move .conda to local and avoid pio kaleido saving due to error on mac

.gitignore

@@ -32,3 +32,4 @@ tensorflow-2.4.1-py3-none-any.whl
 !*.env.example
 
 process.lock
+.conda/

docker-compose.dev.yml

@@ -27,6 +27,7 @@ services:
     working_dir: /app
     volumes:
       - .:/app
+      - ../optinist-docker-volumes/.conda/pkgs:/app/.conda/pkgs
 
       # optinist data outputs directories
       - ../optinist-docker-volumes/.snakemake/:/app/.snakemake

studio/app/common/dataclass/histogram.py

@@ -1,9 +1,8 @@
 from typing import Optional
 
+import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
-import plotly.express as px
-import plotly.io as pio
 
 from studio.app.common.core.utils.filepath_creater import join_filepath
 from studio.app.common.core.utils.json_writer import JsonWriter
@@ -38,8 +37,9 @@ def output_path(self) -> OutputPath:
         return OutputPath(path=self.json_path, type=OutputType.HISTOGRAM)
 
     def save_plot(self, output_dir):
-        fig = px.histogram(x=self.data[0], nbins=20)
+        plt.figure()
+        plt.hist(self.data[0], bins=20)
         plot_file = join_filepath([output_dir, f"{self.file_name}.png"])
-        pio.write_image(fig, plot_file)
-
+        plt.savefig(plot_file)
+        plt.close()
         save_thumbnail(plot_file)

studio/app/common/dataclass/line.py

@@ -1,8 +1,7 @@
 from typing import Optional
 
+import matplotlib.pyplot as plt
 import pandas as pd
-import plotly.express as px
-import plotly.io as pio
 
 from studio.app.common.core.utils.filepath_creater import join_filepath
 from studio.app.common.core.utils.json_writer import JsonWriter
@@ -32,8 +31,9 @@ def output_path(self) -> OutputPath:
 
     def save_plot(self, output_dir):
         for i in range(len(self.data)):
-            fig = px.line(y=self.data[i], x=self.columns)
+            plt.figure()
+            plt.plot(self.columns, self.data[i])
             plot_file = join_filepath([output_dir, f"{self.file_name}_{i}.png"])
-            pio.write_image(fig, plot_file)
-
+            plt.savefig(plot_file)
+            plt.close()
             save_thumbnail(plot_file)

studio/app/common/dataclass/pie.py

@@ -1,9 +1,8 @@
 from typing import Optional
 
+import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
-import plotly.graph_objects as go
-import plotly.io as pio
 
 from studio.app.common.core.utils.filepath_creater import join_filepath
 from studio.app.common.core.utils.json_writer import JsonWriter
@@ -39,17 +38,10 @@ def output_path(self) -> OutputPath:
         return OutputPath(path=self.json_path, type=OutputType.PIE)
 
     def save_plot(self, output_dir):
-        fig = go.Figure(
-            data=[
-                go.Pie(
-                    labels=self.columns,
-                    values=self.data[0],
-                    sort=False,
-                    direction="clockwise",
-                )
-            ]
-        )
+        plt.figure(figsize=(8, 8))  # Optional: Adjust the figure size as needed
+        plt.pie(self.data[0], labels=self.columns, counterclock=False, startangle=90)
+        plt.axis("equal")  # Equal aspect ratio ensures the pie chart is circular.
         plot_file = join_filepath([output_dir, f"{self.file_name}.png"])
-        pio.write_image(fig, plot_file)
-
+        plt.savefig(plot_file)
+        plt.close()
         save_thumbnail(plot_file)

studio/app/common/dataclass/polar.py

@@ -1,8 +1,8 @@
 from typing import Optional
 
+import matplotlib.pyplot as plt
+import numpy as np
 import pandas as pd
-import plotly.express as px
-import plotly.io as pio
 
 from studio.app.common.core.utils.filepath_creater import join_filepath
 from studio.app.common.core.utils.json_writer import JsonWriter
@@ -33,14 +33,20 @@ def output_path(self) -> OutputPath:
 
     def save_plot(self, output_dir):
         for i in range(len(self.data)):
-            fig = px.line_polar(
-                r=self.data[i],
-                theta=self.columns,
-                direction="counterclockwise",
-                start_angle=0,
-                line_close=True,
+            # Convert theta to radians
+            theta = np.linspace(0, 2 * np.pi, len(self.columns))
+            plt.figure()
+            ax = plt.subplot(111, polar=True)
+            ax.plot(theta, self.data[i])
+            ax.set_theta_direction(-1)  # Counterclockwise
+            ax.set_theta_offset(np.pi / 2.0)  # Start angle at 0
+            ax.plot(
+                [theta[-1], theta[0]],
+                [self.data[i][-1], self.data[i][0]],
+                linestyle="-",
+                linewidth=2,
             )
             plot_file = join_filepath([output_dir, f"{self.file_name}_{i}.png"])
-            pio.write_image(fig, plot_file)
-
+            plt.savefig(plot_file)
+            plt.close()
             save_thumbnail(plot_file)

studio/app/optinist/microscopes/OIRReader.py

@@ -450,9 +450,9 @@ def _get_image_stacks(self) -> list:
                         single_plane_buffer = np.ctypeslib.as_array(ctypes_buffer_ptr)
 
                         # construct return value (each channel's stack)
-                        result_channels_stacks[channel_no, serial_loops_index] = (
-                            single_plane_buffer
-                        )
+                        result_channels_stacks[
+                            channel_no, serial_loops_index
+                        ] = single_plane_buffer
                         serial_loops_index += 1
 
                         frame_manager.release_image_body()

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

@@ -154,6 +154,7 @@ def util_download_model_files():
                 with open(file_path, "wb") as f:
                     f.write(response.content)
 
+
 def mm_fun(A: np.ndarray, Y: np.ndarray) -> np.ndarray:
     """
     This code is a port of the CaImAn-MATLAB function (mm_fun.m).

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

@@ -8,3 +8,4 @@ dependencies:
   - scikit-image=0.19.*
   - protobuf=3.20.*
   - caiman>=1.9.9, <=1.9.12
+  - matplotlib

studio/app/optinist/wrappers/caiman/conda/caiman_with_expdb.yaml

@@ -2,12 +2,13 @@ channels:
   - defaults
   - conda-forge
 dependencies:
-  - python=3.8
+  - python=3.9
   - cython
   - numpy=1.22.*
   - scikit-image=0.19.*
   - protobuf=3.20.*
   - caiman>=1.9.9, <=1.9.12
+  - matplotlib
 
   # for expdb
   - gcc=12

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

@@ -5,6 +5,7 @@ dependencies:
   - gcc=12
   - numpy=1.23
   - scipy=1.10
+  - matplotlib
   - pip:
     - isx==1.0.*
     - pynwb==2.6.0

studio/config/docker/Dockerfile.dev

@@ -36,6 +36,23 @@ RUN mkdir -p /opt/miniforge && \
     conda clean -y --tarballs
 ENV PATH $PATH:/opt/miniforge/bin
 
+ENV CONDA_ALWAYS_COPY=1
+
+# Setup conda dir
+RUN mkdir -p /app/.conda/pkgs \
+    && mkdir -p /app/.conda/envs \
+    && chown -R optinist:www-data /app/.conda \
+    && su optinist -c 'cat > /home/optinist/.condarc << EOF
+pkgs_dirs:
+  - /app/.conda/pkgs
+envs_dirs:
+  - /app/.conda/envs
+channels:
+  - conda-forge
+  - defaults
+channel_priority: flexible
+EOF'
+
 # setup cron
 RUN ln -snf /usr/share/zoneinfo/Asia/Tokyo /etc/localtime && echo "Asia/Tokyo" > /etc/timezone && \
     apt-get install --no-install-recommends -y cron rsyslog && \
@@ -111,4 +128,3 @@ 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
-