605 lines
24 KiB
Python
605 lines
24 KiB
Python
import sys
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import os
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root_dir = os.path.abspath(os.curdir)
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sys.path.append(root_dir)
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import pandas as pd
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import numpy as np
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#import g5505_file_reader
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import src.g5505_utils as utils
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#import input_files.config_file as config_file
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import src.hdf5_vis as hdf5_vis
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import src.g5505_file_reader as g5505f_reader
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import h5py
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import yaml
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import shutil
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import logging
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# Define mapping from extension to their file reader
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ext_to_reader_dict = {'.ibw': g5505f_reader.read_xps_ibw_file_as_dict,
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'.txt': lambda a1: g5505f_reader.read_txt_files_as_dict(a1,False),
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'.TXT': lambda a1: g5505f_reader.read_txt_files_as_dict(a1,False),
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'.dat': lambda a1: g5505f_reader.read_txt_files_as_dict(a1,False),
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'.h5': lambda a1,a2,a3: g5505f_reader.copy_file_in_group(a1,a2,a3,False)}
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def read_mtable_as_dataframe(filename):
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""" Reconstruct a Matlab Table encoded in a .h5 file as a Pandas DataFrame. The input .h5 file
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contains as many groups as rows in the Matlab Table, and each group stores dataset-like variables in the Table as
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Datasets while categorical and numerical variables in the table are represented as attributes of each group.
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Note: DataFrame is constructed columnwise to ensure homogenous data columns.
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Parameters:
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filename (str): .h5 file's name. It may include location-path information.
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Returns:
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output_dataframe (pd.DataFrame): Matlab's Table as a Pandas DataFrame
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"""
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#contructs dataframe by filling out entries columnwise. This way we can ensure homogenous data columns"""
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with h5py.File(filename,'r') as file:
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# Define group's attributes and datasets. This should hold
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# for all groups. TODO: implement verification and noncompliance error if needed.
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group_list = list(file.keys())
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group_attrs = list(file[group_list[0]].attrs.keys())
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#
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column_attr_names = [item[item.find('_')+1::] for item in group_attrs]
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column_attr_names_idx = [int(item[4:(item.find('_'))]) for item in group_attrs]
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group_datasets = list(file[group_list[0]].keys()) if not 'DS_EMPTY' in file[group_list[0]].keys() else []
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#
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column_dataset_names = [file[group_list[0]][item].attrs['column_name'] for item in group_datasets]
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column_dataset_names_idx = [int(item[2:]) for item in group_datasets]
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# Define data_frame as group_attrs + group_datasets
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#pd_series_index = group_attrs + group_datasets
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pd_series_index = column_attr_names + column_dataset_names
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output_dataframe = pd.DataFrame(columns=pd_series_index,index=group_list)
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tmp_col = []
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for meas_prop in group_attrs + group_datasets:
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if meas_prop in group_attrs:
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column_label = meas_prop[meas_prop.find('_')+1:]
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# Create numerical or categorical column from group's attributes
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tmp_col = [file[group_key].attrs[meas_prop][()][0] for group_key in group_list]
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else:
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# Create dataset column from group's datasets
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column_label = file[group_list[0] + '/' + meas_prop].attrs['column_name']
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#tmp_col = [file[group_key + '/' + meas_prop][()][0] for group_key in group_list]
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tmp_col = [file[group_key + '/' + meas_prop][()] for group_key in group_list]
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output_dataframe.loc[:,column_label] = tmp_col
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return output_dataframe
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def create_group_hierarchy(obj, df, columns):
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"""
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Input:
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obj (h5py.File or h5py.Group)
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columns (list of strs): denote categorical columns in df to be used to define hdf5 file group hierarchy
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"""
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if not columns:
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return
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# Determine categories associated with first categorical column
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unique_values = df[columns[0]].unique()
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if obj.name == '/':
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obj.attrs.create('count',df.shape[0])
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obj.attrs.create('file_list',df['filename'].tolist())
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for group_name in unique_values:
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group = obj.require_group(group_name)
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group.attrs.create('column_name', columns[0])
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sub_df = df[df[columns[0]]==group_name] # same as df.loc[df[columns[0]]==group_name,:]
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group.attrs.create('count',sub_df.shape[0])
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group.attrs.create('file_list',sub_df['filename'].tolist())
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# if group_name == 'MgO powder,H2O,HCl':
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# print('Here:',sub_df.shape)
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create_group_hierarchy(group, sub_df, columns[1::])
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def is_nested_hierarchy(df) -> bool:
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"""receives a dataframe with categorical columns and checks whether rows form a nested group hierarchy.
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That is, from bottom to top, subsequent hierarchical levels contain nested groups. The lower level groups belong to exactly one group in the higher level group.
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"""
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# TODO: generalize the code to check for deeper group hierachies.
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def are_nested(df, col, col_nxt):
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""" Checks whether low level LL groups can be separated in terms of high level HL groups.
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That is, elements of low-level groups do not belong to more than one HL group."""
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# Compute higher level group names/categories
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memberships = df[col_nxt].unique().tolist()
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# Compute upper-level group memberships of low-level groups
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col_avg_memberships = df.groupby(col).mean()[col_nxt].unique()
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# Check whether all low-level groups have an actual hlg membership. That is, their avg. hlg membership is in the hlg membership.
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return all([col_avg_memberships[group_idx] in memberships for group_idx in range(len(col_avg_memberships))])
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df_tmp = df.copy()
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# Create relabeling map
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for column_name in df_tmp.columns:
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category_index = pd.Series(np.arange(len(df_tmp[column_name].unique())), index=df_tmp[column_name].unique())
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df_tmp[column_name] = category_index[df_tmp[column_name].tolist()].tolist()
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df_tmp.plot()
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return all([are_nested(df_tmp,'level_'+str(i)+'_groups','level_'+str(i+1)+'_groups') for i in range(len(df_tmp.columns)-1)])
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def get_parent_child_relationships(file: h5py.File):
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nodes = ['/']
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parent = ['']
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#values = [file.attrs['count']]
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# TODO: maybe we should make this more general and not dependent on file_list attribute?
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#if 'file_list' in file.attrs.keys():
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# values = [len(file.attrs['file_list'])]
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#else:
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# values = [1]
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values = [len(file.keys())]
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def node_visitor(name,obj):
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if name.count('/') <=2:
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nodes.append(obj.name)
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parent.append(obj.parent.name)
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#nodes.append(os.path.split(obj.name)[1])
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#parent.append(os.path.split(obj.parent.name)[1])
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if isinstance(obj,h5py.Dataset):# or not 'file_list' in obj.attrs.keys():
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values.append(1)
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else:
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print(obj.name)
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try:
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values.append(len(obj.keys()))
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except:
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values.append(0)
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file.visititems(node_visitor)
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return nodes, parent, values
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def get_groups_at_a_level(file: h5py.File, level: str):
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groups = []
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def node_selector(name, obj):
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if name.count('/') == level:
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print(name)
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groups.append(obj.name)
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file.visititems(node_selector)
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#file.visititems()
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return groups
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def annotate_root_dir(filename,annotation_dict: dict):
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with h5py.File(filename,'r+') as file:
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file.attrs.update(annotation_dict)
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#for key in annotation_dict:
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# file.attrs.create('metadata_'+key, annotation_dict[key])
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def is_valid_directory_path(dirpath,select_dir_keywords):
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activated_keywords = []
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if select_dir_keywords:
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for item in select_dir_keywords:
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if len(item.split(os.sep))>1:
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is_sublist = all([x in dirpath.split(os.sep) for x in item.split(os.sep)])
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activated_keywords.append(is_sublist)
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else:
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activated_keywords.append(item in dirpath)
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else:
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activated_keywords.append(True)
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return any(activated_keywords)
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def transfer_file_dict_to_hdf5(h5file, group_name, file_dict):
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"""
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Transfers data from a file_dict to an HDF5 file.
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Parameters:
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h5file (h5py.File): HDF5 file object where the data will be written.
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group_name (str): Name of the HDF5 group where data will be stored.
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file_dict (dict): Dictionary containing file data to be transferred.
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Required structure:
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{
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'name': str,
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'attributes_dict': dict,
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'datasets': [
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{
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'name': str,
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'data': array-like,
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'shape': tuple,
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'attributes': dict (optional)
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},
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...
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]
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}
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"""
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if not file_dict:
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return
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try:
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# Create group and add their attributes
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group = h5file[group_name].create_group(name=file_dict['name'])
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# Add group attributes
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group.attrs.update(file_dict['attributes_dict'])
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# Add datasets to the just created group
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for dataset in file_dict['datasets']:
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dataset_obj = group.create_dataset(
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name=dataset['name'],
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data=dataset['data'],
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shape=dataset['shape']
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)
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# Add dataset's attributes
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attributes = dataset.get('attributes', {})
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dataset_obj.attrs.update(attributes)
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except Exception as inst:
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print(inst)
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logging.error('Failed to transfer data into HDF5: %s', inst)
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def create_hdf5_file_from_filesystem_path(output_filename : str,
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input_file_system_path : str,
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select_dir_keywords = [],
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select_file_keywords =[],
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top_sub_dir_mask : bool = True,
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root_metadata_dict : dict = {}):
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"""
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Creates an .h5 file with name "output_filename" that preserves the directory tree (or folder structure)
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of a given filesystem path.
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The data integration capabilities are limited by our file reader, which can only access data from a list of
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admissible file formats. These, however, can be extended. Directories are groups in the resulting HDF5 file.
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Files are formatted as composite objects consisting of a group, file, and attributes.
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Parameters:
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output_filename (str): Name of the output HDF5 file.
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input_file_system_path (str): Path to root directory, specified with forward slashes, e.g., path/to/root.
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select_dir_keywords (list): List of string elements to consider or select only directory paths that contain
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a word in 'select_dir_keywords'. When empty, all directory paths are considered
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to be included in the HDF5 file group hierarchy.
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select_file_keywords (list): List of string elements to consider or select only files that contain a word in
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'select_file_keywords'. When empty, all files are considered to be stored in the HDF5 file.
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top_sub_dir_mask (bool): Mask for top-level subdirectories.
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root_metadata_dict (dict): Metadata to include at the root level of the HDF5 file.
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Returns:
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str: Path to the created HDF5 file.
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"""
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allowed_file_extensions = list(ext_to_reader_dict.keys()) # list(config_file.select_file_readers(group_id).keys())
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if '/' in input_file_system_path:
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input_file_system_path = input_file_system_path.replace('/',os.sep)
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else:
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raise ValueError('input_file_system_path needs to be specified using forward slashes "/".' )
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for i, keyword in enumerate(select_dir_keywords):
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select_dir_keywords[i] = keyword.replace('/',os.sep)
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# Copy input_directory into the output_dir_path, and work with it from now on
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output_dir_path = os.path.splitext(output_filename)[0].replace('/',os.sep)
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path_to_filenames_dict = utils.copy_directory_with_contraints(input_file_system_path,
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output_dir_path,
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select_dir_keywords,
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select_file_keywords,
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allowed_file_extensions)
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# Set input_directory as copied input directory
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root_dir = output_dir_path
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with h5py.File(output_filename, 'w') as h5file:
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number_of_dirs = len(path_to_filenames_dict.keys())
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dir_number = 1
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for dirpath, filtered_filenames_list in path_to_filenames_dict.items():
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start_message = f'Starting to transfer files in directory: {dirpath}'
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end_message = f'\nCompleted transferring files in directory: {dirpath}'
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# Print and log the start message
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print(start_message)
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logging.info(start_message)
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# Check if dirpath is valid. TODO: This is perhaps redundant by design of path_to_filenames_dict.
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if not is_valid_directory_path(dirpath,select_dir_keywords):
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continue
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# Check if filtered_filenames_list is nonempty. TODO: This is perhaps redundant by design of path_to_filenames_dict.
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if not filtered_filenames_list:
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continue
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group_name = dirpath.replace(os.sep,'/')
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group_name = group_name.replace(root_dir.replace(os.sep,'/') + '/', '/')
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# Flatten group name to one level
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offset = sum([len(i.split(os.sep)) if i in dirpath else 0 for i in select_dir_keywords])
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tmp_list = group_name.split('/')
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if len(tmp_list) > offset+1:
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group_name = '/'.join([tmp_list[i] for i in range(offset+1)])
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# Group hierarchy is implicitly defined by the forward slashes
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if not group_name in h5file.keys():
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h5file.create_group(group_name)
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#h5file[group_name].attrs.create(name='filtered_file_list',data=convert_string_to_bytes(filtered_filename_list))
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#h5file[group_name].attrs.create(name='file_list',data=convert_string_to_bytes(filenames_list))
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else:
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print(group_name,' was already created.')
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for filenumber, filename in enumerate(filtered_filenames_list):
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file_ext = os.path.splitext(filename)[1]
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#try:
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if not 'h5' in filename:
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#file_dict = config_file.select_file_readers(group_id)[file_ext](os.path.join(dirpath,filename))
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file_dict = ext_to_reader_dict[file_ext](os.path.join(dirpath,filename))
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transfer_file_dict_to_hdf5(h5file, group_name, file_dict)
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else:
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source_file_path = os.path.join(dirpath,filename)
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dest_file_obj = h5file
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dest_group_name = f'{group_name}/{filename}' #group_name +'/'+filename
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ext_to_reader_dict[file_ext](source_file_path, dest_file_obj, dest_group_name)
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# Update the progress bar and log the end message
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utils.progressBar(dir_number, number_of_dirs, end_message)
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logging.info(end_message)
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dir_number = dir_number + 1
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if len(root_metadata_dict.keys())>0:
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annotate_root_dir(output_filename,root_metadata_dict)
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#output_yml_filename_path = hdf5_vis.take_yml_snapshot_of_hdf5_file(output_filename)
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return output_filename #, output_yml_filename_path
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import os
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#import src.hdf5_lib as h5lib
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import src.g5505_utils as utils
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import h5py
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import src.metadata_review_lib as metadata_lib
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def save_processed_dataframe_to_hdf5(df, annotator, output_filename): # src_hdf5_path, script_date, script_name):
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"""
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Save processed dataframe columns with annotations to an HDF5 file.
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Parameters:
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df (pd.DataFrame): DataFrame containing processed time series.
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annotator (): Annotator object with get_metadata method.
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output_filename (str): Path to the source HDF5 file.
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"""
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# Convert datetime columns to string
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datetime_cols = df.select_dtypes(include=['datetime64']).columns
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if list(datetime_cols):
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df[datetime_cols] = df[datetime_cols].map(str)
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# Convert dataframe to structured array
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icad_data_table = utils.dataframe_to_np_structured_array(df)
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# Get metadata
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metadata_dict = annotator.get_metadata()
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# Prepare project level attributes to be added at the root level
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project_level_attributes = metadata_dict['metadata']['project']
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# Prepare high-level attributes
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high_level_attributes = {
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'parent_files': metadata_dict['parent_files'],
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**metadata_dict['metadata']['sample'],
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**metadata_dict['metadata']['environment'],
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**metadata_dict['metadata']['instruments']
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}
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# Prepare data level attributes
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data_level_attributes = metadata_dict['metadata']['datasets']
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for key, value in data_level_attributes.items():
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if isinstance(value,dict):
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data_level_attributes[key] = utils.parse_attribute(value)
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# Prepare file dictionary
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file_dict = {
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'name': project_level_attributes['processing_file'],
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'attributes_dict': high_level_attributes,
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'datasets': [{
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'name': "data_table",
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'data': icad_data_table,
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'shape': icad_data_table.shape,
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'attributes': data_level_attributes
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}]
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}
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# Check if the file exists
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if os.path.exists(output_filename):
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mode = "a"
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print(f"File {output_filename} exists. Opening in append mode.")
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else:
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mode = "w"
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print(f"File {output_filename} does not exist. Creating a new file.")
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# Write to HDF5
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with h5py.File(output_filename, mode) as h5file:
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# Add project level attributes at the root/top level
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h5file.attrs.update(project_level_attributes)
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transfer_file_dict_to_hdf5(h5file, '/', file_dict)
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def create_hdf5_file_from_dataframe(ofilename, input_data, approach : str, group_by_funcs : list, extract_attrs_func = None):
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""" Creates an hdf5 file with as many levels as indicated by len(group_by_funcs).
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Top level denotes the root group/directory and bottom level denotes measurement level groups.
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Parameters:
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input_data (pd.DataFrame) :
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group_by_funcs (list of callables or strs) : contains a list of callables or dataframe's column names that will be used
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to partition or group files from top to bottom.
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Callables in the list must assign a categorical value to each file in a file list, internally represented as a DataFrame,
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and they thus return a pd.Series of categorical values.
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On the other hand, strings in the list refer to the name of categorical columns in the input_data (when this is a DataFrame)
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Returns:
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"""
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# Check whether input_data is a valid file-system path or a DataFrame
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is_valid_path = lambda x : os.path.exists(input_data) if isinstance(input_data,str) else False
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if is_valid_path(input_data):
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file_list = os.listdir(input_data)
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# Navigates file-system folders/directories from top to bottom.
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#for dirpath, dirnames, filenames in os.walk(input_data,topdown=True):
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#df = pd.DataFrame(file_list,columns=['filename'])
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df = utils.augment_with_filetype(df)
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elif isinstance(input_data,pd.DataFrame):
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df = input_data.copy()
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else:
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raise ValueError("input_data must be either a valid file-system path or a dataframe.")
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# Create group columns to form paths
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if utils.is_callable_list(group_by_funcs):
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grouping_cols = []
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for i, func in enumerate(group_by_funcs):
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grouping_cols.append('level_'+str(i)+'_groups')
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df['level_'+str(i)+'_groups'] = func(df)
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elif utils.is_str_list(group_by_funcs) and all([item in df.columns for item in group_by_funcs]):
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grouping_cols = group_by_funcs
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else:
|
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raise ValueError("'group_by_funcs' must be a list of callables (or str) that takes input_data as input an returns a valid categorical output.")
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|
|
# Concatenate group columns to form paths
|
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df['group_path'] = df[grouping_cols].apply(lambda row: '/'.join(row.values.astype(str)), axis=1)
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|
|
if approach == 'botton-up':
|
|
# TODO: implement botton-up approach
|
|
if is_nested_hierarchy(df.loc[:,grouping_cols]):
|
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print('Do something')
|
|
else:
|
|
raise ValueError("group_by_funcs do not define a valid group hierarchy. Please reprocess the input_data or choose different grouping functions.")
|
|
|
|
elif approach == 'top-down':
|
|
# Check the length of group_by_funcs list is at most 2
|
|
#if len(group_by_funcs) > 2:
|
|
# # TODO: extend to more than 2 callable elements.
|
|
# raise ValueError("group_by_funcs can only contain at most two grouping elements.")
|
|
|
|
with h5py.File(ofilename, 'w') as file:
|
|
|
|
# Create groups based on concatenated paths
|
|
for path in df['group_path'].unique():
|
|
file.create_group(path)
|
|
# TODO: incorporate remaining cols (i.e., excluding the group columns) as either metadata or datasets
|
|
|
|
#create_group_hierarchy(file, df, grouping_cols)
|
|
|
|
file.attrs.create(name='depth', data=len(grouping_cols)-1)
|
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|
|
print(':)')
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|
|
|
else:
|
|
raise ValueError("'approach' must take values in ['top-down','bottom-up']")
|
|
|
|
|
|
#for i, value in enumerate(df['level_'+str(0)+'_groups'].unique().tolist()):
|
|
|
|
# 2. Validate group hierarchy, lower level groups must be embedded in higher level groups
|
|
|
|
# 3. Create hdf5 file with groups defined by the 'file_group' column
|
|
#
|
|
# Add datasets to groups and the groups and the group's attributes
|
|
|
|
#return 0
|
|
|
|
def main_mtable_h5_from_dataframe():
|
|
|
|
#import os
|
|
ROOT_DIR = os.path.abspath(os.curdir)
|
|
# Read BeamTimeMetaData.h5, containing Thorsten's Matlab Table
|
|
input_data_df = read_mtable_as_dataframe(os.path.join(ROOT_DIR,'input_files\\BeamTimeMetaData.h5'))
|
|
|
|
# Preprocess Thorsten's input_data dataframe so that i can be used to create a newer .h5 file
|
|
# under certain grouping specificiations.
|
|
input_data_df = input_data_df.rename(columns = {'name':'filename'})
|
|
input_data_df = utils.augment_with_filenumber(input_data_df)
|
|
input_data_df = utils.augment_with_filetype(input_data_df)
|
|
input_data_df = utils.split_sample_col_into_sample_and_data_quality_cols(input_data_df)
|
|
input_data_df['lastModifiedDatestr'] = input_data_df['lastModifiedDatestr'].astype('datetime64[s]')
|
|
|
|
# Define grouping functions to be passed into create_hdf5_file function. These can also be set
|
|
# as strings refering to categorical columns in input_data_df.
|
|
|
|
test_grouping_funcs = True
|
|
if test_grouping_funcs:
|
|
group_by_sample = lambda x : utils.group_by_df_column(x,'sample')
|
|
group_by_type = lambda x : utils.group_by_df_column(x,'filetype')
|
|
#group_by_filenumber = lambda x : utils.group_by_df_column(x,'filenumber')
|
|
else:
|
|
group_by_sample = 'sample'
|
|
group_by_type = 'filetype'
|
|
group_by_filenumber = 'filenumber'
|
|
|
|
output_filename_path = os.path.join('output_files','thorsten_file_list.h5')
|
|
|
|
create_hdf5_file_from_dataframe(output_filename_path,input_data_df, 'top-down', group_by_funcs = [group_by_sample, group_by_type])
|
|
#create_hdf5_file_from_dataframe('test.h5',input_data_df, 'top-down', group_by_funcs = [group_by_sample, group_by_type, group_by_filenumber])
|
|
|
|
annotation_dict = {'1-Campaign name': '**SLS-Campaign-2023**',
|
|
'2-Users':'Thorsten, Luca, Zoe',
|
|
'3-Startdate': str(input_data_df['lastModifiedDatestr'].min()),
|
|
'4-Enddate': str(input_data_df['lastModifiedDatestr'].max())
|
|
}
|
|
annotate_root_dir(output_filename_path, annotation_dict)
|
|
|
|
#display_group_hierarchy_on_a_treemap(output_filename_path)
|
|
|
|
print(':)')
|
|
|
|
if __name__ == '__main__':
|
|
|
|
#main()
|
|
main_mtable_h5_from_dataframe()
|
|
#main_5505()
|
|
|
|
print(':)')
|
|
|