def standalone_main():
# Load command line options
parser = OptionParser(usage="usage: %prog [options] [summary_files]...")
parser.add_option( "-r", "--run_dir_file", dest="run_dir_file",
metavar="FILE",
help="file to read list of run directories from")
parser.add_option( "-o", "--output_dir", dest="output_dir",
metavar="DIR",
help="directory where to write plot files")
parser.add_option( "-f", "--filter", dest="filter_names",
metavar="REGEXP",
type="string",
action="append",
help="filter matching filenames according to the supplied regular expression",
)
parser.add_option( "-i", "--indexes", dest="indexes",
metavar="NUM",
type="string",
action="append",
help="which indexes that would generate multiple pages of plots to use",
)
parser.add_option( "--log", dest="make_logs",
default=False,
action="store_true",
help="make debugging log files per plot file")
# Parse command line arguments
(options, args) = parser.parse_args()
# Initialize logging
L2_Log_Util.init_logging()
# Gather list of run directories to gather information from
run_dirs = []
for arg_dir in args:
run_dirs.append(arg_dir)
if options.indexes != None:
indexes = []
for idx_arg in options.indexes:
indexes += OCO_TextUtils.index_range_list(idx_arg)
else:
indexes = None
if options.run_dir_file != None:
if not os.path.exists(options.run_dir_file):
parser.error("Run directory file '%s' does not exist" % options.run_dir_file)
with open(options.run_dir_file, 'r') as run_dir_fh:
run_dirs += [ file_dir.strip() for file_dir in run_dir_fh.readlines() ]
plot_run_comparisons(run_dirs, output_directory=options.output_dir, filename_filters=options.filter_names, page_indexes=indexes, debugging_logs=options.make_logs)
def create_dispersion_from_ascii(l1b_file, out_disp_file, disp_in_file, sounding_id=None, index_scheme=None):
asc_l1b_obj = OCO_Matrix(l1b_file)
if sounding_id == None:
sounding_id = asc_l1b_obj.header['sounding_id']
if disp_in_file == None:
raise IOError('No dispersion file specified')
latitude = float(asc_l1b_obj.header['sounding_latitude'].split()[0])
sza_r = math.radians(float(asc_l1b_obj.header['sounding_solar_zenith'].split()[0]))
saz_r = math.radians(float(asc_l1b_obj.header['sounding_solar_azimuth'].split()[0]))
time_stamp = asc_l1b_obj.header['frame_time_stamp']
time_struct = OCO_TextUtils.convert_timestamp_to_struct(time_stamp)
pixel_ranges = asc_l1b_obj.pixel_ranges()
aband_data = asc_l1b_obj['Radiance'][slice(*pixel_ranges[0]), 0]
disp_in_obj = OCO_Matrix(disp_in_file)
dispersion_coefs = disp_in_obj[DISPERSION_ASCII_COLUMN_IDENT].transpose()
create_scene_dispersion_file(sounding_id, latitude, sza_r, saz_r, time_struct, aband_data, dispersion_coefs, out_disp_file, index_scheme=index_scheme)
def plot_gosat_summ(summary_files):
if len(summary_files) > 1:
summary_names, common_part = OCO_TextUtils.extract_run_names(
summary_files, return_common=True)
else:
common_part = summary_files[0]
plot_data = {}
for curr_summ_file in summary_files:
file_obj = OCO_Matrix(curr_summ_file, as_strings=True)
plot_data = file_obj.as_dict(DICT_KEY_COLUMN, existing_dict=plot_data)
figure_index = 0
x_axis_index = []
for curr_yaxis in PLOT_TYPES:
for curr_filter in PLOT_FILTERS:
legend_names = []
plot_objs = []
fig = None
curr_axis = None
for leg_idx, curr_legend in enumerate(LEGEND_VALUES):
# Extract plot data
x_data = []
y_data = []
for scene_name, scene_data in plot_data.items():
if not re.search(curr_filter[0],
scene_name) or not re.search(
curr_legend[0], scene_name):
continue
if not scene_data.has_key(
X_AXIS[0]) or not scene_data.has_key(
curr_yaxis[0]):
continue
print 'Using scene: ', scene_name, 'for', curr_filter[
1], curr_legend[1]
x_value = scene_data[X_AXIS[0]]
y_value = scene_data[curr_yaxis[0]]
if len(X_AXIS) >= 3:
axis_match = re.search(X_AXIS[2], x_value)
x_value = axis_match.group()
if len(X_AXIS) >= 4:
if not x_value in x_axis_index:
x_axis_index.append(x_value)
x_value = x_axis_index.index(x_value)
try:
x_value = float(x_value)
except:
pass
y_value = float(y_value)
if abs(y_value - FILL_VALUE) > 1e-2:
y_value *= curr_yaxis[2]
insert_point = bisect.bisect(x_data, x_value)
x_data.insert(insert_point, x_value)
y_data.insert(insert_point, y_value)
if len(x_data) > 0:
if fig == None:
fig = pyplot.figure(figure_index)
fig.clf()
curr_axis = pyplot.subplot(111)
curr_plot_obj = pyplot.plot(x_data, y_data, 'x')
plot_objs.append(curr_plot_obj)
legend_names.append(curr_legend[1])
if len(plot_objs) > 0:
figure_index += 1
curr_axis.set_xlabel(X_AXIS[1])
curr_axis.set_ylabel(curr_yaxis[1])
curr_axis.set_title('%s -- %s' % (curr_filter[1], common_part))
leg = curr_axis.legend(
plot_objs,
legend_names,
loc='lower right',
borderpad=0.1,
labelspacing=0.05,
borderaxespad=0.2,
)
pyplot.show()
def plot(matrix, abscissa, abscissa_string, out_filename=None, det_windows=True):
if (matrix.dims[0] == 0 or matrix.dims[1] == 0): return
letter = pyx.document.paperformat.Letter
# Number of spectral points
size = matrix.dims[0]
# All pages will be stored in this object
d = pyx.document.document(pages=[])
# starting pixel indices for each window. The last entry is
# the total number of pixels.
windows = matrix.pixels[:] # Make a copy instead of using a reference
if (len(windows) == 0):
if det_windows and matrix.filename.find("high_res") == -1:
windows = [ wini * (matrix.dims[0] / 3) for wini in range(3) ]
else:
windows = [0]
windows.append(matrix.dims[0])
# Run through the columns
for index in range(0, matrix.dims[1]):
# Don't bother plotting wavelength
try:
if (matrix.labels_lower.index("wavelength") == index): continue
except ValueError:
pass
try:
xindex = matrix.labels_lower.index(abscissa)
if (xindex == index): continue
except ValueError:
xindex = -1
pass
# Plot each window separately
for w in range(0, len(windows) - 1):
# Look for the abscissa_string. If present, use that as
# the x axis.
if (xindex != -1):
xaxis = matrix.data[windows[w]:windows[w+1], xindex]
xtitle = abscissa_string
else:
xaxis = range(0, windows[w+1] - windows[w])
xtitle = "Index"
# Build the list object holding the data for this window.
list = [(xaxis[0], matrix.data[windows[w], index])]
for i in range(0, windows[w+1] - windows[w]):
list.append((xaxis[i], matrix.data[i + windows[w], index]))
# use the list to create the data object to plot
title=OCO_TextUtils.escape_underscore(os.path.dirname(matrix.filename))
data = pyx.graph.data.points(list, title=title, x=1, y=2)
# Assign the axis ranges.
xmin = xaxis[0]
xmax = xaxis[windows[w+1] - windows[w] - 1]
ymax = None
ymin = None
if (min(matrix.data[windows[w]:windows[w+1], index]) ==
max(matrix.data[windows[w]:windows[w+1], index])):
ymax = 1
ymin = -1
# create the graph object
g = pyx.graph.graphxy(width=100,
key=pyx.graph.key.key(pos="br",
symbolwidth=5*pyx.unit.t_cm),
x=pyx.graph.axis.linear(min=xmin,
max=xmax,
title=xtitle),
y=pyx.graph.axis.linear(min=ymin,
max=ymax,
title=matrix.ytitle[index]))
# plot the data
g.plot(data, [pyx.graph.style.line([pyx.color.rgb.red,
pyx.style.linewidth.THICK])])
# Add the title
filename = OCO_TextUtils.escape_underscore(matrix.filename)
title = "%s: Index %d, window %d" % (filename, index, w)
g.text(g.width/2, g.height + 0.4, title,
[pyx.text.halign.center, pyx.text.valign.bottom,
pyx.text.size.Large])
# Add this plot to the document
d.append(pyx.document.page(g,
paperformat=letter,
margin=3*pyx.unit.t_cm,
fittosize=1,
rotated=1, centered=1))
# Write the postscript file
if out_filename == None:
out_filename = "%s.pdf" % matrix.filename
print 'Writing: %s' % out_filename
d.writetofile(out_filename)
def plotRMS(matrix, ref, abscissa, abscissa_string, out_filename=None, pressure_matrix=None, det_windows=True, ratio=False):
if (matrix.dims[0] == 0 or matrix.dims[1] == 0): return
if (ref.dims[0] == 0 or ref.dims[1] == 0): return
# Number of spectral points
size = matrix.dims[0]
# All pages will be stored in this object
d = pyx.document.document(pages=[])
# starting pixel indices for each window. The last entry is
# the total number of pixels.
windows = matrix.pixels[:] # Make a copy instead of using a reference
if (len(windows) == 0):
if det_windows and matrix.filename.find("high_res") == -1:
windows = [ wini * (matrix.dims[0] / 3) for wini in range(3) ]
else:
windows = [0]
windows.append(matrix.dims[0])
# Get pressure levels to be used for partial derivate files to name the indexes
if pressure_matrix != None:
pressure_list = pressure_matrix.data[:, 0]
else:
pressure_list = []
# Run through the columns
for index in range(0, min(ref.dims[1], matrix.dims[1])):
# Don't bother plotting wavelength or wavenumber
if len(matrix.labels) > 0:
if (matrix.labels[index].lower() == "wavelength"): continue
if (matrix.labels[index].lower() == "wavenumber"): continue
try:
xindex = matrix.labels_lower.index(abscissa)
if (xindex == index): pass # continue
except ValueError:
xindex = -1
pass
# This is the canvas that holds both graphs
c = pyx.canvas.canvas()
curr_ypos = 0
# Plot each window separately
num_windows = len(windows) - 1;
for winEndIdx in range(num_windows, 0, -1):
winBegIdx = winEndIdx-1
# Look for the abscissa_string. If present, use that as
# the x axis.
if (xindex != -1):
xaxis = matrix.data[windows[winBegIdx]:windows[winEndIdx], xindex]
xtitle = abscissa_string
else:
xaxis = range(0, windows[winEndIdx] - windows[winBegIdx])
xtitle = "Index"
selfdata = matrix.data[windows[winBegIdx]:windows[winEndIdx], index]
refdata = ref.data[windows[winBegIdx]:windows[winEndIdx], index]
if ratio:
residual, rms = OCO_Statistics.Ratio_RMS(selfdata, refdata)
else:
residual, rms = OCO_Statistics.Residual_RMS(selfdata, refdata)
if (rms < 0):
print "residual has NaN's"
return
# Set up strings used to plot and for verbose output on screen
if len(matrix.labels) > index:
index_name = matrix.labels[index]
elif len(pressure_list) > 0 and matrix.filename.find('_pd') > 0:
#print 'pll:', len(pressure_list), 'index:', index
# Use pressure level for label
index_name = "Pressure %.2f" % pressure_list[index]
else:
index_name = "Index %d" % index
if num_windows > 1:
plot_description = "%s: %s, window %d" % (matrix.filename, index_name, winBegIdx)
else:
plot_description = "%s: %s" % (matrix.filename, index_name)
if ratio:
rms_description = "Ratio RMS = %f" % (rms)
else:
rms_description = "RMS = %f%%" % (rms * 100)
print "%s, %s" % (plot_description, rms_description)
# build the lists to plot
list0 = [(xaxis[0], selfdata[0])]
list1 = [(xaxis[0], refdata[0])]
if ratio:
diff = [(xaxis[0], residual[0])]
else:
diff = [(xaxis[0], residual[0]*100.)]
for i in range(0, windows[winEndIdx] - windows[winBegIdx]):
list0.append((xaxis[i], selfdata[i]))
list1.append((xaxis[i], refdata[i]))
if ratio:
diff.append((xaxis[i], residual[i]))
else:
diff.append((xaxis[i], residual[i]*100.))
# Create the PyX data structures
title = OCO_TextUtils.escape_underscore(os.path.dirname(matrix.filename))
data0 = pyx.graph.data.points(list0, title=title, x=1, y=2)
title = OCO_TextUtils.escape_underscore(os.path.dirname(ref.filename))
if (ref.filename != matrix.filename):
title = "%s%s" % (title, OCO_TextUtils.escape_underscore(ref.filename))
data1 = pyx.graph.data.points(list1, title=title, x=1, y=2)
data2 = pyx.graph.data.points(diff, x=1, y=2)
# Assign the axis ranges.
xmin = xaxis[0]
xmax = xaxis[windows[winEndIdx] - windows[winBegIdx] - 1]
ymax = None
ymin = None
if (min(residual) == max(residual)):
ymax = 1
ymin = -1
# This is the lower graph
if ratio:
y_title_txt = "ratio"
else:
y_title_txt = "difference"
g1 = c.insert(pyx.graph.graphxy(width=100, ratio=1.5*num_windows,
ypos=curr_ypos,
x=pyx.graph.axis.linear(min=xmin, max=xmax,
title=xtitle),
y=pyx.graph.axis.linear(min=ymin, max=ymax,
title=y_title_txt)))
# Plot the differences
g1.plot(data2,
[pyx.graph.style.line([pyx.color.rgb.red,
pyx.style.linewidth.THICK])])
# Add the title
if ratio:
title="Ratio RMS = %f" % (rms)
else:
title="Residual RMS = %f\%%" % (rms * 100)
g1.text(g1.width/2, curr_ypos + g1.height + 0.4, title,
[pyx.text.halign.center, pyx.text.valign.bottom])
curr_ypos += g1.height+6.0
# Find the y axis range
ymax = None
ymin = None
if (min(selfdata) == max(selfdata)
and min(refdata) == max(refdata)
and min(refdata) == min(selfdata)):
ymax = 1
ymin = -1
# This is the upper graph
g0 = c.insert(pyx.graph.graphxy(width=100, ratio=1.5*num_windows,
ypos=curr_ypos,
key=pyx.graph.key.key(pos="br", symbolwidth=5*pyx.unit.t_cm),
x=pyx.graph.axis.linkedaxis(g1.axes["x"]),
y=pyx.graph.axis.linear(min=ymin, max=ymax, title=matrix.ytitle[index])))
# Now plot the values
g0.plot([data0, data1],
[pyx.graph.style.line([pyx.color.gradient.Rainbow,
pyx.style.linewidth.THICK])])
# Add the title
title = OCO_TextUtils.escape_underscore(plot_description)
g0.text(g0.width/2, curr_ypos + g0.height + 0.8, title,
[pyx.text.halign.center, pyx.text.valign.bottom])
curr_ypos += g0.height+15.0
# Add this plot to the document
d.append(pyx.document.page(c,
paperformat=pyx.document.paperformat.Letter,
margin=pyx.unit.t_cm,
fittosize=1,
rotated=0, centered=1))
# Write the postscript file
if out_filename == None:
out_filename = "%s_RMS.pdf" % matrix.filename
print 'Writing: %s' % out_filename
d.writetofile(out_filename)
def plot_gosat_summ(summary_files):
if len(summary_files) > 1:
summary_names, common_part = OCO_TextUtils.extract_run_names(summary_files, return_common=True)
else:
common_part = summary_files[0]
plot_data = {}
for curr_summ_file in summary_files:
file_obj = OCO_Matrix(curr_summ_file, as_strings=True)
plot_data = file_obj.as_dict(DICT_KEY_COLUMN, existing_dict=plot_data)
figure_index = 0
x_axis_index = []
for curr_yaxis in PLOT_TYPES:
for curr_filter in PLOT_FILTERS:
legend_names = []
plot_objs = []
fig = None
curr_axis = None
for leg_idx, curr_legend in enumerate(LEGEND_VALUES):
# Extract plot data
x_data = []
y_data = []
for scene_name, scene_data in plot_data.items():
if not re.search(curr_filter[0], scene_name) or not re.search(curr_legend[0], scene_name):
continue
if not scene_data.has_key(X_AXIS[0]) or not scene_data.has_key(curr_yaxis[0]):
continue
print 'Using scene: ', scene_name, 'for', curr_filter[1], curr_legend[1]
x_value = scene_data[X_AXIS[0]]
y_value = scene_data[curr_yaxis[0]]
if len(X_AXIS) >= 3:
axis_match = re.search(X_AXIS[2], x_value)
x_value = axis_match.group()
if len(X_AXIS) >= 4:
if not x_value in x_axis_index:
x_axis_index.append(x_value)
x_value = x_axis_index.index(x_value)
try:
x_value = float(x_value)
except:
pass
y_value = float(y_value)
if abs(y_value - FILL_VALUE) > 1e-2:
y_value *= curr_yaxis[2]
insert_point = bisect.bisect(x_data, x_value)
x_data.insert(insert_point, x_value)
y_data.insert(insert_point, y_value)
if len(x_data) > 0:
if fig == None:
fig = pyplot.figure(figure_index)
fig.clf()
curr_axis = pyplot.subplot(111)
curr_plot_obj = pyplot.plot(x_data, y_data, 'x')
plot_objs.append( curr_plot_obj )
legend_names.append( curr_legend[1] )
if len(plot_objs) > 0:
figure_index += 1
curr_axis.set_xlabel(X_AXIS[1])
curr_axis.set_ylabel(curr_yaxis[1])
curr_axis.set_title('%s -- %s' % (curr_filter[1], common_part))
leg = curr_axis.legend( plot_objs,
legend_names,
loc='lower right',
borderpad = 0.1,
labelspacing = 0.05,
borderaxespad = 0.2,
)
pyplot.show()
