def _pct2rgb(self, src_filename, dst_filename):
"""!Create new dataset with data in dst_filename with bands according to src_filename
raster color table - modified code from gdal utility pct2rgb
@return new dataset
"""
out_bands = 4
band_number = 1
# open source file
src_ds = gdal.Open(src_filename)
if src_ds is None:
grass.fatal(_("Unable to open %s " % src_filename))
src_band = src_ds.GetRasterBand(band_number)
# Build color table
lookup = [
Numeric.arrayrange(256),
Numeric.arrayrange(256),
Numeric.arrayrange(256),
Numeric.ones(256) * 255,
]
ct = src_band.GetRasterColorTable()
if ct is not None:
for i in range(min(256, ct.GetCount())):
entry = ct.GetColorEntry(i)
for c in range(4):
lookup[c][i] = entry[c]
# create the working file
gtiff_driver = gdal.GetDriverByName(self.gdal_drv_format)
tif_ds = gtiff_driver.Create(
dst_filename, src_ds.RasterXSize, src_ds.RasterYSize, out_bands
)
# do the processing one scanline at a time
for iY in range(src_ds.RasterYSize):
src_data = src_band.ReadAsArray(0, iY, src_ds.RasterXSize, 1)
for iBand in range(out_bands):
band_lookup = lookup[iBand]
dst_data = Numeric.take(band_lookup, src_data)
tif_ds.GetRasterBand(iBand + 1).WriteArray(dst_data, 0, iY)
return tif_ds
def write_level(self, dataset, table_name, zoom_level, overview_level, matrix_width, matrix_height):
"""
Write one zoom/resolution level into pyramid data table.
@param dataset: Input dataset.
@param table_name: Name of table to write pyramid data into.
@param zoom_level: Zoom/Resolution level to write.
@param overview_level: Index to overview to use.
@param matrix_width: Number of tiles in X.
@param matrix_height: Number of tiles in Y.
@return: True on success, False on failure.
"""
in_band_count = dataset.RasterCount
out_band_count = in_band_count
src_bands = list()
expand_palette = False
for i in range(in_band_count):
if overview_level == 0:
src_bands.append(dataset.GetRasterBand(i + 1))
else:
src_bands.append(dataset.GetRasterBand(i + 1).GetOverview(overview_level - 1))
if self.format == 'image/jpeg' and in_band_count == 1 and \
src_bands[0].GetRasterColorInterpretation() == GCI_PaletteIndex:
out_band_count = 3
expand_palette = True
if expand_palette:
color_table = src_bands[0].GetRasterColorTable()
if color_table is not None:
color_table_size = max(256, color_table.GetCount())
lut = [numpy.arrayrange(color_table_size),
numpy.arrayrange(color_table_size),
numpy.arrayrange(color_table_size),
numpy.ones(color_table_size) * 255]
for i in range(color_table_size):
entry = color_table.GetColorEntry(i)
for c in range(4):
lut[c][i] = entry[c]
else:
lut = None
for tile_row in range(matrix_height):
for tile_column in range(matrix_width):
if not self.write_tile(src_bands, out_band_count,
table_name, zoom_level,
tile_row, tile_column, expand_palette, lut):
print("Error writing full resolution image tiles to database.")
return False
return True
def _pct2rgb(self, src_filename, dst_filename):
"""!Create new dataset with data in dst_filename with bands according to src_filename
raster color table - modified code from gdal utility pct2rgb
@return new dataset
"""
out_bands = 4
band_number = 1
# open source file
src_ds = gdal.Open(src_filename)
if src_ds is None:
grass.fatal(_('Unable to open %s ' % src_filename))
src_band = src_ds.GetRasterBand(band_number)
# Build color table
lookup = [Numeric.arrayrange(256),
Numeric.arrayrange(256),
Numeric.arrayrange(256),
Numeric.ones(256) * 255]
ct = src_band.GetRasterColorTable()
if ct is not None:
for i in range(min(256, ct.GetCount())):
entry = ct.GetColorEntry(i)
for c in range(4):
lookup[c][i] = entry[c]
# create the working file
gtiff_driver = gdal.GetDriverByName(self.gdal_drv_format)
tif_ds = gtiff_driver.Create(dst_filename,
src_ds.RasterXSize, src_ds.RasterYSize, out_bands)
# do the processing one scanline at a time
for iY in range(src_ds.RasterYSize):
src_data = src_band.ReadAsArray(0, iY, src_ds.RasterXSize, 1)
for iBand in range(out_bands):
band_lookup = lookup[iBand]
dst_data = Numeric.take(band_lookup, src_data)
tif_ds.GetRasterBand(iBand + 1).WriteArray(dst_data, 0, iY)
return tif_ds
def sample_from( display = True ):
test_x = [ [x] for x in numpy.arrayrange(0,5,.05) ]
test_y = infpy.gp_sample_from( gp, test_x )
if display:
from pylab import figure, plot, show, fill, title
figure()
infpy.gp_plot_prediction( gp.X, test_y )
title('Log likelihood: %f\n%s' % ( gp.log_p_y_given_X, gp.k.params ) )
show()
def findPeak(image):
for n in range(image.shape[1]):
a = numpy.zeros((image.shape[0], 3))
b = image[:, n]
a[:, 0] = numpy.arange(image.shape[0])
a[:, 0] **= 2
a[:, 1] = numpy.arrayrange(image.shape[0])
a[:, 2] = numpy.ones(image.shape[0])
fit = scipy.linalg.lstsq(a, b)
c = fit[0]
row = -c[1] / (2.0 * c[0])
def predict_values( display = True ):
test_x = [ [x] for x in numpy.arrayrange(0,5,.04) ]
( f_star_mean, V_f_star, log_p_y_given_X ) = gp.predict( test_x )
if display:
from pylab import figure, plot, show, fill, title
figure()
infpy.gp_plot_prediction( test_x, f_star_mean, V_f_star )
plot(
[ x[0] for (x, v) in training_points ],
[ v for (x, v) in training_points ],
'rs' )
infpy.gp_title_and_show( gp )
def demo():
data = Numeric.arrayrange(w*h)
## fftdata = FFT.fft(data)
## fftdata2 = FFT.fft(data2)
## fftdata3 = (fftdata + fftdata2) / 2.
## invfftdata = FFT.inverse_fft(fftdata3)
## data = invfftdata.real
data = data.astype('l')
im = Image.new("RGBA", (w, h))
print len(data.tostring("raw", "RGBX", 0, -1))
print len(im.tostring("raw", "RGBX", 0, -1))
im.fromstring(data.tostring("raw", "RGBX", 0, -1),"raw", "RGBX", 0, -1)
root = Tkinter.Tk()
image = ImageTk.PhotoImage(im)
x = Tkinter.Label(root, image=image)
x.pack()
root.mainloop()
def demo():
data = Numeric.arrayrange(w * h)
## fftdata = FFT.fft(data)
## fftdata2 = FFT.fft(data2)
## fftdata3 = (fftdata + fftdata2) / 2.
## invfftdata = FFT.inverse_fft(fftdata3)
## data = invfftdata.real
data = data.astype('l')
im = Image.new("RGBA", (w, h))
print len(data.tostring("raw", "RGBX", 0, -1))
print len(im.tostring("raw", "RGBX", 0, -1))
im.fromstring(data.tostring("raw", "RGBX", 0, -1), "raw", "RGBX", 0, -1)
root = Tkinter.Tk()
image = ImageTk.PhotoImage(im)
x = Tkinter.Label(root, image=image)
x.pack()
root.mainloop()
def hist(v, nbins=10, vmin=None, vmax=None, show=None, p=None):
global _matlab
p = _matlab.get_plot(p)
if vmin is None:
vmin = float(min(v))
if vmax is None:
vmax = float(max(v))
binwidth = (vmax - vmin) / float(nbins - 1)
x = numpy.arrayrange(vmin, vmax + binwidth, binwidth)
y = numpy.zeros(x.shape, int)
for i in range(len(v)):
n = int(round((float(v[i]) - vmin) / binwidth, 0))
try:
y[n] = y[n] + 1
except IndexError:
pass
xx = numpy.zeros(2 * len(x) + 3)
yy = numpy.zeros(2 * len(y) + 3)
xx[0] = x[0]
yy[0] = 0
for i in range(0, len(x)):
xx[1 + 2 * i], xx[1 + 2 * i + 1] = x[i], x[i] + binwidth
yy[1 + 2 * i], yy[1 + 2 * i + 1] = y[i], y[i]
xx[1 + 2 * i + 2] = x[i] + binwidth
yy[1 + 2 * i + 2] = 0
xx[1 + 2 * i + 3] = x[0]
yy[1 + 2 * i + 3] = 0
p.add(biggles.FillBelow(xx, yy), biggles.Curve(xx, yy))
p.yrange = 0, max(y)
if show is not None:
p.show()
_matlab.LAST = p
return p
def hist( v, nbins=10, vmin=None, vmax=None, show=None, p=None ):
global _matlab
p = _matlab.get_plot( p )
if vmin is None:
vmin = float(min(v))
if vmax is None:
vmax = float(max(v))
binwidth = (vmax - vmin) / float(nbins-1)
x = numpy.arrayrange( vmin, vmax+binwidth, binwidth )
y = numpy.zeros( x.shape, int )
for i in range(len(v)):
n = int(round((float(v[i]) - vmin) / binwidth, 0))
try:
y[n] = y[n] + 1
except IndexError:
pass
xx = numpy.zeros( 2*len(x) + 3 )
yy = numpy.zeros( 2*len(y) + 3 )
xx[0] = x[0]
yy[0] = 0
for i in range(0, len(x)):
xx[1+2*i],xx[1+2*i+1] = x[i],x[i]+binwidth
yy[1+2*i],yy[1+2*i+1] = y[i],y[i]
xx[1+2*i+2] = x[i]+binwidth
yy[1+2*i+2] = 0;
xx[1+2*i+3] = x[0];
yy[1+2*i+3] = 0;
p.add( biggles.FillBelow(xx, yy), biggles.Curve(xx, yy) )
p.yrange = 0, max(y)
if show is not None:
p.show()
_matlab.LAST = p
return p
# ----------------------------------------------------------------------------
# Ensure we recognise the driver.
dst_driver = gdal.GetDriverByName(format)
if dst_driver is None:
print('"%s" driver not registered.' % format)
sys.exit(1)
# ----------------------------------------------------------------------------
# Build color table.
ct = src_band.GetRasterColorTable()
ct_size = ct.GetCount()
lookup = [
Numeric.arrayrange(ct_size),
Numeric.arrayrange(ct_size),
Numeric.arrayrange(ct_size),
Numeric.ones(ct_size) * 255,
]
if ct is not None:
for i in range(ct_size):
entry = ct.GetColorEntry(i)
for c in range(4):
lookup[c][i] = entry[c]
# ----------------------------------------------------------------------------
# Create the working file.
if format == "GTiff":
sys.exit(1)
src_band = src_ds.GetRasterBand(band_number)
# ----------------------------------------------------------------------------
# Ensure we recognise the driver.
dst_driver = gdal.GetDriverByName(format)
if dst_driver is None:
print('"%s" driver not registered.' % format)
sys.exit(1)
# ----------------------------------------------------------------------------
# Build color table.
lookup = [ Numeric.arrayrange(256),
Numeric.arrayrange(256),
Numeric.arrayrange(256),
Numeric.ones(256)*255 ]
ct = src_band.GetRasterColorTable()
if ct is not None:
for i in range(min(256,ct.GetCount())):
entry = ct.GetColorEntry(i)
for c in range(4):
lookup[c][i] = entry[c]
# ----------------------------------------------------------------------------
# Create the working file.
def readLiftOver( infile, chromosome,
chromosome_size = 250000000,
report_step = 1000000 ):
"""read a matrix. There probably is a routine for this in Numpy, which
I haven't found yet.
"""
if options.loglevel >= 2:
print "## started reading mapping information"
sys.stdout.flush()
map_position = numpy.zeros( (chromosome_size,), numpy.int)
## signed character for chromosme, negative values for negative strands
map_chromosome = numpy.zeros( (chromosome_size,), numpy.int8 )
map_id2chromosome = ["",]
map_chromosome2id = {}
n = 0
for line in infile:
n += 1
if not (n % report_step):
if options.loglevel >= 2:
print "# iteration %i" % n
sys.stdout.flush()
if line[:5] == "chain":
( chr_x, size_x, strand_x, first_x, last_x,
chr_y, size_y, strand_y, first_y, last_y,
dontknow) = line[:-1].split(" ")[2:]
if strand_x == "-":
raise "what shall I do with negative strands?"
x = int(first_x)
## revert coordinates for negative strands (it seems that
## the mapping file uses reverse coordinates, while liftover
## output doesn't)
## add 1 to coordinates, because 0 is flag for unmappable.
if strand_y == "-":
invert = True
## no +1, because already one past current residue (due to open
## bracket)
y = int(size_y) - int(first_y)
else:
invert = False
y = int(first_y) + 1
if chr_x != chromosome:
keep = False
else:
keep = True
if options.loglevel >= 3:
print "# adding alignment", line[:-1]
continue
elif line.strip() == "":
keep = False
continue
elif keep:
data = map(int, line[:-1].split("\t"))
if len(data) == 3:
size, increment_x, increment_y = data
else:
size, increment_x, increment_y = data[0], 0, 0
# add position
if invert:
map_position[ x:x+size ] = numpy.arrayrange( y, y-size, -1 )
else:
map_position[ x:x+size ] = numpy.arrayrange( y, y+size, 1 )
if chr_y not in map_id2chromosome:
map_chromosome2id[chr_y] = len(map_id2chromosome)
map_id2chromosome.append( chr_y )
id = map_chromosome2id[chr_y]
if strand_y == "-": id = -id
# add chromsome
map_chromosome[x:x+size] = id
x += increment_x + size
if invert:
y -= increment_y + size
else:
y += increment_y + size
if y < 0:
raise "illegal mapping: %i -> %i for %s %s:%s-%s(%s) to %s %s: %s-%s(%s)" % ( x, y,
chr_x, strand_x, first_x, last_x, size_x,
chr_y, strand_y, first_y, last_y, size_y )
return map_position, map_chromosome, map_chromosome2id, map_id2chromosome
time = 4 # data length in seconds
sample_length = int(time * record.frequency) # data length in sample units
end_time = start_time + time # end position in seconds
signals_num = record.nsig # number of signals in record
# default annotation file has .atr extension
default_ann = record.annotation()
## read all annotations for given range
annotations = default_ann.read(int(start_time * record.frequency),
sample_length)
## drawing stuff follows
ylims = (-1.5, 1.5)
t = numpy.arrayrange(start_time, end_time, 1 / record.frequency)
vl = numpy.arange(start_time, end_time, 0.2)
hl = numpy.arange(ylims[0], ylims[1], 0.5)
f = pylab.figure()
f.subplots_adjust(hspace=0.00001)
axes = []
ax = pylab.subplot(signals_num, 1, 1)
pylab.title('ECG record %s' % record.name)
annotation_lines = [ann.time / record.frequency for ann in annotations]
def mark_annotations(ax):
annotation_font = {
if frmt is None:
frmt = GetOutputDriverFor(dst_filename)
dst_driver = gdal.GetDriverByName(frmt)
if dst_driver is None:
print('"%s" driver not registered.' % frmt)
sys.exit(1)
# ----------------------------------------------------------------------------
# Build color table.
ct = src_band.GetRasterColorTable()
ct_size = ct.GetCount()
lookup = [
Numeric.arrayrange(ct_size),
Numeric.arrayrange(ct_size),
Numeric.arrayrange(ct_size),
Numeric.ones(ct_size) * 255
]
if ct is not None:
for i in range(ct_size):
entry = ct.GetColorEntry(i)
for c in range(4):
lookup[c][i] = entry[c]
# ----------------------------------------------------------------------------
# Create the working file.
if frmt == 'GTiff':
sys.exit(1)
src_band = src_ds.GetRasterBand(band_number)
# ----------------------------------------------------------------------------
# Ensure we recognise the driver.
dst_driver = gdal.GetDriverByName(format)
if dst_driver is None:
print('"%s" driver not registered.' % format)
sys.exit(1)
# ----------------------------------------------------------------------------
# Build color table.
lookup = [ Numeric.arrayrange(256),
Numeric.arrayrange(256),
Numeric.arrayrange(256),
Numeric.ones(256)*255 ]
ct = src_band.GetRasterColorTable()
print ct
if ct is not None:
for i in range(min(256,ct.GetCount())):
entry = ct.GetColorEntry(i)
for c in range(4):
lookup[c][i] = entry[c]
def doit(src_filename, dst_filename, band_number=1, out_bands=3, frmt=None):
# Open source file
src_ds = gdal.Open(src_filename)
if src_ds is None:
print('Unable to open %s ' % src_filename)
return None, 1
src_band = src_ds.GetRasterBand(band_number)
# ----------------------------------------------------------------------------
# Ensure we recognise the driver.
if frmt is None:
frmt = GetOutputDriverFor(dst_filename)
dst_driver = gdal.GetDriverByName(frmt)
if dst_driver is None:
print('"%s" driver not registered.' % frmt)
return None, 1
# ----------------------------------------------------------------------------
# Build color table.
ct = src_band.GetRasterColorTable()
ct_size = ct.GetCount()
lookup = [
Numeric.arrayrange(ct_size),
Numeric.arrayrange(ct_size),
Numeric.arrayrange(ct_size),
Numeric.ones(ct_size) * 255
]
if ct is not None:
for i in range(ct_size):
entry = ct.GetColorEntry(i)
for c in range(4):
lookup[c][i] = entry[c]
# ----------------------------------------------------------------------------
# Create the working file.
if frmt == 'GTiff':
tif_filename = dst_filename
else:
tif_filename = 'temp.tif'
gtiff_driver = gdal.GetDriverByName('GTiff')
tif_ds = gtiff_driver.Create(tif_filename, src_ds.RasterXSize,
src_ds.RasterYSize, out_bands)
# ----------------------------------------------------------------------------
# We should copy projection information and so forth at this point.
tif_ds.SetProjection(src_ds.GetProjection())
tif_ds.SetGeoTransform(src_ds.GetGeoTransform())
if src_ds.GetGCPCount() > 0:
tif_ds.SetGCPs(src_ds.GetGCPs(), src_ds.GetGCPProjection())
# ----------------------------------------------------------------------------
# Do the processing one scanline at a time.
progress(0.0)
for iY in range(src_ds.RasterYSize):
src_data = src_band.ReadAsArray(0, iY, src_ds.RasterXSize, 1)
for iBand in range(out_bands):
band_lookup = lookup[iBand]
dst_data = Numeric.take(band_lookup, src_data)
tif_ds.GetRasterBand(iBand + 1).WriteArray(dst_data, 0, iY)
progress((iY + 1.0) / src_ds.RasterYSize)
# ----------------------------------------------------------------------------
# Translate intermediate file to output format if desired format is not TIFF.
if tif_filename == dst_filename:
dst_ds = tif_ds
else:
dst_ds = dst_driver.CreateCopy(dst_filename, tif_ds)
tif_ds = None
gtiff_driver.Delete(tif_filename)
return dst_ds, 0
sys.exit(1)
src_band = src_ds.GetRasterBand(band_number)
# ----------------------------------------------------------------------------
# Ensure we recognise the driver.
dst_driver = gdal.GetDriverByName(format)
if dst_driver is None:
print('"%s" driver not registered.' % format)
sys.exit(1)
# ----------------------------------------------------------------------------
# Build color table.
lookup = [Numeric.arrayrange(256), Numeric.arrayrange(256), Numeric.arrayrange(256), Numeric.ones(256) * 255]
ct = src_band.GetRasterColorTable()
if ct is not None:
for i in range(min(256, ct.GetCount())):
entry = ct.GetColorEntry(i)
for c in range(4):
lookup[c][i] = entry[c]
# ----------------------------------------------------------------------------
# Create the working file.
if format == "GTiff":
tif_filename = dst_filename
else:
import infpy, numpy, math from pylab import plot x = numpy.arrayrange(0.0,5.0,.01) plot( x, [ math.exp( infpy.LogNormalDistribution( 0.1, 1.0 ).log_pdf( x1 ) ) for x1 in x ] ) plot( x, [ math.exp( infpy.LogNormalDistribution( math.log( 0.03 ), 1.0 ).log_pdf( x1 ) ) for x1 in x ] ) plot( x, [ math.exp( infpy.LogNormalDistribution( 1.0, 1.0 ).log_pdf( x1 ) ) for x1 in x ] )
src_band = src_ds.GetRasterBand(band_number)
# ----------------------------------------------------------------------------
# Ensure we recognise the driver.
dst_driver = gdal.GetDriverByName(format)
if dst_driver is None:
print('"%s" driver not registered.' % format)
sys.exit(1)
# ----------------------------------------------------------------------------
# Build color table.
lookup = [
Numeric.arrayrange(256),
Numeric.arrayrange(256),
Numeric.arrayrange(256),
Numeric.ones(256) * 255
]
ct = src_band.GetRasterColorTable()
if ct is not None:
for i in range(min(256, ct.GetCount())):
entry = ct.GetColorEntry(i)
for c in range(4):
lookup[c][i] = entry[c]
# ----------------------------------------------------------------------------
# Create the working file.
# ----------------------------------------------------------------------------
# Ensure we recognise the driver.
dst_driver = gdal.GetDriverByName(format)
if dst_driver is None:
print('"%s" driver not registered.' % format)
sys.exit(1)
# ----------------------------------------------------------------------------
# Build color table.
ct = src_band.GetRasterColorTable()
ct_size = ct.GetCount()
lookup = [Numeric.arrayrange(ct_size),
Numeric.arrayrange(ct_size),
Numeric.arrayrange(ct_size),
Numeric.ones(ct_size) * 255]
if ct is not None:
for i in range(ct_size):
entry = ct.GetColorEntry(i)
for c in range(4):
lookup[c][i] = entry[c]
# ----------------------------------------------------------------------------
# Create the working file.
if format == 'GTiff':
tif_filename = dst_filename
def readLiftOver(infile,
chromosome,
chromosome_size=250000000,
report_step=1000000):
"""read a matrix. There probably is a routine for this in Numpy, which
I haven't found yet.
"""
if options.loglevel >= 2:
print "## started reading mapping information"
sys.stdout.flush()
map_position = numpy.zeros((chromosome_size, ), numpy.int)
# signed character for chromosme, negative values for negative strands
map_chromosome = numpy.zeros((chromosome_size, ), numpy.int8)
map_id2chromosome = [
"",
]
map_chromosome2id = {}
n = 0
for line in infile:
n += 1
if not (n % report_step):
if options.loglevel >= 2:
print "# iteration %i" % n
sys.stdout.flush()
if line[:5] == "chain":
(chr_x, size_x, strand_x, first_x, last_x, chr_y, size_y, strand_y,
first_y, last_y, dontknow) = line[:-1].split(" ")[2:]
if strand_x == "-":
raise "what shall I do with negative strands?"
x = int(first_x)
# revert coordinates for negative strands (it seems that
# the mapping file uses reverse coordinates, while liftover
# output doesn't)
# add 1 to coordinates, because 0 is flag for unmappable.
if strand_y == "-":
invert = True
# no +1, because already one past current residue (due to open
# bracket)
y = int(size_y) - int(first_y)
else:
invert = False
y = int(first_y) + 1
if chr_x != chromosome:
keep = False
else:
keep = True
if options.loglevel >= 3:
print "# adding alignment", line[:-1]
continue
elif line.strip() == "":
keep = False
continue
elif keep:
data = map(int, line[:-1].split("\t"))
if len(data) == 3:
size, increment_x, increment_y = data
else:
size, increment_x, increment_y = data[0], 0, 0
# add position
if invert:
map_position[x:x + size] = numpy.arrayrange(y, y - size, -1)
else:
map_position[x:x + size] = numpy.arrayrange(y, y + size, 1)
if chr_y not in map_id2chromosome:
map_chromosome2id[chr_y] = len(map_id2chromosome)
map_id2chromosome.append(chr_y)
id = map_chromosome2id[chr_y]
if strand_y == "-":
id = -id
# add chromsome
map_chromosome[x:x + size] = id
x += increment_x + size
if invert:
y -= increment_y + size
else:
y += increment_y + size
if y < 0:
raise "illegal mapping: %i -> %i for %s %s:%s-%s(%s) to %s %s: %s-%s(%s)" % (
x, y, chr_x, strand_x, first_x, last_x, size_x, chr_y,
strand_y, first_y, last_y, size_y)
return map_position, map_chromosome, map_chromosome2id, map_id2chromosome
def main(argv):
frmt = None
src_filename = None
dst_filename = None
out_bands = 3
band_number = 1
gdal.AllRegister()
argv = gdal.GeneralCmdLineProcessor(argv)
if argv is None:
sys.exit(0)
# Parse command line arguments.
i = 1
while i < len(argv):
arg = argv[i]
if arg == '-of' or arg == '-f':
i = i + 1
frmt = argv[i]
elif arg == '-b':
i = i + 1
band_number = int(argv[i])
elif arg == '-rgba':
out_bands = 4
elif src_filename is None:
src_filename = argv[i]
elif dst_filename is None:
dst_filename = argv[i]
else:
Usage()
i = i + 1
if dst_filename is None:
Usage()
# ----------------------------------------------------------------------------
# Open source file
src_ds = gdal.Open(src_filename)
if src_ds is None:
print('Unable to open %s ' % src_filename)
sys.exit(1)
src_band = src_ds.GetRasterBand(band_number)
# ----------------------------------------------------------------------------
# Ensure we recognise the driver.
if frmt is None:
frmt = GetOutputDriverFor(dst_filename)
dst_driver = gdal.GetDriverByName(frmt)
if dst_driver is None:
print('"%s" driver not registered.' % frmt)
sys.exit(1)
# ----------------------------------------------------------------------------
# Build color table.
ct = src_band.GetRasterColorTable()
ct_size = ct.GetCount()
lookup = [
Numeric.arrayrange(ct_size),
Numeric.arrayrange(ct_size),
Numeric.arrayrange(ct_size),
Numeric.ones(ct_size) * 255
]
if ct is not None:
for i in range(ct_size):
entry = ct.GetColorEntry(i)
for c in range(4):
lookup[c][i] = entry[c]
# ----------------------------------------------------------------------------
# Create the working file.
if frmt == 'GTiff':
tif_filename = dst_filename
else:
tif_filename = 'temp.tif'
gtiff_driver = gdal.GetDriverByName('GTiff')
tif_ds = gtiff_driver.Create(tif_filename, src_ds.RasterXSize,
src_ds.RasterYSize, out_bands)
# ----------------------------------------------------------------------------
# We should copy projection information and so forth at this point.
tif_ds.SetProjection(src_ds.GetProjection())
tif_ds.SetGeoTransform(src_ds.GetGeoTransform())
if src_ds.GetGCPCount() > 0:
tif_ds.SetGCPs(src_ds.GetGCPs(), src_ds.GetGCPProjection())
# ----------------------------------------------------------------------------
# Do the processing one scanline at a time.
progress(0.0)
for iY in range(src_ds.RasterYSize):
src_data = src_band.ReadAsArray(0, iY, src_ds.RasterXSize, 1)
for iBand in range(out_bands):
band_lookup = lookup[iBand]
dst_data = Numeric.take(band_lookup, src_data)
tif_ds.GetRasterBand(iBand + 1).WriteArray(dst_data, 0, iY)
progress((iY + 1.0) / src_ds.RasterYSize)
tif_ds = None
# ----------------------------------------------------------------------------
# Translate intermediate file to output format if desired format is not TIFF.
if tif_filename != dst_filename:
tif_ds = gdal.Open(tif_filename)
dst_driver.CreateCopy(dst_filename, tif_ds)
tif_ds = None
gtiff_driver.Delete(tif_filename)
# ----------------------------------------------------------------------------
# Ensure we recognise the driver.
dst_driver = gdal.GetDriverByName(format)
if dst_driver is None:
print('"%s" driver not registered.' % format)
sys.exit(1)
# ----------------------------------------------------------------------------
# Build color table.
ct = src_band.GetRasterColorTable()
ct_size = ct.GetCount()
lookup = [Numeric.arrayrange(ct_size),
Numeric.arrayrange(ct_size),
Numeric.arrayrange(ct_size),
Numeric.ones(ct_size) * 255]
if ct is not None:
for i in range(ct_size):
entry = ct.GetColorEntry(i)
for c in range(4):
lookup[c][i] = entry[c]
# ----------------------------------------------------------------------------
# Create the working file.
if format == 'GTiff':
tif_filename = dst_filename
# Adapted for numpy/ma/cdms2 by convertcdms.py import numpy # Tutorial for xmgrace module, using Numeric only # it is recomended to run it usibng parser.py or just read it print 'it is recomended to run this file using parser.py or just read it' TEMPDIR = './' # First let's create some data npoints = 50 X = numpy.arrayrange(npoints, dtype='d') X = X / float(npoints) * 2. * numpy.pi Y1 = numpy.ma.sin(X) Y2 = numpy.ma.cos(X) Y3 = numpy.ma.tan(X) # Now the real grace thing, plot the 2 on one graph and the diff on # another graph from genutil import xmgrace # first we need to import xmgrace module x = xmgrace.init() # create our xmgrace object # First let's set our graphs area # graph 0, exist by default, but we need to add 1 graph, therefore: x.add_graph() # adds one graph to our graph list (x.Graph) # Let's change the orientation of the page to portrait
# Adapted for numpy/ma/cdms2 by convertcdms.py import numpy # Tutorial for xmgrace module, using Numeric only # it is recomended to run it usibng parser.py or just read it print 'it is recomended to run this file using parser.py or just read it' TEMPDIR = './' # First let's create some data npoints = 50 X = numpy.arrayrange(npoints, dtype='d') X = X / float(npoints) * 2. * numpy.pi Y1 = numpy.ma.sin(X) Y2 = numpy.ma.cos(X) Y3 = numpy.ma.tan(X) # Now the real grace thing, plot the 2 on one graph and the diff on another graph from genutil import xmgrace # first we need to import xmgrace module x = xmgrace.init() # create our xmgrace object # First let's set our graphs area # graph 0, exist by default, but we need to add 1 graph, therefore: x.add_graph() # adds one graph to our graph list (x.Graph) # Let's change the orientation of the page to portrait x.portrait()
