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catia.py

Source:catia.py

1###############################################################################2#                                                                             #3# Copyright (C) 2013-2014 Edward d'Auvergne                                   #4#                                                                             #5# This file is part of the program relax (http://www.nmr-relax.com).          #6#                                                                             #7# This program is free software: you can redistribute it and/or modify        #8# it under the terms of the GNU General Public License as published by        #9# the Free Software Foundation, either version 3 of the License, or           #10# (at your option) any later version.                                         #11#                                                                             #12# This program is distributed in the hope that it will be useful,             #13# but WITHOUT ANY WARRANTY; without even the implied warranty of              #14# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the               #15# GNU General Public License for more details.                                #16#                                                                             #17# You should have received a copy of the GNU General Public License           #18# along with this program.  If not, see <http://www.gnu.org/licenses/>.       #19#                                                                             #20###############################################################################21# Module docstring.22"""Functions for interfacing with Flemming Hansen's CATIA program."""23# Dependencies.24import dep_check25# Python module imports.26from os import F_OK, access, chdir, getcwd, sep27PIPE, Popen = None, None28if dep_check.subprocess_module:29    from subprocess import PIPE, Popen30import sys31# relax module imports.32from lib.dispersion.variables import EXP_TYPE_CPMG_SQ33from lib.errors import RelaxError, RelaxDirError34from lib.io import mkdir_nofail, open_write_file, test_binary35from pipe_control.mol_res_spin import check_mol_res_spin_data, spin_loop36from pipe_control.pipes import check_pipe37from specific_analyses.relax_disp.checks import check_model_type, check_spectra_id_setup38from specific_analyses.relax_disp.data import loop_frq, loop_offset_point, return_param_key_from_data39def catia_execute(file='Fit.catia', dir=None, binary=None):40    """Create the CATIA input files.41    @keyword file:          The main CATIA execution file.42    @type file:             str43    @keyword dir:           The optional directory to place the files into.  If None, then the files will be placed into the current directory.44    @type dir:              str or None45    @keyword binary:        The name of the CATIA binary file.  This can include the path to the binary.46    @type binary:           str47    """48    # The current directory.49    orig_dir = getcwd()50    # Test the binary file string corresponds to a valid executable.51    test_binary(binary)52    # The directory.53    if dir == None:54        dir = orig_dir55    if not access(dir, F_OK):56        raise RelaxDirError('CATIA', dir)57    # Change to the directory with the CATIA input files.58    chdir(dir)59    # Catch failures and return to the correct directory.60    try:61        # Execute CATIA.62        cmd = binary + ' < Fit.catia'63        pipe = Popen(cmd, shell=True, stdin=PIPE, stdout=PIPE, stderr=PIPE, close_fds=False)64        # Close the pipe.65        pipe.stdin.close()66        # Write to stdout.67        for line in pipe.stdout.readlines():68            # Decode Python 3 byte arrays.69            if hasattr(line, 'decode'):70                line = line.decode()71            # Write.72            sys.stdout.write(line)73        # Write to stderr.74        for line in pipe.stderr.readlines():75            # Decode Python 3 byte arrays.76            if hasattr(line, 'decode'):77                line = line.decode()78            # Write.79            sys.stderr.write(line)80    # Failure.81    except:82        # Change back to the original directory.83        chdir(orig_dir)84        # Reraise the error.85        raise86    # Change back to the original directory.87    chdir(orig_dir)88def catia_input(file='Fit.catia', dir=None, output_dir='output', force=False):89    """Create the CATIA input files.90    @keyword file:          The main CATIA execution file.91    @type file:             str92    @keyword dir:           The optional directory to place the files into.  If None, then the files will be placed into the current directory.93    @type dir:              str or None94    @keyword output_dir:    The CATIA output directory, located within the directory specified by the dir argument.  This directory will be created.95    @type output_dir:       str96    @keyword force:         A flag which if True will cause all pre-existing files to be overwritten.97    @type force:            Bool98    """99    # Data checks.100    check_pipe()101    check_mol_res_spin_data()102    check_spectra_id_setup()103    check_model_type()104    # Check that this is CPMG data.105    for id in cdp.spectrum_ids:106        if cdp.exp_type[id] != 'SQ CPMG':107            raise RelaxError("Only CPMG type data is supported.")108    # Directory creation.109    if dir != None:110        mkdir_nofail(dir, verbosity=0)111    # Create the R2eff files.112    write_r2eff_files(input_dir='input_r2eff', base_dir=dir, force=force)113    # Create the parameter files.114    write_param_files(global_file="ParamGlobal.inp", set_file="ParamSet1.inp", dir=dir, force=force)115    # Create the main execution file.116    write_main_file(file=file, dir=dir, output_dir=output_dir, force=force)117    # Create the output directory as needed by CATIA (it does not create it itself).118    mkdir_nofail(dir + sep + output_dir, verbosity=0)119def write_main_file(file=None, dir=None, output_dir=None, f_tol=1e-25, max_iter=10000000, r1=False, force=False):120    """Create the main CATIA execution file.121    @keyword file:          The main CATIA execution file.122    @type file:             str123    @keyword dir:           The directory to place the files into.124    @type dir:              str or None125    @keyword output_dir:    The CATIA output directory, located within the directory specified by the dir argument.  This directory will be created.126    @type output_dir:       str127    @keyword r1:            A flag which if True will cause the R1 data to be used for off-resonance effects.128    @type r1:               bool129    @keyword force:         A flag which if True will cause a pre-existing file to be overwritten.130    @type force:            bool131    """132    # The file.133    catia_in = open_write_file(file_name=file, dir=dir, force=force)134    # The R2eff input sets.135    for frq in loop_frq():136        frq_label = int(frq*1e-6)137        file_name = "data_set_%i.inp" % frq_label138        catia_in.write("ReadDataset(%s)\n" % file_name)139    # Write out the data.140    catia_in.write("ReadParam_Global(ParamGlobal.inp)\n")141    catia_in.write("ReadParam_Local(ParamSet1.inp)\n")142    catia_in.write("\n")143    # The R1 data for off-resonance effects.144    if r1:145        catia_in.write("ReadParam(Omega;%s;0;1)\n" % shift_file)146        for frq in loop_frq():147            frq_label = int(frq*1e-6)148            param = "R1iph_%s" % frq_label149            r1_file = "R1_%s.out" % frq_label150            catia_in.write("ReadParam(%s;%s;0;1)\n" % (param, r1_file))151        catia_in.write("\n")152    # Fix these off-resonance parameters.153    catia_in.write("FreeLocalParam(all;Omega;false)\n")154    for frq in loop_frq():155        frq_label = int(frq*1e-6)156        param = "R1iph_%s" % frq_label157        catia_in.write("FreeLocalParam(all;%s;false)\n" % param)158    catia_in.write("\n")159    # Minimisation.160    catia_in.write("Minimize(print=y;tol=%s;maxiter=%i)\n" % (f_tol, max_iter))161    catia_in.write("\n")162    # Plotting.163    catia_in.write("PrintParam(%s/GlobalParam.fit;global)\n" % output_dir)164    catia_in.write("PrintParam(%s/DeltaOmega.fit;DeltaO)\n" % output_dir)165    catia_in.write("PrintData(%s/)\n" % output_dir)166    catia_in.write("\n")167    # Calculate the chi-squared value (not sure why, it's calculated in the minimisation).168    catia_in.write("ChiSq(all;all)\n")169    # Exit the program.170    catia_in.write("exit(0)\n")171    # Close the file.172    catia_in.close()173def write_param_files(global_file=None, kex=1500.0, pA=0.95, set_file=None, dir=None, r1=False, force=False):174    """Create the CATIA parameter files.175    @keyword global_file:   The name of the global parameter file.176    @type global_file:      str177    @keyword set_file:      The name of the parameter set file.178    @type set_file:         str179    @keyword dir:           The base directory to place the files into.180    @type dir:              str181    @keyword r1:            A flag which if True will cause the R1 data to be used for off-resonance effects.182    @type r1:               bool183    @keyword force:         A flag which if True will cause a pre-existing file to be overwritten.184    @type force:            bool185    """186    # Open the global parameter file.187    param_file = open_write_file(file_name=global_file, dir=dir, force=force)188    # Set the starting values.189    param_file.write("kex = %s\n" % kex)190    param_file.write("pb = %s\n" % (1.0-pA))191    # Close the file.192    param_file.close()193    # Open the 1st parameter set file.194    set_file = open_write_file(file_name=set_file, dir=dir, force=force)195    # The parameter format.196    params = ['Delta0']197    values = [0.5]198    if r1:199        for frq in loop_frq():200            params.append("R1iph_%s" % frq_label(frq))201            values.append(1.5)202    for frq in loop_frq():203        params.append("R0iph_%s" % frq_label(frq))204        values.append(5.0)205    if r1:206        params.append("Omega")207        values.append(0.0)208    # Write out the format.209    set_file.write("format = (")210    for i in range(len(params)):211        if i != 0:212            set_file.write(';')213        set_file.write(params[i])214    set_file.write(")\n")215    # Um?!?  The average values maybe?216    set_file.write("* = (")217    for i in range(len(values)):218        if i != 0:219            set_file.write(';')220        set_file.write("%s" % values[i])221    set_file.write(")\n")222    # Close the file.223    set_file.close()224def frq_label(frq):225    """Convert the frequency in Hz to a label in MHz.226    @param frq: The frequency to convert.227    @type frq:  float228    @return:    The frequency in MHz as a label.229    @rtype:     str230    """231    # Convert and return.232    return str(int(frq*1e-6))233def write_r2eff_files(input_dir=None, base_dir=None, force=False):234    """Create the CATIA R2eff input files.235    @keyword input_dir: The special directory for the R2eff input files.236    @type input_dir:    str237    @keyword base_dir:  The base directory to place the files into.238    @type base_dir:     str239    @keyword force:     A flag which if True will cause a pre-existing file to be overwritten.240    @type force:        bool241    """242    # Create the directory for the R2eff files for each field and spin.243    dir = base_dir + sep + input_dir244    mkdir_nofail(dir, verbosity=0)245    # Determine the isotope information.246    isotope = None247    for spin in spin_loop(skip_desel=True):248        if hasattr(spin, 'isotope'):249            if isotope == None:250                isotope = spin.isotope251            elif spin.isotope != isotope:252                raise RelaxError("CATIA only supports one spin type.")253    if isotope == None:254        raise RelaxError("The spin isotopes have not been specified.")255    # Isotope translation.256    if isotope == '1H':257        isotope = 'H1'258    elif isotope == '13C':259        isotope = 'C13'260    elif isotope == '15N':261        isotope = 'N15'262    # Loop over the frequencies.263    for frq, mi in loop_frq(return_indices=True):264        # The frequency string in MHz.265        frq_string = int(frq*1e-6)266        # The set files.267        file_name = "data_set_%i.inp" % frq_string268        set_file = open_write_file(file_name=file_name, dir=base_dir, force=force)269        id = frq_string270        set_file.write("ID=%s\n" % id)271        set_file.write("Sfrq = %s\n" % frq_string)272        set_file.write("Temperature = %s\n" % 0.0)273        set_file.write("Nucleus = %s\n" % isotope)274        set_file.write("Couplednucleus = %s\n" % 'H1')275        set_file.write("Time_equil = %s\n" % 0.0)276        set_file.write("Pwx_cp = %s\n" % 0.0)277        set_file.write("Taub = %s\n" % 0.0)278        set_file.write("Time_T2 = %s\n"% cdp.relax_time_list[0])279        set_file.write("Xcar = %s\n" % 0.0)280        set_file.write("Seqfil = %s\n" % 'CW_CPMG')281        set_file.write("Minerror = %s\n" % "(2.%;0.5/s)")282        set_file.write("Basis = (%s)\n" % "Iph_7")283        set_file.write("Format = (%i;%i;%i)\n" % (0, 1, 2))284        set_file.write("DataDirectory = %s\n" % (dir+sep))285        set_file.write("Data = (\n")286        # Loop over the spins.287        for spin, mol_name, res_num, res_name, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True):288            # The file.289            file_name = "spin%s_%i.cpmg" % (spin_id.replace('#', '_').replace(':', '_').replace('@', '_'), frq_string)290            spin_file = open_write_file(file_name=file_name, dir=dir, force=force)291            # Write the header.292            spin_file.write("# %18s %20s %20s\n" % ("nu_cpmg(Hz)", "R2(1/s)", "Esd(R2)"))293            # Loop over the dispersion points.294            for offset, point, oi, di in loop_offset_point(exp_type=EXP_TYPE_CPMG_SQ, frq=frq, return_indices=True):295                # The key.296                key = return_param_key_from_data(exp_type=EXP_TYPE_CPMG_SQ, frq=frq, offset=offset, point=point)297                # No data.298                if key not in spin.r2eff:299                    continue300                # Write out the data.301                spin_file.write("%20.15f %20.15f %20.15f\n" % (point, spin.r2eff[key], spin.r2eff_err[key]))302            # Close the file.303            spin_file.close()304            # Add the file name to the set.305            catia_spin_id = "%i%s" % (res_num, spin.name)306            set_file.write(" [%s;%s];\n" % (catia_spin_id, file_name))307        # Terminate the set file.308        set_file.write(")\n")...

parsemetsv2folia.py

Source:parsemetsv2folia.py

1#!/usr/bin/env python32import argparse3import sys4import os5try:6    from pynlpl.formats import folia7except ImportError:8    print("ERROR: PyNLPl not found, please install pynlpl (pip install pynlpl)",file=sys.stderr)9    sys.exit(2)10#sys.path.append(os.path.dirname(__file__))11#import tsvlib12#import tsv2folia.tsvlib as tsvlib # USE THIS LINE ON FLAT SERVER but comment it out when testing locally13import tsvlib # USE THIS LINE WHEN TESTING LOCALLY but do not forget to comment this line out when committing14EMPTY = ['', '_']15POS_SET_URL = "https://github.com/proycon/parseme-support/raw/master/parseme-pos.foliaset.xml"16# The TSV file shouls have the following fields:17# 0: token ID (restarting from 1 at every sentence)18# 1: surface form19# 2: nsp (optional) -> the string 'nsp' if the current token should be appended to the previous without space 20# 3: MWEs (optional) -> the list of MWEs this word belongs to in the format 1[:MWE_type1]; 2[:MWE_type2]; ...21def convert(filename, targetfilename, rtl, lang_set_file):22    doc = folia.Document(id=os.path.basename(filename.replace('.tsv','')))23    if rtl:24        doc.metadata['direction'] = 'rtl'25    doc.metadata['status'] = 'untouched'26    doc.declare(folia.Entity, lang_set_file) #ENTITY-SET definition    27    doc.declare(folia.AnnotationType.POS, set=POS_SET_URL) #POS-SET definition 28    text = doc.append(folia.Text)29    with open(filename,'r',encoding='utf-8') as f:30        for tsv_sentence in tsvlib.iter_tsv_sentences(f):31            folia_sentence = folia.Sentence(doc, generate_id_in=text)32            text.append(folia_sentence)33            for tsv_word in tsv_sentence:34                folia_word = folia.Word(doc, text=tsv_word.surface, space=(not tsv_word.nsp), generate_id_in=folia_sentence)35                folia_sentence.append(folia_word)36                if tsv_word.pos:37                    folia_word.append(folia.PosAnnotation(doc, cls=tsv_word.pos, annotator="auto", annotatortype=folia.AnnotatorType.AUTO))38            mwe_infos = tsv_sentence.mwe_infos()39            if mwe_infos:40                folia_mwe_list = folia.EntitiesLayer(doc)41                folia_sentence.append(folia_mwe_list)42                for mweid, mweinfo in mwe_infos.items():43                    assert mweinfo.category, "Conversion to FoLiA requires all MWEs to have a category"  # checkme44                    folia_words = [folia_sentence[i] for i in mweinfo.word_indexes]45                    folia_mwe_list.append(folia.Entity, *folia_words, cls=mweinfo.category, annotatortype=folia.AnnotatorType.MANUAL)46    doc.save(targetfilename)47#This function can be called directly by FLAT48def flat_convert(filename, targetfilename, *args, **kwargs):49    if 'rtl' in kwargs and kwargs['rtl']:50        rtl=True51    else:52        rtl = False53    setdefinition = kwargs['flatconfiguration']['annotationfocusset']54    try:55        convert(filename, targetfilename, rtl, setdefinition)56    except Exception as e:57        return False, e.__class__.__name__ + ': ' + str(e)58    return True59set_path = 'https://github.com/proycon/parseme-support/raw/master/'60set_options = {61    #"parseme": {62    #    'set_file': set_path + "parseme-mwe.foliaset.xml",63    #    'rtl': False64    #}65    "english": {66        'set_file': set_path + "parseme-mwe-en.foliaset.xml",67        'rtl': False68    },69    "farsi": {70        'set_file': set_path + "parseme-mwe-farsi.foliaset.xml",71        'rtl': True72    },73    "germanic": {74        'set_file': set_path + "parseme-mwe-germanic.foliaset.xml",75        'rtl': False76    },       77    "hebrew": {78        'set_file': set_path + "parseme-mwe-hebrew.foliaset.xml",79        'rtl': True80    },81    "lithuanian": {82        'set_file': set_path + "parseme-mwe-lt.foliaset.xml",83        'rtl': False84    },85    "other": {86        'set_file': set_path + "parseme-mwe-other.foliaset.xml",87        'rtl': False88    },89    "romance": {90        'set_file': set_path + "parseme-mwe-romance.foliaset.xml",91        'rtl': False92    },93    "italian": {94        'set_file': set_path + "parseme-mwe-it.foliaset.xml",95        'rtl': False96    },97    "portuguese": {98        'set_file': set_path + "parseme-mwe-pt.foliaset.xml",99        'rtl': False100    },101    "slavic": {102        'set_file': set_path + "parseme-mwe-slavic.foliaset.xml",103        'rtl': False104    },105    "yiddish": {106        'set_file': set_path + "parseme-mwe-yiddish.foliaset.xml",107        'rtl': True108    },109    "maltese": {110        'set_file': set_path + "parseme-mwe-maltese.foliaset.xml",111        'rtl': False112    },113}114def valid_input_file(file_name):115    if not file_name.endswith('.tsv') and not file_name.endswith('.parsemetsv'):116        raise argparse.ArgumentTypeError("File name must end with '.tsv'")117    return file_name118parser = argparse.ArgumentParser(description="Convert from TSV to FoLiA XML.")119parser.add_argument("FILE", type=valid_input_file, help="An input TSV file")120parser.add_argument("--stdout", action="store_true", help="Output data in stdout")121parser.add_argument("--language", type = str.lower, choices = set_options.keys(), help="The input language", required=True) 122 123class Main(object):124    def __init__(self, args):125        self.args = args126    def run(self):127        sys.excepthook = tsvlib.excepthook128        lang_options = set_options[self.args.language]129        filename = self.args.FILE130        targetfilename = "/dev/stdout" if self.args.stdout else filename.rsplit(".",1)[0] + '.folia.xml'131        rtl = lang_options['rtl']132        lang_set_file = lang_options['set_file']        133        convert(filename, targetfilename, rtl, lang_set_file)134def main():135    Main(parser.parse_args()).run()136#####################################################137if __name__ == "__main__":...

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