Changes:

 - Fixed simulation failing to start when intervals statistics and snapshots are empty.
 - Fixed statistics and snapshot intervals not being saved into the session file.
 - The units for intervals are now in seconds and can be input in scientific from, i.e. '1e-5'.
 - Minor refactoring of file viewers

README.rst

@@ -46,7 +46,7 @@ By using the same input data, it is possible to inspect electron scattering prof
 
 Installation
 ---------------
-The simulation requires Python 3.7 or later.
+The simulation requires Python 3.9 or later.
 
 Package is available via PyPi: :code:`pip install febid`
 

febid/__main__.py

@@ -48,7 +48,7 @@ def welcome():
     print(intro)
     command_functions = {
         'show_file': febid.show_file.show_structure,
-        'show_animation': febid.show_animation.show_animation,
+        'show_animation': febid.show_animation.render_animation,
         'gui': start_ui,
         'no_gui': Starter().start
     }

febid/libraries/vtk_rendering/show_animation_new.py

@@ -3,16 +3,17 @@
 """
 import os, time
 import sys
+import numpy as np
+import pyvista as pv
+import vtk
 from datetime import datetime
 from PyQt5.QtWidgets import QApplication
 from PyQt5.QtWidgets import QFileDialog as fd
 
-import numpy as np
-import vtk
-
-import febid.libraries.vtk_rendering.VTK_Rendering as vr
+from febid.libraries.vtk_rendering.VTK_Rendering import Render, read_field_data
 from febid.Structure import Structure
 
+
 def ask_directory():
     os.chdir('../../..')
     init_dir = os.getcwd()
@@ -21,6 +22,7 @@ def ask_directory():
     app.quit()
     return directory
 
+
 def open_file(directory=''):
     """
     Gather files and timestamps sorted in the order of creation
@@ -35,7 +37,7 @@ def open_file(directory=''):
     # directory = '/Users/sandrik1742/Documents/PycharmProjects/FEBID/code/Experiment runs/gr=0'
     files = sorted(os.listdir(directory))[:]
     n = 0
-    for i in range(len(files)-1, -1, -1):
+    for i in range(len(files) - 1, -1, -1):
         if os.path.splitext(files[i])[1] != '.vtk':
             files.pop(i)
             n += 1
@@ -51,13 +53,17 @@ def open_file(directory=''):
 
     return files, times
 
+
 def show_animation(directory=None, **kwargs):
     if not directory:
         directory = ask_directory()
+    if not directory:
+        return
     result = show_animation(directory, **kwargs)
     return result
 
-def show_animation(directory, show='precursor'):
+
+def render_animation(directory, show='precursor'):
     """
     Show animated process from series of vtk files.
     Files must have consequent creation dates to align correctly
@@ -77,14 +83,14 @@ def show_animation(directory, show='precursor'):
 
     # Getting data for initialization
     structure = Structure()
-    vtk_obj = vr.pv.read(os.path.join(directory, files[0]))
+    vtk_obj = pv.read(os.path.join(directory, files[0]))
     structure.load_from_vtk(vtk_obj)
     cell_size, deposit, precursor, surface_bool, semi_surface_bool, ghosts_bool = structure.cell_size, \
-                                                                                 structure.deposit, \
-                                                                                 structure.precursor, \
-                                                                                 structure.surface_bool, \
-                                                                                 structure.semi_surface_bool, \
-                                                                                 structure.ghosts_bool
+        structure.deposit, \
+        structure.precursor, \
+        structure.surface_bool, \
+        structure.semi_surface_bool, \
+        structure.ghosts_bool
     # Determining rendered dataset
     if show not in ['precursor', 'deposit', 'temperature']:
         raise RuntimeError(f'The specified dataset \'{show}\' is not supported.')
@@ -102,7 +108,7 @@ def show_animation(directory, show='precursor'):
         mask_name = 'deposit'
     data = structure.__getattribute__(show)
     mask = structure.__getattribute__(mask_name)
-    t, sim_time, beam_position = vr.read_field_data(vtk_obj) # getting deposition process features
+    t, sim_time, beam_position = read_field_data(vtk_obj)  # getting deposition process features
     # Preparing left corner text with times
     text = ''
     if t:
@@ -111,12 +117,12 @@ def show_animation(directory, show='precursor'):
         text += f'Simulation time: {sim_time:.7f} s \n'
 
     # Setting the setup scene
-    render = vr.Render(cell_size)
+    render = Render(cell_size)
     render.add_3Darray(data)
     render.p.add_text('Adjust the scene for the animation \n and close the window.', position='upper_edge')
     cam_pos = render.show()
     # Setting the first frame
-    render = vr.Render(cell_size)
+    render = Render(cell_size)
     # Creating an arrow at beam position
     if beam_position is not None:
         x_pos, y_pos = beam_position
@@ -134,7 +140,7 @@ def show_animation(directory, show='precursor'):
     render.p.mesh.cell_data[vtk.vtkDataSetAttributes.GhostArrayName()] = index.ravel()
     render.p.mesh.set_active_scalars(data_name)
     # Adding text
-    t, sim_time, beam_position = vr.read_field_data(vtk_obj)
+    t, sim_time, beam_position = read_field_data(vtk_obj)
     text = ''
     if t:
         text += f'Time: {t} \n'
@@ -148,14 +154,14 @@ def show_animation(directory, show='precursor'):
     render.p.add_text(text, position='upper_left', font_size=font_size, name='time')
     render.p.add_text(stats, font_size=font_size, position='upper_right', name='stats')
     render.show(interactive_update=True, cam_pos=cam_pos)
-    init_layer = np.count_nonzero(deposit==-2) # substrate layer
-    total_dep_cells = [np.count_nonzero(deposit[deposit<0])-init_layer] # total number of fully deposited cells
-    growth_rate=[] # growth rate on each step
+    init_layer = np.count_nonzero(deposit == -2)  # substrate layer
+    total_dep_cells = [np.count_nonzero(deposit[deposit < 0]) - init_layer]  # total number of fully deposited cells
+    growth_rate = []  # growth rate on each step
 
     # Animation
     for i in range(1, len(files)):
         # Reading data
-        vtk_obj = vr.pv.read(os.path.join(directory, files[i]))
+        vtk_obj = pv.read(os.path.join(directory, files[i]))
         # Loading the structure
         structure.load_from_vtk(vtk_obj)
         cell_size = structure.cell_size
@@ -167,14 +173,14 @@ def show_animation(directory, show='precursor'):
         if show == 'deposit':
             mask = surface_bool
         if show == 'temperature':
-            mask = deposit<0
+            mask = deposit < 0
         # Calculating deposition process features
         total_dep_cells.append(np.count_nonzero(deposit[deposit < 0]) - init_layer)
         volume = int((total_dep_cells[i] + deposit[surface_bool].sum()) * cell_size ** 3)
         delta_t = (times[i] - times[i - 1]).total_seconds()
         if delta_t < 1: delta_t = 1
         growth_rate.append(cell_size ** 3 * (total_dep_cells[i] - total_dep_cells[i - 1]) / delta_t * 60 * 60)
-        t, sim_time, beam_position = vr.read_field_data(vtk_obj)
+        t, sim_time, beam_position = read_field_data(vtk_obj)
         # Setting up text
         # Left corner
         text = ''
@@ -186,17 +192,17 @@ def show_animation(directory, show='precursor'):
         stats = f'Cells: {total_dep_cells[i]} \n\
                 Height: {int(np.nonzero(deposit)[0].max() * cell_size)} nm \n\
                 Volume: {volume} nm^3 \n\
-                Frame {i+1}/{len(files)}'
+                Frame {i + 1}/{len(files)}'
         # Updating arrow position
         if beam_position is not None:
             x_pos, y_pos = beam_position
             x, y = int(x_pos / render.cell_size), int(y_pos / render.cell_size)
             max_z = structure.deposit[:, y, x].nonzero()[0].max()
             render.arrow.SetPosition(x_pos, y_pos, max_z * render.cell_size + 30)  # relative to the initial position
         # Redrawing the 3D object if necessary
-        if render.p.mesh.n_cells != data.size: # must redraw if shape changes
+        if render.p.mesh.n_cells != data.size:  # must redraw if shape changes
             data_visibility = render.p.renderer.actors[data_name].GetVisibility()
-            render.p.remove_actor(data_name+'_caption')
+            render.p.remove_actor(data_name + '_caption')
             render.y_pos = 5
             render.p.button_widgets.clear()
             render.p.remove_actor(data_name)
@@ -207,7 +213,7 @@ def show_animation(directory, show='precursor'):
             render.p.mesh.cell_data[vtk.vtkDataSetAttributes.GhostArrayName()] = index.ravel()
             render.p.mesh.set_active_scalars(data_name)
         else:
-            render.p.mesh[data_name] = data.ravel() # new data, ravel() sends a view
+            render.p.mesh[data_name] = data.ravel()  # new data, ravel() sends a view
         # Updating hidden cells
         index[mask == 0] = vtk.vtkDataSetAttributes.HIDDENCELL
         index[mask == 1] = 0  # surface_bool is not bool type and cannot be used directly as index
@@ -216,19 +222,20 @@ def show_animation(directory, show='precursor'):
         render.p.actors['stats'].SetText(3, stats)
 
         # render.p.mesh.cell_data[vtk.vtkDataSetAttributes.GhostArrayName()] = index.ravel()
-        p=data[mask]
+        p = data[mask]
         # Updating the scalar bar
         try:
-            render.p.update_scalar_bar_range([np.partition(p[p!=p.min()], 4)[2], p.max()])
-        except: pass
+            render.p.update_scalar_bar_range([np.partition(p[p != p.min()], 4)[2], p.max()])
+        except:
+            pass
         render.update()
-    else: # finishing with a static scene
+    else:  # finishing with a static scene
         # Clearing the scene
         render.y_pos = 5
         render.p.button_widgets.clear()
         render.p.clear()
         # Reading data
-        vtk_obj = vr.pv.read(os.path.join(directory, files[-1]))
+        vtk_obj = pv.read(os.path.join(directory, files[-1]))
         # Loading the structure
         structure.load_from_vtk(vtk_obj)
         cell_size = structure.cell_size
@@ -241,18 +248,18 @@ def show_animation(directory, show='precursor'):
         render.p.update_scalar_bar_range([np.partition(p[p != p.min()], 4)[2], p.max()])
         render.p.mesh.cell_data[vtk.vtkDataSetAttributes.GhostArrayName()] = index.ravel()
         render.p.mesh.set_active_scalars(data_name)
-        t, sim_time, beam_position = vr.read_field_data(vtk_obj)
+        t, sim_time, beam_position = read_field_data(vtk_obj)
         text = ''
         if t:
             text += f'Time: {t} \n'
         if sim_time:
             text += f'Simulation time: {sim_time:.7f} s \n'
         render.p.add_text(text, position='upper_left', font_size=font_size)  # showing time passed
-        render.p.add_text(f'Cells: {total_dep_cells[i-1]} \n'  # showing total number of deposited cells
+        render.p.add_text(f'Cells: {total_dep_cells[i - 1]} \n'  # showing total number of deposited cells
                           f'Height: {int(np.nonzero(deposit)[0].max() * cell_size)} nm \n'  # showing current height of the structure
                           f'Volume: {volume} nm^3 \n'
                           f'Growth rate: {int(np.asarray(growth_rate).mean())} cell/h \n'  # showing average growth rate
-                          f'Frame {i+1}/{len(files)} \n', position='upper_right', font_size=font_size)
+                          f'Frame {i + 1}/{len(files)} \n', position='upper_right', font_size=font_size)
         if beam_position is not None:
             x_pos, y_pos = beam_position
             x, y = int(x_pos / render.cell_size), int(y_pos / render.cell_size)
@@ -264,6 +271,7 @@ def show_animation(directory, show='precursor'):
         cam_pos = render.show(interactive_update=False)
     return cam_pos
 
+
 if __name__ == '__main__':
     filenames = None
     try:
@@ -272,4 +280,4 @@ def show_animation(directory, show='precursor'):
         print(e.args)
         if not filenames:
             filenames = ask_directory()
-    show_animation()
+    show_animation()

febid/libraries/vtk_rendering/show_file.py

@@ -6,32 +6,44 @@
 import pyvista as pv
 from PyQt5.QtWidgets import QApplication
 from PyQt5.QtWidgets import QFileDialog as fd
-from febid.libraries.vtk_rendering import VTK_Rendering as vr
+
+from febid.libraries.vtk_rendering.VTK_Rendering import Render, read_field_data
 from febid.Structure import Structure
 
-def ask_filenames():
+
+def check_allowed_extensions(filenames, allowed_extensions=['vtk']):
+    for filename in filenames:
+        if not any(filename.endswith(ext) for ext in allowed_extensions):
+            return False
+    return True
+
+
+def ask_filenames(allowed_extensions=['vtk']):
     os.chdir('../../..')
     init_dir = os.getcwd()
     app = QApplication(sys.argv)
-    filenames = fd.getOpenFileName(None, 'Select the file to view', init_dir, 'VTK files (*.vtk);;All files (*)')[0]
+    extensions = ', '.join([f'*.{ext}' for ext in allowed_extensions])
+    filenames = fd.getOpenFileName(None, 'Select the file to view', init_dir, f'VTK files ({extensions});;All files (*)')[0]
     app.quit()
     return filenames
 
+
 def show_structure(filenames=None, **kwargs):
     if not filenames:
         filenames = ask_filenames()
     result = render_structure(filenames, **kwargs)
     return result
 
-def render_structure(filenames, solid=True, deposit=True, precursor=True, surface=True, semi_surface=True, ghost=True):
 
+def render_structure(filenames, solid=True, deposit=True, precursor=True, surface=True, semi_surface=True, ghost=True):
     font_size = 12
     cam_pos = None
     if type(filenames) not in [list, tuple]:
         filenames = [filenames]
     for filename in filenames:
         print(f'Opening file {filename}')
         vtk_obj = pv.read(filename)
+        print(f'Data arrays: {vtk_obj.array_names}')
         structure = Structure()
         structure.load_from_vtk(vtk_obj)
         d = structure.deposit
@@ -47,35 +59,33 @@ def render_structure(filenames, solid=True, deposit=True, precursor=True, surfac
         if p.min() < 0:
             p_er += 1
         print(f'Checking data.....', end='')
-        if d_er+p_er:
+        if d_er + p_er:
             print(f'bad cells encountered in data arrays!')
             if d_er:
                 print(f'\t Solid-cell data contains bad cells:')
                 if d.max() > 1:
-                    print(f'\t  Found {np.count_nonzero(d>1)} cells above unity, maximum value is {d.max()}')
+                    print(f'\t  Found {np.count_nonzero(d > 1)} cells above unity, maximum value is {d.max()}')
                 if d.min() < -2:
-                    print(f'\t  Found {np.count_nonzero(d<-2)} cells below zero, minimum value is {d.min()}')
+                    print(f'\t  Found {np.count_nonzero(d < -2)} cells below zero, minimum value is {d.min()}')
             if p_er:
                 print(f'\t Surface precursor density data contains bad cells:')
                 if p.max() > 1:
-                    print(f'\t  Found {np.count_nonzero(p>1)} cells above unity, maximum value is {p.max()}')
+                    print(f'\t  Found {np.count_nonzero(p > 1)} cells above unity, maximum value is {p.max()}')
                 if p.min() < 0:
-                    print(f'\t  Found {np.count_nonzero(p<0)} cells below zero, minimum value is {p.min()}')
+                    print(f'\t  Found {np.count_nonzero(p < 0)} cells below zero, minimum value is {p.min()}')
         else:
             print('ok!')
-        t, sim_time, beam_position = vr.read_field_data(vtk_obj)
-        render = vr.Render(structure.cell_size)
-        cam_pos = render.show_full_structure(structure, True, solid, deposit, precursor, surface, semi_surface, ghost, t, sim_time, beam_position, cam_pos=cam_pos)
+        t, sim_time, beam_position = read_field_data(vtk_obj)
+        render = Render(structure.cell_size)
+        cam_pos = render.show_full_structure(structure, True, solid, deposit, precursor, surface, semi_surface, ghost,
+                                             t, sim_time, beam_position, cam_pos=cam_pos)
     return cam_pos
 
 
 if __name__ == '__main__':
     filenames = None
-    try:
-        filename = sys.argv[1]
-    except Exception as e:
-        print(e.args)
-        if not filenames:
-            filenames = ask_filenames()
-
+    if len(sys.argv) > 1:
+        filenames = sys.argv[1:]
+        if not check_allowed_extensions(filenames):
+            raise ValueError('Only .vtk files are allowed!')
     show_structure(filenames, solid=True, deposit=True, precursor=True, surface=True, semi_surface=True, ghost=True)

febid/start.py

@@ -207,13 +207,15 @@ def _run_febid_interface(self):
         Compile simulation parameters and start the simulation
         """
         sim_volume_params = self.get_simulation_volume_parameters()
-        saving_params = {'gather_stats': False, 'gather_stats_interval': None, 'save_snapshot': False, 'snapshot_interval': None,
-                         'filename': None}
+        saving_params = {'gather_stats': False, 'gather_stats_interval': None, 'save_snapshot': False, 'save_snapshot_interval': None,
+                         'filename': ''}
         flag1, flag2 = self._params['save_simulation_data'], self._params['save_structure_snapshot']
-        saving_params['gather_stats'] = self._params['save_simulation_data']
-        saving_params['gather_stats_interval'] = float(self._params['simulation_data_interval'])
-        saving_params['save_snapshot'] = self._params['save_structure_snapshot']
-        saving_params['save_snapshot_interval'] = float(self._params['structure_snapshot_interval'])
+        gather_stats = saving_params['gather_stats'] = self._params['save_simulation_data']
+        if gather_stats:
+            saving_params['gather_stats_interval'] = float(self._params['simulation_data_interval'])
+        save_snapshot = saving_params['save_snapshot'] = self._params['save_structure_snapshot']
+        if save_snapshot:
+            saving_params['save_snapshot_interval'] = float(self._params['structure_snapshot_interval'])
         flag1, flag2, flag3 = self._params['save_simulation_data'], self._params['save_structure_snapshot'], self._params['show_process']
         if flag1 or flag2:
             try: