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Commit 0b0310c4 authored by Yan Zhaojun's avatar Yan Zhaojun
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test

parent e6ed2c85
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csst_mci_sim/CTI/CTI.py
View file @ 0b0310c4
......@@ -14,14 +14,6 @@ parameters in parallel and serial direction.
"""
import numpy as np
# try:
# import cdm03bidir
# #import cdm03bidirTest as cdm03bidir #for testing purposes only
# except ImportError:
# print('import CTI module')
# #print ('No CDM03bidir module available, please compile it: f2py -c -m cdm03bidir cdm03bidir.f90')
#CDM03bidir
class CDM03bidir():
......@@ -59,7 +51,7 @@ class CDM03bidir():
self.params.update(self.values)
#read in trap information
trapdata = np.loadtxt(self.values['parallelTrapfile'])
trapdata = np.loadtxt(self.values['dir_path']+self.values['paralleltrapfile'])
if trapdata.ndim > 1:
self.nt_p = trapdata[:, 0]
self.sigma_p = trapdata[:, 1]
......@@ -70,7 +62,7 @@ class CDM03bidir():
self.sigma_p = [trapdata[1],]
self.taur_p = [trapdata[2],]
trapdata = np.loadtxt(self.values['serialTrapfile'])
trapdata = np.loadtxt(self.values['dir_path']+self.values['serialtrapfile'])
if trapdata.ndim > 1:
self.nt_s = trapdata[:, 0]
self.sigma_s = trapdata[:, 1]
......@@ -95,100 +87,8 @@ class CDM03bidir():
Set up the logger.
"""
self.logger = True
if self.log is None:
self.logger = False
def radiateFullCCD(self):
"""
This routine allows the whole CCD to be run through a radiation damage mode.
The routine takes into account the fact that the amplifiers are in the corners
of the CCD. The routine assumes that the CCD is using four amplifiers.
There is an excess of .copy() calls, which should probably be cleaned up. However,
given that I had problem with the Fortran code, I have kept the calls. If memory
becomes an issue then this should be cleaned.
:return: radiation damaged image
:rtype: ndarray
"""
ydim, xdim = self.data.shape
out = np.zeros((xdim, ydim))
#transpose the data, because Python has different convention than Fortran
data = self.data.transpose().copy()
for quad in self.values['quads']:
if self.logger:
self.log.info('Adding CTI to Q%i' % quad)
if quad == 0:
d = data[0:self.values['xsize'], 0:self.values['ysize']].copy()
tmp = self.applyRadiationDamage(d, iquadrant=quad).copy()
out[0:self.values['xsize'], 0:self.values['ysize']] = tmp
elif quad == 1:
d = data[self.values['xsize']:, :self.values['ysize']].copy()
tmp = self.applyRadiationDamage(d, iquadrant=quad).copy()
out[self.values['xsize']:, :self.values['ysize']] = tmp
elif quad == 2:
d = data[:self.values['xsize'], self.values['ysize']:].copy()
tmp = self.applyRadiationDamage(d, iquadrant=quad).copy()
out[:self.values['xsize'], self.values['ysize']:] = tmp
elif quad == 3:
d = data[self.values['xsize']:, self.values['ysize']:].copy()
tmp = self.applyRadiationDamage(d, iquadrant=quad).copy()
out[self.values['xsize']:, self.values['ysize']:] = tmp
else:
print( 'ERROR -- too many quadrants!!' )
self.log.error('Too many quadrants! This method allows only four quadrants.')
return out.transpose()
def radiateFullCCD2(self):
"""
This routine allows the whole CCD to be run through a radiation damage mode.
The routine takes into account the fact that the amplifiers are in the corners
of the CCD. The routine assumes that the CCD is using four amplifiers.
There is an excess of .copy() calls, which should probably be cleaned up. However,
given that I had problem with the Fortran code, I have kept the calls. If memory
becomes an issue then this should be cleaned.
:return: radiation damaged image
:rtype: ndarray
"""
ydim, xdim = self.data.shape
out = np.empty((ydim, xdim))
#transpose the data, because Python has different convention than Fortran
data = self.data.copy()
for quad in self.values['quads']:
if self.logger:
self.log.info('Adding CTI to Q%i' % quad)
if quad == 0:
d = data[:self.values['ysize'], :self.values['xsize']].copy()
tmp = self.applyRadiationDamage(d, iquadrant=quad).copy()
out[:self.values['ysize'], :self.values['xsize']] = tmp
elif quad == 1:
d = data[:self.values['ysize'], self.values['xsize']:].copy()
tmp = self.applyRadiationDamage(d, iquadrant=quad).copy()
out[:self.values['ysize'], self.values['xsize']:] = tmp
elif quad == 2:
d = data[self.values['ysize']:, :self.values['xsize']].copy()
tmp = self.applyRadiationDamage(d, iquadrant=quad).copy()
out[self.values['ysize']:, :self.values['xsize']] = tmp
elif quad == 3:
d = data[self.values['ysize']:, self.values['xsize']:].copy()
tmp = self.applyRadiationDamage(d, iquadrant=quad).copy()
out[self.values['ysize']:, self.values['xsize']:] = tmp
else:
print( 'ERROR -- too many quadrants!!')
self.log.error('Too many quadrants! This method allows only four quadrants.')
return out
# if self.log is None:
# self.logger = False
def applyRadiationDamage(self, data, iquadrant=0):
......@@ -255,7 +155,6 @@ class CDM03bidir():
#################################################################################
###modify
import sys
#sys.path.append('../so')
from ifs_so import cdm03bidir
# from ifs_so.cdm03.cpython-38-x86_64-linux-gnu import cdm03bidir
......@@ -275,220 +174,6 @@ class CDM03bidir():
class CDM03():
"""
Class to run CDM03 CTI model, class Fortran routine to perform the actual CDM03 calculations.
:param data: input data to be radiated
:type data: ndarray
:param input: input parameters
:type input: dictionary
:param log: instance to Python logging
:type log: logging instance
"""
def __init__(self, input, data, log=None):
"""
Class constructor.
:param data: input data to be radiated
:type data: ndarray
:param input: input parameters
:type input: dictionary
:param log: instance to Python logging
:type log: logging instance
"""
try:
import cdm03
except ImportError:
print( 'No CDM03 module available, please compile it: f2py -c -m cdm03 cdm03.f90')
self.data = data
self.values = dict(quads=(0,1,2,3), xsize=2048, ysize=2066, dob=0.0, rdose=8.0e9)
self.values.update(input)
self.log = log
self._setupLogger()
def _setupLogger(self):
"""
Set up the logger.
"""
self.logger = True
if self.log is None:
self.logger = False
def radiateFullCCD(self):
"""
This routine allows the whole CCD to be run through a radiation damage mode.
The routine takes into account the fact that the amplifiers are in the corners
of the CCD. The routine assumes that the CCD is using four amplifiers.
There is an excess of .copy() calls, which should probably be cleaned up. However,
given that I had problem with the Fortran code, I have kept the calls. If memory
becomes an issue then this should be cleaned.
:return: radiation damaged image
:rtype: ndarray
"""
ydim, xdim = self.data.shape
out = np.zeros((xdim, ydim))
#transpose the data, because Python has different convention than Fortran
data = self.data.transpose().copy()
for quad in self.values['quads']:
if self.logger:
self.log.info('Adding CTI to Q%i' % quad)
if quad == 0:
d = data[0:self.values['xsize'], 0:self.values['ysize']].copy()
tmp = self.applyRadiationDamage(d, iquadrant=quad).copy()
out[0:self.values['xsize'], 0:self.values['ysize']] = tmp
elif quad == 1:
d = data[self.values['xsize']:, :self.values['ysize']].copy()
tmp = self.applyRadiationDamage(d, iquadrant=quad).copy()
out[self.values['xsize']:, :self.values['ysize']] = tmp
elif quad == 2:
d = data[:self.values['xsize'], self.values['ysize']:].copy()
tmp = self.applyRadiationDamage(d, iquadrant=quad).copy()
out[:self.values['xsize'], self.values['ysize']:] = tmp
elif quad == 3:
d = data[self.values['xsize']:, self.values['ysize']:].copy()
tmp = self.applyRadiationDamage(d, iquadrant=quad).copy()
out[self.values['xsize']:, self.values['ysize']:] = tmp
else:
print ('ERROR -- too many quadrants!!')
self.log.error('Too many quadrants! This method allows only four quadrants.')
return out.transpose()
def radiateFullCCD2(self):
"""
This routine allows the whole CCD to be run through a radiation damage mode.
The routine takes into account the fact that the amplifiers are in the corners
of the CCD. The routine assumes that the CCD is using four amplifiers.
There is an excess of .copy() calls, which should probably be cleaned up. However,
given that I had problem with the Fortran code, I have kept the calls. If memory
becomes an issue then this should be cleaned.
:return: radiation damaged image
:rtype: ndarray
"""
ydim, xdim = self.data.shape
out = np.empty((ydim, xdim))
#transpose the data, because Python has different convention than Fortran
data = self.data.copy()
for quad in self.values['quads']:
if self.logger:
self.log.info('Adding CTI to Q%i' % quad)
if quad == 0:
d = data[:self.values['ysize'], :self.values['xsize']].copy()
tmp = self.applyRadiationDamage(d, iquadrant=quad).copy()
out[:self.values['ysize'], :self.values['xsize']] = tmp
elif quad == 1:
d = data[:self.values['ysize'], self.values['xsize']:].copy()
tmp = self.applyRadiationDamage(d, iquadrant=quad).copy()
out[:self.values['ysize'], self.values['xsize']:] = tmp
elif quad == 2:
d = data[self.values['ysize']:, :self.values['xsize']].copy()
tmp = self.applyRadiationDamage(d, iquadrant=quad).copy()
out[self.values['ysize']:, :self.values['xsize']] = tmp
elif quad == 3:
d = data[self.values['ysize']:, self.values['xsize']:].copy()
tmp = self.applyRadiationDamage(d, iquadrant=quad).copy()
out[self.values['ysize']:, self.values['xsize']:] = tmp
else:
print ('ERROR -- too many quadrants!!')
self.log.error('Too many quadrants! This method allows only four quadrants.')
return out
def applyRadiationDamage(self, data, iquadrant=0):
"""
Apply radian damage based on FORTRAN CDM03 model. The method assumes that
input data covers only a single quadrant defined by the iquadrant integer.
:param data: imaging data to which the CDM03 model will be applied to.
:type data: ndarray
:param iquandrant: number of the quadrant to process
:type iquandrant: int
cdm03 - Function signature::
sout = cdm03(sinp,iflip,jflip,dob,rdose,in_nt,in_sigma,in_tr,[xdim,ydim,zdim])
Required arguments:
sinp : input rank-2 array('d') with bounds (xdim,ydim)
iflip : input int
jflip : input int
dob : input float
rdose : input float
in_nt : input rank-1 array('d') with bounds (zdim)
in_sigma : input rank-1 array('d') with bounds (zdim)
in_tr : input rank-1 array('d') with bounds (zdim)
Optional arguments:
xdim := shape(sinp,0) input int
ydim := shape(sinp,1) input int
zdim := len(in_nt) input int
Return objects:
sout : rank-2 array('d') with bounds (xdim,ydim)
.. Note:: Because Python/NumPy arrays are different row/column based, one needs
to be extra careful here. NumPy.asfortranarray will be called to get
an array laid out in Fortran order in memory. Before returning the
array will be laid out in memory in C-style (row-major order).
:return: image that has been run through the CDM03 model
:rtype: ndarray
"""
#read in trap information
trapdata = np.loadtxt(self.values['trapfile'])
nt = trapdata[:, 0]
sigma = trapdata[:, 1]
taur = trapdata[:, 2]
iflip = iquadrant / 2
jflip = iquadrant % 2
if self.logger:
self.log.info('nt=' + str(nt))
self.log.info('sigma= ' + str(sigma))
self.log.info('taur= ' + str(taur))
self.log.info('dob=%f' % self.values['dob'])
self.log.info('rdose=%e' % self.values['rdose'])
self.log.info('xsize=%i' % data.shape[1])
self.log.info('ysize=%i' % data.shape[0])
self.log.info('quadrant=%i' % iquadrant)
self.log.info('iflip=%i' % iflip)
self.log.info('jflip=%i' % jflip)
# #call Fortran routine
# CTIed = cdm03.cdm03(np.asfortranarray(data),
# iflip, jflip,
# self.values['dob'], self.values['rdose'],
# nt, sigma, taur)
###modify
import sys
sys.path.append('../CTI')
import cdm03
#################################################################################
CTIed = cdm03.cdm03(np.asfortranarray(data),
jflip, iflip,
self.values['dob'], self.values['rdose'],
nt,sigma,taur )
return np.asanyarray(CTIed)
#################################################################################################################
......
csst_mci_sim/mci_data/mci_all_9K.config
View file @ 0b0310c4
......@@ -14,20 +14,22 @@ prescan = 27
overscan = 320
#charge trap information file
parallelTrapfile=MCI_inputdata/cdm_euclid_parallel.dat
serialTrapfile=MCI_inputdata/cdm_euclid_serial.dat
parallelTrapfile=MCI_inputdata/data/cdm_euclid_parallel.dat
serialTrapfile=MCI_inputdata/data/cdm_euclid_serial.dat
#cosmetic defects input file
cosmeticsFile_b =MCI_inputdata/Cosmetics_b.txt
cosmeticsFile_g =MCI_inputdata/data/Cosmetics_g.txt
cosmeticsFile_r =MCI_inputdata/Cosmetics_r.txt
cosmeticsFile_r =MCI_inputdata/data/Cosmetics_r.txt
cosmeticsFile_i =MCI_inputdata/data/Cosmetics_i.txt
###comicray information file
cosmicraylengths=MCI_inputdata/cdf_cr_length.dat
cosmicraylengths=MCI_inputdata/data/cdf_cr_length.dat
cosmicraydistance=MCI_inputdata/cdf_cr_total.dat
cosmicraydistance=MCI_inputdata/data/cdf_cr_total.dat
......
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