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cellblender_mol_viz.py
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cellblender_mol_viz.py
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# ##### BEGIN GPL LICENSE BLOCK #####
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your option) any later version.#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software Foundation,
# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
#
# ##### END GPL LICENSE BLOCK #####
# <pep8 compliant>
"""
This file contains the classes for CellBlender's Molecule Visualization.
"""
import cellblender
# blender imports
import bpy
from bpy.app.handlers import persistent
from bpy.props import BoolProperty, CollectionProperty, EnumProperty, \
FloatProperty, FloatVectorProperty, IntProperty, \
IntVectorProperty, PointerProperty, StringProperty
#from bpy.app.handlers import persistent
#import math
#import mathutils
# python imports
import mathutils
import array
import glob
import os
import random
import re
import json
# CellBlender imports
import cellblender
import cellblender.parameter_system as parameter_system
import cellblender.cellblender_release as cellblender_release
import cellblender.cellblender_utils as cellblender_utils
from cellblender.cellblender_utils import timeline_view_all
from cellblender.cellblender_utils import mcell_files_path
# Mol Viz Operators:
global_mol_file_list = []
def create_color_list():
""" Create a list of colors to be assigned to the glyphs. """
mcell = bpy.context.scene.mcell
mcell.mol_viz.color_index = 0
if not mcell.mol_viz.color_list:
for i in range(8):
mcell.mol_viz.color_list.add()
mcell.mol_viz.color_list[0].vec = [0.8, 0.0, 0.0]
mcell.mol_viz.color_list[1].vec = [0.0, 0.8, 0.0]
mcell.mol_viz.color_list[2].vec = [0.0, 0.0, 0.8]
mcell.mol_viz.color_list[3].vec = [0.0, 0.8, 0.8]
mcell.mol_viz.color_list[4].vec = [0.8, 0.0, 0.8]
mcell.mol_viz.color_list[5].vec = [0.8, 0.8, 0.0]
mcell.mol_viz.color_list[6].vec = [1.0, 1.0, 1.0]
mcell.mol_viz.color_list[7].vec = [0.0, 0.0, 0.0]
# Matrix Form: Assemble obj2 onto obj1 at location of obj1
def assemble_mat(obj1, obj2):
# get tform matrices of obj1 and obj2
m1 = obj1.matrix_world.copy()
m2 = obj2.matrix_world.copy()
# compute inverse of tform matrix of obj2
m2i = m2.inverted_safe()
# create rotation and translation tform matrix for binding site of assembly
r = mathutils.Matrix.Rotation(pi/8,4,'Y')
t = mathutils.Matrix.Translation((0,-2, 0))
bsm = r*t
# create complete composite tform matrix for assembly
assem = m2i*m1*bsm
# Apply the assembly tform matrix to obj2
obj2.matrix_world = obj2.matrix_world*assem
@persistent
def read_viz_data_load_post(context):
print ( "load post handler: cellblender_mol_viz.read_viz_data_load_post() called" )
bpy.ops.mcell.read_viz_data()
@persistent
def viz_data_save_post(context):
# context appears to be None
print ( "save post handler: cellblender_mol_viz.viz_data_save_post() called" )
if 'global_mol_file_list' in dir(cellblender.cellblender_mol_viz):
if len(cellblender.cellblender_mol_viz.global_mol_file_list) > 0:
# There is a non-empty file list, so check if this file path matches the current viz directory
print ( "New file name = " + str(bpy.data.filepath) )
mv = bpy.context.scene.mcell.mol_viz
if not mv.manual_select_viz_dir:
print ( "Viz not manually selected" )
bfn = os.path.abspath(str(bpy.data.filepath))
mfd = os.path.abspath(str(mv.mol_file_dir))
print ( "Blend: " + bfn )
print ( "Viz: " + mfd )
if not mfd.startswith(os.path.splitext(bfn)[0] + "_files" + os.sep + "mcell" + os.sep ):
print ( "Paths don't match, so clear mol-viz information" )
# This is being saved as a different file than was used to generate the visualization data
cellblender.cellblender_mol_viz.global_mol_file_list = []
mv.mol_file_dir = ''
# __import__('code').interact(local={k: v for ns in (globals(), locals()) for k, v in ns.items()})
# Operators can't be callbacks, so we need this function for now. This is
# temporary until we make importing viz data automatic.
def read_viz_data_callback(self, context):
# print ( "read_viz_data_callback" )
bpy.ops.mcell.read_viz_data()
class MCELL_OT_update_data_layout(bpy.types.Operator):
bl_idname = "mcell.update_data_layout"
bl_label = "Update Layout Data"
bl_description = "Update the Data Layout based on most recent run of this project."
bl_options = {'REGISTER'}
def execute(self, context):
# print ( "MCELL_OT_update_data_layout operator" )
mcell = context.scene.mcell
mcell.mol_viz.update_data_layout(context)
return {'FINISHED'}
class MCELL_OT_read_viz_data(bpy.types.Operator):
bl_idname = "mcell.read_viz_data"
bl_label = "Read Viz Data"
bl_description = "Load the molecule visualization data into Blender"
bl_options = {'REGISTER'}
def execute(self, context):
global global_mol_file_list
# Called when the molecule files are actually to be read (when the
# "Read Molecule Files" button is pushed or a seed value is selected
# from the list)
mcell = context.scene.mcell
mol_viz = mcell.mol_viz
choices_list = mol_viz.choices_list
mol_file_dir = ''
if mol_viz.manual_select_viz_dir:
# mol_file_dir comes from directory already chosen manually
mol_file_dir = mol_viz.mol_file_dir
print("manual mol_file_dir: %s" % (mol_file_dir))
else:
# mol_file_dir comes from directory associated with saved .blend file
mol_viz_top_level_dir = None
files_path = mcell_files_path() # This will be the full path from "/"
# Check to see if the data is in an output_data directory or not
if os.path.exists(files_path) and 'output_data' in os.listdir(files_path):
# New "output_data" layout
# Read the viz data from the first data path in the potential sweep
f = open ( os.path.join(files_path,"data_layout.json"), 'r' )
layout_spec = json.loads ( f.read() )
f.close()
data_layout = layout_spec['data_layout']
sub_path = ""
for level in data_layout:
if level[0] == '/DIR':
# This is typically the top level directory
sub_path = os.path.join ( sub_path, level[1][0] )
elif level[0] == '/FILE_TYPE':
# This is typically either "viz_data" or "react_data" ... force "viz_data
sub_path = os.path.join ( sub_path, 'viz_data', '' )
elif (level[0] == '/SEED'):
# Seed selection is handled in another part of the application so pass
pass
else:
# This is a parameter sweep subdirectory, use the parameter name and currently selected index
selected_index = 0
try:
selected_index = choices_list[level[0]]['enum_choice']
except:
pass
sub_path = os.path.join ( sub_path, level[0] + ("_index_%d" % selected_index) )
mol_viz_top_level_dir = os.path.join(files_path, sub_path)
else:
# Old "non-output_data" layout
# Force the top level mol_viz directory to be where the .blend file
# lives plus "viz_data". The seed directories will live underneath it.
mol_viz_top_level_dir = os.path.join(files_path, "viz_data", "")
mol_viz_top_level_dir = os.path.relpath(mol_viz_top_level_dir)
mol_viz_seed_list = glob.glob(os.path.join(mol_viz_top_level_dir, "*"))
mol_viz_seed_list.sort()
# Clear the list of seeds (e.g. seed_00001, seed_00002, etc) and the
# list of files (e.g. my_project.cellbin.0001.dat,
# my_project.cellbin.0002.dat)
mol_viz.mol_viz_seed_list.clear()
# Add all the seed directories to the mol_viz_seed_list collection
# (seed_00001, seed_00002, etc)
for mol_viz_seed in mol_viz_seed_list:
new_item = mol_viz.mol_viz_seed_list.add()
new_item.name = os.path.basename(mol_viz_seed)
if mol_viz.mol_viz_seed_list:
# If you previously had some viz data loaded, but reran the
# simulation with less seeds, you can receive an index error.
try:
active_mol_viz_seed = mol_viz.mol_viz_seed_list[
mol_viz.active_mol_viz_seed_index]
except IndexError:
mol_viz.active_mol_viz_seed_index = 0
active_mol_viz_seed = mol_viz.mol_viz_seed_list[0]
mol_file_dir = os.path.join(mol_viz_top_level_dir, active_mol_viz_seed.name)
mol_file_dir = os.path.relpath(mol_file_dir)
mol_viz.mol_file_dir = mol_file_dir
# mol_viz.mol_file_list.clear()
global_mol_file_list = []
mol_file_list = []
if mol_file_dir != '':
mol_file_list = [ f for f in glob.glob(os.path.join(mol_file_dir, "*.dat")) ]
mol_file_list.sort()
if mol_file_list:
# Add all the viz_data files to global_mol_file_list (e.g.
# my_project.cellbin.0001.dat, my_project.cellbin.0001.dat, etc)
for mol_file_name in mol_file_list:
global_mol_file_list.append(os.path.basename(mol_file_name))
# If you previously had some viz data loaded, but reran the
# simulation with less iterations, you can receive an index error.
try:
mol_file = global_mol_file_list[mol_viz.mol_file_index]
except IndexError:
mol_viz.mol_file_index = 0
mol_file = global_mol_file_list[mol_viz.mol_file_index]
create_color_list()
set_viz_boundaries(context)
# Set the mol_file_index to match the cursor as closely as possible
cursor_index = context.scene.frame_current
if len(mol_file_list) > cursor_index:
mol_viz.mol_file_index = cursor_index
elif len(mol_file_list) >= 1:
mol_viz.mol_file_index = len(mol_file_list) - 1
else:
mol_viz.mol_file_index = 0
try:
mol_viz_clear(mcell, force_clear=True)
mol_viz_update(self, context)
except:
print( "Unexpected Exception calling mol_viz_update: " + str(sys.exc_info()) )
return {'FINISHED'}
# Mol Viz callback functions
def set_viz_boundaries( context ):
global global_mol_file_list
mcell = context.scene.mcell
# mcell.mol_viz.mol_file_num = len(mcell.mol_viz.mol_file_list)
mcell.mol_viz.mol_file_num = len(global_mol_file_list)
mcell.mol_viz.mol_file_stop_index = mcell.mol_viz.mol_file_num - 1
#print("Setting frame_start to 0")
#print("Setting frame_end to ", len(mcell.mol_viz.mol_file_list)-1)
bpy.context.scene.frame_start = 0
# bpy.context.scene.frame_end = len(mcell.mol_viz.mol_file_list)-1
bpy.context.scene.frame_end = len(global_mol_file_list)-1
timeline_view_all ( context )
"""
if bpy.context.screen != None:
for area in bpy.context.screen.areas:
if area != None:
if area.type == 'TIMELINE':
for region in area.regions:
if region.type == 'WINDOW':
ctx = bpy.context.copy()
ctx['area'] = area
ctx['region'] = region
bpy.ops.time.view_all(ctx)
break # It's not clear if this should break or continue ... breaking for now
"""
class MCELL_OT_select_viz_data(bpy.types.Operator):
bl_idname = "mcell.select_viz_data"
bl_label = "Read Viz Data"
bl_description = "Read MCell Molecule Files for Visualization"
bl_options = {'REGISTER'}
filepath: StringProperty(subtype='FILE_PATH', default="")
directory: StringProperty(subtype='DIR_PATH')
def __init__(self):
self.directory = bpy.context.scene.mcell.mol_viz.mol_file_dir
def execute(self, context):
global global_mol_file_list
mcell = context.scene.mcell
if (os.path.isdir(self.filepath)):
mol_file_dir = self.filepath
else:
# Strip the file name off of the file path.
mol_file_dir = os.path.dirname(self.filepath)
mcell.mol_viz.mol_file_dir = mol_file_dir
mol_file_list = [ f for f in glob.glob(os.path.join(mol_file_dir, "*")) if not f.endswith(os.sep + "viz_bngl") ]
print ( "Select found " + str(len(mol_file_list)) + " files" )
mol_file_list.sort()
# Reset mol_file_list and mol_viz_seed_list to empty
# mcell.mol_viz.mol_file_list.clear()
global_mol_file_list = []
for mol_file_name in mol_file_list:
# new_item = mcell.mol_viz.mol_file_list.add()
# new_item.name = os.path.basename(mol_file_name)
global_mol_file_list.append(os.path.basename(mol_file_name))
create_color_list()
set_viz_boundaries(context)
mcell.mol_viz.mol_file_index = 0
mol_viz_update(self, context)
return {'FINISHED'}
def invoke(self, context, event):
# Called when the file selection panel is requested
# (when the "Set Molecule Viz Directory" button is pushed)
print("MCELL_OT_select_viz_data.invoke() called")
context.window_manager.fileselect_add(self)
return {'RUNNING_MODAL'}
class MCELL_OT_mol_viz_set_index(bpy.types.Operator):
bl_idname = "mcell.mol_viz_set_index"
bl_label = "Set Molecule File Index"
bl_description = "Set MCell Molecule File Index for Visualization"
bl_options = {'REGISTER'}
def execute(self, context):
global global_mol_file_list
mcell = context.scene.mcell
# if mcell.mol_viz.mol_file_list:
if global_mol_file_list:
i = mcell.mol_viz.mol_file_index
if (i > mcell.mol_viz.mol_file_stop_index):
i = mcell.mol_viz.mol_file_stop_index
if (i < mcell.mol_viz.mol_file_start_index):
i = mcell.mol_viz.mol_file_start_index
mcell.mol_viz.mol_file_index = i
# print ( "Set index calling update" )
mol_viz_update(self, context)
return{'FINISHED'}
#CellBlender operator helper functions:
@persistent
def frame_change_handler(scn):
""" Update the viz data every time a frame is changed. """
mcell = scn.mcell
curr_frame = mcell.mol_viz.mol_file_index
if (not curr_frame == scn.frame_current):
mcell.mol_viz.mol_file_index = scn.frame_current
bpy.ops.mcell.mol_viz_set_index()
# Is the following code necessary?
#if mcell.mol_viz.render_and_save:
# scn.render.filepath = "//stores_on/frames/frame_%05d.png" % (
# scn.frame_current)
# bpy.ops.render.render(write_still=True)
def mol_viz_toggle_manual_select(self, context):
""" Toggle the option to manually load viz data. """
global global_mol_file_list
mcell = context.scene.mcell
mcell.mol_viz.mol_file_dir = ""
mcell.mol_viz.mol_file_name = ""
# mcell.mol_viz.mol_file_list.clear()
global_mol_file_list = []
mcell.mol_viz.mol_viz_seed_list.clear()
if not mcell.mol_viz.manual_select_viz_dir:
bpy.ops.mcell.read_viz_data()
mol_viz_clear(mcell)
def get_mol_file_dir():
""" Get the viz dir """
mcell = bpy.context.scene.mcell
# If you previously had some viz data loaded, but reran the
# simulation with less seeds, you can receive an index error.
try:
active_mol_viz_seed = mcell.mol_viz.mol_viz_seed_list[
mcell.mol_viz.active_mol_viz_seed_index]
except IndexError:
mcell.mol_viz.active_mol_viz_seed_index = 0
active_mol_viz_seed = mcell.mol_viz.mol_viz_seed_list[0]
filepath = os.path.join(
mcell_files_path(), "viz_data/%s" % active_mol_viz_seed.name)
filepath = os.path.relpath(filepath)
return filepath
# Note: why is self here? This isn't a class method...
def mol_viz_update(self, context):
""" Clear the old viz data. Draw the new viz data. """
mcell = context.scene.mcell
if global_mol_file_list:
if mcell.mol_viz.mol_file_index > len(global_mol_file_list) or mcell.mol_viz.mol_file_index < 0:
mcell.mol_viz.mol_file_index = 0
filename = global_mol_file_list[mcell.mol_viz.mol_file_index]
mcell.mol_viz.mol_file_name = filename
filepath = os.path.join(mcell.mol_viz.mol_file_dir, filename)
# Save current global_undo setting. Turn undo off to save memory
global_undo = bpy.context.preferences.edit.use_global_undo
bpy.context.preferences.edit.use_global_undo = False
mol_viz_clear(mcell)
if mcell.mol_viz.mol_viz_enable:
mol_viz_file_read(mcell, filepath)
# Reset undo back to its original state
bpy.context.preferences.edit.use_global_undo = global_undo
return
def mol_viz_clear(mcell_prop, force_clear=False):
""" Clear the viz data from the previous frame. """
mcell = mcell_prop
scn = bpy.context.scene
scn_objs = bpy.context.scene.collection.children[0].objects
meshes = bpy.data.meshes
objs = bpy.data.objects
if force_clear:
mol_viz_list = [obj for obj in scn_objs if (obj.name[:4] == 'mol_') and (obj.name[-6:] != '_shape')]
else:
mol_viz_list = mcell.mol_viz.mol_viz_list
for mol_item in mol_viz_list:
mol_name = mol_item.name
mol_obj = scn_objs.get(mol_name)
if mol_obj:
hide = mol_obj.hide_viewport
mol_pos_mesh = mol_obj.data
mol_pos_mesh_name = mol_pos_mesh.name
mol_shape_obj_name = "%s_shape" % (mol_name)
mol_shape_obj = objs.get(mol_shape_obj_name)
if mol_shape_obj:
mol_shape_obj.parent = None
scn_objs.unlink(mol_obj)
objs.remove(mol_obj)
meshes.remove(mol_pos_mesh)
mol_pos_mesh = meshes.new(mol_pos_mesh_name)
mol_obj = objs.new(mol_name, mol_pos_mesh)
scn_objs.link(mol_obj)
if mol_shape_obj:
mol_shape_obj.parent = mol_obj
mol_obj.instance_type = 'VERTS'
mol_obj.use_instance_vertices_rotation = True
mols_obj = objs.get("molecules")
mol_obj.parent = mols_obj
mol_obj.hide_viewport = hide
# Reset mol_viz_list to empty
for i in range(len(mcell.mol_viz.mol_viz_list)-1, -1, -1):
mcell.mol_viz.mol_viz_list.remove(i)
"""
def old_mol_viz_file_read(mcell_prop, filepath):
mcell = mcell_prop
try:
# begin = resource.getrusage(resource.RUSAGE_SELF)[0]
# print ("Processing molecules from file: %s" % (filepath))
# Quick check for Binary or ASCII format of molecule file:
mol_file = open(filepath, "rb")
b = array.array("I")
b.fromfile(mol_file, 1)
mol_dict = {}
if b[0] == 1:
# Read Binary format molecule file:
bin_data = 1
while True:
try:
# Variable names are a little hard to follow
# Here's what I assume they mean:
# ni = Initially, array of molecule name length.
# Later, array of number of molecule positions in xyz
# (essentially, the number of molecules multiplied by 3).
# ns = Array of ascii character codes for molecule name.
# s = String of molecule name.
# mt = Surface molecule flag.
ni = array.array("B")
ni.fromfile(mol_file, 1)
ns = array.array("B")
ns.fromfile(mol_file, ni[0])
s = ns.tobytes().decode()
mol_name = "mol_%s" % (s)
mt = array.array("B")
mt.fromfile(mol_file, 1)
ni = array.array("I")
ni.fromfile(mol_file, 1)
mol_pos = array.array("f")
mol_orient = array.array("f")
mol_pos.fromfile(mol_file, ni[0])
# tot += ni[0]/3
if mt[0] == 1:
mol_orient.fromfile(mol_file, ni[0])
mol_dict[mol_name] = [mt[0], mol_pos, mol_orient]
new_item = mcell.mol_viz.mol_viz_list.add()
new_item.name = mol_name
except:
# print("Molecules read: %d" % (int(tot)))
mol_file.close()
break
else:
# Read ASCII format molecule file:
bin_data = 0
mol_file.close()
# Create a list of molecule names, positions, and orientations
# Each entry in the list is ordered like this (afaik):
# [molec_name, [x_pos, y_pos, z_pos, x_orient, y_orient, z_orient]]
# Orientations are zero in the case of volume molecules.
mol_data = [[s.split()[0], [
float(x) for x in s.split()[2:]]] for s in open(
filepath, "r").read().split("\n") if s != ""]
for mol in mol_data:
mol_name = "mol_%s" % (mol[0])
if not mol_name in mol_dict:
mol_orient = mol[1][3:]
mt = 0
# Check to see if it's a surface molecule
if ((mol_orient[0] != 0.0) | (mol_orient[1] != 0.0) |
(mol_orient[2] != 0.0)):
mt = 1
mol_dict[mol_name] = [
mt, array.array("f"), array.array("f")]
new_item = mcell.mol_viz.mol_viz_list.add()
new_item.name = mol_name
mt = mol_dict[mol_name][0]
mol_dict[mol_name][1].extend(mol[1][:3])
if mt == 1:
mol_dict[mol_name][2].extend(mol[1][3:])
# Get the parent object to all the molecule positions if it exists.
# Otherwise, create it.
mols_obj = bpy.data.objects.get("molecules")
if not mols_obj:
bpy.ops.object.add(location=[0, 0, 0])
mols_obj = bpy.context.selected_objects[0]
mols_obj.name = "molecules"
#mol_viz_list
if mol_dict:
meshes = bpy.data.meshes
mats = bpy.data.materials
objs = bpy.data.objects
scn = bpy.context.scene
scn_objs = bpy.context.scene.collection.children[0].objects
z_axis = mathutils.Vector((0.0, 0.0, 1.0))
#ident_mat = mathutils.Matrix.Translation(
# mathutils.Vector((0.0, 0.0, 0.0)))
for mol_name in mol_dict.keys():
mol_mat_name = "%s_mat" % (mol_name)
mol_type = mol_dict[mol_name][0]
mol_pos = mol_dict[mol_name][1]
mol_orient = mol_dict[mol_name][2]
# Randomly orient volume molecules
if mol_type == 0:
mol_orient.extend([random.uniform(
-1.0, 1.0) for i in range(len(mol_pos))])
# Look-up mesh shape (glyph) template and create if needed
mol_shape_mesh_name = "%s_shape" % (mol_name)
mol_shape_obj_name = mol_shape_mesh_name
mol_shape_mesh = meshes.get(mol_shape_mesh_name)
if not mol_shape_mesh:
bpy.ops.mesh.primitive_ico_sphere_add(
subdivisions=0, radius=0.005, location=[0, 0, 0])
mol_shape_obj = bpy.context.active_object
mol_shape_obj.name = mol_shape_obj_name
mol_shape_obj.track_axis = "POS_Z"
mol_shape_mesh = mol_shape_obj.data
mol_shape_mesh.name = mol_shape_mesh_name
else:
mol_shape_obj = objs.get(mol_shape_obj_name)
# Look-up material, create if needed.
# Associate material with mesh shape.
mol_mat = mats.get(mol_mat_name)
if not mol_mat:
mol_mat = mats.new(mol_mat_name)
mol_mat.diffuse_color = mcell.mol_viz.color_list[
mcell.mol_viz.color_index].vec
mcell.mol_viz.color_index = mcell.mol_viz.color_index + 1
if (mcell.mol_viz.color_index >
len(mcell.mol_viz.color_list)-1):
mcell.mol_viz.color_index = 0
if not mol_shape_mesh.materials.get(mol_mat_name):
mol_shape_mesh.materials.append(mol_mat)
# Create a "mesh" to hold instances of molecule positions
mol_pos_mesh_name = "%s_pos" % (mol_name)
mol_pos_mesh = meshes.get(mol_pos_mesh_name)
if not mol_pos_mesh:
mol_pos_mesh = meshes.new(mol_pos_mesh_name)
# Add and place vertices at positions of molecules
mol_pos_mesh.vertices.add(len(mol_pos)//3)
mol_pos_mesh.vertices.foreach_set("co", mol_pos)
mol_pos_mesh.vertices.foreach_set("normal", mol_orient)
# Create object to contain the mol_pos_mesh data
mol_obj = objs.get(mol_name)
if not mol_obj:
mol_obj = objs.new(mol_name, mol_pos_mesh)
scn_objs.link(mol_obj)
mol_shape_obj.parent = mol_obj
mol_obj.instance_type = 'VERTS'
mol_obj.use_instance_vertices_rotation = True
mol_obj.parent = mols_obj
# bpy.context.view_layer.update()
# utime = resource.getrusage(resource.RUSAGE_SELF)[0]-begin
# print (" Processed %d molecules in %g seconds\n" % (
# len(mol_data), utime))
except IOError:
print(("\n***** File not found: %s\n") % (filepath))
except ValueError:
print(("\n***** Invalid data in file: %s\n") % (filepath))
"""
import sys, traceback
def mol_viz_file_dump(filepath):
""" Read and Dump a molecule viz file. """
tot = 0
try:
# Quick check for Binary or ASCII format of molecule file:
mol_file = open(filepath, "rb")
b = array.array("I")
b.fromfile(mol_file, 1)
mol_dict = {}
if b[0] == 1:
# Read MCell/CellBlender Binary Format molecule file, version 1:
print ("Reading binary file " + filepath )
while True:
try:
# ni = Initially, byte array of molecule name length.
# Later, array of number of molecule positions in xyz
# (essentially, the number of molecules multiplied by 3).
# ns = Array of ascii character codes for molecule name.
# s = String of molecule name.
# mt = Surface molecule flag.
ni = array.array("B") # Create a binary byte ("B") array
ni.fromfile(mol_file, 1) # Read one byte which is the number of characters in the molecule name
ns = array.array("B") # Create another byte array to hold the molecule name
ns.fromfile(mol_file, ni[0]) # Read ni bytes from the file
s = ns.tobytes().decode() # Decode bytes as ASCII into a string (s)
mol_name = "mol_%s" % (s) # Construct name of blender molecule viz object
mt = array.array("B") # Create a byte array for the molecule type
mt.fromfile(mol_file, 1) # Read one byte for the molecule type
ni = array.array("I") # Re-use ni as an integer array to hold the number of molecules of this name in this frame
ni.fromfile(mol_file, 1) # Read the 4 byte integer value which is 3 times the number of molecules
mol_pos = array.array("f") # Create a floating point array to hold the positions
mol_orient = array.array("f") # Create a floating point array to hold the orientations
mol_pos.fromfile(mol_file, ni[0]) # Read the positions which should be 3 floats per molecule
mol_type_name = "Volume"
tot += ni[0]/3
if mt[0] == 1: # If mt==1, it's a surface molecule
mol_orient.fromfile(mol_file, ni[0]) # Read the surface molecule orientations
mol_type_name = "Surface"
print ( mol_type_name + " Molecule " + s + " contains " + str(tot) + " instances" )
except EOFError:
# print("Molecules read: %d" % (int(tot)))
mol_file.close()
break
except:
print( "Unexpected Exception: " + str(sys.exc_info()) )
# print("Molecules read: %d" % (int(tot)))
mol_file.close()
break
else:
print ( "Dump doesn't read text files." )
except IOError:
print(("\n***** IOError: File: %s\n") % (filepath))
except ValueError:
print(("\n***** ValueError: Invalid data in file: %s\n") % (filepath))
except RuntimeError as rte:
print(("\n***** RuntimeError reading file: %s\n") % (filepath))
print(" str(error): \n" + str(rte) + "\n")
fail_error = sys.exc_info()
print ( " Error Type: " + str(fail_error[0]) )
print ( " Error Value: " + str(fail_error[1]) )
tb = fail_error[2]
# tb.print_stack()
print ( "=== Traceback Start ===" )
traceback.print_tb(tb)
print ( "=== Traceback End ===" )
except Exception as uex:
# Catch any exception
print ( "\n***** Unexpected exception:" + str(uex) + "\n" )
raise
def remove_compartment_and_state(name):
# Remove states and compartment, e.g. @EC:Syk(a~Y,l~Y,tSH2)@CP -> Syk
split_by_colon = name.split(':')
if len(split_by_colon) == 2:
em_no_start_compartment = split_by_colon[1]
else:
em_no_start_compartment = name
em_no_compartment = em_no_start_compartment.split('@')[0]
em_no_components = em_no_compartment.split('(')[0]
return em_no_components
def get_used_molecule_names(name):
# example of input:
# '@EC:scov2(s!1,s!2,s!3,s!4,s!5).spike(v!1,a)@CP.spike(v!1,a)@CP'
# output:
# ['scov', 'spike']
res = set()
split_by_dot = name.split('.')
for em in split_by_dot:
# remove compartment and states
res.add(remove_compartment_and_state(em))
return sorted(list(res))
def mol_viz_file_read(mcell, filepath):
""" Read and Draw the molecule viz data for the current frame. """
mv = mcell.mol_viz
if (mv.viz_code in ['custom','both']):
script_text = None
if mv.internal_viz_file_name in bpy.data.texts:
# It's an internal file
script_text = bpy.data.texts[mv.internal_viz_file_name].as_string()
elif mv.internal_viz_file_name.startswith ( os.path.sep ):
# It must be an external file starting with an os.sep (typically '/')
script_file = open ( os.path.join ( os.path.dirname(bpy.data.filepath), mv.internal_viz_file_name[1:] ), 'r' )
print ( "Reading script text from " + str(script_file) )
script_text = script_file.read()
if script_text != None:
# Store the filepath for this frame in a place where it can be used by the custom code
mcell.mol_viz.frame_file_name = filepath
# Convert the text to code (this might be done earlier when the file is selected)
code = compile ( script_text, "<string>", 'exec' )
# Execute the code
exec ( code )
if mv.viz_code == 'custom':
return
# check whether the viz file is not empty (may happen for ASCII files)
if os.path.getsize(filepath) == 0:
return
dup_check = False
try:
# begin = resource.getrusage(resource.RUSAGE_SELF)[0]
# print ("Processing molecules from file: %s" % (filepath))
# Quick check for Binary or ASCII format of molecule file:
mol_file = open(filepath, "rb")
b = array.array("I")
b.fromfile(mol_file, 1)
mol_dict = {}
if b[0] == 1 or b[0] == 2:
ver = b[0]
# Read MCell/CellBlender Binary Format molecule file, version 1:
# print ("Reading binary file " + filepath )
bin_data = 1
while True:
try:
# ni = Initially, byte array of molecule name length.
# Later, array of number of molecule positions in xyz
# (essentially, the number of molecules multiplied by 3).
# ns = Array of ascii character codes for molecule name.
# s = String of molecule name.
# mt = Surface molecule flag.
if ver == 1:
ni = array.array("B") # Create a binary byte ("B") array to read one byte
else:
ni = array.array("I") # Create a binary integer ("I") array to read 4 bytes
ni.fromfile(mol_file, 1) # Read one or four bytes which is the number of characters in the molecule name
ns = array.array("B") # Create another byte array to hold the molecule name
ns.fromfile(mol_file, ni[0]) # Read ni bytes from the file
mol_name_from_file = ns.tobytes().decode() # Decode bytes as ASCII into a string (s)
mt = array.array("B") # Create a byte array for the molecule type
mt.fromfile(mol_file, 1) # Read one byte for the molecule type
ni = array.array("I") # Re-use ni as an integer array to hold the number of molecules of this name in this frame
ni.fromfile(mol_file, 1) # Read the 4 byte integer value which is the number of molecules (v2) or 3 times the number of molecules (v1)
if ver > 1:
num_mols = ni[0]
num_floats = 3*ni[0]
mol_ids = array.array("I") # Molecule ids are gnored in cellblender
mol_ids.fromfile(mol_file, num_mols)
else:
num_floats = ni[0]
mol_ids = None
mol_pos = array.array("f") # Create a floating point array to hold the positions
mol_orient = array.array("f") # Create a floating point array to hold the orientations
mol_pos.fromfile(mol_file, num_floats) # Read all the positions which should be 3 floats per molecule
if mt[0] == 1: # If mt==1, it's a surface molecule
mol_orient.fromfile(mol_file, num_floats) # Read all the surface molecule orientations
if mcell.cellblender_preferences.mcell4_mode:
elem_mol_names = get_used_molecule_names(mol_name_from_file)
else:
# MCell3(R) in binary viz mode already splits the complexes into individual molecules
elem_mol_names = [mol_name_from_file]
for elem_mol_name in elem_mol_names:
mol_name = "mol_%s" % (elem_mol_name) # Construct name of blender molecule viz object
# we must append positions and orientations if this mol type already exists
if mol_name not in mol_dict:
mol_dict[mol_name] = [mt[0], mol_pos, mol_orient] # Create a dictionary entry for this molecule containing a list of relevant data
else:
mol_dict[mol_name][1].extend(mol_pos)
mol_dict[mol_name][2].extend(mol_orient)
if len(mcell.mol_viz.mol_viz_list) > 0:
for i in range(len(mcell.mol_viz.mol_viz_list)):
if mcell.mol_viz.mol_viz_list[i].name[4:] == mol_name:
dup_check = True
if dup_check == False:
new_item = mcell.mol_viz.mol_viz_list.add() # Create a new collection item to hold the name for this molecule
new_item.name = mol_name # Assign the name to the new item
except EOFError:
# print("Molecules read: %d" % (int(tot)))
mol_file.close()
break
except:
print( "Unexpected Exception: " + str(sys.exc_info()) )
# print("Molecules read: %d" % (int(tot)))
mol_file.close()
break
else:
# Read ASCII format molecule file:
# print ("Reading ASCII file " + filepath )
bin_data = 0
mol_file.close()
# Create a list of molecule names, positions, and orientations
# Each entry in the list is ordered like this (afaik):
# [molec_name, [x_pos, y_pos, z_pos, x_orient, y_orient, z_orient]]
# Orientations are zero in the case of volume molecules.
mol_data = [[s.split()[0], [
float(x) for x in s.split()[2:]]] for s in open(
filepath, "r").read().split("\n") if s != ""]
for mol in mol_data:
# generate one molecule for each used elementary molecule because
# we do not have shapes/glyphs for all complexes
elem_mol_names = get_used_molecule_names(mol[0])
for elem_mol_name in elem_mol_names:
mol_name = "mol_%s" % elem_mol_name
if not mol_name in mol_dict:
mol_orient = mol[1][3:]
mt = 0
# Check to see if it's a surface molecule
if ((mol_orient[0] != 0.0) | (mol_orient[1] != 0.0) |
(mol_orient[2] != 0.0)):
mt = 1
mol_dict[mol_name] = [mt, array.array("f"), array.array("f")]
new_item = mcell.mol_viz.mol_viz_list.add()
new_item.name = mol_name
mt = mol_dict[mol_name][0]
mol_dict[mol_name][1].extend(mol[1][:3])
if mt == 1:
mol_dict[mol_name][2].extend(mol[1][3:])
# Get the parent object to all the molecule positions if it exists.
# Otherwise, create it.
mols_obj = bpy.data.objects.get("molecules")
if not mols_obj:
bpy.ops.object.add(location=[0, 0, 0]) # Create an "Empty" object in the Blender scene