fix and adjust caiman cnmf

pyproject.toml

@@ -78,7 +78,7 @@ lauda = "*"
 Pillow = "*"
 pymatreader = "^0.0.32"
 xmltodict = "*"
-matplotlib = "==3.7.*"
+matplotlib = "3.7.*"
 scikit-image = "0.21"
 
 [tool.poetry.group.dev]

studio/app/optinist/wrappers/caiman/cnmf.py

@@ -5,7 +5,6 @@
 import requests
 import scipy
 
-from studio.app.common.core.experiment.experiment import ExptOutputPathIds
 from studio.app.common.core.logger import AppLogger
 from studio.app.common.core.utils.filepath_creater import (
     create_directory,
@@ -215,7 +214,7 @@ def caiman_cnmf(
     from caiman.source_extraction.cnmf import cnmf, online_cnmf
     from caiman.source_extraction.cnmf.params import CNMFParams
 
-    function_id = ExptOutputPathIds(output_dir).function_id
+    function_id = output_dir.split("/")[-1]  # get function_id from output_dir path
     logger.info(f"start caiman_cnmf: {function_id}")
 
     # NOTE: evaluate_components requires cnn_model files in caiman_data directory.

studio/app/optinist/wrappers/caiman/params/caiman_cnmf.yaml

@@ -27,7 +27,7 @@ init_params:
   # NOTE: K would affect performance.
   # Set lower values (like 4) for faster processing. (eg., for development)
   # K: 2000  # for production.
-  K: 4
+  K: 10
 
   gSig: [4, 4]
   ssub: 1

studio/app/optinist/wrappers/expdb/conda/expdb.yaml

@@ -8,3 +8,4 @@ dependencies:
   - pip:
     - isx==1.0.*
     - pynwb==2.6.0
+    - matplotlib==3.7.*

studio/config/docker/Dockerfile

@@ -76,10 +76,10 @@ RUN pip3 install --no-cache-dir --upgrade pip && \
     pip3 install poetry && \
     poetry config virtualenvs.create false
 
-# export requirements.txt from poetry and
+# export requirements.txt from poetry and install
 # * Some module versions are adjusted directly for batch environments.
-RUN poetry export -f requirements.txt -o requirements.studio.txt --without-hashes && \
-    sed -e '/^h5py/d' -e '/^opencv-python/d' requirements.studio.txt > requirements.batch.txt
+RUN poetry export -f requirements.txt -o requirements.studio.txt && \
+    sed -e '/^h5py/d' requirements.studio.txt > requirements.batch.txt
 
 RUN pip3 install -r requirements.studio.txt
 

studio/config/docker/Dockerfile.dev

@@ -76,10 +76,10 @@ RUN pip3 install --no-cache-dir --upgrade pip && \
     pip3 install poetry && \
     poetry config virtualenvs.create false
 
-# export requirements.txt from poetry and
+# export requirements.txt from poetry and install
 # * Some module versions are adjusted directly for batch environments.
-RUN poetry export -f requirements.txt -o requirements.studio.txt --without-hashes && \
-    sed -e '/^h5py/d' -e '/^opencv-python/d' requirements.studio.txt > requirements.batch.txt
+RUN poetry export -f requirements.txt -o requirements.studio.txt && \
+    sed -e '/^h5py/d' requirements.studio.txt > requirements.batch.txt
 
 RUN pip3 install -r requirements.studio.txt
 
@@ -111,4 +111,3 @@ USER optinist
 COPY studio/app/optinist/wrappers/caiman/run_download_model_files.sh ./
 RUN bash run_download_model_files.sh && rm run_download_model_files.sh
 USER root
-

studio/config/docker/Dockerfile.test

@@ -34,4 +34,7 @@ COPY pyproject.toml poetry.lock ./
 RUN pip3 install --no-cache-dir --upgrade pip && \
     pip3 install poetry && \
     poetry config virtualenvs.create false
-RUN poetry install --no-root --with test
+
+# export requirements.txt from poetry and install
+RUN poetry export -f requirements.txt -o requirements.studio.txt --with test
+RUN pip3 install -r requirements.studio.txt