# Define cone geometry
cylinderHeight = 90.3332804037
coneUpperRadius = 635.3 / 2.
coneLowerRadius = 448.5 / 2.
# Slice
center = [249.00918273645539, 263.82920110192839]
imagingRadius = 216.742098118
#--------------------------------------------------------
# Embryo setup
#--------------------------------------------------------
# Create embryo
emb = pyfrp_embryo.embryo("Test")
# Set experimental details
emb.setDataResMu(dataResMu)
emb.setSliceDepthMu(sliceDepth)
emb.offsetBleachedPx = [
center[0] - sidelength / 2., center[1] - sidelength / 2.
]
# Geometry
emb.setGeometry2Cone(center, coneUpperRadius, coneLowerRadius, cylinderHeight)
# Update geometry properties in geo-file
emb.geometry.updateGeoFile()
# Create default ROIs
# Define cone geometry
cylinderHeight=90.3332804037
coneUpperRadius=635.3/2.
coneLowerRadius=448.5/2.
# Slice
center=[249.00918273645539, 263.82920110192839]
imagingRadius=216.742098118
#--------------------------------------------------------
# Embryo setup
#--------------------------------------------------------
# Create embryo
emb=pyfrp_embryo.embryo("Test")
# Set experimental details
emb.setDataResMu(dataResMu)
emb.setSliceDepthMu(sliceDepth)
emb.offsetBleachedPx=[center[0]-sidelength/2.,center[1]-sidelength/2.]
# Geometry
emb.setGeometry2Cone(center,coneUpperRadius,coneLowerRadius,cylinderHeight)
# Update geometry properties in geo-file
emb.geometry.updateGeoFile()
# Create default ROIs
emb.genDefaultROIs(emb.geometry.getCenter(),imagingRadius,rimFactor=rimFactor,sliceHeightPx=-sliceDepth)
emb.newAnalysis()
volSize = 30
# Add circular domain
d.addCircleByParameters([256, 256],
300,
0,
volSize,
genLoop=True,
genSurface=True)
# Add attractor mesh around center
v = d.vertices[0]
v.addToAttractor(attrField=None, LcMin=5., LcMax=20., DistMin=30., DistMax=60.)
# Write to file
d.writeToFile(sys.argv[1])
# Create embryo
emb = pyfrp_embryo.embryo("test")
# Set newly generated geofile as geometry
emb.setGeometry2Custom([256, 256], fnGeo=sys.argv[1], dim=2)
# Create mesh
sim = emb.newSimulation()
sim.mesh.genMesh()
# Plot mesh
sim.mesh.plotMesh()
raw_input()
sidelength = 140.
sliceDepth = 15.
sliceWidth = 5
center = [256, 256]
rimFactor = 0.8
# Simulation parameters
D = 50
steps = 1001
tEnd = 1500
# Start timer
starTime = time.time()
# Create embryo
emb = pyfrp_embryo.embryo("Demo")
# Define where data is
emb.setDataFolder(sys.argv[1])
# Set data parameters
emb.setDataResMu(dataResMu)
emb.setFrameInterval(frameinterval)
# Set experimental details
emb.setDataResMu(dataResMu)
emb.setSideLengthBleachedMu(sidelength)
emb.setSliceDepthMu(sliceDepth)
# Create a .geo file of a 2 dimensional domain
d = pyfrp_gmsh_geometry.domain()
def buildEmbryoWizard(fn,
ftype,
name,
nChannel=0,
enc="uint16",
fnDest=None,
createEmbryo=True,
recoverIdent=['recover', 'post'],
bleachIdent=['bleach'],
preIdent=['pre'],
cleanUp=True,
colorPrefix='_c00'):
"""Creates embryo object ready for analysis from microscope data.
(1) Extracts microscope data into .tif files
(2) Builds folder structure
(3) Moves image files in proper folders
(4) Creates embryo object and automatically sets filepaths properly
Args:
fn (str): Path to embryo folder
ftype (str): Type of microscopy file, such as lsm or czi
name (str): Name of embryo
Keyword Args:
nChannel (int): Defines which channel of the images contains relevant data
fnDest (str): Path of embryo data structure
createEmbryo (boo): Flag if embryo object should be created
recoverIdent (list): List of identifiers for recovery data
bleachIdent (list): List of identifiers for bleach data
preIdent (list): List of identifiers for pre-bleach data
cleanUp (bool): Clean up .tif files from other channels afterwards.
Returns:
pyfrp.subclasses.pyfrp_embryo.embryo: Created Embryo in case of success, otherwise -1
"""
# Fix path
fn = slashToFn(fixPath(fn))
# Make sure that input directory exists
if not os.path.isdir(fn):
printError(fn + " does not exist.")
return -1
# Get all files of right type
l = glob.glob(fn + '/*' + ftype)
if len(l) == 0:
printError(fn + "does not contain images of type " + ftype)
return -1
# Extract images using Bioformats
for f in l:
r = pyfrp_img_module.extractBioFormats(f,
fn,
debug=True,
series=0,
channel=nChannel,
enc=enc,
outputformat='tif')
if r == -1:
return -1
# Check for output directory
if fnDest == None:
fnDest = fn
fnDest = slashToFn(fixPath(fnDest))
# Create folder structure
makeEmbryoFolderStruct(fnDest)
# Sort image files in structure
sortImageFiles(fn,
fnDest,
ftype,
nChannel=nChannel,
recoverIdent=recoverIdent,
bleachIdent=bleachIdent,
preIdent=preIdent,
colorPrefix=colorPrefix,
cleanUp=cleanUp)
if createEmbryo:
from pyfrp.subclasses import pyfrp_embryo
emb = pyfrp_embryo.embryo(name)
emb.setDataFolder(fnDest + 'recover/')
a = emb.newAnalysis()
a.setFnPre(fnDest + 'pre/')
return emb
else:
return 1
from pyfrp.subclasses import pyfrp_embryo
import sys
# Create domain
d = pyfrp_gmsh_geometry.domain()
volSize=30
# Add circular domain
d.addCircleByParameters([256,256],300,0,volSize,genLoop=True,genSurface=True)
# Add attractor mesh around center
v=d.vertices[0]
v.addToAttractor(attrField=None,LcMin=5.,LcMax=20.,DistMin=30.,DistMax=60.)
# Write to file
d.writeToFile(sys.argv[1])
# Create embryo
emb=pyfrp_embryo.embryo("test")
# Set newly generated geofile as geometry
emb.setGeometry2Custom([256,256],fnGeo=sys.argv[1],dim=2)
# Create mesh
sim=emb.newSimulation()
sim.mesh.genMesh()
# Plot mesh
sim.mesh.plotMesh()
raw_input()
def buildEmbryoWizard(fn,ftype,name,nChannel=0,enc="uint16",fnDest=None,createEmbryo=True,recoverIdent=['recover','post'],bleachIdent=['bleach'],preIdent=['pre'],cleanUp=True,colorPrefix='_c00'): """Creates embryo object ready for analysis from microscope data. (1) Extracts microscope data into .tif files (2) Builds folder structure (3) Moves image files in proper folders (4) Creates embryo object and automatically sets filepaths properly Args: fn (str): Path to embryo folder ftype (str): Type of microscopy file, such as lsm or czi name (str): Name of embryo Keyword Args: nChannel (int): Defines which channel of the images contains relevant data fnDest (str): Path of embryo data structure createEmbryo (boo): Flag if embryo object should be created recoverIdent (list): List of identifiers for recovery data bleachIdent (list): List of identifiers for bleach data preIdent (list): List of identifiers for pre-bleach data cleanUp (bool): Clean up .tif files from other channels afterwards. Returns: pyfrp.subclasses.pyfrp_embryo.embryo: Created Embryo in case of success, otherwise -1 """ # Fix path fn=slashToFn(fixPath(fn)) # Make sure that input directory exists if not os.path.isdir(fn): printError(fn+ " does not exist.") return -1 # Get all files of right type l=glob.glob(fn+'/*'+ftype) if len(l)==0: printError(fn+ "does not contain images of type " + ftype) return -1 # Extract images using Bioformats for f in l: r=pyfrp_img_module.extractBioFormats(f,fn,debug=True,series=0,channel=nChannel,enc=enc,outputformat='tif') if r==-1: return -1 # Check for output directory if fnDest==None: fnDest=fn fnDest=slashToFn(fixPath(fnDest)) # Create folder structure makeEmbryoFolderStruct(fnDest) # Sort image files in structure sortImageFiles(fn,fnDest,ftype,nChannel=nChannel,recoverIdent=recoverIdent,bleachIdent=bleachIdent,preIdent=preIdent,colorPrefix=colorPrefix,cleanUp=cleanUp) if createEmbryo: from pyfrp.subclasses import pyfrp_embryo emb=pyfrp_embryo.embryo(name) emb.setDataFolder(fnDest+'recover/') a=emb.newAnalysis() a.setFnPre(fnDest+'pre/') return emb else: return 1
sidelength=140.
sliceDepth=15.
sliceWidth=5
center=[256,256]
rimFactor=0.8
# Simulation parameters
D=50
steps=1001
tEnd=1500
# Start timer
starTime=time.time()
# Create embryo
emb=pyfrp_embryo.embryo("Demo")
# Define where data is
emb.setDataFolder(sys.argv[1])
# Set data parameters
emb.setDataResMu(dataResMu)
emb.setFrameInterval(frameinterval)
# Set experimental details
emb.setDataResMu(dataResMu)
emb.setSideLengthBleachedMu(sidelength)
emb.setSliceDepthMu(sliceDepth)