bmtool 0.3.7__tar.gz → 0.3.9__tar.gz

{bmtool-0.3.7 → bmtool-0.3.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bmtool
-Version: 0.3.7
+Version: 0.3.9
 Summary: BMTool
 Home-page: https://github.com/tjbanks/bmtool
 Download-URL: 
@@ -342,6 +342,34 @@ This will plot cells in the `hippocampus` network, using the `pop_name` as the c
 
 All  `point_process` cell types will be ignored since they do not have physical locations.
 
+### Plot 3d cell location and rotation
+Plot the location and rotation of your cells. Plot all of your cells with a single command
+```
+bmtool plot cell rotation
+```
+![bmtool](./figures/rotation3d_1.png "3d Rotation Figure")
+
+Customize your plot by limiting the cells you want or selecting a max number of cells to plot.
+```
+bmtool plot --config simulation_configECP.json cell rotation --group-by pop_name --group CR --max-cells 100 --quiver-length 100 --arrow-length-ratio 0.25
+```
+![bmtool](./figures/rotation3d_2.png "3d Rotation Figure")
+
+Code
+```
+from bmtool import
+from bmtool import bmplot
+
+bmplot.cell_rotation_3d(config=config,
+                     populations=populations,
+                     group_by=group_by,
+                     group=group,
+                     title=title,
+                     max_cells=max_cells,
+                     quiver_length=quiver_length,
+                     arrow_length_ratio=arrow_length_ratio)
+```
+
 ### Plotting Current Clamp and Spike Train Info
 To plot all current clamp info involved in a simulation, use the following command (uses 'simulation_config.json' as default)
 ```

{bmtool-0.3.7 → bmtool-0.3.9}/README.md

@@ -321,6 +321,34 @@ This will plot cells in the `hippocampus` network, using the `pop_name` as the c
 
 All  `point_process` cell types will be ignored since they do not have physical locations.
 
+### Plot 3d cell location and rotation
+Plot the location and rotation of your cells. Plot all of your cells with a single command
+```
+bmtool plot cell rotation
+```
+![bmtool](./figures/rotation3d_1.png "3d Rotation Figure")
+
+Customize your plot by limiting the cells you want or selecting a max number of cells to plot.
+```
+bmtool plot --config simulation_configECP.json cell rotation --group-by pop_name --group CR --max-cells 100 --quiver-length 100 --arrow-length-ratio 0.25
+```
+![bmtool](./figures/rotation3d_2.png "3d Rotation Figure")
+
+Code
+```
+from bmtool import
+from bmtool import bmplot
+
+bmplot.cell_rotation_3d(config=config,
+                     populations=populations,
+                     group_by=group_by,
+                     group=group,
+                     title=title,
+                     max_cells=max_cells,
+                     quiver_length=quiver_length,
+                     arrow_length_ratio=arrow_length_ratio)
+```
+
 ### Plotting Current Clamp and Spike Train Info
 To plot all current clamp info involved in a simulation, use the following command (uses 'simulation_config.json' as default)
 ```

{bmtool-0.3.7 → bmtool-0.3.9}/bmtool/bmplot.py

@@ -409,12 +409,13 @@ def cell_rotation_3d(**kwargs):
     populations_list = kwargs["populations"]
     config = kwargs["config"]
     group_keys = kwargs["group_by"]
-    title = kwargs["title"]
+    title = kwargs.get("title")
     save_file = kwargs["save_file"]
     quiver_length = kwargs["quiver_length"]
     arrow_length_ratio = kwargs["arrow_length_ratio"]
     group = kwargs["group"]
-    max_cells = kwargs["max_cells"]
+    max_cells = kwargs.get("max_cells",999999999)
+    init_vector = kwargs.get("init_vector","1,0,0")
 
     nodes = util.load_nodes_from_config(config)
 
@@ -480,8 +481,19 @@ def cell_rotation_3d(**kwargs):
             #Convert to arrow direction
             from scipy.spatial.transform import Rotation as R
             uvw = pd.DataFrame([U,V,W]).T
-            rots = R.from_euler('zyx', uvw).as_rotvec().T
+            init_vector = init_vector.split(',')
+            init_vector = np.repeat([init_vector],len(X),axis=0)
+            
+            # To get the final cell orientation after rotation, 
+            # you need to use function Rotaion.apply(init_vec), 
+            # where init_vec is a vector of the initial orientation of a cell
+            #rots = R.from_euler('xyz', uvw).apply(init_vector.astype(float))
+            #rots = R.from_euler('xyz', pd.DataFrame([rots[:,0],rots[:,1],rots[:,2]]).T).as_rotvec().T
+
+            rots = R.from_euler('zyx', uvw).apply(init_vector.astype(float)).T
             h = ax.quiver(X, Y, Z, rots[0],rots[1],rots[2],color=color,label=group_name, arrow_length_ratio = arrow_length_ratio, length=quiver_length)
+
+            #h = ax.quiver(X, Y, Z, rots[0],rots[1],rots[2],color=color,label=group_name, arrow_length_ratio = arrow_length_ratio, length=quiver_length)
             ax.scatter(X,Y,Z,color=color,label=group_name)
             handles.append(h)
     if not handles:

{bmtool-0.3.7 → bmtool-0.3.9}/bmtool/plot_commands.py

@@ -136,15 +136,17 @@ def cell(ctx,title,save_file):
 @click.option('--max-cells', type=click.INT, default=999999999, help="max number of cells to display [default: 999999999]")
 @click.option('--quiver-length', type=click.FLOAT, default=10, help="how long the arrows should be [default: 10]")
 @click.option('--arrow-length-ratio', type=click.FLOAT, default=0.2, help="ratio for the arrow of the quiver [default: 0.2]")
+@click.option('--init-vector', type=click.STRING, default="1,0,0", help="comma delimited initial rotation vector specified by pt3dadd [default: 0,0,1]")
 @click.pass_context
-def rotation_3d(ctx,populations,group_by,group,max_cells,quiver_length,arrow_length_ratio):
+def rotation_3d(ctx,populations,group_by,group,max_cells,quiver_length,arrow_length_ratio,init_vector):
     cell_rotation_3d(config=ctx.obj['config'],**ctx.obj['cell'],
                      populations=populations,
                      group_by=group_by,
                      group=group,
                      max_cells=max_cells,
                      quiver_length=quiver_length,
-                     arrow_length_ratio=arrow_length_ratio)
+                     arrow_length_ratio=arrow_length_ratio,
+                     init_vector=init_vector)
     if ctx.obj['display']:
         plt.show()
 

{bmtool-0.3.7 → bmtool-0.3.9}/bmtool.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bmtool
-Version: 0.3.7
+Version: 0.3.9
 Summary: BMTool
 Home-page: https://github.com/tjbanks/bmtool
 Download-URL: 
@@ -342,6 +342,34 @@ This will plot cells in the `hippocampus` network, using the `pop_name` as the c
 
 All  `point_process` cell types will be ignored since they do not have physical locations.
 
+### Plot 3d cell location and rotation
+Plot the location and rotation of your cells. Plot all of your cells with a single command
+```
+bmtool plot cell rotation
+```
+![bmtool](./figures/rotation3d_1.png "3d Rotation Figure")
+
+Customize your plot by limiting the cells you want or selecting a max number of cells to plot.
+```
+bmtool plot --config simulation_configECP.json cell rotation --group-by pop_name --group CR --max-cells 100 --quiver-length 100 --arrow-length-ratio 0.25
+```
+![bmtool](./figures/rotation3d_2.png "3d Rotation Figure")
+
+Code
+```
+from bmtool import
+from bmtool import bmplot
+
+bmplot.cell_rotation_3d(config=config,
+                     populations=populations,
+                     group_by=group_by,
+                     group=group,
+                     title=title,
+                     max_cells=max_cells,
+                     quiver_length=quiver_length,
+                     arrow_length_ratio=arrow_length_ratio)
+```
+
 ### Plotting Current Clamp and Spike Train Info
 To plot all current clamp info involved in a simulation, use the following command (uses 'simulation_config.json' as default)
 ```

{bmtool-0.3.7 → bmtool-0.3.9}/setup.py

@@ -6,7 +6,7 @@ with open("README.md", "r") as fh:
 
 setup(
     name="bmtool",
-    version="0.3.7",
+    version="0.3.9",
     author="Tyler Banks",
     author_email="tbanks@mail.missouri.edu",
     description="BMTool",