Pushing up mods

code/FiberCpp/global_definitions.h

@@ -8,9 +8,9 @@
 
 #define MAX_NO_OF_HALF_SARCOMERES 500
 
-#define MAX_NO_OF_THICK_FILAMENTS 200
+#define MAX_NO_OF_THICK_FILAMENTS 10000
 
-#define MAX_NO_OF_THIN_FILAMENTS 400
+#define MAX_NO_OF_THIN_FILAMENTS 20000
 
 #define MAX_NO_OF_KINETIC_STATES 10
 

code/FiberPy/FiberPy/package/modules/batch/batch.py

@@ -98,7 +98,7 @@ def run_batch(json_batch_file_string=[],
         while threads or my_list:
             if (len(threads) < num_processes) and my_list:
                 t = threading.Thread(target=worker, args=[my_list.pop()])
-                t.setDaemon(True)
+                t.daemon = True
                 t.start()
                 threads.append(t)
             else:

code/FiberPy/FiberPy/package/modules/characterize/characterize_model.py

@@ -127,9 +127,8 @@ def generate_model_files(json_analysis_file_string):
         orig_options_file = os.path.join(temp_dir,
                                          model_struct['options_file'])
         new_options_file = os.path.join(generated_dir, model_struct['options_file'])
-    elif (model_struct['relative_to'] == 'false'):
+    elif (model_struct['relative_to'] == 'False'):
         orig_options_file = model_struct['options_file']
-
         temp, file_name = os.path.split(orig_options_file)
         new_options_file = os.path.join(generated_dir, file_name)
     else:
@@ -1965,4 +1964,12 @@ def characterize_fv_with_pCa_and_isometric_force(json_analysis_file_string,
 
     # Now run the isotonic batch
     batch.run_batch(isotonic_batch_file, figures_only=figures_only)
-
+
+def return_base_dir(struct, file_string):
+    base_dir = ''
+    if ('relative_to' in struct):
+        if (struct['relative_to'] == 'this_file'):
+            base_dir = str(Path(file_string).parent.absolute().resolve())
+        elif not (struct['relative_to'] == 'False'):
+            base_dir = struct['relative_to']
+    return base_dir

code/FiberPy/FiberPy/package/modules/visualization/generate2.py

@@ -26,7 +26,10 @@ def run_render_batch():
         last argument is render_job_file """
 
     # Unpack the arguments
-    render_job_file = sys.argv[-1]
+    for (i,a) in enumerate(sys.argv):
+        print('%i  %s' % (i,sys.argv[i]))
+
+    render_job_file = sys.argv[5]
 
     # Open the render file and pull off the job
     with open(render_job_file, 'r') as f:
@@ -72,7 +75,7 @@ def run_render_job(frame_data, template_data, options_data):
     hs_blend = hs_b.hs_blender(h, frame_data, template_data, options_data,
                                output_image_file)
 
-    bpy.ops.wm.quit_blender()
+    # bpy.ops.wm.quit_blender()
 
     return
 

code/FiberPy/FiberPy/package/modules/visualization/half_sarcomere.py

@@ -25,7 +25,6 @@ def __init__(self, json_file_string):
            hs_data = json_data['hs_data']
            self.t_attach_a_node = json_data['titin']['t_attach_a_node']
            self.t_attach_m_node = json_data['titin']['t_attach_m_node']
-           self.t_slack_length = json_data['titin']['t_slack_length']
            self.t_k_stiff = json_data['titin']['t_k_stiff']
            self.cb_extensions = hs_data['cb_extensions']
            self.hs_id = hs_data['hs_id']

code/FiberPy/FiberPy/package/modules/visualization/hs_blender.py

@@ -55,24 +55,26 @@ def __init__(self, hs, frame, template, options, output_image_file):
 
         # Create thick filaments
         for i, thick_fil in enumerate(self.hs.thick_fil):
-            self.create_thick_filament(i)
+            if (thick_fil.m_y < 3):
+                self.create_thick_filament(i)
 
         # Create thin filaments
         for i, thin_fil in enumerate(self.hs.thin_fil):
-            self.create_thin_filament(i)
+            if (thin_fil.a_y < 2):
+                self.create_thin_filament(i)
 
-        # Set nearest thin filaments
-        # by adding an array into the hs.thick_fil structure
-        self.set_nearest_thin_filaments()
+        # # Set nearest thin filaments
+        # # by adding an array into the hs.thick_fil structure
+        # self.set_nearest_thin_filaments()
 
-        # # # Draws titin filaments
-        self.create_titin_filaments()
+        # # # # Draws titin filaments
+        # self.create_titin_filaments()
 
-        # Create cross-bridges
-        self.create_cross_bridges()
+        # # Create cross-bridges
+        # self.create_cross_bridges()
 
-        # Create mybpc
-        self.create_mybpcs()
+        # # Create mybpc
+        # self.create_mybpcs()
 
         # Hide the primitives
         for p in self.hs_b['primitives']:
@@ -142,6 +144,11 @@ def create_camera(self):
             location=loc,
             rotation=rot)
         bpy.context.object.data.lens = 20
+
+        if ('orthographic' in self.frame['camera']):
+            bpy.context.object.data.type = 'ORTHO'
+            bpy.context.object.data.ortho_scale = self.frame['camera']['orthographic']['ortho_scale']
+            bpy.context.object.data.clip_end = self.options['max_render_distance']
 
         bpy.context.scene.camera = bpy.context.object
 
@@ -153,6 +160,12 @@ def render_screenshot(self):
         """Renders a screen capture of the current geometry."""
 
         bpy.context.scene.render.filepath = self.output_image_file
+
+        print(self.options)
+
+        bpy.context.scene.render.resolution_x = self.options['image_pixels'][0]
+        bpy.context.scene.render.resolution_y = self.options['image_pixels'][1]
+
         bpy.context.scene.frame_set(1)
         bpy.ops.render.render(write_still=True)
         return
@@ -257,6 +270,38 @@ def create_thin_filament(self, thin_id):
         cam_loc = np.asarray([self.frame['camera']['location']['x'],
                               self.frame['camera']['location']['y'],
                               self.frame['camera']['location']['z']])
+
+        # Branch on mode
+        if (self.frame['style'] == 'x_ray'):
+
+            thin_f = self.hs.thin_fil[thin_id]
+            bs_indices = np.arange(0, thin_f.a_no_of_bs)
+
+            for bs_i in bs_indices:
+
+                bs_angle = thin_f.bs_angle[bs_i]
+
+                sph = self.hs_b['primitives']['bs_sphere'].copy()
+                sph.name = ('a_bs_sp_%i_%i' % (thin_id, bs_i))
+
+                bot_x = thin_f.bs_x[bs_i]
+                bot_y = self.yz_scaling * thin_f.a_y + \
+                    self.template['thin_filament']['node']['radius'] * \
+                        np.sin(np.pi * bs_angle / 180.0)
+                bot_z = self.yz_scaling * thin_f.a_z + \
+                    self.template['thin_filament']['node']['radius'] * \
+                        np.cos(np.pi * bs_angle / 180.0)
+
+                # Check distance
+                h = np.linalg.norm(cam_loc - np.asarray([bot_x, bot_y, bot_z]))
+                if (h > self.options['max_render_distance']):
+                    continue
+
+                sph.location=(bot_x, bot_y, bot_z)
+
+                bpy.context.collection.objects.link(sph)
+
+            return
 
         # Set the thin file
         thin_f = self.hs.thin_fil[thin_id]
@@ -1372,6 +1417,22 @@ def create_bs_primitives(self):
             mesh.materials.append(mat)
 
             self.hs_b['primitives'][m_name] = m
+
+        # Create bs_sphere
+        bpy.ops.mesh.primitive_ico_sphere_add(
+            radius = self.template['thin_filament']['sphere']['radius'],
+            enter_editmode=False,
+            subdivisions=4,
+            location=(0,0,0))
+
+        m = bpy.context.object
+        mesh = m.data
+        m_name = 'bs_sphere'
+        mat = bpy.data.materials.new(name=m_name)
+        mat.diffuse_color = self.template['thin_filament']['sphere']['color']
+        mesh.materials.append(mat)
+
+        self.hs_b['primitives']['bs_sphere'] = m
 
     def return_all_filament_y_coords(self):
         """Returns a list of all filament y coordinates"""

code/FiberPy/FiberPy/package/modules/visualization/render.py

@@ -100,7 +100,7 @@ def generate_images(render_batch_file):
             threads.append(t)
         else:
             for thread in threads:
-                if not thread.isAlive():
+                if not thread.is_alive():
                     threads.remove(thread)
 
     return
@@ -126,7 +126,7 @@ def worker(render_file):
         blender_exe_path = options_data['blender_exe_path']
 
         # Generate the command string
-        command_string = ('cd "%s"\n ' % blender_exe_path)
+        command_string = ('c: & cd "%s" & ' % blender_exe_path)
 
         # Deduce the path to this folder
         parent_path = Path(__file__).parent
@@ -142,10 +142,14 @@ def worker(render_file):
 
         # Complete the commmand line
         command_string = command_string + \
-              ('blender -noaudio %s --python "%s" -- -j "%s"' %
-                  (background_string,
-                   generate_path,
-                   os.path.abspath(render_file)))
+              ('blender --python "%s" -- -j "%s" -noaudio %s ' %
+                  (generate_path,
+                   os.path.abspath(render_file),
+                   background_string))
+
+        print('\nCommand string:')
+        print(command_string)
+        print('')
 
         # Write command to temp.bat
         bat_file_string = 'run_job_%i.bat' % render_job['job_number']
@@ -158,7 +162,7 @@ def worker(render_file):
         subprocess.call(bat_file_string)
         time.sleep(1)
         try:
-            os.remove(bat_file_string)
+            # os.remove(bat_file_string)
             print('deleted %s' % bat_file_string)
         except:
             print('No file to delete')

demo_files/myofibrils/sequential_hs/Python_code/multiple_hs_summary.py

@@ -47,13 +47,15 @@ def summary_figure():
     no_of_conditions = no_of_conditions - 1
 
     # Now we can make a figure with one column per condition
-    no_of_rows = 4
+    no_of_rows = 7
     no_of_cols = no_of_conditions
 
     pCa_row = 1
     hs_force_row = 2
     hs_titin_row = 3
     hs_length_row = 4
+    m_pop_row = 5
+    delta_hs_length_row = 6
 
     fig = plt.figure(constrained_layout = False)
     spec = gridspec.GridSpec(nrows = no_of_rows,
@@ -135,14 +137,48 @@ def summary_figure():
             # hs_length
             plot_index = ((hs_length_row-1) * no_of_cols) + i
             for j in range(no_of_hs):
-                col_string = 'hs_%i_length' % (j+1);
+                col_string = 'hs_%i_length' % (j+1)
                 ax[plot_index].plot(d['time'], d[col_string], '-',
                                     color=cmap(cmap_values[j]))
                 if (d[col_string].max() > max_hsl):
                     max_hsl = d[col_string].max()
                 if (d[col_string].max() < min_hsl):
                     min_hsl = d[col_string].min()
-
+
+            # m_pops
+            plot_index = ((m_pop_row-1) * no_of_cols) + i
+            for j in range(no_of_hs):
+                col_string = 'hs_%i_m_pop_1' % (j+1);
+                ax[plot_index].plot(d['time'], d[col_string], '-',
+                                    color=cmap(cmap_values[j]),
+                                    label = 'hs_%i' % (j+1))
+
+            # delta_hs_length_row
+            plot_index = ((delta_hs_length_row-1) * no_of_cols) + i
+            bp = []
+            for j in range(no_of_hs):
+                col_string = 'hs_%i_length' % (j+1)
+                d_hsl_dt = d[col_string].diff()
+                vi = d_hsl_dt.idxmax()
+                ax[plot_index].plot(d['time'], d[col_string].diff(), '-',
+                                    color=cmap(cmap_values[j]),
+                                    label = 'hs_%i' % (j+1))
+                ax[plot_index].plot(d['time'].loc[vi], d_hsl_dt.loc[vi], 'o',
+                                    color=cmap(cmap_values[j]),
+                                    markerfacecolor='none')
+                bp.append(vi)
+
+            # Plot break_points
+            print(bp)
+            bp = np.asarray(bp)
+
+            plot_index = plot_index + no_of_cols
+            for j in range(no_of_hs):
+                print(j)
+                ax[plot_index].plot(j, bp[j],'o',
+                                    color=cmap(cmap_values[j]),
+                                    markerfacecolor='none')
+
     # Apply limits
     for i in range(no_of_conditions):
 
@@ -161,6 +197,20 @@ def summary_figure():
         # HSL
         plot_index = ((hs_length_row - 1) * no_of_cols) + i
         ax[plot_index].set_ylim([min_hsl - 50, max_hsl + 50])
+
+    for i in range(no_of_cols):
+        for j in range(no_of_rows-1):
+            plot_index = j*no_of_cols + i
+            ax[plot_index].set_xlim([0.9, 1.5])
+
+
+    # # Add legend
+    # for i in range(no_of_conditions):
+
+    #     # pCa
+    #     plot_index = ((m_pop_row - 1) * no_of_cols) + i
+    #     ax[plot_index].legend(loc='upper left',
+    #                           bbox_to_anchor=(1.05, 1))
 
 
     ofs = os.path.join(top_data_folder, 'summary.png')
@@ -233,5 +283,5 @@ def superpose_traces():
 if __name__ == "__main__":
     summary_figure()
 
-    superpose_traces()
+    #superpose_traces()