# SpectroscoPy/TextExport.py
# ---------
# Docstring
# ---------
""" Routines for exporting data in plain-text formats. """
# -------
# Imports
# -------
import csv;
import sys;
import numpy as np;
from SpectroscoPy import Constants;
# ---------
# Constants
# ---------
""" Format code for converting floating-point values to text when writing plain-text DAT files. """
_DATFileFloatFormat = "{0:.6f}";
# ------------------------
# Generic Writer Functions
# ------------------------
def WriteData(dataRows, filePath, fileFormat):
""" Write row-wise data to an output file in the specified file format. """
fileFormat = fileFormat.lower();
# Dispatch to the correct writer function for the chosen file format.
if fileFormat == 'csv':
WriteDataCSV(dataRows, filePath);
elif fileFormat == 'dat':
WriteDataDAT(dataRows, filePath);
else:
raise Exception("Error: Unknown file format '{0}'.".format(fileFormat));
def WriteDataCSV(dataRows, filePath):
""" Write row-wise data to an Excel-compatible CSV file. """
outputWriter = None;
# Workaround for a bug in the csv module, where using the csv.writer on Windows inserts extra blank lines between rows.
if sys.platform.startswith("win"):
# Try to open the file with newline = '' set (Python >= 3).
# If this is not possible, issue a RuntimeWarning.
if sys.version_info.major >= 3:
outputWriter = open(filePath, 'w', newline = '');
else:
warnings.warn("CSV files output from Python < 3 on Windows platforms may have blank lines between rows.", RuntimeWarning);
if outputWriter == None:
outputWriter = open(filePath, 'w');
outputWriterCSV = csv.writer(outputWriter, delimiter = ',', quotechar = '\"', quoting = csv.QUOTE_ALL);
for row in dataRows:
outputWriterCSV.writerow(row);
outputWriter.close();
def WriteDataDAT(dataRows, filePath):
""" Write row-wise data to a plain-text DAT file. """
# To generate a nicely-formatted DAT file, we need to know the column widths in advance.
# The brute-force way to do this is to simply call str() on each data item and find the maximum length of the strings to be written in each column.
dataRowsString = [];
for dataRow in dataRows:
dataRowString = [];
for item in dataRow:
# Figure out if item should be formatted as a float.
floatFormat = False;
try:
if isinstance(item, float):
floatFormat = True;
else:
item = float(item);
if not item.is_integer():
floatFormat = True;
except (TypeError, ValueError):
pass;
if floatFormat:
dataRowString.append(
_DATFileFloatFormat.format(item)
);
else:
dataRowString.append(
str(item)
);
dataRowsString.append(dataRowString);
# Calculate column widths and generate format codes.
columnWidths = [len(item) for item in dataRowsString[0]];
for dataRowString in dataRowsString[1:]:
for i, item in enumerate(dataRowString):
columnWidths[i] = max(columnWidths[i], len(item));
columnFormatCodes = [
"{{0: >{0}}}".format(columnWidth)
for columnWidth in columnWidths
];
# Write data.
with open(filePath, 'w') as outputWriter:
for dataRowString in dataRowsString:
# Use four blank spaces as a column separator.
outputWriter.write(
' '.join([formatCode.format(item) for formatCode, item in zip(columnFormatCodes, dataRowString)]) + '\n'
);
# -----------
# Peak Tables
# -----------
def GroupForPeakTable(frequencies, intensities, irRepData, linewidths = None):
"""
Average mode frequencies, intensities and linewidths (if supplied) into groups defined by the (symbol, band_indices) tuples in irRepData.
Returns a tuple of (new_frequencies, new_intensities, irrep_symbols, new_linewidths) lists, each with the same length as irRepData.
Notes:
Band indices should be zero-based.
"""
numModes = len(frequencies);
if len(intensities) != numModes:
raise Exception("Error: The lengths of frequencies and intensities are inconsistent.");
if linewidths is not None and len(linewidths) != numModes:
raise Exception("Error: If supplied, linewidths must have the same number of elements as frequencies and intensities.");
# Check band indices.
includedIndices = set();
for _, bandIndices in irRepData:
for index in bandIndices:
if index in includedIndices:
raise Exception("Error: Band index {0} assigned to multiple ir. rep. groups.".format(index));
if index < 0 or index >= numModes:
raise Exception("Error: Band index {0} is out of bounds for # modes = {1}.".format(index, numModes));
includedIndices.add(index);
if len(includedIndices) != len(frequencies):
raise Exception("Error: The number of bands references in the ir. rep. groups is more than # modes = {0}.".format(numModes));
frequenciesNew, intensitiesNew = [], [];
linewidthsNew = [] if linewidths != None else None;
for _, bandIndices in irRepData:
if len(bandIndices) == 1:
index = bandIndices[0];
frequenciesNew.append(frequencies[index]);
intensitiesNew.append(intensities[index]);
if linewidths != None:
linewidthsNew.append(linewidths[index]);
else:
# Average the frequencies.
frequenciesNew.append(
np.average([frequencies[index] for index in bandIndices])
);
# Sum the intensities.
intensitiesNew.append(
np.sum([intensities[index] for index in bandIndices])
);
if linewidths != None:
# Average the linewidths.
linewidthsNew.append(
np.average([linewidths[index] for index in bandIndices])
);
return (frequenciesNew, intensitiesNew, [symbol for symbol, _ in irRepData], linewidthsNew);
def SavePeakTable(frequencies, intensities, filePath, irRepSymbols = None, linewidths = None, frequencyUnits = None, intensityUnits = None, fileFormat = 'dat'):
"""
Save a set of peak parameters (peak table) to a plain-text file.
Arguments:
frequencies -- list of mode frequencies.
intensities -- list of band intensities.
filePath -- path to output file.
Keyword arguments:
irRepSymbols -- (optional) list of irreducible representation symbols (ir. reps.).
linewidths -- (optional) list of mode linewidths.
frequencyUnits -- units of frequencies and linewidths, if supplied (default: Constants.DefaultFrequencyUnits).
intensityUnits -- units of spectral intensity (default: Constants.DefaultIntensityUnits).
fileFormat -- file format to export to ('csv' or 'dat'; default 'dat');
"""
numModes = len(frequencies);
if intensities == None or len(intensities) != numModes:
raise Exception("Error: intensities cannot be None and must be the same length as frequencies.");
if irRepSymbols != None and len(irRepSymbols) != numModes:
raise Exception("Error: If supplied, irReps must be the same length as frequencies.");
if linewidths != None and len(linewidths) != numModes:
raise Exception("Error: If supplied, linewidths must be the same length as frequencies.");
if frequencyUnits == None:
frequencyUnits = Constants.DefaultFrequencyUnits;
if intensityUnits == None:
intensityUnits = Constants.DefaultIntensityUnits;
# Compile data rows.
headerRow = ["v [{0}]".format(Constants.GetFrequencyUnitLabel(frequencyUnits))];
if irRepSymbols != None:
headerRow = headerRow + ["Ir. Rep."];
headerRow = headerRow + ["I [{0}]".format(intensityUnits)];
if linewidths != None:
headerRow = headerRow + [r"\Gamma [{0}]".format(Constants.GetFrequencyUnitLabel(frequencyUnits))];
dataItems = [frequencies];
if irRepSymbols != None:
dataItems.append(irRepSymbols);
dataItems.append(intensities);
if linewidths != None:
dataItems.append(linewidths);
dataRows = [headerRow] + [dataRow for dataRow in zip(*dataItems)];
# Write output file.
WriteData(dataRows, filePath, fileFormat);
# -----------------
# Simulated Spectra
# -----------------
def SaveSpectrum(spectrum, filePath, frequencyUnits = None, intensityUnits = None, fileFormat = 'dat'):
"""
Save a simulated spectrum to a plain-text file.
Arguments:
spectrum -- a tuple of (frequencies, intensities, intensities_norm) data sets.
filePath -- path to output file.
Keyword arguments:
frequencyUnits -- units of the frequency axis (defaults to Constants.DefaultFrequencyUnits).
intensityUnits -- units of the intensity axis (defaults to Constants.DefaultIntensityUnits).
fileFormat -- file format to export to ('csv' or 'dat'; default: 'dat').
"""
spectrumX, spectrumY, spectrumYNorm = spectrum;
numDataPoints = len(spectrumX);
if len(spectrumY) != numDataPoints or len(spectrumYNorm) != numDataPoints:
raise Exception("Error: The number of frequency and intensity points in spectra are inconsistent.");
if frequencyUnits == None:
frequencyUnits = Constants.DefaultFrequencyUnits;
if intensityUnits == None:
intensityUnits = Constants.DefaultIntensityUnits;
# Compile data rows.
dataRows = [];
dataRows.append(
["v [{0}]".format(Constants.GetFrequencyUnitLabel(frequencyUnits)), "I(v) [{0}]".format(intensityUnits), "I_Norm(v) [AU]"]
);
for dataRow in zip(*spectrum):
dataRows.append(dataRow);
# Write output file.
WriteData(dataRows, filePath, fileFormat);
