import re import pandas as pd import numpy as np from . import version class Table: """Store spreadsheet-like data.""" def __init__(self,data,shapes,comments=None): """ New spreadsheet. Parameters ---------- data : numpy.ndarray or pandas.DataFrame Data. Column labels from a pandas.DataFrame will be replaced. shapes : dict with str:tuple pairs Shapes of the columns. Example 'F':(3,3) for a deformation gradient. comments : iterable of str, optional Additional, human-readable information. """ self.comments = [] if comments is None else [c for c in comments] self.data = pd.DataFrame(data=data) self.shapes = shapes self._label_condensed() def _label_flat(self): """Label data individually, e.g. v v v ==> 1_v 2_v 3_v.""" labels = [] for label,shape in self.shapes.items(): size = int(np.prod(shape)) labels += ['{}{}'.format('' if size == 1 else '{}_'.format(i+1),label) for i in range(size)] self.data.columns = labels def _label_condensed(self): """Label data condensed, e.g. 1_v 2_v 3_v ==> v v v.""" labels = [] for label,shape in self.shapes.items(): labels += [label] * int(np.prod(shape)) self.data.columns = labels def _add_comment(self,label,shape,info): if info is not None: c = '{}{}: {}'.format(label,' '+str(shape) if np.prod(shape,dtype=int) > 1 else '',info) self.comments.append(c) @staticmethod def from_ASCII(fname): """ Create table from ASCII file. The first line can indicate the number of subsequent header lines as 'n header', alternatively first line is the header and comments are marked by '#' ('new style'). Vector data column labels are indicated by '1_v, 2_v, ..., n_v'. Tensor data column labels are indicated by '3x3:1_T, 3x3:2_T, ..., 3x3:9_T'. Parameters ---------- fname : file, str, or pathlib.Path Filename or file for reading. """ try: f = open(fname) except TypeError: f = fname f.seek(0) try: N_comment_lines,keyword = f.readline().strip().split(maxsplit=1) if keyword != 'header': raise ValueError else: comments = [f.readline().strip() for i in range(1,int(N_comment_lines))] labels = f.readline().split() except ValueError: f.seek(0) comments = [] line = f.readline().strip() while line.startswith('#'): comments.append(line.lstrip('#').strip()) line = f.readline().strip() labels = line.split() shapes = {} for label in labels: tensor_column = re.search(r'[0-9,x]*?:[0-9]*?_',label) if tensor_column: my_shape = tensor_column.group().split(':',1)[0].split('x') shapes[label.split('_',1)[1]] = tuple([int(d) for d in my_shape]) else: vector_column = re.match(r'[0-9]*?_',label) if vector_column: shapes[label.split('_',1)[1]] = (int(label.split('_',1)[0]),) else: shapes[label] = (1,) data = pd.read_csv(f,names=list(range(len(labels))),sep=r'\s+') return Table(data,shapes,comments) @staticmethod def from_ang(fname): """ Create table from TSL ang file. A valid TSL ang file needs to contains the following columns: * Euler angles (Bunge notation) in radians, 3 floats, label 'eu'. * Spatial position in meters, 2 floats, label 'pos'. * Image quality, 1 float, label 'IQ'. * Confidence index, 1 float, label 'CI'. * Phase ID, 1 int, label 'ID'. * SEM signal, 1 float, label 'intensity'. * Fit, 1 float, label 'fit'. Parameters ---------- fname : file, str, or pathlib.Path Filename or file for reading. """ shapes = {'eu':(3,), 'pos':(2,), 'IQ':(1,), 'CI':(1,), 'ID':(1,), 'intensity':(1,), 'fit':(1,)} try: f = open(fname) except TypeError: f = fname f.seek(0) content = f.readlines() comments = ['table.py:from_ang v {}'.format(version)] for line in content: if line.startswith('#'): comments.append(line.strip()) else: break data = np.loadtxt(content) for c in range(data.shape[1]-10): shapes['n/a_{}'.format(c+1)] = (1,) return Table(data,shapes,comments) @property def labels(self): return list(self.shapes.keys()) def get(self,label): """ Get column data. Parameters ---------- label : str Column label. """ if re.match(r'[0-9]*?_',label): idx,key = label.split('_',1) data = self.data[key].to_numpy()[:,int(idx)-1].reshape(-1,1) else: data = self.data[label].to_numpy().reshape((-1,)+self.shapes[label]) return data.astype(type(data.flatten()[0])) def set(self,label,data,info=None): """ Set column data. Parameters ---------- label : str Column label. data : np.ndarray New data. info : str, optional Human-readable information about the new data. """ self._add_comment(label,data.shape[1:],info) if re.match(r'[0-9]*?_',label): idx,key = label.split('_',1) iloc = self.data.columns.get_loc(key).tolist().index(True) + int(idx) -1 self.data.iloc[:,iloc] = data else: self.data[label] = data.reshape(self.data[label].shape) def add(self,label,data,info=None): """ Add column data. Parameters ---------- label : str Column label. data : np.ndarray Modified data. info : str, optional Human-readable information about the modified data. """ self._add_comment(label,data.shape[1:],info) self.shapes[label] = data.shape[1:] if len(data.shape) > 1 else (1,) size = np.prod(data.shape[1:],dtype=int) new = pd.DataFrame(data=data.reshape(-1,size), columns=[label]*size, ) new.index = self.data.index self.data = pd.concat([self.data,new],axis=1) def delete(self,label): """ Delete column data. Parameters ---------- label : str Column label. """ self.data.drop(columns=label,inplace=True) del self.shapes[label] def rename(self,label_old,label_new,info=None): """ Rename column data. Parameters ---------- label_old : str Old column label. label_new : str New column label. """ self.data.rename(columns={label_old:label_new},inplace=True) c = '{} => {}{}'.format(label_old,label_new,'' if info is None else ': {}'.format(info)) self.comments.append(c) self.shapes = {(label if label != label_old else label_new):self.shapes[label] for label in self.shapes} def sort_by(self,labels,ascending=True): """ Sort table by values of given labels. Parameters ---------- label : str or list Column labels for sorting. ascending : bool or list, optional Set sort order. """ self._label_flat() self.data.sort_values(labels,axis=0,inplace=True,ascending=ascending) self._label_condensed() self.comments.append('sorted by [{}]'.format(', '.join(labels))) def append(self,other): """ Append other table vertically (similar to numpy.vstack). Requires matching labels/shapes and order. Parameters ---------- other : Table Table to append. """ if self.shapes != other.shapes or not self.data.columns.equals(other.data.columns): raise KeyError('Labels or shapes or order do not match') else: self.data = self.data.append(other.data,ignore_index=True) def join(self,other): """ Append other table horizontally (similar to numpy.hstack). Requires matching number of rows and no common labels. Parameters ---------- other : Table Table to join. """ if set(self.shapes) & set(other.shapes) or self.data.shape[0] != other.data.shape[0]: raise KeyError('Dublicated keys or row count mismatch') else: self.data = self.data.join(other.data) for key in other.shapes: self.shapes[key] = other.shapes[key] def to_ASCII(self,fname,new_style=False): """ Store as plain text file. Parameters ---------- fname : file, str, or pathlib.Path Filename or file for writing. new_style : Boolean, optional Write table in new style, indicating header lines by comment sign ('#') only. """ seen = set() labels = [] for l in [x for x in self.data.columns if not (x in seen or seen.add(x))]: if self.shapes[l] == (1,): labels.append('{}'.format(l)) elif len(self.shapes[l]) == 1: labels += ['{}_{}'.format(i+1,l) \ for i in range(self.shapes[l][0])] else: labels += ['{}:{}_{}'.format('x'.join([str(d) for d in self.shapes[l]]),i+1,l) \ for i in range(np.prod(self.shapes[l]))] if new_style: header = ['# {}'.format(comment) for comment in self.comments] else: header = ['{} header'.format(len(self.comments)+1)] \ + self.comments \ try: f = open(fname,'w') except TypeError: f = fname for line in header + [' '.join(labels)]: f.write(line+'\n') self.data.to_csv(f,sep=' ',na_rep='nan',index=False,header=False)