372 lines
11 KiB
Python
372 lines
11 KiB
Python
import re
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import pandas as pd
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import numpy as np
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from . import util
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class Table:
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"""Store spreadsheet-like data."""
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def __init__(self,data,shapes,comments=None):
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"""
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New spreadsheet.
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Parameters
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----------
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data : numpy.ndarray or pandas.DataFrame
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Data. Column labels from a pandas.DataFrame will be replaced.
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shapes : dict with str:tuple pairs
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Shapes of the columns. Example 'F':(3,3) for a deformation gradient.
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comments : str or iterable of str, optional
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Additional, human-readable information.
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"""
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comments_ = [comments] if isinstance(comments,str) else comments
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self.comments = [] if comments_ is None else [c for c in comments_]
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self.data = pd.DataFrame(data=data)
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self.shapes = { k:(v,) if isinstance(v,(np.int,int)) else v for k,v in shapes.items() }
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self._label_condensed()
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def _label_flat(self):
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"""Label data individually, e.g. v v v ==> 1_v 2_v 3_v."""
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labels = []
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for label,shape in self.shapes.items():
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size = int(np.prod(shape))
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labels += [('' if size == 1 else f'{i+1}_')+label for i in range(size)]
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self.data.columns = labels
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def _label_condensed(self):
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"""Label data condensed, e.g. 1_v 2_v 3_v ==> v v v."""
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labels = []
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for label,shape in self.shapes.items():
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labels += [label] * int(np.prod(shape))
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self.data.columns = labels
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def _add_comment(self,label,shape,info):
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if info is not None:
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specific = f'{label}{" "+str(shape) if np.prod(shape,dtype=int) > 1 else ""}: {info}'
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general = util.execution_stamp('Table')
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self.comments.append(f'{specific} / {general}')
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@staticmethod
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def from_ASCII(fname):
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"""
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Create table from ASCII file.
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The first line can indicate the number of subsequent header lines as 'n header',
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alternatively first line is the header and comments are marked by '#' ('new style').
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Vector data column labels are indicated by '1_v, 2_v, ..., n_v'.
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Tensor data column labels are indicated by '3x3:1_T, 3x3:2_T, ..., 3x3:9_T'.
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Parameters
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----------
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fname : file, str, or pathlib.Path
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Filename or file for reading.
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"""
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try:
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f = open(fname)
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except TypeError:
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f = fname
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f.seek(0)
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try:
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N_comment_lines,keyword = f.readline().strip().split(maxsplit=1)
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if keyword != 'header':
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raise ValueError
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else:
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comments = [f.readline().strip() for i in range(1,int(N_comment_lines))]
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labels = f.readline().split()
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except ValueError:
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f.seek(0)
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comments = []
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line = f.readline().strip()
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while line.startswith('#'):
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comments.append(line.lstrip('#').strip())
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line = f.readline().strip()
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labels = line.split()
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shapes = {}
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for label in labels:
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tensor_column = re.search(r'[0-9,x]*?:[0-9]*?_',label)
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if tensor_column:
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my_shape = tensor_column.group().split(':',1)[0].split('x')
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shapes[label.split('_',1)[1]] = tuple([int(d) for d in my_shape])
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else:
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vector_column = re.match(r'[0-9]*?_',label)
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if vector_column:
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shapes[label.split('_',1)[1]] = (int(label.split('_',1)[0]),)
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else:
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shapes[label] = (1,)
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data = pd.read_csv(f,names=list(range(len(labels))),sep=r'\s+')
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return Table(data,shapes,comments)
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@staticmethod
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def from_ang(fname):
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"""
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Create table from TSL ang file.
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A valid TSL ang file needs to contains the following columns:
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* Euler angles (Bunge notation) in radians, 3 floats, label 'eu'.
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* Spatial position in meters, 2 floats, label 'pos'.
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* Image quality, 1 float, label 'IQ'.
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* Confidence index, 1 float, label 'CI'.
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* Phase ID, 1 int, label 'ID'.
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* SEM signal, 1 float, label 'intensity'.
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* Fit, 1 float, label 'fit'.
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Parameters
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----------
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fname : file, str, or pathlib.Path
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Filename or file for reading.
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"""
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try:
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f = open(fname)
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except TypeError:
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f = fname
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f.seek(0)
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content = f.readlines()
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comments = [util.execution_stamp('Table','from_ang')]
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for line in content:
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if line.startswith('#'):
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comments.append(line.strip())
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else:
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break
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data = np.loadtxt(content)
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shapes = {'eu':3, 'pos':2, 'IQ':1, 'CI':1, 'ID':1, 'intensity':1, 'fit':1}
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remainder = data.shape[1]-sum(shapes.values())
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if remainder > 0: # 3.8 can do: if (remainder := data.shape[1]-sum(shapes.values())) > 0
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shapes['unknown'] = remainder
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return Table(data,shapes,comments)
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@property
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def labels(self):
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return list(self.shapes.keys())
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def get(self,label):
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"""
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Get column data.
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Parameters
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----------
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label : str
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Column label.
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"""
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if re.match(r'[0-9]*?_',label):
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idx,key = label.split('_',1)
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data = self.data[key].to_numpy()[:,int(idx)-1].reshape(-1,1)
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else:
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data = self.data[label].to_numpy().reshape((-1,)+self.shapes[label])
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return data.astype(type(data.flatten()[0]))
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def set(self,label,data,info=None):
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"""
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Set column data.
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Parameters
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----------
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label : str
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Column label.
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data : np.ndarray
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New data.
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info : str, optional
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Human-readable information about the new data.
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"""
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self._add_comment(label,data.shape[1:],info)
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if re.match(r'[0-9]*?_',label):
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idx,key = label.split('_',1)
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iloc = self.data.columns.get_loc(key).tolist().index(True) + int(idx) -1
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self.data.iloc[:,iloc] = data
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else:
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self.data[label] = data.reshape(self.data[label].shape)
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def add(self,label,data,info=None):
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"""
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Add column data.
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Parameters
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----------
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label : str
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Column label.
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data : np.ndarray
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Modified data.
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info : str, optional
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Human-readable information about the modified data.
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"""
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self._add_comment(label,data.shape[1:],info)
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self.shapes[label] = data.shape[1:] if len(data.shape) > 1 else (1,)
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size = np.prod(data.shape[1:],dtype=int)
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new = pd.DataFrame(data=data.reshape(-1,size),
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columns=[label]*size,
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)
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new.index = self.data.index
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self.data = pd.concat([self.data,new],axis=1)
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def delete(self,label):
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"""
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Delete column data.
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Parameters
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----------
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label : str
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Column label.
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"""
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self.data.drop(columns=label,inplace=True)
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del self.shapes[label]
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def rename(self,label_old,label_new,info=None):
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"""
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Rename column data.
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Parameters
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----------
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label_old : str
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Old column label.
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label_new : str
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New column label.
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"""
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self.data.rename(columns={label_old:label_new},inplace=True)
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self.comments.append(f'{label_old} => {label_new}'+('' if info is None else f': {info}'))
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self.shapes = {(label if label != label_old else label_new):self.shapes[label] for label in self.shapes}
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def sort_by(self,labels,ascending=True):
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"""
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Sort table by values of given labels.
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Parameters
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----------
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label : str or list
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Column labels for sorting.
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ascending : bool or list, optional
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Set sort order.
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"""
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self._label_flat()
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self.data.sort_values(labels,axis=0,inplace=True,ascending=ascending)
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self._label_condensed()
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self.comments.append(f'sorted by [{", ".join(labels)}]')
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def append(self,other):
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"""
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Append other table vertically (similar to numpy.vstack).
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Requires matching labels/shapes and order.
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Parameters
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----------
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other : Table
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Table to append.
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"""
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if self.shapes != other.shapes or not self.data.columns.equals(other.data.columns):
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raise KeyError('Labels or shapes or order do not match')
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else:
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self.data = self.data.append(other.data,ignore_index=True)
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def join(self,other):
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"""
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Append other table horizontally (similar to numpy.hstack).
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Requires matching number of rows and no common labels.
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Parameters
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----------
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other : Table
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Table to join.
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"""
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if set(self.shapes) & set(other.shapes) or self.data.shape[0] != other.data.shape[0]:
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raise KeyError('Dublicated keys or row count mismatch')
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else:
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self.data = self.data.join(other.data)
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for key in other.shapes:
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self.shapes[key] = other.shapes[key]
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def to_file(self,fname,format='ASCII',new_style=False):
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"""
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Store as plain text file.
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Parameters
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----------
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fname : file, str, or pathlib.Path
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Filename or file for writing.
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format : {ASCII'}, optional
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File format, defaults to 'ASCII'. Available formats are:
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- ASCII: Plain text file, extension '.txt'.
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new_style : Boolean, optional
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Write table in new style, indicating header lines by comment sign ('#') only.
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"""
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def _to_ASCII(table,fname,new_style=False):
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"""
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Store as plain text file.
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Parameters
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----------
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table : Table object
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Table to write.
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fname : file, str, or pathlib.Path
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Filename or file for writing.
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new_style : Boolean, optional
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Write table in new style, indicating header lines by comment sign ('#') only.
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"""
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seen = set()
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labels = []
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for l in [x for x in table.data.columns if not (x in seen or seen.add(x))]:
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if table.shapes[l] == (1,):
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labels.append(f'{l}')
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elif len(table.shapes[l]) == 1:
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labels += [f'{i+1}_{l}' \
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for i in range(table.shapes[l][0])]
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else:
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labels += [f'{util.srepr(table.shapes[l],"x")}:{i+1}_{l}' \
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for i in range(np.prod(table.shapes[l]))]
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header = [f'# {comment}' for comment in table.comments] if new_style else \
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[f'{len(table.comments)+1} header'] + table.comments
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try:
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f = open(fname,'w')
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except TypeError:
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f = fname
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for line in header + [' '.join(labels)]: f.write(line+'\n')
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table.data.to_csv(f,sep=' ',na_rep='nan',index=False,header=False)
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if format.lower() == 'ascii':
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return _to_ASCII(self,fname,new_style)
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else:
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raise TypeError(f'Unknown format {format}.')
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