def compress(*arg, **karg):
# This function compress the file with a given compress parameter
# compress(file,comression parameter)
fileName = arg[0]
try:
log = karg["log"]
except KeyError:
log = logMod.Log("", nolog=True)
# Open HDF file
try:
sd_id = SD(fileName, SDC.WRITE)
except TypeError:
sd_id = SD(fileName.encode('ascii', 'ignore'), SDC.WRITE)
#open evry data set
for dsname in list(sd_id.datasets().keys()):
sds_id = sd_id.select(dsname)
data = np.copy(sds_id[:])
sds_id[:] = 0
try:
sds_id.setcompress(*arg[1]) # args depend on compression type
except HDF4Error as msg:
log.log('e', Nom, "Error compressing the dataset")
sds_id.endaccess()
sd_id.end()
return
sds_id[:] = data
sds_id.endaccess()
# Close hdf file to flush compressed data.
sd_id.end()
return None
def Open_Datasets(rad_file,tau_file):
f1 = SD.SD('Rad/{0}'.format(rad_file))
g1 = f1.select('EV_250_RefSB')
Radiance_620_d = g1.get()[0,:,:]
scale = g1.attributes()['reflectance_scales'][0]
offset = g1.attributes()['reflectance_offsets'][0]
Radiance_620 = scale*(Radiance_620_d-offset)
LAT = f1.select('Latitude').get()
LON = f1.select('Longitude').get()
f2 = SD.SD('Tau/{0}'.format(tau_file))
COT = access_dataset('Cloud_Optical_Thickness_37',f2)
COTERR = access_dataset('Cloud_Optical_Thickness_Uncertainty_37',f2) #Percentage Uncertainty in COT_data
SZA = access_dataset('Solar_Zenith',f2)
SA = access_dataset('Solar_Azimuth',f2)
VZA = access_dataset('Sensor_Zenith',f2)
VA = access_dataset('Sensor_Azimuth',f2)
REFF = access_dataset('Cloud_Effective_Radius_37',f2) #check - tick
CTH = access_dataset('Cloud_Top_Height',f2) #CHECK - tick
CWV = access_dataset('Above_Cloud_Water_Vapor_094',f2)
#CloudMask = access_dataset('Cloud_Mask_1km',f2)
RAZ = interpolation_fix(SA)-interpolation_fix(VA)
return [VZA,LAT,LON,COT,COTERR,SZA,RAZ,REFF,CTH,CWV,Radiance_620]
def __init__(self, path, mode='r'):
if mode == 'r':
self._hdf = SD.SD(path, SD.SDC.READ)
elif mode == 'w':
self._hdf = SD.SD(path, SD.SDC.WRITE)
else:
raise ValueError("Bad mode=%s" % mode)
self._datasets = self._hdf.datasets().keys()
def proc(indir, outdir, inname, outname):
path = indir + "/" + inname
hdf = HDF(path)
sd = SD(path)
vs = hdf.vstart()
v = hdf.vgstart()
mod_vg = v.attach("MOD_Grid_monthly_CMG_VI")
vg_members = mod_vg.tagrefs()
# print vg_members
mod_vg = v.attach("MOD_Grid_monthly_CMG_VI")
tag, ref = mod_vg.tagrefs()[0]
# print tag, ref
vg0 = v.attach(ref)
# print vg0._name
tagrefs = vg0.tagrefs()
# print tagrefs
for tag, ref in tagrefs:
if tag == HC.DFTAG_NDG:
sds = sd.select(sd.reftoindex(ref))
name = sds.info()[0]
# print name
if name == "CMG 0.05 Deg Monthly NDVI":
sd = SD(path)
sds = sd.select(sd.reftoindex(ref))
ndvi = np.float64(sds.get())
sds.endaccess()
elif name == "CMG 0.05 Deg Monthly EVI":
sd = SD(path)
sds = sd.select(sd.reftoindex(ref))
evi = np.float64(sds.get())
sds.endaccess()
sd.end()
v.end()
data = ndvi
name = outdir + "/" + outname + ".tif"
cols = 7200
rows = 3600
originX = -180.0
originY = 90.0
pixelWidth = 0.05
pixelHeight = -0.05
driver = gdal.GetDriverByName('GTiff')
newRasterfn = name
outRaster = driver.Create(newRasterfn, cols, rows, 1, gdal.GDT_Float32)
outRaster.SetGeoTransform(
(originX, pixelWidth, 0, originY, 0, pixelHeight))
outband = outRaster.GetRasterBand(1)
outband.WriteArray(data)
outRasterSRS = osr.SpatialReference()
outRasterSRS.ImportFromEPSG(4326)
outRaster.SetProjection(outRasterSRS.ExportToWkt())
outband.FlushCache()
def get_data(filename, fieldname, SD_field_rawData):
'''
INPUT
filename: string - hdf file filepath
fieldname: string - name of desired dataset
SD_or_rawData: boolean - 0 returns SD, 1 returns field, 2 returns rawData
RETURN SD/ raw dataset
'''
if SD_field_rawData==0:
return SD(filename) #science data set
elif SD_field_rawData==1:
return SD(filename).select(fieldname) #field
else:
return SD(filename).select(fieldname).get() #raw data
def btd1(mod, rad):
from pyhdf import SD
f = SD.SD(mod)
sds = f.select('Brightness_Temperature')
# sds=f.select('Brightness_Temperature')
#note that the shape of the file, is currently (406,270) this shape can be altered depedending on the file type.
btd = np.repeat(np.repeat((sds.get()[:, 0:406, 0:270] + 15000) * 0.01, 5, axis=1), 5, axis=2).reshape(7, 2030, 1350)
#data is over sampled
#TODO include over sampling
diff = btd[0] - btd[1]
sds = f.select('cloud_top_temperature_1km')
ctt = (sds.get() + 15000) * 0.01
sds = f.select('Cloud_Phase_Optical_Properties')
phase1 = sds.get()
sds = f.select('Cloud_Phase_Infrared_1km')
phase2 = sds.get()
f = SD.SD(rad)
lat=np.repeat(np.repeat(f.select('Latitude').get(),5,axis=0),5,axis=1)
lon = np.repeat(np.repeat(f.select('Longitude').get(), 5, axis=0), 5, axis=1)
sds = f.select('EV_250_Aggr1km_RefSB')
red = (sds.get()[0]+sds.attributes()['reflectance_offsets'][0]) * sds.attributes()['reflectance_scales'][0]
sds = f.select('EV_1KM_RefSB')
_800 = (sds.get()[-1]+sds.attributes()['reflectance_offsets'][-1]) * sds.attributes()['reflectance_scales'][-1]
blue = (sds.get()[2]+sds.attributes()['reflectance_offsets'][2]) * sds.attributes()['reflectance_scales'][2]
grn = (sds.get()[3]+sds.attributes()['reflectance_offsets'][3]) * sds.attributes()['reflectance_scales'][3]
sds=f.select('EV_500_Aggr1km_RefSB')
_2105_band = (sds.get()[-1] + sds.attributes()['reflectance_offsets'][-1]) * sds.attributes()['reflectance_scales'][-1]
_1600_band = (sds.get()[-2] + sds.attributes()['reflectance_offsets'][-2]) * sds.attributes()['reflectance_scales'][-2]
_1200_band = (sds.get()[-3] + sds.attributes()['reflectance_offsets'][-3]) * sds.attributes()['reflectance_scales'][-3]
#TODO add this to your log book to remember that you updated your plots with a linear filter to amplify colour
colour=np.zeros([3,2030,1354])
colour[0]=red
colour[1]=grn
colour[2]=blue
#c=np.where(colour>0.15)
#a1=0.15
#a2=0.37
#max_val=colour[:,:,:].max()
#c2=(a2-a1)/(max_val-a1)
#c1=(1-c2)*a1
#colour[c]=c1+c2*colour[c]
return colour, phase1,phase2,diff,_2105_band,_1600_band,_1200_band,_800,ctt,lat,lon
def h4lookup(path, swath = "Earth UV-2 Swath"):
'''
only look-up datasets, ignore vdata and
"WavelengthReferenceColumn" is that.
'''
hdf = HDF(path)
v = hdf.vgstart()
s2_vg = v.attach(swath)
geo_tag, geo_ref = s2_vg.tagrefs()[0]
dat_tag, dat_ref = s2_vg.tagrefs()[1]
s2_vg.detach()
#--------------------------------------------
# found geoloaction & data fields
#--------------------------------------------
geo_vgs = v.attach(geo_ref); dat_vgs = v.attach(dat_ref)
gvg_tagrefs = geo_vgs.tagrefs(); dvg_tagrefs = dat_vgs.tagrefs()
geo_vgs.detach(); dat_vgs.detach()
tagrefs_list = gvg_tagrefs + dvg_tagrefs
refs_dict = {}
#--------------------------------------------
# create dict in which keys are names in hdf and values are refs
#--------------------------------------------
sd = SD(path)
for tr in tagrefs_list:
tag, ref = tr
if tag == HC.DFTAG_NDG:
sds = sd.select(sd.reftoindex(ref))
refs_dict[sds.info()[0]] = ref
sds.endaccess(); sd.end(); v.end(); hdf.close()
return refs_dict
def read_hdf4(file_name, array_name):
"""
Read 2-D tomographic data from hdf4 file.
Opens ``file_name`` and reads the contents
of the array specified by ``array_name`` in
the specified group of the HDF file.
Parameters
----------
file_name : str
Input HDF file.
array_name : str
Name of the array to be read at exchange group.
x_start, x_end, x_step : scalar, optional
Values of the start, end and step of the
slicing for the whole ndarray.
y_start, y_end, y_step : scalar, optional
Values of the start, end and step of the
slicing for the whole ndarray.
Returns
-------
out : ndarray
Returns the data as a matrix.
"""
# Read data from file.
f = SD.SD(file_name)
sds = f.select(array_name)
hdfdata = sds.get()
sds.endaccess()
f.end()
return hdfdata
def __init__(self, file_path):
self.file_path = file_path
data_file = hdf.SD(file_path, hdf.SDC.READ)
lat_data = pd.DataFrame(data_file.select('Latitude').get())
long_data = pd.DataFrame(data_file.select('Longitude').get())
self.bounding_box = self.__calculate_bounds__(lat_data, long_data)
self.timestamp = dt.datetime.now()
def btd2(mod):
from pyhdf import SD
f = SD.SD(mod)
sds = f.select('Brightness_Temperature')
# sds=f.select('Brightness_Temperature')
btd = np.repeat(np.repeat((sds.get()[:, 0:406, 0:270] + 15000) * 0.01, 5, axis=1), 5, axis=2).reshape(7, 2030, 1350)
diff = btd[0] - btd[1]
sds = f.select('cloud_top_temperature_1km')
ctt = (sds.get() + 15000) * 0.01
sds = f.select('Cloud_Phase_Optical_Properties')
phase1 = sds.get()
sds = f.select('Cloud_Phase_Infrared_1km')
phase2 = sds.get()
# f=SD.SD(rad)
# sds=f.select('EV_250_Aggr1km_RefSB')
# band_600_r=sds.get()[0]*sds.attributes()['reflectance_scales'][0]
# band_800_r=sds.get()[1]*sds.attributes()['reflectance_scales'][1]
# sds=f.select('EV_500_Aggr1km_RefSB')
# plot the brightness temperature differences too.
# sds=f.select('EV_500_Aggr1km_RefSB')
# band_6_r=sds.get()[-1]*sds.attributes()['reflectance_scales'][-1]
# sds=f.select('EV_1KM_Emissive')
# band_7_r=(sds.get()[-5]+sds.attributes()['radiance_offsets'][-5])*sds.attributes()['radiance_scales'][-5]
return diff, ctt
def btd(mod):
from pyhdf import SD
f=SD.SD(mod)
sds=f.select('Brightness_Temperature')
#sds=f.select('Brightness_Temperature')
btd=np.repeat(np.repeat((sds.get()[:,0:406,:]+15000)*0.01,5,axis=1),5,axis=2).reshape(7,2030,15)
"""find a way to improve the phase discrimination at 1km"""
diff=btd[0]-btd[1]
sds=f.select('cloud_top_temperature_1km')
ctt=(sds.get()+15000)*0.01
sds=f.select('Cloud_Phase_Optical_Properties')
phase1=sds.get()
sds=f.select('Cloud_Phase_Infrared_1km')
phase2=sds.get()
sds=f.select('Latitude')
lat=np.repeat(np.repeat(sds.get(),5,axis=0),5,axis=1)
sds=f.select('Longitude')
lon=np.repeat(np.repeat(sds.get(),5,axis=0),5,axis=1)
sds=f.select('cloud_top_height_1km')
cth=sds.get()
sds=f.select('Cloud_Optical_Thickness')
tau=sds.get()*0.009999999776482582
#sds=f.select('EV_1KM_Emissive')
#band_7_r=(sds.get()[-5]+sds.attributes()['radiance_offsets'][-5])*sds.attributes()['radiance_scales'][-5]
return diff,ctt,phase1,phase2,cth,lat,lon,tau
def hdf2txt(hdfFile, txtFile):
try:
hdf = SD(hdfFile) # open the HDF file
attr = hdf.attributes() # get global attribute dictionary
dsets = hdf.datasets() # get dataset dictionary
except HDF4Error, msg:
print "HDF4Error", msg
def get_l2hdf_prod(ifile):
#---------------------------------------------------------------
master_prod_list = ['angstrom','aot_862','aot_865','aot_869','cdom_index','chlor_a','ipar','Kd_490','nflh','par','pic','poc',
'Rrs_410','Rrs_412','Rrs_413','Rrs_443','Rrs_486','Rrs_488','Rrs_490','Rrs_510','Rrs_531','Rrs_547','Rrs_551',
'Rrs_555','Rrs_560','Rrs_620','Rrs_665','Rrs_667','Rrs_670','Rrs_671','Rrs_681','Rrs_645','Rrs_859','Rrs_482','Rrs_561','Rrs_655','adg_giop',
'adg_gsm','adg_qaa','aph_giop','aph_gsm','aph_qaa','arp','a_giop','a_gsm','a_qaa','bbp_giop','bbp_gsm','bbp_qaa',
'bb_giop','bb_gsm','bb_qaa','BT','calcite_2b','calcite_3b','cfe','chlor_oc2','chlor_oc3','chlor_oc4','chl_clark','chl_ocx',
'chl_gsm','chl_octsc','evi','flh','ipar','Kd_lee','Kd_morel','Kd_mueller','Kd_obpg','KPAR_lee','KPAR_morel','ndvi',
'poc_clark','poc_stramski_490','tsm_clark','Zeu_morel','Zhl_morel','Zphotic_lee','Zsd_morel', 'chl_oc2', 'sst','sst4']
prod_list = []
ftype= hdf_cdf_version(ifile)
if ftype == 'hdf4':
f= SD(ifile,SDC.READ)
dsets= f.datasets()
dsNames = dsets.keys()
dsNames= sorted(dsNames)
f.end()
full_var_name= np.asarray(dsNames)
bad_names= np.asarray(['elat','slat','clat','elon','slon','clon','k_no2','cntl_pt_cols', \
'k_oz','tilt','cntl_pt_rows','latitude','vcal_gain','csol_z','longitude', \
'vcal_offset','day','msec','wavelength','detnum','mside','year','l2_flags','F0', 'Tau_r', 'aw', 'bbw', \
'scan_ell','sen_mat', 'sun_ref', 'tilt_flags', 'tilt_ranges','nflag','ntilts','orb_vec','alt_ang','att_ang'])
for vn in full_var_name:
test_index= np.where(bad_names == vn)
if len(bad_names[test_index]) == 0:
prod_list.append(vn)
print ( '\nfull prod list inside of hdf4 get_l2hdf_prod... ' )
print ( prod_list )
return prod_list
if ftype == 'hdf5':
f = Dataset(ifile, 'r')
group_names= f.groups.keys()
var_name= f.groups['geophysical_data'].variables.keys()
var_name= sorted(var_name)
var_name= np.asarray(var_name)
full_list_indx= np.where(var_name != 'l2_flags')
prod_list= var_name[full_list_indx]
f.close()
print ( '\nfull prod list inside of hdf5 get_l2hdf_prod... ' )
print ( prod_list )
return prod_list
def __init__(self, hdfFn):
self.epsgID = None # 4326
self.proj4Str = None # '+proj=longlat +datum=WGS84 +no_defs'
self.ulX = None
self.ulY = None
self.resolution = None
self.sd = pyhdfSD.SD(hdfFn, pyhdfSD.SDC.WRITE | pyhdfSD.SDC.CREATE)
def read_airs_hdfeos(fname, fidx=None, **kwargs):
'''
2016.04.11, Walter Sessions
Moving to IRIS, need to read in radiances for retrieval.
fname str, full path to hdf-eos file
Wait... I should be generating files and making new collocation deals
'''
from pyhdf import SD, SDC
from numpy import recarray, ndarray
#_
hdf = SD(fname, SDC.READ)
#_define record array
dtype = [ ('AIRS_radiance', ndarray),
('AIRS_epoch', ndarray),
('AIRS_latitude', ndarray),
('AIRS_longitude', ndarray) ]
airs = recarray((0,), dtype)
setattr(airs, 'fname', fname)
#_
idx = arange(hdf.select('Time')[:].size) if fidx is None else fidx
def getHDFData(self, sds):
# open the hdf file for reading
hdf=SD.SD(self.filename)
# read the sds data
sds=hdf.select(sds)
data=sds.get()
return data
def get_hdf_SD_file_variables(filename):
"""
Get all the variables from an HDF SD file
:param str filename: The filename of the file to get the variables from
:returns: An OrderedDict containing the variables from the file
"""
if not SD:
raise ImportError(
"HDF support was not installed, please reinstall with pyhdf to read HDF files."
)
variables = None
try:
# Open the file.
datafile = SD.SD(filename)
# List of required variable names.
variables = datafile.datasets()
# Close the file
datafile.end()
except:
logging.error("Error while reading SD data")
return variables
def get_hdf_data(self, sds_name):
# open the hdf file for reading
hdf = SD.SD(self.filename)
# read the sds data
sds_obj = hdf.select(sds_name)
data = sds_obj.get()
return data
def read_hdf4(srcPath, varName, Slice=None, verbose=True):
h4 = SD.SD(srcPath) # 'r')
if Slice == None: Slice = slice(None, None, None)
'''
h4Var = h4.select(varName)
print dir(h4Var)
print h4Var.dimensions()
sys.exit()
'''
try:
h4Var = h4.select(varName)
aOut = h4Var[:][Slice]
except:
print('!' * 80)
print('I/O Error')
print('Blank File? %s' % srcPath)
print('Blank array will be returned [ %s ]' % varName)
print(h4Var.dimensions())
print(Slice)
print('!' * 80)
#raise ValueError
if verbose == True:
print('\t[READ_HDF4] %s [%s] -> %s' % (srcPath, varName, aOut.shape))
# print '\t[READ_HDF4] %s %s -> %s'%( srcPath, h4Var.dimensions(), aOut.shape)
#h4.close()
return aOut
def extract_hdf_radiance(misr_file, shrink_shape=False):
"""
Extract radiance data from the misr_file given and
shrink it if shrink_shape is false
"""
hdf = SD(misr_file)
# Pull radiance data from the hdf file and put it into a list
color_band_ds = [hdf.select('Red Radiance/RDQI'),hdf.select('Green Radiance/RDQI'),hdf.select('Blue Radiance/RDQI')]
# Pull solar zentih data
solar_zenith = hdf.select('SolarZenith')[:,:,:]
# Realign width and height if shrink shape is true
if(shrink_shape == True):
expand_val = shrinked[1]
expand_tuple = shrink_tuple[1]
else:
expand_val = shrinked[0]
expand_tuple = shrink_tuple[0]
red = color_band_ds[0][:,:,:]
green = color_band_ds[1][:,:,:]
blue = color_band_ds[2][:,:,:]
# Get rid of the additional 2 bits on the right of the radiance fdata
red = (np.int16((np.int16(red) >> 2) & 0x3FFF)).astype(np.float_)
green = (np.int16((np.int16(green) >> 2) & 0x3FFF)).astype(np.float_)
blue = (np.int16((np.int16(blue) >> 2) & 0x3FFF)).astype(np.float_)
# Clear out fill data
red[red >= 16378.0] = np.nan
green[green >= 16378.0] = np.nan
blue[blue >= 16378.0]= np.nan
solarZenith_e = np.zeros(expand_tuple)
# Expand the solar zenith data into the current width x height and get rid of data > 90
for i in range(len(solar_zenith)):
solarZenith_e[i] = np.array(solar_zenith[i].repeat(expand_val,axis=0).repeat(expand_val,axis=1))
solarZenith_e[i][solarZenith_e[i] >= 90] = -1
solarZenith_e[i][solarZenith_e[i] < 0] = np.nan
if(shrink_shape == True):
red_s = [0]*len(red)
green_s = [0]*len(red)
blue_s = [0]*len(red)
for i in range(len(red)):
red_s[i] = np.array(shrink(red[i],128,512))
green_s[i] = np.array(shrink(green[i],128,512))
blue_s[i] = np.array(shrink(blue[i],128,512))
if(shrink_shape == True): return np.array(([red_s,green_s,blue_s,solarZenith_e]))
# Return the array of tuples that keep the r, g, b and solar zenith data per pixel
return np.array([red,green,blue,solarZenith_e])
def modisread_day_of_year(folder):
print ' '
print '____________Read Modis Day_of_Year_____________'
print ' '
d = {}
cs_clouds = 1000
granules = modis_granules(folder)
#Chose one File
k = granules.keys()[0]
filename_doy = granules[k]['day_of_year']
print 'read day_of_year: ' + folder + filename_doy
f_doy = SD(folder + filename_doy)
print ' '
for key in ['day_of_year', 'Latitude', 'Longitude']:
d[key] = sp.array(f_doy.select(key).get(), sp.int16)
if key == 'day_of_year':
day_of_year = []
for n in d[key][0].flatten():
#flag=convert_decimal_to_8bit(n)
flag = sp.binary_repr(n, width=16)
day_of_year.append(int(flag)) #0->cloudy, 1->clear
doy = sp.array(day_of_year).reshape(d[key].shape[1:3])
d[key] = doy
print ' done.'
d['day_of_year'] = d['day_of_year'][:, :-1000 / cs_clouds]
d['Latitude'] = d[
'Latitude'][:, :-1000 /
cs_clouds] #remove the right-hand-side edge pixels
d['Longitude'] = d['Longitude'][:, :-1000 / cs_clouds]
print 'image shape: ' + str(d['day_of_year'].shape)
print ' '
return d['day_of_year'], d['Longitude'], d['Latitude']
def co_locate(cal,mod):
from calipso_run_updated_to_analyse import Cal2
try:
c=Cal2(cal)
from pyhdf import SD
#lat=c.coords()[0]
#lon=c.coords()[1]
lat,lon,Image2,Image3=c.file_sort_s()
#c=np.where((lat>-68)&(lat<-48))
#lat=lat[c]
#lon=lon[c]
#different co-ordinate resolutions of each product
#here we are using the r5km resolution
#btd=c.btd_10()
#both products are offset by 20 pixels, meaning the temperature products are offset by 20kms.
#c.close()
f=SD.SD(mod)
subdataset_name='Latitude'
sds=f.select(subdataset_name)
#lat2=np.repeat(np.repeat(sds.get()[:406,:270],5,axis=0),5,axis=1).reshape(2030,1350,order='C')
#sds=f.select('Longitude')
#lon2=np.repeat(np.repeat(sds.get()[:406,:270],5,axis=0),5,axis=1).reshape(2030,1350,order='C')
#x=np.zeros([2030,1354])
lat2=sds.get()[:406,:3]
sds=f.select('Longitude')
lon2=sds.get()[:406,:3]
#x=np.zeros([2030,1354])
cal_index=[]
f.end()
#x=np.zeros([2030,1354])
iterr=[]
iter2=[]
lat1=[]
lon1=[]
coords_x=[]
coords_y=[]
for i in range(len(lat)):
c1=abs(lat2-lat[i])
#print i
c2=abs(lon2-lon[i])
c3=np.sqrt(c1**2+c2**2)
#print c1.min()
c=np.where((c3==c3.min())&(c3.min()<0.025))
if len(c[0])>0:
lat1=lat1+[i for i in range(5*i,5*i+5)]
#iter2.append(c[0])
#btd1.append(btd[i])
coords_x=coords_x+np.arange(5*c[0],5*c[0]+5).tolist()
coords_y=coords_y+np.repeat(5*c[1],5).tolist()
return np.array([coords_x,coords_y]),lat1
except:
print 'did not work'
return [],[]
pass
def hdf4lookup(self, path, swath):
hdf = HDF(path)
sd = SD(path)
vs = hdf.vstart()
v = hdf.vgstart()
vg = v.attach(swath)
vg_members = vg.tagrefs()
vg0_members = {}
for tag, ref in vg_members:
vg0 = v.attach(ref)
if tag == HC.DFTAG_VG:
vg0_members[vg0._name] = vg0.tagrefs()
vg0.detach
vg.detach
lookup_dict = {}
for key in vg0_members.keys():
for tag, ref in vg0_members[key]:
if tag == HC.DFTAG_NDG:
# f = open(swath + '.txt', 'a'); f.writelines('#' + key + '#' + '\n'); f.close()
sds = sd.select(sd.reftoindex(ref))
name = sds.info()[0]
lookup_dict[name] = [tag, ref]
sds.endaccess()
elif tag == HC.DFTAG_VH:
vd = vs.attach(ref)
nrecs, intmode, fields, size, name = vd.inquire()
lookup_dict[name] = [tag, ref]
v.end()
vs.end()
sd.end()
return lookup_dict
def main():
parser = ArgumentParser(description=__doc__)
parser.add_argument('colloc_file', help='HDF collocation output file')
parser.add_argument('shis_file', help='NetCDF SHIS file')
args = parser.parse_args()
colloc_sd = SD.SD(args.colloc_file)
shis_sd = SD.SD(args.shis_file)
idx_sds = colloc_sd.select('SHIS_Index')
idx_ini, idx_fin = idx_sds[0], idx_sds[-1]
t_ini = shis_time(shis_sd, idx_ini)
t_fin = shis_time(shis_sd, idx_fin)
print('SHIS.CPL.COLLOC.{0}.{1}.hdf'.format(t_ini, t_fin))
def L1_Reading(fpath):
sd_obj = SD(fpath, SDC.READ)
Vt_obj = HDF.HDF(fpath).vstart()
m_data = Vt_obj.attach('metadata').read()[0]
Height = np.array(m_data[-2]) # 583高度对应实际海拔
Lats = sd_obj.select('Latitude').get()
Lons = sd_obj.select('Longitude').get()
L_route = np.concatenate([Lats.T, Lons.T]).T
del Lons
surface = sd_obj.select('Surface_Elevation').get()
target_rows = []
distance_list = []
min_distance = 9999999
for location in L_route:
distance = LonLat_Distance(location, LZU_LatLon)
if distance < min_distance:
min_distance = distance
if distance < 50:
target_rows.append(True)
else:
target_rows.append(False)
distance_list.append(distance)
Per532 = np.array(
sd_obj.select('Perpendicular_Attenuated_Backscatter_532').get())
Per532 = cv2.GaussianBlur(Per532, (3, 11), 8)
Per532[Per532 < 0] = 0
Tol532 = np.array(sd_obj.select('Total_Attenuated_Backscatter_532').get())
Tol532 = cv2.GaussianBlur(Tol532, (3, 11), 8)
Tol532[Tol532 < 0] = 0
Par532 = Tol532 - Per532
# proccess Dep data
Dep532 = np.true_divide(Per532, Par532)
Dep532[Par532 <= 0.0003] = 0
Dep532[Par532 <= 0.0000] = 0
Dep532[Dep532 > 1] = 0
Dep532 = cv2.blur(Dep532, (3, 11))
Data_dic = {}
Data_dic['Tol532'] = Tol532
Data_dic['Dep532'] = Dep532
Data_meta = {
'route': L_route,
'surface': surface,
'Lats': Lats,
'target rows': target_rows,
'Height': Height,
'distance': distance_list,
'min distance': min_distance
}
# for key, value in Rd_dic.items():
# value.columns = Height.values[0]
sd_obj.end()
HDF.HDF(fpath).close()
return Data_dic, Data_meta
def __init__(self, *fnames):
"""Initialize the HDF group using the first HDF file"""
N = len(fnames)
#Get the lon&lat coordinates of the common area of the whole group
tops = []
bots = []
lefs = []
ryts = []
for fname in fnames:
hdf_file = SD.SD(fname)
lon = hdf_file.select('Longitude').get()
lat = hdf_file.select('Latitude').get()
hdf_file.end()
lon, lat = autoFlip(lon, 'horizontal', lon, lat)
lon, lat = autoFlip(lat, 'vertical', lon, lat)
tops.append(lat[0][0])
bots.append(lat[-1][-1])
lefs.append(lon[0][0])
ryts.append(lon[-1][-1])
#Intersect with Philippine area, 2.5-22.5 deg lat, 115-130 deg lon
top = min(NP.min([tops]), 22.5)
bot = max(NP.max([bots]), 2.5)
lef = max(NP.max([lefs]), 115)
ryt = min(NP.min([ryts]), 130)
print("Common area (top, bot)(left, right): " + '(' + str(top) + ',' +
str(bot) + ')' + '(' + str(lef) + ',' + str(ryt) + ')')
if top < bot or lef > ryt:
self.proceed = False
print("No common area found")
else:
self.proceed = True
print("Processing: 1/" + str(N))
MXD35L2File.__init__(self, fnames[0])
self.top = top
self.bot = bot
self.lef = lef
self.ryt = ryt
self.interpLonLat()
self.imshowCloudCoast('-1RAW')
self.computeCloudFrac('1RAW')
self.cutCloudWaterCoast()
self.imshowCloudCoast('-2CUT')
self.computeCloudFrac('2CUT')
self.interpCloudWaterCoast()
self.imshowCloudCoast('-3INTERP')
self.computeCloudFrac('3INTERP')
self.N = N
self.members = fnames
def check():
hdf4 = SD.SD(file_path, SD.SDC.READ)
ds = hdf4.datasets()
print ds
cp = hdf4.select("Precipitable_Water_Near_Infrared_Clear")
print " ".join(cp.dimensions().keys()), cp.attributes(), cp.attributes().get('units')
cp.endaccess()
hdf4.end()
def require_SD_info_hdf(file_in):
'''Print and Return SD variable names and dimentions in a HDF-EOS file'''
#--information from input file--
f=SD(file_in,SDC.READ)
var_info=f.datasets()
print("--Variables in ",file_in,"-->")
for name,value in var_info.items():
print(" ",name,": ",value)
return var_info
def read_hdf4(filename, name=None, coords_only=False, **kwargs):
import pyhdf.SD as SD
from pyhdf.error import HDF4Error
try:
_file = SD.SD(filename)
except HDF4Error:
print("Cannot open file: %s" % filename)
raise
# find out which dataset to read
if name is None:
datasets = list(_file.datasets().keys())
variables = []
for d in datasets:
var = _file.select(d)
if len(var.dimensions()) > 1 or var.dim(0).info()[0] != d:
variables.append(d)
if len(variables) > 1:
raise AttributeError("There is more than one non-coordinate "
"variable in the file, and you didn't "
"specify which one you want me to read!")
name = variables[0]
# open dataset
sds = _file.select(name)
# open the coordinate variables
dims = sds.dimensions(full=True)
dimorder = {dims[k][1]: k for k in list(dims.keys())}
coordinates = OrderedDict()
for d in range(len(dimorder)):
coordinates[dimorder[d]] = _file.select(dimorder[d])[:]
# coordinate slicing
slices = get_coordinate_slices(coordinates, kwargs)
# slice the coordinate arrays themselves
for i, c in enumerate(list(coordinates.keys())):
coordinates[c] = coordinates[c][slices[i]]
if coords_only:
return coordinates
# read requested slice from disk
data = sds[slices]
fill = sds.getfillvalue()
if fill is not None and not np.isnan(fill):
data = np.where(data != fill, data, np.nan)
# make sure latitudes go from S to N
if coordinates['latitude'][0] > coordinates['latitude'][-1]:
coordinates['latitude'] = coordinates['latitude'][::-1]
for i in dimorder.keys():
if dimorder[i] == "latitude":
if i == 0:
data = np.flipud(data)
elif i == 1:
data = np.fliplr(data)
else:
raise ValueError("flipping data array for ascending "
"coordinates only works with 2d arrays!")
continue
out = gridded_array(data, coordinates, name)
_file.end()
return out
def h4read(path, ref):
'''
only capable of reading datasets, vdata is not.
'''
sd = SD(path)
sds = sd.select(sd.reftoindex(ref))
data = np.float64(sds.get())
sds.endaccess(); sd.end()
return data