429 lines
12 KiB
Python
429 lines
12 KiB
Python
import re
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import copy
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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.int64,np.int32,int)) else v for k,v in shapes.items() }
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self._label_uniform()
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def __repr__(self):
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"""Brief overview."""
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return '\n'.join(['# '+c for c in self.comments])+'\n'+self.data.__repr__()
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def __getitem__(self,item):
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"""Return slice according to item."""
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return self.__class__(data=self.data[item],shapes=self.shapes,comments=self.comments)
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def __len__(self):
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"""Number of rows."""
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return len(self.data)
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def __copy__(self):
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"""Create deep copy."""
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return copy.deepcopy(self)
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copy = __copy__
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def _label_discrete(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_uniform(self):
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"""Label data uniformly, 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 load(fname):
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"""
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Load from ASCII table file.
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In legacy style, the first line indicates the number of
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subsequent header lines as "N header", with the last header line being
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interpreted as column labels.
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Alternatively, initial comments are marked by '#', with the first non-comment line
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containing the column labels.
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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 load_ang(fname):
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"""
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Load from 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.split('#',1)[1].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)
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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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Returns
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-------
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data : numpy.ndarray
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Array of column data.
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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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Returns
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-------
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table : Table
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Updated table.
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"""
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dup = self.copy()
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dup._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 = dup.data.columns.get_loc(key).tolist().index(True) + int(idx) -1
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dup.data.iloc[:,iloc] = data
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else:
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dup.data[label] = data.reshape(dup.data[label].shape)
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return dup
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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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Returns
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-------
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table : Table
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Updated table.
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"""
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dup = self.copy()
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dup._add_comment(label,data.shape[1:],info)
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dup.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 = dup.data.index
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dup.data = pd.concat([dup.data,new],axis=1)
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return dup
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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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Returns
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-------
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table : Table
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Updated table.
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"""
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dup = self.copy()
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dup.data.drop(columns=label,inplace=True)
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del dup.shapes[label]
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return dup
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def rename(self,old,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 or iterable of str
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Old column label(s).
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label_new : str or iterable of str
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New column label(s).
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Returns
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-------
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table : Table
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Updated table.
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"""
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dup = self.copy()
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columns = dict(zip([old] if isinstance(old,str) else old,
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[new] if isinstance(new,str) else new))
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dup.data.rename(columns=columns,inplace=True)
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dup.comments.append(f'{old} => {new}'+('' if info is None else f': {info}'))
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dup.shapes = {(label if label not in columns else columns[label]):dup.shapes[label] for label in dup.shapes}
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return dup
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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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Returns
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-------
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table : Table
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Updated table.
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"""
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dup = self.copy()
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dup._label_discrete()
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dup.data.sort_values(labels,axis=0,inplace=True,ascending=ascending)
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dup._label_uniform()
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dup.comments.append(f'sorted {"ascending" if ascending else "descending"} by {labels}')
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return dup
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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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Returns
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-------
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table : Table
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Concatenated table.
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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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dup = self.copy()
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dup.data = dup.data.append(other.data,ignore_index=True)
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return dup
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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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Returns
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-------
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table : Table
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Joined table.
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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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dup = self.copy()
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dup.data = dup.data.join(other.data)
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for key in other.shapes:
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dup.shapes[key] = other.shapes[key]
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return dup
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def save(self,fname,legacy=False):
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"""
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Save 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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legacy : Boolean, optional
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Write table in legacy style, indicating header lines by "N header"
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in contrast to using comment sign ('#') at beginning of lines.
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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 self.data.columns if not (x in seen or seen.add(x))]:
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if self.shapes[l] == (1,):
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labels.append(f'{l}')
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elif len(self.shapes[l]) == 1:
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labels += [f'{i+1}_{l}' \
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for i in range(self.shapes[l][0])]
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else:
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labels += [f'{util.srepr(self.shapes[l],"x")}:{i+1}_{l}' \
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for i in range(np.prod(self.shapes[l]))]
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header = ([f'{len(self.comments)+1} header'] + self.comments) if legacy else \
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[f'# {comment}' for comment in self.comments]
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try:
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fhandle = open(fname,'w',newline='\n')
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except TypeError:
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fhandle = fname
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for line in header + [' '.join(labels)]: fhandle.write(line+'\n')
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self.data.to_csv(fhandle,sep=' ',na_rep='nan',index=False,header=False)
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