- Author:
- vickieshim <v.shim@auckland.ac.nz>
- Date:
- 2022-11-10 14:21:43+13:00
- Desc:
- neon file
- Permanent Source URI:
- https://models.cellml.org/workspace/972/rawfile/4380c90088293bf4a66f10486196d638c2eb66e2/generate_argon_document.py
import copy
import json
import os
EXPORT_RELATIVE_PATH = True
#Change this to match the root directory to generate the new file
DIR_2 = '.'
#The name of the newly generated argon document
EXPORT_NAME = 'generated.neon'
VERSION_INFO = {
"OpenCMISS-Argon Version": [
"0",
"2",
"2"
],
}
#Settings for scene viewport, not used a this moment
SCENEVIEWER = {
"Sceneviewer": {
"AntialiasSampling": 0,
"BackgroundColourRGB": [
1,
1,
1
],
"EyePosition": [
295.78381273359287,
2742.141219539055,
-486.04315158466096
],
"FarClippingPlane": 6485.082381619184,
"LightingLocalViewer": False,
"LightingTwoSided": True,
"LookatPosition": [
133.9595184326172,
128.9081916809082,
-829.2242584228516
],
"NearClippingPlane": 132.03169346983802,
"PerturbLinesFlag": False,
"ProjectionMode": "PERSPECTIVE",
"Scene": "",
"Scenefilter": "default",
"TranslationRate": 1,
"TransparencyMode": "FAST",
"TumbleRate": 1.5,
"UpVector": [
0,
0,
1
],
"ViewAngle": 0.6981317007976229,
"ZoomRate": 1
}
}
SCENE_GRAPHICS = {
"Scene": {
"Graphics": [
{
"BoundaryMode": "ALL",
"CoordinateField": "coordinates",
"ElementFaceType": "ALL",
"FieldDomainType": "MESH2D",
"Material": "black",
"RenderLineWidth": 1,
"RenderPointSize": 1,
"RenderPolygonMode": "SHADED",
"Scenecoordinatesystem": "LOCAL",
"SelectMode": "ON",
"SelectedMaterial": "default_selected",
"Surfaces": {},
"Tessellation": "default",
"Type": "SURFACES",
"VisibilityFlag": True
}
],
"VisibilityFlag": True
}
}
TESSELLATION = {
"Tessellations": {
"DefaultPointsTessellation": "default_points",
"DefaultTessellation": "default",
"Tessellations": [
{
"CircleDivisions": 12,
"MinimumDivisions": [
1
],
"Name": "default",
"RefinementFactors": [
12
]
},
{
"CircleDivisions": 12,
"MinimumDivisions": [
1
],
"Name": "default_points",
"RefinementFactors": [
1
]
},
{
"CircleDivisions": 48,
"MinimumDivisions": [
1
],
"Name": "material_preview",
"RefinementFactors": [
1
]
},
{
"CircleDivisions": 12,
"MinimumDivisions": [
16
],
"Name": "update_vis",
"RefinementFactors": [
1
]
}
]
}
}
FIELD_MODULE = {
"Fieldmodule": {
"Fields": [
{
"CoordinateSystemType": "RECTANGULAR_CARTESIAN",
"FieldFiniteElement": {
"ComponentNames": [
"x",
"y",
"z"
],
"NumberOfComponents": 3
},
"IsManaged": True,
"IsTypeCoordinate": True,
"Name": "coordinates"
},
{
"CoordinateSystemType": "FIBRE",
"FieldFiniteElement": {
"ComponentNames": [
"fibre angle",
"imbrication angle",
"sheet angle"
],
"NumberOfComponents": 3
},
"IsManaged": True,
"IsTypeCoordinate": False,
"Name": "fibres"
}
]
},
}
EMPTY_REGION = {
"Fieldmodule": None,
"Scene": {
"Graphics": None,
"VisibilityFlag": True
}
}
SKIP_REGIONS = ['maxilla', ]
def generate_output(currentDir):
data_files = []
for root, dirs, files in os.walk(currentDir, topdown=True):
transformedFound = False
current_dir = {
'node_files': [],
'elem_files': []
}
for file in files:
# print(file)
if file.endswith('_transformed.exnode'):
transformedFound = True
current_dir['node_files'].append(file)
if file.endswith('_transformed.exelem'):
current_dir['elem_files'].append(file)
if transformedFound == False:
for file in files:
if file.endswith('.EXNODE'):
current_dir['node_files'].append(file)
if file.endswith('.EXELEM'):
current_dir['elem_files'].append(file)
if len(current_dir["node_files"]):
data_files.append(current_dir)
argon_document = {
**VERSION_INFO,
#**SCENEVIEWER,
**TESSELLATION
}
root_region = copy.deepcopy(EMPTY_REGION)
bits = []
for index, data in enumerate(data_files):
exnode_file = data["node_files"][0]
region_path = exnode_file
region_parts = region_path.split('/')
region_parts.pop(0)
base_region = root_region
for i in range(len(region_parts) - 1):
current_region = region_parts[i].lower()
if "ChildRegions" not in base_region:
base_region["ChildRegions"] = []
child_region_names = []
for region_info in base_region["ChildRegions"]:
child_region_names.append(region_info["Name"])
if current_region not in child_region_names:
new_child = copy.deepcopy(EMPTY_REGION)
new_child['Name'] = current_region
base_region["ChildRegions"].append(new_child)
child_region_names.append(current_region)
j = child_region_names.index(current_region)
base_region = base_region["ChildRegions"][j]
# base_region["Fieldmodule"] = copy.deepcopy(FIELD_MODULE["Fieldmodule"])
base_region["Scene"] = copy.deepcopy(SCENE_GRAPHICS["Scene"])
#bit = f"'{region_parts[-2].lower()}',"
# if bit not in bits:
# bits.append(bit)
if len(region_parts) > 2 and region_parts[-2].lower() in SKIP_REGIONS:
continue
if "Model" not in base_region:
base_region["Model"] = {"Sources": []}
for node_file in data['node_files']:
exnode_path = node_file # .replace(common_path, '')[1:]
regionName = os.path.dirname(region_path).lower()
if regionName == "":
regionName = exnode_path.replace('_transformed.exnode', '')
base_region["Model"]["Sources"].insert(
0,
{
"FileName": exnode_path,
"RegionName": regionName,
"Type": "FILE"
}
)
for elem_file in data['elem_files']:
exelem_path = elem_file # .replace(common_path, '')[1:]
regionName = os.path.dirname(region_path).lower()
if regionName == "":
regionName = exelem_path.replace('_transformed.exelem', '')
base_region["Model"]["Sources"].append(
{
"FileName": exelem_path,
"RegionName": regionName,
"Type": "FILE"
}
)
#Pick one of the colors below
#if 'MUSCLES' in region_path or 'NECK' in region_path:
# base_region["Scene"]["Graphics"][0]["Material"] = "muscle"
#if 'BONE' in region_path:
# base_region["Scene"]["Graphics"][0]["Material"] = "bone"
#if 'LIGAMENT' in region_path:
# base_region["Scene"]["Graphics"][0]["Material"] = "white"
#if 'SKIN' in region_path:
base_region["Scene"]["Graphics"][0]["Material"] = "brown"
argon_document["RootRegion"] = root_region
#print('\n'.join(bits))
output = os.path.join(currentDir, EXPORT_NAME)
with open(output, 'w') as f:
f.write(json.dumps(argon_document, default=lambda o: o.__dict__, sort_keys=True, indent=2))
print('Generated ' + output)
def main():
data_files = []
print(os.listdir(DIR_2))
for path in os.listdir(DIR_2):
workingDir = DIR_2 + "/" + path
if os.path.isdir(workingDir):
generate_output(workingDir)
if __name__ == "__main__":
main()
model_sources = {
"Model": {
"Sources": [
{
"FileName": "FEMUR.EXNODE",
"RegionName": "/left_lower_limb/bones/femur",
"Type": "FILE"
},
{
"FileName": "FEMUR.EXELEM",
"RegionName": "/left_lower_limb/bones/femur",
"Type": "FILE"
}
]
},
}
