def reformat_gfit_atmosphere(mav_file, out_file, next_spec_srch=None):
print('Reading mav data from %s' % mav_file)
spec_line_start = 1
mav_data = []
mav_fobj = open(mav_file, "r")
file_line_idx = 0
if next_spec_srch == None:
found_spec = True
else:
found_spec = False
for mav_line in mav_fobj.readlines():
line_parts = mav_line.split()
mav_data.append(line_parts)
if mav_line.find('Next Spectrum:') >= 0 and next_spec_srch != None:
if re.search(next_spec_srch, mav_line):
spec_line_start = file_line_idx
found_spec = True
file_line_idx += 1
if not found_spec:
raise ValueError(
'Could not find next spectrum search string: %s in mav file: %s' %
(next_spec_srch, mav_file))
print('Processing for', ' '.join(mav_data[spec_line_start]))
mav_size_row = spec_line_start + 1
mav_header_row = mav_size_row + 2
try:
(num_skip, num_cols,
num_rows) = [int(val) for val in mav_data[mav_size_row]]
except:
mav_header_row = 0
num_skip = -2
num_cols = len(mav_data[0])
num_rows = len(mav_data)
print()
print("Skip: %d, Cols %d, Rows: %d" % (num_skip, num_cols, num_rows))
mav_beg_row = mav_size_row + num_skip + 2
mav_end_row = mav_beg_row + num_rows - 3
mav_all_cols = mav_data[mav_header_row]
print("Column names:", mav_all_cols)
out_col_idx = 0
output_data_matrix = numpy.zeros(
(mav_end_row - mav_beg_row + 1, len(all_col_names)), dtype=float)
for (curr_mav_col, scale) in mav_col_extract:
print('Processing column:', curr_mav_col)
mav_col_idx = mav_all_cols.index(curr_mav_col)
row_idx = mav_end_row - mav_beg_row
for mav_row_data in mav_data[mav_beg_row:mav_end_row + 1]:
new_col_data = float(mav_row_data[mav_col_idx]) * float(scale)
output_data_matrix[row_idx, out_col_idx] = output_data_matrix[
row_idx, out_col_idx] + new_col_data
row_idx -= 1
out_col_idx += 1
print('Writing output file %s' % out_file)
out_mat_obj = OcoMatrix()
out_mat_obj.file_id = 'GFIT Atmospheric State modified from: %s' % (
mav_file)
out_mat_obj.dims = [len(output_data_matrix), len(all_col_names)]
out_mat_obj.labels = all_col_names
out_mat_obj.units = all_unit_names
out_mat_obj.data = output_data_matrix
out_mat_obj.write(out_file)
def reformat_gfit_atmosphere(mav_file, out_file, next_spec_srch=None):
print 'Reading mav data from %s' % mav_file
spec_line_start = 1
mav_data = []
mav_fobj = open(mav_file, "r")
file_line_idx = 0
if next_spec_srch == None:
found_spec = True
else:
found_spec = False
for mav_line in mav_fobj.readlines():
line_parts = mav_line.split()
mav_data.append( line_parts )
if mav_line.find('Next Spectrum:') >= 0 and next_spec_srch != None:
if re.search(next_spec_srch, mav_line):
spec_line_start = file_line_idx
found_spec = True
file_line_idx += 1
if not found_spec:
raise ValueError('Could not find next spectrum search string: %s in mav file: %s' % (next_spec_srch, mav_file))
print 'Processing for', ' '.join(mav_data[spec_line_start])
mav_size_row = spec_line_start + 1
mav_header_row = mav_size_row + 2
try:
(num_skip, num_cols, num_rows) = [int(val) for val in mav_data[mav_size_row]]
except:
mav_header_row = 0
num_skip = -2
num_cols = len(mav_data[0])
num_rows = len(mav_data)
print
print "Skip: %d, Cols %d, Rows: %d" % (num_skip, num_cols, num_rows)
mav_beg_row = mav_size_row + num_skip + 2
mav_end_row = mav_beg_row + num_rows - 3
mav_all_cols = mav_data[mav_header_row]
print "Column names:", mav_all_cols
out_col_idx = 0
output_data_matrix = numpy.zeros((mav_end_row-mav_beg_row+1, len(all_col_names)), dtype=float)
for (curr_mav_col, scale) in mav_col_extract:
print 'Processing column:', curr_mav_col
mav_col_idx = mav_all_cols.index(curr_mav_col)
row_idx = mav_end_row-mav_beg_row
for mav_row_data in mav_data[mav_beg_row:mav_end_row+1]:
new_col_data = float(mav_row_data[mav_col_idx]) * float(scale)
output_data_matrix[row_idx, out_col_idx] = output_data_matrix[row_idx, out_col_idx] + new_col_data
row_idx -= 1
out_col_idx += 1
print 'Writing output file %s' % out_file
out_mat_obj = OcoMatrix()
out_mat_obj.file_id = 'GFIT Atmospheric State modified from: %s' % (mav_file)
out_mat_obj.dims = [len(output_data_matrix), len(all_col_names)]
out_mat_obj.labels = all_col_names
out_mat_obj.units = all_unit_names
out_mat_obj.data = output_data_matrix
out_mat_obj.write(out_file)
