.com/gh/neurodata/brainlit/tree/develop.svg?style=svg)](https://circleci.com/gh/neurodata/brainlit/tree/develop)
+<!---[![CircleCI](https://circleci.com/gh/neurodata/brainlit/tree/develop.svg?style=svg)](https://circleci.com/gh/neurodata/brainlit/tree/develop)-->
 [![Netlify Status](https://api.netlify.com/api/v1/badges/daad6ab0-1d47-4685-b6ab-ecc487a01ba7/deploy-status)](https://brainlit.netlify.app/)
 [![PyPI version](https://badge.fury.io/py/brainlit.svg)](https://badge.fury.io/py/brainlit)
 [![Downloads](https://img.shields.io/pypi/dw/brainlit)](https://img.shields.io/pypi/dw/brainlit)

brainlit/BrainLine/apply_ilastik.py

@@ -154,7 +154,9 @@ def plot_results(
             brain_name = brain_id
         base_dir = data_dir + f"/brain{brain_name}/{dset}/"
         data_files = _find_sample_names(base_dir, dset="", add_dir=True)
-        test_files = [file.split(".")[0] + "_Probabilities.h5" for file in data_files]
+        test_files = [
+            file[: file.rfind(".")] + "_Probabilities.h5" for file in data_files
+        ]
 
         best_fscore = 0
         best_thresh = -1
@@ -316,7 +318,7 @@ def examine_threshold(
     base_dir = data_dir + f"/brain{brain_id}/{dset}/"
 
     data_files = _find_sample_names(base_dir, dset="", add_dir=True)
-    test_files = [file.split(".")[0] + "_Probabilities.h5" for file in data_files]
+    test_files = [file[: file.rfind(".")] + "_Probabilities.h5" for file in data_files]
 
     size_thresh = 500
 

brainlit/BrainLine/util.py

@@ -8,6 +8,7 @@
 from tqdm import tqdm
 from brainlit.BrainLine.imports import *
 import json
+import zarr
 
 
 def download_subvolumes(
@@ -45,7 +46,6 @@ def download_subvolumes(
         data_dir = Path(data_dir)
 
     base_dir = data_dir / f"brain{brain_id}" / dataset_to_save
-    antibody_layer, background_layer, endogenous_layer = layer_names
 
     vols = []
     if "base_s3" in brain2paths[brain_id].keys():