Test some ideas

Dockerfile

@@ -0,0 +1,27 @@
+FROM python:3.11
+
+WORKDIR /app
+
+COPY ./requirements.txt /app/requirements.txt
+COPY ./packages.txt /app/packages.txt
+
+RUN apt-get update && xargs -r -a /app/packages.txt apt-get install -y && rm -rf /var/lib/apt/lists/*
+RUN pip3 install --no-cache-dir -r /app/requirements.txt
+
+# User
+RUN useradd -m -u 1000 user
+USER user
+ENV HOME /home/user
+ENV PATH $HOME/.local/bin:$PATH
+
+WORKDIR $HOME
+RUN mkdir app
+WORKDIR $HOME/app
+COPY . $HOME/app
+
+EXPOSE 8501
+CMD streamlit run app.py \
+    --server.headless true \
+    --server.enableCORS false \
+    --server.enableXsrfProtection false \
+    --server.fileWatcherType none

README.md

@@ -1,11 +1,15 @@
 ---
-title: TestSibernetic
-emoji: 🦀
-colorFrom: indigo
-colorTo: gray
+title: Test Sibernetic...
+emoji: 🐢
+colorFrom: blue
+colorTo: green
 sdk: docker
+app_port: 8501
 pinned: false
-license: mit
 ---
 
-Check out the configuration reference at https://huggingface.co/docs/hub/spaces-config-reference
+## 🧠 Streamlit Docker Template 🔎
+
+Streamlit Docker Template is a template for creating a Streamlit app with Docker and Hugging Face Spaces.
+
+Code from https://docs.streamlit.io/library/get-started/create-an-app

app.py

@@ -0,0 +1,136 @@
+import streamlit as st
+import stpyvista.utils
+
+if "IS_XVFB_RUNNING" not in st.session_state:
+  stpyvista.utils.start_xvfb()
+  st.session_state.IS_XVFB_RUNNING = True 
+
+st.title("Sibernetic simple example")
+
+import pyvista as pv
+import numpy as np
+
+import time
+
+points = []
+types = []
+
+file = "position_buffer.txt"
+
+colours = {1.1: "lightblue", 2.1: "green", 2.2: "turquoise", 3: "#eeeeee"}
+colours = {1.1: "blue", 2.2: "turquoise"}
+
+line_count = 0
+pcount = 0
+
+all_points = []
+all_point_types = []
+
+time_count = 0
+
+logStep = None
+
+include_boundary = False
+
+for l in open(file):
+    ws = l.split()
+    #print(ws)
+    if line_count == 6:
+        numOfElasticP = int(ws[0])
+    if line_count == 7:
+        numOfLiquidP = int(ws[0])
+    if line_count == 8:
+        numOfBoundaryP = int(ws[0])
+    if line_count == 9:
+        timeStep = float(ws[0])
+    if line_count == 10:
+        logStep = int(ws[0])
+
+    if len(ws) == 4:
+        type = float(ws[3])
+
+        if not (type == 3 and not include_boundary):
+            points.append([float(ws[0]), float(ws[1]), float(ws[2])])
+            types.append(type)
+
+    if logStep is not None: 
+        pcount+=1
+        
+        if pcount==numOfBoundaryP+numOfElasticP+numOfLiquidP:
+            print('End of one batch of %i added, %i total points at line %i, time: %i'%(len(points),pcount, line_count, time_count))
+            all_points.append(points)
+            all_point_types.append(types)
+
+            points = []
+            types=[]
+            pcount = 0
+            numOfBoundaryP=0
+
+            time_count+=1
+
+    line_count += 1
+
+#all_points_np = np.array(all_points)
+
+print(f"Loaded positions with %i elastic, %i liquid and %i boundary points (%i total), %i lines"%(numOfElasticP,numOfLiquidP, numOfBoundaryP,numOfElasticP+numOfLiquidP+numOfBoundaryP, line_count))
+print("Num of time points found: %i"%len(all_points))
+
+pl = pv.Plotter(window_size=[800,600])
+pl.set_background("lightgrey")
+
+pl.camera.position = (300, 100, -100.0)
+pl.camera.focal_point = (50,0,100)
+pl.camera.up = (0.0, 1.0, 0.0)
+#pl.add_axes_at_origin(labels_off=False)
+#pl.add_mesh(pv.Cube(center=(50,0,50)))
+
+last_mesh = None
+
+def create_mesh(step):
+    
+    step_count = step
+    value=step_count
+    global last_mesh
+    index = int(value)
+
+    print('Changing to time point: %s (%s) '%(index,value))
+    curr_points = all_points[index]
+    curr_types = all_point_types[index]
+    if last_mesh is None:
+
+        print('Adding mesh...')
+        last_mesh = pv.PolyData(curr_points)
+        last_mesh["types"] = curr_types
+        print(last_mesh)
+        mesh2 = pv.Cube(center=(0,0,0))
+        pl.add_mesh(mesh2)
+
+        last_actor = pl.add_mesh(
+            last_mesh,
+            render_points_as_spheres=True,
+            cmap=[c for c in colours.values()],
+            point_size=3,
+        )
+    else:
+
+        print('Updating mesh...')
+        last_mesh.points = curr_points
+
+    #pl.render()
+
+    time.sleep(0.1)
+    
+    return
+    
+create_mesh(0)
+
+max_time = len(all_points)-1
+#pl.add_slider_widget(create_mesh, rng=[0,max_time], value=max_time, title='Time point')
+#pl.add_timer_event(   max_steps=len(all_points), duration=200, callback=create_mesh)
+
+print('Ready...')
+
+from stpyvista import stpyvista as spv
+## Send to streamlit
+spv(pl, key="pv_cube2")
+

build.sh

@@ -0,0 +1,10 @@
+# Set the platform flag if we're on ARM
+arch=$(uname -m)
+if [[ "$arch" == "arm64" || "$arch" == "aarch64" ]]; then
+    platform_flag="--platform linux/amd64"
+else
+    platform_flag=""
+fi
+
+docker build $platform_flag -t testdox -f Dockerfile .
+

load.py

@@ -0,0 +1,127 @@
+import pyvista as pv
+
+import sys
+import numpy as np
+
+import time
+
+points = []
+
+types = []
+
+file = "pressure_buffer.txt"
+file = "position_buffer.txt"
+if len(sys.argv) == 2:
+    file = sys.argv[1]
+
+colours = {1.1: "lightblue", 2.1: "green", 2.2: "turquoise", 3: "#eeeeee"}
+colours = {1.1: "blue", 2.2: "turquoise"}
+
+line_count = 0
+pcount = 0
+
+all_points = []
+all_point_types = []
+
+time_count = 0
+
+logStep = None
+
+include_boundary = False
+
+for l in open(file):
+    ws = l.split()
+    #print(ws)
+    if line_count == 6:
+        numOfElasticP = int(ws[0])
+    if line_count == 7:
+        numOfLiquidP = int(ws[0])
+    if line_count == 8:
+        numOfBoundaryP = int(ws[0])
+    if line_count == 9:
+        timeStep = float(ws[0])
+    if line_count == 10:
+        logStep = int(ws[0])
+
+    if len(ws) == 4:
+        type = float(ws[3])
+
+        if not (type == 3 and not include_boundary):
+            points.append([float(ws[0]), float(ws[1]), float(ws[2])])
+            types.append(type)
+
+    if logStep is not None: 
+        pcount+=1
+        
+        if pcount==numOfBoundaryP+numOfElasticP+numOfLiquidP:
+            print('End of one batch of %i added, %i total points at line %i, time: %i'%(len(points),pcount, line_count, time_count))
+            all_points.append(points)
+            all_point_types.append(types)
+
+            points = []
+            types=[]
+            pcount = 0
+            numOfBoundaryP=0
+
+            time_count+=1
+
+        
+    line_count += 1
+
+#all_points_np = np.array(all_points)
+
+print(f"Loaded positions with %i elastic, %i liquid and %i boundary points (%i total), %i lines"%(numOfElasticP,numOfLiquidP, numOfBoundaryP,numOfElasticP+numOfLiquidP+numOfBoundaryP, line_count))
+
+print("Num of time points found: %i"%len(all_points))
+
+pl = pv.Plotter()
+pl.set_background("lightgrey")
+
+pl.camera.position = (300, 100, -100.0)
+pl.camera.focal_point = (50,0,100)
+pl.camera.up = (0.0, 1.0, 0.0)
+#pl.add_axes_at_origin(labels_off=False)
+#pl.add_mesh(pv.Cube(center=(50,0,50)))
+
+last_mesh = None
+
+
+def create_mesh(step):
+    step_count = step
+    value=step_count
+    global last_mesh
+    index = int(value)
+
+        
+    print('Changing to time point: %s (%s) '%(index,value))
+    curr_points = all_points[index]
+    curr_types = all_point_types[index]
+    if last_mesh is None:
+
+        last_mesh = pv.PolyData(curr_points)
+        last_mesh["types"] = curr_types
+        print(last_mesh)
+
+        last_actor = pl.add_mesh(
+            last_mesh,
+            render_points_as_spheres=True,
+            cmap=[c for c in colours.values()],
+            point_size=3,
+        )
+    else:
+        last_mesh.points = curr_points
+
+    pl.render()
+
+    time.sleep(0.01)
+    
+    return
+    
+create_mesh(0)
+
+max_time = len(all_points)-1
+pl.add_slider_widget(create_mesh, rng=[0,max_time], value=max_time, title='Time point')
+pl.add_timer_event(   max_steps=len(all_points), duration=200, callback=create_mesh)
+
+pl.show()
+

packages.txt

@@ -0,0 +1,3 @@
+procps
+libgl1-mesa-glx
+xvfb

rebuild.sh

@@ -0,0 +1,2 @@
+docker build --platform linux/amd64 -t testdox -f Dockerfile  --no-cache .
+

requirements.txt

@@ -0,0 +1,4 @@
+streamlit
+pyneuroml
+pyvista
+stpyvista

run.sh

@@ -0,0 +1,9 @@
+# Set the platform flag if we're on ARM
+arch=$(uname -m)
+if [[ "$arch" == "arm64" || "$arch" == "aarch64" ]]; then
+    platform_flag="--platform linux/amd64"
+else
+    platform_flag=""
+fi
+
+docker run -it -p 8501:8501 $platform_flag  testdox