Merge pull request #35 from elephant-track/fix-export

ELEPHANT server v0.6.1 -> v0.6.2
elephant-track · Jan 25, 2025 · 30dd29d · 30dd29d
2 parents ded7ec7 + 3fcb21c
commit 30dd29d
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Showing 6 changed files with 6 additions and 7 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -42,7 +42,6 @@ RUN ln -sf /dev/stdout /var/log/nginx/access.log \
 # install pypi packages
 COPY requirements.txt /tmp/requirements.txt
 RUN python -m pip install -r /tmp/requirements.txt && rm /tmp/requirements.txt
-RUN python -m pip install "tifffile<2022.4.22"
 # RUN pip install memory_profiler line_profiler
 # RUN pip install --no-deps stardist==0.8.3 csbdeep==0.7.2 numba==0.56.0 llvmlite==0.39.0 natsort==8.1.0
 

diff --git a/Dockerfile-test b/Dockerfile-test
@@ -1,4 +1,4 @@
-FROM elephant-server:0.6.0
+FROM elephant-server:0.6.2
 
 LABEL maintainer="Ko Sugawara <[email protected]>"
 

diff --git a/Makefile b/Makefile
@@ -5,7 +5,7 @@ help:
 
 ELEPHANT_GPU?=all
 ELEPHANT_WORKSPACE?=${PWD}/workspace
-ELEPHANT_IMAGE_NAME?=elephant-server:0.6.0
+ELEPHANT_IMAGE_NAME?=elephant-server:0.6.2
 ELEPHANT_NVIDIA_GID?=$$(ls -n /dev/nvidia0 2>/dev/null | awk '{print $$4}')
 ELEPHANT_DOCKER?=docker
 ELEPHANT_RABBITMQ_NODENAME?=rabbit@localhost

diff --git a/elephant-core/elephant/common.py b/elephant-core/elephant/common.py
@@ -1324,7 +1324,7 @@ def export_ctc_labels(config, spots_dict):
             os.path.join(savedir, f'mask{t:0{digits}d}.tif'),
             label[:, None] if n_dims == 3 else label,
             imagej=True,
-            compress=6,
+            compression=("zlib", 6),
         )
         timepoints.discard(t)
     # Save blank images for unlabeled frames
@@ -1334,7 +1334,7 @@ def export_ctc_labels(config, spots_dict):
             os.path.join(savedir, f'mask{t:0{digits}d}.tif'),
             label[:, None] if n_dims == 3 else label,
             imagej=True,
-            compress=6,
+            compression=("zlib", 6),
         )
     if is_zip:
         zip_path = shutil.make_archive('/tmp/archive', 'zip', savedir)

diff --git a/elephant-core/elephant/version.py b/elephant-core/elephant/version.py
@@ -24,4 +24,4 @@
 # ==============================================================================
 """Version definition."""
 
-__version__ = "0.6.0"
+__version__ = "0.6.2"
diff --git a/elephant_server.ipynb b/elephant_server.ipynb
@@ -39,7 +39,7 @@
       },
       "outputs": [],
       "source": [
-        "%env ELEPHANT_SERVER_VERSION = v0.6.0"
+        "%env ELEPHANT_SERVER_VERSION = v0.6.2"
       ]
     },
     {