84 lines
2.7 KiB
Python
84 lines
2.7 KiB
Python
import numpy as np
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#import matplotlib.pyplot as plt
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from netCDF4 import Dataset
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from glob import glob
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def read_NetCDF_file_py(file_name,data_name):
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ncfile = Dataset(file_name,mode='r')
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dataOUT = ncfile.variables[data_name][:]
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ncfile.close()
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return dataOUT
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#end def
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def write_NetCDF_file_py(file_name,data_name,data_IN,data_IN_dtype,lx,ly,lz):
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# Important !
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# Note the dataOUT should have the shape (lz,ly,lx)
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data_IN.shape=(lz,ly,lx) # make sure data_IN has the right shape
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# open a new netCDF file for writing.
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ncfile = Dataset(file_name,'w')
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# create the output data.
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# create the x, y and z dimensions.
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ncfile.createDimension('x',lx)
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ncfile.createDimension('y',ly)
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ncfile.createDimension('z',lz)
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# create the variable (4 byte integer in this case)
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# first argument is name of variable, second is datatype, third is
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# a tuple with the names of dimensions.
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data = ncfile.createVariable(data_name,data_IN_dtype,('z','y','x'))
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data[:] = data_IN
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#data.voxel_unit = 'micrometer'
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#data.voxel_size=5.7
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ncfile.close()
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print '**Info: The *.nc file is written successfully !'
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#end def
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#NOTE: To do a 3-phase segmentation, you need the original segmented image file,
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# which contains 0->solid and 1->pore.
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print "**Info: Need to read the original input segmetned image, "
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print " which contains 0 -> solid and 1 -> pore"
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img_name = "domain1_64_reduced_lbpm.bin"
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print "**Info: Read the image: "+img_name
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img = np.fromfile(img_name,dtype = np.int8)
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input_nc_file_group = glob('OutputData_vis*.nc')
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input_nc_file_var_name = 'Phase'
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output_nc_file_var_name = 'Phase_seg'
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if not input_nc_file_group:
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print "**Error: No input data files: "+input_nc_file_group+" have been found !"
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else:
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for ii in range(len(input_nc_file_group)):
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input_nc_file_name = input_nc_file_group[ii]
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output_nc_file_name = input_nc_file_name[:-3]+'_PhaseSeg.nc'
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print "**Info: Read data file: "+input_nc_file_name
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phase=read_NetCDF_file_py(input_nc_file_name,input_nc_file_var_name)
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(lz,ly,lx) = phase.shape
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img.shape = phase.shape
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# Double check the phase field has the same size as the segmented image
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if phase.size != img.size:
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print "**Error: The size of the loaded segmented image does not match the size of the phase field data !"
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else:
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phase[phase>0.0]=1
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phase[phase<0.0]=2
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phase[img==0]=0
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phase = phase.astype(np.int32)
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write_NetCDF_file_py(output_nc_file_name,output_nc_file_var_name,phase,phase.dtype.char,lx,ly,lz)
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print "**Info: The segmented phase field from the floating phase field has been written."
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#end if
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#end for
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#end if
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