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levelzero.py
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levelzero.py
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from __future__ import print_function, division
import numpy as np
import h5py
from ctypes import *
#import numpy.ctypeslib as npct
from envisat import PhaseConverter
from sciamachy_module import NonlinCorrector
#-- globals --------------------------------------------------------------------
ENVI_FILENAME_SIZE = 63
MAX_UTC_STRING = 28
MAX_CLUSTER = 64
NUM_LV0_AUX_BCP = 16
NUM_LV0_AUX_PMTC_FRAME = 5
NUM_LV0_PMD_PACKET = 200
#-- structures -----------------------------------------------------------------
class dsd_envi(Structure):
_fields_ = [("name",c_char * 29),
("type",c_char * 2),
("flname",c_char * ENVI_FILENAME_SIZE),
("offset",c_uint),
("size",c_uint),
("num_dsr",c_uint),
("dsr_size",c_int)]
class mph_envi(Structure):
_fields_ = [("product",c_char * ENVI_FILENAME_SIZE),
("proc_stage",c_char * 2),
("ref_doc",c_char * 24),
("acquis",c_char *21),
("proc_center",c_char * 7),
("proc_time",c_char * MAX_UTC_STRING),
("soft_version",c_char * 15),
("sensing_start",c_char * MAX_UTC_STRING),
("sensing_stop",c_char * MAX_UTC_STRING),
("phase",c_char * 2),
("cycle",c_short),
("rel_orbit",c_int),
("abs_orbit",c_int),
("state_vector",c_char * MAX_UTC_STRING),
("delta_ut",c_double),
("x_position",c_double),
("y_position",c_double),
("z_position",c_double),
("x_velocity",c_double),
("y_velocity",c_double),
("z_velocity",c_double),
("vector_source",c_char * 3),
("utc_sbt_time",c_char * MAX_UTC_STRING),
("sat_binary_time",c_uint),
("clock_step",c_uint),
("leap_utc",c_char * MAX_UTC_STRING),
("leap_sign",c_short),
("leap_err",c_char * 2),
("product_err",c_char * 2),
("tot_size",c_uint),
("sph_size",c_uint),
("num_dsd",c_uint),
("dsd_size",c_uint),
("num_data_sets",c_uint)]
class sph0_scia(Structure):
_fields_ = [("descriptor", c_char * 29),
("start_lat", c_double),
("start_lon", c_double),
("stop_lat", c_double),
("stop_lon", c_double),
("sat_track", c_double),
("isp_errors", c_ushort),
("missing_isps", c_ushort),
("isp_discard", c_ushort),
("rs_sign", c_ushort),
("num_error_isps", c_int),
("error_isps_thres", c_double),
("num_miss_isps", c_int),
("miss_isps_thres", c_double),
("num_discard_isps", c_int),
("discard_isps_thres", c_double),
("num_rs_isps", c_int),
("rs_thres", c_double),
("tx_rx_polar", c_char * 6),
("swath", c_char * 4)]
"""
struct info_clus
{
unsigned char chanID;
unsigned char clusID;
unsigned char coAdding;
unsigned short start;
unsigned short length;
};
struct mds0_info
{
unsigned char packetID;
unsigned char category;
unsigned char stateID;
unsigned char numClusters;
unsigned short length;
unsigned short bcps;
unsigned short stateIndex;
unsigned int offset;
struct mjd_envi mjd;
struct info_clus cluster[MAX_CLUSTER];
};
struct mds0_aux
{
struct mjd_envi isp;
struct fep_hdr fep_hdr;
struct packet_hdr packet_hdr;
struct data_hdr data_hdr;
struct pmtc_hdr pmtc_hdr;
struct aux_src data_src;
};
struct mds0_det
{
unsigned short bcps;
unsigned short num_chan;
int orbit_vector[8];
struct mjd_envi isp;
struct fep_hdr fep_hdr;
struct packet_hdr packet_hdr;
struct data_hdr data_hdr;
struct pmtc_hdr pmtc_hdr;
struct det_src *data_src;
};
struct mjd_envi
{
int days;
unsigned int secnd;
unsigned int musec;
};
"""
class mjd_envi(Structure):
_fields_ = [("days", c_int),
("secnd", c_uint),
("musec", c_uint)]
class info_clus(Structure):
_fields_ = [("chanID", c_byte),
("clusID", c_byte),
("coAdding", c_byte),
("start", c_ushort),
("length", c_ushort)]
class mds0_info(Structure):
_fields_ = [("packetID", c_byte),
("category", c_byte),
("stateID", c_byte),
("numClusters", c_byte),
("length", c_ushort),
("bcps", c_ushort),
("stateIndex", c_ushort),
("offset", c_uint),
("mjd", mjd_envi),
("info_clus", info_clus * MAX_CLUSTER)]
"""
struct fep_hdr
{
struct mjd_envi gsrt;
unsigned short isp_length;
unsigned short crc_errs;
unsigned short rs_errs;
};
"""
class fep_hdr(Structure):
_fields_ = [("gsrt", mjd_envi),
("isp_length", c_ushort),
("crc_errs", c_ushort),
("rs_errs", c_ushort)]
"""
struct packet_hdr
{
union
{
struct packet_id_breakout
{
#ifdef _SWAP_TO_LITTLE_ENDIAN
unsigned short op_mode:5;
unsigned short vcid:5;
unsigned short :6;
#else
unsigned short :6;
unsigned short vcid:5;
unsigned short op_mode:5;
#endif
} field;
unsigned short two_byte;
} api;
unsigned short seq_cntrl;
unsigned short length;
};
"""
#puff.. if we don't need these in python.. please don't bother with ctypes unions
#class packet_id_breakout(Union):
class packet_hdr(Structure):
_fields_ = [("two_byte", c_ushort),
("seq_cntrl", c_ushort),
("length", c_ushort)]
"""
struct pmtc_hdr
{
union
{
struct pmtc_1_breakout
{
#ifdef _SWAP_TO_LITTLE_ENDIAN
unsigned char ndfm:2;
unsigned char :2;
unsigned char phase:4;
unsigned char sls:2;
unsigned char wls:2;
unsigned char apsm:2;
unsigned char ncwm:2;
#else
unsigned char phase:4;
unsigned char :2;
unsigned char ndfm:2;
unsigned char ncwm:2;
unsigned char apsm:2;
unsigned char wls:2;
unsigned char sls:2;
#endif
} field;
unsigned short two_byte;
} pmtc_1;
unsigned short scanner_mode;
union
{
struct az_breakout
{
#ifdef _SWAP_TO_LITTLE_ENDIAN
unsigned short repeat:12;
unsigned char basic:4;
unsigned char h_w:4;
unsigned char rel:4;
unsigned char corr:4;
unsigned char invert:1;
unsigned char filter:1;
unsigned char centre:1;
unsigned char type:1;
#else
unsigned char type:1;
unsigned char centre:1;
unsigned char filter:1;
unsigned char invert:1;
unsigned char corr:4;
unsigned char rel:4;
unsigned char h_w:4;
unsigned char basic:4;
unsigned short repeat:12;
#endif
} field;
unsigned int four_byte;
} az_param;
union
{
struct elv_breakout
{
#ifdef _SWAP_TO_LITTLE_ENDIAN
unsigned short repeat:12;
unsigned char basic:4;
unsigned char :4;
unsigned char rel:4;
unsigned char corr:4;
unsigned char invert:1;
unsigned char filter:1;
unsigned char centre:1;
unsigned char :1;
#else
unsigned char :1;
unsigned char centre:1;
unsigned char filter:1;
unsigned char invert:1;
unsigned char corr:4;
unsigned char rel:4;
unsigned char :4;
unsigned char basic:4;
unsigned short repeat:12;
#endif
} field;
unsigned int four_byte;
} elv_param;
unsigned char factor[6];
};
"""
class pmtc_hdr(Structure):
_fields_ = [("two_byte1", c_ushort),
("scanner_mode", c_ushort),
("four_byte1", c_uint), # 32 bit.. on a 64 bit build? this is bug.. but well.. also note that c_ulong is 64 bit here!
("four_byte2", c_uint),
("factor", c_byte * 6)]
"""
struct data_hdr
{
unsigned char category;
unsigned char state_id;
unsigned short length;
union
{
struct vector_breakout
{
#ifdef _SWAP_TO_LITTLE_ENDIAN
unsigned char atc_id:6;
unsigned char hsm:2;
unsigned char config_id:8;
#else
unsigned char hsm:2;
unsigned char atc_id:6;
unsigned char config_id:8;
#endif
} field;
unsigned short two_byte;
} rdv;
union
{
struct id_breakout
{
#ifdef _SWAP_TO_LITTLE_ENDIAN
unsigned char :4;
unsigned char packet:4;
unsigned char overflow:4;
unsigned char :4;
#else
unsigned char packet:4;
unsigned char :4;
unsigned char :4;
unsigned char overflow:4;
#endif
} field;
unsigned short two_byte;
} id;
unsigned int on_board_time;
};
"""
"""
struct aux_bcp
{
unsigned short sync;
unsigned short bcps;
union
{
struct flag_breakout
{
#ifdef _SWAP_TO_LITTLE_ENDIAN
unsigned char phase:4;
unsigned char m:1;
unsigned char d:1;
unsigned char eu:1;
unsigned char au:1;
unsigned char pointing:6;
unsigned char :2;
#else
unsigned char au:1;
unsigned char eu:1;
unsigned char d:1;
unsigned char m:1;
unsigned char phase:4;
unsigned char :2;
unsigned char pointing:6;
#endif
} field;
unsigned short two_byte;
} flags;
unsigned int azi_encode_cntr;
unsigned int ele_encode_cntr;
unsigned short azi_cntr_error;
unsigned short ele_cntr_error;
unsigned short azi_scan_error;
unsigned short ele_scan_error;
};
"""
class aux_bcp(Structure):
_fields_ = [("sync", c_ushort),
("bcps", c_ushort),
("two_byte", c_ushort),
("azi_encode_cntr", c_uint),
("ele_encode_cntr", c_uint),
("azi_cntr_error", c_ushort),
("ele_cntr_error", c_ushort),
("azi_scan_error", c_ushort),
("ele_scan_error", c_ushort)]
class data_hdr(Structure):
_fields_ = [("category", c_byte),
("state_id", c_byte),
("length", c_ushort),
("two_byte1", c_ushort),
("two_byte2", c_ushort),
("on_board_time", c_uint)] # 32 bit, contrary to what you'd expect, most likely a ctypes bug
# ("on_board_time", c_ulong)]
class pmtc_frame(Structure):
_fields_ = [("bcp", aux_bcp * NUM_LV0_AUX_BCP),
("bench_rad", c_ushort), # bench_cntrl
("bench_elv", c_ushort), # bench_cntrl
("bench_az", c_ushort)] # bench_cntrl
class mds0_aux(Structure):
_fields_ = [("isp", mjd_envi),
("fep_hdr", fep_hdr),
("packet_hdr", packet_hdr),
("data_hdr", data_hdr),
("pmtc_hdr", pmtc_hdr),
("data_src", pmtc_frame * NUM_LV0_AUX_PMTC_FRAME)] # aux_src structure basically this array of pmtc_frames
"""
struct chan_hdr
{
unsigned short sync;
unsigned short bcps;
unsigned short bias;
unsigned short temp;
union
{
struct
{
#ifdef _SWAP_TO_LITTLE_ENDIAN
unsigned char lu:2;
unsigned char is:2;
unsigned char id:4;
unsigned char clusters:8;
#else
unsigned char id:4;
unsigned char is:2;
unsigned char lu:2;
unsigned char clusters:8;
#endif
} field;
unsigned short two_byte;
} channel;
union
{
struct
{
#ifdef _SWAP_TO_LITTLE_ENDIAN
unsigned char status:3;
unsigned char ratio:5;
unsigned char frame:8;
#else
unsigned char ratio:5;
unsigned char status:3;
unsigned char frame:8;
#endif
} field;
unsigned short two_byte;
} ratio_hdr;
union
{
struct
{
#ifdef _SWAP_TO_LITTLE_ENDIAN
unsigned char cntrl:2;
unsigned char ratio:5;
unsigned short sec:9;
unsigned char mode:2;
unsigned short etf:14;
#else
unsigned short etf:14;
unsigned char mode:2;
unsigned short sec:9;
unsigned char ratio:5;
unsigned char cntrl:2;
#endif
} field;
unsigned int four_byte;
} command_vis;
union
{
struct
{
#ifdef _SWAP_TO_LITTLE_ENDIAN
unsigned char cntrl:2;
unsigned char pet:4;
unsigned char :2;
unsigned char bias:3;
unsigned char :3;
unsigned char comp:2;
unsigned char mode:2;
unsigned short etf:14;
#else
unsigned short etf:14;
unsigned char mode:2;
unsigned char comp:2;
unsigned char :3;
unsigned char bias:3;
unsigned char :2;
unsigned char pet:4;
unsigned char cntrl:2;
#endif
} field;
unsigned int four_byte;
} command_ir;
};
"""
class chan_hdr(Structure):
_fields_ = [("sync", c_ushort),
("bcps", c_ushort),
("bias", c_ushort),
("temp", c_ushort),
("two_byte1", c_ushort),
("two_byte2", c_ushort),
("four_byte1", c_uint),
("four_byte2", c_uint)]
# ("four_byte1", c_ulong),
# ("four_byte2", c_ulong)]
class chan_src(Structure):
_fields_ = [
("cluster_id", c_byte),
("co_adding", c_byte),
("sync", c_ushort),
("block_nr", c_ushort),
("start", c_ushort),
("length", c_ushort),
("data", c_char_p)]
class det_src(Structure):
_fields_ = [("hdr", chan_hdr),
("pixel", POINTER(chan_src))]
class mds0_det(Structure):
_fields_ = [("bcps", c_ushort),
("num_chan", c_ushort),
("orbit_vector", c_int * 8),
("isp", mjd_envi),
("fep_hdr", fep_hdr),
("packet_hdr", packet_hdr),
("data_hdr", data_hdr),
("pmtc_hdr", pmtc_hdr),
("data_src", POINTER(det_src))]
#-- functions ------------------------------------------------------------------
# convert ctypes mjd_envi to float mjd
def convert_mjd_struct_to_float(struct):
d = getattr(struct, "days")
s = getattr(struct, "secnd")
mu = getattr(struct, "musec")
return d + (s + mu/1000000.)/(3600*24.)
class LevelZeroFile:
"""
class that can read data from scia level 0 files
"""
def __init__(self):
self.lib = CDLL('levelzerolib.so')
self.mph = mph_envi()
self.sph = sph0_scia()
self.pc = PhaseConverter()
self.nlc = NonlinCorrector()
self.corrected = False
self.fname = None
def set_file(self, fname):
self.fname = fname
# TODO: can better be done with exact char positions, since this is the way l0 filenames are defined
def get_orbit(self):
if self.fname is None:
raise Exception("no filename set!")
strs = self.fname.split("_")
if len(strs) < 9:
raise Exception("wrong amount of underscores in level 0 file!")
return int(strs[-2])
def print_mph(self):
for field_name, field_type in self.mph._fields_:
print(field_name, getattr(self.mph, field_name))
def print_sph(self):
for field_name, field_type in self.sph._fields_:
print(field_name, getattr(self.sph, field_name))
def print_dsd(self):
for i_dsd in range(len(self.dsd)):
print()
for field_name, field_type in self.dsd[i_dsd]._fields_:
print(field_name, getattr(self.dsd[i_dsd], field_name))
# find the DSD that describes the scia source packets
def find_scia_source_dsd(self):
for dsd in self.dsd:
if getattr(dsd, "name") == "SCIAMACHY_SOURCE_PACKETS":
return dsd
return None
# pre: self.info is present
def find_infos(self, packet_id, state_ids):
infos = []
for inf in self.info:
sid = getattr(inf, "stateID")
if sid in state_ids:
pid = getattr(inf, "packetID")
if pid == packet_id:
infos.append(inf)
return infos
def print_info(self, idx):
for field_name, field_type in self.info[idx]._fields_:
print(field_name, getattr(self.info[idx], field_name))
def print_aux(self, idx):
for field_name, field_type in self.dark_aux[idx]._fields_:
print(field_name, getattr(self.dark_aux[idx], field_name))
def print_det(self, idx):
for field_name, field_type in self.dark_det[idx]._fields_:
print(field_name, getattr(self.dark_det[idx], field_name))
orbit_vector = getattr(self.dark_det[idx], "orbit_vector")
print("orbit_vector:")
for el in orbit_vector:
print(el)
mjd = getattr(self.dark_det[idx], "isp")
print("isp:")
for field_name, field_type in mjd._fields_:
print(field_name, getattr(mjd, field_name))
fep_hdr = getattr(self.dark_det[idx], "fep_hdr")
print("fep_hdr:")
for field_name, field_type in fep_hdr._fields_:
print(field_name, getattr(fep_hdr, field_name))
gsrt = getattr(fep_hdr, "gsrt") # fep_hdr.gsrt mjd_envi struct
for field_name, field_type in gsrt._fields_:
print(field_name, getattr(gsrt, field_name))
packet_hdr = getattr(self.dark_det[idx], "packet_hdr")
print("packet_hdr:")
for field_name, field_type in packet_hdr._fields_:
print(field_name, getattr(packet_hdr, field_name))
data_hdr = getattr(self.dark_det[idx], "data_hdr")
print("data_hdr:")
for field_name, field_type in data_hdr._fields_:
print(field_name, getattr(data_hdr, field_name))
pmtc_hdr = getattr(self.dark_det[idx], "pmtc_hdr")
print("pmtc_hdr:")
for field_name, field_type in pmtc_hdr._fields_:
print(field_name, getattr(pmtc_hdr, field_name))
def get_coadd(self, info):
#info_clus = getattr(info, "info_clus")
info_clus = info.info_clus
num_clus = info.numClusters
print(num_clus)
return getattr(info_clus[38], "coAdding")
# output:
# self.readouts: ch8 detector readouts (1024xN float32)
# self.dark_det_mjds: MJD2000 (float64) of readouts
def read_ch8(self, verbose=False):
#
# open
#
ret = self.lib.OpenFile(self.fname)
if ret < 0:
raise Exception("couldn't open file ["+self.fname+"]. return code = "+str(ret))
#
# read main product header
#
ret = self.lib._ENVI_RD_MPH(byref(self.mph))
if ret < 0:
raise Exception("couldn't read mph")
if verbose:
self.print_mph()
#
# read special product header
#
ret = self.lib._SCIA_LV0_RD_SPH(byref(self.mph), byref(self.sph))
if ret < 0:
raise Exception("couldn't read sph")
if verbose:
self.print_sph()
#
# read dsd's
#
n_dsd = self.mph.num_dsd
if verbose:
print("allocating "+str(n_dsd)+" dsd records..")
dsd_arr_type = dsd_envi * n_dsd
self.dsd = dsd_arr_type()
if verbose:
print(self.dsd)
ret = self.lib._ENVI_RD_DSD(byref(self.mph), byref(self.dsd))
if ret >= 0:
n_dsd = ret
else:
raise Exception("_ENVI_RD_DSD() failed")
if verbose:
self.print_dsd()
#
# read all info packets for dark det and source data
#
dsd = self.find_scia_source_dsd()
if dsd is None:
raise Exception("SCIAMACHY_SOURCE_PACKETS DSD not found!")
num_dsr = getattr(dsd, "num_dsr")
info_array_type = mds0_info * num_dsr
self.info = info_array_type()
ret = self.lib._SCIA_LV0_RD_MDS_INFO(c_uint(n_dsd), byref(self.dsd), byref(self.info))
if verbose:
print("nr info packets =", ret)
info_dark_det = self.find_infos(1, (8,26,46,63,67)) # 1:DET
info_dark_aux = self.find_infos(2, (8,26,46,63,67)) # 2:AUX
n_dark_det = len(info_dark_det)
n_dark_aux = len(info_dark_aux)
if verbose:
print("nr of dark aux =", n_dark_aux)
print("nr of dark det =", n_dark_det)
info_dark_det_type = mds0_info * n_dark_det
info_dark_det_ = info_dark_det_type()
info_dark_det_[:] = info_dark_det[:]
info_dark_aux_type = mds0_info * n_dark_aux
info_dark_aux_ = info_dark_aux_type()
info_dark_aux_[:] = info_dark_aux[:]
#
# read detector data using det info packets
#
chan_mask = 1<<(8-1) # channel 8
det_array_type = mds0_det * n_dark_det
self.dark_det = det_array_type()
det_data_type = c_uint * (1024*n_dark_det)
self.det_data = det_data_type()
mjds_type = c_double * n_dark_det
mjds = mjds_type()
coadds_type = c_ubyte * n_dark_det
coadds = coadds_type()
stateids_type = c_ubyte * n_dark_det
stateids = stateids_type()
n_readouts = self.lib._SCIA_LV0_RD_DET(byref(info_dark_det_), c_uint(n_dark_det), c_byte(chan_mask), byref(self.dark_det), self.det_data, mjds, coadds, stateids)
if n_readouts < 0:
raise Exception("_SCIA_LV0_RD_DET failed! ret="+str(ret))
#
# now get rid of useless packets and shrink data buffer
#
# turn into 2d numpy array and shrink
self.readouts = np.frombuffer(self.det_data, dtype=np.uint32).reshape((n_dark_det, 1024))
#print("TEST", self.readouts[600,0])
self.readouts = np.array(self.readouts[0:n_readouts, :], dtype=np.float64)
#print("shape=", self.readouts.shape, "self.readouts=", self.readouts)
#
# convert all readout metadata to numpy arrays
#
self.mjds = np.array(mjds[0:n_readouts], dtype=np.float64)
self.stateids = np.array(stateids[0:n_readouts], dtype=np.byte)
self.coadds = np.array(coadds[0:n_readouts], dtype=np.byte)
if verbose:
print("my very own mjds:", self.mjds)
#
# convert mjd's to eclipse orbit phase
#
phases, orbits = self.pc.get_phase(self.mjds, eclipseMode=True, getOrbits=True)
self.ephases = orbits + phases
if verbose:
print("my very own ephases:", self.ephases)
#
# read aux data using aux info packets (really not necessary in this case, but ok.)
#
# aux_data_type = mds0_aux * len(info_dark_aux)
# self.dark_aux = aux_data_type()
# ret = self.lib._SCIA_LV0_RD_AUX(byref(info_dark_aux_), c_uint(len(info_dark_aux)), self.dark_aux)
# if ret != len(info_dark_aux):
# raise Exception("_SCIA_LV0_RD_AUX failed!")
#
# close
#
ret = self.lib.CloseFile()
if ret < 0:
raise Exception("couldn't close file. return code = "+str(ret))
# correct nonlinearity
def correct_nlin(self):
self.readouts = self.nlc.correct_ch8(self.readouts)
self.corrected = True
# correct for coadding
def divide_coadd(self):
n_readouts = self.readouts.shape[0]
# print(len(self.coadds))
for i in range(n_readouts):
self.readouts[i,:] /= self.coadds[i]
#print(self.readouts[i,:])
def test_orbit_from_fname(fname):
l0 = LevelZeroFile()
test_fname = "/SCIA/LV0_01/O/SCI_NL__0POLRA20040128_161459_000060052023_00427_10000_2049.N1"
l0.set_file(test_fname)
print(l0.get_orbit(test_fname))
def saveNoise(orbit, exp_time, noise):
idx = orbit_dset[:] == orbit
if idx.sum() > 0:
# replace
i = np.nonzero(idx)[0]
orbit_dset[idx] = orbit
noise_dset[i,:] = noise
else:
# append
ax1 = orbit_dset.len()
orbit_dset.resize(ax1+1, axis=0)
orbit_dset[ax1] = orbit
ax1 = noise_dset.len()
noise_dset.resize(ax1+1, axis=0)
def median_absolute_deviation(a, axis=None):
"""Compute the median absolute deviation.
Returns the median absolute deviation (MAD) of the array elements.
The MAD is defined as ``median(abs(a - median(a)))``.
Parameters
----------
a : array_like
Input array or object that can be converted to an array.
axis : int, optional
Axis along which the medians are computed. The default (axis=None)
is to compute the median along a flattened version of the array.
Returns
-------
median_absolute_deviation : ndarray
A new array holding the result. If the input contains
integers, or floats of smaller precision than 64, then the output
data-type is float64. Otherwise, the output data-type is the same
as that of the input.
Examples
--------
This will generate random variates from a Gaussian distribution and return
the median absolute deviation for that distribution::
>>> from astropy.stats import median_absolute_deviation
>>> from numpy.random import randn
>>> randvar = randn(10000)
>>> mad = median_absolute_deviation(randvar)
See Also
--------
numpy.median
"""
a = np.array(a, copy=False)
a_median = np.median(a, axis=axis)
# re-broadcast the output median array to subtract it
if axis is not None:
a_median = np.expand_dims(a_median, axis=axis)
# calculated the median average deviation
return np.median(np.abs(a - a_median), axis=axis)
#-- main -----------------------------------------------------------------------
if __name__ == "__main__":
import subprocess
import matplotlib.pyplot as plt
import warnings
warnings.simplefilter("error") # warnings to errors
#np.set_printoptions(threshold=np.nan, precision=4, suppress=True, linewidth=np.nan)
from vardark_module import load_varkdark_orbit
from sciamachy_module import get_darkstateid, petcorr, n_chanpix
import envisat
n_pix = n_chanpix
dbname_long = "/SCIA/SDMF31/pieter/vardark_long.h5"
orbit_range = [10000,10010]
cmd = "inquire_scia_db.py --orbit="+str(orbit_range[0])+","+str(orbit_range[1])+" --level=0 --proc=O"
# orbit_range = [44000,44002]
# cmd = "inquire_scia_db.py --orbit="+str(orbit_range[0])+","+str(orbit_range[1])+" --level=0 --proc=P"
text_list = subprocess.check_output(cmd, shell=True)
fnames = text_list.splitlines()
output_fname = "noise_tng.h5"
exp_times = [0.125, 0.5, 1.0]
if h5py.is_hdf5(output_fname):
fout = h5py.File(output_fname, "r+") # assuming all the groups and datasets are already present.
else:
fout = h5py.File(output_fname, "w")
for exp_time in exp_times:
print("creating groups..")
grp = fout.create_group("pet"+str(exp_time))
orbit_dset = grp.create_dataset("orbit", (0,), maxshape = (envisat.last_orbit,), dtype='i')
noise_dset = grp.create_dataset("noise", (0, n_pix), maxshape = (envisat.last_orbit, n_pix), dtype='f')
zero1 = LevelZeroFile()
# zero.set_file("/SCIA/LV0_01/O/SCI_NL__0POLRA20040128_161459_000060052023_00427_10000_2049.N1")
for fname in fnames:
zero2 = LevelZeroFile()
print(fname)
zero2.set_file(fname)
zero2.read_ch8(verbose=False)
zero2.divide_coadd()
zero2.correct_nlin()
#print(zero2.ephases)
#print(zero2.dark_det_mjds)
if zero1.fname is not None:
#
# if we have a complete orbit window then get all the readouts that belong to the actual orbit
#
orbit = zero1.get_orbit()
#print("zero1 fname:", zero1.fname)
#print(zero1.ephases)
#print(zero1.dark_det_mjds)
#print(zero1.ephases, zero2.ephases)
ephases = np.concatenate((zero1.ephases, zero2.ephases))
mjds = np.concatenate((zero1.mjds, zero2.mjds))
readouts = np.concatenate((zero1.readouts, zero2.readouts))
states = np.concatenate((zero1.stateids, zero2.stateids))
orbits = np.trunc(ephases)
idx = orbits == orbit
#print(ephases.shape, orbits.shape, idx.shape)
#print(ephases, orbits, idx)
ephases = ephases[idx]
mjds = mjds[idx]
# print(readouts.shape, readouts[600:700,:])
readouts = readouts[idx,:]
states = states[idx]
wave_phases, wave_orbit, wave, wave_ao = load_varkdark_orbit(orbit, False)
wave_phases = np.mod(wave_phases, 1)
#
# compute and store noise for each exposure time (TODO: separate function?)
#
for exp_time in exp_times:
print("exp_time=", exp_time)
#
# open output group and its datasets
#
grp = fout["pet"+str(exp_time)]
orbit_dset = grp["orbit"]
noise_dset = grp["noise"]
#
# get all readouts for the state id that matches the exposure time
#
stateid = get_darkstateid(exp_time, orbit)
idx = states == stateid
ephases_ = np.mod(ephases[idx],1)
mjds_ = mjds[idx]