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py_mdv.py
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py_mdv.py
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""" Utilities for reading of MDV data into numpy objects
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the name of Argonne National Laboratory nor the names of its
contributors may be used to endorse or promote products derived from this
software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL Scott Collis BE LIABLE FOR ANY
DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-------------------------------------------------------------------------------
Code is adapted from Nitin Bharadwaj's Matlab code
Scott Collis, Argonne National Laboratory,
Computing Environment and Life Sciences Directorate
ARM Climate Research Facility
United States Department of Energy
USE
---
Currently this code works only on polar MDV files which are gzipped.. future
versions will be expanded to load cartesian and deal with non-gzipped files
This will be updates with some examples
REQUIREMENTS
------------
Needs Numpy, datetime, gzip
HISTORY
-------
2011-05-23 Start of development
Scott Collis [email protected]
0.1: basic functionality
2011-05-24
1.0: Added helper functions to calculate cartesian co-ordinates, forced the
init function to get all headers on execute
"""
__author__ = "Scott Collis <[email protected]>"
__version__ = "1.0"
import struct
import gzip
import StringIO
import zlib
from numpy import (array, float32, putmask, NaN, floor, arange, zeros, cos, sin,
pi, arcsin, meshgrid, ones)
import datetime
def radar_coords_to_cart(rng, az, ele, debug=False):
"""
Asumes standard atmosphere, ie R=4Re/3
"""
Re=6371.0*1000.0
#h=(r^2 + (4Re/3)^2 + 2r(4Re/3)sin(ele))^1/2 -4Re/3
#s=4Re/3arcsin(rcos(ele)/(4Re/3+h))
p_r=4.0*Re/3.0
rm=rng*1000.0
z=(rm**2 + p_r**2 + 2.0*rm*p_r*sin(ele*pi/180.0))**0.5 -p_r
#arc length
s=p_r*arcsin(rm*cos(ele*pi/180.)/(p_r+z))
if debug: print "Z=", z, "s=", s
y=s*cos(az*pi/180.0)
x=s*sin(az*pi/180.0)
return x,y,z
class read_mdv:
def __init__(self, filename, **kwargs):
debug=kwargs.get('debug', False) #Noise on or off
#The class initializes by loading the binary data
if debug: print "Opening ", filename
self.fileptr=open(filename, 'rb') #open and add the binary file to the class
#Some information about the MDV file structure
self.MDV_CHUNK_INFO_LEN=480
self.MDV_INFO_LEN=512
self.MDV_LONG_FIELD_LEN=64
self.MDV_MAX_PROJ_PARAMS=8
self.MDV_MAX_VLEVELS=122
self.MDV_NAME_LEN=128
self.MDV_SHORT_FIELD_LEN=16
self.MDV_TRANSFORM_LEN=16
self.MDV_UNITS_LEN=16
self.MDV_N_COORD_LABELS=3
self.MDV_COORD_UNITS_LEN=32
# (x,y) in degrees. Simple latitude-longitude grid.
# Also known as the Simple Cylindrical or Platte Carree projection.
self.PROJ_LATLON = 0
# (x,y) in km. Lambert Conformal Conic projection.
self.PROJ_LAMBERT_CONF = 3
# (x,y) in km. Polar Stereographic projection.
self.PROJ_POLAR_STEREO = 5
# Cartesian, (x,y) in km. This is a simple line-of-sight projection used for single
# radar sites. The formal name is Oblique Lambert Azimuthal projection.
self.PROJ_FLAT = 8
# radar data in native Plan Position Indicator (PPI) coordinates of
# range, azimuth angle and elevation angle. x is radial range (km), y is azimuth angle (deg), z is
# elev angle (deg).
self.PROJ_POLAR_RADAR = 9
# (x,y) in km. Oblique Stereographic projection.
self.PROJ_OBLIQUE_STEREO = 12
# radar data in native Range Height Indicator (RHI) coordinates.
# x is radial range (km), y is elev angle (deg), z is az angle (deg).
self.PROJ_RHI_RADAR = 13
# ***************** COMPRESSION *******************
self.COMPRESSION_NONE = 0# no compression
self.COMPRESSION_ZLIB = 3# Lempel-Ziv
self.COMPRESSION_BZIP = 4# bzip2
self.COMPRESSION_GZIP = 5# Lempel-Ziv in gzip format
# ***************** COMPRESSION CODE *******************
self.TA_NOT_COMPRESSED =791621423
self.GZIP_COMPRESSED = 4160223223
# ***************** TRANSFORM *******************
self.DATA_TRANSFORM_NONE = 0# None
self.DATA_TRANSFORM_LOG = 1# Natural log
# ***************** BIT ENCODING *******************
self.ENCODING_INT8 = 1 # unsigned 8 bit integer
self.ENCODING_INT16 = 2 # unsigned 16 bit integer
self.ENCODING_FLOAT32 = 5 # 32 bit IEEE floating point
# ***************** CHUNK HEADER and DATA *******************
self.CHUNK_DSRADAR_PARAMS = 3
self.CHUNK_DSRADAR_ELEVATIONS=10
self.CHUNK_DSRADAR_CALIB=7
self.DS_LABEL_LEN=40
self.NCHAR_DS_RADAR_PARAMS= 2*self.DS_LABEL_LEN
self.DS_RADAR_CALIB_NAME_LEN=16
self.DS_RADAR_CALIB_MISSING=-9999.0
if debug: print "Getting master header"
self.get_master_header()
if debug: print "getting field headers"
self.get_field_headers(self.master_header['nfields'])
if debug: print "getting vlevel headers"
self.get_vlevel_headers(self.master_header['nfields'])
if debug: print "getting chunk headers"
self.get_chunk_headers(self.master_header['nchunks'])
if debug: print "Reading Chunks"
self.read_chunks()
if debug: print "Calculating Radar coordinates"
self.calc_geometry()
if debug: print "Making usable time objects"
self.append_time()
if debug: print "Calculating cartesian coordinates"
self.append_carts()
if debug: print "indexing fields"
self.index_fields()
def read_list_from_file(self, items, forms, endian, **kwargs):
debug=kwargs.get('debug', False) #Noise on or off
my_dict={}
for i in range(len(forms)):
nbytes=struct.calcsize(forms[i])
if debug: print "reading ", nbytes, " of header data"
bin_data=self.fileptr.read(nbytes)
if 'c' in forms[i]:
my_dict.update({items[i]: "".join(struct.unpack(endian+forms[i], bin_data)).split('\x00')[0]})
else:
my_dict.update({items[i]: struct.unpack(endian+forms[i], bin_data)})
if len(my_dict[items[i]])==1:
my_dict[items[i]]=my_dict[items[i]][0]
return my_dict
def close(self):
#close the mdv file
self.fileptr.close()
def get_master_header(self):
endian='>'
items=["record_len1","struct_id","revision_number","time_gen","user_time","time_begin","time_end","time_centroid","time_expire","num_data_times","index_number","data_dimension","data_collection_type","user_data","native_vlevel_type","vlevel_type","vlevel_included","grid_orientation","data_ordering","nfields","ngates","nrays","nsweeps","nchunks","field_hdr_offset","vlevel_hdr_offset","chunk_hdr_offset","field_grids_differ","user_data_si328","time_written","unused_si325","user_data_fl326","sensor_lon","sensor_lat","sensor_alt","unused_fl3212","data_set_info","data_set_name","data_set_source","record_len2"]
forms=['i','i','i','i','i','i','i','i','i','i','i','i','i','i','i','i','i','i','i','i','i','i','i','i','i','i','i', 'i', '8i', 'i', '5i', '6f', 'f', 'f', 'f', '12f', '%(n)dc' %{'n':self.MDV_INFO_LEN}, '%(n)dc' %{'n':self.MDV_NAME_LEN}, '%(n)dc' %{'n':self.MDV_NAME_LEN}, 'i']
#print len(items)
#print len(forms)
#print forms
my_dict=self.read_list_from_file(items, forms, '>')
self.master_header=my_dict
def get_field_headers(self, nfields):
items=["record_len1", "struct_id", "field_code", "user_time1", "forecast_delta", "user_time2", "user_time3", "forecast_time", "user_time4", "ngates", "nrays", "nsweeps", "proj_type", "encoding_type", "data_element_nbytes", "field_data_offset", "volume_size", "user_data_si32", "compression_type", "transform_type", "scaling_type", "native_vlevel_type", "vlevel_type", "dz_constant", "data_dimension", "zoom_clipped", "zoom_no_overlap", "unused_si32", "proj_origin_lat", "proj_origin_lon", "proj_param", "vert_reference", "grid_dx", "grid_dy", "grid_dz", "grid_minx", "grid_miny", "grid_minz", "scale", "bias", "bad_data_value", "missing_data_value", "proj_rotation", "user_data_fl32", "min_value", "max_value", "min_value_orig_vol", "max_value_orig_vol", "unused_fl32", "field_name_long", "field_name", "units", "transform", "unused_char", "record_len2"]
forms=['i']*17 + ['10i'] + ['i']*9+['4i']+['f', 'f', '%(n)df' %{'n':self.MDV_MAX_PROJ_PARAMS}]+['f']*12+['4f']+['f']*5+['%(n)dc' %{'n':self.MDV_LONG_FIELD_LEN}, '%(n)dc' %{'n':self.MDV_SHORT_FIELD_LEN},'%(n)dc' %{'n':self.MDV_UNITS_LEN},'%(n)dc' %{'n':self.MDV_TRANSFORM_LEN},'%(n)dc' %{'n':self.MDV_UNITS_LEN}, 'i']
fld_headers=[]
for i in range(nfields):
my_dict=self.read_list_from_file(items, forms, '>')
fld_headers.append(my_dict)
self.field_headers=fld_headers
def get_vlevel_headers(self, nfields):
items=["record_len1","struct_id","type","unused_si32","level","unused_fl32","record_len2"]
forms=['i', 'i','%(n)di' %{'n':self.MDV_MAX_VLEVELS}, '4i', '%(n)df' %{'n':self.MDV_MAX_VLEVELS}, '5f', 'i']
vl_headers=[]
for i in range(nfields):
my_dict=self.read_list_from_file(items, forms, '>')
vl_headers.append(my_dict)
self.vlevel_headers=vl_headers
def get_chunk_headers(self, nchunks):
items=["record_len1","struct_id","chunk_id","chunk_data_offset","size","unused_si32","info","record_len2"]
forms=['i']*5 + ['2i', '%(n)dc' %{'n':self.MDV_CHUNK_INFO_LEN}, 'i']
ch_headers=[]
for i in range(nchunks):
my_dict=self.read_list_from_file(items, forms, '>')
ch_headers.append(my_dict)
self.chunk_headers=ch_headers
def get_compression_info(self):
#we assume the file pointer is at the right spot!
items=['magic_cookie','nbytes_uncompressed','nbytes_compressed','nbytes_coded','spare']
forms=['I']*4+['2I']
my_dict=self.read_list_from_file(items, forms, '>')
self.current_compression_info=my_dict
def read_a_field(self, fnum, **kwargs):
debug=kwargs.get('debug', False)
try:
sweep_list= getattr(self, self.field_headers[fnum]['field_name'])
if debug: print 'Getting data from object'
except AttributeError:
if debug: print 'No data found in object, populating'
self.fileptr.seek(self.field_headers[fnum]['field_data_offset'])
items=['vlevel_offsets', 'vlevel_nbytes']
forms=['%(n)dI' %{'n':self.master_header['nsweeps']}]*2
sweep_info_dict=self.read_list_from_file(items, forms, '>')
sweep_list=zeros([self.master_header['nsweeps'], self.master_header['nrays'],self.master_header['ngates']], dtype=float32)
for sw in range(self.master_header['nsweeps']):
if debug: print "doint sweep ", sw
self.get_compression_info()
#print self.current_compression_info
compressed_data=self.fileptr.read(self.current_compression_info['nbytes_coded'])
#pp=open('/tmp/foo2.gz', 'wb')
#pp.write(compressed_data)
#pp.close()
cd_fobj=StringIO.StringIO(compressed_data)
gzip_file_handle = gzip.GzipFile(fileobj=cd_fobj)
n_pts=self.master_header['ngates']*self.master_header['nrays']
if self.field_headers[fnum]['encoding_type'] == self.ENCODING_INT8:
form='>%(n)dB' %{'n':n_pts}
elif self.field_headers[fnum]['encoding_type'] == self.ENCODING_INT16:
form='>%(n)dH' %{'n':n_pts}
elif self.field_headers[fnum]['encoding_type'] == self.ENCODING_FLOAT32:
form='>%(n)df' %{'n':n_pts}
print "using: ", form
decompressed_data = gzip_file_handle.read(struct.calcsize(form))
gzip_file_handle.close()
my_array=array(struct.unpack(form, decompressed_data)).reshape((self.master_header['nrays'],self.master_header['ngates'])).astype(float32)
putmask(my_array, my_array==self.field_headers[fnum]['bad_data_value'], [NaN])
ret_array=my_array*self.field_headers[fnum]['scale']+ self.field_headers[fnum]['bias']
sweep_list[sw, :, :]=ret_array
setattr(self, self.field_headers[fnum]['field_name'], sweep_list)
return sweep_list
def get_all_fields(self):
my_list=[]
for i in range(self.master_header['nfields']):
print "reading field"
my_list.append(self.read_a_field(i))
def read_radar_info(self, nbytes):
weareat=self.fileptr.tell()
items=["radar_id","radar_type","nfields","ngates","samples_per_beam","scan_type","scan_mode","nfields_current","field_flag","polarization","follow_mode","prf_mode","spare_ints","radar_constant","altitude_km","latitude_deg","longitude_deg","gate_spacing_km","start_range_km","horiz_beam_width_deg","vert_beam_width_deg","pulse_width_us","prf_hz","wavelength_cm","xmit_peak_pwr_watts","receiver_mds_dbm","receiver_gain_db","antenna_gain_db","system_gain_db","unambig_vel_mps","unambig_range_km","measXmitPowerDbmH_dbm","measXmitPowerDbmV_dbm","prt_s","prt2_s","spare_floats","radar_name","scan_type_name"]
forms=['i']*12 + ['2i'] +['f']*22 + ['4f', '%(n)dc' %{'n':self.DS_LABEL_LEN}, '%(n)dc' %{'n':self.DS_LABEL_LEN}]
#for i in range(len(forms)):
# print items[i], ':', forms[i]
radar_info_dict=self.read_list_from_file(items, forms, '>')
self.radar_info=radar_info_dict
chunk_read_bytes=self.fileptr.tell()-weareat
#print self.fileptr.tell()-weareat
#print nbytes-chunk_read_bytes
self.fileptr.seek(nbytes-chunk_read_bytes,1)
def get_elevs(self,nbytes):
SIZE_FLOAT=4.0
nelevations=floor(nbytes/SIZE_FLOAT)
#print nelevations
fid_start=self.fileptr.tell()
form='%(n)df' %{'n':nelevations}
eledata=self.fileptr.read(struct.calcsize(form))
elevations=array(struct.unpack(form, eledata))
self.elevations=elevations
chunk_read_bytes=self.fileptr.tell()-fid_start
#print chunk_read_bytes
self.fileptr.seek(nbytes-chunk_read_bytes,1)
#print nbytes-chunk_read_bytes
def get_calib(self, nbytes):
fid_start=self.fileptr.tell()
items=["radar_name","year","month","day","hour","minute","second","wavelength_cm","beamwidth_h_deg","beamwidth_v_deg","antenna_gain_h_db","antenna_gain_v_db","pulse_width_us","xmit_power_h_dbm","xmit_power_v_dbm","twoway_waveguide_loss_h_db","twoway_waveguide_loss_v_db","twoway_radome_loss_h_db","twoway_radome_loss_v_db","filter_loss_db","radar_constant_h_db","radar_constant_v_db","noise_h_co_dbm","noise_h_cx_dbm","noise_v_co_dbm","noise_v_cx_dbm","rx_gain_h_co_dbm","rx_gain_h_cx_dbm","rx_gain_v_co_dbm","rx_gain_v_cx_dbm","zh1km_co_dbz","zh1km_cx_dbz","zv1km_co_dbz","zv1km_cx_dbz","sun_h_co_dbm","sun_h_cx_dbm","sun_v_co_dbm","sun_v_cx_dbm","noise_source_h_dbm","noise_source_v_dbm","power_meas_loss_h_db","power_meas_loss_v_db","coupler_fwd_loss_h_db","coupler_fwd_loss_v_db","zdr_bias_db","ldr_h_bias_db","ldr_v_bias_db","system_phidp_deg","test_pulse_h_dbm","test_pulse_v_dbm","rx_slope_h_co_db","rx_slope_h_cx_db","rx_slope_v_co_db","rx_slope_v_cx_db","I0_h_co_dbm","I0_h_cx_dbm","I0_v_co_dbm","I0_v_cx_dbm","spare"]
forms=[ '%(n)dc' %{'n':self.DS_RADAR_CALIB_NAME_LEN}]+ ['i']*6 + ['f']*51 + ['14f']
radar_calib_dict=self.read_list_from_file(items, forms, '>')
self.calib_info=radar_calib_dict
chunk_read_bytes=self.fileptr.tell()-fid_start
self.fileptr.seek(nbytes-chunk_read_bytes,1)
def read_chunks(self, **kwargs):
debug=kwargs.get('debug', False)
cal_info=[]
self.fileptr.seek(self.chunk_headers[0]['chunk_data_offset'])
for i in range(self.master_header['nchunks']):
self.fileptr.seek(self.chunk_headers[i]['chunk_data_offset'])
#print self.CHUNK_DSRADAR_ELEVATIONS, '==', self.chunk_headers[i]['chunk_id']
if self.chunk_headers[i]['chunk_id']==self.CHUNK_DSRADAR_PARAMS:
if debug:print 'Getting radar info'
self.read_radar_info(self.chunk_headers[i]['size'])
elif self.chunk_headers[i]['chunk_id']==self.CHUNK_DSRADAR_CALIB:#self.CHUNK_DSRADAR_ELEVATIONS:
if debug:print 'getting elevations'
self.get_elevs(self.chunk_headers[i]['size'])
elif self.chunk_headers[i]['chunk_id']==self.CHUNK_DSRADAR_ELEVATIONS:#self.CHUNK_DSRADAR_CALIB:
if debug:print 'getting cal'
self.get_calib(self.chunk_headers[i]['size'])
def calc_geometry(self):
range_km=self.field_headers[1]['grid_minx']+arange(self.master_header['ngates'])*self.field_headers[1]['grid_dx']
if self.field_headers[1]['proj_type']==self.PROJ_RHI_RADAR:
self.scan_type='rhi'
el_deg=self.field_headers[1]['grid_miny']+arange(self.master_header['nrays'])*self.field_headers[1]['grid_dy']
az_deg=self.vlevel_headers[1]['level'][0:self.master_header['nsweeps']]
if self.field_headers[1]['proj_type']==self.PROJ_POLAR_RADAR:
self.scan_type='ppi'
az_deg=self.field_headers[1]['grid_miny']+arange(self.master_header['nrays'])*self.field_headers[1]['grid_dy']
el_deg=self.vlevel_headers[1]['level'][0:self.master_header['nsweeps']]
self.az_deg=az_deg
self.range_km=range_km
self.el_deg=el_deg
def append_time(self):
time_objects=['time_begin', 'time_end', 'time_centroid']
time_dict={}
base_time=datetime.datetime(1970, 1, 1, 00, 00)
for obj in time_objects:
time_dict.update({obj: base_time+datetime.timedelta(seconds=self.master_header[obj])})
self.times=time_dict
def append_carts(self):
#simple calculation involving 4/3 earth radius
xx=zeros([self.master_header['nsweeps'], self.master_header['nrays'],self.master_header['ngates']], dtype=float32)
yy=zeros([self.master_header['nsweeps'], self.master_header['nrays'],self.master_header['ngates']], dtype=float32)
zz=zeros([self.master_header['nsweeps'], self.master_header['nrays'],self.master_header['ngates']], dtype=float32)
if self.scan_type=='rhi':
rg,ele=meshgrid(self.range_km, self.el_deg)
for aznum in range(self.master_header['nsweeps']):
azg=ones(rg.shape, dtype=float32)*self.az_deg[aznum]
x,y,z=radar_coords_to_cart(rg, azg, ele)
zz[aznum, :, :]=z
xx[aznum, :, :]=x
yy[aznum, :, :]=y
if self.scan_type=='ppi':
rg,azg=meshgrid(self.range_km, self.az_deg)
for elnum in range(self.master_header['nsweeps']):
ele=ones(rg.shape, dtype=float32)*self.el_deg[elnum]
x,y,z=radar_coords_to_cart(rg, azg, ele)
zz[elnum, :, :]=z
xx[elnum, :, :]=x
yy[elnum, :, :]=y
self.carts={'x':xx, 'y':yy, 'z':zz}
def index_fields(self):
flds=[self.field_headers[i]['field_name'] for i in range(len(self.field_headers))]
self.fields=flds