Read LCM Coords

01.read_lcm_values.py

def read_lcm_values(fn):  # {{{
    series_type = None

    series_data = {}

    with open(fn) as f:
        vals = []

        for line in f:
            prev_series_type = series_type
            if re.match(".*[0-9]+ points on ppm-axis = NY.*", line):
                series_type = "ppm"
            elif re.match(".*NY phased data points follow.*", line):
                series_type = "data"
            elif re.match(".*NY points of the fit to the data follow.*", line):
                series_type = "completeFit"
                # completeFit implies baseline+fit
            elif re.match(".*NY background values follow.*", line):
                series_type = "baseline"
            elif re.match(".*lines in following.*", line):
                series_type = None
            elif re.match("[ ]+[a-zA-Z0-9]+[ ]+Conc. = [-+.E0-9]+$", line):
                series_type = None
    
            if prev_series_type != series_type:  # start/end of chunk...
                if len(vals) > 0:
                    series_data[prev_series_type] = np.array(vals)
                    vals = []
            else:
                if series_type:
                    for x in re.finditer(r"([-+.E0-9]+)[ \t]*", line):
                        v = x.group(1)
                        try:
                            v = float(v)
                            vals.append(v)
                        except ValueError:
                            print("Error parsing line: %s" % (line,))
                            print(v)
    return series_data
    # }}}

README.md

Basic Python function to read LCModel COORD data : return is a dict containing:

• ppm : points on the ppm scale
• data : data to be fit, on the ppm scale
• completeFit : the model fit, including baseline
• baseline : the modelled baseline (not present if NOBASE is set, which is the default for mega-press and certain other modes)

In response to: https://forum.mrshub.org/t/questions-about-lcmodel-coordinate-files/1141

Note that this does not extract other parameters from the COORD file, and does not attempt to read individual metabolite fits (where NEACH is specified)

For MATLAB, consider:

• https://github.com/chenkonturek/MRS_MRI_libs/blob/master/MRS_lib/io/mrs_readLcmodelCOORD.m
• https://github.com/CIC-methods/FID-A/blob/master/inputOutput/io_readlcmcoord.m
• https://github.com/CIC-methods/FID-A/blob/master/inputOutput/io_readlcmcoord_getBackground.m

I believe versions of the above may also be incorporated into Osprey https://github.com/schorschinho/osprey