''' Analysis tools for mcstas component files and instrument files. ''' import re import os from os.path import splitext, join import subprocess from datetime import datetime ''' Component parser used by initial versions of mcgui. (More recent implementations exist.) ''' class ComponentParInfo(object): ''' Component parameter info, used as ComponentParser.pars ''' def __init__(self, par_info=None): if par_info: self.par_name = par_info.par_name self.type = par_info.type self.default_value = par_info.default_value self.doc_and_unit = par_info.doc_and_unit par_name = '' # parameter par_name type = '' # can be "string" or "int", but is mostly empty default_value = '' doc_and_unit = '' # doc string and unit (no linebreaks) class ComponentParser(object): ''' Component file parser. ''' def __init__(self, comp_file): if comp_file == '': raise Exception('ComponentParser: "comp_file" may not be an empty.') self.file = comp_file self.name = None self.info = None self.description = None # info section all in one string (multiple lines) self.pars = [] # list of McComponentParInfo self.mcdisplay = None # optional MCDISPLAY section self.__hasParsed = False def parse(self): ''' main parse component for info function ''' if self.__hasParsed: return # load component from file text = open(self.file).read() if text == '': raise Exception('parse: component file is empty.') # get component info, description and par docs from header section self.info, self.description, header_P_section = self.__parseComponentHeader(text) # get component par_name from main section self.name = self.__parseComponentName(text) # get component pars from main section and match with par docs from header section self.pars = self.__parseComponentPars(text) self.__matchDocStringsToPars(self.pars, header_P_section) self.__hasParsed = True def parseDisplaySection(self): ''' optional: call to parse MCDISPLAY section and save in member "mcdisplay" ''' # load component from file text = open(self.file).read() if text == '': raise Exception('parse: component file is empty.') pat = 'MCDISPLAY\s*\%\{([-+.\w\s=<>,/*{}\"\'()\.&$=?;:*|]*)\%\}' sr = re.search(pat, text) if sr: self.mcdisplay = sr.group() else: self.mcdisplay = 'missing MCDISPLAY string' @staticmethod def __parseComponentHeader(text): # identify the start and end positions of the I, D and P sections pos_I = text.find('%I') pos_D = text.find('%D') pos_P = text.find('%P') pos_E = text.find('%E') # validate match for %I, %D, %P and %E positions if pos_I == -1: raise Exception('parseComponentHeader: Missing %I tag.') if pos_D == -1: raise Exception('parseComponentHeader: Missing %D tag.') if pos_P == -1: raise Exception('parseComponentHeader: Missing %P tag.') if pos_E == -1: raise Exception('parseComponentHeader: Missing %E tag.') # extract strings for I, D and P sections text_I = ComponentParser.__removeStarsFromLines(text[pos_I+1: pos_D]) text_D = ComponentParser.__removeStarsFromLines(text[pos_D+1: pos_P]) text_P = ComponentParser.__removeStarsFromLines(text[pos_P+1: pos_E]) return text_I, text_D, text_P @staticmethod def __parseComponentName(text): re_out = re.search('DEFINE\s+COMPONENT\s+(\w*)', text) if re_out: return re_out.group(1) @staticmethod def __parseComponentPars(text): ''' parse definition parameters and setting parameters from the main component section ''' # get definition parameters result_1 = [] re_out = re.search(r'DEFINITION\s+PARAMETERS\s*\([-+.\w\s=,/*{}\"]+\)', text) if re_out: result_sub, substituted_text = ComponentParser.__substituteCurlyPars(re_out.group(0)) result_1 = ComponentParser.__parseParLine(substituted_text) # restitute curly pars default values for r in result_1: for s in result_sub: if r.par_name == s.par_name: r.default_value = s.default_value # get setting parameters result_2 = [] re_out = re.search(r'SETTING\s+PARAMETERS\s*\([-+.\w\s=,/*{}\"]+\)', text) if re_out: result_sub, substituted_text = ComponentParser.__substituteCurlyPars(re_out.group(0)) result_2 = ComponentParser.__parseParLine(substituted_text) # restitute curly pars default values for r in result_2: for s in result_sub: if r.par_name == s.par_name: r.default_value = s.default_value return result_1 + result_2 @staticmethod def __substituteCurlyPars(text): # Extract stuff like def_par={1.0, 2.0, 3.0} which contains commas inside a curly bracket. # Returns curly bracket (name, default value), and text with such values replaced by placeholder string curly = re.findall(r'(\w+)=(\{[-+.\w\s,/*\"]*\})', text) result = [] substituted_text = str(text) # get par_info into the par info par_info structure: for p in curly: par_info = ComponentParInfo() par_info.par_name = p[0] par_info.default_value = p[1] result.append(par_info) # reduce substituted_text = substituted_text.replace(par_info.par_name + '=' + par_info.default_value, par_info.par_name + '=' + par_info.par_name + '_substituted') return result, substituted_text @staticmethod def __parseParLine(text): # assuming no curly brackets - these must have been processed and removed from text # always return something result = [] allowed = r'[-+.\w\s=,/*{}\"]' # get the text in parenthesis out1 = re.search(r'\(([-+.\w\s=,/*{}\"]+)\)', text) if not out1: return result # TODO: error handling # get comma separated sections comma_sep = re.findall(r'([-+.\w\s=/*\"]+),*', out1.group(1)) # get par_info into the par info par_info structure: for p in comma_sep: par_info = ComponentParInfo() out = re.search(r'(\w+)\s+([\w\-]+)\s*=\s*([-+.\w/*\"]+)', p) if out: # type par_name = def_val par_info.type = out.group(1) par_info.par_name = out.group(2) par_info.default_value = out.group(3) else: # par_name = def_val out = re.search(r'([\w\-]+)\s*=\s*([-+.\w/*\"]+)', p) if out: par_info.par_name = out.group(1) par_info.default_value = out.group(2) else: # par_name par_info.par_name = p.strip() result.append(par_info) return result @staticmethod def __matchDocStringsToPars(pars, header_P_section): # sets docstring values on objects in the "pars" list of McComponentParInfo parnames = [] for i in range(len(pars)): parnames.append(pars[i].par_name) lines = header_P_section.splitlines() lastpar = None for i in range(len(lines)): line = lines[i] # check for colon out = re.search(r'(.*):(.*)', line) if out: # assume that stars in lines have already been stripped candidate = out.group(1).strip() if candidate in parnames: # candidate is a known par name j = parnames.index(candidate) pars[j].doc_and_unit += out.group(2).strip() + ' ' lastpar = pars[j] elif lastpar: lastpar.doc_and_unit += out.group(2).strip() elif lastpar and ComponentParser.__stringIsEmptyLine(line): # empty line, close lastpar appending lastpar = None elif lastpar: # continuation line, append to lastpar lastpar.doc_and_unit += line.strip() @staticmethod def __stringIsEmptyLine(s): out = re.match(r'[\s\t\r\n]*', s) empty = False if out: empty = out.group() == s return empty @staticmethod def __removeStarsFromLines(text): result = '' text_lns = list(iter(text.splitlines())) for l in text_lns: l = l.lstrip('*') l = l.strip() result += '\n' result += l return result.strip('\n') @staticmethod def __parseInstrumentDef(text): re_out = re.search('DEFINE\s+INSTRUMENT\s+([a-zA-Z0-9_]*)\s*\(([-+.a-zA-Z0-9_ \t\n\r=,/*{}\"]*)\)', text) if re_out: return re_out.group(1) ''' Utility functions related to mccode file handling. ''' ''' Utility functions for parsing instrument and component files. ''' def read_header(file): ''' Reads lines of a slash-star commented section, from file-object. Returns acc. read lines as text. ''' lines = [] while True: try: l = file.readline() lines.append(l) except: break if not re.match('[ ]*\*', l): if not re.match('[ ]*\/\*', l): break elif re.search('[ ]*\*\*\*\*', l): break return ''.join(lines) class InstrCompHeaderInfo: field_cols = ['name', 'author', 'date', 'origin', 'site', 'short_description', 'description', 'test'] lst_cols = ['params', 'params_docs', 'links'] def __init__(self): self.name = '' self.filepath = '' # instr params self.params = [] # comp params self.setparams = [] self.defparams = [] self.outparams = [] # comp category self.category = '' # doc info self.author = '' self.date = '' self.origin = '' self.site = '' self.short_descr = '' self.description = '' self.test = '' self.params_docs = [] self.links = [] @staticmethod def __len__(): return len(InstrCompHeaderInfo.field_cols) + len(InstrCompHeaderInfo.lst_cols) @staticmethod def colname(idx): if idx >= 0 and idx <= 7: return InstrCompHeaderInfo.field_cols[idx] elif idx >= 8 and idx <= 10: return InstrCompHeaderInfo.lst_cols[idx-8] else: raise Exception("InstrCompHeaderInfo.colname: invalid index") def __getitem__(self, idx): if idx == 0: return self.name elif idx == 1: return self.author elif idx == 2: return self.date elif idx == 3: return self.origin elif idx == 4: return self.site elif idx == 5: return self.short_descr elif idx == 6: return self.description elif idx == 7: return self.test elif idx == 8: return self.params elif idx == 9: return self.params_docs elif idx == 10: return self.links else: raise Exception("InstrCompHeaderInfo.__getitem__: idx must be in range(%s)." % str(len(self))) def __setitem__(self, idx, value): if idx == 0: self.name = value elif idx == 1: self.author = value elif idx == 2: self.date = value elif idx == 3: self.origin = value elif idx == 4: self.site = value elif idx == 5: self.short_descr = value elif idx == 6: self.description = value elif idx == 7: self.test = value elif idx == 8: self.params = value elif idx == 9: self.params_docs = value elif idx == 10: self.links = value else: raise Exception("InstrCompHeaderInfo.__setitem__: idx must be in range(%s)." % str(len(self))) def __str__(self): lst = [self.name, self.author, self.date, self.origin, self.site, self.short_descr, self.description, self.test] lst2 = [' '.join(d) for d in self.params_docs] lst3 = [' '.join([str(c) for c in p]) for p in self.params] lst4 = [l for l in self.links] return '\n'.join(lst) + '\n\n- params docs:\n' + '\n'.join(lst2) + '\n\n- params:\n' + '\n'.join(lst3) + '\n\n- links:\n' + '\n'.join(lst4) def parse_header(text): ''' Parses the header of an instrument or component file ''' # get rid of stars and empty padding lines lines = text.splitlines() new_lines = [] for i in range(len(lines)): l = lines[i] new_lines.append(l.strip('*').strip()) # strip spaces then left stars text = '\n'.join(new_lines) # get tag indices, and deal with cases of missing tags tag_I=0 tag_D=1 tag_E=2 tag_P=3 tag_L=4 lst = [text.find('%I'), text.find('%D'), text.find('%Ex'), text.find('%P'), text.find('%L')] # missing %Example tag if lst[tag_E] == -1: lst[tag_E] = lst[tag_P] # existing %I tag with missing %D tag handled like this if lst[tag_I] > lst[tag_D] and lst[tag_E] > lst[tag_D]: lst[tag_D] = lst[tag_E] # if %E is actually %End: if lst[tag_E] > lst[tag_P] and lst[tag_P] != -1: lst[tag_E] = lst[tag_P] for i in range(len(lst)-1): if lst[i] > lst[i+1]: lst[i+1] = lst[i] if lst[tag_L] == lst[tag_P]: lst[tag_L] = len(text) # cut header into some sections bites = [text[lst[i]:lst[i+1]].strip() for i in range(len(lst)-1)] bites.append(text[lst[tag_L]:]) info = InstrCompHeaderInfo() # get author, date, origin, revision m1 = re.search('Written by:([^\n]*)\n', bites[tag_I]) if not m1: m1 = re.search('Author:([^\n]*)\n', bites[tag_I]) if m1: info.author = m1.group(1).strip() m2 = re.search('Date:([^\n]*)\n', bites[tag_I]) if m2: info.date = m2.group(1).strip() m3 = re.search('Origin:([^\n]*)\n', bites[tag_I]) if m3: info.origin = m3.group(1).strip() m4 = re.search('Version:([^\n]*)\n', bites[tag_I]) if m4: info.version = m4.group(1).strip() m5 = re.search('\%INSTRUMENT_SITE:[^\n]*\n(.*)', bites[tag_I], flags=re.DOTALL) if not m5: m5 = re.search('Origin:[^\n]*\n(.*)', bites[tag_I], flags=re.DOTALL) if m5: # ignore some comments descrlines = [] # remove all "*:" lines for l in m5.group(1).strip().splitlines(): if not re.match('[^\n]*:', l, flags=re.DOTALL): descrlines.append(l) info.short_descr = '\n'.join(descrlines).strip() # description descr = bites[tag_D] if re.match('\%Description', descr): descr = descr.replace('%Description', '').strip() elif re.match('\%D', descr): descr = descr.replace('%D', '').strip() info.description = descr # test / example tst = bites[tag_E] info.test = tst # params par_doc = None for l in bites[tag_P].splitlines(): m = re.match('(\w+):[ \t]*\[([ \w\/\(\)\\\~\-.,\":\%\^\|\{\};\*]*)\][ \t]*(.*)', l) par_doc = (None, None, None) if m: par_doc = (m.group(1), m.group(2), m.group(3).strip()) info.params_docs.append(par_doc) else: m = re.match('(\w+):[ \t]*(.*)', l) if m: par_doc = (m.group(1), "", m.group(2).strip()) info.params_docs.append(par_doc) # links for l in bites[tag_L].splitlines(): if re.match('\s*%', l) or l.strip() == '' or re.match('\/', l): continue info.links.append(l) return info def read_define_instr(file): ''' Reads lines from file obj until DEFINE INSTRUMENT, then reads lines until \). Parses this statement and returns the result in organized form. ''' lines = [] for l in file: if not re.match('DEFINE[ \t]+INSTRUMENT[ \t]+', l): continue else: lines.append(l.strip()) break if len(lines) > 0 and not re.search('\)', lines[-1]): for l in file: lines.append(l.strip()) if re.search('\)', l): break return ' '.join(lines) def read_define_comp(file): ''' appends all read lines to return list ''' end_conds = ('SHARE', 'DECLARE', 'INITIALIZE', 'TRACE') lines = [] # get to DEFINE COMPONENT statement for l in file: lines.append(l.strip()) if not re.match('DEFINE[ \t]+COMPONENT[ \t]+', l): continue else: break for l in file: m = re.match('[ ]*(\w+)', l) lines.append(l.strip()) if m and m.group(1) in end_conds: break # look for closing if not re.search('\)', lines[-1]): for l in file: lines.append(l.strip()) if re.search('\)', l): break return '\n'.join(lines) def get_comp_category(filepath): ''' extract first folder name from file path ''' head = os.path.split(filepath)[0] firstdir = os.path.split(head)[1] # handle special case - sub folder of "contrib" folder if firstdir not in ('sources', 'optics', 'samples', 'monitors', 'misc', 'contrib', 'union','sasmodels','astrox','obsolete'): head2 = os.path.split(head)[0] seconddir = os.path.split(head2)[1] return seconddir return firstdir def parse_define_comp(text): text = text.replace('\n', ' ') text = text.replace(' = ', '=') text = text.replace(' =', '=') text = text.replace('= ', '=') name = re.search('DEFINE[ \t]+COMPONENT[ \t]+(\w+)', text).group(1) m = re.search('DEFINITION[ \t]+PARAMETERS[ \t]*\(([\w\,\"\s\n\t\r\.\+\-=\{\}]*)\)', text) defpar = [] if m: defpar = parse_params(m.group(1)) m = re.search('SETTING[ \t]+PARAMETERS[ \t]*\(([\w\,\"\s\n\t\r\.\+\-=\{\}]*)\)', text) setpar = [] if m: setpar = parse_params(m.group(1)) m = re.search('OUTPUT[ \t]+PARAMETERS[ \t]*\(([\w\,\"\s\n\t\r\.\+\-=]*)\)', text) outpar = [] if m: outpar = parse_params(m.group(1)) return (name, defpar, setpar, outpar) def clean_instr_def(defline): ''' takes a typical output of read_define_instr() and extracts the "params string" for use with parse_params ''' m = re.search('\(([^(^)]*)\)', defline) try: return m.group(1) except: return None def parse_params(params_line): ''' creates a list of 3-tuples (type, name, devault_value)) from a "params string" ''' params = [] def par_rec(substr, lst): try: # handle parameter sections including curly bracket default values (case 2) m1 = re.match('([^,{]+),(.*)', substr) # not comma or curl, then a comma m2 = re.match('([^,{]+\{[^}]*\}\s*),(.*)', substr) # not comma or curl, then not a right curl, then a right curlt, then a comma if m1: lst.append(m1.group(1)) substr = m1.group(2) elif m2: lst.append(m2.group(1)) substr = m2.group(2) else: # the end return lst # continue recursion return par_rec(substr, lst) except Exception as e: print("error", e) # split the line into parts corresponding to each parameter definition params_line = params_line.lstrip('(').rstrip(')') # secure brackets stripped if '{' in params_line: # NOTE: this may exceed python max recursion depth in some cases, e.g. guide_four_sides_10_shells # however, this version is required for parsing {a,b,c} style default values # TODO: reimplement into a while-based iteration rather than a recursion parts = par_rec(params_line, []) else: parts = [s.strip() for s in params_line.split(',')] # parse each parameter for part in parts: tpe = None dval = None name = None if re.search(r'^ ', part): part = part[1:] if re.match('double ', part): part = part.replace('double ', '').strip() if re.match('string ', part): tpe = 'string' part = part.replace('string ', '').strip() if re.match('vector ', part): tpe = 'vector' part = part.replace('vector ', '').strip() if re.match('int ', part): tpe = 'int' part = part.replace('int ', '').strip() if re.search('"', part): m=re.match('(.*)\s*=\s*"(.*)"', part) dval = '"' + m.group(2) + '"' name = m.group(1).strip() elif re.search('=', part): m = re.match("(.*)=(.*)", part) dval = m.group(2).strip() name = m.group(1).strip() else: name = part.strip() if name not in (None, "", ): params.append((tpe, name, dval)) return params def parse_define_instr(text): ''' Parses a DEFINE INSTRUMENT statement from an instrument file. Not robust to "junk" in the input string. ''' try: m = re.match('DEFINE[ \t]+INSTRUMENT[ \t]+(\w+)\s*\(([\w\,\"\s\n\t\r\.\+:;\-=]*)\)', text) name = m.group(1) params = m.group(2).replace('\n', '').strip() except: return '', [] return name, parse_params(params) def read_declare(file): raise Exception('Read_declare: not yet implemented.') def read_initialize(file): raise Exception('Read_initialize: not yet implemented.') def read_trace(file): raise Exception('Read_trace: not yet implemented.') def read_finally(file): raise Exception('Read_finally: not yet implemented.') def get_instr_site_fromtxt(text): m = re.search('\%INSTRUMENT_SITE:[ \t]*(\w+)[ \t]*\n?', text) if m: return m.group(1) else: #raise Exception('Tag "%INSTRUMENT_SITE" not found.') return '' def get_instr_site(instr_file): ''' extracts and returns the rest of the line, from the text file instr_file, containing "%INSTRUMENT_SITE:" ''' try: f = open(instr_file, 'rb') text = f.read().decode() f.close() except: text = ''; print("WARNING: \n Attempt to parse instrument header faliled for: \n %s" % instr_file) site = '("%INSTRUMENT_SITE:" tag not found)' start = text.find('%INSTRUMENT_SITE:') if start > -1: end = text.find('\n', start) site = text[start+17:end].strip() return site def get_instr_comp_files(mydir, recursive=True, instrfilter=None, compfilter=None): ''' returns list of filename with path of all .instr and .comp recursively from dir "mydir" 181211: added recursive, defaults to True to preserve backwards compatibility 191114: added instrfilter and compfilter, which filters results based on filename (before the dot) ''' instrreg = None if instrfilter: instrreg = re.compile(instrfilter) compreg = None if compfilter: compreg = re.compile(compfilter) files_instr = [] files_comp = [] for (dirpath, _, files) in os.walk(mydir): for f in files: # get instr files if splitext(f)[1] == '.instr': if instrfilter is not None: if instrreg.match(splitext(f)[0]): files_instr.append(join(dirpath, f)) else: files_instr.append(join(dirpath, f)) # get comp files if os.path.splitext(f)[1] == '.comp': if compfilter is not None: if compreg.match(splitext(f)[0]): files_comp.append(join(dirpath, f)) else: files_comp.append(join(dirpath, f)) if not recursive: break return files_instr, files_comp def save_instrfile(instr, text): ''' Creates and/or saves instrument file, makes sure the file extension is .instr. Returns file par_name, or empty string if no file was saved/created. ''' if instr == '': return '' if str(instr).find('.') >= 0: if os.path.splitext(str(instr))[1] != '.instr': instr = instr + '.instr' else: instr = instr + '.instr' # TODO: add try-finally and error handling f = open(str(instr), 'w', newline='\n') f.write(text) f.close() return instr def get_file_text_direct(file): ''' Opens a file for reading binary, reads it, decodes the results and returns the text. Fixes an occational issue on MacOSX. ''' f = open(file, 'rb') text = f.read().decode() f.close() return text def get_file_contents(filepath): ''' returns file contents if file exists ''' if os.path.exists(str(filepath)): return get_file_text_direct(filepath) else: return '' def run_subtool_noread(cmd, cwd=None): ''' run subtool to completion in a excessive pipe-output robust way (millions of lines) ''' if not cwd: cwd = os.getcwd() try: process = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, stdin=subprocess.PIPE, shell=True, universal_newlines=True, cwd=cwd) process.communicate() return process.returncode except Exception as e: ''' unicode read error safe-guard ''' print("run_subtool_noread (cmd=%s) error: %s" % (cmd, str(e))) return -1 def run_subtool_to_completion(cmd, cwd=None, stdout_cb=None, stderr_cb=None): ''' Synchronous run subprocess.popen with pipe buffer reads, one-string command 'cmd' and running in directory 'cwd'. ''' def call_if_not_none(fct, *args): ''' shorthand utility for calling a function if it is defined, and otherwise ignoring it ''' if fct: fct(*args) if not cwd: cwd = os.getcwd() try: # open the process with all bells & whistles process = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, stdin=subprocess.PIPE, shell=True, universal_newlines=True, cwd=cwd) # flush until EOF for stdoutdata in process.stdout: call_if_not_none(stdout_cb, stdoutdata.rstrip('\n')) for stderrdata in process.stderr: call_if_not_none(stderr_cb, stderrdata.rstrip('\n')) return process.returncode except Exception as e: ''' unicode read error safe-guard ''' print("run_subtool_to_completion: An error occurred, %s" % str(e)) return -1 def start_subtool_then_return(cmd, cwd=None): ''' Asynchronous run subprocess.popen, using one-string command 'cmd' in directory 'cwd'. ''' def call_if_not_none(fct, *args): ''' shorthand utility for calling a function if it is defined, and otherwise ignoring it ''' if fct: fct(*args) if not cwd: cwd = os.getcwd() # open the process with all bells & whistles process = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, stdin=subprocess.PIPE, shell=True, universal_newlines=True, cwd=cwd) return process.returncode def dumpfile_pqtg(scene, filenamebase='mcplot', format='png'): ''' save as png file. Pdf is not supported, althouhg svg kind-of is ''' import pyqtgraph.exporters import pyqtgraph as pg outputfile = '%s.%s' % (filenamebase, format) # Check for existance of earlier exports if os.path.isfile(outputfile): index=1 outputfile = '%s_%i.%s' % (filenamebase, index, format ) while os.path.isfile(outputfile): index += 1 outputfile = '%s_%i.%s' % (filenamebase, index, format) if format=='png': exporter = pg.exporters.ImageExporter(scene) exporter.export(outputfile) elif format=='svg': exporter = pg.exporters.SVGExporter(scene) exporter.export(outputfile) # This is where PDF export would be handled via conversion from SVG # elif format=='pdf': # exporter = pg.exporters.SVGExporter(scene) # exporter.export(outputfile) # import subprocess # # TODO: error handling # process = subprocess.Popen('svg2pdf %s %s.pdf' % (outputfile, '%s_%i.%s' % (filenamebase, index, 'pdf')), # stdout=subprocess.PIPE, # stderr=subprocess.PIPE, # shell=True, # universal_newlines=True) else: raise Exception('png, and svg are the only supported file formats (format=%s)' % format) if os.path.isfile(outputfile): print('Graphics output ' + outputfile + ' saved') def get_datetimestr(): return datetime.strftime(datetime.now(), "%Y%m%d_%H%M_%S")